title: Zeaxanthin augments CD8+ effector T cell function by enhancing TCR stimulation

city: Chicago

first: Ruitu

last: Lyu

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

summary: The detailed mechanisms underlying regulatory significance of dietary components in modulating anti-tumor immunity remain largely unknown. Here, we applied a co-culture screen approach using a blood nutrient compound library to identify zeaxanthin, a dietary carotenoid pigment found in many fruits and vegetables that is important for eye health, as an immunomodulator that enhances cytotoxicity of CD8+ T cells towards tumor cells. Oral zeaxanthin, but not lutein, a carotenoid with similar structure, enhances anti-tumor immunity in vivo. Integrated multi-omics mechanistic studies reveal that zeaxanthin directly promotes T-cell receptor (TCR) stimulation on CD8+ T cell surface, leading to improved intracellular TCR signaling for effector T cell function. Hence, zeaxanthin treatment augments effectiveness of immune checkpoint inhibitor in vivo and human TCR-engineered CD8+ T cells to induce cell death in co-cultured tumor cells. Our findings uncover a previously unknown immunoregulatory function of zeaxanthin, which has translational potential as a dietary element in immunotherapy.

overall_design: KAS-seq profiling of gene expression induced by Zeaxanthin in mouse CD8 T cells.

first: Freya Q

last: Zhang

first: Jiacheng

first: Jing

last: Chen

first: Hao

last: Fan


title: ANTXR1/TEM8 Blockade Prevents Heart Failure through Suppression of TGF-β Signaling

status: Public on Aug 21 2025

city: Frederick

first: GuoJun

last: Yu

state: MD

address: 560 CHANDLER STREET

department: Cell Biology

country: USA

institute: National Institutes of Health

type: Expression profiling by high throughput sequencing

summary: Heart disease, a leading cause of mortality worldwide, is in urgent need of improved therapies.  Here, ANTXR1/TEM8, a transmembrane protein required for collagen uptake, was found to promote heart failure. In preclinical intervention studies, genetic disruption of Antxr1 prevented heart deterioration following acute myocardial infarction, a phenotype that was mirrored by treatment with ANTXR1 neutralizing antibodies. ANTXR1 pharmacologic blockade also improved heart function in models of pressure overload and obesity-induced heart disease with preserved ejection fraction. Exploratory studies to further unravel the mechanism, including single cell transcriptomics, revealed a striking ANTXR1-antibody driven improvement in post-infarct scar formation followed by attenuation of late-stage, chronic TGFβ-mediated extracellular matrix remodeling.  Thus, ANTXR1 function during heart failure is both maladaptive and druggable, providing promising new avenues for therapeutic intervention.

overall_design:
AngII/PE study: The mice were implanted with osmotic pump containing angiotensin II/phenylephrine (ANG II/PE) to induced hypertension heart disease.
MI study: The mice were subjected to permanent ligation of left anterior descending artery to cause ischemia in the left ventricle of the heart.
T8Ab: Anti-Antxr1 antibody that was injected to mice through intraperitoneal injection.
The high quality single cells were purified from each group using Multi Tissue Dissociation Kit 2 (Miltenyi) and scRNA-seq library were prepared using 10x genomics kits and sequenced using NovaSeq 6000. Finally all the scRNA-seq dataset were analyzed using Seurat program.

first: Nicola

last: Boccella

first: Lino

last: Tessarollo

first: Brad

last: St. Croix


title: CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts

status: Public on Aug 22 2025

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

state: Missouri

institute: Stowers Institute for Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Danio rerio
Oryzias latipes

platform_organism:
Danio rerio
Oryzias latipes

overall_design: Refer to individual Series


title: Single-cell mRNA-regulation analysis reveals cell type-specific mechanisms of type 2 diabetes

city: Malmo

first: Dmytro

last: Kryvokhyzha

address: Jan Waldenströms gata 35

department: Clinical Sciences

country: Sweden

institute: Lund University

summary: Perturbed secretion of insulin and other pancreatic islet hormones is the main cause of type 2 diabetes (T2D). The islets harbor five cell types that are potentially altered differently by T2D. Whole-islet transcriptomics and single-cell RNA-sequencing (scRNAseq) studies have revealed differentially expressed genes without reaching consensus. Here, we demonstrate that unprecedented insights into T2D disease mechanisms can be obtained by network-based analysis of scRNAseq data. We developed differential gene coordination network analysis (dGCNA) and analyzed islet scRNAseq data from 16 T2D and 16 non-T2D individuals. dGCNA revealed T2D-induced cell type-specific networks of dysregulated genes with remarkable ontological specificity, thus allowing for a comprehensive and unbiased functional classification of genes involved in T2D. In beta cells eleven networks of genes were detected, revealing that mitochondrial electron transport chain, glycolysis, cytoskeleton organization, cell proliferation, unfolded protein response and three networks of beta cell transcription factors are perturbed, whereas exocytosis, lysosomal regulation and insulin translation programs are instead enhanced in T2D. Furthermore, we validated the ability of dGCNA to reveal disease mechanisms and predict the functional context of genes by showing that TMEM176A/B regulates beta cell microfilament organization and that CEPBG is a key regulator of the unfolded protein response. In addition, when comparing beta- and alpha and cells, we found substantial differences, reproduced across independent datasets, confirming cell type-specific alterations in T2D. We conclude that analysis of networks of differentially coordinated genes provides outstanding insight into cell type-specific gene function and T2D pathophysiology.

overall_design: The CEBPG gene was knocked out with siRNA, to investigate it's effect of on the expression of other genes in the rat INS-1 832/13 cells.


title: Diurnal time mouse kidney bulk RNA-seq

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

summary: 24 mice (both sexes) were dissected in the middle of the active and inactive periods (ZT6 and ZT18) without treatment. The study aimed to compare the different properties of the kidney between the two time points.

overall_design: Deidentified total RNA from mouse kidney samples, collected during the middle of the active and inactive periods, was used to generate cDNA libraries using 100 ng of RNA with the Illumina platform.

middle: A

first: Phi

middle: H

last: Nguyen

first: Nha

middle: V

last: Huynh

first: Anna

last: Montgomery


title: Multiomic assessments of LNCaP and derived cell strains reveal determinants of prostate cancer pathobiology [scRNA-seq]

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

summary: Comparative Molecular Analyses of LNCaP and Substrains Identify Drivers of Cancer Be-havior and Therapy Resistance

overall_design: To collect single cell suspension, cells were trypsinized and washed once in PBS and re-suspended in cell culture media followed by hemocytometer cell count to ensure cell viability above 70%.  The cell suspension were loaded into Chromium Next GEM Chip G (10x Genomics , PN#1000120) with 3′ v.3.1 beads (10x Genomics , PN#2000164) and partitioning oil.  Individual cells were barcoded using a 10× Chromium Controller (10x Genomics). RNA from the barcoded cells were subsequently reverse-transcribed and amplified with a Chromium Single Cell 3′ v3.1 Reagent Kit (10x Genomics, PN#1000123).  Libraries were subsequently constructed from 25% of amplified cDNA traces from pre-vious step with reagents from a Chromium Single Cell 3′ v3.1 Library Kit (10x Genomics, PN#1000190). The cDNA and library traces were quantitated and identified by Tapestation.  Sequencing were performed with an Illumina NextSeq 2000 P3.  All cells grown in RPMI1640 supplemented with 10%FBS and 1%Pen/Strep antibiotic.

first: Armand

last: Bankhead

first: Tony Lok Heng

last: Chu

first: Pete

last: Nelson


title: An Allele Agnostic Mutant KRAS Inhibitor Demonstrates Broad Spectrum Tumour Growth Inhibition in Pancreatic Ductal Adenocarcinoma

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

summary: KRAS is among the most frequently mutated oncogenes in cancer, and for decades, efforts at pharmacological blockade of its function in solid cancers have been unsuccessful. A notable advance in this endeavor is the recent development of small molecule KRAS inhibitors, which enable direct targeting of the mutant oncoprotein. Here, we comprehensively evaluate the pre-clinical efficacy of BI-2493 (henceforth, “panKRASi”), a first-in-class allele agnostic mutant KRAS inhibitor, in pancreatic ductal adenocarcinoma (PDAC). We report effective tumor growth suppression across a broad range of models, including cell lines, organoids, patient-derived xenografts (PDXs), syngeneic orthotopic models, and prolonged survival in genetically engineered mouse models. Overall, transcriptomic, proteomic, and phospho-proteomic profiling of panKRASi-treated models confirms robust Ras pathway inhibition, along with the sustained regulation of crucial hallmarks essential for tumor maintenance. In panKRASi-treated immune-replete models, we observe increased intratumoral CD8+ effector T cells and decreased infiltration of myeloid cells, along with remodeling of the tumor microenvironment (TME). In the long-term, emergence of resistance to panKRASi monotherapy is associated with increased YAP and MYC signaling within tumor cells, and enhanced expression of immune checkpoints within the TME that impede effective T-cell function and changes in cell composition. Our multifaceted approach identifies potential combinatorial approaches for generating sustained responses to panKRASi.

overall_design: KPPC GEMM (LSL-KRASG12D; Trp53loxP/loxP; Pdx1-Cre) PDAC models. were treated with vehicle, or panKRASi (BI2493, 90 mg/kg) for the indicated timeframes. 1 pancreata/tumor was included per sample.


title: Effect of SLC1A5 overexpression on T cell metabolism and function

city: Pamplona

first: Juan

middle: Jose

last: Lasarte

state: Navarra

address: Avda Pio XII, 55

department: Inmunología e Inmunoterapia

country: Spain

institute: Centro de Investigación Médica Aplicada

summary: Glutamine-dependence of cancer cells reduces local glutamine availability, which hinders anti-tumor T-cell functionality and facilitates immune evasion. We thus speculated that glutamine deprivation might be limiting efficacy of CAR T-cell therapies in cancer patients. We have seen that antigen-specific T cells are unable to proliferate or produce IFN-γ in response to antigen stimulation when glutamine concentration is limited. Using multiple myeloma (MM) as a glutamine-dependent disease model, we found that murine CAR-T cells selectively targeting BCMA in MM cells were sensitive to glutamine deprivation. However, CAR-T cells engineered to increase glutamine uptake by expression of the glutamine transporter Asct2 exhibited enhanced proliferation and responsiveness to antigen stimulation, increased production of IFN-, and heightened cytotoxic activity, even under conditions of low glutamine concentration. Mechanistically, Asct2 overexpression reprogrammed CAR-T cell metabolic fitness, improving basal oxygen consumption rate and glycolytic function that enhanced CAR-T cell persistence in vivo. Accordingly, expression of Asct2 increased the efficacy of BCMA CAR-T cells in syngeneic and genetically-engineered mouse models of MM, which prolonged mouse survival. In patients, reduced expression of Asct2 by MM cells predicted poor outcome to combined immunotherapy and BCMA-CAR T-cell therapy. Our results indicate that reprogramming glutamine metabolism may enhance anti-tumor CAR T-cell functionality in multiple myeloma. This approach may also be effective for other cancers that depend on glutamine as a key energy source and metabolic hallmark.

