title: PEPITEM regulates the synovial microenvironment during immune-mediated inflammatory arthritis to limit disease

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

country: United Kingdom

institute: University of Birmingham

summary: Objective: Here we investigate the status of the adiponectin-PEPITEM pathway in early, treatment naïve, rheumatoid arthritis (RA) and psoriatic arthritis (PsA) and the therapeutic efficacy of PEPITEM administration in preclinical models. Methods: Peripheral blood was isolated from patients with clinical suspect arthralgia and suspected inflammatory arthritis and analysed by flow cytometry or western blot. Effect of PEPITEM treatment on inflammatory arthritis were assessed in mice by histology; scRNAseq, flow cytometry or multiplex analysis. Results: Newly diagnosed RA and PsA patients had significantly reduced expression of adiponectin receptor 2 and its downstream signalling adaptor protein APPL-1 on their peripheral blood mononuclear cells, resulting in diminished response to adiponectin and local synovial concentrations of PEPITEM. Building on these observations, treatment with PEPITEM in three distinct inflammatory arthritis animal models significantly reduced arthritis severity, joint swelling, leukocyte infiltration and expression of several pro-inflammatory mediators (e.g., JE (CCL2), RANTES, IL-16) in the synovium. Mechanistically, PEPITEM treatment suppressed the COX2 and NF-B signalling pathways. Moreover, PEPITEM altered the composition of leukocyte subsets recruited into the joint. Conclusion: Collectively, these findings underscore the importance of understanding the dysregulation of the adiponectin-PEPITEM pathway in different immune-mediated inflammatory diseases (IMIDs), such as RA and PsA. The observed differences in expression and downstream signalling through ADIPOR suggest potential targets for therapeutic intervention to restore the balance of this regulatory pathway to mitigate chronic inflammation and disease progression in these patients, paving the way for its clinical use as an alternative and/or combination therapy for early IMIDs.

overall_design: C57BL/6 mice were immunized by subcutaneous (s.c.) injection with methylated bovine serum albumin (mBSA, 10μg, Sigma-Aldrich) in complete Freund’s adjuvant (CFA, Fisher Scientific)31. On day 21, monoarthritis was induced by intraarticular (i.a.) injection of mBSA (100μg) into the knee. Mice were treated sub-clinically from day 21 by intraperitoneal (i.p.) injection with either vehicle control phosphate buffered saline (PBS) or PEPITEM (300μg, SVTEQGAELSNEER- PEG (352)-Amide; Cambridge Research Biochemicals Limited; Cambridge, UK). Joint thickness (mm) was measured by callipers daily for up to 7 days. Mice were culled by cervical dislocation and lower limbs dissected. Isolated joints were enzymatically digested for 45 min at 37°C in collagenase D (0.1g/ml, Roche) and DNase I (0.01g/ml, Sigma-Aldrich) diluted in RPMI1640 containing 2% fetal calf serum (Biosera) (step 1), prior to filtering using 100m cell strainer (vicedeal). Subsequently joints were subjected to a further incubation with an enzyme mixture containing 0.1g/ml Collagenase Dispase (Roche) and 0.01g/ml DNase diluted in RPMI1640 (Sigma-Aldrich) containing 2% FBS at 37°C for 30 min (step 2). Cells from step 2 were filtered as described and combined with those from step 1 and centrifuged at 400g for 5 min. Samples were incubated in the RBC lysis buffer (Sigma-Aldrich: R7757) for 10 minutes, followed by centrifugation at 400g in PBS and then re-suspension in MACS buffer (0.1mM EDTA (Sigma-Aldrich) and 0.6% BSA (Gibco) in PBS) prior to analysis.  cDNA libraries from FACS sorted CD45+ synovial digested cells were prepared using Chromium Next GEM Single Cell 3’ Kit v3.1 (4 rxns PN-1000269) according to manufacturer’s instructions, with the aim to capture about 10,000 cells/10µl for each biological replicate.

first: Chris

last: Mahony

first: Musserat

last: Wahid

first: Helen

last: McGettrick


title: Necroptosis triggers inflammatory interferon signatures in patient-derived metastatic breast cancer organoids

status: Public on Apr 07 2026

city: Frankfurt a.M.

first: Francesco

last: Pampaloni

address: Max-von-Laue-Str. 15

country: Germany

institute: Goethe University Frankfurt a.M.

type: Expression profiling by high throughput sequencing

summary: Breast cancer (BC) is the most common type of cancer among women worldwide and underlies relapse, disease progression and metastasis. Resistance to chemotherapy and programmed cell death (PCD), including apoptosis, strongly affects BC therapy success and remains a major challenge. Although necroptosis, a lytic, and via damage-associated molecular patterns (DAMP) release, highly immunogenic mode of PCD, might overcome apoptosis resistance, there is an urgent need for physiological and translational human models to model necroptosis and PCD resistance in BC. Here, we apply 3D patient-derived, metastatic human mammary organoids (hMOs) to model apoptosis resistance, necroptosis and inflammatory signaling using single-cell CITE-sequencing, time-lapse live cell brightfield and immunofluorescent confocal microscopy as well as biochemical approaches. Smac mimetic-triggered apoptosis triggered could be confirmed in a panel of BC hMOs. Upon inducing apoptosis resistance with caspase inhibition, BC hMOs rapidly undergo necroptosis with profound MLKL phosphorylation. Necroptotic cell death was preceded by prominent transcriptional upregulation of inflammatory cyto- and chemokines, including interferons, that activate natural killer cells. Finally, necroptosis and the expression and release of inflammatory messengers in metastatic BC hMOs could be attenuated upon the inhibition of linear ubiquitination. We describe a novel experimental platform to model PCD, inflammation and necroptosis that allows therapeutic screening to overcome chemotherapy resistance in patient-derived metastatic BC hMOs. With this platform, we identified necroptosis-induced interferon signaling, suggesting Smac mimetics and necroptosis as potential immunotherapy strategy against metastatic BC.

overall_design: scCITEseq: Following treatment, metastatic breast cancer organoids from three donors were harvested and processed to single cells individually and stained with sample tags (HTOs). Viable cells were sorted using fluorescence-activated cell sorting (FACS) and stained with CITEseq antibodies (ADTs) and analyzed using scCITEseq.

first: Kaja Nicole

last: Wächtershäuser

first: Jana

middle: V

last: Schneider

first: Alec

last: Gessner

first: Geoffroy

last: Andrieux

first: Ivan-Maximiliano

last: Kur

first: Nadine

last: Duschek

first: Andreas

last: Weigert

first: Melanie

last: Boerries

first: Michael

middle: A

last: Rieger

first: Ernst HK

last: Stelzer

first: Sjoerd JL

last: van Wijk


title: Physiologic recovery of Mycobacterium tuberculosis from drug injury: A molecular study of post antibiotic effect in vitro and in vivo

city: Aurora

first: Jo

last: Hendrix

state: CO

department: Pulmonology

country: USA

institute: University of Colorado

summary: Post-antibiotic effect (PAE) describes the delay in bacterial growth that continues after antibiotics are cleared. Here, we evaluated the long-standing hypothesis that PAE reflects the time required for bacteria to recover from drug-induced physiologic damage by comparing Mtb after varying durations of treatment with the HRZE in vitro. Our results revealed that longer drug exposure was associated with greater injury and adaptation during treatment, as well as slower recovery after treatment, i.e., longer PAE. Our observation that PAE in Mtb depends on the duration of drug exposure and correlates with the degree of bacterial injury support the hypothesis that nonlethal physiologic damage contributes to PAE. Molecular evaluation of bacterial physiology provides a new basis for probing recovery from drug exposure and understanding PAE.

sample_organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

overall_design: Mtb in aerobic axenic culture were treated with HRZE for 0, 6, or 48 hours. After treatment stopped, RNA-seq profiling with SEARCH-TB was performed at various timepoints of the PAE phase.

first: Reem

last: Al Mubarak

first: Matthew

middle: J

last: Reichlen

first: Samuel

middle: T

last: Tabor

first: Adeline

last: Bateman

first: Lisa

middle: M

last: Massoudi

first: Karen

last: Rossmassler

first: Firat

last: Kaya

middle: D

last: Zimmerman

first: Holly

last: Nielsen

first: Elizabeth

last: Wynn

first: Martin

middle: I

last: Voskuil

first: Gregory

last: Robertson

first: Camille

last: Moore

first: Nicholas

last: Walter


title: Pulsed photobiomodulation reprograms the tumor immune microenvironment to restore local T cell–mediated antitumor immunity

city: Xiamen

first: chuanfang

middle: C

last: Chen

state: Fujian

address: No.4221, Xiang'an South Road, Xiang'an District

department: College of Life Science

country: China

institute: XIAMEN university

summary: We have employed a single cell sequencing approach using 10X Genomics scRNA-seq to study MC38 tumor infiltrated immune cell under Photobiomodulation(PBM) treatment. PBM, also termed low-level laser therapy (LLLT), is a non-invasive, drug-free physical modality that uses defined light wavelengths to modulate cellular functions.  This study represents the first transcriptomic analysis of how PBM reshapes the tumor microenvironment and inhibits MC38 tumor growth.

overall_design: MC38 tumor cells were subcutaneously implanted into C57BL/6 mice. PBM treatment started at day 7 daily, while tumors were harvest at day 14. Tumor infiltrated CD45+ immune cell were sorted  for scRNA-seq.

first: Xiunan

last: Wang

first: Chuanfang

first: Yuling

last: Hong

first: Jia

last: Zhang

first: Shih-Chin

last: Cheng


title: Pediatric Cancer Dependencies Accelerator

city: Memphis

first: Pediatric Cancer Dependencies

last: Acclerator

state: TN

address: 262 Danny Thomas Blvd

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Zone-specific hepatocytes orchestrate the early onset of host defence mechanisms during Staphylococcus aureus bloodstream infection

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

institute: Helmholtz Institute for RNA-based Infection Research

summary: Bloodstream infections (BSI) cause substantial morbidity and mortality, with Staphylococcus aureus among the most lethal pathogens. The liver plays a central role in host defence against blood-borne microbes, yet how its zonal organization shapes this response remains unclear. In a murine model of S. aureus bacteraemia, the liver sequestered ~90% of bacteria within 4 h and markedly reduced bacterial loads by 24 h, indicating rapid activation of local immune defences. Single-cell RNA sequencing identified periportal and midzonal hepatocytes, and to a lesser extent pericentral hepatocytes, as the principal responders. Besides acute-phase proteins, periportal and midzonal hepatocytes strongly upregulated Bmper, a regulator of bone morphogenetic protein signalling and a likely new mediator of the hepatic acute-phase response. Expansion of Kupffer cells, essential for bacterial clearance, was also observed and was primarily driven by local proliferation. These findings demonstrate that hepatocyte zonation orchestrates early hepatic immune responses during S. aureus BSI.

overall_design: Single-cell RNA sequencing (scRNA-seq) of livers from C57BL/6 mice after intravenous infection with S. aureus at 4 and 24 hours post-infection.

first: Obiageli Vivian

last: Nwofor

first: Qian

first: Robert

last: Geffers

first: Antoine-Emmanuel

last: Saliba

first: Oliver

last: Goldmann

first: Eva

last: Medina


title: RNA-seq of mononuclear immune cells isolated from breast cancer wound fluid after IORT or surgery alone

city: Neuherberg

first: Benedek

last: Dankó

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

summary: This dataset comprises RNA-seq profiles from mononuclear immune cells purified from wound fluid of breast cancer patients who received intraoperative radiotherapy (IORT) or surgery only (control). Samples were collected on postoperative day 2 and processed for total RNA extraction and 3′-end mRNA sequencing. The study aims to characterize the transcriptional immune landscape in the early wound-healing phase following IORT.

