title: Single cell transcriptomics of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [scRNA-seq cART+3HP]

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: We studied components of TB immunity that remain impaired after cART in the lung compartment, versus those that are restored by concurrent 3 months of once weekly isoniazid and rifapentine (3HP) and cART in the rhesus macaque (RM) model of LTBI and Simian Immunodeficiency Virus (SIV) co-infection. Concurrent administration of cART+3HP did improve clinical and microbiological attributes of Mtb/SIV co-infection compared to cART-naïve or -untreated RMs. While RMs in the cART+3HP group exhibited significantly lower granuloma volumes after treatment, they, however, continued to harbor caseous granulomas with increased FDG uptake. cART only partially restores the constitution of CD4+ T cells to the lung compartment in co-infected macaques. Concurrent therapy did not further enhance the frequency of reconstituted CD4+ T cells in BAL and lung of Mtb/SIV co-infected RMs compared to cART, and treated animals continued to display incomplete reconstitution to the lung. Furthermore, the reconstituted CD4+ T cells in BAL and lung of cART+3HP treated RMs exhibited an increased frequencies of activated, exhausted and inflamed phenotype compared to LTBI RMs. cART+3HP failed to restore the effector memory CD4+ T cell population that was significantly reduced in pulmonary compartment post SIV co-infection. Concurrent therapy was associated with the induction of Type I IFN transcriptional signatures and led to increased Mtb-specific TH1/TH17 responses correlated with protection, but decreased Mtb-specific TNF responses, which could have a detrimental impact on long term protection.

overall_design: These cells were isolated from bronchoalveolar lavage of rhesus macaques co-infected with Mtb/SIV and treated with cART+3HP

first: Riti

last: Sharan

first: Yi

last: Zou

first: Korri

last: Weldon

first: Zhao

last: Lai

first: Deepak

last: Kaushal


title: YTHDF3 Promotes the Translation of m6A-Enriched Mitosis-Associated Genes to Attenuate the Responsiveness to Neoadjuvant Chemotherapy in Esophageal Cancer [RIP-seq]

status: Public on Nov 03 2025

city: zhengzhou

first: Xiangyu

last: Wang

state: Henan

address: No. 100 Science Avenue

country: China

institute: Zhengzhou University School of Basic Medical Sciences

summary: Neoadjuvant chemotherapy (NACT) is a pivotal treatment strategy for esophageal cancer, significantly improving patient prognosis and 5-year survival rates. However, a substantial proportion of patients exhibit resistance to NACT and consequently fail to benefit from it. As NACT responsiveness is influenced by multiple distinct molecular pathways, it is essential to systematically investigate the mechanisms underlying poor therapeutic responses. In this study, we found that YTHDF3 directly enhances the m6A-dependent translation of key mitotic regulators, CDCA8 and INCENP, thereby reducing cellular sensitivity to NACT.

overall_design: To investigate the transcriptome-wide targets of YTHDF3, RNA immunoprecipitation sequencing (RIP-seq) was performed using an anti-YTHDF3 antibody in KYSE30 esophageal cancer cells. This approach enabled the identification of YTHDF3-bound mRNAs under endogenous conditions, providing insights into its regulatory role in post-transcriptional gene expression.

first: Xiang

middle: Y

first: Ting

last: wang

first: Si

middle: M

last: Zhao

first: Zi

middle: G

last: Dong


title: Heterogeneity and Homogeneity in Treg responses to Interleukin-2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Activation of Piezo1 induces heterogeneity in LSK cells leading to HSC proliferation and myelopoiesis [scRNA-seq]

city: Hangzhou

first: Xinjiang

last: Lu

address: Yuhangtang road No.866

institute: Zhejiang University

summary: Bone marrow haematopoietic stem cells (HSCs) are mobilised into blood under various stresses.  Although they are exposed to shear stress during circulation, the role of mechanical stimulation in regulating HSCs remains unknown. Piezo1, a mechanosensory ion channel, was implicated in regulation of haematopoietic cells. We analysed the transcriptional heterogeneity of LSK cells from mice treated with the Piezo1 agonist Yoda1 for 2 weeks. Our study demonstrated that activation of Piezo1 promoted HSC proliferation and differentiation toward the myeloid lineage, as evidenced by an increase in HSC numbers and the upregulation of myeloid transcription factors.

overall_design: LSK cells were sorted from the bone marrow of control and Yoda1-treated mice.

first: Tongyao

last: Shang

first: Li

first: Shibo

last: Ying


title: Heterogeneity and Homogeneity in Treg responses to Interleukin-2 [RNAseq1: IL2/JES6-1 timecourse]

summary: IL2 is an immune-regulatory cytokine that is crucial for the development and maintenance of Tregs. Here we investigate how temporal IL2 stimulation affects Treg gene expression and chromatin landscape via RNASeq and ATACSeq

overall_design: We tested IL2/JES6 and IL2 immunocytokines F10 and F511 compared to PBS in Foxp3IRES-GFP mice, harvesting cells at 1 to 128 hours post-injection for bulk RNA-seq.

first: Kumba

last: Seddu

first: Kaitavjeet

last: Chowdhary

first: Odhran

last: Casey

first: Molly

last: Henderson

last: Cao

first: Jakub

last: Tomala

first: Liang

last: Yang

first: Jamie

last: Spangler

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: EGF activation of POMC gene transcription is mediated by STAT3

city: Montreal

first: Arthur

middle: Jules

last: Gouhier

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

summary: Classical activation of the hypothalamic-pituitary-adrenal axis (HPA) is exerted by stimulation of pituitary POMC gene transcription and ACTH release by the hypothalamic hormone CRH. In parallel, inflammatory cytokines such as IL6 and LIF also stimulate ACTH release and POMC transcription through the JAK/STAT pathway. In recent years, a particular interest in the role of the EGF pathway for POMC activation was sparked by the identification of causative mutations in the USP8 gene that have been implicated in formation of pituitary corticotrope adenomas that are the hallmark of Cushing’s disease. These mutations were associated with persistent upregulation of the EGF/EGFR pathway and its putative role in ACTH hypersecretion. In the present work, we reassessed the signalling pathways that are activated in response to ACTH in pituitary corticotrope cells using the AtT-20 cell model. We confirmed activation of the MAP kinase pathway by EGF but also show activation of the AKT/mTOR and JAK/STAT pathways. Whereas activation of all three pathways appears essential for stimulation of cell proliferation, only the JAK/STAT pathway and more specifically STAT3, enhances POMC gene transcription. This action is mapped to a single STAT binding element of the POMC promoter in contrast to activation by the other STAT-activating cytokines LIF and IL6. Further, EGF signalling is specifically enhanced by STAT3 but not STAT1 in contrast to LIF-dependent activation. All together, the data identified a unique STAT3-dependent target on the POMC promoter that mediates EGF activation of POMC gene transcription.

overall_design: To investigate the transcriptional effect of the EGF receptor (EGFR) in corticotrope cells AtT-20, we performed RNA-seq in AtT-20 and AtT-20-EGFR with or without EGF treatment for 3 or 18 hours.

first: Ryhem

last: Gam

first: Kevin

last: Sochodolsky

first: Aurelio

last: Balsalobre

first: Yves

last: Gauthier

first: Jacques

last: Drouin


title: Targeting the histone methyltransferase DOT1L rewires CD8 T cells and enhances their intrinsic cytotoxic activity towards tumor cells [RNAseq_WT_KO_DMSO_EPZ]

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: Insights into the epigenetic mechanisms of CD8 T cell differentiation are delivering novel opportunities for modulating fate decisions and immune responses. The histone methyltransferase DOT1L is emerging as a central epigenetic regulator in immune cells. However, its cell-intrinsic role in CD8 T cell programming remains unclear as positive as well as negative roles have been ascribed to DOT1L. Here, we determined the cell-intrinsic role of DOT1L in mouse CD8 T cells using conditional ablation. In contrast to deletion of Dot1L early in the T cell lineage, conditional ablation of Dot1L in isolated mature CD8 T cells in vitro did not compromise the in vivo proliferative capacity and anti-tumor reactivity. In vitro, Dot1L knock-out CD8 T cells showed accelerated and enhanced antigen-specific cytotoxic activity towards tumor cells. Mechanistically, transcriptome and proteome profiling revealed that loss of DOT1L results in an altered cell-identity program with loss of T-cell and gain of NK-cell features. This role of DOT1L was linked to its catalytic activity since treatment with specific DOT1L inhibitors phenocopied genetic deletion of Dot1L. Our findings show that ablation of DOT1L activity is well-tolerated in mature CD8 T cells, rewires their cell identity in a tunable way towards the NK-cell lineage and enhances their cytolytic activity cell intrinsically.

overall_design: RNAseq on expanded murine CD8 T cells (day 8) to investigate the effect of DOT1L genetic ablation (n=3 biological replicates) or catalytic inhibition (n=4 biological replicates) on the transcriptome. For catalytic inhibition, cells were treated for 8 days with either EPZ-5676 (DOT1L inhibitor; 10 mM) or DMSO (vehicle control).

first: Muhammad

middle: A

last: Aslam

first: Muddassir

last: Malik

first: Eliza

last: Kwesi-Maliepaard


title: Targeting the histone methyltransferase DOT1L rewires CD8 T cells and enhances their intrinsic cytotoxic activity towards tumor cells [RNAseq_DMSO_SGC]

overall_design: RNAseq on expanded murine CD8 T cells (day 8) to investigate the effect of loss of DOT1L catalytic activity on the transcriptome. Cells (n=4 biological replicates) were treated for 8 days with either SGC-0946 (DOT1L inhibitor; 10 mM) or DMSO (vehicle control).

first: Willem-Jan

last: de Leeuw

first: Tibor

last: van Welsem


title: Normocaloric Diet induces represión on immune response genes in liver of C57BL/6 mice

city: Juarez

first: Isui Abril

last: Garcia Montoya

state: Chihuahua

address: Plutarco Elias Calles  1210

department: Químico Biológicas

country: Mexico

institute: Universidad Autónoma de Ciudad Juárez

summary: Gene expression profiles in the Liver of C57BL/6 mice with DIO   vs. those who received a Normocaloric diet . Normocaloric diet induce  the downexpression of inflammation-related genes and signaling pathways.

overall_design:
M22K_14_14: Pools of total RNA were made per study group (five mouse per group): Normocaloric   mice (test group) and obese mice (reference). The reverse transcription polymerase chain reaction (RT-PCR) was performed and the resulting complementary DNAs were labeled with Cy5 (Normocaloric) or Cy3 (Obesity.control). Hybridation analysis used the mouse 65-mer oligo library from Sigma-Genosys to compare the expression of 23,232 gene-specific oligonucleotide probes for mouse.
M22K_14_15: Pools of total RNA were made per study group (five mouse per group): Symbiotic  mice (test group) and Normocaloric mice (reference). The reverse transcription polymerase chain reaction (RT-PCR) was performed and the resulting complementary DNAs were labeled with Cy5 (Symbiotic) or Cy3 (Normocaloric.control). Hybridation analysis used the mouse 65-mer oligo library from Sigma-Genosys to compare the expression of 23,232 gene-specific oligonucleotide probes for mouse.
M22K_14_16: Pools of total RNA were made per study group (five mouse per group): Symbiotic  mice (test group) and Obese mice (reference). The reverse transcription polymerase chain reaction (RT-PCR) was performed and the resulting complementary DNAs were labeled with Cy5 (Symbiotic) or Cy3 (Obesity.control). Hybridation analysis used the mouse 65-mer oligo library from Sigma-Genosys to compare the expression of 23,232 gene-specific oligonucleotide probes for mouse.

