title: Single-cell RNA-Seq analysis of colonic mesenchyme lacking tumor necrosis factor receptor 1

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

summary: Our study reports a role for tumor necrosis factor receptor 1 (TNFR1) in maintaining colonic mesenchymal cell diversity. Through scRNA-seq profiling, we show that a TNFR1-deficient mesenchyme has a reduced transcriptional diversity of mesenchymal cell populations, with a near complete loss of a cluster enriched in TNF, IFN, and cytokine signaling genes, which include MMP9, CD200, TNFRSF9, and TRAF1. We show that the transcriptional clustering of mesenchymal cells is consistently distinct and unique to the TNFR1-/- genotype. TNFR1-/- mesenchymal cells cluster as a single population, compared to control mesenchymal cells that cluster into 3 sub-populations. Through in vivo immunostaining in control and TNFR1-/- mice we show that the TNF signaling cluster localizes to the sub-epithelial niche and therefore may play an important role in the crosstalk between epithelial stem cells and mesenchyme-driven immune signaling in health and disease.

overall_design: To assess the role of TNFR1 signaling in the colonic mesenchyme and its interaction with the epithelial stem cell niche, we investigated primary sub-epithelial mesenchymal cell populations isolated from control (TNFR1+/-) or TNFR1-/- mice and grown in vitro for 5 days. These populations were dissociated into a single-cell suspension and profiled using single-cell RNA-Seq.

first: Safina

last: Gadeock

middle: Y

first: D

last: Polk


title: Digital proteomics by DNA sequencing

status: Public on Jul 01 2025

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

country: USA

institute: Frederick National Labroatory for Cancer Research

summary: The simultaneous measurement of many different proteins presents a major challenge to the fields of surgical and clinical pathology, and there is a genuine need for the development of a more direct, quantitative approach to multiplex analysis of proteins in tissues and clinical assays. Here we present a novel, high-throughput immunoassay, driven by the hypothesis that highly sensitive, multiplex protein characterization can be obtained by coupling the unique specificity of antibodies with massively parallel sequencing to detect and quantitate antigens from formalin-fixed, paraffin-embedded tissue (FFPE) and in solution. The method involves conjugating antibodies with a universal anchor oligonucleotide that is hybridized with a second oligonucleotide specifying the sample, antibody, and a unique molecule identifier, akin to “make, model and serial” number.  Recovery of the data-rich oligonucleotide from mixtures of antibodies from samples such as histological tissue sections, (herein breast carcinoma) or extracts in an ELISA-type format, enabling error free-amplification that increases the sensitivity and expands the range of analysis.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
To profile the abundance of select targets in breast carcinoma, libraries of antibody-oligonucleotide heteroconjugates of defined stoichiometry were constructed for ER, PR, Her2, and EGFR. Each conjugate was tagged with a barcode of nucleotides providing metadata to the cognate antigen for the antibody as well as for each antibody molecule in the library. Breast carcinoma tissue arrays were incubated with mixtures of different antibody libraries. Additionally, target antigens were evaluated in an ELISA-like assay. Following antibody binding in either case, the barcoded oligonucleotides were purified, amplified by PCR, and sequenced. The number of unique sequence identifiers was used to determine the relative amounts of each protein. Routine immunohistochemistry (IHC) and ELISAs were performed in parallel to sequencing experiments.

The oligonucleotides_barcodes that used for identifying target unique oligios for this study are provided in the oligonucleotides_barcodes.txt.

first: George

last: Miles

first: David

last: Levens


title: Single-cell RNA-sequencing data of microfluidic spinal cord-like structures

status: Public on Jun 30 2025

city: Ann Arbor

first: Jeyoon

last: Bok

state: MI

address: 2350 Hayward Street

department: Mechanical Engineering Department

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: We analysed scRNA-seq data in human pluripotent stem cell-derived embryonic spinal cord model. This in vitro system recapitulates some key aspects of spinal cord DV patterning as well as neural crest migration.

overall_design: scRNA-seq was performed on dissociated cells from microfluidic spinal cord-like structures at day 12.

first: Jianping

last: Fu


title: EMT-ciliary signaling in quasi-mesenchymal-stem-like cells drives therapeutic resistance and is a druggable vulnerability in triple-negative breast cancer

city: Nantes

first: jennifer

last: Derrien

address: 8 quai moncousu

country: France

institute: INSERM

summary: Cancer therapeutic resistance is mediated, in part, by phenotypic heterogeneity and the plasticity of tumor cells, the latter being enabled by Epithelial-Mesenchymal Transition (EMT). However, EMT in human cancer therapeutic response remain poorly understood. We developed patient-derived organoids (PDOs) from human triple-negative breast cancer (TNBC) and investigated their response to chemotherapy. We found that chemotherapy treatment kills the bulk of tumor cells in PDOs, but there is selective survival of malignant cells that had activated an EMT program, entered a quasi-mesenchymal, stem cell-like state and display primary cilia. We developed a family of small-molecule inhibitors of ciliogenesis and show that treatment with these inhibitors, or genetic ablation of primary cilia, is sufficient to suppress this chemoresistance via NFB-induced cell death. We conclude that an EMT-ciliary signaling axis induces chemoresistance in quasi-mesenchymal stem-like cells to help tumors evade chemotherapy and represents a druggable vulnerability in human TNBC.

overall_design: Cancer cells dissociated from tumor tissue samples were used to generate PDOs. PDOs were dissociated and cells were processed for scRNAseq. PDOs from two different patient samples were used in the study. Non-treated PDOs were analyzed. Additionally, PDOs treated with DMSO (control: CTL) or doxorubicin or taxol or Nao-3 were used in the study.

first: Vincent J.

last: Guen

first: Jennifer


title: Phosphorylated TLR3 nuclear translocation in cancer cell promotes metastasis and chemoresistance

city: Hangzhou

first: zixin

last: wang

state: Zhejiang Province

address: No. 866, Yuhangtang Road, Xihu District

department: Institute of Immunology

country: China

institute: Zhejiang University School of Medicine

summary: Aberrant expression and subcellular location of innate sensors in cancer cells, such as Toll-like receptors (TLRs), correlates with pro-tumoral inflammation and cancer progression, but the mechanism is still largely unknown. Deciphering the proinflammatory mediators in tumor microenvironment will contribute to the development of cancer therapeutics. By using immunohistochemistry in pancreatic ductal adenocarcinoma (PDAC) and multiple other cancer samples, here we found that cancer cell TLR3, a well-known cytoplasmic dsRNA sensor, translocated to the nucleus especially upon chemotherapy stress. Nuclear TLR3 increased the invasive and proliferative properties, and inhibited chemotherapy-induced apoptosis of cancer cells in vitro. Meanwhile, mice bearing cancer cells with nuclear TLR3 exhibited increased liver metastasis and shortened survival. Mechanistically, phosphokinase JAK1 was responsible for TLR3 phosphorylation at S155 to induce its nuclear translocation in cooperation with a nuclear transport factor importin α5. Chemotherapeutic stress induced the aberrant aggregation of dsRNA in the nucleus, which potentially contributed to nuclear TLR3 activation. Then nuclear TLR3 recruited protein arginine methyltransferase 5 (PRMT5) and bound to c-Myc to promote symmetrical dimethylation and multimerization of c-Myc, resulting in the activation of c-Myc downstream target genes and pro-tumoral signaling pathways. Accordingly, high levels of cancer cell nuclear TLR3 in clinical samples predicted patients’ worse prognosis with shorter disease-free survival, overall survival and poor response to neoadjuvant chemotherapy. Therefore, the identification of nuclear TLR3 provides new insight into non-classical functions of innate immune sensors in cancer, and JAK1/TLR3/PRMT5/c-Myc axis may sever as a new prognostic indicator and potential therapeutic target to overcome chemoresistance.

overall_design: RNA-seq profiling of of Panc1 cells with TLR3 knockout, NES-TLR3 or NLS-TLR3 rescue.

first: Zixin

last: Wang

first: Yan

last: Gu

first: Yanfang

first: Ziqiao

first: Xinyuan

last: Chen

first: Haoze

first: Wei

last: Zhang

first: Gang

last: Jin

first: Xuetao

last: Cao


title: The spatial differences of root apex contribute to improved drought tolerance as induced by drought priming in wheat

city: Nanjing

first: Xiao

state: Jiangsu

address: No. 1 Weigang Road

institute: Nanjing Agricultural University

summary: Drought priming is a promising approach to improve drought tolerance, and root apex plays important role in coping with drought adversities in plants. It has been observed that less inhibition of root growth under drought stress was found in paralleling with the enhanced drought tolerance induced by drought priming in wheat. However, the contribution and mechanisms of root apex to the improved tolerance induced by drought priming remains unknown. Here, the transcriptome and proteome of three different zones along the root axis under drought stress were investigated. The two zones distal from the root apex showed more sensitive to drought priming and the later drought stress than the zone proximal to the root apex, as exemplified by the principal component analysis of the different expressed genes (DEGs) among treatments. The DEGs which decreased by drought stress, while higher expressed in primed plants than non-primed plants, might play critical roles in enhanced root growth in primed plants. These genes were mainly involved in the pathways related to cell membrane sensing, plant hormone signaling, stress defense and cell more modification. Moreover, the plant hormone pathway showed positive correlated between transcriptome and proteome analysis, and genes network analysis hinted that ABA receptor and aquaporin could be potential markers in regulation of priming induced root growth and drought stress tolerance.

overall_design: The different zones of root apex were dissected under a computer visual assistant anatomic microscope.The transcriptome of three different zones along the root axis under drought stress were investigated

first: Dong

last: Jiang


title: What effects do arbutin at 0.25 μM and three concentration gradients of SP helical peptides have on the gene expression of melanoma cells?

city: Guangzhou City

first: zhou

last: wei

address: No. 100, Outer Ring Road, Guangzhou University Town, Xiaoguwei Street, Panyu District

institute: Guangdong University of Technology

summary: Previous studies have shown that arbutin has the effect of inhibiting melanin formation in melanoma cells. Therefore, we comparatively observed the effects of arbutin and SP helical peptides on the morphology, tyrosinase activity, melanin content and cell proliferation rate of mouse melanoma cells. We found that this compound, SP helical peptides, also has the effect of inhibiting melanin production, and the inhibitory effect of SP helical peptides is concentration-dependent. Therefore, based on previous studies, this experiment designed the following experimental scheme: to observe the differences in gene expression of melanoma cells under the action of arbutin and different concentrations of SP helical peptides, with or without.

overall_design: RNA-Seq of wild melanoma cells and melanoma cells treated with different condition compounds.


title: SOX3 facilitates granulosa cell proliferation and suppresses cell apoptosis through modulating PI3K/AKT pathway by targeting SPP1

city: Hefei

first: Qiang

last: Hong

address: Hefei

institute: Anhui Medical University

summary: The goals of this study are to compare the differentially expressed genes between OE-NC and OE-SOX3 KGN cell lines  based on RNA-seq data and some of these genes were validated by qRT–PCR. Further, the differentially expressed genes were devided into up-regulated and down-regulated genes for GO, GSEA and KEGG analysis.

