title: Integrative single-cell analysis reveals malignant archetypes and proliferative hierarchies in multiple myeloma [Part 4 of 4: Illumina NovaSeq X; MARS_v2]

first: Ido

last: Amit

summary: Multiple myeloma (MM) is a plasma cell malignancy characterized by substantial genomic and biological heterogeneity, limiting disease classification and development of more targeted therapies. Here, we present a population-level single-cell atlas of MM and detailed clinical annotations from 342 patients representing MM disease and treatment continuum. Our analysis identifies five distinct malignant transcriptional archetypes (MM1–MM5), and a proliferative module variably expressed across archetypes. This proliferation signature emerges as a context-dependent program with independent prognostic value across archetypes. Combined archetype classification with proliferation scoring defines therapeutic resistance, genomic instability, and clinical outcomes. External validation using the CoMMpass cohort confirms the biological robustness and prognostic relevance of this stratification across platforms. Leveraging the resolution of our single-cell atlas, we applied a computational pipeline for therapeutic target discovery based on malignancy, cell-type specificity and tissue restriction. This approach highlights FCRL2 as a promising MM-specific therapeutic target, with selective expression in malignant plasma and B cells at both transcriptomic and protein levels. This integrative analysis provides a clinically actionable blueprint for patient-specific stratification and precision medicine in plasma cell malignancies.

overall_design: this submission includes single-cell RNA sequencing data from bone marrow aspirates collected from 322 multiple myeloma patients plus 20 healthy donors from hip surgery as controls. Samples represent patients with pre-myeloma stages (MGUS, SMM), newly diagnosed multiple myeloma (treatment-naive) and relapsed/refractory multiple myeloma with various prior treatment exposures, compared to normal bone marrow from healthy controls. Disease stage information is available for all samples, while additional clinical data including survival, FISH results, treatment response, and treatment history are available for subsets of samples. The study focuses on plasma cells, with tumor microenvironment cells captured but not analyzed in this dataset.

first: Mor

last: Zada

first: Anna

last: Kurilovich

first: Noam

last: Shapira

first: Shuang-Yin

last: Wang

first: Reut

last: Sharet-Eshed

first: Paulina

last: Chalan

first: Florian

last: Ingelfinger

first: Shlomit

last: Kfir-Erenfeld

last: Asherie

first: Chamutal

last: Gur

last: Gurevich-Shapiro

first: Iuliana

last: Vaxman

first: Rotem

last: Shalita

first: Maya

last: Ben Yehuda

first: Pascale

last: Zwicky

first: Michelle

last: von Locquenghien

first: Kfir

last: Mazuz

first: Eyal

last: David

first: Natan

last: Melamed

first: Irit

last: Avivi

first: Assaf

last: Weiner

first: Polina

last: Stepensky

first: Yael

last: Cohen


title: Transcriptomic Reprogramming of T Cells Underlies Rituximab Efficacy in Idiopathic Nephrotic Syndrome

status: Public on Jul 29 2026

city: Nagoya City

first: Yu

last: Watanabe

state: Aichi Pref

address: 65, Tsurumai Town, Showa Ward

department: Molecular Oncology

country: Japan

institute: Nagoya University

type: Expression profiling by high throughput sequencing

summary: Rituximab efficacy in patients with steroid-dependent idiopathic nephrotic syndrome is associated with distinct T cell metabolic profiles and transcriptional responses revealed by single-cell RNA-sequencing.

overall_design: This study investigated T cell transcriptomic responses to RTX therapy in six adult SD-MCD patients. Responders maintained steroid-free remission >6 months post-treatment; non-responders relapsed within 6 months or could not discontinue steroids. PBMCs were collected before and one month after RTX administration. scRNA-seq and TCR profiling were performed using 10x Genomics platform.

first: Eri

last: Koshi-Ito

first: Chikao

last: Onogi

first: Asuka

last: Horinouchi

first: Koichi

last: Ogami

first: Seiko

last: Yoshino

first: Shitaro

last: Komatsu

first: Akihito

last: Tanaka

first: Kazuhiro

last: Furuhashi

first: Shoichi

last: Maruyama

first: Hiroshi

middle: I

last: Suzuki


city: Toon

first: Yuko

last: Matsuoka

state: Ehime

address: Shitsukawa

department: Immunology

institute: Ehime university

summary: T-cell function is epigenetically regulated, however its precise role in tumor immunity is not fully understood. Ezh2 promotes transcriptional silencing through trimethylation of histone H3K27. We previously reported that the methylation level of histone H3K27 decreases in terminally differentiated and senescent T cells. In this study, we analyzed the role of Ezh2 in the differentiation of effector CD8⁺ T cells and antitumor immunity. In a mouse tumor model, T-cell-specific Ezh2 KO mice exhibited reduced initial tumor growth compared to wild-type (WT) mice, but tumors grew rapidly after day 7. The number of CD8⁺ T cells in tumor-infiltrating lymphocytes (TILs) was significantly decreased in Ezh2 KO mice. We found that although the expression of effector molecules was rapidly increased in Ezh2 KO CD8⁺ T cells compared to WT cells, apoptotic cell death was also rapidly induced after activation. RNA-sequencing revealed that the expression of effector signature genes was upregulated in Ezh2 KO effector CD8⁺ T cells, along with the expression of apoptosis-related genes. These findings suggest that Downregulation of Ezh2 promotes the differentiation of short-lived effector CD8 T cells and weakens antitumor immunity.  These findings suggest that downregulation of Ezh2 promotes the differentiation of short-lived effector CD8⁺ T cells and impairs sustained antitumor immunity. Maintaining appropriate levels of H3K27 trimethylation may be essential for the long-term persistence of effective antitumor T cell responses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and Ezh2-deficient CD8⁺ T cells at days 3 and 5 after TCR stimulation.

first: Kenji

last: Takagi

first: Junpei


title: Tumor Antigen–Independent Targeting of Solid Tumors by Armored 1 Macrophage-Directed anti-TREM2-CAR T Cells

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

country: Israel

institute: Weizmann Institute of Science

summary: Chimeric antigen receptor (CAR) T cell therapy has shown remarkable clinical efficacy in  hematological malignancies and, more recently, in autoimmune diseases. However, its application in solid tumors has been limited by tumor antigen heterogeneity, antigen escape, and the immunosuppressive tumor microenvironment (TME), which is particularly shaped by tumor associated macrophages (TAMs). To overcome these barriers, we developed a novel CAR T cell strategy targeting human TREM2⁺ immunosuppressive TAMs. Macrophage-directed anti- TREM2-CAR T cells demonstrated potent anti-TREM2 activity in both in vitro assays and in solid tumor models in vivo. To further enhance intratumoral T cell function, we incorporated a CAR T cell responsive synthetic DNA biosensor comprising NFAT motifs that enable localized secretion of interleukin-12 upon CAR activation. In murine tumor models, this “armored” TREM2-targeted CAR-T cell approach led to robust remodeling of the TME and tumor-draining lymph nodes, characterized by TREM2⁺ TAM depletion, enhanced T and NK cell infiltration and activation, and complete tumor eradication, independent of tumor antigen expression.

overall_design: To improve CAR T efficacy against solid tumors, we designed a highly specific armored-CAR T cells targeting TREM2+ tumor associated macrophages (TAMs). In addition, we placed a proinflammatory cytokine cargo under transcriptional regulation, downstream of antigen activation signal. Altogether, our armored-hTREM2 CAR T cell was designed to alter the tumor microenvironment by both elimination of TAMs and potent cytokine secretion, only upon TREM2 -antigen recognition.

first: Gal

last: Yagel

first: Dana

last: Rimini

first: Michelle

last: von Locquenghien

first: Roberto

last: Avellino

first: Pascale

last: Zwicky

first: Oren

last: Barboy

first: Gaya

last: Granot

first: Ken

last: Xie

first: Shir

last: Shlomi-Loubaton

first: Eyal

last: David

first: Kfir

last: Mazuz


title: OXTR Overexpression Induces Polycystic Ovary Syndrome-like Phenotype via prolactin/p-STAT3 Signaling in Mice. [RNA-seq]

city: Shenyang,China

first: Dan

last: Li

address: No. 146, Huanghe North Street, Yuhong District, Shenyang City, Liaoning Province，China

country: China

institute: Shenyang Medical College

summary: Polycystic ovary syndrome (PCOS), a prevalent endocrine disorder, represents the most common cause of anovulatory infertility. While the oxytocin receptor (OXTR) is well-characterized in parturition and lactation, its role in follicular development remains undefined. In this study, we establish that global OXTR overexpression in female mice (++Oxtr) recapitulates cardinal PCOS features, including hyperandrogenism, oligo-ovulation, and fertility impairment. ++Oxtr females exhibited distinct ovarian pathology marked by follicular atresia, cystic changes, hemorrhage, and deficient corpus luteum formation. These morphological alterations coincided with profound endocrine dysregulation, featuring hyperprolactinemia, suppressed LH secretion, and progesterone deficiency - contrasting with preserved fertility in ++Oxtr males. Mechanistically, we identified an OXTR-PRL-p-STAT3 axis as central to PCOS pathogenesis. Corresponding to hyperprolactinemia, persistent activation of nuclear p-STAT3 (Tyr705) in ++Oxtr granulosa cells - absent in WT controls at pregnancy - epigenetically upregulated folliculogenesis genes (Lhcgr, Pgr, Leptin, CYP17A1) while impairing ovulation. Therapeutic intervention with bromocriptine normalized prolactin and progesterone levels, partially restoring ovarian function. Notably, ++Oxtr females developed metabolic dysfunction characterized by insulin resistance and gonadal adiposity despite maintaining lean phenotypes. Our findings position OXTR as a novel upstream regulator of PCOS pathogenesis with hyperprolactinemia, suggesting bromocriptine may have therapeutic value in hyperprolactinemic PCOS cases. These insights open new avenues for targeted PCOS interventions.

overall_design: To explore the molecular mechanism of OXTR regulating follicle development, RNAseq was used to analyze differentially expressed genes (DEGs) of ++Oxtr against WT ovaries of females in diestrus. 250 DEGs were identified, 174 up and 76 down.

first: ShuiLian

last: Wang

first: XinYue

last: Bao

first: Ziying

last: Liu


title: Acetate Activates Cytototoxic CD8⁺ T Cells in Melanoma

city: Guangzhou

first: Zhiwen

last: Zhang

address: Lujing Road 2

institute: Southern Medical University

summary: Acetate suppressed melanoma progression in vitro and in vivo in a CD8+ T cell-dependent manner.

overall_design: Comparative transcriptomic profiling of CD8⁺ T cells before and after acetate treatment. Total RNA was extracted from mouse CD8⁺ T cells (acetate-treated and control) using TRIzol reagent


title: OXTR Overexpression Induces Polycystic Ovary Syndrome-like Phenotype via prolactin/p-STAT3 Signaling in Mice [CUT&Tag]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To explore the molecular mechanism of prolactin/p-STAT3 regulating follicle development, CUT&Tag analysis of WT ovaries of females in diestrus was used to identify  p-STAT3 and H3K4me3 targets. Key follicle development genes, including Lhcgr, Pgr, and Lepin were with strong p-STAT3 and H3K4me3 enrichment.


