title: Single-cell analysis reveals the immune landscape of benzene-exposed patients and a distinct FCGR3B+ monocyte population

city: Chongqing

first: Lei

last: Li

address: No. 301, Dashi Road, Nanping, Nan’an District

institute: The First Affiliated Hospital of Chongqing Medical and Pharmaceutical College

summary: Benzene is a known environmental and occupational pollutant associated with immune dysfunction and leukemia. However, the specific immune alterations induced by chronic exposure remain poorly understood. Using single-cell RNA sequencing of peripheral blood mononuclear cells from 16 benzene-exposed individuals (3-28 years of exposure), we identify significant changes in immune cell composition and gene expression. Notably, we observe an expansion of early-stage B cells, altered NK cell subsets, and an increase in terminally differentiated effector memory T cells, suggesting chronic inflammation and immune suppression. We also identify a novel population of proliferating FCGR3B+ monocytes, absent in healthy controls, which may contribute to benzene-induced immune dysregulation. This study provides new insights into the immune microenvironment in benzene exposure and potential therapeutic targets.

overall_design: Peripheral blood was collected from benzene-exposed patients (10 mild cases, 6 moderate cases), and peripheral blood mononuclear cells were isolated for subsequent single-cell transcriptomic sequencing.


title: Linoleic acid supports mitochondrial function and promotes the survival of human effector memory regulatory T cells

status: Public on Oct 01 2025

city: Cincinnati

first: Claire

last: Chougnet

state: OH

address: 240 Albert Sabin Way

department: Immunobiology

country: USA

institute: Cincinnati Children's Hospital Medical Center

type: Expression profiling by high throughput sequencing

summary: Regulatory T cells (Treg) maintain immune tolerance and their dysfunction contributes to cardiovascular disease (CVD). Among Treg subsets, effector-memory Treg (emTreg) are highly suppressive but metabolically vulnerable, relying on sustained mitochondrial function. We previously found that High Density Lipoproteins (HDL) selectively bind to emTreg and promote their survival. Our new data show that HDL deliver linoleic acid (LA), a dietary omega-6-PUFA, to primary human emTreg, promoting their mitochondrial metabolism and decreasing their apoptosis. LA enhanced emTreg mitochondrial membrane potential and decreased oxidative stress and mitochondrial shrinkage. Mechanistically, we uncovered that blocking ALOX15, which oxidizes LA into bioactive lipids that support mitochondrial integrity, abolished LA protective role. Importantly, we found that this protective pathway is impaired in the context of increased CVD risk. Together, our findings further explain the functional links between HDL and and Treg homeostasis and could open new therapeutic avenues to preserve Treg anti-inflammatory function

overall_design: RNA-seq profiling of primary human effector memory regulatory T cells from 3 different healthy subjects treated with PBS (control), HDL, or linoleic acid for 3 h

first: Laura

last: Atehortua

first: Alzbeta

last: Godarova

first: Colin

middle: C

last: Anderson

first: Daniel

last: Stephenson

first: Julie

middle: A

last: Reisz

first: Maria

middle: E

last: Moreno-Fernandez

first: Sean

last: Davidson

first: Angelo

last: D'Alessandro


title: Proteolytic disruption of renal endothelial glycocalyx in sepsis: Dexamethasone inhibition via TLR4/NF-κB/MMP axis

city: HANGZHOU

first: MINGJIE

last: FU

state: ZHEJIANG

address: 79#QINGCHUN ROAD

country: China

institute: THE FIRST AFFILIATED HOSPITAL OF ZHEJIANG UNIVERSITY

summary: Investigate the differences in gene expression in the kidneys of mice with sepsis, and by comparing with the sham operation group, analyze the differentially expressed genes and signaling pathways.

overall_design: Compare the differences in gene expression between the kidneys of CLP sepsis mice and those of the sham-operation mice

first: Mingjie

last: Fu


title: The transcriptional profile of the bacteriophage-resistant AB43

city: Yangzhou

first: JIngchen

last: Hao

address: No. 136, Jiangyang Middle Road

institute: Yangzhou University

summary: Capsule is a critical virulence factor that significantly contributes to phage resistance in Acinetobacter baumannii. To investigate the interplay between capsule-based defense and phage predation, we applied phage selection pressure to A. baumannii to generate isogenic phage-resistant mutants. Utilizing transcriptomic analysis, we subsequently characterized the global alterations in the biological regulatory network of a capsule-deficient, phage-resistant mutant in comparison to its parental strain. This approach allowed us to identify key transcriptional reprogramming events associated with the acquisition of phage resistance in the absence of a functional capsule.

overall_design: RNA-seq profiles of bacteriophage-resistant AB43

first: Jingchen


title: Demyelination-Induced Glutamatergic Imbalance Mediates Hippocampal Hyperexcitability

city: Riverside

first: Seema

last: Tiwari-Woodruff

state: CA

address: 900 University Avenue

department: Biomedical Sciences

institute: University of California-Riverside School of Medicine

summary: Chronic demyelination is a hallmark of multiple sclerosis (MS) and is associated with increased seizure susceptibility. In this study, we used the cuprizone (CPZ) diet induced demyelination model to investigate the progression of hippocampal demyelination and its impact on seizure activity and neurotransmitter dysregulation. Using EEG recordings, immunohistochemistry, Western blotting, ELISA, Golgi staining, and NanoString transcriptomics, we found progressive hippocampal demyelination accompanied by a striking increase in seizure incidence, from 38% at 6 weeks to 88% by 12 weeks. Structural degeneration of the CA1 pyramidal layer was marked by reduced dendritic arborization and loss of parvalbumin interneurons. Hippocampal glutamate levels increased as early as 3 weeks and remained elevated, with values (~2.2 µM) reaching excitotoxic thresholds, along with astrocyte reactivity (glial fibrillary acidic protein) and downregulation of astrocytic glutamate transporter-1, and glutamate aspartate Transporter-1 and modification of aquaporin-4 in CA1. Stratum pyramidal and stratum radiatum region-specific alterations in glutamate transporters and related enzymes (glutamine synthetase, glutamic acid decarboxylase 67, vesicular glutamate transporter 1), further supported neurotransmitter imbalance. Transcriptomic profiling revealed widespread downregulation of myelin, neuronal, astrocytic, glutamatergic, and GABAergic genes at 6 weeks, with partial recovery by 12 weeks. Together, these findings establish a mechanistic link between chronic hippocampal demyelination, glutamate dysregulation, and epileptogenesis offering potential molecular targets for therapeutic intervention in MS-associated epilepsy.

overall_design: Gene expression profiling analysis of mRNA data from demyelainted C57Bl/6J hippocampus mouse samples. Samples were collected from 6- and 12-week Cuprizone-treated and control mice.

first: Anderson

last: Alyssa

first: Ajayi

last: Moyinoluwa


title: Effects of DECR1 deletion on cardiomyocytes

city: SHANGHAI

first: ZHENG

last: YANG

address: FENGLIN STREET

department: ZHONGSHAN HOSPITAL

institute: FUDAN UNIVERSITY

summary: To elucidate the non-ischemic roles of Decr1 in cardiomyocytes, we studied the phenotypic effects of its knockdown in the absence of ischemic or hypoxic stress.

overall_design: The study comprised two groups: a control group receiving a non-targeting reagent and an experimental group subjected to Decr1 knockdown.

first: Zheng

last: Yang

first: Ao

last: Chen

first: Binbin

last: Yu

first: Yan

last: Xia

first: Chenguang

first: Zhangwei

first: Juying

last: Qian


title: scRNA-seq of human CD45+ cells proliferated in the salivary grand or peripheral blood of CD8T cells depleted PBMC-transferred humanized mice

city: Yokohama-shi

first: Yuzo

last: Koda

address: 1000 Kamoshida, Aoba-ku, Yokohama-shi, Kanagawa

country: Japan

institute: Mitsubishi Tanabe Pharma Corporation

summary: We found that the transfer of PBMCs depleted of CD8 T cells into immunodeficient mice resulted in the development of Sjögren's syndrome-like salivary gland symptoms without causing GVHD. To characterize the human immune cells infiltrating the salivary glands, we examined the profiles of human immune cells in the salivary glands or peripheral blood of humanized mice by 10x Genomics single-cell RNA sequencing (scRNA-seq). We revealed that human Tph-like cells co-expressing IL-21 and CXCL13 were highly infiltrated in the salivary glands of CD8 T cell-depleted humanized mice.

overall_design: Peripheral blood or salivary glands were collected from immunodeficient mice transplanted with either human PBMCs or PBMCs depleted of CD8 T cells, and mononuclear cells were isolated by density gradient centrifugation. Human CD45+ cells were sorted by fluorescence-activated cell sorting (FACS) using a BD Aria III, and scRNA-seq analysis was performed.

first: Yuki

last: Imura

first: Piruzyan

last: Mariam

first: Sota

last: fujimori

first: Ryota

last: Sato


title: Tissue-specific expression of Drp1 transcript variants

city: Melbourne

first: Feng

last: Yan

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: Dynamin-related protein 1 (Drp1, encoded by DNM1L) is a key regulator of mitochondrial fission, yet its functional role remains controversial, likely due to isoform-specific effects arising from alternative splicing. Conventional short-read RNA sequencing complicates the characterization of full-length isoforms, limiting our understanding of their biological significance. To resolve this, we applied a targeted long-read sequencing approach to capture full-length DNM1L transcripts in primary human left ventricle and iPSC-derived cardiomyocytes. We recovered the complete spectrum of annotated isoforms and found broadly conserved expression patterns, with isoforms 1-4 expressed most abundantly. Recombinant protein assays further revealed that isoform abundance does not directly predict enzymatic activity, emphasizing the need for combined expression and functional analyses. Extending this framework to mouse, we profiled Dnm1l isoforms across six tissues (brain, heart, skeletal muscle, lung, kidney, and spleen) using the same long-read pipeline. All annotated isoforms were recovered, with distinct tissue-enriched expression patterns. Notably, several isoforms displayed strong tissue specificity, with subsets preferentially expressed in brain, heart, or skeletal muscle, suggesting specialized regulatory roles in mitochondrial dynamics. Functional rescue experiments in Drp1-knockout mouse embryonic fibroblasts revealed isoform-dependent differences in mitochondrial fission activity. Isoforms lacking the A-insert within the GTPase domain (e.g., isoforms b and d) robustly restored mitochondrial fragmentation, whereas the canonical brain-enriched isoform (isoform e) and a muscle-enriched isoform (isoform o) exhibited only partial rescue. These results indicate that inclusion of exons 2 and 3 may negatively regulate Drp1 fission activity. Together, our work establishes a cross-species atlas of DNM1L/Dnm1l isoforms, integrating long-read transcriptomics with functional assays. We demonstrate that Drp1 isoform diversity is tightly linked to tissue identity and that structural differences among isoforms critically shape mitochondrial fission activity, offering new insights into the pathophysiology of Drp1 in human health and disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Long-read targeted RNA sequencing of human induced pluripotent stem cell-derived cardiomyocytes, primary human left ventricle and primary mouse tissues (brain, heart, kidney, lung, skeletal muscle and spleen).

first: Jafar

middle: S

last: Jabbari

first: Nadia

middle: M

last: Davidson

first: Shiang

middle: Y

last: Lim


title: RNA-seq of Tph and Tfh cells proliferated in the spleens of CD8T cells depleted PBMC-transferred humanized mice

summary: We found that the transfer of PBMCs depleted of CD8 T cells into immunodeficient mice resulted in the proliferation of human Tph/Tfh cells in the spleen. To characterize the Tph/Tfh cells, we examined the comprehensive gene profiles of these cells in the spleen of humanized mice by RNA sequencing (RNA-seq).

