title: A red clover-based dietary intervention limits nematode egg excretion and reshapes parasite-host-microbiome interplay within the sheep abomasum

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: Helminth infections, such as gastrointestinal nematodes (GIN) are highly prevalent in grazing-based livestock systems, compromising animal health and welfare and causing substantial economic losses. Although anthelmintics remain the primary control strategy, resistance is becoming increasingly widespread. Thus, sustainable alternatives are urgently needed to improve parasite control and support animal health. We formulated a red clover–based forage diet using the biorefinery by-product red clover pulp. In sheep infected with three common GIN species, this diet reduced fecal egg counts by ~40% (P = 0.0006) without negatively affecting feed intake or weight gain. The diet also significantly increased the abundance of Bacteroidales RF16 and Bacteroidales p-251-o5, taxa associated with short-chain fatty acid production, while reducing Methanomethylophilaceae, a family linked to methane production. Moreover, the red clover diet markedly altered the abomasal environment, and these changes were mirrored by shifts in the Haemonchus contortus gut microbiome, whereas the microbiomes of Teladorsagia circumcincta and Trichostrongylus colubriformis remained largely unaffected by diet. These findings highlight a sustainable dietary strategy to reduce GIN transmission and improve ruminant health, while also revealing distinct interactions between host and parasite-associated microbiomes that could be key to designing future control strategies.

overall_design: Ten male and ten female CheviotTexel crossbred [GP6.1]lambs were purchased from Vibygård Lamb (Rønnede, Denmark). The animals were 4–6 months old, weighing approximately 30–44 kg. From birth they were kept in-door in a separate rearing facility with no exposure to pasture, in order to prevent strongyle infections. During the experiment, the animals were housed indoors in and allocated to separate pens based on similar body weight to ensure equal access to feed and reduce aggressive behaviours. Lambs were randomly assigned to three experimental groups after stratification for initial body weight: uninfected animals fed a ryegrass diet (UR), infected animals fed a ryegrass diet (IR), and infected animals fed a red clover diet (IC). In the UR group, animals were housed in three pens, each containing one male and one female. In the IR group, two pens housed one male and one female each, while a third pen contained two females and one male. In the IC group, one pen housed one male and one female, one pen contained two males, and another housed two females and one male. The animals were provided their respective experimental diets immediately upon arrival and underwent a one-week acclimatization period (from Day -7 to day 0). Following acclimatization, each lamb in the IR and IC groups was orally infected with approximately 10,000 T. circumcincta[ST7.1], 8,000 T.colubriformis, and 100 H.contortus of infective third-stage larvae (L3), administered in equal doses over two consecutive days (Day 0 and 1 post-infection??). The animals were sacrificed on days 31 and 32 post-infection.


title: MBD8 acts a conserved cofactor of the histone demethylase LDL2 to regulate flowering time in plants [LDL2_RNAseq]

status: Public on Jun 01 2026

city: Beijing

first: xinjian

last: he

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

type: Expression profiling by high throughput sequencing

summary: Histone demethylases have been extensively characterized in plants, yet how their enzymatic activities are regulated remains largely unknown. Here, we identify that MBD8, a protein harboring a putative methyl-CpG-binding domain (MBD), forms a protein complex with the histone demethylase LDL2 in Arabidopsis thaliana. In this complex, MBD8 functions as a cofactor that is required for efficient LDL2-mediated removal of mono- and di-methylation at histone H3 (H3K4me1 and H3K4me2) across the genome. In the Arabidopsis C24 ecotype, loss-of-function mutations in MBD8 and LDL2 result in indistinguishable late-flowering phenotypes, which are consistent with increased enrichment of H3K4me1 and H3K4me2 at the flowering repressor loci MAF1 and MAF5. Importantly, we demonstrate that the rice (Oryza sativa) MBD8 orthologs MBD708, MBD709, and MBD715 also interact with the LDL2 ortholog Hd18 to form a protein complex, and disruption of these components delays flowering by reprogramming the expression of genes associated with floral transition. Collectively, this study reveals an evolutionarily conserved mechanism in which MBD8 orthologs act as cofactors of LDL2 orthologs to regulate histone demethylation and flowering time in plants.

sample_organism:
Arabidopsis thaliana
Oryza sativa

platform_organism:
Arabidopsis thaliana
Oryza sativa

overall_design: Examination of the mRNA expression of 12-day-old wild type and two mutants in Arabidopsis;Examination of the mRNA expression of 50-day-old wild type and two mutants in Oryza sativa

first: XinJian

last: He


title: Differential effects of chronic Limb ischemia on gene profile changes between rat gastro and soleus muscles

city: Omaha

first: Hanjun

last: Wang

state: Nebraska

address: 984455 University of Nebraska Medical Center 985850 University of Nebraska Medic

department: Anesthesiology

country: USA

institute: University of Nebraska Medical Center

summary: Rat  gastrocnemius and soleus muscles were dissected from the rats 4 weeks post iIlio-femoral endovascular catheter occlusion  (IFCO) or sham surgery. Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. The sham gastroc had a different transcriptomic profile compared to the sham soleus. The gastroc possessed higher expression of myosin heavy chain 4 (MYH4) and troponin subsets (TNNC2, TNNI2, and TNNT3) and other gene markers for type II fibers. In contrast, the soleus highly expressed MYH7, TNNC1, TNNI1, TNNI3, and other type I fiber contractility genes . These results indicate that the gastroc contained greater proportions of type II fibers while the soleus predominantly comprises type I fibers. Gene set enrichment analysis further highlighted fiber composition differences by shBulk RNAseq discovered that over 1800 DEGs were revealed when comparing IFCO soleus and gastroc with the most downregulated DEGs in the gastroc. A total of 816 DEGs were identified between IFCO and sham solei, with 730 upregulated and 86 downregulated genes. Conversely, only 89 DEGs were identified between the IFCO and sham gastrocs, with all but 3 being upregulated.owing upregulation of glycolytic genes, such as glucose phosphate isomerase (GPI), Lactate dehydrogenase A (LDHA), and 6-phosphofructokinase, muscle type (PFKM), within the gastroc, while the soleus upregulated Lactate dehydrogenase B (LDHB) and NADPH oxidase 1 (NOX1). The soleus also has unregulated NADPH dehydrogenase quinone 1 (NQO1), Glutathione peroxidase 1 (GPX1), and RNA Binding Motif Protein 11 (RBM11), consistent with other reports stating that type I fibers possess higher anti-oxidative capacity. In total, almost 1700 DEGs were identified between the sham muscles, with most DEGs being downregulated in the gastroc compared to the soleus.

overall_design: Sham and Ilio-femoral endovascular catheter occlusion; Gastrocnemius vs Soleus


title: Integrated single-cell and genomic analysis reveals CDC73-centered malignant reprogramming in parathyroid carcinoma

city: Seoul

first: Jong-Il

last: Kim

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

summary: Parathyroid carcinoma (PC) is a rare but aggressive endocrine malignancy with limited therapeutic options, and although CDC73 alterations are a major genetic event in PC, their relationships to tumor-cell states and microenvironmental remodeling remain incompletely defined. To address this, we performed integrated whole-exome sequencing (WES) and single-cell RNA sequencing (scRNA-seq) on parathyroid tumors from four patients with PC and four with parathyroid adenoma (PA) to define cell type-specific transcriptional programs and tumor microenvironmental features according to histology and CDC73 status. WES identified CDC73 alterations in two of four carcinomas, both showing evidence of biallelic inactivation. Compared with PA, PC showed relative expansion of endocrine tumor cells, depletion of endothelial cells, enrichment of cell-cycle programs, activation of PI3K/MAPK signaling, and suppression of p53 activity, with these transcriptional changes following a gradient from PA to CDC73-wild-type PC to CDC73-mutant PC. Within endocrine cells, CDC73-mutant carcinomas were distinguished by reduced endocrine-lineage features, decreased ERBB4 and CASR expression, increased UCHL1 and WT1 expression, and selective activation of MYC regulons. Within the tumor microenvironment, carcinomas were characterized by enrichment of MMP11-positive cancer-associated fibroblasts and fibroblast-driven collagen–integrin signaling, whereas CDC73-mutant tumors additionally exhibited preferential accumulation of regulatory T cells and MARCO-positive protumor macrophages, along with BTLA-associated Treg–macrophage interactions. Overall, integrated genomic and single-cell profiling reveals that parathyroid carcinoma comprises coupled endocrine-cell reprogramming and stromal/immune remodeling, with CDC73 mutation defining a distinct malignant state, supporting CDC73-based molecular stratification and nominating tumor-intrinsic MYC programs, and immunosuppressive myeloid-lymphoid crosstalk as candidate biomarkers and therapeutic targets.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on parathyroid tumor samples from eight patients, including four parathyroid adenomas (PA) and four parathyroid carcinomas (PC).


title: MBD8 acts a conserved cofactor of the histone demethylase LDL2 to regulate flowering time in plants [LDL2_ChIPseq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Examination of H3K4me1, H3K4me2 of wild type and two mutants in Arabidopsis.


title: Age-Dependent Transcriptomic and DNA Methylation Alterations in Fibroblasts During Resolving and Persistent Lung Fibrosis

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

type: Methylation profiling by high throughput sequencing

summary: The activation of fibroblasts in response to lung injury is an adaptive and necessary process for physiological repair, but their persistent activation can lead to excessive scarring and impaired fibrosis resolution. Although the model of bleomycin-induced lung fibrosis in young adult mice is often criticized because fibrosis spontaneously resolves, comparisons of this model with aged mice, in which fibrosis persists, can provide important insights into the genes and pathways that modulate persistent vs resolving fibrosis. Changes in DNA methylation are a prominent feature of aging and pulmonary fibrosis. Here, we explore the differential expression and DNA methylation patterns that occur in lung fibroblasts of young and aged mice during persistent and resolving fibrosis.

overall_design: Aged (> 18 months old) and young (6–8 weeks old) mice were given a single dose of bleomycin or saline and were euthanized at day 30, an early time point that distinguishes resolving vs non-resolving fibrosis. Freshly isolated fibroblasts were analyzed for gene expression by RNA-Seq and DNA methylation by reduced representation bisulfite sequencing.

first: Steven

middle: K

last: Huang

first: Eistine

last: Boateng

first: Raymond

middle: G

last: Cavalcante

first: Tho

last: Pham

first: Ahmed

last: Raslan

first: Nunzia

last: Caporarello

first: Anne

middle: M

last: Scruggs

first: Giovanni

last: Ligresti


title: Eomes sustains progenitor CD4⁺ T helper cells to promote anti-tumor immunity during immunotherapy [scRNA]

city: Toulouse

middle: S

last: Dejean

state: Midi-Pyrenees

address: CHU Purpan – BP 3028

country: France

institute: Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)

summary: CD4⁺ T helper (Th) cells contribute to tumor immunity, yet the subsets and differentiation programs involved remain unclear. Here, we show that the transcription factor Eomesodermin (Eomes) is essential for Th–mediated anti-tumor immunity by orchestrating the differentiation and maintenance of an exhausted-like Th cell lineage, which is transcriptionally and functionally distinct from conventional effector or memory Th subsets. This Eomes-dependent program is further enhanced by 4-1BB stimulation, promoting effective Th cell–mediated tumor control. The precursor subset of this lineage (pTh) expresses stemness-associated transcription factors, displays self-renewal capacity, and can differentiate into effector cells capable of controlling tumor growth. At the transcriptional level, Eomes supports the survival, metabolic fitness, and apoptotic resistance of this lineage. Notably, Eomes⁺ pTh cells are directly relevant to human cancer, being detected across multiple tumor types, exhibiting conserved transcriptional features, and representing the most expanded Th cell population upon immune checkpoint blockade therapy.

