title: Increased APOE abundance in the brain in Down syndrome - Alzheimer’s disease compared with early onset-Alzheimer's disease is associated with elevated APP and C- terminal fragment abundance

city: London

first: Yazead

last: Buhidma

state: London

address: 1 Wakefield Street

department: Department of Neurodegenerative Diseases

institute: University College London

summary: Trisomy of chromosome 21, the cause of Down syndrome (DS), is the most commonly occurring genetic cause of Alzheimer’s disease (AD). Here we compare the proteome of the frontal cortex of people who have Down syndrome-Alzheimer’s disease (DSAD) with demographically matched cases of early-onset AD and healthy ageing controls from the general population. We find the abundance of several chromosome 21 encoded proteins are increased in DSAD compared to both comparative groups. Moreover, wider dysregulation of the proteome occurs beyond proteins encoded by chromosome 21, including an increase in the abundance of the key AD protein APOE, in people with DSAD compared to matched cases of early-onset AD. To understand the cell-types which may contribute to these changes in protein abundance we undertook a single-nuclei RNA-sequencing study on the same cases. This demonstrated that trisomy of chromosome 21 altered transcription of these proteins in a range of cell-types. Specifically, APOE expression was raised in subtypes of astrocytes, endothelial cells and pericytes. In our case series, we also found that the abundance of APOE correlates with the abundance of full-length APP and C-terminal-fragments-α but not with amyloid-β, the key constituent of AD plaque pathology. Having increased abundance of APOE may impact the development of, or response to, AD pathology in the brain of people who have DSAD, altering the disease mechanisms, with clinical implications. Overall, these data highlight that trisomy 21 alters both the transcriptome and proteome of people who have DS in the context of AD, and that these differences should be considered when selecting therapeutic strategies for this important group of individuals who are at high risk of early-onset dementia.

overall_design: Nuclei were isolated from frozen frontal cortex grey matter from discovery cohort cases (8 DS-AD, 4 EOAD, and 4 healthy controls). Tissue was transferred directly onto ice-cold sucrose buffer and homogenised by hand. The homogenate was layered on top of a sucrose cushion and nuclei were recovered after centrifugation. Nuclei were resuspended in PBS containing BSA (to prevent clumping) and RNase inhibitors, counted and diluted to 1,000 nuclei/μl. Sequencing libraries were prepared using the “single cell 3’ library kit v3” with the Chromium instrument (10X Genomics). Aiming to obtain libraries for ~5,000 independent nuclei per sample. Libraries were sequenced on an Illumina NovaSeq6000 instrument (UCL Genomics), to an average of at least 100,000 reads/nucleus. Raw sequencing data were processed through the software CellRanger (10X Genomics) to assign each transcript read to its respective nucleus, we performed alignment to the transcriptome, counting reads, and processing of the unique molecular identifier tag to reduce PCR bias. The resulting gene count table was analysed using the Seurat package (version 4.4). Quality control was performed to remove low-quality cells based on the number of detected genes and unique molecular identifiers (UMIs). Cells with an unusually high number of UMIs, suggesting potential doublet events, were also excluded using scDblFinder. Using SCTransform, gene expression data were normalised to adjust for differences in sequencing depth between cells and scaled to correct for cell-to-cell variation in total UMI count. Data were also normalised to remove confounding sources of variation such as mitochondrial mapping percentage, post-mortem delay, age of death, and batch number.

first: Clíona

last: Farrell

first: Frances

last: Wiseman


title: Multi-Omics Analysis of the Immunological State at Baseline and Following SARS-CoV-2 mRNA Vaccination in Lung Transplant Recipients

status: Public on Feb 28 2025

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: Despite their remarkable success, the effectiveness of COVID-19 mRNA vaccines is notably diminished in organ transplant patients. Here, we employed a multi-omics approach to elucidate the immunological state at baseline and following SARS-CoV-2 mRNA vaccination of lung transplant (LTX) patients compared to healthy controls (HC). Our analysis revealed a baseline immune profile in LTX patients that mirrors the immune alterations observed in severe COVID-19 cases and sepsis. This profile is characterized by: (i) elevated pro-inflammatory cytokines in plasma, notably high levels of EN-RAGE and IL-6; (ii) reduced expression of HLA-DR on blood monocytes and dendritic cells (DCs); (iii) diminished cytokine production by blood monocytes and DCs in response to toll-like receptor (TLR) activation; (iv) increased plasma concentrations of microbial products. In addition to these alterations, single-cell RNA-seq analysis revealed 4 transcriptionally distinct clusters of classical monocytes in HC, with a striking enrichment of a unique classical monocyte cluster in LTX patients, differing from the predominant classical monocytes in HC, marked by heightened expression of the S100A family and reduced expression of genes related to cytokine production and antigen presentation. Following vaccination, LTX patients displayed a reduced magnitude and breadth of binding and neutralizing antibody responses, and impaired memory B and T cell responses. Furthermore, there was a blunted innate immune response to vaccination, evidenced by decreased transcriptional signatures linked to antigen presentation, dendritic cell activation, interferon and monocytes at the single-cell level. Integrative multiscale, multiresponse network (MMRN) analysis revealed an inverse correlation between the distinctive baseline immunological state observed in LTX patients and the adaptive immune responses to vaccines. These findings underscore the distinct immunological profile of lung transplant recipients, providing insights into their immunosuppressed condition and reduced immune responses to vaccines.

overall_design: PBMCs from Baseline, day 1 and day 7 timepoints following the vaccination from each cohort were submitted for BD Rhapsody single cell whole transcriptome analysis (WTA), totaling 41 samples from 5 lung transplant patients and 9 healthy individuals.

first: Hu

last: Mengyun

first: Fang

last: Zhuoqing

first: Miranda

last: Molly

first: Ji

last: Xuhuai

first: Maecker

last: Holden

first: Pulendran

last: Bali


title: Proline metabolic reprogramming modulates cardiac remodeling induced by pressure overload in the heart

city: Hangzhou

first: Qingbo

last: Lv

state: Zhejiang

address: 3 East Qingchun Road

country: China

institute: Sir Run Run Hospital, School of Medicine, Zhejiang University

summary: Metabolic reprogramming is critical in the onset of pressure overload-induced cardiac remodeling. Our study reveals that proline dehydrogenase (PRODH), the key enzyme in proline metabolism, reprograms cardiomyocyte metabolism to protect against cardiac remodeling. We induced cardiac remodeling using transverse aortic constriction (TAC) in  both cardiac-specific PRODH knockout and overexpression mice. Our results indicate that PRODH expression is suppressed post-TAC. Cardiac-specific PRODH knockout mice exhibited worsened cardiac dysfunction, while mice with PRODH overexpression demonstrated a protective effect. Additionally, we simulated cardiomyocyte hypertrophy in vitro using neonatal rat ventricular myocytes treated with phenylephrine. Through RNA sequencing, metabolomics, and metabolic flux analysis, we elucidated that PRODH overexpression in cardiomyocytes redirects proline catabolism to replenish tricarboxylic acid (TCA) cycle intermediates, enhance energy production, and restore glutathione redox balance. In summary, our findings suggest PRODH as a modulator of cardiac bioenergetics and redox homeostasis duing cardiac remodeling induced by pressure overload. This highlights the potential of PRODH as a therapeutic target for cardiac remodeling.

overall_design:
To investigate the role of PRODH in the regulation of pressure overload-induced cardiac remodeling, cardiac-specific overexpression of PRODH was achieved through AAV9-mediated delivery system.
Two types of viruses, AAV9-Vector and AAV9-PRODH, were injected into mice, and transverse aortic constriction (TAC) surgery was performed. Four weeks post-surgery, cardiac tissues were collected for the isolation of adult mice cardiac myocytes, followed by the RNA-seq analysis.
The primary aim of our study was to compare the changes of adult mice cardiac myocytes between the TAC group and the Sham group in AAV9-Vector mice, as well as to assess the transcriptomic differences between the AAV9-Vector and AAV9-PRODH groups in mice following TAC surgery.

first: Wenbin

last: Zhang


title: Systemic 4-1BB stimulation augments extrafollicular memory B cell formation and recall responses during Plasmodium infection [scRNA-seq]

status: Public on Feb 27 2025

city: NORTH CHICAGO

first: Rahul

last: Vijay

state: IL

address: 3333 GreenBay Road, BSB 2.450

department: Microbiology and Immunology

institute: Rosalind Franklin University

summary: T-dependent germinal center (GC) output, comprising plasma cells (PC) and memory B cells (MBC), is crucial for the clearance of Plasmodium infection and protection against reinfection. In this study, we examined the effect of an agonistic antibody targeting 4-1BB (CD137), a member of the Tumor Necrosis Factor Receptor Superfamily (TNFRSF), during experimental malaria. We found that exogenous 4-1BB stimulation dramatically enhanced humoral immune memory and protection from reinfection, despite delaying the effector GC response. Although fewer in number, single cell RNA and ATAC sequencing of MBCs from mice that received 4-1BB stimulation revealed clusters with a transcriptional and epigenetic signature indicative of superior recall and proliferative potential. Importantly, our results indicate that these effects are independent of parasite load or the inflammatory milieu but are dependent on IL-9R signaling in B cells. Our study proposes an immunomodulatory approach to enhance the quality of the MBC pool, providing superior protection during infection and vaccination, particularly in the context of malaria.

overall_design: C57BL/6 mice were infected with Plasmodium yoelii and treated with 3H3 (4-1BB agonist antibody) or isotype control on days 5 and 7 post infection. On 38 days post infection, the spleens were harvested and single cell suspensions were stained with CITE-seq antibodies (ADTs) and fluorescently-labeled antibodies. MSP-1 specific (B220+IgD-GL7-CD38+Decoy-MSP1+) and polyclonal (B220+IgD-GL7-CD38+) memory B cells were flow sorted. scRNA-seq (GEX), CITE-seq (ADT) and V(D)J sequencing libraries were prepared according to the manufacturer’s protocol for Chromium Next GEM Single Cell 5’ Reagent Kit v2 with Feature Barcode technology and V(D)J amplification for mouse B cells (10X Genomics).

first: Carolina

last: Caloba

first: Alexandria

middle: J

last: Sturtz

first: Taylor

last: Lyons

first: Lijo

last: John

first: Akshaya

last: Ramachandran

first: Allen

middle: M

last: Minns

first: Anthony

last: Cannon

first: Justin

middle: P

last: Whalley

first: Tania

middle: H

last: Watts

first: Mark

last: Kaplan

first: Scott

middle: E

last: Lindner


title: Role of FGF21 in cardiac hypertrophyII

city: Cincinnati

first: Georgios

last: Siokatas

state: OH

address: 231 ALBERT SABIN WAY

department: Pharmacology and Systems Physiology

institute: University of Cincinnati

summary: Fibroblast Growth Factor (FGF) 21 is a hormone produced mainly by the liver but also other organs, including the heart. FGF21 analogs are used for treating obesity and metabolic syndrome in humans. In this study, we explored involvement of FGF21 in cardiac hypertrophy. Our mouse studies in wild type mice as well as in mice with either hepatocyte-specific or cardiomyocyte-specific FGF21 ablation demonstrated an interorgan liver-heart crosstalk mechanism, which is controlled by initial hepatic FGF21 release followed by induction of cardiomyocyte FGF21 expression. Conclusively, a hepato-cardiac FGF21-based signaling axis governs cardiac hypertrophy.