title: Transcriptional regulation of durum wheat response to abiotic stress

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

summary: Durum wheat (Triticum turgidum L. ssp. durum) is a major cereal and staple in the semi-arid regions of the Mediterranean Basin. After assembling the Platinum-quality reference genome for Svevo durum wheat cultivar, coupling PACBIO HiFi long read 35X sequencing with BIONANO Optical Mapping and Hi-C conformation capture, a complete and accurate gene annotation was then obtained by coupling Illumina RNASeq and Nanopore Isoseq sequencing from multiple tissues. The gene expression was investigated in root and shoot samples collected from plants grown under control condition or subjected to heat, salinity and osmotic stresses or to nitrogen application to create a transcriptional atlas of durum wheat response to abiotic stresses.

overall_design: Durum wheat (Triticum turgidum L. ssp. durum) cv. Svevo leaves and roots were sampled after 4 and 24 hours of treatment application in three biological replicates to produce a transcriptional atlas of durum wheat response to abiotic and nutrient stress application

first: Elisabetta

last: Mazzucotelli

first: Rachel

last: Rusholme-Pilcher

first: Matteo

last: Bozzoli

first: Tiziana Maria

last: Sirangelo

first: Salvatore

last: Esposito

first: Anthony

last: Hall

last: Tuberosa

first: Luigi

last: Cattivelli

first: Marco

last: Maccaferri


title: Maternal obesity influences transcriptomic and metagenomic profiles in term neonates

city: Barcelona

first: Anna

last: Ramos-Triguero

address: C/ del Rosselló, 149

country: Spain

institute: FRCB-IDIBAPS

summary: Maternal obesity impacts neonatal outcomes; however, its influence on fetal gene expression and early gut microbiota composition remains insufficiently characterized. This prospective study was conducted in 62 full-term neonates between 2022 and 2024, analyzing transcriptomic profiles from umbilical-cord blood and metagenomic sequencing of fecal samples at 4 months. The cohort included 31 neonates born to mothers with normal BMI (NBMI) and 31 neonates born to mothers with overweight or obesity (OBMI). Major congenital anomalies, maternal exposure to drugs or antibiotics were exclusion criteria. OBMI neonates demonstrated significant upregulation of genes related to inflammation (MPO, OLR1) and cell-cycle dysregulation (GADD45G, CCNA1). Evidence of altered lysosomal function was observed, with increased expression of CTSG and CLTCL1 and reduced expression of HYAL1. Microbiome analysis revealed a decrease in Bacteroidota and an increase in Proteobacteria in cesarean-delivered neonates. Holdemanella was enriched in vaginally delivered OBMI neonates, suggesting a potential adaptive microbial response. Enrichment of opportunistic pathogens, including Klebsiella, Morganella, and Enterococcus, was observed in cesarean-delivered neonates, indicating a combined effect of maternal obesity and delivery mode on early microbial colonization. These findings suggest that maternal obesity modifies neonatal immune and metabolic gene expression while reshaping gut microbiome composition, with potential implications for long-term health.

overall_design: This pilot study involved full-term infants (37-42 weeks). Mothers were classified into two groups based on BMI: normal weight (NBMI, BMI<25, n=18) and overweight/obese (OBMI, BMI>25, n=20). Sequencing was performed using Illumina-NextSeq (150x2bp). Quality control and preprocessing were performed using FastQC, MultiQC and Trimmomatic, alignment to Homo_sapiens. GRCh38.102 reference genome using STAR and quality control of alignment with Qualimap. Aligned reads were estimated using featureCounts and differentially expressed genes using DESeq2. Gene annotation was performed using org.Hs.eg.db package. Enrichment pathway was achieved using gage and pathview packages.

first: Melina

last: Vieiros

first: Elisabet

last: Navarro-Tapia

first: Laura

last: Almeida-Toledano

first: Cristina

last: Borrás

first: Elena

last: González

first: Alicia

last: Sanchez

first: Rebeca

last: Tarjuelo

first: Oscar

last: García-Algar

first: Vicente

last: Andreu-Fernández

first: Giorgia

last: Sebastiani


title: A tonsil organoid model reveals Epstein-Barr virus infected germinal center B cell states during primary infection

city: Irvine

first: Timothy

last: Yates

state: CA

address: 501 Aldrich Hall

country: USA

institute: UC Irvine

summary: Epstein-Barr virus (EBV) colonizes secondary lymphoid tissues to establish persistent infection and is strongly associated with malignancy and autoimmunity. Our understanding of EBV infection biology is hindered by a lack of models that capture infected B cell activity in the lymphoid tissue microenvironment. We therefore developed an EBV human tonsil organoid model to evaluate key B cell states and antiviral responses, including after primary infection. EBV promoted B cell differentiation into germinal center (GC)-like phenotypes and transcriptomic analyses highlighted numerous B cell transcriptional programs unique to EBV-infected cells. B cell receptor repertoire analysis revealed that most EBV-infected B cells underwent class switching but only rarely participated in somatic hypermutation. CD4 T cells, highly activated by organoid infection, limited EBV+ B cell outgrowth. Our findings demonstrate human tonsil organoids as a physiologically relevant model to investigate key aspects of EBV immunity and pathogenesis.

overall_design: Following EBV infection of primary human tonsil organoids generated from tonsillectomy donors, immune cells were sorted by flow cytometry across a longitudinal time course (days 4, 7, 14, and 21) and profiled by 10x Genomics 5′ single-cell RNA-seq with paired BCR/TCR V(D)J sequencing and feature-barcoded (HTO/TotalSeq) antibody measurements to define EBV-driven B cell states and accompanying T cell responses.

first: Mahina

middle: T

last: Mitul

first: Yizhe

last: Sun

middle: B

first: Suhas

last: Sureshchandra

first: Jenna

middle: M

last: Kastenschmidt

first: Andrew

last: Sorn

first: Zachary

middle: W

last: Wagoner

first: Erika

last: Joloya

first: Arjun

middle: K

last: Nair

first: Allyssa

last: Daugherty

first: Naresha

last: Saligrama

first: Gurpreet

last: Ahuja

first: Qiu

last: Zhong

first: Douglas

last: Trask

first: Carmy

last: Forney

first: Rui

last: Guo

first: Matthew

last: Weirauch

first: Leah

middle: C

last: Kottyan

first: Benjamin

middle: E

last: Gewurz

first: Lisa

last: Wagar


title: P2X7-mediated mitochondrial calcium overload induces CD8+ T cell senescence

city: Ulsan

first: Jun Pyo

last: Jeon

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, Republic of Korea

country: South Korea

institute: Unist

summary: Neutral lipid levels (Bodipy 493/503) were increased in aged CD8⁺ T cells. We thus selectively removed the lipid sensing transcription factor Rxra and Rxrb in T-lineage cells (Cd4-Cre⁺/⁻ Rxra^f/f Rxrb^f/f; hereafter TDKO). Preliminary phenotyping confirmed that TDKO mice harbour a higher frequency of senescent (fSA-βGal⁺) CD8⁺ T cells relative to wild-type (WT) controls, prompting a comparative survey.

overall_design: Naïve (CD44⁻ CD62L⁺) CD8⁺ T cells were FACS-purified from pooled spleen and lymph-node suspensions of 3-month-old WT and TDKO female littermates. Cells were immediately plated onto anti-CD3 (1 μg ml⁻¹) / anti-CD28 (2 μg ml⁻¹)–coated 24-well plates and cultured for 12 hours in complete RPMI-1640 (10 % FBS). After activation, cells were harvested for ATAC-seq.

first: Daehong

last: Kim

first: Yeonseok

last: Chung

first: Sung Ho

last: Park


title: RNA-sequencing of TNF-α-stimulated NCM460 intestinal epithelial cells

city: Nanjing

first: Yuyu

last: Zhu

address: Xianlin

institute: Nanjing University of Chinese Medicine

summary: We report the application of RNA sequencing technology for high-throughput profiling in NCM460 cells. The goal of this study is to search differential gene in indicated groups. Through differential gene analysis, we can find out the specific mechanism of HTRA2 deficiency to alleviate disease development.

overall_design: Finding out differential gene

first: Chunxiu

last: Xiao


title: Transcripts identified by microarray analysis that were deregulated in E11.5+18h cultures of murine ureters upon treatment with IWP-2.

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in murine E11.5+18h ureters upon treatment with IWP-2.

overall_design: Ureters of NMRI embryos (E11.5) were dissected and cultured for 18h in medium containing 10 µM IWP-2 or in medium without IWP-2. Total RNA from these ureters was analyzed by microarray analysis.

first: Andreas

last: Kispert


title: IRF2 is an Essential Transcription Factor with Pathogenic and Prognostic Impact in Multiple Myeloma

city: Pamplona

first: Nahia

last: Gomez-Echarte

address: Avenida Pio XII, 55

institute: CIMA

summary: Multiple Myeloma (MM), the second most prevalent hematologic malignancy, remains incurable, highlighting the need to identify molecular drivers of disease progression and new therapies. Using a CRISPR-Cas9 library screening approach in MM cells, we identified 22 essential transcription factors (TFs), including members of the interferon regulatory factor (IRF) family. Remarkably, in addition to the well-known IRF4, IRF2 emerged as a critical TF in MM. Cut&Run experiments demonstrated that IRF2 binds extensively to chromatin, both independently and in cooperation with IRF1 and IRF4. While IRF2-unique regions were predominantly associated with active promoters, regions bound by IRF2/1/4 were biased towards introns. Functionally, IRF2 contributes to MM cell survival by suppressing necroptosis and promoting cell migration. Notably, IRF2-dependent transcriptional dysregulation was evident in precursor conditions such as MGUS and SMM, suggesting a role in early disease evolution. In addition to its role as early factor, IRF2 levels also seem to influence disease progression, as MMs with higher expression showed worse progression-free survival (PFS) and overall survival (OS) in both univariate and multivariate analyses, even after adjusting for common MM genetic risk factors. In conclusion, IRF2 constitutes an underappreciated essential TF involved in the pathogenesis and clinical behavior of MM. Its inhibition leads to dysregulation of key signaling pathways in MM pathogenesis, highlighting its potential as a therapeutic target.

overall_design: To determine the function of IRF2 TF in MM and to compare it with IRF1 and IRF4, a CUT&RUN experiment was performed in two MM cell lines (KMS-11 and MM.1R) using two antibodies per TF, and also an antibody against BRD4 and IgG as positive and negative controls of the experiment, respectively. Then, the expression of the genes associated with the chromatin regions bound by IRF2 was assessed in different samples of plasma cells from healthy donors, MGUS, SMM, and MM patients. Finally, to define the function of IRF2, an RNA-seq was performed following IRF2 inhibition using two CRISPR/Cas9 sgRNAs in five MM cell lines (KMS-11, MM.1R, RPMI 8226, MM.1S, and KMS-28-BM). This experiment was performed in three biological replicates.

last: Gómez-Echarte

first: Arantxa

last: Carrasco-León

first: Alba

last: Maiqués-Díaz

first: Naroa

last: Barrena

first: Estibaliz

last: Miranda

first: Leire

last: Garate

first: Ane

last: Amundarain

first: Patxi

last: San Martín-Uriz

first: Stella

last: Charalampopoulou

first: Luis

middle: V

last: Valcárcel

first: Beñat

last: Ariceta

first: Paula

last: Rodriguez-Marquez

first: Juan

middle: R

last: Rodriguez-Madoz

first: Kazuya

last: Ishiguro

first: Francisco

middle: J

last: Planes

last: Rodriguez-Otero

first: Constantine

middle: S

last: Mitsiades

first: Jose

last: Martín-Subero

first: Edurne

last: San José-Enériz

first: Felipe

last: Prosper

first: Xabier

last: Agirre


title: Transcripts identified by microarray analysis that were deregulated in E14.5 Tbx18(cre/+);Ctnnb1(flox/flox) (Ctnnb1-cKO) ureters.

