title: Targeting eIF4A-dependent translation in soft tissue sarcoma

status: Public on Dec 14 2025

city: New York

first: Prathibha

last: Mohan

state: NY

address: 1275 York Avenue

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Well-differentiated and dedifferentiated liposarcoma (WD/DDLS), myxofibrosarcoma (MFS), and undifferentiated pleomorphic sarcoma (UPS) are the most common types of genetically complex sarcoma. There is an urgent need to develop effective targeted therapy for the over 50% of patients who eventually die of disease. Despite their genetic complexity, all four sarcoma types rely on the oncogenic translation of Hippo pathway proteins, which requires the RNA helicase eIF4A (DDX2). Pharmacological inhibition of eIF4A using CR-1-31B effectively suppressed tumor growth and induced apoptosis in DDLS, MFS, and UPS patient-derived cell lines and mouse xenografts. Transcriptome-scale ribosome footprinting identified eIF4A-dependent mRNAs in DDLS, MFS, and UPS cell lines. These include Hippo pathway effectors such as YAP1, WWTR1 (TAZ), and TEAD1. Combined knockdown of YAP and TAZ induced apoptosis in DDLS, MFS, and UPS cell lines, implicating them as critical targets. Hence, DDLS, MFS, and UPS rely on the eIF4A-dependent and CR-1-31B-sensitive translation of Hippo pathway oncogenes such as YAP, TAZ, and TEAD. eIF4A thus represents a new, promising therapeutic target for these incurable forms of soft tissue sarcoma.

overall_design: We performed ribosome footprinting and RNA sequencing on six samples of DDLS8817 cells including three untreated samples (DMSO) and three samples that were collected 2 hrs after treatment with (-)CR31B (10nM). DMSO treated samples are indicated as CT and (-)CR31B treated samples are indicate as (-)CR31B.

first: Young-Mi

last: Kim

first: Evan

last: Seffar

first: Nikita

last: Persaud

first: Tomoyo

last: Okada

first: Anirudh

last: Kulkarni

first: Jianan

last: Lin

first: Nathalie

last: Lailler

first: Shaleigh

last: Smith

first: Nicholas

last: Socci

first: Hans-Guido

last: Wendel

first: Samuel

last: Singer


title: KDM3A catalysed formation of hydroxyacetyl-lysine on histone H3K9

status: Public on Dec 15 2025

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone modifications, including Ne-lysine acetylation and methylation, play critical roles in eukaryotic transcription. The addition of acetyl- and methyl-groups and removal of acetyl-groups involves redox neutral reactions, whereas demethylation is O2 dependent, a reaction with potential to enable O2 availability mediated regulation, as occurs for reactions catalysed by the 2-oxoglutarate dependent hypoxia-inducible factor (HIF) hydroxylases. A screen for substrates of the HIF-regulated Jumonji-C (JmjC) lysine demethylase KDM3A led to the finding that purified recombinant KDM3A catalyses oxidation of the Ne-acetyl group of Lys-9 of histone H3 giving an Ne-hydroxyacetyl-lysine residue. Studies employing a Ne-hydroxyacetyl-lysine selective antibody and mass spectrometry support the cellular relevance of Ne-hydroxyacetyl-lysine. The combined biochemical and cellular results reveal evidence for an unanticipated O2-mediated link between histone lysine Ne-acetylation and JmjC catalysis. Future work can explore the biological significance of Ne-hydroxyacetylation, including in the hypoxic response where KDM3A plays a role in regulating HIF target genes.

overall_design: ChIP-seq analysis of histone modifications in HEK293T cells normalised to a Drosphila chromatin spike in, immunopreciitated in same reaction using a secondary antibody

middle: R

first: Jessica

middle: D

last: Kindrick


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling [RNAseq]

status: Public on Jul 21 2025

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

type: Expression profiling by high throughput sequencing

summary: Transcriptional control in eukaryotes relies on the coordinated action of chromatin-based regulatory mechanisms, including control of nucleosome occupancy and chromatin modifications. We previously identified the ChAHP complex – comprising the chromatin remodeler CHD4, transcription factor ADNP, and HP1 proteins – as a repressor of SINE B2 retrotransposons and site-specific regulator of CTCF engagement with chromatin. However, the molecular basis of these functions remained unresolved. Here, we show that ChAHP-associated CHD4 is essential for SINE B2 repression, while HP1 proteins are dispensable. We further demonstrate that CHD4’s remodeling activity is not required for chromatin binding, but is critical for both retrotransposon silencing and efficient CTCF antagonism. We propose ChAHP is a sequence-specific recruiter of chromatin remodeling activity, facilitating transcriptional control and localized modulation of chromatin architecture.

overall_design: RNA-seq and TT-seq experiments for ADNP PXVxL and N-terminal mutants and for CHD4-ADNP wt and mutant fusions were performed independent triplicates in wt and Cas9-engineered mESC.

first: Josip

last: Ahel

first: Michaela

last: Schwaiger

first: Marc

last: Bühler


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling [ChIPseq]

overall_design: ChIPseq experiments for ADNP, CTCF and Pol III were performed in indepdendent biological duplicates or triplicates in wt and Cas9-engineered mESC.


title: Integrative ATAC-seq and Cut&Run Profiling Reveals T-bet/Runx3 Epigenetic Regulation in Antiviral CD8+T Cells

status: Public on Jul 19 2025

city: Suzhou

first: Qiang

last: Shan

address: No. 100, Chongwen Road

country: China

institute: Suzhou Institute of Systems Medicine

summary: Effector CD8? T cells must swiftly activate cytotoxic programs while preserving lineage identity and repressing alternative cell fates. T-bet and Runx3 serve as pivotal transcriptional regulators in this process, yet their integrated regulatory mechanisms have remained elusive owing to insufficient data on chromatin accessibility and binding dynamics. This study provides a systematic analysis of their cooperative and distinct roles in shaping the epigenetic landscape.

overall_design: Through combined ATAC-seq and Cut&Run analyses, we dissect the synergistic and unique contributions of T-bet and Runx3 to the epigenetic architecture of antiviral CD8+ T cells.

first: Xiaoyu


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling [gNOMEseq]

overall_design: gNOMeseq experiments for ADNP PxVxL and N-terminal mutants were performed independent duplicates in mESC.


title: Single-nucleus and spatial transcriptomic profiling of human lung tissue in chronic obstructive pulmonary disease (COPD)

status: Public on Dec 09 2025

city: New Haven

first: Maor

last: Sauler

state: CT

address: 300 Cedar Street

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

country: USA

institute: Yale School of Medicine

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

overall_design: Refer to individual Series


title: Spatial transcriptomic profiling uncovers the molecular effects of the neurotoxicant polychlorinated biphenyls (PCBs) in the brains of adult mice

status: Public on Jul 17 2025

city: Iowa City

first: Snehajyoti

last: Chatterjee

state: IA

address: 169 Newton Road

department: Neuroscience & Pharmacology

institute: University of Iowa

summary: Utilizing spatial transcripomics approach (10x Genomics Visium v2), this study assess the molecular effects of polychlorinated biphenyls (PCB) on the brain.

overall_design: To investigate the effects of polychlorinated biphenyls (PCB) on memory and transcriptomic profiles, we exposed adult male C57BL/6J mice daily to a synthetic PCB mixture. After seven weeks of exposure, the mice were assessed in a spatial object recognition task (SOR) to evaluate long-term spatial memory. Brain sections from PCB and vehicle-exposed male mice, collected one hour after the memory test session, were processed for spatial transcriptomic analyses using the Visium platform.

first: Budhaditya

last: Basu

first: Nicole

last: Breese

first: Sal

last: Lombardi

first: Hui

last: Wang

first: Xueshu

last: Li

first: Destiny

last: Tiburcio

first: Zachary

last: Niemasz

first: Stacy

middle: E

last: Beyer

first: Laura

last: Dean

first: Rachel

middle: F

last: Marek

first: Michal

last: Toborek

first: Hans-Joachim

last: Lehmler


title: In Vitro Validation of DNA-Diffusion and Control Sequences within the AXIN2 Locus [nanopore_plasmid]

status: Public on Jul 13 2025

city: Boston

first: Gue-ho

last: Hwang

state: MA

address: 300 Longwood Ave

institute: Boston Children's hospital

summary: DNA-Diffusion is a novel generative approach leveraging diffusion probabilistic models for the design of cell type-specific DNA regulatory sequences.  To evaluate the capacity of DNA-Diffusion sequences to endogenously alter AXIN2 transcription, we employed a novel MPRA-like system that utilizes CRE-recombinase mediated cassette exchange and long-read sequencing to measure the gene’s transcriptional output in response to enhancer sequences several kilobases away. We evaluated a total of 100 sequences using the AXIN2 endogenous replacement experiment using the following sequence groups: GM12878 DNA-Diffusion, GM12878 Positive Controls, GM12878 Negative Controls, K562 DNA-Diffusion, HepG2 DNA-Diffusion, and shuffled GM12878 DNA-Diffusion. Our findings demonstrate the potential of DNA-Diffusion to design sequences with therapeutic potential, showing their effectiveness in an endogenous setting.

overall_design: The library was constructed with artificial enhancer and barcode combination flanked with a LoxP/Lox2272 pair. The enhancer and barcode combinations were sequenced using Nanopore seuqencing

first: L

last: DaSilva

first: Simon

last: Senan

first: J

last: Kribelbauer

first: GueHo

first: Deplanke

last: Bart

first: Pinello

last: Luca


title: Generation of iPSC-derived CD4+ Th1 cells enhancing chimeric antigen receptor-T cell cytotoxicity

city: Bunkyo

first: Miki

last: Ando

state: Tokyo

address: Hongo 2-1-1

department: Hematology

country: Japan

institute: Juntendo University

summary: CD4+ T cells are anticipated to enhance the overall immune response, including the anti-tumor activity of chimeric antigen receptor (CAR)-T cell therapy. In the past, we established a culture system to generate CD8+ T cells from iPS cells (iPSCs); however, it was challenging to generate CD4+ T cells. Drawing inspiration from the observation that adult T cell leukemia (ATL) cells are consistently CD4+ and possess Treg characteristics, we successfully generated CD4+ Treg cells by reprogramming ATL cells into iPSCs and then differentiating them into T cells. Gene expression analysis of this generation system suggested that RUNX3 serves as a key regulator in T cell differentiation within the ex vivo generation system. By knocking out RUNX3, we demonstrated the generation of antigen-specific CD4+ Th1 cells via the iPSC route, thereby enhancing the activity of CD8+ CAR-T cells against GD2-expressing lymphoma. These technologies hold significant promise for contributing to “off-the-shelf” immunotherapies against malignant tumors, including solid tumors.

