title: T Cell Transcriptome Alterations in Healthy Volunteers Exposed to Three Weeks of Simulated Microgravity

city: Stockholm

first: Nik

middle: V

last: Kuznetsov

address: Nobels vag 16

country: Sweden

institute: Karolinska Institute

summary: Impairment or reduction of lymphocyte-mediated immune response has been observed during space flight or in microgravity simulation conditions, with the underlying mechanisms remaining unclear. T lymphocytes (T cells) play a critical role in human immune response. The immunosuppression encountered by humans in microgravity may be linked to its impact on T cell global transcriptome networks, affecting immune cell-cell interactions. This study involved a unique three-week microgravity simulation conducted with ten healthy male volunteers aged 25-40 using a dry immersion facility. The research aimed to explore the normal responses of the human body to long-term simulated microgravity (SMG) without any specific countermeasures implemented. To investigate the T cell response to SMG, total RNA isolated from T lymphocytes at different time points during the course of SMG was subjected to RNA sequencing. Bioinformatic analysis revealed the impact of SMG on multiple cell signaling pathways, influenced by key regulators that modulated the expression of different genes. The discovery of potential biomarker genes in T cells may offer valuable insights into studying human responses to microgravity, however, further validation of these findings in space is required.

overall_design:
T cell RNA for RNA-seq was extracted from human T lymphocytes obtained from 10 ml blood samples collected one week before SMG treatment, at three time points during a 3-week SMG course, and one week after SMG treatment. T cell response to long-term SMG was investigated by analyzing differential gene expression.

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

Please note that the processed data column headers are removed due to privacy concerns.

first: Nikolai


title: The promising miRNAs, Let-7b-5p and miR-24-3p, have the potential to serve as therapeutic agents targeting pancreatic cancer stem cells.[RNA-Seq]

status: Public on Dec 09 2025

city: Gustavo A. Madero

first: ROSAURA

middle: HERNANDEZ

last: RIVAS

state: Ciudad de México

address: Av. Instituto Politécnico Nacional 2508

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV

type: Expression profiling by high throughput sequencing

summary: Background Due to its aggressive nature and poor prognosis, the development of new therapeutic strategies for pancreatic cancer is urgently needed. A promising approach involves targeting cCancer Sstem Ccells (CSCs), which are crucial in tumor growth, resistance to radiation and chemotherapy, and recurrence. Recent research has emphasized the significant role of microRNAs (miRNAs) in regulating critical aspects of CSC biology, including self-renewal, drug resistance, tumorigenicity, expression of core pluripotency factors and the modulation of genes involved in key signaling pathways. Therefore, a better understanding of how miRNAs control gene expression in Ppancreatic Ccancer Sstem Ccells (PCSCs) may help identify novel miRNAs that could serve as potential therapeutic targets for these cells. Methods /Results To identify miRNAs that are exclusive to PCSCs, the pancreosphere technique was employed to enrich them. Fluorescence-aActivated Ccell Ssorting (FACS) was used in conjunction with the surface markers CD44, CD24, and CD133 to isolate cells positive for these markers (PCSC+) and those negative for them (PCSC-). 31 Differentially Eexpressed miRNAs (DEmiRNAs) were identified using microRNA microarrays (V4.0) by hybridizing RNA from the PCSC+ and PCSC- populations. KEGG analysis revealed that 10 of the 31 downregulated DEmiRNAs are involved in signaling pathways regulating the pluripotency of PCSCs, such as Wnt/β-catenin, TGFβ, MAPK, and PI3K/AKT. These miRNAs target various mRNAs encoding ligands, receptors, and downstream effector molecules of these pathways, with results further corroborated by RT-qPCR  and Western blot analysis. Transfection of mimics of Let-7b-5p and miR-24-3p into PCSC+ cells resulted in their overexpression, which reduced the activity of key signaling pathways and pluripotency factors, inducing differentiation into exocrine and endocrine phenotypes, as corroborated by, RT-qPCR, Western blot and RNA-seq data. FACS, gemcitabine sensitivity, colony formation assays, and in vivo tumorigenicity experiments showed that the overexpression of each of these miRNAs increased the sensitivity of PCTC+ cells to gemcitabine, decreased their numbers, resulted in the formation of smaller spheres, and development of smaller tumors in vivo. Conclusion Our findings highlight the potential of miRNAs Let-7b-5p and miR-24-3p as therapeutic targets. Their ability to regulate key CSC pathways suggests that reintroducing tumor-suppressive miRNAs could reprogram PCSCs and improve patient outcome.

overall_design: RNA-seq profiling of PCSC+ cells transfected with Let-7b-5p or miR-24-3p mimics.

first: Maricela

last: Medrano-Silva

first: Eric

middle: G

last: Salmerón-Bárcenas

first: Elena

last: Arechaga-Ocampo

first: Nicolas

last: Villegas-Sepúlveda

first: Mayte

middle: L

last: Padilla-Cristerna

first: Gergina

last: Hernández-Montes

first: Leopoldo

last: Santos-Argumedo

first: Sonia

middle: M

last: Pérez-Tapia

first: Gabriela

last: Hernández-Galicia

first: Ana

middle: B

last: Sánchez-Argáez

first: Paola

last: Briseño-Díaz

first: Carmen

last: Sánchez-Torres

first: Arturo

last: Aguilar-Rojas

first: Sara

last: Huerta-Yepez

first: Miguel

last: Vargas

first: Rosaura

last: Hernández-Rivas


title: 3D genome architecture of Zynoseptoria tritici IPO323

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

summary: Three-dimensional (3D) genome organization plays a central role in gene regulation and genome stability, yet its functional relevance in fungal pathogens remains largely uncharacterized. Here, we present a high-resolution Hi-C analysis of the wheat pathogen Zymoseptoria tritici, revealing a hierarchical genome organization. The genome adopts a Rabl-like conformation characterized by centromere clustering and the spatial segregation of accessory chromosomes, which remain tethered to core pericentromeres, supporting their mitotic stability. At finer resolution, we identify homotypic interactions among B compartments and self-interacting domains demarcated by distinct histone modifications and insulator-like sequence motifs at their boundaries. A subset of highly insulated domains enriched in heterochromatin and transposable elements forms an inter-domain interaction network. During wheat infection, several self-interacting domains exhibit coordinated transcriptional activity, linking spatial genome folding to dynamic gene regulation. These findings uncover multi-scale principles of nuclear organization in a major fungal plant pathogen and establish a framework for investigating 3D genome function in filamentous fungi.

overall_design: The reference strain Z. tritici IPO32326 was preserved in 50% glycerol at -80°C. Pre-cultures were prepared with inoculations of ~100uL of glycerol stock spore suspension onto solid YMS medium (4 g/L yeast extract, 4 g/L malt extract, 4 g/L sucrose, and 12 g/L of agar) and grown for 4 days at 18°C. Spores were scraped from plates and re-suspended into PBS buffer (8g/L NaCl, 1.44g/L Na2HPO4, 0.2g/L KCl, 0.24g/L KH2PO4) for sample preparation for epigenomics sequencing as described in Möller et al. 202332. Spores were fixed with formaldehyde according to PhaseGenomics instructions (Seattle, Washington, USA). Hi-C experiments were performed with the Phase Genomics Proximo Hi-C Kit (Fungal), which combines four restriction enzymes to ensure homogeneous digestion at AT-rich genomic regions. The resulting libraries were sequenced at Biomarker Technologies GmbH (BMKgene, Münster, Germany). The sequencing was performed with Illumina NovaSeq X, paired-end 150bp reads. Sample preparation, Hi-C experiment, and sequencing were performed for two independent replicates.

first: Ivona

last: Glavincheska


title: The promising miRNAs, Let-7b-5p and miR-24-3p, have the potential to serve as therapeutic agents targeting pancreatic cancer stem cells.

first: ROSAURA

last: RIVAS

summary: Background  Due to its aggressive nature and poor prognosis, the development of new therapeutic strategies for pancreatic cancer is urgently needed. A promising approach involves targeting cCancer Sstem Ccells (CSCs), which are crucial in tumor growth, resistance to radiation and chemotherapy, and recurrence. Recent research has emphasized the significant role of microRNAs (miRNAs) in regulating critical aspects of CSC biology, including self-renewal, drug resistance, tumorigenicity, expression of core pluripotency factors and the modulation of genes involved in key signaling pathways. Therefore, a better understanding of how miRNAs control gene expression in Ppancreatic Ccancer Sstem Ccells (PCSCs) may help identify novel miRNAs that could serve as potential therapeutic targets for these cells.  Methods /Results To identify miRNAs that are exclusive to PCSCs, the pancreosphere technique was employed to enrich them. Fluorescence-aActivated Ccell Ssorting (FACS) was used in conjunction with the surface markers CD44, CD24, and CD133 to isolate cells positive for these markers (PCSC+) and those negative for them (PCSC-). 31 Differentially Eexpressed miRNAs (DEmiRNAs) were identified using microRNA microarrays (V4.0) by hybridizing RNA from the PCSC+ and PCSC- populations. KEGG analysis revealed that 10 of the 31 downregulated DEmiRNAs are involved in signaling pathways regulating the pluripotency of PCSCs, such as Wnt/β-catenin, TGFβ, MAPK, and PI3K/AKT. These miRNAs target various mRNAs encoding ligands, receptors, and downstream effector molecules of these pathways, with results further corroborated by RT-qPCR  and Western blot analysis. Transfection of mimics of Let-7b-5p and miR-24-3p into PCSC+ cells resulted in their overexpression, which reduced the activity of key signaling pathways and pluripotency factors, inducing differentiation into exocrine and endocrine phenotypes, as corroborated by, RT-qPCR, Western blot and RNA-seq data. FACS, gemcitabine sensitivity, colony formation assays, and in vivo tumorigenicity experiments showed that the overexpression of each of these miRNAs increased the sensitivity of PCTC+ cells to gemcitabine, decreased their numbers, resulted in the formation of smaller spheres, and development of smaller tumors in vivo.  Conclusion Our findings highlight the potential of miRNAs Let-7b-5p and miR-24-3p as therapeutic targets. Their ability to regulate key CSC pathways suggests that reintroducing tumor-suppressive miRNAs could reprogram PCSCs and improve patient outcome.  Due to its aggressive nature and poor prognosis, the development of new therapeutic strategies for pancreatic cancer is urgently needed. A promising approach involves targeting cCancer Sstem Ccells (CSCs), which are crucial in tumor growth, resistance to radiation and chemotherapy, and recurrence. Recent research has emphasized the significant role of microRNAs (miRNAs) in regulating critical aspects of CSC biology, including self-renewal, drug resistance, tumorigenicity, expression of core pluripotency factors and the modulation of genes involved in key signaling pathways. Therefore, a better understanding of how miRNAs control gene expression in Ppancreatic Ccancer Sstem Ccells (PCSCs) may help identify novel miRNAs that could serve as potential therapeutic targets for these cells.  Methods /Results To identify miRNAs that are exclusive to PCSCs, the pancreosphere technique was employed to enrich them. Fluorescence-aActivated Ccell Ssorting (FACS) was used in conjunction with the surface markers CD44, CD24, and CD133 to isolate cells positive for these markers (PCSC+) and those negative for them (PCSC-). 31 Differentially Eexpressed miRNAs (DEmiRNAs) were identified using microRNA microarrays (V4.0) by hybridizing RNA from the PCSC+ and PCSC- populations. KEGG analysis revealed that 10 of the 31 downregulated DEmiRNAs are involved in signaling pathways regulating the pluripotency of PCSCs, such as Wnt/β-catenin, TGFβ, MAPK, and PI3K/AKT. These miRNAs target various mRNAs encoding ligands, receptors, and downstream effector molecules of these pathways, with results further corroborated by RT-qPCR  and Western blot analysis. Transfection of mimics of Let-7b-5p and miR-24-3p into PCSC+ cells resulted in their overexpression, which reduced the activity of key signaling pathways and pluripotency factors, inducing differentiation into exocrine and endocrine phenotypes, as corroborated by, RT-qPCR, Western blot and RNA-seq data. FACS, gemcitabine sensitivity, colony formation assays, and in vivo tumorigenicity experiments showed that the overexpression of each of these miRNAs increased the sensitivity of PCTC+ cells to gemcitabine, decreased their numbers, resulted in the formation of smaller spheres, and development of smaller tumors in vivo.  Conclusion Our findings highlight the potential of miRNAs Let-7b-5p and miR-24-3p as therapeutic targets. Their ability to regulate key CSC pathways suggests that reintroducing tumor-suppressive miRNAs could reprogram PCSCs and improve patient outcome.