last: García-Montoya

first: Florinda

last: Jiménez-Vega


title: Piezo1 deficiency induces transcriptomic changes in HSCs [RNA-seq]

first: Xinjiang

last: Lu

summary: We found that haematopoietic cell-specific Piezo1 knockout (KO) inhibits HSC proliferation and myeloid differentiation. To identify the underlying mechanism, we analysed the gene expression profiles of long-term haematopoietic stem cells (LT-HSCs) from Piezo1 KO mice and compared them with those from control mice. Our study demonstrated that the tight junction pathway was one of the enriched terms among downregulated genes in Piezo1 KO HSCs, with a decrease in JAM3 expression.

overall_design: We performed transcriptional profiling using RNA-seq in sorted LT-HSCs from the bone marrow of control and Piezo1 KO mice.

first: Tongyao

last: Shang

first: Li

last: Zhao

first: Shibo

last: Ying


title: PRC1 Mediates the Transcriptional Repressive Function of POGZ in Neurodevelopmental Gene Regulation

city: Harrisburg

first: Jessenia

last: Chavez

state: Pennsylvania

address: 4261 Williamsburg Dr, Apt. A

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: Polycomb Repressive Complex 1 (PRC1) is a family of fundamental epigenetic regulators crucial for gene silencing and mammalian development. Elucidating the PRC1 composition and function in context- and stage-specific functions during differentiation and development is crucial in understanding the impact of PRC1-mediated transcriptional activity in these processes. This study focuses on the identification and characterization of POGZ, a high-risk Autism risk gene, as a novel component of the PRC1 complex in neural cells. Our biochemical analyses demonstrate that POGZ specifically interacts with the PRC1.6 complex to form the novel PRC1-POGZ complex. Functional assays indicate that POGZ elicits strong transcriptional repressor activity that is dependent on RING1B expression. ChIP-Seq studies determined that PRC1-POGZ localizes at neurodevelopmental genes in the embryonic mouse cortex. Although POGZ knockout (KO) does not compromise mESC pluripotency, POGZ ablation in neural precursor cells resulted in severe dysregulation of transcriptomic gene expression, marked by failed activation of key neural marker genes. Mechanistically, PRC1-POGZ target genes involved in multiple aspects of neuronal differentiation were differentially expressed in POGZ KO NPCs, which may explain the observed failed differentiation. The insights gained herein provide critical insights toward understanding how PRC1-POGZ function influences neural cell fate determination.

overall_design: To investigate the effects POGZ KO may have on the transcriptome of WT embryonic stem cells (ESCs) and differentiated neural precursor cells (NPCs). We generated a POGZ KO ESC line via CRISPR/Cas9 technology. POGZ WT and KO ESCs were differentiated in NPCs using a previously established protocol (Hanafiah, et al. 2020). We performed RNA-Seq on POGZ WT and KO ESCs (Day 0) and NPCs (Day 7). Duplicates of each genotype and time point were included in this experiment.

first: Zhonghua

last: Gao

first: James

last: Stafford


title: Heterogeneity and Homogeneity in Treg responses to Interleukin-2  [scATAC-seq1: IL2 2h and PBS Ctl]

first: CBDM

last: Lab

summary: We investigated early effects of IL2 treatment on mouse Treg chromatin accessibility by performing scATAC-seq on splenic Tregs isolated from mice 2h after treatment with recombinant IL2 or PBS vehicle control.

overall_design: Mouse CD4+ regulatory Tregs were isolated from Foxp3-IRES-GFP reporter mice exactly 2h after treatment with 10 μg of recombinant mouse IL2 (PeproTech, 212-12) or PBS vehicle control (in 110 μl volume). Tregs were isolated from the spleen by FACS for scATAC-seq.

first: Kaitavjeet

last: Chowdhary

first: Kumba

last: Seddu

first: Christophe

last: Benoist


title: Individual G-quadruplex targeting with ligand-functionalized CRISPR-Cas9 uncovers transcriptional-dependent functional responses.

city: London

first: Marco

last: Di Antonio

state: United Kingdom

address: 80 Wood Lane

department: Chemistry

country: United Kingdom

institute: Imperial College London

summary: The development of selective ligands to target DNA G-quadruplexes (G4s) has been pivotal in revealing their role in transcriptional regulation. However, most of the ligands described to date lack intra-G4 selectivity, severely limiting their potential for uncovering the biological function of individual G4s across the genome. To overcome these limitations, we developed ATENA (Approach to Target Exact Nucleic Acid alternative structures). ATENA relies on the chemical modification of established G4-ligands to enable their conjugation onto a catalytically inactive Cas9 protein (dCas9) using HaloTag, allowing for the targeting of individual G4s in living cells. We have systematically screened the length of the PEG-linkers connecting the G4-ligands to the HaloTag and sgRNA sequences to attain optimal G4 engagement both in vitro and in cells. Using optimized conditions, we leveraged ATENA to demonstrate how the selective targeting of the well-studied G4 in the promoter of the oncogene c-MYC suppresses its transcription exclusively from the P1 promoter. We also show that positioning ligands in the proximity of regulatory elements suppresses c-MYC transcription in a G4-independent manner, highlighting the importance of appropriate design to measure genuine G4-mediated transcriptional changes. We also demonstrate that selective targeting of a G4 in the PVT1 promoter can either stimulate or repress its transcription depending on the type of G4-ligand used, indicating that functional responses associated with G4-stabilization can highly depend on the type of ligand used. We further harnessed ATENA to study transcriptional perturbation associated with cell-specific G4s, revealing that the functional responses associated with these structures are tightly linked with the expression levels of the targeted gene. Our study provides critical insights into G4-based therapeutic design, offering an innovative platform to investigate G4 biology with high precision.

overall_design: To investigate the intra-G4 selectivity provided by ATENA against DC-34 and PyPDS, we performed  RNA-Seq analysis.

first: Sabrina Pia

last: Nuccio

first: Enrico

last: Cadoni

first: Roxani

last: Nikoloudaki

first: Silvia

last: Galli

first: An-Jie

last: Ler

first: Thomas

middle: E

last: Maher

first: Ella

last: Fan

first: Ling Sum

last: Liu

first: Christopher

middle: R

last: Fullenkamp

first: John

middle: S

last: Schneekloth Jr


title: Whole blood transcriptomic profiling identifies expression signatures for sepsis mortality

city: Philadelphia

first: Blanca

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

summary:
Sepsis is the leading cause of death in U.S. hospitals and affects nearly 50 million people globally per year. Sepsis is defined as the ‘dysregulated host response to infection’, however, identifying specific and targetable immune abnormalities for therapeutic intervention has been challenging. An effective immune response clears pathogen but also protects host tissues from collateral damage. In sepsis, however, broad immune dysregulation causes organ failure and increased risk of mortality. Therapeutic trials targeting known inflammatory markers in sepsis have failed to improve outcomes. Efforts to identify sepsis therapies may have been thwarted by a focus on the wrong targets, undetected or unaccounted-for heterogeneity among study participants, or issues of timing in a highly dynamic immune response and clinical syndrome.
Analysis of the leukocyte transcriptome can reveal elements of the dysregulated host response to infection that characterizes sepsis. We hypothesized that sepsis nonsurvivors have a distinct transcriptional signature, and we thus sought to identify, validate, and contextualize the whole blood transcriptomic changes associated with sepsis mortality in patients with and without septic shock.

overall_design: We conducted a prospective observational cohort study of 161 critically ill sepsis patients with whole blood RNA samples collected within 24 hours of admission to the ICU. Differential gene expression analysis was conducted to identify transcriptomic changes in 1) nonsurvivors versus survivors at 30 days and 2) patients with versus without septic shock, adjusted for age, sex, and absolute neutrophil count. We performed gene set enrichment analysis (GSEA) to describe overrepresented ontological pathways.

first: Nuala

middle: J

last: Meyer

first: Mengyuan

last: Kan


title: MeCP2 Interacts with the Super Elongation Complex to Regulate Transcription

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

first: Jun

last: Sonn

first: Marta

last: Iwanaszko

first: Huda

last: Zoghbi


title: TPO stimulation midulates gene expression of iKMT2A-MLLT3 HSPC

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Investigate the immediate impact of in vivo exposure to exogenous TPO on gene expression,

overall_design: We profiled Evi1highFlt3-LSK iKMT2A-MLLT3 cells after 2 and 5 days on Dox at the single cell level. LT-HSC and MPP1-3 by using a hashtag oligonucleotide and antibody-derived tag labelling strategy for cellular indexing ofoligonucleotide and antibody-derived tag labelling strategy for cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq)

first: Hugues-Etienne

last: Chatel-Soulet

first: Jürg

last: Schwaller

first: Athimed

last: El Taher


title: RNAseq of mRNA from hepatic CD8 T cell populations after low dose and during high dose AdV infection

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

country: Germany

institute: TUM

summary: We aimed at dissecting phenotype, functionality and regulation of antigen-specific hepatic CD8 T cells after low dose or during high dose infection of the liver.

overall_design: Comparison of hepatic CD8 T cell populations in two infection models (n=3 for each sample group). For low dose infection, hepatic T cells were sorted . For high dose infection, hepatic T cells were sorted.

first: Verena

last: König

first: Miriam

last: Bosch

first: Nina

last: Kallin

first: Sainitin

last: Donakonda

first: Rupert

last: Oellinger

last: Engleitner

first: Percy

last: Knolle


title: Independent interacting effects of folate and methylmalonic acid on cardiovascular disease mortality

status: Public on Nov 02 2025

city: Weifang

first: Peng

last: Wang

state: Shandong Province

address: No. 7166, Bao Tong West Street

institute: Shandong Second Medical University

summary: Objective: To investigate the independent and interactive effects of circulating folate and methylmalonic acid (MMA) status on cardiovascular disease (CVD) mortality. Methods: This study included 22,487 individuals from the U.S. National Health and Nutrition Examination Survey (NHANES) between 1999 and 2014. Kaplan-Meier and weighted Cox proportional hazards models were used to assess the associations of folate and MMA with CVD mortality. Restricted cubic splines (RCS) evaluated nonlinear relationships. Additive interaction method explored interactive effects. Sensitivity analysis tested the robustness of the findings. In vitro, CCK-8 assays were performed to assess the combined effects of folate and MMA on H9c2 cardiomyocyte viability. Transcriptomic analysis identified differentially expressed genes (DEGs) and their enriched pathways. Results: During 12.1 years of median follow-up, 1,510 cardiovascular deaths (4.4%) were recorded. RCS analysis demonstrated a U-shaped association between folate levels and CVD mortality, and a linear association for MMA. When MMA ≤ 182 nmol/L, folate levels were not associated with CVD mortality. However, among individuals with MMA > 182 nmol/L, both low and high folate levels were significantly associated with higher CVD mortality, with adjusted hazard ratios (aHRs) of 1.43 (95% CI: 1.19-1.71) and 2.36 (95% CI: 1.85-3.00), respectively (both P < 0.001). An additive interaction between folate and MMA on CVD mortality (RERI: 0.82 [95% CI: 0.06-1.58], API: 0.35 [95% CI: 0.03-0.67]; SI: 1.57 [95% CI: 1.27-2.00]). Sensitivity analyses confirmed these findings. In vitro, MMA (8 mM) significantly enhanced folate-induced (1.6 mM) cytotoxicity, reducing cell viability to 49.26% (P < 0.001). Transcriptomic analysis revealed 53 DEGs under combined treatment, enriched in inflammation-related pathways. Conclusions: Both population-based and experimental evidence suggest that elevated folate and MMA levels independently increase CVD mortality risk, with their interaction synergistically exacerbating cardiovascular outcomes.