overall_design: To assess the gene expression changes that FGF21 stimulates in the heart over the course of cardiac hypertrophy progression, transcriptomic analysis was conducted on mouse hearts at 8 weeks post TAC.

first: Siokatas

last: Georgios

first: Drosatos

last: Konstantinos

first: Mia

last: Sobuj


title: Role of FGF21 in cardiac hypertrophy (8 weeks)


title: KMT2C Deficiency Drives Luminal Transdifferentiation into Double-Negative Prostate Cancer and Sensitizes to Fatty Acid Synthase Inhibition [RNA-Seq]

city: shanghai

first: jiacheng

last: guo

address: yueyang road 320

institute: Shanghai Institute of Nutrition and Health

summary: Double-negative prostate cancer (DNPC), characterized by AR-null tumors with inherent plasticity, predominantly arises following androgen deprivation therapy (ADT). However, the cellular origin, signaling hierarchy, and treatment strategies for this lethal subtype remain unclear. Here, we demonstrate that the loss of KMT2C, a histone H3K4 methylation transferase preferentially mutated in the DNPC subtype, collaborates with ADT to drive the transformation of luminal tumors into DNPC. Our findings reveal that DNPC arises from the transdifferentiation of luminal cells rather than basal cell expansion. This transdifferentiation is orchestrated by the upregulation of ΔNp63, induced by the dual inactivation of AR and KMT2C. Treatment with antiandrogens facilitates KMT2C binding to the enhancers of a subset of AR-regulated genes, compensating for AR inactivation to preserve the luminal identity. Among these, ARPP2 maintains its expression via KMT2C-dependent enhancer-promoter communication following AR inactivation.

overall_design: mRNA profiles of prostate epithelium (EpCAM+; CD24A+; CD49Flow cells) collected from PtenPC−/− and PtenPC−/− mice with and without ADT; mRNA profiles of the organoids of TP, TPK and TPKP mice treated with ENZ; mRNA profiles of prostate organoids(derived from TPK-Sham & TPK-DNPC mice) with and without TVB2640 treatment.

first: Jun

last: Qin

first: Jiacheng

last: Guo


title: Microwave-Induced Tumor-Derived Microparticles Treat Lung Adenocarcinoma by Inducing Immunogenic Cell Death via HMGB1 Shuttling

status: Public on Feb 26 2025

city: Wuhan

first: Xinghui

last: Cao

address: Hangkong Road 13, Wuhan, China

institute: Huazhong University of Science and Technology

summary: Tumor-derived microparticles (TMPs), a subtype of extracellular vesicles, hold great promise in tumor immunotherapies and vaccines, and have demonstrated significant potential as drug delivery systems for clinical tumor treatment. However, concerns remain regarding the potential risks associated with nucleic acid incorporation, alongside the limited antitumor efficacy of ultraviolet irradiation (UV-TMPs) alone. Here, we introduce a microwave (MW)-assisted method for preparing TMPs, termed MW-TMPs. Brief exposure to short-wavelength MW radiation triggered various forms of programmed cell death, including apoptosis, necroptosis, and pyroptosis, promoting the release of TMPs. These resulting MW-TMPs contained fewer nucleic acids and exhibited superior antitumor activity in vivo compared to UV-TMPs.  Mechanistically, MW-TMPs induced immunogenic cell death (ICD) by shuttling HMGB1 and enabled dual targeting of tumor cells by natural killer (NK) and T cells, while reprogramming of suppressive tumor immune microenvironments in LLC lung adenocarcinoma (LUAD) mouse models. When the intervention to LLC mouse models was completed, cell suspensions were prepared by tissue homogenate of fresh subcutaneous tumors. The single-cell suspension was added to the single-cell sorting honeycomb plate and excessive magnetic beads with barcodes were put into the plate. During the phase of cell lysis, the RNA was labeled as bounding to the barcode. Subsequently, reverse transcription of RNA and cDNA synthesis were carried out to obtain cDNA library for subsequent sequencing. Paired-end sequencing was conducted in the Nova seq6000 sequencing platform to get the transcriptome results. BD Rhapsody Analysis pipeline was applied to identify the UMI sequence and the cell tag sequence alignment to the reference genome (GRCm39).

overall_design: LLC cells (5×10^5 cells suspended in 100 μl DMEM solution) were subcutaneously inoculated into the unilateral posterior flanks of C57BL/6 mice (6 weeks). After approximately one week of observation, they were randomized into several groups (n=6) and treated with MW-TMPs, UV-TMPs or PBS every two days totally for five times. The tumor volume and body weight were recorded every other day until the end of the intervention. When the intervention was completed, fresh subcutaneous tumors were stored in MACS tissue storage solution (#130100008) and cell suspensions were prepared by tissue homogenate. The single-cell suspension was added to the single-cell sorting honeycomb plate and excessive magnetic beads with barcodes were put into the plate. During the phase of cell lysis, the RNA was labeled as bounding to the barcode. Subsequently, reverse transcription of RNA and cDNA synthesis were carried out to obtain cDNA library for subsequent sequencing. Paired-end sequencing was conducted in the Nova seq6000 sequencing platform to get the transcriptome results. BD Rhapsody Analysis pipeline was applied to identify the UMI sequence and the cell tag sequence alignment to the reference genome (GRCm39). After removing low-quality cells, the normalization methods “LogNormalize” and “ScaleData” were used to standardize and scale each gene and then linear dimensional reduction was performed according to the PCA score. Uniform Manifold Approximation and Projection (UMAP) techniques were chosen to visualize the cell clusters (the visualized PCA dimension = 38).

first: Yang

last: Jin

first: Mengfei

first: Yali

last: Wu

first: Wenjuan

last: Chen

first: Jingjing

last: Deng


title: RNAseq of Pim1/Pim2 double knockout vs wild-type CD8+ T cells expanded in IL2 or IL15

city: Dundee

first: Laura

last: Spinelli

address: Dow Street

department: Cell Signalling and Immunology

country: United Kingdom

institute: University of Dundee

summary: T cell antigen-receptor (TCR) and cytokine receptor engagement trigger large changes in Serine/Threonine kinase signalling networks to drive T cell activation and differentiation. The role of only few kinase signalling pathways have been studied in detail, and in this context, Pim kinases are an interesting, yet understudied, family of Serine/Threonine kinases, with reported roles in key processes including survival, proliferation, metabolism across a range of cell types. T lymphocytes predominantly express PIM1 and PIM2, which are rapidly induced by TCR, costimulation and cytokine signalling. Using high-resolution mass spectrometry and RNAseq we systematically examine the impact of Pim1/Pim2 double deficiency on in vitro differentiated cytotoxic T lymphocytes (CTL) expanded in the cytokines IL-2 and IL-15 to generate effector or memory T cells respectively. We find that Pim kinases are dispensable for IL-15-driven memory cell differentiation, but that Pim1/2-deficiency has a selective impact on the transcriptome and proteome of IL-2 driven effector CD8 T cells. ~75% of Pim kinase-regulated proteins were not predicted by differences in mRNA in IL-2 expanded CTL. These included proteins that are key for effector cell function: glucose transporters Slc2a1 and Slc2a3 and key effector molecules Granzyme A and B. We find that Pim kinases have this effect via control of protein translation. Another key finding was that the mRNA for key T cell homing receptors Ccr7, S1pr1 and CD62L was increased in Pim1/2-deficienct T cells and that this functionally enhancing homing to secondary lymphoid organs.

overall_design: Lymph node cell suspension from Pim1/Pim2 WT (WT) and Pim1/Pim2 double knockout (Pim dKO) mice were stimulated for 2 days with anti-CD3/anti-CD28 + IL2 or IL15. Cells were split daily into fresh media and IL2 or IL15. On day 3 of culture CD4 T cells were magnetically depleted. CD8 T cell pellets were harvested on day 6 of culture for RNAseq analysis. 3 biological replicates per condition.

first: Julia

last: Marchingo

first: Elizabeth

last: Emslie

first: Shalini

last: Pathak

first: Doreen

last: Cantrell


title: KMT2C Deficiency Drives Luminal Transdifferentiation into Double-Negative Prostate Cancer and Sensitizes to Fatty Acid Synthase Inhibition [scRNA-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Single-cell transcriptomic analysis of prostate epithelium (EpCAM+; CD45-; CD24A+; CD49Flow cells) collected from PtenPC-/- and PtenPC-/- mice with and without ADT; Single-cell transcriptomic and Single-cell genomic analysis of prostatic epithelium in TKPY mice with or without ADT.


title: Multiomic Analysis of Calf Muscle in Peripheral Artery Disease and Chronic Kidney Disease

city: Gainesville

first: Terence

middle: E.

last: Ryan

state: Florida

address: 1864 Stadium Rd

department: Applied Physiology and Kinesiology

institute: University of Florida

summary: This study examines the transcriptional profile at the single-nuclei resolution human gastrocnemius skeletal muscle from 20 patients with Peripheral artery disease (PAD) and 12 patients with both PAD and Chronic Kidney Disease (CKD). In all libraries, muscle specimens were pooled prior to nuclei isolations were performed.

overall_design: Nuclei were isolated from gastrocnemius skeletal muscle from 20 patients with Peripheral artery disease (PAD) and 12 patients with both PAD and Chronic Kidney Disease (CKD).

first: Pass

last: Caroline G.

first: Ryan

last: Terence E.


title: SMARCA4-mutant lung cancer disrupts anti-tumor immunity and immunotherapy response in a STING pathway-dependent manner [CUT&RUN]

city: HOUSTON

first: Yonathan

last: Lissanu

state: TEXAS

address: 1515 Holcombe Blvd

department: Cardiovascular and Thoracic Surgery

institute: md anderson cancer centre

summary: Genomic studies have identified frequent alterations in components of the SWI/SNF (SWItch/Sucrose Non- Fermenting) chromatin remodeling complex including SMARCA4 and ARID1A. Recent independent clinical studies have shown that SMARCA4 mutant lung cancer patients have very poor response to immunotherapy but the mechanism is unknown. Here we showed that SMARCA4 deficiency caused resistance to anti-PD1 immunotherapy and decreased CD4+ T cell and conventional class I dendritic cells (“cDC1s”) percentage in tumor microenvironment (TME) with mouse models. SMARCA4 loss in tumor cells prevented STING pathway sensing cytosolic DNA and cGAMP to reduce type I IFN and inflammatory cytokine gene expression. Importantly, SMARCA4 degradation induced a profound reprograming of the enhancer landscape with marked loss of chromatin accessibility at enhancers of genes involved in type I IFN and inflammatory cytokine, which is associated with nuclear factor NF-κB pathway. Our finding reveals that SMARCA4 loss can have a critical immune modulatory impact in cancer cell intrinsic fashion and suggest that manipulation of SMARCA4 in tumor cells can improve cancer immunotherapy.

overall_design: Total genomic DNA was extracted from H1975 human lung cancer cell line.There are two replicates for each sample.

first: Yawen

last: Wang

first: Md

last: Qudratullah


title: Enforcement of stem-cell dormancy by nucleophosmin mutation is a critical determinant of unrestricted self-renewal during myeloid leukemogenesis

city: Milano

first: Emanuela

last: Colombo

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

summary:
The most frequent mutation in AML patients with normal karyotype affects the Nucleophosmin gene (NPMc+). Different mouse models have shown that NPMc+ mutation can drive leukemia development.
In this study, the impact of NPMc+ expression on the transcriptional program of mouse hematopietic stem cells (HSC) in vivo has been investigated.