overall_design: The miRNAs obtained from PCSC+ and PCSC- were profiled by microarray, in duplicates for each group, by GeneChip microRNA 4.0 array platforms (ThermoScientific). Data analysis was performed using Transcriptome Analysis Console software v.4.0.2 (Affymetrix, Santa Clara, CA, USA), which included quality control, normalization, and data summarization.

first: Maricela

last: Silva

first: Eric

last: Salmerón Bárcenas

middle: A

last: Ocampo

last: Sepúlveda

last: Padilla Cristerna

middle: H

last: Montes

middle: S

last: Argumedo

last: Pérez Tapia

last: Galicia

last: Sánchez Argáez

last: Díaz

last: Torres

last: Rojas

last: Yepez

last: Rivas


title: Rapamycin limits peritendinous fibrosis but does not affect intratendinous healing in a rodent Achilles tendon injury model

city: London

first: Chavaunne

last: Thorpe

address: Royal College Street

country: United Kingdom

institute: Royal Veterinary College

type: Non-coding RNA profiling by high throughput sequencing

summary: Tendon  injuries are common, affecting both athletes and the general population. Healing is often poor, with deposition of fibrotic, disorganised scar-like tissue leading to continued pain, dysfunction and reinjury. While a variety of therapeutics are available clinically to treat tendon injuries, outcomes remain variable and no treatments are able to fully restore tendon structure and function, hence novel regenerative therapies are required. The pathogenesis of many fibrotic diseases is influenced by the mammalian target of rapamycin (mTOR) signalling pathway, which modulates processes required for cell growth and proliferation. Rapamycin, an mTOR inhibitor, is a promising therapeutic for several fibrotic diseases, and can facilitate musculoskeletal tissue repair. Therefore, we used a needle injury model in the rat Achilles tendon to test the hypothesis that rapamycin treatment during the early stages of tendon injury enhances tendon healing via modulation of resident tendon cell populations and autophagy. The results demonstrate that, while rapamycin treatment decreased peritendinous fibrosis and appeared to modulate cell recruitment, it did not enhance healing of lesions within the tendon core, up to three weeks post-injury. Therefore, rapamycin is not an effective therapeutic for tendon injury in young adults. Future studies should establish if rapamycin is able to improve tendon healing in aged animals or with longer-term administration.

overall_design: RNAseq profiling of Evs isolated from serum of rats subjected to tendon injury and treated either with rapamycin or vehicle control, 7 or 21 days post injury

first: Neil

last: Marr

first: Danae

last: Zamboulis

first: Ross

last: Beaumont

first: Zofia

last: Tatarczyk

first: Yu-Mei

last: Chang

first: Richard

last: Piercy

last: Meeson

first: Mandy

last: Peffers

first: John

last: Hildyard

first: Marianne

last: Pultar


title: Single-cell multidimensional profiling of tumor cell heterogeneity in supratentorial ependymomas [scRNA-Seq]

city: Boston

first: Carlos Alberto

middle: Oliveira de

last: Biagi Junior

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

country: USA

institute: Dana Farber Cancer Institute

summary: Supratentorial ependymomas (ST-EPNs) are aggressive and treatment-resistant pediatric brain tumors that form along the human cortex, with suspected origin from radial glia cells. Although histologically similar, ST-EPNs are molecularly classified into six distinct subgroups, many of them remaining understudied. Here, we integrated molecular cell states and spatial architecture to resolve the cellular origins and aberrant differentiation trajectories of ST-EPNs at single-cell resolution. We show that, while all ST-EPNs display a unified origin from neuroepithelial cells, different subgroups harbor highly diverse cell states and differentiation potential associated with neural or ependymal differentiation. Spatial mapping uncovered a higher-order structural tumor organization driven by presence of the mesenchymal state, and refines classical histological features based on detailed molecular resolution. By benchmarking a morpho-molecular cell-state classification system in different disease models and human tumors, we identified four cellular subtypes defined by the architecture of neurite-like extensions that mediate either self-renewal or fast, saltatory invasive phenotypes reminiscent of neurons during neurodevelopment. Collectively, our study provides a comprehensive framework for the study of ST-EPN cellular states, and reveals biologically relevant tumor compartmentalization with potential clinical implication.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design:
Single cell transcriptomic profiling of 44 supratentorial ependymomas (ST-EPNs), three ST-EPN (ZFTA-RELA) models grown as patient derived xenografts (n = 3), adherent (n = 3), spheres (n = 3), or cocultures with rat E19 cortical cells (n = 3). One ZFTA-Cluster 4 model grown in monoculture and coculture with rat E19 cortical cells, and one ZFTA-RELA model gorwn in monoculture and coculture with human iPSCs-derived neurons and astrocytes.

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

first: Daeun

last: Jeong

first: Sara

last: Danielli

first: Kendra

last: Maaß

first: David

middle: R

last: Ghasemi

first: Svenja

middle: K

last: Tetzlaff

first: Ekin

last: Reyhan

last: Oliveira de Biagi Junior

first: Costanza

last: Lo Cascio

first: Sina

last: Neyazi

first: Andrezza

last: Nascimento

first: Rebecca

last: Haase

first: Bernhard

last: Englinger

first: Li

last: Jiang

first: Alicia-Christina

last: Baumgartner

first: Sophia

last: Castellani

first: Cuong

last: Nguyen

first: Jacob

last: Rozowsky

first: Olivia

last: Hack

first: McKenzie

last: Shaw

first: Stefan

last: Pfister

first: Marcel

last: Kool

first: Tomasz

last: Nowakowski

first: Johannes

last: Gojo

first: Lissa

last: Baird

first: Sanda

last: Alexandrescu

first: Kristian

middle: W

last: Pajtler

first: Varun

last: Venkataramani

first: Mariella

last: Filbin


title: Single-cell multidimensional profiling of tumor cell heterogeneity in supratentorial ependymomas [Spatial Transcriptomics]

first: Carlos Alberto

last: Biagi Junior

overall_design:
We used Xenium Analyzer Spatial Transcriptomics to analyze 56 tumor sections from 23 ZFTA-RELA ST-EPN samples.
Please note that the 'xenium_cell_metadata.csv.gz' includes the metaniche and cluster annotations for all Xenium samples.

first: Daeun

last: Jeong

first: Sara

last: Danielli

first: Kendra

last: Maaß

first: David

last: Ghasemi

first: Svenja

last: Tetzlaff

first: Ekin

last: Reyhan

last: Oliveira de Biagi Junior

first: Costanza

last: Lo Cascio

first: Sina

last: Neyazi

first: Andrezza

last: Nascimento

first: Rebecca

last: Haase

first: Bernhard

last: Englinger


title: Transcriptomic analysis of Erwinia amylovora bacteriophage insensitive mutants

city: Guelph

first: Dion

last: Lepp

address: 93 Stone Rd W

country: Canada

institute: Agriculture and Agri-Food Canada

summary: Phage therapy has garnered significant attention due to the rise of life-threatening multidrug-resistant pathogenic bacteria and the growing awareness of the transfer of resistance genes between pathogens. In light of this, phage therapy applications are now being extended to target plant pathogenic bacteria, like Erwinia amylovora that causes fire blight in apple and pear orchards. Understanding the mechanisms of phage resistance development is crucial for enhancing the effectiveness of phage therapy. Despite the challenges of naturally developing a bacteriophage resistant mutant (BIM) of E. amylovora (without traditional mutagenesis methods), this study successfully created a BIM mutant against the podovirus Ea46-1-A1. The parent strain, E. amylovora D7, and the BIM mutant, B6-2 were compared at the transcriptomic level.

overall_design: RNASeq of E. amylovora wild-type and BIM strains


title: High-resolution single-cell transcriptomic comparison of doublesex-expressing neurons across Drosophila species

city: Philadelphia

first: Justin

last: Walsh

state: PA

address: 3740 Hamilton Walk

institute: University of Pennsylvania

summary: Understanding how the cellular and molecular composition of neural circuits change during evolution is essential for deciphering how behavior evolves. Male sexual behaviors in Drosophila species are remarkably diverse, and the underlying sexual circuits are specified by sex determination genes. Here, we employed single-cell transcriptomics to systematically characterize and compare neuron cell types that express the sex determination gene doublesex in adult males across Drosophila species with divergent sexual behaviors. High-resolution profiling to delineate cellular diversity revealed a largely conserved set of cell types across four species, with minimal evolutionary gain or loss and potentially more prevalent changes in cell type abundance. In-depth comparisons between D. melanogaster and D. yakuba showed that transcriptomic conservation and differentially expressed genes between species are predominantly cell-type-specific, suggesting that cell types evolve as highly independent units. We identified widespread species differences in gene expression, particularly in the neuromodulatory signaling pathway, while preserving a conserved circuit layout in sexual identity and neurotransmitter properties. We further generated a female dataset in D. melanogaster to define sex differences in cell types and examine species divergence in relation to sex differences. Finally, we reported marker gene combinations that uniquely define each cell type, providing a foundational resource that enables the design of cell-type-specific genetic reagents. Overall, our study provides fundamental insights into the cellular diversity of sexual circuits and how evolution shapes cell types and gene expression in behavioral adaptations.

