title: ABCA7 variants impact phosphatidylcholine and mitochondria in neurons

city: Cambridge

first: Li-Huei

last: Tsai

state: MA

address: 77 Massachusetts Avenue

institute: MIT

summary: Loss-of-function (LoF) variants in the lipid transporter ABCA7 significantly increase Alzheimer's disease risk (odds ratio circa  2), yet the underlying pathogenic mechanisms and specific neural cell types affected remain unclear. To investigate this, we generated a single-nucleus RNA sequencing atlas of 36 human postmortem prefrontal cortex samples, including 12 carriers of ABCA7 LoF variants and 24 matched non-carriers. ABCA7 LoF variants were associated with transcriptional changes across all major neural cell types. Excitatory neurons, which expressed the highest levels of ABCA7, showed significant alterations in oxidative phosphorylation, lipid metabolism, DNA damage responses, and synaptic signaling pathways. ABCA7 LoF-associated transcriptional changes in neurons were similarly perturbed in carriers of the common AD missense variant ABCA7 p.Ala1527Gly (n = 240 controls, 135 carriers) - predicted by molecular dynamics simulations to disrupt ABCA7 structure -, indicating that findings from our study may extend to large portions of the at-risk population. Human induced pluripotent stem cell (iPSC)-derived neurons carrying ABCA7 LoF variants closely recapitulated the transcriptional changes observed in human postmortem neurons. Biochemical experiments further demonstrated that ABCA7 LoF disrupts mitochondrial membrane potential via regulated uncoupling, increases oxidative stress, and alters phospholipid homeostasis in neurons, notably elevating saturated phosphatidylcholine levels. Supplementation with CDP-choline to enhance de novo phosphatidylcholine synthesis effectively reversed these transcriptional changes, restored mitochondrial uncoupling, and reduced oxidative stress. Additionally, CDP-choline normalized amyloid-beta secretion and alleviated neuronal hyperexcitability in ABCA7 LoF neurons. This study provides a detailed transcriptomic profile of ABCA7 LoF-induced changes and highlights phosphatidylcholine metabolism as a key driver in ABCA7-induced risk. Our findings suggest a promising therapeutic approach that may benefit a large proportion of individuals at increased risk for Alzheimer's disease.

overall_design: RNA-seq profiling of induced neurons derived from two human isogenic iPSC lines, each homozygous for a distinct ABCA7 loss-of-function variant (p.Tyr622* or p.Glu50fs*3), generated from a parental control line lacking ABCA7 loss-of-function variants. Neurons were collected at Day 28, with or without treatment with CDP-choline during the final 14 days.

first: Djuna

last: von Maydell

first: Ping-Chieh

last: Pao

first: Colin

last: Staab

first: Oisin

last: King


title: Recreating pathophysiology of CLN2 disease and demonstrating reversion by TPP1 gene therapy in hiPSCs-derived retinal organoid and retina-on-chip

status: Public on Jul 25 2025

city: Tuebingen

first: Kevin

last: Achberger

address: Oesterbergstrasse 3

country: Germany

institute: University Tübingen

type: Expression profiling by high throughput sequencing

summary: Mutations in tripeptidyl peptidase 1 (TPP1) gene lead to late infantile neuronal ceroid lipofuscinosis CLN2, characterized by lysosomal accumulation of lipofuscins predominantly found in brain and retina. The ocular phenotype is characterized by bilateral outer retinal degeneration that leads to complete vision loss. CLN2 animal models struggle in recapitulating the retinal phenotype observed in patients. Here, we leveraged human induced pluripotent stem cell (hiPSC)-derived retinal organoids (ROs), retinal pigmented epithelial (RPE) cells, and retina-on-chip (RoC) technologies to model CLN2 disease in vitro in patient-specific microphysiological models of the human retina. Using these models, we were able to recreate the major clinical histological hallmark of CLN2 patients, namely the accumulation of lipofuscins containing subunit C of mitochondrial ATP synthase (SCMAS) and lipids mainly in the outer retina. Furthermore, single-cell RNA-sequencing of CLN2 ROs revealed a dysregulation of translational and mitochondrial function in cones. Finally, we demonstrate that an adeno-associated virus (AAV)-mediated TPP1 gene therapy was able to restore TPP1 expression and could decrease and even prevent SCMAS accumulations. In summary, our study produced novel human-relevant microphysiological retinal disease models, uncovered new mechanisms of CLN2 pathophysiology in the human retina, and demonstrated the immense potential of AAV9.hCLN2 gene therapy for CLN2 disease potentially treating and even curing blindness of affected individuals.

overall_design: iPSC-derived retinal organoids (ROs) at d192  of two control lines (CTRL1, CTRL2) and two CLN2 Patients lines untreated (CLN2-1, CLN-2) and treated with AAV9-hCLN2 (AAV9.hCLN2-treated CLN2-1 and AAV9.hCLN2-treated CLN2-2) were subjected to single cell sequencing analysis (10X Genomics). The six samples were distributed into 4 runs and demultiplexed by SNPs using SoupOrCell v2.0 (Heaton et al 2020). Run 1 contained CTRL1 and CLN2-1, Run2 contained CTRL1 and AAV9.hCLN2-treated CLN2-1, Run3 contained CTRL2 and CLN2-2, Run4 contained CTRL2 and AAV9.hCLN2-treated CLN2-2.

first: Serena

last: Corti

first: Kwi Hye

last: Kim

first: Ting

last: Chen

first: Virginia

last: Cora


title: YY1-mediated DNA looping promotes the generation of ecDNA (HiCUT)

city: Tianjin

first: Luning

last: Qin

address: No.38 Tongyan Road, Haihe Education Park, Tianjin, China

country: China

institute: Nankai university

summary: YY1 is a widely expressed transcriptional regulatory factor that is overexpressed in various cancer types, promoting the expression of numerous oncogenes and contributing to cancer progression. It has been identified as a significant biomarker of cancer, correlating with poor prognosis in cancer patients. Moreover, YY1 is an essential regulator of DNA looping, preferentially occupying enhancers and promoters. YY1-mediated enhancer-promoter loops participate in various cancer-related biological functions by regulating gene expression. The circular nature of ecDNA suggests that its formation involves a DNA looping process. Notably, in tumor cells, YY1-mediated DNA looping is closely associated with the activation of multiple oncogenes and immunosuppressive genes, resembling the types of genes carried by ecDNA. Therefore, we investigated the link between DNA looping mediated by YY1 and ecDNA generation. We conducted YY1 HiCUT in COLO320-DM/HSR cells. We found that in COLO320-DM cells, a large number of YY1-mediated loops were located in the MYC amplification region, while only 1% of these loops were observed in the same region in COLO320-HSR cells. The result indicates YY1 mediates DNA looping through dimerization in cells has potential correlation with ecDNA biogenesis.

overall_design: other

last: Wu

first: Tingxue

last: Zhen

first: Tao

last: Sun


title: Epigenetic de-repression of drivers of neuroendocrine prostate cancer [RNA-seq]

city: Boston

first: Varadha Balaji

last: Venkadakrishnan

address: 450 Brookline Ave

department: Department of Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

overall_design: RNA-Seq to understand epigenetic de-repression of drivers of neuroendocrine prostate cancer

first: Venkadakrishnan

last: Varadha Balaji

first: Beltran

last: Himisha


title: BRD4 inhibition leads to MDSC apoptosis and enhances checkpoint blockade therapy.

status: Public on Jul 24 2025

city: Columbus

first: William

middle: E

last: Carson III

state: Ohio

address: 420 W 12th Street, 620 Tzagournis Research Facility

institute: The Ohio State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: BRD4 is an epigenetic reader protein that regulates oncogenes such as myc in cancer.  However, its additional role in shaping immune responses via regulation of inflammatory and myeloid cell responses is not yet fully understood. This work further characterized the multifaceted role of BRD4 in anti-tumor immunity.  NanoString gene expression analysis of EMT6 tumors treated with a BRD4 inhibitor identified a reduction in myeloid gene expression signatures.  Additionally, BRD4 inhibition significantly reduced myeloid derived suppressor cells (MDSC) in the spleens and tumors of mice in multiple tumor models and also decreased the release of tumor-derived MDSC growth and chemotactic factors.  Pharmacologic inhibition of BRD4 in MDSC induced apoptosis and modulated expression of apoptosis regulatory proteins.  A BRD4-myeloid specific knockout model suggested that the dominant mechanism of MDSC reduction after BRD4 inhibition was primarily through a direct effect on MDSC.  BRD4 inhibition enhanced anti-PD-L1 therapy in the EMT6, 4T1 and LLC tumor models, and the efficacy of the combination treatment was dependent on CD8+ T cells and on BRD4 expression in the myeloid compartment.  These results identify BRD4 as a regulator of MDSC survival and provide evidence to further investigate BRD4 inhibitors in combination with immune based therapies.

overall_design: CD11b+ Gr1+ MDSC were isolated by immunomagnetic negative selection from spleens of TNBC 4T1 tumor-bearing mice and treated with DMSO vehicle control or BET inhibitor PLX51107 at 125 nM for 24 hours.

first: Himanshu

last: Savardekar

first: Andrew

last: Stiff

first: Alvin

last: Liu

first: Robert

last: Wesolowski

first: Emily

last: Schwarz

first: Ian

last: Garbarine

first: Megan

last: Duggan

first: Sara

last: Zelinskas

first: Jianying

last: Li

first: Gabriella

last: Lapurga

first: Alexander

last: Abreo

first: Lohith

first: Ryan

last: Parker

first: Julia

last: Sabella

first: Mallory

last: DiVincenzo

first: Brooke

last: Benner

first: Steven

first: Dionisia

last: Quiroga

first: Luke

last: Scarberry

first: Gang

last: Xin

first: Anup

last: Dey

first: Keiko

last: Ozato

first: Lianbo

last: Yu

first: Merve

last: Hasanov

first: Debasish

last: Sundi

first: Richard

middle: C

first: Kari

middle: L

last: Kendra


title: YY1 and Lig3 collaboratively regulate ecDNA biogenesis (CUT&Tag)

first: Luning

last: Qin

summary: Extrachromosomal DNA (ecDNA) is an important carrier for the amplification of proto-oncogenes. It can not only drive cancer progression by increasing the copy number of oncogenes but also influence the transcriptional regulation of oncogenes by increasing chromatin accessibility and regulating chromatin interactions. Currently, the generation of ecDNA is rather complex and the exact mechanism remains unclear. This study aims to investigate the molecular mechanism underlying the generation of ecDNA in order to identify the targets for ecDNA-targeted drug therapies. We analyzed the chromatin landscape in COLO320-DM and COLO320-HSR cells through CUT&Tag. The results of CUT&Tag for Lig3, the open chromatin marker H3K27ac, and the promoter marker H3K4me3 showed that Lig3 was specifically enriched in the MYC ecDNA amplification regions and bound to a large number of open chromatin regions and promoter regions, indicating that Lig3 may be related to the formation of ecDNA and stably bind to ecDNA, thereby maintaining the integrity of the genes carried by ecDNA. Furthermore, we found that there were a large number of merge peaks between Lig3 and YY1 across the whole genome, which were abundantly occupied at the MYC ecDNA amplification sites. Meanwhile, we observed that in COLO320-DM cells (where oncogenes are amplified in the form of ecDNA), there was a significant enrichment of YY1 in the MYC amplification regions, while in COLO320-HSR cells (where oncogenes are amplified on the homogeneously staining regions, HSR), the peaks of YY1 were significantly decreased. Our data suggest that YY1 is essential for the generation of ecDNA. It forms a complex with Lig3 to jointly regulate the formation of ecDNA, and this complex can be detected as it resides on ecDNA for a relatively long period of time. This may also be related to the stability of ecDNA and its involvement in genomic regulation.