overall_design: The mRNA profiles of OE-NC and OE-SOX3 KGN cell lines were generated by deep sequencing.

first: Rui

last: Cai

first: Cong

last: Li

first: Fenfen

last: Xie


title: Divergent therapeutic and prognostic impacts of immunogenic features in undifferentiated pleomorphic sarcoma and myxofibrosarcoma

city: Leiden, The Netherlands

first: Siddh

last: van Oost

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

summary: Undifferentiated pleomorphic sarcoma (UPS) and myxofibrosarcoma (MFS) are genetically complex soft tissue sarcomas with distinct morphological features. Treatment typically involves surgery, often combined with neoadjuvant chemo- or radiotherapy. To better understand the immunobiology of these sarcomas and its associations with treatment response and prognosis, we performed transcriptomic and immunophenotypic profiling. RNA sequencing was performed on 13 UPS and 10 MFS, and immunological profiles were compared with soft tissue sarcoma data from The Cancer Genome Atlas (n = 206 including 44 UPS and 17 MFS). Immune contextures were further evaluated in 14 UPS and 15 MFS using imaging mass cytometry. Characterization of T cell and macrophage infiltration in tumors was further assessed in 23 UPS and 22 MFS through multispectral immunofluorescence and immunohistochemical analysis. UPS and MFS demonstrated immunogenic features compared to other soft tissue sarcomas, with subsets of UPS and MFS demonstrating high T cell infiltration, while UPS demonstrated a higher infiltration by myeloid cells as compared to MFS. Prognostically, T cells and CD68+CD163+ macrophages were associated with metastasis-free survival in UPS but not in MFS. Notably, in UPS, neoadjuvant radiotherapy appeared to induce cytotoxic T cell infiltration and depletion of myeloid cells, whereas these effects were not observed in MFS. These findings highlight important differences in the immunobiology of UPS and MFS with therapeutic and prognostic implications. These differences should be taken into account given the growing availability of immunotherapeutic options for treating patients with soft tissue sarcomas.

overall_design: Frozen tissue was collected from primary tumors from 13 undifferentiated soft tissue sarcoma and 10 myxofibrosarcoma patients to study immune-related gene expression

first: Judith

last: Bovee

first: Noel

last: de Miranda


title: Spatially resolved chimeric analysis reveals extracellular CKB-mediated ATP uptake at the glioma-astrocyte invasive front

city: 成都

first: ping

last: he

address: 17 Renmin South Road, Wuhou District, Chengdu

institute: sichuan university

summary: Glioblastoma (GBM) is a highly invasive primary brain tumor that, although rarely metastasizing outside the brain, frequently infiltrates surrounding brain tissue. This infiltrative growth may exploit the brain’s metabolic support system, which involves various brain-resident cells providing essential nutrients and maintaining energy balance. In this study, we investigated the metabolic dependencies of infiltrative GBM cells by combining spatially resolved transcriptomic profiling with advanced computational methods in xenografted GBM models. Our findings reveal that GBM cells upregulate creatine kinase brain type (CKB) at the leading edge to adapt to local energy deprivation. CKB facilitates the conversion of creatine to phosphocreatine, utilizing ATP supplied by astrocytes to support tumor cell survival and invasion. Targeting CKB with cyclocreatine significantly reduced tumor size and restricted infiltrative growth in vivo, indicating that GBM cells utilize CKB to harness extracellular ATP via the creatine pathway. These findings suggest that targeting CKB in GBM may offer a novel therapeutic strategy to combat infiltrative growth in this aggressive cancer.

overall_design: We generated and analyzed spatially resolved RNA profiles in two GBM models: a GSC xenograft model and a TP53, NF1, and PTEN (TNP)-inactivated human neural stem cell-derived model. This approach enabled us to dissect tumor and tumor microenvironment (TME) interactions across spatial contexts.


title: PAD2-Mediated Histone Citrullination Drives Tumor Progression by Enhancing Cell Proliferation and Modifying the Microenvironment in Pancreatic Cancer

city: Bunkyo-ku

first: Kentaro

last: Umemura

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

country: Japan

institute: Institute of Science Tokyo

summary: Histone citrullination is catalyzed by peptidyl arginine deiminases (PAD) that play a role in gene regulation. However, the clinical significance and molecular mechanisms of histone citrullination and PADs in pancreatic ductal adenocarcinoma (PDAC) remain unclear. This study aimed to investigate the role and potential molecular mechanisms of PADs in PDAC. Histone citrullination was upregulated and strongly associated with PAD2 nuclear expression in human PDAC samples. PAD2 nuclear expression correlated with aggressive tumor characteristics and poor prognosis. PAD2 overexpression increased PDAC cell proliferation, whereas its knockdown had the opposite effect in vitro. PAD2 bound to the promoter regions of PRUNE1 and E2F1, resulting in the activation of their mRNA expression via upregulation of histone citrullination and chromatin accessibility at their promoter regions. PAD2 overexpression enhanced tumorigenicity, and increased PRUNE1 expression and M2 tumor-associated macrophage (M2 TAM) infiltration in subcutaneous and orthotopic PDAC models. In vitro assay showed that macrophages cultured in a conditioned medium from PAD2-expressing PDAC cells exhibited an increase of M2 TAM-related markers in a PRUNE1-dependent manner. Treatment with the PAD2 inhibitors Cl-amidine and AFM-30a selectively impaired the growth and tumorigenicity of PAD2-expressing PDAC cells in vitro and in vivo. Furthermore, the triple-high expression of nuclear PAD2, PRUNE1, and the M2 TAM marker CD206 may serve as independent adverse prognostic factors for human PDAC. Conclusively, PAD2-mediated histone citrullination drives PDAC progression by epigenetically regulating downstream target genes and influencing the tumor microenvironment. The PAD2-PRUNE1-M2 TAM axis may be a promising therapeutic target and prognostic indicator for PDAC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 1) AsPC-1 NC cells and the AsPC-1 PADI2-OE cells, 2) PANC-1 siNC cells and PANC-1 siPADI2 cells, 3) KLM-1 siNC cells and KLM-1 siPADI2 cells.

first: Shu

last: Shimada


title: Enhancing Skeletal Muscle Fiber Types Transition through Substrate Coating Alteration in Myoblast Cell Culture

city: Taipei

first: Hsi

last: Chang

state: Xinyi

address: No. 250, Wuxing Street

department: Pediatrics

country: Taiwan

institute: School of Medicine, College of Medicine, Taipei Medical University

summary: Skeletal muscle diseases often exhibit fiber type-specific characteristics and posing significant clinical challenges, such as Duchenne muscular dystrophy (DMD), sarcopenia, and volumetric muscle loss injuries. Current treatments are primarily palliative, highlighting the need for innovative therapies. The extracellular matrix (ECM) plays a pivotal role in muscle physiology and regeneration by influencing cell differentiation and repair.  Understanding the mechanism of specific ECM coatings affect muscle fiber type differentiation in vitro could elicit the targeted therapies for muscle regeneration. In this study, C2C12GFP myoblasts were differentiated into myotubes on the plates coated with Fibronectin, Collagen I, and Geltrex™. The myoblasts differentiated successfully on all ECM substrates, forming myofiber.  qPCR confirmed myogenic marker expression patterns, with decreased Pax7 and increased Myog by day 7.  Protein analysis (Western blot and immunofluorescence) and transcriptome profiling (RNA-Sequencing) consistently demonstrated that Collagen I enhanced the development of slow-type fibers, evidenced by increased slow myotube protein expression and the upregulation of slow fiber-associated genes (e.g., Myh7, Myl2), potentially via Calcineurin/NFAT, MEF2, MYOD, AMPK, PI3K/AKT and ERK1 pathways. In contrast, Fibronectin and Geltrex™ favored fast-type fiber development, as shown by elevated fast-type fiber protein levels and upregulation of fast fiber-associated genes (e.g., Fyn, Hk2), possibly through HIF1A, FOXO1, NFKB and ERK2 activation.

first: Yhusi

middle: K

last: Riskawati

first: Chuang-Yu

last: Lin

first: Akira

last: Niwa


title: Sustained and specific multiplexed immune checkpoint modulation in CAR T cells induced by targeted epigenome editing

city: Freiburg

first: Claudio

last: Mussolino

address: Breisacherstr. 115

country: Germany

institute: Institute for Transfusion Medicine and Gene Therapy

summary: Engineered T cells equipped with a chimeric antigen receptor (CAR) have shown tremendous clinical success but tumor-mediated stimulation of T cell inhibitory receptors leads to exhaustion, hampering durable remission in patients. Mitigation of this effect via checkpoint inhibition or genome editing to knockout the genes encoding for these receptors has shown promise. Yet, the side effects of these procedures require alternatives. Targeted epigenome editing is a potent strategy to alter gene expression in the absence of DNA modifications. The hit-and-run feature enables durable multiplexed modulation of gene expression with greater safety. Here we describe multiplexed epigenome editing inactivation of two critical exhaustion-related genes, PDCD1 and LAG3, both in primary human T cells and in prostate cancer specific CAR T cells. Epigenetically modified CAR T cells are fully functional and nearly indistinguishable from parental cells in a variety of functional assays. Target gene silencing is durable over multiple cell divisions and repeated CAR-mediated stimulations. Furthermore, transcriptomic analysis revealed minimal off-target effects not directly attributable to the effectors used. We demonstrate that targeted epigenome editing is an effective and safe procedure for multiplexed gene inhibition and that this strategy can be used to engineer CAR T cells with novel desirable features.

overall_design: We have performed bulk RNA-seq to monitor for aberrant transcriptomic changes induced by the DEM included in this study. To this end we have compared the samples with control cells receiving mock electroporation

first: Maria

middle: S

last: Roman Azcona

first: Gianni

last: Monaco

first: Masako

middle: M

last: Kaufmann

first: Toni

last: Cathomen


title: Phf23 regulates embryonic neurogenesis by increasing the level of H3K27ac of Tcf4 [CUT&Tag]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epigenetic regulation is an important cell fate modality that is ubiquitous in neural development and plays an important role in both the fate determination and differentiation of neural stem cells (NSCs). The epigenetic regulator Phf23 is widely expressed in different human tissues and is involved in various biological processes, but its functional role in development has rarely been reported. Here, we found that Phf23 is an important epigenetic regulator that maintains embryonic neurogenesis in mice, and its absence leads to inhibition of the acetylation level of H3K27ac through the function of Hdac2, resulting in the blockage of embryonic NSCs differentiation at embryonic day 13.5 (E13.5). Tcf4, a transcription factor closely associated with neurogenesis, is a key downstream target gene of Phf23 in regulating embryonic neurogenesis, which may provide insights into the neuromodulatory network of the brain and the diagnosis and treatment of clinically relevant diseases.

overall_design: To investigate the distribution of H3K27ac on DNA in Phf23+/+ and Phf23-/- NSCs and attempted to find the downstream target genes directly regulated by Phf23 through H3K27ac, we harvested Phf23+/+ and Phf23-/- NSCs for CUT&Tag-seq, 3 replicate samples per group and each group has a negative control. We then performed differentially expressed genes and average H3K27ac bound peak densities in TSS regions using data obtained from CUT&Tag-seq.


