title: Transcriptomic profiling and IgM and IgT repertoire dynamics in rainbow trout gills following primary and secondary challenge with Lactococcus petauri

status: Public on Jun 14 2026

city: Madrid

first: Aitor

last: Arrogante

state: Madrid

address: Ctra. De La Coruña, Km 7,5

department: Animal Biotechnology

institute: INIA-CSIC

summary: Fish mucosal tissues lack the organized lymphoid structures present in mammals. Although this is also true for the gills, with the gill-associated lymphoid tissue (GIALT) being mainly composed of B and T cells scattered throughout the epithelium and the lamellae, in some species such as rainbow trout (Oncorhynchus mykiss) or Atlantic salmon (Salmo salar), a more organized structure designated as the interbranchial lymphoid tissue (ILT) is also identified. Yet, although many studies have investigated the immune response of the gill to stimulation or pathogen encounter, which have revealed the activation of both innate and adaptive immune elements, how the gills respond to secondary stimulation or whether memory responses are locally orchestrated is still unknown. To provide insights into this matter, in the current study, we have infected rainbow trout by bath with Lactococcus petauri and then re-infected or mock-infected the survivor fish as well as mock-infected controls. At day 4 after the last infection, the fish were sacrificed and gills used to perform an RNAseq transcriptomic analysis and an IgM and IgT repertoire analysis. The number of cells secreting total and specific IgM in gills was also established by ELIspot. Our results demonstrate that memory responses are locally organized in the rainbow trout gills, given that re-infected fish did not up-regulate genes related to inflammation (as happens in the primary infection), but preferentially modified genes related to adaptive immunity, mainly to B cell function, experiencing a significant IgM and IgT clonal expansion. Accordingly, re-infected fish produced increased levels of specific IgM both locally and in serum, although no clonal selection was apparent. These findings advance our understanding of mucosal immunological memory in teleost fish and reveal the gills as a site of localized adaptive immune regulation during secondary responses.

overall_design: The infections with L. petauri were performed by bath. Briefly, fish were placed into two aerated 15 L basins containing either L. petauri at 1 × 1012 CFU/mL or tryptic soy broth (TSB) alone (for mock-infected controls). After 2.5 h of immersion, fish were transferred back to their original 500 L tanks and maintained at 18°C for 30 days. Following this period, a secondary challenge with the same bacterial strain was conducted using the same protocol. For this, survivors from the initially infected group were divided into two tanks of 14 fish each, one being re infected with L. petauri and the other one mock-infected with TSB alone. In parallel, 14 fish from the previously uninfected control group were exposed to L. petauri for the first time, following the same procedure. A remaining 14 control fish were mock-infected with TSB alone. At day 4 after this last infection, 6 fish were sampled from each group. This design yielded four experimental groups: fish not exposed to the bacteria in none of the infection rounds (CC); fish that were not infected in the first round but were infected in the second one (CI), and therefore had seen the bacteria only once, 4 days before the sampling; fish that were infected in the first round but not in the second round, hence had seen the bacteria only once, 34 days before the sampling (IC); and fish that had survived a first infection and were then challenged again with the bacteria (II).

first: Esther

last: Morel

first: Beatriz

last: Abós

first: Samuel

last: Vicente-Gil

first: Pablo

last: Jiménez-Barrios

first: Patricia

last: Díaz-Rosales

first: Pedro

last: Perdiguero

first: Germán

last: Herranz-Jusdado

first: Carolina

last: Tafalla


title: The RNA Binding Protein ZFP36L2 Displays Tissue-Selective mRNA Targeting in Mice [eCLIP-seq]

status: Public on Jun 15 2026

city: Chapel Hill

first: Silvia

middle: B

last: Ramos

state: NC

address: 133 Medical Drive

department: Biochemistry and Biophysics

country: USA

institute: UNC-Chapel Hill

summary: ZFP36L2 (zinc finger protein 36 like 2, C3H type-ZFP) is an RNA-binding protein targeting transcripts rich in adenine-uridine elements (AREs). Previous transcriptomic analysis suggested that ZFP36L2 displays a distinct transcript preference, depending on the tissue of expression. However, this analysis was restricted to a few tissues. Here, we collected RNA-seq data in six tissues and detected a remarkable transcript selectivity.  Given that ZFP36L2 accelerates the degradation of specific ARE-transcripts upon binding, we obtained differential expression transcriptomic data on a Zfp36l2 knock-out mouse model to delve into the mechanisms governing this tissue-specific targeting. Transcriptomic analyzes of up regulated ARE-transcripts in lung, liver, bone marrow, spleen, kidney, and ovary of the Zfp36l2-deficient mouse confirmed that there is high tissue preference in ZFP36L2 targets. We observed only one common up regulated gene, Apol11b, among these six different tissues. However, we do observe common trends, specifically an enrichment in protein coding genes in the up regulated genes, consistent with these RBP primarily targeting genes on their 3’ UTRs. Interestingly, we observed a significant increase in the proportion of IG (immunoglobulin) genes being up regulated. We further performed eCLIP (Enhanced Cross-Linking&ImmunoPreciptation) on a mouse cell line, MLTC-1 cells, to identify direct binding sites of ZFP36L2. AU-Rich Element score (AREscore) analysis revealed enrichment in both up regulated genes and eCLIP peaks, although some differences were observed in flanking residue composition. Our findings provide new insights into the intricate regulatory network orchestrated by ZFP36L2, opening avenues for exploring its potential roles in different tissues.

overall_design: MLTC-1 cells (American Type Culture Collection, CRL 2065) were cultured in RPMI medium with 10% fetal bovine serum, penicillin (100 units/ml), and streptomycin (100 μg/ml), at 37°C in an incubator with 5% CO2 in atmospheric air. MLTC-1 cells at 70-80% confluency from a 100 mm petri dish were trypsinized, washed in cold PBS twice, counted and adjusted to 20 x 106 cells/ml. A total of 80 x 106 cells were resuspended in 4 mL of PBS and placed in a clean 100 mm petri dish, on top of an ice plate, inside the UV cross-linker (Hoefer UVC 500 crosslinker) with 254-nm UV bulbs. The distance from the UV light source to the cells was 11 cm. Then, the cells were exposed to UV cross-link at 254-nm with an energy setting of 400 mJoules/cm2. After the UV crosslink, cells were washed in PBS, counted again and 20 x 106 cells were pelleted in an Eppendorf tube and snap frozen. Enhanced Cross-Linking&ImmunoPreciptation (eCLIP) was performed by EclipseBio BioInnovations Inc (San Diego; https://www.eclipsebio.com/) according to (25) protocol. In short, total RNA was extracted from the frozen pellets of MLTC-1 cells after UV-crosslinking, quantified and analysed for quality using an Agilent4200TapeStation. Twenty ug of RNA with a RIN of 8.35 was used for immunoprecipitation using the validated Abcam ab70775 antibody. As a negative control, in parallel, we used a rabbit IgG antibody (ab313801 from Abcam). Following the immunoprecipitation, the samples were treated with proteinase K. The IP-RNA was first fragmented and used to create a library using an RNA adapter on the 3' end of the target RNA. The RNA was reverse transcribed resulting in cDNAs ligated to single-stranded DNA adapters on the 3' end to serve as identifiers against PCR duplicates. Finally, the paired-end cDNA fragments were amplified to obtain sufficient material for high throughput sequencing.

first: George

last: Stephenson

first: Alain

last: Laederach


title: Screening and functional study of genes related to tuberculous ulcers

status: Public on Jun 11 2026

city: Nanjing

first: Jiayan

last: Qian

address: Affiliated of Nanjing University of Chinese Medicine to Nanjing Integrated Traditional Chinese and Western Medicine Hospital

country: China

institute: Nanjing Integrated Traditional Chinese And Western Medicine Hospital

summary: Transcriptome analysis was performed to systematically compare human tuberculous ulcers with non-tuberculous skin ulcers. Focusing on the former, this study aimed to identify key associated genes, elucidate their expression profiles and functional attributes, and preliminarily dissect the molecular mechanisms governing their pathological progression. By bridging the current gap in the genetic characterization of tuberculous ulcers, this research not only provides novel targets for investigating disease pathogenesis but also establishes an experimental foundation for early clinical diagnosis and targeted therapeutic strategies, thereby holding significant implications for advancing disease prevention and management.（This study used Agilent Human lncRNA V6 microarray. Only normalized expression data were submitted, original raw scan files are not available.）

overall_design: Two-condition experiment, Tuberculous ulcer tissue sample from human vs. non-tuberculous cutaneous ulcer tissue sample from human. Biological replicates: 3 control, 3 case, independently grown and harvested. One replicate per array.

first: Zihui

last: Huang


title: Cortical organoids reveal human-specific role of METTL5 in neurodevelopment via regulation of CHCHD2 [scRNA-seq]

status: Public on Jun 10 2026

city: San Francisco

first: Elena

last: Turkalj

institute: UCSF

type: Expression profiling by high throughput sequencing

summary: METTL5 catalyzes N6-methyladenosine (m6A) modification on 18S rRNA. In humans, loss-of-function mutations in METTL5 cause severe microcephaly and intellectual disability, whereas Mettl5 knockout (KO) animal models display inconsistent and incomplete microcephaly phenotypes. To better model human disease, we generated METTL5-KO human induced pluripotent stem cell (hiPSC)-derived cortical organoids, which exhibited impaired neural progenitor cell (NPC) proliferation and differentiation, leading to reduced ventricle-like structures and more faithful recapitulation of patient phenotypes. Mechanistically, Ribo-seq analysis revealed broad translational changes in METTL5-KO NPCs consistent with cellular stress responses rather than transcript-specific translational changes. Single-cell RNA-seq identified downregulation of CHCHD2, a mitochondrial regulator of oxidative metabolism. Reintroduction of CHCHD2 in METTL5-KO NPCs rescued proliferation and partially rescued oxidative metabolism defects. This suggests dysregulation of CHCHD2 is a driver of METTL5-mediated regulation of neurogenesis. These findings highlight a previously uncharacterized link between METTL5, CHCHD2, and cellular metabolism as essential for proper human brain development.

overall_design: Single-cell RNA sequencing was performed on human iPSC-derived cerebral organoids generated from control (KOLF2.1J) and METTL5 knockout lines to investigate the impact of METTL5 loss on neurodevelopmental cell states and transcriptional programs. Three biological replicates per genotype were analyzed, with each replicate consisting of 3-4 pooled organoids. Organoids were harvested at day 75 of differentiation for sequencing.

middle: M

first: Gugene

last: Kang

first: Michael

middle: C

last: Oldham

first: Caroline

last: Vissers


title: Decoupling oxidative resilience from reprogramming to rejuvenate the RPE and restore vision

city: Cambridge

first: Yuancheng Ryan

last: Lu

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Germanium embedded bioactive fabric reduces bacteria bioburden and modulates fibroblast and macrophage behavior in vitro

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: Surgical site infections (SSIs) occur in 2 to 4% of all surgical cases. Wearable bioactive fabrics (BAF) containing semiconductor germanium are shown to generate negative ions and emit far-infrared radiation that are reported to promote microcirculation, enhancing immunity and antibacterial activity. The objective of this study was to evaluate the impact of BAF on bacterial bioburden, fibroblast migration and proliferation, and inflammation modulation.

