title: Intron retention phenomenon in phospholipase C gamma 1 isoform: how the Harpagophytum procumbens extract works? A cellular and bioionformatic approach.

city: Rome

first: Anna

last: Scotto d'Abusco

address: P.le Aldo Moro, 5

department: Biochemical Sciences

institute: Sapienza University of Rome

summary:
Harpagophytum procumbens is an African plant, commonly known as devil’s claw, used since the times of traditional medicine as a natural remedy for Osteoarthritis (OA) treatment, the most common joint disease. Nowadays, there is no cure for OA disease; all the therapies are aimed to reduce pain and inflammation and improve the patient quality of life. Given the widespread of pathology and its early onset in patients, the use of a natural remedy for the treatment of symptoms in the early stages of the disease allows to avoid the prolonged administration of analgesics and anti-inflammatory drugs responsible of the onset of several side effects, and at the same time achieving good therapeutic results.
In our experimental conditions, the analgesic and anti-inflammatory effect of a H. procumbens extract (HPE) was tested in vitro on human primary synoviocytes isolated from OA patients that underwent total knee replacement surgery. In last years, we demonstrated an anti-nociceptive role of the HPE on endocannabinoid type 2 receptors (CB2) and an antinflammatory effect on MAPK pathway, and we investigated in depth its effects on several signaling pathways. In particular, performing PCR analyses on both HPE-treated and un-treated synoviocytes, we observed a very interesting result on the phospholipase C γ1 enzyme gene expression. Both samples showed two PCR products, a lower band at 300 bp which was the expected product, and a higher band at 500 bp which was an unexpected product. The surprising result of this experiment concerned the HPE ability to modulate the expression of these two PCR products. While in the untreated sample the product at 300 bp was the most expressed, the HPE treatment induced a decrease in this product expression, increasing that of the product with more base pairs. By investigating the composition of this product through a Sanger sequencing analysis, it has been observed that HPE interferes with the PLC γ1 gene splicing process by stimulating the intron retention during the mRNA maturation. We verified that the introns that were retained in our experimental conditions were also described by the Human and Vertebrate Analysis and Annotation (HAVANA) group, however nobody in literature has attributed this effect to HPE by explaining its molecular mechanisms. Moreover, we demonstrate that samples from different patients had diverse treatment responses regarding the phenomenon of intron retention. Indeed, it has been observed that only in approximately 37% of the HPE treated samples the intron retention phenomenon occurred, while in the remaining part of the samples no modulation was observed. However, as well as the mechanism by which the extract inhibited the splicing process was not clear enough, similarly we have not been able to understand what mentioned inter-individual variability depends on.
For these reasons, in the coming months, we plan to conduct and analyze RNAseq experiments in order to understand how HPE works in the intron retention and what factors influence the treatment response among patients. In recent years, much progress has been made in the analysis and identification of retained introns considered, but still many challenges remain open. It has been shown that this phenomenon is involved in many pathologies, such as rheumatoid arthritis, Alzheimer’s disease and carcinogenic processes, with potential biological consequences for gene expression and cell survival. For this reason, understanding how a substance is able to modulate the intron retention phenomenon is the main innovative aspect of this study and opens up new perspectives in several disease therapeutic treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data among HPE-treated synoviocytes and untreated cells and also among patients with different mRNA expression profile (Intron retention or normal splicing).

first: Alessia

last: Mariano

first: Roberto

last: Mattioli


title: Transcriptomic profiling of right ventricular remodeling in MCT rat model treated with CM5480

status: Public on Sep 16 2025

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

type: Expression profiling by high throughput sequencing

summary: To better understand the molecular mechanisms of CM5480 treatment in MCT rats, a RNA sequencing analysis was performed in right ventricles (RV) tissues collected from 5 control-vehicle, 5 control-CM5480, 5 MCT-vehicle, 5 MCT-CM5480 rats.

overall_design: mRNA profiles of RV tissues from control and MCT rats treated with vehicle or CM5480

first: Fabrice

last: Antigny

first: Anaïs

last: Saint-Martin-Willer

first: Grégoire

last: Ruffenach


title: Targeting SUV39H2 Exon Skipping Reversing CDK4/6 Inhibitor Resistance in Breast Cancer

city: yangzhou

first: Yu

last: Shiyi

state: Jiangsu

address: hanjiang district jiangyangzhonglu136, Hanjiang district, Jiangyangzhonglu 136

country: China

institute: yangzhou university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Breast cancer, the most prevalent malignancy among women, is predominantly estrogen receptor-positive (ER+), with ER+ cases accounting for 80% of the total. The combination of CDK4/6 inhibitors and endocrine therapy has become the standard treatment for advanced ER+ breast cancer. However, around 30% of patients exhibit intrinsic resistance, while others eventually develop acquired resistance leading to recurrence and metastasis. Here, we identified reduced exon 2 skipping of SUV39H2 in CDK4/6 inhibitor-resistant breast cancer cells, leading to increased SUV39H2 protein expression and consequent elevation of H3K9me3 levels, collectively suppressing the p53 pathway and promote resistance. Subsequently, we designed antisense oligonucleotides (ASOs) to modulate SUV39H2 exon skipping, which successfully reduced SUV39H2 levels and H3K9me3 modifications, thereby reactivating p53 target genes and restoring drug sensitivity in vitro and in vivo.Our results demonstrate that SUV39H2 serves as both a potential biomarker and therapeutic target for CDK4/6 inhibitor-resistant breast cancer, highlighting its clinical translational value.

overall_design: ATAC-seq in MCF7-ABER cells treated with antisense oligonucleotides (ASO) targeting SUV39H2 or control (Ctr)

first: Shiyi

last: Yu

first: Yawen

last: Yang


title: Tyk2 controls immunosurveillance of colorectal cancer liver metastasis

city: Vienna

first: Katharina

last: Schwertner

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University Vienna

summary: Colorectal cancer liver metastasis (CRLM) is a major clinical problem. However, little is known about immunosurveillance of CRLM. The Janus kinase Tyk2 is involved in several immune processes, but its role in CRLM is unclear. We have developed a murine colorectal cancer (CRC) organoid-based transplantation model to investigate the functions of Tyk2 in CRLM. Organoids with mutations in Apc, Kras, and p53 were injected into the spleen or portal vein of host mice with Tyk2 deletion in different subsets of immune cells as well as into wild-type host mice treated with the Tyk2 inhibitor deucravacitinib. In addition, cancer cell-intrinsic effects on CRLM were investigated using organoids with CRISPR/Cas9-mediated deletion of Tyk2. Our data show that Tyk2 is a key factor controlling CRLM. We found that Tyk2 is not required in cancer cells, macrophages, NK cells, T cells, and Kupffer cells, but controls CRLM via a dendritic cell-dependent mechanism that relies on MHC-I-dependent cross presentation of antigens to CD8+ T cells. Analysis of a scRNA-seq dataset for primary CRC and CRLM revealed that Tyk2 is predominantly expressed in a specific dendritic cell population that is destined to present antigens in tumor-draining lymph nodes. Although our data cannot prove a role for Tyk2 in immune surveillance of CRLM in humans, they should be considered when treating patients with Tyk2 inhibitors.

overall_design: Organoids with mutations in Apc, Kras, and p53 were injected into the spleen of Tyk2flox/flox and Tyk2Δhem mice to model colorectal cancer liver metastasis. After 7 weeks mice were sacrified and RNA was isolated from liver tissue, matastic tissue and liver tissue adjacent to metastases.

first: Dana

last: Krauß

first: Bernadette

last: Mödl

first: Daniela

last: Zwolanek

first: Robert

last: Eferl


title: Effect of latent tuberculosis on individuals compared with healthy controls

city: Karachi

first: Asghar

last: Nasir

state: Sindh

address: Stadium Road

department: Pathology and Laboratory Medicine

country: Pakistan

institute: Aga Khan University

summary: Blood transcriptomes were analyzed in individuals with and without latent tuberculosis infection (LTBI) using the Clariom S RNA microarray assay (Affymetrix).

overall_design: Participants were recruited with and without diabetes and subsequently tested for latent tuberculosis infection (LTBI), resulting in four groups. Blood transcriptomes from all four groups were analyzed using the Clariom S RNA microarray assay (Affymetrix Inc.).

first: Maliha

last: Yameen

first: Kiran

last: Iqbal

first: Javaria

last: Ashraf

first: Zahra

last: Hasan


title: RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria [siZNF207_Rescue_mRNA-Seq]

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

state: Maryland

address: 1050 Boyles Street

country: USA

institute: National Cancer Institute

summary: Despite progress in understanding pre-mRNA splicing, the regulatory mechanisms controlling most alternative splicing events remain unclear. We developed CRASP-Seq, a method that integrates pooled CRISPR-based genetic perturbations with deep sequencing of splicing reporters, to quantitively assess the impact of all human genes on alternative splicing from a single RNA sample. CRASP-Seq identified both known and novel regulators, enriched for proteins involved in RNA splicing and metabolism. As proof-of-concept, CRASP-Seq analysis of an LMNA cryptic splicing event linked to progeria uncovered ZNF207, primarily known for mitotic spindle assembly, as a regulator of progerin splicing. ZNF207 depletion enhances canonical LMNA splicing and decreases progerin levels in patient-derived cells. We further show that ZNF207’s zinc finger domain broadly impacts alternative splicing through direct interactions with U1 snRNP components. These findings position ZNF207 as a U1 snRNP auxiliary factor and demonstrate the power of CRASP-Seq to uncover key regulators and domains of alternative splicing.

overall_design: mRNA-Seq profiling was performed on HEK293 Flp-In cells treated with siRNAs (siNT or siZNF207) for 48 hours and induced to express either ZNF207 or an empty vector for 42 hours.

first: Amit

middle: K

last: Behera

first: Jeongjin

middle: J

last: Kim

first: Shreya

last: Kordale

first: Filip

last: Pekovic

first: Arun

middle: P

last: Damodaran

first: Bandana

last: Kumari

first: Sandra

last: Vidak

first: Ethan

last: Dickson

first: Mei

middle: S

last: Xiao

first: Gerard

last: Duncan

first: Thorkell

last: Andresson

first: Tom

last: Misteli

first: Eugene

last: Valkov


title: RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria [CRASP-Seq]

overall_design: CRASP-Seq assays of six different splicing minigene reporters (FAS exon-6, EZH2 exon-14, SRSF7 poison exon, PKM mutually exclusive exons, LMNA HGPS, LMNA WT) were performed in three different cell lines (HAP1, RPE1, and HepG2) at two different time points (T1 and T4).


title: RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria [siZNF207_mRNA-Seq]

overall_design: mRNA-Seq profiling was performed on HEK293T cells treated for 48 hours with three independent ZNF207 siRNAs or a non-targeting control.


title: RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria [ZNF207_eCLIP-Seq]

overall_design: eCLIP sequencing of ZNF207 (tagged with FLAG at either the N- or C-terminus) was performed in HEK293 Flp-In cells. FLAG-EGFP was used as a negative control.


