title: EBNA Leader Protein is required to reshape chromatin architecture during B cell transformation by Epstein-Barr Virus (CUT&Run)

overall_design: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) was used to assess the binding of the transcription factors YY1, CTCF and the histone modification H3K27ac in B cells before and after transformation, in LCL and Mutu1 cell lines

last: White

last: Luftig


title: Synergistic DNA and RNA binding of the Hox transcription factor Ultrabithorax coordinates splicing and shapes in vivo homeotic functions

status: Public on Jun 08 2025

city: Montpellier FRANCE

first: Julie

last: Carnesecchi

address: 1919, route de Mende team JCL team JCL

department: IGMM

country: France

institute: CNRS

type: Expression profiling by high throughput sequencing

summary: The dual interaction of many transcription factors (TFs) with both DNA and RNA is an underexplored issue that could fundamentally reshape our understanding of gene regulation. We address this central issue by investigating the RNA binding activity of the Drosophila Hox TF Ultrabithorax (Ubx) in alternative splicing and morphogenesis. Relying on molecular and genetic interactions, we uncover a homodimerization-dependent mechanism by which Ubx regulates splicing. Notably, this mechanism enables the decoupling of Ubx-DNA and -RNA binding activity in splicing. We identify a critical residue for Ubx-RNA binding and demonstrate the essential role of Ubx-RNA binding ability for its homeotic functions. Overall, we uncover a unique mechanism for Ubx-mediated splicing and underscore the critical contribution of synergistic DNA/RNA binding for its morphogenetic functions. These findings advance our understanding of co-transcriptional regulation and highlight the significance of TF-DNA/RNA synergistic function in shaping gene regulatory networks in living organisms.

overall_design: Total RNAs were extracted from three independent replicates from Drosophila S2R+ cells expressing 150ng of GFPnls, myc-UbxWT or myc-UbxN51A or co-expressing 150+150ng of myc-Ubx(WT+N51A) or myc-Ubx(WT+N51A-K58A) (Gal4-UAS, actin promoter) using Qiagen RNA extraction kit (RNeasy). RNA quality and integrity were assessed using BioAnalyzer 2100TM (Agilent Technologies). Material handling and mRNA-Seq directional libraries were performed by Novogene with poly(A) selection according to the manufacturer's protocol (Illumina). Sequencing was performed with NovaSeq X Plus Series (8 G raw data per sample) with a read length of 150 bp and paired-end reads. Replicates were validated by FastQC report, and Principal Component Analysis (PCA) was performed to verify the sample similarity. The data were generated and uploaded on the Gene Expression Omnibus according to the ENCODE guideline (see Data Availability section).

first: Constanza

last: Blanco

first: Wan

last: Xiang

first: Panagiotis

last: Boumpas


title: β-Hydroxybutyrate Boosts Plant Immunity through Enhanced histone Kbhb Levels and Gene Expression Regulation [ChIP-seq]

status: Public on Jun 07 2025

city: Wuhan

first: Qiutao

last: Xu

state: Hubei

address: No.1,Shizishan Street · Hongshan District

country: China

institute: Huazhong Agricultural University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We demonstrated functional differences between H3K9bhb and the well-studied H3K9ac, particularly in regulating immune-response genes in rice. Moreover, we show that exogenous application of β-hydroxybutyrate enhances disease resistance in rice by inducing H3K9bhb deposition and stimulating the expression of defense-related genes. Furthermore, we identified SRT1, SRT2, and HDA705 as key players in the removal of histone Kbhb in rice plants.

overall_design: Libraries were constructed using ChIP-seq technologies to obtain data on histone modifications.


title: Human iPSC-derived NK cells armed with CCL19, CCR2B, high-affinity CD16, IL-15, and NKG2D complex enhance anti-solid tumor activity

status: Public on Jun 10 2025

city: Kobe

first: Hironobu

last: Kimura

state: Hyogo

address: Kobe KIMEC Center Bldg. 3F, 1-5-2 Minatojima-Minamimachi, Chuo-ku

country: Japan

institute: HEALIOS K.K.

summary: Studies of chimeric antigen receptor (CAR)-T and -Natural killer (NK) cells have shown promising results in treating hematological malignancies. However, there are still obstacles to effectively treating solid tumors. These include the challenges of CAR-T cell homing and infiltration, the presence of immunosuppressive microenvironments, and the potential for antigen escape in solid tumors. To overcome the known limitations of immune cell therapy, we engineered human induced pluripotent stem cell (hiPSC)-derived NK (eNK) cells armed with CCL19, CCR2B, high-affinity CD16, IL-15, and NKG2D-DAP10 complex. We introduced the six genes into hiPSCs using the piggyBac system and stimulated them to differentiate into NK cells. Overexpression of NKG2D complex and high-affinity CD16 enhanced the antitumor function of the eNK cells. Overexpression of IL-15 prolonged the persistence of the eNK cells in vitro and in vivo. Forced expression of CCR2B enhanced eNK cell tumor infiltration. Forced expression of CCL19 endowed the eNK cells with the ability to recruit dendritic cells. We found that the eNK cells were able to lyse HLA-E-expressing tumor cells, but not normal human cells. These proof-of-concept studies demonstrate the promise of our eNK cells as a novel adoptive cell therapy product for the treatment of solid tumors.

overall_design:
To enhance antitumor activity of NK cells against solid tumors, we generated NK cells derived from gene-engineered hiPSC forced expression of CCL19, CCR2B, high-affinity CD16, IL-15, and NKG2D-DAP10 complex.
To evaluate the effect of transgene integration, we performed comparative gene expression analysis using data obtained from RNA-seq of non-engineered and engineered hiPSCs.
Comparative gene expression profiling analysis of RNA-seq data for non-engineered and engineered hiPSCs.

first: Kodai

last: Saito

first: Tomonori

last: Hosoya

first: Norihiro

last: Tsuneyoshi


title: An engineered hypoxia-response promoter for human umbilical cord-derived mesenchymal stem cell-based therapeutics

city: guangzhou

first: Song

last: Yang

address: zhongshan second load

institute: Guangdong provincial people's hospital

summary: Myocardial infarction, characterized by insufficient blood supply to the heart, leads to ischemia and hypoxia of myocardial tissues, causing injury and decreased cardiac function. Despite improvements in pharmaceutical and interventional therapies, it remains a leading cause of death worldwide. Human umbilical cord mesenchymal stem cells (hUC-MSCs) play an important role in the repair of infarcted myocardium by promoting angiogenesis, reducing inflammation, secreting growth factors and cytokines. However, the harsh hypoxic microenvironment of infarcted myocardial tissue poses a threat to the survival and function of transplanted hUC-MSCs. In this study, we modified the candidate gene promoter of hUC-MSCs under hypoxic conditions and created a promoter that can respond quickly under hypoxic conditions. We found that the modified promoter significantly promoted the transcription efficiency as hypoxia time increased. This indicates that the engineered hypoxia-response promoter can effectively drive gene expression in a hypoxic environment. Furthermore, the transcription efficiency of the modified promoter under normoxic conditions is lower than that of common promoters in eukaryotic organisms, suggesting that this effect can improve the efficacy and safety of hUC-MSC-based myocardial infarction treatment by ensuring that cells function effectively in the damaged hypoxic area.

overall_design: We cultured hUC-MSCs under hypoxic (1% oxygen) and normoxic conditions, respectively. We then collected cell samples from the hypoxic culture group at 2 hours, 6 hours, 24 hours, and 72 hours, and from the normoxic culture group at 24 hours. Total cellular RNA was extracted for transcriptome sequencing analysis. By analyzing and comparing the gene expression changes in hUC-MSCs from each hypoxic time group with those from the normoxic 24-hour group based on the sequencing results, we aimed to identify potential genes with continuously upregulated expression in hUC-MSCs as the hypoxic time increased.

first: Weizhong

last: Zhuang

first: Lishi

last: Zhou

first: Weiwei

last: Kong

first: Wanwan

last: Zou

first: Qikun

last: Zhu

first: Enze

last: Bian

first: Bin

last: Lin

first: Jianzheng

last: Cen

first: Qiang

last: Gao

first: Jimei

last: Chen


title: Failure to resolve inflammation contributes to juvenile onset cardiac damage in a mouse model of Duchenne Muscular Dystrophy

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

country: USA

institute: Childrens National Hospital

summary: Absence of dystrophin protein causes cardiac dysfunction in patients with Duchenne muscular dystrophy (DMD). Unlike boys with DMD, the common mouse model of DMD (B10-mdx) does not manifest cardiac deficits until late adulthood. This has limited our understanding of the mechanism and therapeutic approaches to target the pediatric onset of cardiac pathology in DMD. Here we show that the mdx mouse model on the DBA/2J genetic background (D2-mdx) displays juvenile-onset cardiac degeneration. Molecular and histological analysis revealed that cardiac damage in this model is linked to increased leukocyte chemotactic signaling and an inability to resolve inflammation. These deficiencies result in chronic inflammation and fibrotic conversion of the extracellular matrix (ECM) in the juvenile D2-mdx heart. To address these pathologies, we tested the utility of pro-resolution therapy to clear chronic cardiac inflammation. Use of an N-formyl peptide receptor (FPR) agonist helped physiologically resolve inflammation and mitigate the downstream events that lead to fibrotic degeneration of cardiomyocytes, preventing juvenile onset cardiac muscle loss. These results establish the utility of D2-mdx model to study events associated with pediatric-onset cardiac damage and demonstrates pro-resolution therapy as an alternate to anti-inflammatory therapy for treating degenerative cardiac pathology that leads to cardiomyopathy in DMD.

overall_design: To investigate the transcriptional landscape of the DMD disease condition in  cardiac muscle, a bulk RNASeq analysis was performed using  RNA  extracted from 4 DMD (D2md-x) and 3 Wild type (B10-mdx) age matched 6 week old male mouse heart.

first: Novak

last: James

first: Lischin

last: Amy

first: Uapinyoying

last: Prech

first: Hindupur

last: Ravi

first: Moon

last: Young Jae

first: Bhattacharya

last: Surajit

first: Tiufekchiev-Grieco

last: Sarah

first: Barone

last: Victoria

first: Mázala

last: Davi A. G.

first: Gamu

last: Iteoluwakishi H.

first: Walters

last: Gabriela

first: Jaiswal

last: Jyoti


title: The Tumor-Sentinel Lymph Node Immune Migratome Reveals a Key Role for Migratory CCR7+ Dendritic Cells in Response to Immunoradiotherapy [TCR-seq]

city: La Jolla

first: Joseph

last: Califano

address: 3855 Health Sciences Dr.

institute: Moores Cancer Center, UC San Diego

summary: Surgical ablation or radiation of tumor-draining lymph nodes can eliminate the primary tumor response to immunotherapy, indicating that local tumor response to immunotherapy is mediated by tumor-draining lymph nodes. Here, we show that immunoradiotherapy efficacy is dependent on immune cell migration from tumor to sentinel lymph nodes. Using a tamoxifen-inducible reporter paired with CITE-sequencing in a murine model of oral cancer, we characterized tumor immune cellular migration through lymphatic channels to sentinel lymph nodes at single-cell resolution. Within a structured approach of sequential immunomodulatory radiotherapy and checkpoint inhibition, we demonstrate that lymphatic-sparing, tumor-directed radiotherapy followed by PD-1 inhibition achieves complete and durable tumor responses. Mechanistically, this treatment approach enhances activated, migratory CCR7+ dendritic cell surveillance across the tumor-sentinel lymph node axis, revealing a shift from their canonical role in promoting tolerance to driving antitumor immunity. Overall, this work supports rationally sequencing immune-sensitizing, lymphatic-preserving, tumor-directed radiotherapy followed by immune checkpoint inhibition to optimize the tumor response. By characterizing the tumor-sentinel lymph node immunomigratome that drives durable antitumor response, we reveal a therapeutic opportunity to enhance the response to immunotherapy by optimizing activated dendritic cell migration to tumor-draining sentinel nodes.

overall_design:
WT animals injected with 4MOSC1 tumors were treated with tdRT→αPD-1 with or without sentinel lymph node lymphatic channel ablation (SLN LCA) or non-sentinel lymph node lymphatic channel ablation (nSLN LCA).