overall_design: RNA-seq profiling of four experimental groups of H9c2 cells: control, folic acid (FA)-treated, MMA-treated, and FA&MMA combination-treated.

first: Xinyu

last: Zhang

first: Chunping

first: Jinfeng

first: Xin

last: Liu

first: Shengnan

last: Zhao

first: Tuanwei


title: Conserved heat shock factors control barley heat stress memory through diverged mechanisms - extended replicate

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary: Climate change requires optimizing stress responses in crops. Priming and memory of heat stress (HS) allow plants to improve their tolerance against high temperatures. Here, we investigate HS memory in cultivated barley (Hordeum vulgare) to assess whether the mechanisms underlying priming by and memory of HS are conserved between dicots and monocots. Mutation of the barley orthologs of two key transcriptional regulators of HS memory, HvHSFA2 and HvHSFA3, reduced HS memory. This correlated with altered transcriptional responses of heat-induced genes in the mutants after recurrent HS. Conversely, overexpression of HvHSFA2 increases HS tolerance with no penalty on productivity. While the biological role of HSFA2 and HSFA3 is conserved, their mechanistic functions appear to have diverged, as we did not find evidence that HvHSFA2 is involved in H3K4me-mediated priming. Instead, both factors are globally required to boost induction of HS-responsive genes after recurrent HS. In summary, while barley HS memory depends on the highly conserved HvHSFA2 and HvHSFA3, the underlying transcriptional wiring is different. Our findings provide a tangible route to improve HS tolerance in temperate cereals.

overall_design: Gene expression analysis for Barley wild-type, hsfa2 and hsfa3 mutants with and without heat priming and heat treatment.

first: Loris

last: Pratx

first: Christian

last: Kappel


title: Circulating Extracellular Vesicles in the Pathogenesis of Heart Failure in Patients with Chronic Kidney Disease

city: New York

first: Alex

last: Gallinat

state: NY

address: One Gustave L Levy Place, Box. 1030

department: Cardiovascular Research Institute

institute: Icahn School of Medicine at Mount Sinai

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Cardiovascular disease (CVD) causes more than 50% of deaths in patients with advanced chronic kidney disease (CKD). CVD degree correlates with CKD severity. Clinical studies suggest that kidney-derived factors contribute to the development of CVD in CKD, independently of co-morbidities like hypertension and hyperglycemia. However, to date, no kidney-specific humoral risk factor that triggers direct cardiotoxicity has yet been identified, primarily due to the paucity of studies in patients with reno-cardiac disease. Here, we investigate how, in CKD patients, circulating extracellular vesicles (EVs) facilitate pathological kidney-heart communication, thereby causing cardiotoxicity, impairing cardiac function and contributing to heart failure (HF) progression. Methods and results: EVs isolated from the plasma of patients with CKD (hCKD-EVs), but not healthy controls (hCtr-EVs), were cardiotoxic, significantly inducing apoptosis both in vitro and in vivo and impairing contractility of isolated adult rat primary CMs in vitro. Likewise, EVs isolated from both plasma and kidneys of adenine diet-induced CKD mice were also cardiotoxic. Pharmacologically depleting circulating EVs in CKD mice significantly recovered cardiac function and ameliorated HF, suggesting CKD-EVs play a causal role in HF pathogenesis. Small RNA sequencing and q-RT-PCR validation uncovered distinct miRNAs enriched in both human and mouse CKD-EVs, compared to Ctr-EVs. CKD-EV-miRNA mimics were cardiotoxic to human ventricular AC16 myocytes inducing apoptosis and to iPSC-derived cardiomyocytes, impairing contractility and downregulating contractile gene expression. Interestingly, levels of endogenous primary miRNAs corresponding to CKD-EV-miRNAs were significantly higher in CKD-kidney tissues, specifically in CD45-veCD31-ve renal cells, but not in CKD-livers, CKD-lungs or CKD-PBMCs from peripheral blood, a result that suggests that CKD-EV-miRNAs originate renally. Remarkably, CKD-EV-miRNA levels correlated with established markers of cardiac injury, uncovering the presence of sub-clinical heart disease and demonstrating heterogeneity in CKD patients not yet diagnosed with HF. Conclusion: Collectively, our human subject and mouse studies show that circulating CKD-EVs, carrying distinct renal-derived miRNAs, mediate the molecular crosstalk that contributes to the pathogenesis of HF in CKD. Consequently, CKD-EVs hold promise as diagnostic and prognostic biomarkers for early disease detection and as targets for novel therapeutic interventions in chronic reno-cardiac disease.

overall_design: This study was approved by the institutional review boards of the Mount Sinai Hospital and University of Virginia (IRB# HSR20550). Peripheral blood was collected from adult patients with moderate to advanced chronic kidney disease (CKD) and healthy controls. CKD diagnosis followed KDIGO guidelines, and exclusion criteria included transplant history, active infection, malignancy, immunosuppressive therapy, pregnancy, bleeding disorders, and anemia. Plasma was isolated from blood collected in sodium citrate tubes and sequentially centrifuged to remove cells, platelets, and microvesicles. Extracellular vesicles (EVs) were isolated via ultracentrifugation (120,000 × g, 90 min), and total RNA was extracted using the miRNeasy micro kit (Qiagen).  Small RNA libraries were prepared using the SMARTer smRNA-seq Kit (Takara Bio) and sequenced on an Illumina NovaSeq 6000 (2x150bp, paired-end). Raw reads were processed using Cutadapt to remove adapters and low-quality sequences, retaining reads 18–32 bp in length. Filtered reads were annotated against miRBase v22 for small RNA identification.

first: Xisheng

last: Li

first: Nikhil

last: Raisinghani

first: Carlos

last: Santos-Gallego

first: Shihong

first: Sabrina

last: La Salvia

first: Seonghun

last: Yoon

first: Hayrettin

last: Yavuz

first: Anh

last: Phan

first: Alan

last: Shao

first: Michael

last: Harding

first: David

last: Sachs

first: Carol

last: Levy

first: Navneet

last: Dogra

first: Nicole

last: Dubois

first: Rupangi

last: Vasavada

first: Uta

last: Erdbruegger

first: Susmita

last: Sahoo


title: FUNCTIONAL AND TRANSCRIPTOMIC ANALYSIS OF EXTRACELLULAR VESICLES IDENTIFIES CALPROTECTIN AS A NEW PROGNOSTIC MARKER IN PERIPHERAL ARTERIAL DISEASE (PAD)

city: Pamplona

first: Goren

last: Saenz-Pipaon

state: Navarra

address: Av. Pio XII 55

department: Atherothrombosis

country: Spain

institute: CIMA University of Navarra

summary:
Rationale: Peripheral arterial disease (PAD) is associated with a high risk of cardiovascular events and death and is postulated to be a critical socioeconomic cost in the future. Extracellular vesicles (EVs) have emerged as potential candidates for new biomarker discovery related to their protein and nucleic acid cargo.
Objective: To study prothrombotic activity, cellular origin and transcriptomic profile of circulating EVs and to assess them as prognostic and therapeutic targets in PAD.
Methods and Results: This prospective study included control and PAD patients. Coagulation time (Procoag-PPL kit), EVs cellular origin and phosphatidylserine exposure were determined by flow cytometry in platelet-free plasma (n=45 PAD). Transcriptomic profiles of medium/large EVs were generated using the MARS-Seq RNA-Seq protocol (n=12/group). The serum concentration of the differentially expressed gene calprotectin was validated by ELISA in control (n=100) and PAD patients (n=317). Calprotectin was also determined in EVs and tissues of human atherosclerotic plaques (n=3). Circulating EVs of PAD patients were mainly of platelet origin, predominantly AnnexinV positive and were associated with the procoagulant activity of platelet-free plasma. Transcriptomic analysis of EVs identified 15 differentially expressed genes. Among them, serum calprotectin was elevated in PAD patients (p<0.05) and associated with increased amputation risk before and after covariate adjustment (mean follow-up 3.6 years, p<0.01). The combination of calprotectin with hs-CRP in the multivariate analysis further improved risk stratification (p<0.01). Furthermore, calprotectin was also expressed in femoral plaque derived EVs and tissues.
Conclusions: We found that PAD patients release EVs, mainly of platelet origin, highly positive for AnnexinV and rich in transcripts related to platelet biology and immune responses. Amputation risk prediction improved with calprotectin and was significantly higher when combined with hs-CRP. Our results suggest that EVs can be a promising component of liquid biopsy with prognostic implications in PAD.

overall_design: RNA-Seq was performed in plasma derived extracellular vesicles from controls, PAD patients with intermittent claudication (IC, Fontaine class IIa) and PAD patients with critical limb ischemia (CLI, Fontaine class IV). n=12/group.

first: Patxi

last: San Martín

first: Núria

last: Planell

first: Alberto

last: Maillo

first: Susana

last: Ravassa

first: Amaia

last: Vilas-Zornoza

first: Esther

last: Martínez-Aguilar

first: José

last: Rodriguez

first: Daniel

last: Alameda

last: Lara-Astiaso

first: Felipe

last: Prosper

last: Paramo

first: Josune

last: Orbe

last: Gomez-Cabrero

first: Carmen

last: Roncal


title: mRNA transcriptome sequencing of tumor cells, TRMs, MDMs, Monocytes and CD8+ T cells from tumor lungs of  KrasLSL-G12D/+Lkb1fl/fl (KL), KrasLSL-G12D/+Lkb1fl/flGpx4m/m(KLG4) after  Ad-cre injection and tamoxifen treatment

city: Wuhan

first: 鹏

last: 王

email: wangp00678@163.com, wangp94@whu.edu.cn

state: 湖北省

address: 169 Donghu nan road,Wucang District

institute: 武汉大学

summary: The transcriptional profiling of tumor cells, TRMs, MDMs, Monocytes and CD8+ T cells from tumor lungs of KL and KLG4 mice

overall_design: KL(n=2) and KLG4(n=2) for tumor cells, TRMs, MDMs and CD8+ T, respectively. KL (n=1) for Monocytes.

first: Peng

last: Wang

first: Shengdan

last: Zhang

first: Xin

last: Chen

first: Dandan

last: Lin

first: Bo

last: Zhong


title: Single-cell RNA sequencing of tumor tissues from 12 colorectal cancer (CRC) patients.

city: Shanghai

first: Zhuoqing

last: Xu

address: No. 197, Ruijin Er Road, Shanghai,

department: Ruijin Hospital

institute: Department of General Surgery

summary: Surgical specimens of tumor tissues from 12 colorectal cancer (CRC) patients were included.  All cases were consecutively enrolled and cytologically or histologically confirmed as rectal adenocarcinoma by at least two pathologists, with no history of prior neoadjuvant anti-tumor therapy.

