title: Lysine-specific demethylase 1 regulates hematopoietic stem cell expansion and myeloid cell differentiation [scRNA-seq]

summary: The lysine-specific demethylase 1 (LSD1) regulates hematopoietic stem cell differentiation and has been identified as a therapeutic target in hematological disorders. LSD1 demethylates mono and dimethylated histones 3 at lysine 4 and 9. In addition, it acts as a scaffold for the formation of chromatin-modifying complexes that regulates the transcription of myeloid-lineage-specific genes in complex with GFI1, a transcriptional repressor. While both enzymatic and non-enzymatic functions of LSD1 have been well defined, the relative importance of these two functions in hematopoiesis remains incompletely understood. Here, we investigated the contribution of enzymatic and non-enzymatic functions of LSD1 to myelopoiesis. We show that myeloid differentiation is independent of the enzymatic functions of LSD1 but requires the non-enzymatic, scaffolding function, which directs GFI1 binding to target sequences. In absence of the LSD1 protein, GFI1 DNA binding is diminished and myeloid cell differentiation arrests at an immature, myelomonocytic-like cell stage, which overexpresses Prtn3. We provide functional data implicating Prtn3 as an effector of the stem cell expansion and myeloid maturation block caused by the loss of LSD1.

overall_design: We performed single-cell RNA-sequencing (scRNA-seq) of Lsd1 ko, Lsd1 ko ctrl, Lsd1 ei, Lsd1 ei ctrl, Lsd1 ko BMT and Lsd1 ko ctrl BMT total BM.


title: Invasive Acinetobacter baumannii ABC141 strain relies on the twin-arginine translocation (Tat) export system for adhesion to host cells

status: Public on Aug 12 2025

city: Madison

first: Suzana

middle: P

last: Salcedo

state: Wisconsin

address: 2015 Linden Dr

department: Pathobiological Sciences

country: USA

institute: University of Wisconsin-Madison

type: Expression profiling by high throughput sequencing

summary: Acinetobacter baumannii is associated with severe hospital-acquired multi-drug resistant infections worldwide, causing significant mortality and morbidity in intensive care patients or under prolonged hospitalization. Multiple studies have recently shown that a proportion of circulating clinical isolates establish a transient multiplication niche inside phagocytic and non-phagocytic eukaryotic cells. We have previously demonstrated that the A. baumannii ABC141 strain invades human endothelial and epithelial cells, where it efficiently multiplies without induction of cytotoxicity. Here, we show that ABC141 adhesion, invasion, and intracellular multiplication depend on the growth stage, being most efficient in the exponential growth phase. To define the gene expression signature most favorable to an intracellular lifestyle, a transcriptomic comparison was carried out between exponentially grown ABC141 and cultures at the stationary phase. Although most of the pathways identified reflected growth-related metabolic changes, we observed an upregulation of the twin-arginine translocation (Tat) export system. Analysis of a mutant strain lacking the tatABC operon revealed this secretion system is only required for adhesion to host cells but not invasion and intracellular multiplication. These data highlight a new role for the Tat export pathway in A. baumannii pathogenesis.

overall_design: Transcriptomic analysis using RNA-seq of Acinetobacter baumannii ABC141 grown in LB medium at 37°C. Two conditions were sampled: 15h of growth (OD600 2.2-2.5) and OD600 of 0.5.

first: Charline

last: Debruyne

first: Landon

last: Hodge

first: Karsten

last: Hokamp

first: Carsten

last: Kröger

first: Anna

last: Ershova


title: Tumor-associated Schwann cell remodeling under metabolic stress via lactate sensing orchestrates [ChIP-seq, MeRIP-seq, RNA-seq]

city: Tianjin

first: xueying

last: Li

address: 94 Weijin Road, Nankai District

country: China

institute: Nankai University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Diabetes mellitus (DM) is a known risk factor for pancreatic cancer, but the underlying mechanisms remain elusive. Using in vivo models of diabetes-driven pancreatic tumorigenesis and metabolomics analysis, we demonstrate that metabolic stress induced by DM promotes pancreatic cancer progression by remodeling tumor-associated Schwann cells (TASs), impairing CD8+ T cell function. We discover that Mettl16+ Cd276+ Nectin2+ Schwann cells play a crucial role in mediating the pro-carcinogenic effects of lactate. Remodeled METTL16+ Schwann cells secret immune evasion factors (CD276, NECTIN2), contributing to anti-PD1 resistance. Furthermore, rosuvastatin was identified in this study as a novel METTL16 inhibitor for pancreatic cancer under metabolic stress. In conclusion, our study underscores the critical role of lactate in the metabolic reprogramming of pancreatic cancer mediated by Schwann cell remodeling, revealing novel pathways for therapeutic intervention.

overall_design: ChIP-seq, MeRIP-seq and RNA-seq data analysis for TAS


title: The obesity-linked peptide SP16 regulates adipocytes through GIP and insulin receptor

city: Warthausen

first: Rakesh

last: Santhanam

address: Goetheweg 10

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

summary: Obesity has emerged as a global epidemic and represents a major public health concern due to its profound implications for metabolic diseases. While recent pharmacological interventions primarily aim to reduce food intake, enhancing energy expenditure in adipose tissue offers a promising complementary approach. In this study, we identify that SP16, a synthetic α1- antitrypsin derived peptide, is a novel GIP (gastric inhibitory peptide) receptor agonist. SP16 promotes lipolysis via the cAMP pathway, resulting in increased mitochondrial oxygen consumption in adipocytes. Furthermore, SP16 binds to the insulin receptor, and at high concentrations, it attenuates insulin receptor signaling. In diet-induced obese (DIO) mice, acute SP16 treatment improved glucose clearance, elevated circulating free fatty acids, and decreased leptin levels. Ex vivo analyses of epididymal white adipose tissue corroborated these findings, demonstrating enhanced lipolysis in SP16-treated mice. In conclusion, SP16 emerges as a novel lipolytic peptide with beneficial metabolic effects.

overall_design: For acute treatment, the 9-day old differentiated hMADS cells were treated with DMSO 0.1%, forskolin (10 µM), GIP (10 nM), SP16 (10 µM), SP16 NC (10 µM) for 4 h (37 °C, 5% CO2).For treatment with insulin, 9-day old differentiated hMADS cells were starved with starvation medium overnight (37 °C, 5% CO2). The following day, hMADS cells were incubated with DMSO 0.1%, picropodophyllin 10 µM (PPP, Sigma, 407247), hGIP 10 nM, SP16 10 µM, SP16 NC 10 µM for 30 min. Insulin was added to the corresponding samples and incubated for another 24 h (37 °C, 5% CO2). After the incubation time, the cells were washed with PBS, lysed and RNA was isolated.

first: Thi My Hanh

last: Ngo

first: Daniel P

last: Teufel

first: Alec

last: Dick

first: Daniel

last: Lam

first: Holger

last: Klein

first: Andreas-David

last: Brunner

first: Mafalda

last: M.A. Pereira

first: Alexander

last: Bartelt

first: Anton

last: Pekcec

first: Maude

last: Giroud


title: Keratinocyte-secreted SAA1 induces a population of long-lived antigen-presenting neutrophils that drives Sweet Syndrome

city: Philadelphia

first: Satish

last: Sati

state: Pennsylvania

address: 421 Curie Blvd, BRB 1039

department: Dermatology

institute: University of Pennsylvania

summary: Sweet syndrome (also known as acute febrile neutrophilic dermatosis), is a rare inflammatory skin disorder characterized by erythematous plaques with a dense dermal neutrophilic infiltrate. It remains unknown how neutrophils, which are generally short-lived, persist in the skin of patients with Sweet syndrome. We report that Sweet syndrome skin contains a unique population of long-lived antigen-presenting cell (APC)-neutrophils that are not present in blood or unaffected skin.

overall_design: scRNA-seq of Human neutrophils and skin cells from patient lesional and non lesional skin

first: Jianhe

last: Huang

first: Thomas H

last: Leung


title: Uncovering gene regulatory differences between human and chimpanzee neural cells [CUT&Tag]

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

summary: A major challenge in human evolutionary biology is to pinpoint the genetic differences that underlie phenotypic changes in the human lineage, such as increased neuron number and a prolonged period of neuronal maturation. Here, we used human-chimpanzee tetraploid cells to distinguish changes in gene expression due to cis-acting sequence variants that change local gene regulation, from trans expression changes due to species differences in the cellular environment, in neural progenitor cells and excitatory neurons. Using a CRISPR inhibition screen, transcription factor motif analyses, and downstream single-locus studies, we further characterized cis-acting gene regulatory differences, including changes to FOS, TNIK, FOSL2, and MAZ, that influence neurogenesis and neuronal maturation. This study identifies specific genomic changes that may contribute to human neural specializations and provides a general framework for understanding genetic differences that underlie human traits.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design:
We performed CUT&Tag for H3K27Ac, FOS, FOSL2, and MAZ in human, chimp, and human-chimp neural cells.

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

middle: H

first: Christopher

middle: A

last: Walsh

first: Ava

middle: C

last: Carter

first: Gabriel

last: Koreman

first: Michael

middle: E

last: Greenberg


title: ERK signaling promotes IKKε expression and oncogenic functions in pancreatic cancer cells in association with TBK1

city: Chapel Hill

first: Albert

last: Baldwin

state: NC

address: 450 West Drive

institute: Lineberger Comprehensive Cancer Center

summary: A variety of cancers utilize RAS-regulated signaling pathways to promote oncogenic phenotypes. A widely studied example is pancreatic cancer, where mutant KRAS signaling leads to activation of MEK/ERK kinases and downstream signaling which promotes oncogenic mechanisms, including cell proliferation. Importantly, ERK inhibitors have shown efficacy in some cancer clinical trials. Previously, others have studied the effects of the related kinases TBK1 and IKKε in pancreatic cancer where they have been shown to promote cell survival. Here, we show that RAS/MAPK signaling promotes expression of IKKε through control of protein stability and not through control of RNA levels. RNAseq analysis indicate that TBK1 and IKKε contribute to the expression of a subset of ERK-regulated genes. Potentially related to the effects on IKKε, proteomic analysis reveals that ERK functions to stabilize a relatively large set of proteins independent of RNA regulation. Knockdown of IKKε and TBK1 individually does not affect growth of MIA PaCa-2 pancreatic cancer cells, but dual knockdown significantly inhibits MIA PaCa-2 growth which is mediated through cell death. Concurrent silencing or inhibition of both TBK1 and IKKε also reduces tumor sphere growth in MIA PaCa-2 cells, correlating with a loss of stemness pathways found with RNAseq. The data suggest the importance of regulation of IKKε by ERK in pancreatic cancer cells and of the combined oncogenic activity of TBK1 and IKKε.

overall_design: RNAseq analysis of MIA PaCa-2 pancreatic cancer cells treated for 24H with the ERK1/2 inhibitor SCH772984, the dual TBK1/IKKepsilon inhibitor Compound 1, or DMSO as a control.

