title: Multi-Omic Atlas reveals cytotoxic phenotype and ROS-linked metabolic quiescence as key features of CTL-resistant HIV-infected CD4+ T-cells

first: Alberto

last: Herrera

state: New York

department: Medicine

institute: Weill Cornell Medicine

summary: HIV, although manageable as a chronic condition, currently lacks a safe or scalable cure. Antiretroviral therapy (ART) effectively suppresses HIV replication, preventing disease progression and transmission to sexual partners. However, ART does not affect established 'reservoirs', which are rare cell populations harboring integrated, intact proviruses that can reignite viral replication if ART is discontinued. Cytotoxic T-lymphocytes (CTL) exert sustained pressure on reservoirs of HIV-infected cells that persist through years of antiretroviral therapy (ART). This selects for latently-infected cells, but also potentially for cells that express HIV but possess intrinsic CTL resistance. In this study we confirm the existence of HIV-infected CD4+ T-cells that survive rigorous CTL attack and map CTL susceptibility to cell identities and states defined by single-cell multi-omics (using 10X based ECCITE-seq) and functional metabolic profiling. Our results provide an atlas for elucidating features of CTL resistance in HIV reservoirs, and identify oxidative stress as a therapeutic target to facilitate reservoir elimination.

overall_design: ECCITE-seq gene expression and antibody derived tag profiles (from 4 donors), and TCR clonotype profiles (from 1 donor) were constructed from 'surviving' and 'bystander' HIV-infected CD4+ T-cells using a wild-type clinical HIV stain and the same strain but with a single CTL epitope escape mutation respectively after co-culture together with a HLA-matched CTL clone targeting the escaped epitope in the second virus.

first: Richard

middle: B

last: Jones

first: Paul

last: Zumbo


title: Clec16a maintains the Definitive Hematopoietic Stem and Progenitor Cells via Mitophagy in Zebrafish

status: Public on Jan 06 2026

city: 杭州

first: shuyang

last: cai

state: 浙江省

address: 西湖区余杭塘路866号浙江大学医学院科研楼A615

country: China

institute: zhejiang university

type: Expression profiling by high throughput sequencing

summary: Since clec16a signaling is imperative for HSPCs production in zebrafish, to further determine the regulatory mechanism by which clec16a signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the clec16a morphants groups.

overall_design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which clec16a signaling regulates the HSPCs in vertebrate.


title: Sympathetic innervation regulates metabolic plasticity of skeletal muscle

city: Atlanta

first: Patricia

middle: J

last: Ward

state: Georgia

address: 201 Dowman Drive

country: USA

institute: Emory University

summary: The sympathetic nervous system (SNS), long recognized for its role in physiological regulation of organs, such as heart, vasculature and lungs, has emerged as a key player in skeletal muscle metabolic and neuromuscular junction (NMJ) health. However, the mechanism through which SNS signaling influences skeletal muscle function and adaptation to exercise remains unclear. Using molecular, electrophysiological, immunohistochemical, and high-resolution respirometry techniques, we tested the role of sympathetic innervation to skeletal muscle in response to exercise. Our findings reveal that sympathetic denervation disrupts the NMJ, reducing motor and sympathetic receptor expression, with concomitant deficits in skeletal muscle function. Mechanistically, these deficits are linked to diminished CPT1 enzyme activity, which impairs long-chain fatty acid-mediated oxidation in skeletal muscle mitochondria. These findings reveal a key role for sympathetic innervation in maintaining mitochondrial metabolic function and by extension, skeletal muscle performance, offering novel insight into the interplay between the SNS, exercise, and muscle mitochondria.

overall_design: RNA-seq profiling of EDL from adult mice with the following treatments: unexercised, exercised, sympathectomixed + unexercised, sympathectomized + exercised.

first: Jordan

last: Owyoung

first: HaoMin

last: Sima

first: Junwon

last: Heo

first: Tess

last: Klugherz

first: Tina

last: Tian

first: Garrett

middle: W

last: Cooper

first: Andrew

middle: L

last: Hong

first: Jarrod

last: Call


title: Porcine induced pluripotent stem cells generated in LACID medium

city: Hangzhou

first: Chengchen

last: Zhao

state: Zhejiang

address: Dunyu Road No.600, Xihu District

institute: Westlake University

summary: Pigs are becoming increasingly important for disease model generating, xenotransplantation and interspecies organogenesis due to their similarity to human in anatomy and physiological structure. Porcine induced pluripotent stem cells (piPSCs) induced from porcine somatic cells are believed to support porcine application. But the establishment of piPSCs capable of feeder-free culture, robust development potential, and blastocysts generation through SCNT has yet to be achieved. Further investigation is needed to explore porcine pluripotency. And the reprogramming medium for piPSCs is few optimized. We found that the induced iPS chemically defined medium 3 (iCD3) promoted the formation of epithelium-like colonies in porcine reprogramming. Then Culturing medium containing LIF, activin A, GSK3 inhibitor, IWR-1, (S)-(+)-dimethindene maleate (LACID) was utilized to achieve stable piPSCs. The LACID piPSCs were identified to exist strong pluripotent characteristics. (1) LACID piPSCs had fundamental pluripotent characters, displaying flat morphology, expressing pluripotent transcription factors and surface marker. Stable Feeder-free culture for LACID piPSCs were carried out by laminin 511 coating and the addition with LDN-193189. (2) These cells exhibited a strong ability to differentiate and form teratoma in NOD-SCID mice, containing three germ layers. Additionally, cardiomyocytes, PEFs, and blastoids were achieved successfully by differentiation. (3) These piPSCs had a good ability to proliferate and their genome could be edited using CIRSPR/Cas9 for knock-in and knockout.  Blastocysts from piPSCs were also achieved by SCNT, which indicated the application value of piPSCs for transgenic pig generation. (4) LACID piPSCs could form chimeric blastocysts and contribute to intraembryonic parts of chimeric blastocysts. (5) Compare with other reported porcine stem cells, LACID piPSCs had advantage in the expression of pluripotent gene and signaling pathways regulating pluripotency of stem cells. In summary, LACID piPSCs exhibited favorable pluripotency features, which renders them ideal for investigating porcine medical applications and achieving naïve or more advanced porcine stem cells.

overall_design: Porcine induced pluripotent stem cells (piPSCs) were induced from porcine embryonic fibroblasts. Three piPSC lines were established from single colonies and maintained in LACID medium. The pluripotency of these piPSCs was thoroughly evaluated. Then three cardiomyocyte lines were differentiated from these piPSCs. For feeder free culturation, LACID piPSCs were seeded on the plate coated with laminin 511 and passaged more than three times to achieve stable piPSCs (Laminin). To optimize the culture medium for feeder-free culture, 100 nM LDN-193189 was added to the LACID medium to culture piPSCs on laminin 511. These piPSCs were passaged more than three times to obtain more compact piPSCs (Laminin-LDN). For the defined culture conditions, the basal medium was prepared by mixing DMEM-F12 and Neural basal medium in a 1:1 ratio, supplemented with 1% N2 and 1% B27. This medium was tested for LACID piPSCs culture. After more than three passages, the piPSCs in N2B27-LACID showed more dome-shaped and compact colony morphology.

first: Bingbo

last: Shi

first: Dong

last: Liu

first: Duanqing

last: Pei


title: Mechanistic basis of gene regulation by SRCAP and H2A.Z (Mnase-Seq)

city: Lausanne

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

country: Switzerland

institute: École polytechnique fédérale de Lausanne

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A central problem in gene regulation is to discriminate gene regulatory functions of chromatin composition from the one of chromatin-modifying complexes. This question has been virtually unexplored in the context of the H2A.Z histone variant and its incorporation into nucleosomes by the Snf2 Related CREBBP Activator Protein (SRCAP) complex. Here we combine rapid SRCAP depletion, a SRCAP mutant lacking H2A.Z deposition activity, and quantitative genome-wide approaches to dissect how SRCAP and H2A.Z regulate transcription in pluripotent stem cells. We find that SRCAP exhibits essential H2A.Z-independent functions in preventing DNA binding of lineage-specific transcription factors at enhancers and stimulating transcription factor binding at promoters. In contrast, H2A.Z acts mainly as a transcriptional repressor that requires dynamic reloading by SRCAP throughout the cell cycle. Our study clarifies how the SRCAP-H2A.Z axis broadly orchestrates transcription to promote self-renewal, inhibit differentiation, and maintain plasticity of pluripotent stem cells.

overall_design: MNase-Seq in triplicates in mESC in control condition or depleted for 4h for SRCAP, Mnase digestion was performed with 2 different concentrations : High (100 U/mL) or Low (6.25 U/mL)

first: Armelle

last: Tollenaere

first: Enes

last: Ugur

first: Cedric

last: Deluz

first: Heinrich

last: Leonhardt

middle: M


title: Evaluation of the efficacy of arctiin in promotes inactivated infectious hematopoietic necrosis virus vaccine from immune and metabolic perspectives

city: Lan zhou

first: Pan

middle: Yu

last: Cai

state: Gansu

address: Yin Tan Road Street, An Ning District

department: College of Animal Science and Technology

institute: Gansu Agricultural University

summary: In this study, we prepared an inactivated IHNV vaccine with ARC as adjuvant and attempted to elucidate its immunoprotective mechanism against rainbow trout liver . This study contributes to a better understanding of the immune mechanisms of adjuvanted and inactivated vaccine combinations and lays the foundation for the development of the next generation of IHNV vaccines

overall_design: For the formal experiment, rainbow trout in control group were intraperitoneally injected with PBS, and two experimental groups were intraperitoneally injected with 150 μL inactivated IHNV vaccine (vaccine group) and 150 μL APS combined inactivated IHNV vaccine (APS+vaccine group), respectively. Each experimental group had 200 fish, 100 of which were used for mortality measurements and the remaining 100 for sampling. At 14 days (D 14) after vaccination, 200 fish per group were injected intraperitoneally with 50 µl IHNV (107 TCID50 ml-1) and monitored for mortality for two weeks. The relative percentage of survival (RPS) was calculated using the formula (Sukkarun et al., 2024): 1-(vaccinated group mortality/control group mortality) × 100%. For sampling, the anesthetics and its doses were the same as in the vaccine safety tests. Liver and blood were collected from four fish from each group at D1, D3, D7, D14, D15, D21, D30, D60 and D90 to assay for immune-related gene expression and non-specific enzyme activities. Liver samples from D21 were also used for transcriptomic and metabolomic analyses. In addition, the spleens of three fish for each group were collected at D7, D14, D15, D21, D30, D60 and D90 for histopathological examination.

first: Zhe

first: Yucai

last: Pan

first: Jinqiang

last: Quan

first: Juhao

last: Lu

first: Guiyan


title: Mechanistic basis of gene regulation by SRCAP and H2A.Z (CUT&Tag)

overall_design: Chromatin immunoprecipitation on H2A.Z, histone PTM and several TF in mESC depleted or not for SRCAP


title: Lysosomal sequestration of PARP inhibitors drives heterogeneous accumulation in ovarian cancer to increase efficacy