overall_design: Wound fluid samples were collected on postoperative day 2 from patients undergoing breast-conserving surgery with or without IORT. Mononuclear cells were isolated by Ficoll-like density gradient centrifugation (Biocoll), cryopreserved in 90% FCS + 10% DMSO, and later processed for RNA extraction. RNA-seq libraries were generated using a 3′-end mRNA-seq protocol. Comparative transcriptomic analysis was performed between the IORT and control groups (n = 17 and 20, respectively).

first: Nikko

last: Brix

first: Martin

last: Selmansberger


title: Early-life RNA sequencing of colon stromal cells and iNKT cells

city: Boston

first: Xi

last: Lin

state: MA

address: 77 Avenue Louis Pasteur, Rm641

institute: Brigham and Women's Hospital

summary: The early-life intestinal microenvironment plays a pivotal role in shaping immune cell development, yet the mechanisms regulating colonic invariant natural killer T (iNKT) cells remain incompletely understood. To investigate how embryonic macrophages regulate iNKT cells during early life, we collected Day 9 whole-colon lamina propria cells after embryonic macrophage depletion and performed both bulk RNA sequencing and single-cell RNA sequencing. We also performed bulk RNA sequencing on distinct colonic stromal cell populations, conventional αβT cells, and iNKT cells under homeostatic early-life conditions to identify factors that directly imprint iNKT cells during this developmental period.

overall_design: For scRNA-seq, Day 9 whole colon LP cells were isolated from three CT and three MMDTR mice (DT injection Day 6-8) and pooled by group. Live cells were FACS-sorted for single-cell RNA sequencing. For whole tissue RNA-seq, total RNA from Day 9 whole colon tissue of three CT and three MMDTR mice (DT injection Day 6-8) was extracted used as input material for library preparation and sequencing. For bulk RNA sequencing of FACS-sorted cells, two hundred P1 and P2 stromal cells from four Day 9 or four Day 15 wild-type (WT) mice, two hundred conventional αβT cells and 50 iNKT cells from four Day 9 WT mice, as well as 50 iNKT cells from four Day 9 CT and four MMDTR mice (DT injection Day 6-8), were sorted using BD FACSAria II.

first: Thomas

last: Gensollen


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [RNA-seq_male_female_MEF]

city: Piscataway

first: Joshua

middle: K

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

institute: Rutgers University

summary: Sirtuins are deacetylases implicated in stress responses and longevity in mammals. Although their differential impact on the two sexes has been noted, underlying causes for sex biases in aging and cancer are not known. Here, using Sirtuin 7 (SIRT7) as a model in mice, we probe mechanisms leading to sex differences. We find that Sirt7-/- females have decreased fitness during embryogenesis and throughout life. Intriguingly, SIRT7 preferentially localizes to the X-chromosome, suggesting a potential defect in X-inactivation — the arm of dosage compensation that equalizes X-chromosome expression between XX females and XY males. Indeed, SIRT7 ablation causes increased Xist RNA levels, H3K27me3 enrichment, and gene repression on the inactive X (Xi) chromosome. Surprisingly, however, loss of SIRT7 exerts greatest effects on the active X (Xa). In Sirt7-/- females, the Xa demonstrates 3D structural disorganization, increased chromatin mixing, and acute propensity to break and form chromosome fusions in an Xa-specific manner. Disproportional to autosomes and Xi, the Xa becomes super-acetylated on H3K36 and super-activated in gene expression, resulting in an imbalance in the 2nd arm of dosage compensation — known as “Xa-hyperactivation” — which evolved to balance X-linked gene expression against the genome. These data reveal a crosstalk between sirtuins and dosage compensation and identify a novel regulator of Xa-hyperactivation.

overall_design: RNA-seq profiling of  WT and SIRT7-KO, male or female, primary mouse MEF cells.

first: Nicolas

middle: G

last: Simonet

first: Barry

last: Kesner

first: François

last: Serra

first: Maria

last: Espinosa-Alcantud

first: Anna

last: Lappala

last: Guitart

first: Laia

last: Marin

first: Uri

last: Weissbein

first: Danni

first: Josema

last: Castelló

first: Llorenç

last: Rovirosa

first: Jay

last: Tischfield

first: Lourdes

last: Serrano

first: Berta

middle: N

last: Vazquez

first: Aurora

last: Ruiz-Herrera

first: Bernhard

last: Payer

first: Biola

last: Javierre

first: Alejandro

last: Vaquero

first: Jeannie

last: Lee


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [ChIP_SIRT7_primary_TTF]

first: Joshua

last: Thackray

overall_design: ChIP-seq profiling of SIRT7 enrichment in WT and SIRT7-KO primary mus/cas hybrid TTF cells.

first: Nicolas

last: Simonet

first: Barry

last: Kesner

last: Wang


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [ChIP_SIRT7_MEF]

overall_design: ChIP-seq profiling of SIRT7 enrichment in WT and SIRT7-KO, male or female, primary mouse MEF cells.

first: François

last: Serra

first: Maria

last: Espinosa-Alcantud

first: Anna

last: Lappala

last: Guitart


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [ChIP_H2AX_gH2AX_TTF]

overall_design: ChIP-seq profiling of H2AX and gammaH2AX enrichment in WT and SIRT7-KO mus/cas hybrid TTF cells.

first: Laia

last: Marin

first: Uri

last: Weissbein

first: Danni

last: Castelló

last: Rovirosa


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [ChIP_H2AX_gH2AX_MEF]

overall_design: ChIP-seq profiling of H2AX and gammaH2AX enrichment in WT and SIRT7-KO primary mouse MEF cells.

first: Josema

first: Llorenç

first: Jay

last: Tischfield

last: Serrano

last: Vazquez

last: Ruiz-Herrera


title: Nuclear myosin 1 regulates platelet activation and immune response in mice

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: abu dhabi

address: NYUAD Saadiyat Island

country: United Arab Emirates

institute: Biology

summary: Cellular differentiation involves a complex series of events associated with changes in cellular shape, function, and proliferative capacity. This process is mostly regulated by specific expression of multiple genes which guide the cell through the differentiation process but also ensure proper function of terminal cell types. Over the last decade, the role of cellular metabolism in maintaining the pluripotency of stem cells and subsequent differentiation is getting more attention as there is a direct link between the metabolic status of cells and their differentiation potential. We have recently shown that deletion of Nuclear Myosin 1 (NM1) leads to a molecular switch from oxidative phosphorylation to glycolysis and subsequent tumorigenesis in mice. Here we performed an in vitro analysis of metabolomic profiles associated with NM1 loss and measured the cytokine and chemokine levels in cells to provide evidence for a possible role of NM1 during hematopoiesis. Moreover, we explored the role of NM1 during the differentiation of hematopoietic progenitor stem cells to terminal blood cells by transcriptomic analysis of bone marrow, spleen, and peripheral blood. We found that in bone marrow, NM1 deletion leads to overexpression of genes associated with glycolysis-dependent platelet activation and suppression of the innate immune system genes. Remarkably, these expression patterns are preserved and become more complex in the spleen and peripheral blood. The study therefore provides novel insights into the underlying mechanisms of hematopoietic differentiation and activation of specific blood cell types and suggests NM1 as a potential therapeutic target for blood-related disorders.

overall_design: RNA seq of blood and spleen tissues isolated from NM1 WT and KO mice

first: Tomas

last: Venit

first: Nizar

last: Drou


title: Anti-HIV Immunotoxin and Antibody-Drug Conjugate Targeted by the Same Anti-gp41 Antibody Display Distinct Modes of Cellular Killing

city: Bozeman

first: SETH

middle: H.

last: PINCUS

state: Montana

address: 103 Chemistry and Biochemistry Building

department: Chemistry

institute: Montana State University

summary: Background:  We are developing cytotoxic immunoconjugates (CICs) to eradicate the persistent reservoir of HIV infection, the barrier to a cure. Having identified the most effective monoclonal antibodies (mAbs) for targeting CICs to HIV-infected cells, we investigated the efficacy and mode of killing of different forms of CICs targeted by the same mAb, an immunotoxin (IT) and antibody drug conjugate (ADC). Methods: We compared the in vitro effects of CICs made by conjugating anti-gp41 mAb 7B2 to either deglycosylated ricin A chain (7B2-dgA) or the anthracycline derivative PNU-159682 (7B2-PNU). Cytotoxicity was tested on cell lines stably expressing the HIV envelope. Metabolic and transcriptional analyses of treatment effects were performed on cells persistently infected with HIV.  Results: 7B2-dgA was more potent and acted more rapidly to kill cells. 7B2-PNU induced bystander-cell killing but stimulated cell growth upon low dose or brief exposure. Six hr post treatment, 7B2-dgA elicited both metabolic and transcriptional alterations, whereas 7B2-PNU treated cells did not differ from untreated cells. At 24 hr, the profiles following both treatments differed from untreated cells and from each other. 7B2-dgA treated cells exhibited elevated intracellular levels of many AAs, and early activation of gene pathways for apoptosis and transcriptional control; later transcriptional changes included decreases in expression of enzymes involved in AA synthesis and carbon metabolism.  Conclusions: An IT and ADC, each delivered by the same antibody and tested in the same cell lines showed substantial differences in their mode of killing, of potential clinical significance. The results of this side-by-side comparison of an ADC and IT have implications for the development of CICs to treat other conditions, including cancer.

overall_design: RNA-Seq was performed on H9 CD4+ lymphoma cells that were persistently infected with the  HIV isolate H9/NL4-3. Cells were either untreated or exposed to an anti-HIV immunotoxin (7B2-dgA) or antibody-drug conjugate (7B2-PNU159682). RNA was extracted 6 and 24 hr post treatment.

first: Seth

middle: H

last: Pincus


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [Hi-C]

first: Joshua

last: Thackray

overall_design: CHART-seq profiling of Xist transcript binding in WT and SIRT7-KO hybrid (mus/cas) mouse Tail Tip Fibroblasts (TTF).

last: Simonet

last: Kesner

last: Serra

last: Wang

first: Lourdes

first: Berta

first: Aurora

first: Bernhard

last: Payer

first: Biola

last: Javierre

first: Alejandro

last: Vaquero

first: Jeannie

last: Lee


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [RNA-seq TTF]

overall_design:
RNA-seq profiling of WT and SIRT7-KO hybrid (mus/cas) mouse ES cells at day 0 (LIF treated) and 7 days after LIF withdraw.
RNA-seq profiling of  WT and SIRT7-KO, male or female, primary mouse MEF cells.