overall_design: Genome binding/occupancy profiling by high throughput

first: Ting

last: Wu

first: Tingxue

last: Zhen

first: Tao

last: Sun


title: Epigenetic de-repression of drivers of neuroendocrine prostate cancer [CUT&Run]

first: Varadha Balaji

last: Venkadakrishnan

overall_design: CUT&RUN to understand epigenetic de-repression of drivers of neuroendocrine prostate cancer

first: Venkadakrishnan

last: Varadha Balaji

first: Beltran

last: Himisha


title: Enhancing Transcriptome Mapping with Rapid PRO-seq Profiling of Nascent RNA

city: Miami

first: Pradeep

middle: Reddy

last: Cingaram

state: FL

address: 1501 N.W. 10th Avenue

department: Human genetics

institute: University of Miami

summary: Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping transcriptomes with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq), enabling efficient transcriptome mapping within a single day (∼12 h), increasing ligation efficiency, abolishing adapter dimers, and reducing sample loss and RNA degradation. Rapid PRO-seq allows for transcriptome mapping using 5,000 cells and is applicable to mouse hematopoietic progenitor cells (mHPCs) as well as mouse neurons. Using acute depletion of INTS11 in neuronal cells, we pinpoint a critical role for INTS11 as a regulator of genes in neurodevelopmental disorders. Taken together, rPRO-seq represents a significant advance in the field of nascent transcript analyses and will be a valuable tool for generating patient-specific genome-wide transcription profiles with minimal sample requirements.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
PRO-seq and rPRO-seq were conducted in duplicates using HeLa cells and mHPC cells.
rPRO-seq were conducted in duplicates using HeLa cells and mouse neuronal differentiated (ND) mESC cells.

first: Felipe

last: Beckedorff

first: Jingyin

last: Yue

first: Fan

last: Liu

first: Helena

last: Gomes Dos Santos

first: Harikumar

last: Arigela

first: Ramin

last: Shiekhattar


title: Adhesion G protein-coupled receptor ADGRG1 promotes protective microglial response in Alzheimer’s disease

city: San Francisco

first: Xianhua

last: Piao

state: CA

institute: University of California, San Francisco

summary: Germline genetic architecture of Alzheimer's disease (AD) indicates microglial mechanisms of disease susceptibility and outcomes. However, the mechanisms enabling protective microglial responses remain elusive. Here, we investigate the role of microglial ADGRG1, an adhesion G-protein-coupled receptor (aGPCR) specifically expressed in yolk-sac-derived microglia, in AD pathology using the 5xFAD mouse model. Transcriptomic analyses reveal that ADGRG1 activates the transcription factor MYC, leading to upregulation of genes involved in homeostasis, phagocytosis, and lysosomal functions, thereby promoting a protective microglial state. We demonstrate that deletion of Adgrg1 in microglia impairs MYC activation, resulting in increased amyloid-beta deposition, exacerbated neuronal loss, and cognitive deficits. Functional assays in mouse models and human embryonic stem cell-derived microglia confirm that ADGRG1 is required for Aβ phagocytosis. These findings uncover a GPCR-mediated pathway that drives a protective microglial state via MYC activation, suggesting potential therapeutic strategies to alleviate AD progression by enhancing microglial functional competence.

overall_design: To investigate the role of microglial Adgrg1 in AD pathology, we engineered a novel mouse model and performed snRNAseq on the neocortex of 6-month-old animal. To enrich glial cells, each animal was sorted by DAPI-positive and DAPI-positive NeuN-negative nuclei before sequencing. The genotypes for the testing animals are: Adgrg1+/+;Cx3cr1Cre/+ (Con); Adgrg1fl/fl;Cx3cr1Cre/+ (CKO); 5xFAD;Adgrg1+/+;Cx3cr1Cre/+ mice (ADCon); 5xFAD;Adgrg1fl/fl;Cx3cr1Cre/+ (ADCKO).

first: Beika

last: Zhu

first: Andi

last: Wangzhou

first: Diankun

last: Yu

last: Li

first: Rachael

last: Schmidt

first: Stacy

last: De Florencio

first: Lauren

last: Chao

first: Yonatan

last: Perez

first: Lea

middle: T

last: Grinberg

first: Salvatore

last: Spina

first: Arnold

middle: R

last: Kriegstein

first: William

middle: W

last: Seeley

middle: M

last: Ransohoff

first: Tomasz

last: Nowakowski


title: The Novel Immunocompetent Eµ-SOX11CCND1 Mouse Model Molecularly and Phenotypically Mimics Human Mantle Cell Lymphoma

first: Alessandro

last: La Ferlita

state: OH

department: The James Comprehensive Cancer Center

summary: Mantle Cell Lymphoma (MCL) is an incurable blood cancer affecting older adults with a median survival of 80 months. There is a great need for novel therapies and immunocompetent pre-clinical models that effectively mimic the tumor micro-environment (TME). Most MCL murine models are patient derived xenografts (PDXs), which are immunocompromised, making them suboptimal to test immunotherapies. Previous attempts at an immunocompetent model were less than optimal with limited pathology, narrow phenotype, or the use of genes not implicated in MCL. Here, we present a novel transgenic, immunocompetent mouse model for MCL by expressing two key MCL genes, SRY-Box Transcription Factor 11 (SOX11), and Cyclin D1 (CCND1) under the Eµ enhancer in C57BL/6 mice. The resulting double transgenic mice showed lethal expansion of B1a (CD5+CD19+CD23-) sub-B cell population in lymphatic organs, as well as the liver, lung, and kidney. We subsequently show this population can further adoptively transferred to healthy mice, which develop aggressive MCL. Passage one was profiled and found to express key human MCL driver genes, as well as cell surface marks, including the immune suppressive PD-1 and PDL-1. This model is resistant to ibrutinib and venetoclax, medications currently used for MCL,  but highly responsive to a protein arginine methyltransferase 5 (PRMT5) inhibitor (OS 18 vs. 67 days p<0.01), supporting our previous work showing PRMT5 as a promising target for MCL. This study provides the pathological and genetic characterization needed to utilize the Eµ-SOX11CCND1 model of MCL to improve the preclinical research of immunotherapeutic and immunomodulatory agents.

overall_design: to investigate the transcriptional changes and resemblance of human MCL in the novel Eµ-SOX11CCND1 model, we established an adoptive transfer model and validated our findings in human MCL


title: T cell-inducing heterologous vaccine against elephant endotheliotropic herpesvirus

city: Guildford

first: Falko

last: Steinbach

address: Daphne Jackson Road

department: School of Veterinary Medicine

country: United Kingdom

institute: University of Surrey

summary: We developed a heterologous, recombinant modified vaccinia virus Ankara prime and adjuvanted protein boost vaccine, containing the regulatory protein EE2 and the major capsid protein. The vaccine design focussed on targeting Th1 and cytotoxic T cell responses, which are crucial to herpesvirus immunity. In a proof-of-concept trial, safety and immunogenicity were tested in adult elephants. We used a modified interferon-γ release (IFNG) point-of-care vaccine-specific whole blood assay to determine T cell responses by RT-qPCR first, established to overcome quality-reducing sample transport times to the laboratory. Subsequently, RNA sequencing was utilised to understand transcriptomic changes induced by the vaccine.

overall_design: Blood samples before and after vaccination were taken for RNASeq. Samples were tested both unstimulated and Ag stimulated.

first: Tanja

last: Maehr

first: Javier

last: Lopez

first: Gabby

last: Drake

first: Frederico

last: Ferreira

first: Richard

last: Fraser

first: Rebecca

last: Mckown

first: Reshma

last: Kailath

first: Susan

last: Morris

first: Adam

last: Chambers

first: Leo

last: Graves

last: Walker

first: Katie

last: Edwards

first: Akbar

last: Dastjerdi

first: Helder

last: Nakaya


title: MERFISH profiling of mouse retinal ganglion cell layer on wholemount

status: Public on Jul 23 2025

city: Berkeley

first: Kushal

last: Nimkar

address: Stanley Hall Room 202

department: Chemical and Biomolecular Engineering

institute: UC Berkeley

summary: We optimized a workflow combining imaging-based spatial transcriptomics (MERFISH) and immunostaining on ganglion cell layer retinal flatmounts of C57/Bl6J mice.The MERFISH data shows molecularly-defined retinal ganglion cell types types exhibited non-uniform distributions. We also analyzed local neighborhoods for each cell and registered several RGC types as enriched in the perivascular niche.

overall_design: We recovered the spatial distribution of cell types in the mouse ganglion cell layer (GCL) by using the Vizgen MERSCOPE platform, which measured the expression of 140 genes in each of those cells. Cells were identified via boundary staining provided by Vizgen, and RNA transcripts were assigned to them via cell segmentation. There are 6 biological replicates, 3 of which contain costaining for CD31. Separately, there are 2 biological replicates with costaining of Opn4. Each biological replicate consists of multiple separately imaged tissue regions due to the 12 micrometer imaging limit.

first: Nicole

middle: Y

last: Tsai

first: Mengya

last: Zhao

first: Yujuan

last: Yi

first: Matthew

last: Lum

first: Yixiao

last: Wang

first: Tavita

last: Garrett

first: Kenichi

last: Toma

first: Franklin

last: Caval-Holme

first: Nikhil

last: Reddy

first: Aliza

last: Ehrlich

first: Arnold

last: Kriegstein

first: Michael Tri

middle: H

last: Do

first: Yang

last: Hu

first: Benjamin

last: Sivyer

first: Karthik

last: Shekhar

first: Xin

last: Duan


title: Sphingomyelin regulates the transcriptional machinery in nuclear lipid microdomains

city: Perugia

first: Elisabetta

last: Albi

state: Italy

address: Via Romana

department: Department of Pharmaceutical Sciences

country: Italy

institute: Università degli studi di Perugia

type: Non-coding RNA profiling by high throughput sequencing

summary: Nuclear lipid microdomains rich in sphingomyelin and cholesterol content regulate double-stranded exonuclease-resistant RNA. The study aimed to elucidate the importance of nuclear lipid microdomains in safeguarding nuclear RNA from digestion and to scrutinize all RNA present. Thus, we investigated the impact of sphingomyelinase on nuclear lipid microdomain RNA and conducted RNA extraction, library preparation, and sequencing. Sphingomyelinase treatment makes the RNA susceptible to RNase treatment. Nuclear lipid microdomains exhibit a higher abundance of retained introns, small nuclear RNA, and long intergenic non-coding RNA compared to whole nuclei, with a notable enrichment in miRNA. The high concentration (20%) of miRNAs in nuclear lipid microdomains is justified by the presence of specific nuclear circular RNA as exons circularized with 'retained' introns, referred to as exon-intron circular RNA (EIciRNA) that act as a sponge for miRNAs. Moreover, we demonstrate the presence of ciRNA. The functional analysis indicates that all types of RNase-resistant RNA associated with nuclear lipid microdomains are involved in chromatin organization and brain pathophysiology. In conclusion, nuclear lipid microdomains represent a site of transcription regulation in which circular RNAs, miRNA, and double-stranded mRNA, all resistant to RNase, are stabilized by nuclear sphingomyelin.