overall_design: Mice were injected i.v. with NK1.1-depleting mAbs (50μg/mice, days -2 and 5), engrafted with Vk12653 MM cells (2.106, day 0), subsequently treated with 4-1BBa or control IgG mAbs (20μg/mice, days 10, 13, 16) and mice were euthanized at day 18. At day 18, CD44high CD4+ T cells were isolated from spleen using CD4+ T Cells isolation Kit (Invitrogen) then FACS Aria Fusion (BD Biosciences).

first: Liliana

last: Lucca

first: Arantxa

last: Agesta

first: Chloé

last: Ferrand

first: Anne-Louise

last: Le Dorze

first: Nadège

last: Carrié

first: Arthur

last: Palak

first: Ludovic

last: Martinet


title: Effects of diet and trained immunity on responses to enteric helminth infection in mice

first: Andrew

last: Williams

summary: Mice were “preimmunized” with UV‑inactivated bacterial and viral pathogens, generating a trained immune response but compatible with SPF housing. Preimmunization increased memory T‑cell populations and strengthened baseline Th1‑associated cytokine responses. When combined with dietary interventions, this immune training altered susceptibility patterns to Trichuris muris (Tm) infection. In chow‑fed mice, preimmunization increased susceptibility to Tm, while in SSD‑fed mice, the diet‑associated resistance was largely preserved. Across both diets, preimmunization enhanced Th1‑skewed cytokine responses during infection, consistent with the Th1 dominance of early Tm immunity. These findings demonstrate that immune maturity modulates, but does not eliminate, diet‑associated differences in helminth susceptibility.

overall_design: Female C57BL/6 mice, aged 4 weeks, were utilized for all experiments and were procured from Envigo (The Netherlands). The mice were housed in groups of three to five per cage, with individual ventilation, wood chips, nesting material, and provided with ad libitum access to water and diet. Two and four weeks prior to diet change, mice were preimmunized subcutaneously with 50 uL of the pathogen mix and 50 uL adjuvant (AddaVax, Invivogen, San Diego, CA, US).  Two weeks after lastest preimmunization, the mice were fed either a standard grain-based diet (chow) or a semisynthetic open-source diet (SSD) containing 13 kJ% fat (#E15051; ssniff Spezialdiäten GmbH, Germany). They were maintained on their respective diets for two weeks prior to infection with approximatively 200 L3 stage larvae of Heligmosomoides polygyrus or 40 Trichuris muris eggs. Infections were administered by delivering 0.2 mL of a water-larvae suspension per mouse via oral gavage. The mice were euthanized 21 days post-infection (DPI).

middle: R


title: Mitochondrial Iron Sensitizes Senescent Cancer Cells to Ferroptosis

city: Montreal

first: Audrey

last: Langlois

state: Qc

address: 900 Saint Denis St

department: Biochemistry

country: Canada

institute: University of Montreal

summary: The chemotherapy regimen FOLFIRINOX has been shown to induce senescence in pancreatic ductal adenocarcinoma (PDAC) cells, as well as in immortalized normal human pancreatic ductal epithelium (HPNE-hTERT) cells. To investigate the transcriptional changes associated with treatment-induced senescence in non-malignant cells, RNA sequencing was performed on HPNE-hTERT cells that were either untreated (vehicle control) or treated with FOLFIRINOX for 4 days.

overall_design: A RNA sequencing was performed to compare immortalized normal human pancreatic ductal epithelium (HPNE-hTERT) cells treated with Vehicle (Veh) or FOLFIRINOX (Folfi) for 4 days.

first: Paloma

last: Kalegari

first: Gerardo

last: Ferbeyre


title: scRNA-Seq from Stroma Vascular Cell isolated from abdominal and gluteofemoral human adipose tissue

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

summary: SVF was isolated from ABD and GF-adipose tissue biopsies by collagenase digestion and centrifugation, from 4 women with PCOS. After isolation, cells were counted with a Countess II automated cell counter (Thermofisher Scientific). Single cell suspension (56K/mL) was distributed into eight wells of a 384-well source plate (Takara Bio USA, San Jose, CA) and dispensed onto a iCELL8 350v Chip (Takara Bio USA) using an iCELL8 MultiSample NanoDispenser (Takara Bio USA). We distributed the ABD and GF-SVF of each subject on the same chip. In brief, mRNA from single cells were isolated, converted to full-length cDNA prior to unbiased amplification of 3’ and 5’ ends using SMART-Seq® ICELL8® Application Kit (Takara Bio, USA). Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol and 150bp paired-end sequencing was performed on an Novogene NovaSeq X Plus instrument.

overall_design: SVF was isolated from abdominal and gluteofemoral adipose tissue biopsies from 4 PCOS women.

first: Steven

last: Smith

first: Timothy

middle: F

last: Osborne


title: snRNA-Seq from  abdominal and gluteofemoral human adipose tissue

summary: Adipose tissue biopsies were collected from subcutaneous abdominal and gluteofemadipose tissue from 5 healthy and 5 PCOS women. After isolation, nuclei were counted with a Countess II automated cell counter (Thermofisher Scientific). Single nuclei suspension (56K/mL) was distributed into eight wells of a 384-well source plate (Takara Bio USA, San Jose, CA) and dispensed onto a iCELL8 350v Chip (Takara Bio USA) using an iCELL8 MultiSample NanoDispenser (Takara Bio USA). We distributed the ABD and GF-SVF of each subject on the same chip. In brief, mRNA from single cells were isolated, converted to full-length cDNA prior to unbiased amplification of 3’ and 5’ ends using SMART-Seq® ICELL8® Application Kit (Takara Bio, USA). Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol and 150bp paired-end sequencing was performed on an Novogene NovaSeq X Plus instrument.

overall_design: snRNA-Seq on frozen abdominal and gluteofemoral subcutaneuous white adipose tissue from 5 healthy and 5 PCOS women.


title: The transcriptional cortical adaptations to daily torpor in Phodopus sungorus

city: Hamburg

first: Manuel

middle: Alexander

last: Friese

state: Hamburg

address: Falkenried 94

department: ZMNH

country: Germany

institute: UKE

summary: Torpor is an essential evolutionary strategy that allows mammals to conserve resources under extreme environmental conditions. While the hypothalamus is a key regulator of systemic adaptations to energy scarcity and reduced temperature, it remains unclear how the cortex, with its high metabolic demand, endures this state. Here, we performed RNA sequencing on neuronal and non-neuronal nuclei isolated from the cortex of Djungarian hamsters (Phodopus sungorus) across different seasonal and metabolic states. We found that non-neuronal cells primarily adapt during the seasonal transition from summer to winter phenotype, with differential expression of genes linked to circadian rhythm. In contrast, cortical neurons exhibited major transcriptional changes only between normothermia and hypothermia, marked by increased expression of RNA catabolic pathways. Finally, comparison with published hypothalamic datasets revealed distinct transcriptional programs between the cortex and hypothalamus. Together, these findings highlight cell type- and region-specific adaptations that preserve CNS integrity during metabolic depression.

overall_design: We conducted RNA sequencing on sorted cortical nuclei from Djungarian hamsters under different metabolic and seasonal conditions.

first: Lukas

last: Bal

first: Marcel

last: Woo

first: Nicola

last: Rothammer

first: Elena

last: Haugg

first: Christina

last: Mayer

first: Annika

last: Herwig


title: Nf2 orchestrates β-arrestin2-biased PTH1R signaling to safeguard skeletal integrity

city: Hangzhou

first: Liao

last: junguang

state: Zhejiang

address: 928 2nd Street

institute: Zhejiang Sci-Tech University

summary: Precise spatiotemporal regulation of parathyroid hormone (PTH) and PTH-related peptide (PTHrP) signaling through the PTH1R is fundamental to skeletal development and metabolic bone remodeling, yet the intracellular mechanisms that fine-tune this signaling remain a central unanswered question. Here, we identify neurofibromin 2 (Nf2) as an essential regulator of PTH1R trafficking and signaling. Conditional knockout of Nf2 in chondrocytes results in short-limbed dwarfism, disrupted growth plate organization, and suppressed chondrocyte proliferation and hypertrophy, and a paradoxical bone phenotype marked by trabecular hyperproliferation and cortical thinning. Mechanistically, Nf2 binds to the PTH1R C-terminal domain (464–591 aa) to promote selective receptor internalization via β-arrestin2, without altering Gαs‐mediated cAMP production or initial receptor phosphorylation by GRKs. Loss of Nf2 decouples PTH1R from β-arrestin2‐mediated endocytosis, leading to sustained and amplified signaling through the cAMP‐CREB‐pSOX9 (S181) and VEGF axis. Consequently, Nf2-deficient mice exhibit exaggerated anabolic responses to the PTH1R agonist abaloparatide and are rescued by the inverse agonist cinacalcet. Importantly, Nf2 ablation confers profound resistance to age-related and ovariectomy-induced osteoporosis. These results establish Nf2 as a chondrocyte‐intrinsic gatekeeper of PTH1R signaling and uncover a novel therapeutic paradigm for bone diseases by targeting Nf2‐mediated β-arrestin2 recruitment.

overall_design: RNA-seq profiling of Nf2f/f and Nf2f/f knockout primary cultured chondrocytes with differentiation.

first: Junguang

last: Liao

first: Yiliang

last: He

first: Guiqian

last: Chen


title: Exercise Mitigates Cardiac Dysfunction Post-MI in Ovariectomized Mice via miR-21/Sox7-Mediated Suppression of Cardiac Fibroblast Activation

city: Shanghai

first: meiyu

last: hu

address: 333 Nan Chen Road

institute: Shanghai University

summary: Background: Postmenopausal women have higher risks of myocardial infarction (MI) and subsequent cardiac dysfunction. Exercise is widely recognized to protect the cardiovascular system, but its molecular mechanisms in postmenopausal MI remain not fully understood. This study explored the effects and mechanism of swimming exercise against cardiac dysfunction in ovariectomized (OVX) mice post-MI. Methods: OVX mice were subjected to a 3-week swimming training before MI induction via permanent ligation of left anterior descending artery. Cardiac systolic function was evaluated by echocardiography. Masson, HE, WGA staining, RT-qPCR, and Western blotting were combined to detect the extent of cardiomyocyte hypertrophy, myocardial fibrosis, and apoptosis. To explore the key exercise-effectors, we detected microRNAs (miR-21, miR-146a, miR-155) in serum samples of elderly post-MI women subsequent to exercise rehabilitation training. miR-21 expression was further investigated in heart sample of OVX plus MI mice. The role of miR-21 in vivo was elucidated through miR-21 knockout mice model and AAV9-mediated miR-21 overexpression mice model. The function of miR-21 in vitro were evaluated in cardiac fibroblasts isolated from OVX mice and treated with TGF-β to induce its activation. miR-21 targets were revealed by microarray analysis and verified by luciferase reporter and functional rescue assays. Results: Swimming significantly improved cardiac function in OVX mice post-MI, alleviated cardiomyocyte hypertrophy, reduced myocardial fibrosis, and inhibited apoptosis. miR-21 expression was downregulated by exercise training both in heart of OVX mice post-MI and in serum of elderly women after MI. miR-21 knockout mimicked swimming’s cardioprotective effects towards OVX mice post-MI, while miR-21 overexpression abolished these effects. The overexpression of miR-21 promoted the TGF-β-induced differentiation of cardiac fibroblasts into myofibroblasts and their proliferation, whereas its inhibition blocked TGF-β’s pro-fibrotic role. Microarray analysis and luciferase assays identified Sox7 as a direct miR-21 target, and Sox7 knockdown reversed anti-fibrotic effect of inhibiting miR-21. Conclusion: Swimming protects against post-MI cardiac dysfunction in OVX mice by downregulating myocardial miR-21, thereby upregulating its target gene Sox7 and inhibiting cardiac fibroblast activation. miR-21 and its downstream target Sox7 contributes to cardioprotective effects of swimming, offering a potential target for postmenopausal MI treatment.