first: Mark-Oliver

last: Trowe

summary: Evaluation of the transcriptional changes in E14.5 ureters upon loss of Ctnnb1 in the ureteric mesenchyme.

overall_design: Total RNA from dissected ureters of E14.5 Ctnnb1-cKO and control embryos was analyzed by microarray analysis.

first: Andreas

last: Kispert


title: IFRD1 orchestrates hepatocyte metabolism and macrophage interactions to facilitate liver regeneration [ATAC-Seq - liver primary cells]

city: Hefei

first: Taofei

last: Zeng

state: Anhui

address: 17 Lujiang Road

institute: The First Affiliated Hospital of USTC

summary: Background & Aims Liver regeneration is a tightly regulated process requiring coordinated interactions between hepatocytes and non-parenchymal cells; however, its molecular mechanisms remain incompletely defined. Here, we aimed to investigate the role of interferon-related developmental regulator 1 (IFRD1) in regulating metabolic–immune crosstalk during liver regeneration. Methods We integrated public transcriptomic datasets, human liver disease samples, and multiple in-house–generated experimental models to characterize the dynamic expression of IFRD1 during liver regeneration. Genetic loss-of-function approaches, including global and cell type–specific knockout mice, together with adeno-associated virus–mediated gain-of-function strategies, were combined with single-nucleus RNA-seq, ATAC-seq, metabolic and biochemical assays, protein interaction analyses, and in vivo rescue experiments to elucidate the underlying mechanisms and clinical relevance. Results Hepatocyte IFRD1 was rapidly induced during the early phase of liver regeneration in mice but markedly diminished in human chronic liver disease. Hepatocyte-specific loss of IFRD1 impaired liver repair and regeneration, whereas IFRD1 overexpression enhanced regenerative responses across multiple models, including partial hepatectomy, toxic liver injury, and hepatic ischemia–reperfusion injury. Mechanistically, IFRD1 was required to sustain hepatocyte β-oxidation and mitochondrial ATP production by stabilizing SLC25A5 through competition with the E3 ubiquitin ligase TRIM21. This ATP boost enables chromatin remodeling in hepatocytes, promoting CCL/CXC chemokine expression to recruit CCR2+ monocytes and expand the regenerative GPNMB+ macrophage pool. Notably, IFRD1 overexpression restored liver regenerative capacity after partial hepatectomy in mice with metabolic dysfunction–associated steatohepatitis or DEN-induced liver fibrosis. Conclusions Our findings define IFRD1 as a key immunometabolic regulator of liver regeneration, mediating hepatocyte metabolic control to macrophage-driven regenerative responses, and support the therapeutic potential of targeting IFRD1 to enhance regenerative capacity in liver disease.

overall_design: ATAC-seq was performed on primary hepatocytes from Ifrd1 knockout mice, treated with ATP or PBS as a control, 12 hours after partial hepatectomy (PHx). Chromatin accessibility was assessed to examine the effects of ATP on chromatin remodeling during liver regeneration.

first: Dalong

last: Yin


title: Transcripts identified by microarray analysis that were deregulated in E12.5+18h cultures of murine ureters upon treatment with IWP-2.

summary: Evaluation of the transcriptional changes in murine E12.5+18h ureters upon treatment with IWP-2.

overall_design: Ureters of NMRI embryos (E12.5) were dissected and cultured for 18h in medium containing 10 µM IWP-2 or in medium without IWP-2. Total RNA from these ureters was analyzed by microarray analysis.


first: Nahia

last: Gomez-Echarte

overall_design: To determine the function of IRF2 TF in MM and to compare it with IRF1 and IRF4, a CUT&RUN experiment was performed in two MM cell lines (KMS-11 and MM.1R) using two antibodies per TF, and also an antibody against BRD4 and IgG as positive and negative controls of the experiment, respectively. Then, the expression of the genes associated with the chromatin regions bound by IRF2 was assessed in different samples of plasma cells from healthy donors, MGUS, SMM, and MM patients. Finally, to define the function of IRF2, an RNA-seq was performed following IRF2 inhibition using two CRISPR/Cas9 sgRNAs in two MM cell lines (KMS-11 and MM.1R). This experiment was performed in three biological replicates.

last: Gómez-Echarte

first: Arantxa

last: Carrasco-León

first: Alba

last: Maiqués-Díaz

first: Naroa

last: Barrena

first: Estibaliz

last: Miranda

first: Leire

last: Garate

first: Ane

last: Amundarain

first: Patxi

last: San Martín-Uriz

last: Charalampopoulou

first: Juan R

first: José


title: CD49d governs immune synapse formation through actin rearrangements and synchronizes BCR signaling in CLL

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: B cell receptor (BCR) signaling is a key determinant of chronic lymphocytic leukemia (CLL) pathophysiology. CD49d, the alpha4 subunit of the very late antigen-4 (VLA-4) integrin, can be activated by BCR signals; however, its role in modulating BCR functionality remains unknown. We used mouse models and primary human CLL to address this aspect. We found CD49d being not only required for bone marrow infiltration in TCL1 transgenic mice but also shaping human bone marrow infiltration patterns, along with patient outcome. In mice transplanted with TCL1 transgenic cells, CD49d loss altered leukemic cell localization in splenic niches. CD49d-deficient murine cells and human CD49d-low CLL cells could not form immune synapses to antigen-presenting membranes. CD49d-loss-related F-actin polymerization and transcriptomic defects in cytoskeleton-associated pathways were found in mouse and human. The requirement of CD49d for engraftment and actin organization could be recapitulated in a second murine model with highly aggressive transformed CLL. RNAseq analyses and kinome profiling revealed impaired antigen responsiveness due to kinase transcription and activity shifts in CD49d-deficient murine leukemic cells, recapitulated in human while applying several human BCR signatures.  Finally, in human CLL expressing low CD49d, actin organization was deregulated, along with a desynchronization of Syk and PLCgamma activation. In summary, our findings establish CD49d as a key regulator of BCR functionality, linking integrin signaling to cytoskeletal dynamics and antigen responsiveness in CLL.

overall_design: RNAseq profiling of Spleen and Peritoneal cavity of CLL cells with CD49d deficiency or not.

first: Melanie

last: Boerries


title: Structure-guided discovery and engineering of miniature CRISPR-Cas12m for epigenome editing

first: Kailong

last: Li

institute: Peking University

summary: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq was performed to determine the chromatin occupancy of xCas12m-VPR(anti-HA) at the targeted HBG1 and HBG2 promoters in HEK293T cells

first: Tao

last: Yu

first: Donglin


title: SMARCA4, STK11, and KEAP1 co-loss associates with poor prognosis and upregulation of the TGF-β pathway in lung adenocarcinoma (LUAD) - RNA-seq

city: New York

first: Sam

last: Tischfield

state: NY

address: 1275 York Ave

department: Center for Molecular Oncology

institute: Memorial Sloan-Kettering Cancer Center

summary:
Background
Lung adenocarcinoma (LUAD) is clinically and molecularly defined by oncogenic driver mutations, whose identification has led to the development of driver-targeted therapies and substantial improvements in prognosis for subsets of LUAD patients. However, recent studies synthesizing LUAD tumor sequencing with clinical outcomes have identified intradriver genetic and phenotypic heterogeneity that underlie differential responses to targeted therapy. Genetic inactivation or loss of SMARCA4, which has been observed to co-occur with loss-of-function mutations in STK11 and KEAP1, is especially predictive of poor prognosis and shorter overall survival in LUAD patients, regardless of driver status. Thus, we sought to examine the clinical features and functional associations of SMARCA4 deficiency in LUAD, both on its own and co-incident with STK11/KEAP1 loss-of-function.
Methods
We examined the apparent correlation between SMARCA4 loss and poor prognosis through MSK-IMPACT clinicogenomic analysis and transcriptomic profiling of curated clinical samples. We additionally generated isogenic cell line models with genetic knockouts of SMARCA4, STK11, and KEAP1 to capture phenotypic and transcriptional features of our mutationally-defined genotypes of interest in vitro and in vivo. Lastly, we interrogated the functional dependency of SMARCA4/STK11/KEAP1 triple mutant models on TGF-β signaling to assess its potential as a therapeutic target.
Results
In our clinicogenomic analysis, we observed that remarkably short overall survival and higher frequency of metastasis to multiple sites distinguish SMARCA4/STK11/KEAP1 triple mutant LUAD. Uniquely in the SMARCA4/STK11/KEAP1 triple knockout models, we observed in vitro metastatic behaviors, including enhanced migration and invasion, and lowered organotropism in an in vivo intracardiac xenograft metastasis assay. RNA-Seq and DNase-Seq of these in vitro models and clinical samples identified upregulation of TGF-β signaling and EMT-associated gene expression as a signature unique to SMARCA4/STK11/KEAP1 triple loss, which correlated with concomitant changes in chromatin accessibility. In vitro small molecule inhibition of TGF-β signaling revealed enhanced dependence on this pathway for survival and migration in triple knockout models, nominating TGF-β as a novel therapeutic target in SMARCA4/STK11/KEAP1 co-mutant LUAD.
Conclusions
We identify SMARCA4/STK11/KEAP1 triple mutant LUAD as a prognostically significant disease subset and nominate TGF-β signaling as a potential therapeutic target.

overall_design: To investigate changes in gene expression associated with SMARCA4 expression loss with and without co-expression of STK11 and KEAP1, we generated CRISPR/Cas9 knockout in vitro models in H358 cell lines with knockount combinations matching our co-mutant groups of interest.

first: Emily

last: Costa

first: Álvaro

last: Quintanal-Villalonga

first: Charles

last: Rudin


title: mRNA-seq profiles of porcine ovarian mural granulosa cells from lactational full-fed and restricted-fed sows at two days post-weaning

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: mRNA-seq profiles of mural granulosa cells from full-fed (FF) and restricted-fed (RES) sows were compared. In total, 2,282 differentially expressed genes (DEGs) were identified, of which 1,531 were upregulated and 751 were downregulated in RES. The most enriched pathway was the cell cycle. Key cell cycle regulators and proliferation markers were upregulated, while differentiation markers were downregulated in RES. Several members of the insulin growth factor binding proteins (IGFBP) family, especially IGFBP7, were strongly correlated with FOXO1, CDKN1A (P21), most cell cycle-related genes, and follicle size exclusively in RES sows, but not in FF sows.

overall_design: Female pigs were fed either a full (FF; 6.5 kg/day) or a restricted diet  (RES; 3.25 kg/day) during the last 2 weeks of lactation and then were fully fed for 2 days post-weaning before ovary collection. Successively, the largest healthy follicle of the right ovary was selected per animal, pure mural granulosa cells were isolated by laser capture microdissection, total RNA was extracted and unique molecular identifiers-based low-input RNA-seq was performed.