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Adaptive Biotechnologies (service provider) did not provide FASTQ files due to proprietary content.
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first: Robert

last: Saddawi-Konefka

first: Shawn

middle: M

last: Jensen

first: Bernard

middle: A

last: Fox

first: Richard

last: Bell

first: J

middle: S

last: Gutkind

first: Andrew

last: Sharabi


title: The Tumor-Sentinel Lymph Node Immune Migratome Reveals a Key Role for Migratory CCR7+ Dendritic Cells in Response to Immunoradiotherapy [CITE-seq]

overall_design: CITE-sequencing was performed on cells isolated from sentinel lymph node (sln) and tumors of mice treated with and without immunoradiotherapy (IRT) to characterize immune cell populations involved in antitumor surveillance


title: Tumor-derived exosomal lncRNA SNHG4 promotes triple-negative breast cancer progression by targeting XPO5

status: Public on Jun 24 2025

city: WuHan

first: xinghua

last: Liao

address: Wuhan University of Science and Technology, Hongshan District, Wuhan City, Hubei Province, China

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
Triple-negative breast cancer (TNBC) is the subtype of advanced breast cancer with the shortest survival time and the poorest prognosis, and treatment options are relatively limited.
Exosomes, small extracellular vesicles enriched with bioactive molecules, are critical mediators of intercellular communication and have been implicated in cancer progression. The aim of this study was to investigate the molecular mechanism of exosomes promoting the proliferation and migration of TNBC.

overall_design: Analyzed six samples.

first: Zhi-Wen

last: Wang

first: Hou-Sheng

last: Yang

first: Hong-Shan

last: Guo

first: Yue-Ying

last: Li

first: Jin-Yun

last: Zhong

first: Shu

last: Jiang

first: Jia-Peng

first: Zhong-Yi

first: Chuan-Yi

last: Zhou

first: Jun

first: Xing-Hua

first: Lei

last: Mao


title: Targeting of cannabinoid receptor 1 for antagonism in profibrotic alveolar macrophages mitigates pulmonary fibrosis

status: Public on Jun 06 2025

city: Rockville

first: Resat

last: Cinar

state: Maryland

address: 5625 Fishers lane

institute: National Institute on Alcohol Abuse and Alcoholism

summary: Pulmonary fibrosis (PF) is a life-threatening disease that requires effective and well-tolerated therapeutic modalities. Previously, the distinct pathogenic roles of cannabinoid receptor 1 (CB1R) and inducible nitric oxide synthase (iNOS) in the lungs and their joint therapeutic targeting were highlighted in PF. However, the cell-specific role of CB1R in PF has not been explored. Here, we demonstrate that CB1R in alveolar macrophages (AMs) mediates the release of anandamide into the alveoli, which promotes PF by inducing profibrotic macrophages that are accessible to locally delivered antifibrotic therapy. A multitargeted therapy may improve therapeutic efficacy in PF. Pulmonary delivery of 0.5 mg/kg/day MRI-1867 (zevaquenabant), a peripherally acting hybrid CB1R/iNOS inhibitor, is as effective as systemic delivery of 10 mg/kg/day, and also matches the efficacy of nintedanib in mitigating bleomycin-induced PF. A systems pharmacology approach reveals that zevaquenabant and nintedanib treatments reverse pathologic changes in both distinct and shared PF-related pathways, which are conserved in human and mouse. Moreover, zevaquenabant treatment also attenuated fibrosis and profibrotic mediators in human precision-cut lung slices. These findings establish CB1R-expressing AMs as a therapeutic target and support local delivery of dual CB1R/iNOS inhibitor zevaquenabant by inhalation as an effective, well-tolerated, and safer strategy for PF.

overall_design: We used 52-week-old C57BL/6J mice (aged mice) to generate bleomycin-induced pulmonary fibrosis model by treating mice with either saline or bleomycin (1 U/kg) by a single oropharyngeal administration. The saline group serves as a healthy control group. Bleomycin-administered mice were randomized to equilibrate their body weight reduction and to assign them to different treatment groups at day 10 post-bleomycin. Pharmacological treatments were performed between day 10 and day 28 post-bleomycin with vehicle, MRI-1867 (Dual-inhibitor of CB1R/iNOS, 0.5 mg/kg, oropharyngeal), rimonabant (CB1R antagonist, 10 mg/kg, intraperitoneally), 1400W (iNOS inhibitor, 10 mg/kg, intraperitoneally), and nintedanib (tyrosine kinase inhibitor, 60 mg/kg, orally). Lung tissues were collected on day 28 post-bleomycin for RNAseq analysis.

first: Abhishek

last: Basu

first: Muhammad

last: Arif

first: Lenny

last: Pommerolle


title: A modular CRISPRa system for molecular therapy of FOXG1 syndrome

city: Sacramento

first: Julian

last: Halmai

state: CA

address: 2921 Stockton Blvd

department: Department of Neurology

institute: UC Davis

summary: To date, there is an unmet need for novel approaches that address haploinsufficiency disorders in a targeted and robust manner. Here, we developed a novel, modular tool for transcriptional regulation of genes involved in neurodevelopmental disease in the absence of creating double-stranded breaks. We utilized this novel platform technology to identify sgRNAs that efficiently regulate expression of the intellectual disability gene FOXG1 that utilizes an optimized protein intein system. Using a modular assembly of CRISPR trans-activators, including single and dual VP64 dCas9 fusion proteins, sgRNA-mediated MS2 p65 HSF (MPH) recruitment or the addition of the VPR tripartite effector (VP64, p65, Rta) can induce dynamic gene regulation. We further increased mRNA levels of FOXG1 using duplexed sgRNAs paired with different combinations of transcriptional activators. We demonstrate that FOXG1 gene upregulation results in a significant increase in FoxG1 protein translation. Following treatment of mutant FOXG1 neural stem cells with the CRISPR activators, we observed a significant increase in FOXG1 expression with no-off targets as determined by in silico sgRNA binding prediction paired with RNA-sequencing. This approach holds great promise as a modular platform technology that is readily adapted for gene therapy delivery for those affected by rare genetic conditions.

overall_design: RNAseq from healthy neural stem cells, mutant neural stem cells and CRISPR corrected, isogenic neural stem cells following CRISPRa or no effector transfection

first: Kyle

last: Fink


title: A feed-forward loop between Toll/NF-κB and Rac1 promotes Epithelial to Mesenchymal Transition of Ras-oncogenic hindgut enterocytes in Drosophila

city: Nicosia

first: Yiorgos

last: Apidianakis

address: 1 Panepistimiou Ave.

department: Biological Sciences

country: Cyprus

institute: University of Cyprus

summary: Cancer cell invasion and subsequent metastasis accounts for most cancer related deaths. However, despite recent progress, there is a need to understand how the main pathways involved in oncogenic cell invasion and metastasis amalgamate into multifunctional networks. Using functional transcriptomic analysis of Drosophila Ras oncogenic hindgut enterocytes, we identified a feed-forward loop between the Toll/NF-κB innate immune pathway and Rac1 signaling driving actin cytoskeleton rearrangements, basement membrane degradation, and loss of intercellular adhesion. We find that this network is necessary and sufficient to promote oncogenic hindgut enterocyte invasion and dissemination. The network is orchestrated by Rac1, which promotes actin cytoskeleton alterations, JNK-mediated matrix metalloprotease-mediated basement membrane degradation and Toll-Snail-depended E-cadherin repression, leading to epithelial-to- mesenchymal transition and dissemination. However, Toll pathway positively regulates itself and the Rac1 pathway cytoskeletal genes downstream of the Ras oncogene, while JNK signaling alone does not suffice to induce cell dissemination. The tight crosstalk between Toll and Rac1 pathways reveals an integral role of Toll/NF-κB in Ras-initiated oncogenic epithelial cell migration.

overall_design: Comparative Gene expression analysis of RNA-Seq data between RasV12 expressing and control Drosophila hindguts

first: Myrofora

last: Panagi

first: Alexandros

last: Galaras

first: Pantelis

last: Hatzis


title: Transcriptome profile of thioacetamide treated mice injected with AAV8 TBG eGFP and AAV8 TBG miR34b/c

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: To analyse gene expression differences between TAA treated mice injected with AAV8 TBG eGFP and TAA treated mice injected with AAV8 TBG MiR34b/c

overall_design: Total RNA was extracted from n=5 and n=7

first: R

last: Ferriero


title: Real time quantitative PCR analysis of WT and CX/CX obtained splenic CD8 T Cells

status: Public on Jun 05 2025

city: Pozzilli

first: Daniela

last: Carnevale

address: Via dell'Elettronica

institute: IRCCS Neuromed and "Sapienza" University of Rome

summary: Activated immune cells infiltrate the vasculature during the pathophysiology of hypertension by establishing a vascular-immune interface that contributes to blood pressure dysregulation and organ failure. Many observations indicate a key role of CD8+ T cells in hypertension but mechanisms regulating their activation and interplay with the cardiovascular system are still unknown. In murine model, here we show that a specific member of the phosphoinositide-3-kinases (PI3K) family of lipid kinases, PI3Kγ, is a key intracellular signaling of CD8+ T cells activation and RANTES/CCL5 secretion in hypertension: CCL5-CCR5 signaling is crucial for the establishment of the vascular-immune interface in peripheral organs, lastly contributing to CD8+ tissue infiltration, organ dysfunction and blood pressure elevation. Our studies identify PI3Kγ as a booster of effector CD8+ T cell function, even in the absence of external stimuli. Lastly, an enhanced PI3Kγ signaling mediates the bystander activation of CD8+ T cells and proves effective in transferring the hypertensive phenotype between mice.

overall_design: qPCR gene expression profiling from N=11 mice CD8 T cells. An equal amount of RNA extracted from CD8T Cells was used for each biological replicate


title: β-Hydroxybutyrate Boosts Plant Immunity through Enhanced histone Kbhb Levels and Gene Expression Regulation [RNA-seq]

first: Qiutao

last: Xu

overall_design: Libraries were constructed using  RNA-seq technologies to obtain data on transcription.


