title: Cell-intrinsic platinum response and associated genetic and gene expression signatures in ovarian cancer cell lines and isogenic models [isogenic models]

city: Madison

first: Jessica

last: Lang

state: WI

address: Wisconsin Institutes for Medical Research Room 2766 1111 Highland Avenue

department: Pathology and Laboratory Medicine

institute: UW-Madison

summary: Ovarian cancers are still largely treated with platinum-based chemotherapy as the standard of care, yet few biomarkers of clinical response have had an impact on clinical decision making as of yet. Two particular challenges faced in mechanistically deciphering platinum responsiveness in ovarian cancer have been the suitability of cell line models for ovarian cancer subtypes and the availability of information on comparatively how sensitive ovarian cancer cell lines are to platinum. We performed one of the most comprehensive profiles to date on 36 ovarian cancer cell lines across over seven subtypes and integrated drug response and multiomic data to improve on our understanding of the best cell line models for platinum responsiveness in ovarian cancer. RNAseq analysis of the 36 cell lines in a single batch experiment largely conform with the currently accepted subtyping of ovarian cancers, further supporting other studies that demonstrate that commonly used cell lines are poor models of high-grade serous ovarian carcinoma. We performed drug dose response assays in the 32 of these cell lines for cisplatin and carboplatin, as previous studies have not comprehensively reported this quantity of cell lines and/or the actual IC50s for these drugs. Our results demonstrate that cell lines largely fall either well above or below the equivalent dose of the clinical maximally achievable dose (Cmax) of each compound, allowing designation of cell lines as sensitive or resistant. We performed differential expression analysis for high-grade serous ovarian carcinoma cell lines to identify gene expression correlating with platinum-response. Further, we generated two platinum-resistant derivatives each for OVCAR3 and OVCAR4, as well as leveraged clinically-resistant PEO1/PEO4/PEO6 and PEA1/PEA2 isogenic models to perform differential expression analysis for seven total isogenic pairs of platinum resistant cell lines. While gene expression changes overall were heterogeneous and vast, themes of innate immunity/STAT activation, epithelial to mesenchymal transition and stemness, and platinum influx/efflux regulators. In addition to gene expression analyses, we performed copy number signature analysis and orthogonal measures of HRD scar scores and copy number burden, which is the first report to our knowledge applying field-standard copy number signatures to ovarian cancer cell lines, which revealed unique features of some ovarian cancer models. We also examined markers and functional readouts of stemness that revealed that cell lines are poor models for examination of stemness feature contributions to platinum resistance, as this is likely a transient state. Overall this study serves as a resource to determine the best cell lines to utilize for ovarian cancer research on certain subtypes and platinum response studies, as well as sparks new hypotheses for future study in ovarian cancer.

overall_design: In order to examine gene expression signatures related to platinum resistance, we performed RNAseq on isogenic cell line models of platinum senstivity and resistance.

first: Kristin

last: Adams

first: Jae-Rim

last: Wendt

first: Ryan

last: Moreno


title: Perfluorooctane sulfonate (PFOS) exposure and alcohol-associated liver disease severity in a mouse chronic-binge ethanol feeding model

status: Public on Jun 27 2025

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

country: USA

institute: University of Louisville

type: Expression profiling by high throughput sequencing

summary: Background: Exposure to pollutants including the ubiquitous ‘forever chemical’, Perfluorooctane sulfonate (PFOS) has increasingly been associated with metabolic dysfunction-associated steatotic liver disease (MASLD). Recent epidemiological evidence has identified associations between Per- and polyfluoroalkyl substances (PFAS) exposure and increased liver injury in alcohol consumers, suggesting potential interactions between these exposures. However, the intersection of pollutant exposures and alcohol-associated liver disease (ALD) is not well studied. We hypothesize that pollutants may disrupt hepatic metabolism to modify ALD severity. Recently, we developed a two-hit (ethanol plus pollutant) mouse model, enabling testing of this hypothesis. Here, we elucidate the metabolic and disease-modifying effects of PFOS in this model. Methods: Male C57BL/6J mice were fed isocaloric control or 5% Ethanol (EtOH) Lieber-DeCarli diet for 15 days. From day 6 of feeding, mice were concurrently gavaged with 1 mg/kg PFOS or 2% tween-80 vehicle for 10 days, followed by a 5 g/kg EtOH binge dose and euthanized 5-6 hours later. Results: Approximately 60% of the administered PFOS dose accumulated in liver. PFOS exacerbated EtOH-induced hepatic steatosis and was associated by higher levels of plasma very low-density lipoprotein (vLDL) and alanine aminotransferase (ALT). PFOS upregulated hepatic ethanol-metabolizing enzymes and lowered blood alcohol levels. Ingenuity Pathway Analysis (IPA) Top Toxicity Functions/Lists associated with hepatic gene expression following PFOS co-exposure in EtOH-fed mice included: fatty acid metabolism and liver steatosis; nuclear receptor activation, cytochrome P450, and reactive oxygen species (ROS); apoptosis; liver fibrosis; and hepatocellular carcinoma (HCC). GO/KEGG analyses similarly revealed enrichment in fatty acid, xenobiotic, alcohol, or glutathione metabolic processes; and Peroxisome proliferator-activated receptor (PPAR) signaling. PFOS upregulated hepatic expression of several nuclear receptors (e.g., Pparα, Car, and Pxr) and their P450 target genes (e.g., Cyp4a10, Cyp2b10, and Cyp3a11) by RT-PCR or Western blot, confirming key IPA predictions. Conclusions: PFOS is a metabolism disrupting chemical that worsened ALD severity. PFOS activated hepatic nuclear receptors and enriched hepatic transcriptional pathways associated with steatosis, xenobiotic metabolism, oxidative stress, cell death, fibrosis, and HCC. These data demonstrate a novel mechanism whereby PFOS exacerbates ALD through coordinated dysregulation of lipid homeostasis and liver injury, potentially mediated by nuclear receptor activation. The identification of PFOS as an ALD risk modifier highlight the critical need to evaluate environmental pollutants as potential contributors to liver disease progression in vulnerable populations. More data are required on environmental pollution as a disease modifying factor in ALD.

overall_design: Total RNA was extracted from liver tissue samples (n=6), and RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, Ipswich, MA). Sequencing was performed on an Illumina NovaSeq 6000 S4 flow cell using a 2 x 150 bp paired-end configuration.

first: Frederick

last: Ekuban

first: Matthew

last: Cave

first: Jae

first: Juw

last: Park


title: A 3D genome atlas of breast cancer progression

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series

first: Teun

last: van den Brand

first: Maria

last: Donaldson Collier

first: Koen

last: Flach

first: Sebastian

last: Gregoricchio

first: Isabel

last: Mayayo-Peralta

first: Karianne

last: Schuurman

first: Hans

last: Teunissen

first: Elzo

last: de Wit


title: Allelic bias contributes to heterogeneous phenotypes of NK cell deficiency

city: New York

first: Emily

last: Mace

state: NY

institute: Columbia University Irving Medical Center

summary: While monogenic variants in CDC45-MCM-GINS (CMG) replisome proteins cause human natural killer cell deficiencies (NKD), family members with the same inherited variants often have variable clinical and cellular phenotypes. Using iPSCs from two siblings with the same hereditary compound heterozygous GINS4 variants but variable disease expressivity, we modeled cell proliferation dynamics and the effect of GINS4 variants on NK cell development from pluripotent stem cells. Cell cycle impairment and increased apoptosis were detected in NK cells from patient-derived iPSCs following NK cell lineage commitment but not in pluripotent cells. While this effect was detected in cell lines from both siblings, the efficiency of NK cell differentiation was variable and correlated with differential clinical severity of NKD. Further investigation of allelic expression of inherited GINS4 variants demonstrated equal biallelic expression of GINS4 in pluripotent cells and primary CD34+ progenitors. However, allelic bias in lineage committed NK cells led to over- or under-representation of more damaging inherited GINS4 heterozygous variants that tracked with differential cellular and clinical severity. This study identifies allelic bias as an epigenetic factor that contributes to the phenotypic variations of monogenic diseases and further defines the etiology of NK cell-lineage specific immunodeficiency arising from CMG variants.

overall_design: To better understand the trajectory of human NK cell development from iPSCs, we performed bulk RNA-seq on undifferentiated iPSCs at day0, sorted CD34+ cells on day 6, and separated CD45+ hematopoietic and CD45− non-hematopoietic/mesodermal cells at days 14, 21, and 42. Six cell lines (GINS4 family, C.1, and II.1-Cor) were used.

first: Seungmae

last: Seo

first: Yong-Oon

last: Ahn

first: Sagar

middle: L

last: Patil

first: Jacqueline

last: Armetta

first: Madrikha

middle: D

last: Saturne

first: Everardo

last: Hegewisch-Solloa

first: Nicole

middle: C

last: Guilz

first: Achchhe

last: Patel

first: Barbara

last: Corneo

first: Malgorzata

last: Borowiak

middle: M


title: KIL transcription factors facilitate embryo growth in maize by promoting endosperm elimination via lytic cell death

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

summary: The endosperm is a transient nutritive tissue in plant seeds. During maize grain development, two distinct endosperm cell death processes occur. The endosperm adjacent to the embryo scutellum (EAS) is completely dismantled, whereas the starchy endosperm (SE) retains nutrient-packed cell corpses after grain filling. Here, we show that SE cell death selectively degrades some organelles including mitochondria and the endoplasmic reticulum, while preserving protein bodies, starch granules, and chromatin. In contrast, EAS cells undergo lytic cell death to remobilize stored nutrients through a complex corpse clearance process. Using single-cell transcriptome analysis, we identified two NAC transcription factors, KIL1 and KIL2, as specifically upregulated in the EAS. Dominant and recessive loss-of-function studies demonstrate that these genes redundantly promote cell death execution and corpse clearance in the EAS, but are not required for SE cell death. Reduced EAS cell death in KIL loss-of-function lines significantly impeded embryo growth, indicating that EAS elimination is crucial for optimal embryo development. Notably, kil1 and kil2 gene expression is regulated by DOSAGE-EFFECT DEFECTIVE1, an imprinted paternally expressed endosperm transcription factor. Our findings suggest paternal control over EAS cell death and the embryo-endosperm size ratio in maize, providing new leads to modulate this agronomically important trait.

overall_design: Single-nucleus RNA-seq experiments were performed on nuclei extracted from endosperm of maize (B73) kernels.