overall_design: Spleen was collected from immunodeficient mice transplanted with either human PBMCs depleted of CD8 T cells or HSCs, and mononuclear cells were isolated by density gradient centrifugation. Human Tph/Tfh cells and PD-1/CXCR5 double negative (DN) cells were sorted by fluorescence-activated cell sorting (FACS) using a BD Aria III, and RNA-seq analysis was performed.


title: Virus-derived siRNA mediated inhibition of PRRSV replication in pigs [PAM]

city: Nanjing

first: Yaotang

last: Wu

address: Nanjing Agricultural University, Wei gang 1

institute: Nanjing Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Porcine reproductive and respiratory syndrome (PRRS) is a highly contagious disease caused by porcine reproductive and respiratory syndrome virus (PRRSV). It clinically manifests as fever, bleeding, and respiratory symptoms in pigs of different age groups, as well as reproductive disorders, causing huge economic losses to the global swine industry. RNA interference (RNAi), a highly conserved mechanism mediating post-transcriptional gene silencing, exerts antiviral effects by cleaving viral double-stranded RNA to generate virus-derived siRNA (vsiRNA). VsiRNA-mediated antiviral immunity is widespread in plants and invertebrates, while in mammals, studies have focused on reducing PRRSV viral load in pigs via siRNA delivery. Therefore, PRRSV strains (LY and LY-R) were primarily selected as virus models to infect PAM and Marc-145 cells, respectively. Then, miRNA and vsiRNA analysis were performed and bioinformatics analysis revealed multiple differentially expressed miRNAs following PRRSV infection. Further enrichment analysis indicated that these miRNAs were mainly enriched in metabolic, endocytic, and phosphorylation signaling pathways. Additionally, in Marc-145 cells infected with PRRSV-LY, high abundance of vsiRNA was detected within the PRRSV-N genome. The N-vsiRNA was inserted into vector psilencer4.1. to construct a PS-N plasmid, which is capable of exerting anti-PRRSV (LY, LY-R, and NADC30-like) activity in Marc-145 cells. Finally, the PS-N plasmid was formulated with PLGA-PEI to prepare a nanoparticle mixture, which was delivered to pigs via intramuscular injection to alleviate tissue damage caused by PRRSV-LY infection to a certain extent. In summary, the porcine RNAi system and vsiRNA generated via viral cleavage play a critical role in inhibiting virus replication. This further demonstrates the feasibility of vsiRNA-based antiviral strategies and offers a reference for the prevention and control of various RNA viruses.

overall_design: For PAM experiments, the infection level of PRRSV LY and LY-R is 0.1 MOI. They were incubated at 37℃ with 5% CO2 for 2 h and then cleaned using RPMI 1640. The non-infected virus cells for the Blank group. The RNA samples were collected according to the indicated time (24 h). The group contain the Blank, HPPRRSV, and PRRSV.

first: Jian

last: Lin

first: Qian


title: Effect of renal failure and sex on gene expression in mouse strain 129S1/SvlmJ kidneys

city: Newark

first: Melissa

middle: B.

last: Rogers

state: NJ

address: 185 south orange ave.

department: Biochem. & Molec. Biology

institute: Rutgers NJMS

summary: Sex and genetic background are key, but sometimes overlooked factors, that profoundly impact disease susceptibility and presentation in both humans and disease models. We previously showed that deficiency of KLOTHO protein, an important renal regulator of mineral homeostasis and a cofactor for FGF23, causes different phenotypes in 129S1/SvlmJ (129) and C57BL/6J (B6) mouse strains (Kuro-o et al. Mutation of the mouse Klotho gene leads to a syndrome resembling ageing. Nature 390: 45-51, 1997; Salloum JS, Garsetti DE, Rogers MB. Genetic Background Influences the Impact of KLOTHO Deficiency. Physiological Genomics. 52, 512-516 (2020). The 129 strain was more severely affected, with decreased longevity, decreased body weight, and increased amounts of kidney calcification compared to B6 mice. Here we used RNA seq to profile messenger RNAs in kidneys from control (ctrl) healthy and Klotho homozygous deficient strain 129 mice of both sexes.   The kidney messenger RNA profiles of control and Klotho homozygous deficient strain B6 mice of both sexes has been submitted separately. Comparing and contrasting the genetic architecture leading to different phenotypes associated with specific inbred mouse strains may reveal previously unrecognized and important metabolic interactions affecting chronic kidney disease.  Both sex and kidney status modulated mRNA profiles.

overall_design: The Klotho mutation (Kuro-o et al. Mutation of the mouse Klotho gene leads to a syndrome resembling ageing. Nature 390: 45-51, 1997) was made fully congenic on the 129S1/SvlmJ (129) strain by backcrossing more than 10 times. RNA was extracted from male and female mice between 44 and 54 days of age for RNA-seq profiling. Control mice with healthy kidneys were either homozygous wild type (++)  or heterozygous for the recessive Klotho mutation (Kl+).  Affected mice with renal failure were homozygous for the recessive Klotho mutation (KlKl).

middle: B

first: Tapan

last: Shah

first: Diane

last: Garsetti

first: Yue

last: Wang

first: Khushboo

last: Sahay

first: Hernandez

last: Lindsey


title: Effect of renal failure, sex, and BMP2 modulation on gene expression in mouse aorta

summary: Renal failure and male sex strongly predict cardiovascular disease.  Understanding the impact of sex and kidney function on the biology of cardiovascular disease will clarify the differential presentation, progression, and response to treatments observed in each sex.  Elucidating the molecular differences also may reveal new and effective therapeutic strategies.  Deficiency of KLOTHO promotes ectopic calcification of soft tissues such as aorta, aortic valves and kidneys. The rapid, synchronous onset of calcification particularly in  the 129S1/SvlmJ (129) mouse strain facilitates molecular studies. (Kuro-o et al. Mutation of the mouse Klotho gene leads to a syndrome resembling ageing. Nature 390: 45-51, 1997; Salloum JS, Garsetti DE, Rogers MB. Genetic Background Influences the Impact of KLOTHO Deficiency. Physiological Genomics. 52, 512-516 (2020) We previously assessed microRNA gene expression differences associated with aorta calcification in healthy or Klotho deficient mice. (Tang Y, Shah TA, Yurkow EJ, Rogers MB. MicroRNA Profiles in Calcified and Healthy Aorta Differ: Therapeutic Impact of miR-145 and miR-378. Physiological Genomics. 52: 517–529, 2020) Here we used RNA seq to profile messenger RNAs in aortas from control (ctrl) healthy and Klotho homozygous deficient mice of both sexes with renal disease that causes aortic calcification.   In addition, we profiled messenger RNAs in aortas from male mice bearing a Bone Morphogenetic Protein (BMP)2 regulatory mutation. BMP2 is a potent osteogenic factor involved in pathological vascular and valve calcification. The Bmp2 mutation (Bmp2∆UCS) is a 300 nucleotide deletion of an ultra-conserved sequence (UCS) in the 3’ untranslated region (UTR) of the Bmp2 gene.  This sequence mediates a post-transcriptional block that prevents BMP2 synthesis in specific cell types, including the aortic valves, coronary vasculature, and aorta. (Shah, T.A., Y. Zhu, N.N. Shaikh, M.A. Harris, S.E. Harris, and M.B. Rogers, Characterization of new bone morphogenetic protein (Bmp)-2 regulatory alleles. Genesis, 2017. 55(7)).  All experimental parameters (sex, kidney health, and BMP2 mutation) modulated mRNA profiles.

overall_design: Both the Bmp2 and Klotho mutations were made fully congenic on the 129S1/SvlmJ (129) by backcrossing more than 10 times. RNA was extracted from male and female mice between 44 and 53 days of age for RNA-seq profiling. Control mice with healthy kidneys were either homozygous wild type (++)  or heterozygous for the recessive Klotho mutation (Kl+).  Affected mice with renal failure were homozygous for the recessive Klotho mutation (KlKl).  Additional groups of control or Klotho deficient male mice were homozygous for the BMP2 mutation (∆UCS/∆UCS).


title: Extracellular glutamate drives glioblastoma invasion through NMDA receptor signaling in a three-dimensional engineered biomaterial platform

city: Berkeley

first: Sanjay

last: Kumar

address: 205 Stanley Hall, University of California

department: Bioengineering

institute: University of California, Berkeley

summary: Glioblastoma (GBM) tumors are characterized by an excess of extracellular glutamate, one important source of which is the tumor cells themselves. This abundance of glutamate promotes GBM proliferation, migration, and therapeutic resistance, and causes excitotoxicity in nearby neurons. However, despite glutamate’s clear role in promoting GBM aggression, the exact mechanisms through which excess glutamate drives these phenotypes, particularly 3D invasion, remain incompletely understood. To address this gap, we used a 3D brain-mimetic hyaluronic acid (HA) hydrogel to investigate the role of glutamate signaling in GBM 3D invasion. We demonstrate that inhibiting the glutamate N-methyl-D-aspartate receptor (NMDAR) reduces invasion from 3D tumorspheres, a result that is reproducible across multiple continuous culture models and a patient-derived xenograft cell line. We then conduct glutamate-driven invasion studies in 3D HA-based devices that can be micro-dissected to isolate and differentially analyze invasive and non-invasive cells. Transcriptomic analysis of invasive, non-invasive, and drug-treated populations of cells reveals that NMDAR inhibition suppresses several pathways associated with invasion-relevant processes, including matrix remodeling and collagen deposition. Our work speaks to the potential value of biomaterial platforms for identifying the autocrine and paracrine mechanisms through which neurotransmitters fuel GBM invasion.

overall_design: GBM43 cells were seeded into 3D hyaluronic acid invasion devices and either treated with control cell culture media or with NMDAR inhibitor, MK801. Core and invasive fractions were dissected from control devices. For MK801 treated devices, core and invasive fractions were pooled due to minimal invasive fraction. Cells were isolated from each fraction and RNA was extracted to submit for sequencing.

first: Wilkins

last: Dana

first: Kumar

last: Sanjay


title: Effect of Sulfamethoxazole(SMZ), Trimethoprim (TMP) and Co-trimoxazole (CTX) on gene expression of human placental BeWo cell lines

city: Utrecht

first: Mehrdad

last: Azarmi Aghajan

address: Universiteit Utrecht David de Wied gebouw  Universiteitsweg 99

department: Pharmaceutical Science

country: Netherlands

institute: Utrecht University

summary: Cell–cell junctions, including tight and adherens junctions, are critical for maintaining placental barrier integrity and ensuring proper maternal–fetal exchange. To investigate the impact of co-trimoxazole (CTX) as well as sulfamethoxazole (SMA) and trimethoprim (TMP) on these junctional networks, RNA sequencing was performed on BeWo placental cells exposed to non-cytotoxic concentrations of these three antibiotics for 24 h. Transcriptomic profiling revealed significant differential gene expression in sulfamethoxazole, trimethoprim and co-trimoxazole-treated cells compared to controls, with enrichment of ERK pathway that might be related to tight junctions, adherens junctions, and cell–cell adhesion. These alterations suggested disruption of placental barrier integrity. In addition, co-trimoxazole exposure was associated with activation of the ERK1/2 signaling cascade, reflected by downregulation of multiple dual-specificity phosphatase (DUSP) genes that normally suppress MAPK activity. Together, the RNA-seq findings indicate that CTX interferes with barrier-related gene networks and promotes ERK pathway activation, supporting its potential to compromise placental barrier function.