title: β-Hydroxybutyrate Boosts Plant Immunity through Enhanced histone Kbhb Levels and Gene Expression Regulation [ATAC-seq]

overall_design: Libraries were constructed using ATAC-seq technologies to obtain data on chromatin accessibility.


title: Forced expression of MSR repeat transcripts above a threshold limit breaks heterochromatin organization

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Mouse heterochromatin is characterised by transcriptionally competent major satellite repeat (MSR) sequences and it has been proposed that MSR RNA contributes to the integrity of heterochromatin. We established an inducible dCas9-effector system in mouse embryonic fibroblasts, where we can modulate MSR transcription through the targeting of a dCas9-Repressor or a dCas9-Activator. With this system, we can define a threshold limit of >300-fold deregulation of MSR transcript levels, above which the structural organisation of heterochromatin becomes disrupted. MEF cells expressing MSR RNA above this threshold limit are not viable and the defects in heterochromatin organisation and chromosome segregation cannot be reverted. This study highlights the importance of restricting MSR RNA output to maintain heterochromatin integrity and relates MSR transcript levels to either physiological or pathological conditions. It also reveals that the structural organisation of heterochromatin is governed by the transcriptional chromatin state and associated MSR RNA of the MSR repeats.

overall_design: To investigate the effect of modulating MSR repeat transcription on repeat dysregulation genomewide. MEF cell lines were created where chromatin effectors can be inducibly expressed. These chromatin effectors are targeted to MSR repeats utilizing the CRISPR/dCas9 system: MSR-dCas9-Control, MSR- dCas9-Repressor, MSR-dCas9-Activator.

first: Reagan

last: Ching

first: Thomas

last: Jenuwein


title: Complex I Inhibition combined with TLR Activation in the Breast Tumor Microenvironment Educates Cytotoxic Neutrophils [scRNA-seq]

status: Public on Jun 04 2025

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

summary: Neutrophils have emerged as diverse regulators of tissue states, displaying functions in both the resolution and promotion of tissue inflammation. While neutrophils have widely been associated with tumor promotion, immune suppression, and poor patient outcome, we provide evidence to support direct tumor cytotoxic properties of neutrophils. Using various models of murine breast cancer; we establish that TLR-mediated engagement, combined with complex I inhibition, within the breast tumor microenvironment, acting either directly or indirectly on neutrophils, primes these innate immune cells to acquire direct tumor killing properties, both in vitro and in vivo, and independently of CD8+ T cell immunity. TLR engagement stimulates emergency granulopoiesis, increasing levels of neutrophils in the circulation and infiltrating into tumors without inducing the formation of a pro-metastatic niche. Mechanistically, we show that systemic administration of various TLR agonists, while increasing systemic inflammation, elevates NFkB signalling in neutrophils, to contribute to their tumoricidal functions. Moreover, using bulk- and single-cell RNA sequencing, along with proteomics approaches, neutrophils that are trained to acquire these anti-tumorigenic functions, acquire enhanced secretory granule production and increased expression NADPH-oxidase machinery. Concomitantly, these tumoricidal neutrophils increase production of toxic levels of reactive oxygen species, which can be overcome with myeloperoxidase inhibitors or overexpression of ROS scavengers. Taken together, we describe a new class of neutrophils that possess direct and intrinsic tumoricidal functions, which can be exploited to eradicate immune cold breast tumors which otherwise are refractory to standard immunotherapies, including immune checkpoint blockade.

overall_design: 4 Murine breast tumors, orthotopic syngeneic (MT - FVB) were sent for single-cell RNA-seq sequencing. 4 conditions: Treatment - Saline+PBS, Saline+Phenformin, Poly I:C+PBS, Poly I:C+Phenformin

first: John

last: Heath

first: Alva

last: Annett

first: Josie

last: Ursini-Siegel


title: Complex I Inhibition combined with TLR Activation in the Breast Tumor Microenvironment Educates Cytotoxic Neutrophils.

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

overall_design: Refer to individual Series


title: Analysis of Biased Allelic Enhancer Activity of Schizophrenia-Linked Common Variants

city: qingdao

first: chengwen

last: gao

state: shandong

address: Huangdao Qingdao Shandong

institute: Affiliated Hospital of Qingdao University

summary: Schizophrenia (SCZ) is a neuropsychiatric disorder with heritability estimates between 60% and 80%. Although genome-wide association studies have identified many genetic loci linked to the disorder, most of these are noncoding variants whose functional impacts are not well understood. To bridge this gap, we prioritized potential functional variants linked to SCZ by utilizing a human brain epigenomic roadmap. We assessed the regulatory activity of these variants using an adapted STARR-seq screening method across four cell lines: Neuro-2a, SH-SY5Y, HEK-293T, and PC-12. Furthermore, we pinpointed candidate target genes through functional characterization and investigated their roles using zebrafish models. Our study identified 351 candidate single nucleotide polymorphisms (SNPs). Among these, 46 SNPs exhibited biased allelic enhancer activity, termed baaSNPs, with notable cell-type specificity. Chromatin interaction profiling and expression quantitative trait loci analyses linked these baaSNPs to 217 candidate target genes, and pathway enrichment analysis indicated that these genes are involved in critical neurological processes such as synaptic transmission and GABAergic signaling. One baaSNP in particular, rs13072690, showed regulatory effects across all examined cell lines and was associated with reduced expression of the PCCB gene in multiple brain regions. Heterozygous pccb knockout zebrafish exhibited abnormal behaviors, including hyperactivity, increased anxiety-like responses, and social deficits. In conclusion, our study presents an approach for functionally annotating putative causative variants. These findings enhance our understanding of the genetic factors underlying the disorder.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We employed a modified STARR-seq approach to assess the regulatory activity of SNPs across four cell lines: HEK-293T, SH-SY5Y, Neuro-2a, and PC-12. These lines were selected for their relevance to neuronal biology and experimental utility: HEK-293T cells for high transfection efficiency and robust reporter assays; SH-SY5Y cells for neuronal characteristics; Neuro-2a cells for studying neurodevelopmental signaling; and PC-12 cells for differentiation and neuroendocrine studies.

first: Chengwen

last: Gao

first: Qian

last: Zhang

first: Chuanhong

last: Wu

first: Lixia

last: Peng

first: Mingxuan

first: Baokun

last: Wang

first: Zhiqiang

last: Li


title: The Role of Orphan GPCR GPR153 in Regulating Vascular Damage Responses

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Expression of GPR153 is upregulated in response to damage both in smooth muscle cells and endothelial cells.We found knockdown of GPR153 in SMC reduced the ligation-induced neointima formation, and GPR153 defeciency in EC protect the mice from neuroinflammation. The mechanism of orphan GPCR GPR153 in regulating cell signaling were studied in SMC, EC and HEK293t cell lines.

overall_design: HEK293t cells were transfected with scramble siRNA or GPR153 siRNA, and then transfected with empty vector or GPR153-Myc plasmid. Control group (scramble siRNA, empty vector), GPR153 knockdown group (GPR153 siRNA, empty vector) and GPR153 overexpression group (scramble siRNA, GPR153-Myc plasmid) were sent for mRNA sequencing.

first: Jingchen

last: Shao

first: Jeonghyeon

last: Kwon

first: Nina

last: Wettschureck


title: Complex I Inhibition combined with TLR Activation in the Breast Tumor Microenvironment Educates Cytotoxic Neutrophils [bulk RNA-seq]

overall_design: Murine breast tumor, orthotopic syngeneic (MT - FVB, 4T1 - BALBc). 4 replicates per conditions: Treatment - Saline+PBS, Saline+Phenformin, Poly I:C+PBS, Poly I:C+Phenformin


title: BAHCC1 binds H4K20me1 to facilitate the MCM complex loading and DNA replication

status: Public on Jun 03 2025

city: Durham

first: Yiran

last: Guo

state: North Carolina

address: 3 Genome Ct

institute: Duke University

summary: Mono-methylation of histone H4 lysine 20 (H4K20me1) is increasingly appreciated to be critical for regulating genomic DNA replication, cell cycle progression and DNA damage repair. How exactly H4K20me1 regulates these biological processes remains murky. Here, we report that an evolutionarily conserved tandem Tudor domain (TTD) in the BAH Domain And Coiled-Coil Containing 1 (BAHCC1) protein (BAHCC1_TTD) selectively reads H4K20me1 for facilitating the replication origin activation and efficient DNA replication. Our integrated biochemical, structural, genomic and cellular analyses demonstrated that BAHCC1_TTD preferentially recognizes H4K20me1 to promote the recruitment of BAHCC1 and its interacting partners, notably the Mini-chromosome Maintenance (MCM) complex, to the replication origin sites. Combined actions of the H4K20me1-reading BAHCC1 and the H4K20me2-reading Origin Recognition Complex (ORC) ensure optimal genomic loading of MCM complexes for facilitating DNA replication. Depletion of BAHCC1, or disruption of the BAHCC1_TTD:H4K20me1 interaction, reduces levels of H4K20me1 and MCM loading, leading to defects in replication and cell cycle progression. Together, this study identifies BAHCC1_TTD as a conserved effector transducing the H4K20me1 signals to the recruitment of MCM complexes for facilitating efficient DNA replication.

overall_design: CUT&RUN was used to assess the genomic mapping of BAHCC1, H3K27me3, MCM2 and PHF8 in parental HeLa cells.

first: Greg


title: Embryonic thermal conditioning and post-hatch heat challenge in broiler chicks reveal changes in hypothalamic expression of genes related to appetite, thermoregulation, and stress modulation

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: Embryonic heat conditioning (EHC; exposing the chick embryo to elevated temperatures transiently during incubation) has been associated with greater stress resiliency later in life, although mechanisms are unclear but likely involve the hypothalamus. The objective of this study was to determine the effects of an acute heat challenge at day 4 post-hatch on the transcriptome of several brain nuclei associated with thermal regulation, stress, and appetite, including the paraventricular nucleus of the hypothalamus (PVN), pre-optic anterior/hypothalamic area (POAH), and the nucleus of the hippocampal commissure (nCPa), in broilers that were subjected to control or EHC. The nuclei were collected by punch biopsy at 3 time points relative to the start of heat challenge (0, 2 and 12 hours), total RNA was isolated, and RNA-sequencing was performed. Transcript abundance was quantified and differentially expressed genes (DEG) identified, and gene ontology analyses were performed. In the nCPa, 469 DEGs were identified across the 3 timepoints. There were 0 DEGs at hour 0, 2 at hour 2, and 467 at hour 12. The gene ontology analysis on nCPa hour 12 samples revealed enrichment of 5 biological processes including mitochondrial electron transport, mitochondrial respiratory chain complex 1 assembly, synaptic vesicle lumen acidification, protein export from nucleus, and aerobic respiration. Most of these genes were down-regulated suggesting that these processes were less functional in EHC chicks. In the POAH, total 18 DEGs were identified, with 0 at hour 0, 18 at hour 2, and 0 at hour 12. Fewer differences were observed in the PVN, with only 4 DEGs identified. All 4 were up-regulated in the EHC group, with 2 being involved in hypothalamic thermal responses: vasoactive intestinal peptide transporter 1 (VIPR1) and caprin family member 2 (CAPRIN2). We also compared expression across time. There were no differences identified in the POAH or PVN. In the nCPA, no differences were detected for hour 2 vs. hour 0, however; the comparison between hour 12 and 2 yielded 9 DEGs. All except 1 were down-regulated at hour 12. The hour 12 vs. 0 comparison revealed 49 DEGs of which 24 were downregulated at hour 12. In conclusion, results revealed some pathways associated with energy metabolism that were altered in response to EHC, with most differences in the nCPa. Surprisingly, fewest differences were observed in the PVN. Findings provide some future target regions, such as the nCPa, and metabolic pathways to better understand how EHC affects stress responses and energy homeostasis later in life.