title: Global transcriptional analysis of human FHs 74 Int intestinal epithelial cells after exposure to advanced glycation end products

city: Krems

first: Sabine

last: Geiselhart

address: Dr.-Karl-Dorrek-Straße 30

institute: Karl Landsteiner University of Health Sciences

summary: Advanced glycation end products (AGEs) are formed during the thermal processing of food and have been implicated in the pathogenesis of a series of chronic inflammatory diseases. AGEs are hypothesized to interact with the intestinal epithelium upon the ingestion of thermally processed food, however, their direct effect on intestinal epithelial cells is poorly understood. This study investigates transcriptomic changes in human intestinal epithelial FHs 74 Int cells after exposure to methylglyoxal-modified human serum protein (AGE-HS), S100A12, a known RAGE ligand, and unmodified human serum proteins (HS) in comparison to PBS treated cells. Surprisingly, AGE-HS treatment did not result in significant differential gene expression at standard analysis thresholds, while unmodified HS induced minor transcriptional changes. S100A12 also elicited no significant gene expression alterations. However, GSEA revealed subtle but coordinated changes – AGE-HS treatment induced downregulation of gene sets linked to MYC, interferon responses, and oxidative phosphorylation, paralleling some effects observed with S100A12. Also, KEGG pathway analysis revealed partial overlap between responses to AGE-HS and S100A12 affecting pathways associated with oxidative phosphorylation and neurodegenerative diseases such as Alzheimer, Parkinson, and Huntington disease. This study provides the first global transcriptomic analysis of intestinal epithelial cells treated with AGE-modified proteins. The effects were less pronounced than expected, thus, these data challenge previous reports of robust AGE-induced inflammatory and proliferative effects and emphasize the importance of rigorous endotoxin testing and the use of appropriate controls.

overall_design: RNAseq analysis of FHs 74 Int cells after treatment with methylglyoxal-modified serum proteins or  S100A12 after one and four hours

first: Katharina

last: Schwertner

first: José

last: Basílio

first: Karin

last: Hoffmann-Sommergruber

first: Isabella

last: Ellinger


title: An siRMSD parameter of structural distortion induced by chemical modification is predictive of the off-target effect of siRNA_(2/2)

city: Bunkyo-ku

first: Seongjin

last: An

state: Tokyo

department: Graduate School of Frontier Science

country: Japan

institute: The University of Tokyo

summary: To investigate effects of siRNA with various 2'- modifications on genome-wide off-target effect, we analyzed gene expression profile of HeLa cells transfected by their siRNAs.

overall_design: Total RNAs were extracted from HeLa cells transfected by mock, unmodified, 2'-deoxy-2'-fluoro, or 2'-O-methyl modified siRNA and performed microarray analysis.

first: Kumiko

last: Ui-Tei


title: An siRMSD parameter of structural distortion induced by chemical modification is predictive of the off-target effect of siRNA_(1/2)

summary: To investigate effects of siRNA with various 2'-ribose modifications on genome-wide off-target effect, we analyzed gene expression profile of HeLa cells transfected by their siRNAs.

overall_design: Total RNAs were extracted from HeLa cells transfected by mock, unmodified, 2'-formamido, 2'-deoxy, or 2'-O-methoxyethyl modified siRNA and performed microarray analysis.


title: Ablation of hematopoietic stem cell derived adipocytes reduces tumor burden in syngeneic mouse models of high-grade serous carcinoma

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: In this study we examined the influence of hematopoietic stem cell derived adipocytes (HSCDAs) on the proliferation and metastasis of high-grade serous carcinoma (HGSC), the most common type of ovarian cancer. HSCDAs are a subtype of adipocytes which begin as myeloid cells that traffic from bone marrow to adipose tissue, particularly visceral depots, and then differentiate and accumulate therein. We hypothesized that HSCDAs promote HGSC progression and establish a pro-tumoral niche within peritoneal adipose tissues such as the omentum. We took primary human adipose biopsies and flow sorted the myeloid and mesenchymal populations. We differentiated these adipose precursors in vitro into mature HSCDAs and CMAs, respectively. RNA-Seq analysis showed that HSCDAs have a distinct transcriptional profile from CMAs, including downregulation of cell cycle and upregulation of multiple metabolic and adipogenic pathways. Using ELISA, we found that HSCDAs secreted greater amounts of inflammatory cytokines IL-6 and IL-8 than CMAs. We incubated HGSC cell lines in conditioned media from HSCDAs and CMAs and performed reverse phase protein array (RPPA) and proliferation assays. HGSC cells in HSCDA media had elevated protein markers of epithelial to mesenchymal plasticity, including fibronectin, as well as increased serine phosphorylation of pro-survival AKT1/2. Conversely, HGSC cells in HSCDA media downregulated tumor suppressors including Wnt regulator GSK3β. Depending on the cell line and adipose donor, HGSC cells also showed altered growth rates in conditioned media. We next investigated the role of HSCDAs in HGSC progression and metastasis in vivo. We generated immunocompetent mice that were either HSCDA Proficient (can make both adipocyte subtypes) or Deficient (can only make CMAs). We performed two independent tumor studies using the ID8 (Tp53-/-, Brca2-/-) and SO (Tp53-/-, Brca1/2 wild-type, Hras and Myc amplified) syngeneic models. In both models, overall tumor burden was lower in HSCDA Deficient mice. In the ID8 model, omentum tumors from HSCDA Deficient mice, relative to those from Proficient mice, showed reduced proliferation (Ki67) and apoptosis (cleaved caspase 3). Analysis of bulk RNA-Seq of ID8 omentum tumors from HSCDA Deficient mice revealed downregulation of oxidative phosphorylation, adipogenesis, and fatty acid metabolism. These pathways were enriched in HSCDA cells in vitro, suggesting that ablation of HSCDAs had a significant influence on the tumor metabolic environment. We also observed reduced inflammatory pathways in ID8 tumors from HSCDA Deficient mice, so we interrogated immune cell infiltration into omentum tumors. Compared to HSCDA Proficient mice, tumors from HSCDA Deficient mice showed reduced densities of dendritic cells (DC) and natural killer (NK) cells. By spatial analysis we found fewer DCs, NKs, and B-cells near tumor cells. Overall, our data suggest that HSCDAs can promote HGSC survival and plasticity while downregulating tumor suppressors, and also alter the peritoneal immune and metabolic environment to promote HGSC progression.

overall_design: Primary human adipose biopsies were taken and the myeloid and mesenchymal populations were flow sorted.The adipose precursors were differentiated in vitro into mature HSCDAs and CMAs, respectively. HGSC cell lines were incubated in conditioned media from HSCDAs and CMAs and reverse phase protein array (RPPA) and proliferation assays were performed. The role of HSCDAs in HGSC progression and metastasis in vivo was then investigated. Immunocompetent mice that were either HSCDA Proficient (can make both adipocyte subtypes) or Deficient (can only make CMAs) were generated. Two independent tumor studies were performed using the ID8 (Tp53-/-, Brca2-/-) and SO (Tp53-/-, Brca1/2 wild-type, Hras and Myc amplified) syngeneic models.

first: Elizabeth

middle: R

last: Woodruff

first: Courtney

middle: A

last: Bailey

first: Francis

last: To

first: Joanne

last: Maltzahn

first: Timothy

middle: M

last: Sullivan

first: Meher

last: Boorgula

first: Dwight

last: Klemm

first: Benjamin

middle: G

last: Bitler

first: Zachary

middle: L

last: Watson


title: Maternal administration of probiotics augments IL17-committed γδ T cells  in the newborn lung

city: Brussels

first: David

last: Vermijlen

state: non-US Resident

address: Boulevard de Triomphe, accès 2 (CP205/3)

department: Pharmacotherapy and Pharmaceutics

country: Belgium

institute: Université Libre de Bruxelles

summary: The early-life period is increasingly being recognized as a window of opportunity to shape immunity where microbiota and related probiotics have an important impact. Innate γδ T cells are the first T cells generated in utero populating epithelial tissues such as the lung contributing to tissue protection through, for example, IL17 production. Here, we studied the influence of maternal microbiota and probiotic supplementation during pregnancy on innate γδ T cells in the lung and thymus of newborn mice. Detailed time-kinetic experiments showed that at birth the murine lung T cell population was specifically dominated by IL17-committed γδ T cells expressing an invariant Vγ6Vδ1 TCR. Single-cell-RNA-sequencing showed that the biased IL17-commitment of perinatal lung γδT cells is highly conserved between mice and humans. While maternal microbiota depletion with antibiotics tended to decrease the frequency of the lung Vγ6 T cells of the offspring at birth, the maternal administration of Lacticaseibacillus rhamnosus(L.rhm.), but not of Bifidobacterium animalis subsp.lactis(B.lac.), increased significantly their frequency resulting in the augmentation of the IL17-commitment of the mouse lung T cell compartment. Altogether, our data indicate that the maternal microbiota contributes to the shaping of IL17-committed γδT cells in the lungs of newborns and that maternal administration of specific probiotic strains can enhance this process.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ϒδT cells were sorted from fetal lung samples, followed by 5'-RNA single cell transcriptome and TCR sequening (10x genomics).

first: Yohannes

last: Tafesse

first: Arnaud

last: Köhler

first: Guillem

last: Sanchez Sanchez

first: Patricia

last: Brito Rodrigues

first: Marko

last: Verce

first: Panagiotis

last: Vitsos

first: Isoline

last: Verdebout

first: Moosa

last: Rezwani

first: Maria

last: Papadopoulou

first: Amandine

last: Everard

first: Véronique

last: Flamand


title: RNA-seq in parental and resistant non-small cell lung cancer (NSCLC) cells

city: Shenyang

first: sihong

last: chen

address: Wenhua Road

institute: Shenyang Pharmaceutical University

summary: Crotonylation is a crotonyl-coenzyme A (CoA)-mediated post-translational modification best known for its roles in epigenetic regulation. Histone lysine crotonylation (Kcr) has been reported to be involved in tumor-related biological functions such as DNA damage repair and immune infiltration. Here we find that abnormal reduction of histone Kcr significantly correlates with a poor response to epithelial growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in resistant models of lung cancer cell lines, and in cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models. The crotonyl-CoA-producing enzyme ACSS2 is the key regulator of the resistance-related change of crotonylation. Quantitative crotonylomic, transcriptomic and epigenomic analyses reveal that EGFR-TKI resistance is accompanied by reduced levels of histone 3 lysine 56 crotonylation (H3K56cr) on chromatin, which inhibits transcription of HNF1A and activates the PI3K/AKT signaling pathway.

overall_design: To uncover how histone Kcr regulates target genes and downstream signaling pathways to mediate EGFR-TKI resistance, RNA-seq was performed to analyze transcriptional changes in HCC827 and HCC827_Er cells with 3 replicates.

first: Sihong

last: Chen

first: Xiaoyuan

last: Wang

first: Youwei

last: Su


title: ChIP-seq in parental and resistant non-small cell lung cancer (NSCLC) cells

overall_design: To uncover how histone Kcr regulates target genes and downstream signaling pathways to mediate EGFR-TKI resistance, ChIP-sequence was performed in HCC827 cells and HCC827_Er cells.


