title: Meiotic prophase I disruption as a strategy for non-hormonal male contraception using small-molecule inhibitor JQ1

city: Ithaca

first: Paula

last: Cohen

address: 618 Tower Rd

institute: Cornell University

summary: The small-molecule bromodomain inhibitor JQ1 transiently suppresses spermatogenesis by targeting BRDT, a testis-specific transcriptional regulator required for meiotic and post-meiotic differentiation. To define the transcriptional and cellular consequences of JQ1 exposure and recovery, we performed single-cell RNA sequencing (scRNA-seq) of mouse testes collected from untreated controls, JQ1-treated males, and recovery cohorts following treatment withdrawal. This dataset includes 15 libraries representing all experimental groups and captures germ cell and somatic populations spanning spermatogonial, meiotic, and spermiogenic stages. The data provide a comprehensive transcriptional atlas of JQ1-induced meiotic disruption and subsequent restoration of spermatogenesis, supporting mechanistic and contraceptive studies of BRDT inhibition.

overall_design: Adult male DBA/2J mice were administered the bromodomain inhibitor JQ1 (50 mg/kg daily, 3 weeks, intraperitoneal) or vehicle control. Testes were collected from (i) untreated controls (UC), (ii) vehicle-treated controls (VC-T), (iii) JQ1-treated males at endpoint (T), and (iv) recovery cohorts (R, VC-R) 6 weeks post-withdrawal (R). Single-cell suspensions were prepared from individual testes, and libraries were generated using the 10x Genomics Chromium 3′ v3.1 platform. Sequencing was performed on an Illumina NovaSeq 6000. After Cell Ranger processing and quality control, 15 libraries (3 biological replicates per condition) were retained for downstream integration and analysis using Seurat. The dataset supports examination of JQ1-induced transcriptional changes, germ cell population dynamics, and recovery kinetics.

first: Stephanie

last: Tanis


title: Meiotic prophase I disruption as a strategy for non-hormonal male contraception using small-molecule inhibitor JQ1 [RNA-seq]

status: Public on Mar 23 2026

country: USA

type: Expression profiling by high throughput sequencing

overall_design: Adult male DBA/2J mice received the bromodomain inhibitor JQ1 (50 mg/kg, intraperitoneal, once daily for 3 weeks) or vehicle control. Testes, liver, and kidney were collected to profile both immediate and post-withdrawal effects. Testis single-cell RNA-seq (scRNA-seq) was generated from five cohorts: (i) untreated controls (UC), (ii) vehicle-treated controls at the treatment endpoint (VC-T), (iii) JQ1-treated at the treatment endpoint (T), and recovery cohorts 6 weeks post-withdrawal—(iv) JQ1 recovery (R) and (v) vehicle-treated recovery (VC-R). For scRNA-seq, single-cell suspensions from individual testes were processed with the 10x Genomics Chromium 3′ v3.1 workflow and sequenced on an Illumina NovaSeq 6000; after Cell Ranger QC, 15 libraries (3 biological replicates per cohort) were retained and integrated in Seurat for downstream analyses of JQ1-induced transcriptional changes, germ-cell population dynamics, and recovery kinetics. In parallel, bulk RNA-seq was performed on liver and kidney (n = 10 samples per organ: 3 treatment, 3 recovery at 6 weeks post-withdrawal, and 4 controls comprising untreated and vehicle-treated samples) to assess systemic transcriptional responses and reversibility outside the reproductive tract.


title: Comprehensive analysis of non-tumor lung, liver, and kidney transcriptomes in metastatic osteosarcoma

city: Bethesda

first: Anjali

last: Garg

state: Maryland

address: Building 10, Room 1B53

department: Comparative Oncology Program,NCI

institute: National Institute of Health

summary: Landscape of the peritumoral TME of metastatic osteosarcoma and further underscore the translational relevance of the canine patient as a model of human disease.

overall_design: Our study identifies shared and tissue-specific changes in met-recipient non-tumor lung, liver, and kidney which overlaps with transcriptional alterations described in human cancers.

first: J

middle: A

last: Beck

first: A

first: P

last: Choyke

first: C

last: Mazcko

last: LeBlanc


title: NAE1/UBA3-UBE2M are E1 and E2 Enzymes for the Urm1 Modification in Human Cells

city: Houston

first: Wenyue

last: Cao

state: TX

address: 7255 Helix Park Ave

institute: Texas A&M University

summary: Ubiquitin-related modifier 1 (Urm1) is an evolutionarily conserved ubiquitin-like protein. In eukaryotes, it serves dual roles as a sulfur donor for tRNA modification and a posttranslational protein modifier. Urm1 is proposed to be a primitive protein modifier and a potential precursor to the more complex ubiquitin system. However, no specific activating enzyme (E1), conjugating enzyme (E2), or ligase (E3) has been reported for the Urm1 modification cascade in human cells. In this study, we design an activity-based Urm1 probe to covalently capture cysteine enzymes functioning in the Urm1 signaling pathway. Through proteomic characterization and cell-based validation, we identify NAE1/UBA3 and UBE2M as E1 and E2 enzymes, respectively, for the urmylation pathway under both normal and oxidative stress conditions. Our results also indicate that DCN1 serves as an E3 ligase for the Urm1 modification in human cells. Bioinformatic analysis further reveals that genetic knockdown of NAE1, UBE2M, and Urm1 affects overlappingly genes associated with pathways controlling cellular response to stress conditions or with implications in liver diseases. Urm1 serves a protective role against oxidative stress. Pevonedistat, a potent NAE1 inhibitor that blocks protein urmylation in human cells, exhibits strong synergy with cisplatin, an agent known to induce oxidative stress, in killing liver cancer cells effectively.

overall_design: To understand gene expression patterns regulated by URM1 and its two controlling enzymes NAE1/UBA3 and UBE2M, transcriptomic profiling was performed on HEK293T cells treated with three siRNAs targeting NAE1, UBE2M, and URM1 genes.


title: Inflammaging in aged tissues drives remodeling of the CD8+ T cell compartment

city: St. Louis

first: Maxim

last: Artyomov

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: Aging profoundly reshapes the immune cell landscape, with particularly strong effects on CD8+ T cells, including a marked decline in naïve cells and the emergence of age-associated GZMK+ CD8+ T cells (TAA cells). Although TAA cells make up a significant fraction of the aged CD8+ T cell compartment, the pathway underlying their differentiation remains unknown. In this study, we demonstrate that TAA cell development is cell-extrinsic and requires antigen exposure within aged non-lymphoid tissues. Using a novel TNFΔ69AU/+ mouse model, we show that systemic low-grade inflammation, characteristic of inflammaging, accelerates CD8+ T cell aging and promotes early accumulation of TAA cells. Through detailed analysis of TAA cell heterogeneity, we identified a progenitor subpopulation enriched in the aged adipose tissue. Using heterochronic transplantation, we show that adipose tissue acts as a functional niche, supporting progenitor maintenance and driving the conversion of young CD8+ T cells into the aged phenotype. Taken together, our findings reveal how aging of non-lymphoid tissues orchestrates the reorganization of the CD8+ T cell compartment and highlight adipose tissue as a promising target for therapeutic strategies aimed at modulating immune aging.

overall_design: Splenic CD3e+CD8+ T cells were sorted from young and middle-aged TNFΔ69AU/+, as well as from young, middle-aged, and old WT controls.

first: Irina

last: Shchukina

first: Carlos

last: Rodriguez-Hernandez

first: Maksim

last: Kleverov

first: Heather

last: Ruiz

first: Gwendalyn

last: Randolph


title: Transcriptomic profiling of chlorogenic acid and taurine treatment in human skin cells provides insights into cellular senescence mechanisms

city: Gangnam-gu

first: Hong-Hee

last: Won

address: 81, Irwon-ro

country: South Korea

institute: SungKyunKwan University

summary: Chlorogenic acid (CGA) and taurine are well-known antioxidant compounds that have been demonstrated to reduce cellular senescence in the skin. Given their potential synergistic effects, co-treatment with CGA and taurine may enhance their individual efficacy. However, the biological mechanisms underlying their skin-protective effects remain underexplored. This study aimed to identify genes responsive to CGA and taurine and elucidate their anti-senescence-associated pathways. To this end, we conducted transcriptome-wide RNA sequencing to profile gene expression changes of human epidermal keratinocytes, melanocytes, and fibroblasts by treatment of CGA, taurine, and their combination. The differential expression analysis identified 197 differentially expressed genes (DEGs) in response to the compounds, of which 62 were prioritized as aging-related DEGs based on their involvement in skin aging pathways from functional enrichment analysis and supporting evidence from public databases and prior studies. By identifying key genes and pathways that might contribute to the cellular longevity in human skin, this study provides molecular insights for developing anti-aging strategies with potential applications in dermatology.

overall_design: RNA-seq profiling of skin keratinocytes, melanocytes, and fibroblasts treated with chlorogenic acid and taurine, chlorogenic acid alone, taurine alone, or left untreated.

first: Beomsu

last: Kim

first: Joong-Gon

last: Shin

first: In-Shik

last: Hong

first: Yeeun

last: Ahn

first: Jung Yeon

last: Seo

first: Jae Young

first: Sooyeon

last: Lee

first: Seung-Hyun

last: Jun

first: Eui Taek

last: Jeong

first: Hyunbin

last: Cho

first: Miso

last: Park

first: Dansay

first: Nae Gyu

last: Kang

first: Yunkwan


title: RNF25 confers tolerance to azacytidine-induced mRNA damage by curbing activation of the integrated stress response

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

summary: Excessive RNA damage activates cellular stress responses, triggering cell death. However, pathways that negatively regulate RNA damage responses are largely uncharacterized. Using genetic screens, we here find that the ubiquitin ligase RNF25 provides tolerance to RNA damage caused by the nucleoside analogue azacytidine, a chemotherapeutic agent used to treat acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Mechanistically, azacytidine is incorporated into mRNA, where it causes lesions that stall elongating ribosomes, leading to cytotoxic activation of the GCN2-dependent integrated stress response (ISR). RNF25 prevents ISR hyperactivation by ubiquitylation of ribosomal protein eS31, suppresses cell death upon azacytidine treatment. Our study reveals an mRNA damage tolerance mechanism that determines cellular survival in response to azacytidine, highlighting RNA damage-induced stress response as a potentially critical component of chemosensitivity in AML and MDS.

overall_design: Ribosome profiling of HAP1 cells treated or not with 20 uM azacytidine for 4 hours.

first: Selay

last: Kaya

middle: D

first: Carla

middle: M

last: Engel

first: Julian

last: Stingele


title: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 30) [I38]

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: This study is part of the immgenT Open Source Project, specifically from IGT38, which focuses on a pan-organ and time course analysis of T cells in acute LCMV (Armstrong) infection at day 30 post-infection. The dataset includes T cells isolated from multiple organs: spleen, prostate, submandibular gland, bone marrow, mesenteric lymph node, small intestine epithelium, small intestine lamina propria, lung, and mediastinal lymph node. 7-week-old male C57BL/6J mice infected intraperitoneally with 2×10^5 PFU LCMV Armstrong, and T cells were analyzed at 60 days post-infection (dpi). The study includes both endogenous T cells and adoptively transferred P14 and SMARTA TCR transgenic T cells. Mice received IV 100,000 SMARTA (CD45.1.2) and 50,000 P14 (CD45.1) T cells one day before infection.