overall_design: RNA sequencing of untreated BeWo cell line (Control cells), as well as Sulfamethoxazole, Trimethoprim, Co-trimoxazole, and DMSO treated BeWo cell line

last: Azarmi

first: Saskia

last: Braber


title: SteMClass: A Novel DNA Methylation-Based Classifier for iPSC In Vitro Differentiation States

city: Berlin

first: Eilis

last: Perez

address: Charitéplatz 1

country: Germany

institute: Charité Universitätsmedizin Berlin

type: Genome binding/occupancy profiling by genome tiling array

summary: Human induced pluripotent stem cells (iPSCs) hold great promise for regenerative medicine, disease modelling, and drug discovery, but most downstream applications require differentiation into specialised cell types not covered by current quality control assays. Here, we present “SteMClass”, a proof-of-concept DNA methylation-based classifier that standardises iPSC differentiation state identification across protocols with one test. We curated a reference cohort of 15 iPSC lines differentiated into seven distinct states (n = 97), performed array-based DNA methylation profiling, and trained a random forest model to classify the eight distinct differentiation states. In nested cross-validation, SteMClass achieved a Brier score of 0.0264, and on an independent cohort (n = 58) attained 96.5% accuracy (Cohen’s K = 0.959) with a 3% rejection rate. Applied to external data (n = 241), performance was 76.5% accuracy (Cohen’s K = 0.593) with a 16.6% rejection rate and enabled the detection of potentially inefficient differentiations. SteMClass is compatible with all Illumina methylation array versions, and accessible via an interactive web interface that supports classification and exploration of DNA methylation profiles. By providing a harmonised, single-assay framework for iPSC-derived differentiation state characterisation, SteMClass improves reproducibility and comparability across studies, paving the way for robust quality control standards and accelerating clinical translation.

overall_design: iPSCs were differentiated into seven distinct cell states, and DNA was extracted from harvested pellets using the Maxwell® RSC system (Promega) with kits appropriate for fresh, frozen, or PFA-fixed samples, yielding comparable methylation quality. DNA quantity was assessed with the Quantus/QuantiFluor® ONE dsDNA system (Promega), followed by bisulfite conversion using the EpiTect Fast Bisulfite Kit (Qiagen). Converted DNA was analysed on Infinium MethylationEPIC BeadChip arrays (v1.0 or v2.0) and scanned with the Illumina iScan System.

first: Eilís

first: Valeria

last: Fernandez-Vallone

first: Daniel

last: Teichmann

first: Philipp

last: Euskirchen

first: Christin

last: Siewert

first: Brendan

last: Osberg

first: Peggy

last: Wolkenstein

first: Harald

last: Stachelscheid

first: David

last: Capper


title: Gene expression levels of WT, rep1, and ngs1 mutants of Yarrowia lipolytica grown in GlcNAc medium

city: Wuhan

first: Xiang-Dong

last: Gao

state: Hubei

address: Luojiashan, Wuchang district

institute: Wuhan University

summary: We determined the mRNA levels of genes in Yarrowia lipolytica wild-type, rep1, and ngs1 mutants that carry PACT1-4NAG plasmid in YNB-GlcNAc medium

overall_design: Yarrowia lipolytica WT/pYL27, WT/pYL27-4NAG, rep1/pYL27-4NAG, and ngs1/pYL27-4NAG strains were grown in YNB-GlcNAc medium. Total RNAs were extracted and sequenced (RNA-Seq).

first: Zhen-Hua

last: Wang


title: Hematopoietic Tet2 inactivation enhances the response to checkpoint blockade immunotherapy

city: Toronto

first: Suraj

last: Bansal

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre, UHN

summary: Somatic mutations inactivating TET2 are among the most common drivers of clonal hematopoiesis (CH). While TET2 inactivation is associated with monocyte-derived inflammation and improved chimeric antigen-receptor-T cell function, its impact on immunotherapy response is unknown. In murine models, hematopoietic Tet2 mutation enhanced the immune checkpoint blockade (ICB) response via the combined presence of phagocytes, CD4 and CD8 T cells. Mechanistically, in Tet2-mutant tumor-infiltrating leukocytes (TILs), ICB preferentially restricted cell states linked to tumor progression while inducing anti-tumor states. Tet2-mutant monocytes activated costimulatory programs, while Tet2-mutant T cells showed enhanced T cell memory signatures, alongside decreased exhaustion and regulatory phenotypes. This murine data was clinically relevant, since tumors from colorectal cancer and melanoma patients with TET2 driver mutation-CH (TET2-CH) showed enhanced immune infiltration, inflammation, and T cell activation. In melanoma patients treated with ICB, TET2-CH was associated with 6-fold greater odds of clinical benefit. Collectively, our data establishes that hematopoietic Tet2 inactivation primes leukocytes for anti-tumor states associated with immunotherapy response and provides a potential biomarker for personalized therapy.

overall_design: 9 weeks after rescue with Tet2wt or Tet2het bone marrow cells, C57Bl6/J mice were subcutaneously implanted with 250,000 MC-38 cells in the right flank. 17 days post-tumor implantation Tet2wt or Tet2het rescued mice were matched by tumor-size and assigned to receive 300 μg of anti-PD-1 blocking antibody (5 mice per genotype) or rat IgG2a isotype control (3 mice per genotype) every 2 days for 3 doses. Mice were euthanized 48 hours after the final dose and live, CD45+ tumor-infiltrating leukocytes were isolated using Fluorescence-Activated Cell Sorting. Single cells were processed using Chromium 10X 5’ Single Cell and Chromium Single Cell Mouse TCR Amplification kits.

first: Vincent

last: Rondeau

first: Marco

last: Buttigieg

first: Andy

middle: G

last: Zeng

first: Darryl

last: Chan

first: Michelle

last: Chan-Seng-Yue

first: Liqing

last: Jin

first: Jessica

last: McLeod

first: Meghan

last: Kates

first: Elisa

last: Donato

first: Patrick

last: Stelmach

first: Caitlyn

last: Vlasschaert

first: Yitong

last: Yang

first: Aarushi

last: Gupta

first: Sofia

last: Genta

first: Enrique

last: Sanz Garcia

first: Liran

last: Shlush

first: Mauricio

last: Ribeiro

first: Marcus

middle: O

last: Butler

first: Sagi

last: Abelson

first: Mark

middle: D

last: Minden

first: Samuel

last: Saibil

first: Steven

first: Michael

middle: J

last: Rauh

first: Andreas

last: Trumpp

first: John

last: Dick

first: Robert

last: Vanner


title: Aging drives a program of DNA methylation decay in plant organs [RNA-Seq]

first: Dawei

last: Dai

address: 2151 Berkeley Way

summary: Epigenetic changes are a hallmark of aging in mammals, but their molecular mechanics are poorly understood. DNA methylation is a biomarker for biological age, which may predict age more accurately than date of birth. However, limitations in mammalian models make it difficult to identify mechanisms underpinning age-related DNA methylation changes and dissect causal relationships. Here, we show that the short-lived model plant species Arabidopsis thaliana exhibits a loss of epigenetic integrity during aging, causing DNA methylation decay in repressive chromatin and the expression of transposable elements. We show that the rate of epigenetic aging can be manipulated by extending or curtailing lifespan, and that shoot apical meristems are protected from this aging process. We demonstrate that a program of transcriptional repression suppresses DNA methylation maintenance pathways during aging, and that mutants of this mechanism display a complete absence of epigenetic decay, whilst physical aging remains unaffected. This presents a new paradigm in which a gene regulatory program sets the rate of epigenomic information loss during aging.

overall_design: Refer to individual series

first: Ben

last: Williams


title: Aging drives a program of DNA methylation decay in plant organs [EM-Seq]

type: Methylation profiling by high throughput sequencing


title: CAGE-seq Profiling of Transcription Start Site Usage in mock-infected and human cytomegalovirus (HCMV) infected human embryonic lung fibroblasts (HELF) cells (human)

city: Shenyang

first: Yang

last: Li

address: No. 36. Sanhao street, Heping District

institute: Shengjing Hospital of China Medical University

summary: CAGE-seq (Cap Analysis of Gene Expression coupled with deep sequencing) was used to map transcription start site (TSS) usage in human embryonic lung fibroblast (HELF) cells in response to infection with the human cytomegalovirus (HCMV) HAN strain. Total RNA from infected cells at 72 hours post-infection and mock-infected controls was profiled. The analysis detected 224,206 and 292,294 CAGE transcription start sites (CTSSs) in infected and mock samples, respectively, which grouped into 20,532 and 26,407 transcript clusters (TCs). Comparative analysis identified 3,302 consensus clusters with significant shifts in TSS positions, spanning 2,487 protein-coding genes and 134 non-coding RNAs. These findings reveal extensive infection-associated remodeling of promoter choice across the host transcriptome.

overall_design:
This study profiled TSS usage by CAGE-seq in human embryonic lung fibroblast (HELF) cells under two conditions: cells infected with the HCMV HAN strain(moi=3) and harvested at 72 hours post-infection, and mock-treated controls. Total RNA from each condition was used to generate CAGE libraries that capture capped 5′ transcript ends, and sequencing was performed on an Illumina HiSeq X Ten with 150-bp paired-end reads. Infection status was the primary variable, with mock-infected HELF cells serving as the reference control, enabling direct comparison of genome-wide TSS usage between conditions and detection of infection-associated TSS shifts.
Raw data uploaded to SRA under Bioprojects: PRJNA1299111 and PRJNA1291936

first: Yanping

last: Ma

first: Qiang

last: Ruan

first: Zhongwei

last: Zhao


title: Virus-derived siRNA mediated inhibition of PRRSV replication in pigs [Marc-145]

first: Yaotang

last: Wu

overall_design: For Marc-145 cell experiments, the infection level of PRRSV LY and LY-R is 0.1 MOI. They were incubated at 37℃ with 5% CO2 for 2 h and then cleaned using RPMI 1640. The non-infected virus cells for the Blank group. The RNA samples were collected according to the indicated time (24 h). The group contain the Blank, HPPRRSV, and PRRSV.

first: Jian

last: Lin

first: Qian

last: Yang


title: RNA Sequencing Analysis of HCI-H1703 Cells Expressing Wild-Type (wt) PPM1G versus PPM1G Knockdown (Sh-PPM1G)

city: Shangha

first: Zhi-xin

address: No. 507 Zhengmin Road, Yangpu District

institute: Tongji University, School of Medicine

summary: We established NCI-H1703 cells with stable PPM1G knockdown using short hairpin RNA (shRNA) technology. Subsequently, we performed data acquisition and analysis of high-throughput RNA sequencing (RNA-seq) by comparing these PPM1G-knockdown cells with wild-type NCI-H1703 cells.

overall_design: NCI-H1703 cells with PPM1G knockdown were constructed using short hairpin RNA (shRNA) technology. Both sh-PPM1G and wild-type (WT) tumor cells were seeded into cell culture flasks. When cell confluency reached 80%-90%, the cells were treated with 0.25% trypsin-EDTA solution: an appropriate volume of trypsin was added to cover the cell layer, and the flasks were incubated in a cell culture incubator for 1-2 minutes. Once cells appeared rounded and began to detach under microscopic observation, serum-containing medium was added to terminate digestion. The cell suspension was transferred to centrifuge tubes and centrifuged at 1500 rpm for 5 minutes. After discarding the supernatant, cell pellets were collected, gently resuspended in pre-chilled PBS, and centrifuged again for washing, repeating this process 2-3 times to completely remove residual medium components. The cells were then frozen in liquid nitrogen and sent to Hangzhou Astrocyte Technology Co., Ltd. for subsequent RNA sequencing (RNA-seq) procedures and data acquisition.