first: Haoran

last: Feng

first: Zichao

last: Guo

first: Wenqing

last: Jia

first: Tao

first: Kun

last: Liu

first: Ren

last: Zhao

first: Xi

last: Cheng


title: RPA directly stimulates Mer3/HFM1 helicase processivity to ensure normal crossover formation in meiosis

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Meiotic crossover formation is critical for generating viable gametes and enhancing genetic diversity. The helicase Mer3 (HFM1 in humans) is a highly conserved factor essential for promoting crossovers and ensuring their proper distribution. Here, we identify replication protein A (RPA) as a direct interactor of budding yeast Mer3. We demonstrate that this interaction is conserved between human HFM1 and RPA. Cross-linking mass spectrometry and structural modelling with AlphaFold2 reveal a conserved and specific Mer3-RPA interface. Single-molecule magnetic tweezers assays demonstrate that direct RPA interaction is required for Mer3 helicase processivity under conditions of low DNA tension. Consistently, mer3 mutant deficient in RPA binding exhibit reduced crossover frequencies and accumulate unresolved recombination intermediates during budding yeast meiosis. Via genome-wide localisation experiments, we link this effect to a weakened recruitment to double-strand break sites of the mer3 mutant. Our findings provide mechanistic insights into coordination of meiotic recombination by the Mer3 helicase through interactions with the canonical DNA repair machinery, highlighting a conserved mechanism underlying crossover control during sexual reproduction.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces mikatae

overall_design: 5 samples total: each comes from two independent replicates each of anti-FLAG ChIP in spo11∆-Mer3-His6FLAG3, Mer3-His6FLAG3 and Mer3-8A-His6FLAG3 S. cerevisiae cells at 3h (spo11∆-Mer3-His6FLAG3) and 3h and 4h (Mer3-His6FLAG3 and Mer3-8A--His6FLAG3) in meiosis combined with 10% of spike-in S. mikatae Zip4-His6FLAG3 cells at 4h in meiosis


title: DRUG-seq of high-density neutrophils (HDNs), mature low-density neutrophils (M-LDN), and immature low-density neutrophils (IM-LDN) in patients with colorectal cancer

summary: High-density neutrophils (HDNs), mature low-density neutrophils (M-LDN), and immature low-density neutrophils (IM-LDN) were isolated from peripheral blood of nine treatment-naïve colorectal cancer (CRC) patients with histologically confirmed diagnoses, followed by gene expression profiling of these neutrophil subsets using Digital RNA with pertUrbation of Genes (DRUG) sequencing.

first: Yuchen

first: Jianting

last: Huo

first: Zifeng

first: Fangqian

first: Han

last: Gao

first: Zeping

last: Lv

first: Wangyi

first: Abudumaimaitijiang

last: Tuersun

first: Suyue

last: Yu

first: Wenchang

last: Li

first: Yaping

last: Zong

first: Xiaohui

last: Shen

first: Jingkun

first: Aiguo

last: Lu


title: Pharmacological rescue of motor neuron health by riluzole in patient-derived motor neurons

city: Melbourne

first: Christopher

last: Bye

state: Victoria

address: University of Melbourne

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

summary: Heterogeneous and predominantly sporadic neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) remain highly challenging to model. Patient-derived induced pluripotent stem cell (iPSC) technologies offer great promise for these diseases, however large-scale studies demonstrating accelerated neurodegeneration from sporadic patients are limited. We generated an iPSC library from 100 sporadic ALS (SALS) patients and conducted population-wide phenotypic screening. SALS patient-derived motor neurons recapitulated key aspects of SALS, including reduced survival, accelerated neurite degeneration correlating with donor survival, transcriptional dysfunction, and pharmacological rescue by riluzole. Here we sought to determine if riluzole treatment reversed the disease process in patient-derived motor neurons by RNAseq profiling of riluzole treated vs untreated motor neurons from 9 ALS donors.

overall_design: RNAseq profiling of patient-derived motor neurons from 9 ALS donors treated with DMSO or riluzole (2.5uM) from day 36 onwards. Samples collected at day neurite collapse reaches 50% of peak health in DMSO treated (LD50).

first: Bye

last: Christopher

first: Qian

last: Elizabeth

first: Lim

last: Katherine

first: Morgan

last: Steven


title: Targeting the histone methyltransferase DOT1L rewires CD8 T cells and enhances their intrinsic cytotoxic activity towards tumor cells [ChIPSeq_DMSO_EPZ_SGC]

first: Fred

last: van Leeuwen

summary: Insights into the epigenetic mechanisms of CD8 T cell differentiation are delivering novel opportunities for modulating fate decisions and immune responses. The histone methyltransferase DOT1L is emerging as a central epigenetic regulator in immune cells. However, its cell-intrinsic role in CD8 T cell programming remains unclear as positive as well as negative roles have been ascribed to DOT1L. Here, we determined the cell-intrinsic role of DOT1L in mouse CD8 T cells using conditional ablation. In contrast to deletion of Dot1L early in the T cell lineage, conditional ablation of Dot1L in isolated mature CD8 T cells in vitro did not compromise the in vivo proliferative capacity and anti-tumor reactivity. In vitro, Dot1L knock-out CD8 T cells showed accelerated and enhanced antigen-specific cytotoxic activity towards tumor cells. Mechanistically, transcriptome and proteome profiling revealed that loss of DOT1L results in an altered cell-identity program with loss of T-cell and gain of NK-cell features. This role of DOT1L was linked to its catalytic activity since treatment with specific DOT1L inhibitors phenocopied genetic deletion of Dot1L. Our findings show that ablation of DOT1L activity is well-tolerated in mature CD8 T cells, rewires their cell identity in a tunable way towards the NK-cell lineage and enhances their cytolytic activity cell intrinsically.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for H3K79me2 on isolated CD8 T cells (N=2 biological replicates) expanded for 8 days in medium containing 0.1% DMSO, 10 mM EPZ-5676 or 10 mM SGC-0946. Chromatin from S. cerevisiae containing HA tagged H3 and lacking H3K79 methylation was spiked into all samples and co-immunoprecipitated to normalize and quantify the data.

first: Teun

last: van der Brand

first: Willem-Jan

last: de Leeuw

first: Muddassir

last: Malik

first: Tibor

last: van Welsem


title: Waves of cell death modulate the abundance and maturation of human retinal ganglion cells

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

address: 1622 Locust Street

department: Ophthalmology

institute: University of Pittsburgh

summary: Retinal ganglion cells (RGCs) are the projection neurons that transmit visual information from the retina to the brain via the optic nerve. A substantial proportion of RGCs are eliminated by programmed cell death during development to regulate their final number, yet how cell death impacts RGC development in human retinas remains poorly understood. Here, we characterized the timing and cell-type-specificity of cell death in human fetal retinas and retinal organoids. We identified two waves of apoptosis: an early wave targeting retinal neuronal precursors and a late wave affecting RGCs and other neurons. In addition to these two waves of apoptosis, organoids displayed a distinct wave of necrosis in the innermost core region that eliminates nearly all RGCs during long-term culture. To investigate the functions of the apoptotic waves during retinal development, we differentiated BAX/BAK double mutant organoids that are deficient for apoptosis. In these mutant organoids, RGC survival was improved, RGC neurogenesis and maturation were delayed, and RGCs were lost through a compensatory increase in necrosis. Our data suggest that the waves of developmental apoptosis promote human RGC neurogenesis and maturation. Together, our results highlight the roles of cell death in human RGC development and the challenges in retinal organoid design. Overcoming these obstacles would improve the utility of retinal organoids for modeling optic neuropathies like glaucoma

overall_design: Wildtype or BAX/BAK double mutant organoids human retinal organoids at different ages were lysed into a single nuclei suspension and run on the 10x Genomics Chromium Single Cell System platform using the Single Cell Multiome ATAC + Gene Expression chemistry. Libraries were sequenced on Illumina NovaSeq X and processed through the Cell Ranger pipeline using the GRCh38 reference genome.

first: Jingliang

last: Zhang

first: Brian

last: Guy

middle: P

first: Caterina

last: Tiozzo

first: Meghana

last: Sreenath

first: Ya-Wen

last: Chen

first: Seth

last: Blackshaw

first: Robert

last: Johnston Jr


title: Transcriptomic Profiling Reveals the Role of Hedgehog Signaling as a Biomarker and in the Pathogenesis of Ménétrier’s Disease

city: New Haven

first: Won Jae

last: Huh

state: CT

address: 310 Cedar Street

institute: Yale University

summary: Both Ménétrier’s disease (MD) and juvenile polyposis syndrome (JPS) are rare premalignant conditions that can lead to gastric cancer. MD is an acquired disease without known causative mutations that is characterized by increased expression of an EGF receptor (EGFR) ligand, transforming growth factor-alpha (TGFα), in the stomach. JPS is inherited in an autosomal dominant pattern and is caused by BMPR1A or SMAD4 mutations. Although there are distinct clinico-pathological features that differ between the two diseases, they also share similar features that often lead to misdiagnosis. To identify diagnostic markers for MD and to better understand the pathogenesis of the disease, we performed transcriptomic profiling of stomach tissues from normal (NL), MD, and JPS patients. Comparative analysis between MD and JPS revealed both common and differential gene signatures. Common gene signatures included estrogen receptor signaling, integrin signaling, mTOR signaling, and others, which may be responsible for histopathological similarities. Among differential gene signatures, we found that Hedgehog (Hh) signaling is upregulated in MD and confirmed that protein expression of Hh signaling downstream targets, GLI1 (glioma-associated oncogene homolog 1) and HHIP (Hedgehog-interacting protein), is higher in MD than in JPS, particularly in foveolar cells by immunohistochemistry. We also showed that treatment with an Hh pathway inhibitor partially rescued the histopathological phenotypes in an MD mouse model. This study provides valuable insights into the potential mechanisms underlying the similar clinico-pathological features observed in MD and JPS. We also identified GLI1 and HHIP as diagnostic markers that can help to distinguish MD from JPS. Furthermore, Hh signaling was shown to play an important role in the pathogenesis of MD and can function as a potential therapeutic target.

overall_design: To compare the transcriptomic profile between MD and JPS, total RNA was extracted from the stomachs of  3 MD, 3 JPS, and 3 normal (NL) individuals. Then RNA sequencing was performed.

first: Miyoung

last: Shin

first: Tryston

middle: T

last: Gabriel

first: Fred Kwame

last: Ofosu

first: Jiali

first: Tricia

last: Wang

first: Matthew

last: Bechard

last: Coffey


title: MeCP2 Interacts with the Super Elongation Complex to Regulate Transcription (RNA-Seq)

first: Ali

last: Shilatifard

summary: Loss-of-function mutations in methyl-CpG binding protein 2 (MECP2) cause the neurodevelopmental disorder, Rett syndrome (RTT). The molecular mechanisms underlying MeCP2 function remain poorly understood. Here, using a MECP2 gain-of-function Drosophila model, we screened for genetic modifiers of MECP2-induced toxicity. Our approach identified several subunits of the Drosophila super elongation complex (SEC), a P-TEFb containing elongation factor that releases promoter-proximally paused RNA polymerase II (RNA pol II), as genetic interactors of MECP2. MeCP2 directly interacts with AFF4, the scaffold of the SEC, and facilitates its binding on a subset of genes that regulate neuronal development and synaptic function in the mouse cortex. Furthermore, genes with reduced AFF4 binding showed reduced RNA pol II binding in their genebody and decreased RNA expression in Mecp2 null mice. Taken together, we propose that MeCP2 interacts with the SEC to facilitate the release of RNA pol II and thereby support gene expression.