sample_organism:
Drosophila melanogaster
Drosophila teissieri
Drosophila yakuba
Drosophila santomea

overall_design: We collected doublesex expressing neurons from males of four Drosophila species and female D. melanogaster via FACS and analyzed by scRNAseq

middle: T

first: Ian

middle: P

last: Junker

first: Yu-Chieh David

last: Chen

first: Yen-Chung

first: Helena

last: Gifford

first: Yun

last: Ding


title: 2’-O-Methyl-guanosine 3-base RNA fragments mediate essential natural TLR7/8 antagonism

city: Clayton

first: Michael

last: Gantier

state: Victoria

address: 27-31 Wright St

department: Centre for Innate Immunity and Infectious Disease

country: Australia

institute: Hudson Institute of Medical Research

summary: Daily phagocytic clearance of billions of apoptotic cells is fundamental to the maintenance of homeostasis and is normally immune silent. Toll-like receptors (TLR) 7 and 8 are phagosomal innate immune sensors known to instigate inflammation in response to guanosine, uridine, and ~2-3 base long degradation products from endosomal RNAs. Exactly how TLR7 and TLR8 evade activation by degradation products from host-RNAs is currently unknown. The activity of the mouse TLR7 inhibitory sequence GGC-v1 was tested on primary bone marrow-derived macrophages (BMDMs) derived from Tlr7Y264H gain-of-function mutant mice. This Tlr7Y264H gain of function mutation results in constitutive engagement of TLR7 through an increased affinity for guanosine. Overnight treatment of Tlr7Y264H mutant BMDMs with GGC-v1 or the small molecule TLR7/8 inhibitor Enpatoran led to significant down regulation of 20 out of the 22 genes regulated by GGC-v1 that were also down-regulated by Enpatoran, indicating that TLR7 sensing was effectively dampened.

overall_design: Primary bone marrow derived macrophages (BMDMs) from 9-11 week-old Tlr7Y264H heterozygous gain-of-function female mice were extracted and differentiated for 5 days in complete DMEM supplemented with L929 conditioned medium, prior to 24 h incubation with 5 µM GGC-v1 or 100 nM Enpatoran and total RNA purification for RNA sequencing.

first: Sunil

last: Sapkota

first: Alexandra

last: McAllan


title: 830 nm Pretreatment in Mice Enhances Endurance in Acute Exercise

first: Nashwa

last: Cheema

address: 55 Fruit St

institute: Massachusetts General Hospital

summary: Fatigue is defined by the reduction of a muscle’s strength and performance during exercise and continuous activity will result in musculoskeletal injury. Light therapy has been shown to have several beneficial physiologic effects in a wide range of tissues. The musculoskeletal system can be irradiated with wavelengths in red and near infrared (NIR) regions which penetrate deep into the body. Photobiomodulation therapy (PBMT) reduces pain, inflammation and enhances physical performance. However, the mechanism(s) of cellular responses by PBM in muscle is not clearly understood. Therefore, the goal of this study is to improve our understanding of the mechanism(s) of action of PBM effects on the musculoskeletal system, in exercised and healthy muscle. We investigate the application of 830 nm and its effect on sedentary muscle and fatigue induced in intense exercise in mice. In sedentary mice, PBM increased the gene expression for muscle tissue development, including cFos, which is critical for activating satellite cells that repair muscle. Immunostaining for cFos expression confirmed an increase in number of activated satellite cells in PBM treated muscle. We performed a treadmill fatigue assay and collected muscle tissue for histological and biochemical analysis. We observed that PBM treated mice had increased performance, reduced muscle fiber damage and altered mitochondrial structure. RNA sequencing from fatigued TA suggested that PBM treatment had increased gene expression of tissue regeneration and remodeling, suggesting tissue adaptation and muscle repair after exercise with PBM. In conclusion, our study suggests that 830 nm may have altered the muscle by activating regenerative genes that protect the tissue from exercise induced cellular stress.

overall_design: We performed Differential Gene Expression analysis from the RNA-seq data of 12 sedentary (6 non-PBM and 6 PBM treated) and 12 fatigue (6 non-PBM and 6 PBM treated) male mice.

first: Namrata

last: Ghag

first: Linh

last: Pham

first: Emma

last: Wise

first: Christiane

last: Fuchs

first: Rox

last: Anderson

first: Joshua

last: Tam


title: Sp100A isoform induces the histone chaperone, HIRA to localize to PML nuclear bodies

city: Bethesda

first: Alison

middle: Anne

last: McBride

state: MD

address: 33 North Drive

department: DIR

institute: NIAID

summary: PML nuclear bodies (PML-NBs) are dynamic subnuclear structures important for chromatin dynamics and anti-viral defense. In this study we investigate the role of Sp100 isoforms in promoting localization of the H3.3 histone chaperone HIRA to PML-NBs in human keratinocytes. Sp100 knockout (KO) cell lines were generated using CRISPR-Cas9 technology and shown to display normal keratinocyte differentiation and PML-NB formation. However, HIRA and its associated complex members (UBN1 and ASF1a) failed to localize to PML-NBs in the absence of Sp100, even after interferon stimulation. Exogenous expression of the four main isoforms of Sp100 showed that the Sp100A isoform is the primary driver of HIRA localization to PML-NBs, with the SUMO interacting motif (SIM) playing an important role. These findings highlight the functional diversity of the Sp100 isoforms in modulating chromatin dynamics at PML-NBs.

overall_design: RNA-seq analysis of Sp100 wildtype and knockout human Normal Immortalized Keratinocyte (NIKS) cell lines that were untreated (0hr IFN) or stimulated with 25 ng/mL Human Interferon Alpha 2a for 12 or 48 hours. Each condition has three biological replicates.

first: Ashley

last: Della Fera

first: Warda

last: Arman

first: Maceo

last: Powers

first: Alix

last: Warburton


title: Abatacept Restores Dysregulated Transcriptomic and Proteomic Profiling in LRBA Deficiency and CTLA-4 Insufficiency

city: Doha

first: Bernice

last: Lo

address: Al Luqta

department: Research

country: Qatar

institute: Sidra Medicine

summary: This study investigates the effectiveness of abatacept via flow cytometric and multi-omics approaches in treating lipopolysaccharide-responsive beige-like anchor (LRBA) deficiency, an immune disorder characterized by infections, autoimmunity, and lymphoproliferation. Integrative analyses revealed that long-term abatacept use boosted the naive T-cell pool through increased thymic output while simultaneously reducing memory T cells and cytokine productions of CD4+ T cells and decreasing autoreactive B cells. Abatacept also normalized the imbalanced T helper (TH) 1 and TH17 responses. By using targeted and single-cell transcriptomics together with plasma proteomic analyses, we observed a complex interaction involving upregulated CD28 and T-cell receptor signaling pathways, accompanied by increased expression of inhibitory checkpoint proteins to maintain immune homeostasis in the absence of the cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4). The immune dysregulation involved multiple pathway repercussions, including upregulation of inflammatory pathways, cytokine and chemokine-mediated responses, antimicrobial peptides, interferon-related genes, complement system, and toll-like receptor signaling, which normalized under abatacept. Thus, targeted treatment can re-establish the broadly disturbed immune regulation in LRBA deficiency.

overall_design: Patient blood samples were collected before and after abatacept treatment and PBMCs were separated using ficoll density gradient, cryopreserved, then put through single cell RNA sequencing.


title: Multi-omics exploration demonstrated the antidepressant effects of chrysophanol on Diabetes-depression comorbidity rats via inflammatory, and neurodegenerative axes

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

country: China

institute: Nissi Biotech

summary: The escalating prevalence of diabetes-depression comorbidity (DDC) necessitates novel therapies targeting shared pathophysiological pathways, which needs to decipher the underlying molecular mechanisms. This study elucidates the therapeutic potential of chrysophanol, a natural anthraquinone, in streptozotocin (STZ) and chronic unpredictable mild stress (CUMS)-induced DDC rat model. Behavioral assessments, biochemical profiling, and integrated multi-omics analyses (RNA-seq and proteomics) were employed to decipher underlying mechanisms. Successful model establishment was confirmed by prolonged immobility time in the tail suspension test (p < 0.01) and reduced general health scores. Chrysophanol treatment restored serum brain-derived neurotrophic factor (BDNF) levels (p < 0.01) and ameliorated dyslipidemia (total cholesterol: p < 0.05). RNA-seq results revealed that chrysophanol regulated expression of hundreds of genes, which were enriched in synaptic vesicle cycling (downregulation of Sh3gl2, Camk5), CNS myelination, and axonal ensheathment pathways. Proteomic profile demonstrated the suppression of neurodegenerative markers and activation of axonal regeneration pathways. Notably, chrysophanol downregulated synaptic proteins associated with leukocyte chemotaxis (Pla2g7, Mdk) and glutamatergic synapses (Itpr2, Slc1a1) while upregulating axonal development, regeneration, and PPARγ signaling proteins, suggesting anti-inflammatory effects and disease-modifying potential through synaptic/axonal regulation (Apoa4, Apoa1, Apod). Integrated multi-omics identified overlapping targets linked to neuronal repair (Ankrd27) and iron metabolism (Fth1). These findings establish chrysophanol as a multitarget agent alleviating DDC via synergistic restoration of neuroplasticity, suppression of neuroinflammation, and rebalancing of metabolic homeostasis, providing a mechanistic foundation for developing chrysophanol-based therapies for diabetes-associated neuropsychiatric disorders.

overall_design: RNA-seq profiling of Ctrl, Model, ChryM after oral gavage of chrysophanol for 14 consecutive days.

first: Xujian

last: Hu


title: Salmonella typhimurium targets distal colonocytes to trigger infection [RNA-seq]

city: Xi'an

first: Shanshan

last: Li

state: Shannxi

address: Chang'an District

institute: Xi'an Jiaotong University

summary: In order to ascertain the dynamic changes of transcriptomics throughout the whole cycle of Salmonella infection in the mouse intestine and offer basic support for the single-cell and spatial transcriptome data analysis in this research, we gavaged BALB/c mice with Salmonella and carried out transcriptome sequencing on the colon tissues at five time points during the entire infection cycle.

overall_design: Bulk RNA sequencing of colonic tissues from Salmonella-infected BALB/c mice across five time points (d0, d1, d3, d5, d7; n=3 per group).

first: Ruifen

last: Zhang

first: Dan

last: Xu


title: RNA sequencing analysis of kidney tissues in MRL/lpr lupus-prone mice and C57BL/6 controls

city: Beijing

first: Zhiying

last: Gao

state: Beijing

address: Peking Union Medical College Hospital (Dongdan campus), No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing,China 100730

department: Department of Nephrology

institute: Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences

summary: To investigate the molecular mechanisms of LN, we performed RNA sequencing on the kidneys of 8- and 17-week-old female MRL/lpr and C57BL/6 mice.

overall_design: RNA sequencing was performed to assess differential gene expression in the kidneys of MRL/lpr lupus mice versus C57BL/6 wild-type mice

first: Yan

last: Qin

first: Xuemei


title: Salmonella typhimurium targets distal colonocytes to trigger infection [Spatial Transcriptomics]

summary: To quantify the extent of Salmonella infection in different large intestine segments, we performed spatial transcriptomics to analyse which clusters of cell populations were most infected by Salmonella and determined susceptibility in the distal colonocyte of mice.  To further identify that Salmonella infection-associated genes and pathways were were both significantly expressed in distal intestinal segments following Salmonella infection, we used spatial transcriptomics data to delineate the different spots on a cell-by-cell basis for subsequent cellular annotation. Our analyses reveal the susceptibility of  DCC upon Salmonella infestation.