first: Hao

last: Cao

first: Han-wen

last: Hu

first: Jian-Xiong

first: Hui

first: Jiefu

last: Wang


title: RNA-seq profiling of gene expression in mock-infected and human cytomegalovirus (HCMV)–infected human embryonic lung fibroblasts (HELF) at 72 hours post infection (two biological replicates per condition)

summary: RNA-seq was performed to quantify host gene-expression changes in human embryonic lung fibroblast (HELF) cells following infection with the human cytomegalovirus (HCMV) HAN strain. HELF cells harvested at 72 hours post infection and mock-infected controls were profiled, with two biological replicates per condition (HELF_1/2 for mock; HCMV_HELF_1/2 for infected). Libraries were sequenced on an Illumina platform with paired-end 150-bp reads, and reads were aligned to the human reference genome (GRCh38) for gene-level quantification. The submission includes a cross-sample expression matrix (raw counts and FPKM) and a differential-expression results table comparing infected versus mock conditions, enabling reuse of the dataset for downstream analyses. Raw FASTQ files are deposited in SRA under the corresponding BioProject and BioSample accessions.

overall_design:
This study uses a two-group design to measure infection-dependent transcriptional responses in HELF cells. Four bulk RNA-seq samples were generated: mock-infected HELF cells (biological replicates n=2, HELF_1 and HELF_2) and HCMV-infected HELF cells collected at 72 h post infection (n=2, HCMV_HELF_1 and HCMV_HELF_2). Infection status is the primary variable, with mock-infected cells serving as the reference control. All samples were sequenced on an Illumina instrument with paired-end 150-bp reads, and gene-level expression was quantified against GRCh38, allowing direct comparison between conditions and replicate-aware differential-expression analysis.
Raw data uploaded to SRA under PRJNA1310581 and PRJNA1310170


title: Transcriptional and epigenetic targets of MEF2C in human microglia contribute to cellular functions related to autism risk and age-related disease [monocytes]

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

type: Genome binding/occupancy profiling by high throughput sequencing

summary: MEF2C is a transcription factor with wide ranging roles and has specifically been implicated in restraining the microglial inflammatory response, participating in nervous system development, and contributing to aging and neurological disease. While MEF2C murine models have provided critical insights, the homeostatic and disease-associated functions of MEF2C in human microglia remain unclear. To examine this question, we profile microglia differentiated from isogenic, CRISPR-modified MEF2C haploinsufficient and knockout induced-pluripotent stem cell (iPSC) lines. A combination of transcriptomic, epigenetic and functional analyses revealed that loss of MEF2C leads to a hyperinflammatory microglial phenotype with broad impairment in phagocytosis, lipid accumulation, lysosomal dysfunction and elevated basal inflammatory cytokine and inflammasome activation. Transcriptomic and epigenetic approaches identified substantial overlap between reduced microglial MEF2C expression and primary brain idiopathic autism datasets, suggesting a broader role of microglial MEF2C dysregulation in idiopathic autism especially as relates to the transcription factors repressive functions. Reduced MEF2C expression has been associated with brain aging, and we find that reduction in MEF2C leads to a premature aging or senescence associated phenotype in microglia.  These findings are extended to a murine xenotransplantation model wherein reductions in MEF2C expression in human microglia leads to an ameboid hyperinflammatory phenotype with lysosomal and lipid dysfunction. Taken together, these studies reveal novel aspects of microglial MEF2C function that contribute to homeostasis and development of neurological disease.

overall_design:
To investigate the effect of the in MEF2C genotype, we generated a cohort of we profile microglia differentiated from isogenic, CRISPR-modified MEF2C haploinsufficient and knockout induced-pluripotent stem cell (iPSC) lines. We additionally examined the expression profiles of monocytes in vitro for comparison.
We then performed gene expression profiling of these in vitro monocytes as well as ATAC-seq analysis. We then integrated this data with our exisiting MEF2C datasets.

first: Celina

last: Nguyen

first: Emily

last: Hansen

first: Cristina

last: Mora

first: Claudia

last: Han

first: Zahara

last: Keulen

first: Nathan

last: Spann

first: Jing

first: Gabriela

last: Ramirez

first: Samantha

last: Mak

last: Trescott

first: Mohammedparsa

last: Khakpou

first: Avalon

last: Johnson

first: Fatir

last: Qureshi

first: Michael

middle: R

last: La Frano

first: Kiana

last: Mohajeri

last: Talkowski

first: Olivia

last: Corradin

first: Marie-Eve

last: Tremblay

first: Christopher

middle: K

last: Glass

first: Nicole

last: Coufal


title: Transcriptional and epigenetic targets of MEF2C in human microglia contribute to cellular functions related to autism risk and age-related disease.

first: Anna

last: Warden

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

overall_design: Refer to individual Series


title: Transcriptional and epigenetic targets of MEF2C in human microglia contribute to cellular functions related to autism risk and age-related disease [ATAC-Seq]

overall_design:
To investigate the effect of the in MEF2C genotype, we generated a cohort of we profile microglia differentiated from isogenic, CRISPR-modified MEF2C haploinsufficient and knockout induced-pluripotent stem cell (iPSC) lines.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for transcription factor MEF2C as well as the histone modifications H3K27ac for acetylation and ATAC-seq in iPSC-derived microglia with different MEF2C genotypes--Control (+/+), haploinsufficient HET  (+/-) and knockout (-/-).

first: Celina

last: Nguyen

first: Emily

last: Hansen

first: Cristina

last: Mora

last: Han

last: Wang


title: Transcriptional and epigenetic targets of MEF2C in human microglia contribute to cellular functions related to autism risk and age-related disease [ChIP-Seq]

first: Claudia

first: Zahara

last: Keulen

first: Nathan

last: Spann

last: Ramirez

last: Mak

last: Trescott


title: Paternal microplastic exposure alters sperm small non-coding RNAs and elicits offspring metabolic dysfunctions in mice

first: Changcheng

last: Zhou

state: California

department: School of Medicine

institute: University of California, Riverside

summary: Microplastics (MPs) has been known for its toxicity on various organs and cells in humans, and its exposure leading to disease. Nevertheless, the toxic effects and underlying mechanisms on the profile of small non-coding RNAs (sncRNAs) in sperm, as well as their effects on embryo development, are not well understood. We recently developed the novel RNA sequencing (RNA-seq) technique, PANDORA-seq to overcome the limitations of traditional RNA sequencing. In this study, we elucidated the sncRNA changes using PANDORA-seq in mouse sperm after four weeks of oral gavage with MPs. We also examined the effects of sncRNAs on mouse embryonic stem cells (mESCs). MP exposure significantly altered sncRNA biogenesis-related genes in the testis and cauda epididymis, but not in the caput epididymis. PANDORA-seq revealed that a sncRNA landscape including transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs) in the sperm was changed by MPs gavage. Interestingly, transfections of changed sncRNA, tsRNA-Glu-CTC and 5S ribosomal RNA (5S rRNA), in mESC changed pluripotency, inflammation, and cardiovascular development related genes. In conclusion, exposure to MPs may alter the sncRNA profile in sperm, which could affect embryonic development and increase the risk of inheritable diseases such as atherosclerosis and metabolic disorders.

overall_design: To investigate the potential effects of MPs exposure on offspring health, 8-week-old male C57BL/6J WT mice were orally gavaged with either water or 10 mg/kg body weight/day of polystyrene microplastics (MPs, 1.1 μm mean particle size) for 4 weeks before mating with 12-week-old unexposed female WT mice. We profiled the sncRNA changes using PANDORA-seq in mouse sperm after 4 weeks of oral gavage with MPs to link the metabolic phenotype observed in F0 males with their offsprings. In addition, we also examined the effects of altered sncRNAs on mouse embryonic stem cells (mESCs).

first: Seung Hyun

last: Park

first: Jianfei

last: Pan

first: Xudong

last: Zhang

first: Ting-An

last: Lin

first: Sijie

last: Tang

first: Tong

first: Qi

last: Chen


title: Microplastic exposure promotes atherosclerotic lesion formation through endothelial dysfunction in LDL receptor-deficient mice

summary: Microplastics (MPs) have emerged as ubiquitous environmental contaminants due to widespread plastic use. However, whether MP exposure promotes atherosclerosis remains unclear. In this study, we investigated the atherogenic effects of MPs in low-density lipoprotein receptor-deficient (LDLR⁻/⁻) mice. We found that nine weeks of MP treatment significantly increased atherosclerotic lesion size in the aortic root of male LDLR⁻/⁻ mice. Single-cell RNA sequencing revealed that MP exposure promoted the formation of macrophage-like endothelial cells in the aorta. These findings highlight the potential cardiovascular risks of MP exposure and underscore its implications for both human and environmental health.

overall_design: We treated C57BL/6J LDLR⁻/⁻ mice fed a low-cholesterol diet (LCD) with 1 µm microplastics (10 mg/kg) for nine weeks and assessed atherosclerotic lesion size, macrophage content, and expression of inflammation-related genes. In addition, we performed single-cell RNA sequencing of the aorta to identify cell types and gene expression changes to elucidate the underlying mechanisms.

first: Qianyi

last: Ma

first: Matthew

last: Campen

first: Hong


title: H4K16ac and RNAPol2 CUT&Tag of Drosophila Melanogaster and Bacillus Grandii

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

institute: Institute of Molecular Biology (IMB)

summary: This experiment was designed to investigate the epigenetic basis of sex chromosome dosage compensation. Such mechanisms often operate through epigenetic modifications, including histone modifications, which alter chromatin structure and gene expression. In Drosophila melanogaster, dosage compensation is achieved by upregulating the single X chromosome in males through acetylation of histone H4 at lysine 16 (H4K16ac). We therefore used D. melanogaster as a positive control to validate our approach. In contrast, the mechanism of dosage compensation in Bacillus grandii remains unknown. By profiling H4K16ac in this species, we aim to test whether this histone modification may have been convergently recruited to mediate dosage compensation.

sample_organism:
Drosophila melanogaster
Bacillus grandii

overall_design: For D. melanogaster, CUT&Tag targeting H4K16ac was performed using five heads per sample for both males and females. For B. grandii, a single head per individual was used for each sample. In B.grandii, we profiled H4K16ac together with RNA polymerase II. Remark: In absence of an appropriate reference genome of Bacillus grandii we used NCBI genome assembly Brsri_v3 of Bacillus rossius redtenbacheri (GCF_032445375.1) as reference genome instead.

first: Frederic

last: Zimmer

first: Annika

last: Fox

first: Qiaowei

first: Peter

last: Andersen

first: Ann-Kathrin

last: Huylmans

first: Tanja

last: Schwander

first: M Felicia

last: Basilicata

middle: I

last: Keller Valsecchi


title: Identification of Upf2 and Upf3 targets in N. castellii using RNA-Seq

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Here, we performed total RNA-Seq in mutant strains of N. castellii lacking the NMD core factors Upf2 and Upf3, in order to identify lncRNAs and mRNAs that are regulated by NMD in this species.