first: Adam

last: Graves

first: Angana

last: Mukherjee

first: Runying

last: Yang

first: Angie

last: Mordant

first: Thomas

last: Webb

first: Kirsten

last: Bryant

first: Laura

last: Herring


title: Chromosome segregation dynamics during the cell cycle of Staphylococcus aureus

city: Oeiras

first: Adrian

last: Izquierdo Martinez

state: Lisboa

address: Avenida da República

country: Portugal

institute: ITQB NOVA

summary: Research on chromosome organization and cell cycle progression in spherical bacteria, particularly Staphylococcus aureus, remains limited and fragmented. In this study, we established a working model to investigate chromosome dynamics in S. aureus using a Fluorescent Reporter Operator System (FROS), which enabled precise localization of specific chromosomal loci. This approach revealed that the S. aureus cell cycle and chromosome replication cycle are not coupled, with cells exhibiting two segregated origins of replication at the start of the cell cycle. The chromosome has a specific origin-terminus-origin conformation, with origins localizing near the membrane, towards the tip of each hemisphere, or the “cell poles”. We further used this system to assess the role of various proteins with a role in S. aureus chromosome biology, focusing on the ParB-parS and SMC-ScpAB systems. Our results demonstrate that ParB binds five parS chromosomal sequences and the resulting complexes influence chromosome conformation, but play a minor role in chromosome compaction and segregation. In contrast, the SMC-ScpAB complex plays a key role in S. aureus chromosome biology, contributing to chromosome compaction, segregation and spatial organization. Additionally, we systematically assessed the impact of proteins linking chromosome segregation to cell division—Noc, FtsK, SpoIIIE, and XerC—on origin and terminus number and positioning. While these proteins have been studied previously, our work uniquely standardizes comparisons by using the same strain background, growth conditions, and analytical approaches for all mutants. This work provides a comprehensive study of the factors governing chromosome dynamics and organization in S. aureus, contributing to our knowledge on chromosome biology of spherical bacteria.

overall_design: ChIP-seq of ParB-FLAG and mNeonGreen-FLAG in Staphylococcus aureus cells.


title: scRNA-seq of mouse periodontal ligament labeled with LepR-cre; R26-tdTomato; Runx2-GFP

city: Tokyo

first: Toshihide

last: Mizoguchi

address: 2-9-18 Kanda-Misakicho, Chiyodaku

department: Oral Health Science Center

country: Japan

institute: Tokyo Dental College

summary: We employed a cell sequencing approach using 10x Genomics scRNA-seq to study the genetic profiling of LepR+ cells in the periodontal ligament (PDL). It has been suggested that PDL-derived LepR+ cells maintain hard tissue homeostasis by differentiating into hard tissue-forming cells such as osteoblasts and cementoblasts. In this study, we generated LepR-cre; R26-tdTomato; Runx2-GFP mice, and performed scRNAseq using their PDL cells. This study is the first genetic profiling of a LepR-cre-labeled population in PDL.

overall_design: PDL cells of LepR-cre; R26-tdTomato; Runx2-GFP mice were collected by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq

first: Satsuki

last: Shidara

first: Shinichirou

last: Ito

first: Akihide

last: Tokuyama


title: Uncovering gene regulatory differences between human and chimpanzee neural cells [scRNA-seq]

first: Janet

last: Song

overall_design:
We performed a CRISPR inhibition screen of 106 cis-regulated open chromatin regions in human and chimpanzee neural progenitor cells to assess their effect on nearby gene expression.

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

first: Christopher

last: Walsh


title: Uncovering gene regulatory differences between human and chimpanzee neural cells [ATAC-seq]

overall_design:
We performed ATAC-seq on human, chimpanzee, and human-chimpanzee neural cells.

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

first: Ava

last: Carter

first: Gabriel

last: Koreman


title: Blooming Resilience: Transcriptomic Insights into Cotton Flower Responses to Boll Weevil Infestation

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

country: Brazil

institute: UFRJ

summary: The global demand for cotton fiber continues to rise, but pests and pathogens significantly hinder cotton production, causing substantial losses. Among these, the cotton boll weevil (Anthonomus grandis) is one of the most destructive pests. To investigate the molecular responses of cotton (Gossypium hirsutum) to boll weevil infestation, we evaluated the global gene expression of floral buds using mRNA-seq. Additionally, we analyzed the expression of non-coding RNAs, including microRNAs (miRNAs) and long intergenic non-coding RNAs (lincRNAs). Infestation by cotton boll weevil larvae triggered a rapid and drastic transcriptional reprogramming, with 1,656 and 1,698 genes modulated after two and twelve hours, respectively. Gene ontology enrichment analysis revealed significant regulation of defense-related and developmental processes, including photosynthesis, primary metabolism, and cell organization. Transcription factor families such as ERF, WRKY, GRAS, and NAC were strongly affected, highlighting their roles in coordinating defense responses. The jasmonate pathway showed intensive modulation, alongside secondary metabolite pathways like terpenoids and phenylpropanoids, which contribute to plant defense mechanisms. Non-coding RNAs also played a critical role in the response. We identified 921 unique known and novel miRNAs, with 36 modulated by the infestation, and predicted 98,850 putative lincRNAs, several of which were differentially expressed. Understanding the genetic and molecular mechanisms underlying cotton’s defense against boll weevil, particularly during early infestation stages, is vital for developing biotechnological strategies to reduce pest damage. Our findings provide critical insights to enhance cotton resilience against herbivores.

overall_design: RNA-seq profiling of cotton floral buds in response to boll weevil herbivory. Evaluations were done after 2h, 12h and 48h of inestation.

last: Arge

first: Marcio

last: Alves-Ferreira


title: Tumor-associated Schwann cell remodeling under metabolic stress via lactate sensing orchestrates [scRNA-seq]

first: xueying

last: Li

overall_design: Pancreas of 15-week DM-KPC and NDM-KPC mice were used as single-cell RNA-seq analyses


title: Differential gene expression in leukemia is driven by enhancer heterogeneity

city: Oxford

first: Alastair

last: Smith

state: England

address: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

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

overall_design: Refer to individual Series


title: Germline transmission of cryopreserved mouse spermatogonial stem cells maintained on the International Space Station

city: Kyoto

first: Takashi

last: Shinohara

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo

department: Graduate School of Medicine

institute: Kyoto University

type: Methylation profiling by high throughput sequencing

summary: Spermatogonial stem cells (SSCs) undergo self-renewal division to maintain spermatogenesis. In this study, we used SSCs for long-term cryopreservation in space flight. We derived germline stem cell (GS) cultures from DBA/2 mouse testes by supplementing GDNF and FGF2 (Kanatsu-Shinohara et al., 2003, Biol. Reprod. 69, 216-616). GS cells were cryopreserved in the ISS for 6 months. Frozen GS cells were thawed upon return to Earth and their gene expression profiles were analysed.

overall_design: In this dataset, we include the DNA methylation data obtained from cultured spermatogonia (GS cells) derived from transgenic mouse line C57BL6/Tg14(act-EGFP-OsbY01) that was bred into DBA/2 background. Each group contains 3 biological replicates.

first: Mito

last: Kanatsu-Shinohara

first: Yusuke

last: Shiromoto


title: Oligonol enhances brain cognition function in high-fat diet-fed mice

city: Hwasun

first: Juhyun

address: Seoyang-ro 264

department: Department of Anatomy

country: South Korea

institute: Chonnam National University Medical School

summary: Oligonol, a low-molecular-weight polyphenol derived from lychee fruit, is well recognized for its antioxidant properties, blood glucose regulation, and fat mass reduction capability. However, its effect on the central nervous system remains unclear. Here, we investigated the effects of oligonol on brain in a high-fat diet (HFD) fed mouse model, and SH-SY5Y neuronal cells and primary cultured cortical neuron under insulin resistance conditions. HFD mice were orally administered oligonol (20 mg/kg) daily, and SH-SY5Y cells and primary cortical neurons were pretreated with 500 ng/mL oligonol under in vitro insulin resistance conditions. Our findings revealed that oligonol administration reduced blood glucose levels and improved spatial memory function in HFD mice. In vitro data demonstrated that oligonol protected neuronal cells and enhanced neural structure against insulin resistance. We confirmed RNA sequencing in the oligonol-pretreated insulin-resistant SH-SY5Y neuronal cells. Our RNA-sequencing data indicated that oligonol contributes to metabolic signaling and neurite outgrowth. In conclusion, our study provides insights into therapeutic potential of oligonol with respect to preventing neuronal cell damage and improving neural structure and cognitive function in HFD mice.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq. Comparative gene expression profiling analysis of RNA-seq data confirmed the effect of oligonol treatment in SH-SY5Y cells where insulin resistance was induced.

first: Seo

middle: Y

last: Choi

last: Ahn

first: Danbi

last: Jo

first: Oh

last: Kim


title: UHRF2 mediates resistance to DNA methylation reprogramming in primordial germ cells [RRBS]

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

summary: In mammals, primordial germ cells (PGCs) undergo global erasure of DNA methylation with delayed demethylation of germline genes and selective retention of DNA methylation at young retrotransposons. However, the molecular mechanisms of persistent DNA methylation in PGCs remain unclear. Here we report that resistance to DNA methylation reprogramming in PGCs requires UHRF2, the paralog of the DNMT1 cofactor UHRF1. PGCs from Uhrf2 knock-out mice show loss of retrotransposon DNA methylation, while DNA methylation is unaffected in somatic cells of Uhrf2-/- mice. Furthermore, Uhrf2-deficient PGCs show precocious demethylation of germline genes and overexpress meiotic genes in females.

overall_design:
To explore the dynamics of DNA methylation during epigenetic reprogramming in PGCs, we performed DNA methylation analysis by RRBS at all stages of PGC development in the mouse from E9.5 to E17.5.
To study the role of Dnmt1 and Uhrf2 in PGCs, we performed DNA methylation analysis by RRBS in PGCs isolated from E13.5 embryos carrying a conditional knockout of Dnmt1 and PGCs isolated from Uhrf2-deficient and WT control E13.5 embryos. To expand our study of the role of Uhrf2, we also performed  DNA methylation analysis by RRBS in Uhrf2-deficient and WT control E8.5 embryos, postnatal organs (brain, liver, heart) and spermatozoa. Finally, we studied the consequences of Uhrf2 deficiency on the transcriptome by performing RNA-seq in Uhrf2-deficient and WT control E8.5 embryos, and Uhrf2-deficient and WT control PGCs isolated from E13.5 embryos.

first: Ambre

last: Bender

last: Dumas


title: UHRF2 mediates resistance to DNA methylation reprogramming in primordial germ cells [RNAseq_E8.5]


title: UHRF2 mediates resistance to DNA methylation reprogramming in primordial germ cells [RNAseq_PGCs]


title: Effect of AtSMC3 depletion and mutation of Topoisomerase VI complex on the transcriptome of 2-week-old Arabidopsis thaliana plants.

