title: Plant hormone and peptide signaling converge in the genetic network regulating cambium activation in Arabidopsis roots [Agilent microarray]

city: Helsinki

first: Tiina

last: Blomster

address: Viikinkaari 1 (P.O. Box 65)

country: Finland

institute: University of Helsinki

summary: Plant secondary growth is driven by two concentric meristems, the inner vascular cambium and outer cork cambium. The periclinal cell divisions of both meristems, providing thickness and protection to plant organs, are activated with a delay after the primary development. Cytokinins and a set of downstream transcription factors are key players in promoting transition from primary to secondary development, however it is unknown whether other factors play a role in this transition. Here, using time-course transcriptome analysis of cytokinin-treated, cytokinin deficient isopentenyltransferase1,3,5,7 (ipt1,3,5,7) mutant we show that during cambium activation cytokinins positively regulate auxin and TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF) peptide signaling in Arabidopsis (Arabidopsis thaliana) root. Correspondingly, mutants defective in TDIF peptide signaling displayed reduced cytokinin-induced secondary growth and auxin signaling was found to be required for proper cytokinin response. Additionally, auxin and cytokinin signaling transiently overlapped in activating procambial cells and acted additively in promoting secondary development. Network analysis revealed that transcription factors belonging to the DNA-BINDING WITH ONE FINGER (DOF) and ETHYLENE RESPONSE FACTOR (ERF) gene families are regulated by cytokinin during cambium activation and mutant analysis demonstrated delayed cambium activation and xylem formation phenotypes. Overall, we find that cytokinin, auxin and TDIF form a tightly intertwined network of positive regulators for activation of secondary growth in the Arabidopsis root indicating extensive redundancy in this process.

overall_design:
Three-dye gene expression study with three biological replicates. Time course study with four time points, mutant vs. wild type comparison, young vs. old root comparison.
Please note that each raw data file contains raw data for three samples as indicated in the corresponding sample description field.

first: Riccardo

last: Siligato

first: Riikka

last: Mäkilä

first: Wiktoria

last: Fatz

first: Munan

last: Lyu

first: Maria Angels

last: de Luis Balaguer

first: Lingling

last: Ye

first: Iris

last: Gildea

first: Omid

last: Safronov

first: Panu

last: Somervuo

first: Kamil

last: Růžička

first: Jarkko

last: Salojärvi

first: Rossangela

last: Sozzani

first: Melis

last: Kucukoglu Topcu

first: Ari Pekka

last: Mähönen


title: Plant hormone and peptide signaling converge in the genetic network regulating cambium activation in Arabidopsis roots [axr3-1_RNA-Seq]

status: Public on Mar 13 2026

type: Expression profiling by high throughput sequencing

overall_design: Auxin signaling is inhibited by the expression of auxin resistant 3-1 (axr3-1). We used the estradiol-inducible pANT:XVE>>axr3-1-YFP line to profile the transcriptomic interaction of auxin and cytokinin signaling in vascular cambium. Samples from roots with already active cambium treated with estradiol (5µM EST), cytokinin (1µM BAP) or both (5µM EST+1µM BAP) were harvested with the DMSO-treated controls at 4h and 24h time points for RNA-Seq. Experiments for both time points were performed in triplicate.


title: Depolymerizing F-actin accelerates the exit from pluripotency to enhance stem cell-derived islet differentiation [Multiomics]

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

country: USA

institute: Washington University in St. Louis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we performed single-cell RNA sequencing and single-nuclei multiomic sequencing (RNA + ATAC) at various stages during the differentiation of human pluripotent stem cells to stem cell-derived islets after treatment with the actin depolymerizing compound latrunculin A (latA) during the first 24 hours of differentiation. We show that depolymerizing F-actin with latA during the first 24 hours of definitive endoderm formation (stage 1) facilitates rapid exit from pluripotency and alters Activin/Nodal, BMP, JNK-JUN, and WNT pathway signaling dynamics. These signaling changes influence downstream patterning of the gut tube, leading to improved pancreatic progenitor identity and decreased expression of markers associated with other endodermal lineages. Continued differentiation generates islets containing a higher percentage of β cells that exhibit improved maturation, insulin secretion, and ability to reverse hyperglycemia. Furthermore, this latA treatment reduces enterochromaffin cells in the final cell population and corrects differentiations from hPSC lines that otherwise fail to consistently produce pancreatic islets, highlighting the importance of cytoskeletal signaling at the onset of directed differentiation.

overall_design: Human pluripotent stem cells were differentiated to stem cell-derived islets (SC-islets). During the first 24 hours of differentiation in stage 1, 0.175uM latA was added to half the samples. Multiomic (RNA + ATAC) sequencing was performed at the definitive endoderm stage (stage 2, day 1) and on the final differentiated SC-islets (stage 6, day 15), comparing latA-treated cells with untreated cells (control).

first: Nathaniel

last: Hogrebe

first: Mason

last: Schmidt

first: Punn

last: Augsornworawat


title: Human scFv based, ALPPL2-specific CAR expressing T cells induce potent antitumor activity in an IL15-dependent manner

city: Seattle

first: Andras

last: Heczey

state: WA

address: 4800 Sand Point Way NE

institute: Seattle Children's Hospital

summary: Chimeric antigen receptor (CAR) T cells have robust antitumor activity against hematologic malignancies and have the potential to benefit patients with solid tumors. Immune recognition of murine proteins expressed in adoptively transferred T cells and lack of homeostatic in the tumor microenvironment can limit expansion and persistence of CAR T cells. CARs generated only from human sequences reduce the risk of immune mediated rejection and Interleukin-15, which promotes T cell survival and fitness can improve the expansion and persistence of T cells. In this study, we report a CAR T construct (ABBz) assembled from only human sequences including an scFv specific to ALPPL2 selected through an unbiased, high-throughput screen of human antibody-based, phage-displayed scFv library based on binding specificity, stringency, and low dissociation constant. We demonstrate specificity to the antigen, effective cytolytic function, and cytokine production induction in ABBz T cells. We detail key transcriptomic, phenotypic and functional changes specific to IL15 coexpression in ABBz T cells. Lastly, we demonstrate that ABBz CAR T cells have robust anti-tumor activity which is further enhanced through IL15 co-expression resulting in increased cytolytic capacity and superior expansion secondary to reduced apoptosis of CAR T cells.

overall_design: RNA-Seq profiles paired and in triplicate of ABBz and 15.ABBz CAR at baseline and 2 rounds of co-culture with Capan-1 target cells

first: David

last: Cunningham

first: Junquan

last: Liu

last: de la Cerda

first: Nisha

last: Gatwai

first: Amy

last: Courtney

first: Linji

last: Guo

first: Purva

last: Rathi

first: Yao

last: Qizhi Cathy

first: Ningyan

last: Zhang

first: Zhiqiang

last: An


title: Cross-Species Transcriptomic Integration Reveals a Conserved, MIRO1-Mediated Macrophage-to-T Cell Signaling Axis Driving Immunosuppression in Glioma [snRNA-Seq]

status: Public on Mar 12 2026

city: Palo Alto

first: Xinnan

last: Wang

state: CA

address: 1201 Welch Road, MSLS Building, Rm P151

department: Neurosurgery

institute: Stanford University

summary: We generated single-nucleus RNA sequencing (snRNA-seq) data from murine gliomas treated in vivo with a MIRO1-binding compound or vehicle control. Tumors were dissociated and processed for nucleus isolation followed by high-throughput transcriptomic profiling to characterize cell-type-specific gene expression programs within the tumor microenvironment (TME). The dataset captures malignant cells and diverse stromal and immune populations, including macrophages, microglia, and T cells, enabling analysis of treatment-associated transcriptional changes at single-cell resolution. These data provide a resource for investigating mitochondrial-associated transcriptional regulation and immune microenvironment remodeling in murine glioma.

overall_design: Single-nucleus RNA-seq profiling of nuclei isolated from orthotopic GL261-Luc mouse glioma tissues following intracranial treatment with 10 μM MIRO1-binding compound (MR3) or vehicle control (DMSO) on days 11 and 18 post-implantation, with tissues collected on day 22 for transcriptomic analysis.

first: Menghan

last: Li

first: Brandon

last: Bergsneider

first: Zehui

last: Du


title: Total RNA Sequencing analysis of total RNA and RNA isolated from mitochondrial pellets in CSDE1-knockdown sensory neurons

city: Daegu

first: Hoyong

last: Jin

address: E4-222, 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

country: South Korea

institute: DGIST

summary: CSDE1 is an RNA-binding protein that associates with a subset of mitochondria-related transcripts. We previously observed that RNAs encoding mitochondrial proteins localized to the mitochondrial inner membrane (MIM), intermembrane space (IMS), matrix, and outer membrane (MOM) are enriched within the CSDE1-bound RNA pool. To determine whether CSDE1 regulates the abundance and mitochondrial localization of mitochondria-associated RNAs in sensory neurons, we performed RNA sequencing of both total RNA and RNA extracted from isolated mitochondria isolated from CSDE1-knockdown sensory neurons. CSDE1 knockdown was achieved using lentiviral transduction, and sequencing results were compared with control neurons infected with empty vector (pLKO).

overall_design: Dorsal root ganglia (DRG) were dissected from embryonic day 13.5 (E13.5) mouse embryos. To enrich for neuronal populations, dissociated DRG cells were cultured in medium containing 5-fluoro-2′-deoxyuridine (FDU) to eliminate non-neuronal cells. Sensory neurons were transduced with lentivirus expressing shRNA targeting CSDE1 or control empty vector (pLKO). Total RNA and RNA extracted from isolated mitochondria were isolated from cultured neurons. RNA sequencing was performed to compare transcriptomic changes in total RNA and RNA extracted from isolated mitochondria between control and CSDE1-knockdown conditions.

first: Ho-Yong

first: Yong-Cheol

last: Cho


title: Plant hormone and peptide signaling converge in the genetic network regulating cambium activation in Arabidopsis roots [ipt1,3,5,7_RNA-Seq]

first: Tiina

last: Blomster

overall_design: To study cytokinin-dependent gene expression during secondary growth activation, isopentenyltransferase1,3,5,7 (ipt1,3,5,7) mutants were treated with cytokinin (1µM BAP) for 4h and compared to mock-treated (1h DMSO) ipt1,3,5,7 mutant.

first: Riccardo

last: Siligato

first: Riikka

last: Mäkilä

first: Wiktoria

last: Fatz

first: Munan

last: Lyu

first: Maria Angels

last: de Luis Balaguer

first: Lingling

last: Ye

first: Iris

last: Gildea

first: Omid

last: Safronov

first: Panu

last: Somervuo

first: Kamil

last: Růžička

first: Jarkko

last: Salojärvi

first: Rossangela

last: Sozzani

first: Melis

last: Kucukoglu Topcu

first: Ari Pekka

last: Mähönen


title: Conserved enhancer association of piRNAs and the implication in germ cell fate surveillance

city: Taipei City

first: Shau-Ping

last: Lin

state: select a state

address: 4F, No. 81, Chang-Xing St.,

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

type: Non-coding RNA profiling by high throughput sequencing

summary: We collected fetal testes of gestational weeks 12-22 abortuses from Taiwan to investigate human piRNA profiles correlating to the time window of epigenetic landscape establishment, along with those from the USA. We identified numerous human piRNAs in second-trimester fetal testes that corresponded to small nucleolar RNAs. Additionally, a substantial proportion of human fetal testicular piRNAs mapped to super-enhancers and typical enhancers, a phenomenon conversed across mouse and chicken species. Notably, many of the pre-pachytene germline piRNAs mapped to enhancers active in various adult somatic lineages, implying they may regulate enhancer activities and safeguard germ cell identity by reducing aberrant expression of somatic genes.

