title: Single-cell transcriptomic analysis suggests potential differences in the developmental stage and quantity of adipose progenitor cells between bovine intramuscular and subcutaneous fat

city: BLACKSBURG

first: Zhendong

last: Tan

state: VA

address: 175 West Campus Drive

institute: Virginia Tech

summary: Background: Intramuscular fat (IMF), the white adipose tissue deposited between skeletal muscle fibers, is a key determinant of beef quality due to its contribution to meat, flavor, juiciness and tenderness. However, IMF develops later and grows more slowly, compared to other fat depots such as subcutaneous fat (SF) in cattle. The cellular and molecular mechanisms underlying the delayed development and slower growth of IMF compared to other fat depots remain poorly understood. Results: We performed single-cell RNA sequencing (scRNA-seq) on the stromal vascular fractions (SVFs) from IMF and SF of adult Angus crossbred steers as well as the mononuclear cell fractions (MCFs) from skeletal muscles of newborn Angus crossbred bull calves, with each tissue type collected from two animals. A total of 14,802 cells from 6 animals were sequenced. A clustering analysis revealed that these cells comprised ten cell types, including adipose progenitor cells (APCs), muscle satellite cells (MuSCs), myoblasts, smooth muscle cells, and various immune cell populations. The SF SVF from adult cattle harbored a significantly higher proportion of APCs than the IMF SVF. The MCFs from newborn calves did not contain detectable APCs. A subclustering analysis revealed that the APCs comprised six subpopulations (C0–C5), among which C3 and C5 were absent in the IMF SVF while C1 was markedly less abundant in the IMF SVF than the SF SVF. A gene set variation analysis and a pseudotime trajectory analysis showed that C1 and C3 represented more differentiated APCs, with higher expression of genes involved in adipogenesis, such as PPARG, ADAM12, and PPARGC1A, whereas subclusters C0 and C4 represented undifferentiated, uncommitted APCs, with higher expression of genes involved in DNA replication and cell adhesion, compared to the other subclusters. Conclusions:Overall, this single-cell transcriptomics study suggests two potential differences in APCs between IMF and SF in adult cattle: (1) IMF contains fewer APCs than SF; (2) APCs in IMF are adipogenically less committed and differentiated compared to APCs in SF. These differences may explain why IMF develops later and grows more slowly than SF in cattle. This study also suggests that, in cattle, intramuscular fat begins to develop postnatally, challenging the widely held belief that it forms during late gestation.

overall_design: Stromal vascular fractions (SVFs) were isolated from intramuscular fat (IMF) and subcutaneous fat (SF) of adult Angus crossbred steers (n = 2 per tissue type). Mononuclear cell fractions (MCFs) were isolated from longissimus dorsi skeletal muscles of newborn Angus crossbred bull calves (n = 2). Single-cell RNA sequencing (scRNA-seq) libraries were prepared using the 10x Genomics Chromium Single Cell 3’ platform and sequenced on an Illumina NovaSeq 6000. The study aimed to compare the abundance, subpopulation composition, and differentiation states of adipose progenitor cells (APCs) between IMF and SF, and to determine whether APCs are present in neonatal skeletal muscle.

first: Pengcheng

last: Lyu

first: Honglin

last: Jiang


title: Chronic stress disrupts hepatic kynurenine pathway to subvert hepatic CD8+ T cell immunity and promote liver cancer

status: Public on Nov 04 2025

city: Jinan

first: Renhui

last: Sun

state: Shandong

address: 44 Wenhua west road

country: China

institute: Shandong University

type: Expression profiling by high throughput sequencing

summary: Chronic psychological stress is associated with liver disease mortality, yet the reasons are unclear. Here we describe a stress-responsive brain-liver regulatory circuit that impairs CD8+T cell immunity and promotes the progression of liver cancer. Specifically, psychological stress-mediated dysregulation of catecholamine/β2-adrenergic receptor (ADRB2) signaling leads to reduced number and effector functions of liver CD8+ T cells by suppressing the expression of quinolinate phosphoribosyl transferase (QPRT) in hepatocytes and shifting hepatic Kyn metabolism from de novo nicotinamide adenine dinucleotide (NAD+) synthesis to kynurenic acid (KA) production. Notably, ADRB2/QPRT expression in human hepatocytes correlates with NAD+ and KA levels, as well as CD8+T cells frequency and function in human liver tissues.

overall_design: To investigate chronic stress-induced liver CD8+T cell injury, liver CD8+T cells from control and CUMS mice were purified for RNA-seq.


title: Minimal edit, maximal effect: extended survival SCID pigs with single amino acid deletion [RNA-Seq]

city: Seoul

first: Min-Hee

last: Kang

state: Seoul

address: 120 Neungdong-ro

department: Stem Cell and Regenerative Biotechnology

country: South Korea

institute: Konkuk University

summary: Severe combined immunodeficiency (SCID) represents a critical area of research for understanding human immune disorders and developing therapeutic interventions. While murine models have provided valuable insights, their translational relevance is limited by physiological differences from humans. Here, we established and characterized a novel RAG2 biallelic knock out (RAG2bKO) model using TALEN-mediated gene editing, which demonstrates extended viability in specific pathogen-reduced facilities while maintaining complete immunodeficiency. Our model exhibits a precise in-frame deletion of a single histidine residue (p.His109del) in the RAG2 protein, resulting in structural destabilization and functional impairment. Comprehensive phenotypic analysis revealed complete thymic aplasia, splenic hypoplasia, and ablation of mature T and B lymphocytes. RNA-seq and H3K4me3 ChIP-seq approaches, including transcriptomic and epigenomic analyses, demonstrated conserved dysregulation of immune pathways across lymphoid tissues, with significant suppression of adaptive immune pathways and compensatory upregulation of innate immune mechanisms. The RAG2bKO pigs showed extended survival up to one year in controlled environments, representing a significant improvement over existing models. This large animal model provides a robust platform for studying SCID pathogenesis, evaluating long-term therapeutic interventions,

overall_design: To investigate the transcriptomic consequences of RAG2 deficiency, we performed RNA sequencing on lymphoid tissues (lymph node, spleen and thymus) from RAG2 biallelic knockout (RAG2bKO) pigs and their wild-type (WT) littermates.

first: Jin-Hoi

last: Kim

first: Kiho

last: Lee

first: Jeongho

last: Hwang

first: Kwonho

last: Hong


title: Lactyl-HDAC1-Mediated Epigenetic Gating of Angiogenic Transcription via Metabolic Reprogramming [RNA-seq]

city: Ganzhou

first: Weijian

last: Zhu

address: No. 1, Hexie Blvd

institute: Gannan Medical University

summary: While angiogenesis serves as a cornerstone of embryogenesis and a defining feature of pathological progression, a critical gap persists in understanding how metabolic signaling precisely converges with nuclear reprogramming to ignite vascular growth. Here, we demonstrate that glucose-derived lactate via glycolysis induces site-specific lactylation at lysine 412 (K412) of histone deacetylase 1 (HDAC1), triggering transcriptional activation of pro-angiogenic genes such as VEGFA. Mechanistically, HDAC2 forms a nuclear complex with HDAC1 to suppress its lactylation modification in the cytoplasm, whereas alanyl-tRNA synthetase (AARS1) promotes its lactylation in cytoplasm to prevent HDAC1 nuclear translocation, leading to nuclear accumulation of H3K56 acetylation and chromatin remodeling that selectively activates angiogenesis-related transcriptional programs. In zebrafish models, HDAC1-K412 mutation caused embryonic lethality, and site-specific lactylation dynamically increased during cardiac development. In the HDAC1 K412A mutation knock-in mouse model, the results showed that this site prevents vascular proliferation in the retinas of streptozotocin (STZ)-induced diabetic mice. Pharmacologically, we found that the HDAC1 activator Exifone suppressed its lactylation and inhibited vascular growth. Strikingly, Exifone attenuates pathological neovascularization in embryonic chick models and halts aberrant vascular proliferation within the retinal vasculature of STZ-diabetic mice. Our findings reveal HDAC1 lactylation as a metabolic-epigenetic nexus governing angiogenesis, providing mechanistic insights into not only obscures developmental principles but hampers therapeutic targeting of aberrant vascularization in diseases ranging from cancer to diabetes.

overall_design: RNA-seq profiling of wildtype HUVEC cells after 12-hour treatment with high glucose (25 mM) or low glucose (5 mM).

first: Chunbo

last: Zhang

first: Jianing

last: Zhong


title: Minimal edit, maximal effect: extended survival SCID pigs with single amino acid deletion [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To investigate the epigenomic landscape alterations due to RAG2 deficiency, we performed Chromatin Immunoprecipitation sequencing (ChIP-seq) targeting the active promoter mark H3K4me3. Lymphoid tissues (lymph node, spleen and thymus) from RAG2 biallelic knockout (RAG2bKO) pigs and their wild-type (WT) littermates were used.


title: The outcomes of caloric restriction are driven by enhanced glucocorticoid rhythms.

city: Neuherberg

first: fabiana

last: quagliarini

address: Ingolstaedter Landstr 1

country: Germany

institute: helmholtz munich

summary: Caloric restriction extends lifespan and healthspan across species, with feeding times synchronized to circadian rhythms further maximizing its benefits. However, the mechanisms linking diet, diurnal rhythms, and lifespan are not fully understood. In mice, the time point most strongly tied to dietary effects on lifespan coincides with the peak of glucocorticoid secretion (ZT12, lights-off). Caloric restriction raises circulating glucocorticoid hormone levels, but their functional relevance remains untested. We show that the glucocorticoid receptor (GR) is critical for the effects of caloric restriction. Hepatocyte-specific GR mutant mice fail to respond to caloric restriction indicating that increased glucocorticoid amplitudes support its benefits. Using multiomics techniques in murine liver, we find that nutrient deprivation elicits a nuclear switch from active STAT signaling to increased FOXO1 activity, enabling the GR to activate a unique diet-specific gene expression program. Taken together, our results suggest that glucocorticoid rhythms are crucial for caloric restriction-induced metabolic reprogramming.

overall_design: Wild-type and glucocorticoid receptor hepatocyte-specific knock-out (GR-LKO) mice were treated to 40% caloric restriction (CR) or night-restricted fed (NRF) as control. Then we harvested their liver, and isolation the liver nuclei through centrifugation.

first: Konstantinos

last: Makris

first: Ioannis

middle: K

last: Deligiannis

first: Liwei

first: Fania

last: Feby Ramadhani

first: Celia

middle: P

last: Martinez-Jimenez

first: Fabiana

last: Quagliarini

first: Nina Henriette

last: Uhlenhaut


title: Lactyl-HDAC1-Mediated Epigenetic Gating of Angiogenic Transcription via Metabolic Reprogramming [ChIP-seq]

overall_design: ChIP-seq of H3K56ac in wildtype HUVEC cells after 12-hour treatment with high glucose (25 mM) or low glucose (5 mM).