first: Nicolas

first: Barry

first: François

first: Maria

last: Espinosa-Alcantud

first: Anna

last: Lappala

last: Guitart

first: Laia

last: Marin

first: Uri

last: Weissbein

first: Danni

last: Castelló

last: Rovirosa

last: Tischfield

last: Serrano


title: Elucidating early intestinal stem cell response to bacterial infection

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

summary: Intestinal stem cells (ISCs) are the regenerative force of the gut epithelium. Lgr5+-ISC have been shown to respond to changes in their microenvironment by coping with different metabolites, adapting to caloric changes, and recovering from injury and inflammation. However, how pathogenic bacteria affect adult stem cell regeneration and, as a consequence, the overall tissue adaption to infection has yet to be explored in depth. Here, we interrogated early Lgr5+ ISC responses to an enteric intracellular pathogen by profiling individual IECs from the mouse small intestine. Utilizing GFP-labeled Salmonella enterica, we isolated intracellular invaded cells to elucidate invasion programs of epithelial cell subsets. In particular, we identified a Salmonella-specific infection signature comprised of antimicrobial peptide (AMP) genes, including the Defensin gene family. Our findings demonstrate that Salmonella enterica targets differentiated Paneth, enterocytes, and stem/progenitor cells at these early stages of infection. In response, a rapid Lg5+ ISC-driven cellular remodeling to enterocyte and Paneth lineages expressing AMP genes is initiated to combat the intruders. Importantly, we uncovered an ISC differentiation program via inflammasome activation to protect the crypt environment, while eliminating infected stem cells from the overall stem cell pool. This novel Lgr5+ stem cell defense mechanism not only protects the gut epithelium from persistent bacterial infection but also promotes tissue regeneration. We propose epithelial remodeling to AMP-secreting cells as a novel innate immune response to handle different gut stresses mediated by Lgr5+ ISCs to maintain organizational principles of gut homeostasis and physiology.

overall_design: The data here is from a single-cell RNAseq experiment by 10x (v3), comparing small intestine epithelium under normal, 12, 24 hours post-infection by Salmonella enterica, 24 hours post-infection by Listeria.

first: Hofree

last: Matan

first: Biton

last: Moshe

first: Lebon

last: Sacha


title: Spatially resolved profiling and Footprint Analysis of the Steroid Nuclear Receptors Reveals a Role for the Disordered N-Terminal Domains in Genome Targeting and AP-1 Interaction

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

institute: Weizmann Institute of Science

summary: Transcription factors (TFs) regulate gene expression by binding to cis-regulatory regions within vast genomes. In budding yeast, intrinsically disordered regions (IDRs) emerged as key effectors of genome preferences, but whether this holds in the complex mammalian genomes remains unclear. Mammalian TFs are enriched with long IDRs, exemplified by the disordered N-terminal domains (NTDs) of the nuclear steroid receptors (SRs). Here, by comparing genomic locations of three SRs and their truncation mutants, we show that the NTDs direct the selection of SR target sites. Footprint analysis revealed that SR mutants lacking the NTD become dependent on the AP-1 motif and further suggest that the NTD can direct genome recognition independent of co-binding TFs, which we confirmed by testing SR binding across the budding yeast genome. Our results suggest that IDRs assist in defining the TF binding targets, opening new avenues for modulating activities of therapeutically relevant TFs.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens
Mus musculus

overall_design: Binding of Nuclear steroid receptors and their mutants was profiled using ChEC-seq in 2 different systems. Mammalian cell-lines - NMuMG (mouse) and HepG2 (human), and yeast (S.Cerevisiae)

first: Zigdon

last: Inbal

first: Shoham

last: Achinoam

first: Mindel

last: Vladimir

first: Manadre

last: Wajd

first: Yahav Har-Shai

last: Dekel

first: Antebi

last: Yaron

first: Barkai

last: Naama


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [ChIP_SIRT7_TTF]

first: Joshua

last: Thackray

overall_design: ChIP-seq profiling of SIRT7 enrichment in WT and SIRT7-KO hybrid (mus/cas) mouse TTF cells.

first: Nicolas

last: Simonet

first: Barry

last: Kesner

first: François

last: Serra

first: Maria

last: Espinosa-Alcantud

last: Lappala

last: Guitart

last: Marin

last: Weissbein

last: Wang

first: Josema

first: Llorenç

first: Jay

first: Lourdes

first: Berta

last: Vazquez

first: Aurora

last: Ruiz-Herrera

first: Bernhard

last: Payer

first: Biola

last: Javierre

first: Alejandro

last: Vaquero

first: Jeannie

last: Lee


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [RNA-seq ES]

overall_design: RNA-seq profiling of WT and SIRT7-KO hybrid (mus/cas) mouse ES cells at day 0 (LIF treated) and 7 days after LIF withdraw.

first: Anna

first: Laia

first: Uri

first: Danni

last: Castelló

last: Rovirosa

last: Tischfield

last: Serrano


title: Single-Cell Cas12a Platform for Screening and CRISPRi

city: South San Francisco,

first: Carolina

last: Galan

state: CA

address: 1 DNA Way

institute: Genentech

summary: To overcome the challenges of pre-crRNA sequence recovery during single-cell RNA sequencing, we optimized guide RNA expression vectors and established a degron-based, enhanced Cas12a system for scalable genetic perturbation. Using this new platform, we performed Perturb-seq screens to accurately capture pre-crRNAs and profile gene editing-induced effects on the transcriptome across multiple cell types and target genes. This dataset provides the single-cell transcriptomic profiles demonstrating the efficacy of our improved Cas12a and HyperLbCas12a systems for highly multiplexed gene knock-out and transient suppression.

overall_design: Plasmid libraries consisting of dual pre-crRNAs were transduced into H358-enAsCas12a or H358-enAsCas12a-FKP12F36V cells. In the case of H358-enAsCas12a-FKBP12F36V, prior to 10x processing, cells were cultured in 1µM dTAGV-1 (Tocris Bioscience, 6914) for 24h or 48h. dTagV1 was continuously supplied until the step of reverse transcription. Gene expression libraries were prepared according to the 10X Genomics according to the manufacturer’s protocol  (CG000316 or CG000418); CRISPR libraries for direct-capture Perturb-seq and direct-capture CROP-seq constructs were created according to 10x genomics user manuals (CG000316 or CG000418).

first: Valentina

last: Snetkova

first: Romain

last: Lopez

first: Antonio

middle: R

last: Rios

first: Takamasa

last: Kudo

first: Kristel

last: Dorighi

first: Søren

last: Warming

first: Benjamin

last: Haley


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [H3K36Ac_TTF]

first: Joshua

last: Thackray

first: Nicolas

last: Simonet

first: Barry

last: Kesner

first: François

last: Serra

first: Maria

last: Espinosa-Alcantud

last: Lappala

last: Guitart

last: Marin

last: Weissbein

last: Wang

first: Josema

first: Llorenç

first: Jay

first: Lourdes

first: Berta

last: Vazquez

first: Aurora

last: Ruiz-Herrera


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [H3K27me3_TTF]

overall_design: ChIP-seq profiling of H3K27me3 enrichment in WT and SIRT7-KO hybrid (mus/cas) mouse TTF cells.

first: Anna

first: Laia

first: Uri

first: Danni

last: Castelló

last: Rovirosa

last: Tischfield

last: Serrano

first: Bernhard

last: Payer

first: Biola

last: Javierre

first: Alejandro

last: Vaquero

first: Jeannie

last: Lee


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [CHART-seq]

first: Joshua

last: Thackray

first: Nicolas

last: Simonet

first: Barry

last: Kesner

last: Serra


title: Monocyte infiltration induces CNS arginine catabolism to fuel neuroinflammation

city: Vienna

first: Omar

last: Sharif

address: Schwarzspanier Strasse

department: Centre for Physiology and Pharmacology, Vascular Biology and Thrombosis research

country: Austria

institute: Medical University of Vienna

summary: Inflammatory responses are associated with recruitment of monocyte-derived cells (Mdcs) into tissues. While tissue-specific Mdc reprogramming is well-established, how Mdc inflitration alters tissue metabolism remains unclear. Here, using a murine neuroinflammation model coupled with genetic fate-mapping, metabolomics, and metabolite imaging, we identify that central nervous system (CNS) Mdc infiltration is associated with substantial metabolic changes, assigning disease-linked metabolites (DLMs) therein. Particularly, we found increased arginine catabolism driven by lesion-associated Arginase-1 (Arg1)-expressing Mdcs promoted oxidative damage, lipid accumulation and Mdc dysfunction. Genetic Arg1-deficiency within Mdcs during neuroinflammation increased extracellular arginine and was associated with rewiring of the CNS metabolic landscape, including attenuated DLMs. This was accompanied by enhanced Mdc-driven anti-inflammation, regulatory T cell expansion, and improved disease outcome. Opposing effects were observed upon dietary arginine deficiency.  Together, our work highlights key roles for Mdcs in CNS metabolism and reveals the pleiotropic beneficial effects of arginine in neuroinflammation.

overall_design: viable CD3-Ly6G-CD45+CX3CR1+Arg1+ cells were isolated and FACS sorted from spinal cords of EAE-induced Arg1tm1Lky animals and compared to viable CD3-Ly6G-CD45+CX3CR1+Arg1-

first: Martina

last: Kerndl

first: Andrea

last: Vogel

last: Komljenovic

first: Gernot

last: Schabbauer


title: Single-Cell Transcriptomic and Chromatin Accessibility Atlas of Peripheral Blood Mononuclear Cells Reveals Immune Cell Heterogeneity and Breed- Specific Characteristics in Duroc and Meishan Pigs

city: Yangzhou

first: Cui

last: Du

state: Jiangsu

address: NO.88 University South Road

institute: Yangzhou University

summary: In this study, we applied scRNA-Seq to profile the PBMCs from Meishan and Duroc pigs which are two strains with distinctive immune traits, and applied scATAC-Seq to Duroc PBMCs. We expect this study will improve the understanding about the immune heterogeneity and inter-breed immune variations in pigs, and reveal novel immune cell populations, immune genes and regulators that would facilitate future biomedical studies. MS(Meishan pig); DR(Duroc pig).

first: Wenbin

last: Bao

first: Hairui

last: Fan


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [H3K36Ac_ES]

overall_design: ChIP-seq profiling of H3K36Ac enrichment in WT and SIRT7-KO hybrid (mus/cas) mouse ES cells at day 0 (LIF treated) and 7 days after LIF withdraw.

first: François

first: Maria

last: Espinosa-Alcantud

first: Anna

last: Lappala

last: Guitart

first: Laia

last: Marin

last: Weissbein

last: Wang

first: Josema

last: Castelló

first: Llorenç

last: Rovirosa

first: Jay

last: Tischfield

first: Lourdes

last: Serrano

first: Berta

last: Vazquez

first: Aurora

last: Ruiz-Herrera


title: Intravitreal AAV delivery induces integrin-dependent ocular inflammation and activation of complement, antiviral and DNA damage responses

city: Philadelphia

first: Jon

middle: E

last: Chatterton

state: PA

address: 3025 Market St

institute: Roche Therapeutics

summary: Intravitreal (IVT) AAV administration is a promising, non-invasive strategy for retinal transduction. However, IVT AAV delivery is often associated with dose-limiting inflammation, and corticosteroid treatment used to manage ocular uveitis is contra-indicated in some patients. Therefore, novel immunomodulatory strategies are needed, requiring further understanding of AAV-triggered immunity mechanisms. Here we characterized immune responses to AAV2.7m8 in mice and pigs. IVT AAV delivery in mice revealed a key role for peripheral leukocytes in mediating ocular inflammation, while the response in pigs was predominantly driven by microglia activation and monocyte infiltration.  Analysis of ocular humors identified MCP-1 and IP-10 as common AAV-induced inflammation markers in both species, with subsequent identification of MIP-1α, IL-6, and complement factor C3a as additional markers in pigs. We also detected DNA damage foci in treated retinas, including in regions exhibiting low or absent transgene expression, but with significant presence of vector genomes. Finally, snRNAseq detected significant transduction of retinal ganglion cells, identified astrocytes and microglia as the main sources of MCP-1 and IP-10, and revealed marked induction of interferon and pro-inflammatory signaling across all retinal cell populations. Thus, our work identified new markers of ocular inflammation and potential targets to modulate AAV-induced uveitis.

