title: FoxO factors are essential for maintaining organ homeostasis by acting as stress sensors in airway epithelial cells

city: Kiel

first: Judith

last: Bossen

address: Am Botanischen Garten 3-9

department: Molecular Physiology

institute: CAU Kiel, Zoological Institute

summary: Airway epithelia have the challenging task of maintaining functional and structural homeostasis, even when exposed to various stress factors. Transcription factors of the FoxO family can fulfill this complex task, as they act as integration hubs that translate extrinsic and intrinsic information into a physiologically appropriate response. We could show that FoxO factors in Drosophila, mouse, and human airway epithelial cells (AECs) respond to stressors like hypoxia, temperature, or oxidative stress by nuclear translocation. A complex activation pattern is revealed in human cell culture systems, which differs between individual hFOXO factors and cell types. Studies with Drosophila showed that hypoxia was the only stressor that induced a dfoxo-dependent, local immune response activation. Since Drosophila has only one ortholog of FoxO, it was possible to show that the absence of dfoxo in the airways strongly increases the stress sensitivity of the airways. This stress sensitivity finds its counterpart in mouse models of chronic and acute asthma, with reduced mFoxO expression in the lung, particularly mFoxO1 and mFoxO3A. Finally, it is also reflected in asthma patients who show reduced hFOXO transcripts in their sputum samples. We conclude that active FoxO signaling in AECs is necessary to respond appropriately to stressors. Impaired FoxO signaling limits this ability and thus promotes disease development.

overall_design: RNA-Seq of trachea from FoxO kockout animals and animals with tracheal FoxO overexpression, compared to their respective controls

first: Karin

last: Uliczka

last: Roeder


title: Characterizing immune signatures of seasonal coronaviruses HCoV-229E and -OC43 in human nasal airway epithelial cells

status: Public on Jul 01 2025

city: London

first: Efstathios

last: Giotis

address: Norfolk Place

department: Infectious Diseases

country: United Kingdom

institute: Imperial College London

type: Expression profiling by high throughput sequencing

summary: Seasonal coronaviruses, including HCoV-229E, -NL63, -OC43, and -HKU1, are prevalent worldwide, predominantly causing mild, self-limiting upper respiratory (re-)infections in adults, often presenting as the common cold. However, in individuals with compromised immune systems, these viruses may lead to more severe illness and even fatalities. Recently, there has been a renewed interest in studying HCoVs due to their amenability to handling in reduced biosafety containment, offering valuable alternatives to SARS-CoV-2 for preclinical screening and the development of antiviral treatments. Despite their significance, research on HCoVs has been hindered by limited host-genomic data. To address this, we performed RNA-sequencing on 3D air-liquid interface human nasal airway epithelial cells (hNECs) infected with the alphacoronavirus HCoV-229E and the betacoronavirus HCoV-OC43. These hNECs were derived from pooled adult donors and exhibited pseudostratified mucociliated differentiation, faithfully replicating the complexities of normal airway biology. Our study aimed to identify specific immune signatures associated with HCoV infections in a physiologically relevant model. By elucidating the host responses induced by different seasonal coronaviruses, we can gain valuable insights into their pathogenesis and interactions with the respiratory epithelium. This knowledge may pave the way for the development of targeted therapeutics and prophylactics to combat HCoV infections effectively.

overall_design: In this study, we aimed to investigate variations in gene expression among different human coronaviruses (HCoV). To achieve this, primary human nasal epithelial cells (hNECs) were subjected to single infections with HCoV-229E, and -OC43 at a multiplicity of infection (MOI) of 0.01, while another group remained uninfected, all maintained at 33°C. RNA samples were collected from both uninfected and virus-infected hNECs at 24 and 72 hours post-infection to assess gene expression changes. The RNA samples' quality and integrity were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies) before proceeding with library preparation. Strand-specific RNA-sequencing was performed at Novogene (Cambridge, UK). Subsequently, FASTQ files were processed using Partek Flow to obtain reliable data for downstream analysis. Differentially expressed genes were identified by applying stringent criteria, including statistical significance (P < 0.005) and fold change (>2), utilizing two replicates for each condition. By comparing the gene expression patterns, we aimed to uncover the pathways impacted by viral infections. This comprehensive examination of gene expression differences among HCoV strains in hNECs will provide valuable insights into the molecular responses of respiratory epithelial cells to different coronaviruses, potentially contributing to the development of targeted therapeutic strategies.

middle: S

first: Tukur

last: Abdullahi

first: Riaz

last: Somji


title: STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging [Xenium]

status: Public on Jun 30 2025

city: Memphis

first: Jasmine

last: Plummer

state: TN

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

country: USA

institute: St. Jude Children's Research Hospital

summary: Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular diversity, but remains constrained by scalability, high costs, and the destruction of cells during analysis. To overcome these challenges, we developed STAMP (Single-Cell Transcriptomics Analysis and Multimodal Profiling), a highly scalable approach for the profiling of single cells. By leveraging transcriptomics and proteomics imaging platforms, STAMP eliminates sequencing costs, enabling single-cell genomics of hundreds to millions of cells at an unprecedented affordability. Immobilizing (‘stamping’) cells in suspension onto imaging slides, STAMP supports single-modal (RNA or protein) and multimodal (RNA, protein and H&E) profiling, while retaining cellular structure and morphology. Its flexible, ultra-high-throughput formats facilitate the analysis of single or multiple samples in the same experiment, enhancing experimental scalability and adaptability. We demonstrate STAMP's versatility across diverse experimental contexts, including the profiling of peripheral blood mononuclear cells (PBMCs), cell lines and stem cells. We also stamped cells and nuclei from dissociated tissues from mouse organs to simulate the generation of cell atlases. Accessibility was further enlarged by analyzing nuclei from archival formalin fixed and paraffin embedded (FFPE) tissue samples. Combining RNA and protein profiling, we applied STAMP for high-throughput immuno-phenotyping of millions of blood cells, providing multimodal insights into cellular heterogeneity. We highlight the capability of STAMP to identify ultra-rare cell populations, simulating clinical applications for detecting circulating tumor cells (CTCs). By capturing lineage dynamics during stem cell differentiation and subtle changes in in vitro activated PBMCs, we further showed its utility for large-scale perturbation studies. These results validate STAMP as a first-of-its-kind single-cell imaging analysis strategy. We present data for 10,962,092 high quality cells/nuclei and 6,030,429,954 high quality transcripts. By replacing sequencing with imaging, STAMP enables high-resolution cellular profiling that is more accessible, scalable, and cost-effective. STAMP has the potential to transform our ability to map biological diversity and dynamics, significantly advancing research and clinical applications.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In this study, we transformed four advanced imaging platforms—Xenium Analyzer (10X Genomics), CosMx Spatial Molecular Imager (NanoString Technologies/Bruker), MERSCOPE (Vizgen), and PhenoCyler Fusion (Akoya Biosciences)—into scalable, flexible single-cell profiling tools. We termed this approach Single-Cell Transcriptomics Analysis and Multimodal Profiling (STAMP) through imaging.    STAMP leverages single-molecule imaging to analyze hundreds to millions of individual cells with unprecedented flexibility and scalability. The platform supports both single-modal (RNA or protein) and multimodal (RNA, protein, and H&E) profiling in single- or multi-sample configurations. We validated its performance across diverse sample types and experimental conditions, comparing its quality control metrics to classical single-cell analysis methods.    To assess scalability, STAMP was applied to cell populations ranging from hundreds to millions, demonstrating adaptability to varying sample sizes. It successfully profiled both whole cells and nuclei (from fresh-frozen and FFPE samples), enabling the analysis of archival tissues. Functional applications included:    -Immunophenotyping millions of peripheral blood mononuclear cells (PBMCs), capturing subtle compositional and transcriptional shifts induced by in vitro perturbations.  -Detection of ultra-rare cell populations, such as circulating tumor cells (CTCs), which are often undetectable using conventional scRNA-seq methods.  -Cellular differentiation and lineage tracing, where STAMP was used to study human embryonic stem cell (hESC) differentiation induced by bone morphogenetic protein 4 (BMP4), effectively modeling early embryonic gastrulation.  -Application to induced pluripotent stem cells (iPSCs), highlighting STAMP’s potential for large-scale perturbation and drug screening studies.


title: A subset of group S1 bZIP transcription factors controls resource management during starvation and recovery in Arabidopsis

city: Wuerzburg

first: Christoph

last: Weiste

address: Julius-von-Sachs Platz 2

department: Pharmaceutical Biology

country: Germany

institute: University of Wuerzburg

summary: To unravel the individual functions of group S1 bZIP transcription factors during dark induced senescence, we made use of Arabidopsis wildtype (WT) as well as single (bzip1 and bzip53) and higher-order S1 bzip mutants (bzip1/53, bzip2/11/44, bzip1/2/11/44/53) and performed RNAseq analysis during the day (Zeitgeber time 6) and extended night conditions (6h, 30h and 78h).

overall_design: We performed RNAseq from 3 biological replicates per genotype (whole rosettes of 4 weeks old wild type (WT, Arabidopsis ecotype Col-0), single (bzip1, bzip53), double (bzip1/bzip53), triple (bzip2/11/44) and quintuple (bzip1/2/11/44/53) bZIP mutants) and conditions (light (ZT6) or extended night (6, 30 or 78 hours)

first: Theresa

last: Wildenhain

first: Cezary

last: Smaczniak

first: Alexander

last: Marsell

first: Jan

last: Draken

first: Daniel

last: Maag

first: Philipp

last: Kreisz

first: Markus

last: Krischke

first: Martin

middle: J

last: Müller

first: Kerstin

last: Kaufmann

first: Wolfgang

last: Dröge-Laser


title: Gene expression profile of sorted CD45+ immune cells from the colons of WT and 5XFAD littermate controlled mice

city: Novato

middle: A

last: Winer

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for research in Aging

summary: Alzheimer's disease (AD) is associated with changes in the gut including dysbiosis. We used single cell RNA sequencing (scRNA-seq) to understand changes in the immune landscape associated with AD

overall_design: Pooled colon immune cells from 3 female littermate controlled mice at 9-months of age from WT and 5XFAD groups were isolated using fluorescense-activated cell sorting (FACS) of LiveCD45+ cells and analyzed using scRNA-seq.