overall_design: RNA was purified from controls and NPMc+ expressing FACS sorted LT-HSC and subjected to microarray analysis. Three biological replicates have been performed.

first: Pier

middle: G

last: Pelicci


title: The temporal refinement of Dach1 is a key step in the functional maturation of primary somatosensory neurons

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: During somatosensory neurogenesis, neurons are born in an unspecialized transcriptional state, with several transcription factors following a broad-to-restricted expression dynamic as development proceeds, supporting neuron subtype identities. The relevance of this temporal refinement remains however unclear, these broad-to-restricted transcription factors being selectively involved in neurons in which they are ultimately maintained. Here we found that Dach1 encodes for a bona fide broad-to-restricted transcription factor retained and required in tactile somatosensory neurons. Within developing nociceptors, we demonstrate that Prdm12 contributes to Dach1 extinction. Using genetic approaches to prevent its temporal restriction during somatosensory development, we reveal that Dach1 refinement is a prerequisite for the appropriate transcriptional maturation of somatosensory subtypes from which it becomes ultimately excluded. These findings highlight the essential role played by Dach1 during somatosensory neuron development. They further demonstrate that the broad-to-restricted temporal pattern followed by several transcription factors is physiologically relevant to achieve appropriate transcriptional maturation of somatosensory neurons.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E18.5 developing somatosensory neurons of embryos conditionally depleted from Dach1 function following Wnt1 mediated Cre activity and control embryos that do not express the Cre recombinase

first: Tûnde

last: Szemes

first: Maren

last: Sitte

last: Salinas-Riester

first: Eric

last: Bellefroid

first: Simon

last: Desiderio


title: Rescuing early Parkinson-induced hyposmia prevents dopaminergic system failure

city: Basel

first: Jasper

last: Janssens

address: Mattenstrasse 26

department: DBSSE

country: Switzerland

institute: ETH Zurich

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

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Refer to individual Series


title: SMARCA4-mutant lung cancer disrupts anti-tumor immunity and immunotherapy response in a STING pathway-dependent manner [H1792_RNA-seq]

overall_design: Total RNA was extracted from H1792  human lung cancer cell line.There are two replicates for each sample.


title: SMARCA4-mutant lung cancer disrupts anti-tumor immunity and immunotherapy response in a STING pathway-dependent manner II

overall_design: Genomic DNA was extracted from H1975 and HCC44 human lung cancer cell line.There are two replicates for each sample.


title: An evolutionarily ancient transcription factor drives spore morphogenesis in mushroom-forming fungi

city: Szeged

first: Zhihao

last: Hou

address: Temesvári krt. 62

country: Hungary

institute: HUN-REN Biological Research Centre Szeged

summary: Sporulation is the most widespread means of reproduction and dispersal in fungi and, at the same time, an industrially important trait in crop mushrooms. In the Basidiomycota, sexual spores are produced on specialized cells known as basidia, from which they are forcibly discharged with the highest known acceleration in nature. However, the genetics of sporulation remains poorly known. Here, we identify a new, highly conserved transcription factor, sporulation-related regulator 1 (srr1), and systematically address the genetics of spore formation for the first time in the Basidiomycota. We show that Srr1 regulates postmeiotic spore morphogenesis, but not other aspects of fruiting body development or meiosis, and its role is conserved in the phylogenetically distant, but industrially important, Pleurotus spp. (oyster mushrooms). We used RNA sequencing to understand genes directly or indirectly regulated by Srr1 and identified a strongly supported binding motif for the protein. Using an inferred network of putative target genes regulated by Srr1 and comparative genomics, we identified genes lost in secondarily non-ballistosporic taxa, including a novel sporulation-specific chitinase gene. Overall, our study offers systematic insights into the genetics of spore morphogenesis in the Basidiomycota.

overall_design: RNA-Seq data of the young fruiting body gill tissue in the wild type and SRR1 mutant of Coprinopsis cinerea

first: Zsolt

last: Merényi

first: Yashu

last: Yang

first: Yan

last: Zhang

first: Árpád

last: Csernetics

first: Balázs

last: Bálint

first: Botond

last: Hegedüs

first: Csenge

last: Földi

first: Hongli

last: Wu

last: Kristóffy

first: Edit

last: Ábrahám

first: Nikolett

last: Miklovics

first: Máté

last: Virágh

first: Xiao-Bin

last: Liu

last: Zsibrita

first: Ildiko

last: Karcagi

first: Wei

last: Gao

first: László

last: Nagy


title: SMARCA4-mutant lung cancer disrupts anti-tumor immunity and immunotherapy response in a STING pathway-dependent manner [RNA-Seq]

first: Yonathan

last: Lissanu

overall_design: Total RNA was extracted from H2122 human lung cancer cell line.There are three replicates samples for parental and SMARCA4 knockout cell line with vehicle treatment.

first: Yawen

last: Wang

first: Md

last: Qudratullah


title: SMARCA4-mutant lung cancer disrupts anti-tumor immunity and immunotherapy response in a STING pathway-dependent manner [H1975 and HCC44]

overall_design: Total RNA was extracted from H1975 and HCC44 human lung cancer cell line.There are two replicates for each sample.


title: Proteasome inhibition induces alteration of DNA methylation profile by attenuating the synthesis of DNA methyltransferase 1 and 3B in colorectal cancer II

city: Shenzhen

first: Kun

last: Sun

state: Guangdong

address: Rm A1921, Guangming International Innovation Center,

institute: Shenzhen Bay Laboratory

type: Methylation profiling by genome tiling array

summary: Proteasome is an essential organelle in guarding cellular protein homeostasis. Here, we report that inhibition of proteasome alters the profile of DNA methylation in colorectal cancer (CRC) by blocking the synthesis of DNA methyltransferases (DNMTs). We found that treating CRC cells with proteasome inhibitors (PIs) suppress the translation of DNMT1 and DNMT3B by inactivating AKT and mammalian target of rapamycin (mTOR), dependent on the accumulation of p300, an acetyltransferase inactivating AKT by mediating its acetylation modification. Furthermore, we demonstrated downregulation of DNMT1 and DNMT3B protects cancer cells against PI treatment, potentially by reprogramming the transcriptome of CRC cells; highlighting the key role of DNMTs in response to proteostasis disturbance

overall_design: To evaluate the landscape of DNA methylation in CRC, we treated HT29 cells with MG132 (0.2μM) for 21 passages and using the DMSO-treated cells as control. We used Infinium MethylationEPIC v2.0 BeadChip to profile DNA methylation at passage 14 and 21, respectively.

first: Yuling

last: Sheng

first: Dingxue

last: Hu

first: Changzheng

last: Du


title: KMT2C Deficiency Drives Luminal Transdifferentiation into Double-Negative Prostate Cancer and Sensitizes to Fatty Acid Synthase Inhibition [CUT&Tag]

first: jiacheng

last: guo

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of KMT2C,AR,ΔNp63 and nSREBF1C binding prostate organoids (derived from TP&TPK) with and without ENZ treatment.；Examination of histone modifications (H3K4me1,H3K27ac and H3K4me3) prostate organoids (derived from TP&TPK) with and without ENZ treatment;Examination of histone modification (H3K4me1) in prostate organoids (PDO-WGH) with and without the KMT2C-T316S mutation.

first: Jun

last: Qin

first: Jiacheng

last: Guo


title: KMT2C Deficiency Drives Luminal Transdifferentiation into Double-Negative Prostate Cancer and Sensitizes to Fatty Acid Synthase Inhibition [ATAC-seq]

summary: Double-negative prostate cancer (DNPC), characterized by AR-null tumors with inherent plasticity, predominantly arises following androgen deprivation therapy (ADT). However, the cellular origin, signaling hierarchy, and treatment strategies for this lethal subtype remain unclear. Here, we demonstrate that the loss of KMT2C, a histone H3K4 methylation transferase preferentially mutated in the DNPC subtype, collaborates with ADT to drive the transformation of luminal tumors into DNPC. Our findings reveal that DNPC arises from the transdifferentiation of luminal cells rather than basal cell expansion. This transdifferentiation is orchestrated by the upregulation of ΔNp63, induced by the dual inactivation of AR and KMT2C. Treatment with antiandrogens facilitates KMT2C binding to the enhancers of a subset of AR-regulated genes, compensating for AR inactivation to preserve the luminal identity. Among these, ARPP2 maintains its expression via KMT2C-dependent enhancer-promoter communication following AR inactivation. Consequently, KMT2C inactivation reduces ARPP2 expression, leading to p65-dependent upregulation of ΔNp63 and subsequent DNPC development. In our DNPC model, we identified a selective reinstatement of fatty acid synthesis, facilitated by the ΔNp63-dependent SREBP1 transcriptome. This sustains DNPC growth through intensified HRAS palmitoylation and activation of the RAS-MAPK signaling pathway. Our findings underscore the role of KMT2C as an epigenetic checkpoint in restraining DNPC transdifferentiation. This highlights an elevated risk for KMT2C-mutated patients receiving ADT and underscores the potential therapeutic targeting of fatty acid synthesis against DNPC.

overall_design: Examination of chromatin accessibility in prostate organoids (derived from TP/TPK) with or without ENZ treatment.


title: The immune checkpoint regulator CD40 potentiates myocardial inflammation

city: Saint Louis

first: Jesus

last: Jimenez

state: MO

address: Clinical Sciences Research Building, Rm. 9900 4939 Children's Place, Campus Box 8086

institute: Washington University School of Medicine

summary: Immune checkpoint therapeutics including CD40 agonists have tremendous promise to elicit antitumor responses in patients resistant to current therapies. Conventional immune checkpoint inhibitors (PD-1/PD-L1, CTLA-4 antagonists) are associated with serious adverse cardiac events including life-threatening myocarditis. However, little is known regarding the potential for CD40 agonists to trigger myocardial inflammation or myocarditis. Here, we leverage genetic mouse models, single cell sequencing, and cell depletion studies to demonstrate that an anti-CD40 agonist antibody reshapes the cardiac immune landscape through activation of CCR2+ macrophages and subsequent recruitment of effector memory CD8 T-cells. We identify a positive feedback loop between CCR2+ macrophages and CD8 T-cells driven by IL12b, TNF, and IFN-γ signaling that promotes myocardial inflammation and show that prior exposure to CD40 agonists sensitizes the heart to secondary insults and accelerates LV remodeling. Collectively, these findings highlight the potential for CD40 agonists to promote myocardial inflammation and potentiate heart failure pathogenesis.

overall_design: To reveal the cardiac immune landscape of CD40 agonist treated mice, we performed CITE-sequencing (CITE-seq) of heart tissue from control (C57BL6J treated with Rat IgG antibodies, n=4) and anti-CD40 (C57BL6J treated with anti-CD40 agonist antibodies, n=4) mice. We constructed 2 libraries (control: L1; disease: 2) from DRAQ5+DAPI- cells purified from pooled enzymatically digested hearts by FACS.