first: Nicolas

last: Doll

first: Yannick

last: Fierlej

first: Thomas

last: Eekhout

first: Lisa

last: Elias

first: Clément

last: Bellot

first: Geng

last: Sun

first: Carolin

last: Grones

first: Stijn

last: Aesaert

first: Griet

last: Coussens

first: Riet

last: De Rycke

first: Maria

last: Šimášková

first: Emilie

last: Montes

first: Chloé

last: Plagnard

first: Peter

last: Rogowsky

first: Yemisrach

last: Abebaw

first: Mohammed

last: Bendahmane

first: Laurens

last: Pauwels

last: Widiez

first: Moritz

middle: K

last: Nowack


title: Single-cell transcriptome profiling reveals blast cell heterogeneity and identifies novel therapeutic target IKZF2 in t(8;21) acute myeloid leukemia (CUT&Tag)

city: Tianjin

first: Wenbing

last: Liu

address: No. 288 Nanjing Road

country: China

institute: Institute of Hematology and Blood Diseases Hospital

summary: To clarify the role of AML1-ETO in aberrant hematopoiesis, we generated conditional AML1-ETO knock-in mice. Our research indicated AML1-ETO induction impaired bone marrow hematopoietic reconstitution and resulted in aberrant accumulation of Lin-Sca-1+c-Kit+ (LSK) cells. To clarify the potential mechanism, we compared gene expression profiling and epigenetic alterations of LSK cells between AML1/ETO mouse (conditional knock-in of Runx1-Runx1t1; Mx1-Cre mouse model) and the control mouse (AML1/ETO mice without Mx1-Cre).

overall_design: Genome binding/occupancy profiling by high throughput sequencing of LSK cells for AML1/ETO mouse and control mouse.

first: Jianxiang

last: Wang

first: Shaowei

last: Qiu

first: Yu


title: Cell-intrinsic platinum response and associated genetic and gene expression signatures in ovarian cancer cell lines and isogenic models

first: Jessica

last: Lang

overall_design: We performed RNAseq on 36 ovarian cancer cell lines of various subtypes with a range of responses to platinum therapy to investigate their associated genetic and gene expression signatures.

first: Kristin

last: Adams

first: Jae-Rim

last: Wendt

first: Ryan

last: Moreno


title: A 3D genome atlas of breast cancer progression [ChIP-seq]

first: Wilbert

last: Zwart

summary: During cancer development and progression massive alterations in gene expression have been observed. The regulation of genes occurs within the context of the 3D genome. However, the impact of disease progression on the 3D structure of the genome remains poorly understood. Using breast cancer as a model we have profiled the 3D genome throughout the natural course of the disease; from development to progression. Uniquely, we analysed tumours from the same patients, enabling us to gauge the extent of changes that happen upon metastasis. Our results show that the organization of genome at the level of topologically associating domains (TADs) and compartments upon tumorigenesis and metastasis, is remarkably stable. However, in pleural metastases, representing heavily pretreated progressive disease, the 3D genome is massively affected, and highly heterogeneous between patients, both on the compartment and TAD level. Our data reveal that disease progression in breast cancer is associated with a progressive unravelling of the 3D genome.

overall_design:
ChIP-seq has been perfomed on fresh-frozen tissue derived from healthy breast (HB), primary breast cancer (PB), BCa-derived liver metastasis (LM). Immunoprecipitation has been performed for ERa (sc-542, SantaCruz).  Raw paired-end fastq.gz files for both immunoprecipitated DNA and input samples are available under controlled access at the EGA database; project number EGAS50000000444 (DataSet: EGAD50000000642)

***************************************************************
Raw data are derived from patient data, for this reason we deposited the raw sequences at the EGA (for both datasets). The corresponding EGA study accession number is EGAS50000000444 (https://ega-archive.org/studies/EGAS50000000444).
***************************************************************

first: Teun

last: van den Brand

last: Donaldson Collier

first: Koen

last: Flach

first: Sebastian

last: Gregoricchio

first: Isabel

last: Mayayo-Peralta

first: Karianne

last: Schuurman

first: Hans

last: Teunissen

first: Elzo

last: de Wit


title: Single-cell transcriptome profiling reveals blast cell heterogeneity and identifies novel therapeutic target IKZF2 in t(8;21) acute myeloid leukemia (ATAC-seq)


title: Microglia–neuron crosstalk through Hex–GM2–MGL2 maintains brain homeostasis

status: Public on Jun 26 2025

city: Freiburg

first: Chintan

last: Chhatbar

address: Breisacher strasse 64

department: Department of Neuropathology

country: Germany

institute: Uniklinikum Freiburg

summary: We used snRNA-sequencing to understand trancriptomic response of CNS cell nuclei  after de-enrichment of NeuN+Olig2+ nuclei after fluorescence based sorting.

overall_design: CNS nuclei were isolated from frozen CNS tissue specimen, stained with anti-NeuN and anti-Olig2, FACS purified (DAPI+NeuN-Olig2-), and analyzed with snRNA-seq

first: Marco

last: Prinz


title: Dissociating Mechanisms That Underlie Seasonal and Developmental Programs for the Neuroendocrine Control of Physiology in Birds

city: Glasgow

first: Tyler

last: Stevenson

address: Jarret Building

department: School of Biodiversity, One Health, and Comparative Medicine

country: United Kingdom

institute: University of Glasgow

summary: Long-term programmed rheostatic changes in physiology are essential for animal fitness. Hypothalamic nuclei and the pituitary gland govern key developmental and seasonal transitions in reproduction. The aim of this study was to identify the molecular substrates that are common and unique to developmental and seasonal timing. Adult and juvenile quail were collected from reproduc tively mature and immature states, and key molecular targets were examined in the mediobasal hypo thalamus (MBH) and pituitary gland. qRT-PCR assays established deiodinase type 2 (DIO2) and type 3 (DIO3) expression in adults changed with photoperiod manipulations. However, DIO2 and DIO3 remain constitutively expressed in juveniles. Pituitary gland transcriptome analyses established that 340 tran scripts were differentially expressed across seasonal photoperiod programs and 1,189 transcripts dis played age-dependent variation in expression. Prolactin (PRL) and follicle-stimulating hormone subunit beta (FSHβ) are molecular markers of seasonal programs and are significantly upregulated in long pho toperiod conditions. Growth hormone expression was significantly upregulated in juvenile quail, regardless of photoperiodic condition. These findings indicate that a level of cell autonomy in the pitu itary gland governs seasonal and developmental programs in physiology. Overall, this paper yields novel insights into the molecular mechanisms that govern developmental programs and adult brain plasticity.

overall_design: Five-week-old male Japanese quail (Coturnix japonica) were acclimated to a long photoperiod for 2 weeks. Then birds were placed on nonstimulatory photoperiods to induce gonadal involution and collected in short days (8L) after 8 weeks. A subset of short-day birds (n=5) was humanely killed using cervical dislocation followed by decapitation. Another group (n=5) was placed on stimulatory photoperiods to induce gonadal growth and collected in a long photoperiod after 8 weeks. Newly hatched chicks were acclimated to a long photoperiod for 5 days. Birds were divided into 2 groups and assigned to either a long (16L, n=4) or short (8L, n=5) photoperiod for 5 days. On posthatch day 10, chicks were killed by cervical dislocation followed by decapitation. For all birds (adults and chicks), brain and pituitary tissues were frozen on dry ice and stored at -70 Celsiius. During collections, the pituitary stalk was severed, leaving the pars tuberalis attached to the mediobasal hypothalamus. Pituitary tissue including the pars distalis was dissected from the sella turcica and retained for both qRT-PCR analyses and Oxford Nanopore RNA-sequencing.

first: Timothy

middle: A

last: Liddle

first: Gaurav

last: Majumdar

first: Calum

last: Stewart

first: Maureen

last: Bain

middle: J


title: Spatial Transcriptomic Landscape of Canine Oral Squamous Cell Carcinoma

city: Davis

first: Stephanie

last: Goldschmidt

state: CA

address: one shields ave

department: VSR

institute: UC-Davis

summary: Canine Oral Squamous Cell Carcinoma (COSCC) is the second most common oral tumor in dogs, and the most relevant for comparative human trials as a spontaneous large animal model of disease. Thus, complete knowledge of the genomic landscape is essential for identifying therapeutic vulnerabilities and early biomarkers of disease across species. Historical genomic work has focused primarily on bulk sequencing, with only one publication using a laser capture dissection technique. The present study describes the complete molecular landscape of COSCC with spatial distinction between the surface tumor, deep invasive front, tumor microenvironment, and peritumoral dysplasia compared to matched normal samples. Each region demonstrated distinct molecular signatures. Genes related to epithelial growth factor (EGFR) and epithelial mesenchymal transformation (EMT) were upregulated in peri-tumoral dysplasia and surface cancer. Additionally, KRAS, SSP1 and KRT14 were upregulated in cancer, therefore combining these read outs may be useful in differentiating high grade dysplasia from malignant tissue at a molecular level. The primary tumor infiltrating leukocyte present in the tumor stroma were M2 macrophages. IL-10 expression was also significantly higher in the stroma, suggesting that tumor associated macrophages were directly related to establishing an immunosuppressive environment via cytokine secretion. The other predominant leukocytes were T-cells, with CD4+ T-cells being most common. CD4+ T cells expressed transcripts for both stimulatory (adaptive immunity with B cells and ICOS) and inhibitory molecules (CTLA4). However, the observed increase in CTLA4 suggests that this inhibitory signal may be preventing a robust anti-tumor immune response representing a therapeutic target for COSCC.

overall_design: Spatial transcriptomic analysis of canine oral squamous cell carcinoma and non-malignant tissues was performed on the NanoString GeoMx Digital Spatial Profiler platform utilizing the GeoMx Canine Cancer Atlas assay to assess the expression of 1,962 genes

first: Clifford

last: Tepper

first: Jack

last: Goon

first: Maria

last: Soltero-Rivera

first: Robert

last: Rebhun

first: Andrew

last: Birkeland

first: Xiao-Jing

last: Wang

last: Davis

first: Stephenie

last: Liu

first: Brian

last: Murphy

first: Natalia

last: Vapniarski-Arzi


title: Humanized lung implant model of Staphylococcus aureus infection

city: Newark

first: Dane

last: Parker

state: NJ

address: 205 South Organge Ave, G-1208

department: Pathology, Immunology and Laboratory Medicine

institute: Rutgers New Jersey Medical School

summary: We investigated the utility in using a humanized mouse model of infection with autologous lung tissue implanted into the mice. The immune response to S. aureus was investigated along with the response of S. aureus to this tissue environment.

sample_organism:
Staphylococcus aureus
Homo sapiens

platform_organism:
Staphylococcus aureus
Homo sapiens

overall_design: RNA-seq analysis of human lung implants in humanized mice before and after infection with S. aureus. S. aureus gene expression in planktonic vs in human lung implants.


title: Sequence-to-expression approach to identify etiological non-coding DNA variations in P53 and cMYC-driven diseases [RNA-seq]

city: Houston

first: Wenbo

last: Chen

address: 7000 Fannin Street

institute: The University of Texas Health Science Center at Houston

summary: Most DNA variants associated with common complex diseases fall outside the protein-coding regions of the genome, making them hard to detect and relate to a function. Although many computational tools are available for prioritizing functional disease risk variants outside the protein-coding regions of the genome, the precision of prediction of these tools is mostly unreliable and hence not close to cancer risk prediction. This study brings to light a novel way to improve prediction accuracy of publicly available tools by integrating the impact of cis-overlapping binding sites of opposing cancer proteins, such as P53 and cMYC, in their analysis to filter out deleterious DNA variants outside the protein-coding regions of the human genome. Using a biology-based statistical approach, DNA variants within cis-overlapping motifs impacting the binding affinity of opposing transcription factors can significantly alter the expression of target genes and regulatory networks. This study brings us closer to developing a generally applicable approach capable of filtering etiological non-coding variations in co-occupied genomic regions of P53 and cMYC family members to improve disease risk assessment.