overall_design: Gene expression profiling in wildtype and Mecp2 null cortex at 7-weeks of age

first: Jun

last: Sonn

first: Marta

last: Iwanaszko

first: Huda

last: Zoghbi


title: Spatiotemporal transcriptomic and metabolomic landscapes of wild soybean seed development reveal regulatory mechanisms of nutrient accumulation [scRNA-Seq]

city: Harbin

first: Peiyan

last: Liu

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: Seed development is pivotal in soybean’s lifecycle, directly determining yield and nutritional quality related to oil and protein contents. However, spatiotemporally resolved mechanisms underlying cell differentiation and nutrient accumulation during seed growth remain elusive, especially in wild soybean (Glycine soja Sieb. et Zucc.), which harbors rich genetic diversity for quality traits. Here, spatial transcriptomics and metabolomics were combined to dissect their dynamics in G. soja seeds at the mid-maturity stage. Differential expression analysis characterized the distinct accumulation patterns between adaxial and abaxial embryo parenchyma cells, revealing abaxial cells are enriched in protein metabolism pathways while adaxial cells focus on lipid metabolism pathways, which is consistent with previous studies reporting spatial nutrient accumulation in G. soja seeds. Meanwhile, pseudotemporal trajectory analyses briefly supported a sequential transcriptional regulation pattern for these differences. Cell-cell communication analysis further uncovered potential signaling interactions mediating cell-type-specific differences across seed cells. Key genetic regulators and differential metabolites were identified through spatial transcriptomics and metabolomics co-expression analysis, with GsMAPK23-4 screened as a core candidate linked to cotyledon nutrient metabolism. Functional validation confirmed GsMAPK23-4 modulates seed quality: knockout mutants had significantly higher amino acids and proteins. These findings elucidate the cellular characteristics and differentiation processes in G. soja seeds at the mid-maturity stage, providing a molecular basis for understanding this phase and generating targets to improve soybean yield and quality.

overall_design: two samples from soybean seeds


title: MeCP2 Interacts with the Super Elongation Complex to Regulate Transcription (ChIP-Seq)

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of AFF4 and total RNA Pol II in wildtype and Mecp2 null cortex at 7-weeks of age


title: Inhibition of the inflammasome ameliorates orthologous polycystic kidney disease

city: Freiburg

first: Katharina

last: Moos

address: Breisacherstr. 153

department: Medical Faculty

institute: University of Freiburg

summary: ADPKD is the most common genetic renal disease, leading to renal failure in the vast majority of affected individuals. Standard therapy consists of blood pressure control and salt restriction. Tolvaptan further delays renal failure but side effects prevent its widespread use. Novel therapeutic approaches are needed. Recent evidence has identified inflammation as an important driver of ADPKD. Here we show a strong inflammatory signature in transcriptomes of early ADPKD in the mouse. IL1β and IL18, effectors of inflammasome activation, are among the top upregulated transcripts. Inflammasomes act as part of the innate immune response to danger signals, including crystals. Induction of calcium oxalate crystals through dietary intervention in Pkd1 mutant mice aggravated the cystic phenotype. Treatment of Pkd1 mutant mice with the inflammasome inhibitor MCC950 significantly ameliorated the ADPKD phenotype. Analogous results were obtained through genetic silencing of the essential inflammasome component Asc in ADPKD mice. Interference with inflammasome activation in the ADPKD animals resulted in better renal function and decreased IL18 excretion in the urine. These findings identify inflammasome inhibition as a promising concept for the treatment of ADPKD.

overall_design: We performed a transcriptional screen in mice with a time dependent targeted deletion of Pkd1. Pkd1flox/flox.Pax8rtTA.Tet-O-Cre mice underwent tetracycline induced tubular deletion of Pkd1 during postnatal week 5 and 6. At 10 weeks, the kidneys were analyzed by RNAseq and the transcripts compared to kidneys from non-cystic Pkd1flox/flox.Tet-O-Cre control animals lacking Pax8rtTA.

first: Junwei

first: Manuel

last: Rogg

first: Shaya

last: Sasanpour

first: Vera

last: Strassl

first: Manaswita

last: Jain

first: Sato

last: Magassa

first: Björn

last: Neubauer

first: Benedikt

last: Kloos

first: Simone

last: Braeg

last: Saller

first: Svenja

last: Wöhrle

first: Frank

last: Bienaimé

first: Oliver

last: Gorka

first: Melanie

last: Boerries

first: Amandine

last: Viau

first: Olaf

last: Gross

first: Christoph

last: Schell

first: Wolfgang

last: Kuehn


title: Spatiotemporal transcriptomic and metabolomic landscapes of wild soybean seed development reveal regulatory mechanisms of nutrient accumulation [Spatial Transcriptomics]

first: Peiyan

last: Liu


title: Biomolecular tracking by FIRESCAPE reveals distinct modes of clearance, damage induction and cellular uptake for extracellular histone H3

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

summary: The study of chromatin has mostly been restricted to defining its function in the nucleus, where histone proteins fulfil vital roles in packaging genomic DNA and regulating transcription. However, chromatin components are often released into the extracellular space, either intentionally via cellular secretion or during disease or damage-induced cell death. These extracellular chromatin components, depending on the context, can consist of free histones, free DNA, intact nucleosomes (histone octamers wrapped by DNA), or heterogeneous, higher order structures such as neutrophil extracellular traps (NETs). They have been associated with diverse pathologies such as inflammation, cancer, and sepsis, and distinct toxic effects, most notably the damaging effects of free histones over intact nucleosomes. Extracellular chromatin components are emerging, suggested biomarkers for various associated diseases, yet there is a widely acknowledged lack of methods that distinguish between them and their unique functions in circulation. Here, we explore the fate and effects of extracellular free histone H3 by utilizing FIRESCAPE ([18F]-Fluorine Isotopic Radiolabeling Enabling Scanning of Clearance After Proteolytic Events), a novel radiolabeling concept that leverages the unique, high-sensitivity properties of the radioisotope 18F and residue-specific protein editing chemistry. By installing true 18F-containing protein sidechain mimics site-specifically into histone H3, FIRESCAPE enabled in vivo scanning of the half-lives, proteolytic susceptibility, and clearance of single residues in a protein of interest, at microdoses far below toxic levels (low nanomole). This now precisely reveals the remarkably distinct distribution, half-lives, damage-inducing abilities, and accumulation of free extracellular histones in cellulo and in vivo, comparing them to other chromatin states such as intact nucleosomes where appropriate. Free extracellular histones are rapidly cleared from circulation, first mediated by proteolysis of the histone tail. However, direct injection of free histones versus nucleosomes into tissue (brain) that is unprotected by such proteolysis provokes a starkly different response: free histones exhibited limited diffusion and swiftly promoted damage both in cell culture and in vivo, in contrast to the largely passive and benign nature of intact nucleosomes. Synthetic extracellular histone H3 uptake was observed and characterized with biochemical, genomic, and proteomic methodologies, revealing apparent deposition into chromatin indistinguishable from native H3 in localization and post-translational modification (PTM) accumulation, yet paired with cellular and tissue damage. These exploratory studies now provide much-needed clarity to the distinct fates and effects of extracellular histones versus nucleosomes, in particular the strongly damaging effects of free histones, their rapid uptake into cells, and an associated histone-specific proteolysis pathway via the removal of the histone tail.

overall_design: This study tested whether extracellular histones could penetrate cells and incorporate into chromatin in an in vivo context. To do this, histone H3 (containing a C-terminal dual FLAG-HA epitope tag) was intracranially injected into rats, followed by brain excision, crosslinking, and ChIP-seq against the HA mark, endogenous histone H3 mark, or input control. This study found widespread chromatin incorporation of the injected HA tagged histone H3, with similar occupancy throughout the genome to endogenous histone H3, only in the conditions in which the histone was injected, and not a PBS mock injection.


title: Therapeutic selective targeting of MMP-12 in B lymphocyte for the treatment of severe allergic airway disease

city: Nanjing

first: Xijie

last: Zhang

address: 300 Guangzhou Road, Gulou District

department: Department of Respiratory and Critical Care Medicine

institute: the First Affiliated Hospital of Nanjing Medical University

summary: Inducible Bronchus-Associated Lymphoid Tissue (iBALTs), the tertiary immune organs in the lungs, have been implicated in various pulmonary diseases. The formation and roles of iBALTs related to severe asthma, however, remain unclear. iBALTs was located near the area of bronchi and vessels in the severe asthma murine model induced by  house dust mite (HDM) extract and lipopolysaccharides (LPS). Repeated sensitizations promoted the formation of iBALTs, which disappeared 2 weeks post last HDM challenge. The neutralizing antibody of CXCL13 prevented the formation of iBALTs but failed to relieve the airway inflammation. B lymphocytes dominated in iBALTs. Compared with the control group, severe asthma group had increased IgE secreting cells. Bulk RNA-seq reveled the elevated MMP-12 in pulmonary B cells. MMP408, a specific MMP-12 inhibitor, reduced iBALTs formation. Moreover, AAV-6 targeting down MMP-12 in B lymphocytes blocked iBALTs and ameliorated the inflammation. These results indicated that MMP-12 from B lymphocytes motivated the aggregation of B lymphocytes, promoted the formation of iBALTs and further sharpened the inflammation of severe asthma.

overall_design: To investigate the possible effect of pulmonary B cells on the formation of iBALTs in severe asthma mice, we isolated the murine B cells from single-cell suspension of lung tissue via B220+ microbeads (130-049-501, Miltenyi Biotec). Then, we explored the differetial expressed genes between control mice and asthma mice by RNA-seq.

first: Xinyu

last: Jia

first: Min

first: Manni

last: Zhu

first: Zhengxia

last: Wang

first: Zhongqi

last: Chen

first: Ningfei

last: Ji

first: Mao

last: Huang

first: Mingshun


title: Bisulfite-sequencing of LX-2 cells

status: Public on Nov 01 2025

first: An

address: Aerodrome Road 13

institute: Huazhong University of Science and Technology

type: Methylation profiling by high throughput sequencing

summary: Liver fibrosis is characterized by deposition of excessive extracellular matrix (ECM). The major source of ECM is activated hepatic stellate cells (HSCs).NSUN2 is one of the m5C methyltransferases, mainly responsible for the methylation of tRNA and mRNA and plays a significant role in RNA m5C methylation. The purpose of this Bisulfite-seq is to explore the role of NSUN2 acting as m5C methyltransferases during HSC activation.

overall_design: The changes of m5C modification in LX-2 cells after TGF-β1 stimulated were investigated by Bisulfite-sequencing.

