title: Staphylococcus aureus delays wound repair by harnessing the agr quorum sensing system to target keratinocyte lipid metabolism [bulkRNA-seq]

first: Michelle

last: Bagood

summary: NHEKs wounded by scratch and incubated with CM for 24 hours were evaluated by bulk RNAseq. Principal component analysis of these data revealed wounded NHEKs exposed to S. hominis products clustered close to control keratinocytes, suggesting these groups have similar transcriptomes, while the presence of S. aureus products caused variation shift in the transcriptome to result in a distinct cluster away from control. This was supported by a heatmap of differential gene expression of S. aureus and S. hominis CM treatment showing broad S. aureus-mediated suppression of genes induced by S. hominis. Conversely, upregulation of many genes by S. aureus were downregulated by S. hominis.

overall_design: Bulk RNA-sequencing was performed on normal human keratinocytes cultured with or without sterile conditioned media from commensal and pathogenic staphylococcus treatment [in vitro].


title: The evolution and heterogeneity of lethal metastatic bladder cancer subtypes

status: Public on Aug 01 2025

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

country: USA

institute: FHCRC

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Tumour genotype shapes blood biomarker expression for use in pancreatic cancer detection and diagnosis

city: Edinburgh

first: Alan

last: Serrels

address: Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University of Edinburgh

summary: Typically diagnosed late, when systemic metastasis has already occurred, pancreatic ductal adenocarcinoma (PDAC) has one of the worst 5-year survival rates of any cancer type. For many patients with advanced disease, current chemotherapy regimens offer only modest benefit despite significant toxicity and surgical resection, the only treatment option with curative potential, is not possible. Therefore, while new treatments are much needed, diagnosing patients at an ‘earlier’ disease stage when surgery remains possible and the window of opportunity for treatment response is longer will be critical to improving patient outcomes. In this regard, the identification of biomarkers from biospecimens that can be easily sampled from patients remains the focus of considerable research, however success has not been forthcoming. Using a suite of novel genetically defined murine isogenic models of early PDAC, engineered using CRISPR-Cas9 gene editing, we sought to address whether loss-of-function mutations in common driver genes, and thus the genetic heterogeneity inherent to the disease, may represent an important confounding factor in the identification of a one-size-fits-all biomarker suitable for early detection. Focussing on the multi-omics analysis of blood, we show that both loss of Cdkn2a and / or Smad4 on the background of a KrasG12D Trp53-/- genotype has profound effects on the profile of differentially expressed RNA species including protein coding RNAs, lncRNAs, snoRNAs, scRNAs, snRNAs and miRNAs, and on plasma protein expression, when compared to both healthy controls and chemically induced pancreatitis. In addition, we find that loss of Smad4, a genomic event that occurs following progression from PanIN to PDAC, substantially limits the availability of blood biomarkers. These findings identify the need to move towards genotype-specific biomarker signatures and uncover a potential role for Smad4 loss in limiting opportunities for the early detection of pancreatic cancer.

overall_design: To investigate the impact of common driver gene loss-of-function on blood biomarker expression we isolated RNA from whole blood from mice harbouring pancreatic tumours established from cell lines engineered to model different genetic backgrounds common to human pancreatic cancer.

first: Marta

last: Canel


title: UBR5 Mediates Menin Inhibitor Dependent Menin/KMT2A Complex Stability [RNA-seq]

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

summary: The chromatin adaptor protein Menin (MEN1) is required by acute leukemias driven by mixed lineage leukemia 1 gene rearrangements (KMT2A-r) for sustained leukemogenesis. Menin inhibitors (MIs), which disrupt the Menin-KMT2A interface leading to downregulation of Menin-KMT2A oncogenic transcriptional programs, have shown promising results in recent clinical trials treating acute myeloid leukemia (AML). Decreased Menin protein stability has been observed following treatment with several MIs though proteasomal degradation, though the biological mechanisms that control Menin stability are not well understood. Here we interrogate and compare five clinical MIs and two pre-clinical compounds to characterize the mechanism by which MIs induce Menin degradation and demonstrate that the loss of the Menin-KMT2A interaction results in decreased protein stability of Menin and KMT2A. We have identified the HECT E3 ubiquitin ligase UBR5 as a regulator of Menin protein stability and demonstrate that UBR5 binds to similar sites as the Menin/KMT2A complex on chromatin. Loss of UBR5 leads to transcriptional rescue of Menin-KMT2A target genes leading to decreased sensitivity to all MIs. Thus, we present UBR5 as an important regulator of Menin/KMT2A complex stability and Menin destabilization/subcellular localization as a designable feature of Menin inhibition targeting KMT2A-r leukemias.

overall_design: Using RNA-seq to test gene expression changes upon UBR5 depeltion and treatment with the Menin inhibitors KO-539 (25nM) and JNJ-6617 (25 nM) for three days.

first: Jevon

middle: A

last: Cutler

first: Jonathan

last: Tsai

first: Charlie

last: Hatton


title: UBR5 Mediates Menin Inhibitor Dependent Menin/KMT2A Complex Stability [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Using Chromatin enrichment strategies including ChIP-seq and biotinylated protein capture on chromatin to test genomic localization patterns of Menin, KMT2A, UBR5, IKAROS, MEIS1, NRF1 and ZNF692.


title: A-to-I editing and adr mutant gene expression in C. elegans germlines

city: BLOOMINGTON

first: Emily

middle: Ann

last: Erdmann

state: IN

address: 1001 E Third Street

department: Biology

institute: Indiana University

summary: In this study, we performed high-throughput RNA-seq on young adult germline samples from wild-type and adr-2(-) C. elegans hermaphrodites. A-to-I editing sites were identified using SAILOR. Differential gene expression analysis was performed using DESeq2.

overall_design: Germlines were isolated from synchronized young adult C. elegans hermaphrodites raised at 20 degrees C. Strains used include N2 and BB20 (adr-2(ok735)). RNA was extracted and poly-A selection was performed prior to library preparation.

first: Heather

last: Hundley


title: A high-fidelity RNA-targeting Cas13X downregulates connexin43 in astrocytes: A novel neuroprotective strategy for glaucoma

city: Shanghai

first: Guoli

last: Zhao

address: 131 Dongan Road

country: China

institute: Fudan University

summary: Glaucoma is a neurodegenerative disease characterized by the progressive degeneration of retinal ganglion cells (RGCs) and their axons, ultimately leading to irreversible vision loss. Elevated intraocular pressure (IOP) is the primary risk factor; however, neurodegeneration continues even after effective IOP management, underscoring the need for neuroprotective therapies. This study investigates the role of connexin43 (Cx43), which is extensively expressed in retinal macroglia, in regulating microglial activation and optic nerve degeneration in glaucoma. We employed a high-fidelity CRISPR-Cas13 (hfCas13X) system to selectively target and knock down Cx43 expression in astrocytes. Our findings reveal that Cx43-mediated ATP release through hemichannels exacerbates microglial activation and neuroinflammation, thereby contributing to RGC loss. Notably, in a mouse model of chronic ocular hypertension (COH) glaucoma, knocking down Cx43 in astrocytes using the hfCas13X system significantly promoted the survival of RGCs and the integrity of the optic nerve, and improved visual function. The hfCas13X system, which offers high-fidelity RNA editing with minimal off-target effects, represents a novel and promising therapeutic strategy for glaucoma, highlighting the potential of gene editing technologies in the management of neurodegenerative diseases.

overall_design: RNA-seq from retinal cells of control and WT-G3w and Cx43ko-G3w mice to investigate the neuroprotective mechanisms of conditional astrocyte Cx43 knockout in glaucoma.

first: Zhen

last: Li

first: Mingjie

first: Shuying

first: Qing

last: Xia

first: Shuoyu

last: Xu

first: Yu

last: Zhang

first: Yi

last: Wang

first: Fang

first: Yuling

last: Liu

first: Yunhui

last: Guo

first: Ruoxi

first: Han

last: Zhou

first: Hong

first: Wenwen

last: Ding

first: Yongchen

first: Yanying

last: Miao

first: Zhongfeng


title: Nicotinamide Mononucleotide alleviates aging defects of Hutchinson-Gilford progeria syndrome

city: HangZhou

first: Yuyan

address: Yuhang Tang Road

institute: Zhejiang university

summary: Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic disorder characterized by mutations in the LMNA gene, resulting in progerin accumulation and accelerated aging, with limited therapeutic options currently available. This study demonstrates the significant therapeutic potential of nicotinamide mononucleotide (NMN) in alleviating HGPS phenotypes at both cellular and organismal levels. Using patient-derived induced pluripotent stem cell-mesenchymal stem cells (iPSC-MSCs), we demonstrated that enhancing NAD+ biosynthesis through NMN supplementation effectively restored mitochondrial function, reduced DNA damage and inflammatory markers, and mitigated oxidative stress. Furthermore, in G608G transgenic mouse models receiving NMN administration over four months, we observed significant improvements in fertility and gonadal function, enhanced cardiovascular parameters, ameliorated skin pathology, and extended lifespan. These comprehensive findings establish NMN supplementation as a promising therapeutic strategy for HGPS and potentially other aging-related disorders.

overall_design: To compare the different genes expression between G608G MSCs and G608G MSCs treated with NMN.

first: Ling

first: Mengchen

last: Wu


title: Viral genome sequencing data of HOS-Bat ACE2 TMPRSS2 cells infected with BANAL-20-236 at passage 10

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

type: Genome variation profiling by high throughput sequencing

summary: The BANAL-20-236 virus was passaged in HOS-TMPRSS2 cells expressing ACE2 of R. ferrumequinum, R. sinicus, and R. shameli to study virological properties in vitro.

overall_design: Serially passaged the virus 10 times in the HOS-TMPRSS2 cells expressing R. ferrumequinum, R. shameli, or R. sinicus ACE2 with three independent wells for each Rhinolophus bat ACE2. The cultured supernatants in passage 10 were used to extract RNA for Viral genome sequencing

first: Luo

last: Chen

first: Shigeru

last: Fujita

first: Alfredo

last: Hinay Jr

first: Jumpei

last: Ito


title: A scalable two-step genome editing strategy for generating full-length gene humanized mice at diverse genomic loci

city: Minato

first: Manabu

last: Ozawa

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

institute: The University of Tokyo

summary: Full-length gene-humanized mice, generated by replacing mouse loci with their human counterparts including untranslated and regulatory regions, offer a powerful in vivo platform to study human gene function. However, reliable humanization of large genomic regions remains challenging due to limitations in DNA insert size, complex protocols, and reliance on specialized materials.  Here, we present a streamlined approach that enables full-length gene humanization through two sequential CRISPR-assisted homologous recombination steps in embryonic stem cells. This method supports targeted knock-in of genomic fragments exceeding 200 kbp and is applicable across multiple mouse strains. Humanized alleles generated using this strategy recapitulate human-like splicing isoforms and organ-specific gene expression, and restore essential functions in hematopoiesis, spermatogenesis, and survival. Furthermore, disease-associated mutations can be introduced into humanized alleles to generate in vivo models of human genetic disorders. This versatile platform enables creation of physiologically relevant, fully gene-humanized mouse models for broad applications in biomedical research.

first: Hideto

last: Mori

last: Taguchi


title: Single cell study on PBMCs collected from Rhesus macaques treated with IL-15/IL-15Ra ex-vivo