overall_design: T cells were isolated from individual organs using mechanical dissociation, enzymatic digestion (collagenase I or DTE), and anti-CD45 intravenous labeling to distinguish tissue-resident from circulating cells. Sorted CD3e+ or IV- CD3e+ were profiled using single-cell RNA sequencing (10x Genomics), combined with CITE-seq (TotalSeq C) and paired TCR α/β sequencing. Samples were pooled using hashtags.

first: Giovanni

last: Galletti

first: Sara

last: Quon

first: Nicole

middle: E

last: Scharping

first: Kennidy

last: Takehara

first: Amir

last: Ferry

first: Ananda

last: Goldrath

first: Ian

last: Magill

first: David

last: Zemmour

first: Christophe

last: Benoist


title: True cyst formation underlies persistence and drug tolerance in Tritrichomonas foetus

city: Chascomús

first: Andrés

middle: Mariano

last: Alonso

state: Buenos Aires

address: Av. Intendente Marino Km 8.2

country: Argentina

institute: INTECH

summary: Tritrichomonas foetus, a protozoan parasite responsible for bovine and feline trichomonosis, has traditionally been considered to form only pseudocysts. Here, we reveal that T. foetus produces true cysts characterized by chitin like components-rich, fibrillar walls, cytoskeletal reorganization, and resistance to detergent treatment. Cystogenesis is induced by environmental stresses such as nutrient deprivation, alkaline pH mimicking the bovine preputial milieu, and exposure to metronidazole, a frontline antiparasitic drug. This encystation enhances parasite survival and suggests a novel drug-resistance mechanism. Transcriptomic profiling identifies key pathways involved in cyst wall biosynthesis and regulation, including Myb-like transcription factors and calcium/calmodulin dependent kinases. Encysted parasites also undergo DNA replication without cytokinesis, suggesting a strategy for rapid multiplication through multiple fission upon excystation. Our findings fundamentally reshape the understanding of T. foetus biology, highlight a critical stage in its transmission cycle, and have significant implications for therapeutic and diagnostic strategies in veterinary parasitology

overall_design: RNAseq profiling for T. foetus K strain incubated in standard culture media (untreated) and under nutrient restriction conditions for 48 hours (treated).

first: Lucrecia

middle: S

last: Iriarte

first: Andres

first: Cristian

middle: I

last: Martinez

first: Maria

last: Prandi

first: Luiz

last: Barros

first: Marcos

last: Ferrante

first: Natalia

last: de Miguel

first: Veronica

last: Coceres


title: Sprayable Nanozyme Hydrogel Epigenetically Reprograms Inflammation for Diabetic Wound Regeneration [Chip-seq]

status: Public on Mar 22 2026

city: Cheonan-si

first: Amal

middle: George

last: Kurian

state: Chungcheongnam-do

address: Pharmacy Bldg, Dankook University

department: Department of Nanobiomedical Science and Tissue regeneration Engineering

institute: Institute of Tissue Regeneration Engineering

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chronic diabetic wounds present a critical clinical challenge due to persistent inflammation and compromised healing. Here we report a novel sprayable nanozyme hydrogel that epigenetically reprograms macrophages to suppress inflammation and coordinate regeneration. Ultrasmall copper-based nanozymes (CuNZ, ~4 nm) synthesized via an eco-friendly one-pot method demonstrated potent multi-radical scavenging activity. When integrated into gelatin methacryloyl (Gel), CuNZ@Gel exhibited excellent sprayability, conformal skin coverage, and long-term storage stability, offering substantial translatable potential. Notably, the nanozyme hydrogel induced distinct epigenetic modifications in macrophages by remodeling chromatin accessibility, effectively shifting gene expression from pro-inflammatory to anti-inflammatory profiles. This epigenetic modulation persisted under oxidative stress, actively suppressing inflammatory while facilitating regenerative responses. In diabetic wound models, CuNZ@Gel significantly accelerated healing through its coordinated antioxidant, anti-inflammatory, and pro-regenerative actions. Unlike conventional passive dressings, our sprayable nanozyme hydrogel proactively reprograms the wound microenvironment via epigenetic antioxidant mechanisms, offering novel insights and strategy for managing chronic diabetic wounds and inflammatory skin complications.

overall_design: Chip-Seq

first: Amal George

first: Jeong-Hui

last: Park

first: Shanika

last: Karunasagara

first: Archita

last: Gupta

first: Shreyas Kumar

last: Jain

first: Tanza

last: Baby

first: Ueon Sang

last: Shin

first: Sak

last: Lee

first: Buuvee

last: Bayarkhangai

first: Rajendra

middle: K

last: Singh

first: Jung-Hwan

first: Kam

middle: W

last: Leong

first: Hae-Won

last: Kim


title: Constitutive activation of canonical Wnt signaling in hem progenitors suppresses the fate of hem-derived Cajal-Retzius cells

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: B304 TIFR Homi Bhabha road

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

summary: Cajal-Retzius cells (CR cells) are the earliest born neurons in the cerebral cortex, and have been implicated in neuronal migration and development of cortical circuitry. One of the sources of CR cells is the cortical hem, which is rich in morphogens of the canonical WNT signaling family. In this study we examine the effect of stabilization of β-CATENIN (gain of function, GOF) in the mouse cortical hem and show that although neurons are still produced, they do not acquire a CR cell identity. The trajectory of differentiation examined using single-cell transcriptomics revealed that upon β-CATENIN GOF, hem-derived CR cells do not display a TBR2+ stage characteristic of immature CR cells. This effect is only seen when β-CATENIN GOF is driven in hem progenitors and is not seen upon β-CATENIN GOF in postmitotic CR cells. These data suggest that a TBR2+ stage may be important for hem-derived CR cell development and that this step appears to be sensitive to levels of stabilized β-CATENIN in hem progenitors.

overall_design: This database contains transriptomes from the telencephalic midline of E11.5 and E14.5 mouse embryos, from Lmx1aCre::Ai9 and Lmx1aCre::Ai9::b-cat gof backgrounds. A subdissected region around the cortical hem, including Cajal-Retzius cells and parts of the hippocampal primordium, were used as input. 5 male embryos were dissected (both hemispheres) for the E11.5 libraries, and 3 male embryos were dissected (both hemispheres) for the E14.5 libraries.


title: ST8Sia6-dependent glycosylation restrains gut inflammation and pathogenic Th1 and Th17 programs

city: Rochester

first: Virginia

middle: Smith

last: Shapiro

state: MN

address: 200 First St SW

department: Immunology

institute: Mayo Clinic

summary: Single-cell suspensions of small bowel lamina propria, small bowel epithelium, and whole colon were purified from mice sufficient, deficient, and heterozygous for sialic acid transferase ST8Sia6. Cells were enriched for CD45 expression, hashtagged according to genotype, and analyzed by 10x scRNA sequencing using the Illumina Novaseq 6000 as well as by 10X CITEseq to identify hashtags.

overall_design: Small intestines and colons were isolated from 1 ST8Sia6 knockout mouse, 1 ST8Sia6 heterozygote mouse, and 2 ST8Sia6 sufficient wildtype mice. The cells from the small intestinal lamina propria, the small intestinal epithelium, and the whole colon (lamina propria and epiethelium combined) were subjected to a percoll gradient and enriched for immune cells using the StemCell Mouse CD45 Positive Selection Kit. The samples were tagged with Biolegend TotalSeq hashtags based on their genotype: KO=C0301, het=C0302, WT=C0303. This procedure was done 3 independent times for combined 10X scRNA sequencing and 10X CITEseq using the Illumina Novaseq 6000. Processed data was aligned using CellRanger, and cells with fewer than 200 genes or greater than 8000 genes, cells with 20% or greater mitochondrial gene counts, and cells with less than 300 or more than 50000 molecules detected were filtered out.

first: Sydney

middle: B

last: Crotts


title: HDAC3 Regulates Transcriptional Networks Governing Decidualization

city: Columbia

first: Jae-Wook

last: Jeong

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

summary: Hdac3d/d mice showed defective decidualization as early as day 3, establishing this as a key time point for molecular assessment. To identify the signaling pathways regulated by Hdac3 during decidualization, RNA-seq was performed on the stimulated uterine horns of Hdac3f/f and Hdac3d/d mice on day 3

overall_design: We used RNA-sequencing to determine the differences in uterine gene expression resulting from Hdac3f/f and Hdac3d/d mice  at decidualization day 3

first: Jeong

last: Jae Wook

first: Kim

last: Tae Hoon


title: Sprayable Nanozyme Hydrogel Epigenetically Reprograms Inflammation for Diabetic Wound Regeneration [mRNA-seq]

first: Amal

last: Kurian

overall_design: mRNA seq profiling of RAW 264.7 macrophage cells treated with hydrogels for 48 hours

first: Amal George

first: Jeong-Hui

last: Park

first: Shanika


title: GmMYB21a improves male fertility of CMS-based restorer line under high-temperature stress in soybean

status: Public on Mar 21 2026

city: Nanjing

first: Jilei

last: Gan

address: No. 666, Binjiang Avenue, Jiangbei New District, Nanjing, Jiangsu Province

country: China

institute: Nanjing Agricultural University

summary: High-temperature (HT) stress during flowering causes male sterility and yield loss in soybean. MYB transcription factors are key regulators under abiotic stress, yet their function and mechanism in regulating male fertility under HT stress in soybean are not fully understood. In this study, a MYB transcription factor GmMYB21a in soybean was identified. GmMYB21a was induced by HT stress in soybean restorer line and was specifically expressed in pollen. Through overexpression and knockout experiments, we demonstrated that GmMYB21a positively regulates pollen fertility and germination under HT stress. Overexpression of GmMYB21a significantly enhanced these traits in restorer line, whereas knockout plants exhibited the opposite effect. Transcriptome sequencing revealed that GmMYB21a overexpression upregulated numerous stress-responsive genes, particularly those involved in flavonoid biosynthesis and sugar metabolism. In addition, molecular experiments confirmed that GmMYB21a bound to the flavonoid synthesis gene GmCHI2-A and promoted its expression. In summary, our research indicated GmMYB21a enhanced the HT-tolerance of male fertility in soybean restorer line through reactive oxygen species scavenging and flavonoid synthesis. This study aims to elucidate the thermotolerance mechanism in soybean male fertility and identify genetic resources for breeding HT-tolerant restorer lines.

overall_design: RNA-seq profiling of wildtype TL and  overexpression line GmMYB21a-OE2 at normal temperature and high temperature treatment.

first: Hongjie

last: Wang

first: Yujuan

last: Gu

first: Xianlong

last: Ding

first: Shouping

last: Yang


title: Tumors Hijack Immune-Privileging Regulons via Distinct Cell Types to Confer T Cell Desertion and Immunotherapy Resistance Across Various Cancers

city: Pittsburgh

first: Xiaosong

state: Pennsylvania

address: 5150 Centre Ave

institute: University of Pittsburgh

summary: Immune checkpoint blockade (ICB) has transformed oncology, yet most patients fail to respond, suffer from hyper-progressive disease, or face severe immune-related toxicities, underscoring the urgent need for biomarkers that identify non-responders. Here we show that tumors co-opt an immune-privileging regulon signature (IMPREG) mirroring transcriptional programs of immune-privileged organs - to enforce T-cell desertion and ICB resistance across solid tumor types. Single-cell and spatial transcriptomic analyses reveal that tumors activate IMPREG through three distinct cellular routes: malignant cells adopting immature neuronal states, cancer-associated fibroblasts assuming myofibroblast identities, or endothelial cells - each creating localized niches of immune suppression and antigen-presentation collapse. Across 4 discovery and 36 validation clinical datasets, IMPREG consistently predicts immunotherapy resistance in 14 distinct cancer types, functioning as an orthogonal marker independent of established biomarkers. Crucially, IMPREG-expressing tumors show enhanced sensitivity to EGFR inhibitors or anti-angiogenic therapies in specific tumor entities. These findings suggest IMPREG as a dual-utility predictive biomarker for personalized treatment stratification.