first: Chunwei

last: Shi


title: Variant-specific interaction of kinectin 1 with the multi–tRNA synthetase complex regulates ER sheet organization

city: Sendai

first: Masaki

last: Hosogane

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

country: Japan

institute: Tohoku university

summary: Kinectin 1 (KTN1) is an integral endoplasmic reticulum (ER) sheet protein that functions in ER organization and translation elongation. Alternative splicing introduces sequence diversity into the cytoplasmic region of KTN1, but the functional relevance of these variants has remained unclear. Here we show that the multi–tRNA synthetase complex (MSC), composed of eight aminoacyl-tRNA synthetases and three nonenzymatic proteins, specifically interacts with KTN1 in a manner dependent on the alternative exon V2 and glutamine-tRNA synthetase (QARS). Using V2 exon-specific knockout cells and KTN1 knockout cells with variant-specific resucue, we found that the V2 exon is required for KTN1-mediated recruitment of the MSC to the ER, where it promotes the formation of rough ER stacks. These findings define a variant-specific role for KTN1 in anchoring the MSC to the ER, and suggest that this interaction underlies a noncanonical activity of the MSC in regulating ER sheet organization.

overall_design: Ribo-seq together with RNA-seq (for normalization of Ribo-seq reads) of KTN1 knockout HeLa cells rescued by doxycycline(dox)-inducible one single variant of KTN1, either KTN1 V2 exon(+) or KTN1 V2 exon(-).


title: The conserved Prp40 WW domains facilitate non-canonical intron splicing via bridging 5'-splice-site and branch-site interaction

city: Taipei

first: LUH

last: TUNG

address: No. 128 Sec. 2 Academia Rd. Nankang Dist

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: Precise regulation of molecular interactions is essential for the proper execution of cellular pathways. In pre-mRNA splicing, the spliceosome must accurately process introns containing both canonical and non-canonical splice-site sequences, the latter often requiring additional regulatory mechanisms. Here, we investigate how cells cope with introns carrying non-canonical splice signals, focusing on spliceosomal components that recognize the 5′ splice site (5′SS) and branch point sequence (BPS). Unexpectedly, we find that the N-terminal WW repeats of the U1 snRNP protein Prp40, previously considered non-essential, play a critical role in facilitating the recognition and splicing of introns with suboptimal 5′SS and BPS elements. We provide genetic and biochemical evidence supporting this function and propose a structural model consistent with predictions from AlphaFold3. Together, our findings reveal a previously underappreciated role for Prp40 in fine-tuning splice-site recognition and ensuring robust splicing of non-canonical introns.

overall_design: RNA-seq profile of wild-type (PRP40) yeast cells which were cultured in 50 ml of liquid YPD medium at 30°C to reach OD600=0.8.

first: Luh

last: Tung

first: Chung-Shu

last: Yeh

first: Hsin-Hung

last: Lin

first: Hsin-Yue

last: Tsai

first: Shang-Lin

last: Chang

first: Hsuan-Kai

first: Amy

last: Larson

first: Fu-Lung

first: Chia-Ling

last: Hsu

first: Jeffery

last: Pleiss

first: Cheng-Fu

last: Kao

first: Wei-Hau

first: Tien-Hsien


title: DRUG-seq of High-Density Neutrophils (HDNs) from Colorectal Cancer Patients with or without GM-CSF Stimulation

first: Zhuoqing

last: Xu

summary: High-density neutrophils (HDNs) were isolated from peripheral blood of three treatment-naïve colorectal cancer (CRC) patients with histologically confirmed colorectal adenocarcinoma, then divided into PBS-treated controls (Ctrl) and GM-CSF-treated groups (GMCSF, 10 ng/mL, 16 hours) prior to Digital RNA with pertUrbation of Genes (DRUG) Sequencing analysis of stimulation-dependent gene expression profiles.

first: Haoran

last: Feng

first: Wenqing

first: Yuchen

last: Zhang

first: Jianting

last: Huo

first: Zifeng

first: Fangqian

first: Han

last: Gao

first: Zeping

last: Lv

first: Wangyi

last: Liu

first: Abudumaimaitijiang

last: Tuersun

first: Suyue

last: Yu

first: Wenchang

last: Li

first: Yaping

last: Zong

first: Xiaohui

last: Shen

first: Xi

last: Cheng

first: Jingkun

last: Zhao

first: Aiguo

last: Lu


title: Conserved heat shock factors control barley heat stress memory through diverged mechanisms

first: Isabel

last: Bäurle

summary: Climate change requires optimizing stress responses in crops. Priming and memory of heat stress (HS) allow plants to improve their tolerance against high temperatures. Here, we investigate HS memory in cultivated barley (Hordeum vulgare) to assess whether the mechanisms underlying priming by and memory of HS are conserved between dicots and monocots. Mutation of the barley orthologs of two key transcriptional regulators of HS memory, HvHSFA2 and HvHSFA3, reduced HS memory. This correlated with altered transcriptional responses of heat-induced genes in the mutants after recurrent HS. Conversely, overexpression of HvHSFA2 increases HS tolerance with no penalty on productivity. While the biological role of HSFA2 and HSFA3 is conserved, their mechanistic functions appear to have diverged, as we did not find evidence that HvHSFA2 is involved in H3K4me-mediated priming. Instead, both factors are globally required to boost induction of HS-responsive genes after recurrent HS. In summary, while barley HS memory depends on the highly conserved HvHSFA2 and HvHSFA3, the underlying transcriptional wiring is different. Our findings provide a tangible route to improve HS tolerance in temperate cereals.

overall_design: Gene expression analysis for Barley wild-type, hsfa2 and hsfa3 mutants with and without heat priming and heat treatment.

first: Loris

last: Pratx

first: Christian

last: Kappel


title: YTHDC1 Regulates m6A-Dependent TERT mRNA Stability to Modulates Ovarian Cancer Senescence

city: Xiamen

first: Hong

middle: Xiao

last: ting

state: fujian province

address: 4221 South Xiang'an Road, Xiang'an District, Xiamen, Fujian

department: Medical School

institute: Xiamen university

summary: The m6A reader protein YTHDC1 is implicated in the pathogenesis of diverse cancer types. In this study, we identify YTHDC1 as a critical regulator of senescence in ovarian cancer cells. We demonstrate that knockdown of YTHDC1 inhibits cell proliferation and promotes cellular senescence.Mechanistically, depleting YTHDC1 diminishes the stability of TERT mRNA in an m6A-dependent manner, thereby reducing TERT expression at both the mRNA and protein levels. This reduction leads to decreased telomerase activity, ultimately triggering senescence. Notably, the senescence phenotype induced by YTHDC1 knockdown can be rescued by the exogenous expression of TERT.

overall_design: RNA-seq profiling analysis of control (shCtrl) and YTHDC1-knockdown (shYTHDC1) A2780 cells.

last: Xiaoting

first: Wang

last: Fen

first: Zhao

last: Zhengyang


title: A ketogenic diet improves memory in females in the APOE4 mouse model of Alzheimer’s disease.

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

summary: The 𝜀4 allele of Apolipoprotein E (APOE4) is the strongest genetic risk factor for Alzheimer’s disease (AD), affecting approximately 68 million Americans. APOE4 carriers exhibit cerebral metabolic deficits decades before clinical onset. We previously demonstrated that ketogenic diet (KD), a low-carbohydrate, high-fat diet promoting ketone metabolism, confers cognitive benefits in aged and PS1/APP mice. Here, we evaluated the effects of KD in a humanized APOE4 AD mouse model. KD significantly improved composite cognitive performance and spatial working memory, with pronounced effects in females. Synaptic plasticity, measured via long-term potentiation (LTP), was likewise enhanced exclusively in females. Transcriptomic and protein analyses revealed KD-induced activation of CREB pathway, marked by increased phosphorylation of ERK and CREB in female brains. Moreover, KD selectively reduced pro-inflammatory cytokine levels in females. These findings demonstrate sex-specific neuroprotective effects of KD in APOE4 mice and suggest its potential therapeutic role in mitigating AD risk in APOE4-positive women.

overall_design: RNA was isolated from 10 mg of frozen murine brain cortex (N = 4–6 per group; 22-month-old ApoE4 males/females on control or ketogenic diet), using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. Extracted RNA was used for NGS library preparation following Illumina’s instruction (TruSeq Stranded Total RNA Library Prep Gold), while sequencing was performed on NovaSeq 6000 (Illumina) running in a 50-bp paired-end mode.

first: Jacopo

last: Di Lucente

first: Jennifer

last: Rutkowsky

first: Alfredo

last: Errico Provenzano

first: Giuseppe

last: Persico

first: Zeyu

last: Zhou

first: Lee-Way

last: Jin

first: Jon

last: Ramsey

first: Claire

last: Montgomery

first: Kyoungmi

last: Kim

first: Marco

last: Giorgio

first: Izumi

last: Maezawa

first: Gino

last: Cortopassi


title: scRNA-seq of NeuroD1-astrocyte therapy post-TBI mouse

city: 广州

first: shuo

last: zhang

address: 黄埔大道西601号

institute: 暨南大学

summary: Astrocytes, the most abundant glial cells in the central nervous system (CNS), play a critical role in brain injury responses. While NeuroD1 overexpression in astrocytes has been shown to reverse glial scar formation and promote tissue repair in mouse models of traumatic brain injury (TBI), the underlying molecular mechanisms remain incompletely understood. To address this, we performed single-cell transcriptomic analysis on a controlled cortical impact (CCI) mouse model using recombinant adeno-associated virus (rAAV)-mediated astrocyte-specific NeuroD1 overexpression.Our findings demonstrate that NeuroD1 overexpression suppresses microglial activation and mitigates brain damage post-TBI. Single-cell RNA sequencing revealed significant shifts in astrocyte subtypes, with upregulated neuroinflammatory pathways and downregulated oxygen metabolism in TBI mice. Conversely, NeuroD1 overexpression reshaped astrocyte subpopulation dynamics, enhanced oxygen metabolism-related gene expression, and attenuated neuroinflammatory signaling. This study provides a comprehensive transcriptomic dataset detailing cellular and astrocyte subtype-specific changes following NeuroD1-mediated brain repair. These insights advance our understanding of cell fate modulation in TBI and support the development of NeuroD1-based gene therapies, offering a valuable resource for future TBI research and therapeutic strategies.

overall_design: RNA-seq was performed on pooled lesion-area samples from adult male FVB mice at 7- and 14-day time points: untreated controls, mice subjected to needle-stick injury, and mice that received ND1 treatment after injury.

first: Shou

last: Zhang

first: Shanggong

last: Liu

first: Rongjie

last: Chen

first: Feng

last: Liao

first: Gong

first: Wenliang

last: Lei


title: Extracellular vesicles from human umbilical cord mesenchymal stem cells protect grafted islets against endoplasmic reticulum stress-induced mitochondrial dysfunction by modulating XBP1-based calcium homeostasis

first: baicheng

last: kuang

state: China/Hubei province

address: Jiefang Street 1095

institute: Institute of Organ Transplantation,Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Islet transplantation is an ideal option for diabetes while early graft lose serves as a major obstacle. Human umbilical cord mesenchymal stem cells (hucMSC) have multiple functions including the maintenance of cellular homeostasis. However, it is unknown whether extracellular vesicles (EVs) derived from hucMSC (hucMSC-EVs) provide protective effects against transplant-related trauma-induced islet injury. Here, we isolated and purified hucMSC-EVs, and found that hucMSC-EVs promoted grafted islet survival, and enhanced glycemic control following co-transplantation in a syngeneic streptozotocin (STZ)-induced mouse model of diabetes. After co-cultured for 12 h or 24 h, labelled hucMSC-EVs with PKH67 were readily internalized by NIT-1 β cells and islets. In tunicamycin (Tm) and thapsigargin (Tg) induced specific endoplasmic reticulum stress (ERS) cell injury models, hucMSC-EVs treatment improved cell viability and β cells function both in NIT-1 cells and ex vivo primary islets. Bulk RNA-seq demonstrated that hucMSC-EVs treatment significantly involved in ERS and the negative regulated mitochondrial apoptotic pathway. While ERS promoted interactions between endoplasmic reticulum (ER) and mitochondria, hucMSC-EVs alleviated ERS, maintained calcium homeostasis, and improved mitochondrial energy metabolism. Notably, the downregulation of XBP1 by hucMSC-EVs fine-tuned ER-mitochondria communication via reducing inositol-1,4,5-trisphosphate receptors at mitochondria-associated membranes (MAMs). Reduced XBP1 also activated Nrf2, restoring mitochondrial calcium homeostasis under ERS. miRNA analysis identified miR-182-5p enriched in hucMSC-EVs that specifically targeted XBP1 mRNA, leading to its degradation and downregulation. These findings demonstrate that hucMSC-EVs protect grafted islets by blocking XBP1 and restoring calcium homeostasis, thus suggesting their potential as a cell-free therapy for improving islet transplantation outcomes.