overall_design:
The experimental plan includes: a) purification of nuclear lipid microdomains from HN9.10e cells in the absence or presence of liposomes with equimolecular concentrations of cholesterol and sphingomyelin; 2) localization in the cells of sphingomyelin and cholesterol/sphingomyelin complex with specific fluorescent probes; 3) verification of the impossibility of purifying nuclear lipid microdomains after treatment with sphingomyelinase which degrades sphingomyelin, an essential lipid for their structure; 4) lipid extraction and lipidomics analysis of whole nuclei and nuclear lipid microdomains; 5) extraction and sequencing of RNA in nuclei and nuclear lipid microdomains
Please note that the "Pool-ID-1_S1_*_expression_values.xlsx' data was generated from all Pool-ID-1_S1_L00* (multiplexed) raw data pooled together and is linked to the Pool rep1 sample records. Briefly all samples were pooled together and sequenced in different lanes, then fastq files were demultiplexed, according to specific barcodes, and used for subsequent gene expression quantification.

first: Carmela

last: Conte

first: Michela

last: Bulfoni

first: Federico

last: Fiorani

first: Samuela

last: Cataldi

first: Nicolò

last: Gualandi

first: Ornella

last: Calderini

first: Mercedes

middle: G

last: Gil

first: Giorgia

last: Vesca

first: Rita

last: Paroni

first: Michele

last: Dei Cas

first: Cataldo

last: Arcuri

first: Alessandra

last: Mirarchi

first: Tommaso

last: Beccari

first: Roshibide

last: Kobayashi

first: Mario

last: Tomishige

first: Francesco

last: Curcio


title: RNA-seq analysis of Calreticulin(Calr) knockout LLC cells identified ER stress response

city: Beijing

first: Lijian

last: Wu

state: Beijing

address: 30 Shuangqing Rd, Haidian District, Beijing

department: School of Medicine

institute: 清华大学

summary: To investigate the mechanisms by which Calreticulin inactivation increases tumor sensitivity to T cell-mediated anti-tumor immunity, LLC cells were transduced with sgRNA targeting Calreticulin or a control sgRNA, and transcriptome changes were profiled using paired-end RNA-seq. Our data demonstrated that Calr KO induces an ER stress response.

overall_design: LLC cells were transiently transduced with plasmids expressing Cas9 and sgRNA targeting Calreticulin or a control sgRNA, and cultured in vitro for 10 days to achieve knockout efficiency. For each group, cells were seeded into 6-well plates in triplicate and harvested by TRIzol after 48 hours. Comparative gene expression profiling was then performed.

first: Yiteng

last: Jin

first: Deng

last: Pan


title: p52:ETS1: a transcriptional complex essential for germinal center formation [RNA_Seq_preGCB]

status: Public on Jul 26 2025

city: Singapore

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive, Proteos

department: Institute of Molecular and Cell Biology (IMCB)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

summary: It is well-established that the five transcription factors of the NFκB family form homo/hetero dimers amongst themselves to regulate gene expression by binding DNA. Our study challenges this paradigm by showing that p52 activates transcription without directly binding DNA but as part of a hetero-tetrameric partnership with ETS1, a transcription factor outside the NFκB family. By generating a knock-in mouse model (p52ki/ki) with three mutated residues on p52 required for its interactions with ETS1 but not with RelB, we demonstrate that the p52:ETS1 complex is the hitherto undiscovered regulator of transcription factors, OCT1 and OBF1, known to be critical for the germinal centre (GC) program. Consequently B cell-intrinsic expression of p52:ETS1 complex is indispensable for splenic GC B cell formation and T cell-dependent antibody responses. Functionally, loss of p52:ETS1 interaction led to diminished antigen-specific IgE thereby protecting mice from allergic responses. Collectively, our expand our current knowledge of NFkB signalling and provide new therapeutic targets for the treatment of allergic diseases.

overall_design: RNA-Seq profiling of WT and p52 knock-in mouse spleen pre-GC and GC B cells.

first: Dhakshayini

last: Morgan

first: Biyan

last: Zhang

first: Kerem

last: Fidan


title: Extragenous ILC2s infiltration into the brain after ischemic stroke

city: Hangzhou

first: An

last: Ping

state: Zhejiang

address: 88, Jiefang Road

institute: Zhejiang University

summary: Group 2 innate lymphoid cells (ILC2s) are key players in immune regulation and tissue repair in barrier immunity, but they are rarely seen in the brain. We investigated whether ILC2s in the peripheral circulation during the acute phase could infiltrate the brain parenchyma. We first transfer ILC2s intravenously into the MCAO mice and performed RNA sequencing of ILC2s isolated from the blood and the brain at different time points after MCAO.

overall_design: We collected the transferred ILC2s from the blood at day 1 (bld_1d, n=6) and day 5 (bld_5d, n=6), also from the brain at day 5 after MCAO (br_5d, n=6) for RNA-seq

first: Fan

last: Yang

first: Lingxiao

last: Lu

first: Xiaotao

first: Jianan

first: Huaming

last: Li

first: Yichen

last: Gu

first: Ziyang

first: Jianmin

first: Ligen

last: Shi


title: Expressed mutated genes in Sezary syndrome and their potential prognostic value in patients treated with Extracorporeal Photopheresis

city: Ferrara

first: Cristian

last: Bassi

state: Ferrara

address: Via Fossato di Mortara 70

department: Medicina Traslazionale e per la Romagna

institute: Università di Ferrara

summary: Background. Sézary syndrome (SS) is an aggressive and leukemic variant of Cutaneous T-cell Lymphoma (CTCL) with an incidence of 1-case per million people per year. It is characterized by a complex and heterogeneous profile of genetic alterations that has so far precluded the development of a specific and definitive therapeutic intervention.Methods. Deep-RNA-sequencing (RNA-seq) data were used to analyze the single nucleotide variants (SNVs) carried by 128 putative CTCL-driver genes, previously identified as mutated in genomic studies, in longitudinal SS samples collected from 17 patients subjected to extracorporeal photopheresis (ECP) with Interferon-α. Results obtained were integrated with Whole Exome Sequencing (WES) data. SNVs were validated using the Sanger method. Pathway analysis was performed with g:Profiler web server (https://biit.cs.ut.ee/gprofiler/gost). Statistical analyses were performed with GraphPad PRISM 8 software.Results.Nonsynonymous SNVs were identified in 56 genes. Integration of RNA-seq with WES data revealed that about half of these genes contained somatic mutations. Among them, the most frequently transcribed mutated genes were TET2, JAK3, NCOR1, PDCD11, RHOA, and TP53.Nearly all the remaining genes had germline-restricted mutations, and included ARID1A, ATM, ATR, CREBBP, POLD1, and POT1 genes, which are involved in DNA repair, homologous recombination, and chromatin remodeling, and the CROCC gene, implicated in centrosome cohesion. Monitoring of the mutated genes, identified within an enlarged panel of CTCL associated genes, revealed their reduction in almost 70% of SS patients as well as a significant decline of total number of mutations (SNVs) during ECP treatment. Several mutated genes persisted post-therapy, representing novel candidates associated with ECP resistance that could also have a potential prognostic relevance.Notably, these genes mainly converge on pathways related to DNA repair (ATR, ATRIP, POLD1, TP53, TP53BP1/2) which might represent novel targets to be explored in combination with ECP.Conclusions. This is the first evaluation in SS of expressed mutations in a large panel of CTCL-driver genes. Also innovative is the monitoring of mutated genes in patients' malignant lymphocytes during ECP, a first-line treatment of In review CTCL, which highlights novel candidates associated with ECP resistance that might unmask novel pharmacological vulnerabilities to be exploited during ECP for a personalized treatment

overall_design: RNA sequencing was conducted on 35 SS samples derived from 16 SS patients with 2 serial samples and 1 patient with 3 serial samples and three control samples (healthy donors)


title: PALB2 and 53BP1 govern post-resection homologous recombination DNA repair

city: Philadelphia

first: David

last: Glass

state: PA

address: 333 Cottman Ave

institute: Fox Chase Cancer Center

summary: Homologous recombination (HR) requires the resection of DNA breaks and RAD51 filament formation. Protein complexes that control end resection have been characterized, but regulators of RAD51 loading are not well defined. PALB2 is a mediator of BRCA2-RAD51 DNA break localization; it can also bind BRCA1, or form homodimers with DNA binding activity, via its coiled-coil (CC) domain. Here, we created a CC mutated mouse allele (Palb2CC) that disrupts CC-mediated interactions. While Palb2CC/CC embryos were not viable; remarkably, intercrossing with mice lacking 53BP1, an inhibitor of PALB2-chromatin contacts, produced live-births. However, Palb2CC/CC53bp1-/- mice were tumor-prone and cells had limited RAD51 foci. HR remained inefficient because the CC domain was required for PALB2 to bind to single-stranded (ss)DNA overhangs and subsequently promote PALB2 and RAD51 accumulation.  These findings underscore the role of ssDNA binding in localizing PALB2 to DNA breaks, while establishing genetic interactions that control post-end resection steps in mammalian HR.

overall_design: Mouse embryonic fibroblasts (MEFs) with different Brca1 and Palb2 genotypes were assayed for their DNA end resection capacity. Cas9-expressing MEFs were treated with mg115 (a multiguide RNA that induces DNA breaks at 115 genomic locations in the mouse genome) for 18 hours to allow Cas9 cutting and end resection to proceed, then harvested for END-Seq.

first: Yifan

last: Wang

first: Yan

last: Coulombe

first: Wei-Ting

last: Yueh

first: Gregory

middle: D

last: Conway

first: Larissa

last: Milano

middle: J

first: Amélie

last: Rodrigue

first: Melissa

last: Thomas

first: Joseph

last: Nacson

first: Dongbo

first: Andrea

last: Bernhardy

first: Robert

last: Betsch

first: Alyssa

last: Russo

first: Kathy

middle: Q

last: Cai

last: Testa

first: Mark

last: Andrake

first: Roland

last: Dunbrack

first: Gaorav

middle: P

last: Gupta

first: Bing

last: Xia

first: Eloise

last: Dray

first: Jean-Yves

last: Masson

first: Neil

last: Johnson


title: Time-Resolved Photocatalytic Proximity Labeling Uncovers ER Proteome Dynamics Underlying UPR to Apoptosis Transition [RNAseq_EMC2_knockdown]

last: Zhou

address: ChengFu Road

department: College of Chemistry and Molecular Engineering

institute: Peking University

summary: Apoptosis is a critical outcome of stress-induced processes, with the endoplasmic reticulum (ER) playing a central role in apoptotic protein processing and stress signal transduction. Profiling the ER proteome during stress to cell death offers valuable insights into these processes, but existing methods often suffer from a loss of in situ information or requirement of genetic manipulation. In this study, we introduce CAT-ER, a novel non-genetic ER proteomics system that provides in situ labeling, spatiotemporal resolution, and compatibility across diverse cell types. By combining an ER-targeted iridium photocatalyst with a thio-quinone methide (thioQM) probe, CAT-ER achieves high specificity in enriching ER proteins, comparable to traditional enzymatic methods. Importantly, CAT-ER is free of genetic manipulation, allowing its use in hard-to-transfect cell types like HeLa and immune cells (e.g., Raji, Jurkat, and RAW264.7). Given the high spatiotemporal resolution of CAT-ER, we revealed dynamic ER proteome changes during thapsigargin (Tg)-induced unfolded protein response (UPR) to apoptosis. Notably, NFIP2 mitigated ER stress by halting translation when UPR initiated, while compromised EMC2 delayed apoptosis during prolonged stress. These findings provide novel insights into the molecular dynamics linking the UPR and apoptosis. Collectively, CAT-ER serves as a versatile tool for spatiotemporal proteomic analysis without the need for genetic manipulation, offering a powerful approach to study ER dynamics in various biological contexts.