city: Marseille

first: Christophe

last: Laloi

state: France

address: 163 avenue de Luminy

department: Biology

institute: Aix-Marseille Université

summary: To investigate the potential interplays between topoisomerase VI and  cohesin complexes in the field of oxidative stress signaling, we generated the ess line, which supresses the expression of the cohesin subunit AtSMC3 at 2 weeks. We performed a comparative study with the caa39 hypomorphic line which is mutated for the A-subunit of Topoisomerase VI complex.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for caa39 and ess lines.

first: Florent

last: VELAY

first: Cécile

last: LECAMPION

last: LALOI


title: Thyroid Hormone Promotes Fetal Neurogenesis [scRNA-Seq]

status: Public on Aug 11 2025

city: Chicago

first: Federico

last: Salas-Lucia

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: The University of Chicago

summary: Maternal low thyroxine (T4) serum levels during the first trimester of pregnancy correlate with cerebral cortex volume and mental development of the progeny, but why neural cells during early fetal brain development are vulnerable to maternal T4 levels remains unknown. In this study, using iPSCs obtained from a boy with a loss-of-function mutation in MCT8—a transporter previously identified as critical for thyroid hormone uptake and action in neural cells—we demonstrate that thyroid hormones induce transcriptional changes that promote the progression of human neural precursor cells along the dorsal projection trajectory. Consistent with these findings, single-cell, spatial, and bulk transcriptomics from MCT8-deficient cerebral organoids and cultures of human neural precursor cells underscore the necessity for optimal thyroid hormone levels for these cells to differentiate into neurons. The controlled intracellular activation of T4 signaling occurs through the transient expression of the enzyme type 2 deiodinase, which converts T4 into its active form, T3, alongside the coordinated expression of thyroid hormone nuclear receptors. The intracellular activation of T4 in NPCs results in transcriptional changes important for their division mode and cell cycle progression. Thus, T4 is essential for fetal neurogenesis, highlighting the importance of adequate treatment for mothers with hypothyroidism.

overall_design: scRNA seq profiling of human induced pluripotent stem cells derived neural precursor cells comparing control (CS01ictr) vs MCT8-deficient (cs58imct8) neural precursor cells and control vs control treated with 1nM T4

first: Sergio

last: Escamilla

first: Amanda

last: Charest

first: Hanzi

last: Jiang

first: Randy

last: Stout

first: Antonio

last: Bianco


title: PDZK1 Protects Against RPE Senescence by Targeting the 14-3-3ε-mTOR Axis to Attenuate Early Diabetic Retinopathy [MG_HG]

city: Guangzhou

first: Junbiao

last: Zhang

state: Guangdong

address: No. 183, Zhongshan Avenue West

department: Ophthalmology

institute: The Third Affiliated Hospital of Southern Medical University

summary: In diabetic retinopathy (DR), hyperglycemia induces retinal pigment epithelium (RPE) cell senescence via downregulation of PDZK1. PDZK1 overexpression counteracts senescence by binding 14-3-3ε to modulate mTOR signaling, reducing oxidative stress and enhancing autophagy. Both genetic PDZK1 restoration and pharmacologic senolysis (Nutlin-3a) attenuate retinal senescence and ameliorate early DR pathology, establishing the PDZK1-14-3-3ε-mTOR axis as a therapeutic target

overall_design: Cells were cultured for 48 hours in either control medium containing 5.5 mM D-glucose and 32 mM mannitol, or in high-glucose (HG) medium containing 37.5 mM D-glucose, followed by RNA extraction for sequencing.

first: Jian

last: Zhao

first: Yanli

last: Liu

first: Lili

last: Wang

first: Chunxi

last: Huang

first: Wei

last: Chi

first: Meixia

last: An


title: Expression of TKS4 isoforms, TKS5 isoforms, WIP, WASL, CR16, and TTP in MCF7 cell line, with TKS4 knockout, TKS4L isoform overespression and TKS4b isoform overespression

city: Kyiv

first: Serhii

last: Kropyvko

address: 150, Zabolotnogo str.

department: Department of Functional Genomics

country: Ukraine

institute: Institute of Molecular Biology and Genetics NAS of Ukraine

summary: The expression of multiple TKS4 isoforms, TKS5 isoforms, WIP, WASL, CR16, and TTP was assessed in MCF7 cell line, with TKS4 knockout, TKS4L isoform overespression and TKS4b isoform overespression

overall_design: qPCR analysis via Taq-Man fluorescent probe of multiple TKS4 isoforms, TKS5 isoforms, WIP, WASL, CR16, and TTP was assessed in MCF7 cell line, with TKS4 knockout, TKS4L isoform overespression and TKS4b isoform overespression. Study was performed in triplicates


title: Single-cell RNA sequencing clarifies dermal fibroblast subset representation in vitro and reveals variable persistence of keloid disease-associated features

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

institute: King's College London


title: Pancreatic cells are resistant to KRASQ61L expression due to hyperactivation of ERK/MAPK signaling and induction of apoptosis

city: Charleston

first: Guy

middle: Aaron

last: Hobbs

state: SC

address: 86 Johnathan Lucas, HCC 702

institute: Medical University of South Carolina

summary: The RAS family of small GTPases is among the most frequently mutated gene families in human cancer. In pancreatic ductal adenocarcinoma (PDAC), ~95% of cases harbor an activating KRAS mutation, primarily at codon 12, 13, or 61, with G12D the most common overall (40%). In contrast, the KRASQ61L mutation, though constitutively active, is virtually absent in PDAC patient tumors. This suggests that KRASQ61L may engage in distinct, allele-specific signaling that limits its ability to drive tumorigenesis. Determining the mechanisms that limit the occurrence of this mutation will aid in our understanding of the critical KRAS effectors and pathways that drive tumorigenesis. To investigate these mechanisms, we utilized a tightly controlled doxycycline-inducible KRAS expression system in an isogenic, immortalized pancreatic cell line, enabling direct comparison of KRASQ61L to the common PDAC mutant KRASG12D. Using TurboID proximity labeling alongside RNA sequencing, we mapped early effector interactions and transcriptional responses, revealing that KRASQ61L induces greater hyperactivation of the ERK/MAPK pathway, resulting in increased nuclear translocation of ERK1/2. Finally, pancreatic cells are highly tolerant to overexpression of KRASG12D, but KRASQ61L overexpression leads to impaired proliferation and increased apoptosis. These findings provide experimental support for the long-standing "Goldilocks" model of oncogenic signaling, where too much ERK/MAPK pathway activation is detrimental to tumorigenesis. Our work offers a mechanistic explanation for the relative absence of KRASQ61L in PDAC and contributes to our understanding of KRAS allele-specific vulnerabilities, which can inform future therapeutic strategies targeting KRAS-driven pancreatic cancer.

overall_design: This RNA sequencing experiment was performed to investigate how different KRAS mutations impact transcriptional programs in a human pancreatic ductal epithelial context. We used HPNE (human pancreatic nestin-expressing) cells engineered to express doxycycline-inducible versions of wild-type KRAS (KRASWT), or one of three oncogenic KRAS mutants: KRASG12D, KRASG12R, or KRASQ61L.  Each isogenic cell line (HPNE-KRASWT, HPNE-KRASG12D, HPNE-KRASG12R, HPNE-KRASQ61L) was treated with doxycycline for 48 hours to induce transgene expression.

first: Rachel

last: Burge

first: Silvia

last: Vaena


title: STAT1-dependent expression in kidney endothelium from mice challenged with LPS

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary: Severe systemic inflammatory reactions, including sepsis, often lead to shock, organ failure and death, in part through an acute release of cytokines that promote vascular dysfunction. However, little is known about the vascular endothelial signaling pathways regulating the transcriptional profile in failing organs. Among all the cytokines altered during a cytokine storm, IL-6 levels are particularly informative, as they correlate with systemic disease severity and are highly predictive of mortality. Here, we show that loss of endothelial expression of the IL-6 pathway inhibitor, SOCS3, promotes a type I interferon (IFNI)-like gene signature in response to endotoxemia in mouse kidneys and brains. In cultured primary human endothelial cells, IL-6 induces a transient IFNI-like gene expression in a non-canonical, interferon-independent fashion. We further show that STAT3, which we had previously shown to control IL-6-driven endothelial barrier function, is dispensable for this activity. Instead, IL-6 promotes a transient increase in cytosolic mitochondrial DNA and requires STAT1, cGAS, STING, and the IRFs 1, 3, and 4. Inhibition of this pathway in endothelial-specific STING knockout mice or global STAT1 knockout mice leads to reduced severity of an acute endotoxemic challenge and prevents the endotoxin-induced IFNI-like gene signature. These results suggest that permeability and DNA sensing responses are driven by parallel pathways downstream of this cytokine, provide new insights into the complex response to acute inflammatory responses, and offer the possibility of novel therapeutic strategies for independently controlling the intracellular responses to IL-6 in order to tailor the inflammatory response.

overall_design: STAT1KO (JAX #012606) or control C57Bl/6J (JAX #000664) were challenged with 250 ug of LPS and sacrificed 15 hours later. Whole organ RNA was oobtained from an aliquot of kidney single cell suspensions, while the reminder was processed for endoothelial cell enrichment prior to RNA isolation. Each experimental group includes two male and two female mice.

first: Martino

last: Nina

first: Bossardi Ramos

last: Ramon

first: Adam

last: Alejandro Pablo


title: Single-cell RNA sequencing clarifies dermal fibroblast subset representation in vitro and reveals variable persistence of keloid disease-associated features [bulk-RNAseq]

summary: In vitro models of scarring and fibrosis are essential to improve our understanding of disease mechanisms and ultimately develop much-needed effective therapeutic strategies. This is particularly true for keloids, the example of pathological scarring exploited in this study, as there is no animal model. Our emerging appreciation of fibroblast heterogeneity from relatively new single cell RNA sequencing (scRNA-seq) information leaves a knowledge gap about what is represented in typical fibroblast cultures. Specifically, it is important to know whether quantitative differences in fibroblast subtypes observed in pathological tissues are represented and/or whether disease-associated molecular alterations of subtypes are maintained.  This study performed scRNA-seq on patient-matched keloid and normal adjacent dermis immediately ex vivo, which was compared to sc- and bulk-RNA-seq on primary dermal fibroblast cultures from the same samples after 4+ passages. Freshly dissociated tissue showed anticipated differences in cell proportions in keloid versus normal skin; however, comparably for both tissue types, there was an assimilation of fibroblast subtypes after culture. Cultured cells clustered conspicuously from the original populations, with evidence of only minor heterogeneity persisting. Cells displayed, to varying degrees, elements of each of the original subset signatures; FAP+/SFRP2+ mesenchymal features were strongest. Pseudo-bulk analysis of ex vivo mesenchymal subpopulations showed cell-intrinsic keloid versus normal skin transcriptional differences consistent with current disease understanding; however, only a subset of these persisted in vitro. Cell-cell communication analysis provides potential strategies to maintain specific cell populations and their in vivo phenotypes. As an example, we report that culture with ascorbic acid (stimulating cell-derived extracellular matrix) enriched the mesenchymal signature. The data presented herein provide resources supporting greater understanding of, and strategies to refine, essential human fibroblast culture models.