overall_design: For bulk RNA-seq, NIT-1 cells treated with hucMSC-EVs or PBS for 16 h, followed by an additional 8 h of Tm exposure were obtained and total RNA was isolated by Trizol Reagent

first: Baicheng

last: Kuang

first: Jimeng

last: Ruan

first: Hao

last: Yan

first: Shiqi

last: Gu

first: Tongwen

last: Ou

first: Nianqiao

last: Gong


title: Enhancer Remodeling-Driven Mevalonate Pathway Confers Resistance to KRAS Inhibitor in Colorectal Cancer

first: yao

middle: yu

last: Guo

address: 广州

institute: Sun-Yat san university

summary: This study investigates the resistance mechanisms to pan-KRAS inhibitors in colorectal cancer (CRC). We established a panel of patient-derived organoids (PDOs) and cell lines with differential sensitivity to pan-KRAS inhibitors. Integrated epigenomic (ChIP-seq for H3K27ac and H3K4me3) and transcriptomic (RNA-seq) profiling revealed that enhancer remodeling drives compensatory activation of the mevalonate (MVA) pathway in resistant models. The MVA pathway upregulation facilitates KRAS membrane trafficking via protein farnesylation, thereby sustaining ERK activation and conferring resistance to KRAS inhibitors. Pharmacological inhibition of the MVA pathway using statins restores therapeutic sensitivity and enhances efficacy of KRAS inhibitors in cellular, PDO, and PDX models.

overall_design: This study includes RNA-seq and ChIP-seq analyses of KRAS inhibitor-sensitive and resistant models. For RNA-seq: 1) LS174T parental vs resistant cells; 2) DLD1 cells treated with BI-2865 for 24h; 3) PDO cohorts with differential sensitivity to BI-2865. For ChIP-seq: H3K27ac and H3K4me3 profiling in LS174T parental vs resistant cells. Biological replicates were included for all experiments.

first: Yaoyu

first: J

last: Tan


title: mtROS-driven Sp1-dependent retrograde signaling promotes colorectal tumor progression via SIRT3-PAGM5 axis-governed mitochondrial homeostasis

city: Chengdu

first: Jiaqiang

last: Deng

state: Sichuan

address: No.24, South Section 1, 1st Ring Road

institute: Sichuan university

summary: Mitochondrial-nuclear communication is critical for maintaining mitochondrial integrity and cellular metabolic adaptation. While mitochondrial dysfunction triggers compensatory retrograde signaling, the molecular mechanisms underlying defect sensing and resolution remain poorly defined. Here, we demonstrated that mitochondrial reactive oxygen species (mtROS) trigger Sp1 stabilization and nuclear translocation, which directly activate transcription of the NAD+-dependent deacetylase SIRT3 through specific promoter binding, revealing a redox-sensitive regulatory axis controlling mitochondrial homeostasis. Mechanistically, SIRT3 sustains mitochondrial integrity through site-specific deacetylation (K141) of mitochondrial phosphoglycerate mutase 5 (PGAM5). Furthermore, SIRT3-mediated deacetylation of PGAM5 was instrumental in promoting Pink1/parkin-dependent mitophagy, thereby maintaining mitochondrial homeostasis. Alternatively, we identified the mitochondrial-nuclear retrograde signaling cascade comprising Sp1, SIRT3 and PGAM5 as a novel driver of colorectal tumorigenesis. Taken together, our findings reveal that mtROS act as pivotal signaling mediators linking mitochondrial perturbations to the nuclear transcriptional adaptation response via the Sp1-SIRT3-PGAM5 retrograde signaling axis. This retrograde signaling cascade enables adaptive transcriptional reprogramming to restore mitochondrial homeostasis, thereby endowing tumor cells with increased stress tolerance.

overall_design:
HCT116 cells treated with mtROS inducers (Men (32 μM), 4-HPR (10 μM), or AMA (10 μM)  for 12 h were determined via RNA sequencing. The control cells were treated with DMSO (0.1%).
RNA-seq profiling of HCT116 cells following treatment with mtROS inducers.

first: Fangdong

last: Zou


title: Inflammation associated microglial expansion disrupts hippocampal glial network communication, driving postoperative neurocognitive impairment

city: Beijing

first: Yuxiang

last: Zheng

address: No. 17, Panjiayuan Nanli, Chaoyang District

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Postoperative neurocognitive impairment (PNCI) significantly affects the recovery and long-term outcomes of elderly patients, with central nervous system (CNS) inflammation serving as the key pathogenic driver of its development. As the resident immune cells of the CNS, microglia play a crucial role in regulating perioperative inflammation and maintaining homeostasis. However, the contribution, phenotypic heterogeneity, and communication network of perioperative microglia in the development of PNCI remain insufficiently characterized. In this study, 18-month-old mice underwent surgery and developed PNCI. Single-cell RNA sequencing was performed, which identified eight microglial subpopulations and six astrocytic subpopulations in hippocampus. Postoperatively, the percentage of microglial subpopulations underwent dramatic changes, with inflammation associated microglia (IAM) increasing more than 14-fold and transition state microglia (TSM) increasing more than 33-fold. These alterations were accompanied by a marked enhancement of intercellular communications among glial cells, particularly driven by the activation of TNF signaling pathway in IAM. This pathway, along with its associated regulatory network, critically modulated the function of astrocytes and endothelial cells, thereby playing a pivotal role in CNS inflammation and the subsequent development of PNCI. Notably, administration of TNF inhibitor etanercept attenuated IAM activation and glial network communication in the hippocampus, which was associated with improved cognitive performance in PNCI mice.

relation:
Reanalysis of: GSM8281758
Reanalysis of: GSM8281759
Reanalysis of: GSM8281760
Reanalysis of: GSM8281761
Reanalysis of: GSM8281762
Reanalysis of: GSM8281763

overall_design:
In this study, six aged mice were randomly assigned to two groups: control group and surgery group. The mice in surgery group received anesthesia and laparotomy, while control group received 50% oxygen for 30 minutes. All mice were sacrificed by decapitation 24 hours after procedure. The brain tissue was rapidly removed, and the hippocampi were dissected out and immediately frozen in liquid nitrogen.

This study represents a re-analysis of all of the raw data generated for GSE267933.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Wenjie

last: Xu

first: Zizheng

last: Suo

first: Yinyin

last: Qu

first: Lina

last: Lin

first: Enze

first: Dengyang

last: Han

first: Meikui

last: Wu

first: Hongyi

last: Li

first: Hui

first: Ting

last: Xiao

first: Cheng

last: Ni


title: SWI/SNF complexes modulate gene expression and the development of physical dependence following prolonged ethanol exposure

city: Richmond

first: Laura

last: Mathies

address: 1220 East Broad Street

institute: Virginia Commonwealth University

summary: Long term exposure to high doses of ethanol causes the development of physical dependence, which is reflected in withdrawal symptoms when ethanol is removed; this contributes to the development of alcohol use disorder in humans. We used Caenorhabditis elegans to understand the transcriptional changes that occur after extended ethanol exposure that underlie physical dependence and withdrawal effects. After an 18 hour exposure to an intoxicating concentration of ethanol, worms develop physical dependence that is observed upon withdrawal from ethanol as an increase in their preference for thicker parts of a bacterial lawn, a behavior we term Withdrawal-Induced Bordering (WIB). We found that WIB is transient, resolving within six hours of removal from ethanol, suggesting it is driven by short-term gene expression changes. We identified 1870 genes with differential expression immediately after ethanol exposure but not after six hours of withdrawal, these are candidate mediators of WIB. We reasoned that epigentic regulation may be involved in these gene expression changes, and found that the SWI/SNF chromatin remodeling complex, known to be important in the response to acute ethanol exposure, is required for normal WIB. swsn-9 mutants demonstrated attenuated WIB, suggesting that there are swsn-9-dependent and swsn-9-independent components of WIB, and we identified 1031 ethanol-responsive genes whose regulation requires swsn-9. WIB phenocopies reduced npr-1 activity, and two genes implicated in the npr-1 signaling pathway, jmjc-1 and dod 24, were transiently regulated after extended ethanol exposure. We found that dod-24 mutants have attenuated WIB, suggesting that dod-24 plays a role in this withdrawal phenotype.

overall_design: Two strains were used in this study - wild type (N2) and swsn-9 mutant (RA503). L4 stage worms were treated with either 0 mM ethanol or 400 mM ethanol for 18 hours prior to gene expression analysis. One set of wild-type samples was allowed to recover in the absence of ethanol for 6 hours prior to gene expression analysis (N2R).

first: GinaMari

last: Blackwell

first: Andrew

last: Davies

first: Jill

last: Bettinger


title: Acetyl transferase EP300 deficiency leads to chronic replication stress mediated by defective fork protection at stalled replication forks

city: New Brunswick

first: Advaitha

last: Madireddy

state: NJ

address: Little Albany Street

institute: Rutgers Cancer Institute

summary: Mutations in the epigenetic regulator and global transcriptional activator, E1A binding protein (EP300), is being increasingly reported in aggressive hematological malignancies including adult T-cell leukemia/lymphoma (ATLL). However, the mechanistic contribution of EP300 dysregulation to cancer initiation and progression are currently unknown. Independent inhibition of EP300 in human cells results in the differential expression of genes involved in regulating the cell cycle, DNA replication and DNA damage response. Nevertheless, specific function played by EP300 in DNA replication initiation, progression and replication fork integrity has not been studied. Here, using ATLL cells as a model to study EP300 deficiency and an EP300-selective PROTAC degrader, as a pharmacologic tool, we reveal that EP300-mutated cells display prolonged cell cycle kinetics, due to pronounced dysregulations in DNA replication dynamics leading to persistent genomic instability. Aberrant DNA replication in EP300-mutated cells is characterized by elevated replication origin firing due to increased replisome pausing genome-wide. We demonstrate that EP300 deficiency results in nucleolytic degradation of nascently synthesized  DNA at stalled forks due to a prominent defect in fork stabilization and protection. This in turn results in the accumulation of single- single-stranded DNA gaps at collapsed replication forks, in EP300-deficient cells.  Inhibition of Mre11 nuclease rescues the ssDNA accumulation indicating a dysregulation in downstream mechanisms that restrain nuclease activity at stalled forks. In addition, Importantly, we find that the absence of EP300 results in decreased expression of BRCA2 protein expression and a dependency on POLD3-mediated error-prone replication restart mechanisms. The overall S-phase abnormalities observed lead to under-replicated DNA in G2/M that instigates mitotic DNA synthesis. This in turn is associated with mitotic segregation defects characterized by elevated micronuclei formation, transmission of unrepaired inherited DNA lesions in the subsequent G1-phase and accumulation of cytosolic DNA in EP300-deficient cells. However, EP300 deficient cells show a significant defect in innate immune system activation. Importantly, EP300Mut cells are sensitive treatments (PARPi, POLQi and Rev1i) that are cytotoxic to BRCA-deficient cancers. Overall, we demonstrate that the DNA replication dynamics of EP300-mutated cells recapitulate features of BRCA-deficient cancers. Altogether, these results suggest that mutations in EP300 cause chronic DNA replication stress, persistent genomic instability and innate immune system evasion underlie aggressive chemo-resistant tumorigenesis in humansdue to the inability to protect stalled replication forks from collapse.