overall_design: 72 tumor tissues were procured from the Health Sciences Tissue Bank of University of Pittsburgh.

first: Bashir

last: Lawal

first: Akshat

last: Gupta

first: Renu

last: Sharma

first: Rohit

last: Bhargava

first: Yue


title: Perturb-seq uncovers pathological obstacles to direct cardiac reprogramming in vivo

city: Beijing

first: Yang

last: Zhao

address: Peking University, No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: We investigated the mechanism underlying Calr suppression-enhanced cardiac reprogramming. As CALR functions as an ER-resident chaperone and Ca2+-binding protein, with Ca2+ acting as a second messenger in fate-determining pathways, particularly cardiogenesis we performed RNA-seq on MGTMyoS-induced MICFs transduced with shCalr or shNT at days 7 and 14 in vitro

overall_design: RNA-seq profiling on MICFs with Calr knock down or shNT at day0, day7, day14.

first: Yihong

last: Cai

first: Junbo

first: Ruohan


title: GLS1 governs vascular smooth muscle cell phenotypic switching and aortic dissection via glutamate metabolism

status: Public on Mar 20 2026

first: Hailong

last: Cao

state: Jiangsu

address: 87 Dingjiaqiao

department: Department of Cardiac Surgery

institute: Zhongda hospital

summary: To evaluate the roles of glutaminase 1 (GLS1) in vascular smooth muscle cells (VSMCs) phenotypic switching and aortic dissection (AD). Integrative transcriptomic analyses were performed to identify the candidate genes involved in VSMC phenotypic switching in AD. The expression of GLS1 in VSMCs was assessed by qRT-PCR, Western blot and immunofluorescence. RNA-sequencing analysis was performed to recapitulate possible changes in the transcriptome profile of GLS1 in VSMCs. We identified GLS1 as a potential regulator in AD. GLS1 expression was significantly downregulated in VSMCs from both human AD aortic tissues and mouse models. Mechanistically, down-regulation of GLS1 impaired glutamate metabolism, leading to reduced levels of glutathione and α-ketoglutarate, thereby promoting mitochondrial dysfunction and accumulation of reactive oxygen species, which activated the PI3K/AKT pathway and ultimately triggered VSMC phenotypic switching. These findings revealed a critical role of GLS1-mediated glutamate metabolism in VSMC phenotypic switching and suggest a promising therapeutic target for AD.

overall_design: RNA-seq profiling of human aortic smooth muscle cells (HASMCs) infected with adenovirus containing empty vector (Ad-Vector) or GLS1-encoding plasmids (Ad-GLS1), followed by treatment with PDGF-BB or control (n = 3)

first: Wei

last: Xie


title: Adenovirus phagocytosis by neutrophils triggers a pro-inflammatory response

city: Montigny-Le-Bretonneux

first: Sophie

last: Dupré

address: 2 av. de la Source de la Bièvre

department: Versailles Saint Quentin University

country: France

institute: Paris Saclay Université

summary: To determine if  transcriptional changes also occur during human neutrophils adenoviruses interaction, a single-cell RNA sequencing study was performed on blood purified PMNs exposed to human serum (HS) alone or to HS-opsonized Ad5.

overall_design: Human Neutrophils (PMNs) were extracted from the blood obtained from healthy donors (EFS  agreements). PMNs (5 × 10^5) per condition were resuspended in HBSS. HBSS, HS or HS-opsonized Ad5 (MOI 10^4 vp/cell) were incubated with PMNs for 30 min at 4°C. After washing with HBSS, samples were incubated 90 min at 37°C then filtered to discard aggregates. PMNs were counted with Trypan Blue to assess cell viability (that was around 80%) then transferred in DNA LoBind tubes. RNA sequencing was performed with 10X Genomics Chromium 3’ single-cell RNAseq by Gustave Roussy Institute genomics facility

first: Laurans

last: Salomé

first: Remy

last: Jeulin

first: Benihoud

last: Karim

first: Dupré-Crochet

last: Sophie


title: Iron Limitation-Induced Modulation of Transcription in Chlamydia trachomatis

city: Lausanne

first: Daniel

last: Rodriguez Rozo

address: Avenue de Cour 10

department: IMUL

country: Switzerland

institute: CHUV

summary: Chlamydia trachomatis (C. trachomatis) is an obligate intracellular bacterial pathogen responsible for trachoma and sexually transmitted infections. Like other Chlamydiota members, such as Waddlia chondrophila, C. trachomatis undergoes a biphasic developmental cycle alternating between infectious elementary bodies (EBs) and replicative reticulate bodies (RBs). Under stressful conditions, RBs differentiate into non-dividing aberrant bodies (ABs), a reversible state associated with persistence. Here, we investigate how early iron deprivation affects transcriptional regulation in C. trachomatis. We performed RNA sequencing to compare transcriptional profiles between EBs and RBs and between RBs and ABs induced by iron chelation with 2,2′-bipyridyl at 8 hpi. In EBs, 29% of genes were downregulated and 30% upregulated compared to RBs, revealing extensive transcriptional remodeling. At 24 hpi, ABs displayed downregulation of two-component system (TCS) genes (atoS, atoC, and chxR), while genes encoding inclusion membrane proteins (Incs) and the trpRBA operon were upregulated. These findings show how C. trachomatis adapts transcriptionally to iron deprivation, revealing stress- and time-dependent changes in metabolism, stress responses, and host–pathogen interactions. Persistence alters the developmental cycle while maintaining inclusion integrity and modulating host interactions, contributing to chronic infection. Uncovering the mechanisms driving persistence may offer crucial insights into chlamydial pathogenesis.

overall_design: RNA-seq was used to profile gene expression across the developmental stages of C. trachomatis. HEp-2 cells were infected and sampled at time points corresponding to reticulate bodies (24 hpi), elementary bodies (72 hpi), and aberrant bodies induced by BPDL-mediated iron limitation (added at 8 hpi and harvested at 24 hpi). Three biological replicates were generated for each condition.

first: Simone

last: Adams

first: Carole

last: Kebbi-Beghdadi

first: Trestan

last: Pillonel

first: Sébastien

last: Aeby

first: Gilbert

last: Greub


title: Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response [bulk RNA-Seq]

city: DUARTE

first: Naseeb

middle: Kaur

last: Malhi

email: naseebmalhi@gmail.com, nmalhi@coh.org

state: CA

address: 1500 E Duarte Road

department: DMRI

institute: City of Hope

summary: Diabetes mellitus (DM) significantly accelerates vascular diseases like peripheral arterial disease (PAD). Endothelial cells (ECs) and macrophages (MΦs) singularly and synergistically are important contributors to DM-associated vascular dysfunction. Single-cell (sc) profiling technologies are revealing the true heterogeneity of ECs and MΦs, but how this cellular diversity translates to cell-cell interactions, and consequentially vascular function, remains unknown. We leveraged scRNA sequencing and spatial transcriptome (ST) profiling to analyze human mesenteric arteries from non-diabetic (ND) and type 2 diabetic (T2D) donors. We generated a transcriptome and interactome map encompassing the major arterial cells and highlighted Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) as a top T2D-induced gene in mononuclear phagocytes (MPs), with concomitant increases of TREM2 ligands in ECs. We verified DM-associated TREM2 induction in cell and mouse models, and found that TREM2 inhibition decreases pro-inflammatory responses in MPs and ECs, as well as increases EC migration in vitro. Furthermore, TREM2 inhibition using a neutralizing antibody enhanced ischemic recovery and flow reperfusion in DM mice subjected to hindlimb ischemia, suggesting that TREM2 promotes ischemic injury in DM. Finally, in human PAD, co-existing DM was associated with greater expression of TREM2 and its interaction with ECs, with a further increase in ischemic tissue compared to patient-matched non-ischemic tissue. Collectively, our study presents the first atlas of human diabetic vessels with single cell and spatial resolution, and identifies TREM2-EC interaction as a key driver of diabetic vasculopathies, the targeting of which may offer an opportunity to ameliorate vascular dysfunction associated with DM-PAD.

overall_design: We performed bulk RNA-seq on THP-1-derived macrophages, with and without siRNA-mediated TREM2 knockdown (100nM),  then 25 mM D-glucose, 5 ng/mL TNF-α (HT) treated.

last: K Malhi

first: Dongqiang

last: Yuan

first: Yingjun

last: Luo

first: Zhen

last: B Chen


title: Transcriptional mechanisms of sex-biased gene expression and their connections to disease-associated variation

city: Durham

first: Angela

middle: G

last: Jones

state: NC

address: 0048B CARL, Box 3053 DUMC

department: MGM

institute: Duke Unversity

summary: Humans display sexual dimorphism across many traits, but little is known about underlying genetic mechanisms and impacts on disease. We utilized single-cell RNA-seq of 480 lymphoblastoid cell lines (LCLs) to identify 1200 genes with significantly sex-biased expression. While reproducibility was highest among LCL datasets, 71% were found to be sex-biased in at least one GTEx tissue, with a core dataset of 21 genes displaying sex-biased expression across all datasets and tissues examined. While 7.7% of sex-biased genes can be directly explained by differences in the number of sex chromosomes, most sex-biased genes (79%) are targets of transcription factors that display sex-biased expression. FOSL1, ZNF730, ZFX, and ZNF726 appear to make the largest contribution to this based on machine learning and linear modeling approaches, and all four of these transcription factors are regulated by the number of X chromosomes. Further, by testing the difference in genetic effect size (β) of conditionally independent expression quantitative trait loci (eQTL) identified in each sex separately, we identified 2,390 sex-biased eQTL (sb-eQTL) across the genome, but evidence of replication in an independent dataset was modest. However, permutation analysis demonstrated that sb-eQTL identified using real sex was more likely to have concordant direction of effect. Further exploratory analysis revealed that these sb-eQTL are enriched in over 100 GWAS phenotypes, including many loci associated with female-biased autoimmune diseases such as multiple sclerosis. Our results demonstrate widespread genetic impacts on sexual dimorphism and identify possible mechanisms and clinical targets for sex differences in diverse diseases.

overall_design: 384 human lymphoblastoid cell lines (LCLs) from the 1000 Genomes project were pooled and analyzed using droplet-based single-cell RNA-seq in 4 samples.

first: Guinevere

last: Connelly

first: Dennis

middle: C

last: Ko


title: Single-nucleus RNA sequencing of human subcutaneous adipose tissue biopsies from 49 Mexican participants

city: Los Angeles

first: Asha

last: Kar

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: University of California Los Angeles

summary: We performed single-nucleus RNA-seq on subcutaneous adipose tissue (SAT) biopsies from Mexicans from Mexico City. The purpose of this study was to understand cell-type and subcell-type level profiles of SAT in Mexicans.

overall_design:
We isolated nuclei from frozen subcutaneous adipose tissue from individuals independently or by pooling biopsy samples in batches of four or five samples. The libraries were constructed using the Chromium Single Cell 3’ v3.1 chemistry and sequenced on an Illumina NovaSeq S4 with a target sequencing depth of 60,000 reads per nucleus.