title: RNA delivery to the corneal endothelium using charge-altering releasable transporters

city: Stanford

first: Sean

last: Wang

state: CA

address: 1291 Welch Rd

country: USA

institute: Stanford University

summary: RNA therapies hold tremendous promise for treating genetic eye diseases. However, their development is limited by the lack of non-viral delivery platforms that can target specific ocular cell types. Here, we describe a charge-altering releasable transporter (CART) that delivers RNA selectively to the corneal endothelium, a non-regenerative cell layer whose dysfunction underlies several blinding conditions. We characterize the safety of CART-RNA nanoparticles in mice and show that they facilitate delivery of diverse RNA cargoes to the corneal endothelium, including circular RNA and CRISPR/Cas9. We verify the feasibility of redosing these nanoparticles and apply them to achieve corneal gene editing. We further demonstrate CART transfection of corneal endothelial cells from a human donor in vitro and in a non-human primate in vivo, supporting translatability to patients. Our findings establish CARTs as a platform for non-viral gene delivery to the eye, with the potential to treat corneal dystrophies and other vision disorders.

overall_design: RNA-seq of sorted cells from Ai9 mouse anterior segments without treatment or 1 week after intracameral injection of Cre mRNA with CART 8. RNA-seq of C57BL/6J mouse anterior segments 48 hours after intracameral injection of EGFP mRNA with or without CART 8.

first: Howard

middle: Y

last: Chang


title: Rat-specific Expression of Placental MATE1 Contributes to Species Difference in Fetal Transfer of Metformin and 1-Methyl-4-phenylpyridinium

city: Tokyo

first: Pharmaceutics

last: Keio

address: 1-5-30 Shibakoen, Minato-ku

department: Pharmacy

country: Japan

institute: Keio University

summary: Metformin readily crosses the human placenta. However, the fetal-to-maternal plasma concentration ratio (F/M ratio) of metformin has been reported to be as low as 0.057 in rats. This study investigated the underlying mechanisms of these interspecies differences by examining the expression and function of candidate transporters, organic cation transporter 3 (OCT3/SLC22A3) and multidrug and toxin extrusion protein 1 (MATE1/SLC47A1), in the placenta across species. Expression analysis at gene and protein levels using RNA-sequencing and absolute quantification by LC-MS/MS revealed minimal species differences in placental OCT3 expression (less than 4-fold for mRNA and protein). In contrast, MATE1 showed almost exclusive expression in the rat placental labyrinth but minimal or undetectable levels were observed in samples prepared from human placental villi and mouse placental labyrinth. To evaluate the function of the placental MATE1, we compared the placental transfer of two MATE1/OCT3 substrates, metformin and 1-methyl-4-phenylpyridinium (MPP+), in pregnant rats and mice in the presence and absence of pyrimethamine, a MATE1 inhibitor. The pyrimethamine was dosed to reach the plasma concentration which specifically inhibits MATE1 based on the measured IC50 of pyrimethamine to rat Mate1 and Oct3, which were 0.015 μM and 100 μM, respectively. The F/M ratios of metformin and MPP+ in the absence of pyrimethamine were half or less in rats compared to mice. Notably, pre-administration of pyrimethamine increased the F/M ratios of metformin and MPP+ by approximately 50% in rats but not mice. These findings demonstrate that functional placental MATE1 expression is specific to rats, which, in part, contributes to the low fetal transfer of cationic compounds compared to other species. This is of significant concern, as it suggests that nonclinical developmental and reproductive toxicity studies of MATE1 substrate drugs in rats may underestimate fetal exposure and toxicity when extrapolated to humans.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: RNA-seq profiling of placental labyrinth of gestational day (GD) 17.5 C57BL/6J mice and GD 20.5 SD rats.

first: Ashukan

last: Suzuki

first: Saki

last: Noguchi

first: Toshiaki

last: Tsuchitani

first: Takuro

last: Ishinabe

first: Masatoshi

last: Tomi


title: Charting the Multi-Level Molecular Response to Palbociclib in ER-Positive Breast Cancer

city: Chapel Hill

first: Archishma

last: Kavalipati

state: North Carolina

address: 120 Mason Farm Rd

department: Pharmacology

institute: UNC Chapel Hill

summary: The addition of CDK4/6 inhibitors to endocrine therapy has significantly improved outcomes in HR+/HER2- breast cancer. However, variable patient responses and acquired resistance remain a clinical challenge. We therefore defined the comprehensive molecular response to palbociclib, the most clinically used CDK4/6 inhibitor. Global analyses of gene expression, protein abundance, splicing, and chromatin accessibility revealed broad patterns and specific changes that result from CDK4/6-inhibition in breast cancer cells. We uncovered unexpected feedback between CDK4/6 and estrogen-response signaling, which has clear clinical implications. We also revealed a widespread alternative splicing program that partially overlapped with genes whose expression is regulated, and which is expected to impact protein function. These molecular changes nominated combination therapies that interfere with the activation of CDKs or ERα. Accordingly, co-targeting CDK7, which regulates CDK2, CDK4/6 and ERα, additively impacted cell fitness.  Collectively, these data reveal a complex, multi-tiered response to CDK4/6 inhibition, with implications for therapeutic efficacy.

overall_design:
6 RNA-seq samples total. 3 biological replicates of T-47D treated with 1 uM palbociclib for 24 hours and 3 biological replicates of T-47D treated with DMSO (control) for 24 hours.
6 ATAC-seq samples total. 3 biological replicates of T-47D treated with 1 uM palbociclib for 24 hours and 3 biological replicates of T-47D treated with DMSO (control) for 24 hours

first: Daniel

last: Dominguez

first: Michael

middle: J

last: Emanuele


title: Single Cell Transcriptomics of human carotid artery plaques V2

city: München

first: Jessica

last: Pauli

state: Bayern

address: Biedersteiner Str. 29

department: Molecular Vascular Medicine

institute: TUM Universitätsklinikum (Klinikum rechts der Isar)

summary: We profiled the single-cell transcriptome and analyzed the diversity of cell types present in human atherosclerotic tissue specimens (carotid artery, CAR). Therefore we carried out scRNA-seq from 7 different patients.

overall_design: To profile single-cell transcriptome and analyze the diversity of cell types present in human atherosclerotic tissue specimens (carotid artery, CAR), we carried out scRNA-seq from 7 different patients.

first: Lars

last: Maegdefessel


title: SKIDA1 transiently sustains MLL::ENL-Expressing hematopoietic progenitors during neonatal stages and promotes B-lineage priming [RNA-Seq]

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

summary: To assess cell-autonomouse transcriptional responses to MLL::ENL induction at different ages, we performed Peformed bulk RNA-sequencing on cultured cells.

overall_design: We sorted Lineage-Sca1+KIT+ progenitors from control or MLL::ENL Tet-On-ME mice, induced MLL::ENL in culture and cultured for 48hrs. We performed RNA-seq  at E16, P14, and 8wk.

first: Jonny

last: Mendoza-Castrejon

first: Jeffrey

middle: A


title: Major waves of H2A.Z incorporation during mouse oogenesis and preimplantation embryo development

city: Copenhagen

first: Erkut

last: Ilaslan

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: Epigenomes of mammalian oocytes and embryos undergo major transitions essential for successful development. Here, we provide genome-wide maps of histone variant H2A.Z during twelve stages of mouse oogenesis and preimplantation embryo development and relate it to histone marks and genomic features. This revealed that major waves of H2A.Z incorporation occur early in growing oocytes, forming distinct patterns of maternal, embryonic, and persistent H2A.Z enrichment. Late maternal enrichment is inherited by the zygote, and precedes reduced formation of lamina associated domains and early replication in the maternal genome of 2-cell embryos. Persistent H2A.Z enrichment is strongly associated with CpG islands and H3K4me3 near transcription start sites of active genes, but thousands of maternal and embryonic H2A.Z incorporation sites exist elsewhere, frequently at transposable elements. The persisting H2A.Z enrichments across related developmental stages enable preservation of epigenetic information despite major concurrent changes in H3K4me3, H3K27me3, and DNA methylation. Altogether, this advances our understanding of how histone variants contribute to epigenetic reprogramming during mammalian oogenesis and early development.

overall_design: H2AZ profile in oocytes and early embryos were characterized using picoChIP-seq.

first: Madeleine

last: Fosslie

first: Trine

last: Skuland

first: Michel

last: Choudalakis

first: Mirra

last: Søegaard

first: Jason

last: Halliwell

first: Shaista

last: Khan

first: Marie

last: Indahl

first: Maria

last: Vera-Rodriguez

first: Adeel

last: Manaf

first: Annika

middle: V

last: Geijer-Simpson

first: Rajikala

last: Suganthan

first: Ingunn

last: Jermstad

first: Knut

middle: T

last: Dalen

first: Ragnhild

last: Eskeland

first: Elisabeth

last: Kommisrud

first: Arne

last: Klungland

first: Magnar

last: Bjørås

first: Peter

last: Fedorcsak

first: Gareth

middle: D

last: Greggains

first: Mika

last: Zagrobelny

first: John

last: Dahl

first: Mads

last: Lerdrup


title: Xenium spatial transcriptomics of human carotid artery plaques

first: Jessica

last: Pauli

summary: We performed Xenium single cell transcriptomics on 4 plaques with matched controls (8 samples in total) and 8 additional plaques. A total of 16 samples was sequenced with two panels each.

overall_design: Xenium single cell transcriptomics with 2 Panels on 4 plaques with matched controls (8 samples in total) and 8 additional plaques

first: Lars

last: Maegdefessel

first: Daniel

last: Garger


title: Radon Exposure Delays the Development of Skin Lesions in a Mouse Model of Psoriasis

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary: We used transgenic mice that spontaneously develop chronic psoriatic skin lesions inflicted (CD11c-IL-17Aind/ind mice) to investigate effects induced by multiple radon exposures. Comprehensive transcriptome profiling of non-lesional skin showed downregulation of genes associated with psoriasis initiation, while anti-inflammatory genes were upregulated. Pathway enrichment analysis revealed immunosuppressive effects related to T cell regulation, similar to UV radiation-induced response.

overall_design: Investigation of plaque formation (skin) throughout the observation period; cytokine release (serum), immune status and proliferation marker after sacrification. Transcriptome profiling (skin) was performed.

first: Sylvie

last: Lerchl

first: Julia

last: Wiedemann

first: Andreas

last: Maier

first: Franziska

last: Papenfuß

first: Anna

last: Brand

first: Björn

middle: E

last: Clausen

first: Claudia

last: Fournier


title: SKIDA1 transiently sustains MLL::ENL-Expressing hematopoietic progenitors during neonatal stages and promotes B-lineage priming [scRNA-Seq]

first: Jeffery

last: Magee

summary: To assess changes in transcriptional responses to Skida1 deletion in the context of MLL::ENL, we performed CITE-seq on Tet-Off-ME mice.

overall_design: We sorted Lineage-KIT+ progenitors from P0 livers. We performed CITE-seq on Control, MLL::ENL, or MLL::ENL; Skida1-deleted mice.