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: This single cell RNA-seq experiment is designed to understand the IL-15 response in ex-vivo IL-15 treated PBMCs from Rhesus macaques

overall_design: PBMCs from six Rhesus macaques were treated ex-vivo with heterodimeric IL-15 (IL-15/IL-15Ra).  6, 12, and 24 hours post treatment were collected for sequencing

first: Leanne

middle: S

last: Whitmore

first: Elise

last: Smith

first: Jean

last: Chang

first: Inah

last: Golez

first: Jennifer

last: Tisoncik-Go

last: Gale Jr


title: Transcriptome-wide effects of Tristetraprolin re-expression in an aggressive triple negative breast cancer cell model

city: Baltimore

first: Julia

middle: L

last: Rutherford

address: 108 N Greene St

institute: University of Maryland, Baltimore

summary: While much cancer research has elucidated the importance of regulation at the transcriptional level, regulation at post-transcriptional levels is less studied, and as such, could reveal novel opportunities for targeted therapy development to benefit clinical cancer research.  Tristetraprolin (TTP, also known as ZFP36) is an RNA-binding protein that has been described as a tumor suppressor in multiple cancers. Here, we conduct a global transcriptomic analysis in the MDA-MB-231 cell line, a triple negative breast cancer cell model, to investigate the effects of TTP re-expression on multiple pathways and phenotypes that play key roles in the development and progression of neoplasia.

overall_design: RNA-seq profiling of EV- and TTP-expressing cell lines in MDA-MB-231/tet-off cell model. MDA-MB-231 cells were stably transfected with the tet-off expression system prior to transfection with EV or TTP plasmids. Each line was sequenced in biological quadruplicate

first: Gerald

middle: M

last: Wilson


title: The conserved SEN1 DNA/RNA helicase has multiple functions during yeast meiosis

city: Stony Brook

first: Nancy

last: Hollingsworth

state: NY

address: 306 Life Sciences Building

department: Biochemistry and Cell Biology

institute: Stony Brook University

summary: Diploid Saccharomyces cerevisiae cells undergo meiosis when they are starved of nitrogen in the presence of a non-fermentable carbon source. Nutrient starvation triggers expression of Ime1, a master regulatory protein required to activate transcription of meiotic “early genes” that mediate premeiotic S phase and Prophase I processes, including recombination and chromosome synapsis. During prophase, the highly conserved, topisomerase-like protein, Spo11, generates ~200 double strand breaks that are used to identify homologous chromosomes and generate crossovers between them. DNA-RNA hybrids are formed when an RNA molecule anneals to a complementary strand of DNA and are present at the ends of double strand breaks during Prophase I of meiosis in a variety of organisms. One way of removing DNA/RNA hybrids is degradation of the RNA by RNase H. Phenotypic characterization of organisms lacking RNase H activity has demonstrated that regulation of the level of DNA-RNA hybrids is important for meiotic double strand break repair. Sen1 is an essential 5’-3’ DNA-RNA helicase that can remove DNA-RNA hybrids by unwinding the RNA. Sen1 is orthologous to the mammalian Senataxin (SETX) helicase. Mouse mutants lacking either Senataxin or RNase H activity exhibit male infertility and defects in double strand break repair. SETX is also required for meiotic sex chromosome inactivation, making it unclear whether SETX’s role in meiotic recombination is direct or an indirect consequence due to defects in SETX functions that affect transcription. Using a variety of orthogonal approaches, this work demonstrates that SEN1 has multiple, temporally distinct functions that promote yeast meiosis. First, it enables the timely expression of IME1-regulated early genes. Second, it helps prevent/remove DNA-RNA hybrids that form during premeiotic S phase. Third, it facilitates repair of Spo11 double strand breaks generated during Prophase I, as well as chromosome synapsis.

overall_design: RNA was extacted from SEN1 and sen1-md yeast (Saccharomyces cerevisiae) cells using the Qiagen RNeasy kit  at different times after the onset of meiosis.  Sequencing libraries were generated from enriched PolyA RNA using NEBNext Ultra RNA Library kit and analyzed by Illumina paired end sequencing.

first: Robert

last: Gaglione

first: Jonathan

last: Caradonna

first: Ed

last: Luk

first: Amy

last: MacQueen


title: RNA-seq result of yeast cells grown in glucose and glycerol condition

city: Novato

first: Fan

last: Zheng

state: California

address: 8001 Redwood Blvd, Novato, CA 94945

institute: BUCK INSTITUTE FOR RESEARCH ON AGING

summary: This project investigates transcriptomic changes in Saccharomyces cerevisiae in response to distinct metabolic environments. RNA-seq was performed on wild-type yeast cultured in glucose (fermentative) and glycerol (respiratory) media. The goal is to understand how mitochondrial ribosomal genes and nuclear gene expression are regulated in different metabolic states.

overall_design: Saccharomyces cerevisiae wild-type strain BY4741 was cultured in synthetic complete (SC) medium supplemented with either glucose or glycerol as the carbon source. Total RNA was extracted from cells grown under both conditions and submitted to Novogene for library preparation and RNA sequencing.

first: Zanlin

last: Yu

first: Yifan

last: Cheng

first: Chuankai

last: Zhou


title: Bulk RNA sequencing study on PBMCs collected from cynomolgus macaques treated with IL-15/IL-15Ra ex-vivo

first: Michael

last: Gale

summary: This bulk RNA-seq experiment is designed to understand the IL-15 response in ex-vivo IL-15 treated PBMCs from cynomolgus macaques

overall_design: PBMCs from six cynomolgus macaques macaques were treated ex-vivo with heterodimeric IL-15 (IL-15/IL-15Ra).  2, 6 12, 24, and 48 hours post treatment were collected for sequencing

last: Whitmore

first: Roni

last: Farkash


title: Single cell study on PBMCs from Rhesus macaques treated with IL-15/IL-15Ra

summary: This single cell RNA-seq experiment is designed to understand the IL-15 response in PBMCs from Rhesus macaques

overall_design: Five animals treated with heterodimeric IL-15 (IL-15/IL-15Ra) with increasing doses (5 ug/kg, 10ug/kg, 15 ug/kg) given at three time points (day 0, 3 and 7)

first: Leanne

first: Elise

last: Smith

last: Chang

last: Golez


title: Transcriptomic analysis of lipase TLL during the lipid expression process of Aspergillus niger at different time points.

city: kunming

first: le

last: yang

state: yunnan

address: cuihubeilu

institute: yunnan university

summary: Aspergillus Niger CICC2629 was used as the host strain to express Thermomyces lanuginosus lipase. The enzyme activity and enzymatic properties of the lipase were measured, and the expression ability of exogenous protein in the host strain was investigated using transcriptomics.

overall_design: The WT and lipase TLL expressing strains were collected at different time points (0,24, 48 and 72  hours) when the lipase was produced. Wild-type mycelial samples were collected and cDNA libraries were constructed for each sample for sequencing.

first: Le

last: Yang

first: Xiao yan

last: Shang

first: Zun xi

last: Huang


title: B cells specific for polyomavirus-derived oncoprotein are predictive of Merkel cell carcinoma progression

first: Haroldo

middle: Jose

last: Rodriguez

address: 850 Republican St

department: Medicine

institute: University of Washington

summary: Merkel cell carcinoma usually results from integration of an oncogenic version of the Merkel cell polyomavirus T-antigen. While T-antigen-specific antibodies are produced by most patients with T-antigen-driven MCC and are used to monitor disease recurrence, baseline antibody titers do not associate with MCC outcome. Here, we analyzed the frequency and phenotype of T-antigen-specific and total B cells from MCC patient blood and tumor samples in search of predictive biomarkers of disease outcome. While no blood-associated B cell phenotypes were strongly associated with disease outcome, the presence of detectable T-antigen-specific antibody-secreting and/or germinal center B cells in MCC patient tumor samples accurately predicted disease control. In vitro, B cells engineered to be specific for T-antigen were capable of robust activation T-antigen-specific CD4+ T cells. Together, these results show the predictive power of B cell responses in relation to MCC outcomes and may suggest that cancer-specific B cells enhance anti-tumor immunity.

overall_design:
Count matrices and B cell receptor sequences from single cell RNA sequencing data are included for immune and tumor cells found in Merkel cell carcinoma patient tumors

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

middle: J

first: Justin

last: Taylor

first: Paul

last: Nghiem


title: Myeloid cells are transcriptionally distinct between RhCMV/SIV vaccinated rhesus macaques protected from SIV and unvaccinated SIV-infected animals.

summary: The 68-1 rhesus cytomegalovirus (RhCMV) vector which expresses Simian Immunodeficiency Virus (SIV) genes (Gag/Tat/Nef/5-Pol) is effective in controlling and clearing SIV in rhesus macaques and the human ortholog vector is a vaccine candidate for the prevention of HIV.  Currently the RhCMV/SIV vaccine is only effective in ~55% (referred to as protected animals) of Rhesus Macaques.  A previous study by Barrenäs et al., 2021, showed that significant gene expression changes in a key set of IL-15 linked genes was correlated with a protection outcome. To further our understanding of the transcriptomic state if cells in protected animals and mechanisms of protection induced by the RhCMV vaccine we performed single cell RNA-sequencing on PBMCs from protected, non-protected and unvaccinated animals at longitudinal time points post SIV challenge. We identified monocytes, CD8 T cells and NK cells were primarily responsible for expression of genes in the IL-15 enriched protective signature. Myeloid cells were transcriptionally distinct 1) from all other cell types, 2) between nonprotected and protected vaccinated RMs and 3) between protected and unvaccinated SIV-infected animals.  Specifically, transcriptomics indicated that myeloid cells were more activated and mature in protected animals by the vaccine at pre-challenge and post-challenge time points. This suggests that the transcriptional state of myeloid cells is essential in eliciting a protection outcome and could be used to determine whether an animal will be protected after vaccination.

overall_design: Two cohorts of 15 Rhesus macaques (RM) were administered the 68-1 RhCMV/SIV vector expressing SIV Gag, Rev, Tat and 5-Pol either orally or subcutaneously. A homologous boost was given 18 weeks later.  A third cohort of 15 RMs received a modified 68-1.2 RhCMV/SIV vector expressing the same SIV proteins.  PBMCs were collect at baseline (prior to vaccination), pre-challenge (day 595 after vaccination and right before challenge with SIV) and 28, 56,84, and 140 days post SIV challenge.

first: Jin

last: Dai

first: Jean

first: Jennifer

last: Tisoncik-Go

last: Gale Jr


title: Targeting GLP-1 signaling ameliorates cystogenesis in a zebrafish model of nephronophthisis

city: Freiburg im Breisgau

first: Toma

middle: Antonov

last: Yakulov

address: Hugstetter Str. 55

department: Department of Medicine

country: Germany

institute: University Freiburg Medical Center

summary: Nephronophthisis (NPH) is the leading genetic cause of end-stage renal disease in children and young adults, with no effective disease-modifying therapies currently available. Here, we identify glucagon-like peptide-1 (GLP-1) signaling as a novel therapeutic target for NPH through a systematic drug repurposing screen in zebrafish. By simultaneously depleting nphp1 and nphp4, we developed a robust zebrafish model that recapitulates key features of human NPH, including glomerular cyst formation. Our screen revealed that dipeptidyl peptidase-4 (DPP4) inhibitors (Omarigliptin and Linagliptin) and GLP-1 receptor agonists (Semaglutide) significantly reduce cystogenesis in a dose-dependent manner. Genetic analysis demonstrated that GLP-1 receptor signaling is important for maintaining pronephros integrity, with gcgra and gcgrb (GLP-1 receptor genes) playing a particularly important role. Transcriptomic profiling identified adenosine receptor A2ab (adora2ab) as a key downstream effector of GLP-1 signaling, which regulates ciliary morphology and prevents cyst formation. Notably, nphp1/nphp4 double mutant zebrafish exhibited upregulation of gcgra as a compensatory mechanism, explaining their resistance to cystogenesis. This compensation was disrupted by targeted depletion of GLP-1 receptors or inhibition of adenylate cyclase, resulting in enhanced cyst formation specifically in the mutant background. Our findings establish a signaling cascade from GLP-1 receptors to adora2ab in regulating ciliary organization and preventing cystogenesis, offering new therapeutic opportunities for NPH through repurposing of FDA-approved medications with established safety profiles.