overall_design: Mouse models of colonic tissues from Salmonella-infected BALB/c mice across four time points (d0, d1, d3, d5) were analysed using spatial transcriptomics

first: Kai

last: Ye


title: Whole transcriptome analysis of peripheral blood mononuclear cells from de novo and drug-naive sporadic Parkinson’s disease patients

city: Sant Joan d'Alacant

first: Marina

last: Guillot Fernández

state: Alicante

address: Av. Don Santiago Ramón y Cajal, s/n

country: Spain

institute: Instituto de Neurociencias

summary:
This study investigated gene expression differences in Parkinson’s disease (PD) using blood samples from 23 newly diagnosed, drug-naïve PD patients and 16 healthy controls recruited from two hospitals in Spain. Participants met diagnostic criteria for early-stage PD (Hoehn and Yahr I-II) and had no family history of the disease. Ethical approval and informed consent were obtained.
Peripheral Blood Mononuclear Cells (PBMCs) were isolated, frozen, and processed for RNA extraction. RNA integrity was assessed before whole transcriptome analysis using the Clariom S Array (Affymetrix). Data processing was conducted in R using BioConductor packages. Quality control measures led to the exclusion of one sample, and data were normalized using Robust Multi-array Average (RMA). Lowly expressed genes and probes not mapping to known genes were filtered out, resulting in 38 samples with 18,091 probes

overall_design: The study included a total of 39 blood samples, comprising 23 from de novo, drug-naïve Parkinson’s disease (PD) patients and 16 from healthy, age- and sex-matched controls. Following quality control assessments, one sample was excluded due to failing labeling control thresholds, resulting in a final dataset of 38 samples. Each patient represented a biological replicate. Peripheral Blood Mononuclear Cells (PBMCs) were isolated, and RNA was extracted and assessed for integrity before transcriptome analysis using the Clariom S Array (Affymetrix). Data preprocessing involved normalization and filtering, leading to a final dataset of 18,091 probes.

first: Navarrete

last: Francisco

first: Guillot-Fernández

last: Marina

first: Martínez-Hostyn

last: Lorena

first: Navarro

last: Daniela

first: Molina

last: José A.

first: López-Atalaya

last: Jose P.

first: Manzanares

last: Jorge


title: Transcriptome of 3D cultivated colon cancer cell lines (HCT116, SW620, DLD1) and HCEC-1CT

city: Belgrade

first: Dunja

last: Pavlovic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetics and Genetic Engineering

summary: The study aimed to identify transcripts of the protein-coding genes that could have regulatory role potentially relevant for malignant transformation of the gut mucosa and colon cancer onset and progression. The set of colon cancer cell lines (HCT116, SW620 and DLD1) and immortalized cells derived from healthy gut mucosa (HCEC-1CT) were cultivated in 3D and their transcriptomes were analyzed by RNA sequencing to profile expression for both coding and non-coding transcripts.

overall_design: We performed transcript expression profiling of 3 colorectal cancer cell lines and HCEC-1CT cell line cultivated in 3D using RNA sequencing.

first: Tamara

last: Babic


title: RNA-seq analysis on bioactive micelle PPP8 therapy for Hemin stimulated mouse neurons

city: chongqing

first: Wanli

last: Yu

address: 118 Xingguang Avenue, Liangjiang New District, Chongqing

institute: chongqing medical university

summary: To analyze the effect of micellar PPP treatment on hemin-stimulated neurons, HT22 cells were treated with PBS, 50 μM hemin, or 25 μg/mL micellar PPP8 plus 50 μM hemin for 6 h. HT22 cells treated with PBS (control group), hemin (experimental group), or the combination of PPP8 and hemin (intervention group) were then collected for transcriptome (RNA-seq) analysis.

overall_design: The total RNA was extracted through the culture of neuron cell HT22. Each group was divided into three replicates. There were three groups in total, namely, the experimental group, the control group and the intervention group.Finally, the high-throughput Transcriptome was sequenced on Illumina NovaSeq.

first: Zhiyu

last: Chen

first: Bo

last: Wu

first: Chunfan

first: Ying

last: Han

first: Dewei

last: Zou

first: Jianxiang


title: Investigation of gene stability in equine luteal tissue during mid-luteal phase and early pregnancy

city: Ithaca

first: Jennifer

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: Real- time reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a technique that allows for the quantification of mRNA transcripts present within a tissue of interest. To ensure that quantified amounts of mRNA determined by RT qPCR is due to biological differences rather than a product of variation in testing protocol, results need to be normalized. Normalization has historically relied on the use of reference genes, or genes whose transcript expression does not differ in the tissue of interest independent of the experimental condition. In the field of equine reproductive studies, ACTB and GAPDH have been the most widely used reference genes for normalization of RT-qPCR results. However, recent studies have demonstrated that these genes may have drastically varied expression levels in different tissues and in different physiological states. Our study was aimed at examining different putative reference genes (historic reference genes as well as genes identified by RNA-seq to be stable across different sample types) in equine corpus luteum samples at day 11 and day 13 in pregnant and non-pregnant animals. Stability of genetic expression was evaluated via three stability software analyses (GeNorm, NormFinder and BestKeeper). We hypothesized that the most commonly used historic reference genes (ACTB, GAPDH and B2M) would be the most stably expressed genes in equine corpus luteum samples. COX4I1 and SRP14 were both found to be within the top three most stable genes of all samples for all methods. When assessing the least stably expressed genes, the historic reference genes were frequently identified across the three softwares. Exploration of putative reference genes should be considered when investigating dynamic endocrine organs such as those used in reproductive studies. RT-qPCR studies evaluated with historic genes should be interpreted cautiously.

overall_design: Healthy normal cycling light breed mares (n=8) were enrolled in the study. A transvaginal luteal biopsy was performed in pregnant and non-pregnant mares at day 11 and day 13 post-ovulation. RNA isolation was performed using TRIzol reagent (ThermoFisher) according to the manufacturer's instructions. RNA libraries were prepared using the NEBNext Ultra II Directional Library prep kit (New England Biolabs). RNA sequencing results were used to identify putative stable reference genes across pregnancy status and timepoint.

first: Leah

middle: N

last: Ramsaran

first: Michael

middle: J

last: Byron

first: Stephen

last: Parry

first: Jennine

last: Lection

first: Bradley

last: Back

first: Soon Hon

last: Cheong

first: Mariana

last: Diel de Amorim


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [CUT&Run]

city: Solna

first: Jasper

last: Panten

address: Tomtebodavägen 23

institute: SciLifeLab

type: Genome binding/occupancy profiling by high throughput sequencing

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed CUT&RUN profiling for two Xi-enriched histone marks, H2AK119Ub and H3K27me3 in a clonal neural progenitor cell line with transgenes that allow for the overexpression of Xist on the inactive X chromosome. We perform Xist overexpression experiments for up to three weeks and also test the reversibility of Xist overexpression using washout experiments.

overall_design: Clonal neural progenitor cell lines were generated by differentiating first generation hybrid embryonic stem cells (from a C57BL6/J x CAST/EiJ cross). All cell lines carry an inactive B6 X chromosome and a doxycycline-inducible transgene on the Xi. Doxycyclin treatment for 7 and 21 days was performed in the E6 cell line and allele-specific histone mark occupancy was measured using CUT&RUN. Furthermore, samples after washing out of doxycycline were analyzed to assess reversibility.

first: Edith

last: Heard

first: Agnese

last: Loda

first: Antonia

last: Hauth


title: Growth hormone directly stimulates cartilage stem cells in the human pubertal growth plate via both canonical and non-canonical pathways.

city: Gothenburg

first: Andrei

last: Chagin

state: Västra Götaland

address: Guldhedsgatan 10a

department: Institute of Medicine

institute: University of Gothenburg

summary: Single cell sequencing was used to study human growth plate cartilage subtypes and response to growht hormone stimulation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
For preparation of human single cell suspension, four human adolescent growth plate chondrocytes were isolated from patients with age 11-14 years of age undergoing Epiphysiodesis. The patients are otherwise physiologically healthy. The needle biopsy containing intact growth plate were examined, selected for explant culture and single cell isolation. Samples were either processed directly, or cultured in vehicle/growth hormone supplemented medium for 24 hours prior to single cell sequencing

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

first: Tsz

last: Chu

first: Ostap

last: Dregval

first: Dana

last: Trompet

first: Lars

last: Sävendahl


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [ESC]

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed transcriptomic profiling of X-linked gene expression in clonal neural progenitor cell lines with transgenes that allow for the overexpression of Xist on the inactive X chromosome. Here, we use the F1 hybrid mouse ESC line from which the NPCs were derived as a control to assess the silencing effect of Xist in ESCs.

overall_design: First generation hybrid embryonic stem cells (from a C57BL6/J x CAST/EiJ cross), that carry  a doxycycline-inducible transgene on the B6 allele were used. Doxycyclin treatment for 24 hours was performed in the ESCs and allele-specific expression was measured using RNA-Sequencing.


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [E8.5]

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes XCI. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. We tested whether dox-mediated Xist-overexpression affected the expression levels of escapees in extra-embryonic tissues.

overall_design: To investigate the effect of Xist overexpression on imprinted X-inactivation in extra-embryonic tissues, we crossed TX/Y males carrying the rtTA transactivator (Xptet/Y; R26rtTA/rtTA or Xptet/Y; R26rtTA/WT) with wild-type JF1 females. Xist RNA overexpression was induced by adding doxycycline to the drinking water of pregnant females for 5 days, from E3.5 to E8.5. RNA was extracted from the collected extra-embryonic tissues of each embryo. Libraries were prepared using the Smart-Seq2 protocol, and allele-specific expression was determined for X-linked genes.

first: Emma

last: Kneuss


title: Rroid2 regulates effector and memory CD8+ T cell response during infection in vivo

city: Wien

first: Dietmar

last: Herndler-Brandstetter

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University of Vienna

summary: CD8+ T cell differentiation has been associated with changes in the expression of long noncoding RNA (lncRNAs). Yet, which and how lncRNAs regulate CD8+ T cell responses following infection in vivo remain incompletely understood. We performed deep RNA-seq to map the lncRNA expression landscape of CD8+ T cell subsets during infection and generated lncRNA knockout mouse models to evaluate the in vivo relevance of six lncRNAs. We identified the enhancer lncRNA Rroid2 to regulate effector CD8+ T cell function as well as effector-to-memory differentiation. Rroid2-deficient mice displayed increased CD44dim Foxp3+ regulatory T cells while the development of other immune cells, such as natural killer cells, was not affected. In CD8+ T cells, Rroid2 deficiency resulted in a fine-tuned downregulation of transcription factors Id2 and T-bet and impaired effector CD8+ T cell proliferation and cytotoxicity as well as memory CD8+ T cell generation and recall responses. In contrast to Id2, Rroid2 deficiency affected both KLRG1+ and KLRG1- effector CD8+ T cells. Taken together, Rroid2 represents a key regulatory layer that controls CD8+ T cell responses to pathogens.