title: Single-cell transcriptomic atlases of midgestation fetal-maternal interface from opossum, tenrec, guinea pig, and mouse

city: New Haven

first: Gunter

middle: P

last: Wagner

state: CT

address: 165 Prospect Street

department: Ecology & Evolutionary Biology

institute: Yale University

summary:
The origin of this chimeric fetal-maternal tissue poses a unique evolutionary puzzle. We present a multi-species atlas integrating single-cell transcriptomes from opossum (a marsupial), Malagasy common tenrec (an afrotherian), mouse and guinea pig (rodents) with previous macaque and human data (primates). Invasive trophoblasts share a transcriptomic signature across eutherians, likely representing a cell type family that radiated following the evolution of hemochorial placentation. Our data suggest that decidual stromal cells evolved stepwise from an immunomodulatory cell found in Tenrec, followed by acquisition of an endocrine decidual cell in Boreoeutherian mammals. Finally, we identify evolutionary patterns in ligand-receptor signaling among fetal and maternal cells: Consistent with theoretical predictions, fetal and maternal cells show a strong tendency towards disambiguated signaling, however, a predicted escalatory arms race dynamic between them is restricted to few ligands. We reconstruct the uteroplacental cell-cell communication network of the eutherian common ancestor, and infer accelerated signaling loss in Euarchontoglires and accelerated gains in primates. Unexpectedly, fetal trophoblast cell types display strong integration into maternal signaling networks despite their recent evolutionary origin.
The tailless tenrec Tenrec ecaudatus is an afrotherian mammal native to Madagascar, related to the elephant and aardvark, and is remarkable for retaining a collection of ancestral eutherian traits. The single known description of the decidual tissue of T. ecaudatus was collected by zoologist and explorer R.H. Goetz in 1936 from a female during mid-gestation. We collected fresh, timed-pregnant uteri from T. ecaudatus at mid-gestation (days 28-30) to address: Which cell types are present in the decidua of a basally branching placental mammal, and how do they, if present, interact with other cells? Furthermore, how does gene expression of the tenrec decidual stromal cell differ from the human? We find that the tenrec possesses a uterine process akin to human predecidualization, involving the upregulation of key decidual transcription factors FOXO1 and KLF7 and effector genes such as IL15, and that this cell type is unique to pregnant animals.

sample_organism:
Mus musculus
Cavia porcellus
Monodelphis domestica
Tenrec ecaudatus

overall_design: Cells from midgestation fetal-maternal interface (whole-thickness uterus and placenta) were isolated and subjected to 10x Genomics 3’ v3 single-cell RNA-seq.

first: Silvia

last: Basanta

first: Mihaela

last: Pavlicev

first: Daniel

middle: J

last: Stadtmauer


title: Opposing role of phagocytic receptors MERTK and AXL in Progranulin deficient FTD

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: Genetic mutations in the progranulin gene, GRN, cause frontotemporal dementia and a lysosomal storage disorder. Using single-nuclei RNA sequencing of the post-mortem brain tissue from heterozygous pathogenic granulin variant (GRN+/-) carriers we found dysregulation of microglia, phagocytosis and the phagocytic receptors MERTK and AXL. Exogenous progranulin regulated MERTK and AXL RNA expression in human microglia induced from iPSCs irrespective of GRN mutation status, without directly binding to MERTK or AXL proteins. We generated double knock-out mice and found that constitutive homozygous loss of Grn and Mertk (Grn-/-;Mertk-/-) rescued microglial disease signature while constitutive homozygous loss of Grn and Axl (Grn-/-;Axl-/-) worsened the microglial disease signature. Higher levels of AXL protein, but not MERTK protein, in the post-mortem superior temporal gyrus correlated with worse cross-sectional functional impairment (CDR sum of boxes) by both GRN+/- mutation carriers and non-carrier controls. These data explain in part the inflammation seen in GRN-FTD and are applicable to other inflammatory states in which PGRN, MERTK and AXL play regulatory roles, including cancer, sepsis, stroke, diabetes and obesity. The interaction between GRN, MERTK and AXL opens potential new therapeutic avenues to intervene on this inflammatory axis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Droplet-based single nuclear RNA sequencing from superior frontal gyrus from 7 patients with GRN+/- loss of function mutations and 8 GRN+/+ aged controls without neurological disease; thalamic cells from WT control, single KO mice (Grn-/-, Mertk-/- and Axl-/- mice) and double KO mice (Grn-/-;Mertk-/- and Grn-/-;Axl-/-).

first: Claire

last: Clelland

last: Fan

first: Jon

middle: I

last: Etchegaray

first: Chad

middle: R

last: Altobelli

first: Sally

middle: E

last: Salomonsson

first: Alisha

last: Maltos

first: Aradhana

last: Sachdev

first: Yaqiao

last: Li

first: Yungui

last: Zhou

first: David

last: Le

first: Chao

last: Wang

first: Gillian

last: Carling

first: Lay

last: Kodama

first: Faten

last: Sayed

first: Juan

middle: A

last: Perez-Bermejo

first: Ethan

middle: G

last: Geier

first: Jennifer

last: Yokoyama

first: Howie

last: Rosen

first: Alissa

middle: L

last: Nana

first: Salvatore

last: Spina

first: Lea

middle: T

last: Grinberg

first: William

middle: W

last: Seeley

first: Fanny

last: Elahi

first: Michelle

last: Arkin


title: POSITIONAL TRANSCRIPTOMICS SHED LIGHT ON SITE-SPECIFIC PATHOLOGIES OF THE AORTA

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Pathologies of large vessels, such as atherosclerosis and aneurysms tend to develop at specific sites in the vascular tree. The consistency with which these events emerge suggests that a combination of unique local stressors, particularly physical forces and disturbances in gene expression profiles underlies disease etiology. We sought to investigate whether transcriptional diversity in specific segments of the aorta could be used to identify emergence of site-restricted vascular disease. Transcriptional profiling was performed using single cell RNA-seq in the carotids, aortic arch, thoracic and abdominal aorta across both sexes. Analyses of the data identified sex-invariant region-specific differences that were further validated by immunocytochemistry. Analysis of vascular smooth muscle cell transcriptomics from distinct regions of the aorta and carotids showed a high degree of similarity, but also uncovered skewed expression of a small percentage of transcripts (7.2%) towards particular vascular segments (carotid, aortic arch, thoracic and abdominal aorta). In silico cross-reference of genes known to be associated with vascular disease with the unique transcriptional signatures validated our proposed hypothesis. Specifically, we found correlations between localized-diseased causing GWAS candidate genes and region-enriched signatures. Pair-wise comparison between anatomic regions across sexes identified regional sex-specific gene signatures highlighting prominent regional-sex dependent differences were observed in vSMCs of the thoracic and abdominal aorta, consistent with sex-specific burden of aneurysm in these regions. Of these regional sex-enriched candidates’, Mcam/CD146, showed ventral thoraco-abdominal distribution, enriched expression in females and it was significantly reduced in the AngII / hypercholesterolemic model of aortic aneurysm. Furthermore, induction of aneurysms in mice lacking Mcam/CD146 resulted in larger lesions and accelerated death due to dissection.

overall_design: Carotid arteries and aorta spanning the aortic root to the iliac bifurcation were isolated from 12 week old female and male mice and dissected into 4 segments based on anatomic landmarks.  Samples were segregated by sex and anatomic location and digested into single cell preperations prior to library preperation.

first: Milagros

last: Romay

first: M

last: Iruela-Arispe


title: An Epigenome Atlas of Mouse Adipocytes

city: Schwerzenbach

first: Laura

middle: Catharina

last: Hinte

address: Schorenstrasse 16

country: Switzerland

institute: ETH Zurich

summary: Despite recent advances in the characterization of the mouse adipocyte epigenome, epigenetic characterization of adipocytes in vivo has been limited, particularly across different adipose depots and of more than two epigenetic modifications. In this study, by using the state-of-the art method CUT&Tag and NuTRAP mice to generate paired single mouse datasets we conducted an integrative multimodal analysis of five histone marks – H3K4me3, H3K27me3, H3K4me1, H3K27ac and H3K9me3 – in beige, brown, and white adipocytes from three distinct mouse adipose tissue depots. Our analysis revealed that enhancers distinguished adipocytes by their tissue of origin, with H3K4me1 deposition differentiating between beige and brown adipocytes. Furthermore, diphtheria toxin-mediated ablation of beige adipocytes showed that white adipocytes in inguinal adipose tissue and beige adipocytes did not use a distinct enhancer set and both poised thermogenic genes for expression. In contrast, adipocytes from epididymal adipose tissue actively repressed thermogenic master regulators and exhibited a distinct enhancer profile compared to white adipocytes from inguinal tissue. These paired multimodal data comprise an extensive resource for the further exploration of the mouse adipocyte epigenome which may enable discovery of regulatory elements governing adipocyte identity and gene regulation.

overall_design: Ucp1ERCre x NuTRAP mice were cold exposed at 8 degrees celsius for one week and received tamoxifen during this time. Subesquently mice were either sacrificed or allowed to recover for 8 weeks at 22 or 30 degrees celsius before tissue harvest. AdipoCre x NuTRAP mice were housed either at 22 or 30 degrees before tissue harvest. AdipoCre x NuTRAP x Ucp1DTRGfp mice were old exposed at 8 degrees celsius for one week and were injected with diphtheria toxin or saline thereafter before tissue harvest. Labelled adipocyte  nuclei of brown, inguinal and epididymal adipose tissue were isolated and used for CUT&Tag. 2-3 biological replicates per hPTM and condition. Datasets are paired per mouse.

middle: C

first: Adhideb

last: Ghosh

first: Ferdinand

last: von Meyenn


title: Single cell transcriptomes of zebrafish germline reveal progenitor types and feminization by Foxl2l [scRNA-seq]

first: Bon-chu

last: Chung

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

department: Institute of Molecular Biology

institute: Academia Sinica

summary: Sex determination is distinct from development of other organs for its diversity among species. In zebrafish, the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However, the detail mechanism is still unclear. Here in this study, we found that the transcription factor that belongs to forkhead box family, Foxl2l, is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre-meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all-male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre-meiotic stage at 21 dpf, the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination, wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 days post fertilization (dpf) and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA-seq and single-cell RNA-seq respectively.

overall_design: Trunks of ziwi:egfp;foxl2l-/- or ziwi:foxl2l+/+ containing gonad were dissociated by 0.4% collagenase and 0.5% trypsin at 26 dpf. Germ cells were then sorted by fluorescence activated cell sorter. Around 3000 EGFP+ cell were collected in each genotype. cDNA libraries were constructed by Chromium Next GEM Single Cell 3' Library Construction Kit v3.1 kit (10x Genomics) and was sequenced performed by Illumina NextSeq 500.