overall_design: We performed RNA sequencing analysis comparing nphp1/nphp4 morphant embryos treated with Omarigliptin versus DMSO controls. At 24 hours post fertilization (hpf), embryos were incubated with Omarigliptin (25 µM) or DMSO. At 48 hpf, total RNA was extracted from 15-50 embryos per replicate.

first: Priska

last: Eckert

first: Maike

last: Nöller

first: Merle

last: Müller

first: Rebecca

last: Haas

first: Johannes

last: Ruf

first: Henriette

last: Franz

first: Katharina

last: Moos

first: Jia-ao

last: Yu

first: Dongfang

last: Zhao

first: Melanie

last: Börries

first: Anna

last: Köttgen

first: Gerd

last: Walz


title: Bulk RNA sequencing study of female rhesus macaques given Modified versions of the RhCMV/SIV vector-based vaccines.

first: Michael

last: Gale

summary: This bulk RNA-seq experiment is designed to uncover the transcriptomic response to modified RhCMV vectors in whole blood of female rhesus macaques

overall_design: Female rhesus macaques were given a prime (D0) and boost (D126) of one of three modified RhCMV vector based vaccines. 1) A 68-1 RhCMV/SIV expressing Gag/RTN/Po,l 2) MiR-126R 68-1 RhCMV/SIVgag/rtn/pol  and  3) MiR-126R 68-1 RhCMV/SIVgag/rtn/pol-ST

first: Leanne

last: Whitmore

last: Chang

first: Elise

last: Smith

first: Lynn

last: Law


title: Illumina sequencing of CRAC data obtained with Upf1 in yeast

city: Paris

first: Gwenael

last: Badis

address: 46 rue d'Ulm

department: Genomique fonctionnelle (Section 2)

country: France

institute: IBENS

summary: The nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic cytoplasmic surveillance pathway that degrades aberrant mRNAs carrying premature termination codons (PTC). In yeast, the long distance between the stop codon and the poly(A) tail dictates mRNA detection by NMD factors Upf1, Upf2 and Upf3, and trigger mRNA decay, independent of deadenylation. While Upf1 binds a wide range of mRNAs beyond PTC-containing substrates, the mechanism of its recruitment on non-PTC-containing mRNAs is unknown. Using Nanopore sequencing of Upf1-bound mRNAs, we discovered that known PTC-containing NMD targets have long poly(A) tails, confirming that Upf1 binding occurs rapidly prior to deadenylation. Strikingly, the largest category specifically bound to Upf1 consisted of mRNAs without PTC harboring short poly(A) tails, corresponding to well-translated and stable transcripts. We showed that the degradation of this subpopulation depends on the three Upf factors, revealing a hitherto unknown function of Upf1 and NMD cofactors in mRNA decay.

overall_design: mRNA stranded sequencing  from UPF1_HTP CRAC samples extracted from LMA3730 strain (minus UV as a negative control and plus UV).

first: Toni

last: Gouhier

first: Cosmin

last: Saveanu


title: Bulk RNA sequencing study cynomonolgus macaques treated with escalating doses of IL-15/IL-15Ra

summary: This bulk RNA-seq experiment is designed to understand the IL-15 response in cynomologus macaques

overall_design: Cynomologus macaques were treated with increasing doses ((5,10 and 15 ug/kg)  at Day 0, Day 3 and Day 7 respectively and whole blood samples collected in PAXgene tubes at 10 timepoints

first: Inah

last: Golez

first: Jennifer

last: Tisoncik-Go

last: Gale Jr


title: Spatial organization of tumour cDC1 states correlates with effector and stem-like CD8+ T cells location

city: London

first: Cecile

last: Piot

address: 1 Midland road

institute: Francis Crick

summary: CD8+ T cells are central to targeting and eliminating cancer cells. Their function is critically supported by type 1 conventional dendritic cells (cDC1s), which both prime antigen-specific CD8+ T cells in tumour-draining lymph nodes (tdLNs) and sustain primed CD8+ T cells within tumours. Despite their importance, the spatiotemporal organisation of cDC1s within tumours and their diverse functional roles remain poorly understood. Here, we use scRNAseq and unbiased spatial analysis to construct a detailed map of cDC1 states and distribution within immunogenic mouse tumours during CD8+ T cell-mediated rejection. We reveal two distinct cDC1 activation states characterised by differential expression of genes linked to anti-tumour immunity, including Cxcl9 and Il12b. Strikingly, Il12b-expressing cDC1s are CCR7+ and enriched at tumour borders, where they closely associate with stem-like TCF1+ CD8+ T cells. In contrast, CCR7– Cxcl9-expressing cDC1s are preferentially found within the tumour parenchyma alongside effector CD8+ T cells. Analysis of a published dataset of human tumours similarly reveals a spatial association between CCR7+ cDC1 and stem-like TCF1+ CD8+ T cells. These findings uncover a highly spatially coordinated interaction between cDC1s and CD8+ T cells within tumours, shedding light on the intricate cellular dynamics that underpin effective anti-tumour immunity.

overall_design: scRNAseq of FACS-sorted cDC1s, cDC2s and pre-cDCs from MCA205 LA OVA tumours harvested from WT mice, sGSN-/- and sGSN-/-Clec9a-/- mice.

first: Cécile

first: Caetano

last: Reis e Sousa


title: Epigenetic Editing Balances TCR Suppression and Persistence in CAR T cells

city: Dresden

first: Frank

last: Buchholz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary: Allogeneic chimeric antigen receptor (CAR) T cell therapies offer a scalable, off-the-shelf option for cancer treatment, but their clinical use is limited by the risk of graft-versus-host disease (GvHD), mediated by the endogenous T cell receptor (TCR). Conventional strategies to eliminate TCR expression rely on genome editing tools such as CRISPR/Cas9 or base editing, which introduce permanent DNA changes and pose safety concerns. Here, we present an epigenetic editing approach that enables efficient, specific, and reversible silencing of the CD3ε gene, a critical component of the TCR complex, without altering the genome. Through systematic optimization of the epigenetic editor and guide RNA design, we achieved robust TCR silencing in primary T and CAR T cells while preserving CAR expression, activation, and effector function. Transcriptome analysis confirmed minimal off-target effects. In vivo observation suggest the epigenetically silenced T cells to prevent GvHD while persisting longer than TCR-knockout cells, supporting the notion that transient TCR suppression may help balance safety and long-term efficacy. Our findings establish epigenetic editing as a non-genotoxic alternative to genome editing, offering a flexible and safer route to generate next-generation allogeneic CAR T cells.

overall_design: RNA-seq profiling of human T cells samples from the same donor which were either untreated, mock electroporated, CRISPR/Cas9 TRAC knocked out or CD3E epigenetically silenced

first: Pascal

middle: Y

last: Schönberg

first: Ángela

last: Ovalle

first: Eugenia

last: Crespo

first: Anja

last: Feldmann


title: Cancer cells subvert ZNF93 to escape surveillance by L1 epigenetic sentinels and control APOBEC3B [cutandtag]

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

summary: The primate-restricted KRAB zinc finger protein (KZFP) ZNF93 represses a subset of L1 transposable elements (TEs) that propagated in the human ancestral genome some 20 to 12 million years ago and have all become transposition-incompetent due to inactivating mutations. Here, we demonstrate that these L1 integrants encode a highly genotoxic endonuclease, and that ZNF93 also represses other full-length L1 integrants via indirect effects as well as APOBEC3B. Consistent with the exquisite sensitivity of single-stranded DNA to attack by both the L1 endonuclease and the cytidine deaminase, ZNF93 expression peaks in S phase and correlates with cell proliferation. ZNF93 is induced in most cancers, and ZNF93-depleted cells exhibit defects in DNA synthesis and activation of the replication and DNA damage checkpoints. These results suggest a model whereby ZNF93 is a major guardian of genome integrity subverted by cancer cells to escape L1-mediated epigenetic surveillance and achieve a proper balance of APOBEC3B-induced tumor heterogeneity and overall genome stability.

overall_design: Cut & Tag of H3K9 and H3K4 in WT and

first: Romain

last: Forey


title: Cancer cells subvert ZNF93 to escape surveillance by L1 epigenetic sentinels and control APOBEC3B [RNA-seq_2]

overall_design: RNA-seq of K562 cell lines overexpressing ZNF93


title: miRNA Expression in Firefighters’ Skin and Blood

city: Oklahoma City

first: Chao

last: Xu

state: Oklahoma

address: 801 N. E. 13th Street

department: Biostatistics and Epidemiology

institute: University of Oklahoma Health Sciences Center

summary: Firefighters are routinely exposed to polycyclic aromatic hydrocarbons (PAHs) during fire suppression activities, molecular biomarkers reflecting such exposure remain underexplored. Thus, we explored an integrated exposure assessment framework linking PAH contamination on turnout gear and skin to changes in microRNA (miRNA) expression in skin and blood biospecimens.

overall_design: This prospective study enrolled 25 firefighters. Skin tape strips and blood were collected before and after fire exposure.

first: Jooyeon

last: Hwang


title: Effect of GPR31-signaling on gene expression in LysoDCs during Listeria monocytogenes infection.

city: Shizuoka

first: Katsuhiro

last: Nakanishi

address: 52-1 Yada, Suruga-ku

institute: University of Shizuoka

summary: GPR31 signaling induced dendrite protrusion of lysozyme-expressing dendritic cells (LysoDCs) into basolateral pockets of M cells. To investigate the effect of GPR31 signaling on LysoDC function during infection, we analyzed the gene expression profile of LysoDCs from WT and Gpr31b-deficient mice at 2 days after L. monocytogenes infection.

overall_design: RNA-seq profiling of LysoDCs prepared from Peyer's patches of WT mice and Gpr31b-deficient mice at 2 days after oral infection of L. monocytogenes. The dataset consists of 4 groups: WT/uninfected, KO/uninfected, WT/infected, and KO/infected (n=3 in each group) .

first: Shinichiro

last: Sawa

first: Eiji

last: Umemoto


title: Effects of Short-Term High Fat/ High Sugar Diet on Follicle - Stimulating Hormone Secretion and Ovarian Gene Expression

city: Omaha

first: Sankarasubramanian

last: Jagadesan

state: NE

address: 42end and Emile st

department: Department of Genetics, Cell Biology & Anatomy

institute: University of Nebraska Medical Center

summary: Obesity is associated with decreased reproductive fitness including changes in the hypothalamic-pituitary-gonadal axis. Exposure to high fat diet can impair reproductive function even in the absence of obesity. Here, we tested the effects of a short-term high fat/high sugar (HF/HS) diet on the secretion pattern of follicle-stimulating hormone (FSH) and changes in gene expression in mouse ovaries. We used Fshb null mice expressing either a wild-type human FSHB transgene by which FSH is released constitutively or those expressing a mutant human FSHB transgene by which FSH is re-routed and released from the regulated LH secretory pathway. Mice were maintained on a HF/HS diet or regular chow for 10 weeks and serial blood samples were collected from tail tips for FSH analyses. RNA-Seq analysis was used to determine changes in ovarian gene expression. After 10 weeks on HF/HS diet, the mice did not develop obesity and allowed us to study the effects on FSH secretion characteristics. While area under the curve for FSH was unchanged, the amplitude of FSH was altered in re-routed FSH expressing mice on a HF/HS diet. We identified distinct changes in ovarian gene expression depending on the diet (regular vs. HF/HS) and FSH secretion pattern (constitutive vs. re-routed). Overall, re-routed FSH expressing mice maintained better ovarian gene expression even when fed on HF/HS diet. Thus, our re-routed FSH expressing transgenic mice provide a trackable genetic model to study the long-term effects of HF/HS diet and other metabolic syndromes on FSH secretion characteristics and the consequences on ovarian function.