overall_design: RNA-seq profiling of thapsigargin-treated HeLa cells and DMSO-treated HeLa cells for both 2 hours treatment and 10 hours treatment, in two biological replicates.

first: Zhou

first: Zhang

last: Yan

first: Chen

last: Peng

first: Fan

last: Xinyuan


title: Time-Resolved Photocatalytic Proximity Labeling Uncovers ER Proteome Dynamics Underlying UPR to Apoptosis Transition [RNAseq_thapsigargin_treatment]


title: Macrovascular infiltration and spikes in circulating tumor cells in cancer patients approaching end of life

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

summary: End-of-life neoplastic events related to carcinoma lethality are poorly characterized. With the purpose of exploring biological events in cancer patients nearing death, we conducted an observational, prospective, case-control study enrolling 21 patients with solid tumors and 10 patients without known malignancy, complemented by a retrospective validation cohort of 1,250 cancer patients. In our prospective cohort, we observed remarkable spikes in circulating tumor cell (CTC) counts immediately before death (P < 0.0001), as well as pathological evidence of macrovascular infiltration and large-vessel occlusion obtained through rapid autopsy. In the validation cohort, radiological evidence of macrovascular infiltration emerged as the strongest predictor of poor survival – independent of clinical metastasis – in treatment-homogenous patients with colorectal, lung, ovarian, hepatocellular, or pancreatic cancer (hazard ratio range: 4.0 - 22.4). These findings suggest that spikes in CTC formation and consequent macrovascular failure could be pivotal end-of-life events associated with cancer lethality, providing a rationale for future clinical trials aimed at curbing tumor infiltration into large vessels.

overall_design: Blood samples were obtained via blood draw from multiple locations in patients and controls at  the moment of the autopsy. CTCs were isolated from blood and sequenced using RNA-seq

first: Kelley

last: Newcomer

first: Alessandro

last: Bifolco

first: Sarah

last: Reeves

first: Giada

last: Pontecorvi

first: Simran

last: Asawa

first: Magdalena K.

last: Sznurkowska

first: Manuel

last: Nüesch

first: Lauren L.

last: Ozimski

first: William

last: Gasper

first: Ilona

last: Krol

first: Dario

last: Ghersi

first: Nicola

last: Aceto

first: Matteo

last: Ligorio


title: Tissue-resident memory CD4+ T cells sustain chronic CNS autoimmunity [scRNA-seq & TCR VDJ]

city: Toulouse

first: Ilan

last: Fijalkow

address: CHU Purpan – BP 3028 – 31024 Toulouse Cedex, 3, Toulouse

country: France

institute: Infinity-Toulouse Institute for Infectious and Inflammatory Diseases

summary: Therapeutic options against multiple sclerosis (MS) preventing T cell migration to the central nervous system (CNS) have remarkable clinical effects against the relapsing-remitting (RRMS) form of the disease, while they are poorly effective against its progressive form (PMS). Disability progression in PMS is thought to result from an interplay between smoldering local inflammation and neurodegeneration. The mechanisms sustaining the chronicity of PMS are poorly understood. Here, we investigated the role of tissue-resident memory CD4+ T (CD4+ Trm) cells in sustaining a chronic autoimmune process in the CNS. Our results revealed the presence of bona fide CD4+ Trm cells expressing CD69, CXCR6, P2RX7, CD49a and the transcription factor Hobit in the CNS of mice with chronic experimental autoimmune encephalomyelitis (EAE) and in the brain of patients with PMS. Single-cell transcriptomic analysis uncovered the transcriptional heterogeneity and inflammatory potential of CD4+ Trm cells and, accordingly, these cells preferentially localized within inflammatory lesions. Finally, depletion of both the recirculating and the CNS-resident CD4+ T cell compartments was required to alleviate neurological signs during the chronic phase of EAE. Our results indicate that CD4+ Trm cells contribute to maintain a chronic inflammatory state in the CNS, promoting damage and/or preventing repair, and suggest that new therapeutic strategies for the treatment of PMS should consider targeting the CNS-resident T cell compartment.

overall_design: We carried out a  5'scRNAseq coupled with TCR VDJ sequencing to uncover the transcriptome and the TCR repertoire of conventional CD4+ T cells purified from the brain and the spleen of mice during the chronic phase of EAE (day 60).

first: Aurora

last: Pignata

first: David

last: Frieser

first: Carmen

last: Gonzalez-Fierro

first: Cheng-Chih

last: Hsiao

first: Hendrik

last: Engelenburg

first: Marine

last: Alis

first: Vincent

last: Cazaentre

first: Lucie

last: Nozeran

first: Romain

last: Miranda-Capet

first: Eloise

last: Dufourd

first: Thaïs

last: Vermeulen

first: Amel

last: Aïda

first: Carole

last: Le Coz

first: Klaas

last: Van Gisbergen

first: Nicolas

last: Blanchard

first: Jörg

last: Hamann

first: Joost

last: Smolders

first: Roland

middle: S

last: Liblau

first: Frederick

last: Masson


title: Cannabis and female fertility: an extensive in vitro and clinical investigation

city: Toronto

first: Brandon

last: Wyse

state: ON

address: 790 Bay St

country: Canada

institute: CReATe Fertility Centre

summary: Cannabis consumption and legalization is increasing globally, raising concerns about its impact on fertility. In humans, we previously demonstrated that tetrahydrocannabinol (THC) and its metabolites reach the ovarian follicle. An extensive body of literature describes THC’s impact on sperm, however no such studies have determined its effects on the oocyte. Herein, we investigate the impact of THC on human female fertility through both a clinical and in vitro analysis. We show that follicular fluid THC concentration is positively correlated with oocyte maturation and in vitro, we observe a similar but non-significant increase following THC exposure. In vitro, we report altered expression of key genes implicated in extracellular matrix remodeling, inflammation, and chromosome segregation. Furthermore, THC induces oocyte chromosome segregation errors and increases abnormal spindle morphology. Finally, THC-positive patients exhibit significantly lower embryo euploid rates than matched controls. This study highlights potential reproductive risks associated with cannabis use in females.

overall_design:
Single-oocyte RNAseq of human immature oocytes (GV) that have matured in vitro (MII) following 24h culture with/without THC.

***************************************************************
Raw FASTQ files are not included in this GEO submission due to ethical restrictions and participant privacy concerns associated with human oocyte-derived RNA-seq data.
***************************************************************

first: Cyntia

last: Duval

middle: A

first: Noga

last: Fuchs Weizman

first: Iryna

last: Kuznyetsova

first: Svetlana

last: Madjunkova

first: Clifford

last: Librach


title: Proteostatic Stress Response Drives T Cell Exhaustion and Immune Evasion

first: Weidong

last: Wu

address: 2255 Kenny Rd

institute: Ohio State University

summary: Chronic infections and cancer cause T cell dysfunction known as exhaustion due to persistent antigen exposure, suboptimal co-stimulation and a plethora of hostile factors, which dampens protective immunity and limits the efficacy of immunotherapies1-4. The mechanisms behind T cell exhaustion remain poorly understood. Herein, we dissected the proteome of CD8+ exhausted T cells (Tex) across multiple states of exhaustion in the context of both chronic viral infections and cancer. We found that there was a non-stochastic pathway-specific discordance between mRNA and protein dynamics in T effector (Teff) versus Tex cells. We identified a unique proteostatic stress response (PSR) in Tex cells which we termed TexPSR. Contrary to canonical stress responses with reduced protein synthesis5,6, the TexPSR involves increased global translation activity and an upregulation of specialized chaperones, characterized further by the accumulation of protein aggregates, stress granules and autophagy-dominant protein catabolism. We established that disruption of proteostasis alone can convert Teff to Tex cells, and linked TexPSR mechanistically to persistent Akt signaling. Finally, we found that disruption of TexPSR-associated chaperones in CD8+ T cells improved cancer immunotherapy preclinically and demonstrated that high TexPSR feature in T cells in cancer patients confers poor response to immunotherapy clinically. Our findings collectively highlight TexPSR as a hallmark and a mechanistic driver of T cell exhaustion, raising the possibility of targeting proteostasis as a potential novel approach for cancer immunotherapy.

overall_design: Mouse splenic CD8+ T cells were isolated and induced into exhausted T cells (Tex) through chronic TCR stimulation by 8 days. Effector T cells (Teff) were generated through acute TCR stimulation. Tex and Teff cell were collected and subject to parallel proteomics and bulk RNA-seq analysis.

first: Yi

last: Wang

first: Anjun

last: Ma

first: Zihai

last: Li


title: A nanopore long-read transcriptome in pancreatic cancer cells

city: shanghai

first: shengnan

last: luo

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

summary: This project aims to leverage Oxford Nanopore Technologies (ONT) long-read RNA sequencing to achieve a comprehensive analysis of the human pancreatic cancer transcriptome. Traditional short-read sequencing methods often struggle with accurately reconstructing full-length transcripts and discerning complex splicing events due to their limited read lengths. In contrast, ONT's long-read sequencing can generate reads that span entire RNA molecules, facilitating precise identification of transcript isoforms, alternative splicing patterns, and poly(A) tail length. By applying this technology, we seek to enhance the annotation of the pancreatic cancer transcriptome, uncover novel transcripts, and gain deeper insights into gene expression dynamics. The findings from this study have the potential to advance our understanding of gene regulation and contribute to the development of novel therapeutic strategies.

overall_design: This project employs Oxford Nanopore Technologies (ONT) long-read RNA sequencing to achieve a comprehensive analysis of the human pancreatic cancer transcriptome. Ten pancreatic cancer cell lines are collected, two replicates for each, were used for ONT long-read RNA sequencing. Transcript expression patterns, alternative splicing, poly(A) tail length, and integration with proteomics were performed across pancreatic cancer cells.

first: Shengli

first: Shengnan

last: Luo


title: Single cell transcriptomic of ex vivo-generated lymphoid progenitors from mobilised peripheral blood- or corb blood-derived hematopoietic stem and progenitors cells

city: Milan

first: Monah

last: Abou Alezz

address: Via Olgettina 60

institute: SR-TIGET

summary: We previously established a feeder-free cell therapy platform for the ex vivo generation of lymphoid-primed progenitors using immobilized Delta-like ligand 4 (DLL4), and hereafter known as ProTcell. We demonstrated these progenitors can be generated from hematopoietic stem and progenitors cells originating from cord blood (CB) and mobilized peripheral blood (mPB). In vivo studies demonstrated that adoptive transfer of these progenitors accelerates T cell reconstitution following thymic engraftment (Moirangthem RD et al., 2021 ; Simons L et al., 2018 ; Reimann et al., 2012). To further explore the full therapeutic potential of this cell product, we performed a comprehensive characterization using single-cell RNA sequencing. We confirmed ProTcell samples derived from CB and mPB were highly similar,as they clustered together. Our analysis also revealed the presence of distinct cell subsets within the cellular product characterized mainly by their commitment to lymphoid lineages. We highlighted strong similarities with early stages of T cell development, underscoring the physiological relevance of our system.

overall_design: ProTcell were produced as previously described (Moirangthem RD et al., 2021). 6 batches of ProTcell were generated, 3 from CB and 3 from mPB, and analyzed by single cell RNA sequecing.