overall_design: Female Yucatan minipigs received bilateral intravitreal injections of AAV2.7m8/CAG-GFP or vehicle control, followed by sacrifice at 2, 3, or 4 weeks post-injection. Retinal nuclei were isolated from flash-frozen whole globes, purified by FACS based on DAPI fluorescence, and analyzed using single-nuclei RNA sequencing on the 10x Chromium platform.

first: Helena

last: Costa Verdera

first: Deepa

last: Jamwal

first: Emily

last: Fabyanic

first: Ariel

last: Hippen

first: Madeleine

last: Salvatore

first: Aiping

last: Majowicz

first: David

last: Markusic

first: Virginia

last: Haurigot

first: Klaudia

last: Kuranda


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [H3K27me3_ES]

first: Joshua

last: Thackray

overall_design: ChIP-seq profiling of H3K27me3 enrichment in WT and SIRT7-KO hybrid (mus/cas) mouse ES cells at day 0 (LIF treated) and 7 days after LIF withdraw.

first: Nicolas

last: Simonet

first: Barry

last: Kesner

first: François

last: Serra

first: Maria

last: Espinosa-Alcantud

first: Anna

last: Lappala

last: Guitart

first: Laia

last: Marin

first: Uri

last: Weissbein

first: Danni

last: Wang

first: Bernhard

last: Payer

first: Biola

last: Javierre

first: Alejandro

last: Vaquero

first: Jeannie

last: Lee


title: Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics

status: Public on Apr 06 2026

first: Roy

last: Novoselsky

department: Molecular cell biology

summary: Subcellular RNA localization, including nuclear retention and apical-basal compartmentalization in polarized epithelia plays a central role in post-transcriptional regulation. However, methods for high-throughput mapping of mRNA localization within intact tissue sections remain limited. Here, we apply high-resolution spatial transcriptomics to systematically resolve intracellular mRNA localization across diverse mammalian tissues. We introduce a computational approach that leverages image-derived features to extract subcellular information from spatial data and quantifies transcript localization patterns. Using this framework, we map apical-basal mRNA localization and nuclear retention in gastrointestinal epithelia and in liver hepatocytes. Our analyses reveal conserved and tissue-specific localization signatures that can be readily obtained from standard high-definition spatial transcriptomics experiments. This approach broadens the scope of spatial transcriptomics by enabling routine investigation of intracellular RNA distributions in both healthy and diseased tissues.

overall_design: 10x VisiumHD of FFPE liver samples  from two healthy WT C57BL/6 mice housed under normal conditions. The experiment included fluorescence staining for Atp1a1, Cd31, autofluorescence and DAPI.

first: Ofra

last: Golani

first: Tal

last: Barkai

first: Merav

last: Kedmi

first: Inna

last: Goliand

first: Shalev

last: Itzkovitz


title: Essential lncRNAs in the human transcriptome [CRISPR]

city: New York

first: Wen-Wei

last: Liang

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Mammalian genomes host a diverse array of RNA that includes protein-coding and noncoding transcripts. However, the functional roles of most long noncoding RNAs (lncRNAs) remain elusive. Using RNA-targeting CRISPR-Cas13 screens, we probed how loss of ~5,500 lncRNAs impacts cell fitness across five human cell lines and identified 788 lncRNAs with context-specific or broad essentiality. We confirm their essentiality with individual perturbations and find that the majority of essential lncRNAs operate independently of their nearest protein-coding genes. Using transcriptome profiling in single cells, we discover that loss of essential lncRNAs impair cell cycle progression and drive apoptosis. Many essential lncRNAs demonstrate dynamic expression across tissues during development. Using ~9,000 primary tumors, we pinpoint those lncRNAs whose expression in tumors correlates with survival, yielding new biomarkers and potential therapeutic targets. This transcriptome-wide survey of functional lncRNAs advances our understanding of noncoding transcripts and demonstrates the potential of transcriptome-scale noncoding screens with Cas13.

overall_design: To profile transcriptomic change after essential lncRNA perturbation, we engineered two human cell lines, HAP1 and MDA-MB-231, to express the nuclear-localized RfxCas13d effector under doxycycline-inducible control. Next, we transduced each cell line with the lentiviral gRNA library at a low multiplicity-of-infection (<0.2) to ensure each cell received only a single perturbation and induced Cas13 expression via doxycycline addition. Cells were harvest after 3 days and loaded into a Chromium Controller (10X Genomics). Gene expression (GEX) libraries were prepared using Chromium Single Cell 3ʹ v3 protocol (10x Genomics). bcgRNA (BCG) libraries from CaRPool-seq experiments were prepared using the standard feature barcoding Chromium Single Cell 3ʹ v3 (10x Genomics) workflow and additional steps noted in carpool-seq.com.


title: Fate mapping reveals a prenatal-to-neonatal wave of ILC2s with a history of Cd3g expression - RNA-Seq

city: Oklahoma City

first: Aneta

last: Pankow

state: Oklahoma

address: 825 NE 13th St

department: Arthritis and Clinical Immunology

institute: Oklahoma Medical Research Foundation

summary: Group 2 innate lymphoid cells (ILC2s) are thought to develop in the bone marrow and fetal liver. However, increasing evidence supports the presence of thymic ILC2s in mice and humans. In this study, we introduce a novel fate-mapping mouse model designed to track thymic ILC2s in peripheral tissues. Thymic ILC2s are labeled by ZsGreen whose expression is induced by Cd3giCre. While they are present in the thymus and peripheral tissues, they are not found in the bone marrow. These cells are predominantly abundant during the neonatal stage, when the intense alveolarization and tissue remodeling occur. RNA sequencing revealed elevated expression of cytokine genes, Il13 and Il4, as well as Klrg1 in these cells. They also harbor TCR gene rearrangements suggesting common developmental pathways with T cells. Furthermore, we demonstrate that neonatal ILC2s play a critical role in macrophage polarization in a naphthalene-induced injury lung model. These findings help explore the differences between pediatric and adult immunity and future therapeutic strategies.

overall_design: Gene expression profile was determined by bulk RNA sequencing of 14 days old RORaf/f (C) or RORaf/fIl7riCre (KO) mice. RNA isolated from whole lung tissue from untreated (Untr-2) mice and mice after 2 days (Tr-2), 5 days (Tr-5) and 7 days (Tr-7) days after treatment with naphthalene.

first: Xiao-Hong

last: Sun


title: HyDRA: a pipeline for integrating long- and short-read RNAseq data for custom transcriptome assembly

city: Brisbane

first: Juliet

last: French

address: 300 Herston Rd

country: Australia

institute: QIMRB

summary: Short-read RNA sequencing (RNAseq) remains a cornerstone for transcriptome profiling, but is limited in reconstructing full-length transcripts and capturing transcript diversity. While long-read RNAseq spans entire transcripts and resolves complex structures, this technology is hindered by its high error rates. In parallel, noncoding RNA transcripts remain underrepresented in current references. Here, we present HyDRA (Hybrid de novo RNA Assembly), a pipeline that integrates the accuracy of short reads with the structural resolution of long reads to produce more complete de novo transcriptome assemblies. Benchmarking showed HyDRA to outperform existing methods by up to 40%. Using the HyDRA human ovarian metatranscriptome, we identified >50,000 high-confidence long noncoding RNAs, most of which have not been previously detected using traditional methods. Although long-read RNAseq is advancing, the vast availability of short reads ensures HyDRA’s ongoing role in capturing high-confidence, cell-type specific transcripts and advancing our understanding of transcriptomic complexity and the noncoding genome.

overall_design: Short-read RNAseq data from primary and immortalized fallopian tube secretory epithelial cells (FT194, FT282, FC-0081-2839, FC-0081-4853, and ABC-TC5521) and ovarian surface epithelial cells (IOSE397, IOSE7576, ABC-TC3743, 7310-donor1-24593, and 7310-donor2-7859) and long-read RNAseq data from immortalized fallopian tube secretory epithelial cells (FT194) and ovarian surface epithelial cells (IOSE397)

first: Isabela

last: Almeida

first: Xue

last: Lu

first: Stacey

last: Edwards

first: Mainá

last: Bitar


title: Transcriptomic and Functional Analysis of Fibroid Extracellular Vesicles

city: torrance

first: Omid

last: Khorram

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

summary: This study aimed to characterize large and small RNA transcriptomic changes in extracellular vesicles from cultures of fibroid explants and matched myometrial explants.

overall_design: Analysis of large and small RNA transcriptomic changes from RNA-seq data in three sets of extracellular vesicles from cultures of fibroid explants and matched myometrial explants.

first: Tsai-Der

last: Chuang

first: Abigail

last: Wiseman

first: Gabriela

last: Alfaro

first: Shawn

last: Rysling

first: Nhu

last: Ton

first: Daniel

last: Baghdasarian


title: NAT10-mediated N4-acetylcytidine modification drives RNA splicing of PML to alleviate adipose-derived stem cell senescence and promote diabetic wound healing

city: Beijing

first: wuhan

last: wei

address: No. 33, Badachu Road, Shijingshan District

department: Plastic Surgery Hospital

institute: Chinese Academy of Medical Sciences

summary: Cellular senescence in adipose-derived stem cells (ADSCs) limits their application in diabetic wounds. Alternative splicing generates multiple isoforms that play critical roles in modulating stem cell senescence. N-acetyltransferase 10 (NAT10) regulates N4-acetylcytidine (ac4C) modification, which has been implicated in RNA splicing. As the role of NAT10 in ADSCs remains elusive, this study aimed to investigate the function of NAT10 in ADSC senescence and RNA splicing.

overall_design: Cellular senescence was assessed using senescence-associated β-galactosidase staining, western blot for senescence markers p21 and p16, and qRT-PCR analysis of senescence-associated secretory phenotype (SASP) expression. RT-PCR analysis was performed to explore the potential role of NAT10 in RNA splicing.