first: Jonny

last: Mendoza-Castrejon

first: Jeffrey


title: Global characterization of Dictyostelium discoideum gene expression changes under hypoxic conditions

city: Villeubanne

first: Julie

last: hesnard

state: FRANCE

address: HESNARD

country: France

institute: Institut Lumière Matière

summary: Aerobic eukaryotes utilize oxygen (O2) to oxidize metabolites and generate ATP. The protist kingdom lacks the Hypoxia Inducible Factor-dependent transcriptional response network to accommodate low O2 though possesses a HIF prolyl hydroxylase that initially mediates the response. To address the scale and scope of hypoxic responses in protists, we characterized transcriptomic and proteomic changes when the social amoeba Dictyostelium is subjected to low (1%) O2 under nutritive conditions over 24 h followed by reoxygenation. Remarkably, 32% of the transcripts quantified were differentially expressed during hypoxia, with greatest changes associated with early (1 h) and late phases (24 h). Protein changes were modestly correlated with and generally lagged behind transcriptional changes. Correlated changes were observed for transcripts and proteins associated with various metabolic, anabolic, and catabolic pathways, as well as chromosome organization, cell cycling, vesicular trafficking, and signaling. Analysis of 4 marker genes showed extremely rapid responses that were graded over a range of O2 levels, with differential responses to inhibitors affecting protein synthesis and mitochondria. Overall, the amoebal response to a low but non-toxic O2-level resulted in massive remodeling of the transcriptome and proteome.

overall_design: Dictyostelium AX3 cells were placed under hypoxic conditions (1% O2) for 24 hours and then reoxygenated for 5 hours (20% O2). Cells were collected for transcriptomic (and proteomic) analysis at 1h, 5h, and 24h of hypoxia, and at 1h and 5h of reoxygenation. Cells were also collected from the culture tube at t0 (21% O2).Transcripts sequencing, alignment with the reference genome, and bioinformatic processing to obtain differential expressions (compared to t0) with a relative FDR were performed by the company GenXpro (GenXpro GmbH, Germany).

last: Hesnard

first: Hanke

last: van der Wel

first: Olivier

last: Cochet-Escartin

first: Stephane

last: Joly

first: Elisabet

last: Gas-Pascual

first: Jean-Paul

last: Rieu

first: Christopher

middle: M

last: West

first: Christphe

last: Anjard


title: Transcriptomics insights into the functional role of tick Ixodes ricinus midgut proteins metalloprotease and antigen p23

city: Ciudad Real

first: Rita

last: Vaz-Rodrigues

address: Ronda de Toledo 12

department: SaBio

country: Spain

institute: Instituto de Investigación en Recursos Cinegéticos (IREC) - University of Castilla-La Mancha (UCLM)

summary: Ticks are hematophagous ectoparasites that impact human and animal health worldwide. Tick saliva contains multiple biomolecules capable of disrupting host immunity, occasionally causing emergent tick-borne allergies like the alpha-Gal syndrome (AGS). Current results highlight a knowledge gap in characterizing tick salivary biomolecules, without alpha-Gal modifications, that influence host response to alpha-Gal and may be implicated in the AGS. This study aimed to functionally characterize biomolecules antigen p23 (A0A0K8RKR7) and metalloprotease (A0A0K8RCY8) based on their role in Ixodes ricinus tick feeding and reproduction, determined after gene knockdown by RNA interference and further transcriptomics analysis. Silencing the expression of antigen p23 and metalloprotease did not result in any significant differences in tick engorgement and egg batch weights compared to the GFP control group. Transcriptomics analysis revealed a total of 438 differentially expressed genes (DEGs) were found in the antigen p23-silenced group, including 149 upregulated and 78 downregulated genes. GSEA analysis following antigen p23 gene knockdown identified significantly upregulated pathways associated with protein production and suppressed routes mostly correlated with ion transport, lipid metabolism, catalytic activity, protein modification, and G-protein activity. Partially silencing metalloprotease in tick midguts led to the identification of 182 DEGs, comprising 104 upregulated and 78 downregulated genes. Ablation of endogenous metalloprotease led to the upregulation of several biological and functional pathways associated with RNA splicing and significantly suppressed routes connected with detoxification, protein modification, catalytic activity and molecule binding. These findings provide valuable insights into tick physiology, providing a foundation for further research on tick-host interactions and AGS pathogenesis.

overall_design: Total RNA from 3 groups (antigen p23, metalloprotease and GFP control) was submitted to RNA-seq anaysis. Samples included the midguts of nine Ixodes ricinus female ticks per group divided into three biological replicates, each containing three ticks per pool.

first: Vincent

middle: C

last: Duru

first: Ard

last: Nijhof

first: José

last: de la Fuente


title: Rise in KRT17 sensitizes platinum-resistant ovarian cancer organoids to targeted therapies

first: Mirjana

last: Kessler

address: Pettenkoferstrasse 8a

department: Department of Obstetrics and Gynecology

institute: Ludwig Maximilian University Munich

summary: Variable responses to platinum chemotherapy and the development of resistant disease drive high mortality in high-grade serous ovarian cancer (HGSOC), the deadliest gynecological malignancy. Here, we developed the organoid drug resistance assay (ODR-test) to quantify the patient-specific efficacy of platinum treatment and generated post-platinum lines (ptGPC) as an in vitro model of platinum-resistant ovarian cancer (PROC). We observed a gradual increase in resistance of ptGPC lines, mirroring the clinical outcomes of patients. We have performed RNA-seq analysis from two different donor organoid lines, before carboplatin exposure and paired ptGPC lines of long-term expandable organoids that successfully overcame in vitro drug treatment. By differential expression analysis, we have identified target genes that mediate the cellular response to platinum and play a role in the development of resistant phenotype in ovarian cancer. We have found that carboplatin treatment triggers sustained reprogramming and ptGPC organoids from different donors show common changes in cell adhesion and cytoskeletal organization, indicating the existence of conserved mechanisms that lead to an increase in resistance.

overall_design:
Total mRNA Isolated from ovarian cancer patient-derived organoids, wt, and ptGPC lines (obtained through ODR-testing- after carboplatin challenge and reseeding ) has been sequenced and analyzed. In parallel, phenotypic changes in ptGPC organoids have also been investigated on the proteome level. Regulation of candidate mediator genes was validated by qPCR, while global changes in cellular architecture and tissue organization were visualized by confocal imaging. An increase in resistance of ptGPC lines has been demonstrated by repeated carboplatin challenge and quantification of organoid forming efficiency. Direct involvement of the rise in KRT17 levels in promoting platinum resistance, and altering the sensitivity of organoids to targeted testing was demonstrated by the generation of genetically modified organoids and in parallel ODR testing.   Raw sequences are not provided due to data protection concerns. Their release would require special approval from the relevant regulatory authority.

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Raw sequences from patients underlies strict privacy lows and requires institutional approval and restricted acces.
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first: Juliane

last: Reichenbach

first: Juliana

last: Schmid

first: Sophia

last: Hierlmayer

first: Tingyu

last: Zhang

last: Sophia Geweniger

first: Tobias

last: Straub


title: A phase 1 study of the CDK9 inhibitor voruciclib in relapsed/refractory acute myeloid leukemia and B-cell malignancies

city: Duarte

first: Edward

middle: C.

last: Dominguez

address: 1500 E. Duarte Rd.

department: Toni Stephenson Lymphoma Ctr

institute: City of Hope

summary: The anti-apoptotic protein myeloid cell leukemia-1 (Mcl-1) contributes to the pathophysiology of acute myeloid leukemia (AML) and certain B-cell malignancies. Dependence on Mcl-1 is associated with resistance to venetoclax. Voruciclib, an oral cyclin-dependent kinase (CDK) inhibitor targeting CDK9, indirectly decreases Mcl-1 protein expression and synergizes with venetoclax in preclinical models. This dose escalation study evaluated voruciclib in patients with previously treated hematologic malignancies (registered as NCT03547115). Initially, voruciclib was administered daily continuously on a 28-day cycle (Group I). After two patients with prior allogeneic stem cell transplantation had a dose limiting toxicity (DLT) of interstitial pneumonitis at 100 mg, voruciclib administration was changed to days 1-14 of a 28-day cycle (Group II). Forty patients, 21 with AML and 19 with B-cell malignancies, were enrolled. Patients had a median of 3 prior lines of therapyies (range, 1-8). Dose escalation in Group II was stopped at 200 mg, a dose that achieved plasma concentrations sufficient for target inhibition, without DLTs observed.  The most common adverse events were diarrhea (30%), nausea (25%), anemia (22%), fatigue (22%), constipation (17%), dizziness (15%) and dyspnea (15%). In AML, one patient achieved a morphologic leukemia-free state and two had stable disease. There was a Voruciclib treatment led to a decrease in MCL1 mRNA expression, downregulation of MYC and NF-κB transcriptional gene sets, and reduced phosphorylation of RNA polymerase II . Voruciclib on intermittent dosing was well tolerated, with no DLTs, paving the way for evaluation of the combination of voruciclib with venetoclax in patients with previously treated AML.

overall_design: Patients ≥ 18 years of age with a diagnosis of AML, CLL, or B-cell NHL (DLBCL, mantle cell lymphoma, follicular lymphoma and marginal zone lymphoma) were eligible if they had disease progression after ≥ 2 prior standard therapies, no prior CDK9 inhibitor exposure, ECOG performance status of 0 or 1, and adequate renal and hepatic function. To identify gene expression changes in response to voruciclib, transcriptomics analysis was conducted by bulk RNA-Seq on pre- and post-treatment PBMC samples from AML, DLBCL, and CLL patients who were dosed with voruciclib.

first: Carly

last: Roleder

first: Alexey

last: Danilov


title: THOC5-Dependent Posttranscriptional Control Maintains Vascular Smooth Muscle Cells Homeostasis Against Chronic Kidney Disease Related Vascular Calcification [RIP-seq]

city: Wuhan

first: yuyao

last: wang

address: 1095 Jiefang Avenue, Wuhan City, Hubei Province

institute: Tongji Hospital affiliated to Tongji Medical College of Huazhong University of Science & Technology

summary: Background: Despite transcriptional control mechanisms of VSMC osteogenic transition having been extensively studied, posttranscriptional regulation is still awaiting elucidation. In the present study, we explore the mechanism of THOC5-dependent VSMCs osteochondrogenic switching. Methods: Von Kossa staining and immunohistochemistry staining were used to detect calcification and expression of THOC5 respectively. Thoc5 shRNA and Thoc5 overexpression lentivirus were used to modulate the expression of Thoc5. RNA-Seq combined with RIP-Seq was used to explore the target mRNAs that directly bind to THOC5, and FISH was used to confirm its subcellular localization. Results: Immunohistochemical staining showed significantly increased THOC5 expression in the calcified artery of CKD patients. Besides, calcification-induced increase of THOC5 expression was found in both in vivo and in vitro calcification models. The overexpression of Thoc5 relieves the calcification and osteogenic differentiation of VSMCs significantly in vitro, which is mainly manifested by the reduction of calcium ion deposition and the decreased expression of osteogenic markers. Furthermore, RNA-Seq revealed that THOC5 overexpression in osteogenic-induced VSMCs closely resembled the gene expression changes induced on TGF-β treatments in cultured VSMCs. In addition, overexpression of THOC5 alleviates the exacerbation of calcification in vivo. Our previous studies found that THOC5 displayed limited binding to VSMCs genomic DNA, so RIP-Seq was selected to detect target genes of THOC5. It was found that THOC5 directly interacts with Guanylate exchange factors (GEFs) mRNAs, and is required for their export. Thereby THOC5 maintaining RhoA GTPase activation contributes to increasing the expression of VSMCs contraction marker, which maintains the contraction phenotype of VSMCs. ROCK (Rho-kinase) inhibitor Y-27632 reversed the protective role of THOC5 on osteoblastic transdifferentiation and calcification, as well as the maintenance of the spindle morphology of VSMCs. Conclusions: Our data introduce the binding of THOC5 to GEFs as a novel mechanism contributing to maintaining VSMCs homeostasis and imply THOC5 as a potential intervention node for vascular calcification diseases.