overall_design: murine CD8+ BCMA CART cells were genetically modified to overexpress SLC1A5 or mock. Cells were then left untreated or activated in BCMA coated plates for 16h. After this incubation, total RNA was extracted and analyzed by RNAsec

first: Juan .J

first: Flor

last: Navarro

first: Teresa

last: Lozano


title: Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Mouse CUT&Tag]

city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

country: China

institute: Fudan University

summary: CHD7 (Chromo-Helicase-DNA binding protein 7) is an ATP-dependent chromatin remodeler required for neural development. To elucidate the molecular mechanism of the function of CHD7 in neurodevelopment, we performed high-throughput sequencing by RNA-seq, ATAC-seq and CUT&Tag on day 14 human cortical organoids derived from control and CHD7 KO H9 hESCs , as well as RNA-seq and CUT&Tag on E10.5 mouse forebrain which Chd7 was specifically depleted in neuroepithelial cells. We found that CHD7 activates neural stem and progenitor cell-specific transcription factors via regulating chromatin accessibility and modification of histone marks H3K27me3 and H3K4me3 in both human cortical organoids and mouse forebrain.

overall_design: Chd7 was conditionally KO by Sox1 cre. E10.5 forebrain tissues were micro-dissected for CUT&Tag.

first: Zhuxi

last: Huang

first: Fei

last: Lan

first: Weijun

last: Feng


title: Distinct roles for NF-κB in hematopoietic stem cells and the bone marrow milieu in promoting hematopoietic aging

city: Los Angeles

first: Apeksha

last: Singh

state: CA

address: 570 Boyer Hall

institute: University of California, Los Angeles

summary: Hematopoietic aging is characterized by chronic inflammation associated with myeloid bias, hematopoietic stem cell (HSC) accumulation, and functional HSC impairment. Yet it remains unclear how inflammation promotes aging phenotypes. Nuclear factor κB (NF-κB) both responds to and directs inflammation, and we present an experimental model of elevated NF-κB activity (“inhibitor of κB deficient” [IκB–]) to dissect its role in hematopoietic aging phenotypes. We find that while elevated NF-κB activity is not sufficient for HSC accumulation, HSC-autonomous NF-κB activity impairs their functionality, leading to reduced bone marrow reconstitution. In contrast, myeloid bias is driven by the IκB– proinflammatory bone marrow milieu, as observed functionally, epigenomically, and transcriptomically. A single-cell RNA sequencing (scRNA-seq) HSPC labeling framework enables comparisons with aged murine and human HSC datasets, documenting an association between HSC-intrinsic NF-κB activity and quiescence but not myeloid bias. These findings delineate separate regulatory mechanisms that underlie the three hallmarks of hematopoietic aging, suggesting that they are specifically and independently therapeutically targetable.

overall_design: CD45.1+ bone marrow was transplanted into young CD45.2 WT and IκB– recipient mice. After 15 weeks, CD45.1+ (donor) Lin- Sca1+ cKitHi (LSK) were isolated from the bone marrow of the bilateral femur and tibia by flow sorting, and analyzed by scRNA-seq.

first: Jennifer

middle: J

last: Chia

first: Alexander

last: Hoffmann


title: Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Human CUT&Tag]

overall_design: CUT&Tag analysis of  Day 14 human brain organoids in H9 and H9 CHD7 KO cells which were established by CRISPR-Cas9.

first: Ming

last: Zhu


title: The pericardium forms as a distinct structure during heart formation

city: Aurora

first: Christian

last: Mosimann

state: Colorado

address: 12801 E. 17th Avenue

department: Department of Pediatrics, Section of Developmental Biology

institute: University of Colorado School of Medicine Anschutz Medical Campus

summary: The heart integrates diverse cell lineages into a functional unit, including the pericardium, a mesothelial sac that supports heart movement, homeostasis, and immune responses. However, despite its critical roles, the developmental origins of the pericardium remain uncertain due to disparate models. Here, using live imaging, lineage tracking, and single-cell transcriptomics in zebrafish, we find the pericardium forms within the lateral plate mesoderm from dedicated anterior mesothelial progenitors and distinct from the classic heart field. Imaging of transgenic reporters in zebrafish documents lateral plate mesoderm cells that emerge lateral of the classic heart field and among a continuous mesothelial progenitor field. Single-cell transcriptomics and trajectories of hand2-expressing lateral plate mesoderm reveal distinct populations of mesothelial and cardiac precursors, including pericardial precursors that are distinct from the cardiomyocyte lineage. The mesothelial gene expression signature is conserved in mammals and carries over to postnatal development. Light sheet-based live-imaging and machine learning-supported cell tracking documents that during heart tube formation, pericardial precursors that reside at the anterior edge of the heart field migrate anteriorly and medially before fusing, enclosing the embryonic heart to form a single pericardial cavity. Pericardium formation proceeds even upon genetic disruption of heart tube formation, uncoupling the two structures. Canonical Wnt/β-catenin signaling modulates pericardial cell number, resulting in a stretched pericardial epithelium with reduced cell number upon canonical Wnt inhibition. We connect the pathological expression of secreted Wnt antagonists of the SFRP family found in pediatric dilated cardiomyopathy to increased pericardial stiffness: sFRP1 in the presence of increased catecholamines causes cardiomyocyte stiffness in neonatal rats as measured by atomic force microscopy. Altogether, our data integrate pericardium formation as an independent process into heart morphogenesis and connect disrupted pericardial tissue properties such as pericardial stiffness to pediatric cardiomyopathies.

sample_organism:
Danio rerio
Rattus norvegicus

platform_organism:
Danio rerio
Rattus norvegicus

overall_design: We sought to probe whether pericardial progenitors are a transcriptionally distinct cell population in the emerging LPM and what gene expression signature defines them. We conducted a 10xGenomics-based single-cell RNA-sequencing (scRNA-seq) analysis of zebrafish LPM cells at 10 hpf (tailbud stage, end of gastrulation) when the LPM has coalesced into its bilateral stripe architecture. We asked if this differential transcriptome signature between the myocardium and pericardium is also detectable in mammalian systems and remains in more mature hearts. We compiled cluster-defining LPM gene lists for myocardium versus mesothelium/pericardium as informed from our zebrafish scRNA-seq and prior work. We then compared the expression of these select gene lists to bulk RNA-sequencing of isolated pericardia and left ventricle myocardia from neonatal 3-week-old rats (Rattus norvegicus).

first: Hannah R

last: Moran

first: Rebecca

last: O'Rourke


title: Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Human ATAC-seq]

overall_design: Chromatin accessibility profile using ATAC-seq on day 14 cortical organoids derived from H9 and H9 CHD7 KO cells which were established by CRISPR-Cas9.


title: Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Mouse RNA-seq]

overall_design: Chd7 was conditional KO by Sox1 cre. E10.5 forebrain tissues were micro-dissected for RNA-seq.


title: Treatment of prostate cancer cell lines with Androgen Receptor and Receptor Tyrosine Kinase inhibitors

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: Androgen receptor (AR)-targeted therapy is the mainstay of systemic treatments for recurrent and metastastic prostate cancer given the tumor cell's dependency on testosterone signaling for growth and survival. However, numerous bypass pathways have been nominated that may circumvent AR in the context of AR-targeted therapies. In this project, we tested whether AR and receptor tyrosine kinase (RTK) activity opposed each other and if inhibition of one promoted the activation of another. We assessed the impact of AR or RTK inhibition in three prostate cancer cell lines over a 5-day time course. We then performed paired-end RNA-seq to assess differential gene expression. Our findings suggest that the AR and HER2 pathways dynamically interact with each other at the transcriptional level.

overall_design: Differential gene expression in the LAPC-4, LNCaP and 22Rv1 cell lines treated with charcoal-stripped serum (CSS), abiraterone (ABI), enzalutamide (ENZ), afatinib (AFA), dacomitinib (DAC), gefitinib (GEF), lapatinib (LAP), neratinib (NER), sunitinib (SUN), vandetanib (VAN)

middle: G


title: Kidney Single-Cell Atlas Reveals Macrophage Heterogeneity in Progression and Regression of Cisplatin Induced AKI [scRNA-seq]

city: Nanjing

first: Bingquan

last: Deng

state: Jiangsu

address: Nanjing Medical University, No.109 Longmian Avenue, Jiangning District

institute: Nanjing Medical University

summary: Macrophages (MФs) play an important role in the repairment of acute kidney injury (AKI). The heterogeneity of renal MФ subsets during pathogenesis of AKI are still remain elusive. We used single cell RNA sequencing (scRNA-seq) to analyze the heterogeneity of renal MФs

overall_design: AKI mice model were constructed by intraperitoneal injection of 20mg/kg cisplatin. Different phases (Sham, day 3 and day 7 time points after injection) kidney single-cell suspensions were harvested for scRNA-seq study.

first: Shensen

last: Li

first: Changchun

last: Cao


title: Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Human RNA-seq]

overall_design: To investigate the gene expression change upon loss of CHD7 during the differentiation from ESC to cortical organoids, we established H9 CHD7 KO cell lines by CRISPR-Cas9 technology.


title: Comparative transcriptomics of lateral hypothalamic cell types reveals conserved growth hormone-tachykinin dynamics in feeding [bulk RNA-Seq]

status: Public on Aug 20 2025

city: South San Francisco

first: Kimberle

last: Shen

address: 1 Dna way

institute: Genentech

summary: The lateral hypothalamus (LH) is a highly heterogenous brain region regulating hunger and motivated behaviours. Inzebrafish, the LH exhibits distinct neural activity across hunger, feeding and satiety staes. In this study, we have generated a zebrafish LH transcriptomic dataset to profile cellular diversity and molecular signatures underlying feeding behaviour.

first: Vindhya

last: Chaganty

first: Caroline

last: Wee


title: Neoadjuvant Intense ADT for High Risk Prostate Cancer: Baseline Analysis

summary: The purpose of this study was to develop better ways of detecting prostate cancer before and after pre-operative treatment, and to test the feasibility of multi parametric magnetic resonance imaging (mpMRI) for the localization and detection of focal prostate cancer both before and after pre-operative treatment with ADT and enzalutamide. In this study, patients with intermediate and high risk prostate cancer received six months of neoadjuvant intense androgen deprivation therapy prior to radical prostatectomy. Biopsies were acquired prior to treatment. Tissue from biopsy and radical prostatectomy were subjected to sequencing and analysis for determination of features associated with response or resistance to treatment.

overall_design:
To identifty the genetic features of resistance or response to neoadjuvant intense ADT, we performed laser capture microdissection and whole transcriptome sequencing of prostate cancer tissues from the biopsies of patients prior to undergoing six months of systemic therapy. At the conclusion of therapy, each biopsy was mapped to the corresponding region of final pathology and assigned responder or nonresponder status.