overall_design: Small RNA-seq profiling was conducted on human fetal testes collected from abortuses at gestational weeks (GW) 12 to 22 due to genetic or other non-gonadal-related phenotypic abnormalities. Sample collection was performed at National Taiwan University Hospital under approved IRB protocols.

first: Yen-Tzu

last: Tseng

first: Pin-Jui

last: Kung

first: Hsien-Hen

first: Luca CW

last: Cheng

first: Yi-Tzang

last: Tsai

first: Kai-Wei

last: Chang

first: Hung-Chih

last: Kuo

first: Hong-Nerng

last: Ho

first: Hsin-Fu

last: Chen


title: Trans-Histone Crosstalk-Mediated Establishment of Mutually Exclusive H3K79 Methylation Zones [ChIP-Seq]

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

institute: Yonsei University

summary: Histone H3 lysine 79 (H3K79) methylation plays critical roles in various cellular processes, including development and DNA repair, potentially through modulation of chromatin structure and gene expression. Despite its importance, the genome-wide distribution patterns, mechanisms of establishment, and functional distinctions among its mono-, di-, and tri-methylated forms (H3K79me1, me2, and me3) remain largely unclear. Here, we generated genome-wide maps of H3K79me1, H3K79me2, and H3K79me3 using ChIP-seq and found that each methylation state is predominantly associated with a unique subset of genes, which we term state-specific H3K79 methylation zones. These zones are mutually exclusive and are stably maintained even during global transcriptional reprogramming. We further demonstrate that H2B ubiquitination mediated by the Rad6-Bre1 complex is essential for the integrity of these methylation zones. Specifically, deletion of RAD6 leads to the complete loss of the H3K79me3 zone and its conversion into an H3K79me1-enriched region. Interestingly, the H3K79me1 zone is also significantly diminished upon RAD6 deletion, indicating that H2B ubiquitination supports both the maintenance and establishment of specific methylation zones. Similar disruption of the H3K79me1 landscape is observed upon loss of H4K16 acetylation. Functionally, H3K79me1 and H3K79me3 appear to have opposing roles in transcriptional regulation as loss of H3K79 methyltransferase Dot1 results in transcriptional activation of genes within the H3K79me1 zone and repression of genes within the H3K79me3 zone. Together, our findings reveal that distinct H3K79 methylation states define specific and functionally divergent chromatin domains, whose establishment and maintenance depend on trans-histone crosstalk and contribute to opposing transcriptional outputs.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) was performed in yeast to profile genome-wide distributions of H3K79me3, H3K79me2, and H3K79me1. Changes in H3K79me2, H3K79me1, and Dot1 occupancy upon RAD6 deletion were analyzed. Additionally, the dynamics of H3K79 methylation before and after nutrient starvation were examined.

first: Na Hyun

last: Park

first: Hwa-Ryeon

last: Kim

first: Jae-Seok

first: TaeSoo


title: SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [ChIP-Seq, 2]

city: Oxford

first: Mafalda

last: Almeida

address: South Parks Rd

department: Biochemistry

country: United Kingdom

institute: University of Oxford

summary: The non-coding RNA Xist mediates X chromosome inactivation (XCI) in mammals, functioning in cis to direct heterochromatin formation over a single X chromosome in cells of early female embryos. Prior studies have determined that Xist transcription and turnover are modulated to maintain the correct level of Xist RNA to inactivate a single X chromosome. The underlying molecular mechanisms are poorly understood. In this study we demonstrate that RNA-dependent recruitment of the H3K9me3 methyltransferase SETDB1 and the HUSH complex across the transcribed Xist locus functions to suppress Xist transcription during establishment of XCI. Thus, degron-mediated acute depletion of SETDB1 or core HUSH subunits abrogates allelic H3K9me3 deposition, increasing Xist transcription, accumulation of Xist RNA, and the rate of X chromosome gene silencing. Our findings support a model in which the SETDB1/HUSH pathway coordinates Xist transcription rates to maintain optimal Xist RNA levels, ensuring the silencing of a single X chromosome.

overall_design: Calibrated native ChIP for H3K9me3 in wild-type iXist-ChrXCast, iXist-ChrX129 and TsixStop mESC and NPC differentiation timnepoints and F121-F1 mESC. Calibrated native ChIP for H3K9me3 in FKBP12F36V-SETDB1 iXist-ChrXCast mESC (clones A12A10, P2F7) and in differentiation timepoints in the presence or absence of SETDB1. Calibrated native ChIP for H3K9me3 in FKBP12F36V-KAP1 (clones A4A11,A4C11,A4F3), FKBP12F36V-MPP8 (clones E10 and H1) and FKBP12F36V-TASOR (clones H4 and F8) iXist-ChrXCast mESC in the absence or presence of KAP1, MPP8 and TASOR respectively.

first: Guifeng

last: Wei

first: Adam

last: Cawte

first: Tatyana

middle: B

last: Nesterova

first: Neil

last: Brockdorff


title: GSK3α functions as a stemness checkpoint across multiple stem cell states

status: Public on Mar 16 2026

city: Omaha

first: Litao

last: Tao

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

summary: Mouse embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) represent the naïve and primed pluripotent states, respectively, each requiring distinct culture conditions. In this study, we show that BRD0705, a selective GSK3α inhibitor, significantly enhances the self-renewal of both ESCs and EpiSCs. When combined with IWR1, BRD0705 sustains long-term maintenance of ESCs in a naïve state and EpiSCs in a primed state, even preserving their unique identities under long-term co-culture. Single-cell RNA sequencing and histone mark profiling confirm that this regimen maintains distinct gene expression and epigenetic signatures corresponding to each pluripotent state. Importantly, unlike pan-GSK3 inhibitors CHIR-99021 (CHIR), BRD0705 acts independently of β-catenin signaling, unveiling a novel mechanism for supporting pluripotency. Finally, BRD0705/IWR1 also supports the maintenance of the formative pluripotent stem cells and neural stem cells. Collectively, we propose that GSK3α inhibition may preserve diverse stem cell states by insulating stem cells from differentiation cues and promoting their intrinsic self-renewal capacity. We believe our findings lay the foundation for universal stem cell culture methods with significant regenerative medicine applications.

overall_design: Change the β-catenin-/-ESCs culture medium to N2B27 overnight before RNA extraction, then treat with Ctr, BRD0705, or CHIR for 30 minutes respectively. Total RNA was extracted using the GeneJET RNA purification kit. For RNA-seq library preparation, 1 g total RNA was used to prepare the RNA-seq library with the Truseq RNA Library Prep Kit V2 with RiboZero (Illumina).

first: Duo

last: Wang

first: Xiukun

first: Gunag

last: Hu

first: Qi-Long

last: Ying


title: Trans-Histone Crosstalk-Mediated Establishment of Mutually Exclusive H3K79 Methylation Zones [RNA-Seq]

overall_design: Analysis of transcriptional responses in wild type and dot1Δ strains during nutrient starvation.


title: SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [RNA-Seq]

overall_design: Calibrated single crosslinked ChIP for RNAPol II, RNA PolII Ser5P, RNA PolII Ser2P in FKBP12F36V-SETDB1 iXist-ChrXCast mouse embryonic stem cells (clones A12A10, P2F7 and G6D2) expressing Xist under a doxycycline inducible promoter in the presence and absence of SETDB1. Double crosslinked ChIP for MPP8 and KAP1 in FKBP12F36V-SETDB1 iXist-ChrXCast mouse embryonic stem cells (clones A12A10 and P2F7) expressing Xist under a doxycycline inducible promoter in the presence and absence of SETDB1.


title: SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation

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

overall_design: Refer to individual Series


title: SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [4sU-seq]

overall_design: 4sU-seq of FKBP12F36V-SETDB1 iXist-ChrXCast mouse embryonic stem cells (clones A12A10, P2F7 and G6D2) expressing Xist under a doxycycline inducible promoter in the presence and absence of SETDB1.


title: ADNP regulates chromatin architecture and lineage fidelity during neural differentiation

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

summary: Activity-dependent neuroprotective protein (ADNP) is frequently mutated in autism spectrum disorder and causal in its namesake neurodevelopmental syndrome. In mouse embryonic stem cells (mESCs), ADNP forms the ChAHP complex to function in gene regulation as well as genome organization, where it competes with binding of the architectural protein CTCF. However, it is unclear whether these functions persist in differentiated cells. To shed light on this question, we have established an ADNP-degron cell line to examine CTCF binding, gene expression and chromatin organization upon ADNP loss in neural progenitor cells (NPCs).

overall_design: ChIP, RNA-seq, and Hi-C was performed on ADNP-degron E14 mouse embryonic stem cells and neural progenitor cells. Cells with or without treatment with asunaprevir and dTAG-13 were collected for genomics experiments.

first: Nathaniel

last: Rell

first: John

last: Doherty

first: Kuo-Chen

last: Fang

first: Kavitha

last: Sarma


title: Aged Differentiated Cells Reverse into Native Stemness-Like State by Niche Cytokines to Sustain Lifelong Homeostasis and Tissue Repair

city: Haifa

first: Shalini

last: Dimri-Wagh

state: Haifa

address: 1 Efron Street

department: Department of  Genetics and Developmental Biology

country: Israel

institute: Technion Israel Institute of Technology

summary: To study the molecular mechanisms driving dedifferentiation and stem cell plasticity during tissue regeneration, we performed single-cell RNA sequencing at multiple time points-Day 2, Day 5, Day 10, and Day 40,following complete ablation of the limbal stem cell (LSC) population. The primary goal was to characterize the transcriptional reprogramming processes that enable differentiated epithelial cells to reacquire stem cell-like properties and restore the LSC pool. Specifically, we aimed to determine (1) the extent to which dedifferentiated cells recapture native stem cell phenotypes, (2) whether this plasticity is maintained in late differentiated and aged cells, and (3) the niche signals that regulate this process. Our data reveal that differentiated cells undergo extensive transcriptional remodeling, becoming virtually indistinguishable from native LSCs, and functionally sustain long-term tissue homeostasis and repair after repeated injury. Remarkably, this plasticity is retained even in late differentiated and aged cells. Mechanistically, we identify macrophage-derived cytokines as key niche factors promoting dedifferentiation and stemness reacquisition. This dataset provides a comprehensive transcriptional resource of corneal regeneration, offering insights into stem cell plasticity and immune-niche interactions with implications for regenerative medicine and limbal stem cell deficiency therapies.

overall_design: To investigate dedifferentiation during limbal regeneration, the limbal epithelium-including the marginal conjunctiva and peripheral cornea was surgically removed using a rotating ophthalmic Alger brush. At defined time points post-injury (Days 2, 5, 10, and 40), the regenerating limbal epithelial tissue along with the underlying stromal tissue (~0.5 mm) was harvested. Additionally, limbal regions from uninjured eyes were collected as controls. Tissues were enzymatically dissociated using Collagenase A and Trypsin into single-cell suspensions and subjected to single-cell RNA sequencing (scRNA-seq) to profile dynamic transcriptional changes occurring during the dedifferentiation process.