overall_design: Strand-specific total RNA-seq in WT, upf2-delta & upf3-delta cells of N. castellii

first: Ugo

last: Szachnowski

first: Constance

last: Creux

first: Quentin

last: Fouilleul

first: Marina

last: Lefrère

first: Antonin

last: Morillon


title: Eomesodermin+ CD4 T cells are critical for curative immunotherapy outcomes

city: Brisbane

first: Kate

last: Gartlan

state: Queensland

address: 300 Herston Road

institute: QIMR Berghofer

summary: IL-10-producing CD4+ type-1 regulatory T cells (Tr1) promote immune tolerance during chronic infection, autoimmunity, and transplantation. However, specific Eomes-dependent stages of Tr1 differentiation and function remain unclear. Using preclinical models of bone marrow transplantation (BMT) and chimeric antigen receptor (CAR) T cell immunotherapy, we demonstrate a Tr1 differentiation trajectory in vivo from Eomes+IL-10– to Eomes+IL-10+ subsets with the acquisition of cytokine, cytolytic and exhaustion features. The Eomes+CD4+ fraction represents the dominant cytotoxic subset after BMT, mediating graft-versus-leukemia effects while limiting inflammation. In CD19-targeted CAR T cell immunotherapy, Eomes drives the same CD4+ Tr1 phenotype that controls cytolysis, whilst mitigating immune toxicity and promoting persistence. In patients receiving commercial CD19-targeted CAR T cells with long term disease control, Eomes+ Tr1 cells represent a stable population comprising 40-80% of the CD4+ CAR T cell population. Hence, Eomes controls both regulatory and cytotoxic programs in CD4+ T cells, essential for curative immunotherapy outcomes.

overall_design: B6D2F1 recipients were transplanted with TCD BM (5x10^6) and naive CD4+ T cells (0.5x10^6) from EomesmCherry/IL-10GFP donors. Spleens (n = 16) were taken on day +14 and pooled from every 4 mice leading to 4 replicate samples (rep 1-4) contaning 4 mice each.  CD4+ T cells were enriched with MACS selection and FACS sorted to P1 (Eomes- IL10-), P2 (Eomes+ IL10-) and P3 (Eomes+ IL10+) based on the expression of mCherry and GFP. The sort-purified cells were subsequently sent to Macrogen (Seoul, South Korea) for RNA sequencing.

first: Ping

last: Zhang

first: Shruti

last: Bhise

middle: H

first: Geoffrey

last: Hill


title: Transciptome profile of liver tissues from CD163KO mice after 8 weeks of Western diet.

city: Odense M

first: Jonas

last: Graversen

address: Campusvej 55

department: Health, IMM

country: Denmark

institute: University of Southern Denmark

summary: Liver macrophages have a high expression of the macrophage-specific scavenger receptor CD163 but during metabolic dysfunction-associated steatohepatitis (MASH) development CD163 undergoes increased shedding and downregulated expression in the liver in humans. Herein, we derived a hepatic-transcriptome based dataset to understand the development of early hepatic steatosis in CD163 knockout mice and their littermate controls.

overall_design: RNA-seq profiling of liver tissue obtained from C57BL/6NTac (CD163tm1(KOMP)Vlcg) mice after 8 weeks of chow (n=4-5 per genotype) or Western diet (n=15 pr. genotype).

first: Maria

last: Skytthe

first: Søren

last: Moestrup


title: Single-cell transcriptome combined with spatial transcriptome to investigate the molecular mechanism associated with autophagy of clear renal cell carcinoma

city: Fuzhou

first: Wu

last: Jiayue

state: Fujian

address: No. 134, Dongjie Street, Gulou District, Fuzhou City

institute: Fujian province hospital

summary: Background: There are no obvious diagnostic markers in the early stages of ccRCC and current targeted therapeutic regimens are susceptible to drug resistance. Our goal is to explore the molecular mechanisms associated with autophagy during the development of ccRCC and to identify molecular markers of prognostic value using scRNA-seq data in combination with stRNA-seq data. Methods: We performed single-cell sequencing of 6 ccRCC samples (3 tumours and 3 controls), stRNA-seq data from 12 samples (GSE175540), and bulk RNA-seq data from 614 patients (TCGA-KIRC). The cell subpopulations were artificial annotated, and the cell pathway activity were assessed. Autophagy-related genes(ARGs) obtained by intersecting autophagy databases with single-cell data and key clusters were identified using AUCell, Subsequent analyses included ligand-receptor interactions and SCENIC,. Combining single-cell genomics and spatial genomics, we used RCTD to visualise cell spatial distribution, analysed spatial cell interactions, studied cell trajectories using stLearn. Finally, identified prognostic-related genes and constructed a nomogram model using LASSO regression and AUCs, based on the risk score, divided into high- and low-risk groups and underwent immune infiltration analysis.. Additionally, we analysed the spatial distribution of prognostic genes. Results Through single-cell sequencing data, we manually annotated 14 cell subpopulations, with TAE being the key cluster. By cross-referencing with the autophagy database, we obtained 216 ARGs. Further CellChat analysis revealed complex interactions. The SCENIC analysis identified the top 5 regulons with the highest RSS scores (EGR1, DDIT3, IRF1, XBP1, and KLF4) and associated 204 transcription factors (TFs). Through spatial transcriptomics analysis, we further determined the cell distribution from a three-dimensional perspective and visualised the spatial dynamics during cell development, the MISTy indicated strong interactions between TAE, fibroblasts, and T cells. By combining ligand-receptor interaction analysis in single cells, we identified the MIF-(CD74+CD44) pathway as having the highest signal intensity, with colocalization indicating a strong correlation between the two. Finally, by analysing the TCGA-KIRC data, we developed a prognostic model based on nine genes (KLF6, UBE2S, PMAIP1, NFKBIZ, CES2, RCN1, C1S, SRSF2, and PKHD1). The high-risk group exhibited significantly poorer survival outcomes, and the spatial distribution of prognostic genes was also visualized. Conclusion: Our study offers new insights into the pathogenesis of autophagy-related clear cell renal cell carcinoma (ccRCC) and potential therapeutic targets.

overall_design: Three pairs of ccRCC tumor tissues and their matched normal tissues were collected. After dissociation with tissue digestion solution and lysis with red blood cell lysis buffer suspensions were obtained for scRNA-seq.

first: Jinfeng

last: Wu


title: Comprehensive architecture of the bacterial RNA Interactome

city: Amsterdam

first: Gaurav

last: Dugar

address: Science Park 904

department: Bacterial Cell Biology

institute: University of Amsterdam

summary: RNA-based regulation is ubiquitous in all microbes yet generating a global map of RNA–RNA interactions has been a formidable challenge. Here, TRIC-seq is introduced as an unbiased approach to map transcriptome-wide RNA–RNA interactions in several bacterial species. Applying TRIC-seq to Escherichia coli captured thousands of unique interactions, unveiling not only the targets of regulatory small RNAs (sRNAs) but also novel non-canonical regulatory interactions involving ribosomal RNAs, transfer RNAs, and messenger RNAs, including a widespread interaction between the 3’ extension of the 16S rRNA and the 5'UTRs of stress-response mRNAs. Unsupervised clustering of the interactome revealed a highly modular architecture, clustered by sRNA interactions. TRIC-seq is presented as a genetics-free approach that can be applied to any bacteria to de novo reveal regulatory RNAs along with their regulons at high specificity and resolution. TRIC-seq revealed a vast, functionally coherent cluster of mRNAs that aggregates and is excluded from ribosomes, providing compelling evidence for bacterial RNA condensates that share key properties with eukaryotic stress granules. TRIC-seq’s robust mapping provides a powerful platform to uncover RNA structures and generating foundational data for the next generation of biological models.

sample_organism:
Myxococcus xanthus
Stutzerimonas stutzeri
Escherichia coli
Staphylococcus aureus

overall_design: TRIC-seq of wild type microbes grown to stationary phase - E. coli, S. stutzeri, M. xanthus and S. aureus. TRIC-seq captures global RNA-RNA interactions in bacteria using a in-situ proximity ligation approach in bacteria


title: Single cell gene expression profile from mouse lung tissue

city: Ann Arbor

first: Jae-Won

last: Shin

address: 1011 N University Ave Room K1030, Ann Arbor, MI 48109

institute: University of Michigan

summary: The majority of the cells consist of immune cells. From lung tissue after repetitive bleomycin-induced fibrotic injury, followed by treatment with immune cloaking gel-coated mesenchymal stromal cells

overall_design: The cells were isolated by lung tissue digestion with enzyme mix from Tumor Dissociation Kit (#1119; Miltenyi), followed by filtration through 40-micron strainer and confirmation of cell viability above 90%. n = 2-3 mice were pulled for each group.

first: Ik-Sung

last: Cho

first: Amal

last: Yaghmour

first: Mark

last: Sanborn

first: Maria Paula

last: Zappia

first: Maxim V

last: Frolov

first: Jalees

last: Rehman


title: Mapping of Chromatin Architecture and Enhancer-Promoter Interactions in the Cochlea

city: Omaha

first: Litao

last: Tao

state: NE

address: 2500 California Plaza

institute: Creighton University

summary: Chromatin interactions, particularly those between promoters and distal enhancers, enable precise gene regulation in specialized tissues, like the cochlea in the inner ear. Disruptions in these long-range interactions between enhancers and gene promoters are linked to hereditary hearing loss. For many genes important to cochlear development and function, the distal regulatory elements that control their expression remain unknown. Identifying these elements and studying their regulatory roles is challenging due to their distance from target genes and the spatial complexity of chromatin architecture. To address this, we employed Micro-C, a high-resolution chromatin conformation capture technique that enables nucleosome-level mapping of chromatin interactions, to construct a cochlea-specific chromatin interaction map. We then integrated epigenomic and transcriptomic data to interpret enhancer-promoter interactions involved in gene regulation.

overall_design: Cochlea organs from P0/1 C57Bl/6 animals were disssected and dissociated for Micro-C, ATACseq, histone or CTCF Cut&Run

first: Tuba

last: Ege

first: Celia

last: Bloom

first: Mi

last: Zhou

first: Huizhan

last: Liu


title: Loss of miR-9-2 Causes Cerebral Hemorrhage and Hydrocephalus by Widespread Disruption of Cell-Type-Specific Neurodevelopmental Gene Networks

city: Seattle

first: Timothy

last: Cherry

state: WA

department: Developmental Biology and Regenerative Medicine

institute: Seattle Children's Research Institute

summary: MIR-9-2 is a broadly and highly expressed microRNA in the developing brain and is frequently deleted in 5q14.3 Microdeletion Syndrome, a rare but severe neurodevelopmental disorder. Despite this, little attention has been paid to the unique contributions of MIR-9-2 to neurodevelopment and disease. We find that deletion of this microRNA leads to embryonic cerebral hemorrhages and severe hydrocephalus, while disrupting gene networks across a wide range of cell types in the developing brain, thus revealing underappreciated and non-redundant molecular, cellular, and system-wide functions for MIR-9-2 in neurodevelopment.

overall_design: Following E2A-Cre germline deletion of miR-9-2 in Mir9-2tm1Mtm transgenic mice, embryonic day (E)12.5 and E16.5 cerebral cortices were harvested from homozygous knock-out and wild-type littermate controls for snRNA-seq processing and analysis.

first: Santiago

middle: P

last: Fregoso

first: Manith

last: Atapattu

first: Lulu

last: Callies

first: Deja

last: Monet

first: Amy

last: Leonardson

first: Lindsay

last: Clark

first: Stella

last: Xu


title: Low blood S-methyl-5-thioadenosine is associated with postoperative delayed neurocognitive recovery