***Raw Data will be submitted to dbGAP***

first: William

middle: L

last: Dahut


title: Bulk RNA Sequencing of Wild Type and Cisplatin Induced AKI (3d and 7d groups) Mice Kidneys

summary: To investigate  the gene expression transition of injury pattern (progression stage) to repair pattern (regression stage) from 3 days to 7 days after acute injury of kidney tissue.

overall_design: Different AKI phases of renal mRNA profiles was generated by RNA-seq using Illumina 4000 platform


title: A high-resolution temporal transcriptomic dataset of porcine wound healing

city: Santa Cruz

first: Ksenia

last: Zlobina

state: California

address: 1156 High Street

department: Applied Mathematics

institute: University of California Santa Cruz

summary: The dataset contains observations from an acute wound healing experiment in pigs. Wound samples for RNAseq were taken from both wound edges and wound centers and were collected at multiple time points from day 0 to day 21 post-wound onset.

overall_design: Six domestic pigs (Yorkshire-mix breed, females, 45-50 Kg, pig ID: 1323, 1324, 1325, 1326, 1327, and 1328) were utilized. Twelve full-thickness, circular excision wounds (2 cm in diameter, wound ID: A, B, C, D, E, F, G, H, I, J, K, and L) were created in each animal. Baseline (Day 0) excised skin tissue was collected. During the post-operative period, wound biopsy samples from wound edge and wound center were collected on post-operative days 1, 2, 3, 4, 5, 6, 7, 9, 11, 13, 15, 16, 19, and 21. The biopsy samples were sent for RNA sequencing analysis.

first: Hsin-Ya

last: Yang

first: Manasa

last: Kesapragada

first: Fan

last: Lu

first: Anthony

last: Gallegos

first: Guillermo

last: Villa-Martinez

first: Moyasar

last: Alhamo

first: Kan

first: Cynthia

last: Recendez

first: Marco

last: Rolandi

first: Athena

middle: M

last: Soulika

first: Elham

last: Aslankoohi

first: Min

last: Zhao

first: Marcella

last: Gomez

first: Rivkah

last: Isseroff


title: The gene expression effects of DSG2 knockout in A431 epidermoid cell line

city: Clinton

first: Austin

middle: Young

last: Shull

state: SC

address: 503 South Broad Street, Box 130

department: Biology

institute: Presbyterian College

summary: Desmogleins are transmembrane cadherin proteins and obligate members of the desmosome, a cell-cell adhesion complex which connects adjacent cells and provides structural integrity to tissues. While Desmogleins are well-known for their importance in maintenance of cell-cell junctions, several studies have also highlighted their role in signaling crosstalk with cell-matrix adhesions and the extracellular matrix (ECM). We have recently shown that Desmoglein-2 (Dsg2) controls cell spreading on ECM substrates (fibronectin and collagen) and phosphorylation of focal adhesion proteins via Rap1 GTPase signaling. In our current study, we show that loss of Dsg2 in keratinocytes enhances the expression of ECM proteins and matrix metalloproteinases (MMPs), an effect that was not recapitulated upon loss of Desmocollin-2 (Dsc2) or loss of Dsg2 in other epithelial cell types. Signaling pathways well-known to control ECM function (TGF-B and Rho) were shown to have no effect on Dsg2-mediated changes in ECM and MMP gene expression, but an analysis of global transcriptome changes by RNA sequencing identified major changes in NF-kappaB (NF-KB)-mediated signaling in Dsg2-deficient cells. Interestingly, NF-KB (RelA) activation is elevated in Dsg2-deficient cells, and knockdown of RelA rescued both the enhanced expression of ECM/MMP genes and the enhanced migratory ability of Dsg2-deficient cells. Taken together, this study has identified an important link between Dsg2 and NF-KB signaling involved in controlling matrix production and remodeling, which has relevance for multiple processes in the epidermis such as wound healing and psoriasis.

overall_design: RNAseq profiling of A431 control cell lines compared to A431 cell lines with CRISPR/Cas9 KO of DSG2

middle: Y

first: Adi

middle: D

last: Dubash


title: The essential role of CTCF binding site at TAD boundaries in modulating Ifng locus chromatin interactions and transcriptional regulation [Hi-C]

city: Fukushima

first: Masayuki

last: Sekimata

address: Fukushima-shi

country: Japan

institute: FukushimaMedical University

summary: Interferon gamma (IFN-g) is a vital cytokine for host defense and tumor surveillance. Its gene expression in T cells is precisely controlled by long-range enhancer-promoter interactions within the Ifng locus. These interactions depend on topologically associating domains (TADs) and intra-TADs, whose boundaries are maintained by the architectural protein CTCF. Despite their importance, the specific contributions of these boundaries to Ifng regulation and their interplay in domain formation are poorly understood. Here, using CRISPR-Cas9 genome editing in mice combined with chromosome conformation capture (3C) and RNA-seq, we explored how chromatin loop dynamics within the TAD modulate Ifng expression. We found that deleting a single CTCF binding site (CBS) at the TAD boundary impaired Th1-associated immune response to Cryptococcus neoformans infection and B16 melanoma cells. This deletion significantly weakened enhancer-promoter interactions and enhancer-driven Ifng activation. Interestingly, disrupting a CBS at an intra-TAD boundary had no impact on Ifng transcription. This study highlights the essential role of CBS elements at TAD boundaries in shaping the chromatin architecture to enable enhancer-promoter communication and subsequent gene regulation.

overall_design: HiC (region capture micro-C) of wildtype Th1 cells and their knockout Th1 cells (CBS-70 and CBS+66) at Day3 of Th1 differentiation

first: Kazuya

last: Muto

first: Daiki

last: Yoshida

first: Toshiyuki

last: Suzuki

first: Natsuo

last: Yamamoto

first: Naokazu

last: Inoue

first: Akiko

last: Murakami-Sekimata

first: Ken

last: Iseki


title: Transcriptional regulon controlled by tyrosine phosphatases in Porphyromonas gingivalis

city: Louisville

first: Richard

last: Lamont

state: KY

address: 570 S Preston St.

department: Oral Immunology and Infectious Diseases

institute: University of Louisville School of Dentistry

summary: Tyrosine phosphorylation/dephosphorylation posttranslational modification (PTM) of proteins in bacteria can control their function and location.  While PTM of transcriptional regulators and DNA-binding proteins impacts gene transcription, little is known regarding the transcriptional landscape regulating tyrosine phospho-relay circuitry.  In this study, we performed RNA-Seq of Porphyromonas gingivalis strains with mutations in ltp1 and php1 genes encoding the two major tyrosine phosphatases, a low molecular weight family enzyme and a histidinol phosphate phosphoesterase family enzyme, respectively.  Additionally, strains were tested in both in vitro and in vivo (mouse abscess) conditions.  Both the Δltp1 and the Δphp1 mutants exhibit little transcriptional difference to the parental strain cultured in vitro, which would tend to exclude a significant role of the phosphatases in P. gingivalis gene regulation under nutrient-rich, low-stress conditions.  While the Δphp1 mutant also clustered closely to the parental strain in the abscess condition, there were a number of differentially regulated genes (DEGs) associated with transporter systems.  In the mouse abscess condition, DEGs in Δltp1 included one of the efflux ABC transporter systems also regulated in the Δphp1 mutant.  However, the primary biological process populated by DGEs in Δltp1 involved genome stability.   Comparison of the parental strain between the in vitro and in vivo condition indicated that DNA metabolic processes, including recombination and transposition, were significantly upregulated in vivo.  Hence, Ltp1 specifically may be involved in the control of adaptation to in vivo conditions, while Ltp1 and Php1 have both common and enzyme-specific activities.

overall_design: We investigated the role that the bacterial tyrosine phosphatases Ltp1 and Ptk1 have on the transcriptome of Porphyromonas gingivalis during mouse infection and during in vitro culture conditions. This was performed by either inoculating mice with either the parental wildtype (WT) ATCC 33277 strain or isogenic deletion mutants lacking either Ltp1 (Δltp1) or Php1 (Δphp1) then collecting abscess material, or inoculating standard TSB media supplemented with hemin and menadinone then collecting washed cell pellets and subjecting both sets of samples to RNASeq.

first: Gatphan

middle: N

last: Atassi

first: Kendall

middle: S

last: Stocke


title: The essential role of CTCF binding site at TAD boundaries in modulating Ifng locus chromatin interactions and transcriptional regulation [RNA-seq]

overall_design: RNA-seq profiling of wildtype Th1 cells and their knockout Th1 cells (CBS-70 and CBS+66) at Day3 of Th1 differentiation


title: Spatial crosstalk modeling of the tumor microenvironment uncovers CCR5-mediated glia-to-glia signaling as a key regulator of brain metastases

first: HONG

last: ZHAO

address: 6565 Fannin Street

institute: Houston Methodist Hospital

summary: Glial cells play a critical role in shaping the tumor microenvironment in brain metastases, facilitating disease progression through complex tumor-glial and distinct glia-to-glia signaling pathways. To investigate these interactions, we conducted RNA sequencing of astrocytes, microglia, and oligodendrocytes at various stages of brain metastasis progression, combined with spatial transcriptomics and crosstalk analysis using the CCCExplorer tool. Our analysis uncovered that while glial cells converge on tumor-promoting pathways such as Ras and Gap junction signaling in tumor cells, they also engage in distinct autocrine and paracrine signaling critical for their own communication. Unique ligand-receptor pairs including OSM-OSMR, CCL4-CCR5, CXCL16-CXCR6, IL1A/B-IL1R, and TNF-TNFR were identified as drivers of glial crosstalk, which sustains the tumor-supportive niche. Targeting CCL4-CCR5-mediated glial signaling with maraviroc, an FDA-approved antiviral drug, reduced brain metastasis progression by 62% (p=0.004) without direct cytotoxicity to tumor cells. These findings highlight the novelty of targeting distinct glial autocrine and paracrine signaling as a therapeutic approach, shifting the focus from tumor cells to disrupting the glial niche that supports brain metastasis growth.

overall_design: Brain metastasis mouse model under vehicle and maraviroc treatment for 14 days, mouse brains were dissected and analyzed using Visium spatial transcriptomics

first: JIANTING

last: SHENG

first: STEPHEN

last: WONG


title: NRF2 Activation in Cancer Cells Suppresses Immune Infiltration into Tumor Microenvironment

city: Sendai

first: Takafumi

state: Miyagi

address: 2-1 Seiryo-machi, Tohoku University

institute: Tohoku University

summary: Clinical observations have revealed that NRF2 hyperactivation in cancer cells is often associated with immune suppression in the tumor microenvironment. However, it remains unclear whether NRF2 hyperactivation directly reduces immune cell infiltration into tumors. To address this question, we established a syngeneic mouse model using transplantation of 3LL lung cancer-derived cells with either NRF2 hyperactivation via Keap1 gene deletion or concomitant Keap1-Nrf2 gene deletion. A series of flowcytometry, histological analysis, and comprehensive gene expression profiling demonstrated that immune cell infiltration was significantly reduced in KEAP1-deleted tumors, with marked decrease in CD45-positive cells, particularly myeloid and monocytic populations. In contrast, concomitant deletion of NRF2 restored immune cell infiltration in the KEAP1-deleted tumors. These findings provide convincing lines of evidence that NRF2 activation in cancer cells suppresses immune cell infiltration into tumors. Our study sheds light on the mechanistic basis by which NRF2 activation contributes to cancer malignancy.