overall_design: Passage-8-9 keloid and normal skin dermal cells extracted from a single patient were cultured with and without ascorbic acid (N=4 replicates/group, 2x P8 technical replicates; 2x P9 technical replicates) for 5 days and processed for bulk-RNA sequencing.

first: Lock

last: Amy

first: Drudi

last: Elena

first: Freydina

last: Dasha

first: Stramer

last: Brian

first: Denk

last: Franziska

first: Shaw

last: Tanya


title: Altered molecular signaling pathways in the hippocampus of rhesus monkeys following chronic alcohol use

city: Jackson

first: Harry

last: Pantazopoulos

state: MS

address: 2500 North State Street

department: Psychiatry and Human Behavior

institute: University of Mississippi Medical Center

summary: Context-induced relapse is a significant factor limiting recovery from alcohol use disorder (AUD).  However, the molecular processes in the hippocampus, a critical region for contextual memory, impacted by chronic alcohol use remain poorly understood. We used a non-human primate model to test the hypothesis that chronic alcohol use impacts hippocampal molecular pathways that may serve as therapeutic targets for context-induced relapse and memory processing issues associated with chronic alcohol use. We conducted RNAseq profiling on hippocampal samples from adult male rhesus monkeys with chronic alcohol use (n=7) and controls (n=5) from the Monkey Alcohol Tissue Research Resource (MATRR).  We identified 2,291 differentially expressed genes (DEGs) in subjects with chronic alcohol use, including genes implicated in genome-wide association studies (GWAS), such as GLP2R and GABBR2. Downregulated pathways included chemical synaptic transmission, trans-synaptic signaling, and neuron development, and upregulated pathways involved mitochondrial function. Targeted pathway analysis highlighted significant downregulation of synaptic signaling pathways (e.g., axonal fasciculation) and upregulation of mitochondrial processes (e.g., electron transport).  Leading-edge analysis revealed several downregulated genes involved in synaptic signaling including GRIN2B, CACNA1C, and NLGN1 and upregulated genes such as NDUFS3 and MT-ND1  involved in mitochondrial processes.  Drug repurposing analysis identified several targets including epidermal growth factor receptor (EGFR) inhibitors, and L-type calcium channel blockers as potential therapeutic targets.  Our results provide critical insights into molecular pathways underlying hippocampal pathology in chronic alcohol use, emphasizing the roles of mitochondrial function, synaptic regulation and calcium channels in the hippocampus, and offering potential novel therapeutic targets.

overall_design: RNAseq profiling of hippocampal tissue samples from adult male rhesus monkeys with chronic alcohol use and controls

first: Tanya

last: Pareek

first: John

middle: M

last: Vergis

first: Sinead

last: O’Donovan

first: Xiaolu

last: Zhang

first: Donna

last: Platt

first: Kathleen

last: Grant

first: Robert

last: McCullumsmith

first: Barbara

last: Gisabella


title: CD45 sequestration lowers the signaling threshold in lymphocytes and enhances anti-tumor immunity

city: Cambridge

first: K.

middle: Dane

last: Wittrup

state: MA

address: 500 Main St

institute: MIT

summary: CD45 plays a central role in immune signal regulation by controlling the spatial dynamics of phosphatase activity through steric segregation of its bulky rigid extracellular domain. To modulate CD45 activity, here we develop and characterize protein engineering approaches to induce multivalent clustering of CD45, effectively mimicking the endogenous local receptor sequestration during immune synapse formation. In doing so, we engineer a biologic that enables precise, tunable control over CD45 surface localization and activity. CD45 sequestration exhibited striking synergy when administered in combination with intratumorally anchored IL-12 therapy, markedly delaying tumor progression and extending survival in syngeneic murine melanoma and carcinoma models. Immune profiling revealed that CD8⁺ T cells are essential mediators of this synergistic antitumor response. Mechanistically, IL-12 initiates a wave of antigen generation and T cell priming, while CD45 sequestration subsequently enhances tumor-specific CD8⁺ T cell activation, expansion, and functional states within the tumor-draining lymph node. These findings suggest that CD45 sequestration lowers the activation threshold of T cells, broadens the tumor-reactive T cell repertoire, and therefore promotes more robust tumor-specific T cell responses. Altogether, we establish CD45 as a promising novel target for cancer immunotherapy, capable of potentiating strong anticancer immune responses.

overall_design: Mice bearing B16F10 tumors, left untreated, treated with alum IL-12, or treated with alum IL-12 + CD45 XL (n = 4-5/group) were harvested 48 h. after the completion of treatment and sorted for CD8+ T cells specific for the immunodominant p15E retroviral antigen in the tdLN for downstream scRNA-seq.  Tumor-draining inguinal lymph nodes (tdLN) were harvested, manually dissociated, and filtered through a 5 mL round-bottom tube with cell-strainer cap (Falcon) using the blunt rubber end of a 1mL syringe plunger (BD Falcon). All lymph node material was used in FACS sorting. Viability was assessed with Zombie Aqua dye (BioLegend, 1:1000) in PBS for 20 minutes at room temperature. Subsequent washes and surface staining were performed in PBS supplemented with 1% bovine serum albumin (Sigma). Samples were resuspended in buffer containing Fc block (clone 93, eBioscience, 1:50) and AlexaFlour 647 labeled p15E tetramer (H2-Kb MuLV env 574-581, NIH Tetramer Core) at 1:100 for 30 min at RT. Extracellular staining was performed at 4oC for 30 min. Cells were also stained with Totalseq C anti-mouse hashing antibodies (BioLegend, 1:100) before FACS. For p15E+ CD8+ T cell sorting cells were sorted on a Sony MA900 and gated on FSC and SSC, Live, CD45+, CD8+, CD44+, and p15E Tetramer+. Cells were subsequently processed according to the 10x Genomics 5` Immune Profiling v3 protocol.

first: Lauren

last: Duhamel

first: Yiming

middle: J

first: William

last: Pinney III

first: Elizabeth

last: Fink

first: Qingyang

last: Zhao

first: Anna

last: Romanov

first: Jordan

last: Stinson

first: Luciano

last: Santollani

first: Joseph

middle: R

last: Palmeri

first: Owen

middle: T

last: Porth

first: Darrell

last: Irvine

first: Dane


title: Sequencing data of a novel piperine derivative HJ-23 against colorectal cancer

city: JiangSu

first: Zhang Meiqi

address: 59 Cangwu Road, Haizhou District, Lianyungang City

institute: 江苏海洋大学

summary: In order to explore the mechanism of HJ-23, we used RNA-seq technology to extract and analyze the total RNA of cells treated with DMSO and HJ-23, and analyzed the RNA data.

overall_design: After reaching 80% density, HCT116 cells were divided into two groups, with no less than 5×10^6 cells in each group. One group was treated with 30µM HJ-23 drug, and the other group was treated with DMSO as a control. Both groups of cells were incubated at 37°C. One day later, the original culture medium was removed and washed with 2 mL PBS using an RNaseA-free pipette tip. 1 mL of total RNA extraction reagent (Biyuntian, China) was added to the culture dish until the cells were completely covered. The culture dish was gently shaken and allowed to stand for 2-3 minutes. Mixed by blowing with an RNaseA-free pipette tip and aspirated into an RNaseA-free cryovial. Quickly frozen in liquid nitrogen and stored in a -80°C freezer. Subsequent RNA sequencing analysis was performed by Sangyo Bioengineering (Shanghai).

first: Meiqi

first: Wenhao

last: Chen


title: A stem cell model identifies two alternative cell fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)


title: Regulation of the oxidative stress response by the E3 ligase TRIP12

city: Berkeley

first: Andrew

last: Ingersoll

state: CA

address: 1951 Oxford St

department: MCB

institute: University of California, Berkeley

summary: Centered on the transcription factor NRF2, the oxidative stress response counteracts reactive oxygen species (ROS) to ensure cell and tissue homeostasis. While unstressed cells constantly degrade NRF2, ROS inhibit the respective E3 ligase, CUL3KEAP1, to stabilize NRF2 and elicit antioxidant gene expression. Following ROS clearance, cells must rapidly reinstate NRF2 degradation, but mechanisms underlying this dynamic regulation are poorly understood. Here, we identify TRIP12, an essential E3 ligase dysregulated in Clark-Baraitser Syndrome and Parkinson’s Disease, as a component of the oxidative stress response. TRIP12 is a ubiquitin chain elongation factor that acts after CUL3KEAP1 to extend K29-linked conjugates for efficient NRF2 degradation. TRIP12 accelerates stress response silencing as CUL3KEAP1 is being restored, but limits NRF2 activation during stress. The need for dynamic NRF2 regulation therefore comes at the cost of less responsive stress signaling, suggesting that TRIP12 inhibition could be exploited to bolster the oxidative stress response in neurodegenerative diseases.

overall_design: To investigate the role of KEAP1 and CCNF on C2C12 myoblast function, cells were siRNA depleted of KEAP1, CCNF, or both to determine which genes were differentially expressed.

first: Devlon

last: McCloud

first: Jenny

last: Hu

first: Michael

last: Rape


title: RNA-seq of Melanoma cell lines M257, M238, 451Lu, 451LuR treated with PUFA/Fe3+ compared to untreated controls

city: Leuven

first: Sahar

last: Motamedi

address: Herestraat 49, Nieuwstraat

department: Oncology

country: Belgium

institute: KU Leuven

summary: here we assess the effect of PUFA/Fe3+ on gene expression in human melanoma cell lines in 2 time points (18 and 36 H).

overall_design: We performed RNAseq on 4 melanoma cell lines treated with PUFA/Fe3+ or control.


title: Investigation of the global translational response to oxidative stress in the model archaeon Haloferax volcanii reveals untranslated small RNAs with ribosome occupancy [Ribo-Seq]

city: Baltimore

first: Emma

last: Dallon

state: Maryland

address: 3400 N Charles St Levi 235

institute: Johns Hopkins University

summary: Oxidative stress induces a wide range of cellular damage, often causing disease and cell death. While many organisms are susceptible to the effects of oxidative stress, haloarchaea have adapted to be highly resistant. Several aspects of the haloarchaeal oxidative stress response have been characterized, however little is known about the impacts of oxidative stress at the translation level. Using the model archaeon Haloferax volcanii, we performed RNA-seq and ribosome profiling (Ribo-seq) to characterize the global translation landscape during oxidative stress. We identified 281 genes with differential translation efficiency (TE). Downregulated genes were enriched in ribosomal and translation proteins, in addition to peroxidases and genes involved in the TCA cycle. We also observed upregulated TE for many transporters and membrane-bound proteases, highlighting the importance of membrane dynamics during oxidative stress. We additionally identified 42 small noncoding RNAs (sRNAs) with ribosome occupancy. Size distributions of ribosome footprints revealed distinct patterns for coding and noncoding genes, with 12 sRNAs matching that of coding genes, and mass spectrometry confirming the presence of seven small proteins originating from sRNAs. However, the majority of sRNAs with ribosome occupancy had no evidence of coding potential. Of these ribosome-associated sRNAs, 12 had differential ribosome occupancy or TE during oxidative stress, suggesting that they may play a regulatory role during the oxidative stress response. In combination with the evidence of regulation at the translation level during oxidative stress, this demonstrates the complexity of gene regulation during stress response.