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Elderly individuals display metabolite alterations that may contribute to development of cognitive impairment following surgery and anesthesia. However, these relationships remain largely unexplored. The study aims to assess the S-methyl-5-thioadenosine (MTA) is associated with postoperative delayed neurocognitive recovery (dNCR). We assess altered metabolites following anesthesia/surgery in both mice and patients to identify blood biomarkers of dNCR. Preoperative and postoperative plasma metabolites are determined by widely targeted metabolomics. The brains of mice with anesthesia/surgery show decreased MTA and activated MTA phosphorylase. Mice also show that preoperative administration of MTA can prevent inflammation and cognitive decline. In clinical patients, we detect lower preoperative serum MTA levels in those who developed dNCR. Both low preoperative and postoperative blood MTA levels are associated with increased risk of postoperative dNCR. These results suggest that anesthesia/surgery induces cognitive decline through methionine synthesis pathways and that MTA could be a perioperative predictor of dNCR.

overall_design: Control and sevoflurane anesthetized hippocampi of aged mice, followed by snRNA-seq.

first: Lei

last: Zhang

first: Haoli

last: Mao

first: Hong

last: Jiang

first: Jiao

last: Zhu

first: Zhenjie

last: Miao


title: Regulatory T cell stability determines the efficiency of bile duct regeneration during cholangitis.

city: Edinburgh

first: Wei-Yu

last: Lu

address: 4-5 Little France Drive

department: Institute for Regeneration and Repair

country: United Kingdom

institute: University of Edinburgh

summary: Cholangiopathies such as Primary Sclerosing Cholangitis (PSC) cause damage to the bile ducts and fibrosis with no effective cure. A reduction and impairment in the function of regulatory T cells (Tregs) occur in PSC. Yet, it is currently unknown what consequence this has on bile duct regeneration. We investigate whether Tregs regulate bile duct regeneration and the dynamics of Tregs turnover during bile duct injury. We used the transgenic Foxp3GFPDTR model to mimic reduced Tregs infiltration to the liver during bile duct injury and showed that reduced intrahepatic Tregs limits bile duct regeneration. Fate mapping of Tregs (Foxp3CreERTAi14) showed that Tregs acquire a pro-inflammatory phenotype within the inflammatory microenvironment, even after IL2 mediated Tregs expansion. Ox40L expression correlates with fibrosis in PSC patients. In the 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine (DDC)-diet mouse model of experimental cholangiopathy, combining IL2-complex administration and blocking Ox40L decreases periportal fibrosis level, increases Treg number and reduces the pro-inflammatory phenotype of Tregs. These results indicate that Tregs mediate cholangiocyte response to biliary injury, and Tregs downregulate Foxp3 and acquire an inflammatory phenotype in an inflammatory microenvironment. Enhancing Treg numbers through IL2 complex administration and blocking Ox40 signalling simultaneously suppress the inflammatory phenotype of Tregs and reduce bile duct damage and fibrosis.

overall_design: Bulk RNA sequencing of freshly isolated EpCAM+ cholangiocytes from transgenic Foxp3GFPDTR  mice which received DDC diet for 10 days. PBS / 1ug/kg Diphteria Toxin was given intraperitoneally  every 48 hours after the commence of DDC diet.

first: Naruhiro

last: Kimura

first: Man Chun

last: Wong


title: Dupilumab normalizes the eosinophilic esophagitis disease transcriptome

city: Tarrytown

first: Wei Keat

last: Lim

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

summary: Dupilumab, which blocks interleukin (IL)-4 and IL-13 signaling, is approved in eosinophilic esophagitis (EoE) and several other type 2 inflammatory diseases. We show that dupilumab normalizes the dysregulated esophageal transcriptome in pediatric, adolescent, and adult patients with EoE, including both eosinophil-related and eosinophil-independent biologic pathways.

overall_design:
Changes in the esophageal transcriptome were analyzed from pre- and post-treatment esophageal biopsies provided by patients with EoE who participated in one of three placebo-controlled clinical trials of dupilumab including pediatric, adolescent and adult patients.
This study includes RNA-seq data for 2887 samples.

Term definitions:

VISIT:
SCR: screening
EOT: end of treatment
ET: early termination
U1:  unscheduled
WK24: week 24
WK52: week 52

TREATMENT:
pbo: placebo
qw: weekly
q2w: every 2 weeks
lo: low-exposure
hi: high-exposure

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

first: Wei


title: JMJD3 and UTX as Key Targets for Gene-Modified Mesenchymal Stem Cell Therapy in Cartilage Tissue Engineering

city: Caen

first: Catherine

last: Baugé

address: Esplanade de la paix

institute: Université de Caen Normandie

summary: Histone methylation plays a critical role in cartilage development, making it an appealing target for improving cartilage engineering protocols. In this study, we evaluated the roles of JMJD3 (KDM6B) and UTX (KDM6A), both demethylases of histone H3 at lysine 27 (H3K27), in chondrogenesis and their application in gene-modified mesenchymal stem cell therapy for cartilage tissue engineering. Our findings revealed that JMJD3 is specifically upregulated during chondrogenesis in hBM-MSC, and is crucial for this differentiation process. In contrast, UTX was found to be dispensable for chondrogenesis. Nevertheless, both JMJD3 and UTX share the ability to demethylate similar gene loci, thereby promoting the expression of chondrogenic signature genes, which suggests functional redundancy. Notably, the genes encoding these H3K27me3 demethylases emerge as strong candidates for enhancing gene-modified mesenchymal stem cell therapy for cartilage tissue engineering, as their overexpression during chondrogenesis significantly increased the formation of thicker cartilage discs enriched with type II collagen. These findings emphasize the potential of transient JMJD3 transduction, along with a lesser emphasis on UTX, as effective strategies for improving gene-modified mesenchymal stem cell therapy in cartilage tissue engineering.

overall_design: ChIP-seq of H3K4me3 and H3K27me3 in human bone marrow-derived mesenchymal stem cells. Cells were collected from 2 different patients.

first: Lyess

last: Allas

first: Juliette

last: Aury-Landas

first: Quitterie

last: Rochoux

first: Anais

last: Julien

first: Eva

last: Lhuissier

first: Marion

last: Lenté

first: Sybille

last: Brochard

first: Alexis

last: Veyssiere

first: Karim

last: Boumédiene


title: Novel molecular signatures of peripheral Regulatory T Cells in Kidney Disease associated with Type 1 Diabetes

city: Campbelltown

first: Mugdha

middle: V.

last: Joglekar

state: NSW

address: Cnr Goldsmith and David Pilgrim Ave

institute: Western Sydney University

summary: Diabetic kidney disease (DKD) is a common complication of type 1 diabetes (T1D). T1D and some kidney disorders are often associated with abnormalities in regulatory T cells (Tregs). However, it is unknown if Treg subsets, and their molecular architecture are altered during the onset and progression of DKD in T1D. We addressed this critical knowledge gap by characterising changes in Tregs isolated from 31 participants (10 control, 13 with T1D, and 8 T1D with albuminuria) using flow cytometry, RNA-sequencing, and microRNA profiling. We identified that the effector and central memory Tregs were significantly different between groups. Similarly, multiple gene transcripts were also significantly different between groups that also overlapped with other publicly available datasets. Machine-learning based data analyses discovered a set of important microRNAs associated with clinical eGFR values. Importantly, our analyses identified two differentially expressed Treg ligand genes (LRRC4B, TGM2), which interacted with the receptors on kidney cells (PTPRD/F/S, ADGRG1) in silico, providing potential mechanistic insights into the role of Tregs in DKD progression. Together, our work supports the yet unappreciated role of Tregs in DKD and opens new research avenues to further consolidate their causal relationship.

overall_design: RNA-seq data on Treg cells samples from donors which do not have diabetes, have Type 1 Diabetes (T1D) without albuminuria, or have T1D with albuminuria.

first: Amita

last: Bansal

first: Soon Wei

first: Wilson KM

first: Giles

last: Best

first: Steven

last: James

first: Sarah

last: Glastras

first: Alexia

last: Pena

first: Cheng Xue

last: Qin

first: Sih Min

last: Tan

first: Devy

last: Deliyanti

first: Darling M

last: Rojas-Canales

first: Mugdha V

first: Elif I

last: Ekinci


title: Fibroblast-directed melanocyte recruitment via Cxcl12-Cxcr4 cascade promotes post-inflammatory hyperpigmentation and skin barrier protection in zebrafish

city: Shenzhen

first: Zhao

last: Shizheng

address: Shenzhen

department: LIFS

institute: Undefined

summary: Post-inflammatory hyperpigmentation (PIH), a prevalent dermatological condition, is classically attributed to melanocyte overactivation in situ. However, the precise triggers and physiological significance of melanocyte responses remain elusive. Using an acetic acid corrosion-induced zebrafish PIH model, here we demonstrate that  melanocyte migration to the inflammatory site is a key pathogenic driver of hyperpigmentation. This migration is  largely orchestrated by fibroblasts, but not macrophages or neutrophils, which secrete the chemokine cxcl12a upon injury, recruiting melanocytes via the cxcl12a-cxcr4a signaling axis. Beyond hyperpigmentation, we reveal that melanocytes function as a dual protective barrier against both UV-induced DNA damage and microbial invasion in response to acetic acid corrosion-induced injury. Our findings provide new insights into PIH pathogenesis and uncover the non-canonical barrier functions of melanocytes in skin inflammation and repair.

overall_design: In this experiment, we have conducted acetic acid corrosion in four trunk sites in 2 dpf embryos,cut the trunk region at 3 dpf, dissociated the embryos into single cell suspension and performed FACS sorting of dsRed positive fibroblasts. In each biological replicate, around 30 embryos were harvested and 500 fibroblsts were sorted into lysis buffer. Smartseq2 protocol was utilized for double strand cDNA library construction.

first: Shizheng

last: Zhao


title: Transcriptomic profiling of DYT-TOR1A patients-derived iPSC reveals dysregulation in extracellular matrix, lipid metabolism, and Chr22q11.23

city: London

first: Nuria

last: Seto-Salvia

address: 1 Wakefield St

department: Clinical and Movement Neuroscience

institute: UCL Queen Sq Institute of Neurology

summary: DYT-TOR1A is an early-onset generalised movement disorder characterised by involuntary muscle contractions, leading to abnormal postures and repetitive movements. The trinucleotide GAG in-frame deletion (ΔGAG) in the TOR1A gene is the most common Mendelian form of dystonia. The TOR1A gene encodes for TorsinA protein, involved in several molecular functions, including chaperone activity, protein quality control, synaptic vesicle recycling, vesicular trafficking, protein folding, homeostasis of the nuclear envelope integrity, and lipid metabolism. There is increasing evidence that DYT-TOR1A dystonia is a neurodevelopmental disorder, beginning in the period where structural and functional abnormalities manifest early in physiological maturation. Recent publications have highlighted the importance of the extracellular matrix and lipid metabolism in dystonia, processes important to cellular neurodevelopment. In is study we aimed to elucidate the gene expression profiles of mutant DYT-TOR1A patient-derived iPSCs to identify key pathways and differentially expressed proteins involved in the early stages of neurodevelopment. Our goal was to identify key molecular pathways and regulatory networks involved in early neurodevelopment that may be disrupted in the presence of the ΔGAG mutation. Through differential gene expression analysis, we sought to uncover potential alterations related to extracellular signalling, lipid homeostasis, and nuclear regulatory mechanisms. This study aims to advance our understanding of the early developmental mechanisms underpinning DYT-TOR1A dystonia and provide a foundation for further investigation into disease-specific molecular targets.

overall_design: RNA-seq profiling of induced pluripotent stem cells of symptomatic patients of DYT-TOR1A dystonia and healthy controls.