overall_design: We generated murine 3LL lung cancer cell lines with NRF2 activation by deleting the Keap1 gene using the CRISPR-Cas9 genome editing method and generated KEAP1 and NRF2 double knockout(DKO) 3LL cells to determine whether NRF2 activation is responsible for the decrease of immune cell infiltration in KEAP1-KO tumors. We performed RNA-sequence analysis using RNA samples from WT,KEAP1 KO and KEAP1 NRF2 DKO 3LL cells. we established a syngeneic mouse model using transplantation of 3LL lung cancer-derived cells with either NRF2 hyperactivation via Keap1 gene deletion or concomitant Keap1-Nrf2 gene deletion. We performed RNA-sequence analysis using RNA samples from WT,KEAP1 KO and KEAP1 NRF2 DKO 3LL transplantated tumors.

first: Huaichun

last: Wen

first: Anqi

last: Zhang

first: Miu

last: Sato

first: Mahiro

last: Matsumoto

first: Yuka

last: Takahashi

first: Yushi


title: PLA2 driven lipid remodelling in ARMS tumorigenic cells

city: Singapore

first: Reshma

last: Taneja

address: National University of Singapore Dept of Physiology, Blk MD9 Level 2, 2 Medical Drive,

department: Physiology

country: Singapore

institute: National University of Singapore

summary: Alveolar rhabdomyosarcoma (ARMS) is an aggressive pediatric soft tissue sarcoma with poor relapse-free survival, especially in metastatic cases. Tumor-initiating cells (TICs) are implicated in recurrence and therapy resistance in ARMS, but their metabolic adaptations remain poorly understood. Emerging evidence suggests that lipid metabolism supports stem-like properties in cancer, yet the role of lipid remodeling enzymes in TIC function has not been defined. Here, we investigate the transcriptomic and metabolic profiles of ARMS TICs using tumorsphere-derived and adherent cells from cell line and patient-derived xenograft models. Gene expression and lipid species differences were analyzed using RNA sequencing, gene set enrichment analysis, qPCR, and mass spectrometry. Lipid droplet accumulation was assessed using Oil Red O and BODIPY staining, and functional dependence on PLA2 activity was evaluated using Darapladib. Seahorse assays were used to examine glycolytic and mitochondrial flux, and in vitro and in vivo assays assessed tumorsphere formation, migration, and tumorigenicity. We found that tumorspheres exhibited upregulation of lipid metabolism, especially multiple PLA2 isoforms, and downregulation of glycolytic gene expression. Lipidomic profiling revealed enrichment of linoleic acid-derived triglycerides and lysophospholipids, alongside increased PLA2 activity. Tumorspheres accumulated lipid droplets and upregulated lipid storage regulators PPARG and CD36. Inhibition of PLA2 with Darapladib impaired TIC self-renewal, migration, and in vivo tumor growth, without affecting mouse body weight. These effects were rescued by exogenous linoleic acid supplementation, implicating PLA2-mediated lipid signaling in TIC maintenance. Despite suppressed glycolysis and partial sensitivity to fatty acid oxidation blockade, TICs remained functionally intact under metabolic stress, demonstrating high metabolic flexibility. Collectively, these findings identify PLA2-driven lipid remodeling as a key metabolic adaptation in ARMS TICs that supports stem-like function independently of canonical energy pathways, highlighting PLA2 as a promising therapeutic target in pediatric sarcomas.

overall_design: ARMS cell line Rh41 and Rh30 and PDX cells RHB280217 were grown in adherent and tumorsphere conditions. Total RNA was extracted from adherent and tumorsphere-derived Rh30, Rh41, and RHB280217 samples using the RNeasy Mini Kit (Qiagen), followed by quality assessment with an Agilent 2100 Bioanalyzer. RNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit and sequenced on an Illumina NovaSeq 6000 platform, generating 150-bp paired-end reads

first: Amogh

last: Gupta

first: Bharathi

last: Ramanathan

first: Dipanwita

last: Das


title: Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy [RNA-Seq - cell line]

first: Moran

last: Amit

address: 1515 Holcombe Blvd

department: Head & Neck Surgery

institute: University of Texas - MD Anderson Cancer Center

summary: Peri-neural invasion (PNI) is a well-established poor prognostic factor in multiple cancer types. However, the mechanisms driving the PNI's detrimental clinical effect remain elusive. Here, we provide clinical and mechanistic insights into PNI and cancer-induced injury of tumor-associated nerves (TANs) and their role in resistance to anti-PD-1 therapy. Our work demonstrates that poor response to anti-PD-1 therapy in cutaneous squamous cell carcinoma (cSCC), melanoma, and gastric cancer is associated with PNI and TANs injury. Ultrastructural electron microscopy analysis reveals that direct contact between cancer cells and nerve fibers leads to cancer-induced nerve injury (CINI) via myelin degradation. Injured neurons respond by autonomously initiating an interleukin (IL)-6 and interferon (IFN) type I inflammatory response. This inflammatory response alters the immune activity in the peri-neural niche in melanoma, cSCC, and pancreatic adenocarcinoma, leading to an immuno-suppressive activity aimed at nerve healing and regeneration. As the tumor grows, the CINI burden increases, the inflammatory signal within the niche becomes chronic, and eventually skews the general immune tone within the tumor microenvironment to a suppressive and exhaustive state. The CINI-driven anti-PD-1 resistance can be reversed by targeting multiple steps in the CINI signaling process: denervating the tumor, conditional knockout of the transcription factor mediating the injury signal within neurons (cKO-Atf3), knockout of the IFN-a receptor signaling (Ifnar1-/-), or by combining anti-PD-1 and anti-IL-6-receptor blockade. Our findings demonstrate the direct immuno-regulatory roles of TANs and their therapeutic potential.

overall_design: Human neurons were co-cultured with the human cutaneous squamous cell carcinoma IC8 cell line (obtained from the laboratory of Drs. Irene Leigh and Catherine Harwood, UK 23), the human oral squamous cell carcinoma PCI-13 cell line (obtained from the laboratory of Dr. Jeffrey Myers, MD Anderson Cancer Center, USA), or with the human epidermal keratinocyte HEK cells (ATCC, PCS-200-011). Sensory or motor neurons were cultured to assess the impact of nerves’ degenerative/regenerative status on immunotherapy in vitro.Neurons were plated on laminin-coated (Life Technologies, Cat# 23017015) round glass coverslips set in 12-well plates. Two hours after plating, the wells were flooded with 1 mL of warm (37°C) Ham’s F12 culture medium (Sigma-Aldrich) supplemented with 10% EV-depleted fetal bovine serum (Gibco, Thermo Fisher Scientific) and 1% penicillin/streptomycin and incubated at 37°C in 5% CO2 and 95% air. The carcinoma cells were plated (1:10 neuron: cancer cells ratio), and cultures were grown in RPMI 1640 medium containing 10% EV-depleted fetal bovine serum in 37°C and 5% CO2 incubation conditions, for 72 hours, with or without anti-PD1 antibody (Cemiplimab, 1000ug/ml,  or RMP1-14, 100ug/ml, InVivoMAb Antibodies, BioXCell, for human and murine, respectively), before neuron sorting and RNA extraction.

first: Tongxin

last: Xie


title: Paraspeckle Protein NONO Regulates Active Chromatin by Allosterically Stimulating NSD1

city: WASHINGTON

first: Jia-Ray

last: Yu

state: DC

address: 7144 13th PL NW

institute: Virginia Tech

summary: NSD1 is a key histone methyltransferase that catalyzes di-methylation of lysine 36 of histone H3 (H3K36me2), essential for active chromatin domains. While the loss of NSD1 activity halts embryonic development and its aberrant gain drives oncogenesis in leukemia and glioma, the regulatory mechanisms remain poorly understood. Here, we uncover that NSD1 requires allosteric activation through the aromatic pocket of its PWWP2 domain. Surprisingly, NSD1-PWWP2 binds to a non-canonical target, nuclear paraspeckle protein NONO, and this protein-protein interaction allosterically stimulates NSD1. Mouse embryonic stem cells (mESC) engineered with mutations in the aromatic pocket of NSD1-PWWP2 cannot differentiate into neural progenitor cells (NPC), and genetic depletion of NONO partially phenocopied this defect, potentially explaining the neurodevelopmental disorder phenotypes in NSD1- and NONO-deficient diseases. Our work uncovered a mechanism driving active chromatin domain formation, an implication in the interplay between nuclear paraspeckles and active chromatin, and a vulnerability of NSD1 for therapeutic interventions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The study seeks to interrogate 1) the gene expression profiles affected by NSD1 or NONO in mESC undergoing neural differentiation, and 2) How NSD1 and NONO affect each other's chromatin occupancy and H3K36me2 global levels on chromatin in HEK293T and mESC. For 1), WT, NSD1-KO, and NONO-KO mESC were differentiated by retinoic acid (RA) for 0, 3, or 6 days. Total RNAs were extracted and polyA selected for pair-end (PE) sequencing for 40M reads each. For 2), ChIP using H3K36me2, NSD1, or NONO antibody were conducted in WT, NSD1-KO, and NONO-KO HEK293T and mESC.

first: Shenglin

last: Mei

first: Justin

last: Demmerle


title: DNA G-quadruplex profiling in skeletal muscle stem cells reveals functional and mechanistic insights [MicroC]

city: Hong Kong

first: Feng

last: Yang

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

department: Chemical Pathology

institute: The Chinese University of Hong Kong

summary: DNA G-quadruplexes (G4s) are non-canonical secondary structures formed in Guanine-rich DNA sequences and recent studies demonstrate G4s play important roles in modulating multiple biological processes through a variety of gene regulatory mechanisms. Emerging G4 profiling permit global mapping of endogenous G4 formation. Here in this study, we map the G4 landscapes in skeletal muscle stem cells (MuSCs) which are essential for injury induced muscle regeneration. Throughout the myogenic lineage progression of MuSCs from quiescent to activated to differentiated cells, we uncover dynamic endogenous G4 formation with a pronounced G4 induction when MuSCs become activated and proliferating. We further demonstrate that G4 induction promotes MuSC activation thus the regeneration process. Mechanistically, we found that promoter associated G4s regulate gene transcription in through facilitating DNA looping. Furthermore, we found that G4 sites are enriched for transcription factor (TF) binding events in activated MuSCs and MAX binds to G4 structures to promote E-P looping and gene transcription. The above uncovered global regulatory function/mechanism are further dissected on the paradigm of CCNE1 promoter demonstrating CCNE1 is a bona fid G4/MAX regulatory target in activated MuSCs. Altogether, our findings for the first time demonstrate the prevalent and dynamic formation of G4s in MuSCs and the mechanistic role of G4s in promoting gene expression and MuSC activation/proliferation.