overall_design: To elucidate how miR-21 exert its effects, we performed RNA-seq of hearts samples harvested from mice of 3 weeks post-MI to identify differentially expressed genes between control OVX mice and miR-21 overexpressed OVX mice that subjected to first swimming training and then MI surgery (Four group: AAV9-Empty+Control+MI-3W; AAV9-OE miR-21+Control+MI-3W; AAV9-Empty+Swim+MI-3W; AAV9-OE miR-21+Swim+MI-3W).


title: Single-cell RNA sequencing of alveolar macrophages in GRP75 knockdown mice with SARS-CoV-2 N protein-induced lung injury

city: hangzhou

first: REN

last: YICHAO

state: zhejiang

address: zhejianghangzhou

institute: zhejiang university

summary: This study investigates the role of GRP75 (Hspa9)-mediated mitochondria-associated membranes (MAMs) in SARS-CoV-2 nucleocapsid (N) protein-induced acute lung injury. Using single-cell RNA sequencing of lung macrophages from control and GRP75 knockdown mice, we demonstrate that N protein promotes GRP75-dependent ER-mitochondria tethering, leading to mitochondrial calcium overload and proinflammatory macrophage activation. GRP75 knockdown attenuates N protein-induced lung injury by reprogramming alveolar macrophage identity from a pro-inflammatory Car4+ state to a metabolically quiescent Hspa9-low state.

overall_design: scRNA-seq profiling of lung cells from three experimental groups: (1) Control shRNA, (2) N protein + Control shRNA, and (3) N protein + GRP75 shRNA. Macrophages were enriched by FACS and pooled with unfractionated lung cells at 4:1 ratio.

first: Yichao

last: Ren

first: Ruoxi

last: zang

first: Jianguo

last: Xu

first: Qiang

last: Shu


title: USP22 Facilitates Gastric Cancer Progression via Hippo/YAP axis

city: Jinan

first: Jie

last: Zhang

address: 247 Beiyuan Street, Tianqiao District, Jinan, Shandong Province, China

institute: Sgandong University

summary: Gastric cancer (GC) is one of the most common malignancies in the digestive system. Previous studies demonstrated that the dysregulation of the Hippo pathway and hyperactivation of the YAP/TEAD transcriptional axis played important roles in GC progression, although the underlying mechanisms remain incompletely understood. Our study demonstrated that the deubiquitinase USP22 plays a pivotal role in regulating the Hippo pathway in GC, where its inhibition markedly suppresses YAP/TEAD activity and tumor progression. Mechanistically, USP22 interacts with YAP and inhibits its K48-linked polyubiquitination, thereby enhancing YAP protein stability and Hippo/YAP axis activity in GC. Intriguingly, YAP can transcriptionally upregulate USP22 by binding to its promoter region, establishing a positive feedback loop that promotes gastric cancer progression. Collectively, our findings reveal a reciprocal activation mechanism between USP22 and the Hippo pathway in gastric tumorigenesis, identifying USP22 as a promising novel therapeutic target.

overall_design: In this study, we used AGS human gastric cancer cells as the primary experimental samples, with cells transfected with siControl serving as the negative control group and cells transfected with two independent siUSP22 sequences as the experimental groups. The experimental conditions were strictly controlled: cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37°C in a humidified incubator with 5% CO₂, and all transfections were performed at 70–80% confluence. The key variables under investigation included the expression levels of YAP downstream target genes (e.g., CTGF, CYR61), which were analyzed by RT-qPCR at 48 h post-transfection to assess the regulatory effect of USP22 on the Hippo signaling pathway in gastric cancer.

first: Ting

last: Zhuang

first: Jian

last: Zhu

first: Yinlu

last: Ding


title: RSAD2/VIPERIN and CMPK2 Coordinate  an Immunometabolic Response to Epstein-Barr Virus

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Epstein-Barr Virus (EBV) infection and reactivation in B-lymphocytes is tightly regulated by host antiviral response genes. In the present study, we identify interferon stimulated genes RSAD2 (radical S-adenosyl methionine domain-containing 2) and CMPK2 (Cytidine/Uridine Monophosphate Kinase 2) as key modulators of EBV expression and cellular response during EBV infection and reactivation. EBV primary infection and reactivation lead to a coordinated upregulation of RSAD2 and CMPK2. Depletion of RSAD2 reduced cell viability and limited EBV reactivation, while depletion of CMPK2 led to reactivation of EBV lytic gene expression during latency. Transcriptomic analysis revealed that RSAD2 and CMPK2 have overlapping functions in regulating IFN-signaling pathways, as well as oxidative phosphorylation, protein translation, and unfolded protein response during reactivation. Despite distinct subcellular localizations, RSAD2 at the Endoplasmic Reticulum (ER), and CMPK2 in mitochondria, both genes converge on shared immunometabolic pathways, including control of Gasdermin D (GSDMD) associated pyroptosis and ATF-4 associated unfolded protein response (UPR). EBV reactivation induced formation of antiviral ribonucleotide ddhCTP during lytic EBV reactivation which was strictly dependent on RSAD2. Knockdown of RSAD2 and CMPK2 had significant effects on global metabolites consistent with a remodeling of glycolysis, fatty acid biosynthesis and degradation of superoxides. These observations demonstrate that RSAD2-CMPK2 function in a coordinated ER-mitochondria stress-Interferon signaling axis that shapes EBV reactivation and host immune control, including a novel layer of immunometabolic regulation modulating viral latency and reactivation.

overall_design: RNAseq profiling after RSAD2 and CMPK2 knockdown in Mutu I cells. Cells were transduced with lentiviruses for shControl, shRSAD2 or shCMPK2. After lentivirus knockdown, cells were  treated with sodium butyrate (NaB) + TPA (12-O-tetradecanoylphorbol-13-acetate) for 24 h to induce lytic EBV reactivation or were left untreated. Cells treated with NaB+TPA are refered to as "Induced" and untreated cells are refered to as "Uninduced".

first: Urvi

last: Zankharia

first: Adam

last: Glass

first: Qing

first: Janvhi

last: Machhar

first: Wujuan

first: Aaron

last: Goldman

first: Ying

last: Ye

first: Bhanu Chandra

last: Karisetty

first: Jayamanna

first: Andrew

last: Kossenkov

first: Jozef

last: Madzo

first: Sun

last: Chung

first: Samantha

last: Soldan

first: Jason

last: Lamontagne

first: Steven

last: Jacobson

first: Lawrence

last: Harris

first: Tyler

middle: L

last: Grove

first: Chengyu

last: Liang

first: Paul

last: Lieberman


title: The long non-coding RNA ACHLYS modulate biological condensates to regulate alternative splicing in root development

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

institute: CNRS

summary: Alternative splicing (AS) enables eukaryotes to dynamically adjust RNA and protein isoforms encoded in one gene. Long non-coding RNAs (lncRNA) have emerged as novel regulators of AS through multiple modes of action, including interactions with splicing factor (SF) proteins. Here, we used Arabidopsis thaliana lateral root development to dissect the specificity of lncRNAs in AS regulation. Data mining and a transient expression screen allowed us to identify novel lncRNAs interacting in vivo with the well-characterized SFs Nuclear speckle RNA binding protein (NSRa) and glycine-rich RNA-binding protein 7 (GRP7) that are differentially expressed during lateral root organogenesis. We identified 4 lncRNAs affecting more than 250 AS events in plant cells, whereby most AS events are unique for each lncRNA. Notably, 19% of the AS events linked to two NSRa-recognized lncRNAs are identical and positively correlated. One lncRNA was named ACHLYS and is highly conserved in several Brassicaceae whereas another was the recently characterized FLAIL lncRNA. ACHLYS knockdown (KD-ACHLYS) and overexpressing lines (OE-ACHLYS) modulate AS regulation in plants and affect root architecture. In parallel, we performed NSRa-iCLIP to determine in vivo genome-wide NSRa binding sites. Interestingly, NSRa binding sites are locally enriched in ACHLYS-dependent AS introns and ACHLYS itself. A specific ACHLYS-induced AS event requires NSRa function showing that ACHLYS defines AS targets through NSRa interaction on specific transcripts. In vitro assays indicate that direct interaction of NSRa with ACHLYS promotes NSRa phase separation. Furthermore, overexpression of  ACHLYS in NSRa-GFP plants results in increased accumulation of NSRa in nuclear speckles. Our data revealed that ACHLYS can modulate NSRa condensates in vivo and binds to NSRa for modifying AS patterns, suggesting a new mechanism where lncRNAs can fine tune spliceosomal regulation and the transcriptome output in eukaryotic organogenesis.

overall_design: RNAseq of 7th Arabidopsis (ecotype Columbia) leaf transietly overexpressing lncRNA and RNAseq  of 10-day-old Arabidopsis seedlings (ecotype Columbia) of AT2G15292 and AT1G04107 35S overespressing and RNAi knockdown seedlings

first: Michel

last: Heidecker

first: Pablo

last: Mammi

first: Thorsten

last: Bergelt

first: Aurelie

last: Christ

first: Martin

last: Lewinski

first: Tino

last: Köster

first: Céline

last: Charon

first: Yu

last: Jin

first: Sebastian

last: Marquardt

first: Thomas

last: Blein

first: Jérémie

first: Dorothee

last: Staiger

last: Crespi


title: Spatially resolved gene expression and tumour-microenvironment interactions across malignant transformation in IDH-mutant glioma

city: Toronto

first: Alyona

last: Ivanova

state: ON

address: 686 Bay Street

institute: The Hospital for Sick Children

summary: Isocitrate dehydrogenase (IDH)-mutant gliomas represent most lower-grade diffuse gliomas in young adults. Although IDH-mutant gliomas initially behave indolently relative to IDH-wildtype counterparts, they undergo inevitable malignant transformation. The mechanisms driving this progression remain poorly defined. We analyzed a rare longitudinal cohort of two patients with IDH-mutant diffuse gliomas, each with matched WHO grade 2, 3, and 4 tumours. Spatial transcriptomics (NanoString GeoMx and 10X Visium), combined with differential expression, spatially variable gene analysis, and gene ontology enrichment, were used to define transcriptional programs underlying progression. Across both patients, higher-grade tumours demonstrated reduced proliferation and a shift toward a migratory, invasive phenotype. Grade 4 samples showed upregulation of genes involved in cell adhesion, axon guidance, cytoskeletal remodeling, and neural development. Spatial analyses localized these programs to tumour invasive margins. GO enrichment highlighted pathways related to neuron projection development, focal adhesion, and lamellipodium organization. Findings were clinically validated using Cox proportional hazards models with LASSO and Elastic Net regularization in a Pan-Cancer Atlas cohort. Elevated expression of invasion-associated genes correlated with shorter progression-free survival and an invasiveness gene signature predicted overall survival  . These findings identify candidate molecular drivers of progression and potential targets for timepoint-specific therapeutic intervention.