overall_design: Utilizing an in vitro study design, BAF was compared to control fabric (CF, non-bioactive, without inclusion of semiconductors) and untreated (UT) groups, using indirect assays in which the BAF fabric was not in direct contact with cells or bacteria, but instead separated by an air gap. These assays assessed the effects of BAF proximity on bacterial killing (Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922), fibroblast cell confluence, wound density, macrophage cytokine production, and macrophage differential gene expression.

first: Lynn

last: Pezzanite

first: Lyndah

last: Chow


title: Cortical organoids reveal human-specific role of METTL5 in neurodevelopment via regulation of CHCHD2

overall_design: Human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells (NPCs) from control and METTL5 knockout lines were used to investigate the effects of METTL5 loss on gene expression and translation. A total of six biological samples were included, consisting of three independent biological replicates per genotype (control and METTL5 knockout). For each biological replicate, matched RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) libraries were generated from the same sample. The experimental variables were genotype (control vs. METTL5 knockout) and assay type (RNA-seq vs. Ribo-seq), enabling direct comparison of transcriptional and translational changes within the same biological samples.

first: Isabelle

last: Liu


title: Correlated protein-RNA associations and a requirement for HNRNPU in the long-range recruitment of Polycomb Repressive Complexes by the lncRNAs Airn and Kcnq1ot1 PLOS Genetics

first: Joseph

middle: Mauro

last: Calabrese

address: 120 Mason Farm Road

institute: UNC Chapel Hill

summary: The lncRNAs Airn and Kcnq1ot1 recruit Polycomb Repressive Complexes (PRCs) and repress genes over multi-megabase genomic intervals, but how they interact with proteins to direct repression remains poorly understood. We conducted formaldehyde-linked RNA-immunoprecipitations (RIPs) of 27 proteins from mouse trophoblast stem cells (TSCs), using a protocol exhibiting similar signal-to-non-specific signal and post-lysis reassociation ratios as crosslinking immunoprecipitation (CLIP) and crosslinking affinity purification (CLAP). Patterns of protein associations across Airn and Kcnq1ot1 were more similar to each other than to nearly all other transcripts and partitioned to extents that mirrored the degree of repression each lncRNA induced, implying connections to mechanism. Indeed, HNRNPU, a factor essential for Xist's localization to chromatin, was enriched over Airn and Kcnq1ot1 and required to maintain normal levels of PRC1- and PRC2-directed chromatin modifications across the Airn and Kcnq1ot1 target domains, yet was dispensable for both lncRNAs’ localization to chromatin and for their association with PRC1. HNRNPU depletion caused a greater reduction in PRC-directed chromatin modifications and gene repression across the inactive X chromosome and the ~15 Mb Airn target domain than across the ~3 Mb Kcnq1ot1 domain. Perhaps relatedly, HNRNPU depletion significantly reduced overall levels of the Xist and Airn but not the Kcnq1ot1 lncRNAs. Our study reports architectures of protein association along Airn and Kcnq1ot1 compared to the transcriptome at large, highlights shared and distinct features between the two lncRNAs, and provides new perspective on the role of HNRNPU in long-range chromatin regulation by lncRNAs.

overall_design: ChIP-sequencing in CRISPR RBP knockdown mouse Trophoblast Stem Cells (mTSCs).

first: McKenzie

last: Murvin

first: Shuang

last: Li

first: Zhiyue

last: Zhang

first: Rachel

middle: E

last: Cherney

first: Mauro


title: Correlated protein-RNA associations and a requirement for HNRNPU in the long-range recruitment of Polycomb Repressive Complexes by the lncRNAs Airn and Kcnq1ot1

summary: The lncRNAs Airn and Kcnq1ot1 recruit Polycomb Repressive Complexes (PRCs) and repress genes over multi-megabase genomic intervals, but how they interact with proteins to direct repression remains poorly understood. We conducted formaldehyde-linked RNA-immunoprecipitations (RIPs) of 27 proteins from mouse trophoblast stem cells (TSCs), using a protocol exhibiting similar signal-to-non-specific signal and post-lysis reassociation ratios as crosslinking immunoprecipitation (CLIP) and crosslinking affinity purification (CLAP). Patterns of protein associations across Airn and Kcnq1ot1 were more similar to each other than to nearly all other transcripts and partitioned to extents that mirrored the degree of repression each lncRNA induced, implying connections to mechanism. Indeed, HNRNPU, a factor essential for Xist's localization to chromatin, was enriched over Airn and Kcnq1ot1 and required to maintain normal levels of PRC1- and PRC2-directed chromatin modifications across the Airn and Kcnq1ot1 target domains, yet was dispensable for both lncRNAs’ localization to chromatin and for their association with PRC1. HNRNPU depletion caused a greater reduction in PRC-directed chromatin modifications and gene repression across the inactive X chromosome and the ~15 Mb Airntarget domain than across the ~3 Mb Kcnq1ot1 domain. Perhaps relatedly, HNRNPU depletion significantly reduced overall levels of the Xist and Airn but not the Kcnq1ot1 lncRNAs. Our study reports architectures of protein association along Airn and Kcnq1ot1 compared to the transcriptome at large, highlights shared and distinct features between the two lncRNAs, and provides new perspective on the role of HNRNPU in long-range chromatin regulation by lncRNAs.

overall_design: RNA-sequencing  in WT and CRISPR RBP knockdown mouse Trophoblast Stem Cells (mTSCs).


title: Melanoma stem cells drive macrophage reprogramming to a hybrid phenotype, modulating melanoma stemness and compromising NK cell-mediated immunity

status: Public on Jun 08 2026

city: Milan

first: Michela

last: Francesconi

state: Brescia

address: Via Giovanni Antonio Amadeo, 42

country: Italy

institute: Istituto Nazionale dei Tumori

summary: Melanoma stem cells may contribute to tumor progression not only through intrinsic plasticity, but also by shaping the immune microenvironment. However, their interaction with the monocyte-macrophage compartment remains poorly understood. Melanosphere cultures derived from A375 and WM115 melanoma cell line were used as an in vitro model enriched for stemness-associated features. THP-1 monocytes were differentiated under a standardized low-dose PMA protocol and exposed to stem cell-conditioned media (SC-CM). Monocyte migration, macrophage transcriptomic and secretory profiling, effect of macrophage CM on NK cytotoxicity, melanoma stem cell phenotype and exploratory clinical relevance in the TCGA melanoma cohort were assessed. Both melanosphere models were enriched for stemness-associated programs and secreted high levels of CCL2. SC-CM promoted THP-1 migration, which was reduced by CCR2 inhibition. RNA-seq showed that SC-CM induced a shared but non-canonical macrophage phenotype enriched for inflammatory, interferon-related, pro-angiogenic, and immune-regulatory programs. Conditioned media from SC-educated macrophages impaired NK-cell cytotoxicity through heat-labile soluble mediators and induced cell line-dependent changes in melanoma stemness-associated transcriptional regulators. In TCGA, a high A375-educated macrophage score was associated with shorter overall survival, whereas the WM115-derived score showed a similar but non-significant trend. Melanoma stem cells actively shape the monocyte-macrophage compartment by promoting monocyte recruitment and inducing an inflammatory and immunomodulatory macrophage program with downstream effects on NK-cell function and melanoma cell-state regulation. These findings support a bidirectional melanoma stem cell-macrophage axis that warrants validation in more physiological systems.

overall_design: RNA-seq profiling was performed on A375 and WM115 melanoma cell lines cultured either under adherent conditions or using a melanosphere enrichment protocol. For THP-1 experiments, cells were seeded at 5 × 10^5 cells per well in 6-well plates and differentiated with 20 nM phorbol 12-myristate 13-acetate (PMA) for 72 h. The resulting macrophages were defined as non-polarized macrophages (M0). M0 macrophages were subsequently exposed to melanoma stem cell-conditioned media for 24 h, while 20 nM PMA was maintained in the culture medium under all experimental conditions. Total RNA was extracted at the end of the treatment.

first: Tiziana

last: Triulzi

first: Michele

last: Sommariva


title: Exploratory investigation of changes in blood transcriptome following mepolizumab treatment for asthma

city: Rochester

first: Emma

last: Durrenberger

state: Minnesota

address: 200 First St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary:
Objective: To evaluate the effects of mepolizumab therapy on the blood transcriptome in patients with severe eosinophilic asthma (SEA) and to determine whether changes in gene expression predict responsiveness to mepolizumab treatment.
Methods: Fourteen consecutive patients diagnosed with SEA were prospectively enrolled. Each patient had sequential blood samples obtained pre-initiation and at 4, 8, and 12 weeks post-initiation of mepolizumab. Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples for bulk RNA sequencing. Paired differential expression (DE) gene analysis was performed comparing baseline gene expression versus all timepoints. Changes in gene expression were also compared between responders versus nonresponders to mepolizumab treatment. Finally, gene set enrichment analysis was evaluated across timepoints and its interaction with the response to mepolizumab treatment.
Results: Principal component analysis of all genes demonstrated a homogeneous distribution, which did not separate into distinct groups based on either timepoint or therapeutic response. At week 12, 149 genes had significant DE (FDR < 0.05) compared to baseline. When performing all-way timepoint comparisons, 74 genes (63 protein-coding) were found to be downregulated at weeks 4, 8 and 12 compared to baseline, but no differences were observed between post baseline timepoints. Twenty-eight genes (16 protein-coding) did change with progression of time and were associated with response to therapy, and 56 protein-coding genes distinguished responders and nonresponders. At week 12, nonresponders had a high enrichment of genes involved with signaling pathways, including cytokines, growth factors, cell differentiation markers, and protein kinases.
Conclusion: In this exploratory study, mepolizumab use was associated with limited global transcriptomic separation with some preliminary differential-expression and enrichment findings. No definitive mechanistic or predictive response signatures were identified due to the study limitations. Future studies, including larger cohorts followed for longer durations with interrogation of specific immune subsets, may offer additional insight into the pathophysiology of severe eosinophilic asthma and into predicting response to mepolizumab treatment.

overall_design:
prospective, observational cohort
Fourteen consecutive patients diagnosed with SEA were prospectively enrolled. Each patient had sequential blood samples obtained pre-initiation and at 4, 8, and 12 weeks post-initiation of mepolizumab. Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples for bulk RNA sequencing. Paired differential expression (DE) gene analysis was performed comparing baseline gene expression versus all timepoints. Changes in gene expression were also compared between responders versus nonresponders to mepolizumab treatment. Finally, gene set enrichment analysis was evaluated across timepoints and its interaction with the response to mepolizumab treatment.