title: Nucleocytoplasmic Shuttling of TAX1BP3: an Indispensable Player in Vascular Proliferative Diseases by Regulating YAP-TEAD Transcriptional Activity [RNA-seq]

city: Guangzhou

first: yulong

last: zhong

state: Guangdong Province

address: 1838 Guangzhou Avenue North

department: physiology

institute: Southern Medical University

summary:
BACKGROUND: The phenotypic switching of vascular smooth muscle cells (VSMCs) plays a crucial role in vascular homeostasis. Protein-protein interactions (PPIs) mediated by PDZ domains is essential for cardiac functions. However, little is known about the role of PDZ proteins in regulating the phenotypic switching of VSMCs. In this study, we aim to explore the role of TAX1BP3, a singular PDZ protein, in maintaining the contractile phenotype of VSMCs.
METHODS: Subcellular localization of TAX1BP3 was assessed in isolated VSMCs and arteries from mice or donors with in-stent restenosis and atherosclerosis. VSMC-specific Tax1bp3 knockout mice were generated to determine the relevant phenotypes in a carotid artery wire injury model. RNA sequencing, ATAC-sequencing, computational prediction of complex structures, and coCo-immunoprecipitation (Co-IP) were performed to elucidate the underlying molecular mechanisms. AAV-mediated Tax1bp3 gene delivery and recombinant TAX1BP3 were employed to investigate the potential translational relevance.
RESULTS: TAX1BP3 exhibited dynamic nucleocytoplasmic shuttling during phenotypic switching of VSMCs. Deficiency of TAX1BP3 facilitated the transition from a contractile to a synthetic phenotype and aggravated neointima formation following vascular injury in mice. The integration of RNA sequencing and ATAC sequencing unveiled that TAX1BP3 primarily regulated the cell cycle progression and cell proliferation of VAMCs through YAP-TEAD transcription activity. The computational prediction of TAX1BP3/YAP1 complex structures and protein interaction related experiments revealed TAX1BP3 and TEAD1 compete for binding to YAP through its TEAD binding domain via a non-canonical PDZ manner. AAV-mediated Tax1bp3 gene delivery markedly attenuated post-injury neointima formation and the progression of atherosclerosis. Recombinant TAX1BP3 administration effectively reduced VSMCs proliferation and intimal hyperplasia following vascular injury in vitro and in vivo.
CONCLUSIONS: Our results identified TAX1BP3 , a novel nucleocytoplasmic protein, a singular PDZ protein, that competitively interacts with YAP/-TEAD complex in a non-canonical PDZ manner and exerted its protective role in phenotypic switching and vascular intimal hyperplasia primarily through the regulation of cell proliferation.

overall_design: To further elucidate the function and mechanism by which TAX1BP3 modulates VSMC phenotypic switching. We conducted RNA sequencing analysis on HASMCs that were either infected with VEC or Ad-TAX1BP3 adenovirus.

first: Canzhao

last: Liu

first: Shanshan

last: Ai

first: Hanyan

last: Yang

first: Yulong

last: Zhong


title: Nucleocytoplasmic Shuttling of TAX1BP3: an Indispensable Player in Vascular Proliferative Diseases by Regulating YAP-TEAD Transcriptional Activity [YAP_ChIP-seq]

overall_design: Performing in situ ChIP-seq on YAP to specifically study the impact of TAX1BP3 on the YAP binding regions.


title: A novel nuclear protein complex controlling the expression of developmentally regulated genes in Toxoplasma gondii [CUT&TAG]

city: wuhan

first: xue

last: lilan

state: 请选择...

address: shizishan

institute: huazhong agriculture university

summary: Toxoplasma gondii is a ubiquitous protozoan parasite with a complex life cycle containing multiple developmental stages. The parasites have distinct gene expression patterns at different stages to enable stage specific life activities, but the underlying regulatory mechanisms are largely unknown. In this study, we identified a nuclear complex that controls the expression of developmentally regulated genes, especially merozoite specific genes. This complex consists of the AP2 family transcription factor AP2Ⅻ-5, the epigenetic factors MORC and HDAC3, as well as a novel AP2Ⅻ-5 interacting protein 1 (AIP1) that stabilizes this complex. At the tachyzoite stage when the parasites proliferate rapidly by asexual endodyogeny, AP2Ⅻ-5 binds to the promoter regions of developmentally activated genes and recruits MORC and HDAC3 to suppress their expression. When sexual commitment and merozoite development is triggered, the abundance of AP2Ⅻ-5 decreases and its suppression on target genes is relieved. In contrast to MORC and HDAC3, which regulate Toxoplasma development but are also essential for tachyzoite growth, AP2Ⅻ-5 and AIP1 are dispensable for tachyzoite proliferation in vitro. These data suggest that while MORC and HDAC3 have broad regulatory activities, forming a complex with AP2Ⅻ-5 and AIP1 enables them to specifically regulate gene expression during development.

overall_design: Chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq) to determine the HDAC3 binding sites in the genomes of ME49 and ΔⅫ-5 strains using CUT&Tag.

first: Lilan

last: Xue

first: Bang

last: Shen


title: Gene expression profile at single cell level of immune cells following spinal cord injury

city: Nanjing

first: Ziyang

last: Zheng

address: Longmian Avenue NO.101

institute: The first affiliated hospital of nanjing medaical university

summary: Immune cells infiltrate extensively into the lesion area after spinal cord injury and persist chronically, playing a crucial role in the inflammation and recovery of spinal cord injury. Here we investigated gene expression levels at single cell level of immune cells which distribute in the uninjured spinal cord and the lesion area at 1, 3, 7, 14, and 28 days after spinal cord injury. Heterogeneity analysis was performed to reveal the immune response after injury and how it is altered over time.

overall_design: Immune cells were collected from spinal cord tissues of uninjured mice (8- to 10-weeks-old C57BL/6) and mice with spinal cord injury on days 1, 3, 7, 14, and 28. Single-cell RNA sequencing was used to profile immune cells in the spinal cord.

first: Siming

last: Dai

first: Xuan

last: Zhao

first: Chenxi

last: Zhang

first: Jian

first: Shujie

first: Guoyong

last: Yin


title: Nucleocytoplasmic Shuttling of TAX1BP3: an Indispensable Player in Vascular Proliferative Diseases by Regulating YAP-TEAD Transcriptional Activity [ATAC-seq]

overall_design: To comprehensively understand the transcriptional changes in TAX1BP3 overexpression HASMCs, ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) was performed to assess alterations in chromatin accessibility.


title: Multi-epigenome-wide analyses and meta-analysis of child maltreatment in judicial autopsies and intervened children and adolescents [ABI]

city: Eiheiji-cho, Yoshida-gun

first: Shota

last: Nishitani

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

department: Research Center for Child Mental Development

institute: University of Fukui

type: Methylation profiling by genome tiling array

summary: Child maltreatment (CM) is associated with adverse physical, psychological, and neurodevelopmental outcomes later in life. Epigenetic modifications, particularly DNA methylation, have been proposed as potential mechanisms underlying these long-term effects. To identify robust CM-associated methylation signatures, we conducted epigenome-wide analyses across three independent cohorts: judicial autopsy cases (CM:11, Controls:7), toddlers shortly after social intervention (CM:36, Controls:49), and adolescents who underwent brain MRI (CM:61, Controls:62). Each cohort was analyzed separately, followed by a meta-analysis to identify common methylation sites associated with CM exposure. The meta-analysis identified four significant CpG sites located within the ATE1, SERPINB9P1, CHST11, and FOXP1 genes. Among these, methylation of FOXP1 was consistently associated with structural brain alterations, including increased gray matter volume (GMV) in the orbitofrontal cortex (OFrC) and middle/posterior cingulate gyrus (MPCG), and decreased GMV in the occipital fusiform gyrus (OFuG). These brain regions are implicated in emotional regulation, memory retrieval, and social cognition, suggesting a potential neurobiological mechanism linking CM to later psychopathology. Furthermore, methylation risk scores (MRS) derived from these four CpGs successfully discriminated individuals who experienced early-life adversity in an independent validation dataset, achieving an area under the receiver operating characteristic curve (AUC) of 0.672, highlighting their potential utility as biomarkers. Gene ontology and pathway analyses revealed enrichment of cholinergic and glutamatergic synaptic transmission pathways, supporting their involvement in traumatic memory formation. Our findings provide novel insights into the epigenetic mechanisms underlying CM and identify potential biomarkers for early detection, prevention, and therapeutic intervention, ultimately contributing to breaking the intergenerational cycle of maltreatment.

overall_design:
Samples from CM cohort Adolescent Brain Imaging
Bisulfite-converted saliva DNA were hybridized into the Illumina Infinium Methylation EPIC Kit array

first: Akemi

last: Tomoda


title: Clonal sharing of CD8+ T-cells links skin and joint inflammation in psoriatic arthritis

city: London

first: Lucy

last: Durham

address: 1st Floor, New Hunt's House, Guy's Campus, Newcommen Street

department: Centre for Inflammation Biology and Cancer Immunology

country: United Kingdom

institute: King's College London

summary: We hypothesised that skin and joint inflammation in psoriatic arthritis is linked in terms of CD8+ T-cell phenotype and clonality. We employed scRNAseq to directly compare the transcriptional signature and T-cell receptor repertoire of memory T-cells from paired skin and synovial tissue+/-fluid from patients with psoriatic arthritis. We identified an enrichment of type-17 CD8+ tissue-resident memory (TRM) cells in both skin and joint, with a stronger IL-17 signature in the skin than the joint. Importantly, we identified several T-cell clones that are shared between the skin and the joint. Shared clones tended to have the same phenotype at both sites, characterised by increased expression of genes associated with a cytotoxic, tissue-resident phenotype. This supports the hypothesis that skin and joint inflammation is linked in terms of T-cell clonality and raises the possibility that specific T-cells migrate between these compartments to propagate inflammation across both sites.

overall_design: Single cell RNA and TCR sequencing analysis of memory T cells  from blood, skin, synovial fluid and synovial tissue from patients with psoriatic arthritis

middle: E

first: Elizabeth

middle: H

last: Gray

first: Frances

last: Humby

first: Nora

last: Ng

first: Sarah

last: Ryan

first: Rosie

last: Ross

first: Giovanni

last: Povoleri

first: Rosamond

last: Nuamah

first: Kathy

last: Fung

first: Athul

last: Menon

first: Pawan

last: Dhami

first: Bruce

middle: W

last: Kirkham

first: Leonie

last: Taams


title: Multi-epigenome-wide analyses and meta-analysis of child maltreatment in judicial autopsies and intervened children and adolescents [TSC]

overall_design:
Samples from CM cohort Toddler Social Cognition
Bisulfite-converted buccal epithelial DNA were hybridized into the Illumina Infinium Methylation EPIC Kit array


title: Multi-epigenome-wide analyses and meta-analysis of child maltreatment in judicial autopsies and intervened children and adolescents

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

overall_design: Refer to individual Series


title: Multi-epigenome-wide analyses and meta-analysis of child maltreatment in judicial autopsies and intervened children and adolescents [JAC_BR]

overall_design:
Samples from CM cohort Judicial Autopsy
Bisulfite-converted brain DNA were hybridized into the Illumina Infinium Methylation EPIC Kit array

first: Masataka

last: Nagao


title: Methylation-based signature to distinguish indolent and aggressive prostate cance

status: Public on Sep 15 2025

city: Saint Louis

first: Christopher

middle: A.