first: Junedh

last: Amrute

first: Pan

last: Ma

first: Xiaroan

first: Shibali

last: Das

first: Raymond

first: Yohei

last: Komaru

first: Andreas

last: Herrlich

first: Matthias

last: Mack

first: Kory

last: Lavine


title: Temporal co-regulation of microRNA arms among cell types after myocardial infarction [RNA-Seq]

city: Frankfurt am Main

first: Marcel

last: Schulz

address: Theodor-Stern-Kai 7, Haus 26

institute: Goethe University and Uniklinikum Frankfurt

summary: Acute myocardial infarction (AMI) is one of the leading causes of mortality worldwide. MicroRNAs (miRNAs) shape the transcript repertoire and control cellular functions. Imprecise cleavage of miRNA hairpins during biogenesis and downstream enzymatic processing alters mature miRNA arm abundance. Using small and total RNA sequencing, miRNA temporal dynamics and regulatory effects were studied in four cell types of the heart upon myocardial infarction. We define differentially processed miRNAs, which have changes in their arm ratios and have effects on target gene regulation. The identified miRNA subsets are enriched in templated isomiR modifications and show associations with RNA binding proteins, biogenesis and other processing factors. Our analysis reveals antagonistic functions co-regulated by the processed miRNA arms, beyond known pathways involved in cardiac regeneration. This study highlights novel insights into disease mechanisms controlled by dysregulated microRNA processing concerning acute damage response as well as long-time adaptation after AMI.

overall_design: Small and total RNA-seq at 6 timepoints, in 4 cell types post AMI. The samples correspond to four major cell types of the heart viz. CM or cardiomyocytes, EC or endothelial cells, FB or fibroblasts and HC or hematopoietic cells. The day corresponds to the time point the small and the total RNA was collected post AMI.

first: Ranjan

middle: K

last: Maji

first: Stefanie

last: Dimmeler


title: Temporal co-regulation of microRNA arms among cell types after myocardial infarction [smallRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Small and total RNA-seq at 6 timepoints, in four cell types post AMI. The samples correspond to four major cell types of the heart viz. CM or cardiomyocytes, EC or endothelial cells, FB or fibroblasts and HC or hematopoietic cells. The day corresponds to the time point the small and the total RNA was collected post AMI.


title: Radiation-induced amphiregulin drives tumor metastases

city: Chicago

first: Arpit

last: Panda

address: 924 E. 57th Street, Suite 104

department: Department of Chemistry

institute: University of Chicago

summary: In this study, we demonstrate that radiation induces the epidermal growth factor receptor (EGFR) ligand amphiregulin (AREG) in tumor cells, which stimulates distant metastasis proliferation in both patients and pre-clinical murine tumor models. Using single-cell RNAseq (sc-RNAseq), we characterized the effects of AREG-induction on immune cells in the lung metastatic microenvironment of B6 mice.

overall_design: AREG-sufficient or AREG-KO Lewis lung carcinoma (LLC) tumors were implanted into the flanks of B6 mice and flank tumors were treated with high-dose irradiation, 12 days after tumor injection. Sc-RNAseq was performed on the CD45+ cells from lung tissue (site of metastases) five days after irradiation of the subcutaneous flank tumor.

first: Panda

last: Arpit

first: Piffko

last: Andras

first: Yang

last: Kaiting


title: SMARCA4-mutant lung cancer disrupts anti-tumor immunity and immunotherapy response in a STING pathway-dependent manner [ChIP-seq3]

first: Yonathan

last: Lissanu

overall_design: Total genomic DNA was extracted from H1975 human lung cancer cell line.

first: Yawen

last: Wang

first: Md

last: Qudratullah


title: Transcriptomic Profiling Provides Insight into the Molecular Basis of Heterosis in Philippine-Reared Bombyx mori Hybrids

status: Public on Feb 25 2025

city: Quezon City

first: Ma. Anita

middle: Mascareñas

last: Bautista

state: Metro Manila

address: Ma. Regidor St., National Science Complex

department: National Institute of Molecular Biology and Biotechnology

country: Philippines

institute: University of the Philippines Diliman

summary: The Bombyx mori parental strains Lat21 and B221 from the Department of Science and Technology - Cordillera Administrative Region (DOST-CAR) Sericulture Facility in La Trinidad, Benguet are crossed to produce the hybrids NC144 (Lat21♀ X B221♂) and CN144 (B221♀ X Lat21♂). These hybrids exhibited heterosis in field studies conducted in the 1980s. This study aims to provide evidence for the observed heterosis in the molecular basis for heterosis in B. mori hybrids NC144 and CN144 through RNA sequencing of whole silkworm larvae. Withe the sequencing data, it was possible to identify differentially expressed genes (DEGs) among: 1) the parental strains and their hybrids, and 2) the two hybrids. DESeq2 found 384 DEGs in the hybrids (reference: Parents; 202 upregulated, 182 downregulated) and 819 DEGs in NC144 (reference: CN144; 66 upregulated, 753 downregulated). Amon these are DEGs encoding for heat shock proteins and antimicrobial peptides, which have potentials use as markers for marker-assisted breeding. Additionally, the inducible nature of these genes in the presence of stressors like extreme temperature and bacteria, suggests that they could also be used as diagnostic tools for stress assessment.

overall_design: RNA from whole Bombyx mori larvae of 2 Philippine-reared parental strains and their 2 hybrids, 3 bioreplicates each strain

first: Ma. Ysabella Elaine

middle: D

last: Conde

first: Jose

last: Planta


title: DNA METHYLATION SIGNATURES OF CERVICAL PRE-INVASIVE AND INVASIVE DISEASE: AN EPIGENOME-WIDE ASSOCIATION STUDY

city: London

first: Sarah

last: Bowden

address: IRDB 3rd floor, Du cane Road

department: Department Surgery and Cancer

institute: Imperial College London

summary: Epigenetic alterations are essential in the development of cancers, while epigenome-wide exploration in cervical cancer has been limited. In this epigenome-wide association study (EWAS) we explore differential DNA methylation signatures associated with CIN (cervical intraepithelial neoplasia) grade 3 and cervical cancer, to better understand potential drivers and biomarkers of cervical carcinogenesis. 247 women were recruited between 2014-2020 (N=119 benign, N=74 CIN3/CGIN (cervical glandular intraepithelial neoplasia) and N=54 cancer). Methylation signatures were obtained from exfoliated cervical cells and sequenced using the Illumina 850k array. Logistic regression and conditional analyses were used to test for independent associations between Cytosine-phosphate-Guanine (CpG) sites and case-control status, with adjustment for batch, chip, age, and human papillomavirus (HPV) status. 409 CpG sites were strongly associated with CIN3/cancer (P-value <5x10-8). Following conditional analysis, two CpG sites located in PAX1 (cg16767801) and NREP-AS1 genes (cg23642047) were independently associated with case status; yielding an area under the curve (AUC) of 0.92 (AUC=0.97 for invasive disease). In a validation dataset (CIN3 only) PAX1/NREP-AS1 yielded a combined AUC of 0.77. Methylation markers offer promise for use in cervical screening particularly as triage tests and self-sampling. We have identified a novel combined methylation marker that offers a high accuracy for detection of CIN3 or worse.

overall_design: In a cohort of 247 women we performed an epigenome-wide association study of CIN3 and cervical cancer versus benign controls, in the presence and absence of HPV infection, with the aim of detecting the strongest signals associated with high-grade cervical lesions, for potential translation to a diagnostic test for cervical screening.

first: James

last: Flanagan


title: The Sotos syndrome gene Nsd1 safeguards bivalent developmental enhancers in poised states through restraining excessive H3K27me3 deposition [Cut & Tag]

city: New York

first: Jie

last: Li

state: New York

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell Medicine

summary: Germline haploinsufficiency of Nsd1 is implicated as the etiology of Sotos syndrome, a developmental genetic disorder manifesting skeletal overgrowth and intellectual disability. However, the underlying molecular mechanisms remain largely elusive to date. Here we employed mouse embryonic stem (ES) cell in vitro differentiation as a developmental model system to tackle this question. We found that Nsd1 is indispensable for faithful differentiation of mouse ES cells into three primary germ layers, particularly the meso-endoderm lineages such as heart, vascular, and skeletal systems. Time-series gene expression profiling revealed that Nsd1 facilitates not only the basal expression but also differentiation-accompanied rapid induction of certain key meso-endoderm linage-specifying transcription factor genes such as T and Gata4. Mechanistically, Nsd1 directly binds to putative distal bivalent enhancers of these genes under ES state, where it antagonizes excessive H3K27me3 through depositing H3K36me2 and conversely maintains the active H3K27ac mark, thereby safeguarding these enhancers at poised or primed states that are highly responsive to developmental cues. In agreement, rescue assays showed that Nsd1-catalyzed H3K36me2 depends on intact PHD1-4, PWWP2, and SET domains to a similar degree, disruption of either one severely abolished Nsd1’s ability to revert the defective differentiation phenotype. Additionally, Nsd1 is likely continuously required to sustain the activation of certain developmental genes, as it continues to reside at these genes after differentiation induction, albeit recruited by a different set of transcription factors. Altogether, our results provide novel molecular insights into how Nsd1 perturbations derail the normal developmental pathways and cause human disease.

overall_design: Cut&Run for 12XHA-tagged Nsd1 using anti-HA antibody at day 4 of differentiating mouse embryonic stem cells

first: Gang


title: The Sotos syndrome gene Nsd1 safeguards bivalent developmental enhancers in poised states through restraining excessive H3K27me3 deposition [ChIP-seq]

overall_design: ChIP-seq for 3XFlag or 12XHA-tagged Nsd1 using either anti-Flag or anti-HA antibody in mouse embryonic stem cells


title: An Nrf2-NF-kB cross-talk controls hepatocyte proliferation in the normal and injured liver

city: Zurich

first: Sabine

last: Werner

address: Otto-Stern-Weg 7

department: Department of Biology

summary: The liver has remarkable regenerative and detoxification capacities, which require the Nrf2 and NF-kB transcription factors. Although their individual functions in hepatocytes are well characterized, knowledge about their cross-talk in the adult liver is limited. Therefore, we deleted the genes for Nrf2, the NF-kB subunit p65 or both genes in adult hepatocytes of mice using AAV8-Cre viruses. Loss of p65  or both genes caused spontaneous liver inflammation and necrosis, combined with a progressive increase in hepatocyte proliferation. Gene expression profiling identified individual and common target genes of both transcription factors, including genes involved in the control of cell proliferation.

overall_design: Control (C57BL6/j), Nrf2 flox/flox, p65 flox/flox and Nrf2:p65 double floxed mice were injected with AAV8Cre to induce a hepatocyte specific knockout of the respective genes. 12 days after injection, mice were euthanized and the liver was perfused with Liberase TM solution followed by low speed centrifugation of the cell suspension and additional centrifugation in Percoll density media. Total RNA was isolated from freshly-isolated hepatocytes and subjected to library preparation using the TrueSeq stranded protocol. After single end sequencing in an Illumina Novaseq machine, reads were aligned to the mouse genome GRCm39 using Salmon softwere. Differential expression was done using DESeq2.