first: Hao

last: Ho

first: Ching-hsin

last: Yang

first: Yan-wei

last: Wang

first: Ker-Chau

last: Li


title: gene expression profile of lung immune cells isolated from mock- or SARS-CoV-2 infected mice at single cell level

city: Wuhan

first: Xianliang

last: Ke

state: Hubei

address: No. 44, xiaohongshan street

institute: Wuhan Institute of Virology, Chinese Academy of Science

summary: Aging is one of  the greatest rick factor of COVID-19. We use single cell RNA sequencing to compare the immune responses in the lung bewteen aged (19-month-old) and young (3-week-old) mice.

overall_design: 3-week or 19-month-old C57BL/6J mice were mock infected or infected with a mouse adapted SARS-CoV-2 virus. At three days post-infection, lungs were harvested from three mice from each group,pooled for digestion with enzyme mix ( Liberase, 33.3 μg/mL, and DNaseI 133.3 ug/mL ) at at 37 ℃ for 30 min with rotation. The released cells were subjected to red blood cell lysis. 12,000 cells from each group were loaded in the lane with 10x Chromium (10x Genomics, USA) for single cell sequencing following the instructions of the Chromium Single Cell 3′ Reagent Kit v3 .

first: Xian

last: Lin

first: Jin

first: Xiaoqin

last: Jian

first: Minqi

last: Chen

first: Chang

last: Ye

first: Quanjiao


title: Phf23 regulates embryonic neurogenesis by increasing the level of H3K27ac of Tcf4 [RNA-seq]

first: ping

last: he

overall_design: To investigate the mechanism of Phf23 loss leading to blocked differentiation of embryonic NSCs, we harvested Phf23+/+ and Phf23-/- NSCs for bulk RNA-seq, and 4 replicate samples per group. We then performed gene expression profiling analysis using data obtained from RNA-seq.


title: Generation of mature epicardium derived from human-induced pluripotent stem cells via inhibition of mTOR signaling

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

summary: Reactivating the human epicardium post-cardiac injury holds promise for cardiac tissue regeneration. Despite successful differentiation protocols yielding pure, self-renewing epicardial cells from induced pluripotent stem cells (iPSCs), these cells maintain an embryonic, proliferative state, impeding adult epicardial reactivation investigation. We introduce an optimized method that employs mammalian target of rapamycin (mTOR) signaling inhibition in embryonic epicardium, inducing a quiescent state that enhances multi-step epicardial maturation. This yields functionally mature epicardium, valuable for modeling adult epicardial reactivation. Furthermore, we assess cardiac organoids with cardiomyocytes and mature epicardium, probing molecular mechanisms governing epicardial quiescence during cardiac maturation. Our results highlight iPSC-derived mature epicardium's potential in investigating adult epicardial reactivation, pivotal for effective cardiac regeneration. Additionally, the cardiac organoid model offers insight into intricate cardiomyocyte-epicardium interactions in cardiac development and regeneration.

overall_design:
Exmination of mTOR inhibition in 3 embryonic epicardial cell types.
Epicardium tissue was peeled from adult mouse heart and analyzed using RNA-seq. Human heart organoids were generated from 1390C1 cell line; after a 7-day treatment, untreated or Torin1-treated heart organoids were analyzed using scRAN-seq.

first: Yu

last: Tian

first: Antonio

last: Lucena-Cacace

first: Rodolfo

last: Allendes Osorio

first: Yasuko

last: Matsumura


title: Recapitulate Organotypic Mesenchyme and Endothelium via Vascularized Lung and Intestine Organoids

status: Public on Jun 29 2025

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Organotypic mesenchyme and endothelium are pivotal during organ development. To generate these context-specific cell types, we established human pluripotent stem cell (hPSC)-derived meso-endoderm spheroids and vascularized primitive gut tube organoids and benchmarked this process via single-cell RNA-seq.

overall_design: Day-3 meso-endoderm spheroids, Day-7 vascularized anterior foregut and mid/hindgut, and Day-21 vascularized lung organoid, small intestine, and colon organoids were generated. In Day-3 group, meso-endodermal spheroids receiving four different BMP4 treatment durations were sequenced; in Day-7 group, two vascularized anterior foregut organoids (receive 0 or 1-day BMP4 treatment from day 0-3) and three vascularized mid/hindgut organoids (receive 1, 2, or 3-day BMP4 treatment from day 0-3) were sequenced; in Day 21 group, one vascularized lung organoid, one vascularized small intestine, and one vascularized colon organoid were sequenced.

first: Yifei

last: Miao

first: Mingxia

last: Gu


title: FASTKD5 processes mitochondrial pre-mRNAs at non-canonical cleavage sites

city: Miami

first: Ahram

last: Ahn

state: FL

address: 1600 NW 10th Ave

department: Biochemistry and Molecular Biology

institute: University of Miami

summary: The first post-transcriptional step in mammalian mitochondrial gene expression, required for the synthesis of the 13 polypeptides encoded in mtDNA, is endonucleolytic cleavage of the primary polycistronic transcripts. Excision of the mtDNA-encoded tRNAs releases most mature RNAs; however, processing of three non-canonical mRNAs not flanked by tRNAs (CO1, CO3, CYB) requires FASTKD5. To investigate the molecular mechanism involved, we created knockout human cell lines to use as assay systems. The absence of FASTKD5 produced a severe OXPHOS assembly defect due to the inability to translate two unprocessed non-canonical mRNAs and predicted altered folding patterns specifically at the 5’-end of the CO1coding sequence. Structural features 13-15 nt upstream of the CO1 and CYB cleavage sites suggest FASTKD5 recognition mechanisms. Remarkably, a map of essential FASTKD5 amino acid residues revealed RNA substrate specificity; however, a key, putative active site residue was required for processing all three non-canonical pre-RNAs. Mutating this site resulted in a substantial increase in binding affinity with all client RNA substrates. A reconstituted in vitro system showed that wild-type, but not mutant, FASTKD5, was able to cleave client substrates correctly. These results establish FASTKD5 as the missing piece of biochemical machinery required to completely process the primary mitochondrial transcript.

overall_design: This study was designed to investigate the structure of human mitochondrial mRNAs. Briefly, mitochondria isolated from HEK-293T cells were incubated with DMS and RNA was extracted from isolated mitochondria. An off the shelf IDT RNAseq library preparation kit was used in conjunction with TGIRT to mediated mutagenesis where DMS modifications occur. This sequencing data was then aligned to the mitochondrial genome and structural models were developed using SEISMIC-RNA (Rouskin Lab) and RNAstructure (Mathews lab).

first: Antoni

last: Barrientis

first: Michele

last: Brischigliaro

first: Seungwoo

last: Hong


title: Effect of treating HRMVECs with nutlin-3 and/or norrin

city: Minneapolis

first: Harald

last: Junge

state: Minnesota

address: Room 310A LRB, 2001 6th Street SE

department: OVNS

institute: University of Minnesota

summary: To identify transcripts controlled by elevated P53 in HRMVECs we inhibited the MDM2/P53 interaction using nutlin-3. To identify cross-talk of P53 and beta-catenin dependent signaling, the experiment was performed in the presence or absence of the frizzled4 ligand norrin. Expression of beta-catenin-dependent signaling response genes induced by norrin, e.g., AXIN2 and APCDD1, were inhibited by nutlin-3. Nutlin-3 furthermore altered the expression of several gene sets, e.g., known p53 regulated genes (e.g., CDKN1A, MDM2), genes that potentially regulate beta-catenin-dependent signaling (including NCAPH, NEURL2, DRAXIN, DKK1), mediators of blood-retina barrier function (including SOX18, KIF11, ABCG2, MFSD2A), and mediators of inflammatory signaling  and leukocyte extravasation (including ICAM1, CCL2, SELE, and CXCL1). The gene expression changes mediating inflammatory signaling and leuokocyte interactions substantially overlap with those expression changes observed in endothelial cells under high glucose conditions and diabetes mellitus.

overall_design: HRMVECs were treated for 24 hours: unstimulated, stimulated with norrin only, stimulated with nutlin-3 only, and stimulated with both norrin and nutlin3. Nutlin-3 was used at 10 µM, norrin (R+D Systems) was used at 200 ng/ml. Nutlin-3 was solved in DMSO. DMSO was added as necessary to keep the DMSO concentration at 0.1% v/v in all groups. Quadruplicate samples of four groups were subjected to paired-end RNA-seq of ribodepleted RNA. Ca. 20 mio reads per sample were obtained.

first: Chi

last: Zhang


title: Lurasidone Induces Developmental Toxicity and Behavioral Impairments in Zebrafish Embryos

status: Public on Jun 27 2025

city: hangzhou

first: Hongjian

last: Gong

state: zhejiang

address: yuhang street 866

institute: zhejiang university

summary: Lurasidone, a second-generation antipsychotic, is widely used for treating schizophrenia and bipolar disorder due to its favorable metabolic profile. However, its potential developmental neurotoxicity remains poorly understood. This study investigated the effects of lurasidone on zebrafish embryos, combining morphological, behavioral, transcriptomic, and neurotransmitter analyses. Zebrafish embryos were exposed to lurasidone at 0, 0.4, 4, and 8 mg/L concentrations from 5 to 120 hours post-fertilization (hpf). Results revealed dose-dependent developmental toxicity, including reduced survival and hatching rates, shorter body length, and increased pericardial and yolk sac edema. Behavioral assessments showed significant impairments in locomotion and touch response, particularly at higher concentrations. Transcriptomic analysis identified 1,907 differentially expressed genes, with upregulation of circadian regulation pathways and downregulation of cell cycle and oxidative phosphorylation pathways. Neurotransmitter profiling indicated significant reductions in glutamate, dopamine, and GABA levels, suggesting disruptions in excitatory/inhibitory balance. These findings highlight lurasidone's potential neurodevelopmental risks, particularly during critical developmental periods. The study underscores the importance of further research to assess the safety of lurasidone in vulnerable populations, such as pregnant women and young patients.

overall_design: comparative gene expression profiling analysis of RNA-seq data for zebrafish 5dpf larve and its drug-exposured derivatives(4 mg/L Lurasidone).

first: Wentian

last: Li

first: Fang

last: Wang

first: Zhe

last: Feng

first: Qianqian

last: Cheng

first: Yuqing

last: Huang

first: Han

last: Xiao


title: Epigenetic profiling of neuronal and non-neuronal signal in major depressive disorder

city: New York City

first: Jaroslav

last: Bendl

state: New York

address: One Gustave L. Levy Place, Department of Genetics and Genomics Sciences, Box 1210

department: Genetics and Genomics Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Characterization of cell type specific (NeuN+/NeuN-) open chromatin by ATAC-seq assay in orbitofrontal cortext of postmortem tissue samples from 19 MMD cases and 18 controls.

overall_design: Open chromatin profiles (ATAC-seq assay) in FANS-sorted neuronal and non-neuronal nuclei from orbitofrontal cortex of 19 MDD cases and 18 controls.