first: Qi

first: Jaap

last: Keijer

first: Katja

last: Teerds

first: Nicoline

last: Soede


title: Interferon regulatory factor 5 regulates bone remodeling via orchestration of osteoclast lineage-osteoblast coupling

city: wuhan

first: Huan

last: Zhao

address: 1，University Park Road

institute: Wuhan University

summary: Bone remodeling is orchestrated by the balanced activity of bone-resorbing osteoclasts and bone-forming osteoblasts. Interferon regulatory factor 5 (IRF5), a member of the IRF family of transcription factors, serves as a critical regulator of macrophage immune-related activity. However, macrophages also serve as the precursor cell of osteoclasts where the role of IRF5 in osteoclast-mediated bone remodeling in vivo remains undefined. Here, we find that IRF5 exhibits nuclear localization specifically in preosteoclasts during macrophage-osteoclast transition in vitro. In turn, myeloid cell-specific Irf5 conditional knockout (Irf5ΔM/ΔM) mice exhibit a significant osteopenic phenotype. Unexpectedly, osteoclast activity remained unaltered, while osteoblastic bone formation was significantly reduced. Interestingly, while conditioned media from wild-type preosteoclasts and osteoclasts increase the osteogenic potential of osteoblastic cells, this stimulatory activity was largely abrogated in conditioned media recovered from Irf5ΔM/ΔM preosteoclasts and osteoclasts. Genome wide analysis further revealed that the Irf5-deficient osteoclast lineage displays major changes in transcriptional programs related to extracellular matrix organization, bone development, and Notch signaling. Taken together, we have identified IRF5 as a novel osteoimmune transcription factor that coordinates bone remodeling by regulating osteoclast lineage-mediated bone coupling, thus providing novel insights into developing effective preventive and/or therapeutic strategies against metabolic bone diseases.

overall_design: RNA-seq profiling the differentially expressed genes between wild type (WT) and Irf5 knockout cells, including bone marrow-derived macrophage (BMM), preosteoclast (POC) and osteoclast (OC).

first: Li

last: Wang

first: Stephen

last: Weiss

first: Lingxin

last: Zhu


title: An Immunocompetent Transplantable Mouse Model of Basal Cell Carcinoma

city: Kgs Lyngby

first: Martin

last: Wiinberg

state: Hovedstaden

address: Produktionstorvet 423

department: Department of Health Technology

country: Denmark

institute: Technical University of Denmark

summary: Basal cell carcinoma (BCC) is the most common type of cancer, yet mouse models of BCC are limited. Existing BCC mouse models such as the Ptch1+/--K14-CreERT2p53fl/fl-tumor (GEM-BCC) model rely on genetic engineering. These models are essential for studying BCC carcinogenesis but are complicated to integrate into preclinical treatment evaluation studies due to the spontaneous growth of multiple tumors with heterogenous growth. This study describes the establishment of an immunocompetent transplantable BCC (Tp-BCC) mouse model suitable for preclinical treatment evaluation. By in vivo passaging GEM-BCC tumor cells, we were able to establish a Tp-BCC model. We compared microstructural features, tumor microenvironment and transcriptional profile of the Tp-BCC model with its parental GEM-BCC model using histology, flow cytometry and RNA sequencing. Tp-BCC tumors displayed synchronized growth and shortened time until tumor formation compared to GEM-BCC tumors. Tp-BCC tumors showed micro-nodular histological structure and had a tumor immune microenvironment composition similar to the GEM-BCC tumors. Hedgehog signaling pathway-related genes were similarly expressed except for Igf2. The transcriptional profile of Tp-BCC model was less variable than the GEM-BCC model. This study demonstrates that the Tp-BCC model resembles the clinically relevant GEM-BCC model while providing an immunocompetent high-throughput model for evaluating treatments of BCC.

overall_design: A cell-derived transplantable BCC tumor model (Tp-BCC) was generated by subcutaneous inoculating BCC cells from the genetically engineered induced murine tumor model, Ptch1+/-K14-CreERT2p53fl/fl (GEM-BCC). This model is meant for higher throughput drug screening in an immunocompetent host. Features of Tp-BCC model including tumor growth, histology, tumor immune microenvironment and gene expression were investigated and compared with its parental tumor model, GEM-BCC, to characterize similarities and differences.

first: Kristian

last: Pedersen

first: Catharina

last: Lerche

first: Thomas

middle: L

last: Andresen

last: Litman

first: Merete

last: Haedersdal

first: Uffe

middle: H

last: Olesen


title: Functional divergence of Capicua isoforms explains differential tissue vulnerability in neurological disease

city: Houston

first: Hamin

last: Lee

state: TX

address: 1 Baylor Plaza, Jan and Dan Duncan Neurological Research institute

institute: Baylor College of Medicine

summary: Many neurological diseases attack specific brain regions despite widespread expression of the disease-related protein. Spinocerebellar ataxia type 1 (SCA1) primarily affects the cerebellum, though Ataxin-1 (ATXN1) is widely expressed. We previously showed that intensified interaction between mutant ATXN1 and Capicua (CIC) drives SCA1 pathogenesis in the cerebellum, whereas ATXN1 loss augments amyloid beta production in the hippocampus and cortex. CIC, however, forms a complex with ATXN1 and its paralog, Ataxin-1-like (ATXN1L)—yet knockout of either yields completely different phenotypes. To determine whether this could be due to CIC having two isoforms, we generated mice bearing either the long (CIC-L) or short (CIC-S) isoform. Loss of CIC-L led to cognitive deficits, whereas loss of CIC-S caused perinatal lethality, phenocopying, ATXN1 and ATXN1L knockout mice, respectively. Furthermore, CIC-L preferentially interacts with ATXN1, and CIC-S with ATXN1L. Our data underscore the importance of isoform–paralog interplay in studying regional vulnerability in neurodegenerative diseases.

overall_design: RNA-seq of Cic-S-KO and Cic-L-KO mice and their pooled littermate control WTs was performed on P6 lung and 12-week-old cortex and cerebellum.

first: Huda

middle: Y

last: Zoghbi


title: RNA-seq for AML cell line in either the absence or presence of ENO1

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for AML cell line in either the absence or presence of ENO1.

overall_design: 3 MV4-11 samples with no treatment and 3 MV4-11 samples with ENO1 knockdown

first: Jian

last: Pan

first: Yijun

last: Wu

first: Chun

last: Yang

first: Shaoyan

last: Hu


title: HOMEODOMAIN-LIKE shapes chromatin architecture and rewires leaf epidermal patterns [RNA-seq]

city: Taipei

first: Chin-Min

last: Ho

address: A423, Institute of Plant and Microbial Biology, Academia Sinica

country: Taiwan

institute: Academia Sinica

summary: During Arabidopsis (Arabidopsis thaliana) leaf epidermis development, precursor cells divide and differentiate to form distinct patterns of trichomes, pavement cells, and stomata. The mechanisms governing these developmental transitions remain unclear. We identified the homeodomain-like protein HDL, which is required for heterochromatin compaction through interactions with the histone deacetylase HDA6 and the methyltransferase KRYPTONITE during the cell cycle. Mutants of HDL showed a prolonged interphase, fewer cell divisions, and greater endoreduplication, resulting in fewer stomata and more trichomes. Chromatin immunoprecipitation and ATAC-sequencing revealed higher chromatin accessibility in HDL-bound regions and lower chromatin accessibility along the promoters of stomata-related genes, which also showed reduced expression in hdl mutants. These findings highlight the importance of chromatin organization in maintaining cell division potential and transcriptional control.

overall_design: RNAseq profiling of HOMEODOMAIN-LIKE mutant (hdl) and WT using 9dpg leaf epidermal cells sorted with AtML1pro:RCI2A-mCherry reporter

first: Ansar

last: Ali

first: Chi

last: Kuan

first: Tsai-Chen

last: Chen

first: Fu-Yu

last: Hung

first: Pei-Yu

last: Lin

first: Ding Hua

first: Guan-Jun

first: Hui-Chun

first: Shao-Li

first: Yun-Ru

last: Feng

first: Chung-Ju Rachel

last: Wang

first: Pao-Yang

first: Keqiang

first: Chin-Min Kimmy


title: CUT-TAG of ENO1 for AML cell line

first: Fang

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore CUT-TAG results of ENO1 in AML cell line.

overall_design: CUT-TAG for ENO1 in MV4-11 cell line

first: Jian

first: Yijun

first: Chun


title: Impact of METTL1 on global gene expression in AML

city: Duarte

first: Rui

last: Su

address: 1500 E Duarte Rd

institute: City of Hope

summary: Methyltransferase 1 (METTL1) is an enzyme responsible for the m7G modification of tRNAs. Our studies indicated that METTL1 is highly expressed in AML samples and its elevated level predicts poor prognosis of AML patients. Knockout (KO) of METTL1 in AML cells significantly suppressed their growth, promoted myeloid differentiation in vitro, and substantially delayed leukemogenesis in vivo. Additional rescue assays demonstrated the functions of METTL1 in AML primarily depended on its enzymatic activity. To delineate the molecular mechanism through which METTL1 exerts its biological functions in AML, we conducted transcriptome-wide RNA sequencing with Mono-mac-6 AML cells following METTL1 KO.

overall_design: We introduced the single-guide RNAs (sgRNAs) targeting METTL1 (sgMETTL1.3 and sgMETTL1.6) or the control sgRNA (sgNS) into Cas9 single-clone of Mono-mac-6 AML cells via lentivirus transduction. The transduction-positive AML cells were selected with blasticidin (10 μg/ml; Cat #: ant-bl-1, InvivoGen) and hygromycin B (200 μg/ml; Cat #: ant-hg-5, InvivoGen) for 1-2 weeks. METTL1 KO efficacy was confirmed by Western blot. Then, the total RNAs were extracted from each group with QIAzol and the poly(A)+ RNAs were enriched from total RNAs for library construction and sequencing. For each group, we included 2 replicates.

first: Lei

last: Dong

first: Lili

last: Ren


title: HOMEODOMAIN-LIKE shapes chromatin architecture and rewires leaf epidermal patterns [ATACseq]

first: Chin-Min

overall_design: ATACseq profiling of HOMEODOMAIN-LIKE mutant (hdl) and WT using 9dpg leaf epidermal cells sorted with AtML1pro:RC12A-mCherry reporter

first: Ansar

first: Chi

first: Tsai-Chen

first: Fu-Yu

first: Pei-Yu

last: Lee


title: HOMEODOMAIN-LIKE shapes chromatin architecture and rewires leaf epidermal patterns [ChIPseq]

overall_design: H3K9me2 profiling of HOMEODOMAIN-LIKE mutant and WT using 8dpg seedlings

first: Ding Hua

first: Guan-Jun

first: Hui-Chun

first: Shao-Li

first: Yun-Ru

first: Chung-Ju Rachel


title: CDK12 as an entry point for combination therapy in high-risk neuroblastoma [RNA-seq]

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

summary: High-risk neuroblastoma (HR-NB) patients undergo aggressive treatments, yet more than half succumb to the disease. HR-NB cells are marked by chronic replicative stress, partly driven by MYCN amplification, and targeting DNA damage response (DDR) pathways presents a promising therapeutic approach. BRCA1 and CDK12, located on the recurrently gained 17q region in HR-NB, play essential roles in maintaining genomic stability. In this study, we hypothesized that pharmacological inactivation of CDK12 could induce a BRCAness phenotype, making NB cells vulnerable to synthetic lethal targets. We evaluated the efficacy of CDK12 inhibitors and protein degraders in a panel of NB cell lines and organoids. Molecular effects of CDK12 inactivation were investigated through immunoblotting and RNA-sequencing. A high-throughput compound screen combining CDK12-targeting agents with a library of ~200 drugs revealed that single-agent treatment with CDK12 inhibitors or degraders induced significant NB cell death in vitro. This was accompanied by a BRCAness signature, including decreased BRCA1 and RAD51 levels, increased DNA damage, and downregulation of DNA repair genes. Additionally, we observed upregulation of immune pathways, suggesting potential for enhancing immunogenicity in HR-NB. The combinatorial drug screen revealed strong synergy with DNA-damaging agents, PARP inhibitors, Ras/MAPK inhibitors, and other compounds. These findings confirm CDK12 as a novel therapeutic target, and the induction of a BRCAness phenotype provides a basis for combination treatments.