first: Andrii

last: Kuklin


title: The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway

city: St. Louis

first: Hao

last: Chen

address: 4370 Duncan Ave

institute: Washington University School of Medicine in St. Louis

summary: Precise control of protein ubiquitination is essential for brain development, and hence, disruption of ubiquitin signaling networks can lead to neurological disorders. Mutations of the deubiquitinase USP7 cause the Hao-Fountain syndrome (HAFOUS), characterized by developmental delay, intellectual disability, autism, and aggressive behavior. These neurological and behavioral manifestations indicate important unknown roles of USP7 specificially in the nervous system. Here, we report that conditional deletion of USP7 in excitatory neurons in the mouse forebrain triggers diverse phenotypes including growth delay, sensorimotor deficits, learning and memory impairment, and aggressive behavior, resembling clinical features of HAFOUS. USP7 deletion induces neuronal apoptosis in a manner dependent of the tumor suppressor p53. However, most behavioral abnormalities in USP7 conditional mice persist despite p53 loss. Strikingly, USP7 deletion in the brain perturbs the synaptic proteome and dendritic spine morphogenesis independently of p53. Integrated proteomics and subsequent ubiquitin biochemical analysis identify the RNA splicing factor Ppil4 as a novel neuronal substrate of USP7. Consistent with the role of Ppil4 in RNA splicing, loss of USP7 disrupts splicing program of synaptic genes in the cerebral cortex. Improtantly, knockdown of Ppil4 in cortical neurons impairs dendritic spine morphogenesis, phenocopying the effect of USP7 loss on dendritic spines. These findings reveal a novel USP7-Ppil4 ubiquitin signaling link that regulates neuronal connectivity in the developing brain, with implications for our understanding of the pathogenesis of HAFOUS and other neurodevelopmental disorders.

overall_design: We performed bulk RNA-seq of the cerebral cortex of 5 pairs of Usp7 cKO; Trp53+/- mice and Usp7 WT; Trp53+/- mice at age P18. The 5 pairs of mice were litter- and sex-controlled.

first: Isabel

last: Risch

first: Obi

middle: L

last: Griffith

first: Malachi

first: Azad

last: Bonni

first: Albert

last: Kim


title: The Sotos syndrome gene Nsd1 safeguards bivalent developmental enhancers in poised states through restraining excessive H3K27me3 deposition [RNA-Seq]

overall_design: RNA-seq profiling and comparison of wild-type vs Nsd1-knock out mouse embryonic stem cells collected at 3 different time points (day 0, day 2, day 4) during in vitro differentiation


title: SMARCA4-mutant lung cancer disrupts anti-tumor immunity and immunotherapy response in a STING pathway-dependent manner

first: Yonathan

overall_design:
Total RNA was extracted from H2122 human lung tumor xenograft.There are four replicates samples for parental and SMARCA4 knockout tumors with vehicle treatment.
Total RNA transcriptome from these samples were profiled by RNA-seq.

first: Yawen


title: Rescuing early Parkinson-induced hyposmia prevents dopaminergic system failure [human]

first: Jasper

last: Janssens

summary:
The diagnosis of Parkinsonism is based on motor symptoms that are caused by reduced dopaminergic output
However, decades earlier, patients report non-motoric problems, including hyposmia
It is not known if non-motor and motor defects are causally connected
Here we used single-cell transcriptome sequencing (10x) of young and olf fly mutants (whole brain)
and human patients (three regions: nucleus basalis of Meynert, nucleus accumbens and putamen).
This atlas reveals early defects in cholinergic neurons that are recapitulaed across species

overall_design: snRNA-seq (10x Genomics ) of frozen human brains + scRNA (10x Genomics) of fresh fly brains

first: J

first: U

last: Pech

first: S

last: Aerts

first: P

last: Verstreken


title: Alteration of global transcription by saccharin in Acinetobacter baumannii AB5075

city: Uxbridge

first: Ronan

last: McCarthy

address: Kingston Ln

institute: Brunel University London

summary: We perform RNA-seq comparing a treatment with 1% saccharin to a mock treatment in A. baumannii AB5075 in order to describe the alterations in global transcription produced by this artificial sweetener. A. baumannii AB5075 cultures were grown in LB medium in the presence of 1% saccharin or a water control (3 biological replicates per condition) until reaching mid-exponential phase. At this point, cells were harvested, treated with RNAlate for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample. As a result, 165 genes appeared upregulated in the presence of saccharin, whereas 215 were downregulated. In highlights, the gene functional groups showing the strongest transcriptional alterations were those related to pili and frimbriae biogenesis, involved in biofilms formation, adhesion and twitching motility.

overall_design: Three independent replicates of A. baumannii AB5075 were grown to mid-exponential phase in LB medium supplemented with 1.33% acesulfame K and compared to three independent replicates grown in the same conditions but receiving a mock treatment (equivalent volume of water).

first: Rubén

last: de Dios

first: Evgenia

last: Maslova

middle: R


title: RBPMS inhibits bladder cancer migration and invasion by downregulating the MYC pathway through alternative splicing of ANKRD10

city: Wuhan

first: Jingtian

last: Yu

address: 169 Donghu

institute: Wuhan University

summary: RNA-binding proteins (RBPs) are pivotal mediators of the alternative splicing (AS) machinery of pre-mRNA, allowing the generation of diverse protein structures and functions from a single gene. Research has demonstrated that the AS process in bladder cancer (BLCA) is significantly dysregulated and plays a crucial role in the development, progression, aggressiveness, and therapeutic resistance of this disease. We conducted comprehensive screening and analysis of the TCGA-BLCA cohort, specifically focusing on genes with significant differences in expression levels between carcinoma and adjacent non-cancerous tissues. Among the 500 differentially expressed genes, 5 RNA-binding proteins were identified. Only the RNA-binding protein mRNA processing factor (RBPMS) demonstrated a consistent downregulation in BLCA and was correlated with an unfavorable prognosis for affected patients. Subsequent in vitro and in vivo experiments revealed that RBPMS exerted inhibitory effects on the epithelial-mesenchymal transition (EMT) pathway and the migratory potential of BLCA cells. RNA-Seq analysis identified ANKRD10 as a key target mRNA regulated by RBPMS in BLCA. RBPMS depletion in BLCA cells resulted in AS of ANKRD10 and increased ANKRD10-2 expression. ANKRD10-2 functioned as a transcriptional co-activator of MYC proteins, thereby augmenting their transcriptional activity. Furthermore, ANKRD10-2 knockdown significantly rescued the migration enhancement induced by RBPMS depletion in BLCA cells. Taken together, this study revealed a mechanism whereby RBPMS suppresses the migration and invasion of BLCA cells by attenuating MYC pathway activity via the AS of ANKRD10.

overall_design: To investigate the downstream mechanisms by which RBPMS and ANKRD10 transcripts regulate bladder cancer, we performed three RNA sequencing. The first time, we performed RNA sequencing on three sets of duplicates of RBPMS-WT and RBPMS-KO in 5637 cells. The second time, we performed RNA sequencing on three sets of duplicated Vector, ANKRD10-1 overexpressing and ANKRD-2 overexpressing 5637 cells. For the second time, we performed RNA sequencing on three sets of replicates of siNC, siANKRD10-1 and siANKRD-2 in 5637 cells.

first: Mengxin

last: Lu


title: Single cell RNA-sequencing analysis of human nonunion tissue

city: Sacramento

first: Thomas

last: Ambrosi

state: California

address: 2700 Stockton Blvd

institute: UC Davis

summary: 10X Genomics single cell RNA-sequencing of freshly isolated nonunion tissue from 63-year old male was conducted to interrogate non-hematopoietic tissue composition. The goal was to generate a dataset that can be compared with publicly available datasets of normal fracture tissue and cells associated with bone healing.

overall_design: Nonunion tissue was harvested during corrective surgery 300 days after initial injury. After mechanical and enzymatic preparation, the single cell solution was stained for flow cytometry and 3x10 6 PI-CD45-CD235a- cells were sorted into a collection tube containing FACS buffer. Cells were then processed with 10X Chromium Next GEM Single Cell 3ʹ GEM kit (10X Genomics Inc, v3.1) according to manufacturer’s instruction to target 10,000 cells. A library ('Nonunion') was generated for partial lane sequencing on a NovaSeq6000.

first: Charles

last: Chan


title: Human Skeletal Stem Cell Diversity

summary: We have used SmartSeq2 to sequence single phenotypic human skeletal stem cell (SSCs) and downstream lineage populations purified via FACS from fetal skeletal tissues and patient specimens. SSC populations were isolated based on their previously reported surface marker profiles. A human SSC (CD45-CD235a-CD31-TIE2-CD146-PDPN+CD73+CD164+), a human bone-cartilage-stroma-progenitor (BCSP; CD45-CD235a-CD31-TIE2-CD146+PDPN+) and an osteoprogenitor (OP; CD45-CD235a-CD31-TIE2-CD146+PDPN-) were investigated.

overall_design: SmartSeq2 single cell RNA sequencing of freshly, prospectively, flow cytometrically purified single skeletal stem cell and lineage population from human fetal tissue (17-20 weeks gestational age) and patient specimens (18-77 years of age).

first: Rahul

last: Sinha


title: The temporal refinement of Dach1 is a key step in the functional maturation of primary somatosensory neurons

first: Gabriela

last: Salinas

summary: During somatosensory neurogenesis, neurons are born in an unspecialized transcriptional state, with several transcription factors following a broad-to-restricted expression dynamic as development proceeds, supporting neuron subtype identities. The relevance of this temporal refinement remains however unclear, these broad-to-restricted transcription factors being selectively involved in neurons in which they are ultimately maintained. Here we found that Dach1 encodes for a bona fide broad-to-restricted transcription factor retained and required in tactile somatosensory neurons. Within developing nociceptors, we demonstrate that Prdm12 contributes to Dach1 extinction. Using genetic approaches to prevent its temporal restriction during somatosensory development, we reveal that Dach1 refinement is a prerequisite for the appropriate transcriptional maturation of somatosensory subtypes from which it becomes ultimately excluded. These findings highlight the essential role played by Dach1 during somatosensory neuron development. They further demonstrate that the broad-to-restricted temporal pattern followed by several transcription factors is physiologically relevant to achieve appropriate transcriptional maturation of somatosensory neurons.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E18.5 developing somatosensory neurons of embryos conditionally overexpressing the Dach1 gene following Cre activity mediated from the Advillin gene and control embryos that do not express the Cre recombinase

first: Tûnde

last: Szemes

first: Maren

last: Sitte

last: Salinas-Riester

first: Eric

last: Bellefroid

first: Simon

last: Desiderio


title: A cell type-specific expression atlas of small and total RNA in the heart after myocardial infarction

first: Marcel

last: Schulz

summary:
This SuperSeries is composed of the SubSeries listed below.
Each sample is annotated as the cell type viz. CM or cardiomyocytes, EC or endothelial cells, FB or fibroblasts and HC or hematopoietic cells. The day corresponds to time point post AMI.

overall_design: Refer to individual Series

first: Ranjan

last: Maji

first: Stefanie

last: Dimmeler


title: Microevolution of Cryptococcus neoformans in high CO2 converges on mutations isolated from patients with relapsed cryptococcosis

status: Public on Feb 24 2025

city: Iowa City

first: Damian

last: Krysan

state: IA

address: 25 South Grand, 2040 ML

department: Division of Pediatrics & Infectious Disease

institute: University of Iowa Hospitals and Clinics

summary: Cryptococcus neoformans is an environmental fungus that causes an estimated 180,000 deaths annually and transitions from the external environment to the host environment to cause disease. CO2 concentrations in the atmosphere (0.04%) are dramatically lower than in mammalian tissues (5%). Environmental C. neoformans strains that cannot tolerate 5% CO2 are much less virulent than CO2-tolerant strains. Microevolution at elevated CO2generated loss-of-function mutations in the nucleotide binding protein Avc1 that confer CO2 tolerance to CO2-intolerant strains. Mechanistically, Avc1 positively regulates the expression of plasma membrane transporters including PDR9, a phospholipid floppase that negatively modulates CO2 fitness. Deletion of AVC1 in five CO2-intolerant environmental strains increased competitive fitness in host CO2 and in a mouse infection model. Importantly, strains with similar AVC1 mutations have emerged in patients with relapsed cryptococcosis. Therefore, this microevolutionary convergence strongly suggests that adaptation to host CO2 is a significant driver of C. neoformans fitness during infection.

