title: Pan-ERBB inhibitors synergize with KRAS inhibitors in rectal cancer

status: Public on Aug 06 2026

city: Göttingen

first: Jonas

last: Buchloh

address: Robert-Koch-Straße 40

institute: University Medicine Göttingen

summary:
Background: Emerging RAS inhibitors show promise in treating KRAS-mutated malignancies, but resistance mechanisms limit their clinical efficacy. Given recent clinical findings associating KRAS mutations with reduced response to neoadjuvant therapy in rectal cancer (RC), we aimed to investigate their impact on treatment outcomes and explore potential therapeutic strategies.
Methods: We conducted a retrospective analysis of 390 RC patients to evaluate the association of KRAS mutations with disease-free survival (DFS) and response to therapy. We assessed the efficacy of KRAS inhibitors in RC cell lines, patient-derived organoids (PDOs), and patient-derived cell lines (PDCLs), and explored adaptive resistance mechanisms through transcriptomic profiling and unbiased drug screening experiments.
Results: Mutant KRAS was associated with a reduced DFS and RCs harboring G12C and G12V mutations had less complete pathological responses. KRAS-mutated RC cells demonstrated adaptive resistance to KRAS inhibitors, characterized by transcriptomic restoration of oncogenic pathways, including MYC and E2F and upregulation of ERBB2/3 gene expression. Consistently, drug screening identified EGFR family inhibitors as potent combinatorial partners, effectively overcoming KRAS inhibitor tolerance by inducing apoptosis. In patient-derived models, the novel pan-RAS inhibitor RMC-6236 combined with EGFR inhibitors demonstrated significant synergistic effects and prevented long-term tumor outgrowth.
Conclusion: Our findings highlight the negative impact of KRAS mutations, particularly G12C and G12V, on RC treatment outcomes. Adaptive resistance by transcriptomic upregulation of ERBB genes limits the efficacy of KRAS inhibitors. Combining these with pan-ERBB inhibitors enhances anti-tumor effects in patient-derived cellular RC models showing its potential as alternative to the combination with anti-EGFR antibodies.

overall_design: SW1463 cells were seeded and were treated after 24 hours by 50 nM Sotorasib for 24h, 6 days and 10 days. mRNA-isolation, library preperation and paired-end sequencing with 20 Million reads/sample followed


title: Blocking the Gut–Liver IgA Axis Attenuates Macrophage-Mediated Inflammation and Injury in Alcohol-Associated Liver Disease [Spatial Transcriptomics]

status: Public on Aug 04 2026

city: Seoul

first: Mingu

last: Kim

address: 222, Banpo-daero

country: South Korea

institute: The Catholic university of Korea

summary: We profiled spatial gene expression in mouse liver and intestine FFPE tissue sections using the 10x Genomics Visium Spatial Gene Expression for FFPE (v2, Mouse) platform. Samples included control and ethanol-fed groups with or without fingolimod (FTY720). Processed data include spatially resolved gene-by-spot count matrices generated by Space Ranger.

overall_design: FFPE tissue sections were processed on the Visium CytAssist instrument and sequenced on an Illumina platform (paired-end; Read1 contains spatial barcode/UMI and Read2 captures transcript-derived sequence). Data were processed with Space Ranger to generate spatial feature-barcode matrices and QC summaries for each sample.

first: Min Gu

first: Kwon Yong

last: Tak

first: Pil Soo

last: Sung


title: ADT-030, a novel PDE10 inhibitor, demonstrates potent antitumor activity in pancreatic ductal adenocarcinoma

city: Birmingham

first: Sujith

last: Sarvesh

state: Alabama

address: 1824 6th Ave S

department: Medicine

country: USA

institute: University of Alabama at Birmingham

type: Expression profiling by high throughput sequencing

summary: Phosphodiesterase 10A (PDE10) was previously reported to be overexpressed in various cancers and essential for cancer cell proliferation and survival. Here, we studied a novel PDE10 inhibitor, ADT-030, and found it to potently and selectively inhibit KRAS mutant PDAC cell proliferation and clonogenicity by inducing G2/M arrest and apoptosis. ADT-030 also inhibited migration. These effects were mediated by increased cAMP/cGMP levels and activation of PKA/PKG. The growth inhibitory activity of ADT-030 was associated with reduced β-catenin and RAS signaling. Notably, ADT-030 also inhibited the growth of KRASG12D and KRASG12C mutant PDAC cells resistant to allele-specific KRAS inhibitors. Oral administration of ADT-030 significantly suppressed tumor growth, reduced lung and liver metastasis, and increased survival without systemic toxicity in syngeneic and patient-derived xenograft (PDX) models. ADT-030 also increased chemotherapy response in orthotopic PDAC models. Immune phenotyping and single cell RNA revealed remodeling by ADT-030 with a more favorable immune suppressive tumor immune microenvironment to activate anti-tumor immunity. These results show that ADT-030 is a promising drug development candidate capable of simultaneously targeting key oncogenic signaling pathways, resulting in tumor-intrinsic and immunomodulatory effects for the treatment of KRAS-mutant PDAC.

overall_design: In vivo studies followed established guidelines and adhered to the approved protocol of the UAB-IACUC. 4-5 weeks old male C57BL6/J mice (The Jackson Laboratory #000664; RRID:IMSR_JAX:000664) were subjected to isoflurane anesthesia, followed by an intra-abdominal incision to access the spleen and pancreas. A Matrigel suspension (40 μL), containing KPC-f-luc (1 × 10^5), 2838c3-f-luc (1 × 10^5), or KPCML1-f -luc (1 × 10^5) cells was injected into the pancreas. The skin and abdominal wall were then closed by suturing. Following a week, mice were confirmed with successful engraftment of tumor by PerkinElmer IVIS Lumina III In Vivo Imaging System (RRID:SCR_025239) and randomized into four groups (n=5 per group) for KPC and 2838c3, two groups for KPCML1, and five groups for KPCML1 with ADT-030 and chemotherapy combination studies. Mice were given oral dosages as follows. The first group received a vehicle, and the other three groups received ADT-030 at varying oral doses (50, 100, and 150 mg/kg). In additional studies with KPCML1 cells implanted mice received vehicle, ADT-030 (150 mg/kg),  PF-2545920 (10 mg/kg, IP) daily for 4 weeks, gemcitabine (50 mg/kg, IP), nab-paclitaxel (30 mg/kg, IP), weekly twice. Tumor tracking and response to therapy was monitored using D-luciferin injection and were conducted bi-weekly throughout the studies. The total luminescence from tumor-bearing regions was quantified using the Living Image in vivo imaging software. Body weights of the animals were measured twice a week. At termination, all animals were subjected to imaging of the whole body, followed by euthanasia, at which time tumors were collected, weighed, and used for subsequent experiments.

first: Dhana Sekar

middle: B

last: Reddy

first: Ganji

middle: P

last: Nagaraju

first: Bassel

middle: F

last: El-Rayes


title: Vaccination with BCG reduces tau pathology and improve memory behaviors in the PS19 dementia mouse model

city: Baltimore

first: Somnath

last: Shee

state: MD

address: 1550 Orleans St, CRB2 Building, Room-176

department: Medicine, Infectious diseases

institute: Johns Hopkins University

summary: Retrospective studies among non-muscle invasive bladder cancer (NMIBC) patients have reported significant reductions (12–78%) in Alzheimer's disease (AD) incidence among BCG recipients versus controls. To understand the underlying mechanisms and discover novel therapeutic targets, we tested Mycobacterium bovis BCG Pasteur in a PS19 (P301S) mice model, which develop tauopathy-dependent neurodegeneration. We showed that BCG reduced hippocampal phospho‑tau, microgliosis, and astrocyte activation while preserving neuronal markers. In vivo T2-MRI showed mitigated atrophy, with simultaneously increasing glutamate‑weighted CEST‑MRI readouts. Additionally, BCG improved survival and body weight, and amended cognitive physiology. Bulk-RNA sequencing of the hippocampus revealed- (1) restoration of the transcriptomics landscape of PS19 mice towards non-carrier controls after BCG-therapy, and interestingly (2) augmented antigen processing coupled with reduced neuroinflammation. Brain myeloid cell profiling by multicolor flow cytometry revealed decreased CD45hi-activated microglia subpopulation, without increasing total microglia, alongside elevated CD80 (Trained immunity marker) on peripheral myeloid cells. Functionally, primary brain myeloid cells displayed greater uptake of FITC‑tau fibrils and higher lactate production, indicating enhanced phagocytosis and glycolytic metabolism. Together, these findings indicate that (1) BCG-driven myeloid reprogramming limits neuroinflammation, enhances tau clearance, and rescues cognitive defects in a tauopathy model, and (2) BCG therapy merit consideration for human clinical trials against AD.

overall_design: To examine whether BCG-therapy can attenuate this disease progression, hemizygous PS19 female mice were either injected with phosphate buffered saline (1X PBS; sham) or wild-type BCG Pasteur AERAS strain (2x 106 colony-forming units (CFU)) subcutaneously into the dorsal neck (scruff) region of mice. Age-matched littermates non-carrier mice were sham-treated and represent healthy controls (AMC UT). Three monthly BCG doses were administered starting at 3-months age, followed by no-treatment phase of 3-4 months. Mice were sacrificed at 9-10 months age, hippocampus tissue from mouse brains were isolated. To understand the cellular mechanism underlying the BCG-driven protective effects, we performed bulk RNA-sequencing of the hippocampal tissue from sham-treated PS19 mice, BCG-treated PS19 mice and the age-matched non carrier controls.

first: Wiiliam

last: Bishai


title: Systematic discovery of potential regulators of transcriptional variability reveals NAP1L1 as a transcriptional stabilizer in mouse ESCs

city: Jerusalem

first: Tamar

last: Segal

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: Embryonic stem cells (ESCs) maintain their capacity to generate all different cell types of the developing embryo. When grown in serum, ESCs display transcriptional heterogeneity of several key pluripotency-related genes (e.g. Nanog). This transcriptional variability was suggested to support ESC pluripotency by enabling them to differentiate along different lineages simultaneously. We hypothesized that expression heterogeneity is a regulated process, mediated by transcriptional (de)stabilizers. To test this systematically, and to identify potential ESC regulators of transcriptional variability, we compared single-cell RNA-seq (scRNA-seq) with ChIP-seq datasets to identify variable and stable genes in ESCs. One of the potential ‘stabilizer’ proteins we identified is Nucleosome Assembly Protein 1-Like 1 (NAP1L1), a member of the NAP1 family. NAP1L1 participates in many cellular functions, including nucleosome maintenance, chromatin remodeling, cell division, and transcription. To test its potential ‘stabilizer’ function, we recruited NAP1L1 to the Nanog promoter via fusion with dCAS9. Immunofluorescence (IF) and single-molecule fluorescence in situ hybridization (smFISH) analyses of Nanog expression revealed that NAP1L1 directly stabilizes both RNA and protein expression levels. To further explore NAP1L1’s function genome-wide, we generated Nap1l1-knock-out (KO) ESCs. scRNA-seq experiments comparing Nap1l1-KO and WT ESCs, revealed increased gene expression variability in Nap1l1-KO cells. To reveal the potential mechanism by which NAP1L1 exerts its stabilizing activity we identified NAP1L1-interacting partners by co-IP followed by Mass-Spectrometry experiments, revealing DPPA3 as a key interacting partner. Taken together, we provide a systematic discovery platform for regulators of transcriptional variability and identify NAP1L1 as a transcriptional stabilizer in ESCs.