first: John

middle: F

last: Fullard

first: Panos

last: Roussos


title: Influence of the autoinducer-2 dependent quorum sensing on gene expression of asymptomatic bacteriuria E. coli isolate 83972

city: Muenster

first: Ulrich

last: Dobrindt

state: NRW

address: Mendelstrasse 7

department: Institute of Hygiene

institute: University of Münster

summary: To analyze the effect of AI-2-dependent quorum sensing on gene expression at the transcriptional level of E. coli 83972, we performed an RNA-seq analysis of wild type strain and the lsr-complemented variant 83972 attB::lsr.

overall_design: Both strains were cultivated in LB, and samples were taken in the lag phase, during mid-exponential growth, and during the transition to the stationary phase. Total RNA was isolated from three biological replicates of each strain and time point for RNA-seq analysis

first: Marla

last: Keizers

first: Michael

last: Berger


title: Transcriptome profiling and co-expression network analysis of 96 Haematococcus pluvialis samples

city: Ningbo

first: Bin

last: Hu

address: No.169 Qixing South Road, Meishan Street, Beilun District, Ningbo City, Zhejiang Province, China

institute: Ningbo university

summary: Haematococcus pluvialis is a microalga known for producing the red carotenoid, astaxanthin. Key research areas to improve productivity include optimizing vegetative biomass, enhancing astaxanthin content, and controlling secondary cell wall formation. In this study, RNA-seq was conducted on 96 H. pluvialis samples under various treatments and time points, generating 96.7 GB of high-quality data (2,080,511,173 clean reads, quality score > 30). Gene expression was quantified as transcripts per million (TPM), and genes with similar expression patterns were clustered. A co-expression network, constructed with a soft threshold of β=7 (R² > 0.9), identified 39 co-expression modules, each averaging 732 genes. Additionally, the re-annotation process provided functional descriptions for around 8,600 previously uncharacterized genes. Gene functional classification analysis revealed their involvement in metabolic pathways related to genetic information processing and primary/secondary metabolite metabolism. This dataset provides a valuable resource for exploring the molecular mechanisms involved in critical processes such as growth regulation, astaxanthin accumulation, and secondary cell wall synthesis in H. pluvialis.

overall_design: Low-light cultivation stage: The algal cells were collected in the logarithmic phase (without any treatment, sample size: 3), the plateau phase (without any treatment, sample size: 3), and the plateau phase (1.8 g/L sodium acetate, sample size: 3).High-light stress cultivation stage:The algal cells were collected on the following days: the first day (without any treatment, sample size: 6), the first day (with 1 mM KI, sample size: 3), the first day (with nitrogen deprivation, sample size:  3), the first day (with nitrogen repletion, sample size: 3), the first day (with 1 mM fructose diphosphate, sample size: 3), and the first day (with 5 mM fructose diphosphate, sample size: 3);  the second day(without any treatment, sample size: 3), the second day(with 0.5 g/L NaCl plus 0.5 mM CMP, sample size: 3);  the Sixtieth hour(without any treatment, sample size: 3),the Sixtieth hour(Mutant, sample size: 3);  the Third day(without any treatment, sample size: 9), the Third day(1 mM Xanthosine, sample size: 6), the Third day(with 1 mM taurine, sample size: 3);  the Fifth day(without any treatment, sample size: 3),the Fifth day(1 mM KI, sample size: 3), the Fifth day(with nitrogen deprivation, sample size: 3),the Fifth day(nitrogen repletion, sample size: 3),the Fifth day(1 mM fructose diphosphate, sample size: 3),the Fifth day(5 mM fructose diphosphate, sample size: 3), the Fifth day(1 mM Uridine, sample size: 3), the Fifth day(1 mM Guanine, sample size: 3);  the Tenth day(without any treatment, sample size: 3),the Tenth day(1 mM KI, sample size: 3).Harvest the algal cells, immediately freeze them in liquid nitrogen, and perform transcriptome sequencing.  Each treatment had at least three biological replicates, resulting in a total of 96 sequencing samples.

first: Kai

last: Liu

first: Feichao

last: Du

first: Hailiang

last: Xing

first: Xiaoyuan

last: Su

first: Tao

first: Feng

last: Chen

first: Yujie

last: Qin

first: Zhaozhen

last: Dong

first: Xue

last: Sun

first: Liuquan

first: Jagroop

last: Pandhal

first: Nianjun

last: Xu

first: Chaoyang


title: Chromatin accessibility and cell cycle progression are controlled by the HDAC-associated Sin3B protein in murine hematopoietic stem cells

status: Public on Jun 28 2025

city: Farmington

first: Harshpreet

last: Chandok

address: 10 Discovery Dr

institute: The Jackson Laboratory

summary: Blood homeostasis requires the daily production of millions of terminally differentiated effector cells that all originate from hematopoietic stem cells (HSCs). HSCs are rare and exhibit unique self-renewal and multipotent properties, which depend on their ability to maintain quiescence through ill-defined processes. Defective control of cell cycle progression can eventually lead to bone marrow failure or malignancy. In particular, the molecular mechanisms tying cell cell re-entry to cell fate commitment in HSCs remain elusive. Previous studies have identified chromatin coordination as a key regulator of differentiation in embryonic stem cells. Here, we utilized genetic inactivation of the chromatin-associated Sin3B protein to manipulate cell cycle control and found dysregulated chromatin accessibility and cell cycle progression in HSCs. Single cell transcriptional profiling of hematopoietic stem and progenitor cells (HSPCs) inactivated for Sin3B reveals aberrant progression through the G1 phase of the cell cycle, which correlates with the engagement of specific signaling pathways, including aberrant expression of cell adhesion molecules and the interferon signaling program in LT-HSCs. In addition, we uncover the Sin3B-dependent accessibility of genomic elements controlling HSC differentiation, which points to cell cycle progression possibly dictating the priming of HSCs for differentiation. Our findings provide new insights into controlled cell cycle progression as a potential regulator of HSC lineage commitment through the modulation of chromatin features.

overall_design: To investigate the function of SIn3B on murine hematopoiesis, conditional knockouts (cKO) of Sin3B in the hematopoietic system were generated by crossing Sin3B-flox mice with Vav1-iCre mice on a C57BL/6 background. Two cKO mice and two wild type mice were humanely sacrificed as adults, and bone marrow was isolated and subjected to cKit enrichment with magnetic beads. Lineage-cKit+Sca-1+ cells were then sorted by FACS and then samples from each genotype were pooled. Cells were stained with TotalSeq Hashtag Oligonucleotide-antibodies against CD45 (BioLegend). Cells were then washed and the 10X Genomics Chromium Single Cell 3' Kit was used to generate single cell suspension and cDNA synthesis/library preparation. Libraries were sequnced on an Illumina NovaSeq and demultiplexed using 10X Genomics CellRanger software. For stress conditions, two mice of the same genotypes as above were given 5-Fluorauracil (100mg/kg) 9 days before harvest.

first: Calderon

last: Alexander

first: David

last: Gregory


title: SMCHD1 controls the structure and accessibility of heterochromatin and functions as an organizer of genome compartments (RNA-Seq)

city: Grand Rapids

first: Gerd

last: Pfeifer

address: 333 Bostwick Ave. NE

institute: Van Andel Research Institute

summary: Structural Maintenance of Chromosomes flexible Hinge Domain containing 1 (SMCHD1) is an SMC-like protein that plays an important role in X chromosome inactivation and is mutated in two human diseases, a muscular dystrophy, and a rare developmental disorder. Here we characterized the function of SMCHD1 in human myoblasts and focused on its role on autosomes. We found that SMCHD1 colocalizes with Lamin B1 and the constitutive heterochromatin mark H3K9me3. Loss of SMCHD1 leads to a loss of heterochromatin at nuclear lamina regions and to extensive changes of the epigenome on most chromosomes. In SMCHD1-deficient cells, about half the regions that normally bind SMCHD1 loose H3K9me3, acquire long stretches of DNA hypermethylation and gain a variety of active chromatin marks including H3K4me3, H3K4me1, histone H3K27 acetylation, and H3K36 di- and trimethylation. Three-dimensional chromatin analysis using HiC shows that long range contacts between different heterochromatin blocks (B compartments) on the same chromosome are diminished while there is extensive formation of new topologically associated domains (TADs) and loops anchored at newly created CTCF/RAD21 binding sites. Inactivation of SMCHD1 promotes many inactive (B) to active (A) compartment transitions. These transitions are accompanied by activation of about 200 previously silenced genes with potential implications for the etiology and progression of SMCHD1-linked diseases. Our data suggest that SMCHD1 functions as a genome compartment organizer and as an important anchor for heterochromatin domains at the nuclear lamina ensuring that lamina- associated domains are protected from histone and DNA modification enzymes that typically operate in active chromatin.

overall_design: Comparative gene expression profiling analysis of RNAseq data in SMCHD1 knockout and wildtype LHCN-M2 cells.

first: Zhijun

last: Huang


title: SMCHD1 controls the structure and accessibility of heterochromatin and functions as an organizer of genome compartments (ChIP-Seq)

overall_design:
chromatin state maps (H3K27ac, H3K4me1, H3K4me3, H3K36me2,H3K36me3 and H3K9me3) and binding profiles for the Pol II RNA polymerase II, CTCF insulator protein and RAD21 cohesion protein were generated by ChIP-seq in WT and SMCHD1 knockout LHCN-M2 cells.
Binding profiles of the H3K27me3 and H2AK119ub1 were generated by ChIP-seq in WT and SMCHD1 knockout LHCN-M2 cells.


title: SMCHD1 controls the structure and accessibility of heterochromatin and functions as an organizer of genome compartments (HiC)

overall_design: Assessing chromatin conformation by in situ HiC on WT and SMCHD1KO cells.


title: Temporal analysis of doxorubicin-induced cardiac toxicity and hypertrophy

city: Taipei City

first: An-Chi

last: Wei

address: No. 1, Sec. 4, Roosevelt Rd., Da’an Dist.

department: Graduate Institute of Biomedical Electronics and Bioinformatics

institute: National Taiwan University

summary: Doxorubicin (DOX) is a potent anti-cancer drug that could induce cardiotoxicity in human bodies. To elucidate the underlying mechanisms behind DOX-induced toxicity, we conducted RNA sequencing on AC16, a well-established immortalized cardiac cell line, after treating it with DOX for 2, 4, and 6 days. We then performed RNA-Seq analysis on the obtained data. Our findings reveal significant alterations in key pathways within the AC16 cells treated with DOX, including disruptions in the MAPK cascade, apoptosis, inflammation, immune response, angiogenesis, and cardiac hypertrophy.

overall_design: To investigate the doxorubicin-induced cardiomyopathy, we performed RNA sequencing on the AC16 cells treated with DMEM, or 2, 4, and 6 days of doxorubicin.

first: Yu-Te

last: Lin

first: Yi-Ju

last: Lee

first: Wen-Wei

last: Tseng

first: Zih-Hua

first: Huai-Ching

last: Hsieh

first: Ko-Hong

first: Jin-Yu


title: Heritable Tissue-Specific Gene Expression Associates With Chronic Wound Microbial Species

city: Lubbock

first: Khalid

last: Omeir

state: Texas

address: 2901 Main St.