overall_design:
GD2-CARTs^MEBV-CD4rejTs:
GD2-CARTs collected before and after co-culture with EBV-specific CD4 reprogrammed T cells (EBV-CD4rejTs). Healthy donor PBMC were activated by T cell Transact  in the presence of 100 U/mL IL-2 .Three days later, activated T cells were plated on 24-well plates coated with RetroNectin and retroviral GD2-CAR supernatant was added to each well to generate GD2-CARTs. GD2-CARTs collected before co-culture were used as the baseline control, whereas GD2-CARTs collected after co-culture were analyzed to assess transcriptional changes associated with co-culture with EBV-CD4rejTs.
ATL-WT vs. ATL-Overexpression:
wild-type (WT) and RUNX3-overexpressing ATL-derived reprogrammed T cells (ATL-rejTs). WT and RUNX3-overexpressing ATL-rejTs were generated using the same differentiation protocol, with RUNX3 introduced by retroviral transduction in the RUNX3-overexpression group. Cells from both groups were collected at day 7 (D7) and after TCR stimulation (post-stim), resulting in four experimental conditions: ATLCD4rejTsWTD7, ATLCD4rejTsWTPost-stim, ATLRUNX3OverexpressionD7, and ATLRUNX3OverexpressionPost-stim.
CD8rejTs vs. RUNX3 KOrejTs:
wild-type (WT) CD8 reprogrammed T cells (iTabZ-WT) generated from a healthy donor, and WT RUNX3-knockout reprogrammed T cells (iTabZ-KO). Both groups were generated using the same differentiation protocol, with RUNX3 disrupted in the knockout group. Cells were collected at weeks 0, 1, and 3, resulting in six experimental conditions; iTabZ-WT-1W,  iTabZ-WT-3W,  iTabZ-WT-5W,  iTabZ-KO-1W, iTabZ-KO-3W, iTabZ-KO-5W.

first: Yoshiki

last: Furukawa


title: In Vitro Validation of DNA-Diffusion and Control Sequences within the AXIN2 Locus [gRNA]

overall_design: To validate enhancer sequences in the AXIN2 locus, a cell line (MEC1) was created with a stably integrated CRE recombinase and an RMCE landing pad within the AXIN2 gene and perturbated the RNA expression using a library that includes various enhancer DNAs, barcodes, and LoxP/Lox2272 sites. The mRNA expressions were analyzed from barcode sequences obtained from mRNA and gDNA using NextSeq sequencing.


title: In Vitro Validation of DNA-Diffusion and Control Sequences within the AXIN2 Locus [mRNA]

overall_design: To validate enhancer sequences in the AXIN2 locus, a cell line (MEC1) was created with a stably integrated CRE recombinase and an RMCE landing pad within the AXIN2 gene and perturbed the RNA expression using a library that includes various enhancer DNAs, barcodes, and LoxP/Lox2272 sites. The mRNA expressions were analyzed from barcode sequences obtained from mRNA and gDNA using NextSeq sequencing.


title: RNA Sequencing-Based Profiling of Differentially Expressed MicroRNAs in Endothelial Cells from Offspring of Hypertensive Pregnancies

status: Public on Jul 08 2025

city: Cheras

first: Adila A

last: Hamid

state: Kuala Lumpur

address: Jalan Yaacob Latif, Bandar Tun Razak

department: Physiology

country: Malaysia

institute: National University of Malaysia

type: Non-coding RNA profiling by high throughput sequencing

summary: Offspring of mothers with hypertensive disorders of pregnancy (HDP) are at increased risk of developing endothelial dysfunction and cardiovascular disease (CVD) in adulthood. MicroRNAs (miRNAs), as key regulators of endothelial cells, may contribute to the early onset of endothelial dysfunction. However, there are limited studies characterizing the miRNA profile of endothelial cells in offspring of HDP. Therefore, this study aims to determine the miRNA expression profile of human umbilical vein endothelial cells (HUVECs) isolated from the offspring of HDP.

overall_design: RNA-seq profiling of HUVECs which were isolated from the umbilical cords of normal and hypertensive pregnancies.

first: Nurul Iffah

last: Mohd Isa

first: Aslah Nabilah

last: Abdull Sukor

first: Saiful Effendi

last: Syafruddin

first: Mohd Faizal

last: Ahmad

first: Shahidee

last: Zainal Abidin

first: Azizah

last: Ugusman

first: Mohd Helmy

last: Mokhtar


title: Global cell-state and gene-program representations reveal conserved and context-specific perturbation responses of cells

status: Public on May 05 2026

city: Cambridge

first: Reuben

last: Saunders

address: 455 Main St

institute: Whitehead Institute

summary: Mammalian organisms comprise numerous types of cells with distinct gene-expression states, which arise from single zygotes differentiating on a complex landscape of cell states. The surge of single-cell transcriptomic data from human and other animals offer the possibility of constructing a global cell-state map, which will be foundational for understanding the molecular basis of normal tissue functions and dysfunction in diseases. However, this challenging task requires computationally efficient integration of many large datasets and accurate removal of artifactual batch effects while preserving true biological variations. Here, we developed a contrastive learning model that combines the strong batch-correction power of pairwise integration with the computational scalability of deep learning and used this model to construct a global cell-state map from human and mouse single-cell transcriptomic data. This model outperforms other state-of-the-art foundation models for batch correction and dataset integration. The resulting global cell-state manifold enables projection and annotation of cell states, generation of cell-state trajectories, and prediction of causal genes driving cell-state transitions. To further illustrate its power for understanding the molecular basis of cell-state transitions, we performed genome-scale perturb-seq experiments on human embryonic stem cells and systematically mapped the cell states induced by genetic perturbations to the global cell-state manifold. We identified gene programs that are differentially regulated both under normal development and upon genetic perturbations and distinct classes of perturbation-induced cell-state transitions that are aligned with or orthogonal to normal cell differentiation. The global cell-state manifold and related computational tools provide a powerful resource for understanding cell states and transitions in health and disease.

overall_design: Genome-scale CRISPRi Perturb-seq experiment in hESCs. Cells were transduced with a lentiviral library targetting thousands of genes and were analyzed by scRNA-seq.

first: Xingjie

last: Pan

first: Joseph

last: Replogle

first: Jonathan

last: Weissman

first: Xiaowei

last: Zhuang


title: Spatial Transcriptomics Uncovers the Hybrid Molecular Identity, Ciliated Phenotype, and Immune Signature of Adenomyosis Lesions

status: Public on Dec 06 2025

city: Liverpool

first: Alison

last: Maclean

state: Merseyside

address: Crown Street

department: Department of Women's and Children's Health

institute: University of Liverpool, Institute of Life Course and Medical Sciences

summary: Adenomyosis is a common gynaecological condition characterised by ectopic endometrial tissue within the myometrium, causing debilitating symptoms with limited treatment options. Despite its prevalence, the pathogenesis of adenomyosis remains poorly understood, hindering the development of targeted therapies for true disease modification rather than symptom management. The objective of this study was to elucidate the spatial transcriptomic profile of adenomyosis lesions with matched eutopic endometrial subregions, with a focus on specific cell types and tissue compartments. The study was designed to identify differentially expressed genes, functionally enriched pathways, and cell-cell communication networks within adenomyosis lesions compared to matched endometrial subregions, and to nominate potential drug targets for future therapeutic development.  We show that adenomyosis lesions exhibit a distinct transcriptome intermediate between matched endometrium and myometrium, with enhanced epithelial ciliation and altered biological pathways. We reveal that lesion transcriptome is more like the endometrial basalis than the functionalis, displaying increased olfactory signalling, altered oxidative phosphorylation and ATP synthesis, and an altered immune microenvironment suggestive of chronic inflammation. In silico drug screening identified potential compounds that can reverse the adenomyosis lesion transcriptome. These findings provide insights into the molecular landscape of adenomyosis lesions and pave the way for developing novel, lesion-specific treatments that could potentially spare the eutopic endometrium and offer alternatives to hysterectomy.

overall_design: Full-thickness endometrial biopsies and matched myometrium containing adenomyosis lesions were prospectively collected from ten premenopausal women undergoing hysterectomy for pelvic pain and/or heavy menstrual bleeding. Paraffin-embedded human uterine biopsies underwent NanoString GeoMx digital spatial profiling. NanoString GeoMx DSP uses a pool of ~20,000 transcript-specific RNA probes, links each of the probes to a unique, probe specific barcode through a UV cleavable linker. The probe pool was hybridized to target mRNAs on tissue slides (overnight), and slides were then stained using fluorophore-labelled antibodies (“morphology markers”; here panCK, CD45, CD31) and imaged on the GeoMx profiler platform. A total of 6 regions of interest (ROIs) were selected per tissue sample (luminal epithelium, endometrial functionalis, endometrial basalis, adenomyosis lesions, and two myometrial regions), and UV light was applied to release and collect the DSP barcodes from selected ROIs. Photocleaved oligonucleotides from ROI aspirates, containing target-specific readout tags and unique molecular identifiers (UMIs), were used for library preparation. Libraries were quality-checked using a Bioanalyzer system (Agilent) and quantified with a Qubit high-sensitivity DNA kit. Sequencing was conducted on an Illumina NovaSeq system using NovaSeq S1 flow cells with paired-end 2 x 50 bp reads, generating approximately 1300 million clusters per cell. Digital count conversion (DCC) files were produced for each target probe.

first: Emily

last: Johnson

first: Corie

last: Rushworth

first: Christopher

middle: J

last: Hill

first: Eva

last: Caamano-Gutierrez

first: Dharani

middle: K

last: Hapangama


title: Scaffolding-dependent CASP1 constrains excessive cell-intrinsic inflammatory signaling in leukemia [THP1]

status: Public on Dec 05 2025

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: The inflammatory cytokine Interleukin-1b (IL-1b is implicated in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). IL-1b processing is regulated by Caspase-1 (CASP1), a protease that is initially expressed as an inactive zymogen (Pro-CASP1) and can be cleaved into its active form. CASP1 cleaves both pro-IL-1b and Gasdermin-D (GSDMD), which mediates IL-1b secretion and consequently pyroptotic cell death. Despite its known role in inflammation, the contribution of CASP1 to leukemogenesis has not been adequately investigated. To address this, we generated Pro-CASP1 knockout (CASP1KO) MDS/AML cell lines and patient-derived samples. As expected, CASP1KO cells were unable to induce pyroptosis or produce IL-1b. Surprisingly, however, these cells also exhibited impaired leukemic cell expansion, increased myeloid differentiation, and significantly reduced leukemic burden when xenografted into mice. Similarly, Casp1-/- pre-leukemic and AML mouse cells were impaired in their clonogenic potential and leukemia development. Notably, restoring IL-1b expression did not rescue the growth defects, suggesting that IL-1b is not the primary driver of CASP1’s role in MDS/AML. Mutation or inhibition of the CASP1 protease activity did not impact MDS/AML cells, indicating that CASP1’s pro-leukemic function is independent of its proteolytic activity. Transcriptomic and functional analyses of CASP1KO cells revealed excessive NF-kB and inflammatory signaling. Suppression of NF-kB activity restored leukemic cell function and viability, indicating that CASP1 acts as a negative regulator of NF-kB activation. We performed a proximity proteomic and computational prediction analysis and identified RPTOR, a component of the mTORC1 complex, as a key interactor of CASP1. Knockdown of RPTOR in CASP1KO cells reduced excessive NF-kB activity and rescued the leukemic growth defect, suggesting that the CASP1–RPTOR interaction regulates NF-kB signaling in leukemia. To target the scaffolding function of CASP1, we developed a PROTAC degrader (dCASP1-55). dCASP1-55 induced NF-kB activation and reduced the colony-forming potential of MDS/AML cells, supporting its potential as a targeted therapy. CASP1 functions as a critical organizational center regulating NF-kB signaling through mTORC1 in MDS/AML, while IL-1b expression is a secondary contributing event.