last: Maher

state: Missouri

address: Division of Oncology

institute: Washington University School of Medicine in Saint Louis: Washington University in St Louis School of Medicine

type: Methylation profiling by high throughput sequencing

summary: Prostate cancer management faces significant challenges in distinguishing indolent from aggressive disease, particularly since most patients are intermediate-risk and therefore hinders the ability to recommend standardized treatment recommendations. Moreover, current prognostic tools including Gleason scoring and tumor staging demonstrate limited accuracy for predicting disease progression and tumor recurrence. DNA methylation serves as a stable epigenetic modification that directly regulates gene expression, making it an ideal biomarker for cancer prognosis. Therefore, this study leveraged whole-genome enzymatic methylation sequencing on 120 patients to develop a novel prognostic signature for aggressive prostate cancer progression. We analyzed 20,849 differentially methylated regions (DMRs) and employed multiple machine learning approaches to identify optimal biomarkers. This revealed a 14-region DNA methylation signature that can serve as independent prognostic prediction factors outperforming traditional clinical indices. Further, when combined into a risk score it achieved a clinically meaningful odds ratio. This methylation-based approach provides actionable information for treatment decisions and surveillance strategies, representing a significant advancement toward precision medicine in prostate cancer management through biologically-informed risk stratification.

overall_design: Clinical outcomes were followed until loss connection, with tumor progression defined by the occurrence of any of the following: death, tumor recurrence, PSA recurrence, or lymph node metastasis. To stratify the degree of malignancy of the tumor itself, patients with GS = 7 and surgical T stage ≤ 2c were classified as low-risk, those with GS ≥ 9 or surgical T stage ≥ 3b as high-risk, and the remaining patients as intermediate-risk.

first: Liao

last: Muheng

first: Webster

last: Jace

first: Ly

last: Amy

first: Rozycki

last: Emily

first: Maher

last: Christopher


title: Multiomic Analysis of Lung Tumors Defines Pathways Activated in Neuroendocrine Transformation

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

summary: To investigate the molecular mechanisms of neuroendocrine (NE) transformation, adenocarcinomas (LUAD) to small cell lung cancer (SCLC), in lung cancer.

overall_design: We performed EPIC (methyl-capture) in transformed lung adenocarcinoma and small cell lung cancer clinical specimens, together with control, never-transformed lung adenocarcinomas and small cell lung cancer.

first: Alvaro

last: Quintanal-Villalonga

first: Charles

last: Rudin


title: Single cell RNA sequencing of patient-derived origanoids of prostate cancer reveals specific markers for prostatic ductal adenocarcinoma

city: Tokyo

first: Yuto

last: Baba

address: 35 Shinanomachi Shinjuku-ku

institute: Keio University School of Medicine

summary: We have performed a single cell RNA sequencing using 10x Genomics platform on patient-derived origanoids (PDO) established from advanced prostate cancer patients. PDOs are classified into different clusters according to their phenotypes. Among the five PDOs, KBO159, which was established from prostatic ductal adenocarcinoma (PDA), expressed unique molecular signatures that were considered potential novel biomarkers for PDA, when integrated with our results of spatial transcriptomic analysis.

overall_design: Once established, the PDOs were dissociated into single cells and subjected to single-cell RNA sequencing.

first: Takashi

last: Watanabe

first: Yukihide

last: Momozawa

first: Takeo

last: Kosaka


title: Neuroprotective mechanisms of secreted factors from glial progenitor cells, obtained from human induced pluripotent stem cells

city: Moscow

first: Evgeny

last: Karpulevich

address: Alexander Solzhenitsyn Street 25

country: Russia

institute: ISP RAS

summary: In this study, we investigated the mechanisms of neuroprotection of factors secreted by glial progenitror cells obtained from human induced pluripotent stem cells. We earlier got data on their neuroprotective action on the model of glutamate excitotoxicity in vitro, traumatic brain injury in vivo as well as proteomic analysis. The experiment was reproduced on cortical neuron cultures from Wistar rat pups (P0, 10 DIV). At 10 day of culturing, the drugs were added. The comparison groups were: extracellular vesicles, proteins of the 3-100 kDa fraction and total secretome. Total RNA was collected 4 hours after addiction of drugs for transcriptome analysis to identify signaling pathways activated in cells by drugs.

overall_design: The experiment was reproduced on cortical neuron cultures from rat pups (P0, 10 DIV). At 10 day of culturing, the drugs were added. Concentrations of the drugs: extracellular vesicles - 10 mkg/ml,  3-100 kDa proteins - 15 mkg/ml, total secretome - 45 mkg/ml. The negative control was intact cultures. Three repeats were performed for each group and control. The comparison groups were: extracellular vesicles, proteins of the 3-100 kDa fraction and total secretome. Total RNA of cells was collected 4 hours after addiction of drugs for transcriptome analysis

first: Anastasiia

last: Gurianova

first: Diana

last: Salikhova


title: Non-remnant triglyceride-rich lipoproteins due to lipoprotein lipase deficiency increase atherosclerosis in mice

first: Ira

last: Goldberg

state: NY

address: 435 E. 30th St, Science Building, 617

department: Division of Endocrinology, Diabetes and Metabolism

institute: New York University Grossman School  of Medicine

summary: Although hypertriglyceridemia and postprandial lipemia associate with greater atherosclerosis, partially metabolized triglyceride-rich lipoproteins termed remnants rather than nascent lipoproteins have been implicated as the culprits. Whether chylomicrons are inherently atherogenic remains unclear. To test whether increased levels of nascent triglyceride-rich lipoproteins (TRLs)  in the absence of markedly reduced LDL-C levels contribute to atherosclerosis, we created mice with induced whole-body lipoprotein lipase (LpL) deficiency combined with LDL receptor (LDLR) deficiency. On an atherogenic Western-type diet (WD), male and female mice with induced global LpL deficiency (iLpl-/-) and LDLR knockdown (Ldlrkd) developed hypertriglyceridemia and elevated cholesterol levels; all the increased cholesterol was in chylomicrons or large VLDL. After 12 weeks on a WD, atherosclerotic lesions both in the brachiocephalic artery and the aortic root were more severe in iLpl-/-/Ldlrkd mice than control Ldlrkd mice. Aorta from hypertriglyceridemic mice had changes in the transcriptomes of endothelial cells, macrophages, and smooth muscle cells indicating vascular inflammation. Our data show that intact TRLs contribute to atherosclerosis, explain the association of postprandial lipemia and vascular disease, and prove that non-remnant TRLs are not benign.

overall_design: We induced LpL deficiency in LDL receptor knockout mice to assess the contribution of unhydrolyzed triglyceride-rich lipoproteins to atherosclerosis. LDLR KO mice with or without concomitant LpL deficiency were fed a western diet for 12 weeks, after which their aortic roots and brachiocephalic arteries were isolated for assessment of atherosclerotic lessions. In addition, we performed single cell RNA sequencing analysis of aortic arches from LDLR KO with or without concomitant LpL deficiency.

first: Ainara G

last: Cabodevilla

first: Maria Concepcion

last: Izquierdo

first: Debapriya

last: Basu

first: Waqas

last: Younis

first: Munichandra B

last: Tirumalasetty

first: Qing Robert

last: Miao

first: Dimitris

last: Nasias

first: Jenny E

last: Kanter

first: Tse Wing

last: Ho

first: Jana

last: Gjini

first: Edward A

last: Fisher

first: Jeffrey

last: Kim

first: Warren L

last: Lee

first: Karin E

last: Bornfeldt

first: Ira J.


title: Localized FLASH Radiotherapy Reduces Long-Term Skin and Muscle Damage While Preserving Systemic Homeostasis

city: Pisa

first: Giulia

last: Furini

address: Via Giuseppe Moruzzi 1

department: Institute of Clinical Physiology (IFC)

country: Italy

institute: National Research Council (CNR)

summary: Radiotherapy (RT) is a cornerstone treatment for nearly 50% of cancer patients, yet its efficacy remains limited by cumulative damage to healthy tissues over time. Delivering RT at ultra-high dose rates (FLASH-RT) represents a transformative strategy, as it appears to maintain tumor control, while sparing the surrounding normal tissue—a phenomenon termed FLASH effect. Here, we compared electron FLASH-RT and conventional RT (CONV-RT) on skin and muscle tissue of naïve mice assessing tissue integrity and gene expression. Bulk RNA sequencing revealed striking differences: FLASH induced minimal transcriptional disruption in skin and muscle, whereas CONV-RT triggered thousands of differentially expressed genes, including massive activation of fibrosis, inflammation, cell death-related pathways in skin, and broad dysregulation of genes linked to muscle function, remodeling and the unfolded protein response. Histological and ultrastructural analyses corroborated the findings, showing reduced immune infiltration in the skin and preserved tissue architecture both in skin and muscle following FLASH. In conclusion our study not only confirms the protective nature of FLASH but also provides novel mechanistic insights into the cascade linking local injury to systemic dysfunction under CONV-RT, reinforcing the translational potential of FLASH to expand the therapeutic window of radiotherapy.

overall_design: C57BL/6J mice were exposed to 35 Gy electron irradiation to the left hindlimb by either FLASH-RT or conventional (CONV-RT) modality. Sham, not irradiated mice served as controls. 70 days post  treatment, skin and muscle tissues from the irradiated area were collected and the trascriptomic profile investigated by RNA-Seq.

first: Eduarda

last: Mota Da Silva

first: Alice

last: Usai

first: Gaia

last: Scabia

first: Claudia

last: Kusmic

first: Filippo

last: Rossi

last: Asero

first: Roberto

last: Cusano

first: Riccardo

last: Berutti

first: Jessica

last: Milia

first: Rossano

last: Atzeni

first: Margherita

last: Maffei


title: Identification of cells exhibiting elevated ERBB network activity in KRas/ Myc-driven lung tumours

city: Glasgow

first: Robin

last: Shaw

address: Switchback Road

institute: CRUK Scotland Institute

summary: Our lab has identified a completely unexpected requirement for ERBB signalling in KRAS‐driven Lung Adenocarcinoma (LuAd). We have shown that this requirement is present from the very outset of lung tumour initiation, and, crucially, we have found a pronounced increase in ERBB signalling during progression from low grade adenocarcinoma to locally invasive disease. We hypothesize that this increased activity, which manifests as strongly elevated expression of multiple EGF/ERBB-family ligands, such as Amphiregulin (AREG), and paracrine activation of ERBB2 on infiltrating macrophages, may be exploited for early detection of KRAS‐ driven malignancy. Alongside a more general increase in AREG expression as tumours progress to higher grade disease, we find individual cells that express extremely high levels of AREG mRNA. We refer to these cells as AREG super-expressers and their lineage identity is unknown. Cell morphology suggests they maybe epithelial, however, unlike the bulk of tumours, these cells fail to express the lung epithelial marker SPC and staining for cytokeratins is inconclusive. Their detection at and adjacent to the tumour:normal interface suggests that they maybe disseminating tumour cells undergoing EMT. Alternatively, they may belong to another lung-resident or infiltrating population, induced to express AREG through direct contact with tumour cells. Immediately adjacent to progressing tumours we find large numbers of F4/80-positive macrophages that stain strongly for tyrosine phosphorylated ERBB2 (p-Tyr-ERBB2), suggesting paracrine activation in response to local production of ERBB ligands. The aim of this part of the work is to identify the cell lineage of the AREG superexpressers and to investigate the effect of ERBB-inhibition using the multi-ERBB inhibitor Neratinib.

overall_design: scRNA-seq was performed on whole-tumour cell suspensions from lungs of SPC-Cre+ KrasG12D+/-;MYC+/+ (KM) genetically engineered mice 8-9 weeks after transgene induction. Three days prior to culling, mice received daily (3 doses total) intraperitoneal injections of neratinib in peanut oil (80mg/kg), peanut oil, or were left untreated (n=3 per group).

first: Bjorn

last: Kruspig

first: Sarah

last: Laing

first: Ximena L.

last: Raffo-Iraolagoitia

first: Ann

last: Hedley

first: Ya-Ching

last: Hsieh

first: Kristina

last: Kirschner

first: Crispin

last: Miller

first: Daniel J.

last: Murphy


title: Ex Vivo Immuno-Oncology Platform Reveals Spatial T Cell Infiltration Patterns Linked to ATR Inhibition Responses in High-Grade Serous Ovarian Cancer

city: Helsinki

first: Anna

last: Vähärautio

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: To characterize the tumor microenvironment (TME) of recurrence-stage high-grade serous ovarian cancer (HGSC) at the single cell level, we performed single-cell RNA sequencing (scRNA-seq) for a total of four samples from three patients. This data set includes scRNA-seq read count data and cell type annotations for each sample.

overall_design:
Gene expression profiles and cell type annotations of single cells from recurrent tumor tissue from 4 samples of 3 HGSC patients.