overall_design: Micro-C of MuSC

first: Huating

last: Wang

first: Xiaona

last: Chen

first: Suyang


title: Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy [RNA-Seq FFPE]

overall_design: The study protocol of the clinical trial is available online (NCT04154943). This manuscript reports patients enrolled in the University of Texas MD Anderson Cancer Center (Houston, Texas, USA) and Moffitt Cancer Center (Tampa, Florida, USA). After a screening period of up to 28 days, patients received neoadjuvant cemiplimab 350 mg intravenously every 3 weeks until unacceptable toxicity, disease progression, or withdrawal of consent. After completion of neoadjuvant treatment, the protocol window for surgery was study days 75–100. If the patient met the criteria for early discontinuation of cemiplimab during the neoadjuvant period, the treating physician could divert the patient to surgery earlier. Pretreatment biopsy specimens were subjected to histopathologic assessment for confirmation of diagnosis and to permit morphologic comparison between tumor tissue before treatment and any residual tumor following therapy. Pathologic response was assessed in the posttreatment surgical specimens according to standard pathologic evaluation recommendations 2 and re-reviewed by a dedicated dermatopathologist (PN) to standardize reporting. The primary endpoint was pathologic complete response (pCR), defined as the absence of viable tumor in post-treatment surgical specimens, determined per independent central pathology review. Major pathologic response (MPR) was a secondary endpoint defined by the presence of >0% but ≤10% viable tumor cells in post-treatment surgical specimens.

first: Neil

last: Gross


title: DNA G-quadruplex profiling in skeletal muscle stem cells reveals functional and mechanistic insights [4C]

overall_design: 4C-seq of DMSO and PDS MuSC

last: Zhang


title: Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenetic maintenance

city: Munich

first: Christoph

last: Geisenberger

address: Thalkirchnerstr. 36

country: Germany

institute: Institute of Pathology

type: Methylation profiling by high throughput sequencing

summary: DNA methylation and histone modifications encode epigenetic information. Recently, major progress was made to measure either mark at single-cell resolution. However, a method for simultaneous detection is lacking, preventing study of their interactions in complex systems. To bridge this gap, we developed scEpi2-seq. This technique provides single-molecule and single-cell readout of histone modifications and DNA methylation and reveals how DNA methylation maintenance is influenced by the local chromatin context.

overall_design: Single cell analysis of histone modifications and DNA methylation

first: Jeroen

last: van den Berg

first: Vincent

last: van Batenburg

first: Buys

last: de Barbanson

first: Anna

last: Lyubimova

first: Joe

last: Verity-Legg

first: Alexander

last: van Oudenaarden

first: Xiufei

first: Yibin

last: Liu

first: Chun-Xiao

last: Song

last: de Ridder


title: DNA G-quadruplex profiling in skeletal muscle stem cells reveals functional and mechanistic insights [RNA-seq]

overall_design: RNA-seq of MuSC


title: The essential role of CTCF binding site at TAD boundaries in modulating Ifng locus chromatin interactions and transcriptional regulation [ChIP-seq]

first: Masayuki

last: Sekimata

overall_design: ChIP-seq of CTCF in wildtype Th1 cells and their knockout Th1 cells (CBS-70 and CBS+66) at Day3 of Th1 differentiation

first: Kazuya

last: Muto

first: Daiki

last: Yoshida

first: Toshiyuki

last: Suzuki

first: Natsuo

last: Yamamoto

first: Naokazu

last: Inoue

first: Akiko

last: Murakami-Sekimata

first: Ken

last: Iseki


title: scRNAseq analysis in control and Goblet-Y/T-Scgb1a1CreERT mouse lung tissues.

city: Boston

first: Xaralabos

last: Varelas

state: MA

address: 72 E. Concord St

department: Department of Biochemistry and Cell biology

institute: Boston University Chobanian & Avedisian School of Medicine

summary: This experiment aims to examine the global cellular response in the lung tissues of Goblet-Y/T-Scgb1a1CreERT mice. Depletion of Yap and Taz in airway secretory cells resulted in goblet cell metaplasia. To elucidate the underlying cellular response, we utilized scRNA sequencing of lung tissues.

overall_design: Scgb1a1CreERT+ and Scgb1a1CreERT- mice were administered daily intraperitoneal tamoxifen injections for five consecutive days. Seven days after the final dose, the lungs were harvested and processed into single-cell suspensions. The cells were then stained with fluorescently conjugated CD45 antibodies, and CD45+ and CD45- cells were isolated and mixed in a 1:1 ratio for scRNA sequencing.

last: Cheng


title: Tumors hijack macrophages for iron supply to promote bone metastasis and anemia

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

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

overall_design: Refer to individual Series


title: An autochthonous model of lung cancer in the Naked Mole-Rat (Heterocephalus glaber)

status: Public on Aug 19 2025

city: Tampa

first: Joseph

last: Kissil

state: FL

address: 12902 Magnolia Dr

department: Molecular Oncology

institute: H Lee Moffitt Cancer Center and Research Institute

summary: There is growing interest in understanding the mechanisms underlying differences in cancer incidence among species. The naked mole-rat (NMR) is often referenced as “cancer-resistant” and prior studies focused on identifying mechanisms explaining this. However, efforts to assess this in vivo have been limited. Herein, we provide evidence that the NMR presents as a novel autochthonous model of lung tumor initiation, driven by an introduction of the oncogenic Eml4-Alk fusion protein using CRISPR-mediated genome editing. While in mice the inversion alone is sufficient to drive tumorigenesis, the inversion alone was insufficient to drive tumorigenesis in the NMR lung and tumor development required additional losses of the tumor suppressors p53 and pRb. Our findings suggest that the proposed “resistance” of the NMR to the development of cancer may reflect tumor initiation mechanisms that are likely to be comparable to the mechanisms present in human cells.

overall_design: We have utilized single cell RNA sequencing on lung tumors from NMRs. We infected NMRs with 3 different oncogeneic events thru CRISPR adenovirus and allowed tumors to form in the lungs. After 15 weeks, we harvested the lungs of 3 tumor-bearing NMRs and processed them for single cell RNA sequencing.

first: Alyssa

last: Shepard

first: Daniel

middle: K

last: Lester

first: Mingxiang

last: Teng


title: DNA G-quadruplex profiling in skeletal muscle stem cells reveals functional and mechanistic insights [CUT&RUN]

first: Feng

last: Yang

overall_design: CUT&RUN seq of G4,MAX and H3K4me3 in MuSC

first: Huating

last: Wang

first: Xiaona

last: Chen

first: Suyang

last: Zhang


title: Bacterial metabolites modulate beneficial GVH/GVL responses and require regulation by intestinal STING

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

summary: The intestinal epithelium is constantly exposed to the intestinal microbiome. Here we used single cell RNA sequencing to reveal how murine small intestinal organoids and specific cell types react to stimulation with the bacterial metabolites Desaminotyrosin (DAT) and indole-3-carboxaldehyde (ICA)

overall_design: Small intestinal organoids were isolated from WT or STING Goldenticket (GT) mice and stimulated for four days with the given metabolite. After 4 days organoids were dissagregated, sorted into single cells and profiled by single-cell RNA-seq. Expression profiles were compared to unstimulated control organoids

first: Göttert

last: Sascha

first: Heinrich

last: Paul

first: Strieder

last: Nicholas

first: Gebhard

last: Claudia

first: Rehli

last: Michael

first: Poeck

last: Hendrik


title: Repeats mimic pathogen-associated patterns across a vast evolutionary landscape [RIP-Seq]

city: Toronto

first: Sajid

last: Marhon

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

summary: An emerging hallmark of many human diseases is transcription of typically silenced repetitive DNA containing pathogen-associated molecular patterns (PAMPs).  These PAMPs engage the innate immune system via pattern recognition receptors (PRRs) – a phenomenon known as “viral mimicry.” We propose a statistical physics framework to quantify viral mimicry by measuring “selective forces” that enrich PAMPs compared to a genome-wide reference distribution. We validate our predictions by identifying repeats that bind different PRRs and show viral mimicry in different repeat families across eukaryotic genomes, suggesting shared mechanisms drive emergence and retention. We propose two non-exclusive evolutionary hypotheses. The first ‘repeat-centric’ hypothesis posits PAMPs are integral to the repeat lifecycle and are therefore enriched as they mediate repeat expansion. The second ‘organism-centric’ hypothesis proposes viral mimicry functions as a cell-intrinsic feedback mechanism for sensing and reacting to transcriptional dysregulation, which provides a selective pressure to maintain PAMPs in genomes.

overall_design: RIP-Seq experiment to assess binding of transcripts of N2102Ep cell line (known to have hight LINE1 expression) to LINE1 ORF1p and ZCCHC3 protein. Two replicates were done for each condition. Also all experiments were done with salt concentraion of 300mM and 500mM during protein and RNA capture.

first: John

last: LaCava

first: Siyu

last: Sun


title: Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy [Spatial Transcriptomics]

city: Houston

first: Moran

last: Amit

overall_design: Cutaneous squamous cell carcinoma samples were processed for spatial transcriptome analyses using the Visium (10X Genomics. We conducted transcriptional phenotyping of each sequenced tissue section based on the molecular characteristics of tumor-associated nerves and tumor immune infiltrate, utilizing gene signatures obtained from the literature. Nerves were evaluated according to the Cancer-Induced Nerve Injury (CINI) signature, which included the following genes: TAGAP, KCNJ8, COL1A1, PECAM1, TMEM119, ATF3, JUN, KLF6, NOCT, LMO7, CSF1, ENTPD1, UCHL1, PINK1, BHLHE41, ITGAM, CHL1, SNCA, SCPEP1, and VEGFA. The immune infiltrate was assessed using two signatures: Anti-tumoral Immunity (CD8A, PRF1, GZMB, IL12A, IFNG, IRF8, CD86, NOS2, TNF, and IL2) and Immunosuppression (IDO1, CTLA4, FOXP3, IL10, IL6, CD163, MSR1, MRC1, PDCD1, PDCD1LG2, and CD274). The strength of the correlation between the CINI and the immune signatures was evaluated.

first: Michael

last: Migden


title: Global transcriptomics and targeted metabolite analysis reveal the involvement of the AcrAB efflux pump in physiological functions by exporting signaling molecules in Photorhabdus laumondii

city: Montpellier

first: Anne

last: Lanois

address: 75 rue du Truel CC54

country: France

institute: INRA

summary: In Gram-negative bacteria, resistance-nodulation-division (RND)-type effluxeffluxpumps, particularly AcrAB-TolC, play a critical role in mediating resistance to antimicrobial agents and toxic metabolites, contributing to multidrug resistance. Photorhabdus laumondii is an entomopathogenic bacterium that has garnered significant interest due to its production of bioactive specialized metabolites with anti-inflammatory, antimicrobial, and scavenger deterrent properties. In previous work, we demonstrated that AcrAB confers self-resistance to stilbenes in P. laumondii TT01. Here, we explore the pleiotropic effects of AcrAB in this bacterium. RNA sequencing of ΔacrA compared to wild type revealed growth-phase-specific gene regulation, with stationary-phase cultures showing significant downregulation of genes involved in stilbenes, fatty acid, and anthraquinone pigment biosynthesis, as well as genes related to cellular clumping and fimbrial pilin formation. Genes encoding putative LuxR regulators, type VI secretion systems, two-partner secretion systems, and contact-dependent growth inhibition systems were upregulated in ΔacrA. Additionally, exponential-phase cultures revealed reduced expression of genes related to motility in ΔacrA. The observed transcriptional changes were consistent with phenotypic assays, demonstrating that the ΔacrA mutant had altered bioluminescence and defective orange pigmentation due to disrupted anthraquinone production. These findings confirm the role of stilbenes as signaling molecules involved in gene expression, thereby shaping these phenotypes. Furthermore, we showed that AcrAB contributes to swarming and swimming motilities independently of stilbenes. Collectively, these results highlight that disrupting acrAB causes transcriptional and metabolic dysregulation in P. laumondii, likely by impeding the export of key signaling molecules such as stilbenes, which may serve as a ligand for global transcriptional regulators.