overall_design: We performed RNA-seq and Ribo-seq using wild-type H. volcanii cultures with and without oxidative stress treatment, using four biological replicates for each condition. We additionally performed RNA-seq on 3 sRNA knockout strains with oxidative stress treatment, using three biological replicates for each. Three biological replicates of wild-type, with and with stress treatment, were included as controls.

first: Haley

last: Moran

first: Sadhana

last: Chidambaran

first: Arman

last: Kian

first: Betty

last: Huang

first: Stephen

last: Fried

first: Jocelyne

last: DiRuggiero


title: Thyroid Hormone Promotes Fetal Neurogenesis [bulk RNA-Seq]

first: Federico

last: Salas-Lucia

overall_design: RNA seq profiling of human induced pluripotent stem cells derived neural precursor cells comparing control (CS01ictr) vs MCT8-deficient (cs58imct8) neural precursor cells and control vs control treated with 1nM T4

first: Sergio

last: Escamilla

first: Amanda

last: Charest

first: Hanzi

last: Jiang

first: Randy

last: Stout

first: Antonio

last: Bianco


title: Single-cell RNA sequencing clarifies dermal fibroblast subset representation in vitro and reveals variable persistence of keloid disease-associated features [scRNAseq]

first: Franziska

last: Denk

summary:
In vitro models of scarring and fibrosis are essential to improve our understanding of disease mechanisms and ultimately develop much-needed effective therapeutic strategies. This is particularly true for keloids, the example of pathological scarring exploited in this study, as there is no animal model. Our emerging appreciation of fibroblast heterogeneity from relatively new single cell RNA sequencing (scRNA-seq) information leaves a knowledge gap about what is represented in typical fibroblast cultures. Specifically, it is important to know whether quantitative differences in fibroblast subtypes observed in pathological tissues are represented and/or whether disease-associated molecular alterations of subtypes are maintained.

This study performed scRNA-seq on patient-matched keloid and normal adjacent dermis immediately ex vivo, which was compared to sc- and bulk-RNA-seq on primary dermal fibroblast cultures from the same samples after 4+ passages. Freshly dissociated tissue showed anticipated differences in cell proportions in keloid versus normal skin; however, comparably for both tissue types, there was an assimilation of fibroblast subtypes after culture. Cultured cells clustered conspicuously from the original populations, with evidence of only minor heterogeneity persisting. Cells displayed, to varying degrees, elements of each of the original subset signatures; FAP+/SFRP2+ mesenchymal features were strongest. Pseudo-bulk analysis of ex vivo mesenchymal subpopulations showed cell-intrinsic keloid versus normal skin transcriptional differences consistent with current disease understanding; however, only a subset of these persisted in vitro. Cell-cell communication analysis provides potential strategies to maintain specific cell populations and their in vivo phenotypes. As an example, we report that culture with ascorbic acid (stimulating cell-derived extracellular matrix) enriched the mesenchymal signature. The data presented herein provide resources supporting greater understanding of, and strategies to refine, essential human fibroblast culture models.

overall_design:
scRNAseq: Passage-zero (non-cultured) and passage-4 (cultured) keloid and normal skin dermal cells extracted from a single patient were processed for single cell sequencing.
bulk-RNAseq: Passage-8-9 keloid and normal skin dermal cells extracted from a single patient were cultured with and without ascorbic acid (N=4 replicates/group, 2x P8 technical replicates; 2x P9 technical replicates) for 5 days and processed for bulk-RNA sequencing.

first: Lock

last: Amy

first: Freydina

last: Dasha

first: Denk

last: Franziska

first: Shaw

last: Tanya


title: Majusculamide-o, a Simplified Marine Natural Product Analog, Exhibits Potent and Specific Cancer Cell Cytotoxicity

city: East Lansing

first: Sachi

last: Horibata

state: Michigan

address: 766 Service Rd

department: Pharmacology and Toxicology

institute: Michigan State University

summary: Metastatic solid tumors (e.g., ovary, pancreas, liver, lung, and brain) contribute to a high mortality rate in cancer patients with few therapeutically effective anticancer drugs available for their treatment, highlighting the need to develop agents that target solid tumors. Natural products (NPs) derived from cyanobacteria possess potent anticancer activity, yet most are hard to synthesize and modify to improve therapeutic efficacy. Here, we have efficiently synthesized a simplified analog of the marine NP majusculamide D, majusculamide o (maj-o, 1), that has remarkable potency and selective cytotoxicity towards various metastatic cancer cells. We found that maj-o (1) treatment causes apoptosis in various cancer cell lines of the ovary (OVCAR3), pancreas (PANC1), brain (U251N), and lung (H125) in a dose dependent manner with the least cytotoxic effect towards non-metastatic or primary tumors of the liver (HEPG2) and ovary (OVCAR8). 1 significantly alters gene expression signatures with more treatment time and affect pathway associated with PI3K-Akt signaling. Our finding suggests that maj-o has great potential to serve a lead compound for drug discovery of novel antineoplastics for solid tumors.

overall_design: OVCAR3 cells were plated in 6-well plates with 500k cells per well and treated with 638 nM (500 ng/ml) MJS-O after 24 h. Durations of treatment were either 0 h, 4 h, or 24 h, and the DMSO concentration between samples was normalized. The RNA was isolated and purified using a RNeasy Mini Kit. RNA amounts were quantified with a DS-11 Spectrophotometer (DeNovix). 1 μg of RNA per sample was shipped to the Van Andel Institute Genomics core (333 Bostwick Ave. NE, Grand Rapids, MI 49503) for RNA analysis.

first: Niklas Alexander

last: Wahl

first: Naiara

last: Lebrón-Acosta

first: Michelle

last: Cuevas-Perez

first: Angel

last: Hernandez-Mejias

first: Dmitry

last: Leshchiner

first: Frederick

last: Valeriote

first: Eduardo

last: Caro-Diaz


title: UHRF2 mediates resistance to DNA methylation reprogramming in primordial germ cells

first: Michael

last: Weber

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

overall_design: Refer to individual Series


title: Genome-wide in vivo and ex vivo mapping of R-loops using engineered N-terminal hybrid-binding domain of RNase H3 (enDR3)

city: Warsaw

first: Damian

last: Graczyk

address: ul. Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary: R-loops are nucleic acid structures composed of RNA/DNA hybrid and a displaced single-stranded DNA, which form during transcription. Defective processing of R-loops threatens genome stability, ultimately leading to severe human diseases. The current knowledge of the mechanisms of R-loop processing and regulation is incomplete. New tools to accurately localize R-loop biology across the genome are of key importance to understand R-loop biology. Here, we propose a new method to capture and sequence RNA/DNA hybrids which can be used to map R-loop locations, providing an essential alternative to currently used approaches, such as immunoprecipitation with S9.6 antibody. Our method relies on an engineered N-terminal hybrid-binding domain from bacterial RNase H3 (enDR3). We developed a tandem form of this domain with specific amino acid substitutions, which enhance affinity and specificity for RNA/DNA hybrids. Moreover, we successfully used this protein for genome-wide R-loop profiling based on DRIPc-seq or ChIP-seq techniques which confirmed that enDR3 is useful for R-loop detection in both in vitro and in vivo methods.

overall_design: The engineered N-terminal RNA/DNA hybrid-binding domain from the bacterial RNase H3 enzyme was used to capture R-loops ex vivo or in vivo from HeLa cells. Additionally, the S9.6 antibody ex vivo was used as a control. This approach allowed a direct comparison of three methods using either two different baits in the same hybrid capture protocol or the same bait using DRIPc or ChIP methodologies in one cell line.

first: Marta

last: Jedynak-Slyvka

first: Roman

last: Szczesny

first: Aneta

last: Jurkiewicz


title: Exploration potential regulatory mechanisms in ovarian injury of mice exposed to low-pressure hypoxia through whole transcriptome sequencing analysis

city: Lanzhou

first: mengwen

last: Jiao

state: Gansu

address: No. 333, Nanbinhe Road, Qilihe District

department: Department of Reproductive Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Chronic high-altitude hypoxia causes significant ovarian tissue damage. This study investigates the underlying mechanisms of ovarian injury in mice exposed to hypoxia, aiming to guide targeted therapy development. Mice were divided into either normal pressure (MP, n=15) or hypobaric hypoxia (PU, n=15) and samples from both groups were analyzed using whole-transcriptome sequencing data. Hub genes were identified through differential expression analysis and protein-protein interaction (PPI) network construction before their expression patterns were examined. Subsequently, functional enrichment was conducted. Key miRNAs, lncRNAs, circRNAs, and transcription factors (TFs) were ascertained. Finally, RT-qPCR and Western blotting (WB) were performed. Hmgcr, Ptgs2, and Mmp3 were identified as hub genes, all showing pronounced lower expression in PU samples. RT-qPCR analysis confirmed the downregulation of these genes, with WB analysis further demonstrating a significant reduction in their protein levels in PU samples. These hub genes were predominantly enriched in "oxidative phosphorylation" pathway. Furthermore, lncRNA-miRNA-mRNA, circRNA-miRNA-mRNA, and TF-mRNA regulatory networks were constructed. These networks highlighted key regulatory molecules, including the miRNA mmu-miR-144-3p, 2 lncRNAs (Miat and Neat1), 8 circRNAs (eg. novel_circ_041272-mu-miR-144-3p-Ptgs2), and 1 TF (Etv4). These results provide key insights for targeted ovarian injury therapies under low-pressure hypoxia.

overall_design: Female 8-week-old C57BL/6 mice were purchased from SPF (Beijing) Biotechnology Co., Ltd. (Animal License No.: SCXK (Beijing) 2024-0001). Notably, the mice were maintained under standard laboratory environment with a 12-hour light/dark cycle (07:00–19:00), ambient temperature maintained at 22±2°C, and a relative humidity of 45%–55%. The mice were provided with ad libitum access to standard laboratory chow and drinking water. The experimental animals were randomly divided into two groups: the MP group (Normal Pressure, n=15) and the PU group (Pressure Under Vacuum, n=15). The PU group was placed in a hypobaric hypoxia animal chamber (Guizhou Fenglei Aviation Mechanical Manufacturing Company, Guizhou, China) simulating the conditions of an altitude of 6500 meters, with a pressure of 43.12 kPa. The control group was housed in a normal environment at an altitude of 1588 meters  and a pressure of 83.56 kPa, in Lanzhou, China. All mice were maintained for 15 consecutive days. All animal experiments were strictly conducted in compliance with the international ARRIVE 2.0 guidelines (Animal Research: Reporting of In Vivo Experiments) and were approved by the Institutional Ethics Committee of The 940th Hospital of Joint Logistic Support Force of Chinese People's Liberation Army (Approval No. 2023KYLL299).Animal welfare measures were implemented according to the 2020 American Veterinary Medical Association (AVMA) Guidelines for the Euthanasia of Animals.The detailed procedures were as follows: mice were anesthetized by intraperitoneal injection of 1% sodium pentobarbital (40 mg/kg), followed by cervical dislocation performed by trained personnel, with subsequent collection of blood and ovarian tissue samples for analysis.These samples were used for evaluating the mouse model conditions and performing whole-transcriptome sequencing.