overall_design: RNA-Seq analysis was conducted on untreated and treated Raji and U2OS cells with doxorubicin to identify differentially expressed genes after treatment. The total RNA samples extracted from cancer cells were tested for RNA quality and concentration. Illumina HiSeq2500 platform in a 2x100bp paired-end configuration was used to obtain 35 million reads on average for each library sample.

first: Walid

last: Fakhouri

first: Lisha

last: Zhu

first: Jim

last: Zheng


title: Hair Follicle Epithelial Stem Cells Contributing to Interfollicular Epidermis during Homeostasis [single-cell RNA-seq]

city: Dallas

first: Elnaz

last: Ghotbi

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: The mammalian skin is a crucial barrier, with the epidermis as its protective, renewing outer layer. Loss of epidermal function is lethal, so multiple stem cell populations likely support the interfollicular epidermis (IFE) for survival. Using single-cell RNA sequencing, we show that KROX20 marks a diverse stem cell population in the upper and middle mouse hair follicle (HF), partially overlapping with known HF stem cells. Lineage tracing reveals that Krox20-lineage cells migrate from the HF to the IFE, contributing to both basal and suprabasal layers.

overall_design: Epithelial cells from epidermis of five Krox20-GFP mice at P5 were harvested and FACS sorted for GFP-positive (Krox20-expressing) cells. FACS-sorted cells (GFP-positive) were then used for Single Cell Sequencing.

first: Edem

last: Tchegnon

first: Ze

last: Yu

first: Tracey

last: Shipman

first: Zhiguo

first: Yumeng

last: Zhang

first: Renee

last: McKay

first: Chao

last: Xing

first: Chung-Ping

last: Liao

first: Lu

middle: Q

last: Le


title: Macrophage trafficking contributes to gut-brain crosstalk in hypertension

status: Public on Jun 25 2025

city: Berlin

first: Suphansa

last: Sawamiphak

address: Robert-Rössle-Straße, 10

institute: Max Delbruck Center

summary: The main goal of this study is to investigate the impact of the IDL (Ion-Dyshomeostatic Larvae) condition on the transcriptomic profile of gut-resident macrophages in zebrafish larvae. While control larvae are raised in standard fish water (Danieau’s solution), IDL larvae are exposed to progressively diluted fish water, reaching a final dilution of 1:1500, starting at 2 days post-fertilization (dpf) (Apaydin et al., Cardiovasc Res 2023).

overall_design: Gut and non-gut resident macrophages sorted (csf1a:GAL4; UAS:EGFP) after 3 days of IDL treatment.

first: Forcari

last: Giovanni

first: Sawamiphak

last: Suphansa


title: Time course single-cell RNA-seq and single-cell ATAC-seq data from mESCs treated with retinoic acid

city: Stanford

first: Jingxue

last: Xin

state: California

address: JAMES CLARK CENTER E100A

institute: Stanford University

summary: This study generated  ~41,000 cells for scRNA-seq and ~19,000 cells for scATAC-seq from differentiating mouse embryonic stem cells over a time course. It demonstrates cRegulon method provides specific regulations of TF combinations to characterize identity and transition of cell types during retinoic acid induced mESC differentiation.

overall_design: Embryoid bodies from mESCs were treated with retinoic acid for up to 10 days. The EBs were collected at Day 0 (Not treated with RA), 2, 4, and 10 after treatment. Nuclei isolated from single cell were used to generate scATAC-seq data. Single cells were used to generate scRNA-seq data. The scRNA-seq library was generated using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, PN-1000268) and the scATAC-seq library was generated using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit (10X Genomics, PN-1000175).

first: Wing

middle: H

last: Wong

first: Xi


title: snRNA-seq of Hexb-deficient brain cells

status: Public on Jun 24 2025

first: Maximilian

last: Frosch

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary: We used snRNA-sequencing to analzye all thalamic brain cells derived from Hexb-deficient and competent cells.

overall_design: CNS nuclei were isolated from frozen thalamic specimen, FACS purified, and analyzed with snRNA-seq

first: Marco

last: Prinz


title: Hair Follicle Epithelial Stem Cells Contributing to Interfollicular Epidermis during Homeostasis

first: Elnaz

summary: The mammalian skin is a crucial barrier, with the epidermis as its protective, renewing outer layer. Loss of epidermal function is lethal, so multiple stem cell populations likely support the interfollicular epidermis (IFE) for survival. We show that KROX20 marks a diverse stem cell population in the upper and middle mouse hair follicle (HF), partially overlapping with known HF stem cells. Lineage tracing reveals that Krox20-lineage cells migrate from the HF to the IFE, contributing to both basal and suprabasal layers. Spatial transcriptomics analysis of the skin was used to confirm this migration.

overall_design: Dorsal skin samples were collected from Krox20-CreERT; R26-tdTomato mice at P38 (n=3), induced at P2, with each mouse corresponding to one skin section per slice. For the three biological replicates (three mice), four technical replicates were used across the four capture areas.

first: Edem

last: Chen

first: Renee M.

first: Lu Q.


title: Cytokinins control secondary cell wall formation in the inflorescence stem of Arabidopsis

city: Brno

first: Jan

last: Hejatko

address: Kamenice 5

country: Czech Republic

institute: CEITEC

summary: Spatiotemporal control over developmental programs is vital to all organisms. Here we show that deficiency in cytokinin signaling or biosynthesis leads to early secondary cell wall (SCW) formation in Arabidopsis inflorescence stem that associates with precocious upregulation of a SCW transcriptional cascade controlled by NAC TFs (NSTs/VNDs). We demonstrate that cytokinin signaling through the AHK2/3 and the ARR1/10/12 suppresses the expression of several NSTs/VNDs and SCW formation in the apical portions of stems. Exogenous cytokinin application led to fast downregulation of NST1 and NST3 (NST1/3) and VND6/7 in the WT and reconstituted both proper development and apical-basal gradient of NST1/3 expression in a cytokinin biosynthesis-deficient mutant. We show that AHK2 and AHK3 required functional NST1 or NST3 to control SCW initiation in the interfascicular fibers, further evidencing that cytokinins act upstream of NSTs transcription factors. The premature onset of a rigid SCW biosynthesis and altered expression of NST1/3 and VND6/7 due to cytokinin deficiency led to the formation of smaller tracheary elements (TEs) and impaired hydraulic conductivity. We conclude that cytokinins downregulate NSTs to inhibit premature SCW formation in the apical  part of the inflorescence stem, facilitating thus the development of fully functional TEs and interfascicular fibers.

overall_design: RNA-seq was performed on dissected stem internodes (apical and basal) from wild-type plants and various cytokinin-related mutants or overexpressors, including mutants in cytokinin receptors (ahk2,3), response regulators (arr1,10; arr1,12; arr10,12; arr1,10,12), cytokinin biosynthesis genes (ipt3,5,7; ipt1,3,5,7), phosphotransfer proteins (ahp1,2,3,4,5), and cytokinin-degrading enzymes (p35S:CKX2; p35S:CKX3).  Plants were grown under long-day conditions until stage 1 of reproductive development, corresponding to the first elongated silique. Stem segments were harvested, total RNA was isolated, and sequencing libraries were prepared using the Illumina TruSeq protocol. Each genotype and tissue type was sampled in biological replicates to enable differential expression analysis. The aim was to identify gene expression changes associated with altered cytokinin pathways that may influence secondary cell wall formation and vascular development.

first: Vojtech

last: Didi

first: Dominique

last: Arnaud

first: Alesia

last: Melnikava

first: Anna

last: Pačinková

first: Roman

last: Hobza

first: Vít

last: Gloser

first: Eva

last: Budinska


title: Marsupial single-cell transcriptomics identifies temporal diversity in mammalian developmental programmes

city: London

first: Sergio

last: Menchero

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Single-cell transcriptomics has demonstrated conserved and divergent programmes of organogenesis in mammals, but existing studies have focused on eutherians. Marsupials exhibit short gestation and complete development externally, necessitating accelerated differentiation of anterior features required for locomotion and feeding. Hence, they represent a unique outgroup for studying temporal shifts in development, known as heterochrony. Here, we generate a single-cell transcriptomic atlas of gastrulation and early organogenesis in a marsupial, the opossum Monodelphis domestica. We identify previously undocumented tissues undergoing heterochrony, and find that transcriptional programmes that form anterior structures initiate earlier and progress faster relative to eutherians. The result is uncoupling of transcriptional and morphological timelines, revealing unforeseen diversity in mammalian developmental sequences. Using our transcriptomic dataset, we identified translation as a candidate control mechanism by which anterior prioritisation is achieved. Our findings provide insight into the asynchronous progression of developmental programmes in marsupials.

overall_design: Opossum (Monodelphis domestica) embryos at four time points encompassing gastrulation and early organogenesis were processed for single-cell RNA-sequencing

first: Christopher

last: Barrington

first: Clare

last: Critcher

first: Wazeer

last: Varsally

first: Gregorio

last: Alanis-Lobato

first: Kathy

last: Niakan

first: James

last: Turner


title: A 3D genome atlas of breast cancer progression [Hi-C]

first: Wilbert

last: Zwart

overall_design:
Hi-C has been perfomed on fresh-frozen tissue derived from healthy breast (HB), primary breast cancer (PB), BCa-derived liver metastasis (LM). Enzymatic digestion has been performed using MboI.  Raw paired-end fastq.gz files are available under controlled access at the EGA database; project number EGAS50000000444 (DataSet: EGAD50000000643)

***************************************************************
Raw data are derived from patient data, for this reason we deposited the raw sequences at the EGA (for both datasets). The corresponding EGA study accession number is EGAS50000000444 (https://ega-archive.org/studies/EGAS50000000444).
***************************************************************

first: Teun

last: van den Brand

first: Maria

last: Donaldson Collier

first: Koen

last: Flach

first: Sebastian

last: Gregoricchio

first: Isabel

last: Mayayo-Peralta

first: Karianne

last: Schuurman

first: Hans

last: Teunissen

first: Elzo

last: de Wit


title: Single-cell transcriptome profiling reveals blast cell heterogeneity and identifies novel therapeutic target IKZF2 in t(8;21) acute myeloid leukemia (RNA-seq)

first: Wenbing

last: Liu

overall_design: Expression profiling by high throughput sequencing of LSK cells for AML1/ETO mouse and control mouse.