overall_design: eggs were kept at 26.6ºC for 12 hours and then were randomly divided into a control and embryonic heat conditioning (EHC) group. These groups were separated into two incubators (Rite Farm Products Pro-1056) and labeled control and EHC, respectively. Both groups from embryonic day (ED) 0-7 were incubated at 37.5ºC and 80% relative humidity. The eggs in the control group continued to be incubated at 37.5ºC until hatch at ED 21. The EHC group was separated from the control group at ED 7 and introduced to an increase in temperature to 39.5ºC and 80% relative humidity for 12 hours per day (07:30–19:30), and 37.5ºC for the remainder of the 24 hours until ED 16. The EHC group then spent the remaining 5 days at 37.5ºC until hatch. After ED 18.5, all eggs were subjected to candling. Infertile eggs and dead embryos were removed from the study. Eggs with viable embryos were transferred to a common hatching incubator (Rite Farm Products Pro-264) and maintained within their separate groups (separate enclosed trays to prevent mixing of treatments) at 36.9ºC and 50% relative humidity for 18 hours. The temperature was gradually decreased to 35ºC until the hatch was collected. Hatched chicks were arbitrarily divided into group cages based on treatment in preparation for the acute day 4 post-hatch heat challenge. The holding room temperature was set at 30ºC, with ad libitum access to food and water, and 24 hr continuous light exposure, similar to our previous studies. On day 4 post-hatch, Control and EHC groups were subjected to an acute heat challenge at 36ºC. Samples were collected at three timepoints: 0 (before heat challenge; baseline), 2 hours, and 12 hours from the start of the increased temperature. Within these three time points, 10 birds were collected and euthanized from control and EHC groups, with 20 birds total for each time point. Chicks were weighed individually, euthanized by decapitation, and sexed via gonad identification.

first: Elizabeth

last: Gilbert


title: RNA-Seq analysis of rat pancreatic tissue from control and acute pancreatitis models

city: 安徽省合肥市新站区

first: 诗亚

last: 马

address: 安徽省合肥市瑶海区银领时代

institute: Anhui Medical University

summary: This study investigates gene expression changes in the pancreas of rats with acute pancreatitis induced by intraperitoneal injection of L-arginine (2*2.5 g/kg, 48 hours) compared to saline-injected controls. High-throughput RNA-Seq was used to explore the transcriptomic differences.

overall_design: Sprague-Dawley rats were randomly divided into control and acute pancreatitis (AP) groups. The control group received an intraperitoneal injection of saline, while the AP group received an intraperitoneal injection of L-arginine at 2*2.5 g/kg. Samples were collected 48 hours after treatment, and total RNA was extracted for transcriptome sequencing using the Illumina Ten platform.

first: Shiya

last: Ma

first: Zhiyu

last: Han

first: Xueying

first: Zhaojian

last: Shen

first: Weili

last: Yu


title: Role of progesterone receptor in inguinal hernia formation via skeletal muscle fibrosis [Hernia_Xenium]

city: Chicago

first: Serdar

middle: E.

last: Bulun

state: IL

address: 303 E Superior Street

department: Obstetrics & Gynecology

institute: Northwestern Feinberg School of Medicine

summary: Inguinal hernia development has been linked to fibrosis and atrophy of the lower abdominal muscle (LAM). We have shown that exogenous adminstration of estradiol (E2) and progesterone (P4) in mice can induce LAM fibrosis, muscle atrophy, and hernia development in mice, and that concurrent inhibition of progesterone receptor signaling using the drug RU486 can prevent this process. Utilizing a combination of single-nuclear transcriptomics and epigenomics, we analyzed the effects of E2 and P4 on the different cell types in the LAM to determine how these compounds contribute to hernia development. Xenium spatial transcriptomics of LAM tissue of treated WT mice allowed for validation of cell type colocalization and differential gene analysis.

overall_design: In this study, LAM sections were harvested from WT mice after 10 weeks of treatment with vehicle, E2+P4, or E2+P4+RU486 and analyzed using Xenium spatial transcriptomics from 10X Genomics.

first: Tianming

last: You

first: Mehrdad

last: Zandigohar

first: Yang

last: Dai

first: Hong

last: Zhao

middle: E


title: Role of progesterone receptor in inguinal hernia formation via skeletal muscle fibrosis [Hernia_Multiomics]

summary: Inguinal hernia development has been linked to fibrosis and atrophy of the lower abdominal muscle (LAM). We have shown that exogenous adminstration of estradiol (E2) and progesterone (P4) in mice can induce LAM fibrosis, muscle atrophy, and hernia development in mice, and that concurrent inhibition of progesterone receptor signaling using the drug RU486 can prevent this process. Utilizing a combination of single-nuclear transcriptomics and epigenomics, we analyzed the effects of E2 and P4 on the different cell types in the LAM to determine how these compounds contribute to hernia development.

overall_design: Multiome-seq: single nuclei were extracted from LAM of WT mice after 10 weeks of treatment with vehicle, E2+P4, or E2+P4+RU486. Joint snRNA and snATAC libaries were prepared using the 10x Genomics platform.


title: Quantitative phase imaging with temporal kinetics predicts hematopoietic stem cell diversity

city: Minato-ku

first: Takaharu

last: Kimura

state: Tokyo

address: 4-6-1 Shirokanedai

institute: The University of Tokyo

summary: Innovative identification technologies for hematopoietic stem cells (HSCs) have advanced the frontiers of stem cell biology. Clinically, the functional quality of HSCs profoundly influences the safety and therapeutic efficacy of stem cell treatments. However, most analytical techniques capture only a single snapshot, disregarding the temporal context. A comprehensive understanding of the temporal heterogeneity of HSCs necessitates live-cell, real-time and non-invasive analysis. Here, we developed a prediction system for HSC diversity by integrating single-HSC ex vivo expansion technology with quantitative phase imaging (QPI)-driven machine learning. By analyzing single-cell kinetics with QPI, we discovered previously undetectable diversity among HSCs that snapshot analysis fails to capture. Our QPI-driven algorithm quantitatively evaluates the stemness of individual HSCs and incorporates temporal information to significantly improve prediction accuracy. This platform marks a paradigm shift from "identification" to "prediction", enabling us to forecast HSC quality by analyzing their past temporal kinetics.

overall_design: Single-cell RNA sequencing : Ex vivo expanded HSCs were collected for single-cell RNA sequencing.

first: Takao

last: Yogo

first: Satoshi

last: Yamazaki


title: Helminth-induced prostaglandin signalling and dietary shifts in PUFA metabolism promote colitis-associated cancer.

city: Cardiff

first: Katherine

middle: Ann

last: Smith

address: Museum Avenue

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

summary: Oxylipins derived from dietary polyunsaturated fatty acids (PUFAs) are key determinants of intestinal health, homeostasis and inflammatory disorders, such as colitis-associated colorectal cancer (CAC). Previous research has independently linked a high dietary omega (ω)-6:ω-3 PUFA ratio, or intestinal helminth infection, to an increased risk of CAC. However, whether these two factors interact to exacerbate disease risk and whether oxylipins contribute to this is unknown. In this study, we report that infection with the helminth Heligmosomoides polygyrus bakeri (Hpb) exacerbates tumour formation when combined with a high ω-6:ω-3 PUFA ratio diet. Dietary increases in tumour burden correlated with heightened levels of arachidonic acid (AA) and AA-derived lipoxygenase (LOX) oxylipins in the colon, including the 12/15-LOX product 12-hydroxyeicosatetraenoic acid, prior to disease onset. Although helminth infection further increased the production of 12/15-LOX oxylipins and increased expression of Alox15, responsible for producing these metabolites, inhibition of cyclooxygenase-dependent prostaglandin production with aspirin prevented helminth-exacerbation of disease. Helminth-infected mice exhibited increased phosphorylation of β-catenin in the colon, which was inhibited by EP2 and 4 antagonists. Moreover, administration of an EP agonist increased tumour burden in naive mice fed a high w-6:w-3 PUFA ratio diet, to the levels seen in helminth-exacerbation of disease. These data suggest that dietary changes in fatty acid composition coordinate with helminth-induced activation of EP signalling to exacerbate tumour development.

overall_design: Naive mice were fed a low omega-6 diet or a modified AIN-76A diet with a high omega-6:omega-3 ratio (mAIN-76A) for one week, then infected with 200 Heligmosomoides polygyrus bakeri L3 larvae for 14 days (Hpb), or maintained as naïve uninfected controls, before RNA-seq analysis of the colon.

first: Ella

middle: K

last: Reed


title: CNS infiltration by Tet2-mutant peripheral myeloid cells protects from Alzheimer’s Disease

city: Houston

first: Hu

last: Chen

state: TX

address: 1250 Moursund St,

department: Pediatrics

institute: Baylor College of Medicine

summary: Bone marrow-derived peripheral immune cells have been found to infiltrate the brain in many neurodegenerative diseases, such as Alzheimer's disease (AD). Using a mouse transplant model of AD (5xFAD mice), we found that loss of the clonal hematopoiesis associated gene Tet2 within peripheral immune cells led to increased myeloid cell brain infiltration when compared to mice with either wildtype or Dnmt3a-mutant peripheral immune cells. scRNA-seq on either CD11a-enriched or CD45-enriched brain cells from 5xFAD mice transplanted with either wildtype, Tet2-/- or Dnmt3a-/- bone marrow, confirmed our finding that loss of Tet2 leads to increased peripheral myeloid cell brain infiltration in AD mice. scRNA-seq identified that the change in infiltrating peripheral immune cells was primarily attributed to increased M1 macrophages and non-classical monocytes in the brains of 5xFAD mice with Tet2-mutant bone marrow. We further identified the upregulation of chemotaxis and migration related pathways in Tet2-mutant infiltrating macrophages and monocytes when compared to wildtype or Dnmt3a-mutant infiltrating cells, providing a mechanism by which loss of Tet2 in peripheral immune cells leads to increased brain infiltration in an AD setting.

overall_design: Single cells were isolated from the brains of 5xFAD mice transplanted with wildtype, Tet2-/- or Dnmt3a-/- bone marrow and sequenced using 10X Genomics scRNAseq. Samples labeled as "main" are CD11a-enriched cells from transplanted 5xFAD mice that were treated with eight weekly doses of 1mg/kg LPS following transplantation. Samples labeled as "validation" are CD45-enriched cells from transplanted 5xFAD mice that did not recieve LPS treatment.