overall_design: RNA Seq profiling of ovries obtained from Constitutive FSH and re-routed FSH expressing Fshb null mice fed on either regular or HF/HS diet for 10 weeks

first: Sara

last: Gilbert

first: Rajendra

middle: T

last: Kumar


title: Bulk RNA sequencing study of Rhesus macaques given Modified versions of the RhCMV/SIV vector-based vaccines.

first: Michael

last: Gale

summary: This bulk RNA-seq experiment is designed to uncover the transcriptomic response to modified RhCMV vectors in whole blood of rhesus macaques

overall_design: Rhesus macaques were given a prime (D0) and boost of one of four modified RhCMV vector based vaccines. 1) A single mrR124-restricted Dpp71 68-1 RhCMV vector expressing full-length (FL) SIVmac239 Gag/Nef and Pol inserts. Also referred to as miR-124-Rh107 DRh110 FL. 2) A single mrR124-restricted Dpp71 68-1 RhCMV vector expression hybrid* (HY) SIVmac239 mismatched Gag/Nef and Pol inserts, [*Conserved region = SIVmac 239 sequence; non-conserved region with average 2 amino acid per 9mer mismatch]   Also referred to as miR-124-Rh107 DRh110 HY. 3) A single mrR124-restricted Dpp71 68-1 RhCMV vector expressing conserved region-only (CON) SIVmac239 Gag/Nef and Pol inserts. Also referred to as miR-124-Rh107 DRh110 CON. And 4) A 3-vectors set of Dpp71 (DRh110) 68-1 RhCMV/SIV vectors (Gag + Retanef + 5’-Pol), given at  5 X 106 PFU (n=10) or 105).

first: Leanne

last: Whitmore

first: Jean

last: Chang

first: Elise

last: Smith

first: Lynn

last: Law

last: Gale Jr


title: Bulk RNA sequencing study on PBMCs collected from rhesus macaques treated with IL-15/IL-15Ra ex-vivo

summary: This bulk RNA-seq experiment is designed to understand the IL-15 response in ex-vivo IL-15 treated PBMCs from rhesus macaques

overall_design: PBMCs from rhesus macaques macaques were treated ex-vivo with heterodimeric IL-15 (IL-15/IL-15Ra).  2, 6 12, 24, and 48 hours post treatment were collected for sequencing

first: Jennifer

last: Tisoncik-Go


title: Intra-tumoral Treg Ablation Activates a CD4-NK Cell Axis to Control CD8 T cell Resistant Tumors

city: Oakland

first: Chenyu

last: Zhang

state: CA

address: 521 33rd St, Unit #2

department: MCB

institute: UC Berkeley

summary: Tumors evade control by CD8+ T cells by losing MHC I expression, necessitating new approaches to improve immunotherapy. NK cells target MHC I-deficient cells but are insufficiently activated to control tumors without help. Here we uncovered a novel approach to control MHC I-deficient tumors by ablating Treg cells intratumorally, which incites potent antitumor NK cell responses without imparting lethal autoimmunity. IT-Treg ablation increased NK cell activation, maturation, expression of effector molecules, and anti-tumor cytotoxic activity. In this setting, conventional CD4+ T cells were required for NK cell activation, due to their production of IL-2 after interacting with conventional type 2 dendritic cells. These results demonstrate an opportunity to reinvigorate antitumor NK cell responses against tumors that evade CD8 T cell responses, by locally depleting Tregs. The findings also highlight the multicellular immunosuppression enforced by Tregs that extends beyond the control of CD8 T cell responses to tumors.

overall_design: Tumors from mice treated with PBS, IT-DT or ITDT + anti-CD4 were resected, and single cell suspensions were prepared. Tumor immune cells were enriched by layering on a lympholyte-M gradient then stained with DAPI, CD19-PECy5, F4/80-PECy5, Ter119-PECy5, CD8a-PECy5, CD3e-APC, CD45-FITC, CD4-BV605, and NK1.1-APC-Cy7 for 30 min on ice. NK cells and CD4 T cells were FACS sorted from tumors pooled from 2-4 mice per replicate, with a yield ranging from 20,000-200,000 cells, with three replicates total.

first: David

last: Raulet

first: Michel

last: DuPage


title: Transcriptome analysis of nphp1(ex15-del4); nphp4(sa38686) double mutant zebrafish

first: Toma

last: Yakulov

summary: Nephronophthisis (NPH) is the most common genetic cause of end-stage renal disease in children and young adults. Mutations in more than 25 genes, called NPHPs, were found to be causative. We performed RNA sequencing analysis to investigate the transcriptional changes in nphp1(ex15-del4); nphp4(sa38686) homozygous mutant zebrafish compared to wild-type siblings. Our analysis revealed significant alterations in gene expression profiles associated with cilia function, cell signaling pathways, and kidney development. This dataset provides insights into the molecular mechanisms underlying NPH pathogenesis and genetic compensation in a zebrafish model of the disease.

overall_design: RNA-seq profiling of nphp1(ex15-del4); nphp4(sa38686) double mutant zebrafish and their wild-type siblings at 48 hpf. Four biological replicates were sequenced for each genotype.

first: Johannes

last: Ruf

first: Priska

last: Eckert


title: H3K27me3 and the PRC1-H2AK119ub pathway cooperatively maintain heterochromatin and transcriptional silencing after the loss of H3K9 methylation [RNA-seq]

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

summary: Heterochromatin is a key architectural feature of eukaryotic chromosomes, essential for cell type-specific gene expression and genome stability. In the mammalian nucleus, heterochromatin is segregated from transcriptionally active euchromatic regions (A compartments), forming large, condensed, and inactive nuclear compartments (B compartments). However, the mechanisms underlying its spatial organization remain incompletely understood. Histone H3 lysine 9 and lysine 27 trimethylation (H3K9me3 and H3K27me3) are two major epigenetic modifications that enrich constitutive and facultative heterochromatin, respectively. Previously, we found that the redistribution of H3K27me3 following the loss of H3K9 methylation contributes to heterochromatin maintenance, while the simultaneous loss of both H3K27me3 and H3K9 methylation induces heterochromatin decondensation in mouse embryonic fibroblasts. However, nearly all B compartments were preserved despite the loss of these repressive chromatin modifications. These findings suggest that other factors are responsible for maintaining B compartments under these conditions. In this study, we explored the role of another repressive chromatin modification, PRC1-mediated H2A K119 monoubiquitylation (H2AK119ub/uH2A), in maintaining heterochromatin structure following the loss of H3K9/K27 methylation. We found that uH2A and H3K27me3 independently accumulate in the B compartments after the loss of H3K9 methylation in iMEFs and cooperatively maintain heterochromatin. Our data indicates that the PRC1- uH2A pathway contributes to maintain heterochromatin organization following the loss of H3K9/K27 methylation in mammalian cells.

overall_design: RNA-seq profiles of H3K9me/H3K27me3/uH2A-depleted immortalized mouse embryonic fibroblasts

first: Yoichi

last: Shinkai


title: H3K27me3 and the PRC1-H2AK119ub pathway cooperatively maintain heterochromatin and transcriptional silencing after the loss of H3K9 methylation [ChIP-seq]

overall_design: ChIP-seq profiles of H3K27me3 and uH2A in immortalized mouse embryonic fibroblasts


title: Cancer cells subvert ZNF93 to escape surveillance by L1 epigenetic sentinels and control APOBEC3B [RNA-seq_3]

first: Julien

last: Duc

overall_design: RNA-seq of SW480, U2932, OCILY7 cell line in WT or ZNF93 KD condition

first: Romain

last: Forey


title: Single-cell transcriptomic profiling of aortic plaque cells from myeloid-specific Lipa overexpression and control mice on an Ldlr-/- background

city: New York

first: Fang

last: Li

institute: Columbia University Irving Medical Center

summary: We performed single-cell RNA sequencing (scRNA-seq) to determine the relative abundance and transcriptomic profiles of cell subclusters in atherosclerotic aortas from control mice and mice with myeloid-specific Lipa overexpression, both on the Ldlr-/- background and fed a Western diet for 16 weeks.

overall_design: We generated a knock-in (KI) mouse model for Cre-loxP–mediated overexpression of Lipa (NM_001111100) on a C57BL/6 background by targeting the Rosa26 locus. Mice heterozygous for the insertion (LipaKI/WT) were bred to obtain homozygous LipaKI/KI mice. We bred LipaKI/KI, Ldlr-/- mice with LysMCre+/-, Ldlr-/- mice, generating mice on an atherosclerosis-prone Ldlr-/- background to assess the impact of myeloid Lipa overexpression on atherosclerosis. The LysMCre+/-, LipaKI/WT, Ldlr-/- mice (M-LipaKI) demonstrated myeloid-specific Lipa overexpression. LysMCre-/-, LipaKI/WT, Ldlr-/- (Ctrl) littermates were used as controls. Aortas were harvested from Ctrl and M-LipaKI mice fed a Western diet for 16 weeks and subsequently enzymatically digested into single cells. Viable single cells, pooled from three male mice, were subjected to scRNA-seq immediately.

first: Chenyi

last: Xue

first: Hanrui


title: The effects of myeloid-specific Lipa overexpression on the transcriptomic profile of aortic plaque macrophages in mice on the Ldlr-/- background and fed a Western diet for 16 weeks

summary: We analyzed the transcriptomic profile of aortic macrophages directly sorted from atherosclerotic aortas of two groups of mice fed a Western diet for 16 weeks: (1) mice with LysMCre-mediated myeliod-specific Lipa overexpression on the Ldlr-/- background; (2) LysMCre-negative littermates on the Ldlr-/- background.

overall_design: We generated a knock-in (KI) mouse model for Cre-loxP–mediated overexpression of Lipa (NM_001111100) on a C57BL/6 background by targeting the Rosa26 locus. Mice heterozygous for the insertion (LipaKI/WT) were bred to obtain homozygous LipaKI/KI mice. We bred LipaKI/KI, Ldlr-/- mice with LysMCre+/-, Ldlr-/- mice, generating mice on an atherosclerosis-prone Ldlr-/- background to assess the impact of myeloid Lipa overexpression on atherosclerosis. The LysMCre+/-, LipaKI/WT, Ldlr-/- mice (M-LipaKI) demonstrated myeloid-specific Lipa overexpression. LysMCre-/-, LipaKI/WT, Ldlr-/- (Ctrl) littermates were used as controls. Whole aortas were harvested from Ctrl and M-LipaKI mice fed a Western diet for 16 weeks and subsequently enzymatically digested into single cells. Viable aortic macrophages (DAPI-CD45+CD11b+CD64+) were sorted and subjected to low-input RNA-seq. n = 4 biological replicates per genotype, with each replicate comprising pooled samples from 2-3 male mice, resulting a total of 10 male mice per genotype.