first: Jianxiang

last: Wang

first: Shaowei

last: Qiu

first: Yu


title: PPARG-centric transcriptional re-wiring during differentiation of human trophoblast stem cells into extravillous trophoblasts [ChIP-seq]

city: AUSTIN

first: Qingqing

last: Guo

address: 2506 Speedway

institute: The University of Texas at Austin

summary: Peroxisome Proliferator-Activated Receptor gamma (PPARG) is a nuclear receptor transcription factor critical for placental development. Using human trophoblast stem cells (TSCs) and their differentiation into extravillous trophoblasts (EVTs) as a model, we show that PPARG is required for both TSC self-renewal and EVT differentiation. ChIP-seq revealed that PPARG occupies distinct sets of regulatory elements in TSCs and EVTs, forming cell-type specific transcriptional networks. Integration with other trophoblast-specific transcription factors suggests that PPARG participates in transcriptional re-wiring during EVT differentiation. Functionally, activation of PPARG promotes EVT invasion, suggesting a potential connection between PPARG signaling and placental pathologies such as placenta accreta. These findings highlight context-specific roles of PPARG in modulating gene expression and cell behavior during human trophoblast development.

overall_design: ChIP-seq for PPARG was performed in human trophoblast stem cells (TSCs) and at multiple stages of extravillous trophoblast (EVT) differentiation, including day 2, 4, 6, and 8.

first: Kim

last: Jonghwan

first: Guo

last: Qingqing


title: bulk RNA-seq of Hexb-deficient microglia

first: Maximilian

last: Frosch

summary: We used bulk RNA-sequencing to analzye microglia derived from Hexb-deficient and competent cells.

overall_design: Brains were homogenized, stained, microglia were FACS-purified, RNA was isolated, cDNA was produced and sequencing libraries were prepared.

first: Marco

last: Prinz


title: Whole transcriptomes analyses of organoids derived from Mist1Cre/ERT2 mice corpus with oxidative stress

city: Shanghai

first: Fan

last: Chen

address: Yueyang Road, No. 320

institute: Center for Excellence in Molecular Cell Science, CAS

summary: Purpose: To explore the molecular mechanisms of Mist1+ cells that are specifically resistance to oxidative stress, and the mechanism that oxidative stress in regulating the stemness of Mist1+ cells, RNA sequencing was performed to analyze the geome-wide change of Mist1+ cells under oxidative stress (high fat diet or Gpx4 knockout) compared with control mice, and further the difference between these two Mist1+ cells. Methods: Total mRNA was extracted from Mist1+ cells which were isolated from corpus of Mist1Cre/ERT2;RFPLSL mice (8 weeks) fed with normal diet and high fat diet. Besides, we formed Mist1+ organoids from Mist1Cre/ERT2;RFPLSL mice and  Gpx4F/F;Mist1Cre/ERT2;RFPLSL mice respectively, organoids were passaged, and total mRNA was extracted from organoids in passage 5, 10 and 15. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina NovaSeq 6000 platform. Results: Our results revealed differentially expressed genes in Mist1+ cells from high fat diet-fed mice compared with normal diet-fed mice. Further KEGG analysis enriched multiple pathways/biological processes including ROS, endocytosis, oxidative phosphorylation, Ras signaling, and ferroptosis. Further GSEA analysis showed that genes associated with stem cell maintenance and differentiation were significantly enriched in the high fat diet group, suggesting that Mist1+ cells enhance their stemness and transcriptional activity in response to oxidative stress induced by a high-fat diet. As for Gpx4 knockout-induced oxidative stress, we found that Gpx4 knockout in Mist1+ cells rewired multiple signaling pathways that drive cell growth, especially Hippo signaling pathway that is closely related with gastric cancer initiation and progression. Conclusion: Our study present the detailed transcripts analysis of Mist1+ cells under oxidative stress (high fat diet or Gpx4 knockout). Based on RNA-seq transcriptome characterization, we conclude a mechanism for Mist1+ cells that are resistance to oxidative stress and act as tumor initiation cells under oxidative stress.

first: Shi

last: Jiao

first: Zhaocai

last: Zhou


title: REV-ERBα regulates brain NAD+ levels and tauopathy via an NFIL3-CD38 axis

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

summary: Nicotinamide adenine dinucleotide (NAD+) is a critical metabolic co-enzyme which is strongly implicated in the pathogenesis of brain aging and neurodegenerative diseases. Prevention of age-related decline in brain NAD+ levels is an attractive therapeutic strategy for combating age-related neurodegeneration, emphasizing the need to fully understand molecular mechanisms regulating brain NAD+ levels. Previous work has shown that the circadian protein REV-ERBα regulates cellular NAD+ levels in cardiac tissue via control of the NAD+ producing enzyme NAMPT. Whether this pathway regulates brain NAD+ levels, however, is unknown. Here, we show that REV-ERBα controls brain NAD+ levels through a distinct pathway involving suppression of the NAD+ consuming enzyme CD38 in astrocytes. Under basal conditions, REV-ERBα suppresses the transcription factor NFIL3 (E4BP4) which itself provides tonic inhibition of CD38 expression, elevating CD38 levels and keeping NAD+ levels low. Deletion of REV-ERBα, either globally or specifically in astrocytes, led to induction of NFIL3, suppression of CD38, increased NAD+, and mitigated protein aggregation, inflammation, and neurodegeneration in a mouse model of tauopathy. This pathway appears to be unique to the brain, as REV-ERBα deletion does not affect NAMPT expression in the brain, does not suppress CD38 in the liver, and has an opposite effect on NAD+ levels in the brain as in the heart. Our data show that the circadian nuclear receptor REV-ERBα can regulate NAD+ via distinct mechanisms in different tissues and define a REV-ERBα-NFIL3-NAD+ downstream pathway controlling brain NAD+ metabolism and neurodegeneration.

overall_design: To analyze the differentially expressed genes among four groups including WT, RKO, PS19, and PS19;RKO, mouse hippocampus RNA samples from each groups were prepared and anlyzed by bulk RNA-sequencing.

first: Jiyeon

last: Lee

first: Erik

middle: S

last: Musiek


title: Early lineage segregation of primary myotubes from secondary myotubes and adult muscle stem cells

city: Lyon

first: Gauthier

last: Toulouse

address: 8 avenue Rockfeller

country: France

institute: CNRS

summary: Myogenesis in amniotes unfolds through two consecutive waves. The primary myotube lineage is characterized by the expression of slow myosin, sometimes in combination with fast myosin, and may serve as a scaffold for the secondary lineage, which expresses exclusively fast myosin. The embryonic origin of these two lineages, their relationship, and their connection to adult muscle stem cells are unknown. Here, we employed innovative strategies, combining novel TCF-LEF/β-catenin signaling reporters with the precise spatiotemporal control of in vivo electroporation in avian embryos, to track limb muscle progenitors from early migration to late fetal stages. Strikingly, we uncovered two distinct progenitor populations co-existing from the earliest stages of limb myogenesis, with specific developmental fates: reporter-positive progenitors exclusively form primary myotubes, while reporter-negative progenitors generate secondary myotubes and adult muscle stem cells. Furthermore, we uncovered a novel function of TCF-LEF/β-catenin signaling in regulating the spatial organization of the primary myotube lineage via CXCR4-mediated control of myoblast migration, likely contributing to its proposed organizing function. By redefining the embryonic origins of these myogenic populations, our findings not only resolve a longstanding question in muscle biology but also provide a crucial molecular entry point for understanding the cellular and molecular underpinnings of muscle fiber type diversity and function.

overall_design: Dissection of electroporated limb bud of chicken embryos with a reporter plasmid (dTomato+) and a transcriptional reporter for TCF/LEF transcription (mVenus+), shorting of the dTomato+ cells and analysis with 10X single-cell RNA-sequencing

first: William

last: Jarassier

first: Valérie

last: Morin

first: Fabien

last: Le Grand

first: Christophe

last: Marcelle


title: snRNA-seq of Hexb-deficient brain cells upon microglia replacement

summary: We used snRNA-sequencing to analzye NeuN-Olig2- thalamic brain cells derived from Hexb-deficient mice upon microglia replacement

first: Frosch

last: Maximilian

first: Shimizu

last: Takashi

first: Prinz

last: Marco


title: Whole transcriptomes analyses of organoids derived from Mist1Cre/ERT2 and Gpx4F/F Mist1Cre/ERT2 mice corpus

summary:
Purpose: To explore the molecular mechanisms of Mist1+ cells that are specifically resistance to oxidative stress, and the mechanism that Gpx4 knockout (oxidative stress) in regulating the stemness of Mist1+ cells, RNA sequencing was performed to analyze the geome-wide change of Mist1+ cells compared with Mist1- cells, and further the difference between Mist1+ cells and Gpx4 KO-Mist1+ cells.
Methods: Total mRNA was extracted from organoids which were isolated from corpus of Mist1Cre/ERT2;RFPLSL and Gpx4F/F;Mist1Cre/ERT2;RFPLSL mice (8 weeks). Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina NovaSeq 6000 platform.
Results: Our results revealed differentially expressed genes in Mist1+ cells when compared with Mist1- cells. Further KEGG analysis enriched multiple pathways/biological processes including ROS, endocytosis, oxidative phosphorylation, transcriptional misregulation in cancer, phagosome, cellular senescence, cell cycle and p53 signaling pathway. Further GSEA analysis showed that Mist1 signature genes were highly enriched in the Mist1+ group when compared to the Mist1- group, and Gpx4 knockout further enriched Mist1 signature genes, suggesting a role for Mist1 as a transcriptional factor in determining cellular resistance towards oxidative stress. At the same time, we found that Gpx4 knockout in Mist1+ cells rewired multiple signaling pathways that drive cell growth, especially Hippo signaling pathway that is closely related with gastric cancer initiation and progression
Conclusion: Our study present the detailed transcripts analysis of Mist1-, Mist1+ and Gpx4 KO-Mist1+ cells. Based on RNA-seq transcriptome characterization, we conclude a mechanism for Mist1+ cells that are resistance to oxidative stress and act as tumor initiation cells under oxidative stress.

overall_design: Total mRNA was extracted from Mist1+, Mist1- and Gpx4 KO-Mist1+ organoids derived from Mist1Cre/ERT2;RFPLSL and Gpx4F/F;Mist1Cre/ERT2;RFPLSL mice (about 8 weeks). The quality was assessed using Agilent 2100, and the profiles were sequenced on the Illumina Hiseq X10.


title: Elementary 3D organization of active and silenced E. coli genome (RNA-Seq)

city: New York

first: Ilya

last: Shamovsky

state: New York

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

summary: Unraveling how genomes are spatially organized and how their 3D architecture drives cellular functions remains a major challenge in biology. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid. Despite progress in characterizing bacterial 3D genome architecture over recent decades, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods like Hi-C. In this study, we developed an enhanced Micro-C chromosome conformation capture, achieving 10 bp resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the E. coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, play key roles in repressing horizontally transferred genes (HTGs). Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, while removing both H-NS and StpA results in their complete disassembly, increased HTGs transcription, and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery.

overall_design: Using the Micro-C technique, we generated contact maps of the E. coli genome at a resolution up to 10 bp. We analyzed wild-type E. coli cells, cells subjected to heat shock, cells treated with different antibiotics and drugs (rifampicin, bleomycin, novobiocin, ciprofloxacin, netropsin), as well as different knockout strains (deltaHNS, deltaStpA, deltaHNSdeltaStpA, deltaFis, deltaMukBEF). We performed gene expression profiling analysis using data obtained from Red-C and RNA-seq. We also performed Hi-C analysis of wild-type E.coli cells.