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

first: Ashwini S

last: Nagaraj

first: Erdogan Pekcan

last: Erkan

first: Anniina

last: Färkkilä


title: Multi-epigenome-wide analyses and meta-analysis of child maltreatment in judicial autopsies and intervened children and adolescents [JAC_BL]

first: Shota

last: Nishitani

overall_design:
Samples from CM cohort Judicial Autopsy
Bisulfite-converted blood DNA were hybridized into the Illumina Infinium Methylation EPIC Kit array

first: Masataka

last: Nagao

first: Akemi

last: Tomoda


title: Mitochondrial Complex II Orchestrates Divergent Effects in CD4+ and CD8+ T Cells

city: Houston

first: Pavan

last: Reddy

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

summary: Mitochondrial metabolism orchestrates T-cell functions, yet the role of specific mitochondrial components in distinct T-cell subsets remains poorly understood. Here, we explored the role of mitochondrial complex II (MC II), the only complex from the electron transport chain (ETC) that plays a role in both ETC and metabolism, in regulating T-cell functions. Surprisingly, MC II exerts divergent effects on CD4+ and CD8+ T cell activation and function. Using T cell-specific MC II subunit, succinate dehydrogenase A (SDHA), deficient mice, we integrated single-cell RNA sequencing and metabolic profiling, with in vitro and in vivo T-cell functional assays to illuminate these differences. SDHA deficiency induced metabolic changes and remodeled gene expression exclusively in activated T-cells. In CD4+ T-cells, SDHA loss dampened both oxidative phosphorylation (OXPHOS) and glycolysis, impaired cytokine production, proliferation, and reduced CD4+ T cell-mediated graft-versus-host disease after allogeneic stem cell transplantation (SCT). In contrast, SDHA deficiency in CD8+ T-cells reduced OXPHOS, but paradoxically upregulated glycolysis and demonstrated enhanced cytotoxic functions in vitro and in vivo. This metabolic reprogramming endowed SDHA KO CD8+ T-cells with superior in vivo antitumor efficacy after immune checkpoint inhibitor therapy and allogeneic SCT. These findings reveal MC II as a bifurcation point for metabolic and functional specialization in CD4+ and CD8+ T-cells.

overall_design: Purified T cells were from WT and SDHA KO mice were stimulated for 48h. Stimulated and unstimulated WT and SDHA KO T cells were analyzed using scRNAseq.

first: Keisuke

last: Seike

first: Shih-Chun

last: Chu

first: Yuichi

last: Sumii

first: Takashi

last: Ikeda

first: Meng-Chih

last: Wu

first: Laure

last: Maneix

first: Dongchang

last: Zhao

first: Yaping

last: Sun

first: Marcin

last: Cieslik


title: SMARCA5 links histone lactylation to metabolic reprogramming and immune evasion [ATAC-seq]

city: Beijing

first: Ji

last: Cong

address: No.17, Panjiayuan Nanli, South Huawei Road

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Lysine lactylation is a lactate-induced post-translational modification that links cellular metabolism to biological processes. However, the functional role of this histone mark in cancers remains largely unexplored, partly due to a lack of knowledge about its reader proteins. Here, we identify SMARCA5 as a bona fide effector of H3K18la. Transcriptomics, metabolomics and epigenetics analyses reveal numerous SMARCA5 target genes, enriched for metabolic regulators including HK2, PFKM, and LDHA. We further demonstrate that SMARCA5 facilitates glycolytic activity by recruiting MYC to the promoters of glycolytic genes. Elevated lactate derived from tumor glycolysis similarly increases H3K18la levels in CD8+ T cells and induces inhibitory receptor expression. Consequently, the glycolysis/H3K18la/SMARCA5/MYC positive feedback loop exacerbates tumor metabolism and promotes immune evasion. Pharmacologic inhibitor of LDHA that interrupts this loop attenuates immune evasion and sensitizes cancer cells to immunotherapy. Collectively, we propose SMARCA5 as a bona fide H3K18la reader that promotes tumor progression and immune escape by coupling cellular metabolism to epigenetic regulation.

overall_design: Comparative chromatin accessibility profiling analysis of bulk ATAC-seq data from SMARCA5 knockdown group and control group in KYSE30 cells


title: SMARCA5 links histone lactylation to metabolic reprogramming and immune evasion [CUT&Tag]

overall_design: Genomic occupancy profiling of SMARCA5, H3K18la and MYC for SMARCA5-deficient and wildtype KYSE30 cells


title: Directional flow-mediated mesenchymal force drives epithelial tube constriction and splitting

city: BOSTON

first: CHANGHEE

last: LEE

state: MA

address: 77 AVENUE LOUIS PASTEUR

department: Genetics

institute: Harvard Medical School

summary: The transformation of a two-dimensional epithelial sheet into various three-dimensional structures is a critical process in generating the diversity of animal forms. Previous studies of epithelial folding have revealed diverse mechanisms driven by epithelium-intrinsic or -extrinsic forces. Yet little is known about the biomechanical basis of epithelial splitting, which involves extreme folding and eventually a topological transition breaking the epithelium. Here, we leverage tracheal-esophageal separation (TES), a critical and highly conserved morphogenetic event during tetrapod embryogenesis, as a model system for interrogating epithelial tube splitting both in vivo and ex vivo. Comparing TES in chick and mouse embryos, we identified an evolutionarily conserved, compressive force exerted by the mesenchyme surrounding the epithelium, as being necessary and sufficient to drive epithelial constriction and splitting. The compressive force is mediated by localized convergent flow of mesenchymal cells towards the epithelium. We further found that SHH secreted by the epithelium functions as an attractor of mesenchymal cells, and the loss of SHH signaling or cell migration abrogates TES, which can be rescued by externally applied pressure. These results unveil the biomechanical basis of epithelial splitting and suggest plausible mesenchymal origin of tracheal-esophageal birth defects.

overall_design: Control E3.5 (N = 6), E4.0 (N = 4), and cyclopamine-treated E4.0 (N = 9) foreguts were dissected and dissociated subject to scRNA-seq processing and analysis

first: Rui

last: Yan

first: Ludwig

last: Hoffmann

first: Panagiotis

last: Oikonomous

first: Deng

last: Li

first: ChangHee

last: Lee

first: Hasreet

last: Gill

first: Alessandro

last: Mongera

first: Nandan

last: Nerurkar

first: L

last: Mahadevan

first: Clifford

last: Tabin


title: Suppression of dormancy through enhanced respiratory electron dissipation extends the lifespan of mycobacterial biofilms

city: Mumbai

first: Amitesh

last: Anand

state: Maharashtra

address: Homi Bhabha Road

department: DBS

country: India

institute: TIFR

summary: Transcriptomics data of life cycle of biofilm.

overall_design: Biofilms were collected after growing for 4, 5 and 6 days in Sauton's media with or without supplementation of 1% sodium nitrate after which their total RNA was extracted.


title: Neonatal microglia replacement in mice modulates seizure severity in adulthood

city: Philadelphia

first: Carleigh

last: O'Brien

state: PA

address: 3600 Civic Center Blvd

institute: University of Pennsylvania

summary: Microglia replacement therapy, where endogenous brain macrophages are depleted and replaced by adoptively transferred surrogates, holds promise for treating pediatric neurologic diseases, but little is known about how early life microglia replacement impacts the brain. We sought to investigate how early postnatal microglia depletion and adoptive macrophage transfer, essential components of microglia replacement, durably impact neural circuits in a mouse model. Using both pharmacologic and genetic models, postnatal microglia depletion worsened adult seizure severity, mortality and neuropathology in a chemical seizure model. Replacement of endogenous microglia by adoptive transfer of monocytes rescued this effect, while transfer of authentic microglia from a donor mouse did not, and even worsened seizure phenotypes. RNA sequencing of transplanted microglia, monocyte-derived surrogates, and endogenous microglia revealed distinct state changes across groups in response to chemically induced seizure, demonstrating that both ontogeny and adoptive transfer significantly impact resident macrophage responses to the excitotoxic brain environment. In sum, we established models for neonatal microglia depletion and replacement, then applied them to identify durable impacts of depletion and reconstitution on the brain environment. We ultimately identified differential responses of macrophages to excitotoxic challenge based on their ontogeny, underscoring focus areas for ongoing preclinical development of microglia replacement therapies.

overall_design: RNA-seq profiling of endogenous microglia, transplanted microglia, and transplanted monocyte-derived microglia in adults at homeostasis and 5 days after kainic acid-induced seizures.

first: Samuelle

last: Delcy

first: Sangeeta

last: Shukla

first: Eli

last: Levitt

first: Akiva

last: Cohen

first: Mariko

last: Bennett

first: Frederick

middle: C


title: Masculinizing Testosterone Therapy Reduces the Incidence of PIK3CA-Mutant/ER⁺ Breast Cancer but Not BRCA1-Associated Triple-Negative Breast Cancer

city: Boston

first: Jan

last: Heng

address: 330 Brookline Ave, Dana 517B

department: Pathology

institute: Beth Israel Deaconess Medical Center

summary: The effects of gender-affirming testosterone therapy (TT) on breast cancer (BC) risk in the general trans masculine population and among BRCA1/2mut carriers are unclear. We found that TT reduced the size but not the number of terminal duct lobular units, increased stromal expression of estrogen receptor (ER), progesterone receptor, and Ki67, and had an immunosuppressive effect. We leveraged preclinical models to assess TT’s effect on BC incidence and biology. Consistent with the human data, TT reduced mouse mammary gland branching and the number of terminal end buds. TT decreased Pik3ca-related ER+ BC incidence by 81% compared to female controls (adj RR 0.19, 95% CI 0.08-0.45), but had no effect on Brca1-related triple negative BC incidence. Our findings clarify that TT modifies the risk for PIK3CA-related ER+ BC but not BRCA1-associated triple-negative BC, emphasizing the ongoing need for surveillance and individualized care in this population.

overall_design: RNASeq profiling of human breast (non cancer) tissue and mouse tumor, comparing samples exposed to testosterone therapy versus no testosterone.

first: Yu Jing Jan

first: Gerburg

last: Wulf


title: Naphthoquinone preferentially pairs with non-proton-pumping NADH dehydrogenase for respiratory electron transport

summary: Naphthoquinones preferentially pair with the non-proton-pumping NADH dehydrogenase, thereby optimizing electron transport in low-potential respiratory chains under aerobic conditions.