overall_design: longitudinal cohort of 2 patients with IDH-mutant diffuse gliomas, each with matched WHO grade 2, 3, and 4 tumours. Patient 1 samples were profiled with GeoMx DSP. Patient 2 samples were profiled with Visium 10X.

first: Shamini

last: Ayyadhury

first: David

last: Munoz

first: Megan

last: Hopkins

first: Farzaneh

last: Aboualizadeh

first: Melanie

last: Spears

last: Wu

first: Trevor

last: Pugh

first: Roel

last: Verhaak

first: Daniel

middle: P

last: Cahill

first: Sunit

last: Das


title: The autoantigen TRIM21 assembles proinflammatory immune complexes following lytic cell death

city: Oxford

first: Lynn

middle: B

last: Dustin

state: Oxfordshire

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

summary: Sjögren’s disease (SjD) causes localized and systemic inflammation and autoantibody production against intracellular proteins such as TRIM21/Ro52 (tripartite motif-containing protein 21). TRIM21, an E3 ubiquitin ligase, binds antibody Fc domains on opsonized pathogens that have escaped extracellular immunity and entered the cytosol. TRIM21 then ubiquitinates these pathogens, driving their proteasomal degradation. How TRIM21 becomes an autoantigen remains unclear. We show that TRIM21 is released upon lytic cell death (pyroptosis/necroptosis) but not apoptosis. Although many cytosolic proteins are released by dead cells, liberated TRIM21 is distinct: its high antibody affinity enables binding to Fc domains of circulating immunoglobulins, forming large immune complexes (ICs). These ICs increase in SjD, where anti-TRIM21 autoantibodies interact with released TRIM21 via Fc and F(ab′)2. TRIM21-ICs are taken up by macrophages, which, in high interferon environments, drive proinflammatory responses, antigen presentation, and metabolic changes. Thus, TRIM21 may perpetuate inflammation and autoantigen presentation, resulting in high immunogenicity.

overall_design: Bulk RNAseq analysis of human monocyte-derived macrophages from 3 donors (D8, D10, and D11) after 6 hours culture with medium only, TRIM21, healthy donor plasma, Sjögren's disease patient plasma, or TRIM21 combined with either healthy donor or Sjögren's disease plasma.

first: Esther

last: Evans

first: Benjamin

last: Demarco

first: Han

last: Cai

first: Madelon

last: de Jong

first: Sarah

last: Hill

first: Marcus

last: Widdess

first: Joannah

last: Fergusson

first: Ryan

last: Glass

first: Gemma

last: Harris

first: Gracie

last: Mead

first: Yavuz

last: Yazicioglu

first: Saba

last: Nayar

last: Fisher

first: Mark

last: Cragg

first: Alexander

last: Clarke

first: Audrey

last: Gérard

first: Jelena

last: Bezbradica


title: Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis

city: Boston

first: Emmanuel

last: Ogbonna

state: MA

address: 200 Longwood Ave

department: Laboratory of Systems Pharmacology

institute: Harvard Medical School; Tufts University School of Medicine

summary: Tertiary lymphoid structures (TLSs) are sites of immune organization in peripheral tissues that arise from chronic inflammation. They play important roles in infection control and cancer but the mechanisms controlling their formation and function remain only partly understood. Here, we combine high-plex imaging, serial-section 3D reconstruction, and optimal trajectory analysis modeling to reconstruct TLSs in human lung infected with Mycobacterium tuberculosis. We find that TLSs are the extended and irregular , spatially heterogeneous structures shape of TLS whose state of maturation, as judged by germinal center (GC) organization, is poorly captured by 2D histopathology or spatial profilingprofiling, making assuagements of developmental stage (early, primary, or secondary) highly error prone. . Using 3D data, we show that TLSs having GCs are diverse in cellular composition, size, and morphology. Organizing this complexityModeling development in 3D using optimal transport (trajectory) analysis reveals multiple pathways of TLS development formation differing that differ in the timing and coordination of follicular dendritic cell network formation,  and GC germinal center consolidation, and positioning within the tissue. These findings highlight the importance of volumetric analysis in understanding immune organization and provide new insights into TLS biology.

overall_design: 3 samples were processed for GeoMx spatial transcriptomics, as described by the manufacturer (Bruker, formerly NanoString Technologies). Guided by immunofluorescence staining (DNA-FITC/525nm, pan-cytokeratin-Cy3/568nm, CD45-Texas Red/615nm, CD20-Cy5/666nm), a total of 161 histopathological regions of interest (ROIs) were selected for human whole transcriptome atlas (WTA) profiling, including 133 TLS ROIs, 7 lymph node ROIs (LN, all from Patient2), and 21 uninvolved lung ROIs (UL, negative control lung alveoli). 16 ROIs from Patient3 (10 TLS, 6 UL ROIs) were excluded from subsequent analysis due to unusually low number of sequencing reads.

middle: C

first: Soheil

last: Talemi

first: Zoltan

last: Maliga

first: Ziyuan

last: Zhao

first: Adrie

last: Steyn

first: Bree

last: Aldridge

first: Peter

last: Sorger


title: Allyl-isothiocyanate affects antimicrobial peptide expression and survival in Drosophila melanogaster

city: Gießen

first: Sonja

last: Dähn

address: Wilhelmstrasse 20

institute: Justus-Liebig-Universität Gießen

summary: The global rise of antibiotic-resistant bacteria highlights the urgent need for alternative strategies to support host defense against infections. Bioactive plant-derived compounds, such as isothiocyanates, have gained attention due to their antimicrobial and immunomodulatory properties. Allyl-isothiocyanate (AITC), a hydrolysis product of glucosinolates found in Brassica vegetables, has demonstrated antimicrobial activity in vitro and the ability to modulate antimicrobial peptide (AMP) expression in cell culture models. However, it’s in vivo effects under metabolically challenging dietary conditions remain poorly understood. In this study, we investigated the impact of dietary AITC supplementation on immune responses and survival in Drosophila melanogaster exposed to a high-sucrose diet (HSD), a dietary condition known to impair metabolic health and immune function. Flies were fed an HSD with or without 0.25 mM AITC and subsequently subjected to oral infection with either Leuconostoc pseudomesenteroides or Pectobacterium carotovorum subsp. carotovorum, which preferentially activate the Toll and Imd signaling pathways, respectively. AMP expression was analyzed by qPCR and RNA sequencing, and physiological consequences were assessed by lifespan analysis. AITC did not affect food intake or basal AMP expression under non-infected conditions. HSD significantly reduced lifespan in both sexes, and AITC supplementation did not rescue this effect. Following infection, both HSD and AITC influenced survival in a sex- and pathogen-specific manner, with AITC frequently exacerbating mortality rather than improving outcomes. While selected AMPs, particularly Attacin D, were modulated in a context-dependent manner, RNA sequencing revealed no consistent transcriptional changes in core Toll or Imd pathway components. Overall, our findings indicate that dietary AITC does not enhance host defense under high-sugar conditions and that its effects on immunity and survival are strongly sex-specific. These results underscore the complexity of diet–immune interactions and caution against extrapolating in vitro antimicrobial effects to in vivo host protection.

overall_design: mRNA-Seq of male and female, 10-day old w1118 Drosophila melanogaster

first: Christian

last: Zimmermann

first: Ronja

last: Merschmann

first: Paul

last: Schmutzler


title: Imbalanced neurogenesis and gliogenesis in the developing neocortex of mice lacking the proteoglycan Tsukushi

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: Development of the mammalian neocortex relies on a tightly controlled schedule, wherein cortical progenitors initially expand by symmetric divisions, then sequentially generate neurons of the deep and superficial cortical layers by asymmetric divisions, and finally give rise to glial cell populations. This sequence of events is orchestrated by a complex network of transcriptional regulators and extracellular signals ensuring a proper balance between cortical expansion, and the production of neurons and glia. Altough the transcription factors governing progenitor self-renewal, neurogenesis and gliogenesis are largely known, the extracellular cues modulating these processes are less understood. Here, we investigate neocortical development in mice lacking the proteoglycan Tsukushi (TSK), which bear hydrocephalus with neurological deficits. We show that TSK is expressed in the cortical plate, where differentiating neurons and glia migrate to form the cortical layers. By single-cell transcriptomics, and validation of key molecular markers at the RNA and protein levels, we report an increased astrogliogenesis at the expense of neurogenesis in TSK-deficient neocortex. These results unveil TSK requirement to balance cortical neurogenesis and gliogenesis and support models linking alterations in neuro-gliogenesis to hydrocephalus.

overall_design: Cerebral cortex tissue was collected from wild-type and TSK knockout mice at embryonic day 14.5 (E14.5) and postnatal day 0 (P0) for single-cell RNA sequencing profiling.

first: Sabrina

last: Quaresima

first: Tenta

last: Ohkubo

first: Arif

last: Istiaq

first: Hideyuki

last: Nakashima

first: Elena

last: Miranda

first: Emanuele

last: Cacci

first: Hirofumi

last: Jono

first: Kinichi

first: Kunimasa

last: Ohta

first: Giuseppe

last: Lupo


title: Transcriptomic profiling of interferon responses induced by IVT sgRNAs in CRISPRi HEK293T cells

city: Ghent

first: Xin

last: Wang

address: Corneel Heymanslaan 10, B

country: Belgium

institute: University Gent

summary: In this study, we investigated the transcriptional responses induced by in vitro–transcribed (IVT) sgRNAs in a CRISPR interference (CRISPRi) system. A total of 906 sgRNAs were generated using a commercially available IVT workflow and delivered to HEK293T cells stably expressing dCas9-KRAB-MECP2. RNA sequencing was performed to profile genome-wide transcriptional changes following sgRNA transfection. Compared with mock-transfected controls, sgRNA-transfected cells exhibited a strong and consistent upregulation of interferon-stimulated genes (ISGs), with prominent enrichment of interferon-α response pathways across the majority of sgRNAs. While most sgRNAs induced robust interferon signaling, a small subset showed a more limited transcriptional response. IFIT1 and IFIT2, two canonical markers of interferon activation, were consistently upregulated and were selected as representative genes for downstream validation. This dataset provides a systematic resource for assessing innate immune activation triggered by IVT sgRNAs in CRISPRi-based perturbation experiments.

overall_design: HEK293T cells stably expressing dCas9-KRAB-MECP2 were transfected with 770 individual IVT sgRNAs. Mock-transfected cells served as controls. RNA sequencing was performed to profile transcriptional responses and assess interferon-related gene induction following sgRNA transfection.