first: Mitchell

last: Pitlick

first: Mrunal

middle: K

last: Dehankar

first: Chantal

last: McCabe

first: Sergio

last: Chiarella

first: Kathleen

last: Bartemes

first: Kay

middle: A

last: Bachman

first: Chung-Il

last: Wi

first: Young

middle: J

last: Juhn

first: Thanai

last: Pongdee


title: Hippuric Acid Suppresses Triple-Negative Breast Cancer via the EGFL8-Notch Signaling Axis

city: Changzhou

first: Tianhan

last: Xu

address: 68 Middle Gehu Road

institute: The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University

summary: Triple-negative breast cancer (TNBC) remains a highly aggressive malignancy with limited therapeutic options due to the absence of well-defined molecular targets. Diet-induced obesity (DIO) promotes TNBC progression by reshaping systemic metabolism and inflammatory responses; however, the key circulating metabolites involved and their mechanisms remain largely unclear. This study aimed to identify key metabolites associated with TNBC progression and further investigate their biological functions and molecular mechanisms. Targeted metabolomics profiling was performed on serum samples from MMTV-PyMT spontaneous breast cancer mice to identify differential metabolites associated with DIO. Hippuric acid was identified as a significantly altered metabolite under DIO conditions. Functional studies demonstrated that hippuric acid markedly inhibited the proliferation, migration, and invasion of TNBC cells, with minimal effects on non-TNBC cells. Transcriptomic analysis identified EGFL8 as a potential downstream target, which was further confirmed by qPCR and functional assays. Overexpression of EGFL8 suppressed malignant phenotypes, whereas its knockdown promoted tumor progression. Rescue experiments showed that EGFL8 partially mitigated the inhibitory effects of hippuric acid on TNBC, suggesting that it functions as an important mediator in this process. Mechanistically, hippuric acid exerted its anti-tumor effects at least in part through modulation of the EGFL8–Notch signaling axis. In conclusion, hippuric acid suppresses TNBC progression via the EGFL8-Notch signaling pathway. These findings highlight a previously unrecognized role of a gut microbiota-derived metabolite in TNBC and suggest its potential as a therapeutic candidate, providing new prospective targets and a theoretical basis for metabolic intervention for TNBC.

overall_design: RNA sequencing profile analysis of 4T1 cells treated with hippuric acid for 24 hours.


title: CXCR3 ameliorates neutrophils-dependent disease severity in SARS-CoV-2 infection by regulating CD4+ T cell recruitment

city: Charlottesville

first: G. Brett

last: Moreau

state: Virginia

address: 345 Crispell Drive

institute: University of Virginia

summary: Understanding the host immune response to SARS-CoV-2 infection is critical for developing effective immunotherapeutic interventions. Using bulk RNA sequencing of lung tissue from mock-infected and mouse-adapted SARS-CoV-2 strain MA-10-infected mice, we identified CXCL9, CXCL10, and CXCL11 as among the most upregulated transcripts. Notably, their shared receptor, CXCR3, was also upregulated, suggesting activation of the CXCL9/10/11–CXCR3 axis in the lungs. Using spectral flow cytometry, we observed that the increased recruitment of CXCR3⁺ immune cells, particularly T cells, innate lymphoid cells (ILCs), and macrophages, correlated with milder disease outcome. Blocking CXCR3 signaling using monoclonal antibodies resulted in worsened disease, which was accompanied by reduced recruitment of T cells, ILCs, and macrophages, and a marked increase in neutrophil infiltration. Depletion of neutrophils using αLy6G antibodies in CXCR3-blocked mice alleviated disease severity, indicating that CXCR3 signaling mitigated neutrophil-driven pathology. CXCR3 blockade failed to exacerbate disease in RAG2⁻/⁻ mice, suggesting that CXCR3-mediated protection requires adaptive immune cells. Adoptive transfer of CD4⁺ T cells from wild type (WT), but not CXCR3⁻/⁻, mice conferred protection in RAG2⁻/⁻ mice. Together, our findings establish a protective role for CXCR3-recruited T cells blocking neutrophil infiltration in the lung, highlighting the mechanistic importance of the CXCL9/10/11–CXCR3 axis in protecting the lung from SARS-CoV-2 infection.

overall_design: Bulk RNAseq was performed on lung tissues collected at Day 6 post-infection from mock-infected and MA10-infected mice.

first: Md Jashim

last: Uddin

first: Claire

last: Flemming

first: Nick

last: Natale

first: Duncan

last: Hart

first: Savannah

last: Brovero

first: Judith

last: Allan

first: William

last: Petri


title: Fasting primes small intestinal regeneration after damage via a microbiome-metabolite-chromatin axis

city: HOUSTON

first: Ajay

middle: Kumar

last: Saw

state: TX

address: 7900 Cambdrige St

department: Department of Genomic Medicine

institute: University Of Texas MD Anderson Cancer Center, Houston, Texas, USA.

summary: Fasting protects the small intestine epithelial cells from high-dose radiation injury, yet the mechanisms linking fasting to epithelial regeneration remain incompletely understood. Akkermansia muciniphila (AKK) is both necessary and sufficient for fasting-induced radioprotection. Selective depletion of AKK abolishes fasting-mediated preservation of SI stem cells, while recolonization restores epithelial integrity and survival. AKK produces the short-chain fatty acid propionate, which, together with host-derived β-hydroxybutyrate (β-OHB), induces histone H3 acetylation (H3K27ac, H3K9ac) and β-hydroxybutyrylation (H3K9bhb) in crypt epithelial cells, remodeling enhancer–promoter landscapes. CUT&Tag and single-cell ATAC-seq analyses show that fasting, in an AKK-dependent manner, expands a Clu⁺Olfm4⁺ “revival” stem cell (persister cells) population enriched for HNF, FOXA, GATA and KLF transcription factor motifs, establishing a pro-regenerative chromatin state that persists through injury-repair phases. CTCF and BORIS activities persist, suggesting a role in maintaining epigenetic memory for intestinal regeneration after radiation. This microbiota–metabolite–chromatin axis primes persister cells for rapid regeneration after damage and offers a strategy to protect normal tissues during radiation therapy.

overall_design: To investigate how tetracycline-induced depletion of AKK affects gene expression in fed versus fasted mice

first: Praveen

last: Barrodia

first: Helen

last: Piwnica-Worms

first: Kunal

last: Rai


title: Molecular and Cellular Adaptations to Extended Hypothermic Oxygenated Perfusion in Donation-After-Circulatory-Death Hearts in a Porcine Model

city: New York

first: Diana

last: Albino

state: NY

department: Surgery

institute: Columbia University

summary: Introduction: Donation after circulatory death (DCD) criteria serves as a potential strategy to expand the organ pool for heart transplantation. However, DCD procurement introduces prolonged warm ischemic times that accelerate endothelial and cardiomyocyte injury. Hypothermic oxygenated perfusion (HOPE) has emerged as a novel metabolic preservation strategy, yet its biological mechanisms remain undefined. We investigated how HOPE preservation modulates cardiomyocyte viability and myocardial metabolic stability after DCD in a porcine model.  Methods and Results: Following induced circulatory arrest and reperfusion with or without in situ normothermic regional perfusion (NRP), porcine hearts were preserved for 2 hours by static cold storage (SCS) or up to 24 hours by HOPE and reanimated using a ex vivo Langendorff circuit, under normothermic conditions. HOPE preservation maintained myocardial structure, cardiomyocyte viability, and sinus rhythm after 24 hours, sixfold beyond the conventional preservation window. Flow cytometry revealed measurable populations of troponin-positive viable cardiomyocytes after 24-hour HOPE, in contrast to complete loss after 24-hour SCS. RNA sequencing and metabolomics demonstrated minimal transcriptional or metabolic shift between 2-hour SCS and 24-hour HOPE hearts, with preservation of oxidative and glycolytic balance and limited inflammatory activation. In contrast, omission of NRP during procurement resulted in marked loss of contractility and cardiomyocyte integrity, underscoring its potential role in pre-preservation harvest in a porcine model.  Conclusions: In a swine model extended hypothermic oxygenated perfusion preservation sustains myocardial and metabolic integrity after circulatory death by minimizing transcriptional and metabolic injury signatures. These findings identify a biologically distinct preservation state that mitigates ischemia-reperfusion injury and may inform novel strategies for organ and tissue preservation.

overall_design: RNA-seq profiling of swine myocardial tissue biopsied following reperfusion with or without NRP, preservation in SCS for 2h or in HOPE for 24h or 2h, and reanimation with 2h of Normothermic Machine Perfusion.


title: Akkermansia muciniphila contributes to fasting-mediated radioprotection by inducing epigenetic and transcriptional changes in small intestinal epithelial cells


title: Fasting primes small intestinal regeneration after damage via a microbiome-metabolite-chromatin axis [RNA-seq]


first: Joseph

last: Calabrese

overall_design: RNA immunoprecipitation-sequencing (RIP-Seq) in mESCs, HEK293Ts, and 1:1 mixed lysates of mouse and human cells.

first: McKenzie

last: Murvin

first: Shuang

last: Li

first: Elizabeth

middle: W

last: Abrash

first: Bridget

last: Peck

first: Samuel

middle: P

last: Boyson

first: Zhiyue

last: Zhang

first: Rachel

last: Cherney

first: Mauro


title: Fasting primes small intestinal regeneration after damage via a microbiome-metabolite-chromatin axis [Cut & Tag]

overall_design: Cut&Tag on histone marks H3K27ac and H3K9ac on small intestinal crypts isolated from Fed (-Tetra), Fast (-Tetra), Fed (+Tetra), Fast (+Tetra).


title: Glucocorticoid transcriptome in the hippocampus of wild-type and GRA knockin mice

city: RTP

first: Thomas

last: Randall

address: 101 TW Alexander

institute: NIEHS

summary: The actions of glucocorticoids are mediated by the glucocorticoid receptor (GR).  In addition to the classic full-length GR isoform (GRA), seven highly conserved receptor isoforms (GRB, GRC1, GRC2, GRC3, GRD1, GRD2, and GRD3) with progressively shorter amino-terminal transactivation domains (NTD) are produced from the single GR gene by alternative translation initiation.  The in vivo function of these seven GR NTD translational isoforms remains unknown. To elucidate the physiological function of the GR NTD translational isoforms, we developed mice (GRA knockin) that express the GRA isoform but not the GRB, GRC1, GRC2, GRC3, GRD1, GRD2, and GRD3 translational isoforms.  RNA-seq was performed on RNA isolated from the whole hippocampus of wild-type (WT) and GRA knockin mice treated with vehicle or the synthetic glucocorticoid dexamethasone (Dex) in an effort to determine how the GR NTD translational isoforms impact the glucocorticoid transcriptome.

overall_design: GRA knockin mice were developed that express the classic full length GRA receptor isoform but lack the seven GR NTD translational isoforms GRB, GRC1, GRC2, GRC3, GRD1, GRD2, and GRD3.  To generate these mice, exon 2 of the GR (Nr3c1) gene was replaced with a mutant version in which the GRA ATG start codon was left intact but the GRB, GRC1, GRC2, GRC3, GRD1, GRD2, and GRD3 ATG start codons were mutated to ATC (isoleucine).    Wild-type (WT) and homozygous GRA knockin mice were adrenalectomized (ADX) at approximately 2.5 months of age to remove endogenous glucocorticoids.  Two weeks after surgery, the ADX WT and GRA knockin mice were injected intraperitoneal with PBS or 1mg/kg dexamethasone (n=5 mice per genotype and treatment group).   After a 6-hour treatment time, mice were euthanized and the hippocampus removed. Total RNA was isolated from the hippocampus using Qiagen RNeasy Mini kit. A TruSeq RNA kit (Illumina, San Diego, CA) was utilized to prepare the poly(A)-enriched RNA-seq libraries that were sequenced on the Illumina NovaSeq 6000 in a 75-base paired-end mode according to the manufacturer’s protocol.