overall_design: Growth of Isochorismate synthase and Chorismate pyruvate-lyase  deficient E. coli MG1655 was performed in their respective evolution media, i.e. minimal media supplemented with glucose (4g/L) as the carbon source. The strains were grown at 37C in two biological replicates for each strain. Total RNA was extracted from the mid-log phase culture for RNA-seq library preparation.


title: mop1 reshapes maize recombination landscape by modulating DNA methylation at MITEs with open chromatin

city: Gainesville

first: Meixia

last: Zhao

state: FL

address: 1355 Museum Drive

department: Microbiology and Cell Science

institute: University of Florida

summary: Meiotic recombination ensures genetic diversity and proper chromosome segregation, but its regulation remains not yet completely understood in many species. Here, we investigate the role of Mediator of paramutation1 (Mop1), a key component of the RNA-directed DNA methylation pathway, in reshaping the recombination landscape in maize. Using high-resolution crossover (CO) mapping, we show that mop1 mutants exhibit sex-specific effects on recombination, with CO numbers significantly reduced in male meiosis but unchanged in females. Sequence analysis of CO-associated motifs reveals increased enrichment of A/T polymer motifs in female mop1 and decreased enrichment of C/G motifs in male mop1 mutants, suggesting a transition to open chromatin states at these regions. Furthermore, we demonstrate that mop1 preferentially introduces new CO sites in females within regions of higher genetic diversity, particularly near miniature inverted-repeat transposable elements (MITEs). Epigenomic profiling reveals that mop1 significantly reduces CHH methylation at MITEs near genes. MITEs that overlap with differentially methylated regions (DMRs) and CO sites exhibit higher levels of histone marks associated with open chromatin, such as H2A.Z and histone acetylation, compared to MITEs outside DMRs or COs. However, the removal of CHH methylation in mop1 at MITEs that introduce COs does not alter the expression of flanking genes. Together, these results highlight the critical role of MOP1 in regulating meiotic recombination by modulating DNA methylation and chromatin states at transposable elements, providing new insights into the epigenetic regulation of meiotic recombination.

overall_design: Transcriptomic analysis of immature anthers undergoing meiosis I from mop1 plants (Mo17/B73;mop1/mop1) and their sibling controls (Mo17/B73;+/+) to identify expression changes associated with crossovers in mop1

first: Hasan

last: Moahmmad Mahmood

first: Zhao

last: Meixia


title: Trophoblast stem cell derivation from naive and primed hPSC enables ELF5 functional analysis (miRNAseq)

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

department: Research Program for Molecular Neurology

type: Non-coding RNA profiling by high throughput sequencing

summary: Human pluripotent stem cells (hPSCs) are valuable tools for studying placental biology, yet their differentiation into bona fide trophoblast stem cells (TSCs) remains challenging. In this study, we established and thoroughly compared naive and primed-derived TSC-like cells with primary human TSCs derived from pre-implantation blastocyst and first-trimester placenta. Comprehensive analyses confirmed expression of trophoblast lineage-specific genes and typical placental features. Detailed transcriptional analyses revealed that naive-derived TSC-like cells resembled embryo and placenta-derived cell lines and differentiated faster and more directly into TSC than primed-derived cells. We used these TSC-like models to study the role of ELF5, a transcription factor indispensable for maintenance and differentiation in mouse TSC. In contrast to the mouse, knockout and knockdown experiments revealed that ELF5 is dispensable for human TSC-like cells self-renewal and differentiation. Our study provides valuable transcriptional data and highlights the utility of hPSC-derived TSC-like cells for modeling the placenta and studying gene function.

overall_design: Small RNA sequencing analysis of naive and primed H9 ESC derived human trophoblast lines as well as trophoblast cell lines bTS5 and CT30.

first: Joonas

last: Sokka

first: Ella

last: Lapinsuo

first: Sami

last: Jalil

first: Masahito

last: Yoshihara

first: Jere

last: Weltner

first: Fredrik

last: Lanner

first: Juha

last: Kere

first: Diego

last: Balboa

first: Timo

last: Otonkoski

first: Ras

last: Trokovic


title: beta-catenin-1 localization and transcriptomic profiling provide insights into the early development of planarians

city: Barcelona

first: Josep

middle: F

last: ABRIL

state: Catalonia

address: Av Diagonal, 643, edifici Prevosti, planta -1, sala IBUB

department: Genetics, Microbiology & Statistics

country: Spain

institute: Universitat de Barcelona

summary: Background: The development of planarians is unique among Spiralians. Instead of the stereotypical spiral cleavage, planarians exhibit a disperse cleavage. There is no apparent gastrulation, and the morphogenesis of the yolk-feeding embryo remains a mystery. In this study, we examine the subcellular localization of βcatenin-1 and the transcriptomic profile during the early embryonic development of Schmidtea polychroa to shed light on these early events. Results: We find that the first nuclearization of βcatenin-1 occurs in yolk cells surrounding the embryonic syncytium. By 24 hours post deposition, βcatenin-1 starts to be nuclearized in blastomeres, coinciding with the activation of signaling and cell motility genes. During morphogenesis of the yolk-feeding embryo, βcatenin-1 is first nuclearized at one pole (gut and pharynx progenitors) and in epidermal progenitors, and afterwards in the embryonic pharynx. At this stage, genes involved in a first morphogenetic event are turned on. Following the yolk ingestion by the embryo, a dramatic transcriptomic shift occurs that coincides with the activation of genes related to cell proliferation. Finally, between 5-7 days post deposition βcatenin-1 is massively nuclearized, and genes involved in the morphogenesis and patterning of the adult tissues get activated. Conclusions: Our findings provide new insights into the early developmental events of Schmidtea polychroa, including cleavage, the involvement of βcatenin-1 in the formation of the embryonic tissues and the morphogenesis of two distinct body plans. These findings are significant to understand the evolution of the peculiar mode of planarian development.

overall_design: RNA-seq time course differential gene expression analysis of Schmidtea polychroa embryonic development from samples at 4, 24, 32, 48, 72, 96, 120, and 168 hours post cocoon deposition, taking 4h as reference time (t_x vs t_4h) or comparisons with previous time points (t_x vs t_(x-1)). The Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GLGS00000000. The version described in this paper is the first version, GLGS01000000.

first: Pablo

last: Coronel-Córdoba

first: Miquel

last: Sureda-Gómez

first: Jose Maria

last: Martín-Durán

first: Francisco

last: Monjo

first: Emili

last: Saló

last: Abril

first: Teresa

last: Adell


title: HCC-derived SNU cell lines as model systems to study HBV life cycle

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Human SNU cell lines derived from hepatocellular carcinomas associated with chronic hepatitis B virus (HBV) infection were examined. The analysis of intracellular RNA and DNA markers of HBV replication and examination of HBV RNA reads coverage of selected regions on HBV-related RNAs and polyadenylation positions within HBV sequence using RNA-sequencing suggested absence of HBV replication in SNU-423, SNU-368 SNU-398, SNU-182, SNU-449, SNU-475, SNU-354, SNU-739 and SNU-387 cells, while SNU-761 and SNU-886 still could maintain residual HBV replication. The undetectable intracellular HBV core antigen (HBcAg) and absence of significant levels of secreted core-associated and virion-associated HBV DNA confirmed the absence or profound suppression of HBV replication in parental SNU cell lines. Various 5'-human-HBV-3' and 5'-HBV-human-3' RNAs transcribed from integrated HBV DNA were found in most of SNU cell lines. The 5'-HBV-human-3' junctions suggested that several SNU cell lines could generate 5'-HBV-human-3' RNAs encoding HBV envelope proteins. The known and novel spliced HBV RNAs were detected in SNU-886, SNU-739, SNU-387, SNU-761, and SNU-354 cells. At least some of them were generated independently of HBV replication. All SNU cell lines could not support efficient HBV replication after transfection with the vector initiating efficient HBV replication in Huh7 cells. This was reflected by three distinct accumulation patterns of HBV replication markers, undetectable intracellular HBcAg, and by the lack of considerable levels of secreted core-bound and virion-associated HBV DNA. Overall, SNU cell lines represent valuable model systems for detailed analysis of integrant-transcribed HBV RNAs, spliced HBV RNAs, and mechanisms of suppression of HBV genome replication.

overall_design: Human SNU cell lines (SNU-423, SNU-368 SNU-398, SNU-182, SNU-449, SNU-475, SNU-354, SNU-739, SNU-387, SNU-761 and SNU-886) developed (by Seoul National University (SNU)) from hepatocellular carcinomas associated with chronic hepatitis B virus (HBV) infection were examined. The RNA markers of intracellular HBV replication (pre-genomic RNA (pgRNA), replication-derived RNAs generated by HBV genome replication and polyadenylated via conventional HBV polyadenylation signal (PAS) (rd-RNAs), and total HBV RNA (including rd-RNAs, cps-RNAs (HBV RNAs polyadenylated via HBV cryptic PAS) and also various RNA species transcribed from integrated HBV DNA depending on the HBV area that they bear) were measured by RT-qPCR assays. The DNA markers of intracellular HBV genome replication (core-associated HBV DNA and covalently closed circular DNA (cccDNA)) were quantified by qPCR assays. These intracellular HBV replication markers were assayed and compared between parental (untransfected) SNU cell lines and two reference cell lines, Hep3B and PLC/PRF/5 (Alexander cells), which also were derived from human HBV-related HCCs. The latter two reference cell lines contained integrated HBV DNA, and had no ongoing HBV replication in them. The intracellular expression of HBV core antigen (HBcAg) was analyzed and compared using immunofluorescence and staining with anti-HBcAg antibodies in parental SNU cell lines, and in control Huh7 cells and HepG2 cells (that were transfected with the plasmid pT-HBV1.3 and were replicating HBV genome). Huh7 cells and HepG2 cells were derived from human HCCs not related to HBV infection. The HBV DNA associated with secreted un-enveloped nucleocapsids (cores) or with HBV virions coated with HBV surface antigen (HBsAg) was assayed and compared in parental SNU cell lines and the above mentioned transfected Huh7 and HepG2 cells using immuno-precipitations (IPs) with anti-HBcAg antibodies or with anti-HBsAg antibodies (respectively) with subsequent measuring of HBV DNA in the pellet and in the supernatant using qPCR, which was designed for the analysis of the relaxed circular HBV DNA (rcDNA). The total RNA harvested from parental SNU cell lines and from Huh7 cells, which were transfected with the plasmid pT-HBV1.3 and were replicating HBV genome, were analyzed by RNA-sequencing that employed poly(A) selection. The generated RNA-seq data was analyzed (i) for HBV RNA reads coverage for the selected regions on HBV genome, which represented the unique areas of HBV genomic sequences that are expected to be present only once on rd-RNAs produced by HBV genome replication; (ii) for polyadenylation sites within HBV sequences, (iii) for 5'-human-HBV-3' RNAs and 5'-HBV-human-3' RNAs that were transcribed from integrated HBV DNA independently of HBV genome replication; and (iv) for spliced HBV RNA species as we did previously (Zaiets, I., S. Gunewardena, S. Menne, S. A. Weinman, and S. O. Gudima. 2023. Sera of individuals chronically infected with hepatitis B virus (HBV) contain diverse RNA types produced by HBV replication or derived from integrated HBV DNA. J. Virol. 97(3):e0195022. doi: 10.1128/jvi.01950-22.. PMID: 36877036. PMCID: PMC10062156). In addition, the above mentioned intracellular HBV genome replication markers, intracellular expression of HBcAg, and secreted core-bound and virion-bound HBV DNA were analyzed and compared in SNU cell lines transfected with the plasmid pT-HBV1.3 (to induce HBV genome replication) and control Huh7 cells and HepG2 cells, which were also transfected with pT-HBV1.3.