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

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

overall_design: Refer to individual Series


title: KMT2A is a prerequisite of malignant transformation during IDH-mutant gliomagenesis [RNA-Seq]

city: Heidelberg

first: Marilin

last: Koch

address: Im Neuenheimer Feld 420

country: Germany

institute: University Hospital Heidelberg

summary: Rationale: IDH1R132H is the defining mutation of low-grade gliomas (LGGs), inflicting broad epigenetic rewiring that leads to malignant transformation. Recent studies demonstrated that cell fate change from astrocyte to LGG is accompanied by redistribution of H3K4 methylation. By modulating H3K4-methyltransferase KMT2A in a conditionally IDH1R132H-expressing human astrocyte model system, we sought to define requirements of IDH1R132H dependent gliomagenesis and identify novel therapeutic targets. Methods: Using KMT2A inhibitor MM-102, we targeted H3K4me3 in IDH1R132H -expressing astrocytes. Flow cytometry for LGG-associated marker L1CAM served as primary read-out. Transcriptional and translational changes were determined with RNA-Seq and Mass spectrometry. Phenotypic profiling included spherogenic, clonogenic, invasion and migration assays; key findings were assessed in patient-derived IDH1R132H glioma lines and validated with an shRNA-mediated knockdown. Epigenetic transformation was characterized with CUT&Tag and the MethylationEPIC array. Downstream targets were assessed utilizing siRNAs. Results:  KMT2A inhibition significantly decreased L1CAM expression and led to broad transcriptional downregulation, including LGG marker genes. Analyses of intersected transcriptomics and proteomics pointed to altered lipid metabolism and migratory capacity. Phenotypic characterization showed impaired invasion, migration, clonal proliferation and sphere formation. Epigenetically, we observed significantly reduced deposition of H3K4me3 at promoters of DEGs and enhanced global DNA methylation. PDGFRA and SCD were identified as KMT2A-dependent downstream targets. Conclusion: Disruption of H3K4me3 methylation by KMT2A inhibition is associated with extensive epigenetic reshaping, resulting in reduced expression of LGG-relevant programs, manifesting phenotypically in decreased tumorigenic potential. Our results suggest that H3K4me3 methylation by KMT2A is essential for low-grade gliomagenesis and maintenance, highlighting KMT2A as a potential therapeutic target.

overall_design: RNA-seq profiling of immortalized IDH1R132H human astrocytes treated with MM-102 resp. mock


title: Mechanistic basis of gene regulation by SRCAP and H2A.Z (RNA-Seq)

overall_design: nuclearRNASeq in duplicates in mESC depleted for 2, 4, 6 or 8h for SRCAP or for 1h and sorted for earlyG1 or lateG1 phase or for mESC expressing wtSRCAP or cdSRCAP


title: Modulating AP-1 enables CAR-T cells to establish an intratumoral stem-like reservoir and overcomes resistance to PD-1 blockade

city: Seattle

first: Shivani

last: Srivastava

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: CAR-T therapy has shown limited synergy with PD-1/PD-L1 blockade, but the mechanisms underlying resistance remain unclear. PD-1⁺TCF1⁺ stem-like T cells mediate responses to PD-1/PD-L1 blockade and are maintained by MHC-dependent interactions with DCs in tumor-draining lymph nodes (dLN). Because CAR-Ts recognize intact antigen, not peptide-MHC, their activation is confined to tumors, potentially preventing maintenance of this critical subset. In ROR1⁺ lung cancer models, ROR1-targeting CAR-Ts rapidly down-regulated TCF1, became exhausted, and were not enhanced by PD-L1 blockade. Overexpression of the AP-1 transcription factor c-Jun, but not BATF, enabled formation of PD-1⁺TCF1⁺ reservoirs in tumors, not dLN, but did not prevent exhaustion, as PD-1 induced post-transcriptional c-Jun down-regulation. Remarkably, PD-L1 blockade restored c-Jun levels, dramatically increased CAR-Ts, and enabled near-complete ROR1+ tumor clearance. These findings identify PD-1 as a suppressor of c-Jun and reveal that MHC-independent CAR-Ts can be engineered to establish intratumoral stem-like reservoirs that overcome resistance to PD-1 blockade.

overall_design: Single cell RNAseq profiling of lung tumors isolated from KP-ROR1 mice: 1) left untreated; 2) treated with cyclophosphamide (Cy) and ROR1 CAR-T cells (SS78); or 3) treated with Cy and cJun.ROR1 CAR-T cells (SS95). Tumors were isolated 9 or 30 days post-treatment, with N=3 mice per group. For analysis of T cells, CD8+ cells were enriched from lung tumor cell suspensions. For TME analysis, total live cells were sorted from lung tumor cell suspensions. ROR1 CAR-T and cJun.ROR1 CAR-T cell infusion products (IP) were also sequenced.

first: Andrew

last: Snyder


title: Mechanistic basis of gene regulation by SRCAP and H2A.Z (EM-Seq)

type: Methylation profiling by high throughput sequencing

overall_design: Enzymatic-Methyl Sequencing in two replicates in mESC depleted for 4h for SRCAP


title: Mechanistic basis of gene regulation by SRCAP and H2A.Z (ATAC-Seq)

overall_design: ATAC-Seq in mESC depleted for 2, 4, 6 or 8h t for SRCAP or for 1h and sorted for earlyG1 or lateG1 phase


title: Mechanistic basis of gene regulation by SRCAP and H2A.Z (ChIP-Seq)


title: Transcriptional response to OSM in small airway epithelial cells [NGS5340]

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

summary: Investigation of OSM-induced transcriptional responses in primary human small airway epithelial cells.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data of 4 different donors treated either with PBS or OSM for 24 hours.

first: Rojo

middle: A

last: Ratsimandresy

first: Salil

last: Uttarwar

first: Mark

middle: S

last: Wilson


title: Assessment of OSMR dependency in pulmonary microvascular endothelial cells [NGS4630]

summary: To investigate OSMR dependency in pulmonary microvascular endothelial cells, cells were preincubated with anti-OSM, or (one of 2) anti-OSMR, or anti-OSM+anti-OSMR antibodies, then stimulated with OSM or PBS for 24 hours.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data of 4 different donors each treated 6 different ways: PBS; OSM+isotype control; OSM+anti-OSMR-1; OSM+anti-OSMR-2; OSM+anti-OSM; OSM+anti-OSMR-1+anti-OSM (combo antibodies).


title: scRNA-seq assessment of the impact of anti-IL6R and anti-OSM in a model of fibrotic lung disease during fibrosis (day 14) [NGS4272]

summary: To determine at the single-cell level the transcriptional impact in the immune, stromal, endothelial and epithelial cell populations in the lung of IL-6 and/or OSM signaling in the bleomycin-induced model of lung injury and fibrosis (day 14).

overall_design: Comparative gene expression profiling analysis of single-cell RNA-seq data from 5 mouse treatment groups (naive; bleomycin+isotype control; bleomycin+anti-IL6R; bleomycin+anti-OSM; bleomycin+anti-IL6R+anti-OSM) 14 days after intra-tracheal administration of saline or bleomycin.

first: Spyros

last: Darmanis

first: Hans

middle: D

last: Brightbill


title: Mechanisms of gene regulation by SRCAP and H2A.Z

first: David

last: Suter

first: Armelle

last: Tollenaere

first: Enes

last: Ugur

first: Susanna

last: Dalla-Longa

first: Cédric

first: Devin

last: Assenheimer

first: J Christof

last: Gebhardt

first: Heinrich


title: Investigation of CD64+ macrophages in bleomycin treated lungs [NGS2117]

summary: Investigation of the comparative transcriptional signatures of CD64+ vs alveolar macrophages at different phases (day 5 and day 14) in the bleomycin-induced model of lung fibrosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from CD64+ or alveolar macrophages in mouse lungs at day 5 and day 14 after receiving saline or bleomycin via intra-tracheal route.

first: Emma

last: Doran

last: Hackney


title: Assessment of OSMR dependency in normal human lung fibroblasts [NGS4564]

summary: To investigate OSMR dependency in normal human lung fibroblasts, cells were preincubated with anti-OSM, or (one of 2) anti-OSMR, or anti-OSM+anti-OSMR antibodies, then stimulated with OSM or PBS for 24 hours.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data of 5 different donors each treated 6 different ways: PBS; OSM+isotype control; OSM+anti-OSMR-1; OSM+anti-OSMR-2; OSM+anti-OSM; OSM+anti-OSMR-1+anti-OSM (combo antibodies).


title: Determining the impact of anti-IL6 and anti-OSM on macrophage and fibroblast biology in a model of fibrotic lung disease [NGS3341]

summary: To determine the comparative effect of anti-IL6 and anti-OSM treatment in lung fibrosis, mice received saline or bleomycin via instillation and then received antibodies via intraperitoneal injection once weekly until take down. At day 14, mice were euthanized, lungs were isolated and lysed in RLT buffer. Total RNA was extracted and sequenced by bulk RNA-sequencing.

overall_design: Comparative gene expression analysis of RNA-seq data from 5 experimental groups. Mice received either saline or bleomycin via intra-tracheal route. Bleomycin-treated mice received either isotype antibodies, or anti-IL6, or anti-OSM, or anti-IL6+anti-OSM antibodies.


title: scRNA-seq assessment of the impact of anti-IL6R and anti-OSM in a model of fibrotic lung disease during resolution (day 24) [NGS4659]

summary: To determine at the single-cell level the transcriptional impact in the immune, stromal, endothelial and epithelial cell populations in the lung of IL-6 and/or OSM signaling in the bleomycin-induced model of lung injury and fibrosis (day 24).

overall_design: Comparative gene expression profiling analysis of single-cell RNA-seq data from 5 mouse treatment groups (naive; bleomycin+isotype control; bleomycin+anti-IL6R; bleomycin+anti-OSM; bleomycin+anti-IL6R+anti-OSM) 24 days after intra-tracheal administration of saline or bleomycin.


title: Akr1b7 functions as a master regulator in ovarian aging

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

country: Japan

institute: Yamaguchi university


title: Akr1b7 functions as a master regulator in ovarian aging [RNA-seq]

summary: At the beginning of ovarian aging, the ovulation of immature oocytes is accelerated, finally leading to the arrest of ovulation despite the remaining oocytes. Here RNA expression in ovarian aging of mice is comprehensively analyzed during the estrous cycle after ovulation stimulation, and an aldo-keto reductase Akr1b7 pathway transiently increased in the young ovary is eliminated in the aged mice. Akr1b7-/- mice enhance the ovulation of immature oocytes, and the KITL expression in Akr1b7-expressed stromal is attenuated, accompanied by oocyte Akt essential for the follicular development inactivation in primordial follicles. The estrous cycle is extended due to the prolonged diestrous stage by a sustained progesterone level in Akr1b7-/- mice ovaries, which is caused by the decline of Cyp17a1, a major metabolite enzyme of progesterone in Akr1b7-expressed theca cell layers. Taken together, the decreased Akr1b7 pathway causes the ovulation of immature oocytes and the prolonged estrous cycle, typical symptoms of ovarian aging.

overall_design: Examination of comprehensive RNA analysis by RNA-seq  in WT and Akr1b7-/- (KO) ovaries at 24h after hCG administration.

first: Keishiro

last: Isayama

first: Kenji

last: Watanabe

first: Masato

last: Ohtsuka

first: Seisuke

last: Kimura

first: Tomoaki

last: Murata

first: Takeshi

last: Honda

first: Masataka

last: Asagiri

first: Shun

last: Sato

first: Hiroshi

last: Tamura

first: Norihiro

last: Sugino


title: A patient-derived ccRCC model that retains native stromal features to assess fibrosis-driven personalized therapeutic response

status: Public on Jan 05 2026

city: Sherbrooke

first: Alexis

last: Perreault

state: Quebec

address: 3001 12e avenue Nord

country: Canada

institute: Université de Sherbrooke

summary: Clear cell renal cell carcinoma (ccRCC) is characterized by a complex tumor microenvironment, in which stromal components such as collagen and cancer- associated fibroblasts (CAF) play a pivotal role in therapeutic resistance. To investigate the contribution of fibrosis to interpatient variability in treatment response, we developed a patient-derived xenograft (PDX) model using the chick chorioallantoic membrane (CAM) assay. This model preserves key stromal features of the original tumors, including collagen types I, III and VII, fibronectin, lysyl oxidases (LOX), and CAF markers such as fibroblast activation protein (FAP) and α-smooth muscle actin (α-SMA). Transcriptomic analyses confirm the conservation of gene expression profiles related to stromal architecture, extracellular matrix composition, and cellular metabolism within the xenografts. In vivo assays across multiple PDXs reveal heterogeneous responses to antifibrotic agents, which correlate with the collagen content of the original tumors. Notably, antifibrotic pretreatment enhances therapeutic efficacy in xenografts derived from tumors with collagen levels ranging from 5 to 25%. This model provides a physiologically relevant platform to assess fibrosis- driven therapeutic responses in ccRCC and supports the integration of stromal profiling into personalized treatment strategies.