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

first: Carlos

last: Aguilar-Salinas

first: Maria Teresa

last: Tusié-Luna

first: Paivi

last: Pajukanta


title: Nrf1 coordinates proteasome and autophagy to maintain cardiac proteostasis

first: miao

last: cui

state: Please select region, state or province

address: 300 LONGWOOD AVE

institute: Boston Children's Hospital

summary: Proteolytic stress frequently arises during disease and aging, particularly in long-lived, post-mitotic cells such as cardiomyocytes. To maintain proteostasis, cardiomyocytes depend on coordinated protein quality control pathways, including the ubiquitin-proteasome system and autophagy. Mechanisms that activate these pathways hold therapeutic potential for heart disease. Here, we demonstrate that transient activation of nuclear factor erythroid 2–like 1 (Nfe2l1, also known as Nrf1), a transcriptional regulator of proteasome activity, specifically in cardiomyocytes during ischemia/reperfusion (I/R) injury improves cardiac function. In addition to regulating the proteasome, we identify a critical role for Nrf1 in activating autophagy, which is essential for its cardioprotective effects. Through multi-omics analyses, we define both transcriptional and post-transcriptional functions of Nrf1 that underlie its cardioprotective activity. Loss-of-function studies in mice demonstrate that Nrf1, but not its homolog Nrf2, is required for autophagy and baseline cardiac function. Together, our findings establish a dual function of Nrf1 in promoting cardiac proteostasis by regulating both proteasomal and autophagic protein quality control pathways. Activating Nrf1 thus offers a therapeutic strategy for treating ischemic heart disease.

overall_design: RNA-seq profling of neonatal rat ventricule cardiomyocytes overepressing LacZ as control and the transcription factor Nrf1 with or without H2O2 treatment.

first: Miao

last: Cui


title: Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response [scRNA-Seq]

overall_design:
We performed scRNA-seq on the intima and whole tissue of mesenteric arteries from non-diabetic and diabetic donors.
Raw data for GSM8881941, GSM8881942, GSM8881946-GSM8881950 previously uploaded in GSE135357. See individual GSM records for details.

first: Viola

first: Xiaofang

last: Tang

last: Chen


title: Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response [Spatial Transcriptomics]

overall_design: We performed spatial transcriptomics profiling using 10x Genomics Visium on mesenteric arteries from non-diabetic and diabetic donors


title: Hyperinnervation inhibits organ-level regeneration in mammalian skin

city: Cambridge

first: Hannah

middle: T

last: Tam

address: 7 Divinity Avenue

department: SCRB

institute: Harvard University

summary: Some mammalian tissues can replace lost cells within one lineage, but organ-level regeneration—restoring diverse cell types across lineages—remains rare. Here we show that late embryonic full-thickness skin injuries heal by regenerating epithelial, mesenchymal, neuronal, and vascular lineages with proper connectivity. However, this ability is lost soon after birth, leading to a failure to restore most cell types and hyperinnervation of the wound bed. Single-cell sequencing identified a postnatal wound-specific fibroblast (PWF) population absent after embryonic wounding. Through an in vivo screen, we discovered three PWF-enriched genes—Timp1, Cxcl12, and Ccl7—that inhibit organ-level regeneration and cause hyperinnervation when overexpressed in embryonic wounds. Reducing hyperinnervation by depleting Cxcl12 in fibroblasts or inhibiting synaptic release enables postnatal skin to regenerate diverse lineages after injury. Our study identifies mechanisms transitioning an organ from regenerative to non-regenerative, discovers fibroblast-driven hyperinnervation as a key barrier, and demonstrates removing this barrier unlocks organ-level regeneration.

overall_design: We first sought to identify the changes that drive the distinct regenerative responses after wounding at E16.5 vs. P5. For this, we performed scRNAseq on E16.5 wounded, P5 wounded, and unwounded age-matched controls skin (2 biological replicates each). We sequenced the wounds 3 days after wounding to capture changes that precede and can potentially lead to the distinct outcomes observed 7 days after wounding.  Second, we sought to test specific genes that might inhibit regeneration in vivo with an AAV-based strategy. To assess which cell types are transduced by AAV, we FACS-purified and single-cell sequenced AAV-positive and -negative cells collected 3 days after E16.5 wounding and AAV transduction.

first: Jingyu

last: Peng

first: Rebecca

last: Freeman

first: Yulia

last: Shwartz

first: Shlomi

last: Brielle

first: Sakshi

last: Garg

first: Siti

last: Rahmayanti

first: Stephen

last: Crocker

first: Devin

last: Coon

first: Ya-Chieh

last: Hsu


title: Endometrial Insights: Unmasking Endometriosis through Single-Cell Profiling and AI-Based Prediction

city: Berne

first: Lea

last: Duempelmann

address: Murtenstrasse 35

department: DBMR

institute: University of Berne

summary: Endometriosis, affecting over 10% of women, presents treatment and diagnostic challenges. To address these issues, we generated the biggest single-cell atlas of endometrial tissue to date, comprising 466,371 cells from 35 endometriosis and 25 non-endometriosis patients without exogenous hormonal treatment. Detailed analysis reveals significant gene expression changes and altered receptor-ligand interactions present already in the endometrium of endometriosis patients, including increased inflammation, adhesion, proliferation, cell survival, and angiogenesis in various cell types. These alterations may enhance endometriosis lesion formation and offer novel therapeutic targets.  Using ScaiVision neural networks, we developed accurate models predicting endometriosis of varying disease severity, including a minimal 11-gene signature-based model. In conclusion, our findings illuminate numerous pathway and ligand-receptor changes in endometriosis endometrium, offering insights into pathophysiology, targets for novel treatments and accurate diagnostic models for enhanced outcomes in endometriosis management.

overall_design: Endometrial biopsies were acquired from participants with and without endometriosis. After dissociating the biopsies into single cells, the cellular content was captured using 10x Genomics technology and sequenced. Subsequently, the resulting data was compiled into an endometrial single-cell atlas.

first: Shaoline

last: Sheppard

first: Angelo

last: Duo

first: Jitka

last: Skrabalova

first: Brett

last: McKinnon

first: Thomas

last: Andrieu

first: Dennis

last: Goehlsdorf

first: Sukalp

last: Muzumdar

first: Cinzia

last: Donato

first: Ryan

last: Lusby

first: Wiebke

last: Solass

first: Hans

last: Bösmüller

first: Peter

last: Nestorov

first: Michael

last: Mueller


title: CarS2 mediated cysteine catabolism drives brown fat development and thermogenesis through persulfidating EBF2

city: Shanghai

first: Xuyun

last: Zhao

state: Shanghai

address: South Chongqing Road

department: Medical school

institute: Shanghai Jiaotong University

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

overall_design: Refer to individual Series


title: CarS2 mediated cysteine catabolism drives brown fat development and thermogenesis through persulfidating EBF2 [Cut & Tag]

summary: Targeting transcriptional regulatory complex is a promising strategy to activate thermogenic fat and treat  obesity. In this study, we focus on identifying critical and special metabolic pathways enriched during brown adipocyte differentiation. By analyzing metabolomics and RNA sequencing results from precursor and mature brown and white adipocytes, we revealed cysteine catabolism pathway is a unique metabolic process that is exclusively increased in the brown adipocyte differentiation. Then, we demonstrated cysteine persulfidation synthase CarS2 is directly induced by EBF2 and mediates cysteine catabolism to produce cysteine persulfide and triggers brown fat protein persulfidation in vitro and in vivo. Loss of CarS2 in thermogenic fat blocks brown and beige fat formation and reduced thermogenesis and energy expenditure in mice. More importantly, CarS2 generates cysteine persulfide and its derivative H2S cell autonomously induces brown adipogenesis and enhances uncoupled respiration by persulfidating EBF2. Mechanistically, the persulfidated EBF2 facilitates its interaction with PPARγ and enhanced the recruitment of the EBF2-PPARγ complex on browning gene promoter, thus driving brown fat development and boosting thermogenic function. Furthermore, the treatment of CarS2 coenzyme PLP or H2S donor elevates brown adipocyte function and ameliorates obesity progression in mice under HFD feeding, indicating a novel metabolite-based strategy for the obesity treatment.

overall_design:
In our study, we found EBF2 is the substrate of CarS2, and was persulfidated in the BAC differentiation.To investigate the role of CarS2 on EBF2 transcription activity in  the BAC differentiation, we seperated and immortalized primary brown adipocytes from CarS2 floxed mice and expressed vector (BAC-V) for control and  a cre recombinase to knock out CarS2 (BAC-cre).
BAC-V and BAC-cre cells were cultured and differentiated to performe Cut & Tag assay by using EBF2 antibody (R&D, AF7006) and H3K27ac antibody(CST,4353).The DNA libiray was sequenced.
we performed promoter binding profile analysis using data obtained from Cut & Tag-seq of BAC-V and BAC-Cre.

first: Hongyong

last: Song

first: Xin

last: Peng


title: CarS2 mediated cysteine catabolism drives brown fat development and thermogenesis through persulfidating EBF2 [BAC and L1 differ]

overall_design:
To investigate the  gene expression profile of BAC cells before and after differentiation, we extracted the RNA of BAC at day 0 and day 4 during the differentiation.we performed gene expression profile using data obtained from RNA-seq before and after BAC differentiation with duplicate.
To investigate the  gene expression profile of 3T3-L1 cells before and after differentiation, we extracted the RNA of 3T3-L1 at day 0 and day 6 during the differentiation.we performed gene expression profile using data obtained from RNA-seq before and after 3T3-L1 differentiation with duplicate.


title: Integrating epigenome-wide Mendelian randomization and multi-omics data validation to identify epigenetic drivers of idiopathic pulmonary fibrosis

status: Public on Mar 19 2026

city: Guangzhou

first: Xingyu

last: Lv

address: No. 107, West Jiangxi Road

department: Sun Yat-Sen Memorial Hospital

institute: Sun Yat-sen University

summary: Idiopathic pulmonary fibrosis (IPF) is a complex disease without clear etiology or effective therapy. While DNA methylation has been implicated in IPF pathogenesis, the tissue-specific causal effects of the epigenetic factors on IPF remain undetermined. Here, we performed epigenome-wide Mendelian randomization using blood-based methylation quantitative trait loci of 420,509 CpG sites and genome-wide association study for IPF to elucidate the causal effects of the CpG sites on IPF. Totally, 452 CpG sites has shown putative causal effects on IPF risk after Bonferroni correction. Among them, 13 CpG sites have shown strong colocalization evidence with genetic factors associated with IPF. Specifically, DNA methylation at CpG sites within MAN2A2 and TRIM27 shows significant differences between IPF lungs and controls, correlating with altered mRNA expressions of these genes in lung tissues. The CpG site in MAN2A2 is a binding site of ZNF384 according to transcription factor databases. RNA sequencing in the TGFβ1-induced alveolar epithelia confirmed significantly reduced expression of MAN2A2 and ZNF384 comparing to the controls. Collectively, our study suggests a putative causal link between DNA methylation within MAN2A2 and IPF risk, wherein lung-specific DNA methylation in MAN2A2 may perturb the interaction between ZNF384 and MAN2A2, revealing novel roles for these genes in IPF pathogenesis.