overall_design: To investigate transcriptomic alterations between WT and the two NAP1L1-KO ESC lines during retinoic acid (RA)-induced differentiation, we performed bulk RNA-seq on cells harvested at days 0, 2, and 4.

first: Elad

last: Dvir

first: Eran

last: Meshorer


title: Blocking the Gut–Liver IgA Axis Attenuates Macrophage-Mediated Inflammation and Injury in Alcohol-Associated Liver Disease [scRNA-seq]

summary: We performed single-cell RNA sequencing (scRNA-seq) of mouse liver cells in an NIAAA ethanol-feeding model. Four samples were analyzed: Control_M, Control_F, EtOH_M, and EtOH_F (n=1 mouse per group). Libraries were prepared using the 10x Genomics Chromium GEM-X Single Cell 3′ RNA library v4 chemistry and sequenced on an Illumina platform with read structure R1(28)–I1(10)–I2(10)–R2(90). Data were processed using Cell Ranger (count) v8.0.1 with the GRCm39-2024-A reference to generate gene expression feature-barcode matrices and standard QC outputs.

overall_design: 10x Genomics 3′ scRNA-seq of mouse liver cells from Control vs EtOH groups in the NIAAA model, including both sexes (Control_M, Control_F, EtOH_M, EtOH_F; n=1 per group). Cell Ranger v8.0.1 was used for alignment and UMI counting with the GRCm39-2024-A reference.


title: Gene expression changes induced by zinc deficiency in intestinal goblet cells

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

summary:
Zn deficiency disturbs synthesis and O-glycosylation of mucins in intestinal goblet cells
Zinc is an essential trace element (TE) required for numerous structural, catalytic, and regulatory protein functions. Approximately 17% of the global population is affected by zinc deficiency, resulting in severe health consequences such as impaired immune function and increased susceptibility to infections and inflammation, as well as severe degeneration of the intestinal epithelium and mucus. The underlying cellular processes, particularly regarding changes of mucus composition, zinc homeostasis and immune defense by human goblet cells are, however, not yet completely understood.

overall_design: 24 samples from 6 conditions with 4 biological replicates each: negative control, zinc-adequate (ZA) medium, zinc-deficient (ZD) medium, IL-8 treatment, cell supernatant from ZD- or ZA-incubated cells

first: Maria

last: Maares


title: Blocking the Gut–Liver IgA Axis Attenuates Macrophage-Mediated Inflammation and Injury in Alcohol-Associated Liver Disease [RNA-Seq]

summary: We generated bulk 3′ mRNA-seq (QuantSeq) profiles to characterize transcriptional responses induced by immunoglobulin A (IgA) in human CD14⁺ monocytes. CD14⁺ monocytes were stimulated on plate-bound IgA (in PBS) for 24 hours or cultured on mock-coated plates incubated with PBS alone. Libraries were prepared using the QuantSeq 3′ mRNA-Seq V2 Library Prep Kit FWD (Lexogen) and sequenced as single-end 100 bp reads on an Illumina NextSeq 2000. This series includes three technical replicates per condition from a single donor.

overall_design: QuantSeq 3′ mRNA-seq (single-end 100 bp; Illumina NextSeq 2000) of human CD14⁺ monocytes after 24-hour stimulation on plate-bound IgA (in PBS) versus mock (PBS-coated), with three technical replicates per condition from a single donor.


title: MED26 facilitates Mediator–Pol II complex assembly and promotes nuclear stress body formation during heat stress

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

country: Japan

institute: Yokohama City University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cells adapt to environmental stress by reprogramming gene expression. During heat stress, the transcription factor HSF1 translocates into the nucleus and activates heat shock–responsive genes, including the lncRNA HSATIII, thereby promoting formation of nuclear stress bodies (nSBs). We show that the Mediator subunit MED26 enhances HSATIII transcription and nSB formation through a mechanism distinct from its role at canonical heat shock protein (HSP) genes. Upon heat stress, MED26-containing Mediator is recruited to both HSP loci and nSBs through interactions with HSF1 and MED15. Notably, phosphorylation of the intrinsically disordered region (IDR) of HSF1 is particularly important for Mediator recruitment to nSBs. Acute loss of MED26 leads to dissociation of both Mediator and Pol II from HSP promoters, whereas at HSATIII loci Mediator is retained despite Pol II dissociation. These results indicate that MED26 acts as molecular switch that facilitates Mediator-Pol II holo-complex assembly at nSBs and promotes nSB formation during heat stress.

overall_design:
Experiment 1: Total RNA-seq prepared from HCT116 cells that stably expressing HSF1-WT and HSF1-S>A upon HS treatment and non-treat as negative control.
Experiment 2:  Total RNA-seq prepared from intrinsic MED26 knocked-down HCT116 cells (dTAG-MED26 cells) upon HS treatment and normal temperature as non-treatment.
Experiment 3: MED26-ChIP-seq prepared from HCT116 cells that stably expressing HSF1-WT and HSF1-S>A upon HS treatment and normal temperature as non-treatment.
Experiment 4:MED1-ChIP-seq prepared from intrinsic MED15 knocked-down HCT116 cells (dTAG-MED15 cells) upon HS treatment and normal temperature as non-treatment.
Experiment 5: MED26-ChIP-seq prepared from intrinsic MED15 knocked-down HCT116 cells (dTAG-MED15 cells) upon HS treatment and normal temperature as non-treatment.
Experiment 6: MED1-ChIP-seq prepared from intrinsic MED26 knocked-down HCT116 cells (dTAG-MED26 cells) upon HS treatment and normal temperature as non-treatment.
Experiment 7: RNAPol II-ChIP-seq prepared from intrinsic MED26 knocked-down HCT116 cells (dTAG-MED26 cells) upon HS treatment and normal temperature as non-treatment.

first: Kexin

last: Li

first: Kazuki

last: Furugori

first: Ryota

last: Abe

first: Hidehisa

last: Takahashi


title: DNA Methylation Changes After Rapid Maxillary Expansion in Mixed Dentition

city: Yokosuka

first: Takayuki

last: Ishiyama

address: Department of Orthodontics, School of Dentistry, Kanagawa Dental University  82 Inaoka-cho

institute: Kanagawa Dental University

type: Methylation profiling by genome tiling array

summary: This study investigated genome-wide DNA methylation profiles in saliva samples from pediatric patients undergoing rapid maxillary expansion and untreated controls.

overall_design: Case-control and longitudinal study comparing genome-wide DNA methylation profiles in saliva samples collected before and after rapid maxillary expansion and from untreated controls using the Illumina Infinium MethylationEPIC v2 BeadChip.

first: Masahiro

first: Atsushi

last: Tajima

first: Tetsutaro

last: Yamaguchi


title: FGF21counteracts metabolic dysfunction in cancer-associated cachexia

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

summary: Cancer-associated cachexia (CAC) is a multifactorial, metabolic wasting syndrome that coincides with cancer malignancies of multiple entities. CAC is characterized by progressive loss of muscle mass and adipose tissue and diminishes therapy responsiveness. Here, we show that the expression of FGF21 is induced in livers of tumor-bearing mice with CAC. FGF21 deficiency promotes weight loss, exacerbates adipose tissue wasting and increases systemic inflammation, pointing towards a protective role of FGF21 in CAC. In line, IL6-mediated STAT3 activation induces FGF21 expression in hepatocytes as well as adipocytes. FGF21 promotes anabolic signaling cascades, increases cellular glucose uptake in response to IL6 exposure and counteracts cytokine-mediated glycerol release, thereby opposing adipose tissue loss in CAC. Eventually, we find that FGF21 is increased in cancer patients with clinical CAC. Together, we reveal a protective role for FGF21 in experimental CAC and identify the protein as a potential biomarker in clinical cachexia.

overall_design: RNA-Seq profiling of whole inguinal adipose tissue of CHX tumor-bearing mice and healthy controls housed at thermoneutrality. Tumor bearing mice were treated with either control AAV, FGF21 AAV or Efruxifermin .

first: Raimund

last: Oberle

first: Österreicher

last: Tamina


title: The WRKY transcription factor FaWRKY71 modulates the response of strawberry fruits to drought stress

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

country: Spain

institute: University of Cordoba

summary: We identified and functionally characterized a ripening-induced WRKY transcription factor, FaWRKY71, that is strongly associated with ripening and drought responses in strawberry. To investigate the role of FaWRKY71 during the ripening process, we generated F. × ananassa transgenic plants to knock down its expression using a construct for gene silencing by RNA interference (RNAi) driven by the constitutive CaMV 35S promoter (35S:FaWRKY71-RNAi).

overall_design: For gene silencing, a conserved region of FaWRKY71 coding sequence wascloned into the pCR8/GW/TOPO entry vector, and finally into pFRN destination vector via Gateway recombination. Stable transformation of strawberry was developed via Agrobacterium tumefaciens AGL0 strain using both with pFRN-FaWRKY71 and pFRN-empty as a control.

first: Facundo

last: Spadoni-Revol

first: Felix J

last: Martínez-Rivas

first: Enriqueta

last: Moyano

first: Rosario

last: Blanco-Portales

first: José L

last: Caballero

first: Juan

last: Muñoz-Blanco

first: Francisco J


title: Deficiency in plastid EF-Tu elicits DNA damage response in Arabidopsis thaliana

city: Jinan

first: Pengcheng

last: Li

address: 23788 Gongye North Road

country: China

institute: Shandong Academy of Agricultural Sciences

summary: Arabidopsis RAB8D (AT4G20360) encodes the plastid translation factor EF-Tu, which is crucial for plant viability. We wondered about the connection between RAB8D deficiency and DNA damage response. RNA-seq results revealed significant upregulation of DNA repair-related genes in rab8d-2, a knock-down mutant of RAB8D. Introducing the knockout allele of ATM (atm-2), SOG1 (sog1-1), NAC044 (nac044-1), or NAC085 (nac085-1) into rab8d-2 significantly reduced the expression of DNA repair-related genes.

overall_design: Transcriptome profiles of 4-day-old seedling roots were compared among genotypes including WT, rab8d-2, atm-2 rab8d-2, sog1-1 rab8d-2, nac044-1 rab8d-2, and nac085-1 rab8d-2.

first: Minghui

last: Zhou

first: Xingjun

last: Wang


title: Genetic relationship between GUN1 and NAC103 in response to plastid translation disruption

summary: To investigate the link between GUN1 and NAC103 in response to plastid translation inhibition, we profiled the seedling root transcriptome after transient spectinomycin treatment. The tested genotypes include WT, gun1-101, nac103-11, and 35S:NAC103-GFP (NAC103-OX, OX103). Our results confirm that NAC103 is a key component of GUN1-mediated plastid signaling in roots.

overall_design: Seeds of WT, gun1-101, nac103-11, and 35S:NAC103-GFP (NAC103-OX) were sterilized with a mixture containing 75% (v/v) ethanol and 0.05% (v/v) Triton X-100 for 10 minutes and then plated onto solid 1/2 Murashige and Skoog (MS) medium containing 1% (w/v) sucrose. The plates were kept in the dark in a refrigerator (4~5°C) for about 3 days and then transferred to a growth chamber (16-h light/8-h dark, 22~23°C). After germination and growing for about 5 days, seedlings were transferred onto solid 1/2 MS medium containing 10 mg/L spectinomycin and incubated for about 24 h. After incubation, root tips (about 0.5 cm in length) were collected and stored at -80°C.