first: Wuhan

last: Wei


title: Mutation-dependent responses to sleep and exercise in clonal hematopoiesis

first: Darwin

last: D'Souza

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

summary: Somatic mutations that cause the clonal outgrowth of mutant hematopoietic stem cells (HSCs), known as clonal hematopoiesis (CH), decay myeloid heterogeneity, activate inflammation, and increase the risk of atherosclerosis. However, whether lifestyle alters myeloid cell diversity by either modulating CH clone expansion or the phenotypic programming of CH mutant cells, thereby impacting atherosclerosis, is unknown. Here, in humans and mice and across mutations in Jak2, Tet2, p53 and Dnmt3a, we demonstrate mutation-dependent responses to lifestyle in CH and show that mutant cells are uniquely and selectively sensitive to lifestyle exposures. Sleep and exercise restrict Jak2 and Tet2 CH and its atherogenic consequences by diminishing the clonal expansion of mutant HSCs and reprogramming mutant bone marrow (BM) HSCs and aortic macrophages, but not their neighboring wildtype (WT) counterparts, through divergent brain-body axes. In two large human datasets, moderate-to-vigorous physical associated with less non-DNMT3A CH. In atherogenic mice with Jak2 or Tet2 but not p53 or Dnmt3a CH, uninterrupted sleep or exercise curtails clone expansion. In Jak2 CH sleep and exercise do so by selectively reprogramming mutant, but not WT, BM HSCs towards anti-proliferative and metabolically healthy phenotypes by tempering BM macrophage-HSC IL-1β signaling. Sleep or exercise also lessens Jak2-, Tet2-, and p53-, but not Dnmt3a-, driven atherosclerosis, partly independent of BM clonal dynamics, by locally reprogramming mutant macrophages in atherosclerotic lesions. In Jak2 mutant, but not adjacent WT, aortic macrophages, uninterrupted sleep reduces cell death, selectively blunting CLEC4E-dependent inflammasome activation and IL-1β generation, consequently diminishing lesions. Exercise, meanwhile, activates PAC1+ neurons in the brain’s locus coeruleus (LC), raising peripheral norepinephrine (NE), and preserves the expression of NE’s adrenergic receptor (ADR) β2 in Jak2V617F, but not cohabitant WT, aortic macrophages. Exercise-mediated NE signaling from the brain’s LC to Jak2V617F aortic macrophages selectively represses their inflammatory programing and atherosclerosis. Together, our findings uncover gene-lifestyle coaction and establish that healthy lifestyles gene-specifically diminish CH and selectively reprogram mutant HSCs and macrophages to maintain myeloid heterogeneity and cardiovascular health.

overall_design: Female Ldlr-/- mice were irradiated and reconsituted with 90% CD45.1WT BM cells and either 10% CD45.2 WT BM cells or 10% Jak2V617Ffl/wtMx1Cre BM cells. Eight weeks later, mice were injected with Poly(I:C) and fed a high cholesterol diet. Ldlr-/-WTBM mice remained sedentary while Ldlr-/-Jak2V617FBM mice remained sedentary or were exposed to SF or exercise for 12 weeks. Aortas were isolated and CD45+ cells were sorted. BM was isolated and mature leukocytes depleted. Cell suspentions were oligotagged for CD45.1 and CD45.2 before scRNAseq. Protocol details can be found in the published manuscript.

first: Teresa

last: Gerhard

first: Zhihong

last: Chen

first: Cameron

last: McAlpine


title: Bulk RNA sequencing of liver NK cells and ILC1s from T-bet WT vs. inducible Ncr1-T-bet Δ/Δ mice

city: Saint Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue, Campus Box 8007

department: Medicine

institute: Washington University School of Medicine

summary: The role of the T-box transcription factors T-bet and Eomes in innate lymphoid cells (ILCs) beyond their development is not well understood. We generated an inducible, NKp46 (Ncr1)-specific T-bet floxed knock-out mouse (Ncr1-T-betΔ/Δ) model. Bulk RNA sequencing of liver NK cells after tamoxifen treatment from T-bet WT (NKp46-CreERT2 x T-bet fl/fl) vs. Ncr1-T-bet Δ/Δ (NKp46-CreERT2 x T-bet fl/fl) mice had minimal transcriptional changes, whereas T-bet-deficient ILC1 exhibited significant gene expression changes. This sequencing data along with their rapid loss in vivo in Ncr1-T-betΔ/Δ mice reveal the requirement for continuous T-bet expression in liver ILC1.

overall_design: T-bet WT mice and T-bet Δ/Δ mice were treated with 1mg tamoxifen by oral gavage for 2 days (Day 1-3), then on Day 3, liver NK cells (YFP+NK1.1+CD49a-CD49b+) and ILC1 (YFP+NK1.1+CD49a+CD49b-) from the same mice were flow sorted. Qiagen RNA easy micro kit was used to extract RNA of cells directly sorted into Buffer RLT + β-mercaptoethanol, following manufacturer’s protocol. Sequencing library was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) and sequenced on Illumina NovaSeq X Plus.

first: Fehniger

last: Todd

first: Wong

last: Pamela

first: Paik

last: Christy

first: Foltz

last: Jennifer


title: Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: Despite therapeutic advances, metastatic colorectal cancer remains a therapeutic challenge as most patients will develop resistance to therapy and will progress. Epigenetic mechanisms are implicated in enabling the acquisition of new phenotypic traits as drivers of colorectal cancer progression, rather than new genetic mutations or expansion of existing mutant clones. It remains unclear, however, which epigenetic mechanisms sustain colorectal cancer plasticity, how they are induced, and how this plasticity generates subclonal diversity that drives the aggressive cancer phenotype. Here we identify the integrated stress response as an inducer of colorectal cancer cell plasticity, subclonal diversity, and tumor progression in the stress-surviving cells. Combined analysis of chromatin accessibility and gene transcription profiling in these cells found the emergence of an endogenous interferon response as a key phenotypic trait associated with subclonal colorectal cancer cell diversity, treatment resistance and heightened aggressiveness. We unveil a new experimental approach to successfully prevent treatment-resistant colorectal cancer progression by combining epigenetic modulators with a cereblon-dependent degrader of GSPT1, a regulator of protein synthesis, to normalize chromatin accessibility and induce colorectal cancer cell death. Collectively, our study identifies the integrated stress response as an inducer of epigenetic and transcriptional plasticity in colorectal cancer cells and highlights a successful approach to therapeutic intervention.

overall_design: RNA expression in a clone of HT-29 cells (596-7 and derived 596-7-R1 clone)

first: Lili

last: Li

first: Taekyu

last: Ha

first: Jing-Xin

last: Feng

first: Michael

last: DiPrima

first: Dunrui

last: Wang

first: Parthav

last: Jailwala

first: Hidetaka

last: Ohnuki

first: Giovanna

last: Tosato


title: FTO Inhibition Depletes Cysteine Metabolism and Sensitizes NSCLC to Radiation Therapy

city: Stanford

first: Erinn

last: Rankin

state: California

address: 269 Campus Dr

department: Rad Onc

institute: Stanford University

summary: Non-small cell lung cancer (NSCLC) remains a leading cause of cancer mortality, underscoring the urgent need for novel therapeutic strategies. Metabolic rewiring is a major cause of therapeutic resistance in tumors. Targeting cysteine metabolism is an attractive strategy due to its crucial role in maintaining oxidative stress. Here we demonstrate that FTO promotes NSCLC growth and survival by orchestrating cysteine metabolism through transcriptional regulation of the cystine transporter SLC7A11 and the de novo transsulfuration pathway enzymes cystathionine β-synthase (CBS) and cystathionine γ-lyase (CTH). Genetic and pharmacological inhibition of FTO reduced cystine uptake and de novo cysteine synthesis, leading to depleted intracellular glutathione (GSH), elevated reactive oxygen species (ROS), and reduced tumor growth. We further show that FTO inhibition increases radiation-induced DNA damage and sensitizes NSCLC cells and xenograft tumors to radiation therapy (RT). These findings establish FTO as a pivotal epitranscriptomic regulator of cysteine metabolism and radiation response in NSCLC, revealing a novel metabolic vulnerability that can be exploited therapeutically. Targeting FTO presents a promising strategy to enhance the efficacy of RT and improve outcomes for patients with NSCLC.

overall_design: H1299 cells were transduced with shRNA containing virus particles (twice) and generated stable KD and WT lines (1 week post infection). RNA was extracted and sent it for sequencing at Novogene.

first: Nishanth

last: Kuganesan

middle: B


title: C2orf74 Orchestrates Germ-Leydig Crosstalk to Reprogram White Adipocyte Identity

city: HeFei

first: zhao

last: li

address: Daoxiangcun

institute: ustc

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

overall_design: Refer to individual Series


title: C2orf74 Orchestrates Germ-Leydig Crosstalk to Reprogram White Adipocyte Identity I

summary: Gender differences in obesity is widely reported, however, identification of gender specific obese gene and characterization of its role in obesity remain elusive. Here, we identify a germ cell specifically expressed gene C2orf74 and demonstrate that C2ORF74 promotes high-fat diet (HFD) induced obesity in male but not female male. Loss of C2ORF74 protects male mice from obesity by boosting testosterone levels and enhancing energy expenditure and browning of white adipose tissues (WAT). We demonstrate that spermatogenic C2ORF74 suppresses testosterone biogenesis in Leydig cells through germ-cell secreted BPIFA3, whose maturation and secretion is dependent on DPM1-mediated glycosylation. Collectively, these findings define a role of spermatogenic C2ORF74 in energy expenditure and adipose browning in a gender specific manner.

overall_design: high fat diet fed WT and C2orf74 male mice at 8 weeks old for 12 weeks and isolated testicular leydig cells ,extract RNA for RNA seq


title: The placentalia specific histone H3.4 promotes germ cell development and reproductive fitness [ChIP-seq]

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary: Genes involved in chromatin remodeling during sperm development are under strong evolutionary pressure to optimize reproductive fitness In mice, the histone H3.4 variant, encoded by the single copy H3f4 gene, is essential for spermatogenesis. H3.4 is highly expressed in spermatogonia and replaces progressively canonical H3 histones during spermatogonial expansion and differentiation. Phylogenetic analysis shows that H3f4 is specific to the placental lineage and originates from an ancestral H3.2 gene existing prior to the divergence of placental and marsupial mammals over 100 million years ago. Situated in a majorly truncated histone cluster, placental H3f4 orthologs show increased synonymous and non-synonymous substitution rates compared to analogous marsupial H3.2 genes. H3f4 carries four non-synonymous substitutions relative to H3.2 genes. To understand the impact of evolutionary sequence divergence on reproductive fitness, we reverted three of four non-synonymously substituted residues in H3f4 to those present in H3.1 (H3f4V24A, H3f4H42R, H3f4S98A) while leaving H3f4C96 intact which is identical to H3.1C96. When expressed from both alleles, neither single nor triple reversion of diverged residues affected spermatogenesis much. In contrast, hemizygous expression of the triply reverted H3f4H3.1 allele on a H3f4-deficiency background caused an >40% reduction in testis weight associated with death of pachytene spermatocytes, impaired differentiation of spermatids and aberrant expression of thousands of genes during spermatid elongation. Hemizygous expression of individual residue substitution alleles revealed that residues V24 and H42 of H3.4 promote spermatogenesis, while residue S98 is neutral. Together, our study shows that H3f4 has been subject to positive evolutionary selection, promoting male reproductive fitness.

overall_design: ChIP-seq for histone variants (H3.4-MYC and H3.3) and for histone hodifications (H3K4me3 and H3K27me3) in FACS-isolated sparmetogenic populations (SgU, SgD, ScLZ, ScPD and rSt)

last: F.M. Peters

first: Pavel

last: A. Komarov


title: The placentalia specific histone H3.4 promotes germ cell development and reproductive fitness [RNA-seq]

overall_design: RNA-seq from FACS-isolated spermatogenic populations (ScLZ, ScPD, rSt and elSt) from mice with H3f4 gene being mutated to either encode for H3.1, or to contain single substitution mutations (H3.4V24A and H3.4H42R)


title: Effect of hydrolyzed corn starch treatment on the gene-expression profiles

status: Public on Apr 05 2026

city: Tokyo

first: Hitomi

last: Hagawa

address: 7-2-1 Hirai, Edogawa-ku

department: Research & Development Headquarters

country: Japan

institute: Lion Corporation

summary:
This study investigates the transcriptional response of normal human epidermal keratinocytes (NHEKs) to treatment with hydrolyzed corn starch containing maltotetraose.
NHEKs were treated with 2.0% hydrolyzed corn starch for 24 h, and total RNA was subjected to gene expression profiling using a Clariom S human array.