overall_design: RNA sequencing of CDK12 inhibitors (dCeMM2, BSJ-4-116, SR-4835, and OKI-1546) in N206 and SH-SY5Y neuroblastoma cell lines, followed by combination drug testing with merestinib in N206 cells.

first: Joshua

last: Goulding

first: Stijn

last: Couwenbergh

first: Kaat

last: Durinck

first: Jan

last: Molenaar


title: Co-deficiency of the BLM and RECQL1 Helicases Causes Synthetic Lethality, Pronounced Replication Stress, and Loss of Chromatid Cohesion

city: Baltimore

first: Robert

last: Brosh

state: Maryland

address: NIH Biomedical Research Center, 251 Bayview Blvd

institute: National Institute on Aging, NIH

summary: The mechanistic basis for chromosomal instability characteristic of RECQ helicase genetic disorders has been elusive, given the complexity and apparent redundancy of cellular pathways important for genome homeostasis. To characterize the genetic interactions of RECQL1 helicase (recently implicated in the rare hereditary disorder RECON syndrome) essential for genome integrity, we performed an acute depletion RNA interference screen and determined a synthetic lethal interaction of RECQL1 with BLM helicase (linked to the cancer-prone disease Bloom syndrome) in cells exposed to a DNA alkylating agent that induces replication stress. The profound replication stress of cells co-deficient in RECQL1 and BLM was marked by elevated DNA damage and chromosomal instability. Strikingly, RECQL1/BLM co-deficiency induced a novel phenotype of premature sister chromatid separation that could be suppressed by depletion of the cohesion unloader WAPL, suggesting that a threshold of replication stress disrupts cohesion establishment. Primary embryonic fibroblasts from transgenic Recql-/- Blm-/- mice recapitulated the replication stress phenotypes of human cells, and the small intestines of Recql-/- Blm-/- mice showed elevated DNA damage. Our findings highlight the important role of either RECQL1 or BLM when the other is deficient, as is the case for each respective hereditary disorder. Moreover, this study suggests a potentially therapeutic vulnerability of cancers harboring somatic mutations in RECQL1, BLM, or other genome caretakers that function in pathways that confer resistance to replication stress.

overall_design: To study the role of Recql and Blm in gene expression, primary MEF cells derived from mice with four different genetic bacgkrounds (WT, Blm-/-, Recql -/-, Blm -/- Recql -/-)  were processed for RNA-sequencing to identify the transcripts differentially expressed in each genetic backgorund compared to wild type cells.

first: Lauren

last: Herr

first: Srijita

last: Dhar

first: Martina

last: Rossi

first: Ethan

middle: D

last: Schaffer

first: Kajal

last: Biswas

first: Sandra

last: Burkett

first: Swagata

last: Mukhopadhyay

first: Arindam

last: Datta

first: Miguel

last: Calvo-Rubio

first: Donna

middle: O

last: Butcher

first: Daniel

last: McNeill

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe

first: Claudia

last: Nicolae

first: Tanay

last: Thakar

first: George-Lucian

last: Moldovan

first: Simonetta

last: Camandola

first: Cristopher

last: Dunn

first: Rafael

last: de Cabo

first: Shyam

last: Sharan

last: Brosh Jr


title: ECD, a novel U5 snRNA binding protein regulates RNA splicing [RNA-Seq, RIP-Seq]

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

summary: The human ecdysoneless protein (ECD) plays a pivotal role in cellular and physiological processes, including the regulation of the cell cycle, cell survival, and embryogenesis. More recently, ECD has been implicated in RNA biogenesis through its regulatory effects on mRNA nuclear export and RNA splicing. In the current study, we identified the mechanism of ECD’s function in RNA splicing. We demonstrate a novel role of ECD as an RNA-binding protein and, through mutational analyses, we show that it utilizes its N-terminal region to interact with RNAs. By employing unbiased approaches such as eCLIP-seq and RNA-seq analyses in hTERT-immortalized mammary epithelial cells (76NTERT), we demonstrate that ECD directly binds to RNA and predominantly utilizes its RNA-binding abilities to regulate RNA splicing. This regulation occurs either through direct binding of ECD to RNA sequences located near splicing sites, one of the top ECD binding motifs identified being purine-rich exonic splicing enhancers or by influencing the biogenesis of the U5 small nuclear ribonucleoprotein particle (U5 snRNP) complex via its direct interaction with U5 snRNA. Notably, this interaction not only maintains the expression of U5 snRNA but also is essential for maintenance of protein components of the U5 snRNP complex, such as PRPF8 and EFTUD2. Consistently, ECD KO in 76NTERT cells lead to widespread aberrant splicing of numerous RNAs leading to alteration in expression of several genes. Importantly, ECD KO or the loss of its RNA-binding function resulted in the downregulation of U5 snRNP components, which functionally culminates into cellular proliferation block. Significantly, full-length ECD but not its RNA binding site mutant failed to rescue cell proliferation blocks upon ECD KO. Collectively, we provide compelling evidence that ECD regulates RNA splicing by directly associating with U5 snRNP and regulating U5snRNP complex to maintain cell proliferation and survival.

first: Achyuth

last: Kalluchi

first: Vimla

last: Band


title: Transcriptomic and Proteomic Signatures Following AS03-adjuvanted Influenza A/H7N9 Vaccine

city: Rockville

first: Johannes

last: Goll

state: MD

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

summary: Vaccines targeting avian influenza virus A/H7N9 are poorly immunogenic. While the immune responses can be improved with oil-in-water emulsion adjuvants such as Adjuvant System 03 (AS03), the cellular mechanisms underpinning the adjuvant effect are incompletely characterized and poorly understood. In this study, we used RNA-sequencing and quantitative proteomics to elucidate the response to two doses of influenza A/H7N9 vaccine, with and without AS03 in six immune cell types. These responses were also compared to those seen after administration of an unadjuvanted seasonal influenza A/H3N2 variant vaccine to identify signatures unique to adjuvanted influenza vaccine and correlated with later antibody responses. Transcriptomic and proteomic analyses revealed that AS03-adjuvanted vaccine uniquely led to upregulation of immune pathways in innate immune cells within 24 hours following vaccination for phagocytosis, antigen presentation and processing, inflammasome activation, NK-cell mediated cytotoxicity, IgA production, and interferon-response pathways. Moreover, while major histocompatibility complex (MHC I and II) upregulation was observed across multiple immune cell types, the neutrophils showed a distinct activation of MHC II, suggesting that neutrophils may play a more important role in antigen presentation than previously understood. Taken together, these data provide a more complete mechanistic understanding of oil-in-water adjuvants and their role in enhancing the immune response for pandemic influenza preparedness.

overall_design:
To characterize differential responses unique to each vaccine.
To understand which of these signals were associated with serum antibody responses.
To develop a systems biology model of the human immune response to these vaccines.

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

last: Creech

first: Kristen

last: Steenbergen

first: Casey

last: Gelber

first: Leigh

last: Howard

first: Kevin

last: Schey

first: Kristie

last: Rose

first: Sandra

last: Yoder

first: Kathryn

last: Edwards


title: Dynamic STING repression orchestrates immune cell functionality across development and maturation.

city: Dallas

last: Yan

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Stimulator of Interferon Genes (STING) is a critical component of the innate immune system. Mechanisms of STING-mediated type I interferon (IFN-I) signaling during infection are well studied in myeloid cells. However, homeostatic STING expression patterns and their regulation, particularly in lymphoid cells, are unknown. We established a Sting1IRES-EGFP reporter mouse to systematically characterize STING expression spatially in tissues and temporally along development of immune cells. Using this reporter and conditional Sting1 transgenic mouse models, we show that STING expression is repressed in neutrophils and forced STING signaling and expression drives systemic inflammatory disease due to secretion of cytokines and chemokines by neutrophils. Additionally, we show that STING expression is temporally restricted during T lymphocyte development at the double positive stage. Forced STING expression and signaling severely impairs T lymphocyte development and reduces thymopoiesis independent of the type I IFN receptor (IFNAR1). Mechanistically, STING expression in the thymus is controlled via epigenetic silencing by DNA methyltransferase 1 (DNMT1). Forced STING signaling in the thymus favors lineage commitment to innate-like gd T cells rather than adaptive ab T cells, revealing a previously unanticipated role of STING in T lymphocyte fate choice. Using two syngeneic tumor models and a cohort of human colorectal cancer patients, we found that tumor-infiltrating CD8+ T lymphocytes gradually repress STING expression as a tumor grows and loss of STING expression strongly correlates with CD8+ T cell exhaustion. Together, our data demonstrates the physiological importance of controlled, rather than ubiquitous STING expression and uncovers STING expression dynamics as an important new dimension of STING pathobiology.

overall_design: RNA sequencing of sorted DP TCRb-/lo-int thymocytes obtained from 5 week old LSL-Sting1-N153S/+ (N1-N4) and LSL-Sting1-N153S;Lck-cre (N5-N8) mice

first: Yan

first: Knox

last: Kennady


title: BRD4 O-GlcNAcylation attenuates phase separation to regulate transcription

city: Beijing

first: Qidong

last: Deng

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

institute: Peking university

summary: BRD4 undergoes liquid-liquid phase separation (LLPS) at super-enhancers (SEs) to facilitate gene control. However, the regulatory mechanisms and transcriptional consequences of BRD4 condensation remain elusive. Here, we show that the BRD4 C-terminal intrinsically disordered region (IDR) is a primary interacting region for O-GlcNAc transferase (OGT), enabling O-GlcNAc modifications at 12 potential sites. O-GlcNAcylation attenuates BRD4 LLPS, leading to small puncta and increased fluidity, which significantly declines occupancy and transcription at SEs. We further demonstrate that loss of O-GlcNAcylation on BRD4 led to elevated gene expression relating to cell cycle and DNA damage, allowing cells less sensitive to DNA damage and promoting faster growth. Therefore, we identify an O-GlcNAc–mediated regulatory mechanism for BRD4 LLPS that governs gene control at SEs, showcasing how O-GlcNAc modifications can influence transcriptional activities at SEs through a phase separation model.

overall_design: To investigate how O-GlcNAcylation on BRD4 C-terminal intrinsically disordered region (IDR) affect BRD4 liquid-liquid phase separation (LLPS) at super-enhancers (SEs) to regulate gene expression.We performed gene expression profiling of RNA-seq and Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for BRD4 in BRD4-WT and BRD4-12A HeLa cells.

first: Guojian

last: Shao

first: Tianyu

last: Wang


title: Pathogenesis elucidation of Ulcerative Colitis Focusing on Appendix Immunity