title: Multimodal Mechano-adaptive Artificial Synovial Fluid Drives In-Situ Engineering of Anti-Pyroptotic Extracellular Vesicles to Arrest Preclinical Osteoarthritis

city: Shanghai

first: Xudong

last: Zhang

address: 1239 Siping Road

department: Department of Orthopedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University

institute: Tongji University: Shanghai, CN

summary: Effective early interventions for knee protection in exercise enthusiasts and pre-clinical symptomatic knee osteoarthritis (OA) patients are lacking. Abnormal mechanical loading initiates a dual pyroptotic loop between chondrocytes and macrophages, converting healthy cartilage to pathology. Herein, we engineered a multifunctional artificial synovial fluid, pPBA@MN UM6@Co (PMUC), to deliver graded protection and repair of early pathogenetic cartilage. Intra articular PMUC builds a persistent hydration layer via water bonding, mimicking native synovial fluid, markedly enhancing lubrication and dissipating mechanical stress. When abnormal stress provokes ultra early cartilage lesions, the ensuing ROS (·OH) surge cleaves boronate esters and glycosidic bonds in PMUC, releasing mannose (Man) and UM6@Co (UC) nanocomplexes. Activation of the hexosamine biosynthetic pathway (HBP) suppresses Caspase-3–GSDME-mediated pyroptosis in chondrocytes while promoting in situ formation and engineering of extracellular vesicle (EV) derived from resident and synovial macrophages. These EVs, functioning as intercellular messengers within the articular cavity, collectively disrupt the chondrocyte-macrophage pyroptosis loop and facilitate matrix regeneration. In high-load exercise and early OA rat models, PMUC prevented further erosion and healed existing defects, achieving full cartilage regeneration and restored locomotor performance within eight weeks. By coupling adaptive lubrication with stress triggered immune-metabolic modulation, PMUC offers the first stage specific strategy that simultaneously protects healthy joints and repairs silent OA, filling a critical clinical gap for exercise enthusiasts and early-stage patients.

overall_design: Transcriptome sequencing was performed on chondrocytes after intervention with PMUC and PBS to observe the differentially expressed genes between the two groups

first: Wei

last: Zhu

first: Peng

last: Wu


title: Transcriptional Landscape Analysis of T-bet/Runx3 in Antiviral CD8+ T Cells via Single- and Double-Knockout RNA-seq

city: Suzhou

first: Qiang

last: Shan

address: No. 100, Chongwen Road

institute: Suzhou Institute of Systems Medicine

summary: Effector CD8+ T cells require tight coordination of cytotoxic gene expression programs with lineage maintenance. T-bet and Runx3 are central to this process, but their combined transcriptional control mechanisms were poorly understood due to sparse transcriptional datasets. This study dissects their cooperative and distinct roles through systematic RNA-seq profiling of knockout models.

overall_design: Using RNA-seq across single and double knockout models, we characterize the transcriptional regulation mediated by T-bet and Runx3.


title: Epigenetic Profiling of T-bet/Runx3 Double Knockout Models via ATAC-seq and Cut&Run in Antiviral CD8+T Cells

summary: The rapid acquisition of cytotoxic functions while maintaining lineage fidelity in effector CD8? T cells relies on precise transcriptional control by T-bet and Runx3. Despite their critical role, the integrated regulatory logic of these factors remained unclear due to limited chromatin accessibility and binding data. This work clarifies their distinct and overlapping contributions through targeted genetic perturbations.

overall_design: Leveraging ATAC-seq and Cut&Run technologies across double knockout models, we investigate the combinatorial and individual roles of T-bet and Runx3 in modulating the epigenetic landscape.


title: Brief high-fat diet exposure imprints TH17-driven inflammatory memory in skin independent of obesity

city: San Francisco

first: Sagar

last: Bapat

state: CA

address: 513 Parnassus Ave

institute: UCSF

summary:
Obesity alters immune responses across inflammatory contexts; however, whether brief dietary changes influence immune function independent of weight gain remains unclear. Here, we demonstrate that transient high-fat diet (HFD) exposure during the onset of psoriasiform inflammation markedly exacerbates disease severity in lean mice. Mechanistically, HFD rapidly increases neutrophil accumulation and NLRP3-dependent IL-1β production in lesional skin, promoting IL-1R1⁺ pathogenic TH17 differentiation and establishment of a chromatin-primed tissue-resident memory CD4⁺ T cell population. Transient HFD exposure during disease onset durably amplifies inflammatory recall responses upon rechallenge, despite subsequent dietary normalization. These findings identify diet on disease onset (DODO) as a critical modifier of inflammatory disease trajectory.

Single-nucleus ATAC-seq of CD4⁺ T cells from recovered skin following diet-modulated IMQ-induced inflammation

Transient high-fat diet (HFD) exposure during the onset of psoriasiform inflammation induces durable transcriptional and epigenomic remodeling in CD4⁺ T cells. To define chromatin accessibility programs associated with inflammatory memory, we performed single-nucleus ATAC sequencing (snATAC-seq) of sorted CD4⁺ T cells isolated from ear skin following recovery from imiquimod (IMQ)-induced inflammation in mice fed either low-fat diet (LFD) or HFD. These data enable identification of differentially accessible regulatory elements and chromatin states associated with diet on disease onset (DODO)-driven inflammatory memory.

overall_design:
Mice were fed either low-fat diet (LFD, 10% kcal fat) or high-fat diet (HFD, 60% kcal fat) for 1 week prior to and during topical imiquimod (IMQ) treatment. Psoriasiform inflammation was induced by daily application of 5% IMQ cream to the ear for 6 consecutive days.
On day 6 of IMQ treatment, lesional ear skin was harvested and enzymatically digested into single-cell suspensions. Immune populations were isolated by fluorescence-activated cell sorting (FACS) prior to single-cell library preparation.
For CD4⁺ T cell profiling, live CD45.2⁺ CD3ε⁺ CD4⁺ T cells were sorted from lesional skin of LFD- or HFD-fed mice and processed using the PIPseq™ T2 3′ Single Cell RNA Kit (Fluent BioSciences). One T2 reaction was used for LFD samples and two independent T2 reactions were used for HFD samples. Libraries were sequenced on an Illumina NovaSeq X platform.
For CD45⁺ immune cell profiling, live CD45⁺ cells were sorted from lesional skin of LFD- or HFD-fed mice and processed using the Chromium Single Cell 3′ Fixed RNA Profiling (Flex) platform (10x Genomics). Libraries were sequenced on an Illumina NovaSeq X platform and aligned using Cell Ranger (GRCm39 reference genome).
Downstream analysis was performed using Scanpy and Seurat following quality control, normalization, clustering, and differential gene expression analysis.

CD4 recovery snATAC-seq:
Mice were fed either low-fat diet (LFD, 10% kcal fat) or high-fat diet (HFD, 60% kcal fat) for 1 week prior to and during topical imiquimod (IMQ) treatment. Psoriasiform inflammation was induced by daily application of 5% IMQ cream to the ear for 6 consecutive days. After resolution of inflammation and recovery, ear skin was harvested.
CD4⁺ T cells were isolated by fluorescence-activated cell sorting (FACS). Nuclei were prepared from sorted CD4⁺ T cells and single-nucleus ATAC libraries were generated using the Chromium Single Cell ATAC v2 kit (10x Genomics) according to the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq X platform to generate paired-end reads.
Raw FASTQ files were processed using Cell Ranger ATAC (10x Genomics) with the GRCm39 mouse reference genome to generate fragment files and peak calls. Downstream analysis was performed using ArchR (v1.0.3), including quality control filtering based on TSS enrichment and fragment counts, dimensionality reduction using iterative LSI, clustering, peak calling using MACS2, and identification of differentially accessible regions between dietary conditions.

first: Zewen

last: Jiang

first: John

middle: M

last: Tayeri

first: Sophie

last: Curio

first: Brittany

last: Davidson

first: Vrinda

last: Johri

first: Jessica

last: Tsui

first: Alexis

last: Combes


title: CCR7+ activated dendritic cells are essential for spontaneous and immunotherapy-driven anti-tumor immunity

city: Manchester

first: Santiago

last: Zelenay

address: Wilmslow Rd, Manchester M20 4BX

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary: Single-cell transcriptomics identifies a convergent activation state of conventional dendritic cells (cDCs) shared by type 1 and type 2 cDCs (cDC1s and cDC2s). These activated DCs (actDCs) are characterized by co-expression of T cell-stimulating and inhibitory molecules. Here, we examined the functional contribution of actDCs to anti-tumor immunity by developing mouse models that leverage CCR7 expression to conditionally label or ablate actDCs. The capacity of cDCs to stimulate tumor-specific cytotoxic T lymphocytes (CTLs) was restricted to the actDC state. cDC1- and cDC2-derived actDCs supported CTL priming through cross-presentation and cross-dressing, respectively, with the latter occurring in a cancer type-dependent manner. actDCs were required for the activation of naive CTLs in tumor-draining lymph nodes and for sustaining effector CTL function within tumors. Consequently, ablation of actDCs impaired spontaneous tumor control and responses to immune checkpoint blockade or adoptive T cell therapy. Thus, the actDC state emerges as a critical determinant of cDC-mediated anti-tumor immunity.

overall_design: 5555 - C57BL/6 mice were injected subcutaneously with 5555 melanoma tumors. Tumors were harvested 4 days post cancer cell inoculation. CT26 - Balb/c mice were injected subcutaneously with CT26 tumors. Tumors were harvested 12 days post cancer cell inoculation. BMDC - Bone marrow from C57BL/6 mice was isolated and plated to generate conventional dendritic cell cultures following an FLT3L/GM-CSF-based differentiation protocol. Dendritic cell cultures in the presence or absence of cancer cells were harvested at day 10. For all experiments, live CD45+ cells were isolated by Fluorescence-activated cell sorting (FACS). Single cell gel beads-in-emulsion and libraries were prepared using the 10X Genomics platform.

first: Eduardo

last: Bonavita

first: Victoria

middle: S

last: Pelly

first: Maria

last: Koufaki

first: Richard

last: Reeves

first: Sudhakar

last: Sahoo


title: Cell-intrinsic functions of PD-L1 activate autophagy and prevent cytokine-induced apoptosis

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: Immune checkpoint inhibitor (ICI) therapy triggers complications which are currently attributed solely to immune activation. We hypothesized that target tissue specific mechanisms also play a role and studied these mechanisms in thyrocytes. We discovered that thyroidal PD-L1 acts as a cytoprotective regulator, promoting cell survival during cytokine-induced stress. PD-L1 suppression in thyrocytes amplified IFNγ-driven stress by aberrantly activating AKT - ERK - mTORC1, inhibiting autophagy, augmenting cellular stress, and triggering apoptosis.  In a mouse model of ICI-thyroiditis, anti-PD-L1 treatment triggered immune activation while promoting thyrocyte apoptosis. Mechanistically, in mice, both pharmacologic and genetic downregulation of thyroidal PD-L1 caused autophagic defects. Our findings reveal a role for PD-L1 in protecting thyroid tissue from cytokine-mediated stress and suggest that anti-PD-L1 tissue toxicity may reflect both an immune-mediated attack and intrinsic cellular vulnerability.  Our data provide a broader framework for understanding ICI adverse events and for guiding the development of treatment strategies.