first: Pierre

last: Gaudeaux

first: Juliette

last: Paillet

first: Marieke

last: Lavaert

first: Noémie

last: Robil

last: de La Grange

first: Tom

last: Taghon

first: Andrea

last: Ditadi

first: Isabelle

last: André

first: Shabi

last: Soheili


title: Modularity of OCT4 underlies its functional diversity in reprogramming and embryonic development  (mES ChIP-seq)

city: Edinburgh

first: Abdenour

last: Soufi

address: 5 Little France Drive

department: School of Biological Sciences

institute: University of Edinburgh

summary: Amongst the multiple cell fates orchestrated by OCT4, its ability to maintain pluripotency is thought to underpin reprogramming. How OCT4 drives pluripotency from diverse cellular contexts is unclear. By systematically dissecting OCT4, we find that reprogramming requires OCT4 domains dispensable for pluripotency maintenance and development throughout gastrulation but important for the embryo competence to develop through late gestation.  Removing OCT4 essential domains in reprogramming leads to more non-specific OCT4 enrichment at accessible somatic sites, unlike removing the non-essential domains, which expands genomic targeting of closed pluripotency sites. Delineating the interaction of OCT4 with chromatin-associated proteins in reprogramming and pluripotency maintenance reveals that OCT4 essential domains engage a unique set of proteins during reprogramming. Remarkably, OCT4 can induce pluripotent and trophoblast stem cells using many similar domains and yet it can be truncated to only induce pluripotency. Our findings demonstrate that the ability of transcription factors to control diverse cell types is encoded within their modular nature.

overall_design: ChIP-seq of OCT4 in mouse embryonic stem cells (mESCs), containing the knockin mutation Pou5F1lin-del in three independent clonal lines (CL1, CL3, and CL7) compared to wildtype (WT).


title: Nrm1 is a bistable switch connecting cell cycle progression to transcriptional control

city: Barcelona

first: Montserrat

last: Vega

state: Barcelona

address: C/ Dr. Aiguader 88, lab 383

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra

summary: Entry into the cell cycle requires activation of G1 cyclin-dependent kinases (CDKs) and the initiation of the G1/S transcriptional program. Unregulated transcription of this gene expression program can lead to genomic instability and aneuploidy. In fission yeast, the MBF complex is the key transcription factor that drives early cell-cycle gene expression. MBF-dependent transcription is triggered in metaphase and is suppressed at the end of S phase by a robust feedback mechanism involving the cyclin Cig2 and the co-repressors Nrm1 and Yox1. Under replicative stress, Yox1 is phosphorylated to release its repressive activity; however, the precise mechanism activating MBF in an unperturbed cell cycle remains unclear. Here, we identify Nrm1 as the primary target of the cell cycle machinery in regulating MBF activity through a two-step control mechanism. We demonstrate that CDK1-mediated phosphorylation of Nrm1 initiates its release, along with Yox1, from chromatin in metaphase. This mechanism overlaps with the irreversible degradation of unphosphorylated Nrm1 (which originates from de novo synthesis or by dephosphorylation of pre-existing Nrm1 during anaphase), preventing its re-association with MBF until the end of the following S phase. These parallel mechanisms, which sense cell cycle status, create a regulated window in which MBF-dependent transcription is relieved from repression, supporting orderly cell cycle progression.

overall_design: Study the role of nrm1 phosphorylation in cell cycle transcription

first: Guillem

last: Murciano-Julià

first: Esther

last: Pazo

first: Isabel

last: Alves-Rodriguez

first: Oriol

last: Bagudanch

first: Roger

last: Anglada

first: Nuria

last: Bonet

first: Sergio

last: Moreno

first: Baldo

last: Oliva

first: Elena

last: Hidalgo

first: Jose

last: Ayté


title: Tumor immune microenvironment-associated prognostic and mifamurtide-response gene signatures for localized osteosarcoma: a correlative study of the ISG/OS2 trial

city: Bologna

first: Emanuela

last: Palmerini

address: via G.C.Pupilli, 1

institute: IRCCS Istituto Ortopedico Rizzoli

summary: A risk-adapted treatment strategy, the ISG/OS-2 trial, evaluated the use of mifamurtide in P-glycoprotein (Pgp)-positive localized osteosarcoma patients. Primary objective was the identification of tumor immune microenvironment (TME) prognostic classifiers in all patients and in those undergoing mifamurtide. RNA from pre-treatment FFPE non-decalcified tissues of 62 patients was analyzed with the PanCancer Immune profiling panel.Thirty three out of sixty-two (53%) Pgp-positive patients underwent chemotherapy (CT) + mifamurtide, 29/62 (47%) Pgp-negative patients received CT alone. Univariate Cox regression, ROC curve and CIBERSORTx algorithm gene deconvolution analyses were performed. A 21-gene signature able to stratify all patients into high-(Hi-R) and low-risk (Lo-R) was identified. TME of Lo-R vs Hi-R, was significantly enriched in T-regs, CD8 T-cells and NK activated cells, and diminished in CD4 T-cells. The 21-gene signature was validated in two independent sets. For patients treated with CT+mifamurtide a 31-gene mifamurtide-related signature able to distinguish Hi-R and Lo-R in terms of OS and EFS  was also identified. In conclusions a validated osteosarcoma TME prognostic gene signature has been identified, regardless of mifamurtide treatment. Importantly, a mifamurtide-related signature was also developed. Tumor-immune interactions possibly implicated in disease progression and treatment response were shown.

overall_design: This is a retrospective, translational study on 62 patients with high-grade osteosarcoma. Inclusion criteria were a diagnosis of localized primary high-grade osteosarcoma included in the ISG-OS2 trial and treated with chemotherapy or chemotherapy and adjuvant mifamurtide. Among these, 33/62 patients (53%) were Pgp-positive and received chemotherapy plus adjuvant mifamurtide, while the 29/62 (47%) Pgp-negative patients underwent chemotherapy alone.

first: Maria Rosaria

last: Sapienza

first: Stefano A

last: Pileri

first: Giorgio

last: Frega

first: Alberto

last: Righi

first: Antonina

last: Parafioriti

first: Alessandro

last: Franchi

first: Claudio

last: Agostinelli

first: Simona

first: Cristina

last: Meazza

first: Virginia

last: Ferraresi

first: Sebastian Dorin

last: Asaftei

first: Luca

last: Coccoli

first: Angela

last: Tamburini

first: Marco

last: Gambarotti

first: Massimo

last: Serra

first: Davide Maria

last: Donati

first: Franca

last: Fagioli

first: Marilena

last: Cesari

first: Elisa

last: Carretta

first: Katia

last: Scotlandi

first: Toni

last: Ibrahim

first: Maria Antonella

last: Laginestra


title: An annotated biobank of triple negative breast cancer patient-derived xenografts featuring treatment-naïve and longitudinal samples throughout neoadjuvant chemotherapy

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: Triple negative breast cancer (TNBC) that fails to respond to neoadjuvant chemotherapy (NACT) can be lethal. Developing effective strategies to eradicate chemoresistant disease requires experimental models that recapitulate the heterogeneity characteristic of TNBC. To that end, we established a biobank of 92 orthotopic patient-derived xenograft (PDX) models of TNBC from the tumors of 75 patients enrolled in the ARTEMIS clinical trial (NCT02276443) at MD Anderson Cancer Center, including 12 longitudinal sets generated from serial patient biopsies collected throughout NACT and from metastatic disease. Models were established from both chemosensitive and chemoresistant tumors and nearly 30% of PDX models were capable of lung metastasis. Comprehensive molecular profiling demonstrated conservation of genomes and transcriptomes between patient and corresponding PDX tumors, with representation of all major transcriptional subtypes.  Transcriptional changes observed in the longitudinal PDX models highlight dysregulation in pathways associated with DNA integrity, extracellular matrix interactions, the ubiquitin-proteasome system, epigenetics, and inflammatory signaling. These alterations reveal a complex network of adaptations associated with chemoresistance. This PDX biobank provides a valuable resource for tackling the most pressing issues facing the clinical management of TNBC, namely chemoresistance and metastasis.

overall_design:
We collected 92 tumors from 75 patients with triple-negative breast cancer, including longitudinal sets throughout NACT and from metastatic disease.  We engrafted those tumors into mice and profiled them by whole exome sequencing and RNA-Seq.

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

first: Amanda

last: Rinkenbaugh

first: Yuan

last: Qi

first: Shirong

last: Cai

first: Jiansu

last: Shao

first: Faiza

last: Hancock

first: Sabrina

last: Jeter-Jones

first: Xiaomei

last: Zhang

first: Emily

last: Powell

first: Lei

last: Huo

first: Rosanna

last: Lau

first: Chunxiao

last: Fu

first: Rebekah

last: Gould

first: Petra

last: den Hollander

first: Elizabeth

middle: E

last: Ravenberg

first: Jason

middle: B

last: White

first: Gaiane

last: Rauch

first: Banu

last: Arun

first: Clinton

last: Yam

first: Alastair

last: Thompson

first: Gloria

middle: V

last: Echeverria

first: Stacy

last: Moulder

first: William

middle: F

last: Symmans

first: Helen

last: Piwnica-Worms


title: Brain-infiltrating ILC2s-derived alpha-calcitonin gene-related peptide promoting angiogenic sprouting accelerates post-stroke angiogenesis

first: An

last: Ping

summary: Group 2 innate lymphoid cells (ILC2s) are key players in immune regulation and tissue repair in barrier immunity, but they are rarely seen in the brain. Since ILC2s can be intrinsically expanded by IL2/IL2 antibody complex, we investigated the transcriptomic changes induced by IL2/IL2 antibody complex (IL2-JES6-1) after ischemic stroke, we performed single-cell RNA sequencing of the CD45high immune cells from the infarcted hemisphere at day 14 after MCAO using 10x Genomics scRNAseq. To investigate the key mechanism of ILC2s-mediated long-term recovery after ischemic stroke, we performed single-cell RNA sequencing of the infarcted hemisphere at day 14 after MCAO using 10x Genomics scRNAseq.

overall_design: Single-cell RNA profiling of brain CD45high immune cells (treated with IL2/IL2Ab complex or PBS) or whole brain cells in MCAO mice (treated with ILC2s or PBS) a 14 dpi.

first: Fan

last: Yang

first: Lingxiao

last: Lu

first: Xiaotao

last: Zhang

first: Jianan

first: Huaming

last: Li

first: Yichen

last: Gu

first: Ziyang

last: Jin

first: Jianmin

first: Ligen

last: Shi


title: Defining Relationships Among Tests for Kidney Transplant Antibody-Mediated Rejection

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

institute: University of Alberta

summary: Effective therapies for kidney transplant antibody-mediated rejection (ABMR) (Mayer et al, 2024) will require accurate diagnoses plus assessment of ABMR activity, and the new tests that were used to show treatment effects in the clinical trial such as donor-derived cell-free DNA (dd-cfDNA) and molecular biopsy analysis (MMDx) could be useful. ). In a partial correlation network, all four tests were correlated, in a hierarchy of inter-test correlations: MMDx ABMR > dd-cfDNA > histology ABMR > and DSA. Surprisingly, DSA correlated at least as strongly with MMDx ABMR as with histologic ABMR, even though DSA is not used in MMDx. When expressed in the same six rejection classes, MMDx diagnosed ABMR more frequently than histology. When histology disagreed with MMDx ABMR, dd-cfDNA, and DSA correlated more strongly with MMDx assessment. However, histology also detected ABMR lesions in some cases that MMDx called no rejection, correlating with subthreshold molecular ABMR activity and dd-cfDNA and DSA (AJT 25:72-87, 2024). Thus, the four-way inter-test correlations extend below current thresholds for diagnosing ABMR. Molecular rejection predicted outcomes better than histologic rejection in Trifecta, confirmed in the earlier INTERCOMEX study. These results map a network of four ABMR-related tests that can add precision to ABMR assessment in trials and clinical management and highlight the need to establish the clinical significance of subthreshold ABMR activity.