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Background: Appendix immunity may be involved in the pathogenesis of ulcerative colitis (UC), but the mechanism is not yet understood. In this study, we aimed to characterize immune cells in the appendix of UC patients. Method: We performed scRNA-seq on appendix cells from UC and non-UC patients. Result:  A wide variety of immune cells were found in the appendix, with a marked increase in IgG-producing Plasma blast in the appendix of UC patients. Conclusion:  The appendix of patients with UC were characterized by an increased number of IgG-producing cells.

first: Takayuki

last: Ogino

last: Okuzaki

first: Shuhei

last: Sakakibara

first: Yosuke

last: Kishi


title: miRNA-mediated cell-to-cell communications boost DNA repair during the Radioadaptative Response in human fibroblasts

status: Public on Jul 30 2026

city: Sevilla

first: Pablo

last: Huertas

address: Av.Americo Vespucio 24

institute: University of Sevilla

summary: The radioadaptive response is a phenomenon in which cells exposed to a low priming dose of ionizing radiation develop increased resistance to a subsequent higher challenging dose for a period of time. Little is known of the molecular components of this response. Here, we focus on determining if during the RAR there are changes in the Homologous Recombination, the more faithful DNA Double Strand break repair pathway. Using immortalized fibroblasts as a model system, we demonstrate that primed cells exhibit faster DNA resection, the initial step of homologous recombination, following a challenging dose, as indicated by RPA foci kinetics. We further establish that the stimulation of resection during the RAR is mostly established and maintained through cell-to cell communication via extracellular vesicles. Indeed, media exchange experiments demonstrated that soluble factors in the conditioned media were sufficient to fully recapitulate the RAR effect. RNA analyses of extracellular vesicles cargo revealed differential expression of miRNAs, particularly miR-126-3p and miR-451a, which we show play crucial roles in modulating the RAR. Notably, inhibition of miR-451a was sufficient to induce the RAR in cells that typically do not exhibit this response. Finally, we identified the p38-CCAR2 axis as a critical regulator of the RAR-mediated DNA end resection boost. p38 activation following priming irradiation block CCAR2 activity, facilitating a more efficient repair process. Collectively, our findings elucidate a novel mechanism by which EV-mediated communication and specific miRNA signaling enhance HR efficiency in response to radiation, offering insights into potential therapeutic applications in radiotherapy.

overall_design: RNA-seq profiling of extracellular vesicles primed vs non-primed 5 hours after the irradiación

first: María del Carmen

last: Domínguez-Pérez

first: Néstor

last: García-Rodríguez


title: Chemical tracking of DNMT1-specific activity during mESC ground state transition

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Cardiac fibroblast deletion of PTBP1 modulates the profibrotic response by alternative splicing

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: In this project we investigate the role of RNA binding protein PTBP1 in cardiac fibrosis through the conditional deletion of PTBP1 in mouse cardiac fibroblasts. We used eCLIP-seq to identify direct RNA targets of PBTP1 in adult mouse hearts that contribute to cardiac fibrosis.

overall_design: Well established eCLIP protocol was used. 2 IP libraries were generated and 2 size matched inputs (SMI) were generated for the study.

first: Sunil

last: Verma

first: Muge

last: Kuyumcu-Martinez

first: Eclipse

last: Bioinnovations

first: Li

last: Quan

first: Shea

last: Ricketts


title: Atg5 inhibits fibroblast activation and promotes alveolar regeneration to alleviate pulmonary fibrosis

city: Tianjin

first: guiying

last: xu

address: No.890 Jinggu Road

institute: Tianjin Haihe Hospital

summary: Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibrotic disease, alveolar epithelial injury and fibroblast activation are two key stages in the progression of the disease. Under injury, autophagy often initiated to maintain cell survival and promote tissue regeneration. Here, we show that autophagy, a conserved cellular process, is upregulated in the mesenchymal cells of lung tissue in IPF patients and in a murine model of bleomycin-induced fibrosis. Our findings indicate that Atg5, a crucial autophagy-related gene, when conditionally deleted in mesenchymal cells, renders mice more susceptible to bleomycin-induced fibrosis. Mechanistically, this is mainly due to the loss of Atg5 exacerbating the activation of fibroblasts induced by TGF-β1, the proliferation of myofibroblasts, and the deposition of extracellular matrix. Intriguingly, as an important niche for alveolar type 2 (AT2) cells, the absence of Atg5 impairing the secretion of factors essential for AT2 cell proliferation and differentiation. These results indicated that autophagy can inhibit the differentiation of fibroblasts into myofibroblasts resulting in extracellular matrix deposition, while promoting alveolar epithelial regeneration. Screening for small molecule compounds that enhance the expression of Atg5 can effectively alleviate the progression of bleomycin-induced lung fibrosis in mice. In summary, our data support the possibility that Atg5 could be a potential clinical target for IPF management.

overall_design: To investigate the role of Atg5 in lung mesenchymal cells in the context of homeostasis and bleomycin injury, we induced Atg5 knockdown in lung mesenchymal cells of Tbx4CreER;Atg5f/f mice by tamoxifen, and then wild-type mice and Tbx4CreER;Atg5f/f mice were treated with either PBS or bleomycin. Lung cells were isolated for analysis on day 14 after bleomycin treatment.

first: Xue

last: Li

first: Guiying

last: Xu

first: Qi

first: Qingwen

last: Ma

first: Hongwei

first: Sisi

first: Yimeng

last: Liu

first: Yueyue

last: Jin

first: Xuan

last: Miao

first: Zuokuan

last: He

first: Jinrui

last: Dong

first: Kuan

first: Jianhai

first: Yu

first: Qiuyang

last: Zhang

first: Junping

last: Wu

first: Wen

last: Ning

first: Huaiyong

last: Chen


title: Depletion of lamin-associated polypeptide 2 alpha leads to chromatin reorganization and redistribution of A-type lamins to open genomic regions [RNA-seq]

city: Vienna

first: Roland

last: Foisner

address: Dr.-Bohr-Gasse 9

country: Austria

institute: Max Perutz Labs, Medical University of Vienna

summary:
Background: Lamins are major regulators of the spatial and functional organization of chromatin. Lamins at the nuclear periphery form the lamina that anchors heterochromatin to the nuclear envelope. A subpool of A-type lamins localizes in the nuclear interior, where they also bind to euchromatic genomic regions. A-type lamin properties and chromatin association are regulated by lamin-associated polypeptide 2alpha (LAP2α). Here we systematically analyze, how LAP2α depletion affects chromatin organization, accessibility and gene expression on a genome-wide level.
Results: LAP2α depletion in mouse dermal fibroblasts positively and negatively affects chromatin accessibility and gene expression throughout the genome, which correlates with changes in chromatin association of A-type lamins and the nucleosomal remodeler proteins BRG1 and CHD4. In particular, A-type lamins translocate to open chromatin regions closer to BRG1 and CHD4 binding sites and deregulated genes, but do not directly accumulate on genes and BRG1 and CHD4-enriched sites. Unsupervised clustering of the datasets on LAP2α-bound genomic regions confirms spreading of A-type lamins to active chromatin regions containing deregulated genes, and an enrichment of chromatin remodelers on a subset of these genomic regions.
Conclusions: LAP2α depletion in fibroblasts leads to a gross rearrangement of chromatin. Genome-wide chromatin reorganization is linked to spreading of A-type lamins to active chromatin regions and accompanied by a restriction of chromatin remodelers to a subset of active genomic regions. These changes correlate with changes in chromatin accessibility and gene expression throughout the genome and particularly in regions, where lamin binding is gained in LAP2α knockout versus wildtype cells.

This research was funded in whole or in part by the Austrian Science Fund (FWF) [P32512-B and P36503-B] to Roland Foisner, and a doctorate program funded by the Austrian Science Fund (FWF) [W1261-B28]. Daria Filipczak is recipient of a DOC Fellowship of the Austrian Academy of Sciences  (ÖAW DOC 25912); This work is also supported by a Marie Jahoda fellowship of the University of Vienna to Nana Naetar.

overall_design: Gene expression profiling by RNA-sequencing of wildtype and Lap2alpha KO mouse dermal fibroblast.

first: Daria

last: Filipczak

first: Fatih

last: Sarigol

first: Daniel

last: Malzl

first: Nana

last: Naetar


title: Low-intensity Pulsed Ultrasound regulates osteoclasts mitochondrial function in the treatment of diabetic periodontitis [scRNA-seq]

city: Chongqing

first: Li

last: houxuan

address: Medical College Road, Yuzhong District,

institute: Chongqing Medical University

summary: Periodontitis and type Ⅱ diabetes mellitus (T2D) have emerged as prevalent global chronic diseases, with a bidirectional relationship existing between them.  Individuals with periodontitis and T2D are susceptible to tooth loss, primarily attributed to alveolar bone resorption resulting from excessive osteoclasts (OC) differentiation.  Although low-intensity pulsed ultrasound (LIPUS) is an established treatment method for bone-related conditions, its mechanism of action on OC remains unclear.  The aim of this research is to examine the effects and mechanism of on OC within a diabetic inflammatory environment.  In summary, our data explored how LIPUS affects OC in the inflammatory environment of diabetes.

overall_design: LIPUS treatment was investigated in diabetic and non-diabetic periodontitis mice using single-cell sequencing of maxillary alveolar bone tissue.

first: Houxuan

last: Li

first: Shuhong

first: Yunchun

last: Kuang

first: Jie

first: Jinlin

last: Song


title: The zebrafish model tackles anti-P2Y12 variability in humans: a translational approach

city: Geneva

first: Pierre

last: Fontana

state: Geneva

address: Rue Michel-Servet 1

department: Medicine

country: Switzerland

institute: University of Geneva

summary: Antiplatelet drugs are a pillar in the treatment strategy to prevent ischemic events in cardiovascular patients. However, the action of existing therapies is nonuniform, and the causative mechanism for this variability remains poorly understood. The differences between the microRNA profiles of individuals have been suggested to impact platelet reactivity and treatment outcomes. microRNA-150 (miR-150) has been previously associated, in several clinical reports, with platelet function variability and cardiovascular events. Therefore, we initiated our analysis by examining the mechanistic role of miR-150 in platelet function. We employed transgenic zebrafish larvae designed to specifically increase miR-150 expression in thrombocytes. Laser-induced caudal vein injury in these animals resulted in a smaller thrombus and decreased thrombocyte accumulation. RNA sequencing of miR-150-overexpressing thrombocytes identified a downregulated transcript encoding microtubule associated serine/threonine kinase-like (mastl), a key regulator of P2Y12 receptor downstream signaling. Overnight treatment of the transgenic fish with clopidogrel, a P2Y12 inhibitor, showed decreased thrombus formation in the control, but not in miR-150-overexpressing animals. This phenotype was reversed by overexpressing mastl. Next, we utilized a VASP phosphorylation assay to show that MASTL deficiency partially protects human platelets from P2Y12 inhibition. Finally, using miRNA:mRNA interaction predictors and experimental assays, we identified MASTL-targeting miRNAs in humans – miR-17-5p and miR-106a-5p – which were significantly upregulated in a population of clopidogrel-resistant patients. Our studies therefore support a model in which miR-150 in zebrafish, and miR-17-5p or miR-106a-5p in humans, modulates MASTL expression, which in turn alters VASP phosphorylation and platelet sensitivity to P2Y12 inhibition.

overall_design: RNAseq profiling of FACS sorted thrombocytes obtained from Tg(itga2b:tagRFP) and Tg(itga2b:miR-150-tagRFP) zebrafish larvae at 5 days post fertilization.