first: Priya

last: Makhijani

first: Fei

last: Wu

first: Julie

middle: K

last: Anderson


title: Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples [Xenium]

city: Houston

first: Ken

last: Chen

state: TX

address: 7007 Bertner Ave

institute: University of Texas MD Anderson Cancer Center

summary: Imaging-based spatial transcriptomics (ST) is evolving as a pivotal technology in studying tumor biology and associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have not been systematically evaluated using rigorously controlled experiments. We use serial 5 m sections of formalin-fixed, paraffin-embedded surgically resected lung adenocarcinoma and pleural mesothelioma samples in tissue microarrays to compare the performance of the ST platforms (CosMx, MERFISH, and Xenium (uni/multi-modal)) in reference to bulk RNA sequencing, multiplex immunofluorescence, GeoMx, and hematoxylin and eosin staining data. In addition to an objective assessment of automatic cell segmentation and phenotyping, we perform a manual phenotyping evaluation to assess pathologically meaningful comparisons between ST platforms. Here, we show the intricate differences between the ST platforms, reveal the importance of parameters such probe design in determining the data quality, and suggest reliable workflows for accurate spatial profiling and molecular discovery.

overall_design: We generated 1 TMAs with lung adenocarcinoma and 2 TMAs with mesothelioma samples. Xenium assay was performed with FFPE TMA sections.

first: Nejla

last: Ozirmak Lermi

first: Luisa

middle: M

last: Solis Soto

first: Cara

last: Haymaker


title: Engineering effector domains of MEF2C and GATA4 enhances cardiac reprogramming

city: Tsukuba

first: SEIICHIRO

last: HONDA

address: 2-1-1 Amakubo

department: Cardiology

country: Japan

institute: University of Tsukuba

summary: The transcription factors MEF2C, GATA4, and TBX5 (MGT) are well established for converting fibroblasts into induced cardiomyocytes (iCMs). However, these reprogramming factors contain effector domains, yet their functional roles in cardiac reprogramming remain largely uncharacterized. Furthermore, whether internal deletions of these domains improve or compromise reprogramming efficiency has not been elucidated. Here we found that the combination of MEF2C and GATA4 mutants (MΔGΔT) elevated reprogramming efficiency by 7-fold to ~21%, achieving robust induction of iCMs with well-defined sarcomeric structures.

overall_design: MEFs were transduced with the retrovirus (MGT, MΔGΔT)  as indicated. Cells were collected after 1 week.

first: Seiichiro

last: Honda

first: Taketaro

last: Sadahiro

first: Masaki

last: Ieda


title: Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples [CosMx]

overall_design: We generated 2 TMAs with lung adenocarcinoma and 2 TMAs with mesothelioma samples. CosMx SMI assay was performed with FFPE TMA sections.


title: Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples [MERFISH]

overall_design: We generated 2 TMAs with lung adenocarcinoma and 1 TMA with mesothelioma samples. MERFISH assay was performed with FFPE TMA sections.


title: Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Cxcl12]

city: San Francisco

first: Nathan

last: Ewing-Crystal

address: 513 Parnassus Ave, HSW12 Room 1201A

department: Laboratory Medicine

institute: University of California, San Francisco

summary: Fibroblasts and immune cells coordinate tissue regeneration and necessary scarring after injury. In the brain, fibroblasts are border-enriched cells whose dynamic molecular states and immune interactions after injury remain unclear. We used single nuclear RNA sequencing at 21 days post photothrombotic (PT) injury to test the role of fibroblast-derived CXCL12 in regulating local immunity after brain injury. We find that loss of fibroblast CXCL12 causes dysregulated immune tone with elevated IFNg signaling.

overall_design: Tissue was collected from wildtype mice and mice with CXCL12-deficient fibroblasts [Col1a2(creER); Cxcl12(flox)]. Bulk lesional nuclei (DAPI+) were isolated and sort-purified from mice at 21 days post injury (dpi) for each condition. 1 male and 1 female mouse were harvested per timepoint/condition and were processed together.

first: Ewing-Crystal

last: Nathan

first: Thomas

middle: D

last: Arnold

first: Ari

middle: B

last: Molofsky


title: Developmental cues from epicardial cells simultaneously promote cardiomyocyte proliferation and electrochemical maturation

city: MINNEAPOLIS

first: Sophie

middle: E

last: Givens

state: MN

address: 312 Church Street SE, Room 7-256

department: Biomedical Engineering

institute: University of Minnesota

summary: Accumulating evidence indicates that maturation limits cardiomyocyte proliferation and conversely, that proliferation occurs rarely in cardiomyocytes of the adult myocardium. Here we  show results that expand on that theory when we co-culture hiPSC-CM with epicardial cells and epicardial-derived cells in two-dimensional (2D) direct co-culture and 3D engineered heart tissues (EHT). In 2D direct co-cultures the percentage of proliferating CM increased at the same time as stark electrophysiologic improvements in calcium handling. Single-cell transcriptomics revealed a significant shift in the bulk CM population in epicardial-CM co-cultures as characterized by more fetal-like myofilament isoforms but with enhanced pathways associated with electrochemical maturation and ventricular development. Co-culture of epicardial cells in the 3D-EHT model showed more limited proliferation but a similar improvement in CM electrophysiologic function. These results indicate that certain aspects of CM maturation are enhanced, especially electrophysiologic properties, by epicardial cells while an embryonic phenotype is maintained (i.e., proliferation and myofilament isoforms). Next, consistent with developmental progression and the initiation of epicardial-to-mesenchymal transition (EMT), epicardial-derived fibroblasts were added to the EHTs containing epicardial cells. Interestingly, we observed significant myofilament maturation and increased force generation by more than an order of magnitude. Taken together, our results suggest that some aspects of CM maturation (i.e., electrochemical) occur during embryonic development when proliferation rates are relatively high and that sarcomere-associated mechanical maturation occurs at later developmental stages when proliferation has largely ceased.

overall_design: Cardiomyocytes and epicardial cells derived from human induced pluripotent stem cells were co-cultured with or without TGF-Beta inhibitors that were used to inhibit epicardial epithelial-to-mesenchymal transition.

first: Brenda

last: Ogle

first: Natalia

last: Calixto Mancipe


title: Inhibition of ACLY enhances tumor immunogenicity and resolves MASH-driven HCC

city: Hamilton

first: DONGDONG

last: WANG

state: Ontario

address: 1200 Main Street West

country: Canada

institute: McMaster University

summary: Immunosuppressive tumor microenvironments are common in cancers such as metabolic dysfunction-associated steatohepatitis (MASH)-driven hepatocellular carcinoma. To further investigate tumor–immune interactions, we performed spatial transcriptomics on livers from MASH-driven HCC mouse models (WD-DEN, WT or Acly KO mice and from WD-CCL4, Vehicle, or EVT0185 (100mg/kg) treated mice).  GO enrichment analysis of spatially resolved tumor cells showed increased fatty acid and lipid metabolism in both Acly KO and EVT0185-treated mice Spatial analysis also revealed a selective increase in B cells, but not T cells, macrophages, or NKT cells, in tumors from Acly KO and EVT0185-treated mice.

overall_design: Two liver samples from WD-DEN HCC mouse models [WT (n=1) or Acly KO (n=1) mice] were used for spatial transcriptomic analysis. Two liver samples from WD-CCl4 HCC mouse models [Vehicle (n=1), or EVT0185 (100mg/kg) (n=1) treated mice] were used for spatial transcriptomic analysis.

first: Jaya

last: Gautam

first: Dongdong

last: Wang

first: Gregory

last: Steinberg


title: Macrophages direct location-dependent recall of B cell memory to vaccination [scRNA-seq and scVDJ-seq]

city: Darlinghurst

first: Wunna

last: Kyaw

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

summary: Vaccines generate long-lived plasma cells and memory B cells (Bmems) that may re-enter secondary germinal centers (GCs) to further mutate their B cell receptor upon boosting and re-exposure to antigen. We show that lymph nodes draining the primary vaccination site harbour a subset of Bmems that reside in the subcapsular niche, generate larger recall responses, and are more likely to re-enter GCs compared to circulating Bmems in non-draining lymph nodes. Depletion of CD169+ subcapsular sinus macrophages impairs Bmem proliferative expansion, secondary GC formation and secretion of affinity-matured antibodies upon boosting of the draining lymph node. This site-specific, niche-dependent control is associated with more rapid secretion of broadly neutralizing antibodies, GC participation and clonal expansion of SARS-CoV-2-specific B cells in healthy volunteers boosted with the BNT162b2 vaccine in the same versus opposite arm. These data reveal an unappreciated role for primed draining lymph node SSMs in Bmem cell fate determination.

overall_design:
To test the impact of boosting location in human subjects, we recruited 30 healthy volunteers who were SARS-CoV-2-naïve and performed a prospective, controlled clinical study of boosting the homologous BNT162b2 mRNA vaccine, which encodes the Ancestral SARS-CoV-2 Spike protein, either in the same (boosted dLN, n=20) or opposite arm (boosted ndLN, n=10) 3 weeks after the priming dose (Figure 7A; Table S3). Fine needle biopsy (FNB) of both axillary lymph nodes were performed in a subset of 18 participants (n=9, boosted dLN; n=9, boosted ndLN) on day 5-7 after the second (booster) vaccine dose. We performed single-cell transcriptomic analysis (5' Gene Expression, VDJ-B) on fine needle biopsy samples  of both axillary lymph nodes from six participants.
Files with 007L (dLN), 007R (ndLN), 010L (dLN), 010R (ndLN), 012L (dLN), 012R (ndLN) are Same arm  (Ipsilateral) vaccine group files.
Files with 008L (ndLN), 008R (dLN), 011L (ndLN), 011R (dLN), 015L (ndLN), 015R (dLN) are Opposite arm (Contralateral) vaccine group files.