first: Katie

last: Matatall

first: Guantong

last: Qi

first: Julia

last: Belk

first: Hind

last: Bouzid

first: Siddhartha

last: Jaiswal

middle: Y

last: King


title: Association of Gut Microbiota and Immune Gene Expression with Response to Targeted Therapy in BRAF-mutated Melanoma

city: Malaga

first: Mora

last: Guardamagna

state: --- Select One ---

address: Severo Ochoa 35

country: Spain

institute: IBIMA

summary:
Gut microbiota has been associated with carcinogenesis and immune regulation. While there is evidence supporting its influence on immunotherapy response in melanoma, its impact on BRAF/MEK-targeted therapy remains unexplored. This study assessed gut microbiota composition and immune-associated genes in melanoma, to generate hypothesis on prognostic and predictive biomarkers for BRAF/MEK inhibitor therapy.
We hypothesize that GM composition may influence responses to treatment or toxicity in patients receiving iBRAF/MEK therapy. Specific microorganisms may serve as prognostic or predictive biomarkers of response, as well as of treatment-related adverse events. Additionally, genes associated with immune activation could further refine prognostic and predictive models. By identifying biomarkers for early prediction of response and microorganisms linked to treatment efficacy and toxicity, our findings aim to contribute to the development of microbiota-modulation strategies that could enhance therapeutic outcomes in specific contexts.

overall_design: Prospective, observational. 24 patients were analyzed for gene expression analyses and 20 patients for gut microbiota (01, 03, 05, 06, 07, 08, 09, 10, 11,15, 16, 18, 20, 21, 22, 23, 25, 26, 27, 28 - gut microbiota data available in the NCBI repository, accession number PRJNA1272598)

first: Miguel

last: Berciano-Guerrero

first: Rocío

last: Lavado-Valenzuela

first: Édouard

last: Auclin

first: Juan

last: Onieva Zafra

first: Isaac

last: Plaza Andrades

first: Javier

last: Oliver

first: Alicia

last: Garrido-Aranda

first: Elisabeth

last: Perez-Ruiz

first: Martina

last: Álvarez

first: María

middle: C

last: Ocaña

middle: I

last: Queipo-Ortuño

first: Isabel

last: Barragán

first: Antonio

last: Rueda-Dominguez


title: Histone deacetylase inhibitors target regulators of DNA replication and the cellular response to DNA replication stress in Ewing sarcoma cells

city: Iowa City

first: David

middle: Jon

last: Gordon

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

summary: DNA replication stress is common feature of multiple tumor types. Histone deacetylases (HDAC) regulate diverse pathways in cancer cells and recent work has identified that HDAC inhibitors downregulate the expression of multiple proteins with critical roles in DNA replication and the cellular response to DNA replication stress, including the RRM1 and RRM2 subunits of ribonucleotide reductase (RNR), CHK1, and WEE1. RNA-seq analysis was performed on a Ewing sarcoma cell line to determine the effects of  HDAC inhibitors on the transcriptome.

overall_design: We performed RNA-seq in a Ewing sarcoma cell line treated with vehicle or HDAC inhibitors, romidepsin and panobinostat.

middle: J


title: Dynamic N6-Methyladenosine profiling during human lung progenitor cell differentiation from iPSCs

city: Guangzhou

first: Huilin

last: Huang

address: #651 East Dong-feng Road

institute: Sun Yat-Sen University Cancer Center

summary: Dynamic RNA N6-Methyladenosine (m6A) modifications are of essential significance in governing RNA synthesis and metabolism during embryonic development. Nevertheless, the comprehensive profile and functional mechanisms of m6A in the early phase of embryonic lung development remain largely elusive. To delineate the dynamic mapping of m6A and investigate the underlying regulatory mechanisms during the process of embryonic lung differentiation, we carried out picogram-scale m6A RNA immunoprecipitation and sequencing (picoMeRIP–seq) through out the stages of endoderm lung progenitor differentiation derived from human induced pluripotent stem cells (iPSCs).

overall_design:
We first induced the generation of definitive endoderm (DE), anterior foregut endoderm (AFE), and lung progenitor (LP) cells from induced pluripotent stem cells (iPSCs). Subsequently, we carried out picogram-scale m6A RNA immunoprecipitation and high-throughput sequencing (picoMeRIP–seq) with the aim of simultaneously capturing the m6A epitranscriptome and transcriptome throughout the entire differentiation process.

***************************************************************
The raw and processed data for this Series are available in the China National Center for Bioinformation (https://ngdc.cncb.ac.cn/) under accession number HRA012195 in compliance with the Chinese government's regulations on human genetic information.
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first: Shenghua

last: Dong

first: Junjie

last: Pang

first: Yushuai

last: Wang

first: Hengyou

last: Weng


title: scRNA-seq of LSK cells isolated from lean and obese mice

city: New York

first: Timothy

middle: Craigin

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University Irving Medical Center

summary: Obesity is known to affect bone marrow hematopoietic stem and progenitor cells (HSPCs). We used single cell RNA sequencing (scRNA-seq) to analyze the differences in HSPCs isolated from lean and obese mice.

overall_design: Male C57Bl6/J mice were fed a low-fat diet (LFD, 10% kcal from fat) or a high-fat diet (HFD, 60% kcal from fat) for 24 weeks, then Lin- Sca-1+ c-Kit+ (LSK) cells were isolated from the bone marrow and single scell RNA seq libraries were prepared using the Chromium Single Cell 3’ Library and Gel Bead Kit v.2 from 10x Genomics

first: Quin

middle: T

last: Waterbury


title: Single cell transcriptional profile of Zika-infected iPSC-derived neural cells

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: We used single cell RNA sequencing to evaluate the transcriptional response to Zika infection in human induced pluripotent stem cell (iPSC)-derived neural cells. We sought to compare the consequences of Zika infection in purified neural progenitor cells (NPCs) to differentiated neural cells (DIFF). As an additional comparator, we  also included NPCs and DIFF cells treated with interferon-beta.

overall_design: NPCs were differentiated into mixed mature neural cell types (DIFF) over 6 weeks; these were compared to freshly passaged NPCs. Cells from both conditions (NPCs and DIFF) were then treated with one of the following four treatment conditions: 1. Zika infection for 48 hours; 2. MOCK infection using NPC-conditioned medium; 3. IFNb treatment for 6 hours; 4. untreated as a control

first: Caleb

last: Stokes

first: Leanne

last: Whitmore

first: Dante

last: Moreno

first: Jennifer

last: Tisoncik-Go

first: Elise

last: Smith

first: Jessica

last: Young

last: Gale Jr


title: Mitochondria-selective primate cell fusions reveal functional consequences of mitochondrial divergence

city: Dallas

first: Leijie

last: Li

state: Texas

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

summary: Interspecies composite cell lines (or hybrid cells) are powerful tools to study genomic divergence between species. However, to date, the only pluripotent composite lines to exist are between human and chimpanzee. In addition, while these human-chimp composite lines contain the nuclear genomes from both species, they only contain the mitochondrial genome from one: human. Here we describe the generation of multiple composite pluripotent stem cell (PSC) lines between human and all other species of great apes (chimpanzee [Pan troglodytes], bonobo [Pan paniscus], gorilla [Gorilla gorilla], and orangutan [Pongo abelii]). In addition, we utilized a strategy based on enforced mitophagy to generate human-great ape composite PSCs that contain either the human or the non-human primate (NHP) mitochondrial genomes.

sample_organism:
Pan troglodytes
Pongo abelii
Homo sapiens

overall_design: To compare composite PSCs harboring human mtDNA vs those that harbor NHP mtDNA by RNA-Seq.

first: Daniel

last: Schmitz

first: Rashmi

last: Dahiya

first: Emily

last: Ballard

first: Jun

last: Wu


title: Quantification of transcript isoforms at the single-cell level using SCALPEL

city: L'Hospitalet de Llobregat

first: Mireya

last: PLASS

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: P-CMRC

institute: IDIBELL

summary: 3' based single-cell RNA sequencing (scRNA-seq) has enabled the study of gene expression at the individual cell level and the development of few methods to quantify transcriptomic variability at the single-cell level. Yet, most of these methods have low sensitivity and specificity. Here, we present SCALPEL, a new tool to quantify and characterize transcript isoforms at the single-cell level using standard 3' based single-cell transcriptomics data. SCALPEL predictions have higher sensitivity than that of other tools and can be validated experimentally. We have used SCALPEL to study the changes in isoform usage during mouse spermatogenesis and in the differentiation of induced pluripotent stem cells (iPSCs) to neural progenitors (NPCs). These analyses confirmed known changes in the 3' UTR length during cell differentiation and allowed the identification of new cell populations and cell type specific microRNA signatures controlling isoform expression in individual cells. Together, our results highlight the importance of isoform quantification to gain insight on the gene regulatory mechanisms at the single-cell level.

overall_design: Human induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs) derived from the same iPSc were dissociated to performe single-cell RNAseq analysis

first: Franz

last: Ake

first: Marcel

last: Schilling

first: Sandra. M

last: Fernández-Moya

first: Akshay Jaya

last: Ganesh

first: Ana

last: Gutiérrez-Franco

first: Lei

last: Plass


title: Chemerin sustains the growth of spongiotrophoblast and sinusoidal trophoblast giant cells through fatty acid oxidation

city: Shenzhen

first: Chen

last: Huang

state: Guangdong

address: 1068 Xueyuan Avenue, Shenzhen University Town

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

summary:
Background
Placental metabolic abnormalities are linked to pregnancy complications such as preeclampsia, gestational diabetes mellitus, and fetal growth restriction. However, little is known about how the metabolic processes regulate placental development and trophoblast differentiation. The adipokine chemerin has elevated serum levels in pregnant women and regulates placental lipid metabolism, potentially playing a role in both placental development and trophoblast differentiation.
Results
In this study, we observed the increased chemerin expression on the serum and placenta from the pregnant mice. Chemerin is highly expressed in the extraembryonic primary parietal trophoblast giant cells and the ectoplacental cone (EPC) trophoblast cells. Excessive chemerin treatment in mice results in the increased placental lipid accumulation, promotes the expansion of glycogen trophoblast cell (GlyT) and syncytiotrophoblast, and restricts the growth of spongiotrophoblast (SpT) and sinusoidal trophoblast giant cell (S-TGC). Chemerin deficiency led to increased expression of placental fatty acid oxidation enzymes and disrupted the proliferation of SpT and S-TGC in the labyrinth. Furthermore, we utilized the fatty acid oxidation inhibitor etomoxir, demonstrated that blocking fatty acid oxidation hinders the proliferation of SpT and S-TGC in the labyrinth.
Conclusions
Our study demonstrated that chemerin-related lipid metabolism is crucial for EPC trophoblast differentiation during placental development, providing evidence that chemerin determines the growth of SpT and S-TGC through fatty acid oxidation. These findings also imply a possible pathological mechanism for pregnancy complications associated with chemerin.