first: Paulina

last: Ciepla

first: Richard

last: Fish

first: Séverine

last: Nolli

first: Sylvie

last: Dunoyer-Geindre

first: Julia

last: Charlon-Gay

first: Jean-Luc

last: Reny

first: Marguerite

last: Neerman-Arbez


title: RNA-seq data of SR30-overexpression transgenic tomato leaves

city: Nanjing

first: Dong

last: Yan

address: NO.1 Weigang

institute: Nanjing Agricultural University

summary: Alternative splicing (AS) plays a vital role in plant responses to biotic and abiotic stress. The modulation of host precursor-mRNA (pre-mRNA) AS is a common pathogenic strategy among distinct pathogens. However, the underlying mechanism by which how plants respond to pathogen-modulated AS remains largely elusive. Here, we fished out a serine/arginine-rich RNA splicing factor (SR) family protein gene, SR30, that promotes tomato susceptibility to P. infestans. To explore the effect of SR30 on host pre-mRNA AS, we examine AS change in SR30 overexpression (SR30-OE) Solanum lycopersicum leaves compared to wild type using paired-end illumina RNA-seq. A large number of AS events are identified, indicating SR30 regulates the AS of tomato pre-mRNA. The overlap between differentially expression genes (DEGs) and differentially alternative splicing genes (DASGs) was low, indicating that most genes were unique to either pre-mRNA splicing or DEGs. SR30 overexpression represses the AS of tomato defense-related genes. Moreover, we also demonstrated that SR30 is upregulated and forms nuclear speckles through phase separation driven by intrinsically disordered regions (IDRs) during Phytophthora infestans. IDR2 and IDR5 deletion mutant SR30ΔIDR2&5 failed to phase separate and promote P. infestans infection. Importantly, the association between SR30 and tomato spliceosome components and the alternative splicing of host defense-related genes are altered in the SR30 in a phase-separate-dependent manner.

overall_design: To investigate the function of SR30 in regulation of pre-mRNA alternative splicing in tomato, we performed RNA-sequencing for six RNA samples from wild type control tomato leaves and SR30-overexpression (SR30-OE) transgenic tomato leaves, using three replicates for each treatment.

first: Suomeng

last: Dong

last: Huang


title: Nrf2-mediated chromatin activation of hyperosmotic response genes attenuates heat-induced renal injury

first: xudan

last: dou

state: Tianjin

address: No.22 Qixiangtai Road

institute: Tianjin Medical University


title: Nrf2-mediated chromatin activation of hyperosmotic response genes attenuates heat-induced renal injury [RNA-seq]

summary: The escalating frequency and duration of extreme weather events, driven by ongoing climate change, are heightening health hazards associated with heat stress. Heat stress can cause whole-body hyperosmolarity and increase risk of chronic kidney disease. Here, we confirmed Nrf2 as the core transcription factor for cellular resistance to hyperosmotic stress through drug screening. Meanwhile, we constructed a mouse model of renal injury caused by high temperature dehydration, genetic deletion of Nrf2 further increased the renal injury and fibrosis. The natural compound SFN, found in cruciferous plants, can be used to activate Nrf2 and alleviate kidney damage caused by high-temperature dehydration. Mechanistically, we performed hyperosmotic stress in kidney collecting duct cells, and through ATAC-seq and ChIP-seq analysis of multiple histone modifications, found that most of the hyperosmotic response genes changed their chromatin state after pharmacological activation of Nrf2. The activation of the chromatin state in hyperosmotic response genes enhances the binding affinity of Nfat5 following exposure to hyperosmotic stress. Together, activation of Nrf2 maintains the active chromatin state of hyperosmotic response genes. Under hyperosmotic stress, the core transcription factor Nfat5 efficiently activates gene expression, thereby assisting cells in resisting hyperosmotic stress. Additionally, activation of Nrf2 by SFN may serve as a potential therapeutic approach for preventing renal injury caused by high-temperature dehydration.

overall_design: mIMCD3 cells were cultured in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) medium containing 10% fetal bovine serum (FBS) at 37°C in a humidified 5% CO2 atmosphere. RNA was extracted from mIMCD3 cells after treatment with DMSO or SFN (10µM) for five hours. RNA was extracted from mIMCD3 cells after treatment with DMSO or SFN (10µM) for five hours, followed by replacement with hypertonic medium (600 mOsm) for one hour.

first: YI

last: Lu

first: Lirong

last: Zhang


title: Nrf2-mediated chromatin activation of hyperosmotic response genes attenuates heat-induced renal injury [ChIP-seq]

overall_design: mIMCD3 cells were cultured in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) medium containing 10% fetal bovine serum (FBS) at 37°C in a humidified 5% CO2 atmosphere. mIMCD3 cells were treated with DMSO or SFN (10µM) for five hours, followed by fixation and sonication, and then Nrf2 or Nfat5 antibodies were added. After treating mIMCD3 cells with DMSO or SFN (10µM) for five hours, the medium was replaced with hypertonic medium (600 mOsm) for one hour, followed by fixation and sonication, and then Nrf2 /Nfat5/different histone antibodies were added.


title: Spatial transcriptomic sequencing of day 7 tumors in G422TN-GBM model

city: Wuhan

first: Hai-Feng

last: Jiang

state: Hubei

address: No.13, Hanghang Road, Baofeng Street, Qiaokou District, Wuhan City, Hubei Province

institute: Huazhong University of Science and Technology

summary: Glioblastoma are difficult to treat because they recur quickly after treatment caused by highly aggressive tumor cells at the distal end of the tumor entity. We created a new G422TN-GBM (TN: triple negative, i.e., wild type IDH1/2, chromosome1/19 Intact and wild type TERT-promoter) model that is highly consistent with the pathological features, immune response and therapeutic response of GBM. Based on this model, we performed spatial transcriptome of intravranial G422TN-tumor at day 7 post implantaion of G422TN-cells.

overall_design: Mice were injected with 50,000 G422TN cells in the striatum. When the tumor grew to the 7th day, the brain tissue was taken for frozen section, and the maximum interface of the tumor was found for spatial transcriptome sequencing.

first: Xiao-Qian

last: Chen

first: Pan-Pan

last: Gao


title: Placenta gene expression postdevelopmental exposure to perfluorooctanoic acid (PFOA) or hexafluoropropylene oxide-dimer acid (HFPO-DA or GenX) in CD-1 mice

city: Research Triangle Park

first: Suzanne

last: Fenton

state: North Carolina

address: 111 TW ALEXANDER DR

department: Mechanistic Toxicology Branch

institute: Division of the National Toxicology Program, National Institute of Environmental Health Sciences

summary: Multiple per- and polyfluoroalkyl substances (PFAS) have been associated with adverse pregnancy and birth outcomes in humans and animals. While the underlying mechanism(s) through which exposure to PFAS may induce these adverse pregnancy and birth outcomes is not known, it has been posited that the placenta may be an important target and/or mediator. We performed whole-transcriptome gene expression analysis to investigate the molecular mechanisms underpinning the effects on placental health after prenatal exposure to two different PFAS, perfluorooctanoic acid (PFOA) and its replacement, hexafluoropropylene oxide-dimer acid (HFPO-DA, commonly referred to as GenX). This dataset is derived from sequencing of the same animals that were reported in GSE199233.

overall_design: Pregnant CD-1 mice were exposed via daily oral gavage from embryonic day (E) 1.5 to E 11.5 (early developmental gestation) or E 17.5 (mature gestation) to PFOA (0, 1, or 5 mg/kg) or GenX (0, 2, or 10 mg/kg). The uterus was removed and the placentas from viable embryos were collected, RNA was isolated (N=5 per dose/group), and transcriptome-wide gene expression was quantified.

first: Bevin

last: Blake

first: Colette

middle: N

last: Miller

first: Helen

last: Nguyen

first: Vesna

middle: A

last: Chappell

first: Trina

middle: P

last: Phan

first: Dhiral

last: Phadke

first: Michele

last: Balik-Meisner

first: Ignacio

last: Tripodi

first: Deepak

last: Mav

first: Ruchir

last: Shah


title: Transcriptomic analysis of embryonic hearts from the Dp1Tyb mouse model of Down syndrome using scRNAseq

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: We performed single cell RNAseq on whole hearts from E13.5 Dp1Tyb embryos and from wild-type littermates.

overall_design: Single cell RNAseq analysis of 5 E13.5 Dp1Tyb embryonic hearts, and 9 wild-type embryonic hearts.

first: Eva

last: Lana-Elola

first: Miriam

last: Llorian


title: RNA-seq of miR-34a-5p treated primary human vascular endothelial cells

city: St. Louis

first: Rajendra

last: Apte

state: MO

address: 660 S Euclid Ave

department: Ophthalmology

institute: Washington University School of Medicine in St. Louis

summary: We identified that miR-34a-5p expression is upregulated in choroidal vascular endothelial cells in a mouse model of laser induced choroidal neovascularization. Therefore, in this experiment we assess the effect of miR-34a-5p treatment on the transcriptome of primary human vascular endothelial cells.

overall_design: We used primary human umbilical vein endothelial cells (HUVECs, ATCC PCS-100-010 ). These cells were maintained in Vascular Cell Basal Media (ATCC PCS-100-030) supplemented with Endothelial Cell Growth Kit-VEGF (ATCC PCS-100-041). We treated HUVECs with either a scrambled control mimic (QIAGEN Cat. #339173) or a hsa-miR-34a-5p mimic (QIAGEN Cat. #339173) for 48h. Then, we washed cells with PBS, isolated RNA, and prepared samples for RNA-sequencing using the RiboErase rRNA depletion kit.

first: Jason

last: Colasanti


title: ERα/miR-26a/ANKRD52 axis regulates progression of MASH- associated HCC in HDTVi HCC models

city: Xi'an

first: Renji

last: Wei

address: Changle West Road, Xincheng District

institute: Fourth Military Medical University

summary: The lack of robust mouse models for metabolic dysfunction-associated steatohepatitis-hepatocellular carcinoma (MASH-HCC) severely hinders mechanistic investigation and therapeutic drug development. Conventional MASH-HCC animal models require a lengthy induction period of more than 10 months, greatly limiting high-throughput mechanistic studies and drug screening.

overall_design: Herein, we combined hydrodynamic tail vein injection (HDTVi) with the Sleeping Beauty (SB) transposon system and oncogenic drivers to generate mouse MASH-HCC models and longitudinally monitor tumor development. Notably, this HDTVi/SB transposon-based strategy achieves successful MASH associated tumor formation within only 1–2 months, drastically shortening the modeling timeline. We recapitulated core MASH-associated pathological features in these mice, including prominent hepatomegaly, elevated circulating liver injury biomarkers, and typical hepatic histologic lesions (hepatocellular ballooning, macrovesicular steatosis, progressive fibrosis), accompanied by robust hepatic inflammatory infiltration. Furthermore, estrogen receptor α (ERα) transcriptionally activates miR-26a, which acts as a critical tumor suppressor to restrain MASH-HCC initiation and progression. Mechanistically, ANKRD52 is a direct, functionally relevant target of miR-26a; this gene accelerates HCC cell proliferation and disease progression via reprogramming hepatic lipid metabolism. In conclusion, our HDTVi/SB transposon-based strategy enables efficient, reliable establishment of murine MASH-HCC models within 1–2 months. Moreover, the ERα-miR-26a-ANKRD52 signaling axis critically modulates the full progression of MASH-HCC.