first: Rama

last: Dhenni

first: Alexandra

middle: C

last: Hoppe

first: Vanessa

last: Venturi

first: Mee Ling

last: Munier

first: Tri Giang

last: Phan


title: Identification of organelle-specific autophagy regulators from tandem CRISPR screens

city: Ottawa

first: Truc

last: Losier

state: ON

address: 451 Smyth Road

department: CMM

institute: University of Ottawa

summary: Autophagy is a conserved degradative process that promotes cellular homeostasis under stress conditions. Under nutrient starvation autophagy is largely non-selective, promoting indiscriminate breakdown of cytosolic components. Conversely, selective autophagy is responsible for the specific turnover of damaged organelles. We hypothesized that selective autophagy may be regulated by distinct upstream signaling from starvation induced autophagy to promote organelle turn-over. To address this question, we conducted kinome-wide CRISPR screens using the DsRed-IRES-GFP-p62 reporter line to identify distinct signaling pathways responsible for the regulation of basal autophagy, starvation-induced autophagy, and two types of selective autophagy, ER-phagy and pexophagy.  The Brunello kinome library was designed to enhance on-target activity while minimizing off-target effects, ensuring the effectiveness and efficiency of our screens. These parallel screens identified established and novel autophagy shared regulators under these conditions, as well as kinases specifically required for ER-phagy or pexophagy. More specifically, CDK11A and NME3 were further characterized to be selective ER-phagy regulators. Meanwhile, PAN3 and CDC42BPG were identified as activator or inhibitor of pexophagy, respectively. Collectively, these datasets provide the first comparative description of the kinase signaling specificity, separating regulation of selective autophagy and bulk autophagy.

overall_design: Following exposure to stress conditions (starvation, ER stress, or peroxisomal stress), DsRed-IRES-GFP-p62 HEK293A reporter line was fixed, sorted into high GFP or low GFP populations by Fluorescence-activated cell sorting (FACS), and analized by NextSeq 500

first: Karyn

last: King

first: Maxime

last: Rousseaux

first: Ryan

last: Russell


title: Lysosomes signal through the epigenome to regulate longevity across generations [III]

first: Qinghao

last: Zhang

email: qinghaoz@bcm.edu, qhzhang87@gmail.com

state: Texas

address: BCM N820, One Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Profiling of H3K79me2 occupancy in wild-type N2 day-1 adult worms subjected to L1 larval starvation (STV) or ad libitum feeding (Fed).

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K79me2 in wild-type N2 day-1 adult worms subjected to L1 larval starvation (STV) or ad libitum feeding (Fed).

first: Meng


title: RNA sequencing of C elegans exposed to natural polyphenols

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: C elegans worms were exposed to either honokiol or magnolol and global transcriptomic profiles determied to eludicate potential modes of action

overall_design: Nematodes were exposed to 200 uM of each compound for one hour prior to RNA extraction. Magnolol (plus DMSO control) were treated in triplicate, and honokiol in duplicate

middle: R


title: Phenotypic variability in SCN1A-associated febrile seizures: transcriptomic and electrophysiological insights from iPSC-derived neurons

city: Catanzaro

first: Barbara

last: Puccio

address: Viale Europa

department: Dept of Surgical and Medical Sciences

country: Italy

institute: Magna Graecia University of Catanzaro

summary: Febrile seizures (FS) are a common childhood neurological condition triggered by fever in children without prior neurological disorders. While generally benign, some individuals, particularly those with complex FS or genetic predispositions, may develop epilepsy or other neurological comorbidities. The mechanisms underlying this transition remain unclear. Mutations in SCN1A, encoding the NaV1.1 sodium channel α-subunit, have been linked to several epilepsy syndromes associated with FS. This study examines phenotypic variability in individuals carrying the same SCN1A c.434T>C mutation, using induced pluripotent stem cell (iPSC)-derived neurons from two siblings with FS. Despite sharing the mutation, only the older sibling developed temporal lobe epilepsy (TLE). Transcriptomic analysis revealed downregulation of GABAergic pathway genes in both siblings’ neurons, aligning with SCN1A-associated epilepsy. However, neurons from the sibling with TLE exhibited additional abnormalities, including altered AMPA receptor subunit composition, changes in GABAA receptor subunit and chloride cotransporter expression, and reduced brain-derived neurotrophic factor (BDNF) levels, indicative of developmental immaturity. Voltage-clamp recordings confirmed impaired GABAergic and AMPA receptor-mediated synaptic activity. These findings suggest that combined GABAergic dysfunction, aberrant AMPA receptor composition, and reduced BDNF signaling contribute to the more severe phenotype and increased epilepsy susceptibility. These findings suggest that combined GABAergic dysfunction, aberrant AMPA receptor composition, and reduced BDNF signaling may underlie the more severe phenotype and increase epilepsy susceptibility in this individual.

overall_design: RNA-seq profiling of iPSC-derived neurons from two siblings carrying the same SCN1A mutation, compared to two healthy controls.

first: Stefania

last: Scalise

first: Alessandro

last: Gaeta

first: Elio

last: Aprigliano

first: Valeria

last: Lucchino

first: Raffaele

last: Covello

first: Mariagrazia

last: Talarico

first: Pietro

middle: H

last: Guzzi

first: Pierangelo

last: Veltri

first: Antonio

last: Gambardella

first: Lilian

last: Lissner

first: Alessandra

last: Morano

last: Cifelli

first: Veronica

last: Alfano

first: Eleonora

last: Palma

first: Gerardo

last: Perozziello

first: Gabriele

last: Ruffolo

first: Giovanni

last: Cuda

first: Elvira

middle: I

last: Parrotta


title: Macrophages direct location-dependent recall of B cell memory to vaccination [CITE-seq]

first: Wunna

last: Kyaw

overall_design: We isolated murine memory B cells from the draining lymph node, non-draining lymph node and spleen and naïve SWHEL B cells from the lymph nodes and spleen that had been adoptively transferred but not immunized and performed single cell transcriptomic profiling

first: Rama

last: Dhenni

first: Alexandra

last: Hoppe

first: Arnold

last: Reynaldi

first: Mee Ling

last: Munier

first: Tri Giang

last: Phan


title: Dysregulated RNA splicing induces regeneration failure in alcohol-associated liver disease

city: URBANA

first: Ullas

middle: Valiya

last: Chembazhi

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: UIUC

summary: Individuals with progressive liver failure due to alcohol-related liver disease (ALD) are at a high mortality risk without liver transplantation. However, our understanding of derailed regenerative responses in ALD is limited. Here, we performed comprehensive multi-omic profiling of healthy and diseased human livers using single nucleus RNA- plus ATAC-seq. We report that hepatic immune milieu alterations prevent hepatocytes from transitioning to a proliferative progenitor-like state, trapping them in a non-functional intermediate state.

overall_design: 10X multi-omics platform based profiling of human livers to obtain matched sn-RNAseq and sn-ATACseq profiles from fresh frozen livers of normal individuals, and SAH and AC patients

last: Valiya Chembazhi

first: Sushant

last: Bangru

first: AnnaMae

last: Diehl

first: Auinash

last: Kalsotra


title: Lysosomes signal through the epigenome to regulate longevity across generations [II]

first: Qinghao

last: Zhang

summary: Profiling of H3K79me2 occupancy in F3 wild-type progeny, designated as second transgenerational (T2) descendants, derived from N2, lipl-4 Tg, or dot-1.3 Tg parents.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K79me2 in F3 wild-type progeny, designated as second transgenerational (T2) descendants, derived from N2, lipl-4 Tg, or dot-1.3 Tg parents at day-1 adulthood.

first: Meng

last: Wang


title: Broccoli consumption alters microbial diversity, host and bacterial gene expression in mice fed a Total Western Diet

city: Beltsville

first: Allen

last: Smith

state: MD

address: 10300 Baltimore Ave, BARC-East, 307C

institute: USDA ARS

summary: Cruciferous vegetables and their derived compounds, such as glucosinolates, have demonstrated anti-inflammatory properties in animal models. In this study, broccoli-supplemented diet induced changes in the gut microbiome and its role in host and bacterial gene expression were examined in mice following consumption of the Total Western Diet (TWD), which is based on NHANES data and represents the composition of a typical American diet. C57BL/6 male mice were fed a TWD for six weeks followed by a supplementation of 0, 0.5, 1 or 2.5% broccoli powder for three weeks. Microbial communities from cecal contents were taxonomically profiled using 16S and metagenomics sequencing, and metatranscriptomics was used to assess functionality of bacterial species. Cecum tissues were also analyzed for host transcriptomics.

overall_design: Three week old C57BL/6 mice were fed the Total Western Diet (TWD) for 6 weeks and then subgroups of mice were fed either the TWD or TWD supplemented with 0, 0.5, 1 or 2.5% broccoli powder for an additional 3 weeks. Mice were then euthanized and cecal contents and various tissues were collected for analyses.

first: Harry

last: Dawson

first: Elizabeth

last: Pletsch

first: Jack

last: Ragonese

first: Adrienne

last: Narrowe

first: Lumei

last: Cheung

first: Celine

last: Chen

first: Thomas


title: Thymic epithelia amplify noise in chromatin accessibility via p53 repression to impose immune tolerance [CUT&Run]

city: Chicago

first: Noah

last: Gamble

state: IL

department: Pathology

institute: University of Chicago

summary: Phenotypic plasticity of somatic cells is a principal feature of vertebrate adaptation as well as a hallmark of tumorigenesis. However, the determinants and mechanisms that regulate the stability of somatic cell identities remain unclear. Here, using the somatic plasticity of thymic epithelial cells – which facilitates the selection of a self-discriminating T cell repertoire – as a physiological model system, we show that stochastic fluctuations in background chromatin accessibility at nucleosome-dense regions are amplified by thymic epithelial cells to ectopically express thousands of genes highly restricted to other specialized cell types. We found broad regions of inaccessible chromatin flanking tissue-specific genes become ‘destabilized’ during thymic epithelial maturation independently of AIRE-induced transcription of these genes, but concurrently with the repression of the tumor suppressor p53. Augmenting p53 activity in thymic epithelial cells reduced noise in chromatin accessibility at nucleosome-dense regions, inhibited ectopic expression of tissue-specific genes and caused multi-organ autoimmunity. Furthermore, we found p53-regulated fluctuations in background chromatin accessibility in lung adenocarcinoma to be associated with high plasticity states that promote tumor progression. Taken together, our findings establish p53-dependent stabilization of nucleosomal barriers to cellular reprogramming as a fulcrum of cell fate integrity that underlies critical components of immune tolerance induction and oncogenic potential.