first: Núria

last: Setó-Salvia

first: Henry

last: Houlden

first: Thomas

middle: T

last: Warner


title: UPF1-dependent glycolysis driven by LINC00887 facilitates macrophage M2 polarization in clear cell renal cell carcinoma

first: Wu

last: Jiayue

summary: Clear cell renal cell carcinoma (ccRCC), a frequent urinary system tumor, is known for its poor patient outcomes. Here, we demonstrate that LINC00887 overexpression in ccRCC drives M2 macrophage polarization via aerobic glycolysis activation and lactate accumulation. Mechanistically, LINC00887 interacted with UPF1, leading to reduced UPF1 levels. UPF1, which is low in ccRCC, restrained cell vitality, proliferation, migration, invasion, and cell cycle progression in ccRCC cells, and stimulated apoptosis. Additionally, UPF1 was found to be negatively correlated with aerobic glycolysis in ccRCC, repressing glycolytic activity and M2 macrophage polarization while bolstering the tumor-killing potential of CD8+ T cells. By combining bioinformatics with experimental data from ccRCC single-cell RNA sequencing, we've demonstrated that reduced UPF1 expression can reprogram glycolytic metabolism, leading to an improved immunosuppressive tumor microenvironment.

overall_design: Two pairs of pathologically confirmed ccRCC tumor tissues and their matched normal tissues were collected.After dissociation with tissue digestion solution and lysis with red blood cell lysis buffer, suspensions were obtained for scRNA-seq.

first: Jinfeng

last: Wu


title: Small cell lung cancer induces synaptic scaling to alter neuronal excitability

city: Nashville

first: Ege

last: Kavalali

state: TN

address: 465 21st Avenue South, 7130A MRBIII

department: Pharmacology

institute: Vanderbilt University

summary: Tumor cell plasticity in novel microenvironments is central to the integration and subsequent growth of metastatic cells. However, the functional consequences of tumor cell integration with central neurons remains understudied. Here, we address this question using small cell lung cancer (SCLC), which has an extraordinary propensity to metastasize to the brain in humans. Transcriptomic and electrophysiological analysis of SCLC cells in neuronal microenvironments reveal a predilection for GABAergic synapse formation between neurons and a subset of adjacent SCLC cells. This functional integration of SCLC with central neurons induces multiplicative synaptic upscaling and dysregulated neuronal excitability. Aberrant excitation in human neurons with SCLC is sustained by synaptic NMDA receptor activation and can be reduced by the FDA approved NMDA receptor blocker memantine. These findings reveal strategies to normalize tumor-induced exacerbation of aberrant neuronal activity.

overall_design: The following samples were generated and analyzed using scRNA-seq:  1) cerebral organoids alone, 2) NCI-H69 cells grown as 2D cell lines, and 3) NCI-H69 cells grown within cerebral organoids.  Samples were processed through the particle-templated instant partition sequencing (PIP-seq) platform using Fluent Biosciences' PIPseqTM T2 3' Single Cell Capture and Lysis Kit v2.0.  cDNA libraries were sequenced on an Illumina NovaSeq 6000 instrument at Vanderbilt University.

first: Aiden

last: Houcek

first: Burak

last: Uzay

first: Geena

last: Ildefonso

first: Tolu

last: Omokehinde

first: Lisa

last: Monteggia

first: Vito

last: Quaranta

first: Amanda

last: Linkous


title: Transcriptome analysis of Aoham4 and Aoham8 in nematode-trapping fungus Arthrobotrys oligospora

city: Kunming City, Yunnan Province

first: Liu

last: Qianqian

address: No.2 Cuihu North Road, Wuhua District

institute: Yunnan University

summary: Transcriptomic analysis revealed that differentially expressed genes in the absence of Aoham4 and Aoham8 were involved in  carbohydrate metabolism, amino acid metabolism, lipid metabolism, transport and catabolism, energy metabolism, and translation.

overall_design: Examination of differential genes in the WT, ΔAoham4 and ΔAoham8 mutant strains and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Qian-qian

last: Liu

first: Jin-kui

last: Yang


title: Highly-conserved lncRNAs regulates the BRCA1 locus under broad-stress responses [RNA-Seq]

city: Cuernavaca

first: Mario

last: Zurita

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: Instituto de Biotecnología - UNAM

summary: RNA polymerase II inhibition triggers a cellular stress response that paradoxically leads to the overexpression of certain transcripts. To investigate the underlying mechanism, we conducted genome-wide assays in human cells treated with triptolide, which disrupts the translocase/DNA helicase activity of XPB, part of TFIIH. Our analysis revealed that XPB activity-independent transcription of genes originate from thermodynamically unstable promoters. Among the upregulated genes, we identified three novel regulatory lncRNAs—TILR-1, TILR-2, and LINC00910 that are highly conserved among primates. Their expression is interdependent, and together, they regulate the nearby BRCA1 locus transcription. We observed that this network of transcripts is also activated in other stress responses, like heat shock and arsenic. We suggest that the BRCA1 locus and its lncRNAs regulators are part of a transcriptional switch that respond to broad stress conditions.

overall_design: RNA-seq in K562 cells treated with 250 nM of triptolide or DMSO during 4 hours

first: Samantha

last: Cruz-Ruiz

first: Raphael

last: Vidal

first: Mayra

last: Furlan-Magaril

first: John

last: Lis


title: Highly-conserved lncRNAs regulates the BRCA1 locus under broad-stress responses [ChIP-exo]

overall_design: ERCC3 ChIP-exo in K562 cells treated with 1 micromolar of triptolide or DMSO during 1 hour


title: Highly-conserved lncRNAs regulates the BRCA1 locus under broad-stress responses [PRO-seq]

overall_design: PRO-seq in K562 cells treated with different triptolide concentrations or DMSO


title: Highly-conserved lncRNAs regulates the BRCA1 locus under broad-stress responses [s]

overall_design: H3K27ac CUT&Tag in K562 cells treated with 250 nM of triptolide or DMSO during 4 hours


title: 3D genome of CD8+ T cells reveals IRF8-mediated exhaustion in cancer [Hi-C]

city: Beijing

first: Ruifeng

last: Li

address: haidian

institute: Tsinghua University

summary: CD8+ T cell responses are essential for anti-tumor immunity, but chronic antigen exposure in cancer can lead to T cell exhaustion, marked by high PD-1 expression. Recent studies have identified progenitor-like CD8+ T cells (Tprog cells) within tumor-infiltrating lymphocytes (TILs) that sustain antitumor responses. These cells can differentiate into terminally exhausted cells (Tterm cells), losing their proliferative and effector functions. Immunotherapy aims to enhance CD8+ TILs functionality, promoting their transition from Tprog to Tterm cells. However, the mechanisms behind this exhaustion remain unclear. Single-cell RNA sequencing and ATAC-seq have revealed distinct profiles and chromatin accessibility between progenitor and terminally exhausted states. Histone modifications predict a loss of enhancer-promoter contacts during this transition. Chromatin structure plays a crucial role in T cell differentiation. We constructed a high-resolution 3D genome map of CD8+ T cell subsets and, through multi-omics integration, identified chromatin structure changes linked to T cell exhaustion, including alterations in topologically associating domains (TADs) and chromatin loops, providing new insights into the genetic basis of CD8+ T cell exhaustion in cancer.

overall_design: To investigate the role of CTCF in CD8⁺ T cell chromatin organization, we performed CRISPR-Cas9-mediated Ctcf knockout in CD8⁺ T cells isolated from Rosa26-Cas9 × OT-I transgenic mice. A single-guide RNA targeting Ctcf(forward: 5′-CACCGGATGAAGACTGAAGTCATGG; reverse: 5′-AAACCCATGACTTCAGTCTTCATCC) was cloned into a pWKO retroviral vector carrying an IRES-BFP cassette. Retrovirus was produced by co-transfecting the sgRNA vector and pCL-ECO into Phoenix cells using calcium phosphate, and supernatants were collected after 48 h. FACS-sorted naïve CD8⁺ T cells were activated with anti-CD3/CD28 for 48 h and transduced with retrovirus via spinfection. Control (Empty, PB⁺) and Ctcf-knockout (FITC⁺) cells were mixed 1:1 and transferred into Tcrb⁻/⁻ mice one day before E.G7 tumor implantation. On day 17, tumor-infiltrating exhausted CD8⁺ T cells were sorted and analyzed by in situ Hi-C.

first: Chen

last: Dong


title: 3D genome of CD8+ T cells reveals IRF8-mediated exhaustion in cancer [RNA-seq]

summary: Exhausted CD8+ T cell differentiation is accompanied by extensive changes in epigenome. However, whether and how higher-order chromatin organization is involved in exhausted CD8+ T cell differentiation is unclear. Here, we showed extensive changes in the three-dimensional genome during exhausted CD8+ T cell differentiation, associated with changes in gene transcription. Moreover, we identified Interferon regulatory factor 8 (IRF8) as an essential transcription factor in re-organization of spatial chromosomal interactions. Irf8 deficiency inhibits the development of terminal exhausted CD8+ T cells and promotes tumor growth. Mechanistically, IRF8 bound to genes associated with exhausted CD8+ T cells differentiation and promoted the formation of chromosomal loops. At the loop anchor regions, IRF8 recruited CTCF to form active chromosomal structure to regulated exhaustion-associated genes. These results thus identify a critical role of IRF8-dependent chromatin topology in gene transcription during exhausted CD8+ T cell differentiation.

overall_design: To assess transcriptional changes associated with IRF8 deficiency in CD8⁺ T cells, 2.5 × 10⁶ FACS-sorted naïve CD45.1/2 wild-type (WT) and CD45.2 Irf8⁻/⁻ P14 CD8⁺ T cells were mixed at a 1:1 ratio and intravenously transferred into CD45.1 congenic recipient mice one day prior to infection with LCMV clone 13. On day 25 post-infection, splenic CD8⁺ T cells were isolated by FACS based on CD45 allelic markers. Total RNA was extracted using TRIzol reagent, and RNA integrity was verified using a Bioanalyzer (Agilent). RNA-seq libraries were prepared using a stranded mRNA-seq kit (e.g., NEBNext Ultra II) and sequenced on an Illumina platform to a depth of ~30 million paired-end reads per sample.


title: Presenilin Ablation in Cholinergic Neurons Induces Accelerated Aging and Systemic Inflammation Insights from ChAT-PS-DKO Mice

city: Shanghai

first: Youwen

last: Si

address: North Zhongshan Road Campus: 3663 N. Zhongshan Rd., Shanghai

institute: East China Normal University

summary: To uncover the underlying causes of cellular senescence observed in 2-month-old DKO mice, expression profiling microarrays were used to analyze gene expression in the cortex and basal forebrain of 2-month-old DKO mice and control mice.

overall_design: Total RNA was isolated from the basal forebrain and cerebral cortex of three 2-month-old control (Con) mice and three 2-month-old double knockout (DKO) mice. Gene expression profiling was conducted using the Agilent SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (Design ID: 074809) at OE Biotech Co., Ltd. (Shanghai, China).