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: RNA-seq profiling of original human ccRCC tumors and associated patient-derived xenografts cultivated on the chorioallantoic membrane of chick embryos for 7 days.

first: Kelly

last: Harper

first: Martine

last: Charbonneau

first: Karine

last: Brochu-Gaudreau

first: Robert

last: Sabbagh

first: Patrick

middle: O

last: Richard

first: Nadia

last: Ekindi-Ndongo

first: Claurio

last: Jeldres

first: Claire

last: Dubois


title: Akr1b7 functions as a master regulator in ovarian aging [superSAGE]

first: Yoichi

last: Mizukami

overall_design: Examination of comprehensive RNA analysis by superSAGE  in YNG and OLD ovaries at 24h–96h after hCG administration.

first: Keishiro

last: Isayama

first: Kenji

last: Watanabe

first: Masato

last: Ohtsuka


title: Dynamics of Stage-specific Immune Remodeling by Neutrophils and Macrophages in Acute Lung Injury

city: chengdu

first: zeng

last: wanqin

state: chengdu

address: No17 renming

institute: Sichuan University

summary: Acute lung injury (ALI) is driven by dysregulated alveolar immune responses. While granulocytes and macrophages are critical effectors, their coordinated molecular reprogramming remains poorly defined. However, the evolving crosstalk and stage-specific functional transitions of these populations have been overlooked. Here, we performed single-cell RNA sequencing (scRNA-seq) of bronchoalveolar lavage fluid from intermediate and late-stage ALI patients to map immune microenvironment remodeling. We observed pronounced granulocyte expansion coupled with macrophage depletion. Granulocytes exhibit distinct trajectories from acute migratory states toward pro-inflammatory, metabolically reprogrammed subsets, dominated by TNF and MAPK signaling. Simultaneously, macrophages transition toward inflammatory M1-like phenotypes, characterized by distinct metabolic reprogramming and reduced oxidative phosphorylation. Furthermore, we identify a granulocyte-centric inflammatory network mediated through TNF, IFN, and RESISTIN pathways, establishing pathogenic feedback loops. Collectively, this study elucidates the transcriptional and metabolic reprogramming driving ALI progression, providing a framework for stage-adapted therapeutic interventions to restore pulmonary homeostasis.

overall_design: We conducted  single-cell RNA sequencing (scRNA-seq) of bronchoalveolar lavage fluid from intermediate and late-stage ALI patients


title: Spatial transcriptomics of maize embryonic leaves

city: Taipei

first: Chi-Chih

last: Wu

address: 128 Academia Road, Section 2, Nankang

department: Biodiversity Research Center

country: Taiwan

institute: Academia Sinica

summary: To explore spatial genetic profiling with histological and cellular features, we conducted 10x Visium transcriptomic system from 8 maize seedling shoots, comprising SAM and serial 5 developing embryonic leaves.

overall_design: Maize seedlings were fresh frozen and sectioned at 12 um thickness onto spatial transcriptomics (ST) gene expression (GE) slides for in situ mRNA capture, library preparation, and sequencing.


title: An integrated drug repositioning analysis identifies rosiglitazone as a repurposing candidate for sarcopenia

city: changsha

first: L

last: S

address: tongzipo roda  NO 172

department: csu

institute: csu

summary: Sarcopenia is characterized by age-related muscle/strength loss and is becoming a highly important public health issue. The development of sarcopenia increases the risk of various adverse health outcomes, including falls, functional decline, frailty, and mortality. Despite its significance, there are no approved drugs to prevent or treat age-related sarcopenia. In this study, we used an integrated drug repurposing approach to repurpose approved drugs for the treatment of sarcopenia. We first used a network-based proximity score to quantify the relationship between disease-gene and drug-gene modules and identify potential repurposing candidates. Then we used summary-data-based Mendelian randomization analysis to explore the potential causal association between drug targets and sarcopenia. In an aging mouse model, we demonstrated that rosiglitazone, an insulin sensitizer used to treat diabetes, could improve endurance exercise performance, and increase grip strength, muscle fiber area, and hind limb muscle mass. Furthermore, we conducted transcriptomics, metabolomics analyses, and 16s RNA sequencing analysis in mice to explore the underlying mechanism of action for rosiglitazone. The results suggested that rosiglitazone may be a promising therapeutic option for alleviating or treating age-related sarcopenia, although additional clinical validation is still needed.

overall_design: After the age of 17 months, mice in the experimental group received a commercially purified diet (AIN-93M) that contained rosiglitazone, while control mice received a standard purified diet (AIN-93M) without rosiglitazone.

first: Hongwen

last: Deng

first: Hongmei

last: Xiao


title: FACS-Based Genome-Wide CRISPR Screening Platform Identifies Modulators of CD47

city: Houston

first: Ling

last: Yin

state: TX

address: 1515 Holcombe Boulevard

institute: MD Anderson Cancer Center

summary: CD47 is a key innate immune checkpoint that enables tumor cells to evade macrophage-mediated clearance. To systematically identify genetic regulators of CD47 surface expression, we performed FACS-based genome-wide CRISPR screens in three murine cancer cell lines, B16 (melanoma), MC38 (colon adenocarcinoma), and EMT6 (breast carcinoma). Comparative analysis of cells with high or low CD47 surface expression using DrugZ revealed CD47 itself as the top hit, validating the screens. Notably, DNAJC13 emerged as a consistent and robust regulator of CD47 expression across all three cell lines. Functional validation using DNAJC13-knockout cells confirmed a significant reduction in CD47 surface levels. Furthermore, in co-culture assays with macrophages, DNAJC13-deficient tumor cells exhibited increased susceptibility to phagocytosis, supporting a functional role for DNAJC13 in innate immune evasion. Finally, we verify that DNAJC13-knockout decrease tumor burden when treated with CD47 blockade. Overall, this study highlights a previously unrecognized regulator of CD47 and demonstrates the utility of high-throughput FACS-based CRISPR screening to uncover modulators of key immune checkpoint pathways.

overall_design: mouse whole genome FACS-based CRISPR-Cas9 knock out screenings in three mouse cancer cell lines: B16F10A,  MC38 and EMT6.

first: Wei

last: He

first: Yifan

last: Wang

first: Huimin

last: Zhang

first: Min

last: Huang

first: Yuelong

last: Yan

first: Siting

last: Li

first: Xu

last: Feng

first: Francisco

last: Saenz

first: Jie

first: Dandan

last: Zhu

first: Chang

last: Yang

first: Tiantian

last: Ma

first: Jialing

last: Fu

first: Junjie

last: Chen


title: Mating regulates growth, metabolism, and digestive efficiency in the female Drosophila midgut

city: Salt Lake City

first: Tahmineh

last: Kandelouei

state: Utah

address: 1950 Circle of Hope Dr.

institute: Huntsman Cancer Institute

summary: Adaptive changes in organ size and function occur in most animals, but how these changes are regulated is not well understood. Previous research found that mating in Drosophila females promotes intestinal stem cell proliferation and increases the overall size of the endodermal portion of the intestine (the “midgut”). Other studies reported mating-dependent changes in feeding behavior, midgut gene expression, and whole-body lipid storage, suggesting altered metabolism. Here, we show that mating dramatically alters female midgut metabolism and digestive function. Mating increased relative levels of TCA cycle intermediates, fatty acids, and ceramides in the gut, increased total midgut lipids and protein, and reduced relative carbohydrate levels. Mating also enhanced the efficiency of protein digestion relative to carbohydrate digestion. Corroborating a previous report, we found that the expression of genes tha mediate protein and carbohydrate and metabolism was similarly altered. In addition, we noted a mating-dependent downregulation of oxidative stress response and autophagy genes. Mating-dependent increases in ecdysone receptor (EcR) signaling were important for increasing TCA cycle intermediates, protein, and ceramides in the female midgut, but had minimal effects on bulk lipid accumulation. Overall, this study contributes to our understanding of the physiological changes that occur during adaptive intestinal growth, and how they are regulated.

overall_design: We first compared the gene expression in mated and unmated flies whole gut (19464X1-8) and gut progenitor cells (19966X1-8) after 48 hours mating. Then, to investigate how ecdysone signaling pathway affects mating-induced changes, we compared mated and unmated flies, each expressing or not expressing EcR-RNAi. We aged the collected virgin flies for 5 days at 29°C to express EcR-RNAi under the control of ubiquitous (Actin-Gal4) (22551X1-16) or EC-specific (Myo1A-Gal4) (24047X1-2, X4-16) drivers. After 5 days of RNAi expression, we set the mating for 48 hours (25°C) by adding males. We then dissected the guts after 48 hours of mating for sample preparation. For mating experiment; mated female flies were cultured with equal number of males, whereas unmated were isolated apart from males from eclosion.  For this experiment, we used 4 replicates per condition/ 15 guts, exept for RNAseq of FACS-sorted progenitor cells that we used 100-150 guts/sample. Mated and unmated flies were age- and genotype-matched. We then performed gene expression profiling analysis using data obtained from RNAseq of mated and unmated flies gut after 48 hours mating.

first: Bruce

last: Edgar

first: Madeline

middle: E

last: Houghton

first: Mitchell

middle: R

last: Lewis

first: Caroline

middle: C

last: Keller

first: Marco

last: Marchetti

first: Xiaoyu

last: Kang


title: Improving anti–CTLA-4 therapies through peptide masking and fragment crystallizable nonfucosylation: preclinical characterization of three novel antibodies

city: Redwood City

first: Amy

last: Jhatakia

address: 700 Bay Road

institute: Bristol Myers Squibb

summary: Background  The anti-cytotoxic T-lymphocyte antigen 4 (CTLA-4) monoclonal antibody, ipilimumab, has shown clinical benefit across multiple tumor types, both as monotherapy and in combination with nivolumab or chemotherapy. However, not all tumors respond, and peripheral effects can lead to immune-related adverse events. We characterized three novel anti–CTLA-4 antibodies: peptide-masked (PROBODY ® conditionally activatable therapeutic [PB]), nonfucosylated (NF), and combined NF- PB (BMS-986288).  Results  NF demonstrated greater T-cell priming and antitumor activity than both ipilimumab and the unmasked PB antibody in cell-based assays and mouse models. Whereas the intact PB antibody showed minimal CTLA-4 binding and peripheral immune activation, unmasking restored its functional activity to levels comparable with those of ipilimumab. Unmasked anti–CTLA-4 NF-PB retained the effectiveness of anti–CTLA-4 NF, and both molecules demonstrated more profound antitumor activity, increased effector memory T-cell response, and prolonged survival in mouse models compared with ipilimumab. Anti–CTLA-4 NF-PB demonstrated reduced peripheral immune responses than anti–CTLA-4 NF or ipilimumab in non-human primates and patients with solid tumors.  Conclusion  Anti–CTLA-4 NF-PB has enhanced antitumor activity, efficacy, and reduced peripheral activity in preclinical models, and has the potential to provide therapeutic benefit in solid tumors.

overall_design:
To capture the T-cell repertoire changes with anti–CTLA-4 treatment in the SEB hCTLA-4 mouse model, whole blood T-cell receptor (TCR) sequencing was performed using the Adaptive Mouse TCRb Immunosequencing platform (Adaptive Biotechnologies, RRID: SCR_018558). Whole blood samples were collected (at pretreatment, day 3, and day 6) in Paxgene tubes, and DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen, Cat# 69504). For data analysis, GLIPH2 was utilized to analyze the local clustering of TCR sequences and to investigate the impact of SEB-specific TCRB motifs. All the TCR sequences from pretreatment samples were used as the reference panel, and sequences from day 3 and day 6 samples were utilized as the input panel. Additionally, all singleton and doubletons (TCR sequences with a count of one and two, respectively) were removed from both the reference and input panels. TurboGLIPH, an R implementation of GLIPH2, was configured and run with the following (default) parameters: sim_depth = 100, min_seq_length = 7, cluster_min_size = 2, and motif_length = (2, 3, 4). After clustering, the resulting cluster list was filtered so that only clusters with clones originating from at least two mice and a Fisher score >0.05 were kept. After filtering the clustering, each clustered clone was first linked back to the mouse/sample from which it originated and then tracked across the remaining samples for that mouse. The number of mice that fell into each treatment group across all days was counted and then plotted for each cluster outputted from GLIPH2. Each point represents how many clones were present for that cluster on a specific day for that treatment group.