title: Intracellular Interleukin-1α in Peritumoral Monocytes Induces IL8 Production and Inhibits Mitophagy to Promote Stemness and Metastasis of Hepatocellular Carcinoma

city: Guangzhou

first: Yonghao

last: Ruan

address: 135 Xin Gang Xi Road, Guangzhou, China

institute: Sun Yat-sen University

summary: In the current study, we found that IL-1α levels were significantly upregulated in peritumoral monocytes compared to nontumor and intratumor counterparts, and glycolytic switch mediated the upregulation of IL-1α via NF-κB signaling. The upregulated IL-1α was neither secreted by nor displayed on cell surface of monocytes. Rather, IL-1α translocated into nuclei to induce the production of IL-8, which effectively enhanced cancer cell stemness and tumor metastasis. Substantial amounts of IL-1α bound to mitochondria to inhibit mitophagy, inducing CA12 expression and macrophages accumulation via ROS-HIF-1α pathway. In accordance, IL-1α levels in peritumoral monocytes were positively correlated with both survival and tumor metastasis of HCC patients. Targeting IL-1α+ monocytes or IL-8 could effectively inhibited tumor progression and enhanced tumor responsiveness to immune checkpoint blockade therapy in mice in vivo. Our results revealed an intracellular regulatory role of IL-1α in modifying the pro-tumor functions of monocytes within specific tumor microenvironments, and pointed to both IL-1α and its downstream IL-8 as potential diagnostic and therapeutic targets for human HCC.

overall_design: To delineate the pro-tumor functions of IL-1α, PBMC-derived monocytes from 2 donors were transfected with siIL1A or siNC, then cells were treated with TSN.

first: Yong-Hao

first: Wan-Ru

last: Ning

first: Yan

last: Wu

first: Limin

last: Zheng


title: Gut Commensal Parabacteroides goldsteinii mitigates LRRK2 Parkinsonism through reducing neuroinflammation and multifaceted effects on gut homeostasis [ST]

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: Our study confirms that gut microbiota is essential for motor dysfunction and neuropathology in LRRK2 G2019S mice. Monoculturing Parabacteroides goldsteinii mitigates age-related motor dysfunction, alpha-synuclein expression, neuroinflammation, and dopaminergic degeneration. Its effects on the gut microenvironment include suppressing the toll-like receptor 4 signaling pathway, facilitating the differentiation of intestinal dendritic cells and macrophages, and promoting anti-inflammatory intraepithelial CD4+ CD8αα+ T cells. It also upregulates tissue repair and immune differentiation pathways, enhances intestinal epithelial junction and mitochondrial function genes, and reduces colonic alpha-synuclein levels.

overall_design: Transcriptomics and spatial transcriptomics analyses to investigate the effects of Parabacterioides goldsteinii on the brain and gut in LRRK2 G2019S mice.

first: CL

last: Hus

first: CH

last: Lin


title: An interferon-induced survival program in dedifferentiated cancer cells drives resistance to immuno-virotherapy

city: Essen

first: Florian

last: Rambow

department: IKIM

institute: University Hospital Essen

summary: Oncolytic virotherapies are currently being explored to improve cancer immunotherapies. How the complex roles of interferons (IFNs) for host defenses against cancer cells and viruses shape responses to immuno-virotherapies is poorly understood. Here, we experimentally show that IFN-unresponsive melanoma cell subpopulations in heterogeneous tumors resist T-cell control but are efficiently eradicated with oncolytic virotherapy. Unexpectedly, T-cell immunity and viral oncolysis were abrogated by the emergence of dedifferentiated, IFN-responsive tumor cell subpopulations. On the molecular level, we discovered that the melanocyte master transcription factor MITF counter-regulates IFNα-mediated anti-viral responses in melanoma cells by dampening the upregulation of IFNα-stimulated anti-viral genes. A subset of these genes overlaps with the IFN-related DNA damage resistance signature (IRDS). The baseline expression of this subset in human melanoma cells is associated with non-response to immune checkpoint blockade in patients. Our results support current approaches targeting cancer cell dedifferentiation and chronic activation of IFN-signaling to advance immunotherapies.

overall_design: To gain insight into the molecular mechanisms how MITF might regulate IFN-mediated anti-viral responses, we employed a functional genomics approach by assessing transcriptomic changes (bulk RNA-seq). We used the MaMel65-tet-on-MITF-eGFP melanoma cell line that was genetically engineered to express MITF tagged with the fluorescent protein eGFP in a doxycycline-inducible manner. Treatment of this cell line with doxycyline for 24 hours induces MITF expression as confirmed by fluorescence microscopy for the eGFP tag. Doxycycline- and vehicle-treated cells were then exposed to 100 IU/ml recombinant human IFNα or to vehicle control for 5 hours and infected with SFV-VA7-mCherry. The experiment was performed by utilizing biological triplicates per condition.


title: METTL3 dependent m6A RNA methylation is required for self-renewal and cell identity maintenance of human trophoblast stem cells

city: Ithaca

first: Weiyu

last: Zhang

address: 215 Tower Rd, Biotechnology Building

department: MBG

institute: Cornell University

summary: N6-methyladenosine (m6A) is the most prevalent mRNA modification with diverse regulatory functions in mammalian cells. However, its significance in the human trophoblast lineage and human placenta development remains largely unexplored. Here, we found that in human pregnancy, METTL3 and METTL14, the primary enzymes responsible for m6A deposition, specifically mark cytotrophoblast cells in the human placenta. By utilizing a METTL3 inducible knockout (iKO) system, we demonstrated the essential role of METTL3 in generating human trophoblast stem cells (hTSCs) from human expanded potential stem cells (hESPCs). Furthermore, METTL3 is critical for the self-renewal ability and cellular identity in the established hTSCs. Mechanistically, METTL3-dependent m6A modification regulates histone modifiers such as EP300 and EZH2 to maintain the epigenetic homeostasis of hTSCs. The depletion of METTL3 in hTSCs results in epigenetic dysregulation, leading to activation of inflammation and premature senescence, which are associated with the preeclampsia phenotype. Notably, our findings from in vitro model show that inhibiting EP300 could efficiently rescue the preeclampsia signature at the transcriptomic level. These results underscore the critical roles of METTL3-dependent m6A RNA methylation in human placentation and the development of placental diseases.

overall_design: We performed single-cell RNA sequencing (scRNA-seq) to analyze global gene expression profiles in P0 and P2 hEPSCs after Dox removal, as well as in differentiated day 3 cells cultured in TSCM with or without Dox.

first: Haifeng

last: Fu


title: Cancer cells subvert ZNF93 to escape surveillance by L1 epigenetic sentinels and control APOBEC3B [RNA-seq_1]

overall_design: RNA-seq of K562 cell line in WT or ZNF93 KD condition


title: CREB5 promotes tumorigenicity and upregulates druggable cell surface modalities in basal-like breast cancer

city: Minneapolis

first: Allison

last: Makovec

address: 425 E River Parkway

institute: University of Minnesota

summary: Basal-like breast cancers (BLBC), of which many are triple negative, have poor outcomes due to the limited targeted therapies available for patients. To address this need, we examined the clinical correlates and functional properties of CREB5, a transcription factor commonly amplified or overexpressed in other metastatic cancers. Using transcriptomic data from TCGA and METABRIC, we found BLBCs harbored the highest levels of CREB5 expression compared to other BC subtypes and that CREB5-high tumors had poor outcomes. In patient-matched primary and metastatic biopsies, CREB5 expression was robust and further increased in BLBCs that develop brain metastasis. CREB5 overexpression in 2 BLBC cell lines increased cell viability, formation of tumorspheres, and led to substantial increases in mRNA and cell surface expression of IL13RA2, a stem cell-like gene in brain cancers. IL13RA2 is a current CAR-T cell target in gliomas, and our work nominates IL13RA2 as a novel potential target in BLBCs.

overall_design: To investigate the regulatory abilities of CREB5 in BLBC, we established CREB5 and Luciferase overexpressed MDA-MB-231 and HCC1806 cell lines using lentiviruses.

first: Ella

last: Boytim

first: Ava

last: Gustafson

first: Liangjun

last: Wang

first: Atef

last: Ali

first: Khalid

last: Ishani

first: Christine

last: Luo

first: Hannah

middle: E

last: Bergom

first: Emily

last: John

first: Sydney

last: Tape

first: Megan

last: Ludwig

first: Samuel

last: Kellen

first: Aiden

last: Deacon

first: Fatemah

middle: I

last: Dewji

first: Camden

last: Richter

first: Lauren

last: Cookle

first: Jonathan

middle: P

last: Rennhack

first: Justin

last: Drake

first: Emmanuel

last: Antonarakis

first: David

last: Largaespade

first: Julie

middle: H

last: Ostrander

last: Hwang


title: Evolutionarily recent TFs partake in human cell cycle regulation [RNA-Seq 4]

first: Julien

last: Duc

summary: The cell cycle is a fundamental process in eukaryotic reproduction, controlled by a highly conserved core signaling cascade. However, the role of recently evolved proteins in cell cycle regulation remains unclear, largely because conservation is often assumed to be essential for function. In this study, we systematically map the influence of evolutionarily recent transcription factors (TFs) on human cell cycle progression. We find that the genomic targets of select recent TFs, many of which belong to the rapidly evolving Krüppel-associated box (KRAB) zinc-finger proteins (KZFP) family, exhibit synchronized cell cycle expression. Systematic perturbation studies reveal that silencing recent TFs disrupts normal cell cycle progression, which we experimentally confirm for ZNF519, a simian-restricted KZFP. Further, we show that the therian-specific KZFP ZNF274 sets the cell cycle expression and replication timing of hundreds of clustered genes. These findings highlight an underappreciated level of lineage specificity in cell cycle regulation and underline the power of forward genetics in comprehensively mapping cell function.

overall_design: Romain, Forey

first: Cyril

last: Pulver

first: Alex

middle: R

last: Lederer

first: Martina

last: Begnis

first: Olga

last: Rosspopoff

first: Joana

last: Carlevaro-Fita

first: Filipe

last: Martins

first: Evarist

last: Planet

first: Charlène

last: Raclot

first: Sandra

last: Offner

first: Alexandre

last: Coudray

first: Arianna

last: Dorschel

first: Didier

last: Trono


title: Gut Commensal Parabacteroides goldsteinii mitigates LRRK2 Parkinsonism through reducing neuroinflammation and multifaceted effects on gut homeostasis [RNA-seq]

first: Chia-Lang

last: Hsu

first: CL

last: Hus

first: CH

last: Lin


title: Evolutionarily recent TFs partake in human cell cycle regulation  [RNA-Seq 2]


title: High-fat diet triggers chemerin-dependent immune reprogramming that exacerbates acute kidney injury

city: Shanghai

first: Bo

last: Deng

address: 639 Zhizaoju Road

department: Division of Nephrology

institute: Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University

summary: Obesity presents a known risk factor for acute kidney injury (AKI), but the precise mechanism underlying this phenomenon remains incompletely elucidated. In this study, we demonstrated that short-term high-fat diet (HFD) feeding aggravated kidney injury in AKI mice. Through multi-omics analysis, we identified chemerin (encoded by Rarres2) as a distinctive renal injury-related adipokine enriched in AKI tubular epithelial cells (TECs), particularly following exposure to HFD. Elevated chemerin levels were confirmed in the serum and kidney biopsy samples of AKI patients with obesity, exhibiting a negative correlation with renal function. Rarres2-/- mice were protected from HFD-induced vulnerability toward AKI as well as different types of AKI after standard diet, emphasizing its direct effect on AKI independent of metabolic factors. Mechanism investigation showed the receptor of chemerin-chemerin chemokine-like receptor 1 (CMKLR1) was expressed on renal mononuclear phagocytic cells (MPCs). By single-cell RNA sequencing (scRNA-seq) analysis, unique Cmklr1hi clusters were identified in renal MPCs following AKI, exhibiting enhanced chemotaxis and pro-inflammatory capacity. Functionally, chemerin acted as a chemoattractant to enhance the chemotaxis of Cmklr1hi MPCs. Finally, supplementation of MPCs-derived cytokines reversed kidney injury in Rarres2-/- mice confirming the role of chemerin-CMKLR1 axis in promoting inflammation and kidney damage. Collectively, we identified chemerin as a specific inflammatory and metabolic target that functions through potent pro-inflammatory Cmklr1hi macrophages. Our study suggests that targeting the chemerin-CMKLR1 axis could be a promising therapeutic strategy for AKI patients, especially those with metabolic syndrome.