last: Dimri Wagh

first: Swarnabh

last: Bhattacharya

first: Gharam

last: Yassin

first: Ofir

last: Shorer

first: Aya

last: Amitai Lange

first: Anna

last: Altshuler

first: Shira

last: Hadad Porat

first: Keren

last: Yizhak

first: Yuval

last: Shaked

first: Michael

last: Mimouni

first: Beatrice

last: Tiosano

first: Ramez

last: Barbara

first: Ruby

last: Shalom Feuerstein


title: 5’tRNA-derived fragments modulate 𝛽-cell homeostasis and islet macrophage activation in type 2 diabetes [RNAseq_BMDM]

city: Lausanne

first: Cristina

last: Cosentino

address: Rue du Bugnon 9

department: Department of fundamental neurosciences

country: Switzerland

institute: Université de Lausanne

summary: During obesity and type 2 diabetes, pancreatic β-cells face chronic environmental stress, while islet-resident macrophages (iMACs) undergo metabolic reprogramming that exacerbates β-cell dysfunction. Stress-induced cleavage of transfer RNAs (tRNAs) generates tRNA-derived fragments (tRFs), whose role in this context is not fully understood. We identify elevated levels of 5’tRFGlu(CTC) and 5’tRFGly(GCC) in β-cells and iMACs from db/db mice and in islets from type 2 diabetic (T2D) patients. Notably, 5’tRFGlu(CTC) is also induced under prediabetic conditions and inversely correlates with insulin secretion. Lipotoxic stress triggers their production via Angiogenin-mediated cleavage. Blocking 5’tRFGlu(CTC) in islets protects against β-cell apoptosis and restores insulin secretion under palmitate stress. Using a β-cell/macrophage co-culture system, we show that β-cell contact shapes a unique macrophage phenotype (iMAC-like) that shifts upon palmitate exposure—recapitulating in vivo observations. Inhibiting 5’tRFGlu(CTC) in iMAC-like cells prevents this activation switch, reduces β-cell stress, and improves insulin secretion. Mechanistically, 5’tRFGlu(CTC) interacts with RNA-binding proteins to regulate transcriptional and post-transcriptional pathways linked to immune activation, ECM remodeling, neurogenesis, and oxidative stress. Our study identifies 5’tRFs as key mediators of islet microenvironment remodeling in diabetes, offering new insights into intercellular stress signaling in metabolic disease.

overall_design: Bone marrow derived macrophages were transfected with an antisense of control (ctr) or with antisense targeting 5'tRFGlu(CTC) (Glu) and then polarized into M2 macrophages. Total RNA was purified with miRNeasy micro kit (Qiagen). Illumina Strand mRNA libraries were prepared and sequenced on NovaSeq 6000 sequencer.

first: Romano

last: Regazzi


title: 5’tRNA-derived fragments modulate 𝛽-cell homeostasis and islet macrophage activation in type 2 diabetes - transcriptomic

overall_design: Mouse pancreatic islets were isolated and dispersed. Mouse islet cells were transfected with antisense oligonucleotides (Ctr, 𝛂Glu) and treated with BSA or palmitate (PA). Total RNA was purified with miRNeasy micro kit (Qiagen). Illumina Strand mRNA libraries were prepared and sequenced on Aviti sequencer.


title: 5’tRNA-derived fragments modulate 𝛽-cell homeostasis and islet macrophage activation in type 2 diabetes [iMAC]

overall_design: tRF profiling of Cd45+, F4/80+, Cd11b+ and Cd11c+ islet macrophages from 8 week-old db/db mice (genetic background BKS.Cg-Dock7m+/+LeprdbJ) and wild type controls (genetic background BKS.Cg-Dock7m+/+) isolated by FACS. Small RNA sequencing data were annotated against the dataset from from http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Mmusc39/Mmusc39-summary.html. High confidence tRNA sequences and mature tRNA sequences were retained, and mtRNA seqences from http://mttrna.bioinf.uni-leipzig.de/mtDataOutput/Search were added. Accesses done in February 2022.


title: 5’tRNA-derived fragments modulate 𝛽-cell homeostasis and islet macrophage activation in type 2 diabetes [beta]

overall_design: tRF profiling of pancreatic beta cells from 8 week-old db/db mice (genetic background BKS.Cg-Dock7m+/+LeprdbJ) and wild type controls (genetic background BKS.Cg-Dock7m+/+) isolated by FACS. Small RNA sequencing data were annotated against the dataset from from http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Mmusc39/Mmusc39-summary.html. High confidence tRNA sequences and mature tRNA sequences were retained, and mtRNA seqences from http://mttrna.bioinf.uni-leipzig.de/mtDataOutput/Search were added. Accesses done in February 2022.


title: Phosphate starvation induces root cell-type specific transcriptional responses and alternative splicing

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas

summary: Optimal plant nutrition is crucial for plant growth, development, and production. Phosphorus (P) is a vital macronutrient for plants, but its availability in soil is often limited. Despite high levels of P in natural soils, much of it is inaccessible to plants. Plants acquire phosphorus as inorganic phosphate (Pi) from the rhizosphere, and Pi starvation triggers adaptive responses to enhance Pi acquisition. These responses include changes in root development and gene transcriptional reprogramming among others. Although several root transcriptomic analyses have identified key genes involved in Pi starvation responses, almost all of them have been conducted with illuminated roots, a condition that masks molecular responses to Pi starvation. In this work, a comparative transcriptomic analysis of specific root cell types identified over 7,000 genes with differential expression in response to Pi deficiency. Additionally, this study highlights the role of alternative splicing in regulating Pi starvation responses and demonstrates that both transcriptional and posttranscriptional responses are cell type specific. Overall, this work provides new insights into the cell-specific responses to Pi starvation, enhancing our understanding of plant adaptation to phosphorus deficiency.

overall_design: To identify novel genes involved in phosphate starvation responses, we carried out a transcriptomic analyses using RNA from  specific cell types of seedlings grown in the D-Root device. RNAseq analyses of polyA mRNAs isolated from roots of GFP/YFP markers  seedlings grown at 22ºC in half strength MS medium with high or low phsophate for 6 days. Afterwards, different cell types were shorted by fluorescence-activated cell sorting (FACS)

first: J

middle: C

first: M

last: P. Gonzalez-Garcia

last: Lanza

middle: A

last: Moreno-Risueño

first: E

last: Caro

first: S

last: Gonzalez-Bodi

first: V

last: Baca-Gonzalez

first: L

last: Serrano

last: Bustillo-Avendaño

middle: M

last: Garcia-Mina

first: A

last: Zamarreño

last: Garnica-Ochoa


title: Single-Cell Chromatin Accessibility Landscape of Developing Perinatal Mouse Skin: A Multi-Omics Approach to Lineage Specification [scATAC-seq and scRNA-seq]

first: Hanjae

last: Lee

address: 103, Daehak-ro, Jongno-gu

institute: Seoul National University

summary: This study presents a time-series scATAC analysis of developing mouse skin. Motif and footprint analyses at the chromatin level, as well as integrated analysis with single-cell and spatial transcriptomic data, enable an in-depth identification of key transcription factors and driver genes involved in fibroblast differentiation and hair follicle formation. This study demonstrates the utility of scATAC analysis combined with multi-omics approaches in providing a comprehensive understanding of skin development. It serves as a valuable reference for future research on skin development and regeneration, supported by an interactive online portal.

overall_design: Dorsal skin from C57BL/6 mice was isolated at embryonic day 18.5 (E18.5) and postnatal days 0, 2, and 4 (PD0, PD2, PD4), followed by scATAC-seq (E18.5, PD0, PD2, PD4) and scRNA-seq (E18.5).


title: Single-Cell Chromatin Accessibility Landscape of Developing Perinatal Mouse Skin: A Multi-Omics Approach to Lineage Specification

overall_design: Formalin-fixed paraffin-embedded (FFPE) tissue sections (5 μm thick) were prepared and subsequently analyzed using the Xenium Analyzer. After deparaffinization and permeabilization, mRNAs were targeted with a custom 50-gene panel of skin markers and driver genes, supplemented by the 10x mouse brain panel (247 genes; https://www.10xgenomics.com/products/xenium-panels). Post-analysis H&E staining was performed, and data visualization was carried out using Xenium Explorer (v3.0). The initial Xenium Analyzer data were reprocessed with the updated Xenium Ranger (v2.0), adjusting nuclei boundary expansion 2 μm.


title: A single-cell atlas revealing cellular heterogeneity across healthy and diseased human thymus

city: Vienna

first: Martin

last: Direder

state: Vienna

address: Lazarettgasse 14

department: Orthopedic and Trauma Surgery

country: Austria

institute: Medical University Vienna

summary: Transcriptional data of B-type thymoma, true thymic hyperplasia and thymic carcinoma

overall_design: Single cell RNA-sequencing gene expression of true thymic hyperplasia, B-type thymoma and thymic carcinoma. Single-cell suspension from all samples were prepared using MACS Miltenyi Tumor Dissociation Kit (Miltenyi). Libraries were generated using Chromium Next GEM Single Cell 5´GEM, Library & Gel Bead Kit v5.2, Chromium Next GEM Chip K Single Cell Kit and Single Index Kit TT Set A (all 10x Genomics, Pleasanton, CA, USA).

first: Maria

last: Laggner

first: Dragan

last: Copic

first: Katharina

last: Klas

first: Daniel

last: Bormann

first: Marie-Therese

last: Lingitz

first: Leonhard

last: Müllauer

first: Ana-Iris

last: Schiefer

last: Mildner

first: Hendrik

middle: J

last: Ankersmit

first: Bernhard

last: Moser

first: Matthias

last: Wielscher

first: Melanie

last: Salek

first: Bahar

last: Golabi

first: Hannes

last: Kühtreiber

first: Wolfgang

last: Weninger

first: Clemens

last: Aigner


title: Igh nuclear speckle association promotes V(D)J recombination

city: Chicago

first: Hammad

last: Farooq

state: IL

address: 835 S Wolcot

department: Microbiology and Immunology

institute: University of Illinois Chicago, College of Medicine

summary: Hi-C analyses of pro-B lymphocytes

overall_design: We report the application of in situ Hi-C for analysis of progenitor (pro)-B cells. We generated genome-wide Hi-C heatmaps for pro-B cells from Rag2-/- and Rag2-/-SiteI.3Pr-/- mice.

first: Amy

middle: L

last: Kenter

first: Khalid

last: Hussain Bhat

first: Sarah

last: Naiyer

first: Jie

last: Liang

first: Saurabh

last: Priyadarshi


title: Promoter mutagenesis and a massively parallel reporter screen of the MAPT locus identifies cis-regulatory elements and genetic variation effects [Oligo MPRA]

status: Public on Mar 11 2026

city: Huntsville

first: Jesse

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Tau neurofibrillary tangles are a hallmark of several neurodegenerative diseases called tauopathies, including frontotemporal dementia and Alzheimer's Disease. Ongoing clinical trials for tauopathies seek to reduce Tau in the brain through immunotherapy, antisense oligonucleotides, and siRNA. MAPT codes for Tau, therefore understanding how the MAPT gene is regulated and the effect of genetic variation at its regulatory elements is likely to have high relevance for tauopathies. We screened a ~3 Mb region including the MAPT locus using 2 different massively parallel reporter assay (MPRA) strategies in KOLF2.1J h-NGN2 neurons and HEK293FT cells, identifying previously unannotated cis-regulatory elements (CREs). Using CRISPR interference (CRISPRi) in mixed neuron cultures, we identified a new CRE for MAPT, as well as 2 CREs for another nearby gene of interest, KANSL1. Known genetic variation from the Alzheimer's Disease sequencing project was tested in a separate MPRA at the top CREs near the MAPT gene, identifying variants with altered regulatory effects including those at previously identified CREs for MAPT. Using a saturation mutagenesis screen of a 2,000 bp region encompassing the MAPT promoter, we assessed regulatory effects of each possible single nucleotide variant in this region. We identified several neuron-specific regulatory variant effects at this region, including a high confidence binding site for the transcription factors EGR2, ZBTB14 and TCLF5 at a region of high MPRA activity and genetic conservation.