first: Igor

last: Zaiets

first: Oleksandra

last: Chazova

first: Severin

middle: O

last: Gudima


title: Effect of knockdown of IGF2BP3 on gene expression of H1299 lung cancer cells

city: Guangzhou

first: Jingwei

last: Li

address: Guangzhou University Town, Panyu District

institute: Sun Yat-sen University

summary: Brain metastases represent a significant cause of morbidity and mortality in non-small cell lung cancer (NSCLC), with limited therapeutic options. The unique brain microenvironment, characterized by low lipid availability, may drive metastatic NSCLC cells to adapt through lipid metabolic reprogramming. In this study, we identify a novel mechanism in NSCLC brain colonization mediated by IGF2BP3-driven lipid metabolism. Elevated IGF2BP3 expression in NSCLC brain colonization correlates with poor prognosis and promotes cancer cell migration, invasion, and brain colonization by activating the lipogenesis pathway. Our findings highlight the critical role of IGF2BP3 in lipid metabolism and propose that targeting IGF2BP3 may provide a promising therapeutic strategy for NSCLC brain metastases.

overall_design: Conparative gene expression profiling analysis of RNA-seq data for H1299 lung cancer cells and its KD dericative (shIGF2BP3).

first: Shumin

last: Ouyang

first: Ziyou

last: Lin


title: Raw sequence reads of Candida albicans Hap31 and Hap32, two subunits of the CCAAT binding complex

city: Hsinchu

first: Dinh-Dong

last: Le

address: No. 101, Section 2, Guangfu Rd

country: Taiwan

institute: College of Life Science - Instituted of Molecular & Cellular Biology

summary: The opportunistic fungal pathogen Candida albicans has recently impacted a substantial portion of the population. The highly conserved CCAAT-binding complex (CBC), also known as the Hap complex in yeast, plays a critical role in multiple cellular functions. Additionally, the cell wall of this pathogen serves as an effective barrier against environmental stresses and undergoes continuous renewal through a complex regulatory network. This network is tightly controlled by numerous cell signaling pathways and transcription factors. Mutants with individual deletions of components of the Hap complex were generated and compared to the wild-type strain to investigate the regulatory role of the CBC in cell wall maintenance and biofilm formation. Additionally, RNA sequencing was performed to uncover novel insights into the regulatory pathways associated with the CBC. Deletion of CBC components significantly impacts the cell wall structure and composition, leading to an imbalance in the cell wall carbohydrate profile, as well as cell wall unmasking, which triggers the activation of the Cell Wall Integrity (CWI) signaling pathway. These alterations subsequently affect the ability to form biofilms on polystyrene surfaces. Notably, the small GTPase Rhb1 is implicated in CBC-mediated CWI maintenance. Moreover, RNA sequencing of the expression profiles of the two Hap3 paralogs suggests their involvement in rRNA processing, ribosomal biogenesis, carbohydrate transport and metabolism, and amino acid biosynthesis, all contributing to cell wall maintenance. Our findings provide novel insights into the molecular pathways that govern cell wall biogenesis. The discovery of this regulatory mechanism is crucial for understanding the relationship between the highly conserved CBC and cell wall maintenance in C. albicans.

overall_design: Candida albicans SC5314 was used as the parent strain. From the the SC5314, deleted mutants of the HAP31, HAP32 genes, and the double-deleted mutants of the HAP31-HAP32 were constructed. Then, RNA sequencing was performed to explore the transcription profile of these mutants. Raw FASTA files were provides in this submission, which are three biology replicated samples from each of the strains, including the SC5314 for the control.

first: Chung-Yu

last: Lan

first: Wen-Han

last: Wang


title: SETD1A Regulates Psychiatric Gene Networks Involved in Genomic Stability and Synaptic Function in Rare and Sporadic Schizophrenia [bulk RNA-seq]

city: Baltimore

first: Tomoyo

last: Sawada

state: MD

address: 855 N Wolfe St

department: Molecular Neurogenetics

institute: Lieber Institute for Brain Development

summary: Rare loss-of-function (LoF) mutations in SETD1A are associated with schizophrenia (SCZ). However, how SETD1A haploinsufficiency leads to SCZ-associated phenotypes and its relevance to patients without these rare mutations is unknown. Here, we identify SETD1A bound loci and regulated genes in human prenatal cortex and isogenic pluripotent stem cell-derived neuronal models engineered with SETD1A LoF variants, including the most common patient mutation. SETD1A preferentially binds the promoters of SCZ and Bipolar risk loci that regulate chromatin remodeling, DNA repair, and synaptic function. Additionally, SETD1A binds to DNA damage prone sites in neural progenitor cells and postmitotic neurons. SETD1A haploinsufficiency causes accelerated neurogenesis, reduced neuronal complexity, and DNA damage accumulation in postmitotic neurons that is rescued by inhibiting the H3K4me2/3 demethylase KDM5. In postmortem SCZ cortical tissue, individuals who lack SETD1A mutations exhibit reduced SETD1A expression, associated with downregulation of SETD1A-regulated genes, implicating SETD1A-H3K4me dysfunction in sporadic SCZ cases. Therefore, restoring the SETD1A-H3K4me epigenetic imbalance may benefit individuals with SETD1A haploinsufficiency as well as a broader psychiatric population without SETD1A mutations.

overall_design: Bulk RNA-seq profiling of isogenic pluripotent stem cell-derived neuronal models engineered with SETD1A LoF variants.

first: Sawada

last: Tomoyo

first: Feltrin

last: Arthur

first: Erwin

last: Jennifer


title: SETD1A Regulates Psychiatric Gene Networks Involved in Genomic Stability and Synaptic Function in Rare and Sporadic Schizophrenia

overall_design: Single Cell RNA-seq profiling of human Cerebral Organoids engineered with SETD1A LoF variants.


title: SETD1A Regulates Psychiatric Gene Networks Involved in Genomic Stability and Synaptic Function in Rare and Sporadic Schizophrenia [CUT&Tag]

overall_design: CUT&TAG profiling from human prenatal frontal lobes and from isogenic pluripotent stem cell-derived neuronal models engineered with SETD1A LoF variants.


title: Neuroprotective effect of secreted factors from glial progenitor cells in a model of glutamate excitotoxicity

first: Evgeny

last: Karpulevich

address: Alexandra Solzhenitsina

department: Information Systems

institute: ISP RAS

summary: In this study, we investigated the mechanisms of neuroprotection of factors secreted by glial progenitro cells. We earlier obtainedn data on their neuroprotective action on the model of glutamate excitotoxicity, as well as proteomic analysis. The model was reproduced on cortical neuron cultures from rat pups (P0, 10 DIV). Before the model reproducing, the samples were added. Next day a solution containing 100 μM glutamate was added to the cultures for 1 hour. The negative control was intact cultures. The addition of 100 μM memantine was a positive control. Three repeats were performed for each group and both controls. The comparison groups were: extracellular vesicles, proteins of the 3-100 kDa fraction and total secretome. Total RNA was collected 4 hours after model reproducing for transcriptome analysis to identify signaling pathways activated in cells by druges under induced glutamate toxicity.

overall_design: A model of glutamate excitotoxicity was reproduced on neuroglial culture (10 DIV). A day before the addition of 100 μM glutamate, examples of extracellular vesicles, proteins of the 3-100 kDa fraction, and total secretome (3-infinity) were added to the cells. 100 μM memantine was used as a positive control. Total RNA was obtained 4 hours after reproducing of the glutamate excitotoxicity model.

first: Diana

last: Salikhova


title: Trophoblast stem cell derivation from naive and primed hPSC enables ELF5 functional analysis (scRNAseq)

first: Jouni

last: Kvist

overall_design: Single cell transcriptomic analysis of naive and primed H9 ESC derived human trophoblast lines, including mid-differentiation day 3 and 6 samples, naive and primed H9 ESC samples, as well as trophoblast cell lines bTS5 and CT30

first: Joonas

last: Sokka

first: Ella

last: Lapinsuo

first: Sami

last: Jalil

first: Masahito

last: Yoshihara

first: Jere

last: Weltner

first: Fredrik

last: Lanner

first: Juha

last: Kere

first: Diego

last: Balboa

first: Timo

last: Otonkoski

first: Ras

last: Trokovic


title: scRNA-seq Analysis of Lung Cells in Influenza A Virus (IAV) Infected Aged Mice

city: Oklahoma City

first: Jordan

last: Metcalf

address: 800 Research PKWY, Rm425

institute: The university of Oklahoma Health Sciences Center

summary: Seasonal influenza causes significant morbidity and mortality worldwide, with 70-90% of these deaths occurring in individuals aged 65 or older. To explore the mechanisms behind this age-related vulnerability, we investigated immune responses and inflammation in the lungs of young and old mice during influenza A virus (IAV) infection. Young (12-week) and old (70-week) C57BL/6J mice were intranasally infected with IAV PR8, and immune responses were assessed at 7 days post-infection (dpi) using single-cell RNA sequencing (scRNA-seq).

overall_design: scRNA-seq profiling in the lungs from old and young mice at day 7 after influenza virus infection

first: Wenxin

last: Wu

first: Jeremy S

last: Alexander

first: Chaoqun

last: Huang

first: Lin

last: Liu

first: Douglas A

last: Drevets

first: Jordan P


title: Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor (bTMP-seq)

city: Milano

first: Stefano

middle: Giustino

last: Manzo

state: MI

address: Via Celoria 26, Dipartimento Bioscienze, Torre A, Piano 4

department: Biosciences

institute: University of Milan

summary: Lamina-associated domains (LADs) are megabase-sized portions of the genome anchored to the nuclear lamina (NL). Factors controlling the tethering of the genome to the NL have remained elusive. Here, we identified DNA Topoisomerase 2 beta (TOP2B) as a prominent regulator of genome-NL interactions. TOP2B depletion leads to the weakening of these interactions in LADs marked by H3K9me3 heterochromatin, and the repositioning of inter-LAD regions (iLADs) to the NL. TOP2B loss affects LAD interactions with Lamin B receptor (LBR) more prominently than with Lamins B1 and B2. LBR loss phenocopies the effects of TOP2B depletion, although the two proteins occupy different portions of the genome. Co-depletion of TOP2B and LBR causes partial LAD/iLADs inversion, mirroring changes typical of oncogene-induced senescence. We propose that a coordinated axis controlled by TOP2B in iLADs and LBR in LADs maintain proper partitioning of the genome between the NL and the nuclear interior.

overall_design: bTMP-seq experiment were performed on hTERT-RPE1 cells control. bTMP intercaletes in negative supercoiled DNA and bTMP-seq provide genome-wide mapping of negative supercoiling in control RPE1 cells.