first: Mengwen

first: Yuewen

last: Zhang

first: Xuan

last: Hou

first: Min

last: He

first: Ling

last: Wang

first: Shaokang

last: Mo


title: Analyzing the effects of benzodiazepines on key virulence-related parameters of Pseudomonas aeruginosa

city: Palma de Mallorca

first: Carlos

last: Juan

address: Crta. Valldemossa 79

country: Spain

institute: Health research Institute of the Balearic Islands

summary: Sedation with benzodiazepines (BZs) has eventual side-effects proved to entail incremented risks for ventilator-associated pneumonia (VAP) (e.g. immunity alterations and nervous/mechanical responses increasing the aspiration of upper respiratory tract-colonizing bacteria), but some knowledge gaps on the topic exist. For instance, it has never been approached whether BZs could cause a modulation of intrinsic bacterial virulence, and/or influence the host-pathogen interaction in neglected contexts (e.g. respiratory epithelium features, or the lytic/opsonic activity of complement) to facilitate VAP development. Thus, to enrich the picture of factors contributing to the BZs-associated higher risk for VAP, we analyzed relevant in vitro, ex vivo and in vivo infection-related parameters to decipher whether they could be affected by these sedatives in the top VAP-causing pathogen Pseudomonas aeruginosa.  While most variables were unaltered (including among others invertebrate infection assays and a rat model of VAP), a significantly attenuated pathogenic impact of infection on human respiratory A549 cells (invasion, cytotoxicity and inflammation reduced up to ≈50%) appeared upon BZ exposure at high therapeutic concentrations (diazepam/midazolam 10 µg/ml), potentially because of effects of the drugs mostly on the cultured cells. These facts could entail a BZs-associated stealth pathogen-like behavior of P. aeruginosa on the respiratory epithelium, consisting of a weak immune activation proportional to the mild damage caused, perhaps favoring VAP onset. Strikingly, BZs triggered a significantly increased biofilm formation (up to ≈2-fold > controls) on plastic plates and endotracheal tubes (supported by the upregulation of various biofilm-related genes and c-di-GMP accumulation), suggesting a groundbreaking idea: the BZ-dependent boosted formation of these P. aeruginosa sessile reservoirs, likely enabling bacterial release to deep airways and thus VAP progression. Animal models with prolonged sedation/ventilation periods should be conducted to confirm that BZs pose an added trigger for VAP through the surprising hitherto unknown phenomena revealed here.

overall_design: RNA-seq prfiling of Pseudomonas aeuginosa (from Denmark collection, DK) grown in planktonic (PL) or biofilm (BF) mode of life in response to midazolam 10 ug/ml treatment (M) vs untreated control (C)

first: Isabel mª

last: Barceló

first: Elena

last: Jordana-Lluch

first: Maria

last: Escobar-Salom

first: Jordi

last: Sansó-Sastre

first: Miguel Ángel

last: Estéve

first: Mar

last: Marí-Riba

first: Àlex

last: González-Alsin

first: Anna

last: Tomàs

first: María

last: Tortosa

first: Gabriel

last: Torrens

first: Sebastián

last: Albert

first: Antonio

last: Oliver


title: Zingerone treats postmenopausal osteoporosis via increased ferroptosis sensitivity by p53-mediated regulation of Sat1 and Gpx4 expression

city: Shenyang

first: Fangming

last: Cao

state: Liaoning

address: 155 Nanjing Street

institute: First Hospital of China Medical University/Department of Orthopedics

summary: Zingerone, a component of dried ginger, has known anti-ulcer and bone growth-promoting effects, but its impact on postmenopausal osteoporosis (PO) is unclear. This study investigates the therapeutic potential and underlying mechanisms of zingerone in PO. A concentration-dependent effect identified on osteoclast precursors: at low concentrations, zingerone maintains low ROS levels, enhance proliferation, and facilitates bone remodelling; at high concentrations, it elevates ROS levels, enhances ferroptosis sensitivity, and suppresses osteoclast formation. Zingerone significantly improves bone mass in an ovariectomised mouse model of PO. Metabolomics identifies 869 differential metabolites linked to glutathione and purine metabolism. Transcriptomics highlights pathways including ferroptosis, leukocyte migration, and cell adhesion. In RAW264.7 cells, zingerone modulates p53, enhances ferroptosis sensitivity, increasing ROS and Fe2+, upregulates Sat1, and downregulates Gpx4, suggesting that zingerone may act via p53-mediated ferroptosis, indicating potential clinical utility. Before clinical application, the dose-dependent effects of zingerone on bone remodelling and its underlying mechanisms warrant further investigation.

overall_design: Novogene Co., Ltd. in Beijing, China conducted RNA sequencing analysis on three replicates of mouse femoral tissue. Differential expression analysis was carried out using the DESeq2 R package for two groups, each with three biological replicates. Differential gene analysis was done using the Limma package in R, with a cut-off threshold of abs(log2) > 0.2. Genes with a p value < 0.05 were deemed significantly differentially expressed. Significantly enriched genes among the DEGs were identified based on corrected p values below 0.05. Statistical enrichment of annotated genes was performed using the KEGG pathway database and the clusterProfiler R package. Additionally, Gene Set Enrichment Analysis (GSEA) was conducted utilizing the clusterProfiler R package. Multiplicative changes in gene expression were calculated for group comparisons, leading to the generation of gene lists based on |log2FC| changes. Pearson correlation analysis was undertaken to assess the correlation between genes and metabolites, with statistical significance set at a p value of less than 0.05.

first: Hao

last: Li

first: Dian

last: Liu

first: Lin

last: Tao


title: Targeting the AKT–EphA2 Axis and Cell–Cell Adhesion Enhances Anoikis Sensitivity in Cancer Cells

city: Galveston

first: Nehal

last: Dwivedi

state: Texas

address: 301 University Blvd

institute: The University of Texas Medical Branch Galveston

summary: Rigidity sensing enables cells to respond to extracellular matrix stiffness and governs survival and apoptotic decisions. Tropomyosin 2.1 (Tpm2.1), a key actin-binding protein, is frequently downregulated in cancer. While re-expressing Tpm2.1 restores rigidity sensing and limits anchorage-independent growth, its ability to fully trigger anoikis, apoptosis induced by loss of matrix attachment, remains unclear. Here, we show that although Tpm2.1 overexpression reduces AKT activation and suppresses survival signaling in suspended breast cancer cells, most cells remain viable without matrix attachment. Time-resolved transcriptomic profiling of apoptotic and non-apoptotic suspended cells revealed compensatory survival programs, including reactivation of PI3K–Akt signaling and upregulation of intercellular adhesion molecules such as ICAM1. Importantly, anoikis resistance can be overcome. Pharmacological inhibition of AKT, EphA2, or ICAM1 in Tpm2.1-expressing cells significantly increases apoptosis under suspension conditions. These findings highlight that while rigidity sensing restoration alone may be insufficient to induce anoikis, it sensitizes cancer cells to targeted therapies, revealing actionable vulnerabilities to  eliminate detached tumor cells.

overall_design: RNA-seq profiling was performed on MDA-MB-231 cells expressing an empty vector (MDA-EV) and cells overexpressing Tropomyosin 2.1 (MDA-Tpm2.1), cultured under attached and suspension conditions for 5 hours, 1 day, 2 days, and 4 days. For each time point, MDA-Tpm2.1 cells in suspension were further separated into apoptotic and non-apoptotic fractions.

first: Anat

last: Galis-Vivante

first: Michael

last: Sheetz

first: Guy

last: Nir


title: Investigation of the global translational response to oxidative stress in the model archaeon Haloferax volcanii reveals untranslated small RNAs with ribosome occupancy [RNA-Seq]

first: Emma

last: Dallon

first: Haley

last: Moran

first: Sadhana

last: Chidambaran

first: Arman

last: Kian

first: Betty

last: Huang

first: Stephen

last: Fried

first: Jocelyne

last: DiRuggiero


title: Metastasis-initiating osteosarcoma subpopulations establish paracrine interactions with both lung and tumor cells to create a metastatic niche

city: Columbus

first: Matt

last: Cannon

state: OH

address: 700 Children's Dr.

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

summary: Osteosarcoma is an aggressive and deadly bone tumor, primarily afflicting children, adolescents, and young adults. Poor outcomes for osteosarcoma patients are intricately linked with the development of lung metastasis. While lung metastasis is responsible for nearly all deaths caused by osteosarcoma, identification of biologically defined, metastasis-targeting therapies remains elusive because the underlying cellular and molecular mechanisms that govern metastatic colonization of circulating tumor cells to the lung remains poorly understood. While thousands of tumor cells are released into circulation each day, very few can colonize the lung. Herein, using a combination of a novel organotypic metastasis in vitro model, single-cell RNA sequencing, human xenograft, and murine immunocompetent osteosarcoma models, we find that metastasis is initiated by a subpopulation of hypo-proliferative cells with the unique capacity to sustain production of metastasis promoting cytokines such as IL6 and CXCL8 in response to lung-epithelial derived IL1α. Critically, genomic and pharmacologic disruption of IL1 signaling in osteosarcoma cells significantly reduces metastatic progression. Collectively, our study supports that tumor-stromal interactions are important for metastasis, and suggests that metastatic competency is driven, in part, by the tumor cell’s ability to respond to the metastatic niche. Our findings support that disruption of tumor-stromal signaling is a promising therapeutic approach to disrupt metastasis progression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell RNAseq was performed on osteosarcoma patient derived xenografts (PDX) and cell culture models. The pdx models are OS-17 lines and either represent primary tibial tumors or lung metastses.

first: James

last: Reinecke

first: Amanda

last: Saraf

first: John

last: Hinckley

first: Amy

last: Gross

first: Helene

last: Le Pommellette

first: Leyre

last: Jimenez Garcia

first: Maren

last: Cam

first: Matthew

first: Sophia

last: Vatelle

first: Berkley

last: Gryder

first: Ruben

last: Dries

first: Ryan

last: Roberts


title: Epigenetic profiling of mouse uteri across reproductive aging

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

summary: Advanced maternal age increases the risk of pregnancy complications because of a higher incidence of karyotypic imbalances in the oocyte. A very important yet much less explored contribution to this risk, however, is the declining capacity of the uterus to adapt to the hormonal stimulus of pregnancy. As such, it has remained unknown what drives the uterine aging phenotype on the molecular and cellular level. Here, we show in mice that maternal aging is associated with a progressive increase in transcriptional variation that is accompanied by a drastic accumulation of activating histone marks. Importantly, the transcriptional signatures associated with uterine aging differ substantially from those of organismal aging. Single-cell deconvolution analysis demonstrates that maternal age-induced effects originate in the epithelial compartment and specifically entail a dramatic up-regulation of the pioneer transcription factor FOXC1,  linked to an accumulation of H3K4me3 and H3K27ac across the locus. FOXC1 over-expression in human endometrial cells causes profound transcriptomic shifts and increases proliferation rates, recapitulating the aging phenotype. Using endometrial epithelial organoids of young and aged mice, we find that aging hallmarks including Foxc1 up-regulation and H3K27ac hyper-enrichment are conserved in vitro. In line with the epithelial hyperplasia phenotype seen in vivo, endometrial epithelial organoids from aged mice are larger and mis-express key factors critical for uterine gland maturity and function, most notably SOX9. Collectively, our data highlight the specific susceptibility of uterine epithelial cells to early-onset aging, with early changes manifesting in an increase in activating epigenetic marks that coalesce on the mis-regulation of FOXC1.