overall_design: NHEKs were cultured in 6-well plates and treated with either culture medium alone (control) or medium containing 2.0% hydrolyzed corn starch for 24 h. Total RNA was extracted from cells and hybridized to Clariom S human arrays. The dataset includes n=3 control samples and n=3 treated samples.

first: Eri

last: Ichikawa

first: Keiko

last: Otake


title: RNA-seq of wild-type human iPSC-derived retinal organoids at different developmental stages

city: Manchester

first: Jacob

last: Sampson

address: Oxford Road

institute: University of Manchester

summary:
Human retinal organoids derived from pluripotent stem cells provide an in vitro system to model key aspects of early human retinal development and to investigate mechanisms underlying developmental eye disorders. Congenital eye diseases, such as microphthalmia, anophthalmia and coloboma, arise from disruptions in gene regulatory programs that control retinal progenitor specification and neuronal differentiation. However, studying these processes in humans is challenging due to limited access to developing retinal tissue.
Here we present a temporal bulk RNA sequencing dataset of retinal organoids collected across multiple stages of differentiation (days 0, 35, 60, 90, 120, and 150). These timepoints span early retinal lineage specification through progressive neuronal differentiation and maturation of retinal cell types. The dataset captures dynamic gene expression changes associated with retinal development and provides a transcriptional framework for studying genes implicated in congenital and developmental retinal disorders.

overall_design: RNA-seq of wild-type human iPSC-derived retinal organoids at days 0 (iPSC), 35, 60, 90, 150 and 180 of organoid differentiation.

first: Srishti

last: Silvano

first: Rick-Lenze

last: van Annika

first: Milena

last: Zitnik-Sergeant

first: Jamie

last: Ellingford

first: Manning

last: Cerys


title: Nanoplastics induces Arrhythmia in Human Stem-cells derived Cardiomyocytes [mouse hearts]

city: Singapore

first: Jeremy

last: Pang

address: 61 Biopolis Drive

country: Singapore

institute: A*STAR

summary: Nanoplastics (NPs), plastic particles ranging from 1–1000 nm, form through weathering and are considered more hazardous than larger plastics due to their ability to penetrate cell barriers and be internalised by biological systems. Most research on NPs has focused on animal models, examining effects on the brain, lungs, and gastrointestinal tract. To enhance physiological relevance, this study investigated the impact of NPs on human cardiomyocytes (CMs) derived from human embryonic stem cells (hESCs). We observed significantly higher cellular uptake of 50 nm NPs compared to 500 nm particles, with dose-dependent accumulation over 3, 5, and 7 days of treatment. This accumulation induced oxidative and endoplasmic reticulum (ER) stress, culminating in arrhythmias by day 7. Complementing these in vitro findings, transcriptome profiling of mice exposed to NPs for 8 weeks revealed disrupted RNA splicing, dysregulated protein translation, and defective protein folding. These molecular changes led to ER stress, apoptosis, and impaired transmembrane ion conductance, contributing to the arrhythmic phenotype. Our findings highlight the detrimental effects of NPs on the human heart. Further research is needed to fully elucidate the mechanisms underlying NP-induced toxicity and to develop strategies for mitigating their adverse effects. This study underscores the urgency of addressing NP pollution to protect human health.

overall_design: RNA-SEQ of Wild Type adult male mice treated with Polystyrene-Nanoplastics over 8 consecutive weeks and control group administered with distilled water.

first: Shirley Pei Shan

last: Chia

first: Jeremy Kah Sheng

first: Winanto

last: Winanto

first: Boon-Seng

last: Soh


title: Epigenetic modulation of polyamine biosynthetic pathways rectifies T cell dysfunction to enhance anti-tumor immunity in lung cancer [ATAC-seq]

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: T cell exhaustion (TEX) represents a critical target for immunotherapy in cancer. Nevertheless, T cells exhibit diminished responsiveness to immune checkpoint inhibitors once they transition to a terminally-exhausted state. Here, we employed an epigenetic drug screen and identified BET inhibitors (BETis) as enhancers of effector functions in primary exhausted T cells from malignant pleural effusions in lung cancer patients. Transcriptomics, metabolomics, and ATAC-seq analyses revealed that BETis reinvigorate TEX by activating the polyamine biosynthesis pathway, expanding intracellular polyamine pools, and altering chromatin accessibility. Genetic and pharmacological inhibition of ornithine decarboxylase (ODC), a key enzyme in this pathway, abolished BETi-mediated immunopotentiation. Single-cell RNA-seq demonstrated BETis reduced terminal TEX while promoting progenitor TEX through activation of the MYC-ODC axis. BETi treatment or adoptive transfer of BETi-treated T cells suppressed malignant pleural effusion formation in a syngeneic lung cancer model. These findings highlight an epigenetic-metabolic approach to enhance TEX plasticity and offers insights for novel cancer immunotherapies.

overall_design: CD3+ T cells were isolated from malignant pleural effusions (MPE) of two lung cancer patients and treated with mock and JQ1 (500nM) for 24-72 hr. At day 7, CD8+ T cells were further isolated from mock- and JQ1-treated CD3+ T cells for ATAC-seq to analyze the chromatin accessibility.

first: Hsing-Chen

last: Tsai


title: Epigenetic modulation of polyamine biosynthetic pathways rectifies T cell dysfunction to enhance anti-tumor immunity in lung cancer [RNA-seq]

overall_design: CD3+ T cells were isolated from malignant pleural effusions (MPE) of three lung cancer patients and treated with mock and JQ1 (500nM) for three consecutive days. At day 7, total cellular RNA was extracted for RNA-seq.


title: The placentalia specific histone H3.4 promotes germ cell development and reproductive fitness

first: Antoine

last: Peters


title: Mechanism of RACK1-dependent ZAKɑ activation at stalled and collided ribosomes

status: Public on Jun 01 2026

city: Copenhagen

first: Zhenzhen

last: Wu

address: Blegdamsvej 3B, Maersk Building,

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: Despite a growing interest in the ribotoxic stress response (RSR), it remains unknown how the upstream p38 and JNK-activating MAP3 kinase ZAKɑ senses translational impairment. Combining Alphafold3 prediction and RNA crosslinking and immunoprecipitation (CLIP), we uncover that ZAKɑ dynamically monitors the mRNA exit channel of elongating ribosomes. This is accomplished by ZAKɑ via its direct interactions with the ribosomal proteins RACK1 and RPS27 as well as with the 18S rRNA helix-26. In this conformation, four RNA-binding peptides in ZAKɑ span across the path of ribosome-exiting mRNA. Progressive elongation effectively threads ZAKɑ off the ribosome, while mRNA stasis stabilizes the interaction allowing for kinase activation. Prolonged binding of ZAKɑ to slow-elongating, stalled and collided ribosomes is associated with sequestration of the SAM domain on RACK1, allowing for transient ZAKɑ dimerization, activation loop trans-autophosphorylation and RSR activation. Our findings highlight how ZAKɑ senses both stalled and collided ribosomes through overlapping mechanisms.

overall_design:
ZAK knockout cells were rescued with a series of ZAKα constructs, indluding:
(1) full-length ZAKɑ;
(2) ZAKɑ with lysine (K) and arginine (R) residues mutated to alanine (A);
(3) ZAKɑ lacking the C-terminal domain (CTD);
(4) ZAKɑ with lysine (K) and arginine (R) residues mutated to alanine (A) and lacking the C-terminal domain (CTD);
(5) ZAKɑ with deletion of the YEATS-Like domain (YLD);
(6) ZAKɑ lacking residues 768-780;
(7) ZAKɑ lacking residues 411-422 and 611-617.
(8) ZAKɑ comprising residues 1-713
Rescued cell lines, except those expressing construct (4) (ZAKα with lysine (K) and arginine (R) residues mutated to alanine (A) and lacking the C-terminal domain (CTD)) and construct (7) (ZAKα lacking residues 411–422 and 611–617), were treated with low-dose anisomycin (0.19 µM) for 15 minutes. Cells expressing constructs (4) and (7) were treated with an equivalent volume of DMSO as a control.

In addition, the full-length ZAKɑ rescue cell line was subjected to the following additional drug treatments:
high-dose anisomycin (76 µM for 15 minutes),
lactimidomycin (15 µM for 1 hour),
CC885 (1 µM for 6 hours) and Harringtonine (30µM for 1 hour)

first: José

middle: F

last: Martínez

first: Andrii

last: Bugai


title: Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors

status: Public on Apr 04 2026

city: Shanghai

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

summary: Depression is a globally prevalent disabling mental illness with serious social hazards. Previous studies suggest that neuroinflammation plays an important role in the pathogenesis of depression, but the underlying mechanism remains elusive. Endogenous retrovirus (ERVs) is a type of transposable elements (TEs), consists around 8% of human genome but are mostly silenced in vivo. Repressive histone modifications H3K9me3 mediated by the methyltransferase SETDB1 plays a key role in maintaining silencing of ERVs. In this study, we constructed Setdb1-CK-cKO (KO) transgenic mice. Behavioral tests showed that the KO mice exhibited anxiety-depression-like behaviors compared to wild type (WT). Cortex snRNA-seq analysis revealed significant changes in astrocytes in addition to excitatory neurons, with the emergence of a new sub cluster of astrocytes in the KO whose transcriptional profile exhibited specific ERVs activation. We observed a large number of GFAP-positive cells in the KO cortex and striatum by Immunostaining, suggesting reactive astrogliosis. Transcriptomic analysis of astrocytes revealed significant upregulation of genes associated with inflammation in the KO cortex, including multiple chemokine genes. To investigate the potential molecular mechanism underlying "endogenous" neuroinflammation in KO mice, we focused on the purinergic receptor P2X7R, which has been reported to play an important role in mediating neuroinflammation and emotional behaviors. Most importantly, we found that the expression of P2rx7 was significantly upregulated in the KO neuron. We applied multiple epigenomic methods (RNA-seq, ATAC-seq, H3K9me3 ChIP-seq) to analyze in detail the molecular mechanism by which SETDB1 regulates the P2rx7 gene expression, and identified a novel enhancer fragment, mE1. We further constructed a SETDB1 knockout human 293T cell line and examined chromatin accessibility by ATAC-seq. We found a regulatory fragment hE1 with enhancer activity, which was present at a similar location in the human P2RX7 locus, suggesting that this mechanism is conserved between human and mouse. Knockout of P2X7R effectively ameliorated neuroinflammation and partially alleviated neuronal dysfunction as well as behaviors in Setdb1-CK-cKO mice.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: H3K9me3 ChIP-seq of sgSETDB1 and control 293T cell line, 3 samples for sgSETDB1 and 2 sample for control. H3K9me3 ChIP-seq of Setdb1-CK-cKO cortex neuronal nuclei, 3 samples per group.

first: Yueyan

last: Zhu

first: Daijing

last: Sun


title: Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors [snRNA-seq]

overall_design: Nuclei were isolated from the cortex of wildtype and Setdb1-CK-cKO mice, two animals for each group.