sample_organism: Photorhabdus laumondii subsp. laumondii TTO1

overall_design: Three independent RNA samples, each corresponding to a pool of total RNA extracted independently from 3 biological replicates cultures of:  TT01 WT grown in LB  harvested in exponential phase (OD= 0.5-0.7) or stationary phase (OD=2.3-4.2) acrA mutant grown in LB  harvested in exponential phase (OD= 0.5-0.7) or stationary phase (OD=2.3-4.2)                                                         mdtA mutant grown in LB  harvested in exponential phase (OD= 0.5-0.7) or stationary phase (OD=2.3-4.2) Deep sequencing, performed using Illumina HiSeq 2000"

first: Linda

last: Hadchity

first: Adrien

last: Chouchou

first: David

last: Roche

first: Jessica

last: Houard

first: Noemie

last: Claveyrolles

first: Alexandra

last: Dauve

first: Jacques

last: Imbert

first: Maxime

last: Gualtieri

first: Alain

last: Givaudan

first: Alyssa

last: Carre-Mlouka

first: Ziad

last: Abi Khattar


title: Salmonella-superspreader hosts require gut regulatory T cells to maintain a disease tolerant state

city: Stanford

first: Blanda

last: Di Luccia

state: CALIFORNIA

address: 299 Campus drive

department: Microbiology and Immunology

institute: Stanford University

summary: Host-pathogen interactions involve two critical strategies: resistance, whereby hosts clear invading microbes, and tolerance, whereby hosts carry high pathogen burden asymptomatically. Here, we investigate mechanisms by which Salmonella- superspreader hosts (SSP) maintain an asymptomatic state during chronic infection. We found that regulatory T cells (Tregs) are essential for this disease-tolerant state, limiting intestinal immunopathology and enabling SSP hosts to thrive, while facilitating Salmonella transmission. Treg depletion in SSP mice resulted in decreased survival, heightened gut inflammation and impairment of the intestinal barrier, without affecting Salmonella persistence. Colonic Tregs from SSP mice exhibited a unique transcriptomic profile characterized by the upregulation type-1 inflammatory genes, including the transcription factor T-bet. In the absence of Tregs, we observed robust expansion of cytotoxic CD4+ T cells, with CD4+ T cell depletion restoring homeostasis. These results uncover a critical host strategy to establish disease tolerance during chronic enteric infection, providing novel insights into mucosal responses to persistent pathogens and chronic intestinal inflammation.

overall_design: T regulatory cells (Treg) were isolated and FACS sorted from the colonic lamina propria of uninfected (UNINF) or infected (INF) F1 mice (C57BL/6 Foxp3DTR x 129X1/SvJ) after 4 weeks of infection with Salmonella Typhimurium SL1344. Alternatively, CD4+ T cells were isolated and FACS sorted from the colonic lamina propria of infected (3) or infected and Treg-depleted  F1 mice (C57BL/6 Foxp3DTR x 129X1/SvJ) after 4 weeks of infection with Salmonella Typhimurium SL1344. These cells were analyzed by scRNA-seq.

first: Liliana

last: Massis

first: Daniel

last: Butler

first: Ramya

last: Narasimhan

first: Sarah

last: Ruddle

first: Trung

last: Pham

first: Jose

last: Vilches-Moure

first: Denise

last: Monack


title: Salmonella-superspreader hosts require gut regulatory T cells to maintain a disease tolerant state.

overall_design: Total RNA extarction from colonic tissues of ΔTreg SSP (n=3) and ΔTreg SSP + anti-CD4 (n=3) mice at 28 days post Salmonella infection


title: Systems approach identifies monocyte imbalance in symptomatic and asymptomatic P. vivax malaria

city: Clayton

first: Stephanie

middle: Irene

last: Studniberg

state: VIC

address: 19 Innovation Walk

department: Microbiology

country: Australia

institute: Infection Discovery Program, Monash Biomedicine Discovery Institute

summary: Although asymptomatic malaria was historically perceived as innocuous, emerging evidence revealed an immunosuppressive signature induced by asymptomatic Plasmodium falciparum infections. To examine if a similar process occurs in Plasmodium vivax malaria, we pursued a systems approach, integrating transcriptional profiling together with previously reported and novel mass cytometry phenotypes from individuals with symptomatic and asymptomatic P. vivax malaria. Symptomatic P. vivax malaria featured upregulation of anti-inflammatory pathways and checkpoint receptors. A profound downregulation of transcripts with roles in monocyte function was observed in symptomatic P. vivax malaria. This reduction in monocyte transcriptional activity was accompanied by a significant depletion of CCR2+CXCR4+ classical monocytes in symptomatic individuals. Despite allowing transcriptional profiles supporting T-cell differentiation, dysregulation of genes associated with monocyte activation and the inflammasome was also evident in individuals carrying P. vivax asymptomatic infections. Our results identify monocyte dysregulation as a key feature of the response to P. vivax malaria and support the concept that asymptomatic infection is not innocuous and might not support all immune processes required to eliminate parasitemia or efficiently respond to vaccination.

overall_design:
RNA-sequencing analysis was performed using bulk PBMCs from study participants with either symptomatic (SM) or asymptomatic (AM) P. vivax malaria, and healthy immune controls (HC) (healthy control participants with immunoglobulin G antibody titres to P. vivax Duffy Binding Protein).

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middle: I

first: Diana

last: Hansen

last: Garnham


title: HiJAKing the hematopoietic system: a low-frequency JAK2V617F clone drives myeloproliferative neoplasm pathology

city: Providence

first: Patrycja

last: Dubielecka

state: RI

address: 1 Hoppin St., Coro West, 5th Fl., Suite 5.36

department: Division of Hematology/Oncology, Department of Medicine

institute: Warren Alpert Medical School of Brown University and Rhode Island Hospital

summary: JAK2V617F is one of the most common mutations in clonal hematopoiesis of indeterminate potential (CHIP) and a major driver of myeloproliferative neoplasms (MPN). To determine the impact of the low frequency JAK2V617F clone on both the hematopoietic system and the bone marrow (BM) stroma, we developed a traceable murine JAK2V617F MPN model where the disease is induced in unconditioned bone marrow transplantation (BMT) recipients. Whole BMT was performed via a single tail vein injection of 5.0x106 cells into unconditioned C57BL/6 Ptprca CD45.1+ recipient mice using CD45.2+ donor cells carrying JAK2V617F isolated from a Poly I:C inducible MPN-like model. BMT resulted in a PV-like phenotype (elevated hematocrit and leukocytosis) with an average donor cell chimerism in peripheral blood of 2.74%. Eight months after BMT, RNA-seq analysis of whole BM sorted according to CD45.1/CD45.2 expression showed significant upregulation of early erythroblast- and myeloid cell-specific transcripts, as well as downregulation of lymphoid transcripts in donor-derived cells compared to controls. Surprisingly, recipient-derived cells also showed upregulation of myeloid- and erythroblast-related transcripts, indicating a skewing of the non-JAK2V617F carrying recipient hematopoietic system towards an MPN-like phenotype. In addition, RNA-seq analysis of the BM stroma from JAK2V617F BMT recipients 28-32 weeks post-BMT indicated significant loss of osteo-mesenchymal transcripts. Consistently, micro-CT imaging indicated loss of trabecular bone. Our model uncovers the impact of JAK2V617F donor cells on the host BM microenvironment and hematopoietic system, driving an MPN phenotype even with low donor cell chimerism within unconditioned recipients. The observation that BMT recipient’s hematopoietic cells, which do not carry JAK2V617F, acquire unique transcriptomic and phenotypic profiles suggests that the MPN clone not only impacts hematopoiesis-supporting stroma but profoundly influences unmutated cells, challenging our current understanding and therapeutic approaches to MPNs and other CHIP-associated diseases.

overall_design: To explore the expansion of JAK2V617F-driven myeloproliferative disease within unconditioned bone marrow transplant (BMT) recipients, we transplanted 5e6 JAK2V617F positive whole bone marrow cells (Donor cells, CD45.2+) into unconditioned wild-type age- and sex-matched recipients (Recipient, CD45.1+). These BMT recipients were compared to age- and sex-matched wild-type control mice (did not recieve any BMT, CD45.1+).  After ~7 months, RNA was isolated from bone marrow sorted from its originating source. From within BMT recipients CD45.2+ cells were the Donor Transplanted cells, CD45.1+ cells were the recipient host cells. CD45.1+ cells were also isolated from wild-type controls.  Additionally, from both wild-type controls and BMT recipients we gated off of all cells that were CD45.1/CD45.2 negative and kept all cells that were also lineage-negative (CD4, CD8, Ter119, CD11b, NK1.1, Ly-6G/Ly-6C, and B220) to enrich for non-hematopoietic stromal cells.  To expore the influence of JAK2V617F positive donor cells within recipient CD11b+bone marrow,  unconditioned wild-type age- and sex-matched controls were compared to BMT recipients. After 52-weeks post BMT RNA was isolated from cells that were double positive for CD45.1+ and CD11b+ from both  unconditioned wild-type controls and BMT recipients.

first: Dennis

last: Bonal

first: Alissa

last: Oakes

first: Anna

last: Chorzalska

first: Makayla

last: Pardo

first: Max

last: Petersen

first: Michael

last: Clarke

first: Seo-Ho

last: Lee

first: John

last: Reagan

first: Adam

last: Olszewski

first: Mark

last: Dooner

middle: O

last: Treaba

last: Morgan

first: Paul

last: Bertone

first: Ting

middle: C

last: Zhao

first: Wentian

last: Yang

first: Corey

middle: E

last: Ventetuolo

first: Gabriela

last: Hobbs

first: Joslyn

last: Mills


title: A conserved subset of cold tumors responsive to immune checkpoint blockade

city: San Francisco

first: Mary Helen

last: Barcellos-Hoff

address: 2340 Sutter Street

department: Radiation Oncology

institute: UCSF

summary: We analyzed transcriptomic data from IMvigor210, TCGA and TISMO datasets to evaluate the predictive value of βAlt, a score representing the negative correlation of signatures consisting of transforming growth factor beta (TGFβ) targets and genes involved in error-prone DNA repair. The immune context of βAlt was assessed concomitant evaluation of tumor-educated immune signatures. An ICB-resistant, high βAlt preclinical tumor model was treated with a TGFβ inhibitor, radiation, and/or ICB and assessed for immune composition and tumor control. Results: Here, we show that high βAlt is associated with an immune-poor context yet is predictive of ICB response in both humans and mice. A high βAlt cancer, in which TGFβ signaling is compromised, generates a TGFβ rich, immunosuppressive tumor microenvironment. Accordingly, preclinical modeling showed that TGFβ inhibition followed by radiotherapy could converted an immune-poor, ICB resistant tumor to an immune-rich, ICB responsive tumor. Mechanistically, TGFβ blockade in irradiated tumors activated natural killer cells that were required to recruit lymphocytes and ICB response. In support of this, natural killer cell activation signatures were also increased in immunepoor mouse and human tumors that responded to ICB

overall_design: RNASeq profiling of 15 F2 mTDT from family F mouse mammary tumors in the BALB/cJ strain. The animals were treated with  TGFβ inhibitor, radiation, and/or immune checkpoint blockage (ICB) inhibitor. Tumors were collected 7 days following treatment for RNA profiling.