overall_design: To investigate the effects of host levels of CO2 compared to enviornmental levels of CO2 on Cryptococcus neoformans gene expression in the environmental isolates A1-35-8 compared to a clinical isolate and reference strain, H99 at 24 hours, in biological triplicate, as well as compared to a A1-35-8 avc1∆ mutant under the same conditions in triplicate.

first: Benjamin

last: Chadwick

first: Laura

middle: C

last: Ristow

first: Emma

last: Blackburn

first: Xiaofeng

last: Xie

first: Xiaorong

last: Lin


title: Effect of felzartamab on the molecular phenotype of antibody-mediated rejection in kidney transplant biopsies

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

summary: A recent randomized controlled trial demonstrated that treatment with CD38 monoclonal antibody felzartamab suppressed antibody-mediated rejection (ABMR) in kidney transplant patients but with recurrence post-treatment in some patients. Felzartamab reduced molecular ABMR activity scores in all 9 patients with baseline ABMR activity, selectively suppressing interferon gamma-inducible and natural killer cell transcripts, with minimal effect on ABMR-induced endothelial transcripts. Suppression was often incomplete when ABMR activity was intense, and molecular recurrence was nearly universal by week 52. However, we also found that felzartamab had parenchymal benefits at week 52, slowing the trajectories of molecular injury scores beyond the treatment period, suggesting that suppression of ABMR activity could potentially slow future progression to kidney failure.

overall_design: The present study examined the molecular effects of 6-months of felzartamab treatment on biopsies from the trial using genome-wide microarray analysis, comparing pre-treatment, end-of-treatment (24 week) and post-treatment (week 52) biopsies from 10 felzartamab and 10 placebo patients.


title: In vivo clonal tracking of human skeletal stem cells with single cell RNA-sequencing readout

first: Thomas

last: Ambrosi

summary: 10X Genomics single cell RNA-sequencing of freshly isolated human skeletal stem cells from the growth plate or periosteum of 17 weeks gestational age fetal bone tissue were collected. The goal of this work was to trace single cell dynamics of human skeletal stem cells in an in vivo setting. Single barcoded human skeletal stem cells were tracked in the graft tissue they formed after xenotransplanation into mice. Single cell analysis assessed tissue composition and was overlayed with barcode readouts to find contributions of individual clones. Differences in stem cell properties and lineage dynamics were assessed between growth plate and periosteal human skeletal stem cells.

overall_design: 1.5-2x10 5 freshly sorted cells of either growth plate (GP) or periosteal (PE) source tissue were seeded into 12-well plate with 1 mL of Opti-MEM Reduced Serum Media containing lentiviral barcode particles generated from CloneTracker XP™ 10M Barcode-3' Library in pScribe5-Venus-Puro plasmid (Cellecta, Cat#BCXP10M3VP-P). Cells were spun in the well plate in plate carriers at 1,500g for 60 min at 24–27 °C. Directly following that step, 3 mL of fresh culture media was added and cells were incubated at 37 °C for 24 h. At this point, the media was changed and cells allowed to further incubate for three days. Cells were then lifted using collagenase and stained with FACS antibodies. Sorted cells with phenotypic hSSC surface marker profile and simultaneous expression of Venus fluorophore were used for renal transplantation assays into NSG mice. To prevent dilution of clones in final readout, 500 Venus+, barcoded hSSCs were mixed with 5,000 Venus-,  non-barcoded hSSC supporter cells of the same source tissue, mixed with 5 µL of Matrigel and transplanted below the renal capsule of mice. Three transplants per hSSC source were conducted. Each mouse was transplanted with hSSCs from the growth plate under the renal capsule of one kidney and with hSSCs from the periosteum contralaterally. After three weeks, kidneys were excised from sacrificed mice and assessed for Venus expression in the graft tissue via microscope. Grafts were then dissected out, pooled by respective hSSC sources and processed for flow cytometric isolation of Venus+ cells. Sorted cells from grafts were processed for 10X genomics single cell RNA-sequencing for interrogation into cell fates and clonal relationships. In addition to 10X libraries (GP, PE) we sequenced specifically amplified barcode regions for GP (GPbc) and PE (PEbc) samples in order to extract clonal barcode information.

first: Debashis

last: Sahoo

first: Charles

last: Chan


title: Multi-omics Analysis of Umbilical Cord Hematopoietic Stem Cells from a Multi-ethnic Cohort of Hawaii Reveals the Intergenerational Effect of Maternal Pre-Pregnancy Obesity and Risk Prediction for Cancers

city: Ann Arbor

first: Lana

last: Garmire

state: Michigan

address: 1600 Huron Parkway

institute: University of Michigan

summary: Maternal obesity is a health concern that may predispose newborns to a high risk of medical problems later in life. To understand the transgenerational effect of maternal obesity, we conducted a multi-omics study, using DNA methylation and gene expression in the CD34+/CD38-/Lin- umbilical cord blood hematopoietic stem cells (uHSCs) and metabolomics of the cord blood, all from a multi-ethnic cohort (n=72) from Kapiolani Medical Center for Women and Children in Honolulu, Hawaii (collected between 2016 and 2018). Differential methylation (DM) analysis unveiled a global hypermethylation pattern in the maternal pre-pregnancy obese group (BH adjusted p<0.05), adjusting for major clinical confounders. Functional analysis revealed significant associations of differentially methylated sites with downregulated cell cycle, lipid synthesis, immune signaling, and metabolic pathways. Utilizing Shannon entropy to evaluate uHSCs methylation levels, we discerned a notable impact of maternal obesity on higher quiescence of uHSCs. Further, the multi-omics integration revealed dysfunction in adipogenesis, erythropoietin production, cell differentiation and DNA repair. This study reveals a significant correlation between pre-pregnancy maternal obesity and multi-omics level molecular changes in the uHSCs of offspring, particularly in DNA methylation. These findings suggest that maternal obesity can lead to alterations that affect physiological pathways in the offspring.

overall_design: Baby cord blood samples from 72 pregnant women (34 obese; 38 non-obese) who delivered at Kapiolani Medical Center for Women and Children in Honolulu, Hawaii (2016-2018) were collected. CD34+/CD38-/Lin- umbilical cord blood hematopoietic stem cells (uHSCs) were collected from cord blood for DNA methylation assay with Infinium HumanMethylation450. A total of 47 matching RNA samples were used for RNA sequencing.

first: Yuheng

last: Du

first: Paula

last: Benny

first: Ryan

last: Schlueter

first: Alexandra

last: Gurary

first: Annette

last: Lum-Jones

first: Cameron

middle: B

last: Lassiter

first: Fadhl

last: AlAkwaa

first: Maarit

last: Tiirikainen

first: Dena

last: Towner

first: W

middle: S

last: Ward

middle: X


middle: A


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


title: A new paradigm for the regulation of A40926B0 biosynthesis

status: Public on Feb 23 2025

city: hangzhou

first: Yanqiu

last: Liu

address: Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang Province, China

institute: Zhejiang University

summary: Compare the difference between Nonomuraea gerenzanensis L70 and wblA disrupted strain RNS-seq.

overall_design: RNA-seq 12 samples

first: Yilei

last: Zheng

first: Ye

last: Xu

first: Xueyan

first: Tianyu

last: Xia

first: Yongquan

last: Li


title: Whole Transcriptome Analysis of Hypothalamus in Mice during Short-Term Starvation

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

country: South Korea

institute: Incheon National University

summary: Molecular profiling of the hypothalamus in response to metabolic shifts is a critical cue to better understand the principle of the central control of whole-body energy metabolism. The transcriptional responses of the rodent hypothalamus to short-term calorie restriction have been documented. However, studies on the identification of hypothalamic secretory factors that potentially contribute to the control of appetite are lacking. In this study, we analyzed the differential expression of hypothalamic genes and compared the selected secretory factors from the fasted mice with those of fed control mice using bulk RNA-sequencing. We verified seven secretory genes that were significantly altered in the hypothalamus of fasted mice. In addition, we determined the response of secretory genes in cultured hypothalamic cells to treatment with ghrelin and leptin. The current study provides further insights into the neuronal response to food restriction at the molecular level and may be useful for understanding the hypothalamic control of appetite.

overall_design: RNA-seq profiling of hypothalamic and hippocampal tissues from fasted and fed (18 hours) eight-week-old male C57BL/6 mice.

first: Jae Geun

last: Kim


title: Signatures of murine PP Th17 derived Tfh cells

city: Columbus

first: Hsin-Jung

middle: Joyce

last: Wu

state: Ohio

address: 1322 Neil Ave, Columbus OH 43201

department: Internal medicine

institute: Ohio State University

summary: To determine the clinical relevance of the murine Th17-derived Tfh signatures in RA patients, we generated both splenic and PP murine Th17-derived Tfh cells signatures using bulk RNA-seq data.

overall_design: To characterize the signature genes of Th17-derived Tfh cells, CD4+ T cells were enriched from the spleen and PP of K/BxN Th17 fate-mapping mice by negative selection kit (Stemcell) and sorted for ZsGreen+ Tfh (CD4+TCRβ+CD25−ZsGreen+CXCR5+PD-1+) and ZsGreen− Tfh (CD4+TCRβ+CD25−ZsGreen−CXCR5+PD-1+). Total RNA were then extracted by Trizol reagent. The signatures were defined as the genes that were upregulated in ZsGreen+ Tfh over ZsGreen– Tfh cells using 1.5 as the cut-off for fold change (p<0.05).  We then investigated these signatures in a cohort of HC and seropostive RA patients from a public scRNA-seq database.

first: Chi

last: Tai

first: Tingting

last: Fan


title: Effect of Nanopore #3 scaffold on gene expression on fibroblasts

status: Public on Feb 22 2025

city: Wenzhou

first: Keqing

last: Shi

address: Fanhaixilu

institute: The First Affiliated Hospital of Wenzou Medical University

summary: Scaffolds with pores can influence cellular fate and tissue microenvironments by altering intracellular and intercellular signaling pathways, which are crucial for guiding tissue regeneration. Despite their significance, the cellular mechanisms behind the response to pores, especially at the nanoscale, are not well understood. Our study shows that scaffolds with different nanopore characteristics can enhance skin regeneration in various ways, with fibroblasts being the primary cellular responders. We have demonstrated that caveolae formation is a critical mechanism by which fibroblasts interact with nanopores. The phosphorylation of caveolin-1 (CAV1) is a key event in this process, enabling caveolae-mediated endocytosis and the subsequent internalization of cellular substances. This initiates a cascade of events involving the internalization of cell surface receptors such as PDGFRβ, activation of tyrosine kinase pathways including PI3K, AKT, and ERK1/2, and the phosphorylation of the transcription factor RUNX1. The nuclear translocation of RUNX1 upregulates the expression of fibroblast growth factor binding protein 3 (FGFBP3), which is a key factor in tissue repair. Additionally, cytoplasmic CAV1 can competitively bind to Filamin-A, releasing CBFβ, which then translocates to the nucleus and enhances RUNX1's DNA-binding affinity, synergistically activating FGFBP3 transcription and promoting tissue healing. Collectively, our findings underscore the importance of considering nanopore characteristics in scaffold design for tissue regeneration and highlight caveolae formation as a central mediator of cellular responses to nanoporous environments, initiating a multitude of biological processes essential for tissue repair and regeneration.