first: Alexey

last: Gavrilov


title: Warm temperature modifies lineage cell fates to reduce stomata production in Arabidopsis

city: Toledo

first: Montaña

last: Mena

state: Toledo

address: Avda. Carlos III s/n

department: Environmental Sciences

country: Spain

institute: UCLM

summary: Stomatal abundance decrease in Arabidopsis triggered by warm-temperature is attributed to PIF4-mediated repression of SPEECHLESS (SPCH) expression. We identified the unknown developmental and transcriptional basis of this adaptive response. We analyzed stomatal lineage progression at warm- and control-T combining live-cell imaging and lineage-cell tracing with epidermal phenotyping, genetics and transcriptomics. Warm-T or PIF4 overexpression caused a fraction of stomatal precursors to lose their identity and become diverted, explaining stomatal index reduction, and hinting at developmental mechanisms underlying lineage progression. Triggering diverted precursor fate required extended exposure to warm-T, below which the process is reversible and stomatal index remains unchanged. Despite heat-induced gene reprogramming silenced key positive drivers of stomatal development as SPCH and MUTE, most lineages progressed and formed stomata. Transcriptomics revealed that warm-T shifted lineages towards uncommitted cell stages, which regained committed fates during recovery at control temperature. This indicates that stomatal development under changing temperatures occurs through partly rewired gene circuits involving alternative pathways.

overall_design: We used short 28ºC pulse treatments to analyze the transcriptional basis of stomatal lineage progression under warm temperature. All treatments began with Col-0 seedlings grown for 3 days at 21ºC (T0). Seedlings were then exposed to control (21ºC) or warm temperature (28ºC) for 16h (T1) and 24h (T2), or grown at 28°C for 16h and shifted back to 21°C for the following 8h (recovery treatment; Recov). RNA-seq data were obtained from three independent biological replicates per time-point and temperature, each consisting of 50 seedlings.

first: Josue

last: Saiz-Perez

first: Montana

first: Carmen

last: Fenoll


title: Functional Genomic Analysis of Glaucoma Pathogenesis Due to gmds Mutation in Zebrafish

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

summary: Glaucoma, a major cause of irreversible blindness, is characterized by optic nerve damage and loss of retinal ganglion cells (RGC). SNPs in the GDP-MANNOSE 4,6-DEHYDRATASE (GMDS) gene have been linked to primary open-angle glaucoma (POAG) and treatment responses. The GMDS gene plays a critical role in fucosylation, a process essential for modifying glycoproteins and glycolipids, yet no mechanism for its role in glaucoma pathology has been described. Our study investigates the effects of gmds haploinsufficiency using a CRISPR/Cas9 induced mutation in zebrafish. RNA sequencing (RNAseq) analysis shows significant downregulation of stress response genes including those of the crystallin family, and increased expression of cell death genes in gmds heterozygous mutant eyes. These gene expression changes correlate with phenotypic alterations, including RGC layer thinning, RGC loss, and reduced optic nerve head width in adult gmds heterozygotes relative to wild type siblings. Our findings provide new insights into the role of GMDS in regulating eye function and suggests that GMDS may influence glaucoma risk by regulating the response to stress. This study provides a layer of functional evidence supporting the predictions made by previous GWAS findings, enhancing our understanding of the genetic basis of glaucoma. It highlights the potential of GMDS as a therapeutic target for mitigating glaucoma-related vision loss, opening new avenues for glaucoma research and treatment development.

overall_design: To investigate transcriptome changes in gmds +/- heterozygous eyes when compared to Wild type silbings. Three Wild type samples (each sample consisting of two eyes from a fish)  and three gmds +/- siblings samples were analysed at two time points: 1 and 2 years of age.

first: Muhammad

middle: T

last: Ameen

first: Hayley

last: Alloway

first: Modeline

last: Longjohn

first: Curtis

middle: R

last: French


title: snRNA-seq of Sandhoff disease brain cells

city: Freiburg

first: Maximilian

last: Frosch

summary: We used snRNA-sequencing to analzye thalamic brain nuclei (NeuN-;Olig2-) derived from Sandhoff disease patients and unaffected controls

overall_design: CNS nuclei were isolated from frozen thalamic specimen, stained with anti-NeuN and anti-Olig2, FACS purified (DAPI+NeuN-Olig2-), and analyzed with snRNA-seq

first: Marco

last: Prinz


title: CREB-family transcription factors and vasopressin-mediated regulation of Aqp2 gene transcription

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary: Water homeostasis is regulated by the peptide hormone arginine vasopressin (AVP), which promotes water reabsorption in the renal collecting duct. The regulation of Aqp2 gene transcription is a key mechanism through which AVP modulates water transport as disruption of this mechanism leads to water balance disorders. Therefore, an important goal is to understand the regulatory processes that control Aqp2 gene transcription. While CREB (CREB1) has been proposed as the primary transcription factor responsible for Aqp2 transcription, recent evidence challenges this view, suggesting that other CREB-like transcription factors, including ATF1 and CREM, may play a role. We employed the CRISPR/Cas9 gene-editing system to delete Atf1, Creb1, and Crem in mpkCCD cells, an immortalized collecting duct cell line. These cell lines were then exposed to the vasopressin analog dDAVP to assess the role of these transcription factors in regulating Aqp2 expression. Deletion of all three transcription factors (ATF1, CREB1, and CREM) led to a significant reduction in the vasopressin-induced upregulation of AQP2 protein, confirming their role in regulating Aqp2 expression. Rescue experiments in triple knockout cells showed that expressing any of the three transcription factors restored the response to vasopressin. RNA-seq data showed that Aqp2 mRNA levels mirrored changes in protein abundance, supporting the idea that these transcription factors affect Aqp2 transcription. Our findings demonstrate that ATF1, CREB1, and CREM have redundant roles in regulating Aqp2 transcription. Our results suggest that these transcription factors might regulate the expression of other unidentified transcription factors involved in Aqp2 regulation.

overall_design: mpkCCD control (unmodified clones) compared to ATF1-KO, ATF1/CREB1-KO or ATF1/CREB1/CREM-KO. Triple-KO cells were then compared to cells with lentiviral rescue of weither ATF1, CREB1 or CREM. Five or three replicates per experiment. Cells were grown in transwells in the presence of 0.1nM dDAVP for 72 hours.

first: Adrian

last: Murillo-de-Ozores

first: Mark

last: Knepper


title: Essential function of the integrator complex in Kaposi's sarcoma-associated herpesvirus lytic replication

city: Gainesville

first: Conner

middle: Mark

last: Traugot

state: FL

address: 2033 Mowry Rd, CGRC 265

institute: University of Florida

summary: The integrator complex (INT) is an essential regulator of RNA biogenesis across evolution. Most current findings describe INT's function in states of equilibrium, presenting a research gap in INT's role in dynamic states, such as in infections and cancers. Viruses hijack cellular RNA machinery to transcribe their genes and produce viral progeny, presenting a unique condition to investigate INT-dependent RNA regulation under perturbation. Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic DNA virus that causes two deadly cancers, Kaposi's sarcoma and primary effusion lymphoma. KSHV undergoes a highly regulated and robust transcription of viral genes upon lytic reactivation, providing a complex and dynamic system to investigate integrator-mediated viral/host RNA regulation. We find that integrator subunit 11 (INTS11), the enzymatic core of INT, is essential for KSHV lytic replication triggered by reactivation or primary infection. Further RNA-seq analyses revealed a dynamic and unique signature of human transcriptomes during each lytic stage, respectively. Although the knockdown of INTS11 resulted in selective upregulation and downregulation of certain human gene transcription, INTS11's loss globally repressed the KSHV transcriptome throughout KSHV lytic replication. This inhibited viral lytic gene expression, viral genome replication, and virion production. Integrator subunits 9 and 6 are also important for KSHV lytic replication. Mechanistically, ChIP-seq analysis showed that INTS11 is increasingly recruited to the KSHV genome with some unique binding patterns as the lytic cycle progresses, suggesting that KSHV hijacks INTS11 during lytic gene transcriptions. In all, our findings reveal the essential roles of the Integrator complex in KSHV lytic replication.IMPORTANCEThe integrator complex (INT) is essential for RNA metabolism and is fundamental to all organisms, but its function and regulation during viral infection are not well described. Kaposi's sarcoma-associated herpesvirus (KSHV) infection establishes lifelong infection and causes two deadly cancers; however, no vaccine is available. Using KSHV as a model, we found that integrator subunit 11 (INTS11), the enzymatic core of INT, is recruited to the KSHV genome under lytic phases and plays an essential role in facilitating global KSHV lytic mRNA transcription and viral production. This reveals the critical role of INT in viral infection, a common and inevitable event in human life.

overall_design: RNA-seq data demonstrating the gene expression in iSLK.219 cells upon shRNA knockdown of host cell INTS11 during KSHV lytic reactivation.

first: Amy

last: Nguen

first: Tianqi

last: Li

first: Kimberly

last: Paulson

first: Tiffany

last: Nelson

first: Mingyi

last: Xie

first: Zhe

last: Ma


title: Elementary 3D organization of active and silenced E. coli genome

first: Ilya

last: Shamovsky

first: Alexey

last: Gavrilov


title: Dietary isoleucine content modulates the metabolic and molecular response to a Western diet in mice

city: Madison

first: Michaela

middle: Elizabeth

last: Trautman

address: 2500 Overlook Terrace

institute: University of Wisconsin Madison

summary: The amino acid composition of the diet has recently emerged as a critical regulator of metabolic health. Consumption of the branched-chain amino acid isoleucine is positively correlated with body mass index in humans, and reducing dietary levels of isoleucine rapidly improves the metabolic health of diet-induced obese male C57BL/6J mice. However, it is unknown how sex, strain, and dietary isoleucine intake may interact to impact the response to a Western Diet (WD). Here, we find that although the magnitude of the effect varies by sex and strain, reducing dietary levels of isoleucine protects C57BL/6J and DBA/2J mice of both sexes from the deleterious metabolic effects of a WD, while increasing dietary levels of isoleucine impairs aspects of metabolic health. Despite broadly positive responses across all sexes and strains to reduced isoleucine, the molecular response of each sex and strain is highly distinctive. Using a multi-omics approach, we identify a core sex- and strain- independent molecular response to dietary isoleucine, and identify mega-clusters of differentially expressed hepatic genes, metabolites, and lipids associated with each phenotype. Intriguingly, the metabolic effects of reduced isoleucine in mice are not associated with FGF21 – and we find that in humans plasma FGF21 levels are likewise not associated with dietary levels of isoleucine. Finally, we find that foods contain a range of isoleucine levels, and that consumption of dietary isoleucine is lower in humans with healthy eating habits. Our results demonstrate that the dietary level of isoleucine is critical in the metabolic and molecular response to a WD, and suggest that lowering dietary levels of isoleucine may be an innovative and translatable strategy to protect from the negative metabolic consequences of a WD.

overall_design: Male and female C57BL/6J and DBA/2J mice were put on one of three diets at 6 weeks of age: a Western Diet Control, a Western Diet Low Isoleucine, and a Western Diet High Isoleucine. After 12 weeks on diet, we euthanized these animals following a 16 hour overnight fast, and liver RNA sequencing was performed.