overall_design: RNA samples derived from TGFβ1-induced A549 cells and control cells were sequenced on the NovaSeq6000 platform (Illumina; USA). Details of RNA sequencing are described in the Supplementary Methods. RNA expression levels were quantified by fragments per kilobase million (FPKM). We compared the mRNA expression levels of target genes and TFs using unpaired two-tailed Student’s t-tests.

first: Zhaoqi

last: Li

first: Luna

last: Hong

first: Shuangyu

last: Yang

first: Fengzhan

last: Ye

first: Linjie

last: Huang

first: Shanping

last: Jiang

first: Huiying


title: CarS2 mediated cysteine catabolism drives brown fat development and thermogenesis through persulfidating EBF2 [AKO and wt Acute cold]

overall_design:
To investigate the role of CarS2 in thermogenic function of brown adipose tissue, we established the CarS2 condition  knock out mice in adipose tissue by cross with adiponectin-cre mice.
AKO mice and wild type littermates were maintained in an 4℃ incubater for 4 hours,then were euthanasia and brown adipose tissue were harvest and frozed immediately with liquid nitrogen.
We performed gene expression profile using data obtained from RNA-seq of BAT from wild type and AKO mice.


title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells [BulkRNA-seq_vitro]

status: Public on Mar 24 2026

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

summary: Although ILC3s are known to differentiate in RORγt-dependent manner, besides ILC3s, RORγt-dependent developmental program is shared among several lymphocytes.However, little is known about the regulatory mechanism of RORγt expression specific to ILC3s. Our data newly idetified cell lineage-specific and two-step regulation of RORγt expression in ILC3 including LTi cells.

overall_design: RORγt-positive cells differentiated in vitro from CLPs from the fetal liver can be classified into two groups based on Runx3 expression. To investigate the functional differences between Runx3-positive RORγt-positive cells and Runx3-negative RORγt-positive cells, bulk RNA sequencing was performed on each cell population.

first: Takuma

last: Fukui

first: Miyuki

last: Watanabe

first: Satoshi

last: Kojo

first: Eriko

last: Sumiya


title: Therapeutic effect of  ANGPTL4 antisense oligonucleotide treatment in pneumonia caused by PAO1 bacteria or PR8 virus

city: Singapore

first: Damien

last: Chua

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University, Singapore

summary: A bacterial pneumonia model represented by Pseudomonas aeruginosa (PAO1) or viral pneumonia model by PR8 virus infection were constructed, and then the drug of antisense oligonucleotide(ASO) for ANGPTL4 is administered for treatment. The inflammatory status of mouse lung tissue is analyzed pathologically and the inflammatory cell count is carried out to evaluate the therapeutic effect of the drug. Similarly, the expression of ANGPTL4 protein in mice is detected and its corresponding lung tissues are analyzed for transcriptomic analysis, and its possible functional pathways are further explored and summarized.

overall_design: In PAO1 infection group, we conducted gene sequencing on four distinct groups of samples: PAO1-infected mice treated with ASO(PAO1-ASO), PAO1-infected mice without treatment(PAO1), healthy mice treated with ASO(Ctrol-ASO), and healthy mice without treatment(Ctrl). In the PR8 infection group, we conducted gene sequencing on four distinct groups of samples: PR8-infected mice treated with ASO(PR8-ASO), PR8-infected mice without treatment(PR8), healthy mice treated with ASO(Ctrl-ASO), and healthy mice without treatment(Ctrl). Each group comprised five samples.

first: Haiyang

last: Fan

first: Shumin

last: Liao

first: Liang


title: m6Am methyltransferase PCIF1 regulates osteogenesis via WNT signaling

city: New Orleans

first: Hong-Wen

last: Deng

state: LA

address: 1440 Canal St, suite 1619G

institute: Tulane University

summary: Skeletal development depends on the self-renewal and differentiation of MSCs. Emerging research underscores the regulatory functions of RNA methylation on bone homeostasis. Here, we show PCIF1, the N6,2′-O-dimethyladenosine (m6Am) methyltransferase, is essential for maintaining bone mass and promoting osteogenic differentiation of MSCs. Multiple complementary analyses—including GWAS, TWAS, and single-cell transcriptomics—collectively point to PCIF1 as a regulator of human bone mineral traits and a marker of early mesenchymal stem cells. Global or MSC-specific Pcif1 deletion elicits osteoporotic pathology in mice, although myeloid cell-specific Pcif1 knockout does not induce femur bone alternation alterations. Mechanistically, Pcif1 knockout decreases m6Am signals of Wnt-related genes (Wnt11, Fzd4, Fgfr2) and accelerates mRNA degradation. This down-regulates active β-Catenin protein, and thus impairs osteogenic function of MSCs. Additionally, the WNT agonist attenuates the osteoporosis-like phenotype induced by Pcif1 deletion. These findings highlight the crucial role of PCIF1-mediated m6Am modification in regulating osteogenesis and suggest potential therapeutic implications for bone disorders.

overall_design: Human femoral head specimens were obtained from patients undergoing total hip arthroplasty. Bone tissues were enzymatically digested to generate single-cell suspensions. Hematopoietic and immune cells were depleted using magnetic-activated cell sorting to enrich osteolineage cell populations. Single-cell RNA sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3′ platform. Libraries were sequenced on an Illumina NovaSeq 6000 instrument using paired-end sequencing.

first: Wei

last: Song

first: Kuan-Jui

last: Su

first: Zhehui

last: Pan

first: Zhong

last: Zhang

first: Qi

last: Yin

first: Weimin

last: Lin

first: Linfeng

last: Liu

first: Yun

last: Gong

first: Bocheng

last: Liang

first: Yimeng

last: Cai

first: Qiwen

first: Hui

last: Shen

first: Quan

last: Yuan


title: Transcriptional and chromatin accessibility profiling of melanoma cells during BRAF inhibitor–induced drug tolerance

city: Nashville

first: Blake

last: Baleami

state: TN

address: 1161 21st Ave S

department: Human Genetic PhD Program

institute: Vanderbilt University

summary: Drug tolerance can emerge rapidly in melanoma following treatment with BRAF inhibitors. This transition has been associated with transcriptional and chromatin state remodeling. To investigate the molecular features of this process, we profiled melanoma cells before and during exposure to a BRAF inhibitor. We generated single-cell RNA sequencing (scRNA-seq), bulk RNA sequencing (bulk RNA-seq), and bulk ATAC-seq datasets from SKMEL5 melanoma cells. Cells were analyzed under untreated conditions and following treatment with 8 µM BRAF inhibitor (PLX4720) for defined time periods corresponding to drug-tolerant states. Bulk RNA-seq was performed on multiple SKMEL5 subclones (SC01, SC07, SC10) to characterize transcriptional responses across biological replicates. scRNA-seq and ATAC-seq were used to profile transcriptional heterogeneity and chromatin accessibility changes associated with drug tolerance.

overall_design: SKMEL5 melanoma cells were cultured under standard conditions and treated with the BRAF inhibitor PLX4720 (8 µM) to induce drug tolerance. Samples were collected under untreated conditions and after defined treatment durations corresponding to drug-tolerant states. In this study, cells treated with PLX4720 for 8 days are referred to as idling cells. Single-cell RNA sequencing (scRNA-seq) and bulk ATAC-seq were performed on untreated cells and on idling cells treated with PLX4720 for 8 days. Bulk RNA sequencing was performed on three independent SKMEL5 subclones (SC01, SC07, SC10) under untreated conditions and following PLX4720 treatment for 3 days and 8 days, with three biological replicates per condition. These datasets were generated to characterize transcriptional and chromatin accessibility changes associated with the emergence of drug tolerance in melanoma cells.

first: Corey

last: Hayford

first: Philip

last: Stauffer

first: B

last: Bishal Paudel

first: Aziz

last: Al'Khafaji

first: Amy

last: Brock

first: Vito

last: Quaranta

first: Daren

middle: R

last: Tyson

first: Leonard

last: Harris


title: Optineurin modulates mTORC2/AKT/STAT3 signaling to control MHC II expression and adaptive immunity against HSV-1

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 900 S. Ashland Ave

department: Research Resources Center

institute: University of Illinois at Chicago

summary: Herpes simplex virus 1 (HSV-1) infection contributes to immunopathogenic diseases and lacks an effective vaccine. Improving antigen presentation is key to better vaccine strategies and more robust immune responses. Here, we show that OPTN, an autophagy receptor traditionally involved in protein recycling, unexpectedly stabilizes RICTOR (mTORC2), a crucial step in enhancing MHC-II surface expression in dendritic cells. OPTN regulates the AKT/mTOR/STAT3 pathway, with AKT2 isoform playing a central role. Using scRNA-seq and transgenic mouse models, we identify the mechanistic details of this pathway. Dysregulation impairs antigen presentation, weakening immunity and vaccine efficacy. Our findings uncover a novel function for OPTN and highlight its role in coordinating innate and adaptive immune defenses, with implications for vaccine development and immune response modulation in HSV-1 and other viral and bacterial diseases.

overall_design: HSV-1 infection was performed by corneal scarification method.Their corneas were scarified in a 3 x 3 grid using a 30-gauge needle followed by the application of HSV-1 McKrae at  5 × 105  PFU.    At 8dpi animals were sacrificed and cLN were harvested from 4 animals in each group and pooled into one sample. cLNs were manually harvested using 5 ml syringe and isolated immune cells were further subjected to DC isolation using Miltenyi kit. Isolated DCs were mixed in a specific ratio with lymphocytes from the same tissue to enrich the DC population.

first: Rashmi

last: Kadam

first: Deepak

last: Shukla

first: Mark

last: Maienschein-Cline

first: George

last: Chlipala


title: Cholesterol-rich diet exacerbates steatohepatitis in the STAM mouse model

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a widespread chronic liver disorder spanning simple steatosis to metabolic dysfunction-associated steatohepatitis (MASH) and fibrosis. Suitable animal models are crucial for therapeutic development, yet many fail to reproduce progression to fibrosing MASH. Here, we employed the STAM model in male C57BL/6J mice to simulate MASLD and investigated whether a high-fat, high-cholesterol (HFHC) diet would intensify disease progression compared with the standard high-fat (HF) diet. HFHC feeding in the STAM model accelerated hepatic lipid accumulation, crown-like structure formation, inflammation, and fibrosis, as demonstrated by histological analyses. Transcriptomic profiling and pathway enrichment confirmed activation of lipid and cholesterol metabolism, regulation of TNF production, and inflammatory signaling. Reactome analysis further indicated alterations in extracellular matrix formation and immune system pathways, consistent with advanced fibrotic progression. In summary, integration of HFHC feeding with the STAM model produced a more severe liver phenotype that better mirrors the pathological spectrum of MASLD.

overall_design: At age of two days male mice were injected with single subcutaneous dose of 200 µg streptocotozin dissolved in 0.1 M citrate buffer (pH 4.5) (STZ, S).  At 4 weeks of age mice were switched to ad libitum feeding of a high-fat diet (HF; Ssniff) or a cholesterol-enriched high-fat diet (HFHC; Altromin). Mice were sacrificed after a 6-hour fast at 8 or 12 weeks of age.