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Adaptive Biotechnologies does not release raw data.
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first: Xin

last: Sun

first: Alessandra

last: Vaccaro

first: Michael

last: Wang

first: Mohammed

last: Nasser

first: Anandaroop

last: Mukhopadhyay

first: Neha

last: Gupta

first: Kyeongah

first: Wei

last: Hu

first: Courtni

last: Newsome

first: Cheuk Hong

last: Leung

first: John

last: Le

first: Mona

last: Yazdani

first: Haiping

last: Guo

first: Lili

first: Monika

last: Pradhan

first: Heather

middle: Y

last: Lin

first: Remie

last: Mandawe

first: Felix

last: Findeisen

first: Jack

last: Lohre

first: Leslie

first: Yun

last: Wei

first: Joshua

last: Dobroff

first: Shaun

last: O'Brien

first: Ke

last: Xu

last: Hammell

first: Karen

last: Price

last: Engelhardt

first: Mark

last: Selby

first: Alan

last: Korman

first: Nicholas

last: Wilson

first: Tina

last: Cascone


title: Combined antagonism of Interleukin 6 and Oncostatin M provide both anti-inflammatory and anti-fibrotic benefit in pulmonary fibrosis

first: Jason

last: Vander Heiden

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Leptin-Activated Crosstalk Among Brain, Brown Adipose Tissue, and Heart Drives Cardiac Protection After Ischemia-Reperfusion Injury [RNA-seq]

city: Jackson

first: Bioinformatics

last: Core

state: MISSISSIPPI

address: 2500 N state street

institute: Molecular and Genomics Core Facility

summary: Cardiovascular disease remains the leading cause of death worldwide, with coronary artery disease being the primary contributor. Our recent studies suggest that activation of leptin receptors (LepRs) in the brain can improve cardiac function following myocardial infarction. However, the mechanism by which this cardioprotective effect is transmitted from the brain to the heart remains unclear. We hypothesize that brain LepR activation stimulates brown adipose tissue (BAT) to secrete extracellular vesicles (EVs) enriched with cardioprotective factors. These EVs may safeguard the heart by modulating cardiac mitochondrial function and collagen deposition.  Our findings indicate that BAT ablation or BAT sympathetic denervation diminishes the cardioprotective effects of brain LepR activation. We also observed an increased concentration of EVs within BAT of rats treated with ICV leptin compared to vehicle-treated controls, an effect abolished by BAT denervation. Furthermore, knockdown of Rab27a in BAT reduced the cardioprotective benefits of brain LepR activation. MicroRNA (miR)-29c-3p was identified as a cargo of leptin-stimulated BAT-derived EVs and appears to play a key role in mitigating cardiac fibrosis after IR injury in leptin-treated animals. Thus, activation of LepR in the brain protects the heart after IR injury via sympathetic mediated BAT-derived EVs enriched with miR-29c-3p.

overall_design: Sprague-Dawley rats with BAT intact, BAT ablation, or BAT sympathetic denervation were implanted with an intracerebroventricular (ICV) cannula for continuous leptin or vehicle delivery over 28 days after cardiac ischemia-reperfusion (IR) injury. Cardiac function was assessed weekly via echocardiography and by ventricular catheterization at the end of the protocol. EVs were isolated from BAT for analysis. Rab27a, a protein required for EV release, was knocked down using adeno-associated virus, and EV tracking was conducted using a double fluorescent reporter mouse model. Our findings indicate that BAT ablation or BAT sympathetic denervation diminishes the cardioprotective effects of brain LepR activation. We also observed an increased concentration of EVs within BAT of rats treated with ICV leptin compared to vehicle-treated controls, an effect abolished by BAT denervation. Furthermore, knockdown of Rab27a in BAT reduced the cardioprotective benefits of brain LepR activation. MicroRNA (miR)-29c-3p was identified as a cargo of leptin-stimulated BAT-derived EVs and appears to play a key role in mitigating cardiac fibrosis after IR injury in leptin-treated animals.


title: S-1 plus chidamide combined with envafolimab as second-line treatment in advanced and metastatic pancreatic cancer (P-henomS/SCOG-P002): A single-arm, exploratory, multicenter, phase 2 trial

city: Suzhou

first: Mengyao

last: Wu

state: Jiangsu

address: No.899 Pinghai Road

institute: The First Affiliated Hospital of Soochow University

summary: Pancreatic ductal adenocarcinoma (PDAC) is an extremely aggressive malignancy with a generally poor prognosis, and there are few effective second-line treatment regimens. We conducted a single-arm, multicenter, prospective Phase II trial (ChiCTR2200058431) evaluating the efficacy and safety of S-1 plus chidamide combined with envafolimab in patients with metastatic PDAC.10×scRNA-seq was adopted to conduct an initial exploration into the potential mechanisms underlying the efficacy of the combination regimen.

overall_design: Mice subcutaneous pancreatic cancer graft models were treated with chidamide at 0, 12.5, and 25 mg/mL. To decipher the complexity of cellular diversity and evolutionary trajectory in immune cell composition in response to chidamide, we obtained one mice tumor of each group after treatment, and the tissues were subjected to scRNA-seq using the 10x Genomics single-cell library.


title: Microbiome-Derived Indole-3-lactic Acid Attenuates Cutibacterium acnes–Induced Inflammation via the Aryl Hydrocarbon Receptor Pathway

city: Seoul

first: Young In

last: Lee

state: Seoul

address: Yonsei-ro 50-1

department: Scar Laser and Plastic Surgery Center

country: South Korea

institute: Yonsei Cancer Hospital

summary: Acne vulgaris is a chronic inflammatory dermatosis where conventional therapies of-ten face limitations in efficacy and safety, necessitating the development of microbi-ome-targeted interventions. This study investigated the immunomodulatory potential of microbiome-derived tryptophan metabolites as a novel therapeutic strategy for Cutibacterium acnes-induced inflammation, focusing on the aryl hydrocarbon receptor (AHR) pathway. We evaluated indole-3-lactic acid (ILA), indole-3-acrylic acid (IAA), and indole-3-propionic acid (IPA) in comparison to tapinarof, utilizing C. ac-nes-stimulated human epidermal keratinocytes and a C. acnes-induced acne mouse model. In vitro, ILA and IPA significantly suppressed C. acnes-driven inflammatory mediators, including TNF-α, IL-1β, and COX2, whereas IAA demonstrated limited ef-ficacy. In vivo, ILA treatment exhibited superior therapeutic activity, markedly reduc-ing inflammatory cell infiltration, epidermal hyperplasia, and IL-1β expression. Tran-scriptomic analysis confirmed that ILA attenuates inflammatory signaling (e.g., IL-17 and TNF pathways) while upregulating AHR-responsive genes such as CYP1A1 and CYP1B1. Collectively, these findings establish ILA as a potent postbiotic that mitigates cutaneous inflammation through selective activation of the AHR. Future studies should prioritize the clinical translation of ILA-based topical fomulations, with rigorous evaluation of their efficacy and safety in well-designed human trials, to support their development as a non-antibiotic therapeutic alternative for acne management.

overall_design: RNA-seq profiling of primary human epidermal keratinocytes in untreated control, Cutibacterium acnes-stimulated, and four different treatment groups (indole-3-lactic acid (ILA), indole-3-acrylic acid (IAA), indole-3-propionic acid (IPA) and tapinarof(TAPI))

first: Sang Gyu

first: Nam Hao

last: Chau

first: Seoyoon

last: Ham

first: Yujin

last: Baek

first: Ngoc Ha

last: Nguyen


title: Differential Cellular Mechanisms Underlie Language and Executive Decline in Amyotrophic Lateral Sclerosis

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center


title: Leptin-Activated Crosstalk Among Brain, Brown Adipose Tissue, and Heart Drives Cardiac Protection After Ischemia-Reperfusion Injury [miRNA-seq]

type: Non-coding RNA profiling by high throughput sequencing


title: Thromboxane receptor activation in dendritic cells mitigates sepsis by suppressing S100a8/a9-mediated neutrophil recruitment

city: Tianjin

first: Ying

last: Yu

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

summary: Dendritic cells (DCs) regulate both innate and adaptive immunity during sepsis. Prostaglandins (PGs), small lipid molecules derived from arachidonic acid via COX enzymes, are crucial regulators of immune homeostasis and inflammation. However, their role in sepsis pathogenesis remains poorly defined. In this study, we identified a significant negative correlation between DC depletion and disease severity in patients with sepsis. Thromboxane (TX) A2 receptor (TP) expression was markedly reduced in blood DCs of patients with sepsis. Patients with low DC-TP expression exhibited an increased blood neutrophil count and a worsening of disease severity. In murine models of sepsis induced by cecal ligation and puncture and lipopolysaccharide challenge, DC-specific TP deficiency exacerbated sepsis by promoting S100a8/a9-mediated neutrophil recruitment, and subsequently neutrophil extracellular trap (NET) formation and lung injury. Genetic and pharmacological inhibition of S100a8/a9-TLR4 axis protected TP-deficient mice from fatal sepsis. Mechanistically, TP signaling suppressed S100a8/a9 expression in DCs via PKCδ-Stat1 signaling, thereby restricting neutrophil infiltration and NETs formation. Finally, the targeted activation of TP in DCs using the nanodrug, DCpep-U-46619, effectively alleviated sepsis-induced lung injury in mice. These findings established TP as a critical immunoregulatory receptor in DCs, highlighting its potential as a therapeutic target for sepsis.

overall_design: Splenic CD45+ immune cells from TPflox/flox and TPflox/floxCD11cCre mice subjected to cecal ligation and puncture (CLP) were sorted for droplet-based single-cell RNA-seq (10x Genomics platform).