title: Elementary 3D organization of active and silenced E. coli genome (HiC)


title: PPARG-centric transcriptional re-wiring during differentiation of human trophoblast stem cells into extravillous trophoblasts [RNA-seq]

first: Qingqing

last: Guo

overall_design: RNA-seq was conducted on human trophoblast stem cells (TSCs) and extravillous trophoblasts (EVTs) at day 8 (EVTd8) under various conditions.

first: Kim

last: Jonghwan

first: Guo

last: Qingqing


title: Gene expression profile at single cell level for human metastatic melanoma samples

city: Boston

first: Jiekun

last: Yang

address: 32 Vassar Street

institute: MIT

summary: There exists great intra- and inter-tumor heterogeneity for metastatic melanomas. We used single cell RNA sequencing (scRNA-seq) to analyze cell type heterogeneity of metastatic melanoma and cell type specific responses to different treatments.

overall_design: We enzymatically digested and dissociated fresh tumor samples and analyzed using scRNA-seq.

first: Genevieve

last: Boland

first: Manolis

last: Kellis


title: Elementary 3D organization of active and silenced E. coli genome (MicroC)


title: BSome-dependent ciliary Hedgehog signaling governs cell fate in the white adipose tissue

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

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

overall_design: Refer to individual Series


title: CAT-seq: A Chemical Strategy for Subcellular-Resolved RNA Profiling and Synchronous Multi-omics Investigation

city: Beijing

first: Qidong

last: Deng

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

institute: Peking university

summary: Understanding cellular functions in health and disease requires dissecting spatiotemporal variations in the subcellular transcriptome. Mitochondria, with their independent RNA metabolism, play pivotal roles in numerous biological processes. Existing methods for mitochondrial RNA profiling suffer from limitations such as low resolution, contamination, and dependence on genetic manipulation. Here, we present CAT-seq, a bioorthogonal photocatalytic labeling strategy that enables high-resolution, in situ profiling of mitochondrial RNA in living cells without genetic manipulation. Through systematic exploration of quinone methide warheads, we identified an efficient RNA labeling probe. Rigorous validation and optimization enabled CAT-seq to successfully profile mitochondrial RNA, track RNA dynamics in HeLa cells, and even the challenging RAW 264.7 macrophages, achieving ~60% specificity. Furthermore, leveraging the unique reactivity of distinct quinone methides, we established an orthogonal labeling system enabling synchronous RNA and protein multi-omics profiling within the same sample. This allows us to unravel the intricate link between mitochondrial RNA and protein changes. Applying synchronous multi-omics to RAW 264.7 cells during immune response revealed an underlying mitochondrial remodeling mechanism behind oxidative phosphorylation pathway reduction. By integrating bioorthogonal photocatalytic chemistry with proximity-based labeling, CAT-seq offers a general, catalytic, and non-genetic approach for subcellular RNA and multi-omics investigations. This opens up exciting avenues for studying diverse physiological and pathological processes with RNA involvement.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mitochondrial RNA is labeled and obtained using CAT-seq in living cells for NGS and RNA modification analysis to track mt-RNA dynamics of RAW264.7 during immune response.

first: Yunpeng

last: Bi

first: Lishan

last: Yu


title: Polyclonal expansion of functional tumor-reactive lymphocytes infiltrating glioblastoma for personalized cell therapy

status: Public on Jun 23 2025

city: Milano

first: Serena

last: Pellegatta

state: Italy/Milano/Lombardia

address: via Giovanni Celoria, 11

country: Italy

institute: Fondazione IRCCS istituto Neurologico Carlo Besta

summary: Tumor-infiltrating lymphocyte (TIL)-therapy has received FDA approval for the treatment of advanced melanoma and shows potential for broader applications in solid tumors, including glioblastoma. In this study, tumor-reactive TILs (tr-TILs) are isolated and enriched for CD137 expression from cavitron ultrasonic aspirator (CUSA) emulsions of 161 adult patients diagnosed with diffuse gliomas. Tr-TILs are successfully expanded in 87 out of the 161 patients, reflecting an expansion rate of 54%. Notably, the presence of IDH1 mutation and the cumulative dose of steroids are identified as significant negative predictors of expansion efficacy. The expanded tr-TILs exhibit distinct phenotypic and molecular dysfunctional features yet show upregulated expression of progenitor/memory-like markers and polyclonal T-cell receptors. Importantly, these tr-TILs demonstrate specific antitumor reactivity against autologous tumor cells in both in vitro and in vivo xenograft models. These findings provide a compelling background for a personalized immunotherapeutic approach while tackling one of the most significant challenges in oncology.

overall_design: TCRvb sequencing of 10 representative tr-TILs samples expanded in vitro to characterize their clonotypic profiles.


title: BBSome-dependent ciliary Hedgehog signaling governs cell fate in the white adipose tissue (RNA-Seq)

summary: The primary cilium has emerged as critical in regulating whole-body energy metabolism, as reflected in the Bardet-Biedl syndrome (BBS) where primary cilia dysfunction leads to obesity due to hyperphagia and white adipose tissue (WAT) remodeling. The regulation of cell fate and differentiation of adipocyte precursor cells (APCs) is key to maintaining WAT homeostasis during obesity. Using mice that recapitulated the BBS patient phenotype (Bbs8-/-), we demonstrate that primary cilia dysfunction reduces the stem-cell-like P1 APC subpopulation by inducing a phenotypic switch into a fibrogenic progenitor state, characterized by extracellular matrix (ECM) remodeling and upregulation of CD9. Single-cell RNA sequencing revealed a direct transition of stem-cell-like P1 cells into fibrogenic progenitors, bypassing the committed P2 cells. Ectopic ciliary Hedgehog signaling upon loss of BBS8 emerged as a central driver of the molecular changes in Bbs8-/- APCs, altering differentiation into adipocytes and lipid uptake. These findings unravel a novel role for primary cilia in governing APC fate, determining the delicate balance between adipogenesis and fibrogenesis. The identified molecular mechanisms provide insights into potential therapeutic targets for obesity.

overall_design: To investigate the effect of ciliary dysfunction in Bbs8-/- mice on APCs, we used FACS to isolate the P1, P2, and P3 APC subpopulations from the iWAT of three lean (7-8 week old) Bbs8+/+ (WT) and Bbs8-/- (KO) mice.

first: Sieckmann

last: Katharina

first: Wachten

last: Dagmar

first: Bonguro

last: Lorenzo

first: Schulte-Schrepping

last: Jonas

first: Beyer

last: Marc


title: Single cell RNAseq dataset of MDA-MB-231 xenograft and matched metastasis

city: Darlinghurst

first: Shabarni

last: Gupta

state: NSW

address: Precinct Loading Dock,, West Street (off Burton Street)

country: Australia

institute: Garvan Institute of Medical Researc

summary: Identifying functionally important cell states and structure within heterogeneous tumors remains a significant biological and computational challenge. Current clustering or trajectory-based models are ill-equipped to address the notion that cancer cells reside along a phenotypic continuum. We present Archetypal Analysis network (AAnet), a neural network that learns archetypal states within a phenotypic continuum in single-cell data. Unlike traditional archetypal analysis, AAnet learns archetypes in simplex-shaped neural network latent space. Using pre-clinical models and clinical breast cancers, AAnet resolves distinct cell states and processes, including cell proliferation, hypoxia, metabolism and immune interactions. Primary tumor archetypes are recapitulated in matched liver, lung and lymph node metastases. This dataset comprises of the 10X genomics based single cell RNAseq on MDA-MB-231 xenografts and matched metastasis used to perform archetypal analysis to understand tumour hetegeneity as a phenotypic continuum.

overall_design: In an MDA-MB-231 mouse model, single-cell RNA-sequencing and spatial RNA-sequencing data were collected for primary tumors, and single-cell RNA-sequencing was collected for lymph node, liver, and lung metastases.

first: Aarthi

last: Venkat

first: Scott

middle: E

last: Youlten

first: Beatriz

middle: P

last: San Juan

first: Carley

last: Purcell

first: Matthew

last: Amodio

first: Daniel

last: Neumann

first: John

middle: G

last: Lock

first: Anton

last: Westacott

first: Cerys

last: McCool

middle: B

last: Burkhardt

first: Andrew

last: Benz

first: Annelie

last: Mollbrink

first: Joakim

last: Lundeberg

first: David

last: van Dijk

first: Jeff

last: Holst

first: Leonard

last: Goldstein

first: Sarah

last: Kummerfeld

first: Smita

last: Krishnaswamy

first: Christine

last: Chaffer


title: Receptor transport protein 4 (RTP4)-mediated repression of hepatitis C virus replication in mouse cells

city: Princeton

first: Aaron

last: Lin

address: Washington Road

department: Molecular Biology

institute: Princeton University

summary: Hepatitis C virus (HCV) exhibits a narrow species tropism, causing robust infections only in humans and experimentally inoculated chimpanzees. The black flying fox orthologue of receptor transport protein 4 (RTP4) was previously shown to be a potent antiviral effector against several ER-replicating RNA viruses, inhibiting viral genome replication. Since the murine but not the human orthologue is a potent inhibitor of HCV we aimed to analyze the potential role for RTP4 in restricting HCV replication in mice. We demonstrate that mouse RTP4 (mmRTP4) functions as a dominant inhibitor of HCV infection. Via interspecies domain-mapping, we identify the zinc-finger domain (ZFD) of murine RTP4 as the essence of its specific HCV inhibition which is consistent with prior work showing that the 3CXXC zinc finger domain of black flying fox RTP4 is necessary and sufficient for antiviral activity. Expression of mouse RTP in HCV-infected Huh7 cells profoundly reduced HCV RNA, NS5A protein production and virion release demonstrating that mmRTP4 can also disrupt already established HCV replication complexes. Bulk RNAseq analysis of HCV-infected samples did not reveal any characteristic antiviral transcriptional signatures following mmRTP4 transduction, indicating that this antiviral activity cannot be readily attributed to induction of an antiviral response. In situ proximity ligation revealed that murine RTP4 associates with the HCV NS5A protein significantly more than human RTP4 during infection. Disrupting RTP4 expression in mice expressing humanized alleles of CD81 and occludin (OCLN) – the species specific cellular factors mediating HCV uptake – did not, however, increase permissiveness irrespective of the immunocompetence of the mice. Collectively, our work provides detailed insights into RTP4’s role in contributing to HCVs narrow host range and will inform downstream development of a more comprehensive small-animal model for this important disease.

overall_design: Comparative gene expression profiling (RNA-seq) of Huh7-Lunet cells infected with HCV-Jc1 (MOI=1) or mock; then transduced with mmRTP4, hsRTP4, blank lentivirus, or mock; at 12, 24, 48, and 72 hours post-infection.