overall_design: Bulk RNAseq profiling of THP1-Cas9 cells  transduced with Lentiviral delivery vectors specific for safe harbor control gene sgAAVS1 (WT), or sgCASP1 (KO), grown in liquid culture, and selected for by cell sorting, and validated by western blot.

first: Emma

last: Uible

first: Kathleen

last: Hueneman

first: Erik

last: Vick

first: William

last: Seibel

first: Kenneth

last: Greis

first: Lynn

last: Lee

first: Timothy

last: Chlon

first: Jorge

last: Henao-Mejia

first: Chandrashekhar

last: Pasare

first: Andrew

last: Volk

first: Daniel

middle: T

last: Starczynowski


title: Osteopontin links acquired resistance to hypoxia-inducing antiangiogenics with refractoriness to anti-PD-L1 agents in breast cancer [II]

city: Madrid

first: Jose Luis

last: Ruiz-Sepulveda

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Translational Research

country: Spain

institute: CNIO

summary: Resistance to antiangiogenics is a major challenge in cancer therapy. These agents can either normalize or exacerbate tumor vascular abnormality and hypoxia. The mechanisms of resistance remain unclear in the latter setting. By integrating data from mouse models and clinical trials, we show that hypoxia-inducing anti-VEGF therapy upregulates programmed cell death ligand 1 (PD-L1), yet fails to sensitize tumors to PD-L1 blockade. Mechanistically, early hypoxic stress triggers epithelial osteopontin (Spp1) production, which recruits monocytes and skews macrophages toward M2 states, suppressing T-cell cytotoxicity. Pharmacologic Spp1 depletion impedes the development of hypoxia, M2 infiltration, restores T-cell activity and enables synergy between antiangiogenics and anti-PD-L1. Genetic dissection – tumor-epithelial Spp1 knockout grafts and bone-marrow chimeras generated by lethal irradiation and reconstitution with Spp1-/- or wild-type hematopoietic donors – show that myeloid Spp1 contributes only marginally compared with epithelial Spp1. These findings identify Spp1 as a central mediator of resistance to hypoxia-inducing antiangiogenics, contribute to a comprehensive model of antiangiogenic resistance, and support Spp1-targeted strategies to personalize immuno/antiangiogenic therapy according to tumor hypoxia.

overall_design: To investigate the effects oh antiangiogenic mediated hypoxia on tumor cell compartment we trated 7-weeks old MMTV-PyMT spontaneous breast tumor mouse models  with 5mg/kg anti-VEGF-A antibody clone B20-4.1.1 twice per week. After 6 weeks of treatment mice where sacrfied and breast tumors extracted. Intratumoral CD45-EPCAM+ tumor cells were FACS-Sorted and RNA extracted to perform 3'RNA-seq experiment.

first: José

middle: L

last: Ruiz-Sepúlveda

first: María

last: Bueno

first: Silvana

last: Mouron

first: Verónica

last: Jiménez-Renard

first: Manuel

last: Muñoz

last: Moradiellos

first: Leonardo

last: Garma

first: Luis

last: García-Jimeno

first: Adam

last: Watson

first: Ghassan

last: Mouneimne

first: Solip

last: Park

first: Rebeca

last: Jimeno

first: Miguel

last: Quintela-Fandino


title: Meiotic cohesin Rec8 imposes fitness costs on fission yeast gametes to drive evolution of parental bias in gene expression

status: Public on Jul 03 2025

city: Lausanne

first: Aleksandar

last: Vjestica

state: Vaud

address: Genopode Building, University of Lausanne

department: Center for Integrative Genomics

institute: University of Lausanne

summary: Differences between partner gametes, which evolved repeatedly in unicellular and multicellular eukaryotes, are central to biological phenomena such as non-Mendelian inheritance and sexual selection1–4. How functional asymmetries first emerge between equivalent partners is poorly understood due to limited experimental evidence. Here, we report that in the isogamous fission yeast Schizosaccharomyces pombe, partner P- and M-gametes differentially invest into zygotic development by making unequal amounts of the conserved meiotic cohesin Rec85. Driven by asymmetric partner communication, P-gametes produce Rec8 before fertilization to promote meiotic fidelity and production of viable spores in zygotes. However, this early Rec8 expression also causes genomic instabilities6 and imposes a fitness cost on P-gametes, revealing a trade-off between sexual success and gamete survival. Using biologically parametrized model and experimental evolution, we show that the Rec8 costs and benefits drive selection for biased parental investment and evolution of mating populations. Our work dissects a molecular mechanism that selects for functional gamete asymmetries in an isogamous species, providing rare experimental evidence for an early step in the evolution of gamete dimorphism.

overall_design: Heterothallic wild-type strains that produce only one gamete type and thus arrest as unmated cells (NMWT) or homothallic fus1Δ mutants, which arrested as mated pairs (F1), were grown exponentially in liquid MSL+N media and then diluted to density of O.D.600 = 1 and incubated at 30°C with 200 rpm agitation for 5 hours. The starved cells were collected by centrifugation, ~2·107 cells concentrated into 20 μL of media and spotted onto MSL-N solid media. After 10 hours of incubation at 25°C, mating efficiency reached approximately 80% and 6 mating spots (~1.2·108 cells) were harvested using inoculation loops, per biological replica (triplicates), for RNA extraction.

first: Celso

last: Martins

first: Harry

last: Booth

first: Clàudia

last: Salat-Canela

first: Zena

last: Hadjivasiliou

last: Vještica


title: Transcriptomic analysis to study interactions between murine host and fungal commensal Candida albicans upon its gastrointestinal colonization

status: Public on Jul 01 2025

city: Providence

first: Richard

last: Bennett

state: RI

address: 171 Meeting St, Biomed Center

department: Molecular Microbiology and Immunology

institute: Brown University

summary: Candida albicans is a ubiquitous fungus in the human gut microbiome as well as a prevalent cause of opportunistic mucosal and systemic disease.  There is currently little understanding, however, as to how crosstalk between C. albicans and the host regulates colonization of this key niche.  Here, we performed expression profiling on ileal and colonic tissues in germ-free mice colonized with C. albicans to define the global response to this fungus.  We reveal that Duox2 and Duoxa2, encoding dual NADPH oxidase activity, are upregulated in both the ileum and colon, and that induction requires the C. albicans yeast-hyphal transition and hyphal-specific toxin candidalysin.  Hosts lacking the IL-17 receptor failed to upregulate Duox2/Duoxa2 in response to C. albicans, while addition of IL-17A to colonoids induced these genes together with the concomitant production of hydrogen peroxide. To directly define the role of Duox2/Duoxa2 in fungal colonization, antibiotic-treated mice lacking intestinal DUOX2 activity were evaluated for C. albicans colonization and host responses.  Surprisingly, loss of DUOX2 function reduced fungal colonization at extended time points (>17 days colonization) and increased the proportion of hyphal cells in the gut.  IL-17A levels were also elevated in C. albicans-colonized mice lacking functional DUOX2 highlighting cross-regulation between DUOX2 on this cytokine.  Together, these experiments reveal novel links between fungal cells, candidalysin and the host IL-17-DUOX2 axis, and that a complex interplay between these factors regulates C. albicans filamentation and colonization in the gut.

overall_design: A group (n=5, 3F,2M) of germ-free mice were colonized with WT-SC5314 strain of Candida albicans for 7 and 21 days. Distal ileum and colon tissues were harvested at 7 days and 21 days post colonization in addition to a control group of non-colonized mice. Bulk RNA sequencing was carried out from these tissues to study any changes in the host gene expression upon C. albicans colonization of the murine gastrointestinal tract.

first: Pallavi

last: Kakade

first: Juan

last: Burgueno

first: Shabnam

last: Sircaik

first: Nicole

middle: O

last: Ponde

first: Jinke

last: Li

first: Iuliana

middle: V

last: Ene

first: Jiwoong

last: Kim

first: Shen-Huan

last: Liang

first: Rebecca

last: Yunker

first: Yasutada

last: Akiba

first: Shipra

last: Vaishnava

first: Jonathan

last: Kaunitz

first: Sing

middle: S

last: Way

first: Andrew

middle: Y

last: Koh

first: Sarah

last: Gaffen

first: Maria

last: Abreu


title: Multiplexed single-cell transcriptomics reveals diverse phenotypic outcomes for pathogenic SHP2 variants

status: Public on Jul 02 2025

first: Ross

middle: M

last: Giglio

institute: Columbia University

summary: The protein tyrosine phosphatase SHP2, encoded by PTPN11, is an important regulator of Ras/MAPK signaling  and  a  signaling  hub downstream  of  receptor  tyrosine  kinases  and  other  transmembrane receptors.  Germline  missense  PTPN11  mutations  cause  developmental disorders  such  as  Noonan Syndrome,  whereas  somatic  mutations  drive diverse  cancers.  While  many  pathogenic  mutations enhance SHP2 catalytic activity, some are inactivating or alter protein-protein interactions, confounding our understanding of how SHP2 dysregulation causes diseases. Here, we perform multiplexed single-cell transcriptional profiling in cells expressing clinically diverse SHP2 variants, with and without receptor tyrosine kinase stimulation. We find that loss of catalytic activity does not phenocopy SHP2 knock-out at the  gene  expression  level,  and  we  show evidence  for  both  convergent  phenotypic  effects  from mechanistically distinct mutations, as well as the divergent effects from structurally similar mutations. These  findings  provide a  framework  for  understanding  how  structural  perturbations  to  SHP2  impact cellular outcomes.

overall_design: Single-cell RNA-seq libraries were generated using three-level single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) of basal or EGF-stimulated HEK 293 SHP2 variant cells. Cells transfected with different SHP2 variants and exposed to varying EGF concentrations were hashed at either 24hr or 96hr and pooled prior to sci-RNA-seq using the sci-Plex nuclear barcoding strategy. This nuclear barcoding strategy relies on fixation of barcode containing well-specific oligos that are specific to a given cell type, replicate, or treatment condition. Cells represent unique timepoint, SHP2 variant, EGF concentration, and replicate.

first: Anne

last: van Vlimmeren

first: José

last: McFaline-Figueroa

first: Neel

middle: H

last: Shah


title: Elucidating the impact of KRAS Gly12 mutants on homeostasis and tumorigenesis in the colonic epithelium

first: Bing

last: Shui

address: 360 Longwood Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: KRAS mutations constitute one of the most prevalent and therapeutically relevant oncogenic drivers in human cancers. Clinical and epidemiological data suggest association between specific KRAS alleles, therapeutic response, and patient outcomes, however, direct experimental validation of these relationships has been limited. In this study, we employed genetically engineered mouse models (GEMMs) to investigate the differential impacts of three most common KRAS Gly12 mutations (KRASG12C, KRASG12D, and KRASG12V) in the context of intestinal homeostasis and tumorigenesis. Although tumors developing from different KRAS Gly12 mutants exhibited no significant histological differences, their effects on survival outcomes of tumor bearing mice and therapeutic response displayed pronounced allele-specific differences. Our transcriptomic analyses revealed both allele-agnostic and allele specific transcriptional programs driven by KRAS Gly12 mutations in colon tumors. The allele-agnostic signature was characterized by enrichment of gene sets associated with MAPK signaling, receptor tyrosine kinase pathways, and immune-modulating pathways, compared to KRAS WT tumors. In contrast, allele-specific signature revealed unique OXPHOS pathway upregulation in KrasG12D tumors and marked enrichment of Notch and Wnt/-catenin signaling pathways in KrasG12C tumors. Inhibition of these pathways, in combination with KRASG12C inhibitor led to either addictive or synergistic reduction in tumor cell viability, in allele-specific manner. Collectively, these findings underscore the importance of understanding the distinct biological effects of KRAS Gly12 mutants on colon tumorigenesis and highlight the therapeutic relevance of allele specific signaling dependencies in colorectal cancer. These results provide key mechanistic insights and provide a foundation for the development of effective, allele-informed therapeutic strategies for KRAS mutant cancers.