first: Robert

last: Oakley

first: Jianying

first: John

last: Cidlowski


title: Transcriptional changes in Drosophila tbph mutants and inducible neuronal TBPH rescue in adult heads at 60 hours post-eclosion

status: Public on Jun 07 2026

city: Trieste

first: Giulia

last: Romano

address: Padriciano 99

institute: ICGEB

summary:
TBPH, the Drosophila ortholog of human TDP-43, is required for normal neuronal function. To identify transcriptional programs altered by loss of TBPH and those restored by neuronal re-expression of TBPH, we performed Affymetrix microarray profiling on adult heads from wild-type (w1118) animals, two independent tbph loss-of-function mutants (tbph^Δ23 and tbph^Δ142), and a tbph mutant line carrying an elav-GeneSwitch-driven UAS-TBPH transgene activated by feeding 5 mM RU-486 for 60 hours post-eclosion (Rescue).
Comparison of mutants vs control identified a shared dysregulated transcriptional signature; comparison of rescue vs mutants identified the subset of these genes whose expression was restored by inducible neuronal TBPH re-expression.

overall_design: Adult Drosophila heads were collected 60 hours post-eclosion from four genotypes (3 biological replicates each, 12 samples total): w1118 (control), tbph^Δ23 mutant, tbph^Δ142 mutant, and a tbph-mutant line carrying elav-GS>UAS-TBPH activated by RU-486 (Rescue). Only the Rescue group received 5 mM RU-486 in food for 60 hours post-eclosion; control and mutant groups were maintained on standard food. Total RNA was extracted, then labeling, hybridization to Affymetrix Drosophila Genome 2.0 Arrays (GPL1322), and scanning were performed at GenoSplice technology (Paris, France) in 2011. Pairwise contrasts: tbph^Δ23 vs w1118; tbph^Δ142 vs w1118; rescue vs tbph^Δ23; rescue vs tbph^Δ142.

first: Feiguin

last: Fabian

first: Romano

last: Giulia


title: Identification of G4 regulated immune-related drug targets for prostate cancer based on G4 screen and machine learning

status: Public on Jun 03 2026

city: Xi'an

first: Yue

last: Hou

state: ShaanXi

address: Changle west road

institute: the Fourth military medical university

summary: Background: G-quadruplex (G4) structures are important epigenetic regulators and potential therapeutic targets in cancer. However, their role in prostate cancer, particularly in relation to the immune microenvironment, remains poorly understood. Methods: We performed BG4 ChIP_x001E_seq to map genome_x001E_wide G4 structures in the prostate cancer cell line C4_x001E_2. Bioinformatics analyses integrated G4_x001E_associated genes with immune pathway enrichment and machine learning algorithms (LASSO, SVM_x001E_RFE, GBM, Naïve Bayes, and GLM) to identify hub genes in prostate cancer progression. Clinical data from GTEx, TCGA, and HPA were analyzed for expression and survival. Functional validation included qPCR, CCK_x001E_8, colony formation, and wound_x001E_healing assays. Druggability was assessed using DrugnomeAI, and AI_x001E_assisted peptide design was performed with RFdiffusion and ProteinMPNN. Results: We identified 1289 prostate cancer_x001E_specific G4 structures, predominantly in promoter regions. Machine learning and immune enrichment analysis pinpointed IKBKB as a key hub gene in prostate cancer progression. IKBKB was overexpressed in prostate cancer tissues, correlated with advanced stage and poor prognosis, and was regulated by promoter G4 structures via transcription factors AR and ERG. IKBKB promoted genome instability, tumor stemness, and immune microenvironment remodeling. G4 stabilization increased IKBKB expression and activated the NF_x001E_κB pathway, enhancing cancer cell viability, proliferation, and migration. Computational screening confirmed IKBKB’s druggability and identified potential inhibitors (e.g., Auranofin). AI_x001E_assisted design generated peptide inhibitors targeting IKBKB and a CRISPR_x001E_dCas9 strategy for G4 disruption.

overall_design: We used BG4 ChIP-seq method to target all endogenous G4 structures in the C4-2 cell line and described the role of G4s in prostate cancer.

first: Chuanjun

last: Shu

first: Changbin

last: Yang


title: A Conserved Natural Killer Cell Transcriptional Fingerprint in Rhesus Macaque Models of Acute Viral Infections [RNA-seq_SIVmac251]

city: Durham

first: Andrew

last: Hudson

address: 1328 Campus Drive

institute: Duke University

summary: In this study, we utilize a rhesus macaque (RM) model to define the transcriptomic profile of NK cells during acute lentiviral infection and to map the changes in this profile as infection progresses to the early chronic phase. Using a novel summary gene set for NK cell cytokine stimulation, we report synchronous metabolic and signaling transcriptional patterns that underlie established features of NK cell dysfunction. We further identify a set of core conserved gene pathways central to RM NK cell activation across diverse acute viral contexts.

overall_design: RNA-seq was performed on bulk-sorted peripheral NK cells from rhesus macaques (N=5) infected with SIVmac251 intrarectally. Blood was sampled on days 0, 7, 70, and 74 post-infection.

first: Kyle

last: Kroll

first: Benjamin

last: Bimber

first: Brady

last: Hueber

first: Griffin

last: Woolley

first: Keith

last: Reeves


title: Spaceflight multi-omics reveals vulnerabilities of human germ cell development

city: Fuzhou

first: Ying

last: Li

state: Fujian

address: No. 2, Xueyuan Road, University Town

institute: Fuzhou University

type: Methylation profiling by high throughput sequencing

summary: Exposure to microgravity, cosmic radiation, and other spaceflight conditions induces significant physiological adaptations in biological systems. While prior studies have characterized effects on stem cell self-renewal and differentiation, the biological impacts of spaceflight on human germ cell development remain unexplored. To address this gap, we deployed automated experimental platforms aboard China's Tianzhou-1 (TZ-1) and Tianzhou-6 spacecraft, enabling fluorescent morphological analysis and multi-omics profiling of stem cell derivatives under orbital conditions. These systems incorporated live-cell imaging, remote operation interfaces from Earth, and integrated sample preservation for time-point-specific specimen capture. Our experiments revealed that spaceflight significantly reduced germ cell yields and dysregulated translational profiles, particularly in cytoskeletal organization and extracellular matrix (ECM) interaction pathways. However, whole-exome sequencing and genome-wide methylation analyses confirmed genomic stability, with no statistically significant mutations during short-term spaceflight. This work establishes an automated platform for real-time analysis of human germ cell differentiation in orbital microgravity and provides a foundation for future space biology research.

overall_design:
To investigate the impact of spaceflight conditions (microgravity and cosmic radiation) on human germ cell development, we deployed optimized automated bioreactors aboard China’s Tianzhou-1 (TZ-1) and Tianzhou-6 (TZ-6) spacecraft. These systems enabled long-term differentiation of human embryonic stem cells (hESCs) into three germ cell lineages—human induced primordial germ-like cells (hiPGCs), human induced ovarian follicles (hiOFs), and human induced spermatogonial stem cells (hiSSCs)—under orbital microgravity, while replicating ground controls under Earth gravity (1g).
Building upon this platform, we conducted integrated multi-omics profiling—including transcriptome-translatome dual-omics sequencing (T&T-seq), whole-exome sequencing (WES), and whole-genome bisulfite sequencing (WGBS)—to quantify spaceflight-induced alterations in gene expression, translational efficiency, genomic stability, and DNA methylation. To spatially resolve cellular adaptations, the bioreactors incorporated real-time imaging, enabling continuous morphological tracking and remote operation from Earth. Furthermore, we performed functional enrichment analysis of differentially expressed genes and proteins to identify pathways dysregulated by spaceflight, with emphasis on cytoskeletal organization, extracellular matrix (ECM) interactions, and metabolic reprogramming. Finally, rigorous statistical validation of genomic stability and cell-type-specific responses  (hiPGCs/hiOFs vs. hiSSCs) established the reproducibility of spaceflight effects across germ cell lineages.

first: Hui

last: Gao

first: Jie

last: Xiong

last: Wang

first: Yongchun

last: Yuan

first: Linjun

first: Jinzhong

last: Xu

first: Wenze

last: Huang

first: Gikin

last: Tan

first: Xiaojuan

last: He

first: Qiangfeng

last: Zhang

first: Tao

first: Kehkooi

last: Kee


title: Reprogramming lineage features promotes epithelial behavior in carcinoma cells

status: Public on Aug 06 2026

city: Dallas

first: Lance

last: Terada

address: 5323 Harry Hines Blvd, MC 8448

institute: University of Texas Southwestern

summary: Cancer cells distort epigenetic control of gene expression, allowing for a remarkable degree of plasticity and loss of cell type identity.  At the same time, expression of identity-discordant lineage determinants can significantly shift cell phenotype by creating lineage hybrid states.  One example is the misexpression of IKZF3, encoding the lymphocyte restricted transcription factor Aiolos, by roughly half of non-small cell lung carcinomas (NSCLC) and the majority of small cell lung carcinomas [1].  During normal lymphocyte development, pre-B progenitors enter a proliferative phase dependent on survival cues from bone marrow stroma.  To progress, Aiolos and its paralog Ikaros (IKZF1) repress multiple adhesion-related genes, releasing cells from this epithelial-type dependence on solid matrix in preparation for their release as mature lymphocytes into the circulation [2, 3].  In lung cancers, unlicensed expression of Aiolos initiates a similar shift from an epithelial to a lymphocyte-like state by repression of multiple adhesion-related genes, resulting in loss of anoikis and consequent metastatic spread [1].  To reverse these lymphoid traits, we created a chimeric epigenetic editor designed to specifically retrieve Aiolos-repressed epithelial adhesion properties.  Here, we demonstrate proof of principle for epithelial lineage restoration by exploiting a lymphocyte developmental pathway.

overall_design: RNA-seq data of H1155 NSCLC cells lentivirally transfected with the empty vector or a chimeric transcription factor studied in this manuscipt

middle: S


title: A distinct cis-regulatory element is required for ILC3s to maintain intestinal tolerance through amplifying RORγt expression [scRNA-seq]

city: Beijing

last: Zhao

state: Beijing

address: No. 1, Qinghuayuan, Haidian District

department: Institute for Immunology

institute: Tsinghua University

summary: RORγt is the linage-specific transcription factor for both ILC3 and T-helper 17 (Th17) counterparts, who take an essential place in regulating intestinal homeostasis. While the biological significance of high RORγt expression and its distinct regulatory mechanisms in ILC3s remains investigation. Through comparing ATAC-seq results on ILC3 and Th17 cells, we identified an open chromatin region (OCR369) which specifically regulates ILC3 RORγt expression and development. Mechanistically, OCR369 is bind by the RORγt activator RUNX3, and is also involved in the chromatin-loop formation between OCR369 and RORγt-promoter. OCR369 depletion also impaired the MHCII+ ILC3s, a group of antigen-presenting cells that regulate RORγt+ Treg cells. And disruption of Th/ Treg balance in the OCR369-deficient mice leads to the spontaneous type 2 inflammation in the small intestine, and impaired generation of oral tolerance. Thus, our study revealed a specific RORγt amplifying mechanism in ILC3 and its important role in maintaining intestinal immune environment and food tolerance.