department: Department of Biological Sciences

institute: Texas Tech University

summary: The reasons for interpatient variability in chronic wound microbiome composition are thought to be complex but are poorly known. To investigate how patients’ genetically regulated tissue expression may influence chronic wound bacterial composition, we performed a microbiome-transcriptome-wide association study. This approach involved estimating for 509 patients their tissue-specific gene expression from DNA genotypes, followed by associating gene expression to the relative abundances of species detected in their wounds as provided on clinical reports to the physician. Comparisons to artery, blood, fibroblast, skeletal muscle, skin, subcutaneous fat, and nerve tissue resulted in 251 transcriptional differences at 109 genes significantly explaining abundances of 39 different species. Overall, these species were detected in 63% of wounds. A similar number of associations per tissue was observed (range 31-39) and many genes were associated at multiple tissues in distinct ways. The cumulative variance across loci for species relative abundance explained ranged from ~5-36%, depending on species. Although the same gene was almost never associated with more than one species, ~14% of enriched pathways were independently enriched for multiple species, which may reflect the diversity of ways microbes interact with partially overlapping attributes of the wound bed. Commonly enriched pathways pertained to collagen formation and modification, cell signaling, cytoskeletal dynamics, interactions with extracellular matrix, transmembrane proteins, among others. This work expands the new perspective that individual genetics may partially determine microbial colonization and infection.

overall_design: DNA was extracted from buccal swabs to genotype patients, from which gene and intron retention levels were estimated for biologically relevant tissue types. Subsequently, tissue-specific expression was associated to chronic wound bacterial abundance.

first: Jacob

last: Ancira

first: Rebecca

last: Gabrilska

first: Craig

last: Tipton

first: Clint

last: Miller

first: Ashley

last: Noe

first: Kumudu

last: Subasinghe

first: Megan

last: Rowe

first: Nicole

last: Phillips

first: Joseph

last: Wolcott

first: Caleb

middle: D

last: Philips


title: SMCHD1 controls the structure and accessibility of heterochromatin and functions as an organizer of genome compartments (DamID-Seq)

first: Gerd

last: Pfeifer

overall_design:
Using DamID-seq to identifify genome-wide patterns of SMCHD1 and LaminB1 in LHCN-M2 cells
Using DamID-seq to identifify genome-wide patterns of  CBX1 and MBD3  in LHCN-M2 cells

first: Zhijun

last: Huang


title: Gene expression profile at single cell level of human cortical brain organoids at day 20.

status: Public on Jun 26 2025

city: Isehara-shi

first: Atsushi

last: Fukuda

institute: Tokai University

summary: We report that NHEJ mediated XIST reactivation in differentiating cell from female hPSCs by single cell  RNA-sequencing.

overall_design: Transcriptome sequencing of 4 total RNA samples from human cortical organoid.


title: Systematic comparison and base-editing-mediated directed protein evolution and functional screening yield superior auxin-inducible degron technology [2]

city: Chicago

first: De

last: Xing

state: IL

address: 264 E Huron St., Suite: 4-121

department: Feinberg School of Medicine, Obstetrics and Gynecology

institute: Northwestern University

summary: Biological mechanisms are inherently dynamic, requiring precise and rapid manipulations for effective characterization. Traditional genetic manipulations operate on long timescales, making them unsuitable for studying dynamic processes or characterizing essential genes, where chronic depletion can cause cell death. We compared five inducible protein degradation systems—dTAG, HaloPROTAC, IKZF3, and two auxin-inducible degrons (AID) using OsTIR1 and AtFB2—evaluating degradation efficiency, basal degradation, target recovery after ligand washout, and ligand impact. This analysis identified OsTIR1-based AID 2.0 as the most robust system. However, AID 2.0's higher degradation efficiency came with target-specific basal degradation and slower recovery rates. To address these limitations, we employed base-editing-mediated mutagenesis followed by several rounds of functional selection and screening. This directed protein evolution generated several gain-of-function OsTIR1 variants, including S210A, that significantly enhanced the overall degron efficiency. The resulting degron system, named AID 2.1, maintains effective target protein depletion with minimal basal degradation and faster recovery after ligand washout, enabling characterization and rescue experiments for essential genes. Our comparative assessment and directed evolution approach provide a reference dataset and improved degron technology for studying gene functions in dynamic biological contexts.

overall_design: CRISPR base editor scanning for in vivo evolution of adapter protein for efficient auxin-inducible degron technology

first: Mazhar

last: Adli


title: Regulation of pancreatic cancer migration by signal convergence in the epigenome [RNA-Seq]

city: Stuttgart

first: Steven

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

summary: Pancreatic ductal adenocarcinoma (PDAC) is frequently diagnosed at an advanced, metastatic stage. PDAC treatment is challenging due to high tumor cell plasticity, tumor heterogeneity, and a dense tumor microenvironment (TME), all of which strongly influence tumor metastasis. While mutations in the KRAS gene characterize PDAC, inflammatory signaling from the TME accelerates tumor progression, metastasis, and therapy resistance. While individual roles of oncogenic and inflammatory signaling in promoting PDAC progression have been studied extensively, the epigenetic and transcriptional mechanisms by which they function combinatorially in metastasis remain unclear. Our study elucidates how inflammatory TNFα and oncogenic MAPK signaling pathways converge to control PDAC cell migration through activation of NF-κB and AP1 transcription factors, respectively. Combining single-cell RNA sequencing (scRNAseq) analyses, multiplex immunofluorescence staining, in vitro, and in vivo studies, we unveil that the simultaneous activation of these pathways with TNFα and EGF induces the expression of specific genes associated with cell motility and migration. We show that combinatorial induced genes are co-bound by FOSL1 and RELA. Remarkably, inhibition of NF-κB transcriptional activity using glucocorticoid receptor (GR) mixed agonists significantly reduces RNA polymerase II across the target genes and inhibits cell migration. These findings highlight the potential of GR agonists, commonly utilized to alleviate chemotherapy side effects, in mitigating PDAC tumor migration. Our study offers promising avenues for developing mechanism-based therapeutic strategies in PDAC management.

overall_design: To explore the epigenetic mechanism by which inflammatory NF-κB signaling converges with oncogenic MAPK signaling to regulate cell migration in pancreatic cancer, we conducted ChIP-seq on the PDAC cell lines AsPC-1 and L3.6pl. The experiment was performed under control conditions and after treatment with EGF (to activate oncogenic signaling), TNFα (to activate inflammatory signaling), and a glucocorticoid agonist (GR). Additionally, siRNA-mediated depletion of the transcription factors FOSL1 and RELA was included.

first: Joana

last: Aggrey-Fynn


title: Immune-related cutaneous adverse events display distinct clinical and molecular characteristics, depending on immune checkpoints targeted

status: Public on Jun 25 2025

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

summary: Background/Objectives: Immune-related cutaneous adverse events (ircAE) are common complications of cancer immunotherapy and provide insight into immune-related ad-verse events (irAE) more broadly. To enhance our molecular understanding, we char-acterized ircAE resulting from single-agent (PD1) and combined immunotherapy reg-imens (P+C). Clinically, maculopapular rashes (MPR) and toxic epidermal necrolysis (TEN) resemble ircAE, providing a valuable basis for investigations. Methods: To in-vestigate the transcriptome and immune infiltrates in ircAE, we conducted transcriptomic analyses and multiplexed immunohistochemistry on skin biopsies from patients re-ceiving PD1 and P+C, as well as those with MPR, TEN, and healthy controls. Results: Principal component analysis revealed distinct transcriptomic clustering between ircAE, MPR, and TEN. Specifically, PD1 ircAE exhibited a gene expression profile similar to TEN, with upregulation of Type-I-response-related genes (e.g., CXCL9 Log2FC 5.34, p<0.0001, CXCL10 Log2FC 6.03, p<0.0001), while P+C ircAE more closely resembled MPR. Immune infiltrates differed significantly between all groups (p=0.002 by PER-MANOVA for all groups). CD4 T-cells were abundant in the dermis of ircAE from any type of immunotherapy. However, PD1 stained positive in 1.07% of CD4 cells with PD1 monotherapy, compared to 0.3%, 0.4%, and 0.08% in P+C, MPR, and TEN, respectively. Conclusions: This study identified distinct molecular and cellular signatures in ircAE depending on the type of immune checkpoint blockade. aPD1-associated ircAE share similarities with the cytotoxic profile of TEN, while P+C more closely mirrored MPR. These findings support the need for tailored management strategies for ircAE, emphasizing personalized therapeutic approaches to minimize treatment interruptions while preserving the efficacy of cancer immunotherapy.

overall_design: Retrospective study, consisting of a comparative analysis of samples from patients developing immune-related cutaneous adverse events following aPD1-based and aCTLA4/aPD1, as well as samples from healthy skin comparators, maculopapular drug rash and toxic epidermal necrolysis

first: Lukas

last: Kraehenbuehl

first: Nicola

last: Winkelbeiner

first: Reinhard

last: Dummer

first: Barbara

last: Meier-Schiesser


title: Intestinal tuft cell subtypes represent successive stages of maturation driven by crypt-villus signaling gradients

city: Utrecht

first: Hugo

last: Snippert

state: Utrecht

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: University Medical Center Utrecht

summary: Plate-based scRNA-seq data of (1) GFP possitive cells sorted from small intestines of ChAT-eGFP mice [in vivo], and (2) fluorescent cell populations sorted from tuft type-specific small intestinal reporter organoids [in vitro].

overall_design:
(1) GFP+EpCAM+DAPI- cells from 3 ChAT-eGFP mice (pooled) were isolated from small intestinal cell suspensions by fluorescence associated cell sorting and subjected to plate-based single-cell RNA sequencing.

(2) Fluorescent populations (GFP+/-; mScarlet-I+/-; DAPI-) from tuft type-specific reporter organoids (ChAT-eGFP;Nrep-mScarlet-I; ChAT-eGFP;Gng13-mScarlet-I; ChAT-eGFP;Folr1-mScarlet-I) cultured in 3 different medium conditions (ENR; ENR+IL4+IL13[crypt]; IL4+IL13+BMP2+BMP4+WNT5a+IL25+NRG1+Acetylcholine[villus]) were isolated by fluorescence associated cell sorting and subjected to plate-based single-cell RNA sequencing.