overall_design: To investigate the role of thyroidal PD-L1 in αPD-L1-induced thyroiditis, we treated NOD.H-2h4 mice with αPD-L1 or isotype control IgG Abs three times/week for two weeks and then harvested the thyroid. To identify genes and pathways dysregulated in the thyroid by PD-L1-blockade, we performed RNA-seq in the thyroid of αPD-L1-treated vs. CTR mice.

first: Mihaela

last: Stefan-Lifshitz

first: Nicola

last: Viola

first: Olga

last: Meshcheryakova

first: Crystal

last: Nieves Garcia

first: Pamela

last: Mattar

first: Zhengzi

last: Yi

first: Marie

last: Louise Aoun

last: C. McAuliffe

first: Jonathan

last: Smith

first: Vikas

last: Mehta

last: V. Smith

first: Adam

last: J. Gersten

first: Rajat

last: Singh

first: Yaron

last: Tomer


title: Topology and Evolution of Global Transcriptional Regulatory Networks Across the Klebsiella pneumoniae Pan-Genome

city: Hongkong

first: Xin

last: Deng

state: 九龍

address: Tat Chee Road, City University of Hong Kong, AC1,B2315

department: BMS

country: Hong Kong

institute: City University of Hong Kong

summary: In this study, we determined 370 transcription factors binding profiles and functions, constructed a comprehensive regulatory network encompassing 9 COG functional categories of one KP isolate .

overall_design: We perfomred DAP-seq experiments of 370 TFs, four timepoints RNA-seq of KP WT strain, and four mutants RNA-seq at two time stages.

first: Beifang

last: Lu

first: Tongtong

last: Feng


title: Integrated RNA, translation, and proteome profiling reveals midbody remnants as selectively organized signaling vesicles

city: Madison

first: Finn

last: Kuusisto

state: WI

address: 1205 University Ave

institute: University of Wisconsin-Madison

summary: This study investigates the differences in mRNA payloads between midbody remnants (MBRs) and whole cell of origin for six cell types, in order to determine type-specific and common enriched genes in MBRs. RNA-seq was performed by the Skop lab for all six cell types. Ribo-seq was performed by the Iwasaki lab on one of the cell types to assess translational differences. Data include raw FASTQ files, processed count tables, and metadata describing each sample.

overall_design: RNA-seq profiling of midbody remnants (MBRs) versus whole cell type of origin for six different cell types. Additional Ribo-seq profiling of MBR versus whole cell type of origin for one of the six cell types.

first: Dantong

last: Zhu

first: Elizabeth

middle: E

last: Torr

first: Kotaro

last: Tomuro

first: Benjamin

last: Minkoff

first: Sophie

last: Lusty

first: Sungjin

last: Park

first: Yuichi

last: Shichino

first: John

last: Favate

first: Premal

last: Shah

first: Randall

middle: D

last: Dahn

first: Michael

last: Sussman

first: Shintaro

last: Iwasaki

first: Justin

last: Wolter

first: Ahna

middle: R

last: Skop


title: Transcriptome of temporal muscle in moyamoya disease

city: Fuzhou

first: Jingyi

last: Chen

address: xinquan road

institute: Fujian Medical University Union Hospital

summary: Objective Indirect revascularization is an effective treatment for moyamoya disease (MMD), but the surgery effect depends on the collateral vessel formation. This study aimed to explore the molecular mechanisms driving angiogenesis in the temporal muscle post-surgery. Methods This study utilized a single-center, prospectively sampled, retrospective cohort design. Temporal muscle tissue was collected, and a comprehensive transcriptome-wide analysis was subsequently conducted. Participants were categorized into Good (Grade A, n=13) and Poor (Grade C, n=12) groups based on Matsushima grading. Results A total of 25 patients were included in the study. Analysis of gene expression between the Good Group and the Poor Group revealed extracellular matrix (ECM) and collagen family promote angiogenesis in temporal muscle. Four children in the Good Group exhibited a high clustering, comparing them to the Poor Group revealed mitochondrial electron transport's crucial role in angiogenesis among children with MMD. Additionally, our analysis demonstrated that fat cell proliferation played a significant role in the adult subgroup. Conclusions This transcriptomic study emphasized the centrality of collagen as the underlying molecular mechanisms that facilitate angiogenesis. In addition, it revealed the significant contributions of the NADH dehydrogenase (complex I) family and fat cell proliferation in this process.

overall_design: Transcriptomic profiling of temporal muscle biopsies from moyamoya disease (MMD) patients undergoing indirect revascularization, comparing angiogenesis-competent  and angiogenesis-deficient cohorts, with subgroup analyses of pediatric (*n*=4) versus adult populations

first: Xiankun

last: Tu


title: COMPASS-like complex participates in the bud dormancy release of tree peony by regulating H3K4me3 modification

city: Qingdao

first: Yuxi

last: Zhang

address: Changcheng Road 700

institute: Qingdao Agricultural University

summary: Bud dormancy release in woody plants is crucial for survival, regrowth, flowering and fruiting. Tree peony (Paeonia suffruticosa), an importantly ornamental and economic plant undergoes bud endodormancy in winter, and effective chilling duration and exogenous gibberellins (GA) can effectively break the dormancy, however, its epigenetic regulation mechanism remains poorly understood. Here, western blotting revealed that H3K4me3 but not H3K4me1 and H3K4me2 was associated with chilling- and gibberellin (GA3)- induced dormancy release.  Chromatin immunoprecipitation sequencing (ChIP-seq) combined with RNAseq results revealed that H3K4me3 enriched near transcription start sites (TSS), and was correlated with the transcriptional activation of dormancy release-related genes (PsEBB3, PsCYCD3.1, PsCYCD3.3, PsBG6, and so on). H3K4me3 enrichment genes (HEGs) common to the differentially-expressed genes (DEGs) were mainly enriched in KEGG pathways such as plant hormone signaling transduction and MAPK signaling. Four COMPASS-like component homologs were screened, among them, PsWDR5a, PsRBL, and PsASH2R were up-regulated by the prolonged chillings and GA3 treatment. PsRBL interacted with PsWDR5a and PsASH2R using yeast two-hybrid, luciferase complementation. Yeast three- hybrid and co-immunoprecipitation assays confirmed that PsRBL bridged the other proteins to form a nuclear-localized complex. Functional analyses showed that PsWDR5a, PsRBL, and PsASH2R significantly promoted budburst and elevated genomic H3K4me3 levels. Our fingings would provide novel insights into the epigenetic regulation of dormancy transitions in woody perennials.

overall_design: ChIP-seq analysis of the H3K4me3 chromatin mark was performed to investigate the dynamics of bud dormancy release induced by chilling. Samples were collected from tree peony buds at 0, 14, and 21 days after chilling.

first: Jingjing

last: Liu

first: Yongli

last: Zhao

first: Shupeng

last: Gai


title: Mutagenicity of N-nitrosodiethylamine and its mechanism of action in liver and bone marrow of Big Blue rats evaluated using in vivo mutation assays and gene expression analysis

city: Jefferson

first: Li

last: Xia

state: AR

address: 3900 NCTR Rd

institute: National Center for Toxicological Research

summary: N-Nitrosodiethylamine (NDEA) has been extensively studied as a carcinogen especially in liver. The detection of NDEA as a contaminant in widely used drugs has led to numerous product recalls in recent years, highlighting the urgent need for improved safety measures. In this study, we examined the tissue-specific mutagenic effects of NDEA using a multi-assay approach, including cII mutation assay, Pig-a assay, Duplex Sequencing (DS), and RNA-sequencing in the liver and bone marrow of Big Blue transgenic rats. Female rats were administered 0, 5, or 10 mg/kg body weight/day of NDEA by gavage for 28 days, with benzo[a]pyrene (75 mg/kg) included as the positive control. The animals were sacrificed 3 days after the end of treatment. Among the assays used, DS demonstrated the highest sensitivity, particularly for detecting low-frequency mutations. Both the cII mutation assay and DS revealed significantly higher mutation frequencies in the liver compared to bone marrow, consistent with the liver’s greater metabolic activation capacity. In contrast, the Pig-a assay in peripheral blood failed to consistently detect mutagenic effects from NDEA exposure. Mutation spectrum analysis by DS revealed a predominance of T > A transversions (35%-38%) and T > C transitions (32%-35%) in the liver, whereas mutations in bone marrow were more evenly distributed. RNA sequencing provided supporting context, revealing significant differences in cytochrome P450 genes in the liver as key contributors to tissue-specific responses. NDEA exposure induced activation of proliferative and pro-tumorigenic pathways such as MYBL2, E2F3, and PRKAR2B signaling in liver. While bone marrow exhibited suppression of translation and immune-related pathways, including EIF2 signaling, following NDEA treatment. These transcriptomic differences likely reflect tissue-specific susceptibility and mode of action. Overall, our study highlights the importance of integrating multiple mutation detection methods to assess tissue-specific genotoxicity. The findings underscore the critical role of metabolic activation and the regulation of proliferative, pro-tumorigenic, translational, and immune pathways in driving NDEA-induced mutagenesis, and support the use of sensitive next-generation sequencing-based approaches to enhance nitrosamine risk assessment.

overall_design: RNA-seq profiling of liver and bone marrow of rats which were gavaged with 0 or 10 mg/kg body weight of NDEA for 28 days and sacrificed 3 days post-treatment.

first: Jian

last: Yan

first: Tao


title: Cytokine-linked remodeling of the immune microenvironment is a hallmark of transformation in follicular lymphoma [VisiumHD]

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

state: MA

address: 75 Ames St

institute: Broad Institute

summary: Across cancer, one of the most frequent examples of histologic transformation is the evolution of follicular lymphoma (FL) to an aggressive large cell lymphoma. Despite recent progress, understanding of the molecular and cellular underpinnings of transformation remains incomplete. Here, we dissect the interplay of tumor and microenvironment cell populations across transformation through a multimodal investigation of 85 FL and transformed FL samples, including single-cell and bulk RNA-sequencing alongside spatial transcriptomics and proteomics. Upon transformation, GPNMB+ macrophages and fibroblasts with matrix-remodeling phenotypes increased while lymph-node organizing populations (e.g. follicular dendritic cells, CCL21-expressing fibroblastic reticular cells) were lost. Transformation was marked by altered spatial distribution of cytokines, impacting macrophage differentiation and T cell infiltration. This detection of secreted stromal and macrophage signals was further evident by non-invasive plasma proteomics. Taken together, our data reveal expansion of macrophages and fibroblasts as key features of transformation with potential diagnostic and therapeutic implications.

overall_design: VisiumHD FFPE profiling was performed on 5 biopsies containing a mixture of indolent and transformed regions

middle: J

first: Stephanie

last: Yiu

first: Laura

last: Beckmann

first: Catherine

last: Wu

first: Gad

last: Getz

first: Sizun

last: Jiang

first: Erin

last: Parry


title: Cytokine-linked remodeling of the immune microenvironment is a hallmark of transformation in follicular lymphoma [bulkRNA-seq]

overall_design:
Bulk RNA sequencing of lymph node biopsies of patients with lymphoma

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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. FASTQs will be submitted to dbGaP separately.
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title: Cytokine-linked remodeling of the immune microenvironment is a hallmark of transformation in follicular lymphoma [GeoMX]

overall_design: GeoMX profiling of two tissue microarrays containing follicular lymphoma biopsies before and after transformation


title: Investigation of the impact of Arylsulfatase L (ARSL) deletion in rat chondrosarcoma (RCS) cell lines