overall_design: We utilize Adult T-cell leukemia/lymphoma (ATLL) cell lines as a model system to investigate the consequences of EP300 deficiency. We also employ an EP300-selective PROTAC degrader as a pharmacologic tool to selectively degrade EP300 in wild-type cell lines to understand the effects on EP300 loss.

first: Mrunmai

last: Niljikar


title: MAP2-mediated integrin dysregulation reprograms cancer cell plasticity to drive liver cancer cell transition to a mesenchymal and stemness state in hepatocellular carcinoma

city: Kong Kong

first: Ut Kei

last: Lou

address: Room 17, 1/F, Laboratory Block, Faculty of Medicine Building, 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

summary: Targeting tumor cell plasticity is central to overcome drug resistance and metastasis. Through lineage-tracing and lineage-ablation studies, our team has previously shown hepatocellular carcinoma (HCC) cells marked by CD133 to represent a functional subset displaying dedifferentiated status with stemness traits, yet there are limited therapies effective for eradicating such resilient cell populations. Here, we explore the therapeutic potential of repurposing an existing drug estramustine phosphate (EMP) for targeting HCC plasticity through inhibiting MAP2, a gene uniquely enriched in CD133+ ‘HCC’ stemness subset but not in CD133+ ‘normal’ regenerative cells. MAP2 is transcriptionally activated by H3K27Ac and its upregulation correlates with aggressive clinical features. Mechanistically, MAP2 sustains tumor plasticity and transition to a mesenchymal state through inducing filamentous actin polymerization and YAP activation, which subsequently disrupts integrin-mediated cell adhesions. Our research offers a promising opportunity for drug repurposing using EMP in combination with sorafenib to target HCC at its stemness roots.

overall_design: RNA-seq profiling of MHCC97L cells with or without MAP2 knockout (97L-sgEV, 97L-sgMAP2-2, 97L-sgMAP2-3) and PLC/PRF/5 cells with empty vector control or MAP2 overexpression (PLC-SAMv2, PLC-MAP2-2).

first: Tin-Lok

last: Wong

first: Huajian

last: Yu

first: Ki-Fong

last: Man

first: Ka-Hei

last: Lam

first: Jia Jian

last: Loh

first: Lei

last: Zhou

first: Yuan

last: Gao

first: Cheng-Han

first: Stephanie

last: Ma


title: Intracellular Delivery of Bone Nanoparticles to Mitigate Irradiation-Induced Damage in Bone Marrow Mesenchymal Stem Cells

city: Milwaukee

first: Xiaolong

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

summary: This study evaluated the therapeutic potential of intracellularly delivered bone-derived nanoparticles (BPs) in mitigating Ionizing radiation (IR)-induced BMSCs damage. We found that IR exposure caused significant BMSCs dysfunction, including reduced proliferation, increased apoptosis, persistent DNA damage, and a shift toward adipogenic differentiation. Treatment with BPs led to efficient intracellular uptake, improved cell morphology, enhanced proliferation, reduced apoptosis, and preservation of balanced differentiation capacity. Transcriptomic analysis via RNA sequencing revealed that BPs restored key molecular pathways disrupted by IR, particularly those involved in cell cycle regulation, extracellular matrix (ECM) remodeling, and apoptosis. By reversing these transcriptional impairments, BPs supported genomic stability and the regenerative function of BMSCs.

overall_design: The third passage BMSCs were seeded at a density of 1 × 105 cells per well in 12-well plates and divided into three experimental groups: Control group: BMSCs without IR exposure or BP co-culture. IR group: BMSCs exposed to IR treatment. IR&BP group: BMSCs exposed to IR followed by BP co-culture.After 7 days of culture, total RNA was extracted from all groups (n=3 per group) using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions. RNA concentration was measured using the Nanodrop ND-1000, and quality was assessed via capillary electrophoresis (Agilent Technologies). RNA sequencing (RNA-Seq) was performed by Novogene Corporation Inc.

first: Wang

last: Bo

first: Ma

last: Xiaolong

first: Nguyen

last: Christopher

first: Stellpflug

last: Austin

first: Li

last: Siqi

first: Han

last: Lu

first: Frei

last: Anne

first: Himburg

last: Heather

first: Gu

last: Linxia

first: Dong

last: Pengfei

last: Shue

first: Mak

last: Michael

first: Wu

last: Rongxue


title: Transcriptome profile of LX-2 cells [SiNSUN2]

city: Wuhan

first: An

last: Zhang

summary: Liver fibrosis is characterized by deposition of excessive extracellular matrix (ECM). The major source of ECM is activated hepatic stellate cells (HSCs).NSUN2 is one of the m5C methyltransferases, mainly responsible for the methylation of tRNA and mRNA and plays a significant role in RNA m5C methylation. The purpose of this transcriptome is to explore the role of NSUN2 acting as m5C methyltransferases during HSC activation.

overall_design:
RNA-seq profiling of  LX-2 cells(con) and TGF-β1 stimulated LX-2 cells (TGFB) and LX-2 cells transfected with NAT10 SiRNA(SiNSUN2) and then stimulated with TGF-β1 (SiNSUN2_TGFB).

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Chunwei

last: Shi


title: Mucosal innate gene signature associated with a mucosal SHIV vaccine and reduced SHIV risk in vaccinated macaques

city: Bethesda

first: Jay

last: Berzofsky

state: MD

address: Building 41 Room D702D

department: Center for Immuno-Oncology

institute: National Cancer Institute

summary: An orally delivered HIV vaccine, which is composed of nanoparticles containing a full-length gp120-CD4 single chain (FLSC) fusion construct plus MVA and molecular adjuvants, has demonstrated 44% vaccine efficacy (p = 0.028) against repeated low-dose intrarectal challenge of rhesus macaques with SHIVSF162P4.  From our previous study, we found that the innate immune responses in the rectal mucosa might contribute significantly to the protection.  Since the vaccine was administered mucosally, it is critical to evaluate the innate responses in the rectal mucosa.  To investigate the possible correlates of protection, we isolated total RNA from the rectal single-cell suspension and ran bulk RNAseq analysis. We distinguished the differentially expressed genes (DEGs) induced by the vaccination and found that gut metabolic pathways, extracellular matrix and antimicrobial humoral responses were altered by mucosal HIV vaccine. We further assessed the genes that were correlated with the number of challenges needed for the animals to be infected.  We observed that cytoskeleton genes such as fibronectin 1, Interleukin-4 and Interleukin-13 signaling, O-linked glycosylation were among the gene signatures that inversely correlated with viral infection risk . These data provide key information on the potential biomarkers to predict the outcome of HIV vaccines and shed light on possible protection mechanisms of mucosal HIV vaccines.

overall_design: RNA-seq profiling of colorectal tissue extracted from rhesus macaques before and after treatement with vaccine.

first: Yongjun

last: Sui

first: Philip

last: Homan

first: Jieqiong

last: Dai

first: Max

last: Lee


title: CpG island hypermethylation and CpG-poor region hypomethylation drive gastric cancer risk after Helicobacter pylori eradication

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

type: Methylation profiling by genome tiling array

summary: Aberrant DNA methylation is deeply involved in the development of gastric cancer (GC) and has emerged as a promising biomarker for risk prediction. In this study, we performed comprehensive DNA methylation profiling of tumor and non-tumor gastric mucosa from patients who developed GC after Helicobacter pylori (H. pylori) eradication (post-eradication GC, PEGC). The normal mucosa of PEGC patients exhibited substantial CpG island (CGI) hypermethylation, comparable to that observed in H. pylori-infected tissues and intestinal metaplasia. We also identified approximately 4,000 CpG sites recurrently hypomethylated in GC using The Cancer Genome Atlas (TCGA)-STAD data, many of which were already hypomethylated in normal mucosa of PEGC. Majority of the hypomethylated sites are located outside of CGIs, and several of them are located near oncogenes such as CDH17, HNF4A, and CD44, and their methylation levels inversely correlated with gene expression. Importantly, we found a strong positive correlation between CGI hypermethylation and CpG hypomethylation, suggesting that both types of epigenetic alterations occur simultaneously from the early stages of carcinogenesis. These findings indicate that CGI hypermethylation and non-CGI hypomethylation are not independent events but represent a coordinated epigenetic landscape that may contribute to persistent GC risk after H. pylori eradication.

overall_design: Genome-wide DNA methylation profiling was performed using Infinium MethylationEPIC BeadChips on tumor and non-cancerous gastric mucosa from post-eradication gastric cancer patients.

first: Gota

last: Sudo

first: Eiichiro

last: Yamamoto


title: Unveiling distinct storage composition and starch properties in developing indica rice grains via transcriptional profiling and enzymatic activity analysis

city: Khon Kaen

first: Maysaya

last: Thitisaksakul

address: Mittrapap Road

department: Biochemistry

country: Thailand

institute: Khon Kaen University

summary: Recently, we observed significant differences in the starch molecular composition and structure between the two Thai indica rice cultivars, RD6 and RD57. However, a comprehensive understanding of the transcriptional regulation of their storage polymers, remains lacking. To address this, we investigated the gene expression patterns and enzymatic activities of key starch and storage protein biosynthetic enzymes in the developing endosperms of these cultivars. The transcriptional profiles of waxy RD6 and high-amylose RD57 rice endosperms were analyzed at 7, 14, 21, and 28 days post-anthesis (DPA). The expression patterns of major differentially expressed genes (DEGs) were cross validated with enzymatic activities and the grain starch and storage protein compositions. Gene expression profiles varied significantly between the RD6 and RD57 rice cultivars, with the most distinct differences observed at 14 days post-anthesis (DPA) and the least at 28 DPA. Temporal dynamics of transcriptome profiles among genes in starch and storage protein biosynthesis revealed active gene expression at 14 DPA and 7 DPA. Collectively, this study provided a comprehensive understanding of the biosynthesis of storage biomolecules through transcriptional profiling of the Thai indica rice. For the breeding and developing new Thai commercial rice varieties with targeted ECQ and health-beneficial traits, understanding the regulatory mechanisms that control starch and storage protein accumulation at both transcriptional and post-translational levels is crucial.

overall_design: RNA-seq profiling of waxy RD6 and high-amylose RD57 rice endosperms at 7, 14, 21, and 28 days post-anthesis (DPA)

first: Wichian

last: Sangwongchai

first: Kwanjeera

last: Wanichthanarak

first: Ammarin

last: In-on