overall_design: RNA-Seq profiling of mouse colonic epithelium collected from Fabp-Cre/+; KrasWT/+ or KrasG12D/+ or KrasG12V/+ or KrasG12C/+ animals; and mouse colonic tumors collected from Fabp-Cre/+; Apcfl/+ animals, the tumor samples also carry one of the following genotypes: KrasWT, KrasG12D, KrasG12C, KrasG12V.

first: Shikha

last: Sheth

first: Moon Hee

last: Yang

first: Kevin

last: Haigis


title: Regional interneuron transcriptional changes reveal pathologic markers of disease progression in a mouse model of Alzheimer’s disease -- Late-stage AD

city: Ann Arbor

first: Mohamed

last: Noureldein

address: 109 Zina Pitcher Place

department: Neurology

institute: University of Michigan

summary: Alzheimer's disease (AD) exhibits imbalance between neuronal excitation and inhibition, likely secondary to interneuron dysfunction. To reveal underlying mediators, we profiled the transcriptome of neuronal subtypes in 5XFAD versus control mice at early- and late-stage disease. Pooled analysis of neuron types showed expected pathways at early-stage (RNA and protein processing pathways) versus late-stage (neurodegenerative pathways) disease. Early-stage interneurons exhibited alterations in AD-related RNA and protein pathways along with canonical neurodegenerative pathways. Early-stage excitatory neurons, however, showed changes in axon guidance and synapse pathways, without representation of neurodegenerative pathways. Classical neurodegenerative pathways were represented only in late-stage excitatory neurons. Late-stage interneurons instead featured neuronal and synapse pathways along with cellular, cancer, and infection pathways. Our results suggest earlier neurodegenerative pathway involvement in interneurons, represented in excitatory neurons only at later stages, possibly indicating earlier inhibitory neuron involvement. These transcriptomic profiles offer insight into potential AD pathophysiology and therapeutic targets.

overall_design: Spatial transcriptomics was performed by GeoMx DSP (NanoString, Seattle, WA), a platform for spatially analyzing gene expression in tissue in a highly multiplexed manner.64 Four slides in total were submitted for spatial transcriptomics. Two slides were for late-stage analysis and were duplicates of 4 brain sections (n=2 5XFAD 30 wk, n=2 controls 30 wk).

last: Chen

first: Eva

last: Feldman


title: Regional interneuron transcriptional changes reveal pathologic markers of disease progression in a mouse model of Alzheimer’s disease -- Early-stage AD

overall_design: Spatial transcriptomics was performed by GeoMx DSP (NanoString, Seattle, WA), a platform for spatially analyzing gene expression in tissue in a highly multiplexed manner.64 Four slides in total were submitted for spatial transcriptomics. Two slides were for early-stage analysis and were duplicates of 4 brain sections (n=2 5XFAD 12 wk, n=2 controls 12 wk)


title: Comparison of untreated and vancomycin-treated macrophages, with or without Candida albicans infection

city: Birmingham

first: Rebecca

last: Drummond

state: Edgbaston

address: IBR 437, University of Birmingham

institute: University of Birmingham

summary: Vancomycin is a widely prescribed antibiotic used in the treatment of Gram-positive bacterial infections. We recently showed that this antibiotic disrupted protective anti-fungal immune responses via microbiome dysbiosis, enhancing susceptibility to invasive candidiasis. Antibiotics are an independent risk factor for developing this life-threatening fungal infection, but whether microbiota-independent mechanisms also drive this association is not clear. Here, we have compared transcriptional responses of mouse bone-marrow derived macrophages at an early time point post-infection (2 hours), comparing back to baseline, using untreated or vancomycin-treated macrophages.

overall_design: Mouse bone-marrow derived macrophages were differentiated in presence of vancomycin or in antibiotic-free conditions. Macrophages were then left uninfected or infected with live Candida albicans yeast (strain SC5413) for two hours. RNA was isolated from all conditions using the Trizol method.


title: Transcriptomic profile at single cell level of adult lungs expressing exogenous BCL2 driven by three mesenchymal cell-specific drivers

status: Public on Jun 25 2025

first: Jichao

address: 3333 Burnet Avenue

department: Pediatrics

institute: University of Cincinnati and Cincinnati Children's Hospital Medical Center

summary: A transient mesenchymal cell in the lung called alveolar myofibroblast (AMF) plays a key role in alveolar formation during postnatal development. However,  AMFs are cleared from the alveoli upon lung maturation. We induce exogenous BCL2 expression in these cells using three lineage-specific drivers (Myh11-CreER, PdgfraCreER, and PdgfrbCreER) to prevent AMF clearance. We use scRNA seq to analyze the transcriptomic changes of AMFs upon BCL2 expression and subsequent persistence in the lung. Additionally, we evaluated the consequences driven by persistent AMFs in other cell lineages at a transcriptional level.

overall_design: Lung cells from mice that overexpressed the prosurvival protein BCL2 (Rosa26 Bcl2/+) in mesenchymal cells were compared to control littermates. Epithelia (ECAD+), endothelial (ICAM2+), immune(CD45+) and mesenchymal cells (ECAD-/ICAM-/CD45-) from adult mouse lungs were isolated using Fluorescence-activated cell sorting (FACS). The transcriptome of each lineage was analyzed using RNA -single cell sequencing.

first: Maria Jose

last: Gacha-Garay

first: Hui

last: Liu

first: Scott

last: Evans

first: Tingting

last: Mills


title: Spatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

summary: Epithelial serous borderline tumors (SBT) are non-invasive neoplastic ovarian lesions that may recur as chemo-resistant low-grade serous cancer (LGSC). While genetic alterations suggest a common origin, the transition from SBT to LGSC remains poorly understood. Here, we integrate cell-type resolved spatial proteomics and transcriptomics to elucidate the evolution from SBT to LGSC and its corresponding metastasis in both the stroma and the tumor. We show that the transition of SBT to LGSC occurs in the epithelial compartment through an intermediary stage with micropapillary features. LGSC overexpressed the c-Met receptor tyrosine kinase and several CNS-specific proteins. In the tumor microenvironment, interconnectivity between cancer and tumor cells and enzymes degrading a packed extracellular matrix suggests functional collaboration between various cells in the tumor organ. Integrating spatial transcriptomics and proteomics, we functionally validate 16 drug targets.

overall_design: ROIs of a total of four cohort groups were studied in the epithelial and stromal compartment on ovarian cancer: serous borderline tumors (SBT), micropapillary SBT (SBT-MP), low-grade serous cancer primary tumors (LGSC-PT) and corresponding metastases (LGSC-Met).

first: Lisa

last: Schweizer

first: Hilary

middle: A

last: Kenny

first: Rahul

last: Krishnan

first: Lucy

last: Kelliher

first: Agnes

last: Bilecz

first: Aasa

last: Shimizu

first: Andreas

last: Metousis

first: Rachelle

last: Mendoza

first: Thierry

last: Nordmann

first: Sarah

last: Rauch

first: Janna

last: Heide

first: Sabrina

last: Richter

first: Yan

last: Li

first: Florian

last: Rosenberger

first: Maximillian

last: Strauss

first: Katherine

middle: C

last: Kurnit

first: Marvin

last: Thielert

first: Edwin

last: Rodriguez

first: Johannes

middle: B

last: Müller-Reif

first: Seiko

last: Yamada

first: Fabian

last: Theis

last: Mund

first: Ricardo

last: Lastra

first: Matthias

last: Mann

first: Ernst

last: Lengyel


title: RNA Pol I activity is required for meiotic chromatin organization and the H3K4me3 gradient essential for oogenesis, independent of ribosome synthesis [RNA-seq]

status: Public on Jun 24 2025

city: Austin

first: Elif

last: Sarinay Cenik

state: TX

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Oogenesis requires extensive and dynamic chromatin remodeling that primes gene promoters for later transcriptional activation during embryonic development. Here, we uncover a pivotal, non-canonical role for RNA Polymerase I (Pol I) in driving these chromatin state transitions during Caenorhabditis elegans oogenesis. Using the auxin-inducible degron system to selectively deplete either Pol I catalytic subunits or ribosome assembly factors, we disentangle the consequences of impaired nucleolar integrity from reductions in ribosome biogenesis. Strikingly, although disrupting ribosome assembly caused minimal effects on oocyte production, loss of Pol I activity led to widespread changes in chromatin accessibility, a dampening of the distal-proximal H3K4me3 gradient required for oogenesis, reduced synapsis, and elevated ATM/ATR phosphorylation, resulting in fewer but significantly larger oocytes. Despite their promoters becoming more accessible, oogenesis genes did not show large changes in steady-state mRNA, consistent with transcriptional repression prior to fertilization. Instead, Pol I depletion prematurely remodeled oogenic chromatin, through a misdirection of H3K4me3 deposition towards promoters normally primed for zygotic genome activation. These findings reveal an epigenetic gating function for nucleolar integrity in oocyte maturation: Pol I preserves three-dimensional chromatin organization and maintains proper spatiotemporal regulation of histone modifications, independent of ribosome production. Given the evolutionary conservation of nucleolar dynamics and histone modifications during gametogenesis, our work suggests that nucleolar stress, whether from environmental factors, aging, or genetic disorders, could broadly compromise fertility by disrupting oogenic chromatin priming.

overall_design:
Gene expression data from dissected gonads of auxin-inducible degron strains used to deplete an RNA Pol I subunit (RPOA-2) or ribosome assembly chaperone (GRWD-1). L4 stage animals were treated with 1 mM auxin (IAA) or EtOH control for 18 hours before germline dissection and RNA-seq. Each replicate includes 20 gonads.
Gene expression data from dissected gonads of auxin-inducible degron strains used to deplete a ribosome assembly chaperone (TSR-2). L4 stage animals were treated with 1 mM auxin (IAA) or EtOH control for 18 hours before germline dissection and RNA-seq. Each replicate includes 20 gonads.

first: Raquel

last: Mejia-Trujillo

first: Qiuxia

last: Zhao

first: Ayesha

last: Rahman


title: Enhancer poising enables pathogenic gene activation by noncoding variants [CUT&Tag]

status: Public on Jun 20 2025

city: Irvine

first: Evgeny

last: Kvon

state: CA

address: 836 Health Sciences Road

institute: University of California, Irvine

summary: Single nucleotide variants within enhancers—non-coding DNA elements that regulate transcription—often lead to aberrant gene activation and contribute to a wide range of genetic disorders (Claussnitzer et al. 2015; Doan et al. 2016; Turner et al. 2017; Yanchus et al. 2022; Lettice et al. 2008). The mechanism by which ectopic gene activation occurs through these gain-of-function enhancer mutations remains poorly understood. Using the ZRS, a benchmark disease-associated enhancer of Sonic hedgehog (Shh), as a model, we demonstrate that poised (i.e., accessible but inactive) chromatin sensitizes Shh to aberrant activation in anterior limb bud, leading to polydactyly. In the anterior limb cells of wild-type mice, Shh is inactive, but the ZRS is accessible and marked by enhancer-associated histone modifications. We demonstrate that this poising signature explains how over 20 independent rare variants within the ZRS cause Shh misexpression in the same anterior limb bud cell population, resulting in similar limb malformations, despite affecting binding sites for different activators and repressors. Disabling pioneer transcription factor binding to the ZRS suppresses its poised state in anterior cells, prevents aberrant activation of the ZRS by rare variants, and fully rescues limb malformations in variant knock-in mice. A thorough examination of other disease-associated enhancers with pathogenic gain-of-function variants revealed that they are all poised in tissues with ectopic activity. We use this poising signature to predict and validate in vivo ectopic forebrain activity of previously uncharacterized autism-associated non-coding variants. Our findings suggest that spatial enhancer poising, likely a byproduct of development, leads to susceptibility to non-coding mutations offering a potential mechanistic explanation for the burden of disease-associated non-coding variants.