overall_design: ChIP-seq of uterine tissue from mice at various ages. Samples are grouped into four age groups, Young (Y), Aged 1 (A1), Aged 2 (A2) and Aged 3 (A3). Two ChIP-seq libraries were prepared for each sample: H3K4me3 and H3K27ac.

first: Aleksandra

middle: O

last: Tsolova

first: Georgia

last: Lea

first: Anshul

middle: S

last: Jadli

first: Anastasios

last: Mastrokolias

first: Ankita

last: Narang

first: Alexa

last: Krala

first: Bethany

middle: N

last: Radford

first: Courtney

middle: W

last: Hanna

first: Gavin

middle: D

last: Kelsey

first: Hilary

last: Critchley

first: Wendy

last: Dean

first: Myriam

last: Hemberger


title: NUDT21 Shapes Macrophage Transcriptomes through alternative polyadenylation in ARDS

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

summary: Defining the molecular mechanisms governing macrophage-driven inflammation is essential for developing targeted interventions for ARDS. One such mechanism could be alternative polyadenylation (APA), a post-transcriptional regulatory process that plays a critical role in gene regulation. Most mammalian genes, including key proinflammatory mediators, contain multiple polyadenylation sites (PAS). APA regulates the addition of poly(A) tails at alternative PAS, generating transcripts with different 3' UTR lengths. One key regulator of APA is Nudix Hydrolase 21 (NUDT21), a critical cleavage factor Im (CFIm) component. However, whether NUDT21-mediated APA plays a role in inflammation during ARDS is not known. Thus, the goal of this study is to identify the APA genes regulated by NUDT21 in macrophages.

overall_design: Comparative analysis of alternative polyadenylation using polyA-click seq (PAC-seq) on Bone marrow derived macrophages collected from mice with myeloid NUDT21 deletion (NUDT21 f/f LysmCre) mice or control LysmCre mice treated with/without 1 ug/ml LPS for 3 hrs.

first: Hui

last: Liu

first: Yu

last: Wang

first: Scott

last: Column

first: Maria

last: Gacha-Garay

last: Shin

first: Rahat

last: Hussain

first: Jayeshkumar

last: Patel

first: Manish

first: Kai-Lieh

last: Huang

first: Eric

last: Wagner

last: Yamalanchili

first: Xiaoyi

last: Yuan

first: Harry

last: Karmouty-Quintana

first: Tingting

last: Mills


title: Identification of two epitypes of IGHV unmutated chronic lymphocytic leukemia with distinct B cell-related epigenetic imprinting and genetic alterations

city: Barcelona

first: Jose Ignacio

last: Martin-Subero

state: Barcelona

address: c/Rosselló, 149-153

institute: IDIBAPS

type: Methylation profiling by genome tiling array

summary: Genetic and epigenetic changes have provided essential insights into the biology and clinical behavior of chronic lymphocytic leukemia (CLL). Overall, increasing number of chromosomal aberrations are related to disease evolution. Complex karyotype (CK) is defined as presence of at least 3 numerical and/or structural aberrations detected by chromosome banding analysis. CK frequently occur in the context of CLLs with unmutated IGHV (U-CLL) and are associated with mutations in ATM or TP53. In this context, the relationship of karyotype complexity and DNA methylation aberrations in CLL remains largely unexplored. In the present study, we selected a highly curated cohort of 52 U-CLL cases with known karyotypes and ATM and TP53 aberration status. An unsupervised Principal Component Analysis using all the CLL samples showed that there is no specific clustering according to karyotype complexity. Although CK was not a major driver of epigenetic variability, a differential methylation (DM) analysis between CK vs non-CK samples led to a small signature of 59 CpGs, suggesting only a subtle relationship between karyotypic complexity and DNA methylation. We noticed that cases with deletions in ATM and TP53 tend to cluster differently in the first two principal components independently of karyotype complexity. A consensus clustering analysis using the 5,000 most variable CpGs confirmed the two clusters, which were enriched in ATMdel (U-CLL C1, P=0.015) and TP53del/mut (U-CLL C2, P=0.004), respectively. U-CLL C1 was also enriched in ATM mutations (P=0.017) and del(13q) (P=0.007), while U-CLL C2 was also related to trisomy 12 (tri12) (P=0.004). Both clusters showed a similarly unfavorable clinical behavior, both in terms of time to first treatment and overall survival. A DM analysis between them resulted in 4,333 differential CpGs. Surprisingly, despite the fact that all the cases are U-CLLs, and therefore germinal center-inexperienced, 2,150 CpGs were modulated in normal B-cell differentiation. Remarkably, 87% of those CpGs showed that cases in the U-CLL C1 cluster are associated with a DNA methylome of less mature B cells (more similar to NBC) whereas cases in the U-CLL C2 were related to more mature B cells (more similar to MBC). A phylogenetic analysis using previously reported CpGs significant for normal B-cell differentiation confirmed this observation. The remaining DM CpGs between the two clusters were largely related to a de novo DNA hypomethylation signature (n=1,679 CpGs) in the U-CLL C2 cluster. In summary, despite not finding a major relationship between complex karyotype and DNA methylation, we discovered the presence of two epitypes in the U-CLL dataset with distinct genetic profiles and methylation signatures related to different levels of epigenetic imprinting, a finding reinforcing the perception that CLL rises from a continuum of B-cell maturation stages.

overall_design: Illumina Infinium MethylationEPIC v1.0 commercial kit

first: Charalampopoulou

last: Eleni Styliani


title: Gradual DNA methylation changes reveal transcriptional factors implicated in metabolic dysfunction-associated steatotic liver disease progression and epigenetic age acceleration

city: Wilrijk

first: Evelien

last: Van Dijck

address: Universiteitsplein 1

institute: University of Antwerp

summary:
Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common chronic liver disease worldwide, but its pathophysiological mechanisms remain elusive. It is a progressive disease, encompassing hepatic steatosis, steatohepatitis with(out) fibrosis and ultimately cirrhosis and hepatocellular carcinoma. DNA methylation (DNAm) is dysregulated in MASLD and may underpin key pathogenic mechanisms. Additionally, aging is associated with MASLD and shares common processes of chronic inflammation and oxidative stress. Therefore, this study focuses on DNAm changes in relation to MASLD progression and epigenetic age acceleration (EAA).
Results: Liver biopsies from 22 MASLD patients were analyzed using Infinium MethylationEPIC BeadChip arrays. Strikingly, progression of MASLD was characterized by gradual DNAm changes, revealing associated KEGG pathways. Additionally, Horvath’s EAA significantly correlated with MASLD stage and individual histological MASLD parameters while LiverClock’s EAA correlated only with MASLD stage. In contrast, both Horvath’s intrinsic EAA and HepClock’s EAA showed no significant correlations. Integrative analyses, leveraging both gradual MASLD and Horvath’s EAA DNAm signatures, gene expression (n = 118), and a MASLD-specific transcriptional regulatory network, identified (regulon-specific) transcription factors  implicated in MASLD and EAA progression, representing a transcription factor-network of redox (ferroptosis), immune, and metabolic/endocrine related epigenetic processes.
Conclusion: Gradual DNAm changes were found to align with progression of MASLD and EAA, with EAA a potential non-biased quantitative biomarker for MASLD. Integrative analysis highlighted potential new therapeutic transcription factor targets, with special emphasis on AEBP1 and emerging nuclear receptors including CAR(NR1I3), MR(NR3C2), GR(NR3C1), and ESRRG, underscoring the potential of epigenetic redox-metabolic therapies for MASLD

overall_design: Liver biopsies from 22 MASLD patients were analyzed using Infinium MethylationEPIC BeadChip arrays. Patients either had no MASLD, MASL, MASH F0-F1 or MASH F2-F4. Differential methylation analysis were conducted on no MASLD vs MASH F2-F4 and linear models were applied to the full MASLD spectrum


title: Genome-wide CRISPR screen for comprehensive identification of human factors involved in alternative polyadenylation based on differential localization of CD47 protein

city: Yokohama

first: Chayanin

last: Wuttinontananchai

state: Kanagawa

address: 4259 Nagatsutacho, Midori Ward

institute: Institute of science tokyo

summary: At least 70% of the human protein-coding genes possess more than one poly(A) site (PAS) and undergo a phenomenon known as alternative polyadenylation (APA), leading to distinct transcripts from a single gene. Previously, it has been demonstrated that shortening or lengthening of mRNA, resulting from the APA, could be observed in physiological and pathological conditions. Nevertheless, factors and cellular mechanisms responsible for the APA are largely unknown. CD47 protein localization was previously demonstrated to be regulated by APA. Here, we showed that core 3′ end processing factors regulate the different CD47 mRNA transcripts. This finding led us to develop an immunofluorescence staining method that simultaneously detects cell surface and intracellular CD47 protein and visualizes altered APA. Using this method, we detected the alterations of CD47 protein localization upon the depletion of the long 3′ untranslated region (UTR) mRNA isoform of CD47 or CFIm25. To systematically elucidate potential novel regulators of APA, we integrated an approach using immunofluorescence staining of cell surface and intracellular CD47 with genome-wide CRISPR screen coupled with pooled single guide RNA (sgRNA) libraries targeting human protein-coding genes. The functional genetic screens and systematic analysis of RNA-seq data revealed POLDIP2 as the potential novel regulator of APA that has global impact on APA regulation. These findings suggest that the study of novel identified APA regulators could lead to a deeper understanding of detailed molecular mechanisms governing APA under physiological and pathological conditions.

overall_design: RNA-seq profiling of wildtype HeLa cells and their POLDIP2 knockdown condition.

first: Junichi

last: Yamamoto

first: Satoshi

last: Sakamoto

first: Yuki

last: Yamaguchi


title: Role of endothelial STING1 in the transcriptional response to LPS

city: Albany

first: Ramon

last: Bossardi Ramos

address: 43 New Scotland Avenue

institute: Albany Medical College

summary: RNA-seq analysis of kidney endothelium and whole kidney from mice 15 hours after an intraperitoneal challenge with 250 micrograms of LPS per mouse.