overall_design: RNA-seq profiling of  placentas from C57BL/6 Wild type mice (4mice) and chemerin knockout mice(4 mice)  at embryonic day 18.5

first: Jiaxuan

last: Cai

first: Suohao

last: Peng


title: Single cell transcriptional profile of Zika-infected human primary fetal brain cells

first: Michael

last: Gale

summary: We used single cell RNA sequencing to evaluate the transcriptional response to Zika infection in human primary fetal brain tissue. Two separate isolates of Asian-lineage Zika virus were used to infect cells, and exogenous treatment with interferon-beta was used as a control.

overall_design: The experimental design consisted of two virally-infected samples, each infected for 48hrs with a separate strain of Zika virus; a Brazilian isolate (BRZ) and a Cambodian isolate (FSS). As a control for viral infection, a third (MOCK) sample was treated with 5% FBS (to mimic viral inoculation medium). A fourth sample was treated with interferon beta (100 IU/mL) for six hours.

first: Caleb

last: Stokes

first: Leanne

last: Whitmore

first: Dante

last: Moreno

first: Jennifer

last: Tisoncik-Go

first: Elise

last: Smith

last: Young

last: Gale Jr.


title: Fusobacterium nucleatum Promotes Metastasis of Breast Cancer via the miR-21-3p/FOXO3 Axis

status: Public on Jun 02 2025

city: qingyuan

first: Zhongzhong

last: Guo

address: No.35, Yinquan North Road, Qingcheng District, Qingyuan Guangdong, China, 511518.

institute: The Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose: This study aims to investigate the impact of Fusobacterium nucleatum (F. nucleatum) infection on distant metastasis in breast cancer and its underlying mechanisms. Materials: Clinical breast cancer samples were collected, and F. nucleatum was identified through bacterial isolation and culture. In vitro and in vivo infection models were established using the isolated bacteria. The impact of F. nucleatum infection on breast cancer cell proliferation and migration was evaluated. High-throughput sequencing and bioinformatics analyses were performed to identify microRNAs exhibiting significant expression changes following F. nucleatum infection. Gene knockdown of miR-21-3p was utilized to assess its role in F. nucleatum-mediated epithelial-mesenchymal transition and cell migration. Online databases predicted the downstream targets of miR-21-3p, which were subsequently validated in cell models. Additionally, the effect of silencing FOXO3 on F. nucleatum-induced cell migration was examined. Results: Both in vitro and in vivo experiments showed that F. nucleatum infection did not affect cell proliferation but significantly enhanced EMT and migration. miR-21-3p was significantly upregulated after infection, and silencing it reduced F. nucleatum-induced migration. FOXO3 was identified as a downstream target of miR-21-3p, and silencing FOXO3 further enhanced cell migration. Conclusion: F. nucleatum promotes breast cancer cell migration through the miR-21-3p/FOXO3 pathway. This study highlights the role of F. nucleatum in breast cancer metastasis and suggests potential therapeutic targets for intervention.

overall_design: Collect fresh clinical breast cancer tissues and adjacent non - cancerous tissues for RNA - sequencing analysis.


title: Chromatin accessibility of hematopoietic stem/progenitor cells (HSPCs) derived from MDS patients before and after disease progression

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

summary: Myelodisplastic syndromes are a oligoclonal disease starting at the level of the stem/progenitor compartment. We used ATACseq to determine  changes in chromating landscape between MDS low and high risk samples.

overall_design: ATAC-seq of CD34+ HSCPs from MDS patients before and after disease progression

first: Paloma

last: Garcia

first: Carl

last: Ward

first: Ildem

last: Akerman


title: Estrogens determine the efficacy of cancer immunotherapy in obese males with melanoma

city: Bern

first: Carole

last: Bourquin

address: Rosenbühlgasse 27

country: Switzerland

institute: University of Bern

summary: Although obesity is a major risk factor for cancer, it may also improve the response to cancer therapy. Here we investigated the impact of obesity on the efficacy of immune checkpoint inhibitors. In male mice, obesity promoted tumor growth but enhanced the response to ICI. In contrast, in non-obese mice, no difference in tumor growth was observed between mice receiving anti-PD-1 or isotype control antibodies.Using transcriptome analysis of bulk tumors, we showed a distinct effect of anti-PD-1 treatment in obese versus non-obese mice. We further compared the gene expression profile of tumors from obese and non-obese mice in absence of treatment to investigate the mechanisms behind the increased efficacy of anti-PD-1 in obese mice. Our findings suggest that estrogens could be an obesity-derived factor modulating the sensitivity to PD-1 blockade in male mice.

overall_design: RNA-seq profiling of bulk B16-F10 tumors isolated from either isotype control or anti-PD-1-treated obese and non-obese male mice.

first: Eloïse

last: Dupuychaffray

first: Hélène

last: Poinot

first: Montserrat

last: Alvarez

first: Betül

last: Taskoparan

first: Eliana

last: Marinari

first: Valérie

last: Dutoit

first: Aurélien

last: Pommier


title: The mechanosensitive adhesion G protein-coupled receptor GPR133/ADGRD1 enhances bone formation – a potential new target for osteoporosis treatment

city: Leipzig

first: Linnaeus

middle: Tapia

last: Bundalian

address: 15 Albert-Scwheitzer Str.

institute: Universitatklinikum Leipzig

summary: Osteoporosis poses an increasing health and socioeconomic burden on aging societies. Current therapeutic options often present potentially severe side effects or lack long-term efficacy, underscoring the need for more effective treatments. Establishing novel drug targets requires an in-depth understanding of their physiological roles. Here, we describe the impact of the adhesion G protein-coupled receptor GPR133/ADGRD1 on osteoblast differentiation and function. Constitutive and osteoblast-specific knockouts of GPR133/ADGRD1 in mice result in reduced cortical bone mass and increased trabecularization in femurs and vertebrae—features characteristic of osteoporosis. Genome-wide association studies in humans link GPR133/ADGRD1 gene variants to differences in bone mineral density and body height. At the molecular level, GPR133/ADGRD1 influences osteoblast function and differentiation through a combined activation mechanism involving interaction with its endogenous ligand PTK7 and mechanical forces. In vitro analysis shows that osteoblast differentiation is driven by cAMP-dependent activation of the b-catenin signaling pathway. Activation of GPR133/ADGRD1 with the receptor-specific ligand AP503 promotes osteoblast function and differentiation both in vitro and in vivo, significantly alleviating osteoporosis in a mouse ovariectomy model. This renders GPR133/ADGRD1 a promising therapeutic target for osteoporosis and other diseases characterized by reduced bone mass.

overall_design: Comparative RNA-Seq profiling of wildtype and Gpr133/ADGRD1-deficient hearts from C57BL/6J mice. The embryonic stem cell line carrying the Adgrd1tm1a(EUCOMM)Wtsi allele was purchased from the European Conditional Mouse Mutagenesis Program (EUCOMM) and injected into 129/SV/J blastocysts. The chimeric mice were crossed with WT C57BL/6J mice for more than 12 generations to exclude potential strain-related effects.

first: Juliane

last: Lehmann

first: Christian

last: Ullmann

first: Luisa

last: Bayer

first: Torsten

last: Schöneberg

first: Martina

last: Rauner

first: Jinpeng

last: Sun

first: Ines

last: Liebscher


title: Genome-wide transcriptome analysis of integrin β1 inhibited primed and naïve human induced pluripotent stem cells.

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

country: Finland

institute: University of Turku

summary: Cell states are governed by cell-intrinsic properties and external cues that regulate cell shape and signaling via cell-cell junctions or adhesions. Integrin β1-mediated adhesion is dispensable in early mouse embryogenesis at pre-implantation but becomes indispensable post-implantation. This implies distinct roles for β1-integrins in the naïve pre-implantation and primed post-implantation pluripotent stem cells (PSC). These, however, remain poorly understood. We investigated β1-integrin control of naïve-like and primed human induced PSC (hiPSC). We find that integrin β1 is active in naïve and primed hiPSCs and the degree of activity varies in vitro on different ECMs. Inhibition of integrin β1 in primed hiPSCs induces naïve-like colony features, reduces actomyosin contraction and ERK activity and alters gene expression, indicative of more naïve-like features. Integrin β1 inhibition supports epigenetic reversion of primed PSC to a naïve-like status, which involves dramatic reorganization of colony morphology, actin and adhesions. Furthermore, continued β1 integrin inhibition facilitates the maintenance of a naïve-like state through gene expression. These data reveal unprecedented integrin-dependent regulation of PSC states and demonstrate how integrin inhibitors may help to fine-tune hiPSC function and properties in vitro.

overall_design: Examination of primed and naïve hiPSCs after integrin β1 function-blocking antibody (MAb13; anti-β1) or IgG (control) treatment (12h in primed, 48h in naïve).

first: Maria

last: Taskinen


title: Olaparib induced NAMPT and circPTTG1IP expression promoted cell survival and contributed to drug resistance in glioblastoma cells

city: 丰台区

first: xiaowei

last: Sha

state: 北京市

address: 北京市丰台区首都医科大学

institute: Capital Medical University

summary: Glioblastoma (GBM) is an aggressive brain cancer that is notoriously resistant to chemotherapy, particularly to Temozolomide (TMZ). In this study, we examined a patient-derived TMZ-resistant GBM cell line and assessed the effects of the PARP inhibitor Olaparib. We observed that while Olaparib exhibited significant tumor inhibition, its required dosage exceeded clinically acceptable levels. Transcriptomic analysis revealed a notable upregulation of nicotinamide phosphoribosyltransferase (NAMPT) in the surviving tumor cells, suggesting that increased intracellular NAD+ levels contributed to their resistance against both Olaparib and TMZ. By optimizing the dosages of Olaparib and FK866, a NAMPT inhibitor, we were able to develop a combination therapy that effectively killed TMZ-resistant GBM cells while adhering to clinically applicable pharmacodynamic and toxicological standards for each drug. This combination was also tested across other TMZ-resistant cell lines and 3D organoids, showing promising potential for clinical application. Additionally, through profiling plasma-detectable circRNA species from the combination treatment, we identified circPTTG1IP as a potential biomarker with negative predictive value. Further analysis indicated that circPTTG1IP might regulate NAMPT expression and NAD+ levels, potentially through its interaction with miRNAs targeting NAMPT. This research provides insights into a novel therapeutic strategy for overcoming TMZ resistance in GBM.

overall_design: Olaparib induced NAMPT expression promoted cell survival and contributed to drug resistance in glioblastoma cells

first: Xiaowei

first: Sifan

last: Meng

first: Jiaqian

last: Li

first: Jing

last: Wang

first: Yang

last: Si

first: Shan

last: Cheng

first: Wei

last: Ding


title: Astrocyte induction of disease-associated microglia is suppressed by acute exposure to fAD neurons in human iPSC triple cultures

city: Boston

first: Courtney

last: Benoit

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: Advancements in human induced pluripotent stem cell (hiPSC) technology have enabled co-culture models for disease modeling in physiologically relevant systems. However, co-culturing protocols face challenges in usability and consistency. Here, we introduce a robust, reproducible hiPSC-derived co-culture system integrating astrocytes, neurons, and microglia. This model leverages cryopreserved cells, enabling co-cultures within 20 days post-thaw. Comparing monocultures and tri-cultures, we show how cell-cell interactions shape transcriptional and functional states across all three cell types. Neurons in tri-culture exhibit increased spine density and activity, while astrocytes and microglia show altered responses to proinflammatory stimulation. Surprisingly, astrocyte co-culture induces upregulation of disease-associated microglia (DAM) genes, including TREM2, SPP1, APOE, and GPNMB. Additionally, while familial Alzheimer’s disease neurons induce a prototypical inflammatory response in microglia, the DAM signature is significantly downregulated. Collectively, this study establishes a versatile human tri-culture model as a valuable resource for dissecting neuron-glia interactions and their role in neurodegenerative disease.