overall_design: RNA-seq analysis of MPEC OT-I cells 14 days post infection and SLEC OT-I cells 7 and 14 days post infection with LM-OVA. Following adoptive transfer of WT and Rroid2 KO OT-I cells and listeria infection, Fluorescence-activated cell sorting (FACS) of transferred OT-I cells from the spleen of infected host mice was performed. RNA was isolated and samples were analyzed with RNA-seq.

first: Julia

last: Erber

first: Thomas

last: Mohr

first: Iros

last: Braozzi


title: Olfr2 drives abdominal aortic aneurysm by promoting monocyte recrutiment

city: Cologne

first: Patrik

last: Schelemei

address: Kerpener Str. 62

department: Internal Med III

country: Germany

institute: University Hospital Cologne

summary: Olfactory receptor 2 is a G-protein coupled receptor expressed on vascular macrophages. Activation by its ligand octanal in conjuction with a toll like receptor 4 stimulus induces the NLRP3 inflammasome with subsequent IL-1alpha and IL-1beta release. In this study we aim to investigate the effects of genetic Olfr2 deficiency on the development of abdominal aortic aneurysm (AAA).

overall_design: RNA seq profiling of sorted Ly6Chigh monocytes from the spleen of Olfr2 WT and KO mice at day 7 after aneurysm induction

first: Holger

last: Winkels


title: Resident CD49a⁺CD103⁺NKG2C⁺ NK Cells Restrict HIV Infection in Human Lymphoid Tissue Explants

city: Barcelona

first: María José

last: Buzón Gómez

state: Barcelona

address: Passeig Vall d'Hebron, 119-129

department: Infectious Diseases

institute: Vall d'Hebron Research Institute

summary: Natural killer (NK) cells are pivotal effectors in antiviral immunity, yet their tissue-specific roles during acute HIV infection remain poorly defined. Using an ex vivo human tonsillar tissue model, we profile NK cell responses to early HIV infection and uncover distinct subsets with specialized functions. We identify a previously uncharacterized memory-like NK population (CD16⁺/⁻CD69⁺CD49a⁺CD103⁺NKG2C⁺) associated with reduced viral burden and enriched in cytotoxic mediators (GNLY, PRF1, GZMB), apoptotic ligands (FASLG, TRAIL), cytokine receptors (IL2RA, ILR2B, IL2RG, IL12RB2, IL18R1) and trafficking molecules (CCL3–5, CCR7, SELL). These cells coexpress NKG2A, suggesting a regulatory balance between activation and inhibition. Although functionally capable of clearing HIV-infected CD4⁺ T cells in a tissue-mimetic environment, they show impaired cytotoxicity and transcriptional signs of exhaustion after infection. Conversely, HIV drives the reprogramming of immature CD16⁻CD69⁺ NK cells toward a more cytotoxic and migratory effector phenotype. These findings reveal dynamic NK cell adaptations in lymphoid tissue during early HIV infection and highlight tissue-resident NK cells as promising targets for immunotherapeutic intervention.

sample_organism:
Homo sapiens
HIV-1 group M

platform_organism:
Homo sapiens
HIV-1 group M

overall_design: Tonsils from a 9-year-old and a 10-year-old child were left overnight in dissection medium to inactivate contaminating microorganisms. Dissection medium included RPMI-1640 medium (Gibco) supplemented with 500 U/ml penicillin (Fisher Scientific), 500 µg/ml streptomycin (Fisher Scientific), 1 µg/ml gentamicin (Gibco), and 5 µg/ml amphotericin B (Gibco). Tonsillar tissue explants (8 mm³ blocks) were cultured on the air-liquid interface on absorbable gelatin sponges (Goodwill). The hemostatic sponges were soaked in RPMI-1640 medium supplemented with 20% Fetal Bovine Serum (FBS) (Gibco), 10 mM HEPES (Biowest), 100 U/ml penicillin, 100 µg/ml streptomycin, and 66 µg/ml amikacin (Vall d’Hebron Hospital pharmacy) (R20 medium). The first day of culture, R20 medium also included 310 µg/ml of timentin (Caisson Labs). Half of the tissue blocks were infected with HIV Bal viral stock (TCID50: 625 units) via dropwise application directly onto the tissue. Medium and sponges were refreshed every 2 days. After 5 days of culture, the tissue blocks were mechanically dissociated and filtered sequentially through 70 µm and 30 µm cell strainers to obtain a single-cell suspension. The CD56+ cell population was enriched from both HIV-infected and uninfected tissue suspensions using the MagniSort™ Human CD56 Positive Selection Kit. Subsequently, CD3- CD56+ cells were further purified by Fluorescence-Activated Cell Sorting (FACS) and analyzed using scRNA-seq.

last: Buzón

first: David

last: Perea

first: Alba

last: González

first: Irene

last: Mota


title: Inducible deletion of DGAT1 and 2 from microglia exacerbates neurodegeneration and endolysosomal lipid accumulation in male PS19 mice.

city: St Louis

first: George

middle: Travis

last: Tabor

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

summary: Brain myeloid cells accumulate neutral lipids in multiple human neurodegenerative disorders and relevant mouse models. These lipid structures are often assumed to be lipid droplets (LDs), and ‘LD-high microglia’ have generally been characterized as maladaptive. While a number of studies have been performed in cell culture and Drosophila models to characterize glial LD dynamics, it is still unclear what roles microglial LD biogenesis play in mammalian tauopathy. To address this question, we induced the deletion of diacylglycerol acyltransferases 1 and 2 (DGATs), enzymes critical for LD formation, from microglia in the PS19 mouse model of tauopathy. We observed that microglial DGAT KO exacerbated neurodegeneration, induced behavioral deficits, and increased the accumulation of brain cholesterol esters in male PS19 mice. Myeloid cell lipids appeared to largely localize to endosomes/lysosomes not LDs, even in control PS19 mice. Our results suggest that microglial DGAT-dependent LD biogenesis is adaptive in advanced tauopathy. Furthermore, the bulk of the lipidic accumulations in brain myeloid cells do not correspond to true LDs, which has important implications for the development of lipid-modulating therapies for neurodegenerative diseases.

overall_design: snRNA-seq profiling of PU.1+ nuclei from 9.5-month-old WT (CfD) and PS19 (PCfD) mice heterozygous for Cx3cr1-CreERT2 and homozygous for floxed DGAT1 and DGAT2 alleles that were treated with tamoxifen or oil at 3 months of age.  CfD-OIL, CfD-TAM, PCfD-OIL, and PCfD-TAM

last: Holtzman

first: Elizabeth

last: West

first: Johannes

last: Schlachetzki

first: Christopher

last: Glass

first: Carisa

last: Zeng

first: Maxim

last: Artyomov


title: FKBP9 Enhances IGF2BP1 Mediated m6A Recognition and Promotes Hepatocellular Carcinoma Progression

city: Nanjing

first: Facai

last: Yang

state: jiangsu

address: No. 87 Dingjiaqiao, Gulou District, Nanjing

institute: Southeast University

summary: Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal malignancies worldwide, with intricate molecular mechanisms driving its progression. Among various post-transcriptional regulatory mechanisms, N6-methyladenosine (m6A) modification has emerged as a critical factor influencing mRNA stability and translation, thereby impacting tumorigenesis. FK506-binding protein 9 (FKBP9), a peptidyl-prolyl isomerase (PPIase), has been implicated in several cancers; however, its specific role in HCC remains largely unexplored, and existing studies have not fully elucidated the molecular interactions and downstream effects of FKBP9 in HCC. In this study, we employed a combination of biochemical, molecular, and cellular techniques, including immunoprecipitation, RNA immunoprecipitation, luciferase reporter assays, and in vivo tumor models, to investigate the functional relationship between FKBP9 and the m6A reader protein Insulin like growth factor 2 mRNA binding protein 1 (IGF2BP1). Our findings demonstrate that FKBP9 directly interacts with IGF2BP1, enhancing its recognition of m6A-modified transcripts, particularly oncogenes such as MYC and Platelet-Derived Growth Factor Subunit B (PDGFB). Functional assays revealed that FKBP9 promotes HCC cell proliferation, migration, and invasion by stabilizing m6A-tagged oncogenic mRNAs. Furthermore, in vivo experiments confirmed that FKBP9 overexpression accelerates tumor growth, whereas MYC inhibition mitigates this effect. This study provides novel insights into the oncogenic role of FKBP9 in HCC by uncovering its regulatory influence on IGF2BP1-mediated m6A RNA recognition. These findings suggest that targeting the FKBP9-IGF2BP1 axis could be a promising therapeutic strategy for HCC.

overall_design: RNA-seq profiling of wildtype Huh7 cells and their knockdown derivatives (shFKBP9, shIGF2BP1), and eild-type HepG2 cells were used for MeRIP-Seq.


title: Salmonella typhimurium targets distal colonocytes to trigger infection

first: Ruifen

last: Zhang

state: Shaanxi

address: No. 28, Xianning West Road, Pengkang Building, Xingqing Campus, Xi'an Jiaotong University

department: School of Life Sciences

institute: xjtu

summary: To clarify how different intestinal cell types respond when facing the key intestinal pathogenic microorganism Salmonella, we conducted single-cell transcriptomic sequencing. The results revealed that a specific cluster of mature colonic epithelial cells was the most susceptible to infection. By describing the transcriptomic changes of this cluster of cells at different time points after infection, we further aimed to explain how this cluster of cells was affected by the infection.

overall_design: Single-cell RNA sequencing of colonic tissues from Salmonella-infected BALB/c mice across five time points (d0, d1, d3, d5, d7; n=2 per group).

first: Dan

last: Xu

first: Stephen

last: Bush


title: A Transcriptome-based Molecular Classification Scheme for Thyroid Eye Disease

city: Shanghai

first: Tianyi

last: Zhu

address: 639 Zhizaoju Road

department: Ophthalmology

institute: Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine

summary: Thyroid eye disease (TED) is an orbital autoimmune disease which severely affects vision, appearance, and quality of life. TED is the most common extrathyroidal manifestation of Graves' disease, which is mainly featured by hyperthyroidism. Current assessments of TED severity and activity, do not effectively guide regimen, especially the selection of target agents. Peripheral blood samples from 161 TED patients and 20 Graves' hyperthyroidism (GH) patients without eye disease were collected for transcriptome sequencing, and corresponding clinical information was systematically compiled. We then comparatively derived a unique gene expression profile for TED compared to GH, and based on this, unsupervised clustering of TED patients using ConsensusClusterPlus was conducted. Next, immune infiltration analysis, weighted gene co-expression network analysis (WGCNA), hub gene screening, and drug sensitivity analysis were performed for different clusters. TED exhibited elevated of autoantigens, immune responses, cellular proliferation, and metabolic disorders than GH. A novel two-cluster classification scheme was established for TED, independent of classical assessment of severity and activity. Cluster 1 patients received more intravenous glucocorticoids and surgeries but experienced less pain and excessive tearing. They had higher peripheral blood lymphocytes, including CD4+ T cells, CD8+ T cells, T follicular helper cells, natural killer cells, and B cells, than cluster 2 patients. WGCNA identified cluster-related gene modules, and least absolute shrinkage and selection operator (LASSO) regression analysis yielded six hub genes (DDR2, LRP1B, NTRK2, PALB2, PTPRD, and SLC25A6) for cluster 1 and three hub genes (MON2, SNORA74B, and STX16) for cluster 2 as potential biomarkers. Considering current TED therapies, cluster 1 patients may prefer insulin-like growth factor 1 receptor (IGF-1R) antibodies, while cluster 2 patients may favor glucocorticoids. We described the specific gene profile of TED compared to GH and built a new molecular classification of TED patients into two clusters with different immune infiltration, hub genes, and drug sensitivity. It paves the way for improved application of precision medicine in TED.