Raw and processed data, including Seurat objects (RDS files), are provided.

first: Julian

last: Buissant des Amorie


title: Identification of functional non-coding variants associated with orofacial cleft [MPRA]

city: Seattle

first: Robert

middle: A.

last: Cornell

state: WA

address: 1959 NE Pacific Street

department: Oral Health Sciences

institute: University of Washington

summary: Oral facial cleft (OFC) is a multifactorial disorder that can present as a cleft lip with or without cleft palate (CL/P) or a cleft palate only. Genome wide association studies (GWAS) of isolated OFC have identified common single nucleotide polymorphisms (SNPs) at the 1q32/IRF6 locus and many other loci where, like IRF6, the gene presumed to be relevant to OFC risk is expressed in embryonic oral epithelium. To identify the functional subset of SNPs at eight such loci we conducted a massively parallel reporter assay in a cell line derived from fetal oral epithelium, revealing SNPs with allele-specific effects on enhancer activity.

overall_design: A massively parallel reporter library was constructed containing candidate cis-regulatory element (CRE) sequences each 161 bp in length, and with non-risk and risk alleles of 889 SNPs. The CREs were cloned upstream of a hsp68 minimal promoter. The MRA library was electroporated into fetal oral epithelial cells (GMSM-K) with four biological replicates. Four RNA libraries, the input plasmid DNA library and three DNA libraries (post-transfection) were sequenced.

first: Priyanka

last: Kumari

first: Ryan

middle: Z

last: Friedman

first: Sarah

last: Curtis

first: Lira

last: Pi

first: Kitt

last: Paraiso

first: Axel

last: Visel

first: Lindsey

last: Rhea

first: Martine

last: Dunnwald

first: Anjali

last: Patni

first: Daniel

last: Mar

first: Karol

last: Bomsztyk

first: Julie

last: Mathieu

first: Hannele

last: Ruohola-Baker

first: Elizabeth

last: Leslie-Clarkson

first: Michael

last: White

first: Barak

last: Cohen


title: Identification of functional non-coding variants associated with orofacial cleft [RNA-Seq]

first: Robert

last: Cornell

overall_design: RNA-sequencing of a fetal oral epithelial cell line (GMSM-K) to characterize its epithelial features.


title: PRC2-mediated apoptosis evasion is a therapeutic target of MDS/AML harboring inv(3)/t(3;3) and monosomy 7

city: Yokohama

first: Hiroyoshi

last: Kunimoto

address: 3-9 Fukuura, Kanazawa

department: Department of Stem Cell and Immune Regulation

institute: Yokohama City University Graduate School of Medicine

summary: Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) harboring both inv(3)/t(3;3) and monosomy 7 (-7) are highly aggressive myeloid cancers whose molecular pathogenesis and therapeutic vulnerability remain elusive. High throughput drug screens, CUT&Tag/RNA sequence and functional assays using human MDS/AML cells revealed that EZH2 inhibitors efficiently induce apoptosis preferentially in MDS/AML with inv(3)/t(3;3) and -7 through activation of GADD45γ-p38-p53 axis. EVI1 activated in 3q-rearranged MDS/AML was responsible for GADD45γ silencing by direct binding to its consensus sequence within GADD45γ promoter and recruitment of PRC2 complex via interaction with EZH2, which can be therapeutically targeted by EZH2 inhibition. MDS/AML with inv(3)/t(3;3) and -7 showed preferential sensitivity to EZH2 inhibition in both mouse model and patient samples. Thus, MDS/AML cells with inv(3)/t(3;3) and -7 possess apoptosis evasion mechanism through EVI1-PRC2-mediated repression of GADD45γ-p38-p53 axis, which is a potential therapeutic vulnerability in MDS/AML patients with these high-risk cytogenetic lesions.

overall_design: To determine whether EZH2 inhibition in MDS/AML cells harboring both inv(3)/t(3;3) and -7 alters transcriptional output related to GADD45-SAPK axis, we cultured YCU-AML1 cells with either vehicle or valemetostat 300nM for 7 days, isolated CD33+ leukemic blast population and performed RNA-sequence (RNA-seq) analysis.


title: 5-methylcytosine regulated CCNL2 promotes cisplatin resistance by ferroptosis inhibition in ovarian cancer

city: ji nan

first: kai

last: zhang

state: shandong

address: Jinan, Shandong, China, wenhua western road

institute: Qilu Hospital of Shandong University

summary: Ovarian cancer (OC) is the most lethal gynecological tumor, primarily due to resistance to chemotherapy. Cyclin L2 (CCNL2), a novel member of the cyclin family, plays an important role in HIV replication. However, its role in OC chemoresistance remains unknown. Here, we demonstrate that elevated expression of CCNL2 indicates a poor prognosis in ovarian cancer. Furthermore, inhibition of CCNL2 reduces malignancy and enhances chemotherapy sensitivity in OC. Additionally, CCNL2 inhibition promotes cisplatin-induced ferroptosis by increasing intracellular iron ion levels. Mechanistically, CCNL2 is upregulated by YBX1 via a 5-methylcytosine (m5C) manner, leading to increased CCNL2 mRNA stability. Given the lack of protein structure data for CCNL2, we performed virtual screening to identify YBX1 inhibitors, targeting its upstream regulation. The inhibitor YB-B1 effectively suppresses YBX1 and CCNL2 expression, and enhances the cytotoxic effect of cisplatin. Together, we highlight the critical role of CCNL2 in ovarian cancer chemoresistance, elucidate its regulatory mechanism, and propose a new approach to address the challenge.

overall_design: To investigate the function of CCNL2 in ovarian cancer cells, HEY cells were transfected with CCNL2-targeting siRNA for 48 hours

first: Kai

last: Zhang

first: Guiyun

last: Cheng

first: Xihan

last: Liu


title: Epigenomic preconditioning of peripheral monocytes determines their transcriptional response to the tumor microenvironment

city: Saint Petersburg

first: Laszlo

last: Halasz

state: Florida

address: 600 5th Ave S

department: Institute for Fundamental Biomedical Research

institute: Johns Hopkins University

summary: Monocytes are recruited to tumors and undergo transcriptional reprogramming resulting in tumor-promoting functions. Epigenomic features, such as post-translational modification of histones and chromatin accessibility, are key determinants of transcription factor binding and thereby play an important role in determining transcriptional responses to the tissue environment. It remains unknown whether systemic tumor-associated signals could alter the epigenomic landscape of peripheral monocytes before they reach the tumor, thus shaping their subsequent response to the tumor microenvironment. Here, we performed genome-wide analyses of multiple histone modifications (H3K4me1, H3K4me3, H3K27ac) and chromatin accessibility in a mouse model and found that the distal tumor caused extensive remodeling of both H3K4me3+ promoters and H3K4me1+ enhancers in peripheral monocytes. Specifically, this involved the repression of interferon-responsive regulatory elements as well as the stablishment of enhancers harboring binding motifs for transcription factor families downstream of pro-inflammatory signaling, such as C/EBP, AP-1 and STAT. Reprogrammed enhancers in peripheral monocytes could be linked to sustained gene expression changes that persisted after tumor infiltration. In addition, key pro-tumor genes upregulated in tumor-infiltrating monocytes showed epigenetic priming already in the circulation. Overall, these results indicate that the epigenomic landscape of peripheral monocytes is altered in response to a distal tumor, and this can shape the transcriptional response of monocytes to the tumor microenvironment.

overall_design: Transcriptomic and epigenetic profiling of Ly6C-hi monocytes from tumor-bearing and healthy mice using high-throughput sequencing (RNA-seq, ATAC-seq, H3K4me3 CUT&Run, H3K4me1 CUT&Tag, H3K27ac CUT&Tag).

first: Mate

last: Kiss

last: Nagy


title: Cell cycle regulation in archaea

city: York

first: Daniela

last: Barilla`

address: Wentworth Way

department: Biology

country: United Kingdom

institute: University of York

summary: Chromosome segregation is a vital process for all organisms. The mechanisms underpinning chromosomal partitioning in the archaeal domain remain elusive. Our group has identified the first chromosome segregation system in thermophilic archaea. Sulfolobus solfataricus partition system consists of SegA, an orthologue of bacterial Walker-type ParA proteins; SegB, an archaea-specific DNA binding protein and a cis-acting DNA region. ChIP-seq experiments disclosed multiple SegB binding sites scattered over the chromosome and revealed a novel DNA binding motif.

overall_design: Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on exponential-growing Sulfolobus Solfataricus (see the supplementary Materials and Methods for the exact treatment that were applied).

first: Azhar

last: Kabli

first: Irene

last: Ng

first: Nicholas

last: Read

first: Ngat

last: Tran

first: Tung

middle: B

last: Le

last: Barilla'


title: Systematic comparison and base-editing-mediated directed protein evolution and functional screening yield superior auxin-inducible degron technology

status: Public on Jun 24 2025

first: De

last: Xing

overall_design: single-cell RNA seq of iPSCs differentiated as embryoid bodies for 21 days

first: Mazhar

last: Adli


title: Disease-associated loci share features with loci that regulate gene expression in response to environmental perturbations

first: Wenhe

last: Lin

state: Illinois

address: 920 E 58th St

institute: University of Chicago

summary: Many of the genetic loci associated with disease are expected to have context-dependent regulatory effects that are underrepresented in the transcriptomes of healthy, steady-state adult tissues. To understand genetic gene regulation across diverse environmental conditions and cellular contexts, we perturbed a broad array of human cell types with three environmental exposures in vitro. With single-cell RNA-sequencing data from 1.4 million cells, we identified hundreds of dynamic eQTLs that regulate molecular responses to perturbation across multiple cellular contexts. These response eQTLs exhibit distinct signatures of regulatory complexity, evolutionary constraint, and functional enrichment that distinguish them from standard, steady- state eQTLs. Similar to GWAS loci, response eQTLs are enriched in distal enhancers and are linked to genes that experienced strong selective constraint, involve in complex regulatory landscapes, and diverse biological functions. We also observed that response eQTLs are more likely than standard eQTLs to colocalize with loci that affect complex traits. Our results highlight the complexity of genetic regulatory effects and suggest that our ability to interpret disease-associated loci may benefit from the pursuit of studies of gene-by-environment interactions in diverse biological contexts.

overall_design: We obtained single-cell RNA-seq data from 51 YRI iPSC-derived hetergeneous differentiating cultures in control, nicotine, caffeine, and ethanol conditions. There are a total of 191 samples.

first: Yoav

last: Gilad


title: SMCHD1 controls the structure and accessibility of heterochromatin and functions as an organizer of genome compartments (WGBS)

first: Gerd

last: Pfeifer

state: MI

type: Methylation profiling by high throughput sequencing

overall_design: Comparative DNA methylation profiling analysis of WGBS data in SMCHD1 knockout and wildtype LHCN-M2 cells.

first: Zhijun

last: Huang


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

city: AUSTIN

first: Qingqing

last: Guo

state: TX

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 and RXRA was conducted in human trophoblast stem cells (TSCs) and fully differentiated extravillous trophoblasts (EVTs) at day 8 (EVTd8). ChIP-seq for PPARG, RXRA, EP300, H3K27ac, NCOA3, MED1, MED12, and MED15 was performed at EVT day 3 (EVTd3) under control conditions and treatment with 1μM T0070907 from EVT day 1 to day 3.

first: Jonghwan

last: Kim


title: Cxcr4 and Cxcr6 Dually Limits T Cell Entry Into the Polyomavirus-infected Brain

city: Montreal

first: Jo Anne

last: Stratton

address: 3801 Rue University

country: Canada

institute: McGill University

summary: Regulation of the T cell response during viral infection of the central nervous system (CNS) is a vital aspect of host response for pathogen clearance but must be tightly regulated as to prevent excess inflammation and pathology. Chemokines are often cited as the source for control of both the CD8 and CD4 T cell response, modulating their migration and proliferation.  Here mouse polyomavirus (MuPyV) is used as in vivo model for JCPyV, the causative agent of Progressive Multifocal Leukoencephalopathy (PML), to investigate the duel control of CXCR4 and CXCR6 on brain T cells. MERFISH single cell spital transcriptomes for the first time reveals the full landscape of MuPyV brain infection and genetic knockout and small molecule antagonists models divulge the T cell response control mechanism. This work points to the potential of new duel targeting therapeutic strategies for PML patients and contributes to central details about the functions of CXCR4 and CXCR6 that are required for full understanding of T cell responses in the CNS.