title: Nrf2-mediated chromatin activation of hyperosmotic response genes attenuates heat-induced renal injury [ATAC-seq]

first: xudan

last: dou

overall_design: mIMCD3 cells were cultured in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) medium containing 10% fetal bovine serum (FBS) at 37°C in a humidified 5% CO2 atmosphere. mIMCD3 cells were treated with DMSO or SFN (10µM) for five hours.

first: YI

last: Lu

first: Lirong

last: Zhang


title: Evolution of CCNB1IP1 regulating emergence and increase of cortical folding in primates

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

institute: Kunming Institute of Zoology

summary: Cortical expansion and folding have gradually increased during primate evolution, reaching the highest in the human brain. Indeed, cortical folding has a concerted relationship with neocortex expansion, underlying evolution of human cognitive functions. However, molecular mechanisms underlying concerted evolution remain largely unknown. Here, using Chinese tree shrew as an outgroup of primate, we identify the Cyclin B1 Interacting Protein 1 gene CCNB1IP1 (also named HEI10) as a key regulator of cortically concerted evolution. CCNB1IP1 has acquired brain expression in primates, and is highly expressed in human neuronal progenitor cells. The expression of CCNB1IP1 has gradually increased along primate brain evolution, coinciding with the increase of cortical size and folding. Mechanistically, we elucidated that overexpression of CCNB1IP1, leading to a decrease of G1 duration, and subsequently causes an increase in basal progenitors and neurons. Furthermore, we generated a novel CCNB1IP1 knock-in mouse model and provide confirmation that CCNB1IP1 can induce cortical folding in otherwise smooth mouse brain. Moreover, the CCNB1IP1 knock-in mouse model exhibited traits associated with enhanced learning and memory abilities. Together, our study reveals how the changes in CCNB1IP1 expression may have contributed to the increase of cortical size and folding during human brain evolution.

overall_design: We performed RNAseq on fetal cortex of Chinese tree shrew.

first: Lei

last: Shi


title: Genomic profiling of estrogen-related receptor identifies adult adipocyte-specific targets in Drosophila

city: Bloomington

first: Lesley

middle: Nicole

last: Weaver

state: IN

address: 1001 E. 3rd Street

department: Biology

institute: Indiana University

summary: Estrogen-related receptor (ERR) is a conserved nuclear receptor required for energy homeostasis. Here, we took a modified DamID genomic profiling approach (NanoDam) to identify ERR-specific targets in adult Drosophila male and female adipocytes. We found that ERR binds to the loci of genes encoding enzymes involved in glycolysis, the pentose phosphate pathway, and beta-oxidation.

overall_design: To determine the regions of the Drosophila genome bound by ERR in adipocytes, we expressed a UAS-NanoDam (contains the Dam methyltransferase fused to a GFP nanobody) construct in the absence and presence of an endogenously C-terminal eGFP-ERR construct for 14 hours. Whole flies were collected and genomic DNA was isolated processing. In this setup, only targets bound by ERR specifically in adipocytes would be methylated.


title: Multi-stage single-cell atlas of a chordate non-embryonic development unveils dedifferentiating bud founder cells

city: Exeter

first: Marie

last: Lebel

address: Stocker Road

department: Biosciences

institute: University of Exeter

summary: Colonial tunicates are the only chordates capable of forming fully functional bodies from somatic tissues through non-embryonic development, or budding. In Botryllus schlosseri, budding produces new individuals (zooids) from a portion of the peribranchial epithelium of a preexisting zooid. While the anatomy of this process has been described in detail, the cellular and molecular mechanisms underpinning bud initiation remain elusive. Here, we present a multi-stage single-cell transcriptomic atlas of a non-embryonic development in a chordate, capturing initiation and development of zooids. We identify an epithelial founder cell population that gains developmental potential through possible dedifferentiation, challenging the long-standing hypothesis that a long-lived, circulating pluripotent stem cell drives new zooid formation. Although some circulating cells exhibit stem-like expression profiles, these populations were either hematopoietic or germline restricted lineages. This atlas provides a foundational resource for understanding the cellular origin and mechanisms underlying agametic development and possibly whole-body regeneration in chordates.

overall_design: Budlets and buds from seven successive blastogenetic stages of Botryllus schlosseri were dissected from colonies, pooled by developmental stage, enzymatically dissociated into single-cell suspensions, fixed with ACME, sorted by FACS, and processed for single-cell RNA sequencing. Circulating cells were extracted from colonies at two different developmental stages, pooled by stage, and immediately processed for single cell RNA sequencing.

first: Alexandre

last: Alié

first: Stefano

last: Tiozzo

first: Tal

last: Scully

first: Allon

middle: M

last: Klein


title: Role of adenosine deaminase in prostate cancer progression

city: Houston

first: Arun

last: Sreekumar

state: Texas

address: One Baylor Plaza

department: Molecular and Cell Biology

institute: Baylor College of Medicine

summary: Prostate cancer (PCa) is the second most common cancer and constitutes about 14.7% of total cancer cases. PCa is highly prevalent and more aggressive in African-American (AA) men when compared to European-American (EA) men. PCa tends to be a highly heterogeneous malignancy with a complex biology that is not fully understood. We use metabolomics as a tool to understand the mechanisms behind PCa progression and disparity. A key enzyme in the purine metabolic pathway, Adenosine deaminase (ADA) was found upregulated in PCa.  In an attempt to understand the significance of high ADA in PCa, we established ADA overexpression models and performed various in vitro and in vivo studies.

overall_design: To understand the significance of ADA at later stages in tumor progression, tet-inducible ADA overexpression cell lines were used in vivo. 22Rv1 and C4-2B cell lines that are more robust and have better in vivo tumorigenicity were used for this study. The cells were injected without ADA induction and were maintained without induction until tumors were formed (50mm3). ADA expression was induced after the tumors reached 50mm3 and the growth rate was monitored until the tumors reached 500mm3. Upon ADA induction, the tumors experienced a growth spurt. The ADA-OE-induced tumors grew faster than the control tumors in both 22Rv1 and C4-2B models. The induction of ADA was verified by qPCR after the tumors were harvested. RNA sequencing was done on these tumors to understand the mechanisms that drivethe tumor growth.


title: Genome-widebinding maps of arabidopsis HDL

city: Taipei

first: Fu-Yu

last: Hung

address: Institute of Plant Biology, National Taiwan University

institute: NTU, IPB

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of HDLpro::HDL-YFP in 10 days old KYPpro::KYP:3xFLAG arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide binding levels of KYP:3xFLAG. ChIP was performed using anti-FLAG antibody (sigma M2), and ChIP DNA were analyzed by Illumina NovoSeq.

overall_design: Chromatin immunoprecipitation was performedwith HDLpro::HDL-YFP arabidopsis. IP DNA was analyzed by Illumina NovaSeq.

first: Chin-min

last: Ho

first: Yun-Ru

last: Feng


title: The evolution of the type I IFN transcriptional response across human populations

city: Boulder

first: Robin

middle: D.

last: Dowell

state: CO

address: 596 UCB

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

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

overall_design: Refer to individual Series


title: Identification of Human Specific Expressed Genes in the Fetal Brain

summary: The expansion of human neocortex is the cornerstone of highly developed cognitive abilities which distinguishes human from primates, but the molecular basis underlying it remains elusive. Here, we comprehensively compared the transcriptomes of neural precursor cells-enriched germinal zone (GZ) and neurons-enriched cortical plate (CP) of neocortex among human, macaque and mouse to identify human specific expressed genes (HSEGs) for each layer. The data identified that the HSEGs have evolved to transfer between the layers and also annotated the primate originated HSEGs. Further, we assessed the contributions of regulatory factors to the evolution of HSEGs. Finally, we analyzed such a new identified HSEG named CCNB1IP1 and discovered that the evolution of cis regulatory elements caused the gene to develop human specific pattern. Subsequent functional results showed that CCNB1IP1 could repress the expression of cell cycle related genes by interacting with E2F1, thereby shortening the length of the G1 phase. Thus, our study is firstly to identify HSEGs in the fetal cortex and reveals how CCNB1IP1 regulated cell cycle progress which contributed to the expansion of human cortex potentially.

overall_design: We performed RNAseq on SH-sy5Y cells transfected by GFP and GFP-CCNB1IP1 expression vectors.


title: The evolution of the p53 transcriptional response across primates

sample_organism:
Gallus gallus
Macaca mulatta
Papio anubis
Gorilla gorilla
Pan paniscus
Pan troglodytes
Pongo pygmaeus
Homo sapiens
Bos taurus
Saimiri boliviensis
Aotus nancymaae
Nomascus leucogenys


title: The KDM1A and KDM7A lysine demethylases cooperate to regulate androgen receptor function in prostate cancer cells [KDM1A & KDM7A inhibitors]

city: Nottingham

first: Nigel

last: Mongan

address: University Park

department: Biodiscovery Institute

institute: University of Nottingham

summary: KDM1A and KDM7A are Androgen Receptor coregulators. Here the KDM1A and KDM7A inhibitors, namoline and TCE-5002 were used to pharmacologically inhibit KDM1A and KDM7A in prosate cancer cells and the effect on androgen regulated gene expression and splicing determined.

overall_design: The roles of KDM1A/LSD1 and KDM7A/JHDM1D on basal and androgen (R1881, 1nM) regulated gene expression and alternative splicing in hormone dependent LNCaP and castrate resistant LNCaP:C42 prostate cancer cells was determined using RNA sequencing. LNCaP and LNCaP:C42 cells were grown in phenol red-free RPMI-1640 medium supplemented with 1% penicillin-streptomycin, 2mM L-Glutamine and 1 mM sodium pyruvate and 10% charcoal-stripped FBS and were treated with androgen (R1881, 1nM), KDM1A inhibitor (namoline, 50µM) and/or KDM7A inhibitor TCE-5002 (100µM) for 72 hours.

first: Jennie

last: Jeyapalan

first: Veronika

last: Metzler

first: Simone

last: de Brot

first: Daisy

last: Haigh

first: Corinne

last: Woodcock

first: Jennifer

last: Lothion-Roy

first: Anna

middle: E

last: Harris

first: Emeli

last: Nilsson

first: Atara

last: Ntekim

first: Jenny

last: Persson

first: Brian

last: Robinson

first: Francesca

last: Khani

first: Kristian

middle: B

last: Laursen

first: Lorraine

last: Gudas

first: Michael

last: Toss

first: Emad

last: Rakha

first: David

last: Heery

first: Catrin

last: Rutland


title: The KDM1A and KDM7A lysine demethylases cooperate to regulate androgen receptor function in prostate cancer cells [siKMD1A & siKDM7A]

first: Nigel

last: Mongan

summary: KDM1A and KDM7A are Androgen Receptor coregulators. Here siRNAs targeting KDM1A and KDM7A were used to deplete KDM1A and KDM7A in prostate cancer cells and the effect on androgen regulated gene expression and splicing determined.

overall_design: A pool of siRNAs were used to deplete KDM1A/LSD1 and KDM7A/JHDM1D in hormone dependent LNCaP and castrate resistant LNCaP:C42 prostate cancer cells and the effect on basal and androgen (R1881, 1nM) regulated gene expression and alternative splicing determined using RNA sequencing.

first: Jennie

last: Jeyapalan

first: Veronika

last: Metzler