overall_design: CUT&Tag followed by sequencing was performed on 30-60k fluorescently-sorted cells from anterior, central, and posterior domains of E11.5 mouse hindlimb buds. H3K4me1, H3K27ac, H3K27me3, and ZIC2 antibodies were used. CUT&Tag direct, protocol version 4 published by the Henikoff lab was used.

first: Ethan

last: Hollingsworth


title: The SIRT6-TDO2/KYNA-mTOR Axis Mediates Synaptic Plasticity and Cognitive Impairments in Fetal Growth Restriction Offspring

status: Public on Jun 04 2025

city: Shanghai

first: Shujuan

last: Chang

address: siping road 1239

institute: tongji university

summary: Fetal growth restriction (FGR) can lead to cognitive impairment in offspring, but the underlying mechanisms remain unclear. This study found that hippocampal excitatory neurons in FGR mice exhibit significantly reduced SIRT6 expression. SIRT6 deficiency upregulates TDO2 via its histone deacetylase activity (independent of ADP-ribosyltransferase function), promoting kynurenic acid (KYNA) accumulation, which suppresses the AKT/mTOR/p70S6K pathway and disrupts synaptic protein synthesis.

overall_design: RNA-seg profiling of the hippocampus at 8 weeks in WT mice and Sirt6 cKO mice

first: Wen

last: Chen

first: Wei

last: Zhu

first: Nana

last: Liu

first: Yuhang

last: Wang

first: Jianguo

last: Li

first: Jiuhong

last: Kang


title: Lymphatic dysfunction drives inflammatory temporomandibular joint osteoarthritis (TMJOA) and pain

city: Los Angeles

first: Ziying

last: Lin

address: 2250 Alcazar St. CSA Clinical Sciences Annex

institute: University of Southern California

summary: Temporomandibular joint (TMJ) arthritis is a craniofacial disorder characterized by joint dysfunction and orofacial pain. Despite of its established roles in fluid and immune regulation, lymphatic regulation, and function in TMJ remain unknown. Using genetic report mouse, uDISCO tissue clearing, and 3D volume imaging, we defined lymphatic vessel morphology, structure, anatomic location in adult mouse TMJ. We demonstrate in a mouse model of TMJ osteoarthritis (TMJOA) that arthritis induces inflammatory lymphangiogenesis and leads to impaired synovial lymphatic functions, including decreases in synovial influx and lymph node fluid drainage. To establish the causative link between lymphatic remodeling and TMJOA, we performed lymphatic loss- and gain-of-function studies. Lymphatic deficiency exacerbated cartilage defects, bone loss, synovitis, synovial fibrosis, and pain behaviors in TMJOA mice. Conversely, lymphatic activation via a hydrogel-mediated VEGF-C delivery to TMJ reduced TMJ pain, inflammation, and arthritis-like pathogenesis. Therefore, we defined lymphatic structure in TMJ and found that lymphatic dysfunction drives TMJOA pathogenesis and pain, suggesting its potential as a therapeutic target.

overall_design: To elucidate the role of lymphatic vessels in TMJ arthritis, we employed a lymphatic loss-of-function approach using Prox1 mutant mice. TMJ arthritis was induced by intra-articular injection of complete Freund’s adjuvant (CFA). Subsequently, TMJs from both wild-type and Prox1 mutant mice were harvested. Single-cell suspensions were prepared from dissected TMJ tissues and subjected to scRNA-seq for transcriptomic profiling and comparative analysis.


title: ChIP and ATAC-seq data related to Rapid transcriptional response to a dynamic morphogen by time integration

status: Public on Jun 13 2025

city: Evanston

first: Shelby

last: Blythe

address: Northwestern University, Hogan Hall, 2205 Tech Drive

institute: Northwestern University

summary: This study on blastoderm stage Drosophila embryos seeks to measure accessible chromatin and the enrichment on chromatin of transcription factors associated with BMP signaling (phospho-Mad, Medea) in either wild-type conditions, or in embryos mutant for the homeodomain transcription factor zerknullt (zen). The associated manuscript demonstrates that zen is a critical transcription co-activator that enables rapid responses to BMP signaling.

overall_design: Two measurement types were performed. 1) Chromatin IP (ChIP) was performed for either phospho-Mad or GFP-tagged Medea (or negative controls) in wild type embryos. GFP-tagged Medea was ChIPped in zen mutant embryos. 2) Chromatin accessibility was measured by ATAC-seq on single wild-type or zen mutant blastoderm stage embryos.

first: Susanna

last: Brantley

first: Anna

last: Chao

first: Stefano

last: Di Talia


title: Rps15 mutation drives B cell malignancy through translational rewiring, oxidative stress and genomic instability

status: Public on Jun 01 2025

city: Boston

first: Catherine

middle: J.

last: Wu

address: 450 Brookline Ave

department: Medical Oncology

summary: Ribosomal protein mutations are increasingly associated with cancer risk and thought to perturb ribosome function. At the same time, they reportedly activate p53, a critical anti-cancer barrier. To determine how these mutations overcome this protective block to enable tumorigenesis, we generated an in vivo model of the hotspot Rps15-S138F mutation identified as a putative driver of chronic lymphocytic leukemia. Under pre-leukemic conditions, this mutation induced protein instability, ribosome biogenesis defects and altered translation resulting in oxidative stress, DNA damage and induction of a p53-dependent response that promote initial cellular hypo-proliferation. However, aged mice with mutated Rps15 eventually developed B-cell leukemia (37% penetrance), which exhibited increased Myc activity with strong pro-survival and proliferation signatures. Mutant Rps15 thus induces both hypo- and hyper-proliferative signals, initially weighted towards cell cycle arrest; and that through translational rewiring, oxidative stress, DNA damage response defects and genomic instability set the stage for the acquisition of additional driving mutations, such as TP53 deletion, that can overcome this cell cycle block to trigger tumorigenesis.

overall_design: Paired RNA-seq and ribo-seq profiling of age-matched Rps15-S138F mutant and wildtype mice

last: Gutierrez

first: Marwan

last: Kwok

first: Neil

last: Ruthen


title: Maternal exposure to ozone during implantation promotes a feminized transcriptomic profile in the male adolescent liver

status: Public on Jun 16 2025

city: Research Triangle Park

first: Colette

last: Miller

state: NC

address: 109 TW Alexander

institute: U.S. Environmental Protection Agency

summary: Maternal exposure to ozone during implantation results in reduced fetal weight gain in rats. Offspring from ozone-exposed dams demonstrate sexually dimorphic risks to high-fat diet feeding in adolescence. To better understand the adolescent hepatic metabolic landscape following fetal growth restriction, RNA sequencing was performed to characterize the effects of ozone-induced fetal growth restriction on male and female offspring. Pregnant Long-Evans rats were exposed to filtered air or 0.8 ppm ozone for 4 hours on both gestation days 5 and 6 (n = 6 / group). At approximately postnatal day 48, liver tissue was obtained for RNA sequencing from offspring. Peri-implantation exposure to ozone in the dam had greater effects on hepatic gene expression in male offspring than in the females. Interestingly, heatmaps of these DEGs suggested that male offspring from ozone-exposed dams had a transcriptomic pattern like that of female offspring. Using a filtered set of highly female-predominant genes (n = 390), 57% were upregulated in the male offspring from ozone-exposed dams. Upregulated canonical pathways included sirtuin and orexin signaling, estrogen receptor signaling, and integration of energy metabolism. Relatively few genes altered in the male offspring from ozone exposed dams were associated with endpoints of sexual maturity, signifying the likely source of the observed feminization was not attributed to sex hormones. This study provides initial evidence that growth restriction in utero may increase the risk of hepatic feminization in male offspring. Additional work is needed to further understand the relationship between developmental undernutrition and feminization in the male liver.

overall_design: Liver sections were collected from ~PND 48 offspring from dams exposed to either filtered air or 0.8ppm ozone at GD 5 and 6. Samples were sequenced using the Illumina NextSeq 500 platform.

middle: N


title: Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [RNA-seq]

status: Public on May 31 2025

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

summary: Recent breakthroughs in single-cell genomics allow probing molecular states of cells with unprecedented detail along the sequence of the DNA. Biological function relies, however, on emergent processes in the three-dimensional space of the nucleus, such as droplet formation through phase separation. Here, we use single-cell multi-omics sequencing to develop a theoretical framework to rigorously map epigenome profiling along the DNA sequence onto a description of the emergent spatial dynamics in the nucleus. Drawing on scNMT-seq multi-omics sequencing in vitro and in vivo we exemplify our approach in the context of exit from pluripotency and global de novo methylation of the genome. We show how DNA methylation patterns of the embryonic genome are established through the interplay between spatially correlated DNA methylation and topological changes to the DNA. This feedback leads to the predicted formation of 30-40nm sized condensates of methylated DNA and determines genome-scale DNA methylation rates. We verify these findings with orthogonal single cell multi-omics data that combine the methylome with HiC measurements. Notably, this scale of chromatin organization has recently been described by super-resolution microscopy. Using this framework, we identify local methylation correlations in gene bodies that precede transcriptional changes at the exit from pluripotency. Our work provides a general framework of how mechanistic insights into emergent processes underlying   cell fate decisions can be gained by the combination of single-cell multi-omics and methods from theoretical physics that have not been applied in the context of genomics before.

overall_design: E14 mESC were cultured in 2i+LIF media. For induction for 2i-relase experiment, the cell been rinsed with PBS before the culture media was changed to serum + LIF medium. 0h, 24h, and 48h after induction of 2i-release single cells were distracted and sc-NMT sequencing was performed.

first: Fabrizio

last: Olmeda

first: Tim

last: Lohoff

first: Stephen

last: Clark

last: Benson

first: Felix

last: Krueger

first: Wolf

last: Reik

first: Steffen

last: Rulands


title: Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [BiSulfite-seq]


title: Direct Reprogramming of Human Fibroblasts into Retinal Progenitor Cells by Small Molecules to Treat Photoreceptor Degeneration

status: Public on May 22 2025

city: Taipei

first: Yueh-Chang

last: Lee

address: No.128, Sec. 2, Academia Rd.