first: Michael

last: Schwoerer

first: Thomas

last: Cafiero

first: Jianche

last: Liu

first: Sebastian

last: Carver

first: Keith

last: Berggren

first: Serene

last: Dhawan

first: Saori

last: Suzuki

first: Brigitte

last: Heller

first: Celeste

last: Rodriguez

first: Aoife

last: O'Connell

first: Hans

last: Gertje

first: Nicholas

last: Crossland

first: Alexander

last: Ploss


title: Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping  to Fold Tcrb Loci for Long-Range Recombination [RNA-Seq]

city: Philadelphia

first: Craig

last: Bassing

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: Cohesin-mediated chromosome looping regulates diverse processes, including antigen receptor (AgR) gene assembly by V(D)J recombination. To understand mechanisms that coordinate genome topologies, we focused on a genetically tractable AgR locus, Tcrb. Cohesin loading and initiating loop extrusion (LE) from a nearby CTCF-binding element (CBE) required the promoter of the most 5’Vb segment, creating long-range contacts with target downstream DJb segments within the recombination center (RC). CBEs flanking the RC have multiple functions: terminators of LE originating in the Vb cluster, initiators of LE in the RC, and insulation of enhancer activity. Deletion of the Tcrb super-enhancer abolished loop extrusion from the neighboring RC but spared longrange contacts, indicating that unidirectional loop extrusion from upstream Vb segments was sufficient. Thus, Vb promoter- or enhancer-dependent cohesin loading initiates LE in opposite directions across the locus to assemble a broad Tcrb repertoire, a finding that has broad implications for genomic architecture and function.

overall_design: RNA-Seq was performed on sorted (B220-, CD19-, CD11b-, CD11c-, NK1.1-, TER119-, TCRβ-, TCRγ/δ-) DN thymocytes from two Rag1-/- mice per experiment with either a WT Tcrb locus or with the indicated mutations.

first: Brittney

last: Allyn


title: Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping  to Fold Tcrb Loci for Long-Range Recombination [MCC]

overall_design: (B220-, CD19-, CD11b-, CD11c-, NK1.1-, TER119-, TCRβ-, TCRγ/δ-) DN thymocytes were sorted from Rag1-/- mice. MicroCapture C was performed using a custom kit from Arima per manufacture instructions. The bait file report details the probe sequences.


title: Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping  to Fold Tcrb Loci for Long-Range Recombination [Gro-Seq]

overall_design: Gro-Seq was performed on sorted (B220-, CD19-, CD11b-, CD11c-, NK1.1-, TER119-, TCRβ-, TCRγ/δ-) DN thymocytes from Rag1-/- mice with either a WT Tcrb locus or with the indicated mutations.


title: Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping  to Fold Tcrb Loci for Long-Range Recombination [Hi-C]

overall_design: Conventional HiC or HiC using the Arima Kit was performed in DN thymocytes from ~5 Rag1-/- mice per experiment with either a WT Tcrb locus or with the indicated mutations.


title: Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping  to Fold Tcrb Loci for Long-Range Recombination


title: Elementary 3D organization of active and silenced E. coli genome

first: Ilya

last: Shamovsky


title: In vivo manipulation of the protein homeostasis network in rhabdomyosarcoma

city: San Francisco

first: Alex

last: Lee

address: 1550 4th Street

institute: UCSF

summary: Dysregulation of the proteostasis network is associated with various diseases including cancer. Previous studies have shown that inhibiting components of this network, such as HSP70 chaperones, can selectively induce cell death in rhabdomyosarcoma (RMS), a common pediatric soft tissue sarcoma. Here we show that inhibiting VCP, an ATPase involved in protein degradation, activates the unfolded protein response and induces apoptosis in RMS, with a preclinical p97 inhibitor showing promising anti-tumor activity in mouse models. The findings confirm the efficacy of targeting the proteostasis network in RMS and suggest that targeting compensatory network components might yield synergistic outcomes.

overall_design: RNA-seq libraries were generated from xenografts subcutaneously injected into the flanks of nu/nu mice treated with either 50 mg/kg CB-5083 or methylcellulose vehicle.

first: Amit

last: Sabnis

first: Kristen

last: Kwong

first: Yue

last: Pan

first: Jacqueline

last: Morales

first: David

middle: V

last: Allegakoen

first: Trever

last: Bivona

first: Peter

last: Wipf

first: Christopher

last: Guerriero

first: Jeffrey

middle: L

last: Brodsky


title: Broad-spectrum antibiotics disrupt homeostatic efferocytosis

city: New York City

first: Justin

last: Perry

address: 1275 York Avenue

department: Immunology Program

institute: Memorial Sloan Kettering Cancer Center

summary: The phagocytic clearance of apoptotic cells, termed efferocytosis, is essential for both tissue homeostasis and tissue health during cell death-inducing treatments. Failure to efficiently clear apoptotic cells augment the risk of pathological inflammation and has been linked to a myriad of autoimmune and inflammatory diseases. Although past studies have elucidated local molecular signals that regulate homeostatic efferocytosis in a tissue, whether signals arising distally also regulate homeostatic efferocytosis remains elusive. Interestingly, clinical evidence suggests that prolonged use of broad-spectrum antibiotics is associated with an increased risk of autoimmune and inflammatory disease development. We therefore hypothesized that intestinal microbes produce molecular signals that regulate efferocytotic ability in tissue phagocytes beyond the intestines. Here, we find that macrophages, the body’s professional phagocyte, display impaired efferocytosis in the peritoneum of broad-spectrum antibiotics (ABX)-treated, vancomycin-treated, and germ-free mice in vivo, the latter of which could be rescued by fecal microbiota transplantation. Mechanistically, the microbiota-derived short-chain fatty acid butyrate directly boosted efferocytosis efficiency and capacity in mouse and human macrophages, with both intestinal and local delivery of butyrate capable of rescuing ABX-induced large peritoneal macrophage (LPM) efferocytosis defects. Bulk mRNA sequencing of butyrate-treated primary macrophages in vitro and single cell mRNA sequencing of LPMs isolated from ABX-treated and butyrate-rescued mice revealed specific regulation of efferocytosis-supportive transcriptional programs. Specifically, we found that the efferocytosis receptor T-cell immunoglobulin and mucin domain containing 4 (TIM-4, Timd4) was downregulated in LPMs of ABX-treated mice which was rescued by oral butyrate and that TIM-4 was required for the butyrate-induced enhancement of LPM efferocytosis capacity in vivo. Strikingly, LPM efferocytosis was impaired well-beyond withdrawal of ABX and, importantly, ABX-treated mice exhibited significantly worse disease in a mouse model of system lupus erythematosus. Collectively, our results demonstrate that homeostatic efferocytosis relies on distal molecular signals and suggest that a defect in homeostatic efferocytosis may contribute to the clinically observed link between broad-spectrum antibiotics use and inflammatory disease.

overall_design: K27ac Cut and Run on Bone Marrow Derived macrophages at rest treated with Butyrate or PBS Control

first: Pedro

last: Saavedtra

first: Steven

middle: Z

last: Joswefowicz

first: Andrew

middle: W

last: Daman


title: Caste- and environment-associated differential expression of odorant receptors in pest ants

first: Kayli

middle: Renee

last: Sieber

address: 882 Newell Drive

department: Biology

summary: We performed bulk RNA-seq analysis of antennae from three notable pest ant species, Camponotus floridanus, Atta sexdens, and Atta cephalotes, in order to characterize caste-specific expression patterns of odorant receptor genes.

sample_organism:
Atta cephalotes
Atta sexdens
Camponotus floridanus

overall_design: RNA was extracted from the antennae of different castes of each species and sequenced to provide transcriptome data.

first: Maya

last: Saar

first: Nicholas

last: Newell

first: Katrina

last: Fernandez

first: Flávia

last: Franco

first: Fernando

last: Sujimoto

first: Charlotte

last: Francoeur

first: Roberto

middle: M

last: Pereira

first: Cameron

last: Currie

first: José

last: Simões Bento

first: Hua

last: Yan


title: MicroRNA-885-5p regulates cell cycle progression in hepatocellular carcinoma cells

city: Pathumwan

first: Archittapon

last: Nokkeaw

state: Bangkok

address: Padtayapatana Building, 1873, Henri Dunant Road

department: Biochemistry

country: Thailand

institute: Chulalongkorn university, faculty of medicine

summary: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by targeting messenger RNA (mRNA) for translational repression or degradation. Dysregulation of miRNAs has been implicated in hepatocellular carcinoma (HCC) development. Here, we identify miR-885-5p as a novel tumor suppressor miRNA in HCC. Analysis of miRNA expression profiles from TCGA and GEO databases revealed downregulation of miR-885-5p in HCC tissues. Overexpression of miR-885-5p significantly suppressed HCC cell proliferation, supporting its tumor-suppressive role. Transcriptomic profiling of miR-885-5p-overexpressing HCC cells identified cell cycle as the most affected pathway by KEGG and GO analyses. Specifically, miR-885-5p induced downregulation of G1/S transition-promoting genes, including CDK6, E2F2, and CCNA2, in HCC cells. Consequently, these cells exhibited reduced BrdU incorporation and G1 phase arrest. Dual luciferase assays confirmed direct interaction of miR-885-5p with the 3' untranslated regions of CDK6, E2F2, and CCNA2 mRNAs. Furthermore, miR-885-5p overexpression sensitized HCC cells to the CDK4/6 inhibitors palbociclib, ribociclib, and abemaciclib. These findings demonstrate that miR-885-5p induces cell cycle arrest and enhances CDK4/6 inhibitor sensitivity in HCC, suggesting its potential as a therapeutic target.

overall_design: A human HCC cell line with control and hsa-miR-885-5p overexpressed using a pri-miRNA plasmid. Three technical replicates were performed for each group.

first: Chaiyaboot

last: Ariyachet


title: Junctophilin-2 Regulates Store-Operated Calcium Entry to Drive Cardiac Fibroblast Activation, Fibrotic Repair, and Angiogenesis After Myocardial Infarction

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

summary: Calcium homeostasis in cardiac fibroblasts (CFs) are thought to play a critical role in myocardial repair and remodeling following injury. Junctophilin-2 (JP2) is a structural protein known to regulate intracellular calcium signaling and excitation-contraction coupling in cardiomyocytes. However, the role of JP2 in CF biology remains unexplored. To investigate the functional role of JP2 in CFs, we transduced primary CFs with adenoviruses expressing GFP, JP2, or a JP2 targetting shRNA and determined differentially expressed genes via RNA-sequencing. JP2 overepression and silencing had opposite effects on the expression of genes associated with fibrosis, migration, and cell division.

overall_design: Primary mouse cardiac fibroblasts were cultured and transducing for 72 hrs with adenoviruses expressing GFP, JP2, and shJP2 before harvesting for RNA-seq profiling.

first: Jinxi

last: Wang

first: Duane

middle: D

last: Hall


title: Single nuclei RNAseq of human Rett syndrome neurons cortical samples after sorting for MECP2 expression

city: Oxnard

first: Abril

last: Morales

address: 1300 East Pleasant Valley Road, Spc 119

institute: University of California, Los Angeles

summary: Here we employed sc-RNA-seq on nuclei from MECP2 Syndrome brain and normal brain to understand the effect of loss of MECP2 on neurons compared to both MECP2+ neurons in isogenic MECP2 Syndrome brain, as well as to WT brain to determine which changes are due directly to loss of MECP2, and in transgenic rats lacking MECP2.