title: Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors [ATAC-seq]

overall_design: ATAC-seq of neuron in wildtype and Setdb1-CK-cKO mice, three animals per group. ATAC-seq of 293T cell line in control and SETDB1 knockout(sg-SETDB1) group, three replicate wells per cell line. ATAC-seq of astrocyte in wildtype and Setdb1-CK-cKO mice, two animals combine to one sample, two samples per group.


title: Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors [ChIP-seq]

overall_design: H3K9me3 ChIP-seq of astrocyte in wildtype and Setdb1-CK-cKO mice cortex, three animals per group.


title: Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors [RNA-seq]

overall_design: Astrocyte specific RNA-seq in wildtype and Setdb1-CK-cKO mice, two animals combine to one sample, two samples per group. Neuronal nuclei RNA-seq in wildtype and Setdb1-CK-cKO mice, three animals per group. Cortex tissue RNA-seq in wildtype, Setdb1-CK-cKO and Setdb1-CK-cKO/P2rx7 knock out mice, three animals per group.


title: Synovial sarcoma with prominent myxoid stroma and negative epithelial markers

status: Public on Apr 03 2026

city: Niigata City

first: Tomohiro

last: Miyazaki

address: 1-757 Asahimachi-Dori, ChuoKu

department: Orthopedics

institute: Niigata University Graduate School of Medical and Dental Sciences

summary: Bulk RNA sequencing was performed on two human synovial sarcoma specimens from a single patient: a primary thigh soft-tissue tumor and a recurrent subcutaneous thigh lesion.

overall_design: Two tumor samples from one patient were subjected to bulk RNA-seq. Sequencing reads were used for quality assessment, alignment/quantification, and fusion transcript screening.

first: Naoki

last: Oike

first: Takashi

last: Ariizumi

first: Hiroyuki

last: Kawashima


title: Genotoxicity profiling reveals distinct platform- and cell type–specific effects in therapeutic gene editing for genetic hyperinflammation

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Base editors enable precise correction of point mutations without requiring DNA double-strand breaks, yet platform– and cell type–specific genotoxicities remain incompletely characterized. Here, we applied cytosine base editing (CBE) to disrupt a cryptic splice-site mutation in the Unc13d locus of Jinx mice, a model of familial hemophagocytic lymphohistiocytosis type 3 (FHL3). Efficient editing (62–89%) in fibroblasts, T cells, and hematopoietic stem cells (HSCs) restored Unc13d splicing, reconstituted cytotoxic T cell function, and protected mice from virus-triggered hyperinflammation after transplantation of edited HSCs. Comparative genotoxicity profiling revealed distinct platform- and cell type–specific patterns: hyperactive CBE induced broader off-target activity and more structural variants than CRISPR–Cas9. While off-target sequence edits persisted, the stability of CBE-induced chromosomal translocations differed between cell types. These findings establish therapeutic base editing for a genetically predisposed hyperinflammatory syndrome and underscore the importance of context-specific safety profiling to guide clinical translation of genome editors.

overall_design: Murine T cells, HSCs and MEF cells were edited using Cas9 nuclease or evoCDA1-BE4max at the Unc13D locus. CAST-Seq was performed to assess the formation of chromosomal translocations between the on-target site and potential off-target sites.

first: Lei

last: Lei

first: Masako

last: M. Kaufmann

first: Jessica

last: Lao

first: Gudrun

last: Thoulass

first: Sandra

last: Ammann

first: Hui

last: Xiao

first: Manuel

last: Rhiel

first: Viviane

last: Dettmer-Monaco

first: Julian

last: Grünewald

first: Jamal

last: Alzubi

first: Bret

last: R. Miller

first: Kristoffer

last: Weißert

first: Linda

last: Gräßel

first: Christoph

last: Schell

first: Anna

last: Lena Illert

first: J. Keith

last: Joung

first: Melanie

last: Boerries

first: Tatjana

last: I. Cornu

first: Stephan

last: Ehl

first: Miriam

last: Erlacher

first: Peter

last: Aichele

first: Toni

last: Cathomen


title: Toll-Like-Receptor 5 Reduces Lung Dysbiosis and Protects Against Pulmonary Fibrosis

city: RTP

first: Thomas

last: Randall

state: NC

address: 101 TW Alexander

institute: NIEHS

overall_design: Refer to individual Series


summary: TLR5 is a pathogen recognition receptor against flagellin that is expressed in various epithelial and immune cells. Mice pretreated with TLR5-agonist are protected against bleomycin-induced pulmonary fibrosis. However, the mechanisms by which TLR5-agonism protects against pulmonary fibrosis remains to be determined. Here, we found innate host defense gene sets to be selectively elevated in sorted type 2 alveolar epithelial.

overall_design: mRNA profiles of TLR5-agonist and vehicle-treated type 2 alveolar epithelial cells were generated by deep sequencing, in triplicate, using using BGI’s unique DNBseq™.

first: Yosuke

last: Sakamachi

first: Lecong

last: Zhou

first: Tom

first: Jian

middle: L

last: Li

first: Stavros

last: Garantziotis


summary: Idiopathic pulmonary fibrosis (IPF) is a devastating pulmonary disease with no curative treatment other than lung transplantation. IPF results from maladaptive responses to lung epithelial injury, but the underlying mechanisms remain unclear. Here, we show that deficiency in the innate immune receptor, toll-like receptor 5 (TLR5), is associated with IPF in humans and with increased susceptibility to experimental fibrosis in mice, while activation of lung epithelial TLR5 through a synthetic flagellin analog protects from experimental fibrosis. Mechanistically, epithelial TLR5 activation induces antimicrobial gene expression and ameliorates dysbiosis after lung injury.  In contrast, TLR5 deficiency in mice and IPF patients is associated with lung dysbiosis. Elimination of the microbiome in mice through antibiotics abolishes the protective effect of TLR5 and reconstitution of the microbiome rescues the observed phenotype. In aggregate, TLR5 deficiency is associated with IPF and dysbiosis in humans and in the murine model of pulmonary fibrosis. Furthermore, TLR5 protects against pulmonary fibrosis in mice, and this protection is mediated by effects on the microbiome.

overall_design: Experimental animals were euthanized using FatalPlus by intraperitoneal administration. Lungs were excised from animals under sterile conditions and were collected into DNA extraction buffer containing ATL buffer and proteinase K (Qiagen) and shaken in a FastPrep Instrument (MP Biomedicals) at 5.0ms-1 for 30s. Following bead-beating, genomic DNA (gDNA) was extracted using the DNeasy Blood and Tissue Kit (Qiagen) in accordance with the manufacturer protocol. The quality and quantity of the isolated gDNA was measured using a 4200 Tapestation System (Agilent). Bacterial DNA was quantified in experimental specimens with a QX200 droplet digital PCR (ddPCR) system (Bio-Rad). 16S V4 amplicon libraries were prepared following a modified Illumina library construction workflow developed by the Schloss Lab. The PCR amplification of the target region was performed using 515F (GTGYCAGCMGCCGCGGTAA) and 806R (GGACTACNVGGGTWTCTAAT) 16S primers. Amplicons were then purified using NGS clean-up and size-select (Macherey-Nagel) in accordance with the manufacturer protocol. For the Tlr5-/- dysbiosis study, wildtype and Tlr5-/- mice were treated with intratracheal bleomycin (3U/Kg) and were euthanized 7-days post administration. For the epithelial Tlr5 knockout dysbiosis study, Tlr5-/- and Tlr5fx/fx Spc-Cre mice were treated with intratracheal bleomycin (3U/Kg) and were euthanized 7-days post administration. For antibiotic (ABX)/bleomycin samples, animals were given a mixture of Ampicillin (1 g/L, Sigma, A1593-25G), Vancomycin (500 mg/L, Sigma, V2002-5G), Neomycin Sulfate (1 g/L, Sigma, N5286-25G), and Metronidazole (1 g/L, M1547-25G) in drinking water and in mash for 4-weeks prior to experimental use and throughout studies. Sucralose (1/50 dilution) was added for palatability. Mice were given bleomycin (3U/Kg), intratracheally, and euthanized at day 7. For TLR5-agonist/bleomycin samples, animals were dosed with 1.5 g of TLR5-agonist subcutaneously (200 L volume in normal saline with 0.01% Tween-80), 30-minutes prior to bleomycin administration. Mice were given bleomycin (3U/Kg), intratracheally, and euthanized at day 7. For the fecal microbiota transfer (FMT) donor samples, naïve wildtype and Tlr5-/- mice were euthanized for lung collection. For the FMT recipient samples, wildtype and Tlr5-/- mice were placed on ABX for 4-weeks and rested for 1-week prior to FMT from Tlr5+/+ or Tlr5-/- donors. FMT was employed in a 2-by-2 design, whereby microbiota-depleted Tlr5-/- and Tlr5+/+ mice (FMT recipients) received FMT from either Tlr5-/- or Tlr5+/+ mice (FMT donors) via 8 oral gavages in 2-weeks.

first: Thomas A

first: Brian

last: Papas

first: Jason

last: Malphurs

first: Benjamin G

last: Wu

first: Yonghua

first: Leopoldo N

last: Segal


title: Eye-conic' spatial transcriptomics of keratoconus corneas

city: Poznan

first: Marzena

last: Gajecka

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

summary: The cornea is a transparent, avascular eye tissue composed of five layers: epithelium, Bowman's layer, stroma, Descemet's membrane, and endothelium, each of which, if affected by keratoconus (KTCN), may exhibit specific morphological changes. Due to the complexity of the tissue, the studies preserving the spatial location should be applied to identify the layer-specific molecular changes in KTCN, for further understanding of the mechanistic aspects of its cone formation.

overall_design: Eight corneas of 8 unrelated Polish male patients with KTCN were included in the study, as well as five normal/non-affected corneas collected postmortem from 5 deceased male donors. The 10 µm-thick corneal cryosections and Visium Spatial Gene Expression Libraries were prepared and processed according to manufacturer's protocol ‘for Fresh Frozen’ (v. 1, 10x Genomics, Pleasanton, CA, USA). The paired-end sequencing was performed using a NovaSeq 6000 sequencer (Illumina, San Diego, CA, USA).

first: Alicja

last: Wysocka

first: Katarzyna

last: Jaskiewicz-Rajewicz

first: Jakub

last: Wozniak

first: Malgorzata

last: Rydzanicz

first: Rafal

last: Ploski

first: Monika

last: Udziela

first: Jacek

last: Szaflik


title: Transcriptomic analysis of therapy-naïve and alectinib-treated H3122 xenograft tumors from NSG and humanized HGF-NSG mice

city: Tampa

first: Bina

last: Desai

state: Florida

address: 12902 USF Magnolia Drive

institute: H. Lee Moffitt Cancer Center

summary: To uncover the identity of the HGF-independent stromal-mediated resistance mechanism(s), we performed transcriptomic analyses of treatment-naïve and alectinib-treated H3122 xenograft tumors from NSG and humanized HGF-NSG (hHGF-NSG) mice. Xenograft tumors of H3122 cell model were used to perform bulk-RNA sequencing. Reads were mapped to both human and murine genomes, enabling simultaneous assessment of the tumor and stromal compartments. Our transcriptional analyses revealed the emergence of the HGF-dependent differences only after six weeks of alectinib treatment. Pathway enrichment analyses revealed marked changes in multiple pathways associated with extracellular matrix (ECM). Altogether, the transcriptomic analysis supported the potential involvement of tumor cell-ECM interactions in HGF-independent mediation of stromal-mediated resistance to alectinib.