overall_design: To identify the key molecules that sensitize HFD-fed mice to AKI, we performed RNA-seq of kidneys from control and cisplatin-treated mice as AKI datasets.Comparative gene expression profiling analysis of RNA-seq data for control and AKI kidneys were analyzed.

first: Zhenkai

last: Wu

first: Shuai

last: Ma

first: Feng

last: Ding


title: Age-associated difference between young-adult and aged ferrets during SFTSV infection

city: Daejeon

first: Dongbin

last: Park

address: 55, Expo-ro

country: South Korea

institute: Institute for Basic Science

summary: This longitudinal scRNA-seq analysis examines age-related differences, focusing particularly on the B cell response, between young-adult and aged ferrets during SFTSV infection.

overall_design: To elucidate age-dependent SFTSV progression, we performed longitudinal single-cell RNA sequencing (scRNA-seq) on the spleen, PBMC, and BM of young-adult and aged ferrets—an established immunocompetent animal model reflecting fatal clinical symptoms of human SFTSV infections. Our analysis revealed distinct age-related differences in immune response

first: Young Ki

last: Choi


title: Anti-B-cell maturation antigen (BCMA) chimeric antigen receptor (CAR) T-cell therapy bb21217 for relapsed and refractory multiple myeloma: results from the phase 1 CRB-402 study

city: Seattle

first: Daniel

last: Zak

address: 188 East Blaine Street, Suite 300

institute: Regeneron

summary: Chimeric antigen receptor (CAR) T-cell therapy enriched for a memory-like phenotype may persist and function longer than a non-enriched product, thereby improving duration of response (DOR). We conducted a phase 1 study with bb21217 (NCT03274219), an anti-B-cell maturation antigen CAR T-cell therapy manufactured in the presence of bb007 (phosphoinositide 3-kinase inhibitor) to enrich for T cells with a memory-like phenotype, in patients with relapsed/refractory multiple myeloma. No new safety concerns were raised with bb21217 therapy. The objective response rate was 69.4% and median DOR was 23.8 (95% confidence interval, 16.8–34.8) months. Analysis of drug product established an association between early memory phenotype and robust expansion and depth of response. Examination of baseline characteristics indicated that tumor burden and prior therapies influenced DOR. This supports the generation of CAR T cells early in a disease course when tumor burden is lower and source material exhibits a more naïve phenotype.

overall_design: RNA-Seq was performed on pre-infusion bb21217 drug products (DPs) for 75 patients participating in CRB-402 (NCT03274219), a two-part, non-randomized, open-label, multi-site, phase 1 study of bb21217 in patients with relapsed/refractory (R/R) Multiple Myeloma (MM).  In Part A (dose-escalation phase), 12 patients received a target dose of 150 × 106 CAR T cells, 6 received 300 × 106 cells and 6 received 450 × 106 cells. In Part B (dose-expansion phase), 8 patients received 300 × 106 cells and 40 patients received 450 × 106 cells. bb21217 Drug Product (DP) was manufactured by transducing autologous T cells with an anti-BCMA02 CAR lentiviral vector as described by Friedman et al. (2018) and culturing in the presence of bb007.

first: Melissa

last: Alsina

first: Nina

last: Shah

first: Maeva

last: Fincker

first: Olivia

last: Finney

first: Anna

last: Truppel-Hartmann

first: Noopur

last: Raje


title: Maternal TDP43 Orchestrates Nuclear Speckle Assembly and Zygotic Splicing Activation During Oocyte-to-embryo Transition in Mouse [RIP-seq]

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: Zygotic splicing activation (ZSA) is an important means for mRNA post-transcriptional regulation during the maternal-to-zygotic transition (MZT) progress, ensuring normal embryonic development. However, the key factors and mechanisms of ZSA regulation are still unclear. Here, we found that nuclear speckle (NS), a key splicing region, is newly established at the 2-cell stage in mice, which is consistent with the period of ZSA. Moreover, NS and TDP43, an important component of paraspeckle, always have a partially adjacent and mutually exclusive localization relationship. TDP43 shuttles from the paraspeckle through liquid-liquid phase separation to perform its function: that is, it acts as a match-maker, binding to the transcribed RNAs on the one hand, and directly binding to the NS proteins on the other hand to ensure the correct assembly of NS. Maternal TDP43 deficiency leads to NS assembly failure in 2-cells, resulting in the inability of transcripts to skip; while injection of excessive TDP43 in zygotes leads to abnormal enlargement of NS in 2-cells, resulting in excessive skipping of transcripts. Both bidirectional ZSA disorders lead to 2-cell arrest in early embryogenesis. The ZSA defect caused by TDP43 deficiency also impairs the cell totipotency-pluripotency conversion. Collectively, our study discovered a NS upstream regulatory factor TDP43, which help maintain the balance of ZSA, providing a new perspective on post-transcriptional regulation of early embryos.

overall_design: Ten embryos per sample were washed in 0.2 BSA in 1X PBS and collected for lysis in 4.2 μl lysis buffer (0.2% Triton X-100, RNase inhibitor, deoxyribonucleotide triphosphate (dNTPs), oligo-dT primers, and 1:1000 ERCC spike-in). Then the samples were reverse transcribed and amplificated using the Smart-seq2 method, as described previously. Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503). Barcoded libraries were pooled and sequenced on the HiSeq X Ten platform with 150-bp paired-end reads.

first: Zuoqi

first: Zhiyan

last: Jiang

first: Yunwen

first: Hengyu


title: Maternal TDP43 Orchestrates Nuclear Speckle Assembly and Zygotic Splicing Activation During Oocyte-to-embryo Transition in Mouse [RNA-seq]

first: Yuke


title: Effects of Tirzepatide on macrophage polarization, inflammatory factors and atherosclerotic genes in RAW264.7 cells under oxidative low-density lipoprotein

city: shenyang

first: mengjie

last: kang

state: 辽宁省

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

institute: Shenyang Medical College

summary: Tirzepatide (TZP) is a novel dual agonist of glucagon-like peptide -1/glucose-dependent insulinotropic polypeptide receptors. TZP represents a significant advance in the treatment of diabetes and obesity. Clinical trials have shown that TZP significantly reduces cardiovascular risk in patients with diabetes or obese patients who are at high CV risk. We report here that TZP exerts anti-atherosclerotic effects by altering macrophage polarization and inflammatory expression. Under oxLDL, the expression of inflammatory factors in RAW264.7 cells increased, and the phenotype of M1 macrophages increased. After TZP treatment, M2 macrophages increased and anti-inflammatory factor expression increased in RAW264.7 cells. In summary, our data provide a new mechanism for TZP in the treatment of oxLDL-induced foam cell formation.

overall_design: RNA-seq profiling gene expression in control RAW264.7 cells, RAW264.7 cells with oxLDL, RAW264.7 cells with tirzepatide, and RAW264.7 cells with oxLDL and tirzepatide

first: Ming-Sheng

last: Zhou

first: Mengjie

last: Kang

first: Hao-Lin

last: Ren

first: Limin

last: Liu

first: Junjia

last: Gao

first: Qian

last: Xu

first: Lu

last: Zhang

first: Hui

last: Jia

first: Qing

last: Chen

first: Yueyang

first: Yue

first: Yuhan


title: H3K27me3 and the PRC1-H2AK119ub pathway cooperatively maintain heterochromatin and transcriptional silencing after the loss of H3K9 methylation [Hi-C]

first: Kei

last: Fukuda

overall_design: Hi-C analysis of H3K9me/H3K27me3/uH2A-depleted immortalized mouse embryonic fibroblasts

first: Yoichi

last: Shinkai


title: Astroglial TNFR2 signaling regulates hippocampal synaptic function and plasticity in a sex dependent manner

city: Miami

first: Roberta

last: Brambilla

state: FL

department: Neurological Surgery

institute: University of Miami Miller School of Medicine

summary: Astrocytes participate in synaptic transmission and plasticity through tightly regulated, bidirectional communication with neurons, both pre- and post-synaptic elements, as well as microglia and oligodendrocytes. A key component of astrocyte-mediated synaptic regulation is the cytokine tumor necrosis factor (TNF). TNF signals via two cognate receptors, TNFR1 and TNFR2, both expressed in astrocytes. While TNFR1 signaling in astrocytes has been long demonstrated to be necessary for physiological synaptic function, the role of astroglial TNFR2 has never been explored. Here, we demonstrate that astroglial TNFR2 is essential for maintaining hippocampal synaptic function and plasticity in physiological conditions. Indeed, GfapcreERT2:Tnfrsf1bfl/fl mice with selective ablation of TNFR2 in astrocytes exhibited dysregulated expression of neuronal and glial proteins (e.g. SNARE complex molecules, glutamate receptor subunits, glutamate transporters) essential for hippocampal synaptic transmission and plasticity. Hippocampal astrocytes sorted from GfapcreERT2:Tnfrsf1bfl/fl mice displayed downregulation of genes and pathways implicated in synaptic plasticity, astrocyte-neuron and astrocyte-oligodendrocyte communication. These alterations were accompanied by increased glial reactivity and impaired astrocyte calcium dynamics, and ultimately translated into functional deficits, specifically impaired long-term potentiation (LTP) and cognitive functions. Notably, male GfapcreERT2:Tnfrsf1bfl/fl mice exhibited more pronounced hippocampal synaptic and cellular alterations, suggesting sex-dependent differences in astroglial TNFR2 regulation of synaptic function. Together, these findings indicate that TNFR2 signaling in astrocytes is essential for proper astrocyte-neuron communication at the basis of synaptic function, and that this is regulated in a sex-dependent manner.