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: In this study, we identified arylsulfatase L (ARSL), which is mutated in X-linked chondrodysplasia punctata (CDPX), as a Golgi-localized enzyme responsible for glycosaminoglycan (GAG) desulfation. To elucidate the cellular and molecular consequences of ARSL deficiency, we performed trasncriptome profiling using RNA-sequencing (RNA-seq) in rat chondrosarcoma (RCS) wild-type (WT) and ARSL knockout (KO) cells.

overall_design: RCS wild-type (WT) and ARSL knockout (KO) cells were cultured, and total RNA was collected 48 hours after seeding for digital mRNA sequencing (mRNA-seq)


title: Cytokine-linked remodeling of the immune microenvironment is a hallmark of transformation in follicular lymphoma [scRNA-seq]

overall_design:
10x 5' single-cell RNA sequencing was performed on lymph node biopsies from patients with indolent and transformed follicular lymphoma

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


title: A Human Single-cell Atlas Identifies OLR1+ Scar-associated Macrophages as a Therapeutic Target for Chronic Liver Disease

city: Edinburgh

first: Eleni

last: Papachristoforou

address: Edinburgh BioQuarter 4-5 Little France Drive

department: Institute for Regeneration and Repair

institute: University of Edinburgh

summary: Chronic liver disease (CLD) is a major global healthcare problem. Irrespective of cause, chronic damage to the liver results in fibrosis, which is associated with adverse clinical outcomes. Immune cells, in particular monocyte-derived macrophages (MDMs), are key regulators of fibrosis and represent an attractive therapeutic target for CLD. However, it has remained unclear which specific subpopulation of MDMs drives pro-inflammatory and pro-fibrotic functions in human CLD and how they might be selectively modulated. Here, we generate an annotated human liver single cell atlas from 42 healthy and 35 CLD patients, identifying 125 transcriptionally distinct cellular states. Leveraging large patient and cell numbers, our atlas resolves rare liver cell states and distinguishes two types of disease-expanded scar-associated macrophages (SAMac), including a specific subpopulation with a pro-inflammatory pro-fibrotic phenotype. The scavenger receptor OLR1 was enriched in pro-inflammatory SAMacs and high hepatic OLR1 expression was associated with increased mortality in CLD patients. A corresponding monocyte-derived OLR1+ SAMac subpopulation expanded in a mouse model of CLD and exhibited a pro-inflammatory phenotype based on single-cell RNA-seq, single-cell ATAC-seq, and flow cytometry analyses. Primary human OLR1+ MDMs promoted fibrogenic signalling in multilineage liver spheroid cultures, whilst specific targeting of OLR1 reduced IL-1β production by human macrophages and attenuated myofibroblast activation. Overall, our annotated human liver single-cell atlas provides a valuable reference to study disease-associated cell states in CLD. We utilise this resource to identify a distinct pro-inflammatory subpopulation of SAMacs and highlight OLR1 as a potential therapeutic target to specifically modulate SAMac function and attenuate liver fibrosis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For mouse carbon tetrachloride (CCl4) studies, C57BL/6JCrl WT mice were administered chronic CCl4 for 4 weeks, followed by harvests at serial timepoints (24 hours, 96 hours and 4 weeks) following the last CCl4 injection. Uninjured age-matched mice were used as controls. Liver and circulating immune cells were isolated by FACS. 3 mice were pooled together for each sample. For single-cell RNA-seq, liver and blood immune cells were profiled at 24 hours, 96 hours and 4 week timepoints as well as age-matched controls. For single-cell ATAC-seq, liver and blood immune cells were profiled at the 24 hour and 4 week timepoints as well as age-matched controls. For mouse bile duct ligation (BDL) studies, C57BL/6JCrl WT mice underwent BDL surgery, followed by harvest at day 14. Uninjured age-matched mice were used as contols.  Liver and circulating immune cells were isolated by FACS. 3 mice were pooled together for each sample. Single-cell RNA-seq was performed on BDL liver and blood immune cells as well as age-matched controls. For human liver needle biopsy scRNAseq, up to 5mm of liver biopsy material was snap frozen immediately following collection. Paired biopsy tissue underwent hisotlogcal staging and patients with histologically normal liver (n=6) or those with MASLD (n=7) were identified. Frozen biopsy tissue from these patients were then subjected to scRNAseq.

first: Prakash

last: Ramachandran

first: Juliet

last: Luft


title: Transcriptome profiling analysis of heat-adapted breeder hen jejunal mucosal tissues in response to acute heat stress

city: Nakhon Ratchasima

first: Yongcai

last: Zhu

address: School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand

country: Thailand

institute: Suranaree University of Technology

summary: Heat stress (HS) can weaken the intestinal integrity and damage the intestinal barrier function of poultry, disrupting nutrient digestion and absorption. However, the underlying molecular mechanism is unclear. Our objective was to examine the gene expression profile of the jejunum by conducting transcriptomic analysis of heat-adapted breeder hens under acute HS (36 °C for a 6-h). Fifty 28-week-old breeder hens were raised individually in a cage and randomly assigned to control and heat-treated groups (25 hens each). Control group hens were maintained at thermoneutral conditions (23 °C) and heat-treated group hens were subjected to acute HS (36 °C for a 6-hour). The heart rate and cloacal temperature were measured in all hens. The jejunal mucosa tissues were collected from 12 randomly selected hens per group for transcriptomic analysis. The acute HS induced significant physiological alterations, with a marked increase in the heart rate and cloacal temperature in hens (P = 0.001). Transcriptome analysis revealed 138 genes with altered expression patterns under acute HS conditions. Of these, 75 genes including heat shock proteins (HSPs) showed upregulated expression, while 63 genes including a key bile acid transport molecule (SLC10A2) exhibited downregulated expression. Functional analysis through gene ontology classification, pathway mapping via the Kyoto encyclopedia of genes and genomes, and protein interaction networks identified several important regulatory genes in thermal response (HSPA8 and HSPA2), energy homeostasis and fat metabolism (PDK4, PPARA, and CD36), glucose transport (SLC2A5), and cholesterol synthesis pathway (SQLE, CYP51A1, and HSD17B7). The findings suggest that acute HS might affect energy utilization, fat metabolism, and glucose transport mechanisms in the jejunal mucosa of breeder hens. The upregulation of HSPs appears to serve as a protective mechanism, potentially preserving intestinal nutrient processing capacity under acute HS. These findings provide foundational knowledge for further investigation into the molecular mechanisms governing HS responses in avian intestinal function and may inform strategies for maintaining gut health in commercial poultry operations exposed to environmental challenges.

overall_design:
Fifty 28-week-old breeder hens were raised individually in a cage and randomly assigned to control and heat-treated groups (25 hens each). Control group hens were maintained at thermoneutral conditions (23 °C) and heat-treated group hens were subjected to acute HS (36 °C for a 6-hour). The heart rate and cloacal temperature were measured in all hens. The jejunal mucosa tissues were collected from 12 randomly selected hens per group for transcriptomic analysis.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Satoshi

last: Kubota

first: Phocharapon

last: Pasri

first: Sutisa

last: Khempaka


title: Transcriptome profiling analysis of heat-adapted and heat-sensitive breeder hen jejunal mucosal tissues in response to acute heat stress

summary: Heat stress (HS) can weaken the intestinal integrity and damage the intestinal barrier function of poultry, disrupting nutrient digestion and absorption. However, the underlying molecular mechanism is unclear. Our objective was to examine the gene expression profile of the jejunum by conducting transcriptomic analysis of heat-adapted and heat-sensitive breeder hens under acute HS (36 °C for a 6-h). Fifty 28-week-old breeder hens were raised individually in a cage and randomly assigned to heat-adapted and heat-sensitive groups (25 hens each). After exposure to acute HS for 6 hours, jejunal mucosa samples from the heat-adapted (HA group, n = 3) and heat-sensitive (HS group, n = 3) groups were selected for transcriptome analysis using RNA sequencing (RNA-seq). RNA-seq identified 284 differentially expressed genes, with 155 genes upregulated and 129 downregulated in the heat-sensitive group compared to the heat-adapted group. Gene ontology term (GO) analysis of the DEGs revealed significant enrichment in 555 GO terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway revealed 5 pathways were significantly enriched in upregulated DEGs, including the VEGF signaling pathway, MAPK signaling pathway, steroid biosynthesis, neuroactive ligand-receptor interaction, and cell cycle, and 1 pathway significantly enriched in downregulated DEGs, such as cell adhesion molecules. The protein-protein interaction (PPI) network identified PLK1, CDC7, CDC20, HSPA2, IL6, SLC22A19A, LBFABP, and SLC2A2 as key core nodes, which may play crucial roles in regulating the effects of HS on cell division, immune function, energy and lipid metabolism, and nutrient transport. The findings suggest that acute HS might affect cell division, immune function, energy and lipid metabolism, and organic acids and glucose transport mechanisms in the jejunal mucosa of breeder hens. The DEGs and pathways identified in this study will provide new insights to understand further the molecular mechanisms underlying HS responses in avian intestinal function, suggesting potential targets for nutritional or management strategies to mitigate its effects.


title: FANCM is Required for the PAX3::FOXO1-Driven Oncogenic Program in Rhabdomyosarcoma [CRISPR Screen]

city: Durham

first: Christopher

middle: David

last: Delaney

state: NC

address: 308 Research Drive, LSRC C131

department: Pharmacology and Cancer Biology

institute: Duke University School of Medicine

summary: Alveolar rhabdomyosarcoma (ARMS) is a highly aggressive pediatric soft tissue sarcoma driven by the PAX3::FOXO1 fusion protein. Despite multipronged treatment approaches, survival rates for patients with fusion-positive (FP) ARMS remain poor, underscoring the need for novel therapeutic strategies. Here, we employ sequential multimodal CRISPR/Cas9 genetic screens to identify essential genes in FP ARMS, revealing FANCM, a key component of the Fanconi Anemia pathway, as a critical dependency. FANCM loss selectively impairs FP ARMS cell growth in vitro and in vivo, reduces PAX3::FOXO1 levels, and induces myogenic differentiation. Mechanistically, FANCM depletion exacerbates replication stress, particularly at PAX3::FOXO1 target gene loci, which leads to ATR/ATM-mediated DNA damage signaling and selective downregulation of the fusion-driven oncogenic program. CRISPR exon-tiling screens highlighted FANCM's helicase and DNA-binding domains as essential for its FP-specific dependency, linking FANCM-mediated replication fork binding and downstream ATR signaling to FP ARMS survival. This study positions FANCM as a promising therapeutic target in FP ARMS and introduces a novel paradigm for exploiting replication stress vulnerabilities in oncofusion-driven malignancies.

sample_organism:
Homo sapiens
unidentified

platform_organism:
Homo sapiens
unidentified

overall_design: Five CRISPR/Cas9 screen experiments: 1) Genome-scale essentiality screen in 2D vs 3D culture using the PAX3::FOXO1-positive RMS cell line Rh4 Clone. 2) Custom sgRNA library essentiality screens in six RMS cell lines: Rh4 Clone, Rh4 Native, Rh28, Rh30, RD, and SMS-CTR. 3) PAX3::FOXO1-FLAG flow-based screen in the Rh4 Clone cell line. 4) CKM flow-based screen in four PAX3::FOXO1-positive cell lines: Rh4 Clone, Rh4 Native, Rh28, and Rh30. 5) Exon saturation sgRNA tiling screen of FANCM in the Rh4 Clone and RD cell lines.