overall_design: Four groups: WT+Saline, WT+LPS, STINGiEKO+Saline, STINGiEKO+LPS


title: Dual regulatory role of invariant natural killer T cells in the development and progression of hepatocellular carcinoma

city: Vari

first: Mihalis

last: Verykokakis

address: Fleming 34

country: Greece

institute: BSRC Alexander Fleming

summary: Our project aims to examine the role of Invariant Natural Killer T cells (iNKT) in Hepatocellular Carcinoma (HCC) which is not known. HCC is a leading cause of death and accounts for ~80% of cases of liver cancer worldwide. Because there are no biomarkers that allow the early diagnosis, HCC is diagnosed at late stages when the tumor is developed enough and is resistant to chemotherapy. The liver is characterized by an immunosuppressive environment and due to this environment, liver is prone to HCC development. Once HCC is developed, the function of immune cells that fight the tumor such as dendritic cells, natural killer cells, helper and cytotoxic T cells is suppressed while the function of regulatory T cells and myeloid- derived suppressor cells is enhanced. However, the role of Natural Killer T cells (NKT) is not known. NKT cells is a population of the immune system which is largely enriched in the liver, which recognize lipid antigens by CD1d molecule and can rapidly produce large amounts of various cytokines to enhance the function of other immune populations. Here, we investgated the  role of NKT cell in chemical-induced HCC that recapitulates the development of human HCC usiing genetic models that lack or overproduce NKT cells.

overall_design: Hepatic Invariant Natural Killer T  (iNKT) cells, identifed as CD1D-PBS57-tetramer+Tcrb+ cells,  were isolated through FACS sorting from two healthy WT mice (controls) and three WT mice with DEN-induced hepatocellular carcinoma

first: Maria

last: Papanastasatou


title: Exploiting Sesbania grandiflora’s Genetic Potential for Legume Breeding and Adaptive Responses to Combined Drought and Salt Stress

city: Changsha

first: Guo

last: Purui

address: No.498 Shaoshan South Road

summary: Alfalfa seeds from Gwadar Port, Pakistan were cultivated at Central South University of Forestry and Technology under controlled conditions (28 °C, 70% RH, 12 h light-dark cycle) for two months.

overall_design: Four groups of three samples each


title: Role of endothelial SOCS3 in the transcriptional response to LPS

summary: Translating affinity purification (TRAP)-mediated analysis of kidney endothelial translatome of bulk kidney RNA-seq from mice 15 hours after an intraperitoneal challenge with 250 micrograms of LPS per mouse.

overall_design: Total RNA from kidney or endothelial especific. Four groups: WT+Saline, WT+LPS, SOCS3iEKO+Saline, SOCS3iEKO+LPS


title: Spatially resolved atlas of IPF fibroblastic foci identifies that PAK2 kinase activation is involved in fibrogenesis

city: Tokyo

first: Yu

last: Fujita

address: 3-25-8 Nishishinbashi

institute: The Jikei University School of Medicine

summary: Idiopathic pulmonary fibrosis (IPF) is a fatal interstitial lung disease characterized by progressive fibrosis of the lung parenchyma. To identify potential therapeutic targets for IPF, we conducted spatial transcriptomic analysis and single-cell RNA sequencing (scRNA-seq). Our findings reveal that PAK plays a critical role in the immature fibroblast niche during fibrogenesis, highlighting its potential as a therapeutic target for the treatment of IPF.

overall_design: Lung tissue samples were obtained from three patients diagnosed with idiopathic pulmonary fibrosis (IPF) for analysis. Spatial transcriptomic analysis was performed on nine lung tissue sections derived from these three patients.

first: Naoaki

last: Watanabe

first: Masahiro

last: Yoshida

first: Yuta

last: Hirano

first: Yusuke


title: Next Generation Sequencing assesses 53BP1-regulated gene expression profiling in hTRET-RPE1 cells

city: wuhan

first: wu

last: wei

address: Shuiguohu Subdistrict

institute: Wuhan University

summary: The goal of this experiment is to analyze global gene expression profiles after depletion of 53BP1

overall_design: hTERT-RPE1 53BP1 knock-out cell line used in this study were generated using CRISPR-Cas9 gene editing approach. Cell were transduced with a lentiviral expression vector encoding a single guide RNAs (gRNAs) against 53BP1, and cells expressing the vector containing only Cas9, but no sgRNA, served as control cell lines.

first: Yundong

last: Fu

first: Wei

last: Wu

first: Shuyun

last: Ma

first: Qiang

last: Chen


title: Series-temporal transcriptome profiling of cotton reveals the response mechanism of phosphatidylinositol signaling system in the early stage of drought stress

city: Jinan

first: xiaoge

last: wang

state: Shandong province

address: 23788 Industrial North Road Avenue

department: Institute of Industrial Crops

institute: Shandong Academy of Agricultural  sciences

summary: To investigate the response mechanism in the early stage  of cotton to drought stress, we performed gene expression profiling analysis using data obtained from RNA-seq of roots, stems and leaves from cottons treated with 10% PEG 6000 for 0 min (control), 10 min, 30 min, 60 min and 180 min.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 tissues at 5 time points after PEG treatments.

first: Xiaoge

last: Wang

first: Yongsheng

last: Deng

first: Liying

last: Gao

first: Fanjin

last: Kong

first: Guifang

last: Shen

first: Bing

last: Duan

first: Zongwen

first: Maohua

last: Dai

first: Zongfu

last: Han


title: Transcriptional profiling of ahp4 versus wt in roots and shoots

city: LOUGHBOROUGH

first: Anthony

last: Bishopp

state: Leicestershire

address: College Road

institute: University of Nottingham

summary: Bulk RNA-seq data data sets were generated for mutant and wild-type roots of 7 day old plants, with and without cytokinin treatment

overall_design: Plants were grown for 7d. They were dissected at the hypocotyl to make to pools. Half the pools were treated with 100 nM BA for 2h, the other half with a mock DMSO treatment. Mutant (ahp4-2) and wild-type were compared.

first: Elina

last: Chrysanthou


title: A novel t(5;7)(q31;q21/CDK6::IL3 in immature T-cell acute lymphoblastic leukemia with IL3 overexpression and reactive eosinophilia

city: Perugia

first: Roberta

last: La Starza

address: Piazzale Menghini 9

department: Department of Medicine and Surgery

country: Italy

institute: University of Perugia

type:
Expression profiling by array
Genome variation profiling by SNP array

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

overall_design: Refer to individual Series


title: Rapalink-1 reveals novel TOR dependent genes and the role of agmatinases  in growth and lifespan

city: London

first: Charalampos

last: Rallis

address: Mile End Road

department: School of Biological and Behavioural Sciences

institute: Queen Mary University of London

summary: mTOR is a conserved proaging pathway with characterised inhibitors like rapamycin and torins. A third-generation inhibitor, rapalink-1, has been developed, however, its effects on organismal gene expression and lifespan have not been evaluated. Here, we demonstrate that rapalink-1 affects fission yeast spatial and temporal growth and prolongs chronological lifespan. Endosome and vesicle-mediated transport and homeostasis processes related to autophagy and Pik3, the orthologue of human PI3K, render cells resistant to rapalink-1. Our study reveals mTOR-regulated genes with unknown roles in aging including all fission yeast agmatinases, the enzymes responsible for processing agmatine to putrescine and urea. We identify sensitive and resistant mutants to agmatine and putrescine and show that all fission yeast agmatinase enzymes are required for normal lifespan. Genetic interactome assays for the agmatinase agm1 and further analyses demonstrate that impairing the agmatinergic branch of arginine catabolism results in mTOR activity levels that are beneficial for growth but detrimental for chronological aging. Our study reveals metabolic circuits with possible implications to other systems, including human cells.

overall_design: To compare the effects of Rapamycin and Rapalink-1 on gene expression, S.pombe cells were treated with 100nM of Rapamycin and Rapalink-1 for 5 hours, followed by downstream processing to extract RNA and compare transcriptomic profiles between untreated and treated yeast cells.

first: Rallis

last: Charalampos

first: Kumar

last: Juhi


title: Transcriptome expression of WT and miR164OE seedlings treated with/without heat stress

city: Taipei

first: Jeng-Shane

last: Lin

address: No. 1, Sec. 4, Roosevelt Road

department: Plant Biology

country: Taiwan

institute: National Taiwan University

summary: To understand regulation mechanism of miR164/targets, transcriptomes of WT and miR164 ovexpression plants with/without heat stress  were dissected. 5-day-old seedlings were treated with heat stress at 35oC for 5 days. Total RNAs were isolated for library construction and analyzed by RNA-seq via Solexa platform. Raw sequences were obtained from the Illumina Pipeline softwareIllumina bcl2fastq v2.1.7 and expected to generate 6 G per sample.

overall_design: Examination of transcriptome expression in WT and  miR164OE seedlings treated with/without heat stress


title: Metabolic Cross-Feeding Supports Growth of Candida albicans and Enterococcus faecalis in the Gut Microbiome

city: San Francisco

first: Haley

middle: Elizabeth

last: Gause

country: USA

institute: UCSF

summary: The fungal species Candida albicans and the bacterium Enterococcus faecalis are both common members of the gut microbiome, with co-occurrence of these two species widely reported in dysbiotic gut environments. While prior research suggests these species interact in the gut, the underlying mechanisms of these interactions remain unclear. To explore these interactions further, we utilized dual RNA-sequencing to transcriptionally profile both C. albicans and E. faecalis during co-culture and mono-culture under two conditions: (1) an in vitro condition designed to mimic certain aspects of the gut environment and (2) the germ-free mouse gut. Gene expression analysis revealed that both species strongly upregulate citrate-related genes during co-culture: C. albicans upregulates CIT1 (citrate synthase) which produces citrate, while E. faecalis upregulates its cit operon, responsible for citrate metabolism. In vitro co-cultures revealed that citrate cross-feeding supports increased growth of E. faecalis, which depends both on C. albicans' expression of CIT1 and E. faecalis' expression of the cit operon. A main byproduct of citrate metabolism in E. faecalis is formate, a short chain fatty acid (SCFA) toxic to fungi. Our RNA profiling revealed that C. albicans strongly upregulates three formate dehydrogenases (FDHs) during co-culture, enabling formate detoxification and conferring a growth advantage to C. albicans when grown in E. faecalis conditioned medium. These findings reveal a metabolically driven interaction between C. albicans and E. faecalis in the gut, where cross-feeding of citrate and detoxification of formate facilitates the growth of both species when they are cultured together. Using a simplified fungal-bacterial co-culture system, our studies begin to reveal the mechanistic complexities of metabolic sharing between a eukaryote and a bacterium.

sample_organism:
Enterococcus faecalis
Candida albicans
Mus musculus

overall_design: mono-cultures and co-cultures of Candida albicans and Enterococcus faecalis were grown in 1) hypoxic (0.2% O2, 37C) conditions for 4 hours , and 2) in the gut of Gnotobiotic Mice for 10 days. Total RNA was extracted from cell pellets (in vitro)  or cecal contents (mice) and used to create cDNA libraries for RNA-sequencing

first: Alexander

last: Johnson