title: The influence of cohesin on the short-scale dynamics of intact and damaged chromatin in different phases of the cell cycle

city: Moscow

first: Vladimir

last: Viushkov

address: 1-12 Leninskie Gory

department: Faculty of Biology, Department of Molecular Biology

country: Russia

institute: Lomonosov Moscow State University

summary: Cohesin organizes the genome into spatially segregated loops and topologically associated domains by loop extrusion. In addition, it ensures cohesion of sister chromatids after replication. Thus, cohesin is expected to limit chromatin dynamics by ensuring cohesion and compacting chromatin in the interphase. Nonetheless, loop extrusion is an example of chromatin dynamics; thus, cohesin could promote the dynamics of genomic loci at the scale of individual loops and contact domains. Moreover, given that the extruding activity of cohesin after replication is supplemented by its cohesive activity, the impact of cohesin on chromatin dynamics in different phases of the cell cycle may vary. Of particular interest is the cohesin’s role in the regulation of the dynamics of damaged chromatin, which remains insufficiently studied. Here, we visualized a genomic locus using the CRISPR-Sirius system in human cells with auxin-induced depletion of the cohesin subunit RAD21. Cohesin depletion increased the local spatial dynamics of the visualized locus on a time scale of fractions of a second to one minute. This effect was observed in both replicated and unreplicated chromatin. However, the increase in the mobility of the visualized locus upon cohesin depletion was more pronounced in the former. In addition, we showed that cohesin depletion did not affect the local mobility of double-strand break repair foci visualized using a fluorescent fragment of the repair factor 53BP1. Cohesin depletion did not affect the local mobility of repair foci in either replicated or unreplicated chromatin. The results indicate that cohesin constrains local spatial dynamics of genomic loci. At the same time, cohesive activity of cohesin is not indispensable for restricting chromatin dynamics, although it enhances the confinement effect. On the other hand, repair foci are less mobile structures than point chromatin loci, and cohesin does not affect their dynamics on the studied time scales.

overall_design: ChIP-Seq of RAD21 in untreated wild-type HCT116 cells, as well as in HCT116 cells with auxin-inducbile depletion of RAD21. In later case, two conditions were analyzed - untreated cells and cells treated with a combination of indole-3-acetic acid and alpha-naphthaleneacetic acid for 6 hours.

first: Anastasia

last: Shtompel

first: Sergey

last: Ulianov


title: Expression profile of cassava shoot under heat and cold stress conditions using no-amplification non-tagging CAGE-seq

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

summary: This study provides nAnT-iCAGE-seq data from cassava (Manihot esculenta) exposed to 42°C (heat), 4°C (cold), and control conditions. The dataset includes raw sequencing reads, processed transcription start site (TSS) profiles, and annotations for alternative promoter genes (APGs) and differentially expressed genes (DEGs). Data were generated using Illumina 2000/2500 platforms.

overall_design: nAnTi-CAGE-seq profiling of cassava shoots (ECU72 and KU50 cultivars) under control (25°C), heat (42°C), and cold (4°C) treatments for 5 hours.

first: Ezoe

last: Akihiro

first: Utsumi

last: Yoshinori

first: Sakurai

last: Tetsuya

first: Takahashi

last: Satoshi

first: Takeda

last: Tomoyuki

first: Todaka

last: Daisuke

first: Ogawa

last: Yutaka

first: Ueda

last: Minoru

first: Ishida

last: Junko

first: Tanaka

last: Maho

last: Chikako

first: Motoaki

last: Seki


title: Prostaglandin E2 stimulates opposing effects on inner and outer blood-retina barrier function

first: Amy

middle: Kathryn

last: Stark

summary: Diabetic retinopathy (DR) is the leading cause of vision loss in working-age individuals globally, and the associated complication of diabetic macular edema (DME) is the most frequent cause of vision loss in these patients. The retinal swelling characteristic of DME can be attributed to fluid leakage due to damage to the two blood-retina barriers—the inner barrier composed primarily of retinal microvascular endothelial cells and the outer barrier composed of retinal pigment epithelial cells (RPE). Based on the previously characterized proinflammatory roles of prostanoid signaling in DR, we assayed the distinct prostanoid signaling mechanisms regulating inner and outer blood-retina barrier function using in vitro methods involving monoculture of primary human cells. Prostaglandin E2 (PGE2) stimulation of retinal endothelial monolayers caused a decrease in barrier permeability in electric cell-substrate impedance sensing (ECIS) assays and dextran flux assays. These effects occurred specifically via the EP4 receptor of PGE2. In direct contrast, PGE2 stimulation of RPE monolayers caused an increase in barrier permeability via the EP2 receptor. Other prostanoids did not alter barrier permeability in either monocellular model. RNA sequencing of retinal endothelial and RPE cells with or without PGE2 stimulation revealed significant dysregulation of genes encoding junctional complex components and signaling that likely drive the observed effects on cell barrier resistance. Together these results identify opposing mechanisms of PGE2 signaling in the retina via two distinct receptors, indicating cell type-specific and receptor-specific targets for the potential therapeutic management of DME or other causes of dysfunctional retinal vascular permeability.

overall_design: RNA-seq profiling of human retinal microvascular endothelial cells (hRMEC) and human retinal pigment epithelial cell line ARPE-19 cells stimulated with 100 nM prostaglandin E2 (PGE2) or DMSO vehicle for 6 hours

first: Anna

last: Gilmartin

first: Cayla

last: Ontko

first: Taylor

middle: E

last: Smith

first: Amanda

middle: L

last: Beall

first: Gary

middle: W

last: McCollum

first: John

last: Penn


title: Pseudogenes contribute to the evolution of topological domains across species via forming three-dimensional genome [RNA-Seq_mouse]

first: Liu

last: He

address: No. 5, Dongdan Sanjo, Dongcheng District

institute: Peking Union Medical College

summary: The human genome harbors 15,000 pseudogenes, except very few can transcribe non-coding RNAs or encode truncated proteins, a large number of which without transcriptional capacity are functionally unknown. Here, we proposed and verified that pseudogene DNA sequences can form chromatin contacts that act as anchors of chromatin loops and boundaries of topologically associating domains (TADs). More amazing, due to the sequence-specificity of pseudogenes, TAD boundaries containing them in the human genome were primarily species-specific, including human-specific and primate-specific ones. We found that during primate evolution, by inheritance from parent genes, certain pseudogenes can introduce additional transcription factor-binding sequences, especially CTCF, at their insertion sites to generate species-specific TAD boundaries, and due to the participation in TAD evolution, CTCF binding motifs on pseudogenes were subjected to significantly heightened selection pressure. Deleting these pseudogenes in human embryonic stem cells (hESCs) disrupted the structure of species-specific TADs, whereas inserting them in mouse embryonic stem cells (mESCs) mediated new TADs formation, and pseudogenes involved in three-dimensional (3D) genome formation were critical for maintaining hESCs self-renewal. The structural necessity and biological function of these pseudogenes demonstrated the broad significance of pseudogenes in 3D genome construction and evolution.

overall_design: Two mouse embryonic stem cells (mESCs) knock-in (KI) cell lines were obtained for each of the two pseudogenes, AC106872.1 and KRT18P67. KRT18P67-KI-C4, KRT18P67-KI-B5, AC106872.1-KI-B9, AC106872.1-KI-D11, and wild-type (WT) mESCs were subjected to Hi-C sequencing. To find out how insertion of pseudogenes influence gene expression in mESCs, we also performed RNA-seq for WT, KRT18P67-KI and AC106872.1-KI mESCs, each with two replicates. We also performed Hi-C in KRT18P37 knock-out human embryonic stem cells (hESCs) with two replicates.

first: Mengyao

last: Sun


title: Pseudogenes contribute to the evolution of topological domains across species via forming three-dimensional genome [mESC_KI_Hi-C]


title: Visomitin attenuates pathological bone loss by reprogramming osteoclast metabolism via STAT3/LDHB axis

city: Hangzhou

first: Putao

last: Yuan

address: No. 3, Qingchun Road East

department: Department of Orthopaedic Surgery

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine

summary: A persistently substantial energy demand and metabolic reprogramming endure throughout the entire course of osteoclastogenesis, accompanied by an intensified oxidative stress. Hence, balancing cellular energy metabolism and mataining redox homeostasis offers potential for coordinating osteoclastogenesis and bone loss in pathological conditions. In the present study, we have discovered Visomitin, a novel antioxidant that specifically targets mitochondria, which efficiently decreases intracellular reactive oxygen species levels, inhibits osteoclastogenesis, and impairs bone resorption.

overall_design: BMMs were cultured under osteoclastic differentiation conditions for 5 days, either in the presence or absence of Visomitin treatment. Subsequently, the samples were subjected to transcriptome RNA-seq.

first: Peihua

last: Shi

first: Zhenhua

last: Feng

first: Haotian

last: Yang

first: Hong

last: Xue

first: Ziang

last: Xie

first: Xuewu


title: Pseudogenes contribute to the evolution of topological domains across species via forming three-dimensional genome [hESC_KO_Hi-C]


title: Liver single-nucleus multiome profiling reveals cell-type mechanisms for cardiometabolic traits

city: Chapel Hill

first: Karen

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Genome-wide association studies (GWAS) have identified numerous genetic variants associated with cardiometabolic traits, yet their mechanisms in relevant liver cell types remain unclear. Using multiome single-nucleus RNA and ATAC sequencing on liver samples from 39 individuals, we profiled gene expression and chromatin accessibility in 68,398 nuclei across six primary liver cell types. We identified 306,706 accessible chromatin regions, including 70,884 regions undetected in bulk tissue analyses, predominantly representing less abundant cell types. By mapping quantitative trait loci (QTLs), we detected 1,885 chromatin accessibility QTLs (caQTLs) and 67 expression QTLs (eQTLs), highlighting genetic regulation in the different liver cell types. We integrated cell-type QTLs with GWAS signals and revealed cell-types, genes, and chromatin regulatory elements involved in cardiometabolic traits, such as liver enzymes and cholesterol levels. Importantly, non-hepatocyte cell-type QTL analyses elucidated previously obscured mechanisms, such as an eQTL for ADAMTS12 in liver sinusoidal endothelial cells potentially involved in liver fibrosis, demonstrating how single-nucleus approaches capture regulatory events missed in bulk analyses. Furthermore, we annotated bulk liver caQTLs colocalized with GWAS signals to liver cell types, enhancing functional interpretations and predicting cell-type of action for complex trait associations. Our findings provide a comprehensive, high-resolution map of the hepatic regulatory landscape, advancing the understanding of cellular contexts and molecular mechanisms underlying cardiometabolic diseases.

overall_design: 10x Chromium Single Cell Multiome ATAC + Gene Expression performed on frozen liver tissue from 39 human donors

first: Abdalla

middle: A

last: Alkhawaja

first: Kevin

last: Currin

first: Hannah

last: Perrin

first: Swarooparani

last: Vadlamudi

middle: S

last: Etheridge

first: Kelsy

last: Broadaway

first: Gabrielle

last: Cannon

first: Carlton

last: Anderson

first: Anne

last: Moxley

first: Erin

last: Schuetz

first: Federico

last: Innocenti

first: Terrence

last: Furey


title: Mapping Hap2/Hap3/Hap5 binding sites in yeast using CPD-seq data

city: Pullman

first: John

middle: J.

last: Wyrick

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: Here, we used the cyclobutane pyrimidine dimer-sequencing (CPD-seq) method to map UV damage footprints associated with transcription factor binding to DNA in yeast. We analyzed CPD-seq data from UV-irradiated wild-type yeast cells that were immediately isolated and analyzed (0hr time point) and compared these data to isolated yeast genomic DNA that was UV-irradiated in vitro (naked DNA control). We analyze these data with a machine learning algorithm to identify binding sites of the Hap2/Hap3/Hap5 transcription factor complex across the yeast genome, based on their UV damage footprint. As a control, we UV-irradiated hap5 mutant cells, which renders the complex unable to bind DNA, and mapped UV damage patterns using CPD-seq.

overall_design: We used the CPD-seq method to map UV-induced cyclobutane pyrimidine dimers (CPDs) at single-nucleotide resolution across the yeast genome, both immediately after UV-irradiation of yeast cells (0hr) and in isolated yeast genomic DNA that was UV-irradiated in vitro.

last: Wilson