first: Weijin

last: Qian

first: Jin

last: Liu

first: Chen

last: Liang

first: Huifang

last: Zhou


title: Clazakizumab treatment effects on peripheral blood and kidney transcriptomes in chronic antibody-mediated rejection

city: Cambridge

first: Roy

address: Cambridge Biomedical Campus, Francis Crick Ave

institute: MRC Laboratory of Molecular Biology

summary: There are currently no licenced treatments for antibody-mediated rejection (ABMR), a major cause of late kidney allograft loss. IL-6 is a cytokine that promotes B cell differentiation to plasma cells, T follicular cell (Tfh) polarisation, and monocyte activation, key processes for antibody generation or effector functions. Clazakizumab (CLZ), an IL-6-neutralising antibody, has been used in a phase 2 trial in patients with ABMR, showing potential efficacy in terms of a reduction in donor-specific antibodies and kidney molecular ABMR (MMDx) score. Here we studied the transcriptional changes occurring in paired blood and kidney samples taken following CLZ treatment during this clinical trial. We observed a reduction in ‘FcγR mediated phagocytosis’, ‘complement and coagulation cascades’ and ‘natural killer (NK) cell mediated cytotoxicity’ gene sets in peripheral blood with short-term CLZ treatment, with variable individual responses and some patients showing a rebound in these pathways in longer-term despite ongoing CLZ treatment. We identified a gene module in blood that showed a significant positive correlation with kidney ABMR MMDx score and was down-regulated with CLZ-treatment, potentially identifying a peripheral blood gene set that can be used to non-invasively assess treatment efficacy. In the kidney, CLZ-treatment was associated with a reduction in a “damaged tubule” gene signature and preservation of podocyte signatures, providing further evidence of its therapeutic efficacy in ABMR.

overall_design: Comparative gene expression profiling from peripheral blood taken at 3 timepoints during a phase 2 randomised controlled trial assessing clazakizumab in treatment of late antibody mediated rejection

first: Colin

last: Lee

first: Menna

last: Clatworthy


title: Therapeutic Perturbation of Liver and Bile Duct Cancer through Targeted Inhibition of FSP1 and GCS Induced Ferroptosis

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

summary: Triggering ferroptosis has recently been demonstrated to be a promising approach for cancer treatment. However, the application of current ferroptosis inducers, such as GPX4 inhibitors, was rather limited due to their pharmaceutical or safety issues, which evoking the discovery of new favorable candidates. In this study, we took advantage of a phenotypic screening strategy and discovered (20S)-Protopanaxatriol (hereafter as (20)S-APPT), a derivative of ginsenosides, as a novel ferroptosis inducer both in vitro and in vivo, with desirable safety in particular. Mechanistic investigations revealed that (20)S-APPT induces ferroptosis by targeting plasma-membrane localized CoQ10 oxidoreductase FSP1. Upon FSP1 inhibition, oxidation of arachidonic acid in an ACSL4 dependent way as well as reactive oxygen species produced by mitochondrial oxidative stress are both involved to boost the process of ferroptosis. Intriguingly, we firstly uncovered that inhibition of FSP1 alone is sufficient to induce ferroptotic cell death in a subset of liver and bile duct cancer cells. Furthermore, we unexpectedly found that only the addition of GCS inhibitor BSO, which attenuates intracellular GSH, exerts synergistic effect to induce ferroptosis with FSP1 inhibitors in rest non-responsive cancer cells, while sparing normal cell counterparts intact. Overall, our work helped to gain insights into a new ferroptotic role of FSP1 and further proposed that co-targeting FSP1 and GCS is a hopeful and safe strategy to combat liver and bile duct cancer through triggering ferroptosis, which might facilitate to pave a new way for drug development and further clinical therapeutic intervention in the future.

overall_design: 1. Cell Culture and Treatment. SK-HEP-1 cells were cultured and treated with 10 µM (20)S-APPT for 12h to observe transcriptome changes. 2. RNA-seq library construction. Extract total RNA from both control (ctrl) and (20)S-APPT treated cells. Prepare sequencing libraries using an RNA-seq kit. Sequence libraries on a high-throughput sequencing platform to obtain transcriptome data. 3. Data Analysis. Process raw sequencing data to remove low-quality reads. Align RNA-seq reads to the reference genome. Identify differentially expressed genes between ctrl and (20)S-APPT treated cells.

first: Fanyu


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [Astrocytes]

first: Jasper

last: Panten

summary: X-chromosome inactivation (XCI) silences one copy of the X-chromosome in female cells, but a number of genes escapes XCI. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees in Astrocytes. To this end, we performed RNA-seq analysis profiling of X-linked genes upon doxycycline-induced Xist upregulation and following doxycycline washout.

overall_design: Astrocytes were generated by differentiating NPC clone E6 (C57BL6/J x CAST/EiJ). Doxycyclin treatment for 3 and 7 days (and following wash-out) was performed and allele-specific RNA expression was measured.

first: Edith

last: Heard

first: Agnese

last: Loda

first: Antonia

last: Hauth


title: Epigenetic profiling of hematopoietic stem cells identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

summary: The ability to cope with fluctuations in energy supply is essential for an organism's survival and health. While caloric restriction (CR) provides benefits towards many aspects of aging, it is associated with loss of immune function. The mechanisms by which the hematopoietic stem cells (HSCs) respond to this stress and potentially contribute to this loss of immunity remain unclear. In this study, using both lifelong and short-term CR mice models, we found that reduced energy supply leads to a decrease in total peripheral blood white blood cell production that is myeloid- and thrombo-erythroid-biased. This strategy prioritizes the production of cell types essential for survival, such as red blood cells, platelets, and innate immune cells, at the expense of adaptive immune cell differentiation. Consistent with change in blood composition, HSCs under CR are driven into cell cycle to support the myeloid differentiation rather than self-renewal. Interestingly, despite the altered hematopoietic output, lifelong CR mitigates age-associated transcriptome changes of the HSCs, but these modifications are swiftly lost after ad libitum feeding. Epigenetic profiling identified KDR as a key regulator of the CR response and experimental knockdown of Kdr in aged HSCs reproduced the more youthful aging transcriptome observed in lifelong CR HSCs. Additionally, we show that PU.1 acts as an intracellular regulator of the CR response, regulating HSC self-renewal and differentiation under CR conditions by increased binding to its target genes.

overall_design: RNA-seq, ATAC-seq, ChIP-seq sequencig were performed to compare the epigenome between young and old wild type and calorie restriction HSCs.

first: Le

last: Zong

first: Ferda

last: Tekin-Turhan

first: Wakako

last: Kuribayashi

first: Mayuri

last: Tanaka-yano

first: Keefer

last: Li

first: Isabel

last: Beerman


title: Protein kinase A regulates ferroptosis by controlling GPX4 m6A modification through phosphorylation of ALKBH5

city: Shenzhen

first: YANXI

last: SUN

address: No.66,Gongchang Road

department: School of Medicine

institute: Sun Yat-sen University

summary: GPX4-dependent ferroptosis has emerged as a therapeutic strategy for cancer treatment. Here, we demonstrated that protein kinase A (PKA) participates in the regulation of ferroptosis by controlling the m6A modification of GPX4 in an ALKBH5-dependent manner. Notably, we identified ALKBH5, an m6A demethylase, as a novel target of PKA, which drives phosphorylation-dependent degradation of ALKBH5 protein. Moreover, the deletion of ALKBH5 represses ferroptotic cell death by maintaining GPX4 m6A modification and stability. Thus, by regulating ALKBH5-dependent GPX4 stability, PKA acts as a key regulator of ferroptosis. Our study unveils the involvement of PKA in m6A modification, which could control GPX4-dependent ferroptosis and tumor progression.

overall_design: RNA-seq profiling of HT-1080 cells and their knockout derivatives(sgPKA, sgALKBH5)

first: Xiaocheng

last: Zhao

first: Yanxi

last: Sun

first: Xingwu


title: scRNA of tumor associated lymphatic endothelial cells (LEC) from B16-OVA-VEGFC tumors implanted in Ifnγr1WT (Cre minus) and Ifnγr1iProx1 (Cre plus) mice

city: New York

first: Amanda

last: Lund

state: New York

address: 522 First Ave

institute: NYU Langone Health

summary: In order to determine transcriptional differences between lymphatic endothelial cell (LEC; CD45-CD31+pg38+) from B16-OVA-VEGFC melanoma tumors from Ifnγr1WT (Cre minus) and Ifnγr1iProx1 (Cre plus) mice, we sorted endothelial cells (DAPI-, CD31+, CD45-) from Ifnγr1WT (Cre minus) and Ifnγr1iProx1 (Cre plus) mice separately.

overall_design: B16-OVA-VEGFC (500K) were intradermally implanted in Ifnγr1WT (Cre minus) and Ifnγr1iProx1 (Cre plus) mice. On day fifteen, tumors were collected and three tumors per condition were pooled and stained (DAPI-, CD31+, CD45-) and sorted separately.

first: Karakousi

last: Triantafyllia

first: Cristaldi

last: Vanessa


title: Responses of various cells in the zebrafish olfactory epithelium after treatment with alarm substances

city: wuhan

first: Wenjun

last: Chen

address: No. 7 Donghu South Road, Wuchang, Wuhan

department: Chinese Academy of Sciences

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: We performed single-cell transcriptome sequencing of the olfactory epithelium of AB strain zebrafish. We also applied alarm substances to one of the groups and studied the response of the olfactory epithelium to alarm substances by comparing the proportions of various cell types and transcriptional changes between the experimental and control groups.

overall_design: Zebrafish were exposed to alarm substances and their olfactory epithelium was used for single-cell sequencing. The blank control group used olfactory epithelium from zebrafish of the same strain, age and sex.

first: wenjun

last: chen

first: Haifeng

last: Jiang

first: Cheng

last: Wang

first: Zufa

last: Ding

first: Dan

last: Yu

first: Yang

last: Liu

first: Shunping

last: He

first: Liandong

last: Yang


title: Effect of depletion of Kdm5a on gene expression of zebrafish

city: Taiyuan

first: Yuan

last: Fu

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

department: Department of Biochemistry and Molecular Biology, School of Basic Medicine

institute: Shanxi Medical University

summary: To study Kdm5a regulation of gene expression in zebrafish, we established a Kdm5a-deficient animal model by crispr/cas9.We then performed gene expression profiling on RNA-seq data at two time points, 24h and 48h after fertilization in zebrafish.