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: Retinal progenitor cells (RPCs) hold promise for restoring vision in advanced stages of photoreceptor degeneration. We have developed a technique to directly reprogram human Tenon's fibroblasts (HTFs) into induced RPC-like cells (iRPCs) using small molecules. To explore the transcriptomic profile of iRPCs, we performed bulk RNA-seq analysis of HTFs and FACS-sorted iRPCs. The Gene Ontology (GO) enrichment analysis demonstrated significantly highly enriched GO terms include Proteinaceous Extracellular Matrix, Axon and Dendrite, Synaptic Membrane and Transport Vesicle, Presynapse and Postsynapse, Basement Membrane and Collagen Trimer, Platelet Alpha Granule and ER Lumen. The significantly down-regulated GOs were Spindle and Chromosomal Structures, Sarcomere and Muscle Fiber Components, Cell Adhesion Complexes.

overall_design: RNA-seq profilling of HTFs and their derivatives (iRPCs) at day0 and day6 of chemical reprogramming

first: Pei-Lun

last: Lai

first: Chien-Ying

first: Fang-Ling

last: Chang

first: Shang-Yen

first: Po-Yu

last: Lin

first: Chi-Hsuan

last: Chuang

first: Yu-Xin

last: Chou

first: Zhao-Feng

last: Chen

first: Chih-Lun

last: Cheng

first: Hsuan

first: Chi-Hou

last: Ng

first: Shang-Chih

last: Yang

first: Shang-Fu

first: Wei-Ju

first: Yu-Chieh

last: Ho

first: Kishan

last: Kapupara

first: Cheng-En

last: Zou

first: Yao-Tseng

last: Wen

first: Jean

last: Lu


title: Transcriptomic characterization of the liver microenvironment in cynomolgus macaques treated with TLR8 agonist.

city: Foster City

first: Cameron

last: Soulette

address: 333 Lakeside Dr

institute: Gilead Sciences

summary: RNA-seq data from liver tissues of cynomolgus macaques treated with TLR8 agonist (0.1, 0.5 or 2.5 mg/kg).

overall_design: Cynomolgus macaques (n = 3/sex/group) were dosed via oral gavage on day 1, 8, 15, 22 and 29 with either vehicle [30% (w/v) polyethylene glycol 300 (PEG 300) and 70% (w/v) reverse osmosis water (pH adjusted to 3.0 ± 0.1)], or 0.1, 0.5 or 2.5 mg/kg/dose TLR8 agonist diluted in vehicle at a dose volume of 2 mL/kg. The animals were anesthetized with sodium pentobarbital and euthanized via exsanguination at approximately 4 h (± 30 min) following dosing on day 29. Liver tissue (≥10 mg) was obtained from the left lateral lobe at terminal sacrifice and flash frozen in liquid nitrogen. Isolation of total cellular RNA and RNA-seq was conducted by Expression Analysis (Durham, NC).


title: Analysing environmentally induced genome-wide frameshift

status: Public on May 14 2025

city: stockholm

first: yujie

last: zhang

address: Tomtebodavägen 23

country: Sweden

institute: Karolinska institutet

sample_organism:
Bacillus subtilis
Saccharomyces cerevisiae


title: Analysing environmentally induced genome-wide frameshift in S. cerevisiae using SLAM-Seq

summary: In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation. To measure the RNA degradation, we utilized  SLAM-seq (Herzog, et.al, 2017, PMID: 28945705) in S.cerevisiae in wildtype and NMD mutant (upf1Δ). Our goal with SLAM-seq is to quantify the fraction of the transcriptome that is directly degraded as a result of environmentally induced ribosome frameshifts through an NMD-dependent mechanism.

overall_design:
To perform pulse and chase experiment, RNA molecules were labelled with 4tU for 1h during cell grown at mid exponential phase. Cells were washed and resuspend in prewarmed medium (YPD with MES buffer or CSM with MES buffer) without  4tU and time points were collected at 0, 15 and 30 mins.

Funded by "ERC Synergy grant" (Grant ID 101118521, European Research Council).

first: Yujie

last: Zhang

first: Vicent

last: Pelechano


title: Analysing environmentally induced genome-wide frameshift in S. cerevisiae using ribosome profiling

summary: In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation. To explore this process, we utilized Ribosome profiling (Ingolia, et.al 2009, PMID: 19213877), in S.cerevisiae in low nutrients condition. Our goal with Ribosome profiling was to identify gene- and codon-specific features that contribute to genome-wide frameshifting events.

overall_design:
Ribosome profiling and RNA-seq was carried out on S. cerevisiae grown in CSM medium (3 replicates).

Funded by "ERC Synergy grant" (Grant ID 101118521, European Research Council).


title: Maternal Med12 safeguards trophoblast pluripotency and placental development

status: Public on May 13 2025

city: Fort Collins

first: Michelle

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

summary: For a brief but critical period post-fertilization, the mammalian embryo is entirely dependent on maternal products inherited from the oocyte. Previous research showed that oocyte-specific loss of Med12, an X-linked gene and Mediator complex subunit, leads to female sterility despite normal folliculogenesis and ovulation. Here, we show that loss of maternal Med12 has minimal effect on the oocyte transcriptome and does not manifest in embryonic lethality until post-implantation. Implants derived from Med12-null oocytes demonstrate abnormal placentation at E9.5, with an overabundance of trophoblast giant cells (TGC). This phenotype associates with downregulation of trophoblast pluripotency markers (e.g. Cdx2) and activation of drivers of TGC identity (e.g. Stra13) in the E7.5 extraembryonic ectoderm, revealing a previously undescribed role for Med12 in trophoblast pluripotency maintenance. Notably, we find consistently low Med12 expression in embryos derived from Med12-null oocytes, potentially due to programmed paternal X chromosome inactivation (XCI). To isolate the consequences of maternal Med12 depletion, we introduced an autosomal Med12 transgene and show that embryonic expression of the transgene rescues development of Med12-null oocytes. We conclude that oocyte-specific deletion of Med12 produces a maternal-zygotic double knock-out in extraembryonic tissues due to paternal XCI, leading to loss of pluripotency in the trophoblast, placental malformation, and embryonic death.

overall_design: To investigate the role of oocyte-derived Med12 in mouse oogenesis and embryogenesis, we used a conditional knock-out strategy via Zp3-Cre-mediated recombination to ablate Med12 from oocytes. We then performed comparative gen expression profiling using data obtained from RNA-seq of growing oocytes from 12-day-old females (D12), germinal vesicle (GV) oocytes, metaphase-II stage (MII) oocytes, and E7.5 embryonic tissues from individual implants (ectoplacental cone - EPC, extraembryonic ectoderm - ExE, epiblast - EPI) collected from either (1) Zp3-Cre;Med12fl/fl dams, in which Med12 is ablated from oocytes ("Med12KO"); or  (2)  Med12fl/fl control ("WT") females. Embryonic implants were collected after timed-mating of experimental dams with wild-type male studs of proven fertility.

first: Aleksandar

last: Rajkovic


title: The ImmgenT Open-Source project

first: Liang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

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

Supplementary files current as of 7/8/2025.
v1 - 5/14/2025
v2 - 7/8/2025

overall_design:
The immgen T OpenSource Project is a collaborative effort involving 100 participants across 41 laboratories, working together to create the most comprehensive atlas of T cells in the mouse immune system. Leveraging a common data generation pipeline, the goal is to profile T cells in every body location, capturing their diverse states in response to a broad range of immunological challenges and physiological states (infection, autoimmune, tumor, aging), and how specific gene programs drive this diversity. Profiling was performed at the single-cell level, with multimodal mRNA, surface protein (CITE-seq/TotalSeq, 128 antibody panel), and TCR-VDJ (paired TCRα/TCRβ). Please refer to individual series for a description of each experiment.

UPDATE: [Mar-17-2026] Some processed data files were replaced. See the supplementary file GSE297097_README.txt for details.


title: IL-9 and Blimp-1 protect the transcriptional identity of group 2 innate lymphocytes in allergic asthma [ATAC-seq]

status: Public on May 07 2025

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

institute: University of Pittsburgh

summary: Type 2 inflammation in the lung underlies allergic asthma and promotes tumor metastasis. Type 2 innate lymphoid cells (ILC2s) respond to tissue damage signals including IL-33 and IL-25 and are implicated in type 2 inflammatory diseases of the lung, but the factors that maintain ILC2s ability to produce type 2 cytokines are not known. We show Blimp-1 is a key transcriptional repressor of type 1 genes induced by the type 2 cytokine IL-9 in ILC2s in response to tissue damage signals. Loss of Blimp-1 in ILC2s altered inflammation in response to allergens, but also limited metastatic melanoma in the lung by limiting type 2 cytokines in favor of type I cytokines including IFNg and TNF. Thus, Blimp-1 protects the type 2 identity of ILC2s during lung inflammatory diseases.

overall_design: 2 female Blimp-1IL7RaCre and 2 female ControlIL7RaCre mice match with age were used. Whole lung was harvested and ILC2s were sorted from lung by the following markers: live, lineage-, CD90.2+, CD3-. After sorting, ~15,000 ILC2s cells from each sample were cultured in complete RPMI in 96-well plate with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours. After 72 hours, ILC2s were collected passed down for sequencing.

first: Yibo

last: Zheng

first: Aaron


title: IL-9 and Blimp-1 protect the transcriptional identity of group 2 innate lymphocytes in allergic asthma [RNA-seq]

overall_design: For bulk RNA sequencing evaluating Blimp-1 deficiency (including library WT_1, WT_2, WT_3, KO_1, KO_2 and KO_3), 3 female Blimp-1IL7RaCre and 3 female ControlIL7RaCre mice match with age were used. Whole lung was harvested and ILC2s were sorted from these individual mice by the following markers: live, lineage-, CD90.2+, CD3-. After sorting, ~15,000 ILC2s cells from each sample were cultured in complete RPMI in 96-well plate with 20ng/mL IL-33 and 20ng/mL IL-25 for 72 hours. After 72 hours, ILC2s were collected and RNA was isolated with RNeasy Plus Micro Kit (74034, Qiagen). RNA quality was assessed by RIN score and passed down to library preparation.  For bulk RNA sequencing comparing unstimulated ILC2s ex vivo from lung with stimulated ILC2s (including library 1_unstim, 2_unstim, 3_unstim, 4_unstim, 1_stim, 2_stim, 3_stim and 4_stim), 8 female B6 mice were separated into two groups. Whole lung was harvested and ILC2s were sorted from these individual mice lung by the following markers: live, lineage-, CD90.2+, CD3-. After sorting, ~15,000 ILC2s cells from each sample were cultured in complete RPMI in 96-well plate with or without IL-33 (20ng/mL) according to their group for 24 hours. After 24 hours, ILC2s were collected and RNA was isolated with RNeasy Plus Micro Kit (74034, Qiagen). RNA quality was assessed by RIN score and passed down to library preparation.


title: Dexamethasone-induced transcriptional patterns across different tissues

status: Public on May 05 2025

city: Krakow

first: Michal

last: Korostynski

state: malopolskie

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Maj Institute of Pharmacology PAS

summary: Glucocorticoids act in a highly coordinated manner on various tissues, causing discrete patterns of biological effects. In this study, we aimed to inspect this very sophisticated transcriptional machine by comparing gene expression changes in specific tissues after the administration of a prototypical GR (dexamethasone). We reevaluate the tissue-specific acute effects of dexamethasone on gene expression. We provide a resource summarizing the effects on gene expression of dexamethasone in multiple tissues in mice, as a model organism. This dataset was supported by the National Science Centre, Poland, Grant OPUS 2022/45/B/NZ5/03188.