overall_design: Trifecta-Kidney (ClinicalTrials.gov #NCT04239703) studied 717 indication biopsies to define the relationships among four tests used for ABMR: standard-of-care local histologic biopsy ABMR diagnosis, MMDx ABMR diagnosis, dd-cfDNA, and donor-specific antibody (DSA).


title: p53 maintains lineage fidelity during lung capillary injury-repair in neonatal hyperoxia

city: Chicago

first: Lisandra

last: Vila Ellis

state: IL

address: 303 E Superior

department: Cell and Developmental Biology

institute: Northwestern University

summary: Bronchopulmonary dysplasia (BPD), a prevalent and chronic lung disease affecting premature newborns, results in vascular rarefaction and alveolar simplification. Although the vasculature has been recognized as a main player in this disease, the recently found capillary heterogeneity and cellular dynamics of endothelial subpopulations in BPD remain unclear. Here, we show Cap2 cells are damaged during neonatal hyperoxic injury, leading to their replacement by Cap1 cells which, in turn, significantly decline. Single cell RNA-seq identifies the activation of numerous p53 target genes in endothelial cells (ECs), including Cdkn1a (p21). While global deletion of p53 results in worsened vasculature, endothelial-specific deletion of p53 reverses the vascular phenotype and improves alveolar simplification during hyperoxia. This recovery is associated with the emergence of a transitional EC state, enriched for oxidative stress response genes and growth factors. Notably, this transitional EC gene signature is conserved in an aberrant capillary population identified in human BPD with pulmonary hypertension, underscoring the biological and clinical relevance of our findings. These results reveal a key role for p53 in maintaining endothelial lineage fidelity during pulmonary capillary repair following hyperoxic injury and highlight the critical contribution of the endothelium to BPD pathogenesis.

overall_design: FACS purified cells from p53 null, p53 endothelial mutant, and littermate control were profiled at the indicated time

first: Jonathan

last: Bywaters

first: Jichao

last: Chen


title: ALKBH1-mediated tRNA 5-formylcytidine modification facilitates codon-biased translation and leukemogenesis [RNA-seq]

city: Monrovia

first: Jianjun

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: Here, we show that ALKBH1 is overexpressed in acute myeloid leukemia (AML) and required for AML development/maintenance and leukemia stem cell (LSC) self-renewal, but is dispensable for normal hematopoiesis. ALKBH1 plays a pivotal role in regulating mitochondrion structure/functions and facilitating oxidative phosphorylation (OXPHOS) to generate energy for AML cell survival/proliferation. Mechanistically, we uncover that ALKBH1 specifically promotes 5-formylcytidine (f5C) formation in tRNAs to expand tRNA decoding capacity and promote translation of essential targets. This mechanism/phenomenon is termed “epitranscriptomic Midas touch”, which promotes expression of WDR43 and BCL2, two crucial targets of ALKBH1 in AML. ALKBH1 targeting markedly enhances BCL2 inhibitor (Venetoclax)’s efficacy in AML treatment. Collectively, our studies reveal the functional importance of a previously unappreciated signaling (i.e., ALKBH1/tRNA-f5C/WDR43/BCL2) in AML, and highlight the potential of targeting ALKBH1 for cancer therapy.

overall_design: ALKBH1 KD was induced after 4 days treatment with doxycycline (1 ug/ml), then contrl and ALKBH1 KD cells were treated with DMSO or 100 nM Venetoclax for 48h. Cells were then collected  for total RNA. PolyA-mRNA was further isolated for library preparation and sequencing

first: Chao

last: Shen

first: Keren

last: Zhou

first: Xiaolan

last: Deng


title: Effect of endothelial cell-specific TET2 knockout on mouse lung endothelial cell transcriptome of chow-fed and high fat diet-fed mice

city: London

first: Hannah

middle: Louise Hoskins

last: Green

address: 125 Coldharbour Lane

institute: King's College London

summary: RNA sequencing of mouse lung endothelial cells from male wildtype (TET2fl/fl Cre negative, tamoxifen-injected) or endothelial-specific TET2 knockout mice (TET2fl/fl, Cdh5-CreERT2 positive, tamoxifen-injected) fed either a standard chow diet or a high fat diet for 20 weeks.

overall_design: Mouse lung endothelial cell RNA from 4 groups (3 biological replicates per group): WT_CHOW (TET2fl/fl Cre negative, tamoxifen-injected chow-fed mice), WT_HFD (TET2fl/fl Cre negative, tamoxifen-injected high fat diet-fed mice), KO_CHOW (TET2fl/fl, Cdh5-CreERT2 positive, tamoxifen-injected chow-fed mice), KO_HFD (TET2fl/fl Cdh5-CreERT2 positive, tamoxifen-injected high fat diet-fed mice)

middle: L

first: Alison

middle: C

last: Brewer


title: The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis.

city: Shanghai

first: Jincan

last: He

address: siping road 1239

institute: Tongji university

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

overall_design: Refer to individual Series


title: 5hmC enrichment in HUVEC following treatment with interferon gamma or high glucose

type: Methylation profiling by high throughput sequencing

summary: Hydroxymethylated DNA immunoprecipitation sequencing of HUVEC following treatment with high glucose (25mM) compared to normal glucose (5mM) + mannitol (20mM), or following interferon gamma treatment compared to untreated controls

overall_design: Genomic DNA was isolated from single samples of HUVEC untreated or treated with 25mM glucose or 5mM glucose + 20mM mannitol for 2 weeks, or HUVEC treated with IFNg for 24h. Samples were immunoprecipitated with an anti-5-hydroxymethylcytosine antibody. An input sample (non-immunoprecipitated) from the untreated HUVEC is also included.


title: Limited response of primary nasal epithelial cells to Bordetella pertussis infection [RNAseq_Sort_population]

status: Public on Jul 22 2025

city: Prague

first: Martin

last: Zmuda

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Microbiology of the Czech Academy of Sciences

summary: Bordetella pertussis is a Gram-negative coccobacillus that causes whooping cough or pertussis, a respiratory disease that has recently experienced a resurgence. Upon entering the respiratory tract, B. pertussis colonizes the airway epithelium and attaches to ciliated cells. Here, we used primary human nasal epithelial cells (hNECs) cultured at the air-liquid interface, and investigated their transcriptomic response after infection with the B. pertussis B1917. We also analyzed role of the type III secretion system effector protein BteA in modulating this response.

overall_design: In order to confirm identitty and differentiation of primary human nasal epithelial cells (hNECs) cultured at air-liquid interface, the cells were stained with antibodies against CD271(NGFR) and CD66c (CEACAM6), and Tubulin tracker (Tub). Following the gating of single cells, the cells were sorted into subpopulations, which was followed by transcriptomic profiling. The transcriptomic profiling was performed on hNECs originating from two different donors.

first: Ivana

last: Malcova

first: Barbara

last: Pravdova

first: Ondrej

last: Cerny

first: Denisa

last: Vondrova

first: Jana

last: Kamanova


title: Tissue-resident memory CD4+ T cells sustain chronic CNS autoimmunity

first: Ilan

last: Fijalkow

summary: Therapeutic options against multiple sclerosis (MS) preventing T cell migration to the central nervous system (CNS) have remarkable clinical effects against the relapsing-remitting (RRMS) form of the disease, while they are poorly effective against its progressive form (PMS). Disability progression in PMS is thought to result from an interplay between smoldering local inflammation and neurodegeneration. The mechanisms sustaining the chronicity of PMS are poorly understood. Here, we investigated the role of tissue-resident memory CD4+ T (CD4+ Trm) cells in sustaining a chronic autoimmune process in the CNS. Our results revealed the presence of bona fide CD4+ Trm cells expressing CD69, CXCR6, P2RX7, CD49a and the transcription factor Hobit in the CNS of mice with chronic experimental autoimmune encephalomyelitis (EAE) and in the brain of patients with PMS. Single-cell transcriptomic analysis uncovered the transcriptional heterogeneity and inflammatory potential of CD4+ Trm cells and, accordingly, these cells preferentially localized within inflammatory lesions. Finally, depletion of both the recirculating and the CNS-resident CD4+ T cell compartments was required to alleviate neurological signs during the chronic phase of EAE. Our results indicate that CD4+ Trm cells contribute to maintain a chronic inflammatory state in the CNS, promoting damage and/or preventing repair, and suggest that new therapeutic strategies for the treatment of PMS should consider targeting the CNS-resident T cell compartment.

overall_design: A CITE-seq  analysis  was performed on conventional CD4+ T cells isolated from the brain and spinal cord of mice during both the acute (day 14)  and the chronic phase (day 50) of experimental autoimmune encephalomyelitis (EAE).

first: Aurora

last: Pignata

first: David

last: Frieser

first: Carmen

last: Gonzalez-Fierro

first: Cheng-Chih

last: Hsiao

first: Hendrik

last: Engelenburg

first: Marine

last: Alis

first: Vincent

last: Cazaentre

first: Lucie

last: Nozeran

first: Romain

last: Miranda-Capet

first: Eloise

last: Dufourd

first: Thaïs

last: Vermeulen

first: Amel

last: Aïda

first: Carole

last: Le Coz

first: Klaas

last: Van Gisbergen

first: Nicolas

last: Blanchard

first: Jörg

last: Hamann

first: Joost

last: Smolders

first: Roland

last: Liblau

first: Frederick

last: Masson


title: Single Cell Sequencing of Mouse Embryo at Early and Mid Gestation

first: Meghan

last: Riddell

state: AB

summary: Maternal adaptations are necessary for pregnancy and proper nurturing of a developing embryo. Murine embryogenesis and pregnancy are intensely studied processes, but historically this knowledge has been acquired by analyzing the role of a single molecule at a time. Single cell RNA-sequencing allows for a snapshot of the of cell states for multiple cell populations that can be compared to understand time-dependent pregnancy adaptations, and the dynamic cellular composition of murine embryogenesis during gestation. Here we present scRNA-seq analyses on murine implantation sites at gestational day (GD) 6.5 and 10.5 and examine the temporal changes that occur from early to mid-gestation. These analyses were conducted on C57/bl6J mice to serve as a resource to the community. We have also made an interactive webpage with these datasets, providing way for anyone to further explore genes and cell types of interest without the need for coding skills. The interactive datasets can be found at (link)

overall_design: Uteri from pregnant dams were dissected at GD 6.5 and 10.5 and the gestational sacs were separated. For GD 10.5, the fetus and the placenta were removed. For the GD 6.5 samples, two different gestational sac from two different mice were used. For GD 10.5, two different gestational sac from one dam were used, and the tissues were analyzed using scRNA-seq

first: Juan

last: Garcia Rivas

first: Wendy

last: Duan

first: Bethan

last: Wilson


title: HSF2 drives breast cancer progression by acting as a stage-specific switch between proliferation and invasion

city: Turku

first: Lea

last: Sistonen

address: Tykistökatu 6 A

department: Cell Biology

country: Finland

institute: Åbo Akademi University

summary: Breast cancer is hallmarked by phenotypic transitions enabling abnormal cell proliferation and invasion. The stress-protective transcription factor heat shock factor 2 (HSF2) is associated with cancer, but its function in breast carcinogenesis remains poorly understood. Analysis of human breast tumor samples and mouse in vivo xenografts uncovered that HSF2 expression and activity undergo dynamic changes as a function of tumor progression. HSF2 expression, nuclear localization, and co-expression with the proliferation marker Ki67 are increased in ductal carcinoma in situ (DCIS), suggesting that HSF2 designates hyperplastic cells underlying tumor expansion. In mouse xenografts, HSF2 localization switches from nuclear to cytoplasmic upon DCIS-to-invasive transition. Using cell-based models, we identify canonical TGF-β signaling as the molecular mechanism regulating HSF2. TGF-β-mediated downregulation of HSF2 allowed acquisition of an invasive cell phenotype, which was counteracted by ectopic HSF2. Altogether, we propose that HSF2 acts as a stage-specific switch between proliferation and invasion in breast cancer.