overall_design: Thymic epithelial cells were isolated using a previously published protocol (Kim & Serwold, Methods in Molecular Biology, 2019) with minor modifications. Briefly, thymi from 4-5 week-old mice were harvested and connective tissue was removed. Stromal tissue was perforated using scissors and incubated with rotation in DMEM-F12 (Sigma D6421) at room temperature for for 10min to liberate thymocytes. Remaining stromal tissue was enzymatically digested (0.5mg/mL Collagenase D (Sigma 11088858001), 0.2mg/mL DNaseI (Sigma 10104159001), 0.5mg/mL Papain (Worthington Biochemical LS003126)). Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 and EpCAM+ cells were enriched via positive selection using magnetic anti-Cy7 beads (Miltenyi 130-091-652). Enriched fraction was stained with fluorescently conjugated antibodies for FACS or analysis.  For each condition, 500,000 cells were washed three times in wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× EDTA-free protease inhibitor cocktail, Roche), then bound to Concanavalin-A beads (Bangs Laboratories) according to the manufacturer’s instructions. Cells were incubated with 1:100 dilution of anti-BAF155 antibody (G. Crabtree) for 2 h or overnight at 4 °C in permeabilization buffer (1× permeabilization buffer, eBioscience, 0.5 mM spermidine, 1× EDTA-free protease inhibitor cocktail, 2 mM EDTA). The sample was then incubated with 700 ng ml−1 protein A-MNase (S. Henikoff) in permeabilization buffer at 4 °C for 1 h. Digestion was performed in 0.5× permeabilization buffer supplemented with 2 mM CaCl2 at 4 °C for 1 h. The reaction was stopped by adding 2× Stop buffer (final concentration 100 mM NaCl, 10 mM EDTA, 2 mM EGTA, 20 μg ml−1 glycogen, 25 μg ml−1 RNase A, Thermo Fisher Scientific) and the sample was incubated at 37 °C for 20 min. Protein in the sample was then digested in 0.1% SDS and 250 μg ml−1 proteinase K (New England Biolabs) for 2 h at 56 °C, shaking gently. CUT&RUN fragments were purified using phenol chloroform extraction. CUT&RUN libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina coupled with NEBNext Multiplex Oligos for Illumina (New England Biolabs) with modifications optimized for small fragments as detailed in https://doi.org/10.17504/protocols.io.wvgfe3w. Paired-end, dual-index sequencing was performed on the Illumina NextSeq 500 system.

first: Jason

last: Caldwell

first: Caroline

last: Kaiser

first: Joshua

last: McKeever

first: Alexandra

last: Bradu

first: Sandy

last: Klemm

first: William

last: Greenleaf

first: Narutoshi

last: Hibino

first: Aaron

last: Dinner

first: Andrew

last: Koh


title: Dying occurs as a defined molecular progression in Drosophila rather than as nonspecific physiological collapse

city: Bethesda

first: Kory

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: While we know much about the biology of aging, the biology of dying remains mysterious. Here, we show that old-age death in Drosophila is a discrete and ordered process that follows, but is distinguishable from, aging itself. We apply pseudotime trajectory analysis to transcriptomic data from individual, old flies as they progress toward death. This pseudotime reordering reveals a reproducible molecular organization underlying the process of dying, as demonstrated by systematic changes in the pattern of gene expression as the process advances. Analysis of these transcriptomic changes reveals not only the continuation of some characteristic processes of mid-life aging, but also the activation of a host of novel processes that are not typically associated with aging, and which instead seem to define the progression of an individual towards death. Finally, we reanalyze an existing C. elegans dataset and find that many of the processes we observe changing through the death progression in flies also vary among dying worms, suggesting that features of the death progression have been maintained across a wide span of evolution. These data challenge the idea that dying is simply a nonspecific collapse of physiology that is the inherent conclusion to the dysfunctions of aging.

overall_design: Bulk RNA-Seq profiling of 113 flies representing 73 for natural aging characterization and 40 for supine death phenotype characterization.

middle: W

last: Scott

middle: P

last: Wodrich

first: Hitesh

last: Chaouhan

first: Arvind

last: Shukla

first: Philip

middle: G

last: McQueen

first: Edward

last: Giniger


title: Broccoli consumption alters microbial diversity, host and bacterial gene expression in mice fed a Total Western Diet [RNA-seq]

first: Allen

last: Smith

first: Harry

last: Dawson

first: Elizabeth

last: Pletsch

first: Jack

last: Ragonese

first: Adrienne

last: Narrowe

first: Lumei

last: Cheung

first: Celine

last: Chen

last: Wang


title: Single residues in the histone core domain guide transcription elongation

city: Vienna

first: Zachary

middle: Hugh

last: Harvey

state: Vienna

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

summary: Transcription activity is tightly correlated with a stereotypical suite of chromatin features and modifications, but how/if these are interpreted by transcriptional machinery remains poorly understood. The presence of the histone variants such as H2A.Z is one such feature, known to change the biophysical properties of chromatin. Here we couple phylogenetic analysis to synthetic biology to establish that H2A.Z tunes RNA polymerase II elongation activity through a direct interaction with the transcription machinery. We show that evolution-derived sequence variation in only seven residues located in the short unstructured loop 2 (L2) region of H2A.Z affects RNA polymerase II elongation rates through physical interaction with transcription elongation factor Spt6. Our results establish a direct physical and functional link between transcription and its chromatinized template. Moreover, we proposed that species-specific variations in H2A.Z L2 change the ground state level of transcription and could be exploited for the creation of emergent properties of chromatin.

overall_design: To investigate the effect H2A.Z mutants on transcription more precisely, a series of S. pombe lines wherein the endogenous gene (Pht1) was mutated using standard approaches, and then ChIP-seq was used to profile Pht1.


title: Single residues in the histone core domain guide transcription

summary: The nucleosome is thought to suppress transcription in eukaryotes by acting as a structural barrier. However, once begun, transcription can readily proceed in the presence of nucleosomes, suggesting this model is insufficient. Here, we establish that the ultra-conserved core domain of the ancestral histone H2A.Z informs transcription elongation via direct interaction of its loop 2 region with the transcription elongation factor Spt6. Interrogating H2A.Z sequences representing more than a billion years of eukaryotic evolution in a single synthetic host, we show that Spt6 can distinguish even single-residue substitutions within their loop 2, controlling RNAPII processivity. Our results place the histone core domain at the origin of eukaryotic gene expression, establishing it as a powerful force shaping transcription.

overall_design: To investigate the effect H2A.Z mutants on Spt6 chromatin localization more precisely, a series of S. pombe lines wherein the endogenous gene (Pht1) was mutated using standard approaches, and then ChIP-seq on myc-tagged Spt6 was performed.

first: Jian Yi

last: Kok


title: Thymic epithelia amplify noise in chromatin accessibility via p53 repression to impose immune tolerance

first: Noah

last: Gamble

overall_design: Mouse: Thymic epithelial cells were isolated using a previously published protocol (Kim & Serwold, Methods in Molecular Biology, 2019) with minor modifications. Briefly, thymi from 4-5 week-old mice were harvested and connective tissue was removed. Stromal tissue was perforated using scissors and incubated with rotation in DMEM-F12 (Sigma D6421) at room temperature for for 10min to liberate thymocytes. Remaining stromal tissue was enzymatically digested (0.5mg/mL Collagenase D (Sigma 11088858001), 0.2mg/mL DNaseI (Sigma 10104159001), 0.5mg/mL Papain (Worthington Biochemical LS003126)). Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 and EpCAM+ cells were enriched via positive selection using magnetic anti-Cy7 beads (Miltenyi 130-091-652). Enriched fraction was stained with fluorescently conjugated antibodies for FACS or analysis.  Human: Excised thymic tissue from one patient (3-month-old male) was obtained during the course of corrective cardiac surgery at the Advocate Children’s Hospital, Chicago, IL, USA. Patient was de-identified upon receipt with written informed consent for release of genomic sequence data in accordance with IRB approved protocols by the Advocate Children’s Hospital, University of Chicago, and the National Institute of Health. Connective tissue was removed, and stromal tissue was minced using scissors. Tissue was incubated with rotation in DMEM-F12 (Sigma) at 4C for 20min to liberate thymocytes. Further thymocyte liberation was achieved via enzymatic digestion using 0.5mg/mL Collagenase D (Millipore 11088858001) and 0.2mg/mL DNase I (Sigma 10104159001) at 37C for 20min. Remaining fragments were incubated with rotation in 0.5mg/mL Papain (Worthington), 0.25mg/mL Collagenase D and 0.1mg/mL DNase I at 37C for 20min. Digestion was quenched by addition of FACS buffer. Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 (BioLegend 324245 clone 9C4 1:100) and EpCAM+ cells were enriched via positive selection with magnetic anti-Cy7 beads (Miltenyi). Enriched fraction was stained with DAPI (Invitrogen), CD45 (BioLegend 368508 clone 2D1 1:100), LY51/CD249 (Fisher Scientific BDB564533 clone 2D3/APA 1:100) and HLA-DRA (BioLegend 307622 clone L243 1:100) and sorted on a Symphony S6 (BD Biosciences).  For all multiome experiments, we used the ATAC+GEX single-cell kit and protocol (10X Genomics 1000236 with protocol CG000338 RevE) with minor modifications to sample preparation. Briefly, 40,000 mTECs were FACS-sorted into 1X PBS supplemented with 2% BSA and centrifuged at 300rcf for 5 min. Cells were gently washed in 50uL Lysis Buffer (10mM Tris, 10mM NaCl, 3mM MgCl2 in nuclease-free water) and centrifuged at 300rcf for 5 min. Cells were resuspended in  50uL permeabilization buffer (10mM Tris, 10mM NaCl, 3mM MgCl2, 0.1% Tween20, 0.01% digitonin, and RNase inhibitor (Millipore) in nuclease-free water) and incubated for 5 minutes on ice. Nuclei were gently washed with wash buffer (10mM Tris, 10mM NaCl, 3mM MgCl2, 0.1% Tween20, and RNase inhibitor in nuclease-free water) and centrifuged at 500rcf for 5 min. Finally, nuclei wee resuspended in 5uL chilled diluted nuclei buffer (10X Genomics) and added to transposition mix. Paired-end, dual-index sequencing was performed on the Illumina NextSeq 500 or NovaSeq 6000 platform.