overall_design: About 0.5 cm length of small intestine was cut at ~10 cm to the cecum from naïve 20 weeks old littermates (n=3), extracted RNA using TRIzol reagent (Invitrogen, 15596026CN).Gene expression profiles were compared btween the  Rorc Δ369 and Rorc WT mice

first: Haoyu

last: Liu

first: Panwei

last: Song

first: Wenyan

first: Xiaohuan

last: Guo


title: Transcriptomic profiling of PTX4 overexpression in THP-1 cells

status: Public on Jun 01 2026

city: singapore

first: yi

last: chai

department: CSI

country: Singapore

institute: National University of SIngapore

summary: Our study demonstrated that PTX4 is silenced by promoter hypermethylation in adverse-risk AML patients, and patients with lower PTX4 expression exhibit significantly reduced overall survival. Methylation-specific PCR confirmed PTX4 promoter methylation in multiple AML cell lines including THP-1, and treatment with the demethylating agent 5-azacytidine restored PTX4 expression. To elucidate the molecular mechanisms by which PTX4 exerts its tumor suppressive function, we performed RNA-sequencing analysis of THP-1 cells with stable PTX4 overexpression compared to empty vector controls. Total RNA was extracted from three biological replicates each of THP-1-EV and THP-1-PTX4-OE cells using the RNeasy mini kit (Qiagen). RNA library construction and sequencing were performed by Novogene Singapore using the Illumina NovaSeq 6000 platform with paired-end sequencing. Raw reads were quality-assessed using FastQC v0.11.5, followed by adapter trimming and alignment to the human reference genome (GRCh38/hg38). Pathway analysis demonstrated that PTX4 suppresses oncogenic programs including NF-κB signaling, IL-17 signaling, and Toll-like receptor pathways, while enhancing T cell receptor signaling and MAPK pathways. This dataset provides molecular insights into PTX4-mediated tumor suppression in AML and supports its potential as a therapeutic target through demethylating agents.

overall_design: THP-1 human monocytic cells were stably transduced with either empty vector (EV, n=3) or PTX4 overexpression construct (PTX4-OE, n=3). Total RNA was extracted from three independent biological replicates per condition. RNA libraries were constructed and sequenced on Illumina NovaSeq 6000 platform with paired-end sequencing. Differential gene expression analysis was performed to identify PTX4-regulated genes.

first: Jianbiao

last: Zhou

first: Yi

last: Chai


title: Cellular expression domains of type 3 deiodinase in the meninges, choroid plexus, tanycytes and barrier tissues of the brain

city: Bethesda

first: Hong

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary: Thyroid hormone is necessary to stimulate mammalian brain development but its action must be limited to avoid damage arising from unregulated stimulation. Type 3 deiodinase, a thyroid hormone-degrading enzyme encoded by Dio3, constrains thyroid hormone exposure in the brain and has primarily been described in neuronal populations.  However, detection is difficult because of low, transient expression, often in specialized cell populations.  Here, using Dio3Cre-mediated labeling with a sensitive fluorescent reporter, we uncovered Dio3 expression in non-neuronal cell types in blood-cerebrospinal fluid (CSF) and blood-brain barriers during development in mice.  These barriers control solute transport, suggesting that Dio3 regulates thyroid hormone availability at these cellular interfaces between brain tissues and hormone-bearing fluids.  Dio3 expression was detected in the arachnoid barrier in the meninges, the membranes surrounding the brain, and in the epithelial layer of the choroid plexus, which regulates solute exchange with CSF. Transcriptome analyses corroborated early Dio3 expression in these tissues, beginning even before barrier function matures. Dio3 expression was also detected in tanycytes lining the third ventricle and in pericytes associated with capillaries at the neurovascular interface. These findings suggest a role for Dio3 in regulating thyroid hormone availability at key interfaces of CSF and blood with immature brain tissues.

overall_design: Meninges and choroid plexus tissues were micro-dissected from embryos and neonatal mice at the ages indicated, then immediately frozen on dry-ice in readiness for RNA extraction. RNA from different samples was purified using an RNeasy plus mini or macro kit (Qiagen #74134 or #74034), then (150 -300 ng) used to construct libraries with a SMARTer stranded total RNA sample prep kit (Takara #634875).

first: Ye

first: Lily

last: Ng

first: Douglas

last: Forrest


title: Timely NODAL Inhibition Driven by Consecutive Lefty1 and Lefty2 Is Required for Epiblast Patterning

city: New Haven

first: Minming

last: Wang

state: CT

address: 10 Amistad

department: BBS

institute: Yale University

summary: The mouse genome encodes two Lefty genes, novel TGF-β superfamily members that antagonize the Nodal signaling gradient during symmetry breaking within the gastrulation-stage embryo. Despite their reported roles as modulators of this key morphogen, accurately describing how the Leftys contribute to cell fate determination is hindered due to the challenge of modeling rapid changes in embryonic complexity from static snapshots of internally developing embryos. Here, we generated two high temporal and cellular resolution transcriptional atlases of Lefty1 and Lefty2 mutant embryos and evaluated the effects of these regulators on cell fate specification using a Network Flow Model to describe the processes of gastrulation continuously. Combined with analysis of dynamic Nodal activity in wild-type and mutant embryos, we capture a sequential shift from Anterior Visceral endoderm (AVE)-based Lefty1 to primitive streak (PS)-based Lefty2 control, which our mutant data suggest act to collectively shield the developing embryo from spurious Definitive endoderm (DefEndo) and Extra-embryonic mesodermal (ExM) differentiation. We find that mutation of either Nodal antagonist converges towards a highly similar phenotype, with only the most rostral neural lineages protected in lefty2 mutant embryos as a hallmark of AVE-based patterning.  Collectively, our work highlights the potential of single-cell profiling technologies to decode complex differentiation processes, including addressing how classical morphogens temporally coordinate multiple distinct transcriptional states from the same pluripotent field.

overall_design: single cell RNA-seq analysis of Lefty1 and Lefty2 mutant embryos

first: Zachary

middle: D

last: Smith

first: Yusuke

last: Kijima

first: Helene

last: Kretzmer


title: Methylome profiling enhances risk stratification and reveals context-dependent chemo-resistance mechanisms in acute myeloid leukemia

type: Methylation profiling by genome tiling array

summary: Acute Myeloid Leukemia (AML) is the second most lethal hematologic malignancy, with approximately 30% of patients being refractory to first-line induction therapy. While current risk stratification systems, such as European LeukemiaNet (ELN), use cytogenetic and molecular markers to guide treatment decisions, their predictive accuracy remains suboptimal, particularly in forecasting treatment response. In this study, we performed integrated methylome and transcriptome analysis of diagnostic samples from 145 AML patients, including methylome data on 25 patients, to investigate the molecular basis underlying the discrepancy between predicted and actual treatment outcomes. Unsupervised analysis revealed that while genomic backgrounds strongly influence molecular profiles, treatment response patterns frequently diverge from predictions based on cytogenetic and mutational risk classifications. We identified PTX4 as a novel tumor suppressor gene (TSG) silenced by DNA hypermethylation in patients with adverse-risk AML. Within individual AML subtypes, comparison of refractory/relapsed (RR) cases versus those achieving complete remission (CR) uncovered distinct resistance mechanisms. Furthermore, analysis of hematopoietic developmental trajectories revealed that RR cases exhibit altered epigenetic programming, characterized by preferential methylation changes in regulatory regions, such as polycomb-repressed chromatin states. These results represent both context-dependent and unifying mechanism of treatment resistance that is independent of genetic background. These findings highlight the limitations of current genetic-based risk assessments and underscore the potential of incorporating epigenetic profiling, such as methylome analysis, to more accurately predict treatment response and guide therapeutic strategies in AML.

overall_design: We aimed to profile the DNA methylome of acute myeloid leukemia (AML) patients to investigate mechanisms of treatment response. Bone marrow DNA was analyzed using the Infinium MethylationEpic array in a cohort of 25 patients, including 13 relapsed/refractory (RR) AML patients and 12 patients who achieved complete remission (CR) after standard induction therapy. The patients were selected to represent diverse cytogenetic and molecular subtypes while maintaining balance for age and sex between response groups.


title: Increasing TET expression and 5-hydroxymethylcytosine formation by a carbocyclic 5-aza-2’-deoxy-cytidine antimetabolite [methylation]

city: Saarbruecken

first: Gilles

last: Gasparoni

state: Saarland

address: Campus

department: Genetics Department

country: Germany

institute: Saarland University

summary: Ten-eleven translocation (TET) enzymes are critical epigenetic regulators, which oxidize the methylated cytosine nucleobase 5-methyl-dC (5mdC) in the genome to 5-hydroxymethyl-dC (5hmdC) in an α-ketoglutarate-dependent manner. Because the presence of 5mdC in the promoter region of a given gene silences its expression, this oxidation goes in hand with the reactivation of such silenced genes. In different highly aggressive cancers such as acute myeloid leukemia (AML) and glioblastoma, loss of TET enzyme function and therefore reduced 5hmdC levels pave the way for tumor development. Impairment of TET activity can occur through metabolic inhibition, through loss-of-function mutations in TET genes themselves, and finally through suppression of TET-expression via epigenetic silencing. Reactivation of TET enzyme expression represents a major aim of epigenetic cancer therapy. Here we show that the carbocyclic antimetabolite 5-aza-2’deoxycytidine (cAzadC), which is supposed to suppress the methylation of DNA during replication, leads to a substantial increase of TET2 expression and strongly increasing 5hmdC levels. We show that the treatment with cAzadC goes in hand with the broad reactivation of the cellular anti-tumor responses. With patient-derived xenograft AML-mouse models, we show that this translates into a strongly improved anti-cancer effect in vivo.

overall_design: MOLM-13 cell line was treated with 5-Aza-2’-deoxycytidine (0.5uM) or with carbocyclic AzadC derivative (0.5uM). Cells treated with DMSO only were used as a control. All treatments were performed in triplicates.