first: Jade

last: Moore

first: Jim

last: Gkantalis

first: Ines

last: Guix

first: William

last: Chou

first: Kobe

last: Yeun

first: Ann

middle: A

last: Lazar

first: Matthew

last: Spitzer

first: Alexis

last: Combes


title: Kidney Single-Cell Atlas Reveals Macrophage Heterogeneity in Progression and Regression of Cisplatin Induced AKI.

city: Nanjing

first: Bingquan

last: Deng

address: Nanjing Medical University, No.109 Longmian Avenue, Jiangning District

institute: Nanjing Medical University


title: Dysmorphic neurons express markers of inhibitory glycinergic signaling in focal cortical dysplasia

first: Phedias

last: Diamandis

address: 101 College St

summary: Focal cortical dysplasia (FCD) is a severe neurodevelopmental malformation that often manifests as medically refractory epilepsy. A key histological hallmark of FCD is the presence of cytomegalic dysmorphic neurons (CDNs), which are considered to be major contributors to cortical network hyperexcitability. However, the relatively low frequency of CDNs within resected lesions has challenged their unbiased molecular characterization. Here, we leverage deep learning approaches to objectively map key anatomical compartments of FCD and guide regional spatial transcriptomic profiling. Using this approach, we generate an anatomical transcriptional catalog of type IIb FCD, and uncover non-canonical markers of signaling and neurotransmitter pathways in CDNs that may serve as new therapeutic targets for this debilitating disorder.

overall_design: Spatial transcriptomic sequencing of formalin-fixed paraffin-embedded samples of focal cortical dysplasia IIB was performed. Four sections of excised FCD brain tissue were processed with Visium by 10X Genomics technology.

first: Ameesha

last: Paliwal


title: Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease

city: Hamburg

first: Christian

last: Krebs

state: Hamburg

address: Martinistraße 52

institute: UKE

summary: Rapidly progressive glomerulonephritis (RPGN) is the most aggressive group of autoimmune kidney disease with the worst prognosis. Anti-neutrophil cytoplasmic antibody (ANCA) associated vasculitis, anti-glomerular basement membrane (anti-GBM) and lupus nephritis are the most common causes of RPGN and are characterized by the formation of glomerular crescents and infiltration of leukocytes that eventually lead to glomerulosclerosis and kidney failure. In this work, we used high-resolution spatial transcriptomics of 32 ANCA, 19 lupus nephritis, 6 anti-GBM, and 6 control patients to understand how intercellular signaling between immune and renal tissue cells leads to renal inflammation and glomerular injury. Using 3,218,210 immune and kidney cells, we observed that the biological pathways involved in the sequence of glomerular crescent formation are similar across the diseases. While innate immune cells infiltrated the glomerular compartment relatively early, later increases in adaptive immune cells were largely restricted to the periglomerular regions. These changes in immune cells temporally correlated with increases in glomerular parietal epithelial (PEC) and fibrotic mesangial cells, suggesting disease-relevant functional signaling between these immune and renal cells. Cell communication analysis revealed early disease PDGF signaling from epithelial and mesangial cells to PECs, causing their activation and proliferation. At later stages, TGF-β signaling from macrophages, T cells, epithelial cells, and mesangial cells to PECs triggered the expression of extracellular matrix components resulting in glomerulosclerosis. Our results highlight a spatio-temporally conserved progression into glomerular crescents and sclerosis for ANCA, lupus nephritis, and anti-GBM disease, which is driven by consecutive PDGF and TGF-β signaling to PECs.

overall_design: snRNA-seq of human samples from the kidney, specifically from individuals with ANCA-associated glomerulonephritis, was performed using Single Cell 3' v3.1 (10x Genomics) according to manufacturer's instructions. Libraries were sequenced aiming at 25,000 reads per cell on an Illumina NovaSeq 6000

first: Robin

last: Khatri

first: Saskia

last: Jauch-Speer

first: Ulf

last: Panzer

first: Stefan

last: Bonn

middle: F


title: A simple, fast and cost-efficient protocol for ultra-sensitive ribosome profiling

city: Heidelberg

first: Jiří

last: Koubek

address: INF 345

department: ZMBH

institute: Heidelberg University

summary: Ribosome profiling has become an essential tool for studying mRNA translation in cells with codon-level resolution. However, its widespread application remains hindered by the labour-intensive workflow, low efficiency and high costs associated with sequencing sample preparation. Here, we present a new cost-effective and ultra-sensitive library preparation method that significantly advances the applicability of ribosome profiling.  By implementing bead-coupled enzymatic reactions and product purifications, our approach increases both yield and throughput while maintaining high reproducibility. Demonstrating the sensitivity of the protocol we prepared libraries from as little as 12 fmol of RNA, which expands the feasibility of ribosome profiling from minimal input samples, such as derived from small populations, stressed cells, or patient-derived specimens. Additionally, we validate the versatility of the protocol across multiple species and demonstrate its applicability for RNA-seq library preparation. Altogether, this protocol provides a highly accessible and efficient alternative to existing ribosome profiling workflows, facilitating research in previously challenging experimental contexts.

sample_organism:
Escherichia coli
Saccharomyces cerevisiae
Homo sapiens
Mus musculus

overall_design: Classical ribosome profiling library preparation protocol (Ingolia et al., 2009), new ribosome profiling library preparation protocol (described in the study)

first: Jiri

first: Katharina

last: Jetzinger

first: Shiran

last: Dror

first: Mikel

last: Irastortza-Olaziregi

first: Dana

last: Frank

first: Ilgin

last: Kotan

first: Jaime

last: Santos

first: Frank

last: Tippmann

first: Pascal

last: Lafrenz

first: Henrik

last: Kaessmann

first: Orna

last: Amster-Choder

first: Bernd

last: Bukau

first: Günter

last: Kramer


title: The HY5-NPR1 module governs light-dependent virulence of a plant bacterial pathogen

city: Peking

first: Liu

last: Pengtao

state: Peking

address: West Campus of China Agricultural University, Haidian District, Beijing

department: College of Plant Protection

institute: China Agriculture University

summary: Light is essential for plant development, but its influence on pathogen virulence and immunity remains poorly understood. Here, we found that the Pseudomonas syringae DC3000 type III effector, AvrPtoB, exhibits virulence exclusively upon light exposure. This light-dependent regulation is controlled by the Arabidopsis transcription factor ELONGATED HYPOCOTYL 5 (HY5), a central regulator of photomorphogenesis. AvrPtoB targets HY5 in the nucleus, facilitating its ubiquitination and degradation. Genetic disruption of HY5 eliminates susceptibility to AvrPtoB and compromises plant immunity upon light exposure. HY5 enhances immunity by binding promoters of defense-related genes, activating their expression, and stabilizing the transcriptional coregulator NONEXPRESSOR OF PATHOGENESIS-RELATED (PR) GENES 1 (NPR1) by inhibiting its negative regulators NPR3/4. Both HY5-mediated immunity and light-dependent AvrPtoB virulence require NPR1. By contrast, during darkness, CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1)-mediated HY5 degradation suppresses AvrPtoB virulence and HY5-enhanced immunity. These findings elucidate a mechanism in which light modulates bacterial virulence and plant immunity via an HY5-NPR1 module, advancing our understanding of light-pathogen-host interactions.

overall_design: Total RNA was extracted from leaves of 3-week-old Arabidopsis infiltrated with DC3000 at 0 or 24 hours post infiltration using TRIzol® Reagent

first: Pengtao

last: Liu

first: Zhao

last: Zhao

first: Yaqi

last: Tang

first: Yangyang

last: Zhou

first: Jie

first: Kaiqi

last: Xu

first: Yaxin

last: Chen

first: Xiaoting

last: Li

first: Yaru

first: Li

last: Yang


title: Biphasic control of the B cell transcriptome by mTORC1 and GSK3

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: Dysregulated gene expression in germinal center (GC) B cells is associated with autoimmune disorders and lymphoma. To detect pivotal gene regulators and potential therapeutic targets, we fluorescently labeled 47 key B cell genes and performed genome-wide sgRNA screens in GC-lymphoma cells. We identified 4,440 regulators and 17,638 connections containing regulatory directions and strength. We developed the interactive data portal B-LEARN, to access, analyze and visualize the molecular network data. Mechanistic Target of Rapamycin (mTOR) signaling forms a regulator hub accounting for ~40% of regulators identified. Using reporter cell lines, we evaluated impact of rapamycin, a potent mTOR inhibitor, which repressed cell cycle genes early post-treatment but unexpectedly increased immune response genes later. Glycogen synthase kinase 3 (GSK3) counteracted mTOR for immune gene expression and cell cycle control but not translation. The matching set of reporter cell lines and interactive data portal will be a useful resource for future studies.

overall_design: CRISPR screen, ChIPseq, mRNAseq

first: Jens

last: Kalchschmidt

first: Tomoya

last: Kanno

first: Rafael

last: Casellas

first: John

middle: J

last: O'Shea

first: Solji

last: Park

first: Wendy

last: Dubois

first: Yongbing

first: Pawel

last: Trzaskoma

first: Craig

last: Thomas

first: Louis

last: Staudt


title: Targeting a pathogenic cryptic exon that drives HLRCC to induce exon skipping

city: Bethesda

first: Pedro

middle: Jorge

last: Batista

address: 37 Convent Dr

institute: NCI

summary: Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) arises from the loss of fumarate hydratase (FH) activity, leading to the development of cutaneous and uterine leiomyomas as well as early-onset type 2 papillary renal cell carcinoma. Recently, we identified a pathogenic intronic variant in the FH gene that disrupts splicing by creating a novel splice acceptor site, resulting in the aberrant inclusion of a cryptic exon. This exon introduces a premature termination codon, leading to loss of enzymatic function. To restore FH expression, we aimed to identify strategies to exclude the cryptic exon from the mature mRNA. To this end, we generated a mini-gene GFP reporter system that recapitulates the splicing defect observed in patients. We employed CRISPR-Cas9-mediated genome editing and antisense oligonucleotides (ASOs) to modulate splicing and were able to show that both strategies can successfully promoted exon skipping in a reporter cell line. Furthermore, we were able to shift the balance between the different FH mRNA isoforms in patient derived fibroblasts using ASOs. These findings support the potential of splicing modulation as a therapeutic approach for HLRCC-associated FH non-coding loss-of-function mutations.

overall_design: Sequencing of sgRNA cassettes from genomic DNA extracted from cells before and after sorting for GFP-positive cells—expression of GFP reporters on splicing.

first: Siddhardha

last: Maligireddy

first: Mariana

last: Mandler

first: Judith

last: Lunger

first: Madelien

last: Yuen

first: Sneha

last: Kulkarni

first: Alexendar

middle: R

last: Perez

first: Christina

last: Fitzsimmons

first: Daniel

last: Crooks

first: Raj

last: Chari

first: W. Marson

last: Linehan


title: Transcriptomic profiling of shed cells enables spatial mapping of cellular turnover in human organs

city: Rehovot

first: Tal

last: Barkai

address: Herzl St 234

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: Single-cell atlases provide valuable insights into gene expression states but lack information on cellular dynamics. Understanding cell turnover rates—the time between a cell’s birth and death—can shed light on stemness potential and susceptibility to damage. However, measuring turnover rates in human organs has been a significant challenge. In this study, we integrate transcriptomic data from both tissue and shed cells to assign turnover scores to individual cells, leveraging their expression profiles in spatially resolved expression atlases. By performing RNA sequencing on shed cells from the upper gastrointestinal tract, collected via nasogastric tubes, we infer turnover rates in the human esophagus, stomach, and small intestine. Additionally, we analyze colonic fecal washes to map turnover potential in the human large intestine. Our findings reveal a subset of short-lived, interferon-stimulated colonocytes within a distinct pro-inflammatory microenvironment. Our approach introduces a dynamic dimension to single-cell atlases, offering broad applicability across different organs and diseases.

overall_design:
Bulk RNAseq data of NGT fluids from human patients without upper GI malignancies.