first: Eric

last: de Bony

first: Wim

last: Trypsteen

first: Jasper

last: Anckaert

first: Nurten

last: Yigit

first: Kimberly

last: Verniers

first: Pieter

last: Mestdagh


title: Antifungal effect of volatile organic compounds produced by fruit endophytic Bacillus against Aspergillus niger under postharvest conditions

city: Suzhou

first: Xiaoyu

last: Lin

address: No. 100, Chongwen Road, Suzhou Industrial Park

institute: Suzhou Institute of Systems Medicine

summary: The rapid postharvest deterioration of fresh fruits is closely associated with fungal contamination,particularly by Aspergills niger, which severely compromises storage stability and market value.In this study, a fruit endophytic strain, Bacillus velezensis LY G-26, was isolated and shown toproduce volatile organic compounds (VOCs) with strong antifungal activity. VOCs significantlyinhibited 4. niger mycelial growth, spore gemination, and sporulation, and induced severemembrane disruption and mitochondrial damage. HS-SPME-GC-MS/MS identified 2-nonanone,2,S-dimethylpyrazine, and trans-2,3-dimethylacrylic acid as the primary active VOCs, with2-nonanone exhibiting the strongest inhibition. To enable practical application in food systems,LYG-26 was encapsulated into superabsorbent polymer beads, creating a packaging-compatibleslow-release system. When incorporated into sealed storage containers, the beads continuouslyreleased VOCs and significantly reduced A. niger decay in longan, effectively extending theirpostharvest shelf life. These findings provide a safe and environmentally friendly strategy forpostharvest preservation and shelf-life enhancement.

overall_design: In this study, a fruit endophytic strain, Bacillus velezensis LY G-26, was isolated and shown to produce volatile organic compounds (VOCs) with strong antifungal activity.

first: Tianhe

last: Liu


title: Anopheles albimanus lola knockdown immune response differential transcriptome: effect of Anopheles albimanus lola knockdown on the gene expression profile of the midgut in mosquitoes treated with an immune challenge

city: Mexico

first: Veronica

last: Valverde-Garduño

state: Morelos

address: Av Universidad

department: Centro de Investigaciones en Enfermedades Infecciosas

country: Mexico

institute: Instituto Nacional de Salud Pública

summary: Anopheles mosquitoes are a potential transmitter of viruses and parasites that cause human diseases. An. albimanus is among the main malaria vectors in Mexico and Latin America. Mosquitoes' ability to transmit pathogens (vectorial competence) is directly related to their genetics and immunity. The innate immunity system is the first line of defense against non-self microbial invaders. The mosquito midgut is a crucial entry point for such microbial invaders and for mosquito immune interactions with them. Here, we provide evidence that the lola gene expression is upregulated by immune challenge in three mosquito tissues and cells: the midgut, fat body, and hemocytes. We applied an efficient method for double-stranded RNA (dsRNA)-mediated silencing of this gene expression in vivo as assessed by RT-qPCR. A transcriptome analysis was conducted to investigate the potential involvement of the Lola transcription factor in regulating gene expression. We combined RNAseq with reverse genetics, and our transcriptome analysis revealed that Lola participates in mosquito  defense mechanisms. The knockdown of lola showed that it regulates the expression of genes associated with multiple functions, especially those related to detoxification and immunity. Here, we show for the first time a list of mosquito immunity genes that require Lola expression. These lola-dependent genes include antimicrobial peptides, C-lectins, pattern recognition receptors, Clip-domain serine proteases, ML-domain-containing proteins, enzymes that catalyze the generation and detoxification of reactive oxygen species, and components of the JNK immune signaling pathways in the midgut of An. albimanus. Our studies provide direct evidence of a functional link between JNK signaling and Lola factor in the mosquito midgut. Dysregulation of this pathway may contribute to increased pathogen invasion.

overall_design: RNA-seq profiling of the midguts from mosquitoes treated with lola-dsRNA and stimulated with an immune challenge compared with the expression profile of the midguts from control mosquitoes treated with gfp-dsRNA and stimulated with the same immune challenge as lola knockdown mosquitoes.

first: Verónica

first: Heidi

last: Espadas-Álvarez


title: Human spinal cord organoids recapitulate developmental and disease-associated oligodendrocyte lineage signatures [RNA-Seq]

city: Atlanta

first: Taylor

last: Pio

state: GA

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

summary: These data consist of two RNAseq datasets. The first is a timeline of human spinal organoid (hSpO) gene expression from d75 to d200. The second is gene expression of human primary cortical cells which were immunopanned to enrich for oligodendrocytes, then treated with either vehicle, cytokine cocktail of TNF-α, IL-1α, and C1q (TIC), or IFN-gamma.

overall_design: Human spinal organoids (hSpO) were collected at 5 timepoints in 3 hiPSC lines, and 2 replicates per line/timepoint were sequenced. Three independent samples of primary human cortical tissue were immunopanned to enrich for oligodendrocytes. Cells were treated with vehicle, TIC, or IFN-gamma, then 1-2 replicates of each sample/treatment combination were sequenced.

first: Meghna

last: Bettaiah

first: Supriya S.

last: Wariyar

first: Sabra

last: Mouhi

first: Jimena

last: Andersen


title: Chemotherapy-induced senescent fibroblasts promote NF-kB-mediated tumor aggressiveness, suppressed by Rofecoxib in gastric cancers

city: Suwon-si

first: in-hye

last: Ham

address: 169 Worldcup-ro, Yeongtong-gu

department: surgery

institute: Ajou University School of medicine

summary: Purpose: Chemotherapies for patients with gastric cancers (GCs) has been shown disappointing results in the clinics. The cancer-associated fibroblasts (CAFs) could be considered one cause of the resistance to chemotherapy in GCs. However, the chemotherapy-induced reprogramming of CAFs and its effects on GC progression and chemotherapy resistance have not been elucidated.   Methods: IncuCyte and transcriptome were used to identify chemotherapy-induced senescence of CAFs. Screening for drugs to inhibit the senescence of CAFs was performed. The cell proliferation and migration assays and phospho-protein array were performed to investigate the effects of senescent CAFs on GC cells. Inhibitory effects of screened drugs on CAFs were also evaluated in experimental models. Senescent CAFs and their clinical meanings were also investigated in the human GC tissues undergoing preoperative chemotherapies.  Results: Chemotherapy could alleviate proliferation and widen cytoplasm of CAFs. Some secretory molecules like TNF-α were upregulated in the CAFs with chemotherapy. Chemotherapy-treated CAFs increased the resistance to chemotherapy and the migratory potentials of GC cells. The COX2 inhibitor, one of the screened drugs, has inhibitory effect on chemotherapy-induced senescence CAFs. Consequently, it could suppress GC progression and resistance to chemotherapy. The GC patients with senescent CAFs were significantly correlated with poor histologic response to chemotherapy.  Conclusions: In this study, we are convinced that the chemotherapy-induced senescence of CAFs could have a significant effect on progression and resistance to chemotherapy in GC. Inhibitory drugs for chemotherapy-induced senescence of CAFs could be used to overcome the CAF-induced resistance to chemotherapy in GCs.

overall_design: To investigate the consistent effects of 5-FU induced senescence, we performed microarray analysis on four different CAF lines (CAF47, CAF51, CAF98, and CAF133), comparing untreated controls with 5-FU treated groups for each line.


title: Single-cell RNA sequencing of MC38 subcutaneous allograft tumors in C57BL/6J mice treated with FOLFOX alone or in combination with a composite probiotics

city: lanzhou

first: Hu

last: Chen

state: Gansu

address: Lanzhou University, Lanzhou City, Gansu Province, China, lanzhou, Gansu, 730000, China

institute: Lanzhou University

summary: This study employs single-cell RNA sequencing (scRNA-seq) to investigate the impact of a probiotic consortium, alone or in combination with the chemotherapeutic regimen FOLFOX, on the tumor microenvironment (TME) of MC38 colorectal adenocarcinoma allografts in C57BL/6J mice. MC38 tumor-bearing mice were divided into three experimental groups: untreated control, FOLFOX-treated, and FOLFOX plus composite probiotics-treated. Tumors were harvested at a defined endpoint, dissociated into single-cell suspensions, and subjected to scRNA-seq using the 10x Genomics platform. The resulting data enable high-resolution characterization of transcriptional changes across immune, stromal, and malignant cell populations within the TME. This dataset aims to elucidate how combinatorial probiotic and chemotherapy intervention reshapes cellular composition, cell-state transitions, and intercellular communication networks, potentially revealing mechanisms of enhanced anti-tumor immunity or therapy resistance.

overall_design: This study employed a subcutaneous MC38 colorectal adenocarcinoma allograft model in C57BL/6J mice. Tumor‑bearing mice were randomly allocated into three groups: an untreated control group, an FOLFOX chemotherapy‑only intervention group, and a combined probiotic consortium plus FOLFOX intervention group. Each group included 3 biologically replicated mice (9 samples in total). The probiotic consortium was administered via oral gavage starting one week after tumor inoculation, while chemotherapy was initiated two weeks post‑inoculation. At the predetermined experimental endpoint, subcutaneous tumor tissues were collected and processed into single‑cell suspensions using enzymatic digestion.

first: Qi

last: Jiao


title: Human spinal cord organoids recapitulate developmental and disease-associated oligodendrocyte lineage signatures [scRNA-Seq]

summary: Human spinal organoids (hSpO), assembloids (human cortical organoid assembled to hSpO and 3D human muscle), and assembloids treated with cytokine cocktail TNF-α, IL-1α, and C1q (TIC) were dissociated. All dissociations were enriched for either astrocytes or oligodendrocytes through immunopanning, then sequenced.

overall_design: Each replicate is derived from 7 hSpO or assembloids per condition per line. These experiments were performed in 2 hiPSC lines.


title: Effect of artificial control system (hQSCS) on native transcriptome of S. erythraea during erythromycin fermentation

first: zhengduo

last: wang

institute: east china university of science and technology

summary: Reconstructing an artificial control system orthogonal to the native regulatory network of Saccharopolyspora erythraea is critical for circumventing the constraints imposed by its complex endogenous regulation. Here, we present a transcriptional profiling dataset of S. erythraea strain harboring the heterologous QS control system (hQSCS) during erythromycin fermentation. This dataset was generated to characterize the transcriptional response of host cells upon activation of the heterologous hQSCS. Specifically, RNA sequencing was performed on strain without hQSCS (control) and hQSCS engineered strain (treatment), both cultured in TSB medium for 72 h. Differential expression analysis of this dataset will help determine whether hQSCS exerts regulatory crosstalk with the native transcriptome of S. erythraea, which is essential for verifying the orthogonality of hQSCS. Collectively, this transcriptional dataset provides a valuable resource for investigating the orthogonality of hQSCS in S. erythraea and offers insights into the development of orthogonal control systems for other rare actinomycetes.

overall_design: RNA-seq profiling of S. erythraea with or without hQSCS at 72h of erythromycin fermentation.

first: Zhengduo

last: Wang

first: Haihong

first: Yingrui

last: Hou

first: Lingzhuo

last: Zeng

first: Xi

last: Li

first: Zilong

first: Baoxin

last: Zhang

first: Lu

last: Zhou

first: Lijie

last: Niu

first: Binqing

last: Yuan

first: Huan

last: Zhu

first: ShanShan

first: Menglei

last: Xia

first: Xiaohan

last: Yang

first: Zhiheng

first: Bixiao

first: Weilin

first: Hao

last: Yan

first: Chengyu

first: Zonglin

last: Liang

first: Lixin

first: Weishan


title: Activation of the JNK–ENO1 Axis Promotes Glycolytic Reprogramming and Progression of Retroperitoneal Leiomyosarcoma

city: guangzhou

first: mengye

last: he

state: guangdong

address: guangzhou

institute: guangzhoucunzhongkeji

summary: Retroperitoneal leiomyosarcoma (RPLMS) is a highly aggressive malignancy with limited therapeutic options, and its metabolic underpinnings remain poorly understood. In this study, we identified significant activation of glycolytic pathways in RPLMS through RNA-seq analysis, with enolase 1 (ENO1) markedly upregulated in both tumor tissues and patient-derived cell lines. Functional experiments demonstrated that ENO1 knockdown suppresses proliferation, migration, and glycolytic metabolism in RPLMS cells. Mechanistically, JNK signaling was shown to directly promote ENO1 transcription, thereby driving glycolytic reprogramming. Our findings reveal that the JNK–ENO1 axis plays a critical role in RPLMS progression, suggesting that targeting this pathway may represent a promising therapeutic strategy for this devastating disease.