first: Kris

middle: C

last: Wood


title: FANCM is Required for the PAX3::FOXO1-Driven Oncogenic Program in Rhabdomyosarcoma [ChIP-Seq]

overall_design: Two ChIP-seq  experiments: 1) The RMS cell line Rh4 Native was prepared in triplicate, grown to confluency, and prepared for H3K27Ac ChIP-seq  2) The Rh4 Native cell lines stably expressing  inducible knock-down constructs ishFANCM or seed-matched control hairpin (ishFANCM-SMC), were prepared in triplicate, treated for 2 days with doxycycline (150 ng/mL) to induce hairpin expression, and then prepared for pRPA32-S33 ChIP-seq.


title: Perturbation of the relative abundance of H2A.Z variants alters H3K27me3 enrichment in Arabidopsis thaliana [RNA-Seq]

city: West Lafayette

first: Joe

last: Ogas

state: Indiana

address: 175 S. University Street

department: Department of Biochemistry

institute: Purdue University

summary: H3K27me3 is a histone modification associated with transcriptional repression that plays a pivotal role in differentiation and development in plants and animals. H2A.Z, a histone variant of H2A, is often colocalized with H3K27me3 in Arabidopsis. Previous genome-wide studies have raised the possibility that H2A.Z contributes to H3K27me3 homeostasis in plants. To examine the contribution of H2A.Z to H3K27me3, we made use of hta9 hta11, a plant line which is defective in two of three genes that code for H2A.Z and which has been previously characterized as an H2A.Z-depletion mutant. Surprisingly, ChIP-seq analysis of H2A.Z enrichment revealed that hta9 hta11 plants exhibit a nearly indistinguishable genic H2A.Z enrichment pattern relative to wild type with few genes that are differentially enriched for H2A.Z. Mass spectrometry measurement of histone abundance in hta9 hta11 plants in conjunction with our ChIP-seq analysis indicates that the chromatin of hta9 hta11 plants exhibits altered relative abundance of H2A.Z variants rather than a global depletion of H2A.Z. In contrast, ChIP-seq analysis of H3K27me3 reveals that hta9 hta11 plants exhibit a robustly global reduction in H3K27me3 enrichment, and numerous genes are identified that exhibit altered levels for H3K27me3. In addition, hta9 hta11 plants exhibit differential expression of thermoresponsive genes that have previously been shown to be dependent on H2A.Z. Our combined analyses indicate that specific H2A.Z isoforms play distinct roles in chromatin composition and gene expression in Arabidopsis, particularly with regards to H3K27me3 homeostasis.

overall_design: To investigate the contribution of perturbed chromatin homeostasis to transcript levels in hta9 hta11 plants

first: Jiaxin

last: Long

first: Gustavo

last: Agreda

first: Shelby

last: Sliger

first: Jacob

last: Fawley

first: Pete

last: Pascuzzi

first: Bradley

last: Dickson

first: Bryon

last: Drown


title: FANCM is Required for the PAX3::FOXO1-Driven Oncogenic Program in Rhabdomyosarcoma [RNA-Seq]

summary: Many cancers are driven by mutationally altered transcription factors (TFs) that rewire cells to an oncogenic state. Cells must activate specific mechanisms to tolerate the burden of oncogenic TF activity. To define such mechanisms, we focused on a canonical oncogenic fusion protein-driven cancer, alveolar rhabdomyosarcoma (ARMS), where the PAX3::FOXO1 fusion protein hyperactivates and mislocalizes PAX3 and FOXO1 TF functions. Employing sequential functional genomic CRISPR/Cas9 screens, we identified FANCM, a DNA translocase in the Fanconi anemia pathway, as a selective dependency in PAX3::FOXO1+ ARMS. FANCM loss reduces fusion protein levels, induces myogenic differentiation, and disrupts the PAX3::FOXO1 transcriptional program, thereby halting oncogenic proliferation. Mechanistically, FANCM depletion exacerbates replication stress (RS) and DNA damage signaling, with chromatin-associated RS enriched at PAX3::FOXO1 target gene loci, resulting in selective downregulation of the oncogenic program. CRISPR exon-tiling screens prioritized FANCM's helicase and DNA-binding domains as essential for this dependency, linking FANCM-mediated replication fork binding to sustained oncogenesis.

overall_design: Three RNA-seq profiling experiments: 1) RNA-seq profiling of the PAX3::FOXO1-positive RMS cell line Rh4 Clone upon inducible knock-down of PAX3::FOXO1 via breapoint-targeting hairpin (ishP3F1) compared to control inducible hairpin (ishNTC) after 7 days of doxycycline induction at 100 ng/mL. 2) RNA-seq profiling of the Rh4 Clone cell line upon inducible knock-down of FANCM via ishFANCM, compared to control non-targeting inducible hairpin (ishNTC) or seed-matched control hairpin (ishFANCM-SMC), after 2 days of doxycycline induction at 150 ng/mL. 3) RNA-seq profiling of the Rh4 Clone cell line 24 hours after treatment with irradaition (5 Gy), compared to parental non-treated cells.


title: Improving “mice with natural microbiota” model through controlled microbial exposure

city: Providence

first: Geongoo

last: Han

address: 171 Meeting St.

institute: Brown University

summary: Laboratory-raised specific pathogen-free (SPF) mice have been indispensable for fundamental scientific research, yet their reliability in predicting human clinical outcomes has been questionable. A major factor contributing to this disconnect is the sanitized housing environment, which deprives laboratory mice of physiological microbial exposure critical for immune maturation. Various approaches have been developed to introduce microbes to SPF mice, aiming to mimic human-like microbial experiences and engender adult human-like immune traits. However, many of these methods suffer from significant variability in pathogen exposure and mortality, driven by the uncontrolled nature of microbial exchange. Here we present a simple gavage-fomite (GaF) method that provides controlled exposure to a diverse array of pathogens and commensal while limiting mortality. GaF-treated mice exhibited consistent microbial exposure histories, robust immune maturation characterized by mucosal T-cell distribution and elevated serum inflammatory cytokines, and a systemic immune transcriptional signature closely aligned with that of adult humans. Furthermore, these mice demonstrated enhanced protection against a virulent bacterial challenge. The improved reproducibility, simplicity and effectiveness of the GaF method provides a valuable tool for generating “mice with natural microbiota”, enabling widespread adoption and advancement of both basic and translational research across institutions.

overall_design: To investigate the effects of gavage/fomite method on the systemic immune responses, the cecal contents of pet store mice were gavaged to SPF mice. Dirty beddings were also transferred from pet store mice cages to SPF mice cages twice per week. After at least 60 days of treatments, spleens were harvested and processed for bulk RNA-Seq.

first: Mohammad

middle: H

last: Hasan

first: Jessica

last: Pacia

first: Julian

last: Ramprashad

first: Gregorio

last: Valdez

first: Shipra

last: Vaishnava

first: Lalit

middle: K

last: Beura


title: Perturbation of the relative abundance of H2A.Z variants alters H3K27me3 enrichment in Arabidopsis thaliana [ChIP-Seq]

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for histone variant H2A.Z as well as the histone modification H3K27me3 in wild type (WT) and hta9 hta11 Arabidopsis plants.


title: Drugless Extracellular Hydrogels Enable the Reprogramming of Malignant Glioblastoma

city: Suwon

first: Seunghee

last: Jeong

address: 2066 Seobu-ro, Janna-gu, Suwon, Gyeonggi-do, South Korea

institute: Sunkyunkwan University

summary: Glioblastoma multiforme (GBM) poses a significant challenge in clinical practice due to its poor prognosis and high recurrence rate. Despite several advancements in GBM therapy, it often causes neural cell death near the tumor. Furthermore, the aggressive and invasive nature of GBM frequently leads to recurrence near the resection site. Herein, this study introduces a novel drug-free therapeutic approach by injecting a tumor-reprogrammable and extracellularly activatable hydrogel, termed ‘TREAT’ gel. The soft, injectable hydrogel, which is injected into the tumor resection cavity, adapts to the cavity’s shape, interfaces with residual tumor cells and induces genetic reprogramming of malignant GBM cells, while preserving brain cells and even restoring brain function.

overall_design: Tumor-inoculated and resected mouse brain samples were analyzed, response to the tumor regrowth. Total 4 animals were sampled, with groups including hydrogel-treated and non-treated conditions.

first: Daeun

last: Lee

first: Jaeseung

last: Yei

first: Jungwoo

last: Kim


title: eCLIP-seq of eIF4AIII to profile EJC-localized RNAs

city: Hangzhou

first: Fengli

last: Zhao

state: Zhejiang

address: No. 28 of Shuidaosuo Road

department: State Key Laboratory of Rice Biology and Breeding

institute: China National Rice Research Institute

summary: Various RNA binding proteins participate in different regulatory steps of the RNA lifecycle, affecting various aspects of gene expression. Among these RNA-binding proteins, the exon junction complex (EJC) has been closely linked to RNA since its early production and it is involved in almost every step of the RNA lifecycle. This research focused on plant eIF4AIII as the main subject, investigating its RNA-binding characteristics and how it works as an RNA-binding protein to affect cellular functions and RNA quality control. We found that plant eIF4AⅢ tends to bind to spliced mature mRNA, and it has a classical occupancy near the 3' end of the exon similar to its homologue in other species, and its binding also depends on the splicing events. However, the single-base positioning of eIF4AⅢ binding RNA also exhibits plant-specificity, located 25-28 bp upstream of the exon-exon junction. Data analysis revealed a correlation between the binding half-life of eIF4AⅢ with RNA and the efficiency of RNA degradation in response to NMD in plants. Moreover, when eIF4AⅢ was knocked down, the abundance of intron-retention transcripts increased in plant cells. These results suggest that eIF4AⅢ, as an RNA-binding protein, is involved in the degradation of abnormal transcripts to achieve quality control.

overall_design: eIF4A3-eCLIP-seq was performed using FLAG antibody in eIF4A3-FLAG plants. Herboxidiene wad used to test effect of splicing event. mRNA-seq and total RNA-seq was performed in the same materials as a complementary.

first: Kaiwen

last: Sun

first: Danling

last: Zhu

first: Zhe

last: Wu


title: Age-dependent alterations in the human striatum identify a PPP1R15B-miR-196a node as a modifier of Huntington’s disease phenotypes

city: Saint Louis

first: Victoria

middle: A.

last: Church

state: MO

address: 660 Euclid

institute: Washington University School of Medicine

summary: Polyglutamine expansion in Huntingtin (HTT) causes its aggregation and progressive loss of striatal neurons in Huntington’s disease (HD). HD is a mostly adult-onset neurodegenerative disorder with no disease-modifying therapies. Here we found that human striatal aging is associated with a global upregulation of genes involved in translation, including the translation and proteostasis regulator PPP1R15B (R15B). We used the R15B inhibitor Raphin1 to investigate if the age-associated changes could modify HD pathology. R15B inhibition rescued early learning and late motor deficits in HDYAC128 mice. In striatal medium spiny neurons directly reprogrammed from fibroblasts of symptomatic HD patients (HD-MSNs), Raphin1 reduced the formation of mutant HTT aggregates and neuronal death. Genetic knockdown of R15B also protected HD-MSNs from neurodegeneration whereas its overexpression exacerbated disease phenotypes. Moreover, both human striatum and reprogrammed MSNs exhibited age-dependent decline of miR-196a, a microRNA that directly targets non-conserved sites in human R15B 3’UTR and overexpressing miR-196a lowered mutant HTT aggregation. This work identifies age-dependent alterations in miR-196a and its target R15B and demonstrates the therapeutic potential of reversing these changes in diverse models and readouts of HD. We propose miR-196a and R15B as disease-modifying targets in HD.