overall_design: 2 samples underwent ICV sham (DMEM) injections, 2 samples underwent ICV MuPyV injections.

first: Alexander

last: Kalynn

first: Afanasiev

last: Elia

first: Spencer

last: Sam

first: Stratton

last: Jo Anne

first: Lukacher

last: Aron


title: Impaired AMPK Control of Alveolar Epithelial Cell Metabolism Promotes Pulmonary Fibrosis

city: Philadelphia

first: Michael

last: Beers

state: PA

address: 3450 Hamilton Walk

institute: University of Pennsylvania

summary: Alveolar epithelial type II (AT2) cell dysfunction is implicated in the pathogenesis of familial and sporadic idiopathic pulmonary fibrosis (IPF). We previously demonstrated that expression of an AT2 cell exclusive disease-associated protein isoform (SP-CI73T) in murine and patient-specific induced pluripotent stem cell (iPSC)-derived AT2 cells leads to a block in late macroautophagy and promotes time-dependent mitochondrial impairments; however, how a metabolically dysfunctional AT2 cell results in fibrosis remains elusive. Here, using murine and human iPSC-derived AT2 cell models expressing SP-CI73T, we characterize the molecular mechanisms governing alterations in AT2 cell metabolism that lead to increased glycolysis, decreased mitochondrial biogenesis, disrupted fatty acid oxidation, accumulation of impaired mitochondria, and diminished AT2 cell progenitor capacity manifesting as reduced AT2 self-renewal and accumulation of transitional epithelial cells. We identify deficient AMP-kinase signaling as a key upstream driver of AT2 cell dysfunction and demonstrate that targeting this druggable signaling hub can rescue the aberrant AT2 cell metabolic phenotype and mitigate lung fibrosis in vivo.

overall_design: This data set is composed of samples from four different experiments.  The scRNA samples are derived from SftpcI73T mice 28 days post tamoxifen induction and dosed via intraperitoneal injections with either Metformin or vehicle beginning at day 12 post tamoxifen induction.  Single cell suspension from whole lungs were CD45 and CD31 depeleted prior to library generation.  There is also an RNA-seq data set derived from murine AT2 cells isolated at 3 and 14 days post tamoxifen from SftpcI73T mice using a CD45 depeletion and adhereance binding protocol that enriches for 95% AT2 cells (libraries names AT2-#).  Additionally we have a third data set derived from flow sorted murine AT2 cells isolated at 14 days post tamoxifen from SftpcI73T mice using MHCII and CD51 to enrich for transitional AT2 cells.  Finally we have included an RNA-seq data set from Human iPSC derived cells differentiated into iAT2s and challenged for 24 hours with AICAR.

first: Luis

last: Rodriguez

first: Konstantinos-Dionysios

last: Alysandratos

first: Jeremy

last: Katzen

first: Aditi

last: Murthy

first: Willy Roque

last: Barboza

first: Yaniv

last: Tomer

first: Sarah

last: Bui

first: Rebeca

last: Acin-Perez

first: Anton

last: Petcherski

first: Kasey

last: Minakin

first: Paige

last: Carson

first: Swati

last: Iyer

first: Katrina

last: Chavez

first: Charlotte

middle: H

last: Cooper

first: Apporva

last: Babu

first: Aaron

last: Weiner

first: Andrew

last: Vaughan

first: Zoltan

last: Arany

first: Orian

middle: S

last: Shirihai

first: Darrell

middle: N

last: Kotton


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), extravillous trophoblasts (EVTs) at differentiation day 3 (EVTd3), and fully differentiated EVTs at day 8 (EVTd8) under various conditions.

first: Jonghwan

last: Kim


title: Systematic comparison and base-editing-mediated directed protein evolution and functional screening yield superior auxin-inducible degron technology [1]

first: De

last: Xing

overall_design: RNA-seq profiling degron-tagged RBBP4_mAID iPSCs expressing AID 2.0  or AID 2.1 relative to the parental RBBP4_WT iPSCs

first: Mazhar

last: Adli


title: Novel single-cell preservation and RNA sequencing technology unlocks field studies for Plasmodium natural infections

city: Antwerp

first: Pieter

last: Monsieurs

address: Nationalestraat 155

country: Belgium

institute: Institute of Tropical Medicine

summary: Single-cell RNA sequencing (scRNA-seq) is a powerful technology that can be used to unravel cellular heterogeneity when applied to unicellular eukaryotes, including Plasmodium parasites. scRNA-seq is particularly useful to study complex infections like malaria, with mixed life stages or clones, yet until now it has been primarily limited to in vitro and animal malaria models due to challenges associated with working with malaria natural infections in endemic settings. We validated a novel single-cell RNA sequencing technology for use with Plasmodium parasites by combining optimized sample preparation methods with RNA preservation integrated in a sample capture device, which allows for the separation of the sample collection and library preparation and sequencing. We recovered 22,345 P. knowlesi single-cell transcriptomes from 6 samples, the most extensive P. knowlesi dataset to date. Regardless of preparation methods used, all samples resulted in reproducible circular UMAP projections with consistent cluster localization and high gene expression correlation, which were confirmed by biomarker expression and annotating life stages using the Malaria Cell Atlas P. knowlesi reference dataset. Some variation in life stage recovery was observed, especially for the ring stage. This could be attributed to the inherent differences between sample preparation methods, or as a result of gene and transcript filtering thresholds which should be further investigated and optimized based on what is known about parasite biology. In conclusion, by combining parasite enrichment with a novel scRNA-seq and preservation technology, scRNA-seq can be expanded to field settings, even when limited resources are available.

overall_design: To validate the application of HIVE technology for the analysis of Plasmodium natural infections, we tested different sample processing and loading methods, and assessed the single-cell RNA sequencing results. To create a mock natural infection sample with mixed parasite life stages, we diluted in vitro-cultured P. knowlesi A1-H.1 parasites to 0.8% parasitemia in whole blood. Tested methods for sample processing include two combinations of leukodepletion and parasite enrichment techniques tailored to optimally isolate all life stages present in blood circulation and eliminate uninfected human cells from natural infections, which would otherwise dominate sequencing reads. A schematic representation of the protocols of the 6 samples is provided in Figure 1. For the PNyco method, which only requires a tube centrifuge, we used a Plasmodipur filter to remove human leukocytes, followed by a Nycodenz density gradient to enrich for parasite life stages. Here we found an enrichment to 22% parasitemia after the Nycodenz gradient by microscopy. In the second method, MACSPS, we used a MACS column to enrich for trophozoite and schizont life stages in the magnetic column based on the paramagnetic properties of hemozoin, similar to the MCA method (2). The first elution contains leukocytes, uninfected RBCs, and ring stages which have passed through without binding to the magnetic column. Subsequently, the first elution underwent further processing using a Plasmodipur filter to remove leukocytes, followed by a saponin lysis to remove uninfected RBCs, resulting in the isolation of the ring stage. In the second elution, the trophozoite and schizont stages bound to the magnetic column were released and recovered. The ring stages were then combined with trophozoites and schizonts recovered to obtain an enriched sample containing all life stages. For the HIVE loading, we evaluated two different methods for loading enriched parasite into the HIVEs: one utilizing a plate centrifuge to facilitate the sinking of parasites into the pico-wells, and the other allowing parasites to sink by gravity, eliminating the need for a plate centrifuge if unavailable (C and G, respectively, Figure 1). In addition, we also tested cultured P. knowlesi samples without mixing with whole blood. Parasite enrichment was conducted using two different density gradient centrifugation methods. Half of the cultured parasites were purified using a Percoll gradient (PkCultureP), typically employed to enrich samples for schizonts stages (40), while the other half underwent purification using a Nycodenz gradient (PkCultureN), commonly used for P. knowlesi (33), which recovered a broader range of parasite life stages compared to Percoll. Both methods led to a similar level of enrichment, around 50%, and samples were loaded using centrifugation.

first: Erin

last: Sauve

last: Guetens

first: Roberto

last: Rudge de Moraes Barros

first: Anna

last: Rosanas-Urgell


title: Multi-omics Dissection of MAPK-driven Senescence Unveils Therapeutic Vulnerabilities in KIAA1549::BRAF-fusion Pediatric Low-Grade Glioma Models

city: Jena

first: Romain

last: Sigaud

address: Am Klinikum 1

department: Pediatrics and Adolescent Medicine

institute: UKJ

summary: Pilocytic astrocytomas (PA), the most common pediatric low-grade gliomas (pLGGs), are characterized by genetic MAPK pathway alterations leading to constitutive activation and oncogene-induced senescence (OIS) accompanied with the senescence-associated secretory phenotype (SASP). This study investigates the molecular mechanisms of signaling pathways regulating OIS and SASP in pLGGs using a multi-omics approach. We utilized senescent DKFZ-BT66 cells derived from a primary KIAA1549::BRAF-fusion positive PA to generate RNA-sequencing and phospho-/proteomic datasets before and after treatment with the MEK inhibitor trametinib. Multi-omics factor analysis (MEFISTO) and single sample gene set enrichment analysis (ssGSEA) were employed to identify key OIS effectors and differentially regulated pathways upon MAPK inhibition. Trametinib treatment inhibited MAPK activity, OIS and SASP signatures across all omics levels, functionally underscored by reduced sensitivity towards senolytic drugs. We constructed a pathway network using a prior knowledge approach, mapping n = 106 upregulated and n = 84 downregulated direct downstream effectors of MAPK leading to OIS/SASP. These effectors are associated with better progression-free survival in pLGG patients, independent of tumor site, level of resection, and genetic aberration. Several compounds targeting signaling nodes (SOD-1, IRS1, CDK1/2, CK2) involved in OIS and under MAPK control were identified, of which n = 4 were validated in an additional primary KIAA1549::BRAF fusion pLGG model as potential new therapeutic vulnerabilities for the treatment of pLGG. Our unbiased multi-omics signaling pathway analysis identifies a specific and comprehensive network of MAPK-OIS-SASP interdependencies in pLGGs and suggests new therapeutic strategies for these tumors.

overall_design: DKFZ_BT66 cells (senescent mode) where treated in vitro with 100nM trametinib for 15min, 1h, 6h and 24h. Control samples (DMSO) were also generated. Samples were generated in 3 independant biological replicates.

first: Anja

last: Stefanski

first: Florian

last: Selt

first: Daniela

last: Kocher

first: Diren

last: Usta

first: Daniel

last: Picard

first: Isabel

last: Büdenbender

first: Marc

last: Remke

first: Stefan

middle: M

last: Pfister

first: David

last: Jones

first: Tilman

last: Brummer

first: Olaf

last: Witt

first: Till

last: Milde