overall_design: Background Retroperitoneal leiomyosarcoma (RPLMS) is a rare and aggressive soft tissue sarcoma with limited therapeutic options and poor clinical outcomes. Metabolic reprogramming, particularly aerobic glycolysis, is a hallmark of malignant tumors; however, its regulatory mechanisms in RPLMS remain largely unexplored. This study aimed to elucidate the role and regulatory mechanism of glycolytic reprogramming in RPLMS progression. Methods RNA sequencing (RNA-seq) was performed on retroperitoneal leiomyosarcoma (RPLMS) tissues to identify dysregulated genes. KEGG pathway enrichment analysis was conducted to assess enriched pathways. Patient-derived RPLMS cell lines (FM1 and FM2) were established and characterized for further experimentation. ENO1 expression levels in RPLMS tissues and cell lines were examined using quantitative real-time PCR (qPCR) and Western blotting. Loss-of-function assays were carried out to evaluate the effects of ENO1 knockdown on cell proliferation, migration, invasion, and glycolytic activity. Pharmacological inhibition of the JNK pathway together with ChIP–qPCR analysis confirmed that JNK signaling regulates ENO1 at the transcriptional level. Results RNA-seq analysis revealed significant enrichment of the glycolysis pathway in RPLMS, with enolase 1 (ENO1), a rate-limiting glycolytic enzyme, markedly upregulated. Elevated ENO1 expression was consistently observed in both patient-derived RPLMS cell lines and tumor tissues. Functional assays demonstrated that ENO1 silencing significantly suppressed cell proliferation and migration, while markedly attenuating aerobic glycolysis in RPLMS cells. Mechanistically, transcriptional regulation analyses identified ENO1 as a downstream target of JNK signaling. Activation of the JNK pathway enhanced ENO1 transcription, thereby promoting glycolytic reprogramming in RPLMS cells. Conclusion Our findings demonstrate that aberrant activation of the JNK–ENO1 axis drives aerobic glycolytic reprogramming and malignant progression in retroperitoneal leiomyosarcoma. Targeting JNK-mediated ENO1 transcription may represent a potential therapeutic strategy for RPLMS.

first: Xiaopeng

last: Suo

first: Mengxia

last: Yi

first: Gaoming

first: Wen

first: Gaohua

first: Mengmeng

last: Xiao


title: Time-course relative transcriptional profiles of the targets controlled by the artificial control system (hQSCS) in its ON and OFF states.

city: Shanghai

first: zhengduo

last: wang

summary: After constructing a heterologous QS control system (hQSCS) orthogonal to the endogenous regulatory network in Saccharopolyspora erythraea, we used hQSCS to control the upregulation and downregulation of a series of target genes, thereby activating a metabolic network orthogonal to the host’s native system. To confirm that hQSCS can simultaneously regulate multiple functional modules and maintain differential expression compared to the OFF state over an extended period, we performed time‑course transcriptome analysis on the metabolically engineered industrial strain N9 at multiple time points. Specifically, hQSCS was kept in the OFF state by adding cellulose as an inducer to serve as the control group, whereas the experimental group naturally grew and autonomously triggered and maintained hQSCS in the ON state during the stationary phase. Samples were collected at different growth stages for transcriptome sequencing. Differential expression analysis of this dataset will help determine whether hQSCS can effectively control a metabolic network orthogonal to the endogenous system, which is crucial for the broader application of hQSCS and provides insights for the implementation of orthogonal control systems in other rare actinomycetes.

overall_design: RNA-seq profiling of S. erythraea N9 (industrial strain N6 harboring an orthogonal regulatory and metabolic system) with or without cellulose at a series of time points during erythromycin fermentation.

first: Zhengduo

last: Wang

first: Haihong

last: Chen

first: Yingrui

first: Lingzhuo

first: Xi

first: Zilong

first: Baoxin

first: Lu

first: Lijie

first: Binqing

first: Huan

first: ShanShan

first: Menglei


title: Transcriptomic profiling of oxaliplatin-resistant colorectal cancer cells

city: Shijiazhuang

first: Tianyang

state: Hebei province

address: Heping West Road No. 215

department: Department of Hepatobiliary Surgery

institute: The Second Hospital of Hebei Medical University

summary: RNA-seq analysis comparing parental HCT116 cells with oxaliplatin-resistant HCT116-OXR cells to identify molecular mediators of platinum resistance in colorectal cancer.

overall_design: Oxaliplatin-resistant HCT116-OXR cells were established through 6-month stepwise dose escalation. RNA was extracted from parental HCT116 (n=3) and resistant HCT116-OXR (n=3) cells for transcriptomic comparison.

first: Xiaoyan

first: Guiying

first: Lianmei

last: Zhao


title: Estradiol disrupts constitutive androstane receptor (CAR)-mediated bile acid homeostasis in a murine model of intrahepatic cholestasis of pregnancy (ICP), and this effect is reversed by CAR ligands

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

institute: University of Southern Denmark

summary: Estrogens impair bile acid (BA) homeostasis, leading to intrahepatic cholestasis of pregnancy (ICP). ICP is characterized by elevated serum bilirubin and BAs, severe pruritus, and an increased risk of adverse perinatal outcomes. The constitutive androstane receptor (CAR) regulates genes involved in xenobiotic and BA detoxification. Previous studies suggest that CAR activation is protective in bile duct ligation–induced cholestasis and that major genes involved in BA elimination are downregulated in ethinylestradiol (EE)–induced cholestasis in mice. We examined whether CAR ligands could ameliorate cholestasis and prevent hepatic injury in an EE-induced cholestasis model using biochemical, transcriptomic, and BA metabolomic analyses. We found that estradiol inhibits and downregulates CAR target genes in vitro. Consistently, EE significantly suppresses hepatic CAR target gene expression in vivo, whereas the murine CAR agonist TCPOBOP partially restores the expression of selected detoxification genes, improves plasma alkaline phosphatase levels, and decreases hepatic BA accumulation. In humanized PXR–CAR–CYP3A mice with EE-induced cholestasis, MI763F, a novel and potent human CAR agonist, recapitulates the effects of TCPOBOP on key genes involved in BA metabolism and the BA metabolome, and significantly reduces hepatic BA accumulation. These results demonstrate that CAR ligands counteract EE-mediated disruption of genes involved in BA homeostasis.

overall_design: RNA-seq profiling of hepatic transcriptional responses to the CAR ligand MI-763F in cholestatic humanized PXR–CAR–CYP3A4/3A7 mice

first: Mária

last: Bajnoková

first: Mikkel

last: Alnor

first: Nicolaj

last: Ibsgaard Toft

first: Peter

last: Pávek


title: Pygo2 Loss Induces Tertiary Lymphoid Structure Formation and Enhances Immunotherapy and Castration Responses in Prostate Cancer

city: Notre Dame

first: Ziyu

last: Zeng

state: Indiana

address: 100 Galvin Life Sciences Center

department: Biological Sciences

institute: University of Notre Dame

summary: Prostate cancer (PCa) is widely regarded as an immunologically "cold" tumor, and the presence and regulation of tertiary lymphoid structures (TLSs) in it remain poorly understood. Using a prostate-specific Pten/Smad4 knockout (DKO) model, we found that additional deletion of Pygo2 (TKO) markedly enhanced TLS formation, increased TLS-associated chemokines and cytokines, and promoted lymphocyte organization within the tumor microenvironment. Pygo2 loss also restored androgen receptor (AR) signaling and sensitized tumors to castration. Importantly, combination therapy with castration, CXCR2 inhibition, and immune checkpoint blockade (CSI) further matured TLSs, strengthened B and T cell responses, and induced durable disease control in >80% of TKO mice for more than 42 weeks. Mechanistically, Pygo2 deletion led to DNA damage accumulation and activation of the STING-interferon pathway, whereas STING silencing abolished this response. Collectively, these findings identify Pygo2 as a key regulator of TLS formation, immune activation, and therapy resistance, highlighting it as a promising therapeutic target in castration-resistant prostate cancer.

overall_design: Bulk RNA-seq: DKO (Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L) and TKO (Nkx3.1-CreERT2/+ Pten-L/L Smad4-L/L Pygo2-L/L) tumors with/without CSI treatment (castration + SX-682 CXCR2 inhibitor + anti-PD1/CTLA4). Four grouDKO: DKO, TKO, DKO+CSI, TKO+CSI.scRNA-seq: Same model, three grouDKO analyzed (DKO, TKO, TKO+CSI), n=2 tumors per group, 10x Genomics platform with hashtag barcoding.

first: Yini

last: Zhu

first: Yan

last: Liu

first: Qi

last: Huo

first: Liang

last: Cheng

first: Xin

last: Lu


title: CD4 T cell-derived IL-2 counteracts rapamycin-mediated suppression of CD8 T cell effector differentiation in acute GvHD

city: Suwon

first: Truc

middle: Do Thanh

last: Nguyen

state: All

address: 2066 Seobu-ro, Jangan-gu

institute: Sungkyunkwan University School of Medicine

summary: Graft-versus-host disease (GvHD) remains a major limitation in the success of allogeneic hematopoietic stem cell transplantation. Rapamycin, an mTOR inhibitor, is used to control alloreactive T cell responses, but its effects on differentiation of donor T cell subsets in vivo are not fully understood. We previously identified two major subsets of alloreactive CD8⁺ T cells that arise during acute GvHD, including TCF1⁺ progenitor-like and Tim-3⁺ terminal effector populations. In this study, we examined how rapamycin influences the activation, circulation, and differentiation states of donor CD8⁺ T cells in murine acute GvHD models, both with and without donor CD4⁺ T cell help. Single-cell RNA sequencing was performed on donor-derived T cells collected from multiple experimental conditions to define the transcriptional programs associated with rapamycin treatment, CD4⁺ T cell involvement, and effector commitment. This dataset enables further investigation of the cellular mechanisms regulating T cell differentiation during GvHD under mTOR inhibition.

overall_design: Female C57BL/6 (H-2ᵇ) recipient mice were lethally irradiated and transplanted with donor BALB/c (H-2ᵈ) bone marrow together with either purified CD8⁺ T cells alone or a combination of CD4⁺ and CD8⁺ T cells. Rapamycin was administered in designated experimental groups to evaluate its effects on donor T cell activation and differentiation in vivo. Four experimental conditions were compared: CD8⁺ T cell transfer without rapamycin, CD8⁺ T cell transfer with rapamycin, CD4⁺ + CD8⁺ T cell transfer without rapamycin, and CD4⁺ + CD8⁺ T cell transfer with rapamycin. Donor-derived T cells were isolated from circulation and GvHD target tissues at defined timepoints and analyzed using the 10x Genomics 5′ single-cell gene expression platform. The resulting dataset enables characterization of transcriptional states associated with rapamycin treatment and CD4⁺ helper involvement during acute GvHD.