overall_design: RNA-seq profiling of sorted hippocampal astrocytes from adult naive male mice with ablation of astroglial TNFR2 (GfapcreERT2:Tnfrsf1bfl/fl ) and corresponding controls (Tnfrsf1bfl/fl )

first: Brianna

middle: N

last: Carney

first: Placido

last: Illiano

first: Taylor

last: Pohl

first: Haritha

last: Desu

first: Shwetha

last: Mudalegundi


title: Evolutionarily recent TFs partake in human cell cycle regulation [RNA-Seq 2]

city: Lausanne

first: Julien

last: Duc

institute: EPFL

first: Cyril

last: Pulver

first: Alex

last: Lederer

first: Martina

last: Begnis

first: Olga

last: Rosspopoff

first: Joana

last: Carlevaro-Fita

first: Filipe

last: Martins

first: Evarist

last: Planet

first: Charlène

last: Raclot

first: Sandra

last: Offner

first: Alexandre

last: Coudray

first: Arianna

last: Dorschel

first: Didier

last: Trono


title: A functional subpopulation of human glioma associated macrophages linked to malignant glioma progression [mtscATAC-seq]

first: Kenny

last: Yu

address: 1275 York Ave

department: Neurosurgery

institute: Memorial Sloan Kettering Cancer Center

summary: Malignant gliomas are progressive brain cancers with poor prognosis. Pro-tumorigenic glioma associated macrophages (GAM) have been implicated in disease progression however identification of pathogenic functional subsets is lacking. Macrophage functional specification is driven by transcription factor-associated gene regulatory networks, yet the core regulatory transcription factors that govern GAM functions remain unclear. Here we apply single cell RNA/ATAC sequencing to derive the imprint of the glioma tumor microenvironment on GAM transcriptional program specification and identify cell surface markers to prospectively isolate a functionally distinct subpopulation of GAMs in human samples present high grade tumors irrespective of IDH mutation status. This subset of GAMs, termed malignancy associated GAMs (mGAMs) spatially localize to hypoxic metabolic niches and possess a multitude of pro-tumorigenic functions. mGAMs also share somatic mutations with monocytes, suggesting a common bone marrow origin. mGAMs therefore represent a functional subset of GAMs in humans and a potential therapeutic target.

overall_design: Immune cells were first isolated from dissociated glioma samples via CD45+ MACS followed by FACS purification for mGAM and non-mGAM populations. Peripheral blood from the same patient was collected and PBMCs isolated using gradient separation (Ficoll-Paque PLUS, Cytiva, USA) followed by CD14 MACS sorting to obtain monocytes. Purified viable cells were used as input to the mtscATAC-seq protocol.

middle: K

first: Zaki

last: Abou-Mrad

first: Kristof

last: Törkenczy

first: Isabell

last: Schulze

first: Jennifer

last: Gantchev

first: Gerard

last: Baquer

first: Kelsey

last: Hopland

first: Evan

last: Bander

first: Umberto

last: Tosi

first: Cameron

last: Brennan

first: Nelson

last: Moss

first: Pierre-Jacques

last: Hamard

first: Richard

last: Koche

first: Caleb

last: Lareau

first: Nathalie

last: Agar

first: Taha

last: Merghoub

first: Viviane

last: Tabar


title: A host-directed adjuvant sensitizes intracellular bacterial persisters to antibiotics

city: Chapel Hill

first: Kuan-Yi

last: Lu

state: NC

address: 125 Mason Farm Road

institute: UNC Chapel Hill

summary: Intracellular bacterial reservoirs contribute to antibiotic treatment failure by fostering metabolically dormant persister cells that are highly tolerant to killing. However, strategies to effectively target intracellular persister cells remain limited. Here, we developed a high-throughput screen to identify compounds that modulate the metabolic activity of intracellular Staphylococcus aureus. The identified compound, KL1, increases intracellular bacterial metabolic activity and sensitizes persister populations of S. aureus to antibiotics, without causing cytotoxicity or bacterial outgrowth. KL1 also exhibits adjuvant activity against intramacrophage Salmonella enterica Typhimurium and Mycobacterium tuberculosis, as well as in murine infection models of S. aureus and S. Typhimurium infection. Transcriptomic analysis and further mechanistic studies reveal that KL1 modulates host immune response genes and suppresses the production of reactive species in host macrophages, alleviating a key inducer of antibiotic tolerance. Our findings highlight the potential to target intracellular persisters by stimulating their metabolism.

overall_design: To interrogate the mechanism of action of the compound KL1, RAW264.7 cells infected with S. aureus strain JE2-Lux at an MOI of 20 were treated with and without 40 uM KL1 for 24 h in triplicate and harvested for RNA-seq. Only the host transcripts were analyzed. The data were processed based on the standard procedure by Azenta Life Sciences.

first: Brian

last: Conlon


title: Identification of a novel PDC-E2 epitope in Primary Biliary Cholangitis and application for engineered Treg therapy

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Background and Aims: Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease, characterized by progressive destruction of small intrahepatic bile ducts and portal inflammation. Treatment options are limited with reliance on liver transplantation in advanced cases. The adaptive immune response is implicated in disease pathogenesis by both the presence of anti-mitochondrial antibodies targeting the E2 subunit of the pyruvate dehydrogenase complex (PDC-E2), in 90-95% of patients, and T cells infiltrating the portal tracts in affected individuals. Here, we examined T cell responses to peptides derived from PDC-E2, with a focus on CD4 T cell responses restricted to HLA Class II DRB4*0101, an allele found in 62% of PBC patients, to uncover PDC-E2 epitopes that could be used for Engineered Treg therapy. Approach and Results: Using an Activation Induced Marker assay and single cell RNA-sequencing, we found clonal expansion of CD4 T cells reactive to PDC-E2 epitopes in both conventional (Tconv) and regulatory T (Treg) cells. The TCR repertoires were non-overlapping and private and included TCRs specific for a novel PDC-E2 epitope restricted to DRB4*0101. CD4 Tconv cells from healthy and PBC subjects that responded to the PDC-E2 novel epitope showed phenotypic heterogeneity skewed towards T follicular helper cell subset. Using a TCR specific for this novel PDC-E2 epitope, we created an engineered Treg that suppressed PDC-E2 specific polyclonal CD4 Tconv cells from PBC patients. Conclusions: This study advances the knowledge of PDC-E2 specific T cell responses and introduces a novel PDC-E2 epitope recognized by reactive Tconv and Treg cells. Generation of engineered Treg specific for this epitope with effective suppressive activity provides therapeutic potential as Treg therapy targeting PDC-E2 in PBC.

first: Ritika

last: Tewari

first: Soo Jung

last: Yang

first: Ethan

last: McClain

first: Alex

last: Hu

first: Emma

last: Mortensen

first: Aleah

last: DeSchmidt

first: Janice

last: Chen

first: Aravind

last: Kancharla

first: Akhilesh

last: Singh

first: Eddie

middle: A

last: James

first: David

last: Rawlings

first: Chandra

last: Patel

first: Karen

last: Cerosaletti

first: Jane

last: Buckner


title: Evolutionarily recent TFs partake in human cell cycle regulation [RNA-Seq 1]

first: Julien

last: Duc

address: Station 19 CH-1015 Lausanne

first: Cyril

last: Pulver

last: Lederer

first: Martina

last: Begnis

first: Olga

last: Rosspopoff

first: Joana

last: Carlevaro-Fita

first: Filipe

last: Martins

first: Evarist

last: Planet

first: Charlène

last: Raclot

first: Sandra

last: Offner

first: Alexandre

last: Coudray

first: Arianna

last: Dorschel

first: Didier

last: Trono


title: GhFPF1 positively regulates shade avoidance responses by interacting with the NF-Y transcription factor GhNF-YA3 in cotton

city: Wuhan

first: qingqing

last: li

address: No. 238 Jiefang Road, Wuchang District

department: Department of Respiratory and Critical Care Medicine

institute: Renmin Hospital of Wuhan University

summary: Dense planting can create a shade environment which will stimulate plants to produce a series of shade avoidance responses (SAS). Thus far, slow progress has been made in research into the molecular mechanism of SAS in crops. In this study, we identified GhFPF1 as a positive regulator of SAS in cotton.

overall_design: After mutating GhFPF1 using CRISPR technology, the elongation response of the mutant was weakened under dense planting conditions. The constitutive expression of GhFPF1 resulted in SAS in cotton. GhFPF1 interacted with GhNF-YA3, which is a nuclear factor Y (NF-Y) member downregulated in shade conditions in cotton. Silencing GhNF-YA3 led to SAS in cotton.

first: QiFeng

last: Ma

first: Xiaoyan

last: Wang


title: Folic acid regulates neural mRNA m6A epitranscriptome via one-carbon metabolism in Drosophila and mammals

first: Xiaoyun

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: Folic acid is one of the B vitamins and is involved into neural function and brain development. Increasing evidence showed that folic acid can regulate neural gene function through DNA modification, while regulatory roles of folic acid in RNA modification remain largely unknown. In this study, we investigated the role of folic acid in regulating neural mRNA m6A epitranscriptome in Drosophila and mammals. We found that the folate treatment induced a significant increase in mRNA m6A levels compared to the control group in Drosophila and S2 cells. MeRIP-seq analysis indicated that carbon metabolism pathway and neural-related pathways were mainly affected. Subsequently, we migrated our validation experiments to human cells, our results showed that folate also affected mRNA m6A modification through one-carbon metabolic pathway in human cells, especially in neuronal cells. We also validated the effect of folic acid on mRNA methylation in mice, the results showed that folic acid treatment can significantly increase the expression of m6A-related proteins (Mettl3, Mettl14, FTO) and neural mRNA m6A methylation levels in mice brain. Moreover, we found that folic-acid producing Lactobacillus plantarum can significantly affects the m6A modification of mRNA in the host. In conclusion, we demonstrated that folic acid can participate in mRNA m6A modification through one-carbon metabolic pathway in Drosophila and mammals, and found that it has a significant effect on neural-related genes and pathways.

sample_organism:
Drosophila melanogaster
Mus

platform_organism:
Drosophila melanogaster
Mus

overall_design: In this study, we investigated the regulatory role of folic acid in Drosophila and mammalian neural mRNA m6A table transcriptome. The experimental groups were folate-treated Drosophila and folate-treated S2 cells. meRIP-seq analysis showed that carbon metabolic pathways and neural-related pathways were mainly affected. Subsequently, we knocked down the screened gene DHFR, and the experimental groups were DHFR knockdown cells. We also verified the effect of folic acid on mRNA methylation in mice, and the experimental group was folic acid-treated mice. In addition, we found that folic acid-producing Lactobacillus plantarum significantly affected the m6A modification of mRNA in the host, and the experimental group was Drosophila treated with Lactobacillus plantarum.

first: Anrui

last: Liu

first: Zhengyi

last: Huo


title: Transcriptomic Insights into Drought Tolerance Enhancement in Bread Wheat  Induced by a Microalgae-based Biostimulant

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

summary: Bread wheat (Triticum aestivum) is a staple food crucial for global caloric intake and food security. The current climate emergency demands the development of sustainable agricultural practices, particularly in the context of drought-induced yield reductions in bread wheat. Microalgae-based biostimulants have emerged as promising tools to enhance crop tolerance to drought stress while concurrently mitigating atmospheric CO2 accumulation. This study characterizes the transcriptomic responses to the foliar application of the microalgae-based biostimulant LRMTM in drought-stressed and fully irrigated wheat plants unveiling its mode of action. Drought stress at the tillering stage significantly altered gene expression activating key pathways related to phosphate starvation response (PSR), inositol phosphate signaling, and tocopherol biosynthesis. The application of the microalgae-based biostimulant LRMTM in drought-stressed plants further enhanced the expression of drought-responsive genes, particularly those involved in PSR and carbon fixation. Specific responses to LRMTM treatment in drought-stressed plants were also found related to abscisic acid (ABA) signaling activating genes involved in stomata closure, which plays a critical role in drought tolerance. In fully irrigated plants, LRMTM treatment was also beneficial modulating circadian rhythms, shade avoidance and attenuating stress responses. Phenotypic analysis showed that LRMTM-treated plants exhibited enhanced drought tolerance, increased height and spike length even under fully irrigated conditions. These results indicate that the microalgae-based biostimulant LRMTM not only enhances wheat response to drought but also promotes growth and productivity in both stressed and non-stressed conditions which could contribute to the development of sustainable agriculture in the face of the current climate challenges.