overall_design: To ascertain how THOC5 influences VSMCs global gene expression of VSMCs during the osteogenic transition. We performed RNA sequencing (RNA-Seq) on THOC5 overexpression VSMCs treated with Pi for 6 days . Then, We performed RNA immunoprecipitation sequencing (RIP-Seq) against THOC5 in VSMCs, both with or without Pi treatment, to assess the transcriptomic binding of THOC5.


title: THOC5-Dependent Posttranscriptional Control Maintains Vascular Smooth Muscle Cells Homeostasis Against Chronic Kidney Disease Related Vascular Calcification [RNA-seq]


title: Chameau (HBO1) regulates starvation in a temperature-dependent manner in Drosophila melanogaster

city: Berlin

first: Anuroop

middle: Venkateswaran

last: Venkatasubramani

state: Berlin

address: Robert-Rössle-Straße 10

institute: MDC-Berlin

summary: The body temperature of Drosophila melanogaster depends on the extrinsic temperature. Numerous studies in fruit flies have shown that environmental temperature has an effect on metabolism, lifespan and starvation resilience. We have previously shown that Chameau (Chm), a MYST-domain acetyltransferase, promotes aging but also increases starvation resilience. As starvation resilience is highly temperature dependent, we explored the effect of temperature on starvation resilience in fruit flies with reduced chm expression. Strikingly, we found that an increase of 2°C was sufficient to restore starvation resilience in chm mutants. The increase in temperature rescued the dampened expression of genes involved in insulin, hormone and starvation response as well as a reduced rate of weight loss and misregulation of trehalose, we observed in chm mutants at 23°C. Our data show that whereas Chm has an important role in regulating starvation at 23°C and below, it becomes obsolete at higher temperatures. Our finding that a gene plays an important role only under specific environmental conditions has important implications in light of the recent global change of climate conditions.

overall_design: 2 genotypes at 2 different conditions in 5 biological replicates per genotype and condition

first: Axel

last: Imhof


title: Transcriptome analysis of the effect of Armh4 on aging

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

summary: Here, we determined the impact of the Armh4 gene on aging by performing transcriptome analysis of cardiac tissues from aged and young mice subjected to systemic Armh4 knockout or wild type groups.

overall_design: Normal and healthy c57bl/6j young mice and systemic Armh4 gene knockout mice were raised in a stable environment (room temperature 24±3℃; indoor humidity 55±5%), 12-hour light/12-hour dark cycle, fed normal food, and raised to 25 months of age, and divided into WT_Aged group and KO_Aged group. In addition, the feeding environment of WT_Young group and KO_Young group mice was consistent with that of aged mice, and they were raised for 8 weeks, with at least 6 mice in each group. Mice were anesthetized with inhaled anesthetics and killed by cervical dislocation. The heart was immediately dissected and stored at -80°C.  Select 4 independent biological replicate samples from each of the four separate groups, namely WT_Aged, KO_Aged, WT_Young, and KO_Young, to extract RNA. RNA-seq was provided by Beijing Genomics Institute (BGI)

first: Yu

last: Fang

first: Baosen

first: Ningning

last: Guo

first: Jian

last: Lv


title: CFAP20 salvages arrested RNAPII from the path of co-directional replisomes

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Fine-tuning DNA replication and transcription is crucial to prevent collisions between their machineries, especially at promoters where RNA polymerase II (RNAPII) initiates transcription and forms R-loops. Arrested RNAPII can obstruct DNA replication, which often starts near promoters. The mechanisms that salvage arrested RNAPII during elongation to avoid conflicts with incoming replisomes are unknown. Here, we identify CFAP20 as a key player in rescuing arrested RNAPII in promoter-proximal regions, preventing conflicts with co-directional replisomes. CFAP20-deficient cells accumulate R-loops near promoters and exhibit defects in replication origin firing and fork progression. Co-depleting the Mediator coactivator complex or removing RNAPII engaged with R-loops rescues these defects. Thus, CFAP20 salvages arrested RNAPII under conditions of high Mediator-driven transcription to promote RNAPII elongation, thereby preventing collisions with co-directional replisomes.

overall_design: Wild-type and CFAP20-KO RPE-1 cells were subjected to scEdU-seq as previously described by van den Berg 2024

first: J


title: Methylation Array Signals are Predictive of Chronological Age Without Bisulfite Conversion

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

summary: DNA methylation data has been used to make “epigenetic clocks” which attempt to measure chronological and biological aging. These models rely on data derived from bisulfite-based measurements, which exploit a semi-selective deamination and a genomic reference to determine methylation states. Here, we demonstrate how another hallmark of aging, genomic instability, influences methylation measurements in both bisulfite sequencing and methylation arrays. We found that non-methylation factors lead to “pseudomethylation” signals that are both confounding of epigenetic clocks and uniquely age predictive. Quantifying these covariates in aging studies will be critical to building better clocks and designing appropriate studies of epigenetic aging.

overall_design: Mouse hippocampi were dissected from C57BL/6 mice from the National Institute on Aging colony. Mice were sacrificed between 4 and 24 months of age. Isolated DNA was split into three groups - Converted (standard protocol for methylation array), Unconverted (standard protocol minus bisulfite reagent), and No Touch (standard protocol minus bisulfite reagent and bisulfite heat treatment cycles). Converted and Unconverted samples are fully paired by splitting aliquotted DNA, with a technical replicate included in each condition, while No Touch aliquots cover a subset of samples. The final conditions include 7 aging time points (4, 5, 8, 11, 14, 18, and 24 months) as well as three conditions (Converted, Unconverted, and No Touch).

first: Hunter

middle: L

last: Porter

first: Victor

last: Ansere

first: Ram

last: Babu Undi

first: Walker

last: Hoolehan

first: Cory

middle: B

last: Giles

first: Chase

last: Brown

first: David

last: Stanford

first: Mark

last: Huycke

first: Willard

last: Freeman


title: Ex vivo lung-organoid model for aberrant basaloid cell induction and activation

city: Kashiwa

first: BIN

last: WU

state: Chiba

address: #304, 6-6-2, Kashiwanoha

department: Research

institute: ImmunoGeneTeqs

summary: Lung epithelial cell injury contributes to various lung diseases, impacting lung function and overall human health. Bleomycin (BLM)-induced murine models of pulmonary fibrosis (PF) are commonly utilized to study lung epithelial cell injury. However, the complex microenvironments in inflamed lungs hinder clear causal relationships between cell-to-cell, molecules interaction. To address this limitation, we aimed to establish an ex vivo organoid model of BLM-induced lung injury recapitulating the cellular and molecular responses of BLM-induced lung epithelial injury in vivo.

overall_design: Lung organoids were generated by co-culturing primary murine CD326 positive lung epithelial cells and CD140a positive lung fibroblasts. To clarify transcriptomic changes of BLM-injured lung organoids at single-cell level, we stimulated lung organoids with bleomycin (0.3 ug/ml) in a culture media from day 8 to day 10 post co-cultured. After that, bleomycin was removed from the culture media and the lung organoids were further cultured until day 14 post co-cultured. scRNA-seq analysis was performed at day 14 post co-cultured.

first: Bin

last: Wu

first: Shigeyuki

last: Shichino

first: Satoshi

last: Ueha

first: Rina

last: Matsukiyo

first: Tatsuro

last: Ogawa

first: Kouji

last: Matsushima


title: Glucocorticoid Receptor cistromic reprogramming by caloric restriction and corticosterone treatments.

city: Neuherberg

first: fabiana

last: quagliarini

address: Ingolstaedter Landstr 1

institute: helmholtz munich

summary: In order to examine the impact of two separate corticosterone surges on liver physiology, we conducted genome-wide mapping of GR binding profiles at 6 pm (ZT12) through ChIP-sequencing. This was done using liver samples from mice subjected to either short-term caloric restriction or corticosterone injections. Our findings reveal that both interventions yield unique binding profiles.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Glucocorticoid Receptor (GR) in mouse liver in caloric restriction. In the case of GR, we have ChIP-seq between three different conditions (night-restricted feeding/NR, caloric restriction/CR, and cort-supplementation + NR/CORT+NR).

first: Konstantinos

last: Makris

first: Fania

last: Feby Ramadhani

first: Fabiana

last: Quagliarini

first: Nina

middle: H

last: Uhlenhaut


title: The outcomes of caloric restriction are driven by enhanced glucocorticoid rhythms.

summary: Caloric restriction extends lifespan and healthspan across species, with feeding times synchronized to circadian rhythms further maximizing its benefits. However, the mechanisms linking diet, diurnal rhythms, and lifespan are not fully understood. In mice, the time point most strongly tied to dietary effects on lifespan coincides with the peak of glucocorticoid secretion (ZT12, lights-off). Caloric restriction raises circulating glucocorticoid hormone levels, but their functional relevance remains untested. We show that the glucocorticoid receptor (GR) is critical for the effects of caloric restriction. Hepatocyte-specific GR mutant mice fail to respond to caloric restriction indicating that increased glucocorticoid amplitudes support its benefits. Using multiomics techniques in murine liver, we find that nutrient deprivation elicits a nuclear switch from active STAT signaling to increased FOXO1 activity, enabling the GR to activate a unique diet-specific gene expression program. Taken together, our results suggest that glucocorticoid rhythms are crucial for caloric restriction-induced metabolic reprogramming.

overall_design: This project consist of several bulk RNA-seq datasets, ChIP-seq datasets, and single nuclei multiome dataset. All datasets comes from murine liver samples.

first: Liwei

last: Zhang

first: Ioannis

last: Deligiannis

first: Celia

last: Martinez-Jimenez

first: Nina Henriette


title: Hepatic Glucocorticoid Receptor (GR) drives the diurnal adaptation to Caloric Restriction

summary: We examined the gene expression profiles of liver samples throughout the day/night cycle (ZT0-ZT4-ZT8-ZT12-ZT16-ZT20) from control mice (night-restricted fed) and mice under short-term caloric restriction.

overall_design: Bulk RNA sequencing (RNA-seq) from livers of WT and hepatocyte-deleted for Glucocorticoid Receptor mice (GR liver KO ) upon night restricted feeding (NR) and caloric restriction (CR) with sampling every 4hours at 6 different timepoints (ZT0, ZT4, ZT8, ZT12, ZT16, and ZT20), ZT corresponds to Zeitgeber Time, 6 a.m :ZT0 & ZT12: 6 p.m. Additionally, bulk RNA sequencing (RNA-seq) from livers of night-restricted fed (NR) and caloric restricted (CR) WT mice at Zeitgeber 12 (ZT12; 6 p.m).