first: Maike

last: Däther

first: Elsa

last: Peev

first: Annika

last: Fröhlich

first: Binje

last: Vick

first: Sogol

last: Fatourechi

first: Matthias

last: Heiss

first: Corinna

last: Pleintinger

first: Emmanuel

last: Bisong

first: Hans

last: Hurmiz

first: Davide

last: Guglielminotti

first: Yasmin

middle: V

last: Gärtner

first: Tina

last: Aumer

first: Karsten

last: Spiekermann

first: Jörn

last: Walter

first: Irmela

last: Jeremias

first: Franziska

middle: R

last: Traube

first: Thomas

last: Carell


status: Public on Jun 02 2026

first: Ying

last: Li

first: Hui

last: Gao

first: Jie

last: Xiong

last: Wang

first: Yongchun

last: Yuan

first: Linjun

first: Jinzhong

last: Xu

first: Wenze

last: Huang

first: Gikin

last: Tan

first: Xiaojuan

last: He

first: Qiangfeng

last: Zhang

first: Tao

first: Kehkooi

last: Kee


title: Chemo-omic pipeline enables discovery of prion synaptotoxic pathways and inhibitory drugs

status: Public on May 31 2026

city: Boston

first: David

last: Harris

address: 72 E. Condord St., K-225

department: Biochemistry & Cell Biology

institute: Boston University

summary: Prion propagation, in which the cellular prion protein (PrPC) is conformationally converted into an infectious structure (PrPSc), is now well understood. However, the molecular mechanism responsible for the neurotoxicity of prions remains unclear. Synaptic loss is one of the earliest events in both in vivo and in vitro models of prion disease. We previously developed a neuronal cell culture model to analyze the mechanisms of prion-induced synaptic degeneration in a physiologically relevant setting. Using this system, we showed that exposure of hippocampal neurons to PrPSc engages a NMDAR/p38 mitogen-activated protein kinase (MAPK) signaling pathway that results in rapid, PrPC-dependent loss of synaptic transmission and retraction of dendritic spines. To comprehensively identify the components of this synaptotoxic signaling pathway, we measured changes in the phosphoproteome and transcriptome of hippocampal neurons exposed to PrPSc while they were undergoing the process of dendritic spine retraction. We then used these data as input into the L1000 and P100 databases of transcriptomic and proteomic drug signatures, leading to the discovery of 17 compounds that were able to prevent PrPSc-induced spine retraction. These compounds converged on three protein kinase targets: Ca2+/calmodulin-dependent protein kinase II (CaMKII), protein kinase C (PKC), and glycogen synthase kinase 3β (GSK3β). Using immunocytochemical staining, we confirmed that PrPSc treatment of hippocampal neurons induced phosphorylation of the three kinases and caused their rapid translocation to dendritic spines. Along with N-methyl-D-aspartate receptors (NMDARs) on the neuronal surface, which trigger an initial influx of Ca2+ in response to PrPSc, these kinases constitute key nodes in a signaling network that mediates prion synaptotoxicity. Taken together, our results provide new insights into the mechanisms of prion neurotoxicity, and they identify novel molecular targets and inhibitory compounds that can be utilized for therapy of prion diseases.

overall_design: RNA-seq profiling of wild-type C57BL/6J mouse hippocampal neurons and there PrP knock out derivatives at 30 minutes, 2 hours, 4 hours and 24 hours of exposure to purified PrPSc or Mock materials

first: Nhat

last: Le

first: Robert

last: Mercer

first: Cheng

last: Fang

first: Adam

last: Labadorf


title: BACH1 orchestrates macrophage state transitions to coordinate regenerative inflammation [chimeric BMT]

city: Debrecen

first: Noemí

last: Caballero-Sánchez

address: Egyetem tér 1

department: Biochemestry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary: To delineate the transcriptional changes, we used the cardiotoxin (CTX) acute muscle injury model and profiled the chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) in sorted macrophage populations at different time-points during muscle regeneration. We identified BACH1 a heme-responsive transcriptional repressor, as a novel regulator of this process. Histological analysis reveals that Bach1 myeloid-specific knockout mice present a persistent necrotic fiber as well as delayed tissue repair while FACS and bulk RNA-seq show an abnormal macrophage phenotype switch and deregulation of critical genes involved in regenerative inflammation. To study how BACH1 affects the macrophage subtype specification and cellular composition during muscle repair, we have performed single-cell RNA-seq (scRNA-seq) experiments in control and myeloid specific Bach1 knockout models at different time points post CTX injury in mice. Our results indicate significant differences in the macrophage subsets composition and gene expression profiles demonstrated by the magnitude of expression of critical inflammatory and repair-related genes. In conclusion, by combining single-cell transcriptomics and macrophage-specific knockouts, we revealed a crucial role for BACH1 in regulating macrophage subtype specification and subsequently skeletal muscle regeneration.

overall_design: Following Tiablis Anterior isolation and enzymatic digestion, immune cells were sorted using CD45 magnetic beads (Miltenyi Biotec) and analyzed using scRNA-seq.


title: Evolution of origin sequence and recognition for licensing of Eukaryotic DNA replication

city: Cold Spring Harbor

first: Bruce

last: Stillman

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: The large size of eukaryotic chromosomes necessitates that the initiation of DNA replication occurs at numerous origins of DNA replication. In S. cerevisiae, origins are highly DNA sequence-specific and are recognized by the Origin Recognition Complex (ORC). In contrast, most eukaryotes have lost features in ORC subunits that contribute to DNA sequence-specific recognition, raising the question of how origins are identified. An analysis of origins in the genome of the distantly related budding yeast Yarrowia lipolytica identified considerable variability in origin sequence and structure. High-resolution structures demonstrate that Y. lipolytica origins are recognized by a combination of ORC and Cdc6 in a manner different from S. cerevisiae. The structure of Yarrowia ORC-Cdc6 bound to different origins shows considerable plasticity in protein-DNA interactions. We compare these yeast structures to the structure of human ORC-CDC6 bound to DNA. These studies reveal information on the evolution of origins and origin recognition.

overall_design: EdU pulse labeling of Yarrowia lipolytica DNA at various time points post G0/G1 arrest and release, isolation of DNA and fragmentation, click chemistry pull down of labelled DNA and DNA sequencing.

first: Jack

last: Bauer

first: Narges

last: Zali

first: Om

last: Prakash Chouhan

first: Osama

last: El Demerdash

first: Kaiser

last: Loell

first: Justin

last: Kinney

first: Leemor

last: Joshua-Tor

first: Matt

last: Tuttle


title: Integrated Multi-Omics and Interactome Analysis of CDK8 Inhibition Reveals Erythroid Differentiation Programs and BET Synergy in AML Stem-like Cells

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: Acute myeloid leukemia (AML) with leukemic stem cell (LSC) characteristics represents a therapeutic challenge due to inherent resistance to differentiation. CDK8, a kinase component of the Mediator complex, has emerged as a regulator of oncogenic transcription, yet its role in LSC maintenance and potential as a combination therapy target remains incompletely defined. RVU120 (Romaciclib) and CCT251921 are selective, orally bioavailable small-molecule inhibitors of CDK8. Of them, RVU120 is currently tested as monotherapy in stage II clinical trials for Myelodysplastic Syndrome. Here, we demonstrate that pharmacologic CDK8 inhibition rapidly suppresses STAT5 Ser726 phosphorylation in LSC-like TEX cells, reduces CD34+ populations, and drives erythroid/megakaryocytic differentiation. Integrated time-resolved transcriptomic, proteomic, and phosphoproteomic analyses of TEX cells, revealed highly concordant responses to both inhibitors, with progressive activation of cholesterol biosynthesis, inflammatory signaling, and erythroid-like differentiation. Phosphoproteomic profiling identified a restricted set of altered phosphosites enriched in nucleic acid-binding proteins. Co-immunoprecipitation mass spectrometry mapping of the CDK8 interactome in TEX and AML models identified core proteins, including Mediator components, chromatin remodelers (INO80), and BRD3, a BET family bromodomain protein. CUT&Tag genomic profiling demonstrated that CDK8 inhibition triggers widespread enhancer activation (H3K27ac, H3K4me1) with coordinated redistribution of Polymerase II RNA, BRD3, and MLL4, while uncoupling proliferative from immune-regulatory chromatin programs. Functional screening revealed context-dependent synergy between CDK8 and BET inhibition in AML cell lines and patient-derived xenograft models. These findings position CDK8 as a central node in LSC transcriptional control and establish a mechanistic rationale for combined CDK8-BET inhibition as a precision therapeutic strategy in molecularly defined AML subsets. The Cut&Tag dataset generation was supported by the National Science Center grant (2018/30/E/NZ2/00801).

overall_design: For the genome-wide chromatin survey with Cut&Tag, 300 000 TEX cells were separately treated with 5% DMSO, RVU120, or CCT251921 at 0.5 μM for 24h and 72h, then collected and stored as pellets at -80 °C. At least three biological replicates were prepared.

first: Małgorzata

first: Urszula

last: Pakulska

first: Izabela

last: Rumienczyk

first: Maria

last: Kulecka

first: Jarosław

last: Cendrowski

first: Magdalena

last: Cubulska-Lubak

first: Ewelina

last: Kaniuga

first: Zuzanna

last: Sandowska-Markiewicz

first: Wioletta

last: Slusarczyk-Kacprzyk

first: Krzysztof

last: Goryca

first: Tymon

last: Rubel

last: Bakun

first: Bianka

last: Swiderska

first: Kamila

last: Kruczkowska

first: Piotr

last: Rzepecki

first: Jolanta

last: Korsak

first: Krystyna

last: Kyc-Wachowiak

first: Anna

last: Polak

first: Przemyslaw

last: Juszczynski

first: Milena

last: Mazan

first: Tomasz

last: Rzymski

first: Jerzy

last: Ostrowski


title: BACH1 orchestrates macrophage state transitions to coordinate regenerative inflammation [Individualmouse]

first: Noemí

last: Caballero-Sánchez


title: PD-1 regulates latent effector differentiation of thymic cytotoxic CD8+ T cells

status: Public on May 29 2026

city: Rochester

first: Haidong

last: Dong

state: MN

address: 200 First Street SW

institute: Mayo Clinic

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

overall_design: Refer to individual Series


title: Targeting WNK1 suppresses acute myeloid leukemia progression and enhances sensitivity to venetoclax

city: Shanghai

first: Fangli

last: Chen

address: 1111 XianXia Road

institute: Tongren Hospital, Shanghai Jiao Tong University School of Medicine

summary: The With-No-Lysine (WNK) kinase family plays critical roles in cellular signaling, yet its significance in acute myeloid leukemia (AML) remains unclear. Here, we demonstrate that WNK1 is a novel therapeutic target in AML. Analysis of public databases and primary patient samples reveals that WNK1, but not other WNK family members, is highly expressed in AML, particularly in adverse subtypes such as FLT3-ITD mutated AML. CRISPR dependency scores confirm WNK1 is essential for AML cell survival. Pharmacological inhibition of WNK1 using WNK463 or WNK11 significantly suppresses the proliferation of AML cell lines and primary blasts, induces apoptosis through upregulation of pro-apoptotic proteins Bim and Puma, and impedes tumor growth in mouse xenograft models without significant toxicity. Transcriptomic analysis indicates that WNK1 inhibition downregulates genes involved in DNA replication pathways, including MCM5, CHAF1B, and GINS2, whose high expression correlates with poor prognosis. Importantly, elevated WNK1 expression is associated with resistance to the BCL-2 inhibitor venetoclax, a frontline AML therapy. Combining WNK463 with venetoclax exhibits synergistic anti-leukemic effects in vitro, accompanied by enhanced Bim upregulation. In summary, our study identifies WNK1 as a key oncogenic driver in AML and establishes WNK1 inhibition as a promising therapeutic strategy that suppresses AML progression and sensitizes leukemia cells to venetoclax, providing a rationale for novel combination regimens to overcome drug resistance.

overall_design: To elucidate the potential molecular mechanisms underlying the effective inhibitory effect on AML cells by WNK463, we treated MV4-11 cells with 1 μM of WNK463 or blank control for 48 h, and extracted RNA from these cells for high-throughput transcriptome sequencing.


title: Developing a pan cancer therapy based on DISE inducing short RNAs

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary: Developing DISE inducing sRNAs based on CAG trinucleotide repeat sequences. This RNA seq analysis was designed to identify downregulated mRNAs in both the PC3 prostate tumros and the liver of xenografted nude mice treated with eitehr the control sRNA sNT1 or the CAG repeat based sRNA sCAG, both delivered as lipopolyplexes.