overall_design: To determine the effect of Raphin1 on HD-MSNs, we treated HD-MSNs or control MSNs with Raphin1 for two weeks. We then obtained RNA-sequencing reads and compared the effect of drug treatment in HD-MSNs.

first: V

middle: A

first: A

last: Yoo


title: Multi-platform genomic analysis of matched well- and dedifferentiated liposarcomas identify novel risk and progression determinants

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: To define mechanisms that regulate biological behavior in well- and dedifferentiated liposarcoma (WD/DDLS) subsets, we describe an integrative analysis of DNA sequence, copy number and gene expression in 9 paired WDLS and DDLS samples with validation cohorts and in vitro studies. Amplification of 12q13-15 was common to all WDLS; 6q23-25 amplifications were observed 18% of WDLS and were associated with increased TAB2 and higher local recurrence risk versus non-6q-amplified WDLS. TAB2 knockdown decreased MDM2 protein expression and induced markers of cellular senescence in 6q23-25-amplified WDLS cells but not in non-amplified WDLS of amplified DDLS cells. Amplification of 6q23-25 was not associated with DDLS recurrence risk or progression from WDLS to DDLS. Instead, pathogenic ATRX mutations, recurrent losses in 13q and gains in 8q12-21 accompanied dedifferentiation. Downregulation of the 13q-encoded genes MYCBP2 and IRS2 was observed in DDLS versus WDLS; in vitro, these genes were essential for WDLS cell differentiation. Taken together, this study defines a copy number-driven model of liposarcoma initiation, progression, and differentiation.

overall_design: U133A arrays were used specifically to examine genes dysregulated in WDLS compared to normal fat and tumors with 6q23-25 amplification versus those without the event.

first: Aimee

last: Crago

first: Nicholas

last: Socci

first: Samuel

last: Singer


title: Kidney collecting duct cell type composition is regulated by Notch signaling via modulation of mTORC1 activity

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

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

overall_design: Refer to individual Series


title: Temperature during conidiophore development primes Aspergillus fumigatus spore transcriptome for asexual or sexual development

status: Public on Aug 05 2026

city: Athens

first: Michelle

last: Momany

state: GA

address: 120 Carlton Street

department: Plant Biology

institute: University of Georgia

summary: Aspergillus fumigatus is a thermotolerant saprobe found in soils and plant debris worldwide and an important pathogen of humans causing two million deaths annually. A. fumigatus makes abundant asexual spores (conidia) which are widely distributed by wind and can be inhaled from the environment. In susceptible individuals inhaled conidia break dormancy, germinate and grow in the lung leading to serious disease. Recent work has shown that conidia made at 37°C and 50°C have different morphologies and germination kinetics. While the asexual cycle is well-characterized at 37°C, much less is known about the asexual cycle at 50°C. Here, we combine flow cytometry and transcriptomics to track morphology and gene expression in the hyphae, conidiophores and conidia of A. fumigatus during asexual development at 37°C or 50°C. We show that the temperature during a narrow time window in late-stage conidiophore development dictates resulting conidial morphology, transcriptional program, and germination kinetics. As expected, conidiation at 37°C resulted in upregulation of brlA, the master regulator of asexual development, and its downstream targets in conidiophores and conidia. Surprisingly, conidiation at 50°C resulted in upregulation of MAT1-1, the master regulator of sexual development and its downstream targets in conidiophores and conidia. Our findings suggest that temperature during late conidiophore development transcriptionally primes conidia for asexual, parasexual or sexual development enhancing chances of survival for progeny. Our findings are especially relevant for agricultural compost where a wide gradient of temperatures exists, abundant A. fumigatus has been isolated, and resistance to antifungals is thought to evolve.

overall_design: RNA-sequencing of Aspergillus fumigatus strain CEA10/A1163. Hyphae, conidiophores, and conidia were produced at both 37°C and 50°C conditions and cell types were isolated and RNA was extracted (6 samples). 3 biological replicates for each sample (18 total samples). Isolation of conidia: Conidia were produced on Aspergillus minimal media (AMM) for 3 days at 37°C or 50°C, and harvested in 10 mL of DEPC-treated water (Invitrogen). Isolated conidia were filtered 4x through 22-25 µm Miracloth (Sigma) and washed by centrifuging for 1 minute at 7,000 x g at 4°C and resuspended in 1 mL DEPC-treated water. Conidia were diluted to a common concentration of 1x10^8 conidia/mL for all experiments. Isolation of hyphae was carried out by growing 200 µL of 1x10^8 conidia/mL conidia in 500mL liquid Aspergillus Minimal Medium. Cultures were incubated for 12 hours at either 37°C or 50°C with shaking at approximately 150 rpm. Hyphae were filtered through 22–25 µm Miracloth, washed with DEPC-treated water, and RNA extraction was immediately carried out. Isolation of conidiophores: 200 µL of 1x10^8 conidia/mL conidia were inoculated across Aspergillus Minimal Medium in 60 mm x 15 mm petri dishes (ThermoFisher Scientific).  4 mL of melted H20 agar was layered directly on top to physically isolate developing conidiophores from the underlying hyphae. After 28 and 38 hours of incubation at 37°C or 50°C, respectively, the conidiophores were isolated by gently shaving of the top conidiophore layer using a razor blade. RNA extractions were carried out immediately for each isolated cell type. RNA extractions: Isolated cells were immediately lysed by resuspending cells in  1xTE buffer (Invitrogen) and 425-600 µM beads (Sigma) by vortexing on high for 2 minutes. RNA extractions were carried out utilizing TRIzol according to the manufacturer's protocol (Invitrogen). RNA-sequencing: RNA-sequencing was performed by Plasmidsaurus on RNA extracted from isolated conidia, hyphae and conidiophores produced at 37°C or 50°C. Three biological replicates of each condition were sequenced. Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file. Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation. Differential analyses of RNA-seq data were carried out using DESeq2 v.1.50.2 (BiocManager v1.30.27) in R. Low read counts were filtered out (< 5). All parameters were performed according to standard methods. Resulting differentially expressed genes (DEGs) were filtered based upon adjusted p-value (padj < 0.05) and |Log2FoldChange| > 2.

first: Justina

last: Stanislaw


title: Whole-transcriptome sequencing reveals the inflammatory endotypes and potential biomarkers of antrochoanal polyps

city: Beijing

first: Wentong

last: Ge

address: South Lishi Road

department: Department of Head and Neck Surgery

institute: Beijing Children's Hospital, Capital Medical University, National Center for Children's Health

summary:
Objective: To determine the transcriptome of antrochoanal polyps (ACP) in children and find the patterns of gene expression. In the meantime, by analyzing the gene expression profiles and performing functional network analysis, to investigate inflammatory patterns (endotypes), diagnostic biomarkers, and therapeutic targets of ACP.
Methods: Whole-transcriptome analysis with next-generation sequencing (RNA-seq) was used to identify differentially expressed genes (DEGs) between 6 pairs of ACP and ipsilateral uncinate process (UP) samples from the same patients. The hub genes were identified based on the protein-protein interaction (PPI) network constructed by DEGs. For the enrichment analysis of DEGs, the Gene Ontology (GO) database was employed.
Results: ACP samples were independent of UP samples as determined by PCA analysis. A total of 1419 DEGs were screened, with 604 up-regulated genes and 815 down-regulated genes. 10 hub genes were identified that may play a crucial role in the pathogenesis of ACP: IL6, ITGAM, CXCL8, FN1, EGF, ITGAX, TLR8, FCGR3B, IFNG, LEP, from the PPI network of 1419 significantly DEGs with 942 nodes and 5085 edges. Neutrophil activation, neutrophil-mediated immunity, neutrophil activation involved in immune response, neutrophil degranulation, neutrophil chemotaxis, neutrophil migration, and other neutrophil-related biological processes were significantly enriched by GO analysis.

first: Xiao

last: Xiao

first: Xiaoxu

last: Chen


title: Integrating Transcriptomics, Mendelian Randomization, Machine Learning, and Experimental Validation to Identify Feature Genes in Sepsis with Thyroid Dysfunction_discovery cohort

status: Public on Aug 03 2026

city: Kunming

first: Ye

last: Li

address: Kunming University of Science and Technology

summary: Sepsis is frequently associated with thyroid dysfunction. However, the underlying molecular mechanisms and effective biomarkers for sepsis with thyroid dysfunction remain unclear.

overall_design: In this study, transcriptome sequencing was performed on blood samples collected from sepsis patients with thyroid dysfunction and those with sepsis alone. Differential expression analysis (DEG) and weighted gene co-expression network analysis (WGCNA) were employed to screen candidate genes. Mendelian randomization (MR) analysis was then applied to assess the causal relationship between candidate genes and thyroid dysfunction. Subsequently, LASSO regression and support vector machine recursive feature elimination (SVM-RFE) were utilized to further identify feature genes. Functional exploration of the identified genes involved single-sample gene set enrichment analysis (ssGSEA), immune infiltration analysis, molecular regulatory network construction, drug prediction, and phenome-wide association study (PheWAS).

first: Li

last: Ye


title: Transcriptonal  profiling of 5 dpf pdcd7/cx20 pd1215 zebrafish mutants and WT siblings

first: Daniel

last: Levic

address: 307 Research Drive

department: Cell Biology

institute: Duke University

summary: For this experiment, we sought to characterize gene expression changes and intron splicing events in 5 dpf pdcd7/cx20 pd1215 mutants relative to WT siblings.

overall_design: For RNAseq of 5 dpf pdcd7/cx20 mutants and WT siblings, total RNA from n=40 larvae (3 replicates) was extracted in Trizol, treated with DNase, and then purified using RNA Clean & Concentrator-5 columns (Zymo). Library preparation and sequencing were performed by Medgenome using Illumina Stranded mRNA prep and Illumina NovaSeq PE150 to collect > 125 M paired-end reads.

first: Michel

last: Bagnat

first: Carina

last: Block


title: Integrating Transcriptomics, Mendelian Randomization, Machine Learning, and Experimental Validation to Identify Feature Genes in Sepsis with Thyroid Dysfunction_validation cohort

institute: Kunming University of Science and Technology

overall_design: Quantitative real-time PCR (qRT-PCR) was performed to validate the expression levels of the feature genes in an independent clinical cohort, which included sepsis patients with thyroid dysfunction and those with sepsis alone. This validation aimed to confirm the differential expression patterns observed in the discovery cohort and to assess the clinical applicability of the identified genes.


title: Chronic Kidney Disease Induces Pro-Arrhythmic Remodeling

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

summary: Background: Patients with chronic kidney disease (CKD) are at increased risk of developing cardiac arrhythmogenesis and sudden cardiac death, however the basis for this association is incompletely known. Methods: Here, using murine models of CKD, we examined interactions between kidney disease progression and structural, electrophysiological, and molecular cardiac remodeling. Results: C57BL/6 mice with adenine supplemented in their diet developed progressive CKD. Electrocardiographically, CKD mice developed significant QT prolongation and episodes of bradycardia. Optical mapping of isolated-perfused hearts using voltage-sensitive dyes revealed significant prolongation of action potential duration (APD) with no change in epicardial conduction velocity. Patch-clamp studies of isolated ventricular cardiomyocytes revealed changes in sodium and potassium currents consistent with APD prolongation. Global transcriptional profiling identified dysregulated expression of cellular stress response proteins RNA-binding motif protein 3 (RBM3) and cold inducible RNA-binding protein (CIRP) that may underlay the ion channel remodeling. Unexpectedly, we found that female sex is a protective factor in the progression of CKD and its cardiac sequelae. Conclusion: Our data provide novel insights into the association between CKD and pathologic proarrhythmic cardiac remodeling. Cardiac cellular stress response pathways represent potential targets for pharmacologic intervention for CKD-induced heart rhythm disorders.