overall_design: HS578T cells transfected with plasmids encoding GFP (Mock) and exogenous HSF2 (HSF2oe), treatments: 24 h control and 10 ng/ml TGF-beta 1 (240-B-002, R&D Systems), 2 biological replicates

first: Jenny

last: Pessa

first: Oona

last: Paavolainen

first: Hendrik

last: Hästbacka

first: Mikael

last: Puustinen

first: Alejandro

last: Da Silva

first: Sandra

last: Pihlström

first: Silvia

last: Gramolelli

first: Pia

last: Boström

first: Pauliina

last: Hartiala

first: Emilia

last: Peuhu

last: Joutsen


title: Structure of gut microbial glycolipid modulates host inflammatory response

city: Boston

first: Hyoung-Soo

last: Cho

state: Massachusetts

address: 77 Avenue Louis Pasteur, NRB 1058

department: Immunology

institute: Harvard Medical School

summary: Commensals are constantly shaping the host’s immunological landscape. Lipopolysaccharide (LPS) found in gram-negative microbes have a terminal lipid A in their outer membrane. Here, we report that structural variations in symbiotic lipid A lead to divergent immune responses between the symbiont’s various lipid A structures, each distinct from the responses elicited by classical lipid A. Certain lipid A structures can induce a sustained IFN-β response orchestrated by Cdc42-facilitated TLR4 endocytosis and lipid droplet formation. This lipid A-directed IFN-β response is paramount for colon RORγt+ Treg induction while simultaneously suppressing colonic TH17 and controlling gut inflammation. Intriguingly, the quantitatively dominant penta-acylated lipid A species in Bacteroidetes fails to elicit IFN-β response. Instead, a less abundant tetra-acylated lipid A species sustainably induces IFN-β, thereby contributing to RORγt+ Treg homeostasis. These structural nuances in symbiotic lipid A contribute to maintaining potent regulation of Treg to maintain a healthy endobiotic balance.

overall_design: RNA-Seq data obtained from the mouse bone marrow-derived dendritic cells (mBMDCs) treated with structurally variable synthetic lipid A analogs (3A-MPLA, 4A-MPLA, 5A-MPLA, and 6A-DPLA) for 24 h

first: Ji-Sun

last: Yoo

first: Xinyang

last: Song

first: Byoungsook

last: Goh

first: Alos

last: Diallo

first: Jesang

last: Lee

first: Sumin

last: Son

first: Yoon Soo

last: Hwang

first: Seung Bum

last: Park

first: Sungwhan

last: Oh

first: Dennis

last: Kasper


title: The Role of the Microenvironment on the Localization of Hair and Skin Nonuniform Pigmented Spots in Mice with a Targeted Mutation in the Endothelin B Receptor

city: wenzhou

first: yu

last: chen

address: 270 West Xueyuan Road

institute: Wenzhou Medical University

summary: In mammals, severe mutations in genes encoding factors critical for developing melanocytes often lead to a total loss of melanin-dependent skin and hair pigmentation. However, even null mutations in the gene encoding the G protein-coupled Endothelin-3 receptor EDNRB are associated with locally restricted pigmented spots at the head and tail on an otherwise totally white coat. Here, we investigate the developmental mechanism of these nonuniform pigmented spots in Ednrb-deficient mice and show that the local microenvironment, particularly the presence of enriched KIT ligand (KITL), dictates the appearance of these spots during development. Using a variety of transcriptomic profiling analyses and genetic and biochemical manipulations both in vivo and in vitro, we show that in E11.5 Ednrb-deficient embryos, a high expression level of KITL surrounds melanoblasts in the caudal region but not in the trunk region. The genetic reduction of KITL/KIT signaling in Ednrb-deficient miceleads to a complete loss of these nonuniform pigmented spots in the head and caudal regions. Moreover, the intradermal injection of anti-KIT antibody in the head region of adult Ednrb-deficient mice significantly reduces hair pigmentation in the secondary hair cycle. Furthermore, the exogenous addition of KITL rescues Ednrb-deficient melanoblasts from the neural crest cells in the trunk region, likely by stimulating MITF expression. Hence, these findings underscore the significance of the microenvironment for the appearance and localization of pigment spots and highlight the role of KITL as a major determinant of this microenvironment.

overall_design: To investigate the developmental mechanism of these nonuniform pigmented spots in Ednrb-deficient mice and show that the local microenvironment,the E11.5 Ednrb+/+ and Ednrb-/-  embryonic trunk and caudal region were isolated. Total RNAs of the trunk or caudal region were extracted using TRIzol reagent (Invitrogen) .

first: Huirong

last: Li

first: Yu

last: Chen

first: Ling

last: Hou


title: Defective neutrophil-derived exosomes induce macrophage activation through miR-122-5p in Behçet’s Disease

city: Beijing

first: Wenjie

last: Zheng

address: No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN

institute: Peking Union Medical College Hospital

summary: Background Behçet’s disease (BD) is a life-threatening systemic vasculitis characterized by polymorphonuclear neutrophil (PMN) and macrophage activation. This study aimed to elucidate the potential dysregulation of BD PMN exosomes on macrophage activation. Methods BD PMN exosomes were isolated, quantified, incubated with macrophages, and analyzed by miRNA sequencing (n=4). RNA sequencing of miRNA-transfected macrophages (n=6) was analyzed using transcription factor co-regulation network and miRNA target prediction to identify key regulatory factors, which were validated by dual luciferase reporter assay and miRNA/siRNA transfection. Results BD PMN exosomes were decreased and negatively correlated with CRP. PMN exosomes suppressed IL-6, TNF-α, CD80 and CD86 expressions on macrophages, which were attenuated in BD PMN exosomes. miRNA sequencing showed decreased miR-122-5p in BD PMN exosomes, which targeted IRF5, suppressed TLR4 signaling and IFN-β autocrine, and downregulated macrophage activation. Conclusions BD PMN exosomes were decreased in both quantity and miR-122-5p, which impaired the immunoregulatory potential on macrophages through degrading IRF5 and suppressing IFN-β autocrine, indicating a new interaction mechanism between PMNs and macrophages.

overall_design: Transcriptional profiling of LPS-stimulated THP-1 macrophages with miR-122-5p or control miRNA transfection (n=6 for each group).

first: Hua

first: Xin

last: Yu

first: Chaoran


title: Cell Type Differences in Human Cytomegalovirus Transcription and Epigenetic Regulation with Insights into Major Immediate-Early Enhancer-Promoter Control [PRO-seq]

city: Iowa City

first: Jeffery

last: Meier

state: IA

address: SW34 GH, Department of Internal Medicine, University of Iowa. 200 Hawkins Drive

department: Departments of Internal Medicine and Epidemiology

institute: University of Iowa and Iowa City Veterans Affairs Health Care System

summary: Cell type differences in the human cytomegalovirus (HCMV) transcriptome may result from variations in transcription and/or post-transcription. Here we report unexpected differences in transcription and epigenetic control in late-stage HCMV infection of human differentiated NTera2 cells (D-NT2) compared to fibroblasts, using integrated functional genomic approaches (PRO-Seq, RNA-Seq, DFF ChIP-Seq, rapid viral protein degradation, and promoter mutation and function assays). In D-NT2, but not fibroblasts, RNA polymerase II initiation and elongation at several viral promoters requires viral DNA synthesis and are independent of host P-TEFb, viral IE2, or viral UL87 late transcription factor (LTF). This includes transcription from the enhancer for the major immediate early (MIE) promoter where GC-box sequence mutations increase transcription and mutations in CREB and NF-kB response elements decrease transcription. The GC-box sequence mutations also alter infected cell morphology and gene expression program, whereas mutations in CREB and NF-kB response elements do not. In D-NT2, LTF-driven promoters constitute a smaller proportion of the viral late promoter population and are generally less active. Additionally, viral genomes have more nucleosomes, potentially restricting LTF access. A TBP-IE2-nucleosome complex, with more nucleosome than in fibroblasts, covers the MIE promoter transcription start site, potentially contributing to epigenetically silence of the promoter.

overall_design: PRO-Seq library preparation to extract and sequence nascent RNAs is carefully detailed in the manuscript.

first: Qiaolin

last: Hu

first: Ming

first: Mrutyunjaya

last: Parida

first: Benjamin

middle: M

last: Spector

first: Juan

last: Santana

first: Arya

last: Zandvakili

first: David

last: Price


title: Limited response of primary nasal epithelial cells to Bordetella pertussis infection

first: Martin

last: Zmuda

overall_design: RNA-seq analysis was performed on primary human nasal epithelial cells (hNECs) cultured at air-liquid interface. The transcriptomic response of the cells was assessed following 24-hour infection with Bordetella pertussis B1917 wild type, a BteA deletion mutant, and a BteA-complemented strain, with three biological replicates per condition.

first: Ivana

last: Malcova

first: Barbora

last: Pravdova

first: Ondrej

last: Cerny

first: Denisa

last: Vondrova

first: Jana

last: Kamanova


title: Soluble Nucleoporin, sPOM121, promotes prostate cancer progression and immune evasion through direct promoter regulation at active transcriptional hubs [ChIP-seq]

city: Minneapolis

first: Shijia

last: Zhu

state: Minnesota

address: 1200 Washington Avenue S Suite #175

department: Department of Laboratory Medicine and Pathology

institute: University of Minnesota Medical School

summary: The role of nucleoplasmic residing nucleoporins (NUPs) in solid tumors, including prostate cancer, remain unknown. Here we uncover the clinical relevance and mechanistic role of the off-pore NUP soluble POM121 (sPOM121) as a critical transcriptional regulator enhancing lethal prostate cancer aggressiveness. Mechanistically we found that sPOM121, through its C-terminal domain associates with the chromatin remodeler SMARCA5 at nuclear condensates facilitating transcriptional activation at promoter sites. Indeed, sPOM121 through this mechanism regulates a discrete oncogenic gene network, including B-catenin, leading to tumor progression and immune evasion in prostate cancer. Notably, targeting the sPOM121-B-catenin axis in patient derived pre-clinical and syngeneic mouse models halts prostate cancer aggressiveness and enhances anti-tumor immunity. Together, our findings reveal previously unknown actionable transcriptional rewiring functions of the nucleoplasmic residing NUP, sPOM121, in solid tumors, promoting lethal prostate cancer.

overall_design: ChIP-sequencing experiments were conducted for sPOM121 and SMARC5 in 22Rv1 and DU145 cell lines with input DNA as control.

first: Josep

last: Domingo-Domenech

first: Veronica

last: Rodriguez-Bravo


title: Soluble Nucleoporin, sPOM121, promotes prostate cancer progression and immune evasion through direct promoter regulation at active transcriptional hubs [ATAC-seq]

overall_design: ATAC-sequencing experiments were conducted for sPOM121 knock-down and SMARC5 knock-down in 22Rv1 and DU145 cell lines with normal as controls.