first: Ronglu

last: Du


title: RNA catabolism restricts ERV expression and functionalization [WGBS]

city: Irvine

first: Ivan

last: Marazzi

address: 839 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California

summary: Endogenous retroviruses (ERVs) are remnants of ancient parasitic viral integrations and comprise a sizable portion of the genome in most organisms. Deregulated expression of ERVs in human is associated with a plethora of disease conditions, such as cancer and neurodegeneration. Epigenetic mechanisms silence most ERVs by generating a local repressive environment (heterochromatin) to prevent their expression. However, the mechanisms controlling the fate of ERVs residing in euchromatic regions of the genome (e.g. MERVL elements) are not well understood. Here, by integrating multidimensional epigenetic and genomic analyses, we demonstrate that silencing of euchromatic MERVL elements is achieved via transcription-coupled RNA degradation. Disrupting RNA catabolism promotes RNAPII elongation from MERVL promoters, increases MERVL expression and exonization, creating novel chimeric gene isoforms, and directing embryonic stem (ES) cells toward a terminal undifferentiated state. Our results indicate that RNA catabolism is a core regulatory module of gene networks that safeguards cell identity and potency, restricts MERVL functionalization and suppresses gene birth.

overall_design: Bisulfite-Seq of mESCs and EpiLCs, in both Exosc3 cKO and control genotypes.

first: Denis

last: Torre

first: Yesai

last: Fstkchyan

last: Marrazi


title: RNA-seq analysis of Caenorhabditis elegans exposed to bacterial PNGase enzymes

city: Nanjing

first: Josef

last: Voglmeir

address: 1 Weigang

institute: Nanjing Agricultural University

summary: Peptide:N-glycosidase (PNGase) enzymes produced by bacteria have the potential to influence host cellular physiology. To investigate host transcriptional responses to bacterial PNGase activity, we performed bulk RNA sequencing on whole Caenorhabditis elegans exposed to active PNGaseDJ, PNGaseF, or an inactive PNGase mutant (DJ101A). Differential gene expression and pathway enrichment analyses were used to identify biological programs affected by PNGase exposure.

overall_design: Whole C. elegans animals were exposed to bacterial PNGaseDJ, PNGaseF, or an inactive PNGase mutant (DJ101A). Two independent biological replicates were collected per condition. Total RNA was extracted and subjected to single-end RNA sequencing. Differential gene expression was assessed between each PNGase treatment and the DJ101A control, followed by pathway-level enrichment analysis.

first: Yamin

first: Ran

last: Cao


title: C1q-dependent clearance of alpha-synuclein allows macrophages to transiently limit enteric synucleinopathy in male mice

city: GAINESVILLE

first: Phillip

last: Mackie

state: FL

address: 1149 Newell Drive BLDG 59 L4-151

department: Neuroscience

institute: University of Florida

summary: Here we have utilized the 10x Chromium platform to perform single-cell RNA sequencing on immune cells isolated from mouse duodenum 30 days after inoculation with preformed fibrils of alpha-synuclein or saline (control). This is the first single-cell dataset of the immune landscape during the development of enteric synucleinopathy and thus provides novel insight into the immune response during early stages of enteric neuronal pathology.

overall_design: 30 days after injection with either alpha synuclein preformed fibrils or saline into the duodenal wall, mice were euthanized and the duodenum was harvested and digested. Immune cells were isolated via either FACS or magnetic bead enrichment and then combined for single-cell RNA sequencing using the 10x Chormium platform.

first: Mauli

last: Bhogade

first: Malu

middle: G

last: Tansey

first: Benoit

middle: I

last: Giasson

first: Habibeh

last: Khoshbouei


title: Spatial transcriptomic signatures of cardiac sarcoidosis

city: New York City

first: Yee Hoon

last: Foong

address: NYU Grossman School of Medicine

department: Department of Medicine

institute: New York University

summary: 10X Visium profiling of myocardial tissue from patients with cardiac sarcoidosis

overall_design: 10X Visium profiling of 12 samples of myocardial tissue from 9 patients (8 transplanted, 1 endomyocardial biopsy)

first: Arushi

last: Singh

first: Maria

last: Malik

first: Fang

last: Zhou

first: Cindy

last: Liu

first: David

last: Willet

last: Golombeck

first: Tatiana

last: Zuluaga

first: Hortense

last: Le

first: Avrom

last: Caplan

first: José

last: Durán

first: Glenn

last: Fishman

first: Anthony

last: Aizer

first: Alex

last: Reyentovich

first: Eliot

last: Peyster

first: Randal

last: Goldberg

first: Rami

last: Vanguri


title: MCF-7 cells long-term treated with Fulv plus Abema acquired ESR1 Y537S mutation and exhibited defective RSR and DDR

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: ESR1 mutations are the leading cause of endocrine therapy resistance and progression in ER-positive metastatic breast cancer. ESR1 mutations are detected in ~50% of metastatic breast cancer patients, and identification of effective targeted therapeutics are critically needed. Here, we identified enrichment of dysregulated replication stress and DNA damage responses in multiple ESR1 mutant models. Long-term treatment with endocrine therapy Fulvestrant plus the CDK4/6 inhibitor abemaciclib led to the emergence of a Y537S ESR1 mutation in a cell line, which exhibited dysregulation of replication stress response, enhanced DNA damage response, and synergistic responses to inhibitors of these pathways.

overall_design: RNA-Seq profiling of the MCF-7 parental wild-type ESR1, Abemaciclib resistant MCF-7 with wild-type ESR1, fulvestrant and Abemaciclib reistant MCF-7 treated for 8 months with 3% Y537S ESR1, and fulvestrant and Abemaciclib resistant MCF-7 cells treated for 12 months with 30% Y537S ESR1.

first: Jessica

middle: H

last: Stevens

first: Sarah

middle: K

last: Herzog

first: Guowei

last: Gu

first: Sandra

last: Grimm

first: Kloma

last: Cardoza

first: Autumn

last: Hawkins

first: Hangqing

last: Lin

first: Daniela

last: Ramos

first: Amanda

last: Beyer

last: Edwards

first: Derek

last: Dustin

first: Harry

middle: J

last: Yang

first: Nicole

last: Liang

first: Cristian

last: Coarfa


title: Gene expression of three ivermectin selected resistant Caenorhabditis elegans strains compared to the susceptible N2 strain

city: Toulouse

first: Rémy

last: Betous

address: 23 Chemin des Capelles

department: Animal Health

country: France

institute: INRAE

summary: Ivermectin (IVM) is a cornerstone of nematode control. However, its efficacy is increasingly compromised by emerging resistance in targets parasites. Here, we investigated these mechanisms in three independently evolved Caenorhabditis elegans lineages exposed to stepwise ivermectin selection. Remarkably, these populations, although distinct, converged over time to a comparable and stabilized high level of IVM resistance. RNAseq analysis across lineages revealed a conserved enrichment for ciliary/neuronal pathways including genes expressed in amphid/phasmid, indicating remodeling of the chemosensory/ciliary network as resistance intensifies. All resistant lines also converged on the dye-filling defective (Dyf) phenotype that emerged during selection at stages coinciding with sharp gains in ivermectin tolerance, implicating amphid structure/function in the establishment of durable resistance. Our results support a two-phase associative model in which early PGP-mediated tolerance precedes the emergence of ciliary/amphidial signatures and a Dyf phenotype during selection that durably reduces susceptibility.

overall_design: RNA-seq profiling of three ivermectin-selected resistant Caenorhabditis elegans  strains and of the wild-type N2 strain at the  L4 stage

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: scRNA-seq data from patients undergoing neoadjuvant BO-112 and hypofractionated radiation therapy in soft tissue carcoma

city: Stanford

first: Anusha

last: Kalbasi

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford

summary: We have employed single cell sequencing data to study the tumor microenvironment in patients with soft tissue sarcoma. This includes longitudinal biopsy and surgical specimens during a phase 1 clinical trial (NCT04420975) testing pre-operative hypofractionated radiation therapy with BO-112 (Highlight Therapeutics). As a comparison, we included surgical specimens from a cohort of patients undergoing pre-operative hypofractionated radiation therapy alone (NCT02701153).

overall_design: scRNA-seq was performed on sarcoma tissue from 4 paired samples (pre- and post-treatment) under clinical trial (preoperative RT, BO-112, resection) and 3 post-treatment RT only samples

first: Jie

last: Deng

first: Aastha

last: Pal


title: Sonic hedgehog signaling promotes basal epidermal fibrillin 3 expression for zebrafish fin ray branching

city: Eugene

first: Sam

last: Horst

state: OR

address: 1229 University of Oregon, Room 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

summary: Zebrafish robustly regenerate amputated fins, including restoring branched bony ray skeletons. During fin outgrowth, sonic hedgehog a (shha)-expressing basal epidermal cells (bEps) signal to themselves and adjacent progenitor osteoblasts (pObs) to progressively split pObs into daughter ray pools. Collectively moving bEps pass through a shha-expressing state to define distal shha-positive bEp domains that themselves separate laterally ahead of ray branching. As such, Shh/Smo signaling may promote transient associations between bEps and pObs that gradually splits pOb pools. We used bulk RNA sequencing of caudal fin regenerates after Smoothened (Smo) inhibition followed by a crispant screen to identify fibrillin 3 (fbn3) as a candidate Shh/Smo target gene for ray branching.  Homozygous fbn3 mutant zebrafish regenerated caudal fins with fewer branched rays and increased distances to branch points. Shh/Smo signaling was required specifically for fbn3 induction in bEps but not pObs. Double homozygous mutants showed that fibrillin 2 (fbn2; FBN2 ortholog) redundantly supports fbn3-promoted ray branching. Fbn1-containing microfibrils accumulated at the bEp/pOb interface in fbn3 and, more so, fbn3/2 mutant regenerating caudal fins. Shh/Smo signaling may activate bEp fbn3 expression to locally modify microfibril structure and/or abundance, facilitating bEp-pOb interactions and/or movements underlying ray branching morphogenesis.

overall_design: Samples were collected from shha:GFP zebrafish caudal fin regenerates at 4 days post amputation 5 hours after injection with injection buffer (50% PEG-400, 5% Propylene Glycol, 0.5% Tween-80) or 40 mg/kg of BMS-833923 from Cayman Chemical suspended in injection buffer. Only tissue distal to and including the shha:GFP domains were collected. Each sample is comprised of pools of 4 fin regenerates. This was done to compare transcript levels between controls (buffer injected) and Smoothened-inhibited (BMS-833923) regenerates to identify downstream targets of Sonic hedgehog signaling. All datasets were aligned to Danio rerio GRCz11.

first: Samuel

first: Gabriel

last: Yette

first: Astra

middle: L

last: Henner

first: Scott

last: Stewart

first: Kryn

last: Stankunas


title: Spatial transcriptomic data from longitudinal tumor samples from one patient undergoing neoadjuvant BO-112 and hypofractionated radiation therapy in soft tissue carcoma

summary: We have employed spatial transcriptomic data to study the tumor microenvironment in a single patient with soft tissue sarcoma over time during treatment with hypofractionated preoperative radiation and intratumoral BO-112.

overall_design: spatial transcriptomics were performed using 10X Genomics platform from archival FFPE tumor tissues from longitudinal tumor samples from one patient undergoing neoadjuvant BO-112 and hypofractionated radiation therapy in soft tissue carcoma.

first: Jingyu W.

last: Xu

first: Linh M.

last: Tran

first: Steven M.