first: Jason

last: Caldwell

first: Caroline

last: Kaiser

first: Joshua

last: McKeever

first: Alexandra

last: Bradu

first: Sandy

last: Klemm

first: William

last: Greenleaf

first: Narutoshi

last: Hibino

last: Dinner

middle: S

last: Koh


title: Cold Plasma Generates a Localized Inflammatory Response and Promotes Muscle Repair

city: Philadelphia

first: Theresa

last: Freeman

state: PA

address: 1015 Walnut Street

department: Orthopedic Surgery Research

institute: Thomas Jefferson University

summary: The FDA-approved Renuvion cold plasma device is currently used for dermal skin tightening procedures and subdermal tightening after liposuction. Anecdotally, patients report improved tissue healing outcomes following treatment. The most likely explanation for this is plasma-generated reactive species which are inflammatory but also activate cellular signaling pathways, stimulate antioxidant responses, and activate immune cells. In this study, we aimed to determine the immediate and long-term molecular effects of a single plasma treatment on surgically injured muscle and the soft tissue envelope. We used RNA sequencing, histology, and immunohistochemistry to determine changes to the tissue following treatment. Neutrophils and mast cells rapidly mobilize 6 h after treatment in conjunction with an upregulated cellular antioxidant response. Additionally, genes identified by RNAseq indicate upregulated pro-regenerative muscle-tissue-protective gene transcripts and downregulated apoptotic pathway transcripts in the muscle tissue 6 h after treatment. The histology and RNAseq results from 4- and 14-days post plasma treatment indicate that these early inflammatory and antioxidant events drive muscle regeneration to skew toward myogenic differentiation over adipogenesis. Thus, we conclude that a single plasma treatment results in an immediate inflammatory and antioxidant response that enhances long-term muscle fiber repair through reduced adipogenesis.

overall_design: Gene expression was compared between control and Renuvion treated surgical incisions in Sprague-Dawley rats at three different time points (6 hours, 4 days, and 14 days). The surgical incision was created on the same day as treatment for the 6 hour cohort. For the day 4 and day 14 groups, an initial surgery was done one week prior to the revision surgery with or without Renuvion treatment. The rats were euthanized at 4 and 14 days after the revision surgery. The biceps femoris was excised on the day of euthansia for each rat and snap frozen. The RNA was extracted from the tissue and sent to Novogene for sequencing.

first: Carly

middle: J

last: Smith

first: Amanda

last: Watkins

first: Abigail

last: Lucas

first: Arianna

last: Moniodes

first: Conn

last: Ritchie

first: Thomas

last: Thompson

last: Schaer

first: Brendan

middle: F

last: Gilmore

first: Noreen

last: Hickok


title: Thymic epithelia amplify noise in chromatin accessibility via p53 repression to impose immune tolerance [RNA-seq]

first: Noah

last: Gamble

overall_design: Thymic epithelial cells were isolated using a previously published protocol (Kim & Serwold, Methods in Molecular Biology, 2019) with minor modifications. Briefly, thymi from 4-5 week-old mice were harvested and connective tissue was removed. Stromal tissue was perforated using scissors and incubated with rotation in DMEM-F12 (Sigma D6421) at room temperature for for 10min to liberate thymocytes. Remaining stromal tissue was enzymatically digested (0.5mg/mL Collagenase D (Sigma 11088858001), 0.2mg/mL DNaseI (Sigma 10104159001), 0.5mg/mL Papain (Worthington Biochemical LS003126)). Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 and EpCAM+ cells were enriched via positive selection using magnetic anti-Cy7 beads (Miltenyi 130-091-652). Enriched fraction was stained with fluorescently conjugated antibodies for FACS or analysis.  75,000 primary mTECs were FACS-sorted directly into RULT lysis buffer (Qiagen RNEasy Kit) and total RNA was extracted using manufacturer’s instructions. mRNA was enriched and RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Kit. Paired-end, dual-index sequencing was performed on the Illumina NovaSeq 6000 platform.

middle: A

last: Caldwell

last: Kaiser

last: McKeever

first: Aaron

first: Andrew


title: The B cell maturation antigen (BCMA) is dispensable for long-lived plasma cell survival

city: Erlangen

first: Hans-Martin

last: Jäck

address: Glückstrasse 6

department: Molecular Immunology

institute: Universitätsklinikum Erlangen

summary: Survival of antibody-secreting plasma cells is a prerequisite to establish long-lasting humoral immune protection. The B cell maturation antigen (BCMA) has been proposed to promote APRIL-mediated survival signals in plasma cells. However, the extensive shedding of murine BCMA from the plasma cell surface raises doubts about its ability to function as a signaling receptor. To unequivocally establish whether BCMA is required for long-lived plasma cell survival, we established two independent BCMA-deficient mouse lines and analyzed the survival of antigen-specific plasma cells after immunization. In contrast to published data, we found comparable numbers of long-lived antigen-specific plasma cells after primary and secondary protein and mRNA immunizations in BCMA-deficient mice. In addition, wildtype and BCMA-deficient plasma cells showed comparable transcriptome profiles with no indication for reduced survival signaling. Interestingly, total plasma cell numbers were increased after boost immunization in bone marrow and mesenteric lymph nodes of BCMA-deficient mice. Therefore, BCMA has no intrinsic role in maintaining long-lived plasma cells. We propose a function of BCMA limited to acting as a soluble decoy receptor for APRIL and fine-tuneing the size of the plasma cell population by limiting the availability of survival factors. This finding removes a piece of the puzzle of the mechanisms that contribute to long-lived plasma cell survival.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for splenic and bone marrow plasma cells from BCMA (Tnfrsf17) WT/KO mice under steady state conditions and after Spikevax (mRNA-1273) immunization

first: Sebastian

last: Schulz

first: Shannon

last: Menzel


title: Simultaneously Targeting Ovarian Cancer and Tumor Microenvironment Using Stem Cell-Engineered Off-The-Shelf CAR-iNKT Cells

city: Los Angeles

first: Yichen

last: Zhu

state: California

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

summary: Adoptive cellular therapy has recently transformed the field of cancer immunotherapy, specifically the treatment of hematological malignancies, through the application of chimeric antigen receptor (CAR) T cells. While a tremendous step forward for cell therapy, current CAR T products face barriers to patient accessibility and clinical benefit. Their autologous nature renders the therapies patient selective and costly, and mechanisms of resistance to CAR T cells, including antigen downregulation/antigen-negative relapse, limit long-term therapeutic efficacy. In this letter, we report novel ex vivo HSC-derived mesothelin- CAR engineered NKT (AlloMCAR-iNKT) cell products that are pure, potent, and safe allogeneic cell therapies. AlloMCAR-iNKT cells execute ovarian cancer killing through a CAR-TCR-NK triple-mechanism, do not cause GvHD, and are resistant to allorejection. Our feeder- free, serum-free culture method promotes the speedy clinical translation of HSC engineered cells, and here we validate our system as a versatility platform for the development of designer “off-the-shelf” cellular products with high therapeutic potential to ovarian cancer patients.

overall_design: Gene expression profiling of primary ovarian cancer (OC) patient samples

first: Yan-Ruide

last: Li

first: Sanaz

last: Memarzadeh

first: Lili

last: Yang


title: Mitochondrial complex IV remodeling in tumor-associated macrophages amplifies interferon signaling and promotes anti-tumor immunity (RNA-Seq)

first: Megan

middle: Lynn

last: Clark

address: 421 Curie Blvd, Room 320

institute: University of Pennsylvania

summary: Tumor-associated macrophages (TAMs) play a critical role in the clinical outcome of solid tumors and the efficacy of immune checkpoint blockade (ICB) therapies. Interferon (IFN)-TAMs are a potent anti-tumor TAM subset recently identified in several human cancers, with higher frequencies strongly predicting improved overall survival and ICB responses. Yet the molecular mechanisms governing IFN-TAM gene expression programs and population dynamics remain largely unknown. Herein, we uncover a mitochondrial process where NDUFA4, a subunit of Complex IV of the electron transport chain, serves as a switch that controls TAM functions and tumor immunity. We demonstrate that in response to interferons (IFNs) within the tumor microenvironment, NDUFA4 is dramatically downregulated in TAMs by the cooperative activity of the NDUFA4 homolog NDUFA4L3 and the microRNA miR-147, both encoded by a single highly conserved bifunctional transcript. Notably, repression of NDUFA4 is necessary for the expansion of IFN-TAMs and subsequent anti-tumor immunity via NK and CD8+ T cell recruitment, whereas constitutive NDUFA4 expression supports pro-tumoral TAMs. Unexpectedly, we find that NDUFA4 minimally contributes to mitochondrial respiration but instead primarily functions as a gatekeeper of mitochondrial DNA (mtDNA) release into the cytoplasm. Consequently, NDUFA4 repression enhances mtDNA-induced stimulator of interferon genes (STING) activation, thereby amplifying anti-tumor IFN-induced transcriptional programs in TAMs. Finally, leveraging the exceptional specificity of miR-147 for Ndufa4 mRNA, we demonstrate that RNA-based therapeutics targeting this functional switch enhance ICB efficacy and inhibit tumor growth. In summary, we uncover that tumor microenvironmental cues control the abundance of IFN-TAMs and subsequent anti-tumor immunity through the regulation of NDUFA4 and that this novel functional switch can be exploited for cancer immunotherapies.