overall_design: LentiMPRA in KOLF2.1h-NGN2 Neurons (transduced on day 14, collected on day 18) and HEK293FT cells using 270bp oligos as test sequences

first: Rebecca

last: Hauser

first: Nicholas


title: Immunological mechanisms underlying the clinical heterogeneity of Kikuchi disease: The potential role of atypical memory B cells

city: Taipei

first: Shan-Chi

last: Yu

address: No 7 Chung Shan S Rd

institute: National Taiwan University Hospital

summary: Building on our previous research, which classified Kikuchi disease into three subtypes based on predominant symptoms and fever status—febrile type, febrile lymphadenopathy (FebLAP), and afebrile lymphadenopathy (aLAP)—we further investigated the underlying mechanisms contributing to their distinct clinical differences.

overall_design: Using NanoString nCounter technology, we analyzed the gene expression profiles of 35 Kikuchi disease FFPE lymph node specimens and compared them across the subtypes.

first: Tseng-Cheng

last: Chen

first: Chun-Nan

first: Tsung-Lin

last: Yang


title: Whole-Protein Screening and Multi-Modal Profiling of Antigen-Specific CD4+ T Cells at Single-Cell Resolution

first: Rongyu

last: Zhang

address: 401 Terry Ave N

institute: ISB

summary: Systematic whole-protein screening and comprehensive profiling of antigen-specific CD4+ T cells are crucial for advancing vaccine design and cancer immunotherapies, yet remain technically challenging. Here, we present a high-throughput platform that utilizes large-scale class II single-chain trimer libraries to detect antigen-specific CD4+ T cells, while simultaneously profiling their antigen specificity, TCRα/β sequences, MHC restriction, whole transcriptomes, and patient/timepoint origins at single-cell resolution. Upon rigorous platform validation, we screened the full SARS-CoV-2 spike receptor binding domain in a longitudinal cohort of 22 participants, identifying 2,188 antigen-specific CD4+ T cells and revealing key metrics defining the immunogenicity of class II-restricted viral antigens. We further extended the platform to whole-protein screening of HPV-16 E6/E7 in a cohort of precancerous patients, uncovering HPV-specific CD4 TCRs that, upon extensive characterization, demonstrated strong therapeutic potential. By integrating high-throughput antigen screening with high-dimensional, multi-modal cellular characterization, our approach provides an unprecedented window into CD4+ T cell immunity, potentially guiding vaccine design and next-generation TCR-based cancer immunotherapies.

overall_design: RNA-seq profiling of antigen-specific CD4+ T cells identified through single-chain trimer (SCT) dextramers to characterize the immunological states of cells in response to SARS-CoV-2 and HPV-16 infections at various timepoints.


title: SEPHS2 deficiency reprograms glucose metabolism to activate the pentose phosphate pathway by stabilizing PCK1 through NAD+

city: shenzhen

first: yihuizhi

last: zhang

state: guangdong

address: 1088 Xueyuan Avenue, Nanshan District

department: School of Medicine

country: China

institute: Southern University of Science and Technology

summary: SEPHS2, a key enzyme in synthesizing selenoproteins, which converts hydrogen selenide into selenophosphate. We found that SEPHS2 knockout inhibits oxidative phosphorylation (OXPHOS), but has no effect on glycolysis, as indicated by an seahorse assay. SEPHS2 loss redirects more glucose to the pentose phosphate pathway (PPP). Mechanistically, SEPHS2 knockout elevates NAD+ levels, which are essential for Sirtuin activity. The increase in the activity of SIRT2 leads to deacetylation of PCK1, a posttranslational modification required to prevent PCK1’s ubiquitination and subsequent degradation. Thus, SEPHS2 knockout stabilizes PCK1 by reducing its ubiquitination. Since PCK1 is a key regulator of gluconeogenesis, SEPHS2 knockout promotes gluconeogenesis while reducing cellularglucose uptake, down-regulating oxidative phosphorylation and enhancing the PPP.

overall_design: Differential gene expression caused by A-375 control and SEPHS2 knockout cells were determined by RNA-seq

first: Siyuan

last: Xia

first: Yihuizhi


title: Base editing and nanoparticle transfection of airway cell types essential for treatment of cystic fibrosis

city: Baltimore

first: Garry

middle: R

last: Cutting

state: MD

address: 733 N Broadway

department: Genetic Medicine

institute: Johns Hopkins School of Medicine

summary: Cystic Fibrosis (CF) is a life-limiting genetic disorder caused by deleterious variants in the CFTR gene that results in altered mucous impairing the airway epithelia. Durable correction of these variants in airway cells remain a therapeutic challenge for ~10% of individuals unresponsive to CFTR modulators. A common disease-causing CFTR splice site variant 3120+1G>A was corrected in primary CF airway cells using base editor RNAs. Single-cell RNA sequencing revealed a remarkable increase in detectable CFTR transcript in most CF airway epithelial cell types resulting in notable enrichment of CFTR-expressing ionocytes and secretory goblet cells. Progenitor basal cell subtypes were edited but they decreased as a fraction of total cells and CFTR expressing cells compared to unedited cells.

overall_design: Primary human nasal epithelial cells were isolated and cultured from a CF individual bearing one copy of the 3120+1G>A variant. Following electroporation of ABE8e mRNA/sgRNA4long or sg5long or no sgRNA (mock) to targeting the 3120+1G>A variant, cells were allowed to differentiate for 21 days on air-liquid-interface before undergoing processing for scRNASeq analysis.

first: Erin

middle: W

last: Kavanagh

first: Anya

middle: T

last: Joynt

first: Audrey

last: Pion

first: Alice

last: Eastman

first: Alianna

middle: I

last: Parr

first: Katherine

last: Starego

first: Manav

last: Jain

first: Sydney

last: Shannon

first: Edwin

last: Yoo

first: Gregory

last: Newby

first: Stephany

middle: Y

last: Tzeng

first: Neeraj

last: Sharma

first: Jordan

last: Green


title: A dual role for PGLYRP1 in host defense and immune regulation during B. pertussis infection

first: Ciaran

last: Skerry

address: 685 W. Baltimore Street

institute: University of Maryland School of Medicine

summary: Bordetella pertussis, the etiologic agent of whooping cough, remains a serious public health concern despite widespread vaccination. Improved therapeutics and vaccines are urgently needed to treat and prevent pertussis disease. Host recognition of bacterial peptidoglycan (PGN), including B. pertussis extracellular PGN fragment tracheal cytotoxin (TCT), shapes the immune response to infection. Peptidoglycan recognition proteins (PGLYRPs) are a conserved family of innate immune molecules which bind bacterial PGN. While they function as immune signaling receptors in arthropods, PGLYRPs in mammals have thus far been primarily recognized for their bactericidal activity. Previously thought to function only as antimicrobial peptides in mammals, the immune modulatory roles of this family of peptidoglycan recognition proteins are beginning to gain greater appreciation. Peptidoglycan recognition protein 1 (PGLYRP1) is a secreted antimicrobial protein. However, its role in mammalian host defenses and immune signaling during infection with Gram-negative pathogens, such as B. pertussis, remain largely unknown. Here, we identify a dual role for PGLYRP1 in modulating host immune responses to B. pertussis. Using knockout mice, single-cell and bulk transcriptomics and functional assays, we show that PGLYRP1 has bactericidal activity against B. pertussis in vitro and promotes early bacterial control in vivo. PGLYRP1 also dampens inflammatory responses and impedes bacterial killing later in infection. Mechanistically, PGLYRP1 enhances nucleotide oligomerization domain (NOD)-1 signaling in response to TCT while suppressing NOD2- and triggering receptor expressed on myeloid cells-1 (TREM-1)-mediated inflammatory pathways. TCT-bound PGLYRP1 selectively impairs TREM-1 activation compared to PGNs from other bacteria, revealing a novel bacterial immune evasion strategy. These findings demonstrate that B. pertussis co-opts PGLYRP1 to temper inflammation and alter immune signaling, revealing a novel immune evasion mechanism of manipulating the availability and structure of their exogenous peptidoglycan, revealing implications for host-pathogen evolution, vaccine design and host-directed therapeutics.

overall_design: Mice challenged intranasally with 50 uLs of PBS-sham or B. pertussis (2x10^6 CFU). One hour before challenge with B. pertussis, mice in the AALR group were treated with S1P agonist, AALR. Four days after infection, mice were euthanized, perfused, and lungs were collected.

first: David

last: Rickert

first: Sasha

last: Cardozo

first: Nicholas

middle: H

last: Carbonetti

first: William

middle: E

last: Goldman

first: Karen

last: Scanlon


city: Rochester

first: Zhiquan

last: Wang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

summary: Defining the acute BTK-loss transcriptional program in CLL using a BTK degrader by RNA-seq

overall_design: Primary CLL B cells received various treatments and the gene expression was determined by RNA-seq


title: Stable bioreactor control reveals acidic pH-driven metabolic reprogramming and mitochondrial dysfunction in human lymphoblastoid cells

city: Thuwal

first: Mo

last: Li

address: King Abdullah University Of Science And Technology

country: Saudi Arabia

summary: Human cells require precise pH regulation to maintain optimal physiological functions, yet the molecular impacts of acidic environments remain underexplored due to the lack of technologies capable of precisely controlling the cell culture environment. Here, we employed a gas-only bioreactor to stably control pH, dissolved oxygen, and temperature during the culture of human B lymphoblastoid cells. Integrated transcriptomic, epigenomic, and metabolomic analysis revealed that acidic pH (6.8) induces a metabolic shift towards glycolysis, suppresses energy-intensive processes such as cell proliferation, and triggers intracellular accumulation of lactate and oncometabolites and mitochondrial dysfunction. This environment also elevates reactive oxygen species (ROS) and upregulates inflammatory and immune pathways, leading to heteroplasmic shifts in a pathogenic mitochondrial mutation. Mechanistically, acidic pH caused marked depletion of intracellular NAD⁺ driven in part by PARP1 activation, and restoration of NAD⁺ levels via nicotinamide mononucleotide supplementation or PARP1 inhibition partially rescued cellular proliferation, mitochondrial genomic integrity, and stress-associated transcriptional programs. These findings highlight the critical role of pH homeostasis in cellular metabolism and immune response, offering insights into the cellular adaptations to acidic stress, which may inform therapeutic strategies for conditions like cancer and metabolic disorders.

overall_design: GM12878 cells were thawed from liquid nitrogen stocks and expanded in batch culture until entering logarithmic growth phase. Cells were then transferred to bioreactor culture systems equilibrated to the indicated pH conditions (pH 7.4 or pH 6.8), with dissolved oxygen and pH continuously monitored to ensure stability throughout the experiment. Cells were seeded at a density of approximately 2.5 × 10⁵ cells/mL and cultured for 72 hours. For NAD⁺ precursor supplementation, nicotinamide mononucleotide (NMN, Abcam; Cat# ab223879) was added to the culture medium at a final concentration of 0.5 mM at the start of the bioreactor culture. For inhibition of NAD⁺ consumption, a PARP1 inhibitor (Rucaparib, Sigma; Cat# AMBH2D6FA67F) was added at a final concentration of 5 μM. NMN-treated and PARP1 inhibitor–treated cultures were performed in parallel with untreated controls under both pH conditions. No medium changes were performed during the intervention period to maintain consistent metabolic conditions. At the end of the 72-hour treatment period, cells and conditioned media were harvested for downstream analyses. All intervention conditions were processed in parallel to minimize batch effects. Total RNA was extracted using Qiagen RNeasy mini kit (cat#74106), and the quality was assessed with the Bioanalyzer 2100. The RNA samples with RIN > 7.0 are outsourced to X Genomics for directional library preparation and sequencing.