last: Dubinett

first: Zinaida

last: Good


title: Comparative transcriptome analyses highlight distinct pathogenetic mechanisms for pleuropulmonary blastoma and congenital pulmonary airway malformations I

city: Québec

first: Lucie

last: Jeannotte

state: QC

address: 2260, boulevard Henri Bourassa

department: Biologie moléculaire, Biochimie médicale & Pathologie

institute: Université Laval

summary: Pleuropulmonary blastoma (PPB) and congenital pulmonary airway malformations (CPAM) are two rare cystic lung diseases occurring in childhood. PPB can evolve from a low-grade epithelial cyst lesion to a high-grade sarcoma with poor prognosis, while CPAM usually has a favorable non-tumorous outcome. Clinical similarities complicate diagnosis and may delay appropriate care. PPB is associated with DICER1 mutations that disturb miRNA biogenesis, altering the miRNA repertoire. Conversely, KRAS mutations are detected in CPAM, but their implication remains unclear. To decipher the mechanisms underlying these diseases, we undertook a comprehensive analysis of molecular variations in CPAM and PPB lung lesions using genome-wide RNA-seq and miRNA-seq assays. Each pathology displayed a distinct expression profile revealing a unique etiology. CPAM presented misexpression of bronchial epithelial markers correlating with KRAS mutation, while changes in expression of distal lung epithelial and mesenchymal markers were PPB-specific. PPB also exhibited abnormal gain of expression of developmental transcription factors likely due to perturbed Polycomb Repressive Complex 2 (PRC2) activity. Overexpression of miR-323a-3p, which targets the PRC2 subunit EED, correlated with decreased EED expression. Together, these observations propose a PPB pathogenetic mechanism connecting DICER1 mutations and altered miRNA profile to defective PRC2 activity, misexpression of developmental transcription factors and cancer.

overall_design: To characterize the global transcriptional changes occurring in pleuropulmonary blastoma (PPB) and congenital pulmonary airway malformations (CPAM), we applied bulk RNA sequencing (RNA-seq) to lung lesions from 4 PPB human patients, 4 CPAM human patients and  lung from 4 human controls.

first: Josselin

last: Guéno

first: Nicolas

last: Houde

first: Kim

last: Landry-Truchon

first: Béatrice

last: Frenette

first: William

last: Foulkes

first: Christophe

last: Delacourt


title: Age-independent and targetable transcription factor networks regulate CD8+ T cell senescence in aging humans [RNA-seq_inhibitors]

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

summary: Aging impairs immunity in part through the accumulation of CD8+ T cells with senescence features, including a pro-inflammatory transcriptome and impaired proliferative capacity. Using senescent cell isolation coupled with multiomic profiling, we defined the epigenetic regulation of CD8+ T cell senescence in healthy younger and older humans. We discovered that the transition to senescence was controlled by chromatin state-specific transcription factor (TF) networks whose composition was largely insensitive to donor age. These TF networks mediated widespread enhancer remodeling, causing repression of genes essential for proliferation as well as upregulation of inflammatory and secretory pathways. Inhibition of AP1, KLF5, or RUNX2 modulated the transcriptional output and partially restored the blunted transcriptional response to stimulation of senescent CD8+ T cells. Our data also revealed CD8+ T cell senescence gene signatures predictive of response to CAR-T cell therapy in diffuse large B cell lymphomas. Overall, our study defines the gene regulatory mechanisms of senescence in human CD8+ T cells, provides a resource for the interrogation of CD8+ T cell senescence in disease, highlights TF network perturbation as a viable strategy to manipulate the senescence state of CD8+ T cells, and reveals senescent CD8+ T cell gene signatures as valuable prognostic tools for immunotherapy outcome.

overall_design: RNA-seq profiling of SA-ßGal-low and SA-ßGal-high CD8+ T cells isolated from the peripheral blood from 3 younger donors. The cells were then plated in the presence of IL2 20U/mL and DMSO or 30µM of the respective inhibitors: SR128662, T5224 or CADD522. Cells were cultured for 3 days and subsequently collected for RNA extraction.

first: Paolo S

last: Turano

first: Elizabeth

last: Akbulut

first: Hannah K

last: Dewald

first: Themistoklis

last: Vasilopoulos

first: Patricia

last: Fitzgerald-Bocarsly

first: Utz

last: Herbig

first: Ricardo Iván

last: Martínez-Zamudio


title: Single-cell transcriptome analysis reveals the association between ketone body synthesis and morphogenic profile of intestinal epithelia in neonatal mice II

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: The intestinal epithelium undergoes robust maturation postnatally, yet its early-life characteristics remain poorly understood. Using single-cell RNA sequencing, we analyzed intestinal epithelial cells from neonatal and juvenile mice reared under both specific pathogen-free and germ-free conditions. Among the various cell types comprising the intestinal epithelia, we found that enterocytes, in particular, exhibit markedly different features between these stages. Enterocytes of neonatal mice show reduced expression of secretory host defense-related genes independently of microbial colonization. Conversely, neonatal enterocytes display upregulation of ketogenesis-related genes, which correlates with high expression of genes contributing to cell morphogenesis rather than serving primarily as an energy source. These findings provide novel insights into early-life maturation of intestinal epithelia offering implications for understanding neonatal intestinal pathologies.

overall_design: Small intestinal epithelial cells of neonatal and juvenile mice were isolated by flowcytometry and analyzed using single cell RNA-sequencing.

first: Kyoko

last: Mastuki

first: Taiki

last: Sakaguchi

first: Kiyoshi

last: Takeda


title: Phenylhydrazone-based Endoplasmic Reticulum Proteostasis Regulator Compounds with Enhanced Biological Activity

city: La Jolla

first: Gabriel

last: Kline

address: 10550 N Torrey Pines Rd

institute: Scripps Research Institute

summary: Pharmacological enhancement of endoplasmic reticulum (ER) proteostasis is an attractive strategy to mitigate pathology linked to etiologically-diverse protein misfolding diseases. However, despite this promise, few compounds have been identified that enhance ER proteostasis through defined mechanisms of action. We previously identified the phenylhydrazone-based compound AA263 as a compound that promotes adaptive ER proteostasis remodeling through mechanisms including activation of the ATF6 signaling arm of the unfolded protein response (UPR). However, the protein target(s) of AA263 and the potential for further development of this class of ER proteostasis regulators had not been previously explored. Here, we employ chemical proteomics to demonstrate that AA263 covalently targets a subset of ER protein disulfide isomerases, revealing a molecular mechanism for the activation of ATF6 afforded by this compound. We then use medicinal chemistry to establish next-generation AA263 analogs showing improved potency and efficacy for ATF6 activation, as compared to the parent compound. Finally, we show that treatment with these AA263 analogs enhances secretory pathway proteostasis to correct the pathologic protein misfolding and trafficking of both a destabilized, disease-associated α1-antitrypsin (A1AT) variant and an epilepsy-associated GABAA receptor variant. These results establish AA263 analogs with enhanced potential for correcting imbalanced ER proteostasis associated with etiologically-diverse protein misfolding disorders

overall_design: Total RNASequencing of AA263 analog treated HEK293T cells to determine transcriptional activity of pharmacologic ATF6 activators. RNA was submitted to BGI Genomics Co., Ltd. for strand-specific mRNA sequencing on their DNBSEQ platform with three biological replicates per condition.

middle: M

first: Leonard

last: Yoon

first: Jeffery

middle: W

last: Kelly

first: Rockland

last: Wiseman


title: Title: Lysine acetylation modulates HY5 function in Arabidopsis under high light conditions

city: Münster

first: Jie

last: Shen

address: Schlossplatz 7,  48149 Münster

institute: University of Muenster

summary: To determine the role of HY5 under HL in transcriptional regulation, RNA-seq was performed on 7-day-old Col-0 and hy5 mutant seedlings grown under GL and HL conditions. HY5-dependent and HL-responsive differentially expressed genes (DEGs) were identified by comparing Col-0 vs. hy5 under HL, and GL vs. HL conditions, respectively (Fig. S8A). Using a 2-fold change and p ≤ 0.05 cutoff, 6,929 and 7,378 DEGs were detected in Col-0 and hy5, respectively, with 4,130 genes overlapping (Fig. S8B). Volcano plot analysis identified 615 upregulated and 291 downregulated HY5-dependent genes under HL. Next, transcriptome analysis was conducted using RNA-seq on 7-day-old seedlings of Col-0, hy5, 35S:HY5K87K-GFP/hy5#1, 35S:HY5K87Q-GFP/hy5#1, and 35S:HY5K87R-GFP/hy5#2 grown under GL conditions. Comparison of DEGs between transgenic lines and the hy5 mutant revealed 3,755, 3,450, 5,341, and 5,935 upregulated, and 4,139, 3,584, 5,832, and 6,209 downregulated genes in Col-0 (native HY5), 35S:HY5K87K-GFP/hy5#1 (HY5K87K), 35S:HY5K87Q-GFP/hy5#1 (HY5K87Q), and 35S:HY5K87R-GFP/hy5#2 (HY5K87R) seedlings, respectively.

overall_design: 7-day-old Col-0 (WT), hy5, 35S:HY5K87K-GFP/hy5-1, 35S:HY5K87Q-GFP/hy5-1 and 35S:HY5K87R-GFP/hy5-2 seedlings grown at GL and Col, hy5 exposed to HL treatment were collected for RNA-seq.

first: Iris

last: Finkemeier


title: Age-independent and targetable transcription factor networks regulate CD8+ T cell senescence in aging humans [ATAC-seq_inhibitors]

first: Ricardo

last: Martínez Zamudio

overall_design: ATAC-seq profiling of SA-ßGal-low and SA-ßGal-high CD8+ T cells isolated from the peripheral blood from 3 younger donors. The cells were then plated in the presence of IL2 20U/mL and DMSO or 30µM of the respective inhibitors: SR128662, T5224 or CADD522. Cells were cultured for 3 days and subsequently collected for nuclei isolation and tagmentation.

first: Paolo S

last: Turano


title: Comparative transcriptome analyses highlight distinct pathogenetic mechanisms for pleuropulmonary blastoma and congenital pulmonary airway malformations II

first: Lucie

last: Jeannotte

overall_design: Bulk miRNA-seq analysis was carried out on 3 PPB and 4 control lung specimens to identify differentially expressed miRNAs.

first: Josselin

last: Guéno

first: Nicolas

last: Houde

first: Kim

last: Landry-Truchon

first: Béatrice

last: Frenette

first: William

last: Foulkes

first: Christophe

last: Delacourt


title: Spatial single cell transcriptomic analysis of a lineage-traceable mouse model of DICER1 Syndrome informs tumor developmental hierarchy [RNA-Seq]

city: Vancouver

first: David

last: Huntsman

state: BC

address: 675 W 10th Ave

department: Molecular Oncology

institute: BC Cancer Research Centre

summary: DICER1 syndrome predisposes children and young adults to tumor development across various organs. Most of these cancers are sarcomas, which uniquely express the RNase IIIb domain-deficient form of DICER1 and exhibit histological and molecular similarities regardless of their anatomical origins. To uncover their cellular origin and developmental hierarchy, we established a lineage-traceable genetically engineered mouse model allowing for controlled activation of Dicer1 mutations in Hic1+ mesenchymal stromal cells. This resulted in the development of renal tumors closely mirroring human DICER1 sarcoma histologically and molecularly. Spatial single-cell transcriptomics analysis revealed that a Hic1+Pdgfra+Dpt+Pi16+ fibroblastic progenitor population, corresponding to universal fibroblasts of steady-state kidneys, exhibits the capability to undergo rhabdomyoblastic differentiation or transition into proliferative sarcomatous cells. Investigation of patient samples identified analogous cell states and developmental trajectories. This study uncovers a fibroblastic origin for DICER1 sarcoma and provides a faithful model for future mechanistic and translational investigation.

overall_design:
Hic1+ mesenchymal cells were obtained from Hic1CreERT2/CreERT2:Rosa26LSL-tdTomato and
Hic1CreERT2/CreERT2:Dicerfl/fl-D1693N;Rosa26LSL-tdTomato GEMM mice 4 weeks post tamoxifen treatment, which occurred when mice were 3-weeks-old. Following collection, cells were enriched for tdTomato+ cells via FACS. The resulting cell populations were grown in either Mesencult media or DMEM/F12 media with 10% FBS. Passaged cells were isolated and examined via bulk RNA-seq.