title: A comparative transcriptomic analysis provides new insights into the ecological adaptations in Ichthyophis bannanicus

city: Guangxi Zhuang Autonomous Region

first: wang

last: zhen

address: 1303 East Education Road, Yulin City, Guangxi, China

institute: Yulin Normal University

summary:
Background Banna caecilian (Ichthyophis bannanicus) is the only species of Gymnophiona in China, with unique lifestyles and characteristics. Although there have been some studies on distribution and morphological characteristics in I. bannanicus, little research focused on the molecular level. A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions.
Result To provide new insights into molecular mechanisms of ecological adaptation in I. bannanicus, we performed gene expression analysis across 10 tissues including skin, blood, spleen, liver, kidney, lung, heart, stomach, testis and ovary. By integrating 27 newly generated RNA-seq datasets with 21 publicly available transcriptomes, we performed a systematic gene expression analysis across tissues representing 19 major organ systems, thereby generating a comprehensive and high-resolution transcriptomic atlas for I. bannanicus. We identified 5,092 housekeeping genes (HKGs) and 2,169 tissue-specific genes (TSGs), and conducted weighted gene co-expression network analysis to determine the modules most relevant to each tissue. Functional enrichment indicated that HKGs support basic cellular activities, while TSGs and the module genes are associated with tissue differentiation and specific physiological processes. Our comparative genomic analysis of I. bannanicus and Xenopus tropicalis revealed genes potentially lost in I. bannanicus, including RCVRN.1, GNAT2, SAG, GRK7, SMURF1, NOG, and MAPK14, which may be associated with degeneration of its visual system and limb structures. Notably, cross-species comparison of HKGs, TSGs, and co-expression modules highlighted an enhanced and unique immune capacity in I. bannanicus.
Conclusion Our findings demonstrate that HKGs, TSGs, and co-expression module genes offer valuable perspectives on tissue specialization and evolutionary divergence. The comparative transcriptomic analysis across multiple species and diverse tissue types provides valuable clues into the molecular features that may contribute to ecological adaptation in I. bannanicus.

overall_design: We conducted transcriptomic analysis on ten tissues (liver, kidney, lung, blood, heart, ovary, skin, spleen, stomach, and testis) of Ichthyophis bannanicus.

first: Yongjian

last: Bei

first: Fengli

last: Zhao

first: Jieling

last: Lai

first: Zhen

last: Wang

first: Guifen

last: Li

first: Shaoquan

last: Meng

first: Linzhuang

last: Bai


title: RNA-seq of human heart tissues and human iPSCs

city: Guangzhou

first: Juli

last: Liu

state: Guangdong

address: Zhongshan 2nd road

department: Medical Research Center

institute: Guangdong provincial people's hospital

summary: To know gene expression patterns for human iPSCs (PS) and different heart tissues, including right ventricular (RV), left ventricular (LV) and sinoatrial node (SN) tissues.

overall_design: Human iPSCs (PS) and different heart tissues,

first: Shaoxian

last: Cheng


title: RNA Binding Patterns of Ischemic Heart Failure Prognosis Indicator Eukaryotic Translation Initiation Factor 3m Reveal its Unique Role in Regulation of Nitrative Damage after Myocardial Ischemia-Reperfusion [Ribo-Seq]

city: Shanghai

first: Zilun

last: Wei

address: 180 Fenglin Road

department: Shanghai Institute of Cardiovascular Diseases

institute: Zhongshan Hospital

summary: RNA undergoes various modifications in a manner similar to DNA, thereby opening up the research field of epitranscriptomics. Regulators of mRNA modifications play a role in many molecular processes, biological functions, and disease prognosis. Differential expression profile of RNA modification regulators from HFrEF patients’ hearts remains deficient at present, let alone their affections on the prognosis. A risk score model based on two modifications-related modulators (eIF3m and Nudt12) was built and screened out with a LASSO regression analysis. Translation dysregulation upon eIF3m knock down in cardiomyocytes was examined by combined high-throughput methods of transcriptome sequencing, ribosome profiling, proteome research, and Clip analyses. Metabolic assays and flux analysis were used to characterize the effects of eIF3m and its downstream mediator in metabolic reprogramming with high-level exogenous TNF-α to mimic a highly oxidative inflammatory injury. eIF3m deficiency leads to decoupling of the major steps in translation initiation and elongation. It stabilizes eIF3m-f-h subcomplex through proteasome dependent-polyubiquitination, and controls translational response of specific mRNAs. eIF3m directly binds to Mt2 5’ leader to upregulate its translation in NRCMs and H9c2 cells. eIF3m knockdown induced expression of genes involved in proinflammatory and oxidative stress, resulting in 3-NT modification to a key glycolysis enzyme Pfkfb3 when co-cultured with exogenous TNF-α. CM-specific eIF3m deletion deteriorates cardiac function and increases infarction size after I/R operation, whereas CM-specific eIF3m overexpression reverses the phenotype. Additionally, eIF3m overexpression inhibits whereas RNAi-mediated Mt2 knockdown activates NF-κB signaling and aggravates nitrative damage. Metabolic analyses highlighted the role for eIF3m in promoting glycolysis and biosynthesis required for functional recovery of the myocardium. Our study demonstrates that the prognosis indicator eIF3m alleviates oxidative inflammatory injury and promotes glycolytic reprograming mainly by binding to Mt2 mRNA. Therapeutic strategies enhancing eIF3m level may possess therapeutic potential against I/R injury.

overall_design: The first two sample are replicated sample which belong to control group. Another two sample are also replicated sanples which belong to eIF3m knockdown group.

first: Yongchao

first: Aijun

last: Sun

first: Junbo

last: Ge


title: RNA Binding Patterns of Ischemic Heart Failure Prognosis Indicator Eukaryotic Translation Initiation Factor 3m Reveal its Unique Role in Regulation of Nitrative Damage after Myocardial Ischemia-Reperfusion

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

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Refer to individual Series


title: Comparison of proteogenomic strategies for the generation of zebrafish fit-for-purpose protein databases

city: Lausanne

first: James

last: Holzwarth

state: Vaud

address: EPFL Innovation Park, G

department: NIFSAS

country: Switzerland

institute: Nestlé

summary:
High-quality protein databases (DBs) are essential for optimal analysis of mass spectrometry (MS)-based proteomic data since protein identifications fully rely on the sequences of proteins present in these DBs. The generation of custom protein DB using proteogenomics is an effective way to cope with the absence, incompleteness, or inaccuracy of public resources as well as the specificities of the samples under study.
In this work, we implemented a proteogenomic pipeline with the aim to build protein DBs for zebrafish using both short- and long-read RNASequencing (RNA-Seq and Iso-Seq, respectively). We evaluated the impact of these genomic technologies on the size and quality of the resulting DBs, as well as their influence on protein identification using MS-based proteomics. Specific protein DBs were produced for different zebrafish samples and tissues, i.e., larva, larval tail, muscle, brain and liver. They were compared to assess the relevance of using sample-specific protein DBs for proteomic analysis, and we determined that the current long-read Iso-Seq approach was more appropriate for this goal. Different strategies for DB curation were evaluated to clean and reduce the size of the DBs. Curation resulted in increased numbers of protein identifications. In summary, our study provides relevant observations and methodological recommendations for the generation of protein DBs using proteogenomics applied and application to the proteomic analysis of zebrafish and other species with gaps in annotation of DBs.

overall_design: RNASeq  and proteomics data from 5 different zebrafish tissues

first: Charlotte

last: Macron

first: Corentin

last: Beaumal

first: Matthieu

last: Porchet

first: Jens

last: Stolte

first: Joy

last: Richard

first: Philipp

last: Gut

first: Sylviane

last: Metairon

first: Patrick

last: Descombes

first: Michael

last: Affolter

first: Loïc

last: Dayon


title: RNA Binding Patterns of Ischemic Heart Failure Prognosis Indicator Eukaryotic Translation Initiation Factor 3m Reveal its Unique Role in Regulation of Nitrative Damage after Myocardial Ischemia-Reperfusion [Mt2RNAseq]

overall_design: The first three sample are replicated sample which belong to control group. Another three sample are also replicated sanples which belong to Mt2 knockdown group.

last: Zhao


title: Glucose metabolism influences the adaptive response of osteocytes to mechanical stimuli via CCN1

city: Sapporo

first: Mari

last: Sato

address: Kita13 Nishi7 KIta ku

institute: Hokkaido University

summary: Bone loss is a diabetic-related complication. Chronic hyperglycemia affects bone quality, quantity and function1. Recently, reduced bone response to mechanical loading in diabetic mice have been reported2. However, it remains unclear whether hyperglycemic condition affects mechanosensing of osteocytes known as mechanical sensor cells through the changes of molecular mechanism. In this study, we addressed the identification of mechano-sensitive and glucose-dependent molecular mechanisms in osteocytes. First, we isolated osteocyte related mechanosensitive genes by examining bone tissues and osteocytic cells derived from in vivo and in vitro mechanical loading model. RNA sequencing analysis of a murine bone tissues exposed to 6 weeks of voluntary wheel running showed 146 genes were respond to mechanical loading. Of these genes, 4 genes were also reacted to ultrasound stimulation in murine osteocytic cell line. Only one gene of 4 genes, Ccn1 (cysteine-rich 61, Cyr61), was upregulated by both wheel running exercise in vivo and ultra sound stimulation in vitro. Thus, Ccn1 was considered specific candidate gene for mechanosensing in osteocytes. Next, we examined the effect of glucose level on CCN1 expression induced by mechanical stimuli by using obese mice model and high-glucose-exposed osteocytic cells. The mechanical stress-induced elevation of CCN1 expression was totally abolished by high glucose condition both in mice bone and osteocytic cells. Our findings support a new role of CCN1 as a glucose dependent mechanosensing molecules in osteocytes contributing to diabetic bone abnormality.

overall_design: Male mice at 6 weeks of age were divided into two groups: normal chow diet/sedentary (ND/SED) and normal chow diet/wheel cage running (ND/WCR). Mice in ND/SED groups were individually housed in a normal cage without a running wheel, and mice in ND/WCR group were individually housed in wheel cages with free access to a running wheel (140-mm diameter, 60-mm wide; MELQUEST, Toyama, Japan).  After 6 weeks, mice were removed from the wheel cages or static cages, euthanized under anesthesia and femoral bones were isolated. RNA samples derived from ND/SED mice (n=3) and ND/WCR mice (n=3) were compared.


title: RNA Binding Patterns of Ischemic Heart Failure Prognosis Indicator Eukaryotic Translation Initiation Factor 3m Reveal its Unique Role in Regulation of Nitrative Damage after Myocardial Ischemia-Reperfusion [RNA-Seq]

overall_design: The first three sample are replicated sample which belong to control group. Another three sample are also replicated sanples which belong to eIF3m knockdown group.


title: RNA-seq analysis of differentially expressed genes between WT and shTRIP6 RKO cells.