first: Samhan

last: Alsolami

first: Yiqing

last: Jin

first: Yingzi

last: Zhang


title: SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [ChIP-Seq]

first: Mafalda

last: Almeida

address: South Parks Rd

summary: The non-coding RNA Xist mediates X chromosome inactivation (XCI) in mammals, functioning in cis to direct heterochromatin formation over a single X chromosome in cells of early female embryos. Prior studies have determined that Xist transcription and turnover are modulated to maintain the correct level of Xist RNA to inactivate a single X chromosome. The underlying molecular mechanisms are poorly understood. In this study we demonstrate that RNA-dependent recruitment of the H3K9me3 methyltransferase SETDB1 and the HUSH complex across the transcribed Xist locus functions to suppress Xist transcription during establishment of XCI. Thus, degron-mediated acute depletion of SETDB1 or core HUSH subunits abrogates allelic H3K9me3 deposition, increasing Xist transcription, accumulation of Xist RNA, and the rate of X chromosome gene silencing. Our findings support a model in which the SETDB1/HUSH pathway coordinates Xist transcription rates to maintain optimal Xist RNA levels, ensuring the silencing of a single X chromosome.

overall_design: Calibrated single crosslinked ChIP for RNAPol II, RNA PolII Ser5P, RNA PolII Ser2P in FKBP12F36V-SETDB1 iXist-ChrXCast mouse embryonic stem cells (clones A12A10, P2F7 and G6D2) expressing Xist under a doxycycline inducible promoter in the presence and absence of SETDB1. Double crosslinked ChIP for MPP8 and KAP1 in FKBP12F36V-SETDB1 iXist-ChrXCast mouse embryonic stem cells (clones A12A10 and P2F7) expressing Xist under a doxycycline inducible promoter in the presence and absence of SETDB1.

first: Guifeng

last: Wei

first: Adam

last: Cawte

first: Tatyana

last: Nesterova

first: Neil

last: Brockdorff


title: A Single Small-Molecule-Based Human Embryo Model Reveals V-ATPase Requirement in Mammalian Blastocyst Cavitation

city: barcelona

first: aintzane

last: rueda

state: Choose State

address: C/ del Dr. Trueta, 179, 08005 Barcelona

institute: Sequentia Biotech SL.

summary: Human naïve pluripotent stem cells (nPSCs) can be indued by various combinations of signaling factors to genearte blastocyst-like structures known as blastoids. Despite the rapid advances in human blastoid models, their potential to uncover fundamental mechanisms of early development remains limited, leaving key morphogenetic processes poorly understood. Here, we present a simple and robust system in which dimethyl sulfoxide (DMSO) alone induces blastoid formation from human nPSCs. This model faithfully recapitulates pre- and post-implantation features, including amniotic cavity formation, and reveals a previously unrecognized mechanism of trophectoderm (TE) cavitation. Using this system, we identified lysosome-related genes—particularly those encoding subunits of the proton pump V-ATPase—are essential for blastoid cavitation. DMSO treatment upregulates key V-ATPase subunits (ATP6V0A4 and ATP6V1B1), which are also enriched in the TE of human embryos. Inhibition of V-ATPase disrupted lysosomal acidification, blocked intracellular vacuole formation, and impaired blastoid cavitation. Furthermore, both genetic and pharmacological disruption of V-ATPase function significantly impaired cavitation in mouse and human blastocysts. Thus, our simple DMSO model recapitulates key aspects of human blastocyst development and reveals a conserved mechanism involving V-ATPase–mediated lysosomal acidification during early mammalian embryogenesis.

overall_design: Single cell RNA sequencing was performed to profile the cellular composition and transcriptional landscape of day 6 human preimplantation embryo models (blastoids) generated in vitro. Blastoids were collected at day 6 of differentiation, dissociated into single cell suspensions, and processed for single cell transcriptomic analysis using the 10x Genomics Chromium GEM-X platform. Cells were captured in a single library preparation and sequenced to sufficient depth to enable the identification of major preimplantation lineages and associated transcriptional programs. The resulting dataset provides a high-resolution snapshot of lineage specific gene expression at the day 6 preimplantation stage.

first: Arun Pandian

last: Chandrasekaran

first: Alsolami

last: Samhan

first: Yibo

first: Ling

first: Ismail

last: Shakir

first: Aisha

last: Siddique

first: Gerardo

last: Ramos-Mandujano

first: Baolei

last: Yuan

first: Maya

last: Ayach

first: Alfonso

last: Saera-Vila

first: Zejun

last: Fan

first: Siyi

last: Fu

first: Huoming

first: Saige

last: Xin

first: Kholoud

last: AlDakhil

first: Juan Carlos

last: Izpisua Belmonte

first: Jin

first: Yang

last: Yu


title: RNA-seq analysis for wild-type fibroblasts and patient fibroblasts bearing pathogenic EPG5 mutations

city: London

first: Kritarth

last: Singh

state: England

address: Biosciences Stores, Anatomy Building, Gower street

department: Cell and Developmental Biology

institute: University College London

summary: The aim of this study was to compare RNA-seq profiles of wild-type fibroblasts and patient-derived fibroblasts carrying pathogenic EPG5 mutations. Using an adjusted p-value threshold of < 0.05, we identified 5,303 differentially expressed transcripts in patient fibroblasts harboring a homozygous p.Gln336Arg missense mutation, of which 2,651 were upregulated and 2,652 were downregulated. In patient fibroblasts carrying compound heterozygous truncating mutations (p.Arg299*/p.Pro1827Ala), we identified 6,317 differentially expressed transcripts, including 3,239 upregulated and 3,078 downregulated transcripts, compared with control 1 fibroblasts.

overall_design: Three replicates for each fibroblast line (passage 5): Control 1; Patient 1 (p.Gln336Arg) and Patient 3 (p.Arg299*/Pro1827Ala ). Control fibroblasts sometimes refer to as wild-type.

first: Michael

last: Duchen


title: Benchmarking urinary cell transcriptomes for noninvasive differentiation of BK polyomavirus-associated nephropathy from T cell-mediated rejection

city: New York

first: Manikkam

last: Suthanthiran

state: New York

address: 1300 York Ave, Rm A569

department: Nephrology and Hypertension

institute: Weill Cornell Medicine

summary: BK polyomavirus-associated nephropathy (BKVN) adversely impacts kidney allograft survival and often mimics acute T cell-mediated rejection (TCMR), confounding diagnosis and management. To address this conundrum, we performed unbiased RNA sequencing of urinary cells matched to biopsies classified as BKVN with intragraft inflammation (BKVN-P), BKVN without inflammation (BKVN-N), TCMR, or no rejection (NR). BKVN-N displayed dominant host DNA replication, cell cycle, and repair programs, while BKVN-P samples exhibited expansive innate immune activation, antigen presentation, chemokine upregulation, and epithelial injury. Both BKVN subtypes shared signatures of T cell exhaustion and mature and tolerogenic dendritic cell activation but differed in immune orientation—Th1 predominance in BKVN-N versus Treg and CD8 enrichment in BKVN-P. Compared to TCMR samples, BKVN-P lacked robust TCR/CD28 signaling and was enriched for viral and innate modules; BKVN-N lacked alloimmune activation. B cell exhaustion characterized BKVN-N, while BKVN-P displayed robust B cell activation with metabolic downregulation. A ratiometric urinary cell biomarker, CXCL10 mRNA/CD3E mRNA, distinguished both BKVN subtypes from TCMR with diagnostic accuracy, replicated by RT-qPCR for clinical translation, and confirmed in an independent cohort. These findings demonstrate the utility of urinary cell transcriptomics for resolving viral injury from alloimmunity, enabling precision diagnostics and targeted immunomodulation in kidney transplantation.

overall_design: RNA-seq profiling of urine specimens matched to kidney allograft biopsies classified as BKVN with BKVN-P and BKVN-N, TCMR, and NR.

first: Mueller

last: Franco B.

first: Li

last: Carol

first: Dadhania

last: Darshana M

first: Seshan

last: Surya V.

first: Salinas

last: Thalia

first: Sharma

last: Vijay K.

first: Xiang

last: Jenny Z.

first: Hirsch

last: Hans H.

first: Muthukumar

last: Thangamani

first: Suthanthiran

last: Mannikkam


title: ALS molecular subtypes are a combination of cellular, genetic, and pathological features learned by deep multiomics classifiers (post-mortem cortex)

first: Hemali

last: Phatnani

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Amyotrophic Lateral Sclerosis (ALS) is a complex syndrome with multiple genetic causes and wide variation in disease presentation. Despite this general heterogeneity, several common factors have been identified. For example, nearly all patients show pathological accumulations of phosphorylated TDP-43 protein in affected regions of the motor cortex and spinal cord. Moreover, large patient cohort studies have revealed that most patient samples can be grouped into a small number of ALS subtypes, as defined by their transcriptomic profiles. These ALS molecular subtypes can be grouped by whether postmortem motor cortex samples display signatures of: mitochondrial dysfunction and oxidative stress (ALS-Ox), microglial activation and neuroinflammation (ALS-Glia), or dense TDP-43 pathology and associated transposable element de-silencing (ALS-TE). In this study, we have built a deep layer ALS neural network classifier (DANcer) that has learned to accurately assign patient samples to these ALS subtypes, and which can be run on either bulk or single-cell datasets. Upon applying this classifier to an expanded ALS patient cohort from the NYGC ALS Consortium, we show that ALS Molecular Subtypes are robust across clinical centers, with no new subtypes appearing in a cohort that has quadrupled in size. Signatures from two of these molecular subtypes strongly correlate with disease duration: ALS-TE signatures in cortex and ALS-Glia signatures in spinal cord, revealing molecular correlates of clinical features. Finally, we use single nucleus RNA sequencing to reveal the cell type-specific contributions to ALS subtype, as determined by our single-cell classifier (scDANCer). Single-cell transcriptomes reveal that ALS molecular subtypes are recapitulated in neurons and glia, with both ALS-wide shared alterations in each cell type as well as ALS subtype- specific alterations. In summary, ALS molecular subtypes: (1) are robust across large cohorts of sporadic and familial ALS patient samples, (2) represent a combination of cellular, genetic, and pathological features, and (3) correlate with clinical features of ALS.

overall_design: Expression profiling by high throughput RNA sequencing of ALS patients

first: Maria

last: Pedersen

first: Andrew

last: Rice

first: Alexi

last: Runnels


title: Single-cell RNA/TCR-seq of T cells from murine muscle injury and foreign body response to synthetic biomaterial implants

first: Jennifer

last: Elisseeff

address: 1800 Orleans St

institute: Johns Hopkins

summary: The main objective of this study is to characterize T cell response to tissue injury and foreign body response (synthetic polycaprolactone PCL implant). We isolate T cells  from injured murine muscles with and without fibrotic PCL implants at various timepoints and perform transcriptomic profile using paired single-cell RNA/TCR-sequencing.