first: Yujung

last: Jang

first: Jaeyeop

last: Shin

first: Kunhee

last: Lee

first: Solhwi

first: Euna

last: Yoo

first: Youla

last: Seong

first: Yujin

first: Tae Jin

last: Kim

first: Woong-Yang

last: Park

first: Se Jin

last: Im


title: Effect of Alendronate on Survival and Bone Properties in Nothobranchius furzeri: Insights from a Model of Accelerated Aging

city: Vienna

first: Peter

last: Pietschmann

state: Vienna

address: Währinger Gürtel 18-20

country: Austria

institute: Institute of Pathophysiology and Allergy Research

summary: Alendronate, a nitrogen containing bisphosphonate, effectively inhibits osteoclastic bone resorption and is considered as first line treatment of osteoporosis and Paget´s disease. Additionally, several studies suggest a beneficial effect on mortality that goes beyond life-extending effects attributed to the well-established fracture risk reduction. However, mechanisms of the mortality reducing effect of bisphosphonates are unclear. The turquoise killifish Nothobranchius furzeri (N.furzeri), a well-known model of accelerated aging, exhibits an extremely short life cycle and thus could represent a suitable model for survival studies. The aim of this study was to test the effect of alendronate on the life span and bone properties of N.furzeri. 89 female fish were divided at the age of 16 weeks into a treatment (10µM alendronate, n=44) and a control (n=45) group and monitored for survival. Vertebral bodies of deceased fish were examined by micro-CT and bone histomorphometry. RNA sequencing and gene expression analysis was done from isolated tissues of heart, spleen, liver, muscle and kidney. Comparing both groups, the alendronate group showed a significantly higher survival (p=0.0070). Micro-CT evaluation showed significantly higher values for bone (+2%; p=0.0013) and tissue mineral density (+3%; p=0.0159) in the control group. Bone histomorphometry displayed significant higher values for number of osteoblasts/bone perimeter (p=0.0340) and number of osteoblasts (p=0.0335) in the alendronate group. RNA sequencing revealed differences in both gene expression and biological function with alendronate treatment. Looking at the gene expression levels, we determined a reduced ZNF703 expression in the alendronate group. Our results indicate that alendronate has a positive effect on the survival of N.furzeri and alters bone mineralization. Furthermore, it effects several non-bone related pathways.

overall_design: RNA-seq profiling from heart, spleen, kidney, muscle of the caudal fin and liver of 19 weeks old alendronate treated and untreated Nothobranchius furzeri

first: Maria

last: Butylina

first: Michael

last: Kothmayer

first: José

last: Basílio

first: Katharina

last: Wahl-Figlash

last: Gelles

first: Florian

last: Frommlet

first: Oliver

last: Pusch


title: Unveiling the DNA repair landscape by unlocking the potential of cryopreserved PBMCs with optimal processing

first: Zachary

middle: D

last: Nagel

address: 655 Huntington Avenue

department: Environmental Health

institute: Harvard University

summary: In the field of DNA repair, cryopreserved peripheral blood mononuclear cells (PBMCs) are a feasible model for large-scale human biomonitoring studies. However, the optimal processing of cryopreserved PBMCs to accurately represent real-time and reproducible DNA repair capacity (DRC) for an individual remains uncertain. The literature is inconclusive regarding the preservation of DRC among PBMC subpopulations or whether a particular cell type is a better representative of DRC. Additionally, it is unknown whether an individual’s DRC remains stable over time. This paper utilizes a functional-based Fluorescent Multiplex Host Cell Reactivation assay to evaluate DRC by measuring repair capability of intact PBMCs for various DNA lesions. The results demonstrate significant differences in DRC among PBMC subtypes during resting and stimulated stages, with T cells dominating most of the data obtained from PBMCs in all functional assays examined. The stability of DRC within individuals is maintained for major DNA repair pathways across repeated measurements. Furthermore, the rank order of individual DRC is preserved by transfecting cryopreserved resting human PBMCs. These findings have the potential to revolutionize approaches for handling cryopreserved PBMCs in the field of DNA repair for human bio-monitoring purposes.

overall_design: Different immune cell types, in both resting and proliferative states, were isolated from the peripheral blood mononuclear cells of 11 healthy individuals, and global transcriptome changes were compared across cell types.

first: Sneh

last: Toprani

first: Ting

last: Zhai


title: Yeast Rpd3L histone deacetylase couples nutrient shifts to genome-wide chromatin reprogramming

city: Dallas

first: Saikat

last: Bhattacharya

state: Texas

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

summary: Adaptive transcriptional rewiring underlies the metabolic flexibility of Saccharomyces cerevisiae. We demonstrate that the histone deacetylase Rpd3 mediates nutrient-dependent chromatin reprogramming that coordinates transcriptional shutdown and global acetylation balance during metabolic transitions. Genome-wide analyses reveal that Rpd3 complexes drive rapid, reversible histone deacetylation across promoters and gene bodies, fine-tuning transcriptional output. Rpd3, primarily through the large complex (Rpd3L), localizes at promoters of active genes enriched in H3K9ac and the acetyltransferase Gcn5. Upon nutrient shift, Gcn5 disengages while Rpd3-mediated H3K9 deacetylation enforces repression. Loss of Rpd3 or its Rpd3L-specific subunit, Pho23, disrupts this balance, resulting in the aberrant persistence of growth programs upon starvation and defective activation of respiratory genes in the presence of glucose. HDACs thus can act as metabolic gatekeepers, coupling nutrient cues to chromatin reprogramming and ensuring transcriptional fidelity during metabolic transitions, thereby resolving the long-standing paradox of HDAC enrichment at active promoters.

overall_design: ChIP-Seq of Rpd3, Eaf3 and Pho23 from cells grown in glucose-replete and glucose-deplete media. Rpd3 ChIP-seq was performed in WT, eaf3Δ, or pho23Δ cells

first: Benjamin

last: Sutter

last: Tu


title: The RING E3 Ligase RLIM Drives Oxidative Stress-Induced Stem Cell Dysfunction through MDM2-p53 Signaling

city: 江苏省

first: yajie

last: li

state: China

address: 江苏省徐州市铜山路209号

institute: 徐州医科大学

summary: Chronic diabetic ulcers present a persistent challenge due to delayed wound healing. At the wound site, oxidative stress impairs stem cell survival and differentiation, accelerates senescence, and impairs autophagy. RLIM was identified as a critical regulator in human umbilical cord mesenchymal stem cells (hUCMSCs), where oxidative stress-induced RLIM upregulation leads to MDM2 degradation and stabilization of p53. Functionally, RLIM upregulation under oxidative stress inhibited autophagy, induced cellular senescence, and significantly impaired angiogenesis, cell migration, and immunomodulatory functions, ultimately hindering diabetic wound healing in vivo. These results highlight the RLIM-MDM2-p53 signaling axis as a pivotal pathway governing stem cell senescence and function under oxidative stress, offering promising therapeutic targets to enhance stem cell-based approaches for diabetic wound repair.

overall_design: To identify key regulatory factors involved in the functional impairment of hUCMSCs under oxidative stress, RNA sequencing was performed on hUCMSCs treated with H2O2 and control-treated cells

first: Xiaoyue

last: Li

first: Yajie


title: Probiotics Complex Synergizes with FOLFOX to Enhance Antitumor Response and Ameliorate Chemotherapy-induced Intestinal Toxicity via Upregulation of NAD+ Metabolism

first: Hu

last: Chen

summary: Modulating the gut microbiota can improve chemotherapy efficacy, but strategies that simultaneously reduce toxicity and enhance therapeutic outcomes remain understudied. This study developed a NAD⁺-enhanced composite probiotic formulation (derived from fermented yak milk from the Qinghai-Tibet Plateau) to alleviate FOLFOX-induced intestinal toxicity and enhance efficacy in a colitis-associated colorectal cancer (CAC) mouse model. Metabolomics revealed significant contributions of nicotinic acid and nicotinamide metabolism to the body's response to chemotherapy. Consequently, RNA-seq was employed to validate the criticality of nicotinamide metabolism at the gene expression level: probiotics counteracted FOLFOX-induced NAD⁺ depletion, restored SIRT1/3 activity, and suppressed FoxO3a-mediated chemotherapy resistance. A clinical cohort of 53 gastrointestinal cancer patients confirmed serum NAD⁺ levels correlate with gut microbiota and intestinal toxicity. Collectively, we propose a microbiota-targeting strategy synergizing with FOLFOX, providing a translatable paradigm for precision oncology.

overall_design: BALB/c mice induced with AOM/DSS and confirmed to develop inflammation-associated colonic neoplasia were randomly assigned to the model group (CAC), FOLFOX chemotherapy group (CAC_F), combined probiotic intervention group (CAC_FP), and combined probiotic-loperamide group (CAC_FPL).Unprocessed mice from the same batch were designated as the control group (NC). Samples were collected one week after chemotherapy initiation for RNA-seq analysis.

first: Qi

last: Jiao

first: Xusheng

last: Guo


title: Effect of BMP2, BMP3, BMP4, IL6, LIF, and OSM on the gene expression profiles of two patient-derived glioblastoma neurosphere lines.

city: CA

first: Weaverly Colleen

last: Lee

address: 327 Campus Drive

department: Biology Department

institute: Stanford University

summary: To identify microenvironmental influences on glioblastoma (GBM) cell death response, a secreted factor modulatory screen was conducted on primary patient-derived GBM neurospheres. This screen identified several protein ligands that broadly altered GBM cell death response. To gain a better understanding of the mechanisms by which they alter cell death, we performed RNA-seq on the neurospheres following exogenous addition of the protein ligands.

overall_design: Two patient-derived glioblastoma neurosphere lines were cultured in ultra low adherent 6-well plates. The following day, these were treated with 100 ng/ mL of the recombinant proteins mentioned above. RNA was harvested following 24h of incubation with the ligands. Each experiment consists of two replicates, where the ligand treatments and RNA extractions were performed on separate days.

first: Scott

last: Dixon


title: Mg2+ Modulates H3K27me3 Demethylation via KDM6A to Regulate Myoblast Differentiation and Crosstalk with Osteoclasts

first: Lei

last: Wang

address: No. 639, Zhizaoju Road

institute: Shanghai Ninth People's Hospital

summary: Muscle injury and regeneration mechanisms following bone fractures, which are common in orthopedic conditions, remain incompletely understood. Improving patient prognosis could significantly benefit from metal debris derived from fracture fixation materials that promote muscle repair and prevention; however, the underlying mechanisms are poorly understood. In this study, we unveiled an unexpected role of Mg2+ in regulating repair responses and aging in injured CTX-induced muscles. Supporting this discovery, genetic models in C2C12 cells, both gain- and loss-of-function, demonstrated that muscle-specific Mg2+ supplementation enhanced myoblast differentiation, a process dependent on the H3K27me3 demethylase KDM6A rather than on KDM6B. Additionally, we observed that Mg2+ present in myoblasts inhibited excessive osteoclast activation, partially reversing their tendency to promote muscle atrophy. Our findings illuminate a muscle-bone crosstalk mechanism that bridges the gap between muscle dysfunction and bone injury. This crosstalk represents a potential long-term solution to fractures and disuse muscle atrophy.