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

summary: To investigate the biological function TRIP6 in the colorectal cancer, we established RKO cell lines in which the TRIP6 gene has been knocked down by shRNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RKO cells and its KD derivatives (shTRIP6).

first: Hua

last: Wu


title: RNA Binding Patterns of Ischemic Heart Failure Prognosis Indicator Eukaryotic Translation Initiation Factor 3m Reveal its Unique Role in Regulation of Nitrative Damage after Myocardial Ischemia-Reperfusion [ClIP-Seq]

first: Zilun

last: Wei

overall_design: The first two sample are human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) with Flag-eIF3m overexpression and being immunoprecipitated with eIF3m or IgG antibody; the last two samples are neonatal rat ventricular myocytes (NRVMs) without adventrious transfection and directly  being immunoprecipitated with eIF3m or IgG antibody.

first: Yongchao

last: Sun


title: Effects of low-doses of antiandrogenic substances on Wistar Rat testes [Transcriptome analysis]

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Three antiandrogenic substances (Flutamide, Prochloraz, Vinclozolin) were administered in aqueous preparations at 3 doses: i) Acceptable Daily Intake (ADI) ; ii) No Observed Adverse Effect Level (NOAEL) ; iii) Low Observed Adverse Effect Level (LOAEL) . Pregnant females (20/group) were treated by gavage from gestation day (GD) 6 until postnatal (PND) day 21. After weaning, the offspring received the same test-substance as their mothers by oral gavage. Twenty males were selected to be raised until the weaning (Subset 1, PND 21), the day of sexual maturation (Subset 2, puberty) or early adulthood (Subset 3, PND 83±2). At each subset, testes were used for transcriptome and miRNome analyses.

overall_design: The experimental design comprised 4 animals per groups and 10 experimental conditions (3 drugs, tested at 3 doses, and 1 control) for each time point: PND21 (young), PND30-40 (puberty) and PND83 (adult).   A total of 120 samples were assayed both on mRNA expression arrays and microRNA arrays using a one-color labeling protocol.

first: M

last: Benhamed

first: B

last: Mari

first: K

first: P

last: Barbry

first: A

last: Paquet


title: Effects of low-doses of antiandrogenic substances on Wistar Rat testes [miRNome analysis]


title: Effects of low-doses of antiandrogenic substances on Wistar Rat testes

type:
Non-coding RNA profiling by array
Expression profiling by array


title: Single-nucleus RNA sequencing of ex vivo precision-cut lung slices from normal human lung tissue

status: Public on Nov 03 2025

city: New Haven

first: Maor

last: Sauler

state: CT

address: 300 Cedar Street

department: Section of Pulmonary, Critical Care, and Sleep Medicine

institute: Yale School of Medicine

summary: This study aimed to elucidate how epithelial–macrophage interactions contribute to pulmonary fibrosis. Using bleomycin-induced and genetic mouse models (Mif-2 KO, SPC-Cul3 KO, SPC-Mif KO, CX3CR1-Cd74 KO, PF4-Cd74 KO, and TGF-β transgenic mice), we performed single-cell transcriptomic profiling of lung cells and compared them with wild-type controls.

overall_design: Samples were inflated by injecting 3% low-melting agarose followed by cutting samples into 5x5 mm cubes. Peripheral slices (300 μm) were cut with a vibratome. Sections were placed into 1 mL 10% DMEM with 1% pen-strep in a 24 well plate. hPCLS were washed with HBSS x 2 h, rocking, at 37 degrees, and then treated with vehicle (DMSO) or Fibrotic cocktail (FC) [5 ng/ml recombinant transforming growth factor-β (TGF-β) (240-B, R&D Systems), 5 μM platelet-derived growth factor-AB (PDGF-AB) (PHG0134, GIBCO), 10 ng/ml tumor necrosis factor-α (TNF-α) (210-TA, R&D Systems), and 5 μM 1-Oleoyl lysophosphatidic acid (LPA) (62215, Cayman Chemical)] +/- 50μM 4-IPP drugs in 500 ul of 0.25% DMEM w 1% pen-strep. Every 2 days, the media was changed and treated again. At the end of the 5 days, PCLS were washed in cold PBS x 2 then placed in RNAlater solution (Thermo). Nuclei were isolated from frozen tissue and profiled with snRNAseq.

first: Sang-Hun

last: Kim

first: Jessica

last: Nouws


title: Single-cell RNA Sequencing Reveals Multiple Pathways Involving Pulmonary Immune and Epithelial Cells Through which Aryl Hydrocarbon Receptor Activation Attenuates Acute Respiratory Distress Syndrome

city: Columbia

first: Chloe

last: Weyer-Nichols

state: South Carolina

address: 6311 Garners Ferry Rd

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

summary: Acute Respiratory Distress Syndrome (ARDS) is a severe inflammatory lung disorder triggered by pneumonia, sepsis, trauma, and COVID-19, leading to high mortality. In this study, we investigated the effect of Aryl Hydrocarbon Receptor (AhR) activation by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a potent ligand, on LPS-induced ARDS in mice using single-cell RNA sequencing (scRNA-seq). scRNA-seq revealed sixteen transcriptionally distinct cell clusters in the lungs. AhR activation reversed the decreased pulmonary functions caused by LPS, and significantly reduced pulmonary infiltration of monocytes, neutrophils, and macrophages. Interestingly, AhR activation during ARDS led to increased proportions of alveolar macrophages, and angiogenic and quiescent endothelial cells (AECs and QECs, respectively). Among the downregulated pathways, prostaglandin signaling was the most broadly suppressed across many cell types in the LPS+TCDD group. AhR activation suppressed the neutrophil chemotaxis pathway involving Cxcl2, Cxcl3, and Cxcl10. The damage to endothelial and epithelial cells induced during ARDS was also blocked by AhR activation. This was associated with decreased expression of S100a8 and S100a9. Notably, multiple pathways related to cellular junction organization were enriched following AhR activation. Additionally, Scgb1a1, also called Club cell protein 16 (CC16), primarily secreted by Club cells in the respiratory epithelium, was highly upregulated following AhR activation accounting for lung homeostasis. Together, these findings demonstrate that AhR activation mitigates key inflammatory and barrier-disruptive processes involving multiple cell types in LPS-induced ARDS. These data identify AhR as a central regulator of pulmonary inflammation and epithelial–endothelial integrity and support the future evaluation of AhR-targeted therapeutics as potential treatment for ARDS.

overall_design: Mice were treated with either Vehicle or 30 ug/kg TCDD (i.p.) at 0 hours followed by 10 mg/kg LPS (i.t.) at 24 hours. After 48 hours, whole lungs were collected and prepared for scRNA-seq.

first: Mitzi

last: Nagarkatti


title: ClinASO: a guideline for rapid drug discovery of gapmer antisense oligonucleotidess

city: kunming

first: shunkai

last: chen

address: wujiaying

department: school of life sciences

institute: Yunnan university

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic disorder that threatens global health, yet current treatments lack efficacy and patient compliance. Antisense oligonucleotides (ASOs) offer advantages for chronic metabolic diseases through precision targeting and long-acting effects; however, rational design remains a key barrier to drug development. Here, we established an integrated Gapmer ASO design platform that incorporates SNP filtering, secondary structure prediction, off-target minimization, RNase H cleavage efficiency, and animal model compatibility to systematically identify potent ASO candidates. Targeting acyl-CoA synthetase long-chain family member 4 (ACSL4), we screened a focused panel of candidates and identified a highly efficient ASO that suppressed ACSL4 expression and reduced lipid droplet accumulation in HepG2 cells. Conjugation with N-acetylgalactosamine (GalNAc) yielded gA-28c, which achieved efficient hepatocyte uptake and robust ACSL4 knockdown at low doses (2.5 mg/kg) in vivo, with durable activity for at least 14 days and no detectable hepatotoxicity. In a chronic high-fat diet (HFD) mouse model, gA-28c markedly suppressed hepatic ACSL4, ameliorated steatosis, and restored near-normal liver histology, phenocopying ACSL4 knockout. Unexpectedly,gA-28c also normalized dyslipidemia, significantly lowering circulating cholesterol and lipoproteins, a therapeutic effect not previously observed with genetic ACSL4 depletion. Mechanistically, ACSL4 silencing by gA-28c downregulated lipid metabolic pathways and enhanced triglyceride turnover. Collectively, these findings establish gA-28c as a potent, liver-targeted, and long-acting therapeutic candidate that not only alleviates hepatic steatosis but also improves systemic lipid metabolism, underscoring the promise of ASO therapy for MASLD and hyperlipidemia

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Investigate the gene expression differences in HFD mice treated with gA-28c (2.5mg/kg) every two weeks

first: Shunkai

last: Chen

first: Hao

last: Liu

first: Shijie

last: Guo

first: Jinyi

last: Bi


title: Single-cell and single-nucleus transcriptomic profiling of mouse models and human lung tissues to study pulmonary fibrosis


title: miRNA-Seq of Extracellular Vesicles from Human Placenta–Derived Mesenchymal Stem Cells

city: Seongnam

first: Jae Hyun

last: Park

state: Gyeonggi-do

address: 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-

institute: CHA University

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular vesicles (EVs) released by human placenta–derived mesenchymal stem cells (hpMSCs) are thought to mediate paracrine effects. To characterize their small-RNA cargo, we isolated hpMSC-derived EVs (hpEVs) from conditioned media using size-exclusion chromatography and performed miRNA sequencing.

overall_design: small RNA profiling of EVs released from human placenta-derived mesenchymal stem cells


title: Human Placenta–Derived Mesenchymal Stem Cells Attenuate Hippocampal Aging-Associated Transcriptomic Profiles in Aged Mice

summary: Background Intravenous human placenta–derived mesenchymal stem cells (hpMSCs) can improve tissue function through paracrine effects, but their impact on normal brain aging is not well defined.  Methods Aged female mice (18–19 months) received three intravenous infusions of hpMSCs or PBS at six-week intervals. Hippocampal tissue was collected after the behavioral tests for RNA sequencing.  Results RNA sequencing showed hpMSCs' effectiveness in modulating aging-related neural pathways, particularly by downregulating age-specific genes in the hippocampus, indicative of neural reactivation.  Conclusions Systemic hpMSC administration modulates neural pathways in aged mice.

overall_design: RNA-Seq profiling of hippocampal tissue from hpMSC-treated and PBS-treated aged mice


title: Single-cell RNA-sequencing of ChAT-eGFP+ adipose stromal vascular cells

city: St Louis

first: Alexander

last: Knights

state: MO

address: 4515 McKinley Ave

institute: Washington University

summary: ChAT-eGFP mice were housed at thermoneutrality for three weeks then either kept at thermoneutrality or exposed to acute cold challenge, then inguinal adipose stromal vascular cells were harvested and scRNAseq performed on sorted ChAT-eGFP+ cells. This study represents the first single-cell transcriptomic profiling of cholinergic cells in fat and seeks to understand the regulation of these cells in response to acute cold exposure and thermogenic activation.

overall_design: At five weeks of age, male ChAT-eGFP mice were housed at thermoneutrality (30C) for three weeks, then either kept at thermoneutrality or exposed to acute cold challenge (4C) for 4h. Two biological replicates per condition were used, with each biological replicate comprised of cells from four pooled mice. Inguinal subcutaneous white adipose tissue was harvested then stromal vascular cells were isolated following tissue digestion. Live, single ChAT-eGFP+ cells were FACS-sorted then ~10,000 cells per biological replicate were submitted for 10x Genomics scRNAseq (3' GEX v3).

first: Jun

last: Wu


title: Single-cell RNA-seq of nevus-derived melanocytes and matching perilesional skin melanocytes

city: WOOLLOONGABBA

first: Mitchell

middle: S

last: Stark

state: QLD

address: 37 Kent St

department: Frazer Institute

country: Australia

institute: The University of Queensland

summary: Melanocytic nevi are considered to be benign melanocytic proliferations which are driven primarily via BRAF V600E MAPK activation. Using scRNA-seq we explored the signalling pathways in nevus derived melanocytes compared to perilesional skin.