first: Felix

last: Kommoss

first: Joyce

last: Zhang

first: Branden

last: Lynch

first: Shary

last: Chen

first: Janine

last: Senz

first: Yana

last: Moscovitz

first: Lesley

middle: A

last: Hill

first: Wilder

last: Scott

first: Jonathan

last: Bush

first: Kenneth

first: Andrew

last: Roth

first: Andreas

last: von Diemling

first: Gregg

middle: B

last: Morin

first: Michael

last: Underhill

first: Yemin

last: Wang


title: Impact of Notch signaling on the TAF6delta-driven transcriptome.

city: Paris

first: Arndt

middle: Gerhard

last: Benecke

address: 7 quai Saint Bernard

department: Centre of Neurosciences of Sorbonne Université (Neuro-SU)

institute: Centre National de la Recherche Scientifique

summary:
TAF6delta, a pro-apoptotic transcription factor, induces a gene-expression signature that leads to cell death and upregulates genes in the Notch signaling pathway. To test the impact of Notch on the TAF6delta-driven transcriptome, we performed transcriptome profiling of HeLa cells in the presence of A Notch inhibitor of the gamma-secretase inhibitor class (S2188; CAS  Number 200810-93-1; methyl (2S,3S)-2-[[(2S)-2-[[(4S)-2,2-difluoro-4-[[(2S,3S)-3-methyl-2-[[(2S)-3-methyl-2-[(2-methylpropan-2-yl)oxycarbonylamino]butanoyl]amino]-3-oxopentanoyl]amino]-3-methylbutanoyl]amino]-3-methylpentanoate], a slice-site switching oligonucleotide targeting the TAF6 mRNA (SSO-TAF6delta) alone or in combination and compared those to vehicle (DMSO) treated cells.
The three highest quality recordings from four biological replicates were used for further analysis.

overall_design: HeLa cells were treated in cell-culture with the Notch signaling inhibitor S2188n (CAS Number 200810-93-1, 15µM) of the gamma-secretase inhibitor class, herafter GSI, alone or in conjunction (one hour later) with the splice-site shifting oligonucleotide targeting TAF6, SSO-TAF6delta, for 19 hours. mRNA was extracte, labelled and hybridized to Applied Biosystems ABI 2nd generation human microarrays and chemiluminescence recorded according to standard protocols. Raw data were quality-controlled, scaled, 15µM,and median-normalized, and signal-variance and expression probabilities computed according to Noth et al. (2006) Genomics, Proteomics & Bioinformatics, 4:212-229.

first: Brendan

last: Bell

first: Emmanuelle

last: Wilhelm


title: CITE-seq Analysis of Dendritic Cells in the Gut-Draining Lymph Node at Homeostasis with LIPSTIC Labeling of Akkermansia muciniphila-Presenting Cells

city: Berkeley

first: Shaina

middle: Laufer

last: Carroll

state: CA

address: 405 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Commensal-specific T cells contribute to tissue homeostasis within the intestines, and can influence disease pathology in the context of both cancer and autoimmunity. Antigen presenting cells play a critical role in influencing the differentiation of these T cells, but how the complex network of antigen presenting cells in the intestines drives commensal-specific T cells towards a variety of differentiation trajectories remains poorly understood. We examined the priming of T cells specific for the intestinal commensal bacterial species Akkermansia muciniphila, using the LIPSTIC system combined with single-cell RNA-sequencing to identify the APCs that prime A. muciniphila-specific T cells both at homeostasis when it elicits T follicular helper cells, and during inflammation, when it also elicits TH17 and TH1 cells. We found that A. muciniphila-specific T cells were primed by several transcriptionally distinct subpopulations of migratory cDC2s in both contexts. The identity of these subpopulations did not change with inflammation, but the distribution of presentation across the subpopulations shifted, with increased presentation by inflammatory cDC2s favoring TH1 and TH17 polarization. These results reveal how distinct T cell differentiation trajectories can be determined through varied interactions with multiple, functionally distinct subpopulations of APCs.

overall_design: CITE-Seq: A. muciniphila-specific T cells engineered to express a CD40L-SortaseA fusion protein were adoptively transferred into CD40G5 mice, in which the CD40 gene had been modified to express an additional five N-terminal glycines. The CD40G5 mice were vertically colonized with a simplified microbiota known as Altered Schaedler's Flora plus A. muciniphila. 2.5 days after the T cell transfer, we performed LIPSTIC labeling by repeated injections of an LPETG-biotin peptide to identify APCs that were interacting with A. muciniphila-specific T cells. After 6 injections, gut-draining lymph nodes were harvested from 5 mice and enriched for dendritic cells. Enriched dendritic cells were stained with CITE-seq antibodies (ADTs and HTOs) and then dendritic cells were isolated by fluorescence-activated cell sorting before running on a 10X

last: Ly

first: Ashley

last: Liu

first: Maria

last: Canesso

first: Gabriel

middle: D

last: Victora

first: Daniel

last: Mucida

first: Gregory

last: Barton


title: Interferon stimulated gene ISG20 induces an innate immune defense signature in primary human fibroblasts

city: Ulm

first: Thomas

last: Stamminger

address: Albert Einstein Allee 11

institute: Institute of Virology, Ulm University

summary: ISG20 is an interferon-regulated protein that exhibits RNase activity thereby inhibiting the replication of a broad spectrum of RNA viruses. By single cell RNA sequencing we identified ISG20 and several other interferon-regulated proteins as potential restriction factors against human cytomegalovirus (HCMV) since they were highly expressed in a cluster of HCMV resistant cells. Using an siRNA screening strategy we confirmed the antiviral action of ISG20.

overall_design: Primary human foreskin fibroblast cells were infected with HCMV (strain AD169) at a multiplicity of infection of 0.4 and harvested at 6 hours post-infection for droplet-based single-cell RNA sequencing.

first: Myriam

last: Scherer

first: Anna

last: Reichel

first: Philipp

last: Kirchner


title: Interferon stimulated gene ISG20 induces an innate immune defense signature in primary human fibroblasts [RNA-Seq]

summary: ISG20 is an interferon-regulated protein that exhibits RNase activity thereby inhibiting the replication of a broad spectrum of RNA viruses. We identified ISG20 as a potential restriction factor against human cytomegalovirus (HCMV) that inhibits HCMV gene expression at the early stage of infection. However, neither the half-life of viral nor of cellular RNAs nor of viral DNA was decreased in ISG20-expressing cells. Instead, RNA-seq analysis revealed an innate immune defense signature upon ISG20 expression that comprised a distinct set of interferon-stimulated genes, zinc finger proteins and transposable elements.

overall_design: Lentiviral vectors were used to generate primary human fibroblasts (HFF) with doxycycline-inducible overexpression of ISG20 (HFF/ISG20) alongside control cells (HFF/CTRL). HFF/ISG20 and HFF/CTRL were treated for 24 h with doxycycline before total RNA was isolated and subjected to mRNA sequencing. Results are derived from three biological replicates (rep_1, rep_2, rep_3).

first: Teresa

last: Rummel

first: Caroline

last: Friedel

first: Florian

last: Erhard


title: Age-independent and targetable transcription factor networks regulate CD8+ T cell senescence in aging humans [ATAC-Seq]

first: Ricardo

last: Martínez Zamudio

overall_design: ATAC-seq profiling of SA-ßGal-low and SA-ßGal-high CD8+ T cells isolated from the peripheral blood from 4 younger (20s) 4 older (55+) donors.

first: Paolo S

last: Turano

first: Elizabeth

last: Akbulut

first: Hannah K

last: Dewald

first: Themistoklis

last: Vasilopoulos

first: Patricia

last: Fitzgerald-Bocarsly

first: Utz

last: Herbig

first: Ricardo Iván

last: Martínez-Zamudio


title: Tet2 modulates ER stress responses, β cell death, and autoimmunity in diabetes [snATAC-seq]

city: Farmington

first: Madhav

last: Kothari

state: CT

address: 10 Discovery Drive

institute: The Jackson Lab

summary: In previous studies, we showed that Tet2 controls the responses of beta cells to inflammation in a model of autoimmune Type 1 diabetes, but the specific cell types affected by Tet2  loss in islets was not clear and the molecular mechanisms responsible for the autoimmune responses and beta cell death were unknown. We found that Tet2-deficient islets have fewer islet infiltrating lymphocytes beginning 8-10 weeks after bone marrow transplant, reduced activation of CD8+ T cells, and greater CD8+ T cell repertoire diversity. Transcription factor finding motifs for interferon responses factors and inflammatory signaling molecules were enriched in Tet2-responsive cis-regulatory elements across all KO islet endocrine cells, but we observed beta cell-specific enrichment of TFs modulating homeostatic or ER stress response pathways. To confirm the effects of TET2 in human islets, we induced ER stress with brefeldin A or thapsigargin and inhibited TET2 with Bobcat 339. Pharmacologic TET inhibition reduced expression of ER stress response genes, inflammatory responses, and stress-induced beta cell death. We conclude that Tet2(TET2) can regulate ER stress responses involved in beta cell killing in autoimmune/inflammatory settings.

overall_design: scRNA-seq, snATAC-seq and scTCR-seq of islets from NOD and Tet2KO NOD mice of 10-13 weeks of age

first: Jinxiu

last: Rui

first: Romy

last: Kursawe

first: Mahsa

middle: N

last: Barkestani

first: Romi

last: Genosar

first: Pamela

last: Clark

first: Michael

last: Stitzel

first: Kevan

last: Herold


title: Tet2 modulates ER stress responses, β cell death, and autoimmunity in diabetes [scTCR-seq]

middle: C


title: CITE-seq Analysis of Dendritic Cells in the Gut-Draining Lymph Node in anti-IL10R-treated mice with LIPSTIC Labeling of Akkermansia muciniphila Presenting Cells

first: Shaina

last: Carroll

overall_design: CITE-Seq: Five CD40G5 animals, in which the CD40 gene had been modified to express an additional five N-terminal glycines, were treated with anti-IL10R blocking antibodies and four CD40G5 animals were treated with isotype control antibodies. Prior to treatment, all nine of the CD40G5 mice were vertically colonized with a simplified microbiota known as Altered Schaedler's Flora plus A. muciniphila. Three days after antibody treatment, A. muciniphila-specific T cells engineered to express a CD40L-SortaseA fusion protein were adoptively transferred into these CD40G5 mice as well as one control animal that was not colonized with A. muciniphila.  2.5 days after the T cell transfer, we performed LIPSTIC labeling by repeated injections of an LPETG-biotin peptide to identify APCs that were interacting with A. muciniphila-specific T cells. After 6 injections, gut-draining lymph nodes were harvested from ten mice (the nine that were antibody treated and the one control lacking A. muciniphila) and enriched for dendritic cells. Enriched dendritic cells were stained with CITE-seq antibodies (ADTs and HTOs) and then dendritic cells were isolated by fluorescence-activated cell sorting before running on a 10X

first: Andrew

last: Ly

first: Ashley

last: Liu

first: Maria

last: Canesso

first: Gabriel

last: Victora

first: Daniel

last: Mucida

first: Gregory

last: Barton


title: Involvement of phytohormone responses of rubber leaves after infection of Pestalotiopsis microspora revealed by transcriptome analysis