title: Cell Type Differences in Human Cytomegalovirus Transcription and Epigenetic Regulation with Insights into Major Immediate-Early Enhancer-Promoter Control [DFF-ChIP]

first: Jeffery

overall_design: Nuclei from D-NT2 or HFF cells were rapidly isolated, either without crosslinking or with crosslinking using 1% paraformaldehyde for 10 minutes, followed by immediate quenching with 1.33 M Tris (pH 7.6). The isolated nuclei were then digested with DNA Fragmentation Factor (DFF) to primarily generate mono-nucleosomes. Chromatin was released from the nuclei through light sonication, and immunoprecipitations were performed on the released chromatin. Finally, the nuclei were prepared for DFF ChIP-Seq as detailed in the methods section.

last: Li


title: Human hepatoma Huh-7 cell culture models deficient in apolipoprotein B secretion

city: Mineola

first: M. Mahmood

last: Hussain

state: New York

address: 101 Mineola Blvd.

department: Foundations of Medicine

institute: NYU Grossman Long Island School of Medicine

summary: High plasma apolipoprotein B (apoB)-containing lipoproteins are both a biomarker and causal mediator of many metabolic diseases. Inhibition of apoB and MTP decreases plasma lipid levels but at a risk of lipid accumulation in tissues. Whole body knock out of MTP and APOB are embronically lethal. Therefore, we created a human hepatome cells line (Ako) deficient in APOB gene to understand the global consequences of APOB loss. APOB gene deletion significantly reduced apoB mRNA and protein levels in the Ako cells compared to control cells. These cells supported apoB48 secretion when transfected with apoB48 expression plasmids. These cells did not accumulate significant amounts of triglyceride. KEGG pathway analysis of RNA-Seq data showed a significant increase in DNA replication/repair pathway and complement/coagulation cascade in the Ako cells. The most downregulated pathways included the PI3k-Akt signaling and MAPK signaling pathways. Total proteome analysis of secretory proteins identifed Vitamin D binding protein as the most upregulated protein while apoB was the most dowregulated protein in these cells. Since both APOB and MTP are important part of the lipoprotein assmebly and secretion, we also perfrmed total transcriptome analysis for the MTP deficient Huh-7 (Mko-3) cells. We found differential expression of some the pathways in both Ako and Mko-3 cells such as DNA replication, base excision repair, steroid hormone biosynthesis and pathways reated to breast cancer. These cells may be useful in studying structure-function analysis of apoB peptides and to address the cellular consequences of disruptions in lipoprotein assembly and secretion. However; further detailed studies are needed to establish how apoB regulates these pathways

overall_design: To understand the global consequences of APOB loss, we generated a human hepatoma (Huh-7) cell culture model system deficient in apoB. ApoB deficient Huh-7 cells (Ako) were generated using the CRISPR/Cas9 system. Total RNA for transcriptomics and overnight conditioned media for proteomics was obtained from the Ako and Huh-7 cells (n=3). Statistical analysis was done using Student’s t-test while comparing two groups, p < 0.05 was considered significant

first: Swati

last: Valmiki

first: Sara

last: Rosario

first: Ashley

last: Mooring

first: Binu

last: Prakash

first: Atrayee

last: Chattopadhyay

first: Chandana

last: Prakashmurthy

first: Florencia

last: Schlamp

first: Abulaish

last: Ansari

first: José

middle: O

last: Alemán

first: Nathalie

last: Pamir


title: L-asparaginase monotherapy as an encouraging approach towards acute fulminant chronic active Epstein-Barr virus infection

city: Bunkyo

first: Miki

last: Ando

state: Tokyo

address: Hongo 2-1-1

department: Hematology

country: Japan

institute: Juntendo University

summary: Peripehral blood of a chronic active Epstein-Barr virus disease (CAEBV) patient was taken to examine the gene expression levels of CAEBV patients.

overall_design: We analyzed peripheral blood of a chronic active Epstein-Barr virus disease (CAEBV) patient to investigate the reason for the effectiveness of L-asparaginase in CAEBV patients.

first: Yoshiki

last: Furukawa

first: Jun


title: Early-life ketone body signaling promotes beige fat biogenesis through changes in histone acetylome and β-hydroxybutyrylome [ChIP-seq]

city: Taipei

first: Chung-Lin

last: Jiang

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

summary: Infants experience distinct ketogenesis during the preweaning period, but its physiological significance remains unclear. Here, we show that preweaning ketosis enhances beige fat biogenesis and improves metabolic health in adulthood. To elucidate the underlying mechanisms, we performed multi-omics analyses of inguinal white adipose tissue (iWAT) and its stromal vascular fraction (SVF). Bulk RNA-seq of iWAT was conducted in 8-week-old Hmgcs2 knockout (KO) and control mice housed at room temperature (23 °C) or exposed to cold (4 °C). To further examine the effects of elevated ketosis, we administered oral 1,3-butanediol (1,3BD) or water to pups from postnatal day 2 to 21, and analyzed the iWAT SVF using bulk RNA-seq, single-cell RNA-seq, and ChIP-seq targeting H3K9ac, H3K14ac, and H3K9bhb. These integrative analyses reveal how early-life ketosis programs adipose progenitors to promote beige adipocyte development.

overall_design: To investigate how both loss and enhancement of ketogenesis influence histone modifications in adipose progenitors, SVF was isolated from iWAT depots of P21 control, Hmgcs2 KO, and 1,3BD-supplemented (1,3BD) male mice and cultured overnight. Sonicated chromatin was immunoprecipitated with antibodies against H3K9ac, H3K14ac, and H3K9bhb and subjected to ChIP-seq.

first: Fu

last: Lin

first: Chung

first: Po

last: Yang


title: Systematic discovery of CRISPR-boosted CAR T cell immunotherapies

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: CAR T cell therapy has shown remarkable success in treating blood cancers, but CAR T cell dysfunction is a common cause of treatment failure. Here we present CELLFIE, a CRISPR screening platform for enhancing CAR T cells across multiple clinical objectives. We performed genome-wide screens in human primary CAR T cells with readouts capturing key aspects of T cell biology, including proliferation, target cell recognition, activation, apoptosis and fratricide, and exhaustion. Screening hits were prioritized using a new in vivo CROP-seq method in a xenograft model of human leukemia, establishing several gene knockouts that boost CAR T cell efficacy. Most notably, we discovered RHOG knockout as a potent and unexpected CAR T cell enhancer, both individually and together with FAS knockout, which was validated across multiple in vivo models, CAR designs, and patient-derived cells. Demonstrating the versatility of the CELLFIE platform, we also conducted combinatorial CRISPR screens to identify effective knockout pairs, and saturation base editing screens to characterize RHOG variants. In summary, we discovered, validated, and biologically characterized CRISPR-boosted CAR T cells that outperform standard CAR T cells in widely used benchmarks, establishing a foundational resource for optimizing cell-based immunotherapies.

overall_design:
RNA-seq samples for RHOG knockout and standard (safe harbor locus edited) human primary CAR T cells (CD4 and CD8 cells analyzed separately), stimulated with CD19-positive tumor cells and profiled over time in vitro.

***************************************************************
Raw data were not submitted due to privacy concerns (human donor samples).
***************************************************************

first: Paul

last: Datlinger

first: Eugenia

last: Pankevich

first: Cosmas

last: Arnold

first: Daria

last: Romanovskaia


title: Early-life ketone body signaling promotes beige fat biogenesis through changes in histone acetylome and β-hydroxybutyrylome [scRNA-seq]

overall_design: To profile the cellular heterogeneity of adipose progenitors, we performed single-cell RNA sequencing using the BD Rhapsody™ Single-Cell Analysis System. SVF was isolated from iWAT depots of P21 control, Hmgcs2 KO, and 1,3BD-supplemented (1,3BD) male mice as well as P56 control male mice. After overnight in vitro culture, RNA was extracted and subjected to scRNA-seq.

first: Pei

middle: H

last: Lai


title: Glutaminase as a metabolic target of choice to counter acquired resistance to Palbociclib by colorectal cancer cells

city: Barcelona

first: Míriam

last: Tarrado-Castellarnau

address: Av. Diagonal 643

institute: Universitat de Barcelona

summary: Therapeutic resistance in cancer results from genetic or epigenetic mechanisms that enable cell survival under drug pressure. While several resistance mechanisms to cyclin-dependent kinase inhibitors have been identified, acquired resistance is still a therapeutic challenge. Here, we have systematically analyzed metabolic reprogramming in colorectal cancer cells exposed to Palbociclib, a CDK4/6 inhibitor, or Telaglenestat, a glutaminase inhibitor. Through multiple approaches, we show that Palbociclib and Telaglenestat elicit complementary metabolic responses and are thus uniquely suited to counter the metabolic reprogramming induced by the reciprocal drug. As such, while Palbociclib induced reduced tumor growth in vivo, and Telaglenestat did not show a significant effect, the drug combination displayed a strong synergistic effect on tumor growth. Likewise, initial responses to Palbociclib were followed by signs of adaptation and resistance, which were prevented by combining Palbociclib with Telaglenestat. The combination of Palbociclib and Telaglenestat may effectively forestall acquired resistance to Palbociclib.

overall_design: We have quantified transcript abundance in residual tumors from a mouse xenograft model of HCT116 human colorectal cancer cells exposed to Palbociclib, a CDK4/6 inhibitor, or Telaglenestat, a glutaminase inhibitor. Gene expression was also profiled in two-dimensional monolayer cell cultures explanted from the residual tumors.

first: Carles

last: Foguet

first: Josep

last: Tarragó-Celada

first: Marc

last: Palobart

first: Claudia

last: Hernández-Carro

first: Jordi

last: Perarnau

first: Erika

last: Zodda

first: Ibrahim

last: Polat

first: Silvia

last: Marin

first: Alejandro

last: Suarez-Bonnet

first: Juan José

last: Lozano

first: Mariia

last: Yuneva

first: Timothy

last: Thomson

first: Marta

last: Cascante


title: Early adipose tissue wasting in a preclinicl model of human lung cancer cachexia

city: Burlington

first: Michael

last: Toth

state: VT

address: 149 Beaumont Avenue, HSRF 103

institute: University of Vermont College of Medicine

summary: Cancer cachexia (CC), a syndrome of skeletal muscle and adipose wasting, reduces responsiveness to therapies and increases mortality. There are no approved treatments for CC, which may relate to discordance between pre-clinical models and human CC. To address the need for clinically relevant models of lung CC, we generated inducible, lung epithelial cell specific KrasG12D/+ (G12D) mice. G12D mice develop CC over a protracted time course and phenocopy tissue and tumor, cellular, mutational, transcriptomic, and metabolic characteristics of human lung CC. G12D mice demonstrate early loss of adipose, a phenotype that was apparent across numerous models of CC and translates to patients with lung cancer. Tumor-released factors promote adipocyte lipolysis, a driver of adipose wasting in CC, and adipose wasting was inversely related to tumor burden. Thus, G12D mice model key features of human lung CC and highlight a role for early tumor metabolic reprogramming of adipose tissue in CC.

overall_design: White adipose tissues were excised and lung organoids isolated and cultured from the lungs of Scgb1a1-CreER-TM-KrasLSL-G12D/+ (G12D) or wild-type Scgb1a1-CreERTM mice 3 and 6 weeks after tamoxifen administration. Organoid and white adipose tissue RNA was isolated from G12D or WT mice and prepared and RNAseq profiling carried out.

first: Deena

last: Snoke

first: Jacob

last: Dearborn

first: Devdoot

last: Majumdar

first: David

last: Seward