overall_design: The experiment was designed to investigate the regulatory role of the Kdm6a gene using Chromatin Immunoprecipitation Sequencing (ChIP-Seq) in Mus musculus (mouse) models. The samples were organized into two main pairs of experimental and control groups to study both Kdm6a overexpression and inhibition.


title: Subtype-Specific Dependencies and Drug Vulnerabilities Enable Precision Therapeutics in Head and Neck Cancer

city: Seattle

first: Joel

middle: Markus

last: Vaz

state: WA

address: 1100 Fairview Ave North

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Molecular heterogeneity in head and neck squamous cell carcinoma (HNSCC) is well recognized, yet existing subtype frameworks remain largely descriptive and have not translated into therapeutic decision-making. Here, we establish a mechanistic platform that converts transcriptomic diversity into drug-actionable tumor states. Integrating multi-cohort RNA-seq from 727 tumors across five independent datasets, genome-scale CRISPR dependency maps, and pharmacologic screening, we define distinct tumor survival circuits across HPV-negative HNSCC and nominate subtype-matched therapeutic strategies. These circuits encompass a proliferative axis (MYC, MET/FAK, inflammatory and translational programs), an epithelial-differentiated/adhesion program, an EMT-like state with stromal activation, and mitochondrial/oxidative metabolic states, each mapping to selective liabilities (e.g., mitotic/autophagy control, ERBB/PI3K and cadherin signaling, OXPHOS/mitochondrial translation, and G2/M-integrin-Notch pathways, respectively). We then develop a transcriptomic predictor of EGFR-inhibitor response using machine learning and validate it in prospectively collected, fresh patient-derived 3D microtumors. The resulting 13-gene signature identifies erlotinib-responsive tumors (R = 0.93) and maps biologically to an epithelial-differentiated state, outperforming EGFR expression alone. Our study establishes a subtype-to-dependency-to-therapy framework, enabling precision stratification and providing a clinically feasible path for prospective biomarker deployment.

overall_design:
Freshly processed samples were extracted from tumor tissues and processed for bulk-RNAseq.
contributor: Gujral Lab, gujrallab@fredhutch.org


title: Transcriptome of primed and naïve-like state sheep embryonic stem cells

city: West Lafayette

first: Shyamkumar

last: TS

state: IN

address: 625 Harrison St

department: Comparative Pathobiology

institute: Purdue University

summary: This project investigates the transcriptional profiles of sheep embryonic stem cells (sESCs) maintained in different culture conditions required for the maintenance of distinct pluripotent states. We derived primed-state sESCs from in vivo blastocysts using a chemically defined culture system and characterized their morphology and molecular features. When cultured in defined media previously shown to stabilize naïve pluripotency in human ESCs, sESCs adopted dome-shaped colony morphology, and exhibited features consistent with a naïve-like state. RNA sequencing was performed on both primed and naïve-like sESCs to define gene expression differences, signaling pathway changes, and regulatory networks associated with pluripotency state transitions in sheep.

overall_design: RNA-seq profiling of 2 lines of de novo–derived sheep embryonic stem cells (sESCs) maintained under defined primed pluripotency conditions in feeder-free culture, and naïve-like sESCs cultured in naïve-supportive conditions on both feeders and feeder-free systems.

first: Manuel Alexander

last: Vasquez-Hidalgo

first: Viju V

last: Pillai


title: Integrating AI in characterization receptor and construction signaling network for beta-glucan-engaged trained immunity in zebrafish

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

summary: Trained immunity, a form of innate immune memory, involves the functional reprogramming of innate immune cells, enabling an enhanced nonspecific response to subsequent challenges. While beta-glucan, a fungal cell wall component, is a known inducer of this process in zebrafish, the specific receptor responsible remains unidentified. Here, we identify C-type lectin domain-containing 1 (CLDC1), designated DrDectin-1, as the pivotal beta-glucan receptor in zebrafish through AI-driven bioinformatic screening based on mammalian Dectin-1. Structural analysis suggests key beta-glucan binding residues (D182, Y183, H184). Using cldc1 knockout zebrafish in beta-glucan training and secondary infection models, combined with RNA-seq, H3K4me3 ChIP-seq, and virtual cell modeling, we demonstrate that CLDC1 mediates trained immunity via the Syk-Raf signaling pathways. Our findings identify the long-sought beta-glucan receptor in zebrafish and provide a comprehensive mechanistic framework for innate immune memory in teleosts, with implications for evolutionary immunology and disease management.

overall_design: RNA-Seq profiling of beta-glucan-trained WT annd cldc KO zebrafish after E. piscicida-infection

first: Boning

last: Shao

first: Zhiqiang

first: Hongxing

last: Yu

first: Dahai


title: Integrating AI in characterization receptor and construction signaling network for beta-glucan-engaged trained immunity in zebrafish [ChIP-seq]

overall_design: ChIP-Seq for H3K4me3 in WT and cldc1 KO zebrafish after PBS or β-glucan treatment


title: Bifidobacteria infantis and human milk oligosaccharides have independent effects on immune response and amino acid metabolism in germ-free mouse models

city: College Station

first: Destiny

middle: A

last: Mullens

address: 2253 TAMU

department: Nutrition

institute: Texas A&M University

summary: Early-life microbial colonization is essential for gut and immune development. Human milk oligosaccharides (HMO) support the growth of Bifidobacterium infantis (BI), a keystone infant species. Herein, we studied the individual and combined effects of BI and HMO on immune and colon transcriptomes, and the serum metabolome. Germ-free mice were randomly assigned to four groups [10-14/group: HMO, BI, BI+HMO and control (no HMO or BI)]. HMO and BI+HMO groups received 5 mg/d each of 2′-fucosyllactose, lacto-N-tetraose and 3′-sialyllactose for 14 d. BI and BI+HMO received B. infantis ATCC 15697 (1x10^9 CFU/d) on days 1, 4, and 9.  Mono-colonization with BI increased monocytes, macrophages, B cells, CD4+ T cells, and Treg cells in mesenteric lymph nodes (MLN) relative to control. In the spleen, BI alone increased B cells, dendritic cells, Th17 cells, and ILC3 cells, and enriched serum amino acid metabolism pathways. Additionally, BI influenced colonocyte gene expression, and modulated serum metabolites regulating circadian rhythms. BI+HMO increased MLN Th17 cells and spleen monocytes compared to HMO alone. Collectively, the results of this study highlight the complex interplay between host-microbe-diet interactions and emphasize the importance of considering these interactions when designing strategies to modulate infant health during early life.

overall_design: Mouse colon tissue isolated from germ-free mice orally-gavaged with human milk oligosaccharides and/or Bifidobacteria infantis.

first: Bharath

last: Mulakala

first: Michael

last: Salinas

first: Laurie

last: Davidson

first: Selim

last: Romero

first: Quentin

last: Read

first: Renne

last: Fox

first: Tanya

last: LeRoith

first: James

last: Cai

first: Robert

last: Chapkin

first: Sharon

last: Donovan

first: Laxmi

last: Yeruva


title: Glioblastoma tumorspheres treated with streptonigrin (Sn) and temozolomide (TMZ)

city: Seoul

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

institute: Yonsei University

summary: Glioblastoma (GBM) is the most common and aggressive primary malignant brain tumor, with a median survival of less than two years despite standard therapy. Transglutaminase 2 (TGM2) contributes to tumor progression and poor clinical outcomes. This study evaluated the therapeutic potential of combining streptonigrin (SN), a TGM2 inhibitor, with temozolomide (TMZ), the standard chemotherapeutic agent for GBM. The combination of SN and TMZ significantly reduced cell viability and ATP levels and induced apoptosis more effectively than either agent alone. Moreover, the combination effectively reduced stemness and invasiveness in GBM TSs, along with the expression of related proteins and mRNAs. In vivo, combination therapy prolonged survival in mice and reduced expression of invasiveness-related protein, as shown by immunohistochemistry. These findings suggest that targeting TGM2 with SN enhances the therapeutic efficacy of TMZ in GBM. The combination of SN and TMZ holds promise as a novel treatment strategy for GBM.

overall_design: GBM tumorspheres (TSs) were treated with SN, TMZ, or their combination. Cell viability and ATP production were measured to assess cell proliferation, and mRNA expression were assessed by RNA sequencing.

first: Jun Pyo

last: Hong

first: Je Beom

first: Byungho

last: Lee

first: Ran Joo

last: Choi

first: Jin-Kyoung

last: Shim

first: Tae Hoon

last: Roh

first: Ju Hyung

last: Moon

first: Eui Hyun

first: Wan-Yee

last: Teo

first: Jong Hee

last: Chang

first: Seok-Gu

last: Kang


title: DNA hypomethylating agents potentiate the efficacy of CD3 bispecific T cell engagers [scATAC-seq]

city: Tarrytown

first: Qingqing

last: Wang

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

summary: Bispecific T cell engagers targeting tumor-associated antigens and CD3 are promising novel targeted therapeutic agents for both solid and hematologic cancers. However, prolonged TCR stimulation can lead to chromatin rewiring and T cell dysfunction. Here, we investigate the combination of bispecific T cell engagers with the DNA hypomethylating agent decitabine and observe suppressed tumor growth in preclinical models. Utilizing the PSMAxCD3 bispecific antibody for the treatment of prostate carcinoma and in vivo humanized models, we catalog, at the single-cell level, the dynamics of T cell epigenetic states during bispecific therapy, and in combination with decitabine. Importantly, this combination preserves a progenitor exhausted T cell population and delays acquisition of a dysfunctional state, at both chromatin and protein levels. At the DNA methylation level, TCR stimulation in the presence of decitabine maintains a naive-like pattern in gene loci associated with T cell stemness. This study provides a rich resource for understanding the evolution of T cell states during immunotherapy and mechanistic support for combining epigenetic modifiers with bispecific T cell engagers in the clinic.

overall_design: We used scATAC-seq to profile the epigenetic landscape of immune cells from malignant tissues during bispecific therapy, and in combination with DNA hypomethylating agent decitabine in preclinical models. We also performed reduced representation bisulfite sequencing (RRBS) in these sample cells to investigate the epigenetic landscape..

first: Mark

last: Aleynick

first: Jennifer

middle: E

last: Wu

first: Nikolaos

last: Kourtis


title: DNA hypomethylating agents potentiate the efficacy of CD3 bispecific T cell engagers [BiSulfite-seq]

overall_design: Utilized reduced representation bisulfite sequencing analysis of chronically stimulated T cells with or without decitabine treatment to investigate the DNA methylation pattern change across the genome


title: miRNA expression profiles of mouse ES cells and HeLa cells

city: Yayoi, Bunkyo-ku

first: Hiroki

last: Ono

state: Tokyo

department: Research Division for Applied Life Sciences

country: Japan

institute: Institute for Quantitative Biosciences, The University of Tokyo

type: Non-coding RNA profiling by high throughput sequencing

summary: To analyze relationship between the expression levels and activities of miRNAs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The miRNA expression profiles of mouse embryonic stem cells (129(+Ter)/SvJcl (female mouse) × C57BL/6NJcl (male mouse)) and HeLa cells were analyzed using the AQ-seq method.

first: Hirohide

last: Saito

first: Nozomu

last: Yachie

first: Arman

last: Adel

first: Karin

last: Hayashi