overall_design: For triple culture (TC) conditions, iNs and iAs were differentiated to day 20 and iMGs were differentiated to day 40. On day 20, iAs were dissociated and replated on top of iN cultures. On day 21 (day 40 of iMG differentiation), iMGs were dissociated and replated on top of iN-iA co-cultures. All three cell types were then co-cultured together for an additional six days, after which they were dissociated and analyzed by single-cell RNA-sequencing. For TC samples, four independent culture wells were combined for each culture condition. For monoculture (MC) conditions, cells were differentiated and cultured in parallel to triple cultures under the exact same culturing conditions. For MC samples, four independent monocultures for each cell type (iN, iMG, iA) were pooled.

first: Alex

last: Lish

first: Richard

last: Pearse

first: Tracy

last: Young-Pearse


title: MOZ and HBO1 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia

first: Scott

last: Armstrong

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

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

overall_design: Refer to individual Series


title: MOZ and HBO1 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia [ChIP-Seq]

summary: NUP98 fusion oncoproteins (FOs) are a hallmark of childhood acute myeloid leukemia (AML) and drive leukemogenesis through liquid-liquid phase separation-mediated nuclear condensate formation. However, the composition and consequences of NUP98 FO-associated condensates are incompletely understood. Here we show that MYST family histone acetyltransferase (HAT) complex proteins including MOZ/KAT6A, HBO1/KAT7, and the common MOZ/HBO1 complex subunit BRPF1 associate with NUP98 FOs on chromatin and within condensates.  MYST HATs are molecular dependencies in NUP98-rearranged (NUP98-r) leukemia, and genetic inactivation or pharmacologic inhibition of Moz and Hbo1 impairs NUP98-r cell fitness. MOZ/HBO1 inhibition decreased global H3K23ac levels, displaced NUP98::HOXA9 from chromatin at the Meis1 locus, and led to myeloid cell differentiation. Additionally, MOZ/HBO1 inhibition decreased leukemic burden in multiple NUP98-r leukemia xenograft mouse models, synergized with Menin inhibitor treatment, and was efficacious in Menin inhibitor-resistant cells. In summary, we show that MYST family HATs are therapeutically actionable dependencies in NUP98-r AML.

overall_design: Chromatin immunoprecipitation DNA Sequencing (ChIP-Seq) for HA-tagged NUP98-fusion proteins, Kmt2a, and Brpf1 in NUP98-rearranged murine leukemia cells treated with DMSO, SNDX-5613, PF9363, or combination

first: Emily

middle: B

last: Heikamp

first: Charles

last: Hatton


title: Basal IFNλ2/3 expression regulates tight junction formation in human epithelial cells

city: Gainesville

first: Yagmur

last: Keser

state: Florida

address: 1200 Newell Dr.

department: Molecular Genetics and Microbiology (MGM)

institute: University of Florida

summary: Type III interferons (IFNλs) play crucial roles in antiviral defense and intestinal epithelial barrier integrity. While interferon expression has been primarily studied in response to pathogens, basal interferon expression occurs in pathogen-free environments. However, the mechanisms regulating basal IFNλ expression and its function have not yet been elucidated. Our findings reveal that basal IFNλ2/3 expression correlates with the development of an intact cellular epithelium characterized by formation of tight junctions and establishment of barrier function. We discovered that basal IFNλ2/3 expression depends on cGAS/STING-mediated mitochondrial DNA detection and is inhibited by the Hippo mechanotransduction pathway at low cellular densities. Notably, cells lacking basal IFNλ2/3 fail to develop proper tight junctions and barrier function. Mechanistically, we found that IFNλ2/3 negatively regulates claudin-2 expression, thereby promoting barrier formation as cells become confluent. These results demonstrate a previously unknown function of basal IFNλs in regulating epithelial cell junction formation and highlight their importance not only during pathogen challenges but also in maintaining epithelial cell function under steady-state conditions.

overall_design: To investigate  the interplay between cellular density and basal IFNλ signaling in human intestinal epithelial cells, we generated T84 IFNλ2/3 KO and IFNLR KO cells. T84 WT, IFNλ2/3 KO and IFNLR KO were seeded at high and low density. One day pos-seeding of low density and two-days post-seeding of high density, cells were harvested and sent for RNA sequencing.

first: Camila

last: Metz-Zumaran

first: Zina

middle: M

last: Uckeley

first: Megan

last: Stanifer

first: Steeve

last: Boulant


title: The Serine/Threonine Protein Phosphatase 6 Is Required for Efficient Gametogenesis in Sexual-Stage Plasmodium berghei

city: Shenyang

first: Xiaotong

last: Zhu

state: Liaoning

address: No. 77 Puhe Road Shenyang North NEW AREA

department: Department of Immunology

institute: China Medical University

summary: Protein phosphorylation plays a critical role during the development of malaria parasites. Here, we performed a functional analysis of the Plasmodium berghei Ser/Thr protein phosphatase 6 (PbPP6), which is associated with the plasma membrane of macrogametes and ookinetes. Compared to wild-type P. berghei, the genetic disruption of pbpp6 (∆pbpp6) resulted in reduced asexual growth of the parasites and prolonged survival of infected mice. The ∆pbpp6 parasites showed impaired gametogenesis, particularly affecting male gametogenesis, which substantially decreased both ookinete formation and mosquito transmission. Transcriptomic analysis revealed an over 11-fold downregulation of nek3, a regulator of MAPK2 within the PKG-Ca²⁺ signaling cascade, foreshadowing pathway dysregulation that was further evidenced by significantly diminished intracellular cGMP levels, decreased cytosolic Ca²⁺ mobilization, and reduced DNA replication in activated Δpbpp6 gametocytes. Phosphoproteomic analysis detected increased phosphorylation at the Ser508 site of guanylyl cyclase alpha (GCα), indicating that PbPP6 regulates cGMP-PKG-Ca2+ signaling through modulation of GCα activity during gametogenesis. Additionally, we observed altered expression of messenger ribonucleoproteins in the Δpbpp6 parasites, which may affect the translational repression of stored mRNAs in female gametocytes and impact post-fertilization development in mosquitoes. Collectively, this study highlights the potential of targeting PP6 to disrupt malaria transmission.

overall_design: 1 μg total RNA was extracted from purified gametocytes (The mice were treated with sulfadiazine (Sigma, 20mg/l in drinking water) at 3 dpi for 48 hrs to remove asexual stage parasites, and the activated gametocytes (25℃ for 15 min) were collected by using 48% Nycodenz) of Δpbpp6 and WT parasites using the Qiagen RNeasy kit (Qiagen, Dusseldorf, Germany) as per manufacturer’s instructions. The quantity, purity and integrity of the RNA were evaluated by 1.5% agarose gel electrophoresis and on a NanodropTM OneC spectrophotometer (ThermoFisher). The mRNA-seq libraries were constructed with 2 μg RNA using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China), which eliminates duplication bias in PCR and sequencing steps by using unique molecular identifiers (UMI) of 8 random bases to label the pre-amplified cDNA molecules (91). RNA-seq was performed from three biological replicates of the Δpbpp6 and WT parasites. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina, San Diego, USA). Raw sequencing data were first filtered by Trimmomatic (version 0.36) to remove the low-quality reads, and were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. RNA-seq reads from each sample was aligned to the PbANKA01 of the P. berghei ANKA reference genome using the STAR RNA-seq alignment tool (92). HTSeq tool (v.0.6.1) was used to count transcripts for each gene (93). Cuffdiff v2.1 was used as the default method for normalization (94), while differential expression analysis was conducted using DESeq2 (v.1.28.1) in R (v.4.04) (20). The false discovery rate (FDR) was calculated to control for multiple hypothesis testing. Genes with an adjusted FDR below 0.1 and a minimal log2Fold change (log2FC) of 1 were considered to be significantly differentially expressed. Clustering and PCA were performed in R to estimate sampling distribution in each experiment. GO analysis for differentially expressed genes were performed in PlasmoDB (95), with the Benjamini adjusted P-value cutoff of 0.1to determine statistically significant enrichment.

first: Yonghui

last: Feng

first: Wenyan

last: Gao

first: Chenqing

first: Dan

last: Zhou

first: Lin

last: Sun

first: Liying

first: Liwang

last: Cui

first: Yaming

last: Cao

first: Shuangrui

last: Shi


title: MOZ and HBO1 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia [RNA-Seq]

first: Scott

overall_design:
For RNA-seq experiments in Figure 6, murine NUP98-HOXA9 leukemia cells were treated with  DMSO, 500 nM PF9363, 2 uM SNDX-5613, or a combination of both (500 nM PF9363 + 2 uM SNDX-5613) for 72 hours. For RNA-seq experiments in Figure 7, human CD45+ cells were isolated from animals who were treated with vehicle or PF9363 for 30 days. Mice were sacrificed and bone marrow was harvested at the end of the treatment period on Day 54, and mouse cell depletion was performed to enrich for human CD45+ cells.
For RNA-seq experiments from CRISPR-edited cell lines, murine NUP98-HOXA9 leukemia cells constitutively expressing the CRISPR-Cas9 enzyme were transduced with lentivirus containing sgRNA targeting various components of the Kat6a/6b/7 complex. The plasmid encoding each sgRNA also contains an IRES-RFP. On day 4 following transduction, RFP+ cells were sorted and RNA and DNA were isolated. CRISPR editing efficiency was confirmed using PCR primers to amplify the sgRNA cut site, followed by Sanger sequencing and analysis using the Synthego ICE algorithm. RNA was used to generate RNA-seq libraries for analysis of differential gene expression upon genetic inactivation of each Kat6a/6b/7 component. A non-targeting sgRNA (NTC) was used as a control.

first: Emily

middle: A


title: Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing [WGBS-seq]

city: Badalona

first: José

middle: Luis

last: Sardina

address: Ctra de Can Ruti, Camí de les Escoles, s/n

institute: Josep Carreras Leukaemia Research Institute

type: Methylation profiling by high throughput sequencing

summary: We investigated the genome-wide DNA methylation dynamics occurring during the C/EBPa-driven B cell to macrophage transdifferentiation.

overall_design: We utilized Whole Genome Bisulfite Sequencing (WGBS-seq) to investigate DNA methylation changes across the genome at a nucleotide level during the process of C/EBPa-driven B cell to macrophage transdifferentiation. The analysis was carried out at four distinct time points (0 hours, 24 hours, 96 hours, and 168 hours).