overall_design: PCL particulate was implanted into hindlimb volumetric muscle loss (VML) defects in C57BL/6 wildtype (WT) mice for 1, 6, or 12 weeks. For injury only controls, VML injuries were treated with saline and collected at 1 week. T cells (LiveSSCloCD45+CD3+) were sorted from the muscle with and without fibrotic PCL implants. Sorted T cells were processed for single-cell RNAseq paired with alpha/beta and gamma/delta TCRseq.

first: Anna

last: Ruta

first: Kavita

last: Krishnan

first: Joscelyn

last: Mejias

first: Locke

last: Davenport Huyer

first: Christopher

last: Cherry

first: Frank

last: Yu


title: Single cell RNA-seq of creatine-treated tumor-bearing mice

city: Los Angeles

first: Lili

last: Yang

address: 610 Charles E. Young Dr. East, TLSB 3045

institute: UCLA Lili Yang Lab

summary: Tumor-infiltrating immune cells (TIIs) are highly sensitive to metabolic cues. However, the therapeutic potential of targeting TII metabolism remains underexplored. In order to study the in vivo transcriptomal changes in the tumor microevironment upon creatine treatment, we performed scRNA-seq on creatine-treated tumor-bearing mice. Nontreated mice were included as a control.

overall_design: Tumor-infiltrating immune cells from creatine-treated or control B16-OVA tumor-bearing mice were isolated by fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Elliot

last: Kang

first: James

last: Elsten-Brown

first: Yu-Chen

last: Wang

first: Bo

last: Li


title: Revealing the transcriptional profile of fish muscle cells in vitro and in vivo: insights to improve fish muscle culture

city: Jatai

first: Bruna

middle: Tereza Thomazini

last: Zanella

state: Goias

country: Brazil

institute: Federal University of Jatai (UFJ)

summary: In vitro experiments have contributed to numerous fields of knowledge, including fish skeletal muscle. Despite improved strategies, in vitro assays still show discrepancies with in vivo systems, especially for non-model organisms. In this sense, we characterized the transcriptional profile of pacus (Piaractus mesopotamicus) muscle cells in vitro and in vivo. Processes related to proliferation, glycolytic metabolism, and extracellular matrix were enriched in vitro, while energy production, muscle contraction, and amino acid pro-cessing were enriched in vivo. Through qPCR, the genes fn1a (fibronectin 1a), hk1 (hexokinase 1) and ctnnb1 (catenin beta 1), respectively related to extracellular matrix, glycolytic metabo-lism, and cell proliferation and differentiation, were highly expressed in vitro. The genes ckma (creatine kinase, muscle a), acat1 (acetyl-CoA acetyltransferase 1), mdh2 (malate dehydrogenase 2) and pkmb (pyruvate kinase M1/2b), respectively associated with ATP production, fatty acid oxidation, oxidative and glycolytic metabolism, and the genes musk (muscle, skeletal, receptor tyrosine kinase), chrna1 (cholinergic receptor, nicotinic, alpha 1) and clu (clusterin), in-volved in cell signaling, were highly expressed in vivo. Our findings may support the de-velopment of molecular strategies to enhance muscle cell culture technology and expand knowledge for in vitro meat production, improving sustainable fish farming.

overall_design: Juvenile pacu (Piaractus mesopotamicus) (12-20g) were farmed at 28°C in storage tanks equipped with a water circulation system under 12h light:12h dark photoperiod. The animals were fed ad libitum once a day with commercial food. The fish were euthanized with an overdose of benzocaine, and the fast-twitch muscles were collected from the epaxial region for in vitro (muscle cells: MC) and in vivo (muscle tissue: MT) analysis. For the in vitro experiments, we collected the skeletal muscle of twelve animals for each cell isolation process, and for in vivo experiments, the skeletal muscle of six animals.

first: Érika

last: Perez

first: Mirely

last: Barbosa

first: Jéssica

last: Valente

first: Bruno

last: da Silva Duran

first: Maeli

last: Dal-Pai-Silva


title: Obesity imprints CD4 T cells via DNA methylation, perpetuating immune dysregulation

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

institute: University of Birmingham

summary: Obesity represents a major global healthcare crisis, with childhood obesity rising at an alarming rate. Children with obesity are highly likely to carry it into adulthood, bringing numerous associated health risks. Even more troubling is the emerging understanding of “obesity memory”, which contributes to the frequent issue of weight regain. Here, we show that obesity imprints CD4 T cells through DNA methylation, leading to a long-time lag, spanning years, before adaptive immune homeostasis is restored after weight loss. Differential DNA methylation analysis highlighted autophagy and immune senescence as key mechanisms underpinning this memory of obesity in CD4 T cells. Additionally, saturated fatty acids, in particular palmitate, drive epigenetic changes in CD4 T cells, perpetuating this altered state. Importantly, we identified molecular targets (i.e., Stk26 and Cdkn1c) underpinning key cell functions (autophagy and immune senescence) that could be targeted to promote a return to immune homeostasis alongside weight loss.

overall_design: Mice were placed either on a 14 week chow diet (CD) – 10% lipid (Test diet, USA, T-5755-1817109),14 week high-fat diet (HFD) – 60% lipid (Test diet, USA, T-58Y1-58126) or had a diet reversal (HFD-RE) with 8 weeks of HFD followed by 6 of chow diet. At week 13, mice were subjected to allogeneic immunisation by intraperitoneal injection with a mixture of splenocytes isolated from WT BALB/c and CBA mice (1:1 ratio, 1.5 x106 cell). Spleens were harvested at the end of week 14. Memory CD4 T cells were isolated from spleens using the EasySep Mouse Memory CD4 T cell isolation kit (Stemcell Technologies) according to the manufacturer’s instructions. Total RNA was isolated from the splenic memory CD4 T cells using the RNeasy micro kit (Qiagen) according to the manufacturer's instructions. Quality control check of RNA was done using the Qubit RNA High Sensitivity (HS) and TapeStation HS assays. 40 ng RNA from each sample was run for mRNA-expression analysis on the nCounter-based NanoString instrument (NanoString Technologies) using the nCounter® Mouse PanCancer Immune Profiling Panel (770 targets) (NanoString technologies).

first: C

last: Mahony

last: Mauro


title: A Pilot Phase II Study of Neoadjuvant Fulvestrant plus Abemaciclib in Women with Advanced Low--Grade Serous Carcinoma

city: Houston

first: Ken

last: Chen

state: TX

address: 7007 Bertner Ave

institute: University of Texas MD Anderson Cancer Center

summary: Purpose: Neoadjuvant chemotherapy shows limited activity in low-grade serous carcinoma (LGSOC) of the ovary, fallopian tube, and peritoneum (LGSOC). Given LGSOC’s similarities to hormone receptor- positive (HR+) breast cancer, including clinical benefit from endocrine therapies, we conducted a phase II pilot study to assess the clinical benefit of neoadjuvant treatment with fulvestrant and abemaciclib for women with advanced LGSOC.  Patients and Methods: Women with untreated, unresectable stage III or IV LGSOC were eligible. Patients received fulvestrant (500 mg IM on day 1 and 15 of the first 28-day cycle, then day 1 of subsequent cycles) and abemaciclib 150 mg orally BID. Pre/perimenopausal patients received goserelin 10.8 mg subcutaneously every 12 weeks for ovarian suppression. Imaging re-assessment was performed every 8 weeks using RECIST 1.1 until deemed resectable. Following interval cytoreductive surgery (ICS), patients received 4 cycles of adjuvant fulvestrant and abemaciclib followed by maintenance letrozole. Patients with progressive disease were removed from the study and received standard chemotherapy. The pPrimary endpoint is best overall response clinical benefit rate (BOR CBR).   Results: Fifteen patients were enrolled and evaluable for efficacy. BOR CBR in the neoadjuvant setting was 100%, with  (9/15 patients (60%) achieving partial response (PR), and 6/15 patients (40%) showing stable disease (SD). One patient with radiologic PR had pathologic complete response at ICS. Nine of fifteen patients (60%) underwent ICS – 5 (55.5%) with complete gross resection, 2 (22.2%) with <1cm residual disease, and 2 (22.2%) with suboptimal cytoreduction. Median time on study prior to surgery was 8.38 months.   Conclusion: Neoadjuvant treatment with fulvestrant and abemaciclib was tolerable and demonstrated unprecedented response and CBGR rates in this pilot study. These results compare favorably withto published outcomes of neoadjuvant chemotherapy in LGSOC.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: We performed GeoMx DSP WTA assay with 2 pairs of samples of pre- and post treatment timepoints and 4 additional patients from post treatment timepoint with fulvestrant and abemaciclib combination therapy.

first: Nejla

last: Ozirmak Lermi

first: Luisa

last: Solis Soto

first: Amir

last: Jazaeri


title: DMEM and EMEM as alternate growth media for pathogenic Leptospira

city: Storrs

first: Elsio

middle: Augusto

last: Wunder

state: CT

address: 61 N Eagleville

department: Pathobiology and Veterinary Sciences

institute: University of Connecticut

summary: Pathogenic Leptospira spp. must adapt to diverse environments during their life cycle, yet most laboratory studies rely on in vitro culture conditions that poorly reflect the host environment. This limitation restricts the relevance of transcriptomic studies for understanding leptospiral pathogenesis. In this study, we evaluated genome-wide gene expression of Leptospira interrogans grown in four different in vitro media—EMJH, DMEM, EMEM, and HAN—and compared their transcriptomic profiles to those obtained from bacteria recovered from the whole blood of infected hamsters.

sample_organism: Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130

overall_design: RNA-seq of Leptospira interrogans serovar Copenhageni L1-130 in in vitro conditions like DMEM, EMEM, HAN, EMJH and Whole blood of hamster to mimic host environment.

first: Leandro

last: Garcia

first: Emillie

last: Karovic

first: Candace

last: Banasiewicz

first: Zheng

first: Francesc

last: Lopez-Giraldez

first: Jeffrey

last: P Townsend


title: A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma

city: Philadelphia

first: Kai

last: Tan

state: PA

address: 3501 Civic Center Boulevard

department: Pediatrics

institute: Children's Hospital of Philadelphia

summary: Pediatric high-grade glioma (pHGG) is an incurable central nervous system malignancy that is a leading cause of pediatric cancer death. While pHGG shares many similarities to adult glioma, it comprises distinct disease entities. In this study, we longitudinally profile a molecularly diverse cohort of 16 pHGG patients through single-nucleus RNA and ATAC sequencing, whole-genome sequencing, and CODEX spatial proteomics to capture the evolution of neoplastic and microenvironmental features during disease progression and treatment. We define a set of core pHGG neoplastic cell states and observe differential tumor-myeloid interactions between malignant cell phenotypes. We find that essential neuromodulators and the interferon response are upregulated post-therapy and validated malignant cell-intrinsic targets. We observe an increase in oligodendrocytes upon progression and that they coordinate spatial motifs with proneural tumor cells. This multiomic atlas of longitudinal pHGG captures features of therapy response and provides a scalable reference for the study of pediatric brain tumors.

overall_design: Pediatric HGG cell lines treated with 0 or 4 Gy of ionizing radiation

first: Jonathan

last: Sussman

first: Thomas

last: De Raedt


title: Hepatic Transcriptomic Responses in Pregnant and Non-pregnant Rats Exposed to HFPO-DA: Analyses to Inform the Role of Maternal Effects on Neonatal Toxicity