overall_design: From 5 individual Rett syndrome patient brain samples, we isolated nuclei using sucrose gradient centrifugation and sorted using FACS for neurons with low and high MECP2 expression to study transcriptional changes associated with MECP2 mutation.

first: William

last: Lowry


title: Regulatory T cells poise the myeloid landscape after chemotherapy in lung tumors

city: Paris

first: Alexandre

last: Boissonnas

address: 91 bd de l'hopital

institute: Inserm

summary: Tumor-associated macrophages (TAMs) and regulatory T cells (Tregs) are major immune components of the tumor microenvironment, promoting tumor growth and limiting the efficacy of chemotherapy in almost all cancer indications. While Tregs are well known for their immune suppressive activity toward the adaptive immune system, less is known about their regulatory activity toward the innate compartment. We showed in human and mouse lung cancer, that chemotherapy transiently reduced Treg number and switched the mononuclear phagocyte (MP) landscape toward a pro-inflammatory signature but also an increased TGFβ-expressing TAM accumulation over time. Preventing Treg recovery further increased the recruitment of monocytes and limited TGFβ expression upon TAM differentiation, demonstrating that Tregs dampen the pro-inflammatory status of the MP compartment induced by chemotherapy and promote tumor relapse. Anti-TNFR2 antibody treatment during the Treg recovery phase affected the direct interaction between Tregs and MPs, increased the pro-inflammatory signature of the MPs and improved survival in the mouse model. Targeting the crosstalk between tumor-associated Tregs and the MP compartment limits the reconstitution of an anti-inflammatory environment following chemotherapy and improves therapeutic outcome.

overall_design: Four sorted tumor samples, each pooled from three mice with multifocal lung tumors, were analyzed: untreated (NT), chemotherapy-treated (CP), chemotherapy plus anti-TNFR2-treated (CP_aTNFRII) and local irradiation (IR). The samples include T lymphocyte and myeloid cell populations, analyzed using scRNA-seq.

first: Eleonore

last: Weber-Delacroix

first: Marylou

last: Panouillot

first: Marie

last: Laviron

first: François

last: Lanthiez

first: Tristan

last: Philippe

first: Sandrine

last: Barthélémy

first: Solène

last: Fastenackels

first: Armanda

last: Casrouge

first: Benoît

last: Salomon

first: Ingrid

last: Sassoon

first: Jeremy

last: Baudhuin

first: Ilaria

last: Onorati

first: Mariane

last: Kambouchner

first: Nahla

last: Cucherousset

first: Christophe

last: Combadière

first: Boris

last: Duchemann

first: Marie-Caroline

last: Dieu-Nosjean


title: CDK12/13 inactivation triggers STING-mediated antitumor immunity in preclinical models [RNA-seq]

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: Michigan

address: 1500 E. Medical Center Dr

institute: University of Michigan

summary: Inactivation of cyclin-dependent kinase 12 (CDK12) characterizes an immunogenic molecular subtype of prostate cancer, marked by genomic instability and increased intratumoral T cell infiltration. However, the mechanisms underlying this phenotype and its therapeutic implications remain unclear. Here, we demonstrate that CDK12 inactivation or suppression of its paralog CDK13 activates stimulator of interferon genes (STING) signaling across multiple cancer types. Analysis of clinical cohorts receiving immune checkpoint blockade (ICB) revealed that reduced CDK12/13 expression correlates with improved survival and treatment response. Mechanistically, CDK12/13 depletion or targeted degradation induces transcription-replication conflicts and R-loop accumulation, triggering cytosolic DNA release and subsequent STING activation. Functionally, CDK12/13 degradation significantly delays tumor growth and exhibits synergistic effects with anti-PD1 therapy in various syngeneic tumor models. This combination enhances STING activity and promotes the infiltration and activation of CD8+ T cells within tumors. Notably, the anti-tumor effects of this combination require STING signaling and functional CD8+ T cells. These findings identify CDK12/13 as promising therapeutic targets for enhancing ICB efficacy, highlighting their potential to amplify STING-mediated anti-tumor immunity. This work provides a mechanistic framework for leveraging CDK12/13 antagonists in combination with ICB to improve clinical outcomes in cancer therapy.

overall_design: Myc-CaP cells were treated by CDK12/13 degrader YJ1206 for 24 hours and subjected to RNA-sequencing to evaluate genes differently expressed post CDK12/13 degradation compared to the DMSO-treated cells.

first: Yi

last: Bao

first: Yu

last: Chang

first: Jean

last: Ching-Yi Tien

first: Gabriel

last: Cruz

first: Fan

last: Yang

first: Rahul

last: Mannan

first: Somnath

last: Mahapatra

first: Radha

last: Paturu

first: Xuhong

last: Cao

first: Fengyun

last: Su

first: Rui

last: Wang

first: Yuping

last: Zhang

first: Mahnoor

last: Gondal

first: Jae

last: Eun Choi

first: Jonathan

middle: K

last: Gurkan

first: Stephanie

middle: J

last: Miner

first: Dan

last: Robinson

first: Yi-Mi

last: Wu

first: Licheng

last: Zhou

first: Zhen

first: Ilona

last: Kryczek

first: Xiaoju

first: Marcin

last: Cieslik

first: Yuanyuan

last: Qiao

first: Weiping

last: Zou

first: Ke

last: Ding


title: BBSome-dependent ciliary Hedgehog signaling governs cell fate in the white adipose tissue (scRNA-Seq)

first: Joachim

last: Schultze

overall_design: To investigate the effect of ciliary dysfunction in Bbs8-/- mice on the cells, of the iWAT we isolated the total stromal vascular fraction (SVF) of a lean (7 week old) Bbs8-/- (KO)  and Bbs8+/+ (WT) mouse.

first: Sieckmann

last: Katharina

first: Blank-Stein

last: Nelli

first: Wachten

last: Dagmar

first: Bonguro

last: Lorenzo

first: Schulte-Schrepping

last: Jonas

first: Beyer

last: Marc

first: Becker

last: Matthias

first: Osei-Sarpong

last: Collins


title: Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping  to Fold Tcrb Loci for Long-Range Recombination [CUT&RUN]

first: Craig

last: Bassing

overall_design: CUT&RUN was performed on (B220-, CD19-, CD11b-, CD11c-, NK1.1-, TER119-, TCRβ-, TCRγ/δ-) DN thymocytes were sorted from Rag1-/- mice

first: Brittney

last: Allyn


title: Triggering AHR resolves TGF-β1 induced fibroblast activation and promotes AT1 cell regeneration in alveolar organoids

city: San Diego

first: Bin

last: Fang

state: CA

address: 10675 John Jay Hopkins Dr

department: Discovery Science

institute: Novartis

summary: Regeneration of the alveolar epithelium is necessary to restore tissue architecture and gas exchange capabilities in chronic pulmonary diseases such as fibrosing interstitial lung disease. While it is known alveolar type 2 (AT2) cells give rise to alveolar type 1 (AT1) cells to repair the alveolar epithelium after injury, methods to promote this process under pathological settings are poorly understood. Here, using a complex 3D organoid culture with TGF-β1 dependent impaired AT1 spheroid formation, we performed a high-throughput screen (HTS) with ∼16,800 compounds to identify small molecules that increase number of AT1 spheroids. Longitudinal single cell RNA sequencing (scRNA-seq) revealed that DB-11-BE87 increased AT1 regeneration by reducing TGF-β1 induced fibroblast activation, concurrently with AHR activation in those cells. These studies highlight a novel HTS system to identify factors that can promote AT1 differentiation and suggest AHR activation as a method to counteract pathological TGF-β1 signaling in pulmonary disease.

overall_design: To understand the effect of DB-11-BE87 on mixed distal lung cell cultures, longitudinal scRNA-seq was performed at three different time points (day 1, 3, and 11) following TGF-β1 and compound treatment (DMSO, 10 μM DB-11-BE87, 10 μM QA-92-TQ17) (n=3-4 per group) Compound QA-92-TQ17 was chosen as a minimally active structural analogue of the active DB-11-BE87. As a control, cells freshly dissociated from untreated mouse lung on day 0 were profiled by scRNA-seq.

first: Drew

last: Hagan

first: John

last: Walker

first: Whitney

last: Barnes

first: Guray

last: Kuzu

first: Glenn

last: Federe

first: Rebekah

last: Decker

first: Scott

last: Williams


title: shRNA-mediated knockdown of MEP50 gene in LNCaP cells

city: West Lafayette

first: Chang-Deng

last: Hu

state: IN

address: 201 S. University St, Hansen Life Sciences Building, Room 401A

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

summary: We performed shRNA-mediated knockdown of MEP50 in LNCaP cells via dox-inducible expression system. We sought to compare transcriptome with- and without MEP50 knockdown across three biological replicates

overall_design: Identify differentially expressed genes in LNCaP cells following MEP50 knockdown across three biological replicates

first: Xuehong

last: Deng

first: Andrew

last: Asberry

first: Jun

last: Wan

first: Sheng

last: Liu


title: NOTCH1 reverses immune suppression in small cell lung cancer through reactivation of STING [scRNA-seq]

status: Public on Jun 22 2025

city: Bethesda

first: Nitin

last: Roper

address: 37 Convent Drive

department: Developmental Therapeutics Branch

institute: National Cancer Institute

summary: Downregulation of antigen presentation and lack of immune infiltration are defining features of small cell lung cancer (SCLC) limiting response to immune checkpoint blockade (ICB), While a high MHC Class I, immune-inflamed subset benefits from ICB, underlying mechanisms of immune response in SCLC have yet to be elucidated. Here we show that in the landmark IMpower133 clinical trial high, but not low, NOTCH1 expression is significantly associated with longer survival with the addition of ICB to chemotherapy among ~80% of SCLC patients with neuroendocrine-enriched tumors (ASCL1-enriched, HR 0.39, P=0.0012; NEUROD1-enriched, HR 0.44, P=0.024). Genetic or pharmacologic activation of NOTCH1 in ASCL1 and NEUROD1 SCLC cell lines dramatically up-regulates MHC Class I through epigenetic up-regulation of STING. In syngeneic mouse models, Notch1 activation reprograms SCLC tumors from immune-excluded to immune-inflamed, facilitating durable, complete responses with ICB combined with a STING agonist. STING1 expression is significantly enriched in high compared to low NOTCH1 expressing tumors in IMpower133 thereby validating our proposed mechanism. Our data reveal a previously undiscovered role for NOTCH1 as a critical driver of SCLC immunogenicity and a potential predictive biomarker for ICB in SCLC. NOTCH1 activation may be a therapeutic strategy to unleash anti-tumor immune responses in SCLC and other neuroendocrine cancers in which NOTCH1 is typically suppressed.

overall_design: We performed single-cell RNA-seq of a human SCLC cell line (COR-L88) treated ex-vivo with DMSO, LSD1 inhibition or LSD1 inhibition plus GSI (gamma secretase inhibitor).

first: Yoo

middle: S

last: Kim

first: Xinyu

last: Wen