first: G

last: Valcárcel

first: A

middle: V

last: López-Rubio

first: J

middle: L


title: Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing [RNA-seq, transdifferentiation]

summary: We examine the differential transcriptional dynamics during the C/EBPa-driven transdifferentiation of B-cells into iMacs in cells with experimentally induced hypermethylation of the IL1RN gene promoter.

overall_design: We conducted RNA-seq experiments to examine how gene expression changes in cells that underwent hypermethylation editing at the IL1RN promoter using CRISPR-dCas9-DNMT3A during transdifferentiation. We compared the edited cells (sgIL1RN) to non-edited cells (CTRL) at three different time points (0 days -B cells-, 3 days, and 7 days -iMacs-) using biological duplicates.


title: Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing [dCas9-DNMT3A ChIP-seq]

summary: To investigate the genome-wide occupancy of the DNA methylation editing tool dCas9-DNMT3A in cells harboring non-targeting sgRNAs (CTRL) and cells harboring sgRNAs targeting the IL1RN promoter (sgIL1RN).

overall_design: We analyzed the occupancy of dCas9-DNMT3A using chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq). We compared IL1RN methylation-edited cells (sgIL1RN) with non-edited cells (CTRL) using biological duplicates.


title: Novel enzyme-based reduced representation method for DNA methylation profiling with low inputs

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

summary: DNA methylation at cytosine-phospho-guanine (CpG) residues is a vital biological process that regulates cell identity and function. Although widely used, bisulfite-based cytosine conversion procedures for DNA methylation sequencing require high temperature and extreme pH, which leads to DNA degradation, especially among unmethylated cytosines. This disproportionate damage to unmethylated cytosines contributes to inaccuracies in GC content representation. EM-seq, an enzyme-based cytosine conversion method, has been proposed as a less biased alternative to methylation profiling. Compared to bisulfite-based methods, EM-seq boasts greater genome coverage with less GC bias and has the potential to cover more CpGs with the same number of reads (i.e., higher signal-to-noise ratio). Reduced representation approaches enrich samples for CpG-rich genomic regions, thereby enhancing throughput and cost effectiveness. We hypothesized that enzyme-based technology could be adapted for reduced representation methylation sequencing to enable high-resolution DNA methylation profiling on low inputs samples. We leveraged the well-established differences in methylation profile between mouse CD4+ T cell populations to compare reduced representation EM-seq (RREM-seq) performance against our previously published modified reduced representation bisulfite sequencing (mRRBS). While the mRRBS method failed to generate reliable DNA libraries when using <2-ng inputs (equivalent to DNA from around 350 cells), the RREM-seq method successfully generated DNA libraries from 1–25 ng of mouse and human genomic DNA. These libraries fell within the expected size range, and primer contamination was not observed. Low-input (<2-ng) RREM-seq libraries’ final concentration, regulatory genomic element coverage, and methylation status within the lineage-defining Treg cell-specific super-enhancers were comparable to mRRBS libraries with more than 10-fold higher DNA input. RREM-seq libraries also successfully detected the methylation differences between alveolar Tconv and Treg cells in mechanically ventilated patients with severe SARS-CoV-2 pneumonia. Our results suggest that the RREM-seq method can generate reliable libraries for single-nucleotide resolution methylation profiling using low input clinical samples.

overall_design:
DNA libraries for methylation sequencing were generated using flow cytometry-sorted splenic CD4+ conventional T cells (Tconv cells) and CD4+CD25+FOXP3+ regulatory T cells (Treg cells) from healthy mice and paired alveolar CD4+ Tconv and Treg cells from mechanically ventilated patients with severe SARS-CoV-2 pneumonia.

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Submitter states that missing raw data are being made available for controlled access in dbGaP.
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middle: D

first: Qianli

last: Liu


title: Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing [DNA methylation arrays]

summary: We assessed both on-target and off-target DNA methylation editing events following targeting with dCas9-DNMT3A to the IL1RN locus in cells undergoing B to macrophage transdifferentiation.

overall_design: We used DNA methylation arrays (Illumina Infinium MethylationEPIC v2.0 Bead-Chip arrays) to study genome-wide DNA methylation changes in cells that underwent CRISPR-dCas9-DNMT3A-induced hypermethylation editing at the IL1RN promoter (sgIL1RN) during the C/EBPa-induced transdifferentiation of human B cells (BlaER) into macrophages. We compared these edited cells to non-edited cells (CTRL). The analysis was conducted at two different time points (0 hours -B cells- and 3 days) using biological quadruplicates.


title: Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing [RNA-seq, IL1B treatment]

summary: We analyzed the differential transcriptional response to IL-1β treatment in cells with experimentally induced hypermethylation of the IL1RN gene promoter.

overall_design: We used RNA-seq to investigate how gene expression changes in C/EBPa-B cell-derived macrophages (iMacs) in response to IL-1β treatment after undergoing CRISPR-dCas9-DNMT3A-induced hypermethylation editing at the IL1RN gene. We compared the gene expression in the edited iMacs (sgIL1RN) to that in non-edited iMacs (CTRL) at three different time points (0 hours, 3 hours, and 16 hours), using biological duplicates for each time point.


title: Drosophila males differentially express small proteins regulating stem cell division frequency in response to mating

city: Athens

first: Cordula

last: Schulz

state: ga

address: 136 Cedar Street

institute: University of Georgia, Athens

summary: : The germline stem cells (GSCs) in the male gonad of Drosophila can increase their division frequency in response to a demand for more sperm caused by repeated mating.  However, the molecules and mechanisms regulating and mediating this response have yet to be fully explored. Here, we present the results of a transcriptome analysis comparing expression from the testis tips from non-mated and mated males. An overlapping set of 18 differentially expressed genes (DEGs) from two independent wild-type (wt) strains revealed that the majority of the DEGs encode secreted proteins, which suggests roles for them in cell-cell interactions. Consistent with a role for secretion in regulating GSC divisions, knocking down Signal Recognition Particle (SRP) components within the germline cells using RNA Interference (RNAi), prevented the increase in GSC division frequency in response to mating. The major class of DEGs encodes polypeptides below the size of 250 amino acids, also known as small proteins. Upon reducing germline expression of small proteins, males no longer increased GSC division frequency after repeated mating. We hypothesize that mating induces cellular interactions via small proteins to ensure continued GSC divisions for the production of sperm.

overall_design: mRNA expression comparison of apical testis tissue collected from mated and unmated Canton S1 and Oregon R flies in triplicate.

first: Manashree

middle: S

last: Malpe

first: Leon

middle: F

last: McSwain

first: Heath

last: Aston

first: Karl

last: Kudyba

first: Chen

last: Ng

first: Megan

middle: P

last: Wright


title: Altered cofactor recruitment and nucleosome dynamics underlie bisphenol A's impact on ERα-mediated transcriptional bursting

city: Durham

first: Christopher

middle: R

last: Day

state: NC

address: 111 TW Alexander Dr.

department: ERBL

institute: NIH/NIEHS


title: BAHCC1 binds H4K20me1 to facilitate the MCM complex loading for DNA replication

city: Chapel Hill

first: Gang Greg

last: Wang

state: NORTH CAROLINA

address: 405 West Drive

department: UNC Lineberger Comprehensive Cancer Center; Department of Biochemistry and Biophysics

institute: University of North Carolina at chapel hill

summary: Methylation of histone H4 lysine 20 (H4K20), such as H4K20 mono-methylation (H4K20me1), regulates the biological processes of DNA replication, cell cycle progression, and DNA damage repair. Whereas H4K20me1 is knowingly written by SET8 (also known as PR-Set7) and erased by PHF8 (also known as KDM7B), the mechanism underlying H4K20me1-mediated regulation of DNA replication remains murky. Here, we report that a conserved tandem Tudor domain of BAHCC1 (BAHCC1TTD) specifically reads H4K20me1. Our biochemical, structural and cellular analyses demonstrated that the recognition of H4K20me1 by BAHCC1TTD facilitates the BAHCC1 recruitment onto the replication origins, where BAHCC1 interacts and recruits components of Minichromosome Maintenance (MCM) complex, a critical partner machinery of Origin Replication Complex (ORC) for mediating DNA replication. Combined actions of the H4K20me1-reading BAHCC1 and the H4K20me2-reading ORC ensure optimal genomic loading of MCM proteins. Depletion of BAHCC1, or disruption of BAHCC1TTD:H4K20me1 interaction, affected H4K20me1 homeostasis and MCM complex loading, leading to impaired DNA replication and defective cell cycle progression. Together, this study identifies a conserved BAHCC1TTD as an effector linking H4K20me1 to MCM recruitment for efficient DNA replication.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: CUT&RUN and CUT&Tag based examination of the genomic binding by BAHCC1, MCM complex (MCM2 or MCM3), ORC1 and related histone modifications in HeLa cells. For CUT&RUN, a fixed fraction of Drosophila cell chromatin was added as spike-in normalization controls, and for CUT&Tag, a fixed fraction of MEF cell chromatin was added as spike-in normalization controls.

first: Dongxu

last: Li

first: Greg


title: Altered Cofactor Recruitment and Nucleosome Dynamics Underlie Bisphenol A's Impact on Estrogen Receptor-Mediated Transcriptional Bursting [RNA-seq]

summary: Gene regulation is complex, involving the coordination of hundreds of proteins to initiate transcription.  At individual loci, transcriptional initiation is stochastic, resulting in short periods of nascent RNA synthesis known as transcriptional bursts.  To understand how altered Estrogen Receptor α (ERα) function and cofactor recruitment regulates transcriptional bursting, we utilized single molecule imaging of estrogen responsive genes in Bisphenol A (BPA) treated cells. We observe that cells treated with BPA exhibited TFF1 burst initiation rates and sizes which were indistinguishable from cells induced with Estradiol (E2). However, we observed a 50% reduction in the number of active alleles in BPA treated cells.  This effect is gene specific, as GREB1 was unperturbed.  Although we observed no difference in chromatin accessibility, the TFF1 promoter exhibited an altered structure which coincided with reduced ERα and cofactor binding.  Lastly, deletion of the enhancer locus removed the BPA effect, indicating that enhancer function was perturbed.  Our results demonstrate gene specific effects of altered ERα recruitment and function which lead to a reduction of transcriptionally permissive states. Our work supports the model that the initial estrogen response occurs from alleles in primed transcriptionally permissive states with additional inactive alleles contributing to the cellular response over time.

overall_design: CUT&Tag, ATAC-seq and RNA-seq of MCF7 cells treated with E2 and BPA.

first: Pelin

last: Yesar

first: Gloria

last: Adedoyin

first: Brian

last: Bennett

first: Carson

middle: C

last: Chow

first: Joseph

last: Rodriguez


title: Altered Cofactor Recruitment and Nucleosome Dynamics Underlie Bisphenol A's Impact on Estrogen Receptor-Mediated Transcriptional Bursting [ATAC-seq]


title: Altered Cofactor Recruitment and Nucleosome Dynamics Underlie Bisphenol A's Impact on Estrogen Receptor-Mediated Transcriptional Bursting [CUT&Tag]


title: Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing

first: José

last: Sardina