overall_design: Each nevus was bisected; one half prepared for standard histopathological diagnosis, while the other half was dissected to separate nevus from adjacent non-lesional skin (hereafter referred to as perilesional skin). In nevi that were deemed to have sufficient size to attempt cell culturing, the bisected portion that was not used for diagnostic purposes, was bisected again, with one half prepared for cell culturing. Briefly, the epidermis was separated from the dermis by a 3-hour incubation at 37°C with Dispase II solution (Roche, Rotkreutz, Switzerland) followed by vortexing for 15 seconds and stirring with a pipette tip until the skin layers separated. Samples were then mixed with 2mL melanoblast culture media (MCBD 153 medium [Sigma-Aldrich, St Louis, USA], 10% chelated fetal bovine serum (8), 2% fetal bovine serum, 2mM glutamine, 1.66µg/L cholera toxin, 100nM endothelin-3 [ENZO Life Sciences, Farmingdale, USA], 10ng/mL stem cell factor [Sigma-Aldrich, St Louis, USA], 2.5ng/mL basic fibroblast growth factor 2)  and transferred to a culture plate coated with collagen matrix (Thermo Fisher Scientific Inc, Waltham, USA) to be incubated for 72 hours at 37°C. The melanocytes were grown using media designed to promote the transition of melanocytes back to the melanoblast cell state to allow the expansion of cells in cell culture flasks. From prior experience, melanocytes derived from nevi do not commonly grow very efficiently which may be in part due to the phenomenon of oncogene-induced growth arrest. To overcome growth arrest induced by the presence of the BRAF V600E mutation, once the culture was approximately 50% confluent, cells were treated with a lentiviral CDK4 R24C vector. This vector has previously been shown to allow oncogene driven melanocytes (NRAS Q61K) to enter into the senescence bypass by rendering CDK4 to be insensitive to inhibition by p16 and p15. Stably transduced cell lines were generated by transducing cells in 12- or 6-well plates at approximate 50:1 ratio of viral particles to cells. Wells containing confirmed >99% GFP- or RFP-positive cells were expanded for stock freezing and/or assays.

first: Richard

last: Sturm


title: Progranulin promotes dendritic growth of hippocampal neurons by acting on astrocytes

city: Birmingham

first: Andrew

last: Arrant

state: AL

address: 1825 University Blvd SHEL 1106

institute: University of Alabama at Birmingham

summary: Progranulin is a secreted pro-protein that is trafficked to lysosomes and exerts protective effects in the brain. Progranulin (GRN) mutations, most of which cause progranulin haploinsufficiency, are a major genetic cause of frontotemporal dementia (FTD). Restoring progranulin to people with GRN mutations is a promising treatment strategy, but understanding progranulin’s mechanism of action may enable design of optimal progranulin-based therapies. Progranulin restrains inflammation and promotes neuronal growth and survival, but the mechanisms underlying these effects are unclear. Progranulin is constitutively secreted and interacts with various signaling receptors, but is also taken up and trafficked to lysosomes, where it is necessary for maintaining normal lysosomal function. In previous work, we showed that progranulin acts in lysosomes to promote neuronal survival, but it is not clear if progranulin enhances neuronal growth by acting in lysosomes or through extracellular signaling. To address this question, we employed lentiviral vectors expressing either progranulin (PGRN) or a non-secreted, lysosome-targeted progranulin (L-PGRN). Using lentiviral vectors driven by non-selective (PGK), neuron-selective (hSyn), or astrocyte-selective (GFAP) promoters, we found that delivering L-PGRN to astrocytes, but not neurons, promoted dendritic outgrowth in primary hippocampal cultures. Using transwell co-cultures of astrocytes and neurons, we found that neurons cultured with L-PGRN–transduced astrocytes had greater dendritic outgrowth than those cultured with GFP-transduced astrocytes. Bulk RNA sequencing of primary astrocytes indicated that L-PGRN reduced transcriptomic pathways associated with inflammation and cellular reactivity. Consistent with this result, we found that reducing the number of astrocytes in hippocampal cultures increased dendritic outgrowth and occluded the pro-growth effects of L-PGRN. These data show that under these culture conditions, progranulin secretion is not required to promote dendritic outgrowth. Instead, progranulin may act via a non-cell–autonomous mechanism to suppress secretion of factors from astrocytes that restrain neuronal growth. These data add to a growing body of evidence that progranulin can act on astrocytes to promote neuronal health.

overall_design: Rat primary astrocytes were transduced with lentiviral vectors expressing GFP or L-PGRN, then analyzed four days later by RNA sequencing. Four independent cultures were sequenced. The experiment had a paired design, with a GFP and an L-PGRN–treated sample from each culture.

first: Azariah

middle: K

last: Kaplelach

first: Justin

last: Hall

first: Wren

middle: O

last: Nader

first: Amelia

middle: G

last: Davidson

first: Margaret

last: Ireland

first: Lara

last: Ianov


title: Heterogeneity and Homogeneity in Treg responses to Interleukin-2 [RNAseq2: Differential activation of Immune cell types by IL2-Immunocytokines]

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: IL2 is an immune-regulatory cytokine that activates both effector and T regulatory cells—a dual function leveraged in immunotherapy. However, pure IL2 induces both activation and suppression, and requires toxic doses due to its short half-life. To address this, the Spangler Lab at Johns Hopkins developed IL2 immunocytokines (IL2-ICs)—antibody-conjugated IL2 fusion proteins targeting IL2Ra (Tregs) or IL2Rb (effector cells), with extended serum half-life. We tested IL2-ICs in Foxp3IRES-GFP mice, harvesting cells at 4, 24, and 64 hours post-injection for bulk RNA-seq. Transcriptomic analysis showed IL2-ICs induced sustained IL2 responses with partial cell-type bias.

overall_design: Five treatments were tested: 1: F5111 IL2-IC, which targets IL-2 activity to Treg cells. 2: F10 IL2-IC, which targets IL-2 activity to NK cells. 3 and 4: Two FITC-IL2 controls, in which IL-2 is bound to a biologically irrelevant antibody that does not direct activity to any specific cell type. To match the N297A mutation present in F10 IL2-IC, the corresponding FITC control also included this mutation. 5: PBS, as a negative control. Each treatment was administered to 20 mice: 10 were injected 24 hours before tissue harvest and 10 were injected 4 hours before. Thus, each treatment group included both time points. Spleens were harvested at 4 and 24 hours post-injection. Treg cells, B cells, and NK cells were sorted for low-input bulk RNA sequencing. B cells, which do not respond to IL2-ICs, served as a reference to distinguish differential responses in Treg and NK cells.

first: Kumba

last: Seddu

first: Kaitavjeet

last: Chowdhary

first: Odhran

last: Casey

first: Molly

last: Henderson

first: Yi

last: Cao

first: Jakub

last: Tomala

first: Liang

last: Yang

first: Jamie

last: Spangler

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Single-cell RNA sequencing of lung cells from bleomycin-induced and doxycycline-inducible TGF-β transgenic mouse models of pulmonary fibrosis

first: Maor

last: Sauler

overall_design: Single-cell RNA sequencing was performed on lung cells from wild-type and genetically modified mice, including Mif-2 KO, SPC-Cul3 KO, SPC-Mif KO, CX3CR1-Cd74 KO, PF4-Cd74 KO, and doxycycline-inducible TGF-β transgenic mice. Pulmonary fibrosis was induced by intratracheal bleomycin, with lung tissues collected at day 10 and 14  or by two weeks of doxycycline administration to activate TGF-β transgene expression. Gene expression profiles were compared across models and wild-type controls to identify cell type–specific changes associated with fibrosis progression.

first: Sang-Hun

last: Kim

first: Jessica

last: Nouws


title: A streamlined and comprehensive protocol for the generation and multi-omic analysis of human monocyte-derived macrophages

city: Hanover

first: Brittany

last: Goods

state: New Hampshire

address: 15 Thayer Dr.

institute: Dartmouth College

summary: Macrophages are versatile immune cells with phenotypes ranging from inflammatory (M1-like) to anti-inflammatory (M2-like), shaped by diverse differentiation and polarization conditions. We present a standardized protocol to generate and characterize human macrophages from frozen PBMC-derived monocytes using cytokine profiling, transcriptomics, and snRNA-seq, including depolarization studies. This streamlined approach facilitates reproducible macrophage studies from biobanked samples, advancing both research and therapeutic applications.

overall_design: Monocytes from 3 female donors were isolated from frozen peripheral blood mononuclear cells and differentiated into macrophages over 6 days using 25ng/mL M-CSF in RPMI media with 10% FBS and 1% Penicillin-Streptomycin. On day 7 macrophages were activated into M1-like cells using 10ng/mL LPS and 20ng/mL IFNgamma.

first: Olivia

last: Palmer

first: Laurent

last: Perreard

first: Fred

middle: W

last: Kolling IV

first: Patricia

last: Pioli


title: MNX1 prevents somatostatin expression in human beta cells by repressing PERCC1

city: Paris

first: Farah

last: Kobaisi

address: 123 Bvd Port Royal

institute: Institute Cochin

summary: A highly specific mosaic transcriptional environment guides the fate of pancreatic progenitors during development and next maintains the identity of mature endocrine cells. In mice, one of such transcription factors is MNX1 (motor neuron and pancreas homobox1). It is essential for beta cell development and identity as its deletion in mature beta cells increases their somatostatin expression via an unknown mechanism. Here, we asked whether MNX1 plays a similar role in human beta cells and dissected the molecular players involved in its function. We used the human beta cell line EndoC-BH1, knocked down MNX1 expression using siRNA and performed bulk RNA sequencing searching for MNX1 targets. We next performed loss- (siRNA) and gain- (transduction with lentivectors and lipofections) of function to determine how MNX1 regulates gene expression in human beta cells. SiRNA-mediated downregulation of MNX1 in EndoC-BH1 cells induced the upregulation of somatostatin as well as its transcriptional activator HHEX. RNAseq revealed PERCC1 (Proline and Glutamate Rich with Coiled Coil 1) as being among the highest upregulated genes. SiRNA-mediated loss of PERCC1 upon MNX1 knockdown impaired the upregulation of both SST and HHEX expression, while PERCC1 overexpression upregulated the expression of both HHEX and SST. PERCC1 expression was tightly regulated by HHEX and by its own expression in a positive feedback mechanism. Moreover, NKX2.2 downregulation, whose knockout in mice induces somatostatin upregulation, led to the upregulation of PERCC1, HHEX and SST in EndoC-BH1. Finally, over-expression of PERCC1 in primary mouse beta cells revealed an upregulation of both mouse Hhex and Sst. We discovered a novel MNX1-PERCC1-HHEX regulatory axis in human beta cells. There, MNX1 protects beta cell identity by inhibiting PERCC1, an activator of HHEX and SST expression. PERCC1 might thus be considered as a sharply tuned central hub for SST regulation. Our results increase our knowledge of beta cell plasticity and may have implications for therapeutic strategies aimed at protecting beta cell identity.