city: Gifu

first: Afdholiatus

last: Syafaah

address: Yanagido 1-1

department: UGSAS

institute: Gifu University

summary: The circular leaf disease, caused by Pestalotiopsis spp., is a new primary foliar disease characterized by yellow-brown spots that develop into dark brown spots on rubber leaves. This disease, called leaf fall disease, has recently caused significant economic losses in countries that produce natural rubber. However, the molecular mechanisms involved in the interaction between P. microspora and H. brasiliensis are not well understood. In this study, we carried out transcriptome analysis by RNA-Seq of a susceptible rubber clone (GT-1) after inoculation with the mycelial plug of P. microspora. The analysis brought us to identify 3,799, 7,274, and 4,678 differentially expressed genes (DEGs) at 2, 4, and 6 days post infection (dpi), respectively. In addition to general hypersensitive response (HR) and systemic acquired response (SAR) mediated by salicylic acid and hydrogen peroxide, our Gene Ontology (GO) analysis of the detected DEGs revealed abscisic acid and ethylene responses. Detection of these two phytohormone responses suggests possible involvement of abscisic acid and/or ethylene in the process to lead the leaf fall in susceptible rubbers. Activation of the ethylene signaling by the pathogen infection was also supported by our promoter analysis, which detected GCC box in the putative cis-elements for the response to P. microspora infection. Regarding the down-regulated genes, GO analyses showed suppression of photosynthesis across the infection time points. In addition to global understanding of the transcriptional response of rubber to the pathogen, we extracted general Regulatory Element Group (REG) that are position-dependent cis-regulatory elements and covers half of the elements in a genome, and also established molecular markers for qRT-PCR. Our study provides genomic information and convenient tools for facilitating further exploration of Hevea-Pestalotiopsis interaction

overall_design: RNA-Seq profilling of GT1 mature leaf under Pestalotiopsis microspora infection and mock condition

first: Fetrina

last: Oktavia

first: Masaharu

last: Kawauchi

first: Yuko

last: Makita

first: Minami

last: Matsui

first: Stephany

last: Tumewu

first: Shimizu

last: Masafumi

first: Kazuki

last: Sugekawa

first: Yoshiharu

middle: Y

last: Yamamoto


title: Interferon stimulated gene ISG20 induces an innate immune defense signature in primary human fibroblasts [SLAM-seq]

first: Thomas

last: Stamminger

summary: ISG20 is an interferon-regulated protein that exhibits Rnase activity thereby inhibiting the replication of a broad spectrum of RNA viruses. We identified ISG20 as a potential restriction factor against human cytomegalovirus (HCMV) that inhibits HCMV gene expression at the early stage of infection.In order to investigate whether ISG20 affects the half-life of cellular RNAs via its putative RNase activity, a SLAMseq experiment was performed. Interestingly, ISG20 expression resulted in an overall increased stablilty of cellular RNAs.

overall_design: Lentiviral vectors were used to generate primary human fibroblasts (HFF) with doxycycline-inducible overexpression of ISG20 (HFF/ISG20) alongside control cells (HFF/CTRL). HFF/ISG20 and HFF/CTRL were treated for 24 h with doxycycline before total RNA was isolated and subjected to mRNA sequencing.To label newly synthesized RNA, HFFs were treated with 4-thiouridine (4sU) at a final concentration of 400 µM for 1 h prior to cell lysis. Cells without 4sU treatment were processed in parallel. Results are derived from two biological replicates (rep_1, rep_2).

first: Myriam

last: Scherer

first: Teresa

last: Rummel

first: Florian

last: Erhard


title: Age-independent and targetable transcription factor networks regulate CD8+ T cell senescence in aging humans [RNA-Seq]

first: Ricardo

last: Martínez Zamudio

overall_design: RNA-seq profiling of SA-ßGal-low and SA-ßGal-high CD8+ T cells isolated from the peripheral blood from 4 younger (20s) 4 older (55+) donors. These samples were analzyed in conjunction with previously published samples from accession GSE169009. From this accession, FASTQ files were downloaded and processed as detailed below in 'data processing step'.

first: Paolo S

last: Turano

first: Elizabeth

last: Akbulut

first: Hannah K

last: Dewald

first: Themistoklis

last: Vasilopoulos

first: Patricia

last: Fitzgerald-Bocarsly

first: Utz

last: Herbig

first: Ricardo Iván

last: Martínez-Zamudio


title: Tet2 modulates ER stress responses, β cell death, and autoimmunity in diabetes [scRNA-seq]

first: Madhav

last: Kothari

first: Jinxiu

last: Rui

first: Romy

last: Kursawe

first: Mahsa

last: Barkestani

first: Romi

last: Genosar

first: Pamela

last: Clark

first: Michael

last: Stitzel

first: Kevan

last: Herold


title: Age-independent and targetable transcription factor networks regulate CD8+ T cell senescence in aging humans [CUT&Tag]

overall_design: Cut&Tag profiling of H3K4me1, H3K27me3, H3K27ac and IgG control of SA-ßGal-low and SA-ßGal-high CD8+ T cells isolated from the peripheral blood from 3 younger donors.


title: Adiponectin Modulates the Diurnal Hepatic Transcriptome and Energy Metabolism in Male Mice

city: Lübeck

first: Leonardo

last: de Assis

address: Marie Curie

institute: University of Lübeck

summary: Adiponectin is an adipocyte-derived hormone with insulin-sensitizing and lipid-lowering effects. Its expression and circulating levels show pronounced variation across the day, which opens the possibility that adiponectin influences metabolic programs in target tissues, such as the liver in a time-of-day dependent manner. To test this, we compared liver circadian transcriptome profiles (with sampling at 4-hour intervals) between adiponectin-deficient (ADQ-KO) and wild-type (ADQ-WT) mice. Adiponectin loss led to tonic (i.e., time independent) transcriptional changes in the liver with 1,393 differentially expressed genes (518 up- and 875 downregulated). These included upregulation of chromatin and RNA processing pathways and downregulation of immune and mitochondrial metabolic genes. At the same time, circadian analysis identified a marked reprogramming of transcriptome rhythms in ADQ-KO livers with changes in MESOR (n = 3,369 transcripts), amplitude (n = 386), and phase of gene expression (n = 603). Genes associated with mitochondrial respiration and fatty acid metabolism showed reduced rhythm amplitude and MESOR, whereas glycolytic genes exhibited increased MESOR. One of the identified adiponectin candidate targets and a master regulator of hepatic metabolism, Hif1a, was further studied by functional assays in hepatocytes. Pharmacological adiponectin receptor activation promoted glycolysis and mitochondrial respiration under normoxia, but these effects were attenuated under hypoxia mimicry, consistent with HIF1a-dependent interference. These findings suggest adiponectin as a regulator of liver circadian metabolism, modulating both the timing and magnitude of energy-related gene expression programs, potentially in part through a HIF1a-mediated mechanism.

overall_design: Three- to eight-month-old male ADQ-WT and ADQ-KO mice (B6;129-Adipoqtm1Chan/J; JAX strain 008195) on a C57BL/6J background were group-housed under a 12-hour light, 12-hour dark (LD, ~300 lux in the light phase) cycle at 22 ± 2 °C and a relative humidity of 60 ± 5 % with ad libitum access to standard chow and water. Mice were culled by cervical dislocation at 4-hour intervals, tissues were kept on dry ice and stored at −80 °C. Animal experiments were ethically approved by the Animal Health and Care Committee of the Government of Schleswig-Holstein and in line with international guidelines for the ethical use of animals. Data were reported according to the ARRIVE guidelines. For each timepoint, a total of 3 – 4 mice were used.

middle: V

first: Henrik

last: Oster


title: Uncoupling Insulin Sensitivity From Longevity: A Sex-Dependent Effect of Hepatic Glucagon Signaling

city: Birmingham

first: Alexander

middle: Tate

last: Lasher

state: AL

address: 902 14th St S

department: Biology

institute: University of Alabama at Birmingham

summary: Glucagon, a key hormone in maintaining euglycemia during fasting, also exerts broad metabolic effects, including regulation of lipid oxidation, adiposity, insulin sensitivity, and metabolic rate. However, its role in aging and longevity remains largely unexplored, a significant omission given the extensive research on dietary restriction, fasting, and insulin signaling in lifespan modulation. Here, we investigated the impact of hepatic glucagon receptor (GCGR) signaling on lifespan using a liver-specific GCGR knockout (LKO) mouse model. While male LKO mice exhibited normal lifespan, female LKO mice displayed a significant reduction in survival. Strikingly, and in contrast to prevailing expectations based on metabolic improvements, this shortened lifespan in females occurred despite marked enhancements in metabolic health, including reduced body weight and adiposity, preferential glucose oxidation, elevated metabolic rate, and enhanced glucose tolerance and insulin sensitivity throughout adulthood. Underpinning this detrimental outcome, transcriptomic and biochemical analyses revealed a striking, female-specific activation of pro-inflammatory pathways, notably NF-κB and cGAS-STING signaling, in the liver and kidney of aged LKO mice. These findings identify a novel, sexually dimorphic role for the hepatic glucagon receptor in regulating lifespan, linking its interruption in females to late-life inflammation and reduced longevity despite an otherwise beneficial metabolic phenotype.

overall_design: RNA-seq gene expression of male and female liver-specific glucagon receptor knockout (LKO) or cre negative (CRE-) control mouse liver tissue at 20-22months of age. Mice were maintained on the C57BL/6J genetic background.

middle: T

first: Ben

last: Heckman

first: Parth

last: Sarker

first: Kaimao

last: Liu

first: Liou

last: Sun


title: Tumor Acidosis Remodels the Glycocalyx to Control Lipid Scavenging and Ferroptosis

city: Umea

first: Silvia

last: Remeseiro

state: Vasterbottens lan

address: Johan Bures vag 12, MBC-huset

department: Umea Centre for Molecular Medicine

country: Sweden

institute: Umea University

summary: Cancer cell adaptation to metabolic stress remains a major barrier to effective therapy. Here, we identify a chondroitin sulfate (CS)-enriched glycocalyx in the acidic microenvironment of human glioblastoma (GBM) and CNS metastases. Integrated analyses of patient GBM tumors and in vitro and in vivo models reveal that CS-glycocalyx encapsulation provides a physical barrier to lipid scavenging and mitigates lipid-induced toxicity in acidosis. Mechanistically, HIF and TGFβ signaling converge to induce CS biosynthesis and dynamically reprogram syndecan-1 glycosylation from heparan sulfate (HS) to CS, limiting lipid particle uptake. Dual inhibition of CS biosynthesis and diacylglycerol-O-acyltransferase 1 (DGAT1), which blocks lipid storage, triggers uncontrolled lipid peroxidation and ferroptotic cell death. These findings uncover a stress-adaptive glycan program that insulates tumor cells from lipotoxic stress. Disrupting this glyco-metabolic barrier selectively sensitizes GBM cells in the lipid-rich, acidic microenvironment and reveals a therapeutic vulnerability that may be leveraged to overcome metabolic resilience in aggressive tumors.

overall_design: Two biological replicates (500,000 cells each) were prepared for each of the following U87MG-derived conditions for HIF1α CUT&RUN sequencing (targeting 25 million reads per replicate): NA cells (U87MG cultured at pH 7.4) AA cells (U87MG cultured at pH 6.4) Ctrl cells (U87MG cultured in serum-free media at pH 7.4) DMOG-treated cells (U87MG treated with 0.5 mM dimethyloxalylglycine at pH 7.4) In addition, CUT&RUN was performed using IgG provided in the CUT&RUN Assay Kit (Active Motif, #53180, version 47) to serve as a control for normalization and peak calling in the HIF1α datasets.

first: Anna

last: Bång-Rudenstam

first: Chaitali

last: Chakraborty

first: Itzel

last: Nissen

first: Mattias

last: Belting