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

first: Oran

last: Yakubovsky

first: Yael

last: Korem Kohanim

first: Keren

last: Bahr Halpern

first: Sapir

last: Shir

first: Noa

last: Oren

first: Michal

last: Fine

first: Paz

last: Kelmer

first: Amit

last: Talmon

first: Alon

last: Israeli

first: Niv

last: Penchovich

first: Ron

last: Pery

first: Ido

last: Nachmany

first: Shalev

last: Itzkovitz


title: Developmental trajectories of giant cells induced by Meloidogyne incognita in tomato determined by single-cell RNA-sequencing

city: Knoxville

first: Hewezi

last: Tarek

state: TN

address: 2621 Morgan Circle

institute: niversity of Tennessee, Knoxvile

summary: Plant-parasitic root-knot nematodes (Meloidogyne species) are highly polyphagous parasites that infect a wide variety of plants, including economically important crops. These parasites modulate cellular identity of terminally differentiated root cells to induce the formation of giant-cells and knot-like structures (galls), creating new organs in infected plant roots. In this study, we generated single cell RNA-seq data of galls and neighboring root tissues at two distinct stages of M. incognita infection of tomato plants.

sample_organism:
Solanum lycopersicum
Meloidogyne incognita

overall_design: We generated single-cell transcriptome of Meloidogyne incognita–induced galls on tomato roots at 5- and 10-day post infection (dpi), which represent early- and fully-developed galls. At the same infection stages, about 1 cm of gall-neighboring root tissues were also collected and used as control.

first: Tarek

last: Hewezi

first: Sobhan

last: Bahrami Zadegan

first: Peitong

last: Li


title: A comprehensive benchmark of single-cell Hi-C embedding tools

city: Cleveland

first: Fulai

last: Jin

state: Ohio

address: 2109 Adelbert Rd Building, 7th FL

department: Genetics

institute: Case Western Reserve University

type:
Other
Third-party reanalysis

summary: Embedding is the key step in single-cell Hi-C (scHi-C) analysis which relies on capturing biological meaningful heterogeneity at various levels of genome architecture. To understand the strength and limitations of existing tools in various applications, here we use ten scHi-C datasets to benchmark thirteen embedding tools including Va3DE, a new convolutional neural network model that can accommodate large cell numbers. We built a software framework to decouple the preprocessing options of existing tools and found that no single tool works best across all datasets under default settings. The difficulty levels and preferred resolutions are different between benchmark datasets, and the choice of data representation and preprocessing strongly impact the embedding performance. Embedding cells from early embryonic stages relies on long-range compartment-scale contacts, but resolving cell cycle phases and complex tissue requires short-range loop-scale contacts. Both random-walk and inverse document frequency (IDF) transformation prefers long-range “compartment-scale” over short-range “loop-scale” embedding, while deep-learning methods better overcome sparsity at both scales and are more versatile with different resolutions. Finally, “diagonal integration” with independent data modal is a promising approach to distinguish similar cell subpopulations. Our findings underscore the significance of appropriate priors for scHi-C embedding and offer new insights into genome architecture heterogeneity.

relation:
Reanalysis of: GSE80006
Reanalysis of: GSE129029
Reanalysis of: GSE94489
Reanalysis of: GSE211395
Reanalysis of: GSE84920
Reanalysis of: GSE130711
Reanalysis of: GSE223917
Reanalysis of: GSE213262
Reanalysis of: GSE215353

overall_design:
Single-cell Hi-C datasets spanning early embryogenesis, cell cycle, and differentiated brain cells in both mouse and human.
Data processing: Contact maps were generated by binning the pairs files to ~5-10kb resolution depending on restriction enzyme, and summing neighboring bins to produce lower resolution maps down to 1Mb resolution. Raw count values per-bin are provided without normalization.
Processed data: tab-delimited file contains cell names and metadata
Processed data: tarball contains scool files at multiple resolutions
**********************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
**********************************************************************

first: Dylan

last: Plummer

first: Xiuyuan

last: Lang

first: Shanshan

last: Zhang

first: Yan

first: Jing


title: Inflammation awakens dormant cancer cells by modulating epithelial-mesenchymal phenotypic state [Sum159]

city: Cambridge

first: Jingwei

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

summary: The awakening of dormant disseminated cancer cells is responsible for the clinical relapses of patients whose primary tumors have been cured months and even years earlier. In the present study, we demonstrate that dormant breast cancer cells lodged in the lungs reside in a highly mesenchymal, non-proliferative phenotypic state. The awakening of these cells does not occur because of a cancer cell-autonomous process. Instead, inflammation and wound-healing of the surrounding tissue microenvironment causes them to shift from a highly mesenchymal to a quasi-mesenchymal phenotypic state in which they acquire stemness and proliferative ability. Once awakened, these cells can stably reside in this quasi-mesenchymal state and maintain their stemness, doing so without ongoing heterotypic signaling from the lung microenvironment. EGFR ligands released by the cells of the injured tissue microenvironment, including notably M2 type macrophages, promote dormant cancer cells to move toward this quasi-mesenchymal state, a transition that is essential for the awakening process. An understanding of the mechanisms of metastatic awakening may lead in the future to treatment strategies designed to prevent such awakening and resulting metastatic relapse.

overall_design: For the samples of Sum159 ITGB4 low clone 1 beomycin treated, cells were injected into the mouse lungs through tail vein. At the end point of the experiment, lungs were harvested and dissociated into cell suspension. Cell suspension containing tumor cells were cultured in petri dishes overnight, and in the next day tdtomato+ tumor cells were sorted by FACS. RNA samples were extracted from the sorted tdtomato+ tumor cells and sent for sequencing. For the samples of Sum159 ITGB4 high, Sum159 ITGB4 low clone 1 control, cells were cultured in petri dishes. RNA samples were extracted from these cells and sent for sequencing.

first: Bingbing

last: Yuan


title: Non-coding genetic variants dominant in African American reveal prostate cancer risk

first: David

last: Takeda

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

summary: Prostate cancer (PrCa) manifests substantial variation in incidence rates among distinct populations. African American (AA) men are more likely to be diagnosed with and die from PrCa than European American (EA) men. Despite ongoing advancements in identifying polygenic risk variants from large genome-wide association study (GWAS) cohorts, the genetic mechanisms underlying the higher prevalence of PrCa in AA men remain unclear. A systematic approach that does not rely on extensive cohorts to identify causal regulatory variants contributing to PrCa development is still lacking. Here, by employing a sequence-based deep learning model of prostate regulatory enhancers, we identified ~2,000 essential SNPs (eSNPs) with increased alternative allele frequency in AA and which potentially affect the enhancer function leading to greater PrCa susceptibility. The identified eSNPs potentially mediate PrCa development through two complementary mechanisms: alternative alleles with increased enhancer activity are associated with immune system suppression, while those with decreased enhancer activity are linked to differentiation processes. Interestingly, the eSNPs disrupt the binding of key prostate transcription factors including FOX, AR and HOX families, collectively contributing to PrCa predisposition. Together these eSNPs can be used to assess polygenic risk score that is more effective than previous GWAS-based risk scores in distinguishing individuals with PrCa from the control.

overall_design: ChIP-sequencing of prostate cancer cell lines

first: Shan

first: Kaniz

last: Fatema

first: Sundarraj

last: Nidharshan

first: Arashdeep

last: Singh

first: Padma

last: Rajagopal

first: Dimple

last: Notani

first: Sridhar

last: Hannenhalli


title: Cultured alveolar basal cells differ in their transcriptome, but display similar characteristics and functional properties to airway basal cells

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Basal cells ectopically appear within the lung parenchyma of interstitial lung disease (ILD) patients, however their exact origin, role and function remain poorly understood. By comparing ectopic alveolar to “classical” airway basal cells, we aimed to get a better understanding of the origin and disease-specific characteristics of alveolar basal cells.

overall_design:
Alveolar and airway basal cells were isolated from transbronchial and airway mucosal biopsies of 3 ILD patients. Samples were analyzed by single cell RNA sequencing (scRNA-seq) using the 10X Genomics platform.
--------------------------------------------------
Authors state "Raw data cannot be made available for this dataset on GEO due to patient privacy concerns, and patient consent stipulating that donors can withdraw at any time from the study."

first: Petra

last: Khan

first: Katrin

last: Hostettler

first: Julien

last: Roux


title: Inflammation awakens dormant cancer cells by modulating epithelial-mesenchymal phenotypic state

summary: The awakening of dormant disseminated cancer cells appears to be responsible for the clinical relapses of patients whose primary tumors have been successfully cured months and even years earlier. In the present study, we demonstrate that dormant breast cancer cells lodged in the lungs reside in a highly mesenchymal, non-proliferative phenotypic state. The awakening of these cells is not triggered by a cancer cell-autonomous process. Instead, lung inflammation induced by the chemotherapeutic agent bleomycin effectively awakens dormant cancer cells, providing useful models for studying metastatic awakening. Mechanistically, the awakened cells shift from a highly mesenchymal to a quasi-mesenchymal phenotypic state in which they acquire tumorigenicity and proliferative ability. Once awakened, these cells can stably reside in this quasi-mesenchymal state and maintain their tumor-initiating ability, doing so without ongoing heterotypic signaling from the lung microenvironment. EGFR ligands released by the cells of the injured tissue microenvironment, including notably M2 type macrophages, promote dormant cancer cells to move toward this quasi-mesenchymal state, a transition that is critical for the awakening process. An understanding of the mechanisms of metastatic awakening may lead in the future to treatment strategies designed to prevent such awakening and resulting metastatic relapse.

overall_design: Refer to individual Series