overall_design: RNA seq profiling of EndoCBH1 cells that were transfected with MNX1 siRNA to knock down its expression or transfected with a non-targeting (NT) control

first: Alicia

last: Maugein

first: Alexis

last: Fouque

first: Olivier

last: Albagli-Curiel

first: Philippe

last: Ravassard

first: Raphael

last: Scharfmann


title: The ORB2 RNA-binding protein represses translation of its target transcripts during the Drosophila maternal-to-zygotic transition via its functionally conserved Zinc-binding ‘ZZ’ domain

city: Toronto

first: Howard

last: Lipshitz

state: ON

address: 661 University Ave

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: RNA-binding proteins (RBPs) are key components of the post-transcriptional regulatory machinery. We show that the ORB2 RBP, the Drosophila ortholog of vertebrate Cytoplasmic Polyadenylation Element Binding Protein 2 (CPEB2), binds to hundreds of maternally provided mRNAs in early embryos, identify a U-rich motif enriched in ORB2’s targets, and show that this motif confers ORB2 binding and repression to a luciferase reporter mRNA in S2 tissue culture cells. ORB2’s target transcripts are translationally repressed and unstable during the maternal-to-zygotic transition (MZT), a developmental phase during which a large proportion of maternally provided mRNAs are repressed and cleared.  We show that, when tethered to a luciferase reporter, ORB2 and its human homolog CPEB2 (but not ORB and CPEB1) repress translation and that the C-terminal Zinc-binding (‘ZZ’) domain of ORB2 is sufficient for repression. ORB2 interacts with a suite of post-transcriptional regulators in early embryos; a subset of these interactions is lost upon deletion of the ZZ domain, notably with the Cup repressive complex. Analysis of the early embryo’s translatome in the presence or absence of the endogenous ZZ domain, shows that ORB2’s targets move onto polysomes upon ZZ domain deletion, indicating that this domain mediates translational repression of ORB2’s targets during the MZT. Together, our results assign a function to the ZZ domain and support a significant role for ORB2 in post-transcriptional regulation of maternal mRNAs during the Drosophila MZT.

overall_design:
For each replicate of RIP-seq, 1mL of 0-3h embryo extract (prepared as described above) was supplemented with Triton X-100 to 0.1% final concentration, then diluted in an equal volume of lysis buffer with 0.1% Triton X-100 and cleared again by centrifugation at 4°C, 13 000 RPM for 15 minutes. The supernatant was incubated for 3 to 4 hours at 4°C with end-over-end rotation with 100μL of anti-FLAG M2 affinity gel beads (Sigma) which had been pre-incubated at 4°C with 50μg of purified anti-ORB2 E8 synthetic antibodies blocked with 5μg/μL BSA. After incubation, the lysates were decanted and beads were washed four times with lysis buffer supplemented with 0.1% Triton X-100 and then three times with equilibration buffer: 100 mM NaCl, 100 mM HEPES-NaOH (pH 7.4), 1 mM MgCl2. Fabs and associated RNPs were eluted from the beads with 200 μL of 200μg/μL FLAG-peptide (Sigma) suspended in equilibration buffer at 4°C for 20 minutes. RNA was isolated from the eluate using TRI Reagent (Sigma) according to the manufacturer’s instructions.
RNA was prepared for sequencing using Ribo-Zero Gold rRNA depletion kit and TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to manufacturer’s instructions. Libraries were sequenced using the HiSeq 2500 System, V4 Chemistry (Illumina), with paired-end reads 125nt in length.

first: Timothy

last: Low

first: Hua

last: Luo

first: Chalini

last: Weerasooriya

first: Sichun

last: Lin

first: Stephane

last: Angers

first: Craig

middle: A

last: Smibert


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

first: CBDM

last: Lab

summary: Interleukin-2 (IL2) is the key trophic factor for T Regulatory (Treg) cells, regulating both their differentiation and homeostasis. To understand how temporally regulated responses to IL2 unfold in Tregs, we performed fine time-course analyses at single-cell level induced by IL2 in Tregs in vivo. The data revealed responses that were largely uniform in resting Treg, but diverse among activated or effector Tregs, matching different STAT5 signal transduction efficiency. Individual Tregs displayed divergences in the preponderance of changes downstream of STAT1 or STAT5.

overall_design: We investigated how temporal interleukin-2 stimulation affect regulatory T cell gene expression. To do so, we stimulated FOXP3-GFP mice in vivo with IL2-JES6-1 complex at different time points between 1 to 128hrs and isolated splenic Tregs for each timepoints with PBS control.  Cells were encapsulated using the Chromium Single Cell 5’ v3 platform (10X Genomics). TotalSeq-A hashtag antibodies and samples (0.5 μl per sample for 20 min, BioLegend; hashtag 2, 128hr IL2-treated; hashtag 4, 128hr PBS-treated; hashtag 5, 64hr IL2-treated; hashtag 6, 24hr IL2-treated; hashtag 8, 16hr IL2-treated; hashtag 9, 8hrs IL2-treated; hashtag 10, 4hr IL2-treated; hashtag 11, 2hr IL2-treated; hashtag 12, 2h PBS-treated; hashtag 13, 1hr IL2-treated.

first: Kumba

last: Seddu

first: Kaitavjeet

last: Chowdhary

first: Molly

last: Henderson

first: Jakub

last: Tomala

first: Odhran

last: Casey

first: Yi

last: Cao

first: Diane

last: Mathis

first: Jamie

last: Spangler

first: Christophe

last: Benoist


title: Heterogeneity and Homogeneity in Treg responses to Interleukin-2 [scATAC-seq2: IL2/JES6-1 timecourse]

summary: We investigated the dynamic effects of IL2 exposure on Treg chromatin accessibility over time by performing scATAC-seq on splenic Tregs isolated from mice at mulitple timepoints (1,2,4,8,16,32,64,128hours) after treatment with IL2/JES6-1 complexes or PBS vehicle control.

overall_design: Mouse CD4+ regulatory Tregs from Foxp3-IRES-GFP reporter mice treated with PBS or IL2/JES6-1 complexes and isolated from the spleen by FACS for scATAC-seq at multiple timepoints (1, 2, 4, 8, 16, 32, 64 and 128hours after injection)


first: Howard

last: Lipshitz

overall_design: Total RNA-seq profiling of embryo of wild type and orb2-delta-zz D. melanogaster at 0-1hr, 1-2hr and 2-3hr of  post egg-lay.

first: Timothy CH

first: Craig A


overall_design: polysome gradient RNA-seq profiling of embryo of wild type and orb2∆zz D. melanogaster at 0-1hr, 1-2hr and 2-3hr of post egg-lay.

first: Timothy

last: Low

first: Hua

first: Chalini


title: A streamlined and comprehensive protocol for the generation and multi-omic analysis of human monocyte-derived macrophages [bulk RNA-Seq]

first: Brittany

last: Goods

overall_design: All samples are human monocyte derived macrophages cultured for 6 days in M-CSF at a density of 100,000 cells per well in a 96 well plate. On day 7 macrophages were activated with a cytokine cocktail to induce an M0, M1 or M2-like phenotype and then we characterized the transcriptional signature.

first: Olivia

last: Palmer

first: Laurent

last: Perreard

first: Fred

last: Kolling IV

first: Patricia

last: Pioli


title: Persistent pneumococcal colonisation in anti-retroviral-treated HIV infection is associated with nasal inflammation

city: Blantyre

first: Joseph

middle: Aston

last: Phiri

state: Southern Region

address: Chipatala Avenue

country: Malawi

institute: Malawi Liverpool Wellcome Programme

summary: We have employed a single cell RNA sequencing approach to study the nasal immune and epithelial cells landscape in People Living with HIV (PLHIV) and during the course of anti-retroviral uptake. The landscape ansal immunity is crucial for early control of respiratory pathogens including bacterian and viruses.

overall_design: Cross-sectional observational cohort design recruiting HIV- adults, People Living with HIV on ART for less than three months and people living with HIV on ART for greater than one year. Nasal cells were collected from all the participants using a nasal curette from the inferior turbinate.Single cell suspensions were prepared and libraries were prepared using 10X 5' platform. Samples were sequenced on a NextSeq 5000

last: Aston Phiri

first: Kondwani

last: Charles Jambo


title: Non-canonical functions of UGT2B17 promote castrate-resistant prostate cancer progression

city: Vancouver

first: Nathan

last: Lack

state: British Columbia

address: 2260 Oak st.

institute: Vancouver Prostate Centre

summary: When prostate cancer (PCa) overcomes the androgen receptor (AR) target therapy and progresses to the castrate-resistant prostate cancer (CRPC) stage, it becomes curable. UDP glucuronosyltransferase 2B17 (UGT2B17) is the key enzyme determining androgen bioavailability to AR inside PCa cells. However, whether UGT2B17 promotes CRPC progression remains poorly understood. Here, we report that anti-AR therapy increases UGT2B17 protein stability. UGT2B17 is localized in both the cytoplasm and nucleus to exert multiple non-enzymatic functions. In the cytoplasm, UGT2B17 activates unfolded protein response (UPR) to counteract endoplasmic reticulum (ER) stress for cell survival. UGT2B17 can exert its nuclear functions by stimulating c-Src kinase to activate AR in the absence of androgens. The UGT2B17-Src axis confers PCa cells resistant to DNA damage and promotes cell cycling by passing the G2 checkpoints through de-activating ATM and ATR kinases. We conclude that these non-enzymatic functions of UGT2B17 activate multiple survival pathways to allow CRPC progression.

overall_design: RNA-seq analysis comparing the transcriptome between LNCaP95 and LNCaP(UGT2B17 KO) cell lines

first: Xuesen

last: Dong

first: Tunc

last: Morova


title: Docetaxel treatment upregulates estrogen receptor expression in triple negative breast cancer cells via activating arachidonic acid pathway

city: Xinxiang

first: Xin

last: Zhao

address: Jinsui Avenue

institute: Xinxiang Central Hospital

summary: Triple negative breast cancer (TNBC), the most aggressive subtype of breast cancer,accounts for approximately 15% of all cases. TNBC remains challenging due to a lack of effective treatment strategies, which significantly impacts patient survival outcomes. This study investigates a novel combination therapy using Docetaxel, a microtubule depolymerization inhibitor, and Tamoxifen, an estrogen receptor (ER) antagonist, targeting TNBC, as well as elucidate molecular mechanisms. Synergistic effects of Docetaxel with Tamoxifen in TNBC cells were analyzed at SynergyFinder. Their anti-tumor growth effects were determined in vivo using both nude mice and Balb/c mice. RNA-Seq was conducted to analyze the pathways altered by Docetaxel treatment in TNBC cells. We demonstrate that Docetaxel sensitizes TNBC cells to Tamoxifen, despite the typical ER-negative status of TNBC. Here, we reveal that Docetaxel activates the arachidonic acid signaling pathway, leading to increased prostaglandin E2 (PGE2) production and subsequent upregulation of c-Jun phosphorylation, which in turn induces ESR1 expression. This ERα induction enables Tamoxifen to effectively inhibit TNBC cell proliferation. Given the clinical availability of both drugs, our findings propose a promising, translationally feasible combination strategy to address the therapeutic limitations of TNBC, offering a novel approach to improve outcomes for this high-risk patient population.

overall_design: HCC1937 cells treated with con or 8nM Docetaxel for 24h were collected for RNA-Seq.