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

institute: ToxStrategies

summary: Like other per- and polyfluoroalkyl substances (PFAS), toxicity studies for short-chain HFPO-DA (ammonium, 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate) indicate the liver is the primary target of toxicity in rodents. However, neonatal mortality and decreased birth weight were also reported in rats following oral exposure to HFPO-DA in utero. Exposure-related effects in neonatal rats including hypoglycemia, decreased liver glycogen, and perturbed hepatic gene expression of glucose metabolism and peroxisome proliferator activated receptor (PPAR) pathways also accompanied these findings. A putative rodent-specific adverse outcome pathway (AOP) network was recently developed using these endpoints and assessed for its applicability to PFAS. AOP 1 in this putative AOP network consists of PPARα activation as one of multiple initiating events, and placental insufficiency, neonatal hepatic glycogen deficit, and hypoglycemia as key events leading to neonatal mortality and lower birth weight. To further inform AOP 1 of this putative AOP network and investigate whether this altered carbohydrate metabolism liver phenotype observed in rat neonates also occurs in HFPO-DA-exposed pregnant and non-pregnant adult rats, transcriptomic analysis and glycogen staining were performed on female rat livers from a 15-d developmental or 90-d subchronic toxicity study. HFPO-DA-mediated changes in hepatic gene expression in female rats were consistent with PPAR signaling. Changes in hepatic glycogen content and glucose metabolism-related gene expression were independent of HFPO-DA exposure, indicating that the altered carbohydrate metabolism phenotype observed in neonatal livers does not occur in adult female rats, regardless of pregnancy status. Therefore, key events in this AOP for neonatal mortality and lower birthweight are likely to directly affect the perinatal rat and are not expected to affect the maternal rat liver. Findings from this study were consistent with previous mechanistic studies supporting the rodent-specific PPARα mode of action for HFPO-DA-mediated liver effects in rodents.

overall_design: Comparative gene expression profiling analysis of TempO-Seq data from FFPE liver tissue of pregnant (female) Sprague Dawley rats administered deionized water (vehicle control) or HFPO-DA in deionized water at 10, 100 or 1000 mg/kg by oral gavage once daily during gestation days (GD) 6 to 20, for a total of 15 days (developmental study), or non-pregnant female Sprague Dawley rats orally administered the same HFPO-DA doses daily for 90 days (subchronic study).

first: Chad

last: Thompson

first: Laurie

last: Haws

first: Grace

last: Chappell


title: Herpes simplex virus 1 (HSV-1) R-loops are targets for APOBEC-mediated innate immunity [RNaseH_DRIP-seq]

city: Debrecen

first: Márton

last: Miskei

address: Egyetem tér1.

country: Hungary

institute: University of Debrecen

summary: APOBEC cytidine deaminase enzymes play a crucial role in antiviral innate immunity as they introduce mutations in viral genomes, restrict viral replication, and promote host defense against infections. Special three-stranded nucleic acid structures, called R-loops, have been considered as efficient targets for APOBEC-mediated mutagenesis because they present an ideal substrate, a persistent single-stranded DNA, for the enzyme. However, the relationship between R-loops and APOBEC enzyme activity has not been verified and remains to be elucidated. Here, we reveal a mechanistic link between R-loop formation, APOBEC enzyme binding, and APOBEC mutagenesis at viral R-loop targets during virus infection. In a cellular model involving human T lymphoblastoid leukemia cells infected with Herpes simplex virus 1 (HSV-1), we show that APOBEC3A and APOBEC3G binding sites and mutagenesis signatures occur mainly in viral R-loop structures. C-to-T mutagenesis primarily targets R-loops, which are specifically concentrated in HSV-1 genes that are essential for virus assembly and function. Among these genes, we identified mutation hotspots resulting in amino acid changes, likely leading to inactivation of HSV-1 protein functions. Collectively, our findings show that viral R-loops serve as potent targets for APOBEC-induced mutagenesis, representing an effective strategy to inactivate essential viral proteins and compromise viral activity.

overall_design: The specificity of S9.6 immunoselection was monitored by RNaseH treatment, which degrades the RNA strand of RNA-DNA hybrids

first: Marton

first: Lorant

last: Szekvolgyi


title: Herpes simplex virus 1 (HSV-1) R-loops are targets for APOBEC-mediated innate immunity [DRIP-seq]

overall_design: DRIP-seq experiments to determine the R-loops on the HSV-1 genome.


title: Herpes simplex virus 1 (HSV-1) R-loops are targets for APOBEC-mediated innate immunity [ChIP-Seq]

overall_design: ChIP-seq experiments to find APOBEC3A and APOBEC3G binding sites on the HSV-1 genome.


title: Stable Bioreactor Control Reveals Acidic pH–Driven Metabolic Reprogramming and Mitochondrial Dysfunction in Human Lymphoblastoid Cells

city: THUWAL

first: Samhan

middle: M.

last: Alsolami

address: Thuwal 23955

department: BESE

institute: KAUST

summary: Human cells require pH regulation to maintain physiological function, yet the molecular consequences of acidic environments remain incompletely understood. Here, we employ a gas-only bioreactor to control pH, oxygen, and temperature. Integrated Omics analyses reveal that acidic pH induces a glycolytic metabolic shift, suppresses proliferation, and promotes accumulation of lactate and oncometabolites alongside mitochondrial dysfunction. Acidic conditions increase reactive oxygen species (ROS) and activate inflammatory and immune pathways, leading to heteroplasmic enrichment of a pathogenic mitochondrial mutation. Acidic pH depletes intracellular NAD⁺, partly driven by PARP1 activation. Restoring NAD⁺ through nicotinamide mononucleotide (NMN) supplementation partially rescues proliferation and stress-associated transcription, while elevating NAD+ levels by NMN or PARP1 inhibition reverses heteroplasmic enrichment of mutant mitochondrial DNA. These findings underscore the role of pH homeostasis in coordinating metabolism, redox balance, and immune signaling, and identify NAD⁺ metabolism as a mechanistic link between acidic microenvironments, mitochondrial genome instability, and immune–metabolic remodeling.

overall_design: B-LCL treated with pH 6.8 and pH 7.4 in controlled environment

first: Mo

last: Li


title: A single small molecule-based human embryo model reveals V-ATPase requirement in mammalian blastocyst cavitation

first: aintzane

last: rueda

summary: Human naïve pluripotent stem cells (nPSCs) can be induced by various combinations of signaling factors to generate blastocyst-like structures, termed blastoids. Despite rapid progress in human blastoid models, their potential to uncover fundamental mechanisms of early human development remains limited, leaving key morphogenetic processes poorly understood. Here, we describe a simple and robust system in which dimethyl sulfoxide (DMSO) alone induces blastoid formation from human nPSCs. This model recapitulates key pre- and post-implantation features and exhibits enhanced polar trophectoderm (TE) organization, more efficient attachment within an implantation-relevant window, improved epiblast lumenogenesis associated with amniotic cavity formation, and more robust, sustained expansion of embryonic lineages following attachment. Using this system, we reveal a previously unrecognized mechanism underlying TE cavitation and identify lysosome-associated genes - particularly subunits of the proton pump V-ATPase - as essential regulators of blastoid cavitation. DMSO treatment upregulates key V-ATPase subunits (ATP6V0A4 and ATP6V1B1), which are also enriched in the TE of human embryos. Genetic or pharmacological inhibition of V-ATPase activity disrupts lysosomal acidification, blocks intracellular vacuole formation, and impairs blastoid cavitation, whereas overexpression of V-ATPase subunits rescues this phenotype. Furthermore, genetic and pharmacological perturbations of V-ATPase function significantly compromise cavitation in both mouse and human blastocysts. Finally, DMSO treatment induces membrane biomechanical changes characteristic of early embryonic development, suggesting a mode of action distinct from conventional small-molecule, signaling pathway-based induction strategies. This simple DMSO-based blastoid model recapitulates key aspects of human blastocyst development and reveals a conserved requirement for V-ATPase-mediated lysosomal acidification during early mammalian embryogenesis.

overall_design:
These blastoids were produced using PALLY protocol with and without DMSO. Also, these blastoids were allowed to go on to model peri-implantation in vitro under the same treatment.
D1-D4 samples represent technical replicates.

first: Yiqing

last: Jin

first: Yingzi

last: Zhang

first: Ismail

last: Shakir

first: Alfonso

last: Saera-Vila

first: Arun

last: Chandrasekaran

first: Gerardo

last: Ramos Mandujano

first: Yang

last: Yu

first: Yibo

last: Wang

first: Ling

first: Aisha

last: Siddique

first: Baolei

last: Yuan

first: Maya

last: Ayach

first: Zejun

last: Fan

first: Siyi

last: Fu

first: Huoming

first: Saige

last: Xin

first: Kholoud

last: Khalid AlDakhil

first: Juan Carlos

last: Izpisua Belmonte

first: Jin


title: Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes [snRNA-Seq]

status: Public on Mar 10 2026

city: Heidelberg

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

country: Germany

institute: University Hospital Heidelberg

summary: Breast cancer brain metastases (BCBM) are a severe condition with high demand for improved personalized treatment, but a comprehensive understanding of BCBM immune-microenvironment heterogeneity and susceptibility to immunotherapy is lacking. Here, we multimodally profile the immune niche in a vast, clinically well-annotated cohort of 156 BCBM applying tissue cytometry, bulk and single nuclei RNA-sequencing, flow cytometry, and spatial transcriptomics, complemented by functional studies in patient-derived models. Integrative analyses reveal two immune landscapes predicting prolonged patient survival and not deducible from paired primary tumors: 1) BCBM with a high proportion of CD8 tissue-resident-like memory T cells as major players of tumor immune control. 2) BCBM containing tertiary lymphoid structures. Surrogate signatures of these landscapes are prognostic in independent BCBM and primary breast cancer cohorts, are associated with fewer metastases, and predict immunotherapy response. Our work provides critical insights into anti-tumor immunity in BCBM and identifies novel biomarkers with translational relevance.

overall_design:
We performed single nuclei RNA-sequencing (snRNA-seq) of 28 BCBM. We focused on the TNBC subtype, since TNBC is associated with inferior prognosis of BCBM patients and at the same time is considered immunogenic with ICB use in the clinic. Samples were selected representing the full cohort in terms of CD8 T cell infiltration rate and ecotype variety. We sequenced single nuclei rather than cells for a comprehensive view, preventing potential cell loss by harsh tissue dissociation, and after optimizing the nuclei isolation protocol. This involved controlled tissue preparation and improved in silico doublet detection applying our previously developed demultiplexing pipeline using patient-specific single nucleotide variants (SNP).