first: Wenke

last: Jonas


title: Mapping the miRNA landscape of primitive macrophage extracellular vesicles highlights their pro-vasculogenic effects in engineered human cardiac tissue

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

country: Canada

institute: University of Toronto

type: Non-coding RNA profiling by high throughput sequencing

summary: Resident cardiac macrophages, derived from primitive yolk sac precursors during embryogenesis, have increasingly been recognized for their distinct phenotype and functions in regulating homeostasis of the human heart. However, the profile of their extracellular vesicles (EVs) in cardiac signalling and regulation remains uncharted. Here, we employ differentiation of human pluripotent stem cell (hPSC)-derived primitive macrophages (Mac) for isolation of their secreted EVs and in-depth characterization of EV-miRNA cargo. Primitive macrophages secreted nanoscale EVs that expressed canonical EV markers, and miRNA sequencing highlighted a diverse and unique profile of miRNAs when compared to EVs sourced from other principal cardiac cell lineages and published data from monocyte-derived cells. In particular, we noted the abundance and enrichment of vascular-modulatory let-7 miRNAs and miR-126-3p. Functional screening of Mac-EVs in a 3D model of in vitro cardiac vasculogenesis confirmed enhanced early endothelial cell organization and branching. Establishing a reference for the human Mac-EV miRNome enables further hypothesis-driven mechanistic tests of Mac-EV miRNAs in mediating cardiac physiology and disease, opening the door to identification of therapeutic targets and modalities for cardiac repair.

overall_design: miRNA-seq profiling of extracellular vesicles (EVs) isolated via PEG-based precipitation from conditioned media of human embryonic stem cell (hESC)-derived primitive macrophages (Mac-EVs), human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes (CM-EVs), primary human cardiac fibroblasts (CF-EVs), and primary human cardiac microvascular endothelial cells (HCMVEC-EVs).

first: Karl

last: Wagner

first: Shira

last: Landau

first: Gregory

last: Kent

first: David

middle: F

last: Bodenstein


title: Adeno-associated virus (AAV)-TBX18 does not generate biological pacemaker activity, unlike AAV-Hcn2

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: Gene therapy-based biological pacemakers have been proposed as an alternative to their hardware-based counterparts. In this context, short-term ectopic expression of the T-box transcription factor 18 (TBX18) in the ventricle reportedly generated potent short-term pacemaker function in various animal models. Here, we investigated the effect of adeno-associated virus (AAV)-mediated long-term expression of TBX18, and compared the outcome to that of the pacemaker ion channel Hcn2. Our findings revealed that CMV-driven ectopic TBX18 expression in mouse hearts led to severe cardiac fibrosis. At lower, non-fibrogenic levels, TBX18 maintained its transcriptional function but failed to induce pacemaker phenotypes. TBX18-expressing cells showed suppressed expression of key working myocardial genes, but the pacemaker gene program was not induced. Electrophysiological studies showed abnormal automaticity in TBX18-expressing cells, combined with prolonged repolarization and various current changes. However, no hyperpolarization-activated funny current was detected. In a complete AV-block rat model, AAV-mediated Hcn2 expression induced robust ectopic pacemaker activity in the presence of isoproterenol, whereas TBX18 expression neither generated such activities, nor augmented Hcn2-mediated pacing. In conclusion, at functional non-fibrogenic levels, TBX18 is neither sufficient nor necessary to induce pacemaker activity. In contrast,  Hcn2 generates reliable pacing, making it  a more viable candidate for biological pacemaker development.

overall_design: RNA-seq profiling of neonatal rat ventricular myocytes transduced with AAV-MCS, AAV-Hcn2 and various AAV-TBX18 vectors.

first: Jianan

last: Wang

first: Karel

last: van Duijvenboden

first: Gerard

last: Boink


title: Metabolite-induced DNA damage drives stochastic stem cell loss and clonal hematopoiesis

first: Bertie

last: Gottgens

email: bg200@cam.ac.uk, nkw22@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

summary: DNA damage and mutations in hematopoietic stem cells (HSC) enable clonal hematopoiesis (CH). Such damage occurs throughout life, but its origins remain unknown. Here, we demonstrate that endogenous formaldehyde causes HSC attrition and subsequently CH. We generated conditional mouse models lacking formaldehyde detoxification and Fanconi anemia (FA) DNA repair in blood. Formaldehyde protection was crucial from embryonic HSC emergence and throughout life. Despite a severe deficiency in HSCs, these mice produce blood for many months. To determine what enables this, we employed a new unbiased method for detecting clones which exploits somatic variant data. This revealed initial polyclonal hematopoiesis which diminishes to monoclonal CH, devoid of known genetic selection. Furthermore, in FA children, we find the same transition to monoclonal hematopoiesis. Therefore, DNA damage-induced attrition down to a last functional cell can be a driving force for CH, representing an alternative route to CH other than purely by fitness-enhancing selection.

overall_design: scRNA-seq was performed on Lin− cKit+ hematopoietic progenitor populations from spleen and bone marrow of conditional Adh5 and/or Fancd2 knockout mice and controls, using 10x Genomics 3’ v3 chemistry, to compare transcriptional states across genotypes.

first: Ashley

middle: N

last: Kamimae-Lanning

first: Jill

middle: M

last: Brown

first: Matthias

last: Günther

first: Franziska

last: Hörsch

first: Holly

last: Russell

first: Lise

last: Larcher

first: Frédéric

last: Langevin

first: Tomoya

last: Isobe

first: Nicola

last: Wilson

first: Felix

middle: A

last: Dingler

first: Rebecca

middle: L

last: Cordell

first: Meng

first: Christopher

last: Millington

first: Nina

last: Claudino

first: Ewa

last: Gogola

first: Matthew

last: Nicholls

first: Verena

last: Körber

first: Berthold

last: Göttgens

first: Marella

last: de Bruijn

first: Juan

last: Garaycoechea

first: Jean

last: Soulier

first: Thomas

last: Höfer

first: Ketan

middle: J

last: Patel


title: Pan-cancer single-cell atlas of mouse and human tumor-associated dendritic cells

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Dendritic cells (DCs) are critical inducers of anti-tumor immunity. Yet, a comprehensive mapping of mouse and human DC subsets and states in a cancer context is lacking. Aiming to address this knowledge gap, we have generated pan-cancer mouse and human tumor-associated DC (TADC) scRNA-seq atlases, encompassing 15 mouse tumor models and 10 human cancer types, within which we identified several lineage-defined DC subsets along with functional states. We show that TADCs acquire an inflammatory profile with tumor progression and that tumor-mediated reprogramming occurs within the DCs from lymph nodes of tumor-bearing mice. Importantly, we demonstrate that TADCs are conserved across mice and human, and that gene signatures of different TADC subsets/states correlate with patient outcomes. Overall, we provide an in-depth characterization of the TADC compartment in mouse and human cancers, which can improve our understanding of the tumor microenvironment and contribute to the development of new anti-cancer therapies.

overall_design: E0771 scRNAseq kinetic dataset: CD45+7-AAD- MHC-IIlow-hiCD11c-/+ cells from tumors of orthotopic E0771 breast cancer mouse model, 9, 14 or 21 days post tumor inoculation. B16-F10 scRNAseq dataset: CD45+7-AAD- cells from tumors of B16-F10 melanoma mouse model. LLC-OVA dataset: CD45+7-AAD- cells (tumors and tumor-draining lymph nodes, scRNAseq) or unsorted splenic cells (scRNA/BCR-seq) of a subcutaneous LLC-OVA lung cancer mouse model. KP kinetic CITEseq dataset: CD45+7-AAD- cells from tumors of a spontaneous KrasLSL-G12D/+; Trp53fl/fl  (KP) lung cancer mouse model,  5 weeks  (early stage) or 8 weeks (late stage)  post Cre-induction. PyMT_spontaneous scRNAseq dataset: CD45+Viobility 488/520- cells from tumors of spontaneous MMTV-PyMT breast cancer mouse model. KPM scRNAseq dataset: unsorted cells from the tumors of a spontaneous KrasLSL-G12D/+;p53fl/fl;Msh2fl/fl (KPM) lung cancer mouse model.

first: Caro

last: Aarushi

first: Laoui

last: Damya


title: CLIP-seq analysis of FLAG-DHX29 in HEK293T cells

city: Kyoto

first: Masanori

last: Yoshinaga

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto University

summary: Synonymous codon usage controls global gene expression in both prokaryotic and eukaryotic species. Non-optimal codons are known to induce mRNA decay; however, the underlying molecular mechanism remains poorly understood in human cells. Through genome-wide CRISPR screening, we identified the RNA-binding protein DHX29 as a critical regulator of codon-dependent gene expression. Cryogenic electron microscopy and selective ribosome profiling demonstrated that DHX29 directly interacts with the A-site entrance of the translating 80S ribosome, the binding site for the eEF1A•GTP•aminoacyl-tRNA ternary complex, suggesting a role in monitoring aminoacyl-tRNA sampling. Proteomic analysis further revealed that DHX29 recruits the GIGYF2•4EHP complex to mediate global suppression of non-optimal mRNAs. These findings establish a mechanistic link between synonymous codon usage and the regulation of gene expression.

overall_design: HEK293T cells stably expressing FLAG-DHX29 were treated with DOX 40 ng/ml for 24 hours. Cell lysate were treated with RNase I digestion at 0.01 unit/ml and supjected to CLIP-seq.

first: Hirotaka

last: Toh

first: Shintaro

last: Iwasaki

first: Osamu

last: Takeuchi


title: A Light-Driven Bioactive Nerve Conduit for Trigeminal Neuralgia: Integrated Decompression and Photosynthetic Oxygenation Restores Mitochondrial Function

city: Chengdu

first: Guihua

last: Wei

address: No.111, North 1st Section, 2nd Ring Rd

institute: Southwest Jiaotong University

summary: Vascular compression and concomitant hypoxia exacerbate trigeminal neuralgia (TN), yet current therapies rarely target both pathologies. We developed a photosynthetic nerve guide conduit (SFM-Gel@ NGC) by embedding auto fluorescent microalgae in silk fibroin hydrogel, enabling simultaneous mechanical decompression and oxygen release. The construct exhibited suitable mechanical properties, tunable oxygen generation, and excellent biocompatibility. Under hypoxia, SFM-Gel promoted neuronal cell proliferation and function by reducing ROS and restoring mitochondrial activity, while downregulating HIF-1α and ATP/P2X3 pathways. In a rat TN model, auto fluorescent SFM-Gel@ NGC implantation alleviated mechanical allodynia, repaired nerve morphology, and suppressed BDNF/NGF and ATP/P2X3 inflammatory signaling. Transcriptomic analysis confirmed modulation of hypoxia/ROS/NF-κB pathways during immune/inflammatory responses to compression. This integrated decompression-oxygenation strategy offers a transformative therapy for TN.