overall_design: RNAseq of bone marrow-derived macrophages (BMDMs) from wild-type, Ndufa4l3-miR147-deficient, and Ndufa4-deficient mice stimulated with Interferon-gamma (40ng/ml) for 12 hours. Ndufa4l3miR147KO and Nmes1-Ndufa4l3miR147KO in the sample titles both are referring to the Ndufa4l3miR147KO genotype.

middle: L

first: Jorge

last: Henao-Mejia


title: Mitochondrial complex IV remodeling in tumor-associated macrophages amplifies interferon signaling and promotes anti-tumor immunity (scRNA-Seq)

overall_design: scRNA-sequencing of CD45+ tumor-infiltrating immune cells and CD45+CD11b+ splenocytes which were FACS sorted from 8-week-old male wild-type and Ndufa4-deficient mice (C57BL/6 background) on day 18 post subcutaneous B16-F10 melanoma tumor implantation. Equal numbers of cells from each mouse were sorted per organ (n=3 mice per genotype), then pooled into a single sample for each genotype per organ (4 total samples).


title: H2A.Z sets the transcriptional ground state of chromatin via interaction with Spt6 [RNA-Seq]

first: Zachary

last: Harvey

overall_design: To investigate the effect of primary sequence variation on H2A.Z function, a series of S. pombe lines wherein the endogenous gene (Pht1) were replaced by one of 9 representative H2A.Z sequences from diverse species were subject to mRNA-seq. Experiments were performed on three biological replicates (independent colonies).


title: H2A.Z sets the transcriptional ground state of chromatin via interaction with Spt6 [PRO-Seq]

overall_design: To investigate the effect H2A.Z mutants on transcription more precisely, a series of S. pombe lines wherein the endogenous gene (Pht1) was mutated using standard approaches, and then PRO-seq (Judd, et al. 2020) was performed.


title: Multi-omics informed mechanism-based model of meropenem and tobramycin against hypermutable Pseudomonas aeruginosa

city: Parkville

first: Cornelia

last: Landersdorfer

state: Vic

address: 399 Royal Parade

department: Monash Institute of Pharmaceutical Sciences

institute: Monash University

summary: Hypermutable P. aeruginosa isolates are prevalent in cystic fibrosis and associated with acute exacerbations of chronic lung infections leading to early death and increased resistance emergence.  Achievable epithelial lining fluid concentration-time profiles of meropenem and tobramycin in monotherapy and combination regimens were simulated against two clinical hypermutable P. aeruginosa isolates; CW8 (MICmeropenem=8mg/L, MICtobramycin=8mg/L) and CW44 (MICmeropenem=4mg/L, MICtobramycin=2mg/L) in an 8-day hollow fiber infection model (HFIM). Both isolates were previously characterised with genotypes resembling those of carbapenem- and aminoglycoside-resistant strains. Meropenem at 1 or 2g every 8h (3h infusion) and tobramycin at 5 or 10mg/kg body weight every 24h (0.5h infusion) were studied. Total and resistant bacterial counts were determined. Whole genome sequencing was performed on mutants and whole population samples at 191h, and transcriptomics at 1 and 191h. Mechanism-based modelling of total and resistant populations was informed by the multi-omics analysis.  While all regimens against both isolates produced regrowth, the high dose combination synergistically suppressed resistant regrowth against CW8 up to ~96h. The high dose combination provided some killing against CW44, however failed to prevent resistant regrowth. In CW8, mutations emerged during treatment in pmrB, ampR, and multiple efflux pump regulators; in CW44, mutations in pmrB and PBP2 were observed. In CW8, resistance genes mexB and oprM were downregulated by the combination at 1h and coincided with synergistic killing, with differential expression of outer membrane norspermidine and lipopolysaccharide genes at 191h. Mechanism-based modelling incorporating subpopulation and mechanistic synergy successfully characterized the bacterial response of CW8, while mechanistic synergy was not required for CW44.  Incorporating information from the multi-omics analyses was instrumental in building the mechanism-based model to describe the bacterial response of the hypermutable isolates, whereas MICs and traditional PK/PD indices could not predict the outcomes of the HFIM.

overall_design: To investigate synergistic killing and resistance emergence of P. aeruginosa with transcriptomics. Two clinical P. aeruginosa isolates were exposed to meropenem and tobramycin concentration-time profiles, alone and in combination, in the hollow fiber infection model over 191 h. Samples were taken at 1 and 191h post treatment.

first: Jessica

last: R Tait

first: Akosua

last: Agyeman

first: Deanna

last: Deveson Lucas

first: Carla

last: López-Causapé

first: Rajbahan

last: Yadav

first: Vanessa

last: Rees

first: Beom

last: Shin

first: Roger

last: Nation

first: John

middle: D

last: Boyce

first: Antonio

last: Oliver

middle: B


title: Transposable elements function as mechanical sensors [HiCAR]

city: Durham

first: Tongyu

last: Sun

state: NC

address: 307 research drive

institute: Duke university

summary: Transposable elements (TEs), comprising almost half of the genome, are tightly controlled by intrinsic factors. However, how TEs are modulated by extrinsic mechanical forces remains unknown. To address this question, we culture human embryonic stem cells on hydrogels with different rigidity and comprehensively analyze the changes in transcriptome, epigenome and genome architecture of TEs, and find that TEs are able to sense mechanical forces.  Upon sensing changes in substrate rigidity, a majority of TEs exhibit elevated or declined transcription, accompanied by corresponding chromatin state alterations. Moreover, mechanotransducer YAP binds directly to a subset of TEs, especially LTR7/HERV-H, and its loss partly recapitulates effects of soft substrate on TEs. Notably, mechanical forces are required for TEs’ chromatin interaction through YAP and CTCF cooperation. Functionally, mechano-sensing TE-enhancer directs definitive endoderm formation through the regulation of distal target, FAM189A2. Overall, our results demonstrate that TEs are mechanical sensors, and that TE-enhancers dictate cell fate.

overall_design: Cells were cultured on the hydrogels with different rigidity, and were collected for RNA-seq, ChIP-seq and HiCAR.

first: Yarui

last: Diao


title: Ac4C modification of LncRNA SIMALR promotes nasopharyngeal carcinoma progression through binding eEF1A2 to facilitate ITGB4/ITGA6 translation

city: Guangzhou

first: Liu

state: GuangDong

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

summary: The dysregulation of long non-coding RNAs (lncRNAs) are involved in regulating tumor progression in multiple manner. However, little is known about whether lncRNA is involved in the translation regulation of proteins. Here, we identified that the suppressor of inflammatory macrophage apoptosis lncRNA (SIMALR) was highly expressed in nasopharyngeal carcinoma (NPC) tissues by analyzing the lncRNA microarray. Clinically, the high expression of SIMALR served as an independent predictor for inferior prognosis in NPC patients. SIMALR functioned as an oncogenic lncRNA that promoted the proliferation and metastasis of NPC cells in vitro and in vivo. Mechanistically, SIMALR served as a critical accelerator of protein synthesis by binding eEF1A2 (eukaryotic translation elongation factor 1 alpha 2), one of the most crucial regulators in the translation machinery of the eukaryotic cells, and enhancing its endogenous GTPase activity. Furthermore, SIMALR mediated the activation of eEF1A2 phosphorylation to accelerate the translation of ITGB4/ITGA6, ultimately promoting the malignant phenotype of NPC cells. In addition, N-acetyltransferase 10 (NAT10) enhanced the stability of SIMALR and caused its overexpression in NPC through the N4-acetylcytidine (ac4C) modification. In sum, our results illustrate SIMALR functions as an accelerator for protein translation and highlight the oncogenic role of NAT10-SIMALR-eEF1A2-ITGB4/6 axis in NPC.

overall_design: RNA Immunoprecipitation sequencing (RNA-seq) foreEF1A2 in HONE-1 cells

first: Sha

last: Gong

first: Han

last: Qiao

first: Junyun

last: Wang

last: Liu


title: Tissue-Resident CCR2+ Macrophage TREM-1/3 Signaling is Necessary for Leukocyte Recruitment to Injured Hearts

city: Saint Louis

first: Daniel

last: Kreisel

state: MO

address: 425 S Euclid Ave

department: Department of Surgery

summary: The triggering receptor expressed on myeloid cells-1 (TREM-1) has been shown to amplify inflammatory signals, such as Toll-like receptor signaling, after infections and after sterile injury. While previous studies have demonstrated that TREM-1 activation on circulating immune cells promotes injury, the role of TREM-1 signaling in tissue-resident cells in the propagation of sterile inflammation remains poorly understood. Here, we took advantage of a cardiac transplantation model to dissect how TREM-1/3 expression on heart-resident cells regulates sterile inflammation. Using single cell RNA sequencing, intravital microscopy and positron emission tomography (PET)-based imaging we discovered that TREM-1/3 signaling in donor tissue-resident CCR2+ macrophages promotes CCL3 production and is critical for the recruitment of neutrophils and CCR2+ monocytes early after reperfusion. We demonstrate prolonged allograft survival in TREM-1/3-deficient compared with wildtype hearts. Thus, we identify TREM-1/3 signaling in donor grafts as a potential future therapeutic target to diminish inflammation after heart transplantation.

overall_design: Graft tissue was digested, and single-cell suspensions were prepared as previously reported (18). Cells were stained using DAPI (BD Biosciences), CD45.1 (Clone 104; Invitrogen), CD45.2 (Clone A20; Biolegend) and CD11b (Clone M1/70; Biolegend). Flow cytometric analysis and sorting were performed on a BD FACS Melody cell sorter. Flow cytometrically sorted DAPI-CD45.1+CD45.2-CD11b+ and DAPI-CD45.1-CD45.2+CD11b+ cells were encapsulated with barcoded oligo-dT containing gel beads with the 10X Genomics Chromium controller. Library preparation was performed as per manufacturer recommended protocols at the Genome Technology Access Center at Washington University School of Medicine. Samples were processed using the Chromium Single Cell 3′ Library & Gel Bead Kit (10X Genomics, v3). Libraries were sequenced on the NovaSeq S4 (Illumina), with a target of 50,000 reads per cell and 500 million read pairs per library.