overall_design: RNAseq of ventricles isolated from control (n=8) and CKD (n=8) mice exposed to the high-dose regimen.

first: Benjamin

last: King

first: Shana

last: Mintz

first: Xianming

last: Lin

first: Gregory

last: Morley

first: Alireza

last: Khodadadi-Jamayran

first: Glenn

middle: I

last: Fishman


title: Pleckstrin-2 Promotes Cutaneous Squamous Cell Carcinoma by Recruiting Profilin-1 to the Membrane to Destabilize Cytosolic PTEN

city: Xi'an

first: Guanfei

last: Zhang

address: No.28, Xianning west road

institute: Xi'an Jiaotong University

summary: Cutaneous squamous cell carcinoma (cSCC) is a prevalent skin malignancy driven by ultraviolet-induced genomic damage, and advanced disease remains clinically challenging due to limited therapeutic options. Through integrative transcriptomic and functional analyses, we identify Pleckstrin-2 (PLEK2) as a previously unrecognized oncogenic driver in cSCC. PLEK2 is markedly upregulated in patient tumors, cSCC cell lines, and UV-induced mouse models. Genetic perturbation studies demonstrate that PLEK2 promotes proliferation, migration, epithelial–mesenchymal transition, and tumorigenicity. Mechanistically, PLEK2 recruits Profilin-1 (PFN1) to the plasma membrane through its DEP domain, thereby reducing cytosolic PFN1 pool required for PTEN stabilization. This PFN1 sequestration accelerates PTEN polyubiquitination and degradation, thereby sustaining AKT pathway activation. Upstream, we identify ETS2 as a direct transcriptional activator of PLEK2, establishing an ETS2–PLEK2–PFN1–PTEN axis that drives cSCC progression. These findings delineate a signaling pathway regulating PTEN stability and AKT activation, and provide mechanistic insight into cSCC progression.

overall_design: Sequencing libraries were constructed and sequenced from cSCC cell lines SCL-1 and HSC-1 stably transfected with either shNC or shPLEK2.

first: Meng

last: Liu

first: Lanlan

last: Cui

first: Zongguan

last: Huang

first: Mo

first: Fengyun

last: Sun

first: Zhenzhen

last: Lu

first: Changwei

last: Hu

first: Xiaofei

last: Zhao

first: Yiming

first: Ying

first: Shujun

last: Han

first: Yan

last: Zheng

first: Yongping

last: Shao


title: Novel 3D Approach to Model Non-Alcoholic Fatty Liver Disease using human Pluripotent Stem Cells

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: We aimed to develop an in vitro system that would recapitulate the key features of Non-Alcoholic Fatty Liver Disease (NAFLD). We took advantage of human pluripotent stem cells to establish complex co-cultures including all the cell types known to be involved in disease progression. Cultures were challenged with free fatty acid, to mimic NAFLD, and transcriptomic analyses were used to confirm the presence of a NAFLD signature.

overall_design: We used a total of 5 samples, as follows: 1 control sample (CTRL) and 4 treated samples, each consisting of a different treatment with free fatty acids.

first: Carola

last: Morell

first: Arash

last: Shahsavari

first: Ludovic

last: Vallier


title: Transcriptomic responses of Acinetobacter baumannii ATCC19606 efflux pump mutants under chloramphenicol stress

city: Hamburg

first: Jiabin

address: Martinistr. 52

institute: University Medical Center Hamburg-Eppendorf

summary: Efflux pumps play a key role in antibiotic resistance in Acinetobacter baumannii. Here, we investigated the transcriptomic responses of A. baumannii ATCC19606 mutants lacking the efflux pumps AdeAB, AdeIJ, or CraA under chloramphenicol stress. RNA-seq was performed on wild-type and knockout strains grown in LB medium with or without sub-MIC chloramphenicol. The data reveal strain-specific metabolic remodeling and highlight CraA as a major determinant of chloramphenicol resistance.

overall_design: RNA-seq profiling of wild-type Acinetobacter baumannii ATCC19606 and its isogenic efflux pump knockout mutants (ΔadeAB, ΔadeIJ, and ΔcraA). Samples were cultured in LB medium under two conditions: untreated (control) and treated with sub-inhibitory concentration of chloramphenicol. Biological replicates (2 to 3 per condition) were sequenced using Illumina NovaSeq 6000 (paired-end, 150 bp).

first: Wuen Ee

last: Foong

first: Xinxin

last: Xiang

first: Wenjun

last: He

first: Xuan

last: Yan

first: Klaas M.

last: Pos

first: Heng-Keat

last: Tam


title: 3D Human iPSC-Derived Cardiac Organoids for Antifibrotic Drug Screening

city: palo alto

first: Joseph

last: wu

address: 265 Campus Drive

institute: Stanford university

summary: This experiment is to test the antifibrotic effects of PT30 in cardiac organoids. The cardiac organoids are generated by mixing iPSC-CMs nad iPSC-CFs.

overall_design: iPSC-COs are stimulated by profibrotic cocktail (TGFB+ET1) and treated with PT30

first: Hao

last: Zhang

first: Rihua

last: Huang

last: Wu


title: Androgen receptor determines skeletal muscle sexual dimorphism [RNA-seq]

city: Toon

first: Hiroshi

last: Sakai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

summary: The molecular and functional bases of sexual dimorphism in skeletal muscle remain poorly understood. The androgen receptor (AR) is a major regulator of sex-biased gene expression in muscle, but its genomic targets and associated coregulators in vivo are incompletely defined. Using ChIL-seq and an AirID-AR knock-in mouse, we mapped AR-bound genes and AR-associated proteins in skeletal muscle and identified histone deacetylase–linked corepressors. We further identified myosin binding protein H (Mybph) as a female-biased AR-repressed gene conserved in mouse and human muscle. Mybph loss disrupted sarcomeric organization and selectively delayed postinjury force recovery in female mice. These findings define an in vivo AR regulatory network and identify AR-dependent Mybph repression as a potential mechanism contributing to skeletal muscle sexual dimorphism.

overall_design: RNA-seq profiling of tibialis anterior (TA) muscles from control, orchiectomized (ORX), and DHT-treated orchiectomized male C57BL/6J mice 4 weeks after treatment.

first: Yuuki

last: Imai


title: GAS6 drives chemoresistance and immune escape in ovarian cancer

city: Shanghai

first: Yaodi

last: Shao

address: 2699 West Gaoke Road

institute: Shanghai First Maternity and Infant Hospital

summary: High-grade serous ovarian cancer (HGSOC) has poor prognosis owing to widespread platinum resistance and unsatisfactory efficacy of chemo-immunotherapy, so novel mechanisms of therapeutic failure are urgently required. The GAS6/AXL axis supports tumor survival and immunosuppression, yet how chemotherapy modulates GAS6 expression remains unclear. We demonstrate that chemotherapy elevates GAS6, which activates AXL to trigger NF-κB-mediated transcription of GDF-15. This GAS6-AXL-GDF-15 cascade drives intrinsic platinum resistance and tumor immune evasion. Blocking GDF-15 reverses chemoresistance; combined with anti-PD-1 antibody, it produces synergistic anti-tumor effects. Circulating GAS6 protein reflects activation of this signaling cascade and acts as a non-invasive predictive biomarker for combined GDF-15/PD-1 blockade. Collectively, we identify a chemotherapy-activated GAS6/AXL-NF-κB-GDF-15 pathway that mediates both chemoresistance and immune escape in HGSOC, supporting translational application of GDF-15 inhibitors plus immune checkpoint inhibitors for biomarker-stratified patients.

overall_design: RNA-seq analysis in GAS6-overexpressing ovarian cancer cells


title: RNA sequencing analysis of THP-1 cells treated with chlorquinaldol

city: Wuhan

first: Xiang

last: Zhou

state: Hubei

address: Room 100302, Building 10, Wuhan University of Science & Technology (Huangjiahu District), No.2 West Huangjiahu Road, Hongshan District

department: College of Life Science & Health

summary: Based on our findings that chlorquinaldol can exert a potent antiviral effect both in vivo and in vitro, to explore the molecular mechanisms underlying chlorquinaldol-induced gene expression, we performed RNA sequencing analysis on THP-1 cells treated with either a low-concentration or a high-concentration of chlorquinaldol, using treatment of the STING agonist 3'3'-cGAMP as an antiviral control.

overall_design: THP-1 cells were treated with 0, 20 μM, 50 μM of chlorquinaldol for 8 hours, or treated with 1 μg/mL of 3’-3’-cGAMP for 8 hours as a positive control for innate antiviral signaling. RNA sequencing analysis was performed.

first: Runfa

last: Chen

first: Miaomiao

last: Cai

first: Yuting

last: Dai

first: Boyuan

last: Shen

first: Yinghong

first: Wen

first: Zhijie

last: Cui

first: Jing

last: Yang

first: Zhengfan

last: Jiang


title: Interleukin-33 activated group 2 innate lymphoid cells drive type 2 immune dysfunction in endometriosis

city: Kingston

first: Katherine

middle: B

last: Zutautas

state: Ontario

address: 18 Stuart St. Rm 853

department: Biomedical and Molecular Sciences

country: Canada

institute: Queen's University

summary: Immune dysfunction is a key contributor to endometriosis (EM) pathophysiology, with a type 2-skewed immune response thought to support EM lesion maintenance and establishment. The alarmin interleukin-33 (IL-33) is elevated in EM patient plasma, peritoneal fluid (PF), and lesions compared to controls, and in an EM mouse model IL-33 drives lesion progression, although exact mechanisms remain unclear. Here we validate that IL-33/ST2 signaling contributes to EM pathophysiology, identifying IL-33/ST2 axis dysregulation in EM lesions compared to control endometrial tissue and characterize PF group 2 innate lymphoid cells (ILC2s) with upregulation of ST2+ in severe stage patients. Using ILC2-deficient mice, we demonstrate that ILC2s are critical for the IL-33-driven inflammatory response in EM. IL-33 treatment in EM-induced ILC2-deficient mice resulted in reduced type 2 effector cytokine production and dysregulated immune infiltration, as well as an altered lesion transcriptional signature compared to ILC2-sufficient controls. Notably, reintroducing ILC2s was insufficient to rescue the IL-33-mediated response; however, we identified ILC2 homing to EM lesions.  Finally, we identify ST2 neutralization as a promising therapeutic technique to blunt the IL-33/ILC2 type 2 response in EM.

overall_design: RNAseq profiling of endometriosis lesions from IL-33 treated ILC2-competent (C57Bl/6J, Nmur1iCre-eGFP, and Id2fl/fl) and ILC2-deficient (Nmur1iCre-eGFPId2fl/fl) mice.

first: Danielle

last: Sisnett

first: Dan

last: Vo

first: Alexandra

last: Wodz

first: Katja

last: Jarick

first: Christoph

last: Klose

first: Olga

last: Bougie

first: Bruce

last: Lessey

first: Chandrakant

last: Tayade