overall_design: To elucidate the molecular mechanisms underlying the therapeutic effect of SFM-Gel @NGC-Light on trigeminal neuralgia, a comparative transcriptomic analysis was conducted. Total RNA was extracted from trigeminal ganglia of two experimental groups: the chronic constriction injury of the infraorbital nerve (CCI-ION) model group and the SFM-Gel @NGC-Light treatment group. RNA sequencing was performed on the Illumina NovaSeq 6000 platform (150-bp paired-end). Differential expression analysis identified genes significantly altered by the treatment, followed by functional enrichment analysis of Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and hallmark gene sets. This design aims to define the transcriptomic reprogramming associated with pain alleviation and neural repair.

first: Zaiqi

last: Li

first: Huiyuan

last: Wang

first: Qing

last: Ye

first: Jieling

last: Zhao

first: Mengqi

last: Huang

first: Jialuoyang

last: Chen

first: Xiong

last: Xiong

first: Ludi

last: Zhang

first: Ling

first: Yuee

last: Dai

first: Shuxin

last: Qu


title: CD5L Promotes Efferocytosis and Resolution of Retinal Ischemic Injury

city: Little Rock

first: Rami

last: Shahror

state: AR

address: 4301 West Markham Street

institute: University of Arkansas for Medical Sciences

summary: Ischemia-induced retinopathy is a defining characteristic of prevalent ocular conditions such as diabetic retinopathy and central retinal artery and vein occlusions. Current therapeutic interventions for ischemic retinopathies have shown limited efficacy, highlighting the need for a better understanding of the underlying mechanisms. Histone deacetylase 3 (HDAC3) is a member of the class I histone deacetylase enzyme family, which participates in regulating gene expression by removing acetyl groups from histone proteins. We have recently uncovered the role of myeloid HDAC3 as a potential key inhibitor of efferocytosis following retinal ischemia, the process by which myeloid cells clear dead cells to facilitate tissue repair. Here, we investigated the underlying mechanism by which HDAC3 inhibits efferocytosis through regulating the CD5 antigen-like (CD5L)/cluster of differentiation 36 (CD36) axis, which was identified through RNA-sequencing. We utilized myeloid-specific HDAC3 knockout (KO) mice in our in vivo studies and in vitro macrophage efferocytosis assays. To assess the role of CD5L in retinal injury, we subjected CD5L KO mice to ischemia-reperfusion (IR) and treated wild-type (WT) mice with recombinant CD5L. We evaluated retinal injury outcomes through retinal imaging, neurovascular assessments, and functional tests conducted in vivo. Additionally, we conducted in vitro studies to investigate the underlying mechanisms. RNA sequencing data identified CD5L as a pro-efferocytic molecule that is upregulated in HDAC3 knockout macrophages after exposure to apoptotic cells in vitro. Similarly, CD5L is also upregulated in the retinas of myeloid HDAC3 knockout mice following IR injury, where it colocalized with myeloid cells. HDAC3 suppresses CD5L transcription in an LXR-dependent manner. Experiments conducted with CD5L KO mice and treatment involving recombinant CD5L protein demonstrated a protective role for CD5L against retinal ischemic injury. Additionally, we found that CD36, a receptor for CD5L that facilitates the clearance of apoptotic cells, is upregulated in the retina myeloid cells following IR injury. In vitro experiments indicated that CD5L mediates efferocytosis via CD36.

overall_design: Gene expression profiling analysis of RNA-seq data from HDAC3 knockout and control macrophages after exposure to apoptotic cells, and non apoptotic cells, or no treatment. The expermintes were done in  biological triplcates.

first: Bushra

last: Zaman

first: Piyanan

last: Chuesiang

first: Melissa

last: Wild

first: Esraa

last: Shosha

first: Yuet-Kin

last: Leung

first: Shengyu

last: Mu

first: Nancy

last: Rusch

first: Abdelrahman

middle: Y

last: Fouda


title: Bulk RNA sequencing of CD36⁺ and CD36⁻ cells isolated from hiPSC-derived airway epithelial cells

city: Kyoto city

first: Shimpei

last: Gotoh

state: Kyoto prefecture

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Department of clinical application

institute: Kyoto University CiRA

summary: To investigate whether CD36 can serve as a reliable surface marker for isolating deuterosomal cells from human induced pluripotent stem cell (hiPSC)-derived airway epithelial cells, we sorted CD36-positive and CD36-negative populations at an early stage of differentiation and performed bulk RNA sequencing. CD36⁺ cells were highly enriched for deuterosomal and multiciliated cell markers

overall_design: CD36-positive and -negative cells were isolated by flow cytometry from air–liquid interface (ALI) cultures of airway epithelial cells differentiated from the B2-3 SFTPC-GFP reporter hiPSC line　(Gotoh et al.,2014). This reporter line was originally established from the 201B7 hiPSC line, which was derived from a healthy donor (Takahashi et al., 2007). Total RNA of CD36-positive and CD36-negative cells was isolated using the RNeasy Micro Kit (Qiagen) following the manufacturer’s instructions. RNA integrity for each sample was assessed using the Agilent 2100 BioAnalyzer, with all samples showing an RNA integrity number (RIN) exceeding 9.5.

first: Haruka

last: Yamaki

first: Satoshi

last: Konishi


title: The role of CNS1 in shaping the CD4+ T cell and Treg response to influenza

city: Chapel Hill

first: Jason

middle: Robert

last: Mock

address: 125 Mason Farm Road

institute: University of North Carolina

summary: Regulatory T cells (Tregs) have critical roles in the recovery from acute lung injury (ALI). Recently, the field has gained critical insights into Tregs in ALI, and the diversity of gene expression and function of Tregs throughout ALI is beginning to be described. However, the origins of these Tregs has remained unknown. Here, we utilized a mouse model lacking the conserved noncoding sequence 1 (CNS1) of the Foxp3 promoter, which results in attenuated peripheral Treg induction, to understand the role(s) of peripheral Tregs in the initiation, pathogenesis, and recovery from acute lung injury. We found that CNS1-deficient mice exhibit more severe ALI and delayed resolution. We find that CNS1 may have roles in shaping the T cell response during influenza and that CNS1-deficient Tregs have several cell-intrinsic maladaptive phenotypes, overall giving us insight into the Treg plasticity that may aid in ALI recovery.

overall_design: To understand the cell-intrinsic effects of CNS1 loss, we generated mixed bone marrow chimeric mice to study the intrinsic differences between wild-type Tregs and Tregs lacking CNS1 in the Foxp3 promoter.  These mixed chimeric mice were then given PR8 induced influenza and two time points bead enrichment of regulatory T cell-enriched lymphocytes were obtained and sent for scMulti-omic analysis and compared to a control mixed chimeric mice not exposed to PR8.

first: Morgan

last: McCullough

first: Hong

last: Dang


title: Single-cell RNA sequencing reveals deuterosomal cells during differentiation of hiPSCs into airway multiciliated cells

summary: We performed single-cell RNA sequencing (scRNA-seq) to investigate the differentiation of human induced pluripotent stem cells (hiPSCs) into airway multiciliated cells. The analysis revealed diverse epithelial cell types, including basal, secretory, goblet, and pulmonary neuroendocrine cells, as well as a distinct population of deuterosomal cells. This dataset provides a valuable resource for studying human multiciliogenesis and related diseases.

overall_design: Single-cell libraries were constructed using the Chromium platform (10X Genomics) and the Single Cell 3′ Reagent Kits v3.1 according to the manufacturer’s protocols. Sequencing data were processed using Cell Ranger (v8.0.1) for demultiplexing, alignment to the GRCh38 reference genome (refdata-gex-GRCh38-2020-A, including reporter sequences), and generation of gene count matrices.

first: Koji

last: Tamai


title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells [ATAC-seq]

first: Shinichiro

last: Sawa

overall_design: To elucidate the regulatory mechanisms of RORγt expression specific to ILC3s, we comprehensively performed ATAC-seq across cell lineages and differentiation stages in RORγt-positive cells

first: Takuma

last: Fukui

first: Miyuki

last: Watanabe

last: Kojo

first: Eriko

last: Sumiya


title: Signaling cascades shape functional subpopulations of cortical astrocytes in male wild-type mice and APP/PS1dE9 Alzheimer’s disease model

city: Evry

first: Eric

last: Bonnet

address: 2 rue Gaston Crémieux

institute: CNRGH

summary: Astrocytes are key partners for neurons and can impact diseases such as Alzheimer's disease (AD), as they exhibit multiple reactive changes. Recent single cell/nucleus genomics analyses evidence astrocyte subpopulations coexisting in normal and AD brains. However, the signaling cascades controlling them, their functional characteristics and roles in AD are still unknown. Here, thanks to astrocyte-specific reporters for STAT3 and NF-kB signaling pathways, two regulators of astrocyte reactivity, we report the presence of three astrocyte subpopulations defined by their signaling activity, in the prefrontal cortex of male APP/PS1dE9 mice. These subpopulations are not triggered by amyloid deposition and are also observed in wild-type mice. They show distinct morphologies, molecular signatures and functional profiles. While NF-kB+ astrocytes have larger territories and higher lysosomal activity, STAT3+ astrocytes display enhanced hemichannel activity. The specific inhibition of these subpopulations reduces amyloid plaque size and impacts anxiety, social preference and social memory in AD but not wild-type mice. Our results show how innate signaling shapes astrocyte subpopulations in the mouse cortex, with distinct functions in health and disease.

overall_design: Experiments were carried out on one-year-old male APP/PS1dE9 (APP) mice (Jankowsky et al., 2004) on the C57BL/6J background and their WT littermates. These mice express a chimeric mouse/human APP695 gene containing the Swedish K670M/N671L mutations (APPswe) and human PSEN1 with a deletion in exon 9 (PS1dE9). Mice were injected with two fluorescent lentivirus based reporters for the STAT3 and NF-KB pathways, which target astrocytes. Astrocytes from the mouse PFC were then sorted based on their expression of fluorescent reporters (GFP=STAT3; CFP=NF-kB), into three subpopulations (STAT3, NF-kB, double). The protocol described in (Ceyzeriat et al., 2018) was used to analyze the transcriptome of the three astrocyte subpopulations, except that the lower number of astrocytes sorted per sample was not compatible with RNA quality assessment, and full length double strand cDNA libraries were amplified with 18 LD-PCR cycles. RNAseq libraries were sequenced on a Novaseq Illumina 6000 platform (2x100 bp). Quality control of sequencing data was performed with FastQC (v0.11.9). Reads were mapped on the GRCm39 (mm39) mouse genome assembly with STAR (v2.7.9a) and quantified with RSEM (v1.3.3).