overall_design: RNA sequencing was performed on NIH-3T3 cells cultured on both standard plates and Nanopore #3 scaffold

first: Feixia

last: Guo

first: Wei

last: Xie


title: Influenza virus-induced type I interferons disrupt alveolar epithelial repair and tight junction integrity in the developing lung

city: Philadelphia

first: Alison

last: Carey

state: PA

address: 245 N 15th Street

institute: Drexel University College of Medicine

summary: Type I interferons (IFN-I) are key innate immune mediators which control viral infection in adults. Recently, using a neonatal murine model of influenza A infection (IAV), we demonstrated that IAV-infected murine neonates lacking a functional IFN-I receptor (IFNAR-/-) have significantly improved survival and reduced lung pathology relative to wild-type (WT) neonates. However, the opposite is observed in adults, with IAV-infected IFNAR-/- adults exhibiting enhanced morbidity relative to WT adults, indicating an age-specific IFN-I toxicity in neonates. Therefore, we hypothesized that IAV-induced IFN-I signaling in primary neonatal type II alveolar epithelial cells (TIIECs), the main cell type of IAV infection and initiator of host response in the lung, contributed to age-specific viral pathogenesis.  To investigate the role of IFN-I signaling in TIIECs, we performed RNA-Seq on purified TIIECs in a multifactorial design, comparing 1. IFNAR-/- and WT genotypes, 2. neonatal and adult ages, 3. IAV-infected and uninfected, 4. over a three-day time course.Analysis of purified TIIECs revealed age, not infection status, as the primary driver of transcriptional differences in TIIECs. Subsequent pathway analysis demonstrated IAV-infected IFNAR-/- neonates significantly upregulate cell proliferation, tissue repair and tight junction genes at 2-days post-infection (dpi), compared to WT neonates. Next, to determine if these growth and repair differences persisted later in infection, targeted analysis of repair gene expression and immunofluorescent quantification of pulmonary sealing tight junction molecules ZO-1 and occludin was performed at 6-dpi. Relative to WT neonates, IFNAR-/- neonates had significantly higher whole lung occludin staining and repair gene expression. Together, our data demonstrates IFN-I signaling is extremely pathogenic in the developing lung because by disrupting alveolar repair and pulmonary barrier integrity.

overall_design:
To investigate the role of IFN-I signaling within TIIECs during influenza infection, 3-day-old wild-type (WT) and IFNAR-/- neonates, and 8-week-old WT and IFNAR-/- adults were infected intranasally with PR8-IAV. Primary TIIECs were isolated from the lungs of infected mice at 1-day (24h), 2-days (48h), and 3-days (72h) -post infection. TIIECs were harvetsed from timepoint-matched uninfected WT and IFNAR-/- neonates (4-, 5-, and 6-days old), and uninfected 8-week-old WT and IFNAR adults to serve as controls.
RNA was extracted from Type II alveolar epithelial cell samples and gene expression analysis was performed using RNA-seq.
Comparative gene expression analysis was determined based on differences in genotype (WT vs IFNAR-/-), age (neonate vs adult), treatment (flu-infection vs uninfected), and timepoint (1-, 2-, 3-days post infection).

first: Abigail

last: Onufer

first: Joshua

last: Mell

first: Laura

last: Cort

first: Abhishek

last: Rao

first: Nontokozo

last: Mdluli

middle: J


title: Transcriptomic and epigenetic investigation of Zika virus (ZIKV) and Dengue virus (DENV) infection in human monocyte-derived dendritic cells

city: La Jolla

first: Aaron

middle: F

last: Carlin

address: 9500 Gilman Drive GPL Rm 118

department: Pathology and Medicine

institute: University of California, San Diego

summary: Dendritic cells are key targets for ZIKV and DENV infection. To identify host pathways manipulated by ZIKV and DENV in dendritic cells, we developed a system that enables characterization of genome-wide transcriptional and epigenetic changes in virus-infected and neighboring (bystander), uninfected primary human dendritic cells.

overall_design: We first applied RNA-seq of DENV or ZIKV infected and uninfected bystander human monocyte-derived dendritic cells (moDCs) exposed to unmodified clinical virus strains to identify virus-regulated transcripts. Using ChIP-seq assays, we confirmed that in moDCs, DENV increased recruitment of NF-kB to target gene promoters of DENV-induced genes. We then tested how ZIKV alters NF-kB induction of target genes in infected cells by treating with Kdo2-Lipid A (KLA).

first: Christopher

last: Benner

first: Sujan

last: Shresta


title: PRC1 and PRC2 proximal interactome in mouse embryonic stem cells [ChIP-Seq]

city: Nijmegen

first: Michiel

last: Vermeulen

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen

summary: Polycomb Repressive Complexes PRC1 and PRC2 play a crucial role in silencing lineage-specific genes during early embryogenesis. To provide new insights in polycomb biology, we profiled the proximal interactome (proxeome) of the catalytic subunits RNF2 (PRC1) and EZH2 (PRC2) in mouse embryonic stem cells (mESCs). This revealed >100 proteins proximal to PRC2 and PRC1, which mainly comprise transcription factors, transcriptional regulators and RNA binding proteins. Interestingly, the EZH2 proxeome included both PRC complexes, while the RNF2 proxeome only identified PRC1 subunits. More than half of the PRC2 proximal proteins are shared with PRC1, revealing the molecular constitution of polycomb chromatin domains. We identified several pluripotency-associated transcription factors, including NANOG, for which we confirmed genomic co-localisation with PRC2. Upon PRC2 disruption, NANOG redistributes to specific sites containing its DNA binding motif. Finally, we compared PRC2 proximal interactomes between naïve mESCs, serum-cultured mESCs and embryoid bodies, altogether providing a comprehensive resource in different cellular contexts that may help to further decipher Polycomb biology.

overall_design: To study the effect of fusing (mini)TurboID to Ezh2 on H3K27me3 deposition we performed HA and H3K27me3 ChIP on wild-type cells and cells expressing EZH2-(mini)TurboID. Additionally, we performed ChIP to study the overlap in localization between PRC2-proximal proteins and PRC2.

first: Dick

middle: W

last: Zijlmans

first: Suzan

last: Stelloo

first: Danique

last: Bax

first: Yavor

last: Yordanov

first: Pien

last: Toebosch

first: Maximilian

last: Raas

first: Sigrid

last: Verhelst

first: Lieke

last: Lamers

first: Marijke

middle: P

last: Baltissen

first: Pascal

last: Jansen

first: Guido

last: van Mierlo

first: Maarten

last: Dhaenens

first: Hendrik

last: Marks


title: Patient derived model of UBA5-associated encephalopathy identifies defects in neurodevelopment and highlights potential therapies

status: Public on Feb 21 2025

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital


title: Early Notch signaling programs effector CD8+ T cell differentiation [RNA-Seq]

city: Montréal

first: Nathalie

last: Labrecque

state: QC

address: 110, avenue des Pins O

department: Unité de recherche en immunobiologie des lymphocytes T

institute: Institut de recherches cliniques de Montréal

summary: A better understanding of the mechanisms regulating CD8+ T cell differentiation is essential to develop new strategies to fight infections and cancer. Using genetic mouse models and blocking antibodies, we uncovered cellular and molecular mechanisms by which Notch signaling favors efficient generation of effector CD8+ T cells. Using transcriptional and epigenetic studies, we identified a unique Notch-driven T cell-specific signature. Early Notch signals were associated with chromatin opening in regions occupied by bZIP transcription factors, specifically BATF, known to be important for CD8+ T cell differentiation. Overall, we show that the delivery of early Notch signals controls the molecular and functional fate of CD8+ T cells after infection.

overall_design: For RNA-seq of naive WT vs Notch1/2 KO CD8+ T cells, naive OT-I cells (Zombie dye− CD8+ CD45.2+ CD25− CD69− CD44−) from pooled lymph nodes and spleens were sorted, and a total of 3 individual biological samples from 3 independent experiments were collected for each genotype (6 x 10^5 to 3 x 10^6 cells per sample). For RNA-seq of day 3 WT vs Notch1/2 KO CD8+ T cells, B6-CD45.1 mice were adoptively transferred with WT vs Notch1/2 KO OT-I cells and infected with Lm-OVA. 72h post-infection, activated OT-I cells (Zombie dye− CD8+ CD45.2+ CD44+) from spleens were sorted, and a total of 8 individual biological samples from 3 independent experiments were collected for each genotype (1.9 x 10^4 to 1.1 x 10^5 cells per sample). For RNA-seq of OP9 vs OP9-DLL4-cocutured CD8+ T cells, OT-I cells from pooled lymph nodes were activated in vitro with aCD3/aCD28 for 72h before being co-cultured on OP9 or OP9-DLL4 fibroblasts for 24h. OT-I were harvested and co-cultured on fresh OP9 or OP9-DLL4 for another 24h. 5 days post-activation, OT-I cells were harvested and sorted (Zombie dye−CD8+ CD45.2+ CD44+). A total of 3 individual biological samples from one independant experiment were collected for each condition (1 x 10^5 cells per sample). For RNA-seq of day 3 WT vs Notch1/2 KO CD8+ T cells transduced with empty-RV or BATF-RV, OT-I cells were isolated from pooled lymph nodes and cultured with IL-7, IL-15 and IL-2 to induce homeostatic proliferation. After 48h in culture, cells were spin-transduced with RV supernatant and put back in culture with IL-7, IL-15 and IL-2 for 48h. Transduced OT-I cells were adoptively transferred into B6-CD45.1 mice and infected with Lm-OVA. 72h post-infection, transduced OT-I cells (Zombie dye− CD8+ CD45.2+ CD44+ GFP+) were sorted from spleens. A total of 4 individual biological samples from one independent experiment were collected for each condition (6 x 10^4 to 1 x 10^5 cells per sample).

first: Dave

last: Maurice-De Sousa

first: Laure

last: Le Corre

first: Salix

last: Boulet

first: Frédéric

last: Duval

first: Jean-François

last: Daudelin

first: Livia

last: Odagiu

first: Marion

last: Sarrias


title: Early Notch signaling programs effector CD8+ T cell differentiation [ATAC-Seq]

overall_design: For ATAC-seq, B6-CD45.1 mice were adoptively transferred with WT vs Notch1/2 KO OT-I cells and infected with Lm-OVA. 72h post-infection, splenocytes were purified by negative selection using anti-CD4 and anti-CD19 biotinylated antibodies and streptavidin-conjugated magnetic beads (EasySep Streptavidin RapidSpheres, StemCell Technologies). Activated OT-I cells (Zombie dye− CD8+ CD45.2+CD44+) were then sorted and nuclei isolation was performed.