overall_design: Mice were implanted with PC3 cells s.c. Three weeks after tumor implanation they were i.p. treated six times over two weeks with either sNT1-LPP or sCAG-LPP. 17 days after first treatment RNA was isolated from both the PC3 tumors and the liver of treated mice. RNA was subjected to long RNA sequencing.

first: Elizabeth

last: Bartom


title: Uncovering ectopic GC-like niches for tumor reactive lymphocyte priming in lung adenocarcinoma using Stereo-XCR-seq

city: Shenzhen

first: Zhong

last: Liu

address: 9 Yunhua Road, Meisha Street, Yantian District

institute: BGI

summary: This experiment aims to dissect the spatial immune microenvironment of lung cancer by performing Stereo-XCR-seq on fresh-frozen tumor tissues. First, we conduct rigorous sample quality control, perform serial tissue sectioning, use H&E staining for morphological validation, and capture mRNA in situ on Stereo-seq chips. Subsequently, we enrich TCR and BCR transcripts from the constructed Stereo-seq libraries using our in-house developed sscirPCR strategy, via nested PCR-mediated ligating element addition, splint oligo-induced circularization, and two-round specific PCR amplification, enabling the spatial mapping of lymphocyte clonal dynamics within the tumor tissue to uncover immune evasion mechanisms and inform immunotherapeutic strategies.

overall_design:
Spatial transcriptomics profiling of 11 lung adenocarcinoma (LUAD) patient tissues using Stereo-XCR-seq. Stereo-seq was performed to capture in situ mRNA, followed by TCR/BCR enrichment to profile lymphocyte clonal dynamics within the tumor microenvironment.
***The raw sequencing reads are available in the Genome Sequence Archive (GSA, https://ngdc.cncb.ac.cn/gsa-human) under accession number HRA013757 and HRA018548.

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Raw files for human/patient samples are being made available in GSA (https://ngdc.cncb.ac.cn/gsa/) for controlled access to the personally identifiable sequence data.
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first: Zhan

last: Xiaojuan

first: Huang

last: Mengye

first: Zhang

last: Yang

first: Liu

last: Zhong

last: Chengwu

first: Guo

last: Yanying

last: Yi

first: Zhou

last: Wenwen

first: Yan

last: Yixin

first: Zeng

last: Hui

first: Dong

last: Yingqi

last: Xuan

first: Chen

last: Xiaoyu

first: Yang

last: Haohang

first: Ma

last: Rong

first: Zhu

last: Fan

first: Zheng

last: Xubin

first: Li

last: Xinxing

first: Hou

last: Sen

first: Gao

last: Zhidong

first: Yin

last: Jinwen

first: Chan

last: Francis Ka-ming

first: Wu

last: Qin

first: Deng

last: Senyi

first: Yao

last: Yin

first: Suo

last: Shengbao

last: Chuanyu

last: Longqi

first: Xu

last: Xun

last: Yong

first: Tao

last: Haoran

first: Ai

last: Xinlei

last: Yuliang

last: Tao

first: Sun

last: Hanyong

last: Young

first: Zuo

last: Li

first: Wang

last: Hua

last: Xin

last: Zhifang

last: Jingying

last: Zexian

first: Feng

last: Yu


title: Cancer Therapeutic TKI Osimertinib-induced Cardiotoxicity Is Driven by HDAC-Dependent Epigenetic Repression and Rescued by Vorinostat

city: Shreveport

first: Hind

last: Lal

state: LA

address: 1501 Kings Hwy

department: Cellular Biology and Anatomy

institute: LSU Health Shreveport

summary: Osimertinib, a third-generation EGFR tyrosine kinase inhibitor (TKI), has significantly improved outcomes in non–small cell lung cancer (NSCLC) patients harboring the T790M mutation; however, emerging clinical evidence indicates a substantial risk of cardiotoxicity. Here, we establish the first in vivo preclinical model of osimertinib-induced cardiotoxicity using transverse aortic constriction (TAC) in mice. Osimertinib treatment resulted in profound cardiac dysfunction, impaired hypertrophic remodeling, and increased markers of heart failure and fibrosis. Unbiased transcriptomic profiling revealed a maladaptive myocardial stress response characterized by activation of p53-associated cell death pathways, mitochondrial dysfunction, and negative enrichment of histone acetyltransferase (HAT) complexes, indicating epigenetic repression. Mechanistically, osimertinib-treated hearts exhibited increased expression of multiple histone deacetylase (HDAC) isoforms, reduced acetylation of key histones, and enhanced cardiomyocyte apoptosis via Bax/caspase-mediated pathways. There was only a minimal, transient effect on inflammation, supporting a type I, cell-autonomous cardiotoxic mechanism. Consistent with this, in vitro and in vivo analyses demonstrated suppression of pro-survival ERK/AKT signaling, mitochondrial dysfunction, and activation of intrinsic apoptotic pathways. Given the central role of HDAC activation, we tested whether pharmacologic HDAC inhibition could mitigate osimertinib-induced cardiotoxicity. Treatment with the FDA-approved HDAC inhibitor vorinostat (SAHA) restored histone acetylation, attenuated p53 activation, reduced cardiomyocyte death, and rescued cardiac function in osimertinib-treated mice. Translational studies in human NSCLC-derived PC9 cells further demonstrated that SAHA enhances osimertinib anti-tumor efficacy while alleviating cardiotoxicity. Collectively, these findings define HDAC-dependent epigenetic repression as a key mechanism underlying osimertinib-induced cardiotoxicity and identify HDAC inhibition as a therapeutically actionable strategy to improve both cardiac safety and cancer treatment efficacy.

overall_design: To define the molecular mechanism of Osimertinib-induced cardiotoxicity, we analyzed our RNA-sequencing data generated from TAC placebo and TAC Osimertinib hearts tissues. RNA extraction of left ventricle of heart tissues from TAC placebo and TAC Osimertinib were extracted. Total RNA samples underwent quality control assessment, followed by poly(A)-enriched, strand-specific library preparation by LC Sciences, LLC (Houston, TX). For analysis, raw reads were aligned to the mouse reference genome and transcriptome (GRCm38) using STAR and quantified with RSEM), following the nf-core/rnaseq pipeline. Differential expression analysis was performed using the limma + voom in R, with significance defined as adjusted p-value (FDR) < 0.05. Downstream analyses, including PCA and pathway enrichment (GSEA/g:Profiler), were conducted using standard R-based pipelines.


title: Developing a pan cancer therapy based on DISE inducing short RNAs [DISE-071.RNAseq]

first: Marcus

last: Peter

summary: Developing two different DISE inducing sRNAs. The first is based on the 6mer seed GGGGGC (G5C) and the second on CAG trinucleotide repeat sequences.This RNA seq analysis was designed to identify the most deregulated genes in either HeyA8 or PC3 cells transfected with either of the two Di-sRNAs, each compared to the nontargeting control sNT8.

overall_design: HeyA8 or PC3 cells were transfected with different sRNAs at 10nM and 48hrs after transfection RNA was isolated and subjected to large RNA Seq analysis

first: Elizabeth

last: Bartom


title: Genes responding to O3 are regulated during leaf development in hybrid poplar (Populus tremula x alba)

city: CHAMPENOUX

first: David

last: Cohen

address: rue d'Amance

department: UMR1434 SILVA

country: France

institute: INRAE

summary: Tropospheric ozone (O3) harms vegetation by reducing tree biomass and crop yield. Accurate risk assessment based on O3 uptake depends on quantifying the plant's capacity to cope with O3-generated reactive oxygen species (ROS) at the cellular level. Young leaves were shown to have better ability to deal with O3 stress than mature leaves but the mechanisms behind remain unclear. The aim of this study was to assess the crosstalk between O3 response and leaf development process. Time-course response to O3 (80 and 100 ppb) was studied at transcriptomic and cellular level in a growing leaf (GL) and an expanded leaf (EL) of young poplar. Quantification of hypersensitive response-like (HR-like) and chlorophyll showed that GL was more tolerant to O3 than EL. The response of leaf transcriptome to O3 concerns mostly genes regulated at the developmental level leading to an acceleration of leaf aging and senescence. GL response to O3 was delayed compared to EL suggesting that O3 tolerance at early stages of leaf development may result from an insensitivity to O3-induced senescence. In addition to detoxification mechanisms, understanding this process could offer new perspectives for O3 tolerance improvement or assessment.

overall_design: 72 RNA samples were analyzed (4 replicates*2 leaf position*3 treatments* 3 sampling points) through one experiment.

first: Benjamin

last: Turc

first: Audrey

last: Berthe

first: Irene

last: Hummel

first: Jean-Charles

last: Olry

first: Pierre

last: Vollenweider

first: Yves

last: jolivet

first: Mireille

last: Cabane


title: Developing a pan cancer therapy based on DISE inducing short RNAs [DISE-069.RNAseq]

summary: Developing two different DISE inducing sRNAs. The first is based on the 6mer seed GGGGGC (G5C) and the second on CAG trinucleotide repeat sequences.This RNA seq analysis was designed to identify the most deregulated genes in ID8p53-/-Brca2-/- (DKO) cells transfected with either of the two Di-sRNAs, each compared to the nontargeting control sNT8.

overall_design: ID8 DKO cells were transfected with different sRNAs at 10nM and 48hrs after transfection RNA was isolated and subjected to large RNA Seq analysis


title: Modeling Stimulus-Induced Stress Responses in Microglia-like Cells Using a Commercial iPSC-dCas9-KRAB Line

first: Nicola

last: Kearns

address: 1750 W Harrison St

institute: Rush University Medical Center

summary: This study investigates microglial responses to amyloid-beta (Aβ) and lipopolysaccharide (LPS) using human induced pluripotent stem cell (iPSC)-derived microglia-like cells (iMGLs). iMGLs were exposed to either Aβ or LPS and profiled by single-cell RNA sequencing (scRNA-seq) using the 10x Genomics platform. Transcriptomic analysis revealed both shared and stimulus-specific microglial activation states, characterized by inflammatory signaling, cell death pathways, and lipid metabolism. In parallel, a CRISPR-based pooled survival screen was performed to identify genes critical for microglial survival. Guide RNA representation was measured at multiple differentiation time points (days 12, 24, 36, and 45) to infer gene essentiality during iMGL development. Together, these datasets provide insights into the molecular programs driving microglial stress responses and survival under neuroinflammatory conditions.

overall_design: iPSCs were transduced with a pooled CRISPRi sgRNA library and differentiated into microglia. Genomic DNA was collected at multiple stages of differentiation to assess sgRNA representation, and transcriptomic libraries were prepared using the Illumina iSeq 100 System.

first: Devin

last: Saunders

first: Bernard

last: Ng

first: Faraz

last: Sultan

first: Himanshu

last: Vyas

first: Ricardo

last: Vialle

first: Eric

last: Clark

first: Sashini

last: De Tissera

first: Jishu

last: Xu

last: Bennett

first: Yanling

last: Wang


overall_design: Following Amyloid-β (Aβ) or Lipopolysaccharide (LPS) stimulation, iPSC-derived microglia were isolated using FACS sorting and analyzed via scRNA-seq.