overall_design: Comparative gene expression profiling of RNA-seq data from WT-zebrafish and Kdm5a-KO zebrafish at 24h and 48h after fertilization.

first: Jianting

last: Li

first: Qi

last: Xie

first: Xiaolong

last: Gu


title: Adipose-specific MTP deficiency protects against hepatic steatosis up upregulating PPARα activity

city: Mineola

first: M. Mahmood

last: Hussain

address: 101 Mineola Blvd.

department: Foundations of Medicine

institute: NYU Grossman Long Island School of Medicine

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing health concern. Better understanding of factors that prevent hepatic lipid accumulation may help design new strategies to prevent or treat MASLD. We have previously shown that adipocyte microsomal triglyceride transfer protein (MTP) regulates intracellular lipolysis by inhibiting adipose triglyceride lipase (ATGL) activity. Here, we show that adipose-specific MTP knockout mice (A-Mttp−/−) fed an obesogenic diet exhibit moderately high plasma triglyceride levels and less hepatic steatosis compared to their wild-type counterparts. Mechanistic studies revealed that high plasma triglycerides are due to increased hepatic triglyceride synthesis and production of triglyceride-rich lipoproteins from the livers of A-Mttp−/− mice. In addition, hepatocytes from these mice showed increased fatty acid oxidation and this could be a contributing factor for less hepatic steatosis. Studies aimed at understanding how adipose MTP regulated hepatic triglyceride-rich lipoprotein production and fatty acid oxidation revealed that adipose MTP modulates the release of agonists that activate hepatic PPARα activity. Our study highlights the significance of the regulated movement of fatty acid from adipose tissue to the liver in maintaining a healthy liver. It is likely that adipocyte fatty acid release can be modulated to reduce hepatic steatosis.

overall_design:
Stromal vascular fraction (SVF) isolated from wild type and adipose MTP KO mice were isolated and differentiated into adipocytes. The adipocytes were starved overnight and the conditioned media was collected. The primary hepatocytes isolated from wild type mice was treated with either Mttp flox or Mttp KO adipocyte condition media.
RNA was Isolated from these hepatocytes to perform RNA sequencing.
The data from RNA sequencing was used to indentify differentially expressed genes.

first: Sujith

last: Rajan

first: Michael

last: Verano

first: Thomas

last: Palaia

first: Chandana

last: Prakashmurthy

first: Shahidul

last: Islam

first: Lili

last: Lee

first: Jose

middle: O

last: Aleman

first: Ira

last: Goldberg

first: Edward

last: Fisher

first: Mahmood


title: Single cell RNA-sequencing analysis of the inhibitory effects of Olig2 on astrocyte-to-neuron conversion

city: Guangzhou

first: Zheng

last: Wu

state: Guangdong

address: 601 West Huangpu Road

institute: Jinan University

summary: Collectively, our study reveals the role of Olig2 in hindering the in vivo AtN conversion and idendifies an inducible barrier to neuronal reprogramming.

overall_design: WT mouse cortex was injected with AAV9 hGFAP-Ngn2-tdTomato in the presence of scramble shRNA or Olig2 shRNA.  Virus-infected brain tissue was collected 18, 20, 22 days post injection (n = 2 mice for each time point), and dissociated into single-cell suspension, which was loaded to microfluidic chip, followed by scRNA-seq processing.

first: Chuying

last: Lai

first: Kaiyu

last: Hou

first: Gong

last: Chen


title: Olfr2 deficiency protects from abdominal aortic aneurysm

first: Patrik

last: Schelemei

overall_design: RNA-seq profiling of AAA of Olfr2 WT and Olfr2 KO mice at day 7 after aneurysm induction.

first: Schelemei

last: Patrik

first: Winkels

last: Holger


title: IFNγ-dependent metabolic reprogramming restrains an immature, pro-metastatic lymphatic state in melanoma

first: Amanda

last: Lund

summary: In order to determine the transcriptional changes upon IFNγ treatment on Human Dermal Lymphatic Endothelial Cells (HDLEC), we treated HDLEC in vitro with recombinant human IFNγ or PBS control for 72 hours.

overall_design: HDLECs were seeded in 6-well plates at 60K per well. The following day they were treated with PBS control or IFNγ (0.5ug/ml) in fresh media. Treatment was replenished every day.

first: Karakousi

last: Triantafyllia

first: Cristaldi

last: Vanessa


title: Tracing the molecular route to progression in miRNA biogenesis-defective thyroid lesions [InfiniumMethylationData]

status: Public on Dec 10 2025

city: Hospitalet de Llobregat

first: Barbara

last: Rivera

address: Granvia de l'Hospitalet de Llobregat, 199

institute: IDIBELL

type: Methylation profiling by genome tiling array

summary: Germline and somatic alterations in DICER1 and DGCR8 microprocessors confer risk of developing benign and malignant thyroid lesions, yet the molecular events driving malignant transformation remain unclear. We trace the molecular trajectories from benignity to malignancy in DICER1/DGCR8-mutated thyroid lesions using multi-omic profiling on 27 DICER1/DGCR8-mutated samples. Our findings reveal a progressive, specific, and linear accumulation of genetic alterations, which when combined with enhanced downregulation of miRNAs distinguished DICER1/DGCR8-malignant lesions from their benign counterparts. Compensatory hypomethylation of miRNA encoding genes characterised DICER1/DGCR8-benign lesions, but as the tumors progressed to malignancy, methylation was partly reimposed, reversing the attempts to activate miRNA-encoded genes and further compromising miRNA production. Transcriptomic analyses revealed mutation-specific effects on the microenvironment, whereby DICER1 mutations activated canonical thyroid cancer progression pathways, whereas altered DGCR8 associated with immune-related alterations. This work unveils specific molecular events underlying malignant progression of miRNA-biogenesis related thyroid tumors and identifies potential biomarkers and disease etiology mechanisms.

overall_design: Thyroid lesion-specific genome-wide DNA methylation profiling was investigated in 3 FFT and 9 FFPE samples (5 TFNDs, 4 FTCs, 1 FVPTC, and 2 PDTCs) using the Illumina HumanMethylation EPIC array at GenomeScan (Leiden, The Netherlands). The data from these samples was combined with data from 5 publicly available datasets from the Gene Expression Omnibus (GEO): GSE121377, GSE197860, GSE97466, and GSE77804 and GSE214568 (thyroid data only); and 1 publicly available dataset from ArrayExpress: E-MTAB-10906. All 6 datasets employed Illumina platforms, with four using the EPIC array and two using the Illumina 450K array. Four datasets were also derived from FFT samples while the other two datasets were derived from FFPE samples. From these 6 studies, we included a total of 277 thyroid samples: 21 FVPTCs; 4 PTC, not otherwise specified (PTC-NOS); 6 ATCs; 6 OTAs; 8 OTCs; 60 CPTCs; 57 normal thyroid tissues; 29 TFNDs; 20 FTAs; 8 tall-cell variant PTC; 26 FTCs; 3 PDTCs; 7 NIFTPs; and 22 nodular hyperplasias. Additionally, we included 2 DICER1-mutated FVPTCs and 2 DGCR8-mutated FVPTC from the TCGA-THCA project.

first: Chong

last: Anne-Sophie

first: Roca

last: Carla


title: Gene expression profile in single cells of neonatal murine anemic liver

city: Omaha

first: MohanKumar

last: Krishnan

address: 985870 Nebraska Medical Center

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

summary: In the mice fetus or neonate, the liver is the major hematopoietic organ before the bone marrow takes over, and anemic-associated hypoxia may alter the hematopoietic niche in the liver.  Using scRNA-seq analysis, we analyzed the cell diversity in the neonatal murine anemic liver.  Briefly, C57BL/6 mice from each litter were randomly assigned to two study groups: (a) naive control and (b) phlebotomy-induced anemia. Phlebotomy-induced anemia was performed in mouse pups by facial vein phlebotomy to remove 20µL blood/g body weight on P2, P4, P6, P8, and P10 to reduce the hematocrit (Hct) index from an initial 45-60% range, down to 20-24%. Hematocrits and RBC indices were measured at each phlebotomy; 5 µL blood was diluted 1:20 in Cellpak reagent (Sysmex America, Mundelein, IL; catalog #DCL-310A), and analyzed in the Sysmex XT-2000iV veterinary hematology analyzer. Non-phlebotomized control animals were handled similarly to phlebotomized animals with a daily non-phlebotomizing needle stick. Pups were weighed daily to determine the volume of blood to be drawn. The animals were euthanized 24 h (P11) later, and the liver tissue was processed for scRNA sequencing.

overall_design: We used phlebotomy-induced anemia in C57BL6/J neonatal mouse pups and extracted the liver tissue for single cell isolation by using mouse liver dissociation kit (Miltenyi Biotech).  Single-cell RNA-sequencing was performed on dissociated liver single cells using the Chromium Next GEM Single-Cell 3ʹ Reagent Kits v3.1 (10× Genomics) at the Single Cell & Transcriptomics Core, Johns Hopkins University.  Mice with and without phlebotomy-induced anemia were analyzed by scRNA-Seq and compared as two study groups: (a) naive control and (b) phlebotomy-induced anemia.

first: Conover

last: Talbot Jr


title: Transcriptome analyses of human corneal endothelial cell lines derived from patients with Fuchs Endothelial Corneal Dystrophy

city: Boston

first: Shazia

last: Ashraf

state: Massachusetts

address: Massachusetts Eye and Ear Inf.

institute: Massachusetts Eye and Ear Infirmary

summary: We report differential gene expression profiles of the corneal endothelial cells from Fuchs dystrophy patients with or without the TCF4 gene mutation

overall_design: mRNA expression profiles (RNAseq) of cell lines generated from the corneal endothelial tissues obtained from 3 normal donors, 3 FECD patients with TCF4 mutation, and 4 FECD patients without TCF4 mutation

first: Ula

last: Jurkunas


title: CUT&Tag analysis of the inhibitory effects of Olig2 on astrocyte-to-neuron conversion

first: Zheng

last: Wu

overall_design: WT mouse cortex was injected with AAV9 hGFAP-Ngn2-tdTomato. Virus-infected brain tissue was collected 7 days post injection (n = 12 mice), and dissociated into single-cell suspension, followed by tdTomato+ cells collecting by fluorescent-assisted cell sorting. The tdTomato+ cells were then subjected to CUT&Tag sequencing.


title: Nanoengineered  3D culture substrate enables superior long-term and polyclonal engraftment of genetically engineered hematopoietic stem and progenitor cells