first: Yuriko

last: Terada

first: Wenjun

last: Li

first: Amit

last: Bery

first: Junedh

middle: M

last: Amrute

first: Christian

last: Frye

first: Hao

last: Dun

first: Andrew

last: Koenig

first: Hannah

last: Leuhmann

first: Yongjian

first: Marina

last: Cella

first: Ruben

last: Nava

last: Gelman

first: Kory

last: Lavine


title: Members of the MYB68 subclade orchestrate cork differentiation by regulating stem cell proliferation and suberin deposition

city: Freiburg

first: Laura

last: Ragni

address: Schänzlerstr. 1

institute: University of Freiburg

summary: Plants have developed specialized barriers to isolate the inner tissues from the environment. The periderm is a dynamic barrier comprising a stem-cell niche, the cork cambium, which produces the cork. Cork cells have a unique cell wall impregnated with hydrophobic polymers such as suberin and lignin, which are essential for the barrier function. Despite its importance, the cork differentiation network remains largely unknown. Here, we identify MYB68 subclade transcription factors as activators of suberin biosynthesis and polymerization, as well as repressors of cork cambium proliferation. We further show that suberin deposition in the cork is also regulated by MYBs from other subclades. However, only MYB68 subclade members suppress cell proliferation, revealing both shared and distinct roles of MYB transcription factors. These findings have broad applicability, as tissue-specific manipulation of MYB activity has the potential to improve the traits of biotechnological interest, such as thicker periderms and more suberized cork layers.

overall_design: To investigate how MYB68 and MYB86 control suberin deposition, w performed RNA seq with WT and myb68 my84 roots. We collected only the 2 uppermost cm of 18-day-old roots (plants were grown in vitro 1/2 MS in continuous light at 22C). 3 biological replicates. Each biological is from at least 40 plants

first: David

last: Molina


title: Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Tgfb]

city: San Francisco

first: Nathan

last: Ewing-Crystal

state: CA

address: 513 Parnassus Ave, HSW12 Room 1201A

institute: University of California, San Francisco

summary: Fibroblasts and immune cells coordinate tissue regeneration and necessary scarring after injury. In the brain, fibroblasts are border-enriched cells whose dynamic molecular states and immune interactions after injury remain unclear. We used single nuclear RNA sequencing at multiple timepoints after photothrombotic (PT) injury to test the role of TGFb in regulating fibroblast and macrophage responses to brain injury. We find that inhibition of fibroblast TGFb signaling, or of TGFb activation, impairs profibrotic fibroblast (and macrophage) expansion and function.

overall_design: Tissue was collected from wildtype mice, mice with TGFb-blind fibroblasts [Col1a2(creER); Tgfbr2(flox)], or mice treated with ADWA11 (anti-integrin avb8, 0/7dpi). Bulk lesional nuclei (DAPI+) were isolated and sort-purified from mice at 7 or 21 days post injury (dpi) for each condition. 1 male and 1 female mouse were harvested per timepoint/condition and were processed together.

first: Thomas

last: Arnold

first: Ari

last: Molofsky


title: Dynamic fibroblast-immune interactions shape recovery after brain injury [snRNASeq_Timecourse]

summary: Fibroblasts and immune cells coordinate tissue regeneration and necessary scarring after injury. In the brain, fibroblasts are border-enriched cells whose dynamic molecular states and immune interactions after injury remain unclear. We used single nuclear RNA sequencing at multiple timepoints to profile stromal and immune responses to sterile (photothrombotic, PT) injury. We find that early pro-fibrotic myofibroblasts transition into several states, including meningeal and lymphocyte-interactive fibroblasts.

overall_design: Bulk nuclei (DAPI+) were isolated and sort-purified from WT mice at rest (dural meninges and cortex), 2 days post injury (dpi;  PT lesion and perilesional cortex), 7dpi, and 21dpi. 1 male and 1 female mouse were harvested per timepoint and were processed together. Microanatomical regions from each timepoint were processed separately and barcoded using 10X CellPlex barcodes; microanatomical regions from a given timepoint were combined prior to sorting and sequenced together. Resting dural meninges were enriched for fibroblasts using Col1a2(creER); R26(Sun1GFP) nuclear signal. Mice with impaired Tgfb signaling were harvested at 7 and 21dpi but were discarded after initial clustering and not analyzed separately due to low yield.


title: Lysosomes signal through the epigenome to regulate longevity across generations [I]

city: Houston

first: Qinghao

last: Zhang

address: BCM N820, One Baylor Plaza

institute: Baylor College of Medicine

summary: Profiling of H3K79me2/3 occupany between wild-type N2 worms and lipl-4 transgenic (lipl-4 Tg) worms.

overall_design: Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) was performed for histone modifications H3K79me2, H3K79me3, as well as histone H3, in wild-type N2 worms and lipl-4 transgenic (lipl-4 Tg) worms at day 1 of adulthood.

first: Meng

middle: C

last: Wang


title: Dynamic fibroblast-immune interactions shape recovery after brain injury [Visium]

summary: Fibroblasts and immune cells coordinate tissue regeneration and necessary scarring after injury. In the brain, fibroblasts are border-enriched cells whose dynamic molecular states and immune interactions after injury remain unclear. We used spatial transcriptomics (10X Visium) to spatiotemporally profile CNS wound healing responses, including stromal and immune responses, after photothrombotic (PT) injury.

overall_design: 10um cortical tissue slices including PT lesions were analyzed at rest, 2dpi, 7dpi, and 21dpi. 2 tissue slices were mounted per capture area, with 1 mouse (1 slice/mouse) analyzed at rest and 2dpi, and 2 mice (1 slice/mouse) analyzed at 7dpi and 21dpi (2 additional 21dpi mice, Cthrc1(creER); R26(DTA),  discarded after initial clustering due to undetectable deletion).


title: Dynamic fibroblast-immune interactions shape recovery after brain injury

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

overall_design: Refer to individual Series


title: Expression data of multiple myeloma patients at various stages of disease

city: Seattle

first: Carl

last: Murie

state: Washington

institute: Institute of System Biology

summary: Bone marrow plasma cell samples were obtained from 23 multiple myeloma patients at various stages of disease from the Seattle Cancer Care Institute. RNASeq gene expression profiling was applied to CD138+ purified plasma cells. We trained a machine learning algorithm on mmSYGNAL program activity to develop a risk classification scheme  for multiple myeloma and applied it to the 23 patient’s gene expression profiles. Unlike other risk prediction methods we applied mmSYGNAL was able to accurately predict disease progression risk at primary diagnosis, pre- and post-transplant and even after multiple relapses, making it useful for individualized dynamic risk assessment throughout the disease trajectory.

overall_design: Expression profiling by high throughput sequencing on 23 multiple myeloma patients at various stages of disease

first: Nitin

last: Baliga

last: Coffey

first: Pam

last: Becker


title: Differential gene expression profile of germline STK11 deletion in patient derived fibroblasts

first: Tahir

last: Khan

address: 255 E Chicago Street

institute: Lurie Childrens Hospital

summary: Peutz-Jeghers syndrome (PJS) is a rare autosomal dominant disorder hallmarked by mucocutaneous melanocytic macules and gastrointestinal hamartomatous polyposis associated with germline/somatic pathogenic variants in the tumor suppressor STK11. PJS is clinically heterogeneous, however, the relationship between clinical phenotype and genotype remains elusive. Here, we report a family with variable severity PJS who harbor a heterozygous STK11 whole gene deletion combined with heterozygous variants in PMS2 and TP53AIP1 that segregate with disease severity in the family. RNA-seq analysis followed by qRT-PCR confirmed that expression of STK11, TP53, PMS2, and TP53AIP1 and a large fraction of p53 signaling pathway components, are significantly reduced while Wnt signaling pathway effectors are upregulated in cells from an individual with severe disease

overall_design: To investigate the differnetial gene expression profiles in patient dernmal fibroblasts compared to control fibroblasts

first: Erica

middle: E

last: Davis


title: Sexual reproduction is controlled by successive transcriptomic waves in Podospora anserina

city: Rueil Malmaison

first: Frederique

last: Bidard

address: 1-4 avenue de Bois Préau

department: Biotechnology

country: France

institute: IFPEN

summary: A whole genome microarray approach has been engaged in the heterothallic euascomycete Podospora anserina to identify genes that regulate the key steps of its sexual development. A time-course transcriptional study of 10 developmental stages from fertilization to ascospore maturation has been performed. More than half of the genome (58% of the 10540 CDS) displayed a significant change of transcript levels between at least two developmental stages of the kinetic (i.e. on all comparisons between the 10 developmental stages).

overall_design: With GPL10116 : reference design with a WT strain. Three independant  biological replicates, the common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5,

first: Véronique

last: Berteaux-Lecellier

first: Fabienne

last: Malagnac

first: Grognet

last: Pierre

first: Debuchy

last: Robert

first: Lelandais

last: Gaelle

first: Arnaise

last: Sylvie

first: Muchielli

last: Marie-Hélène

first: Imbeaud

last: Sandrine


title: IL-13 decreases suceptibility to airway epithelial SARS-CoV-2 infection but increases disease severity in vivo [scRNA-seq]

city: Iowa city

first: Alejandro

middle: Pezzulo

last: Colmenares

state: Iowa

address: 169 Newton Road

department: Internal medicine

institute: University of Iowa

summary: Human airway epithelia (HAE) undergo inflammation-induced remodeling in chronic lung diseases such as asthma and chronic bronchitis. The role of type 2 inflammation-induced epithelial remodeling in SARS-CoV-2 infection and the course of COVID-19 is unclear, moreover, there is discrepancy in the literature regarding the potential benefit of treatments that modulate type 2 inflammation. We investigated the role of IL-13-induced inflammation on SARS-CoV-2 binding/entry, replication, and host response in primary HAE cells in vitro and in a model of mouse-adapted SARS-CoV-2 in vivo. IL-13 protected airway epithelial cells from SARS-CoV-2 infection in vitro by decreasing the abundance of ACE2- expressing ciliated cells rather than by neutralization in the airway surface liquid or by interferon-mediated antiviral effects. In contrast, IL-13 worsened the severity of disease in mice in vivo; the effects were mediated by eicosanoid signaling and were abolished in mice deficient in the phospholipase A2 enzyme PLA2G2D. We conclude that IL-13-induced inflammation affects multiple steps of SARS-CoV-2-induced disease pathogenesis. Whereas IL-13-induced inflammation may be protective against initial infection at the airway epithelium, it enhances disease severity once infection progresses in vivo; blockade of IL-13 and/or eicosanoid signaling may be protective against progression to severe lung disease.