first: Tom

last: van Schaik

first: Marcel

last: de Haas

first: Jeremie

last: Breda

first: Mikhail

last: Magnitov

first: Elzo

last: de Wit

first: Anna

last: Manjon

first: Rene

last: Medema

first: Adam

middle: J

last: Buckle

first: Catherine

last: Naughton

first: Nick

last: Gilbert

first: Bas

last: van Steensel


title: Decreased sialylation in the mouse retina elicits complement-related microglia response and bipolar cell loss

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

country: Germany

institute: University Hospital of Bonn

summary: Sialylation plays an important role in self-recognition, as well as keeping the complement and innate immune systems in check. It is unclear whether the reduced sialylation as seen during aging and in mice heterozygous for the null mutant of UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (Gne+/-), an essential enzyme for sialic acid biosynthesis, contributes to retinal inflammation and degeneration. We found a reduction of polysialic  acid and trisialic acid expression in several retinal layers in Gne+/- mice at 9 months of age, which was associated with a higher  microglial expression of the lysosomal marker CD68. Furthermore, the total number of rod retinal bipolar cells was reduced in 12 months old Gne+/- mice, demonstrating loss of these retinal interneurons that are involved in connecting photoreceptors and ganglion cells. Whole-genome transcriptome analysis showed up-regulation of the complement, inflammation, and apoptosis pathways in the retinas of Gne+/- mice. Particularly, increased gene transcript levels of the complement factors C3 and C4 and the pro-inflammatory cytokine Il-1β were observed by semi-quantitative real-time polymerase chain reaction (sqRT-PCR) in 9 months old Gne+/- mice. The Iincreased expression of CD68, as well as the loss of rod bipolar cells, and increased gene transcription of the complement factor C4, were all prevented after crossing Gne+/- mice with complement factor C3-deficient animals.  In conclusion, our data show that retinal hyposialylation in middle-aged Gne+/- mice, at 9 and 12 months of age,  was associated with complement-related inflammation and lysosomal microglia response, as well as rod bipolar cells loss, which was absent in animals with a genetic deletion of complement factor C3.

overall_design: To investigate the effect of reduced sialylation on the retinas of middle-ages mice, we studied the retinas of heterozygous Gne gene knock-out mouse model (Gne+/-) which have about 25% overall reduction in sialic acid, and compared them to Gne+/+ wildtype mice. To investigate whether the effects seen in the Gne+/- mice retinas are driven by the complement system, we crossed both the Gne+/+ wildtype mice and the Gne+/- mice with a complete complement knock-out mouse, resulting in Gne+/+ C3-/- and Gne+/- C3-/- mice. RNA-sequencing was performed on nine months old mice.

first: German

last: Cuevas-Rios

first: Tawfik

last: Abou Assale

first: Jannis

last: Wissfeld

first: Annemarie

last: Bungartz

first: Julia

last: Hofmann

first: Thomas

last: Langmann


title: Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor (RNA-Seq)

first: Stefano

last: Manzo

overall_design: RNA-seq experiment were performed on RPE1SunTag control and depleted for TOP2B. RNA was extracted 5 days post transfection.

first: Tom

last: van Schaik

first: Marcel

last: de Haas


title: Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches [Xenium PDAC]

city: Dallas

first: Huocong

last: Huang

address: NB8.212A, 6000 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research, Department of Surgery and Immunology

institute: UT Southwestern Medical Center

summary: To explore the CAF niches in pancreatic ductal adenocarcinoma (PDAC), we performed Xenium assays in 3 treatment-naïve and 3 chemoradiotherapy-treated human PDAC samples. We found that after the chemoradiotherapy treatment, tissues became more desmoplastic with a larger CAF proportion. And interestingly, we found there was a reduction of cancer cell 1 in the chemoradiotherapy group while the ratio of cancer cell 2 remained similar, suggesting cancer cell 2 was the chemoradiotherapy-resistant cancer cell population. Through differential gene analysis, we found cancer 2 was marked by a high level of SPP1 expression.

overall_design: We designed a custom gene panel comprising 480 genes for cell type recognition and gene functional analysis. Tissue sections were prepared according to the Xenium In Situ for FFPE-Tissue Preparation Guide protocol. FFPE sections were cut to 5 μm and placed in the designated sample area on a Xenium slide.


title: Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches [scRNA-seq]

summary: To understand the microenvironmental changes caused by Spp1 knockout, we digested the tumors from the control and knockout groups into single cell suspension and performed scRNA-seq. The scRNA-seq data suggested a significant increase of T cell infiltration into the stromal Spp1 knockout tumors.

overall_design: For each group, we included 6 tumors. Every two tumors were then pooled together for library construction (three libraries per group). Approximately 10,000 cells were used for library construction with the Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics), following the manufacturer’s protocol. The purified libraries were sequenced on an Illumina NovaSeq 6000. Raw base call (BCL) files from the sequencer were demultiplexed into fastq files. These fastq files were aligned to the mm10 mouse reference genome and quantified using the Cell Ranger pipeline (version 7.2.0, 10x Genomics). The preliminary filtered data generated from Cell Ranger were utilized for all subsequent analyses.


title: Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches [Xenium PM]

summary: One of the most common origins of Peritoneal metastasis (PM) is colon cancer, which occurs in about 20% of colon cancer patients. Given the cancer cell heterogeneity in PM, we first tried to dissect the spatial distribution of CAF and the associated niches at a single cell resolution, we exploited the Xenium In Situ high-plex spatial imaging platform. We performed the Xenium assays with 8 human PM samples of colon origin including one PM-adjacent tissue. Among the 8 PM samples, 3 samples carried a distinct iCMS3 epithelial signature (PM1, PM2, PM3), 2 carried iCMS2 signature (PM6, PM7), while the other 2 samples had a mix of both iCMS2 and iCMS3 signatures (PM4, PM5). We found that the presence of iCMS3 cancer cells was associated with an increase infiltration of lymphocytes and the formation of tertiary lymphoid structures (TLS).


title: Tyrosine kinase Ptk1 couples one carbon metabolism and virulence in an endogenous pathogen

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

summary: Endogenous pathogens can constrain virulence to ensure survival in the host.  Pathogenic state can be controlled by metabolic responses to the prevailing microenvironment; however, the coupling and effector mechanisms are not well understood. Flux through the One Carbon Metabolism (OCM) pathway can modulate virulence of the oral pathobiont Porphyromonas gingivalis, and here we show that this is controlled by tyrosine phosphorylation-dependent differential partitioning of gingipain proteases.  The OCM essential precursor pABA inhibits the low molecular weight tyrosine phosphatase Ltp1, and consequently relieves inhibition of its cognate kinase, Ptk1.  We found that in the absence of pABA, reduced Ptk1 kinase activity blocks extracellular release of gingipains.  Surface retention of gingipains confers resistance to neutrophil mobilization and killing, and virulence in animal models of disease is elevated.  Reciprocally, Ptk1 and gingipains are required for maximal flux through OCM, and Ptk1 can phosphorylate the OCM pathway enzymes GlyA and GcvT.  Further, ALP, an alkaline phosphatase involved in synthesis of DHPPP, which combines with pABA to make DHP, is phosphorylated and activated by Ptk1. Deletion mutants of ptk1 and pabC were more virulent in an in vivo virulence (murine abscess) model.   RNASeq was adopted to compare the transcriptional profile of ptk1 and pabC mutants recovered from abscess material.  We propose, that although the primary function of Ptk1 is to maintain OCM balance, it mechanistically couples metabolism with tunable pathogenic potential through directing the location of proteases.

overall_design: In order to investigate the role that the pABA synthesis enzyme PabC and the bacterial tyrosine kinase Ptk1 has on the transcriptome of Porphyromonas gingivalis during infection, mice were inoculated with either the parental wildtype (WT) ATCC 33277 strain or isogenic deletion mutants lacking either pabC (ΔpabC) or ptk1 (Δptk1) and abscess material collected and subjected to RNASeq.

first: Kendall

middle: S

last: Stocke

first: Satya

last: Pandey

first: Shunying

last: Jin

first: John

middle: D

last: Perpich

first: Lan

last: Yakoumatos

first: Hirotaka

last: Kosaki

first: Daniel

last: Wilkey

first: Zackary

last: Fitzsimonds

middle: P

last: Miller

first: Mukesh

middle: K

last: Sriwastva

first: Michael

last: Merchant

first: Juhi

last: Bagaitkar

first: Silvia

last: Uriarte

first: Jan

last: Potempa


title: Oxidative stress induced telomere instability/damage drives T cell dysfunction in cancer

city: Pittsburgh

first: Greg

last: Delgoffe

address: 5115 Centre Ave.

institute: University of Pittsburgh

summary: The tumor microenvironment imposes immunologic and metabolic stresses sufficient to deviate immune cell differentiation into dysfunctional fates like exhaustion. Our data show that dysfunctional T cells in cancer do not harbor short telomeres indicative of replicative senescence, but rather harbor damaged telomeres, which we hypothesized arose from oxidative stress. Chemo-optogenetic induction of localized mitochondrial or telomeric reactive oxygen species (ROS) using a novel photosensitizer caused DNA damage at telomeres and was sufficient to drive a dysfunctional state in newly activated T cells, with diminished capability for cytokine production. Localizing the ROS scavenger GPX1 directly to telomeres reduced telomere fragility in tumors and improved the function of therapeutic T cells. Protecting telomeres through expression of a telomere-targeted antioxidant protein may preserve T cell function in the tumor microenvironment and drive superior responses to adoptive cell therapies.

overall_design:
1. CD8+ T cells from TRF1-FAP-T or Mito-FAP-T mice (3 each) were stimulated overnight with anti-CD3/CD28 antibodies and treated with 660nm light alone or with MG-2I dye for 1 hour. Twenty-four hours later, RNA was isolated for sequencing (samples TRF1FAP_light-1-3, TRF1FAP_lightdye_1-3, MitoFAP_light1-3, MitoFAP_lightdye_1-3).
2. Separately, Pmel-1 CD8 cells were expanded in-vitro and transduced with control (PMIA) or GPX1-TRF1 expression constructs and infused into B16-tumor bearing mice. Ten-days later, CD8+ T cells were sorted from tumors for RNA-sequencing (samples PMIA_1-4 and GPX_1-4).
1. CD8+ T cells from TRF1-FAP-T or Mito-FAP-T mice (3 each) were stimulated overnight with anti-CD3/CD28 antibodies and treated with 660nm light alone or with MG-2I dye for 1 hour. Cells were then passaged in the presence of IL-2. Seven days later, RNA was isolated for sequencing.

first: Dayana

middle: B

last: Rivadeneira

first: Sanjana

last: Thosar

first: Kevin

last: Quann

first: Billy

last: Gunn

first: Victoria

last: Dean

first: Konstantinos

last: Lontos

first: Ryan

last: Barnes

last: Bruchez

first: Patricia

last: Opresko

middle: M


title: Mouse brains

city: beijing

first: Zhihong

last: Song

address: Taiping Road 27

institute: Beijing Institute of Basic Medical Sciences

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

overall_design: Refer to individual Series


title: m6A-containing RNA in oligodendrocyte  progenitor cells of C57BL/6J mice [MeRIP-Seq]

summary: To explore the genes that undergo m6A modification in oligodendrocyte  progenitor cells, we isolated primary cells in brains of C57BL/6J mice at P4.

overall_design: Analysis of m6A modified genes in oligodendrocyte precursor cells isolated by immuneadsorption from brains of C57BL/6J mice at P4.

first: Ying

last: Zhang

first: Shukun

last: Wang