***************************************************************
Due to data protection regulations, the raw sequencing data have been deposited at GHGA: https://data.ghga.de/dataset/GHGAD48917471237543
***************************************************************

first: Lena

last: Jassowicz

first: Fangyoumin

last: Feng

first: Rolf

last: Warta

first: Marc

last: Zapatka

first: Martina

last: Seiffert


title: Promoter mutagenesis and a massively parallel reporter screen of the MAPT locus identifies cis-regulatory elements and genetic variation effects [RNA-seq]

city: Huntsville

first: Jesse

last: Cochran

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Tau neurofibrillary tangles are a hallmark of several neurodegenerative diseases called tauopathies, including frontotemporal dementia and Alzheimer's Disease. Ongoing clinical trials for tauopathies seek to reduce Tau in the brain through immunotherapy, antisense oligonucleotides, and siRNA. MAPT codes for Tau, therefore understanding how the MAPT gene is regulated and the effect of genetic variation at its regulatory elements is likely to have high relevance for tauopathies. We screened a ~3 Mb region including the MAPT locus using 2 different massively parallel reporter assay (MPRA) strategies in KOLF2.1J h-NGN2 neurons and HEK293FT cells, identifying previously unannotated cis-regulatory elements (CREs). Using CRISPR interference (CRISPRi) in mixed neuron cultures, we identified a new CRE for MAPT, as well as 2 CREs for another nearby gene of interest, KANSL1. Known genetic variation from the Alzheimer's Disease sequencing project was tested in a separate MPRA at the top CREs near the MAPT gene, identifying variants with altered regulatory effects including those at previously identified CREs for MAPT. Using a saturation mutagenesis screen of a 2,000 bp region encompassing the MAPT promoter, we assessed regulatory effects of each possible single nucleotide variant in this region. We identified several neuron-specific regulatory variant effects at this region, including a high confidence binding site for the transcription factors EGR2, ZBTB14 and TCLF5 at a region of high MPRA activity and genetic conservation.

overall_design: RNAseq of  CRISPRi  performed in KOLF2.1J mixed neuron cultures. NPCs were transduced with CRISPRi contstructs targeting the AAV safe harbor locus (negative control), MAPT promoter (positive control), as well as CREs of interest (r1-r14). The cells were  differentiated into mixed neuron cultures, and RNAseq was performed to determine effect on MAPT expression.

first: Rebecca

last: Hauser

first: Nicholas


title: Genetic deletion of cytoglobin exacerbates cardiac hypertrophy and inhibits cardiac fibroblast activation independent of changes in blood pressure

city: Albany

first: David

last: Jourd'heuil

address: 43 New Scotland Ave

department: Molecular and Cellular Physiology

institute: Albany Medical College

summary: Hypertension-mediated left ventricular hypertrophy and cardiac fibrosis often precede heart failure. Recent studies indicate that cytoglobin (Cygb), a globin expressed in the vasculature, increases systemic blood pressure. The present work aims to determine the role of Cygb in angiotensin II (Ang II)-induced cardiac hypertrophy and fibrosis in the mouse. Methods: Males and females global Cygb knockout (Cygb−/−), and wildtype (Cygb+/+) mice were treated with Ang II (1.5 µg/kg/day) for two weeks via subcutaneous osmotic minipumps. Cardiac function was assessed through echocardiography, and hearts were analyzed for changes in hypertrophy, fibrosis, and gene expression. Functional studies were also performed in isolated cardiac fibroblasts. Results: Cygb−/− mice from both sexes showed an increase in cardiac hypertrophy over Cygb+/+ mice. Cardiac functions were also depressed in Cygb−/− males with no changes in females. Importantly, genetic deletion of Cygb did not affect systemic blood pressure in mice, at baseline or after Ang II treatment. We established that Cygb was expressed in fibroblasts and pericytes in humans and mice hearts. Finally, we found that Cygb−/− cardiac fibroblast did not upregulate the expression of genes associated with myofibroblasts following treatment with Ang II. This was reversed following expression of human cytoglobin. Conclusions: Our findings indicate that Cygb plays a protective role in the mouse heart during Ang II-induced cardiac stress. This is the first study detailing the function of Cygb in the heart as a regulator of cardiac hypertrophy. This study also reveals a role for Cygb in regulating cardiac fibroblast activation by Ang II. NEW & NOTEWORTHY: We identified cytoglobin as an important globin in cardiac pathophysiology. Genetic deletion of cytoglobin led to exacerbation of angiotensin II-mediated cardiac hypertrophy in the absence of any effect on systemic blood pressure. Cytoglobin is expressed in cardiac fibroblasts and pericytes and is required for cardiac fibroblast activation to myofibroblast. The present study reveals for the first time a role for cytoglobin in regulating angiotensin II signaling.

overall_design: Bulk RNA-seq was performed on left ventricular tissue from global cytoglobin knockout (Cygb−/−) mice and wild-type (WT) littermate controls after 2 weeks of continuous infusion with angiotensin II (Ang II) via subcutaneous osmotic pumps.Left ventricles were harvested at the end of the 2-week infusion period, RNA was isolated from each individual mouse, and sequencing libraries were prepared for gene expression profiling by bulk RNA sequencing. This design enables comparison of the transcriptional response of the left ventricle to Ang II between WT and Cygb knockout mice in order to identify gene expression programs and pathways that are altered by the loss of cytoglobin during Ang II–induced cardiac stress.

first: Le Gia Cat

last: Pham

first: Kurrim

last: Gilliard

first: Frances

first: Sarahann

last: Mistretta

first: John

last: Schwarz

first: Harold

last: Singer


title: Genome-wide profiling identifies the genetic dependencies of cell death following EGFR inhibition [RNA-Seq]

city: Worcester

first: Michael

last: Lee

state: MA

address: 55 N Lake Ave

institute: Umass Chan Medical School

summary: EGFR is a proto-oncogene that is mutationally activated in a variety of cancers. Small molecule inhibitors targeting EGFR can effectively slow the progression of disease, and in some settings, these drugs even cause dramatic tumor regression. However, responses to EGFR inhibitors are rarely durable, and the mechanisms contributing to response variation remain unclear. In particular, several distinct mechanisms have been proposed to explain how EGFR inhibition activates cell death, and a consensus has yet to emerge. In this study, we use functional genomics with specialized analyses to infer how genetic perturbations affect the drug-induced death rate. Our data clarify that inhibition of PI3K signaling drives the lethality of EGFR inhibition. Inhibition of other pathways downstream of EGFR, including the RAS-MAPK pathway, promotes growth suppression but not the lethal effects of EGFR inhibitors. Taken together, our study provides a “reference map” for the genome-wide genetic dependencies of lethality in response to EGFR inhibitors.

overall_design: RNA-sequencing of PC9 and H1650 non-small cell lung cancer cell lines with and without EGFR inhibitors 10 uM erlotnib and .1 uM osimertinib at 0 and 36 hours.

first: Sydney

last: Porto

first: Gavin

last: Birdsall

last: Harper

first: Megan

last: Honeywell

first: Scott

last: Leighow

first: Tiana

last: Naylor

first: Kelly

last: Ward

first: Mika

middle: K

last: Wesley

first: Justin

last: Pritchard


title: Transcriptome profiling of B16F10 cells and differentiated B16F10 cells induced by forced expresssion of Myod1, Pparg, or by knockdown of Setdb1 using RNA-sequencing.

status: Public on Jun 01 2026

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

summary: The core proeprty of cancer cells is neural stemness, which determines tumorigenicity and pluripotency. Therefore, cancer cells can supposedly be induced to differentiate along different lineages. B16F10 is a mouse melanoma cell line. We found that B16F10 cells differentiated into muscle cells or adipocytes upon induction by muscle or adipocyte differentiation factor Myod1 or Pparg, respectively. Moreover, Setdb1 is an epigenetic modification factor responsible for catalyzing the histone modification H3K9me3. Transcription of Setdb1 gene is enriched in embryonic neural cells during vertebrate embryogenesis. Setdb1 is upregulated in cancer cells and promotes cancers. We found that knockdown of Setdb1 in B16F10 cells led to a neuronal-like differentiation phenotype.

overall_design: Forced expression of mouse Myod1 (B16F10Myod1) or Pparg (B16F10Pparg) in B16F10 cells was perfomed with lentiviral transfection, respectively. In paralell, cells transfected with lentivirus carrying only the empty vector were used as control (B16F10Ctrl). All cells were cultured in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% FBS at 37°C in 5% CO2 for 8 days when significant phenotypic change occurred in cells with forced Myod1 or Pparg expression. Control and differentiated cells were then collected and subjected to RNA-sequencing. Setdb1 was knocked down with specific short-hairpin RNA (shSetdb1) in B16F10 cells using lentiviral infection (B16F10shSetdb1), while cells infected with virus carrying only the empty vector was used as control (B16F10shCtrl). Cells were cultured in DMEM supplemented with 10% FBS at 37°C in 5% CO2 for 7 days when knockdown cells underwent significant phenotypic change. Control cells and knockdown cells were then collected and subjected to RNA-sequencing.

first: Yang

last: Liu


title: Transcriptome profiling of CT26 cells and differentiated CT26 cells induced by forced expresssion of Myod1 or Pparg using RNA-sequencing.

summary: The core proeprty of cancer cells is neural stemness, which determines tumorigenicity and pluripotency. Therefore, cancer cells can supposedly be induced to differentiate along different lineages. CT26 is a mouse colon cancer cell line. We found that CT26 cells differentiated into muscle- or adipocyte-like cells upon induction by muscle or adipocyte differentiation factor Myod1 or Pparg, respectively.

overall_design: Forced expression of mouse Myod1 (CT26Myod1) or Pparg (CT26Pparg) in CT26 cells was perfomed with lentiviral transfection, respectively. In paralell, cells transfected with lentivirus carrying only the empty vector were used as control (CT26Ctrl). All cells were cultured in Roswell Park Memorial Institute 1640 (RPMI 1640) supplemented with 10% FBS at 37°C in 5% CO2 for 9 days when significant phenotypic change occurred in cells with forced Myod1 or Pparg expression. Control and differentiated cells were then collected and subjected to RNA-sequencing.


title: Transcriptome profiling of embryonic stem cells (mESCs) derived from B6 mouse, primitive neural stem cells (NSCs) derived from mESCs, muscle fibers, fat cells, spleen cells and thymus using RNA-sequencing.

summary: The core proeprty of cancer cells is neural stemness, which determines tumorigenicity and pluripotency. Therefore, cancer cells can differentiate along different lineages. Upon differentiation, cancer cells will lose their neural stemness and tumorigenicity. Cancer cells, embrynonic stem cells and neural stem cells are immune-privileged cells and are capable of immune evasion. We used transcriptome profiling to analyze the difference in trasncriptomes and particularly, transcription of immune related genes in a few cell types representing undifferentiated and differentiated states, because immunigenicity is the key for effective anti-tumor immunity and this relies on expression of immune related genes. This analysis generates the clue to the relationship between immune related gene expression and differentiation status of cells.

overall_design: Primitive neural stem cells (NSCs) were obtained by culturing mESCs for 6 days in the defined serum-free medium Ndiff®227, which was used for deriving neuroectodermal cells from ESCs. Muscle, fat, spleen and thymus tissues were obtained from B6 male mice of 4 weeks of age. Skeletal muscle tissue was removed from legs and washed with pre-cooled PBS under sterile conditions. Muscle was then digested with 0.2% type I collagenase at 37°C with 5% CO2 for 50 minutes to obtain free muscle fibers. After neutralizing digestion with serum-containing DMEM and washing with PBS, muscle fibers were collected. Subcutaneous fat tissue was removed from the groin and washed three times with PBS. Fat tissue was cut into small pieces, and digested with 0.1% type I collagenase in a water bath at 37°C for 40 minutes. After termination of digestion, the mixture was filtered through a 100-mesh filter, and centrifuged at 140×g for 5 min. The upper layer of fat cells was collected and washed with PBS. To obtain spleen cells, spleen tissue was pulverized, filtered, centrifuged at 500×g for 5 minutes, and the supernatant was discarded. 500 μl red blood cell lysis buffer was added to the precipitated cells, treated at room temperature for 10 minutes to remove red blood cells. Spleen cells were then collected were collected by centrifugation and PBS washing. Muscle fibers, fat cells, spleen cells and thymus tissue were subjected to RNA-sequencing. NSCs and mESCs, muscle fibers, fat cells, spleen cells  and thymus tissue were subjected to RNA-sequencing.