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

summary: Ex vivo culture of hematopoietic stem and progenitor cells is crucial for gene therapy applications but inadvertently triggers detrimental cellular responses, potentially threatening clinical success. In this study, we employ a biocompatible 3D scaffold with cell-scale resolution to provide mechanical support during ex vivo manipulation. This innovative 3D culture system improves multi-lineage differentiation and engraftment capacity by leveraging mechanobiological control over nuclear morphology, cytoskeleton organization, metabolism, and DNA integrity. Notably, 3D culture enables efficient genetic engineering across multiple platforms, including long-range gene editing, base- and prime-editing, and lentiviral gene addition. Moreover, this scaffold increases the clonal output and the long-term persistence of genetically engineered cells in xenotransplantation experiments and outperforms traditional 2D culture in a clinical protocol for Wiskott-Aldrich Syndrome. Overall, we propose a transformative approach to enhance the efficacy and safety of hematopoietic stem cell-based gene therapies within emerging and pre-existing clinical workflows.

overall_design: Human hematopoietic stem and progenitor cells (HSPCs) were cultured on traditional 2D culture or on innovative 3D culture substrates and bulk RNA sequencing analyses were performed on days 4 or 7 post-thawing

first: Federico

last: Midena

first: Teresa

last: Tavella

first: Raffaella

last: Di Micco


title: Effect of the rhesus theta defensin-1 (RTD-1) on gene expression in human monocytic THP-1 cells. [I]

city: Los Angeles

first: Prasad

last: Tongaonkar

state: CA

address: 7504 NRT, 1450 Biggy St

department: Pathology and Laboratory Medicine

institute: USC

summary: Theta defensins are unique since they are the only cyclic peptides in the animal kingdom.  The theta defensin, Rhesus theta defensin (RTD)-1, first isolated from rhesus macaque neutrophils as a broad-spectrum antimicrobial peptide was subsequently found to regulate gene expression and immune signaling pathways in cell culture and animal models of immune mediated diseases. To gain insights into RTD-1 regulation, we performed RNA sequencing (RNA-seq) to determine the effect of RTD-1 on global gene expression in THP-1 monocytes. Differential gene expression analysis revealed RTD-1 mediated stimulation of interferon and antiviral gene expression pathways potentially priming cells for resistance to viral infections.

overall_design: Monocytic THP-1 cells were treated with 1, 3, 10 µg/ml RTD-1 or with the vehicle (0.01 % acetic acid) for 20 h in the presence or absence of 100 ng/ml Salmonella enterica LPS in RPMI containing 1% FBS and 1% penicillin/streptomycin medium. The RNA isolated from these cells was used for gene expression profiling to identify differentially expressed genes between RTD-1 treated and untreated cells.

first: Katie

last: Trinh

first: Michael

middle: E

last: Selsted


title: Effect of the rhesus theta defensin-1 (RTD-1) on gene expression in human monocytes. [II]

summary: Rhesus theta defensin (RTD)-1, a cyclic antimicrobial peptide, regulates gene expression and immune signaling pathways in cell culture and animal models of immune mediated diseases. To gain insights into RTD-1 regulation of naïve cells, we performed RNA sequencing (RNA-seq) to determine the effect of RTD-1 on global gene expression in human monocytes. Analysis of differentially expressed genes revealed RTD-1 mediated stimulation of interferon and antiviral gene expression pathways in human monocytes.

overall_design: Human monocytes were treated with 10 µg/ml RTD-1 or with the vehicle (0.01 % acetic acid) for 4 h in RPMI medium containing 1% Heat Inactivated FBS, 1% penicillin/streptomyocin and 100 µg/ml normocin. The RNA isolated from these cells was used for gene expression profiling to identify differentially expressed genes between RTD-1 treated and untreated cells.


title: Gene expression profiling of MC38 Zfx KO clones in vitro

city: South San Francisco

first: Dorothee

last: Nickles

address: 1 DNA Way

institute: Genentech

summary: A large fraction of patients with cancer exhibit an intrinsic or adaptive resistance to immunotherapies that aim at boosting T cell responses against tumor cells. To better understand resistance mechanisms in tumor cells, we used CRISPR-Cas9 whole-genome editing to identify mutant tumor cells that are resistant to T cell killing. Among the top hits, we identified the transcription factor zinc-finger protein X-linked (Zfx). Zfx knockout tumor cells are resistant to T cell killing both in vitro and in vivo. Mechanistically we showed that Zfx regulates expression of genes involved in apoptosis pathways and Caspase-3 is one of the central components regulated by Zfx. In addition, ZFX expression is decreased in several human cancer tissues compared to healthy tissues. Female kidney renal clear cell carcinoma (KIRC) patients with high ZFX expression showed significantly better survival compared to patients with low ZFX expression. Our results demonstrate a novel resistant mechanism in tumor cells and suggest that targeting tumor cell intrinsic resistance genes in combination with immune therapies could benefit cancer patients. - The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.

overall_design: To delete Zfx from MC38 tumor cells, CRISPR ribonucleoprotein (RNP) complexes were transfected into cells using CRISPRMAX lipofectamine. The KO was confirmed by PCR. RNA was isolated from in vitro cultured tumor cells with RNeasy (QIAGEN) following manufacturer’s instructions, including DNase treatment steps. Quality control was performed with NanoDrop (Thermo Scientific) and 1 µg RNA was used for RNA sequencing.

first: Ulrike

last: Kaufmann


title: Gene expression profiling of MC38 Zfx KO clones in vivo

overall_design: To delete Zfx from MC38 tumor cells, CRISPR ribonucleoprotein (RNP) complexes were transfected into cells using CRISPRMAX lipofectamine. The KO was confirmed by PCR. RNA was isolated from tumors with RNeasy (QIAGEN) following manufacturer’s instructions, including DNase treatment steps. Quality control was performed with NanoDrop (Thermo Scientific) and 1 µg RNA was used for RNA sequencing.


title: Sequencing and bioinformatics analysis of exosome-derived miRNAs in mouse models of pancreatic injury induced by OSA

city: 泉州

first: 清石

last: 陈

state: 福建省

address: 福建省泉州市鲤城区中山北路34号

institute: 医科大学附属第二医院

summary: The role of exosomal miRNAs involved in the pathogenesis and development of pancreatic injury caused by obstructive sleep apnea (OSA) remains unclear. Here, miRNA sequencing (miRNA-seq) was used to investigate the expression profile of exosomal miRNAs in pancreatic tissue in a mouse model of chronic intermittent hypoxia (CIH) -induced pancreatic injury. A total of 55 newly predicted miRNAs and 277 existing miRNAs were identified in pancreatic tissue exosomes from the mouse model of chronic intermittent hypoxic-induced pancreatic injury. 3 up-regulated and 33 down-regulated miRNAs with differential expression were identified. 8 exosome-derived miRNAs were selected to construct CNC networks to predict target genes. Some targets and pathways were elucidated by GO analysis and KEGG analysis. Our work first comprehensively studied the expression profile of exosome-derived miRNA in pancreatic tissue of mouse models of OSA-induced pancreatic injury, bringing fresh perspectives on managing pancreatic injury brought on by OSA.

first: Qingshi

last: Chen

first: Jiuhuang

last: Lan

first: Yaopeng

last: Guo

first: Dexin

last: Liu


title: Screening for Non-Invasive rsRNA Biomarkers to Assess Embryo Quality Using Ultra-Sensitive Pandora Sequencing Combined with Machine Learning

first: Yi

last: Li

address: 107 Yanjiang Xi  Ave.

department: Department of Obstetrics and Gynecology

institute: Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University

summary: Accurate embryo selection is vital for successful in vitro fertilization (IVF), but current morphological scoring methods are somewhat subjective and do not reflect molecular changes. This study employs ultra-sensitive Pandora sequencing to detect highly modified rsRNAs in culture media, aiming to identify molecular markers for non-invasive embryo quality assessment. Machine learning identified four candidate rsRNAs (5S, 5.8S, 28-1S, 28-2S) associated with embryo quality, with cross-validation demonstrating high predictive accuracy (AUC = 0.955). Quantitative RT-PCR further confirmed that 5.8S and 28-2S levels were significantly higher in the culture media of high-quality embryos. These findings suggest that specific rsRNAs could serve as non-invasive markers for embryo selection, offering new insights into rsRNA functions in embryo development.

overall_design: This is a case-control study. In this study,  the  high-quality embryos and their culture medium were set as the case group while the low-quality embryo and their culture medium were set as the normal control group.

first: Songbang

last: Ou

first: Xinsheng

last: Zhong

first: Xuemin

last: Yang


title: Dysfunction of Unc119, a transducin-binding protein, leads to cone-rod dystrophy through activating JAK-STAT and NF-kB inflammatory pathways in the mouse retina

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

summary: Transducin is a heterotrimeric G protein that is a component of the phototransduction cascade in rod and cone photoreceptor cells of the retina. Gnat1, a rod-specific transducin α-subunit, regulates light/dark adaptation by changing its subcellular localization depending on light. Our previous study revealed that Gnat1 translocation in rod photoreceptor cells under light/dark conditions requires E3 ligase Klhl18-mediated ubiquitination and degradation of Unc119, a Gnat1-binding protein. A mutation in the human UNC119 gene is associated with cone-rod dystrophy (CRD); however, the underlying pathological mechanism remains unclear. In this study, we generated and analyzed Unc119-deficient (Unc119−/−) mice. We found that Unc119-deficienct mouse retina exhibited progressive photoreceptor degeneration, resembling CRD in humans. We also found that Unc119 interacts with Gnat2 in cone photoreceptor cells and that Unc119 is essential for the translocation of Gnat2 to the outer segment in cone photoreceptor cells. RNA-seq and subsequent bioinformatics analysis revealed the predicted activation of the JAK-STAT and NF-κB pathways in the Unc119−/− retina. Treatment of Unc119−/− mice with curcumin, an inhibitor of the JAK-STAT and NF-κB pathways, suppressed inflammation and cone photoreceptor cell degradation in Unc119−/− retinas. Furthermore, a human CRD associated-UNC119 mutant protein inhibited the interaction between UNC119 and GNAT1 or GNAT2. Taken together, the current study suggests that UNC119 dysfunction leads to CRD by affecting the JAK-STAT and NF-κB pathways, and may advance our understanding of the pathological mechanisms of CRD.

overall_design: We performed RNA-seq analysis using retinal RNA from Unc119+/+ and Unc119－/－ mice

first: Koki

last: Kobayashi

first: Taro

last: Chaya

first: Yamato

last: Maeda

first: Yuki

last: Nakashima

first: Ryotaro

last: Tsutsumi

first: Haruka

last: Yamamoto

first: Toshinori

last: Tsujii

first: Takahisa

last: Furukawa


title: Increased pulmonary blood flow leads to alveolar dysplasia at early postnatal developmental stage

city: Shanghai

first: zheng

last: sixie

address: 1678 Dongfang Road

institute: Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong Univerisity School of Medicine

summary: We reported the RNAseq analyses of lung in two groups of mice (5 in each group) at postnatal day 14 (P14). The mice in increased pulmonary blood flow (IPF) group underwent an abdominal surgery by puncture from aorta to inferior vena cava at P7, mice in Sham group underwent the same surgery except for the puncture. The results revealed that there were differentially expressed genes between VO and sham group at P14.

overall_design: RNAseq analyses of lung in volume overload.

first: Sixie

last: Zheng

first: Lincai

last: Ye