overall_design: The microarray experiment was performed in nine tissues (adrenal cortex, perigonadal adipose tissue, hypothalamus, liver, kidney, anterior thigh muscle, pituitary gland, spleen, and lungs) from adult male C57BL/6 mice using whole-genome microarrays. The animals that received DEX 10 mg/kg i.p. four hours before tissue collection. For each tissue, 4-6 samples (each representing RNA pooled from two animals) were hybridized with Illumina MouseWG-6 v2 BeadChip arrays.

first: Marcin

last: Piechota


title: Insights into the Cellular and Molecular Mode of Action behind the Anti-Fibrotic Effects of Nerandomilast

status: Public on Apr 28 2025

city: Biberach an der Riss

first: Christoph

last: Mayr

address: Birkendorfer Str. 65

department: Immunology & Respiratory Diseases Research

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

summary: The quest for innovative pharmacologic interventions in idiopathic pulmonary fibrosis (IPF) is a challenging journey. The complexity of the disease demands a comprehensive approach that targets multiple cell types and pathways. In this study, we explored the anti-fibrotic properties of nerandomilast, a preferential phosphodiesterase 4B inhibitor, focusing on its effects on myofibroblasts (MFs) and endothelial cells. Our findings demonstrate that nerandomilast induces the dedifferentiation of human lung MFs and diminishes their contractility in vitro by interfering with TGFβ and GPCR signaling pathways. Moreover, nerandomilast effectively mitigates features of vascular dysfunction, such as increased vascular permeability and immune cell infiltration, both in vitro and in vivo. This is accomplished by strengthening endothelial junctions and inhibiting the expression of adhesion molecule proteins. Furthermore, in a rat model of bleomycin-induced pulmonary fibrosis, nerandomilast normalizes the specialization of endothelial cell types. The results of this study significantly contribute to the growing knowledge around the potential therapeutic use of nerandomilast in the treatment of IPF by providing valuable insights into its cellular and molecular mode of action

overall_design:
To examine the molecular mechanisms behind Myofibroblast dedifferentiation upon treatment with nerandomilast, we performed NGS of Myofibroblasts. IPF-HLF were pre-stimulated with TGFβ1 for 48h to induce Myofibroblast differentiation, with nerandomilast and/or high-dose PGE2 added in the continued presence of TGFβ1 for a further 24h.

[UPDATE] The processed data file, 1243_tpm_annotated.csv, was corrected for the missing data row identifers on Aug 11, 2026.

first: Dennis

last: Reininger

first: Felix

last: Wolf

first: Susanne

last: Wespel

first: Nadine

last: Laufhaenger

first: Kerstin

last: Geilinger-Kästle

first: Alec

last: Dick

first: Florian

last: Gantner

first: Peter

last: Nickolaus

first: Franziska

middle: E

last: Herrmann


title: Comparative RNA-seq analysis of Arabidopsis thaliana wild-type vs. autophagy atg5 mutant under water deprivation.

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: A comparative analysis between wild-type Arabidopsis thaliana and autophagy´s atg5 mutant to discover differences between these two plants during normal growth and in relationship to water deficit

overall_design: Seeds were germinated in Normal medium o WSM during five days to compare differences in expression of genes during normal or water deciency

first: Luis

last: Castillo-Olamendi

first: Elsa

last: Quezada-Rodríguez

first: Jorge

last: Solís-Miranda

first: Gladys

last: Jiménez-Nopala

last: Vega-Alvarado

first: Patricia

last: León

first: Helena

last: Porta


title: Two-component intranasal vaccine against SARS-CoV-2 Omicron variant

status: Public on Jun 02 2025

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Mucosal immunity plays a pivotal role in providing comprehensive protection against upper-airway infections and effectively limiting the shedding and transmission of SARS-CoV-2. Despite its critical importance, there remains a notable absence of nasal spray vaccines endorsed for global use by the World Health Organization. This could be due to the inability of current intranasal vaccines to induce strong mucosal and systemic responses in humans, thus urgently entailing a next-generation of intranasal COVID-19 vaccines with novel and safe technologies. In this study, we prepared a two-component intranasal vaccine that combines adenovirus vectors with a self-assembled subunit protein. Specifically, the adenovirus vector expresses the spike protein of XBB.1.5 variant (Ad5XBB.1.5), and were mixed with the recombinant protein that developed derived from the receptor binding domain (RBD) of XBB.1.5 (RBDXBB.1.5-HR). Combination of Ad5XBB.1.5 and RBDXBB.1.5-HR elicited superior humoral and cellular immunity against XBB.1.5-included variants compared with the individual components. Importantly, the STING signaling pathway was found to be crucial for the adjuvant effect of the adenovirus vector. In addition, to increase the broad-spectrum neutralizing capacities, a trimeric protein derived from the BA.5 variant (RBDBA.5-HR) was incorporated to formulate a three-component vaccine (Ad5XBB.1.5+RBDXBB.1.5-HR+RBDBA.5-HR), indicating the utilization of a combination of an adenovirus-vectored and subunit protein vaccines has the potential to serve as a next-generation intranasal vaccine platform. Of note, intranasally delivery of two-component vaccine provided protective immunity against live Omicron XBB.1.16 virus challenge in mice. Furthermore, the combination of adenovirus and subunit protein vaccine demonstrates excellent tolerability and safety in human subjects, and is able to induce enhanced mucosal immunity as well as high levels of sera neutralizing antibody in all participants. These findings underscore its suitability for clinical application in the prevention of SARS-CoV-2 variants encompassing XBB lineages.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on female C57BL/6 mice in PBS, as well as on Ad5XBB.1.5+RBDXBB.1.5-HR groups, including Sting-/- mice also receiving Ad5XBB.1.5+RBDXBB.1.5-HR immunization as previously described. Forty-eight hours after the final vaccination, the mice were euthanized for lung tissue collection. The lungs were minced with scissors and treated with tissue dissociation solution to generate a single-cell suspension.

first: Weiqi

last: Hong

first: Xiangyu

first: Xiawei

last: Wei


title: Leucegene: AML sequencing (part 1-6, GRCh38 reference)

status: Public on Apr 23 2025

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: RNA sequencing of human leukemia

overall_design:
The goals of this project are to obtain a comprehensive study of mutations and gene expression in human acute myeloid leukemia (AML). Methods: AML cells were thawed. DNA and RNA (polyA) was extracted and sequences were obtained with an illumina HiSeq 2000 sequencer.
**Re-analysis/re-quantification with new methods and updated reference genome of samples already found in the following Series: GSE49642, GSE52656, GSE62190, GSE66917, GSE67039 and GSE106272**

first: Camille

last: Simon

first: Jalila

last: Chagraoui

first: Jana

last: Krosl

first: Patrick

last: Gendron

first: Geneviève

last: Boucher

first: Pierre

last: Chagnon

first: Simon

last: Drouin

first: Raphaëlle

last: Lambert

first: Claude

last: Rondeau

first: Annie

last: Bilodeau

first: Sylvie

last: Lavallée

first: Martin

first: Caroline

last: Pabst

first: Anne

last: Bergeron

first: Vincent

first: Jonathan

last: Yeh

first: Eric

last: Deneault

first: Jessica

last: Simard

first: Giovanni

last: D'Angelo

first: Bernhard

last: Lehnertz

first: Radia

last: Johnson

first: Clarisse

last: Thiollier

first: Tara

last: McRae

first: Miriem

last: Marquis

first: Frédéric

last: Barabé

first: Brian

last: Wilhelm

last: Marinier

first: Sébastien

last: Lemieux

first: Josée

last: Hébert


title: Leucegene: AML sequencing (part 7)

first: Guy

last: Sauvageau

summary: RNA sequencing of human leukemia

overall_design: The goals of this project are to obtain a comprehensive study of mutations and gene expression in human acute myeloid leukemia (AML). Methods: AML cells were thawed. DNA and RNA (polyA) was extracted and sequences were obtained with an illumina NovaSeq 6000 sequencer.


title: Bronchopulmonary Dysplasia with Pulmonary Hypertension Associates with Loss of Semaphorin Signaling and Functional Decrease in FOXF1 Expression

status: Public on Apr 14 2025

city: Nashville

first: Jennifer

last: Sucre

state: TN

address: 2215 B Garland Ave, 1125 Light Hall

department: Division of Neonatology, Department of Pediatrics

institute: Vanderbilt University Medical Center

summary: Lung injury in preterm infants leads to lifelong structural and functional respiratory deficits, with a risk for bronchopulmonary dysplasia (BPD). In its most severe form BPD is accompanied by pulmonary hypertension (PH).  While impaired alveologenesis and vasculogenesis in BPD are well-described, the molecular mechanisms driving these phenotypes and the cellular dynamics associated with evolving BPD and BPD+PH in humans are not well-described. We performed single-cell RNA sequencing on preterm infant lungs in early stages of BPD, BPD+PH and term infants. Analysis of the endothelium revealed an aberrant capillary cell-state primarily in BPD+PH marked by ANKRD1 expression and a transcriptomic signature not previously described in previously analyzed human lung disease, a finding validated in an expanded repository of human infant lung tissue. Predictive signaling analysis identified deficits in the semaphorin guidance-cue signaling pathway and decreased expression of pro-angiogenic transcription factor FOXF1 within the alveolar parenchyma of the human neonatal lung samples with BPD and BPD+PH. We observed similar trends in the in decreased semaphoring signaling in a murine BPD mouse model and in analysis of ACDMPV single-nuclear sequencing data. These transcriptional deficits in semaphorin signaling common to BPD+PH and ACDMPV suggest a mechanistic link between the developmental phenotype in BPD and ACDMPV, providing a foundation for further exploration of the role of semaphorins in normal alveolar development. Further, these data fill a critical gap in currently available transcriptomic analysis of the normal and diseased lung across the lifespan as searchable atlas of early human lung development and injury.

overall_design: To examine the cellular dynamics and mediators of neonatal lung injury, single-cell RNA sequencing was performed on human neonatal lungs of varying stages of lung injury and chronic lung disease: 1 acute preterm infant with lung injury, 2 BPD samples at term corrected gestational age (CGA), 2 BPD+PH at term CGA, and 2 term infants in the first 3 weeks of life.

first: Shawyon

middle: P

last: Shirazi

first: Nicholas

last: Negretti

first: Christopher

last: Jetter

first: Alexandria

last: Sharkey

first: Shriya

last: Garg

first: Meghan

last: Kapp

first: Devan

last: Wilkins

first: Gabrielle

last: Fortier

first: Saahithi

last: Mallapragada

last: Banovich

last: Wright

first: David

last: Frank

last: Kropski


title: Oncogenic transcription factor targets

status: Public on Apr 17 2025

city: Turku

first: Otto

last: Kauko

address: Tykistökatu 6

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

summary:
Transcription factors ERG and AR (prostate cancer), ER (breast cancer), CTNNB1 (colorectal cancer), GLI1 and PAX3-FOXO1 fusion (Rhabodomyosarcoma) have been shown to be critical for the formation of tumors. The purpose of this study was to identify common targets of these transcription factors.
We used microarrays to study gene expression in response to modulating these transcription factors by RNAi (ERG, CTNNB1, GLI1, PAX3-FOXO1) or their ligands (AR and ER).

overall_design: Cancer cell lines were treated with with two siRNAs in duplicates to knock down the targeted TFs or, in the case of hormone receptor TFs AR and ER, stimulated with their natural ligands to induce the activity of these TFs. RNA was extracted and hybridized on Affymetrix microarrays.