overall_design:
Bulk RNA-sequencing profiling of therapy naïve and alectinib treated (2 weeks and 6 weeks) H3122 xenograft tumors from NSG and hHGF-NSG mice, mapped to human reference genome, to uncover changes in the tumor cell compartment.  See fpkm_hg38.txt.
Also mapped to murine reference genome.  See fpkm_mm10.txt.

first: Andriy

last: Marusyk

first: Sandhya

last: Prabhakaran


title: Single-Cell Transcriptomic Profiling of Male Zebrafish hypothalamus: Investigating the Impact of CCK1/CCK2 Knockout on hypothalamus Function

city: Wuhan

first: Hangyu

last: Li

state: 湖北省

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

summary: This study explores the effects of CCK1 and CCK2 knockout on the hypothalamus of male zebrafish using single-cell RNA sequencing (scRNA-seq). Two groups were analyzed: the CCK1/CCK2 knockout (KO) group and the wild-type (WT) group. hypothalamus tissues were dissociated into single cells, followed by RNA sequencing to examine changes in gene expression. The results show how CCK receptor loss impacts hypothalamus cell function and gene expression, providing insights into the role of CCK in zebrafish hypothalamus regulation and endocrine function.

overall_design: Male zebrafish (6 months old) from two groups, CCK1/CCK2 knockout (KO) and wild-type (WT), were used. hypothalamus tissues from 30 fish per group were collected for analysis.


title: A novel platform for parallel T cell receptor cloning and testing enables anti-neoantigen tumor immunotherapy

status: Public on Apr 02 2026

city: Pittsburgh

first: Warren

last: Shlomchik

address: 5051 Centre Ave

institute: University of Pittsburgh

summary: Tumor-infiltrating CD8 cells recognize neoantigens created by tumor-specific mutations. Nonetheless, even after checkpoint inhibitor therapy, most patients progress. A deeper understanding of anti-tumor responses could facilitate development of better therapies. To enable such studies, we applied TCXpress, a high throughput platform that clones fully expressible TCRs from single cells into retro- or lenti- viral vectors without sequencing or gene synthesis, to study TCRs from CD8 cells infiltrating mouse MC38 tumors. We expressed cloned TCRs in reporter cells and interrogated TCR specificity by coculturing them with B6WT3 cells transduced with tandem minigenes encoding predicted neoantigens. We isolated TCRs reactive against epitopes from mutant Rpl18, ADPGK, PSMD2 and Zc3h7b along with self-reactive TCRs that recognize normal B6 and MC38 cells. Importantly, we successfully treated MC38-bearing mice with T cells transduced with anti-Rpl18 TCRs. These results establish a system that could be used to study many types of T cell responses and validates a therapeutic approach that could be tested in the clinic.

overall_design: Whole genome sequencing of MC38-Leiden cells was performed to identify potential neoantigens compared to reference B6 germline.

first: Alexander

last: Rowe

first: Smriti

last: Chaurasia

first: Wenzhong

last: Wei

first: Lau

last: Garcia-Dieguez

first: Katherine

last: Querry

first: Jonathon

last: Schiebel

first: Christy

last: Smolak

last: Muralles

first: Daniel

last: Wikenheiser

first: Kevin

last: Quann

first: Collin

last: Pirner

first: Kentin

last: Codispot

first: Mark

middle: J


title: Developmental molecular signatures define de novo cortico-brainstem circuit for skilled forelimb movement

city: White Plains

first: Julia

last: Kaiser

address: 784 Mamaroneck Avenue

institute: Burke Neurological Institute

summary:
Skilled motor control requires precise connections between subcerebral projection neurons (SCPN) in the cerebral cortex and their appropriate subcerebral targets in the brainstem or spinal cord. The brainstem has been widely recognized as a key integration and processing hub between “upper” motor centers and spinal circuits involved in execution of movements. Cortical input into the brainstem may fine-tune movement execution and support motor planning and is established by two SCPN supopulations: 1) cortico-brainstem neurons (CBN) that limit their axon extension to supraspinal levels, directly innervating brainstem nuclei, and 2) corticospinal neurons (CSN) that extend their axons into the spinal cord but additionally collateralize within the brainstem. Classical anatomical tracing approaches are not able to distinguish CBN from CSN, since these distinct subpopulations reside interdigitated in cortex, thus precluding the investigation of the function of CBN in skilled motor movement execution and planning until now.
We used a combination of transcriptomics, tracing, and imaging techniques to identify the molecular program that CBN vs. CSN at the time point of initial axon extension. We found that Neuropeptide Y (Npy) is specifically enriched in CBN in lateral cortex, while CART prepropeptide (Cartpt) delineates cervical-projecting CSN, which now provides, for the first time in the field, molecular access to specifically investigate direct cortical input into the brainstem. By using established Cre mouse lines for CBN / CSN specific markers, we now aim to investigate the function and connectivity of these CBN vs. CSN within the brainstem. Our preliminary results suggest a topographic organization of these subpopulations within the brainstem. Selectively silencing of Npy+ CBN within the lateral cortex will allow us to investigate the contribution of CBN to skilled motor movements in the single pellet reaching task and other selected motor tasks. Our results provide a foundation for future studies aiming to unravel the complexity of cortico-brainstem and cortico-spinal circuits, and their contribution to movement control in health and disease.

overall_design: retrograde labeling of SCPN (labeled form cerebral peduncles) vs CSN (labeled from spinal C2) at P0/P2 respectively, tissue collection and single cell dissociation at P1 vs. P3, FACS,  whole cell scRNA-Seq (10x Chromium SC 3')

first: Vibhu

last: Sahni

first: Dimitris

last: Konstantopoulos


title: Single-Cell Transcriptomic Profiling of Male Zebrafish Pituitary: Investigating the Impact of CCK1/CCK2 Knockout on Pituitary Function

first: Hangyu

last: Li

summary: This study explores the effects of CCK1 and CCK2 knockout on the pituitary of male zebrafish using single-cell RNA sequencing (scRNA-seq). Two groups were analyzed: the CCK1/CCK2 knockout (KO) group and the wild-type (WT) group. Pituitary tissues were dissociated into single cells, followed by RNA sequencing to examine changes in gene expression. The results show how CCK receptor loss impacts pituitary cell function and gene expression, providing insights into the role of CCK in zebrafish pituitary regulation and endocrine function.

overall_design: Male zebrafish (6 months old) from two groups, CCK1/CCK2 knockout (KO) and wild-type (WT), were used. Pituitary tissues from 30 fish per group were collected for analysis.


title: SPECIFIC REACTIVITY OF ABASIC SITES WITH POLYAMINES ENABLES THEIR GENOMIC MAPPING

city: Paris

first: Anton

last: Granzhan

address: 45 rue des Saints-Pères

department: UMR8601 LCBPT

country: France

institute: Université Paris Cité

summary: Apurinic/apyrimidinic (AP) sites are among the most abundant DNA lesions and represent key intermediates in the base excision DNA repair pathway. Knowing their genomic distribution is important for understanding the mechanisms of genotoxic agents. Although several methods exist for genomic mapping of AP sites, some of them suffer from limited specificity and/or complex multi-step workflows. Here, we present APX-seq, a novel method based on the recently discovered reaction of AP sites with 1,2-diamines, for highly specific chemical labelling, isolation and enrichment of AP site-containing genomic fragments for subsequent DNA sequencing. Following in vitro optimization and validation, we applied APX-seq to the genome of cultured HepG2 cells. Our finding reveal that AP sites are broadly distributed in the genome and are enriched in euchromatin, consistent with the prior studies. Moreover, we show that treatment with genotoxic agents such as a DNA-alkylating chemical or X-ray radiation, barely alters the genomic landscape of AP sites.

overall_design: APX-seq and AP-seq were performed in HepG2 cells subjected to four conditions: untreated (control), 5 mM MMS treatment, 10 mM MMS treatment, and 6 Gy X-ray radiation (XRD). Cells were harvested at defined time points following treatment for subsequent genomic DNA extraction and AP site profiling.

first: Eka Putra

last: Gusti Ngurah Putu

first: Laurent

last: Cattiaux

first: Nicolas

last: Servant

first: Sophie

last: Bombard


title: Cell size-dependent mRNA transcription drives proteome remodeling [RNA-seq]

city: Stanford

first: Dong Shin

last: You

address: 327 Campus Drive

institute: Stanford University

summary: Increasing cell size drives proteomic changes that impact cell physiology. However, the molecular basis of size-dependent proteome remodeling has remained unclear. Here, we develop an inducible Cyclin D1 expression system in human cells to generate proliferating cells spanning over a two-fold size range. We use this system to make comprehensive genome-wide measurements of mRNA and protein concentrations and stability. We find that protein and mRNA turnover rates are weakly related to cell size, but that mRNA concentrations are strongly size-dependent. This establishes that transcriptional regulation is the basis of proteome remodeling. Live-cell imaging of nascent mRNAs using the MS2 system is used to measure how transcriptional dynamics change with cell size. Larger cells prolong transcriptional bursts and shorten inactive periods between bursts but maintain similar burst amplitudes to achieve transcriptional scaling. Together, our results show how transcription is modulated by cell size to remodel the proteome and alter cell physiology.

overall_design: RNA-seq profiling of CCND1 overexpression or knockdown hTERT-RPE-1 lines with and without induction by doxycycline or DMSO at day 4 and day 5 of treatment. Two replicates are provided

first: Christopher

last: Bohrer

first: Purva

last: Rumde

first: Ioannis

last: Sanidas

first: Matthew

middle: P

last: Swaffer

last: Larson

first: Josh

last: Elias

first: Michael

last: Lanz

first: Jan

middle: M

last: Skotheim


title: “Zipper” Grammar of CTD Governs the Spatial Programing of the Transcription Cycle of RNA Polymerase II [TT-seq]

city: Austin

first: Yan Jessie

last: Zhang

state: TX

address: 100 E 24th St

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: RNA polymerase II transcribes all protein-coding genes in eukaryotes, with its C-terminal domain (CTD) acting as a regulatory platform throughout the transcription cycle. Despite its simple sequence, the conserved heptad repeats encode a regulatory grammar critical for transcription initiation, elongation, and termination. Using structural analysis, single-molecule imaging, and synthetic CTD-engineered Pol II constructs, we defined the minimal sequence requirements across transcriptional stages. We show that while SP motifs are essential phosphorylation sites, flanking residues tolerate variability. In contrast, the periodic positioning of tyrosine residues is indispensable for pre-initiation complex (PIC) assembly through interactions with the Mediator, which are disrupted upon Ser5 phosphorylation triggering promoter escape. This supports a “zipper” model where sequential tyrosine engagement stabilizes PIC assembly and progressive phosphorylation propels Pol II escape. Site-specific Ser2/5 phosphorylation orchestrates 3’-end processing factor recruitment. These findings redefine the functional grammar of the Pol II CTD and explain how a low-complexity sequence achieves regulatory specificity.

overall_design: TT-seq profiling of HEK293 degron cells that were tranfected with an RPB1 with a 26X wildtype CTD or a 26X Y1T and T4Y CTD

first: Qian

first: Haley

middle: A

last: Hardtke


title: “Zipper” Grammar of CTD Governs the Spatial Programing of the Transcription Cycle of RNA Polymerase II [ChIP-Seq]

overall_design: ChIP-seq of GFP-tagged RPB1 with engineered C-terminal domain (CTD) in HEK293T cells.