overall_design: We investigate the effect at the transcriptomic level of the microalgae-based biostimulant LRMTM in drought-stressed and fully irrigated wheat plants.

first: Mercedes

last: García-González

first: Christina

last: Arvanitidou

first: Marcos

last: Ramos-González

first: M

last: García-Gómez


title: Loss of MTCH2 induces E2F4/TFRC-mediated ferroptosis in colorectal cancer

city: Beijing

first: Pu

last: Xing

address: No.52 Fucheng Road

institute: Peking University Cancer Hospital & Institute

summary: Ferroptosis is a specific type of lipid peroxide-mediated cell death which is crucial in tumor suppression. While the mitochondrial carrier homolog 2 (MTCH2) is implicated in lipid homeostasis and mitochondrial metabolism, its role in ferroptosis and colorectal cancer (CRC) remains uncharacterized. Here, we identified MTCH2 as a crucial regulator of ferroptosis in CRC progression. Clinically, high expression of MTCH2 in CRC tissues predicted poor prognosis. Functionally, loss of MTCH2 inhibited azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colorectal tumorigenesis in intestine-conditional Mtch2 knockout (Mtch2cKO) mice and led to accumulation of ferrous ion and enhanced ferroptosis of CRC in vitro and in vivo. Mechanistically, MTCH2 deficiency promoted the proteasome-dependent ubiquitination of E2F4 and attenuated transcriptional inhibition of transferrin receptor (TFRC) by E2F4, ultimately facilitating TFRC-mediated ferroptosis in CRC cells. Taken together, our study reveals the mechanism of MTCH2 deficiency induced ferroptosis to inhibit the progression of CRC, and supports a potential therapeutic strategy targeting the MTCH2/E2F4/TFRC signaling axis in CRC patients with liver metastasis.

overall_design: scRNA-seq of murine CRC from AOM/DSS-induced Mtch2cKO and wild type transgenic mice.

first: Beihai

last: Jiang

first: Xiangqian

last: Su


title: Evolutionarily recent TFs partake in human cell cycle regulation [BRDU]

first: Julien

last: Duc

first: Cyril

last: Pulver

first: Alex

last: Lederer

first: Martina

last: Begnis

first: Olga

last: Rosspopoff

first: Joana

last: Carlevaro-Fita

first: Filipe

last: Martins

first: Evarist

last: Planet

first: Charlène

last: Raclot

first: Sandra

last: Offner

first: Alexandre


title: Next-generation sequencing is useful for quantitative analysis of the transcriptome of HMME-RGD@C3F8 NBs under  low-frequency ultrasound irradiation  combined with Elesclomol-Cu  treated and untreated HCC cells

city: Harbin

first: Yucao

last: Sun

state: Heilongjiang Province

address: No.150, Haping Road, Nangang District

institute: Harbin Medical University Cancer Hospital

summary: Hepatocellular carcinoma has a hidden onset and is often found at an advanced stage clinically. Moreover, because it is insensitive to radiotherapy and chemotherapy, its treatment is often difficult. In this study, we constructed nanobubbles loaded with sonosensitizer HMME and tumor-targeting peptide RGD (HMME-RGD@C3F8 NBs) combined with cuproptosis inducer Elesclomol-Cu to achieve sonodynamic/cuproptosis combined therapy for hepatocellular carcinoma (HCC). Furthermore, to explore the mechanism of the enhanced anti-tumor efficacy of synergistic sonodynamic/cuproptosis therapy, RNA sequencing was performed.

overall_design: The transcripts of two kinds of HCC cells before and after HMME-RGD@C3F8 NBs combined with Elesclomol-Cu under low-frequency ultrasound were detected.

first: Yichi

last: Chen

first: Bolin

last: Wu

first: Wen

last: Cheng


title: Multi-omics analysis revealed the anti-quorum sensing mechanism of theaflavin-3,3´-digallate on Hafnia alvei H4

city: Dalian City

first: xue

last: li

state: Liaoning Province

address: No. 1 Light Industry Court, Ganjingzi District

department: School of food science and technology

institute: Dalian Polytechnic University

summary: Theaflavin-3,3´-digallate (TF3) exhibits anti-quorum sensing (QS) properties against Hafnia alvei H4, a bacterium commonly found in spoiled aquatic products, by interacting with LuxI and reducing AHL concentration. This study investigated the extensive changes in the transcriptional and metabolic profiles of H. alvei H4 induced by TF3 as a QS inhibitor (QSI). The results demonstrated that a subminimal inhibitory concentration of TF3 (31.25 µM) disrupted the QS system of H. alvei H4 by down-regulating the expression of genes involved in QS and decreasing AHL concentrations. The dysfunction of the QS system in H. alvei H4 exacerbated oxidative stress, which in turn altered membrane composition, increased membrane permeability, and disrupted energy metabolism, amino acid metabolism, and nucleotide metabolism, ultimately contributing to the anti-QS effect. Subsequent validation through real-time fluorescence quantitative PCR and enzyme assays corroborated the sequencing results. These findings enhance our understanding of the comprehensive anti-QS effects induced by TF3, which may facilitate its future development and application in ensuring food safety.

overall_design: To study the broad changes in the transcription and metabolic profile of Hafnia alvei H4 induced by TF3 as a QS inhibitor, we treated H. alvei H4 with a subminimal inhibitory concentration of TF3 (31.25 µM), cultured and pretreated together with the control group without TF3 treatment, perform RNA-Seq sequencing.

first: Xue

last: Li

first: Yanan

last: Wang

first: Gongliang

last: Zhang

first: Jingran

last: Bi

first: Hongshun

last: Hao

first: Hongman

last: Hou


title: Maternal ancestry reveals cyclical aging of the mammary gland.

city: New York

first: Edmund

middle: C

last: Jenkins

address: 1468 Madison Avenue

department: Heme/Onc

institute: Icahn School of Medicine at Mt. Sinai

summary: the present provocative data that in addition to the expected progressive age-related  involution, mammary gland aging can occur in a cyclical pattern and is dictated by maternal ancestry. In cyclical aging, mammary glands of 11 and 19 months old mice share genetic and proteomic signatures, which are enriched in breast cancer-related pathways, but are absent at 3 and 14 months. Since incidence of breast cancer shows a bimodal age distribution at 45 (~11m in mice) and 65 (~19m in mice) in human populations, cyclical aging may contribute to these peaks of cancer susceptibility. Conversely, since the mammary glands at 3 and 14 months cluster together hierarchically, the cancer-associated peaks seem separated by a rejuvenation phase. Since cyclical aging is observed in mice with extended lifespan, these findings raise the possibility that if oncogenic mutations are avoided during the pro-oncogenic phases, through its rejuvenation phase, cyclical aging may impact multiple organs leading to extended longevity.

overall_design: We then performed single cells RNAseq analysis on primary  mammary epithelium BL/6NZB females at 3M, 11M, 14M, and 19M of age

first: Doris

last: Germain


title: Effect of Ilf3 knockout on gene expression in AOM/DSS induced CRC

city: GUANGZHOU

first: Baifu

last: Qin

address: Institute of Molecular and Medical Virology, Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, School of Medicine, Jinan University, Guangzhou, Guangdong Province

summary: To study the impact of ILF3 in the context of cancer, we established the AOM/DSS colitis-associated CRC model. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different tumor tissues from  Ilf3-WT and Ilf3-KO mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  Ilf3-WT and Ilf3-KO mice CRC tumor samples

first: Mong-Hong

last: Lee

first: Kai


title: Dynamic magneto-mechanical force in lysosomes instructs durable macrophage repolarization for antitumor immunity.

first: Li

last: Yingze

address: Zhennan Road

institute: Tongji University

summary: Mechanical forces are the emerging physical cue to regulate biochemical signals of immune cells for antitumor immunity. Here, we develop a magneto-mechanical force-triggered lysosomal membrane permeabilization (MagLMP) strategy to dictate durable macrophage repolarization, which leads to dynamic damage of lysosomal membrane via the finely tuned torque-induced vortex. We found that the MagLMP could activate M1-like macrophage repolarization, followed by the mounting of antitumor immunity. Together, we establish an intracellular mechanical strategy to dynamically manipulate innate immune responses in vivo and provide the tool for durable immunotherapy through organelle mechanotransduction.

overall_design: The experiment is aim to investigate the repolarization of macrophages after stimulated by magneto-mechanical force in lysosomes.  Magnetic nanomotors were cocultured with RAW 264.7 macrophages, and then cells were stimulated by rotation magnetic field at the frequency of 1 Hz.


title: DNA-based cell typing in menstrual effluent identifies cell type variation by sample collection method: toward noninvasive biomarker development for women’s health

city: Lebanon

first: Irma

last: Vlasac

state: NH

address: 1 Medical Center Drive.

department: Epidemiology

institute: Dartmouth College

summary: Menstrual effluent cell profiles have potential as noninvasive biomarkers of female reproductive and gynecological health and disease. We used DNA methylation-based cell type deconvolution (methylation cytometry) to identify cell type profiles in self-collected menstrual effluent. During the second day of their menstrual cycle healthy participants collected menstrual effluent using a vaginal swab, menstrual cup, and pad. Immune cell proportions were highest in menstrual cup samples, and epithelial cells were highest in swab samples. Our work demonstrates the feasibility and utility of menstrual effluent cell profiling in population-level research using remotely collected samples and DNA methylation.

overall_design: We profiled DNA methylation from 12 healthy controls matched by collection sample type (swab, pad, menstrual cup) using Illumina Epic Chip V2

first: Hannah

last: Stolrow

first: Brock

last: Christensen

first: Luisa

last: Rivera


title: Transcriptome analysis reveals the molecular mechanism of Baduanjin in improving type 2 diabetes

city: beijing

first: Guangjian

last: Jiang

address: Beijing University of Traditional Chinese Medicine, No. 11 North Third Ring East Road, Beijing City

institute: Beijing University of Chinese Medicine, Beijing

type: Non-coding RNA profiling by high throughput sequencing

summary: Among the many clinical practices that use Baduanjin as a treatment for type 2 diabetes patients, it has shown to be effective, but there is still a lack of research on molecular regulation mechanisms. We detected the levels of lncRNA, circRNA, and mRNA in the blood of type 2 diabetes patients before and after the intervention of Baduanjin for 12 weeks.  Our analysis used sequencing and bioinformatics methods to identify differentially expressed genes, circRNAs, and lncRNAs possibly related to the regulation of diabetes by Baduanjin. From peripheral blood of patients with diabetes before and after Baduanjin intervention, 4244 DE mRNAs, 463 lncRNAs, and 516 circRNAs were determined. Systematic bioinformatics analysis revealed that the DE genes are functionally rich in oxidative phosphorylation and cytokine-cytokine receptor interaction. In addition, the results indicated that the potential ENST00000512668-G0S2 interplay, which has been methodically validated in the lncRNA prediction database, participates in Baduanjin regulation of diabetes by altering oxidative phosphorylation in patients with diabetes. This finding provides molecular targets for improving the use of Baduanjin as adjunctive therapy for diabetes.

overall_design:
Difference of mRNA, lncRNA and circRNA Expression in Blood of Diabetic Patients Before and After Baduanjin Exercise

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Xian-Jie

last: Zhen

first: Jun-Chang

last: Liu

first: Yue-Lin

first: Yue

last: Ma

first: Xin-Hui

last: Huo

first: Yan

first: Bo-Han

last: Lv

first: Yan-Xiang

last: Wu

first: Tian

last: An

first: Guang-Jian