first: David


title: TPX2-mediated autophagy maintains cancer stemness in LUAD

status: Public on May 28 2026

city: 福建省

first: Yali

last: Zheng

address: 福建省厦门市翔安区厦门大学

institute: Xiamen University

summary: Targeting protein for Xklp2 (TPX2) is a mitotic regulator frequently overexpressed in lung adenocarcinoma (LUAD), while its role in cancer stemness and autophagy remains incompletely understood. In this study, integrative bioinformatic analyses based on TCGA and GTEx datasets revealed that TPX2 overexpression in LUAD was associated with poor prognosis, elevated stemness scores, and increased expression of cancer stem cell-related markers. To investigate the molecular mechanisms underlying TPX2-mediated regulation in LUAD, RNA sequencing was performed in PC9 cells following TPX2 knockdown. Transcriptomic profiling and pathway analyses identified significant alterations in autophagy-related signaling pathways. In parallel, co-immunoprecipitation coupled with mass spectrometry (IP-MS) was conducted to characterize TPX2-associated protein interactions and explore potential regulatory networks involved in autophagy. Functional experiments further demonstrated that TPX2 depletion impaired autophagic flux and reduced stemness-associated phenotypes in LUAD cells, whereas TPX2 overexpression exerted opposite effects. These data provide transcriptomic and proteomic resources for investigating the role of TPX2-mediated autophagy in LUAD progression and cancer stemness.

overall_design: RNA-seq profiling was performed in PC9 lung adenocarcinoma cells transfected with shNC or shTPX2 to investigate transcriptomic changes associated with TPX2 depletion.

first: Mingzheng

last: Jiang

first: Hongli

last: Ye

first: Jiwei

last: Li

first: Zhancheng

last: Gao


title: Generation of human hypothalamic appetite-regulating neurons and tanycytes from stem cells

city: Copenhagen

first: Erno

last: Hänninen

address: Blegdamsvej 3B

department: reNEW, Novo Nordisk Foundation Center for Stem Cell Medicine

country: Denmark

institute: University of Copenhagen

summary: The balance between energy intake and expenditure is controlled by the hypothalamus, a small brain region composed of several subregionalised nuclei with high neuronal diversity which are key to controlling appetite and food intake through response to circulating hormones and metabolic. However, the cellular and functional characteristics of this highly specialised neural region has been studied mainly in animal models due to a lack of access to human experimental counterparts. Here, we fine-tuned the differentiation of human pluripotent stem cells toward hypothalamic nuclei, including the arcuate nucleus (ARC), ventromedial hypothalamus (VMH) and paraventricular nucleus (PVN), and we identified key subtype-specific progenitor markers of hypothalamic subregions. We show that the timing for addition and withdrawal of bone morphogenic protein (BMP) was essential for controlling sub-regional specification of tuberal hypothalamic progenitors along the anterior-posterior axis, balancing VMH versus ARC fates. A particular population of SHH-/NKX2.1+/RAX+/FGF10+/TBX3high posterior tuberal progenitors was identified as the source for generation of ARC-associated agouti-related peptide (AGRP) neurons and tanycytes whilst anterior tuberal SHH+/NKX2.1+/RAX+/TBX3low progenitors generated VMH phenotypes including NR5A1 neurons. Upon maturation in 2D, 3D and in vivo, ARC-patterned progenitors gave rise to multiple key appetite-regulating cell types including AGRP, prepronociceptin (PNOC), growth hormone-releasing hormone (GHRH), thyrotropin-releasing hormone (TRH) and pro-opiomelanocortin (POMC) neurons and characteristic tanycyte glial cells. Differentiated ARC cultures showed high transcriptomic similarity to the human ARC and displayed evidence of functionality by AGRP secretion and responsiveness to leptin and fibroblast growth factor 1 (FGF1). In summary, our work provides new insights into the developmental lineages underlying human hypothalamic subregional specification and enables access to highly characterized human hypothalamic ARC cultures, which will provide novel opportunities for investigating the cellular and molecular pathways triggered by obesity-associated genetic variants and appetite-regulating drugs and peptides.

overall_design: Here, we developed a novel ARC differentiation protocol of human embryonic stem cell (hESCs) by recapitulating early tuberal hypothalamic patterning events identified in the chick. To study the cellular composition of our protocol we performed temporal scRNA-seq at day 16, 25, 50 and 70.

first: Zehra

last: Abay-Nørgaard

first: Anika

last: Müller

first: Agnete

last: Kirkeby


title: Generation of human hypothalamic appetite-regulating neurons and tanycytes from stem cells [BMP_data]

overall_design:
Here we used human embryonic stem cell (hESCs) to perform temporal snRNA-seq of different BMP timings (no BMP, BMP 5-7, 5-9, 5-11 and 5-14) at day 16 (early stage) and 50, 60 and 80 (late stage) to see how timing of BMP impacts tuberal hypothalamic development in humans.

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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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title: Sexually Dimorphic Regulation of MiR-29a/c-3p in Human Endothelial Cells: Cell Functions and Transcriptome

city: Madison

first: Siyan

last: Zhang

state: WI

address: PAB1 UnityPoint Health-Meriter Hospital 202 S. Park St.

department: Department of Ob/Gyn

institute: University of Wisconsin-Madison

summary: Preeclampsia (PE) is a major cause of maternal and fetal morbidity and mortality during pregnancy. PE is characterized by widespread endothelial dysfunction in mothers and fetuses. To date, the etiology of PE remains elusive, but the dysregulation of microRNAs (miRNAs) in endothelial cells may contribute to the pathogenesis of PE. We have reported that PE downregulates expression of two miRNAs, miR-29a-3p and miR-29c-3p (miR-29a/c-3p) and knockdown of miR-29a/c-3p impairs functions of human umbilical vein endothelial cells (HUVECs). Herein, we tested the hypothesis that knockdown of miR-29a/c-3p sex-specifically impairs cellular responses to vascular endothelial growth factor-A (VEGFA) and fibroblast growth factor 2 (FGF2) accompanying  with disrupted transcriptome in HUVECs.  MiR-29a/c-3p were downregulated using miR-29c-3p inhibitors in  HUVECs, followed by assessing  chemotactic and proliferative responses to VEGFA and FGF2. RNA-seq analysis was conducted to profile  transcriptomic  changes.  Compared with negative control, miR-29c-3p inhibitors suppressed  over 90% of miR-29a/c-3p in HUVECs at 48 h. MiR-29c-3p inhibitors decreased VEGFA-stimulated chemotaxis by 25% in male, but not female HUVECs. MiR-29c-3p inhibitors did not alter FGF2-stimulated chemotaxis or VEGFA- and FGF2-stimulated proliferation in HUVECs. RNA-seq revealed that miR-29a/c-3p inhibitors differentially altered the transcriptome between female and male HUVECs. Functional enrichment analyses showed that miR-29a/c-3p-regulated genes were differently associated with hypertension, heart, angiogenesis, and immunology in female and male HUVECs.  These data demonstrate that knockdown of miR-29a/c-3p differentially affects cellular responses to angiogenic factors  in female and male HUVECs, in association with disrupted transcriptome. These miR-29a/c-3p-regulated genes might serve as sex-specific therapeutic targets for PE-associated vascular dysfunction.

overall_design: RNA-seq of HUVECs with miR-29a/c-3p knockdown or negative control cells from female and male (n = 3-4 per sex/group) to profile miR-29a/c-3p target transcriptomes and identify sex-specific differences.

first: Si-yan

first: Chi

last: Zhou

first: Jing


title: LDHA/Hedgehog signaling pathway axis regulates lung metastasis in  osteosarcoma

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shituskawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

summary: Osteosarcoma is the most common malignant bone tumor in children and adolescents. Osteosarcoma has a strong tendency of lung metastasis and patients with metastases have poor prognoses. Lactate Dehydrogenase A subunit (LDHA) is one of the key enzymes in glycolysis and is known to be involved in progression and metastases of various cancers. Here, we showed that Ldha knockdown suppressed cell migration and invasion in vitro in murine osteosarcoma cells and decreased lung metastases in vivo. Subsequent RNA-seq analysis revealed that Ldha knockdown was associated with downregulation of the Hedgehog signaling pathway and we demonstrated that pharmacological inhibition of the Hedgehog signaling pathway with vismodegib also suppressed cell migration, invasion and lung metastases in murine osteosarcoma cells as well as Ldha knockdown. Furthermore, in human osteosarcoma cells, we confirmed that LDHA silencing led to the downregulation of the Hedgehog signaling pathway and that cell migration and invasion were suppressed by inhibiting the Hedgehog signaling pathway. Collectively, we elucidated that Ldha-Hedgehog signaling pathway axis is involved in osteosarcoma lung metastases. Our findings might contribute to further understanding for the molecular mechanism of osteosarcoma lung metastases and the development of a novel therapy for them.

overall_design: To determine the role of LDHA in osteosarcoma, we generated osteosarcoma cells with stably silenced LDHA expression using shRNA from murine osteosarcoma cell line LM8. mRNA was extracted from  LM8-shCTL, shLdha1, shLdha2 cells. mRNA profiles were analyzed by deep sequencing using Illumina NextSeq 500.

last: imai

first: Haruhiko

last: Akiyama


title: Individualized transcriptomic changes in malignant and benign prostate identify markers of disease recurrence

status: Public on May 26 2026

city: Turku

first: Matti

last: Poutanen

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: More accurate methods for early prediction of cancer aggressiveness are essential for enhanced prostate cancer (PC) treatment. In this study, the transcriptome profiles from malignant and adjacent benign prostate tissue samples were compared in 41 patients who underwent radical prostatectomy. Hierarchical clustering clearly separated benign and malignant tissues and included expected transcriptional changes associated with carcinogenesis. Using reproducibility-optimized statistical testing (ROTS), we identified 45 genes whose expression differed between paired malignant and benign prostate tissue from the same patient (FDR < 0.05) in patients with and without biochemical recurrence (BCR). Within this individualized approach, two interconnected regulatory pathways underlying the pathogenesis were identified: one centered on FOS, NR4A, and EGR family transcription factors, with strong involvement of TNFα signaling, and another, a less dense network, centered on IL6. Expression of the 45 identified transcripts was also higher in the more aggressive Luminal B-type PC than in Luminal A- and Basal-type PC, further underscoring their association with PC aggressiveness. A machine learning method (SIVS) was then used to further define five transcripts, BPIFB2, C11orf96, DUSP5, NR4A2, and NR4A3, whose individualized malignant to benign expression differences were most strongly associated with an increased risk of BCR, and thus, providing novel information on their potential involvement in processes increasing the PC aggressiveness.

overall_design: RNA-seq was performed for paired Benigin and malignant prostate cancer tissue derived from same prostate cancer patients

first: Julia

last: Mathlin

first: Mats

last: Perk

first: Kalle

middle: T

last: Rytkönen

first: Asta

last: Laiho

first: Tommi

last: Välikangas

first: Arttu

last: Junnila

first: Leena

last: Straus

first: Mikael

last: Högerman

first: Michael

last: Gabriel

first: Malin

last: Hagber-Thulin

first: Gudrun

last: Wahlström

first: Johanna

last: Schleutker

first: Pekka

last: Taimen

first: Peter

last: Boström

first: Laura

middle: L

last: Elo