first: Yiannis

last: Poulot-Becq Giraudon

first: Océane

last: Guillemaud

first: Elisa

last: Degl'Innocenti

first: Vivien

last: Letenneur

first: Karouna

last: Bascarane

first: Tony

last: Barbay

first: Mie

last: Møller Clausen

first: Céline

last: Derbois

first: Martine

last: Guillermier

first: Ludmila

last: Juricek

first: Miriam

last: Riquelme-Perez

first: Tom

last: Lakomy

first: Lucile

last: Benhaim

first: Noëlle

last: Dufour

first: Pauline

last: Gipchtein

first: Fanny

last: Petit

first: Léa

last: Siron

first: Gwennaëlle

last: Aurégan

first: Nathalie

last: Dechamps

first: Marie-Claude

last: Gaillard

first: Alexis

middle: P

last: Bemelmans

first: Rémi

last: Bos

first: Maria-Angeles

last: Carrillo-de Sauvage

first: Giampaolo

last: Milior

last: Rouach

first: Solène

last: Brohard

first: Kévin

last: Muret

first: Carole

last: Escartin


title: Caspase-8 silences cell death-independent constitutive immune activation driven by tonic TNF-α

city: Messina

first: Concetta

last: Beninati

state: ME

address: Via Consolare Valeria 1

department: Human Pathology

country: Italy

institute: University of Messina

summary: Caspase-8 maintains organismal integrity by preventing cell death and secondary inflammation in selected epithelial and endothelial tissues. Here we show that caspase-8 also controls a systemic, cell death-independent inflammatory pathway that is constitutively activated during homeostasis. In vivo, selective caspase-8 inhibition produces, in the absence of other stimuli, marked neutrophilia driven by circulating proinflammatory and chemotactic cytokines. In vitro, caspase-8 inhibition triggers in neutrophils, but not in macrophages, a profound transcriptional response associated with the release of IL-1βand other cytokines. This process requires tonic TNF-α production by neutrophils, which acts autocrinally to sequentially activate RIPK1, RIPK3,MAPKs and NF-κB. The IL-1βrelease induced by caspase-8 inhibition requires gasdermin D and neutrophil serine proteases, but not canonical inflammasome components, such as NLRP3 and ASC, or gasdermin E. Our data unveil the mechanistic features of a neutrophil-centric, pro-inflammatory pathway that can be therapeutically targeted to augment host defenses against pathogenic agents.

overall_design: RNA-seq profiling of murine Neutrophils and Macrophages isolated frombone marrow and treated for 3 h with Caspase-8 inhibitor (z-IETD-fmk 50 µM) or vehicle (DMSO 0,2%).

first: Germana

last: Lentini

first: Francesco

last: Coppolino

first: Agata

last: Famà

first: Giuseppe Valerio

last: De Gaetano

first: Federica

last: Grasso

first: Luigi

last: Fiore

first: Alessia

last: Berbiglia

first: Silvia

last: Carnevale

first: Isabella

last: Venza

first: Egil

last: Lien

first: Terje

last: Espevik

first: Mario

first: Sebastien

last: Jaillon

first: Giuseppe

last: Teti


title: Global transcription changes driven by the second messenger cyclic di-GMP in Acinetobacter baumannii AB0057

city: Southampton

first: Rubén

last: de Dios

state: Hampshire

address: University Road

department: School of Biological Sciences

institute: University of Southampton

summary: In order to know the effect of the second messenger cyclic di-GMP (cdGMP) on the global transcription of A. baumannii AB0057, we performed a differential RNA sequencing (dRNA-seq) experiment comparing two AB0057 derivatives that allow IPTG-induced overexpression of the phosphodiesterase coding gene rocR (decreases cdGMP levels) or a constitutively active version of the diguanylate cyclase pleD (pleD*, increases cdGMP levels). As a result,  98 genes appeared upregulated >2-fold in high cdGMP conditions (overexpressing pleD*) whereas 143 were downregulated. In highlights, the gene functional groups showing the strongest transcriptional alterations were those related to biofilm formation (upregulated) and twitching motility (downregulated).

overall_design: A. baumannii AB0057 derivatives carrying either rocR or pleD* inserted in a miniTn7 transposon  were grown in LB supplemented with IPTG 1 mM (3 biological replicates per strain) until reaching mid-exponential phase (approx. OD600 0.6). At this point, cells were harvested, treated with RNAlater for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample and sequenced, followed by a differential gene expression analysis.

first: Ronan

last: McCarthy


title: Pericytes are organ-specific regulators of tissue morphogenesis

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

institute: Max Planck Institute for Molecular Biomedicine

summary: Blood vessels provide a versatile and adaptable transport system, but recent work has established that endothelial cells, which form the innermost lining of the vascular network, are also a source of molecular signals controlling the behavior of other cell types in the surrounding tissue. Pericytes are another essential component of the vessel wall, but comparably little is known about their signaling interactions with other cell populations during organ growth and patterning. Here, we have used tissue-specific and inducible mouse genetics, high-resolution imaging, single-cell RNA sequencing and cell culture experiments to address the function of three pericyte-derived growth factors in the postnatal development of two model organs, namely lung and brain. We found that Pdgfrb-CreERT2-controlled inactivation of the gene for hepatocyte growth factor (HGF) causes no overt alterations in the postnatal brain but impairs alveologenesis in the lung due to defective interaction with AT2 epithelial cells. Likewise, expression of brain-derived neurotrophic factor (BDNF) by pericytes is not required in the postnatal brain but controls lung development through interactions with the receptor tyrosine kinase TrkB in the pulmonary endothelium. Conversely, pericyte expression of the TGFβ family growth factor Nodal is not required for lung morphogenesis but regulates blood vessel growth and barrier function in the postnatal brain, which we attribute to signaling interactions with endothelial cells, astrocytes and microglia. Taken together, our findings establish that pericytes are a critical source of angiocrine signals that control morphogenetic processes in an organ-specific fashion.

overall_design: For the single cell sequencing of postnatal lung, two Hgf lox/lox  control mice and two Hgf iPCKO P21 old pups or two Bdnf lox/lox  control mice and two Bdnf iPCKO P21 old pups were analyzed, respectively. For the single cell sequencing of postnatal brain, the P12 cerebral cortices belonging to mice from the same genotype were pooled together

first: Seyed Javad

last: Rasouli

first: Rodrigo

last: Diéguez-Hurtado

first: Parisa

last: Ghanbari

first: Anusha

last: Aravamudhan

first: Mara-Elena

last: Pitulescu

first: Ralf

middle: H

last: Adams


title: Epigenetic evolution of IDHwt glioblastomas

city: Rotterdam

first: Bo

last: Deng

address: Dr. Molewaterplein 40

institute: Erasmus MC

summary: Although the genetic evolution of IDH-wildtype glioblastomas has extensively been investigated, limited studies have addressed the epigenetic evolution. Understanding the epigenetic evolution is particularly relevant as demethylation of the MGMT promoter may form a means to treatment resistance.  Methods  We generated whole genome DNA methylation data of 64 matched primary-recurrent samples from IDH-wildtype glioblastoma patients. Data were combined with three publicly available datasets into a final cohort consisting of 418 samples. In the combined dataset, we determined change in genome-wide DNA-methylation. MGMT promoter methylation was defined using the MGMT-STP27 algorithm. CoxPH regression was used to investigate the impact of identified changes on survival.   Results  Our analysis demonstrates that the methylome of IDH-wildtype glioblastomas is highly stable. Changes that do occur can mostly be allocated to differences in tumor purity. Conversion from a MGMT promoter methylated to unmethylated status at progression occurred infrequently, but significantly more often than the converse. Conversion was associated with poorer overall and progression-free survival compared to those that remained MGMT methylated. Similar to previously reported, MGMT promoter methylation status was significantly associated with overall-, progression-free and post-recurrence survival. Despite this large survival difference, very few CpGs were co-methylated with the MGMT methylation status. Of these, the vast majority lied within the MGMT gene body and were inversely correlated with MGMT promoter methylation status.    Conclusions   The methylome of IDH-wildtype glioblastomas is highly stable at tumor progression. This stability is also present in the MGMT promoter.

overall_design: Genome-wide DNA methylation data was generated from 64 samples of patients included in the GSAM (Glioblastoma-Stability of Actionable Mutations) study.DNA methylation profiling for all GSAM samples was performed using the Illumina EPIC (850K) methylation array. For this, tumor DNA was extracted from FFPE tissue using the QIAamp DNA FFPE Tissue Kit (Qiagen), and the quantity of isolated DNA was assessed with a Qubit 3.0 fluorometer (Invitrogen). Genome-wide DNA methylation profiling was done using the Illumina HumanMethylationEPIC (850K) beadchip.

first: Pim

last: French


title: Transfer RNA quantifications in HEK293T cells by tRNA sequencing

first: Masanori

last: Yoshinaga

overall_design: Transfer RNAs in HEK293T cells were quantified by tRNA-seq analysis.

first: Takayuki

last: Ohira

first: Masaki

last: Takegawa

first: Tsutomu

last: Suzuki

first: Osamu

last: Takeuchi


title: Selective ribosome profiling of the DHX29-bound ribosomes in HEK293T cells

overall_design: HEK293T cells expressing FLAG-DHX29 were lysed, and ribosome footprints were isolated from the input and FLAG-DHX29-bound ribosomes. The ribosome footprints were then subjected to Thor-Ribo-Seq analysis.

first: Mari

last: Mito

first: Yuichi

last: Shichino

first: Shintaro

last: Iwasaki


title: Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Respons

city: DUARTE

first: Naseeb

last: Malhi

address: 1500 E Duarte Road

department: DMRI

institute: City of Hope

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

overall_design: Refer to individual Series


title: Effect of DHX29 depletion on mRNA stability in HEK293T cells

overall_design: Control and DHX29-deficient HEK293T cells were generated by transducing Cas9-expressing cells with vectors expressing control and DHX29-targeting gRNAs. The cells were treated with 4-thiouridine for 24 hours and then cultured in media containing uridine for 0, 3, and 6 hours. The samples were analyzed using SLAM-seq.

first: Yitong

last: Wu


title: Effect of DHX29 depletion on gene expression in HEK293T cells

overall_design: Control and DHX29-deficient HEK293T cells were generated by transducing Cas9-expressing cells with vectors expressing control and DHX29-targeting gRNAs, and subjected to RNA-seq analysis.

first: Fabian

last: Hia


title: Effect of DHX29 depletion on gene expression in K562 cells

overall_design: Control and DHX29-deficient K562 cells were generated by transducing Cas9-expressing cells with vectors expressing control and DHX29-targeting gRNAs, and subjected to RNA-seq analysis.


title: Effect of DHX29, GIGYF2, 4EHP, and DHX29/4EHP depletion on gene expression in K562 cells

overall_design: RNA-seq analysis was performed on Control, DHX29-, GIGYF2-, 4EHP-, and DHX29/4EHP-knockdown K562 cells generated by the CRISPRi system.


title: Global transcription changes driven by the second messenger cyclic di-GMP in Acinetobacter baumannii AB5075

first: Rubén

last: de Dios

summary:
In order to know the effect of the second messenger cyclic di-GMP (cdGMP) on the global transcription of A. baumannii AB5075, we performed a differential RNA sequencing (dRNA-seq) experiment comparing two AB5075 derivatives that allow IPTG-induced overexpression of the phosphodiesterase coding gene rocR (decreases cdGMP levels) or a constitutively active version of the diguanylate cyclase pleD (pleD*, increases cdGMP levels)
A. baumannii AB5075 derivatives carrying either rocR or pleD* inserted in a miniTn7 transposon  were grown in LB supplemented with IPTG 1 mM (3 biological replicates per strain) until reaching mid-exponential phase (approx. OD600 0.6). At this point, cells were harvested, treated with RNAlater for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample.
As a result,  154 genes appeared upregulated in high cdGMP conditions (overexpressing pleD*) whereas 188 were downregulated. In highlights, the gene functional groups showing the strongest transcriptional alterations were those related to biofilm formation (upregulated) and twitching motility (downregulated).

overall_design: Three independent replicates of A. baumannii AB5075 carrying either rocR or pleD* in an IPTG-inducible expression system were grown to mid-exponential phase in LB supplemented with IPTG 1 mM and compared between the two sample groups.

first: Ronan

last: McCarthy