first: Mikko

last: Turunen

first: Gong-Hong

last: Wei


title: Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome]

status: Public on May 02 2025

city: LA JOLLA

first: Maria Luisa

last: Amaral

address: 9500 GILMAN DR

institute: UCSD

summary: We performed single-nucleus ATAC-seq (snATAC-seq) to profile chromatin accessibility across eight brain regions from C57BL/6J male and female mice at 2, 9, and 18 months of age. Nuclei were isolated from frozen dissected brain regions, tagmented using barcoded Tn5, and sequenced using combinatorial barcoding or 10x Multiome (female samples). Our analysis reveals region- and age-dependent chromatin changes, highlighting regulatory programs associated with aging in specific brain cell types.

relation:
Reanalysis of: GSM7876941
Reanalysis of: GSM7876944
Reanalysis of: GSM7876911
Reanalysis of: GSM7876915
Reanalysis of: GSM7876920
Reanalysis of: GSM7876919
Reanalysis of: GSM7876951
Reanalysis of: GSM7876950
Reanalysis of: GSM7876899
Reanalysis of: GSM7876903
Reanalysis of: GSM7876889
Reanalysis of: GSM7876890
Reanalysis of: GSM7877041
Reanalysis of: GSM7877045
Reanalysis of: GSM7876980
Reanalysis of: GSM7876981
Reanalysis of: GSM7876894
Reanalysis of: GSM7876955
Reanalysis of: GSM7876940
Reanalysis of: GSM7876939
Reanalysis of: GSM7876901
Reanalysis of: GSM7876958
Reanalysis of: GSM7877006
Reanalysis of: GSM7877008
Reanalysis of: GSM7876907
Reanalysis of: GSM7876905
Reanalysis of: GSM7876924
Reanalysis of: GSM7876923
Reanalysis of: GSM7876960
Reanalysis of: GSM7876961
Reanalysis of: GSM7877023
Reanalysis of: GSM7876957
Reanalysis of: GSM7877039
Reanalysis of: GSM7877043
Reanalysis of: GSM7876912
Reanalysis of: GSM7877069
Reanalysis of: GSM7876904
Reanalysis of: GSM7876982
Reanalysis of: GSM7876902
Reanalysis of: GSM7876972

overall_design:
Single-nucleus ATAC-seq was performed on eight dissected brain regions (AMY, CP, ENT, RLP, NAC, AHC, PHC, FC) from male and female C57BL/6J mice at 2, 9, and 18 months of age. Male samples were processed using combinatorial indexing snATAC-seq; female samples were profiled using the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit. For each brain region and age, 2–3 biological replicates consisting of pooled nuclei from 3–14 mice were used.

Please note that the sample extract protocol has been updated on May 21, 2025.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Sainath

last: Mamde

first: Bing

last: Ren


title: Gene expression profile at single-cell level of helped and helpless LCMV-specific CD8+ effector T cells (day 7 post acute LCMV infection)

status: Public on Apr 09 2025

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

summary: We used single-cell RNA sequencing (scRNA-seq) to obtain transcriptomic profiles of virus-specific CD8+ effector T cells generated in the presence (helped) or absence (helpless) of CD4+ T cells.

overall_design: Young adult B6 mice were treated with isotype control antibody (helped) or depleted of CD4+ T cells (helpless), transferred intravenuously with 5,000 naïve congenic (CD90.1+) T cell receptor transgenic (TCRtg) CD8+ T cells specific for the LCMV GP33-41 determinant (P14 cells), and challenged with LCMV Armstrong (2e5 pfu intraperitoneally). Seven days later, live P14 effector T cells (P14 TE)  were purified from spleens of P14 chimeras by fluorescence activated cell sorting  for downstream scRNA-seq processing.

first: Verena

last: van der Heide

first: Travis

last: Dawson

first: Dirk

last: Homann


title: Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids

status: Public on Apr 02 2025

middle: William

last: McKellar

address: 101 6th Ave

institute: New York Genome Center

summary: The human heart, originating from the splanchnic mesoderm, is the first functional organ to develop, co-evolving with the foregut endoderm through reciprocal signaling. Previously, cardioid models offered new insights on cardiovascular cell lineages and tissue morphogenesis during heart development, while mesoderm-endoderm crosstalk remain incompletely understood. Here, we integrated micropatterned cardioids, CRISPR-engineered reporter hiPSCs, deep-tissue imaging, and single-cell RNA sequencing (scRNA-seq) to explore synergistic mesoderm-endoderm co-development. scRNA-seq with PHATE trajectory mapping reconstructed lineage bifurcations of mesoderm-heart and endoderm-foregut lineages, identifying key cell types in cardiac and hepatic development. Ligand-receptor interaction analysis highlighted mesodermal cells enriched in non-canonical WNT, NRG, and TGF-β signaling, while endodermal cells exhibited VEGF and Hedgehog activity. We found that micropattern sizes influenced cellular composition, cardioid cavitation, contractile functions, and mesoderm-endoderm signaling crosstalk. The cardioids generated from 600 µm diameter circle patterns showed larger cavity formation resembling early heart chamber formation. Our findings establish micropatterned cardioids as a model for mesoderm-endoderm co-development, enhancing our understanding of heart-foregut synergy during early embryogenesis.

overall_design: GCaMP6f reporter hiPSC cell lines were differentiated into cardiac organoids and cultured upon a micropatterned surface allowing for geometric control of multiple sizes. After successful differentiation into cardioids functioning organoids were imaged with samples collected at multiple time points for scRNA-Seq analysis.

first: Plansky

last: Hoang

middle: W

first: Andrew

last: Kowalczewski

first: Nhu

last: Mai

first: Meng

last: Chai

first: Lance

middle: X

last: Lian

first: Yi

last: Zheng

first: Iwijn

last: De Vlaminck

first: Huaxiao

last: Yang

first: Benjamin

middle: D

last: Cosgrove

first: Zhen

last: Ma


title: Chloride Nucleotide-Sensitive Channel 1A (CLNS1A) Regulates Genome Stability and Cell Cycle Progression to Control Pathogenic T Helper 17 Cell Function and Autoimmunity

status: Public on Apr 01 2025

first: Maxwell

last: McDermott

address: 550 1st Ave

institute: NYU Langone Health

summary: RNA-sequencing of myelin-specific 2D2 CD4+ T cells isolated from the spinal cord and spleen of mice with EAE.

overall_design: CD4+ T cells isolated from the spleen of 2D2 mice were activated by stimulation with aCD3 (1ug/ml) and aCD28 (1ug/ml) in the presence of IL1b (20ng/ml), IL6 (20ng/ml) and IL23 (20ng/ml), aIL4 (5mg/ml) for 96 hours to induce pth17 cell differentiation. Samples of naive and pTh17 were collected. pTh17 cells were transferred into Rag1-/- hosts.  Donor 2D2 CD4+ T cells were isolated from the spleen and spinal cord of the Rag1-/- host mice at day 14 after EAE induction, and enriched by FACS.

first: Liwei

last: Wang

first: Stefan

last: Feske


title: Chloride Nucleotide-Sensitive Channel 1A (CLNS1A) Regulates Genome Stability and Cell Cycle Progression to Control Pathogenic T Helper 17 Cell Function and Autoimmunity [RNA-seq]

summary: RNA-sequencing of in vitro differentiated shRenilla (control) and shClns1a transduced pTh17 cells.

overall_design: CD4+ T cells isolated from the spleen of 2D2 mice were activated by plate-bound aCD3 (1 ug/ml) and aCD28 (1 ug/ml) in the presence of IL1b (20ng/ml), IL6 (20ng/ml) and IL23 (20ng/ml), aIL4 (5mg/ml). 24 hours post activation, cells were transduced with shRenilla (control) or shClns1a.  48 hours post activation, cell were detached and cultured in the presence of IL1b (20ng/ml), IL6 (20ng/ml), IL23(20ng/ml), and aIL4 (5mg/ml)  for an additional 72 hours. Cells were restimulated with aCD3 (1 ug/ml) and aCD28 (1 ug/ml) for an additional 0, 6 or 24 hours. Transduced cells were enriched by FACS.


title: Chloride Nucleotide-Sensitive Channel 1A (CLNS1A) Regulates Genome Stability and Cell Cycle Progression to Control Pathogenic T Helper 17 Cell Function and Autoimmunity [CUT&RUN]

summary: CUT&RUN sequencing of CLNS1A and PRMT5 in in vitro differentiated pTh17 cells.

overall_design: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 (1 ug/ml) and aCD28 (1 ug/ml) in the presence of IL1b (20ng/ml), IL6 (20ng/ml) and IL23 (20ng/ml), aIL4 (5mg/ml) for 3 days.


title: Chloride Nucleotide-Sensitive Channel 1A (CLNS1A) Regulates Genome Stability and Cell Cycle Progression to Control Pathogenic T Helper 17 Cell Function and Autoimmunity [ATAC-seq]

summary: Assay for transposase-accessible chromatin with sequencing (ATAC-seq) for shRenilla (control) or shClns1a transduced pTh17 cells restimulated with aCD3/CD28 for 24h.

overall_design: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 (1 ug/ml) and aCD28 (1 ug/ml) in the presence of IL1b (20ng/ml), IL6 (20ng/ml) and IL23 (20ng/ml), aIL4 (5mg/ml). After 24 hours of activation  Cells were transduced with shRenilla or shClns1a, then co cultured for another 24 hours to induce knockdown.  Cells where then deattached, the media was changed, and samples were further cultured in the presence of IL1b (20ng/ml), IL6 (20ng/ml), IL23(20ng/ml), and aIL4 (5mg/ml) for an additional 96 hours.


title: Transcriptomic and metabolomic regulation of temperature-dependent longevity in Drosophila melanogaster

city: Birmingham

first: Alexander

middle: Tate

last: Lasher

state: AL

address: 1300 University Blvd.

department: Biology

institute: University of Alabama at Birmingham

summary: Temperature reduction has been one of the most robust environmental manipulations used to increase lifespan in invertebrates. However, the underlying molecular mechanisms leading to temperature-mediated lifespan extension remains largely unknown. Here, we evaluate how genes and metabolites are altered in response to changes in temperature in the fruit fly, Drosophila melanogaster. Our data show that environmental temperature affects transcriptome much more than the metabolome. Intriguingly, the most affected candidate genes, the Turandot (tot) family genes, have direct effects on longevity in flies.  Specifically, knockdown of tot expression at all temperatures leads to lifespan extension in a sex-specific fashion. Overall, our results imply that individual genes, specifically, the Turandot family of genes that may play a novel role in lifespan regulation in the fruit fly.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for male and female Drosophila melanogaster whole fly body raised at 18, 24, or 28 degrees Celsius.

first: Jessica

last: Hoffman

first: Tate

first: Steven

last: Austad

first: Liou

last: Sun


title: Mouse heart analysis of Txnip PPXY motif mutated to AAXA

city: NY

first: Yoshinobu

last: Nakayama

address: 160 Convent Ave

institute: City College of New York

summary: Cardiomyocyte specific knock in mouse heart with Txnip PPXY motif mutated to AAXA

overall_design: Wild-type mouse hearts versus Knock-in mouse hearts (n=3 each) The control wild-type hearts are the identical as GSE166252.

first: Jun

last: Yoshioka