title: Sex-specific Concordance of Striatal Transcriptional Signatures of Opioid Addiction in Human and Rodent Brains

city: Worcester

first: Ryan

last: Logan

state: MA

address: 366 Plantation Street

institute: University of Massachusetts Chan Medical School

summary: Background: Opioid use disorder (OUD) has emerged as a severe, ongoing public health emergency. Current treatments for OUD are unsuccessful in lead to lasting abstinence in most users. This underscores the lasting effects of chronic opioid use and emphasizes the need to understand the molecular mechanisms of drug seeking and taking, but also how those alterations persist through acute and protracted withdrawal.  Methods: Here, we used RNA sequencing in post-mortem human tissue from males (n=10) and females (n=10) with OUD and age and sex-matched control subjects. We compared molecular alterations associated with human OUD in the nucleus accumbens (NAc) to mouse and rat models of non-volitional (n=3-6 per group per sex) and volitional (n=5-6 per group per sex) exposure to opioids across distinct stages of opioid use and withdrawal (acute and prolonged). Results: We found that the molecular signature in the NAc of females with OUD mirrored effects seen in the NAc of female rodents in a non-volitional paradigm at all stages of exposure. Conversely, males with OUD showed a similar expression profile to rodents with volitional exposure, but only during the acute withdrawal phase. Shared co-expression networks were involved in post-transcriptional modification of RNA and epigenetic modification of chromatin state. Conclusions: Our results provide fundamental insight into the conserved molecular pathways altered by opioids across species, with evidence suggesting that alterations in females with OUD may be driven by drug exposure, while alterations in males with OUD may be driven by volitional intake.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: RNA-sequencing was conducted on prefrontal cortex and nucleus accumbens of Heterogeneous Stock rats and C57BL/6J mice. Both male and female rats and mice were used. Heterogeneous Stock rats underwent oxycodone self-administration, then sacrificed at different times following opioid self-administration. Mice were given either saline solution or morphine solution for oral drinking, then sacrified at different times following opioid drinking. Tissue was collected and gene expression was examined in rats and mice across different times of opioid administration and withdrawal.


title: High PRMT5 levels, maintained by KEAP1 inhibition, drive chemoresistance in ovarian cancer [CRISPR screen]

city: Chicago

first: Harun

last: Ozturk

state: Illinois

address: 303. E. Superior, Lurie cancer center

institute: Northwestern University

summary: Protein arginine methyl transferases (PRMTs) are generally upregulated in cancers. However, the mechanisms leading to this upregulation and its biological consequences are poorly understood. Here, we identify PRMT5, the main symmetric arginine methyl transferase, as a critical driver of chemoresistance in high-grade serous ovarian cancer (HGSOC). Cancer transcriptome analysis shows that HGSOC tumors express the highest levels of PRMT5. Furthermore, PRMT5 levels and its enzymatic activity are further induced in a Platinum (Pt)-resistant state at the protein level. To reveal potential regulators of high PRMT5 protein levels, we optimized intracellular immunostaining conditions and performed an unbiased CRISPR screening to identify regulators of PRMT5 levels in OC cells. These results led to several critical regulators, including KEAP1, a top-scoring negative regulator of PRMT5 protein levels. Our mechanistic studies show that KEAP1 directly interacts with PRMT5, leading to its ubiquitin-dependent degradation under normal physiological conditions. However, Pt-treatment-mediated stress leads to KEAP1 inhibition, resulting in elevated levels of PRMT5, sufficient to confer cells resistant to Pt. At the genomic level, our chromatin immunoprecipitation and sequencing (ChIP) studies show that elevated PRMT5 directly interacts with the promoters of stress response genes and positively regulates their transcription. In line with increased PRMT5 levels in Pt-resistant cells, pharmacological inhibition of PRMT5 selectively renders these cells selectively sensitive to PRMT5 inhibition compared to chemo-naive or normal fallopian epithelial cells. As such, combined PRMT5 inhibition with Pt results in synergistic cellular cytotoxicity in vitro and tumor volume reduction in vivo in otherwise Pt-resistant patient-derived xenograft tumors. Overall, the findings from this study identify PRMT5 as a critical therapeutic target in Pt-resistant HGSOC cells and reveal the molecular mechanisms that lead to high PRMT5 levels in Pt-treated and chemo-resistant tumors.

overall_design: To identify and characterize potential regulators of PRMT5, we conducted a CRISPR-Cas9-based genetic screen using chemoresistant COV362 cells.

first: Mazhar

last: Adli


title: High PRMT5 levels, maintained by KEAP1 inhibition, drive chemoresistance in ovarian cancer [ATAC-seq]

overall_design: To investigate whether PRMT5 bound genes are associated with open chromatin, we performed ATAC-seq.


title: High PRMT5 levels, maintained by KEAP1 inhibition, drive chemoresistance in ovarian cancer [ChIP-seq]

overall_design: To investigate which genes are regulated by PRMT5, we profiled PRMT5 chromatin binding using ChIP-seq in chemo-resistant OVCAR4 cells. We also profiled H3K27ac to determine if PRMT5 binding is associated with active chromatin.


title: High PRMT5 levels, maintained by KEAP1 inhibition, drive chemoresistance in ovarian cancer [RNA-seq]

overall_design: To investigate PRMT5 regulated genes that contribute to chemoresistance, we profiled transcriptome of chemo-naïve, chemo-resistant and chemo-resistant cells treated with PRMT5 inhibitor.


title: RNA sequencing to analyze trasncriptional profiles and screen potential regulators in confined migration

city: Suzhou

first: Peng

last: Shi

address: Renai street,199

institute: Soochow University

summary: To identify potential regulators involved in confined cell migration, we performed transwell migration assay with 3 μm pore size to simulate native physical confined microenvironment. Transmigrated cells were collected for RNA sequencing to analyze transcriptional profile changes in comparison to parental cells.

overall_design: Here are two types of samples, namely control and 3 μm_confine. The control group represents parental MEF cells. The 3 μm_confine group represents MEF cells transmigrated through transwell with 3 μm pore size.

first: Congying

last: Wu


title: A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

summary: The cohesin protein complex is essential for the formation of topologically associating domains (TADs) and chromatin loops on interphase chromosomes. For the loading onto chromosomes, cohesin requires the cohesin loader complex formed by NIPBL and MAU2. Cohesin localizes at enhancers and gene promoters with NIPBL in mammalian cells and forms enhancer-promoter loops. Cornelia de Lange syndrome (CdLS) is a rare, genetically heterogeneous disorder affecting multiple organs and systems during development, caused by mutations in the cohesin loader NIPBL gene (> 60% of patients), as well as in genes encoding cohesin, a chromatin regulator, BRD4, and cohesin-related factors. We also reported CHOPS syndrome that phenotypically overlaps with CdLS and is caused by gene mutations of a super elongation complex (SEC) core component, AFF4. Although these syndromes are associated with transcriptional dysregulation, the underlying mechanism remains unclear. In this study, we provide the first comprehensive analysis of chromosome architectural changes caused by these mutations using cell lines derived from CdLS and CHOPS syndrome patients. In both patient cells, we found a decrease in cohesin, NIPBL, BRD4, and acetylation of lysine 27 on histone H3 (H3K27ac) in most enhancers with enhancer-promoter loop attenuation. In contrast, TADs were maintained in both patient cells. These findings reveal a shared molecular mechanism in these syndromes and highlight unexpected roles for cohesin, cohesin loaders, and the SEC in maintaining the enhancer complexes. These complexes are crucial for recruiting transcriptional regulators, sustaining active histone modifications, and facilitating enhancer-promoter looping.

overall_design: Analysis of protein chromosomal localization by spike-in ChIP-seq  in NIPBL wild-type and mutant 293FT cells

first: Toyonori

last: Sakata

first: Shoin

last: Tei

first: Kosuke

last: Izumi

first: Ian

last: Krantz

first: Masashige

last: Bando


overall_design: Analysis of transcription levels by RNA-seq in NIPBL wild-type and mutant 293FT cells


title: Single-cell RNA sequencing for osteochondral fusions

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

summary: We have developed a protocol to generate hPSC-derived osteochondral fusions that mimick embryonic long bone diaphysis. hPSCs were first differentiated to chondroprogenitors and osteogenesis-committed early chondrocytes. Then they were centrifuged together to genrate a fusion construct. After cultured for 7 days in vitro, the fusion construct was transplanted under the kidney capsule of the NOD/SCID mice to generate a mature osteochondral fusion. The 4-week osteochondral fusion grafts contain full spectrum of cells during endochondral ossification, mimicking the in vivo growth plate tissues of early long bone diaphysis. To exam this tissue in single-cell level for comparison with the published datasets of the true human emrbyo, we conducted single-cell RNA sequencing on the 4-week osteochondral fusion grafts.

overall_design: To collect enough cells for single-cell RNA sequencing, three osteochondral fusions were pooled together and were dissociated to single cells by Liberase after cut into small fragments. Digestion was stopped until no large fragments could be found and the cells were filtered by 40μm strainers. After that, the cells were treated with hemolysis reagents for 10 min at RT. Then 1 mL basal medium composed of DMEM/F12, 10% FBS, 1% pen-strep was added and the cells were centrifuged at 300g for 5 min and were resuspended in the medium mentioned above.


title: Limited Cell-Autonomous Anticancer Mechanisms in Long-Lived Bats

city: Rochester

first: Fathima

last: Athar

address: 500 Joseph C Wilson Blvd.

department: Biology

institute: University of Rochester

summary: Bats are remarkably long-lived for their size with many species living more than 20-40 years, suggesting that they possess efficient anti-aging and anti-cancer defenses. Here we investigated requirements for malignant transformation in primary bat fibroblasts in four bat species - little brown bat (Myotis lucifugus), big brown bat (Eptesicus fuscus), cave nectar bat (Eonycteris spelaea) and Jamaican fruit bat (Artibeus jamaicensis) – spanning the bat evolutionary tree and including the longest-lived genera. We show that bat fibroblasts do not undergo replicative senescence and express active telomerase. Bat cells displayed attenuated stress induced premature senescence with a dampened secretory phenotype. Unexpectedly, we discovered that bat cells could be readily transformed by only two oncogenic perturbations or “hits”: inactivation of either p53 or pRb and activation of oncogenic RASV12. This was surprising because other long-lived mammalian species require up to five hits for malignant transformation. Additionally, bat fibroblasts exhibited increased p53 and MDM2 transcript levels, and elevated p53-dependent apoptosis. The little brown bat showed a genomic duplication of the p53 gene. We hypothesize that bats evolved enhanced p53 activity through gene duplications and transcriptional upregulation as an additional anti-cancer strategy, similar to elephants. In summary, active telomerase and the small number of oncogenic hits sufficient to malignantly transform bat cells suggest that in vivo bats rely heavily on non-cell autonomous mechanisms of tumor suppression.

sample_organism:
Artibeus jamaicensis
Homo sapiens
Mus musculus
Mus spretus
Eptesicus fuscus
Eonycteris spelaea
Myotis lucifugus

overall_design:
We isolated primary wing fibroblasts from four species of bats; little brown bat (Myotis lucifugus) with maximum lifespan (MLS) of 34 years, big brown bat (Eptesicus fuscus; MLS of 19 years), cave nectar bat (Eonycteris spelaea; MLS of over 8 years; related species Eidolon helvum have MLS of 22 years), and Jamaican fruit bat (Artibeus jamaicensis; MLS of 19 years). Cells were treated with two doses of Gamma radiation and response was studied.
We isolated skin tissues from 3 species of bats: big brown bat (Eptesicus fuscus; 4 individuals); cave nectar bat (Eonycteris spelaea; 5 individuals); and Jamaican fruit bat (Artibeus jamaicensis; 3 individuals) for RNA-seq to compare expression difference of TP53

first: Zhizhong

last: Zheng