overall_design: To investigate the role of IL-13 induced inflammation on SARS-CoV-2 in vitro, we treated HAE from 2 donors with 20 ng/mL recombinant IL-13 or 20 ng/mL recombinant IL-17 combined with 10 ng/mL tumor necrosis factor alpha (TNFα) for 4 or 55 days. The cytokines were applied to both apical and basolateral side of HAE. The cells were then infected with SARS-CoV-2 (MOI 0.1), the strain isolated from the first US patient (2019-nCoV/USA-WA1/2020, GenBank:MN985325.1) for 6 or 72 hours.

first: Shreya

last: Ghimire

first: Biyun

last: Xue

first: Kun

last: Li

first: Ryan

last: Gannon

first: Christine

last: Wolford-Lenane

first: Andrew

last: Thurman

first: Huiyu

last: Gong

first: Grace

last: Necker

first: Jian

last: Zheng

first: David

middle: K

last: Meyerholz

first: Stanley

last: Perlman

first: Paul

last: McCray

last: Pezzulo


title: Cald1 regulates osteogenic differentiation of PDLSCs.

city: Chongqing

first: Jie

state: Chongqing

address: 426# Songshibei Road, Yubei District

department: College of Stomatology

institute: Chongqing Medical University

summary: To explore underlying mechanisim of which Cald1 regulates osteogenic differentiation of PDLSCs, RNA -seq was performed on PDLSCs treated with NC shRNA and Cald1 shRNA respectively.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PDLSCs treated with NC shRNA and Cald1 shRNA respectively.

first: Yuejia


title: Cycloheximide resistant ribosomes reveal adaptive translation dynamics in C. elegans

status: Public on Jun 29 2025

city: Austin

first: Qiuxia

last: Zhao

address: 2415 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Protein translation regulation is critical for cellular responses and development, yet how disruptions during the elongation stage shape these processes remains incompletely understood. Here, we identify and validate a single amino acid substitution (P55Q) in the ribosomal protein RPL-36A of Caenorhabditis elegans that confers complete resistance to high concentrations of the elongation inhibitor cycloheximide (CHX). Heterozygous animals carrying both wild-type RPL-36A and RPL-36A(P55Q) exhibit normal development but intermediate CHX resistance, indicating a partial dominant effect. Leveraging RPL-36A(P55Q) as a single-copy positive selection marker for CRISPR-based genome editing, we introduced targeted modifications into multiple ribosomal protein genes, confirming its broad utility for altering essential loci. In L4-stage heterozygotes, where CHX-sensitive and CHX-resistant ribosomes coexist, ribosome profiling revealed increased start-codon occupancy, suggesting early stalling of CHX sensitive ribosomes. Chronic CHX reduced ribosome collisions, evidenced by fewer disomes and unchanged codon distributions in monosomes. Surprisingly, prolonged elongation inhibition did not activate well characterized stress pathways–including ribosome quality control (RQC), the ribotoxic stress response (RSR), or the integrated stress response (ISR)–as indicated by absence of changes in RPS-10 ubiquitination, eIF2α phosphorylation, PMK-1 phosphorylation, or the transcriptional upregulation of ATF-4 target genes. Instead, RNA-normalized ribosome footprints revealed gene-specific changes in translation efficiency, with nucleolar and P granule components significantly decreased while oocyte development genes were increased. Consistent with these observations, we detected premature oogenesis in L4 animals, suggesting that partial translation elongation inhibition reshapes translation efficiency, to fine-tune developmental timing.

overall_design: Comparative gene expression profiling analysis of Disomeseq data for L4 stage matched  rpl-36A(P55Q)/mIn1 heterozygotes treated with or without CHX

first: Elif Sarinay

last: Cenik


title: Cycloheximide resistant ribosomes reveal adaptive translation dynamics in C. elegans [RNA-Seq]

status: Public on Jun 28 2025

overall_design: Comparative gene expression profiling analysis of RNA-seq data for L4 stage matched  rpl-36A(P55Q)/mIn1 heterozygotes treated with or without CHX


title: Ferulic acid ameliorates TLR4-mediated macrophage activation by irreversibly binding to Peroxiredoxin 1 to inhibit its dimerization and secretion

city: 天津市 / 市辖区 / 津南区

first: jin

last: yan

state: Not US or Canada

address: 天津市海河教育园区同砚路38号南开大学药学院

institute: nankai university

summary: This study was designed to investigate whether Ferulic acid (FA) alleviates LPS-induced inflammation, and to identify associated transcriptional changes and signaling pathways.

overall_design: The RAW264.7 macrophages were divided into three experimental groups: the control group (Con), the model group (Mod), and the FA group. The Mod group was exposed to 1 μg/mL of LPS for 24 h to establish the inflammatory model. The FA group was pretreated with 10 μM of FA for 12 h, followed by LPS treatment for 24 h. After treatment, the cells were washed twice with PBS, lysed with TRIzol Reagent, and transferred to cryovials. The samples were then sent to Heyuan Biotechnology (Shanghai) Co., Ltd. for transcriptome analysis.

last: Gao

first: Jin

last: Yan

first: Xingwang

last: Zu

first: Yanyan

last: Xu

first: Shilong

last: Wang

first: Yue

first: Yuanyuan

last: Hou


title: Cycloheximide resistant ribosomes reveal adaptive translation dynamics in C. elegans [Ribo-Seq]

overall_design: Comparative gene expression profiling analysis of Riboseq data for L4 stage matched  rpl-36A(P55Q)/mIn1 heterozygotes treated with or without CHX


title: Multi-omic characterization of human sural nerves across polyneuropathies [Xenium]

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

institute: University Hospital Muenster

summary: Diseases of peripheral nerves termed polyneuropathies (PNPs) are common, mechanistically heterogeneous, and challenging to diagnose. Here, we integrated single nucleusi transcriptomics of peripheral nerves from 33 human PNP patients and four controls (365,708 nuclei) with subcellular spatial transcriptomics. We identified novel and human-specific nerve cell type markers including unexpectedly heterogeneous perineurial fibroblasts. All PNPs shared a loss of myelinating and an increase in repair Schwann cells and endoneurial lipid-associated macrophages. Transcriptional changes affected multiple cells outside of the endoneurium across PNPs, suggesting PNPs as ‘pan-nerve diseases’. Spatially, PNPs showed a previously unknown perineurial hyperplasia and fibrotic dispersion and this was most pronounced in immune-mediated PNPs. Single cell transcriptomics supported the differential diagnosis of PNPs with potential for future unbiased diagnostic classification.

overall_design: Sural nerves were collected from 33 polyneuropathy patients and four controls. The samples were processed with single nucleus RNA sequencing and spatial transcriptomics (Xenium)

first: Gerd

last: Meyer zu Hörste


title: Deciphering NEUROD1's target genes and miRNAs: an integrative analysis in small cell lung cancer

city: Bunkyo-ku, Hongo

first: Hiroshi

last: Takumida

state: Tokyo

department: Respiratory Medicine

institute: Graduate School of Medicine, The University of Tokyo

type: Non-coding RNA profiling by high throughput sequencing

summary: Small cell lung cancer (SCLC) is a particularly challenging tumor to treat, due to its poor prognosis. ASCL1 and NEUROD1 are master regulators that define the molecular subtypes of SCLC, which are characterized by neuroendocrine features. Immunohistochemical studies have demonstrated that these genes can be co-expressed to varying degrees. While the transcriptional functions of ASCL1 have been well-documented, those of NEUROD1, specifically its target genes and miRNAs, remain less explored. The objective of this study was to identify the targets of this gene.

overall_design:
RNA-seq and miRNA-Seq analyses were conducted on Lu134A following NEUROD1 knockout (KO) to identify gene expression changes relative to untreated (WT) and negative control samples (NC).
Furthermore, RNA-Seq analysis was conducted on Lu134A introduced miRNA mimics (negative control (NC) and 139-5p mimic (139)).

first: Akira

last: Saito

first: Masafumi

last: Horie


title: Binding sites of ASCL1 and NEUROD1 in ASCL1/NEUROD1 double-positive cell lines

summary: Small cell lung cancer (SCLC) is divided into four subtypes based on specific transcription regulators: ASCL1, NEUROD1, POU2F3, and YAP1. Around 80% of SCLC cases show neuroendocrine markers, mainly ASCL1 (called SCLC-A) or NEUROD1 (called SCLC-N). In the past, these four subtypes were thought to be completely separate. However, recent studies have shown that they can change into one another. For example, SCLC-N can develop from SCLC-A. Additionally, ASCL1 and NEUROD1 can sometimes be expressed together, although this combined subtype is not well understood. Our previous research (PMID: 35789143) showed that ASCL1 controls certain microRNAs (miRNAs), which helps keep the subtypes separate. However, the exact way NEUROD1 controls transcription in SCLC, especially when it is co-expressed with ASCL1, is still unknown. To investigate transcriptional regulation, we used Cleavage Under Targets and Tagmentation (CUT&Tag) to confirm the binding sites of ASCL1 and NEUROD1 for double positive cells.

overall_design: CUT&Tag in double positive cells (Lu134A) using ASCL1 and NEUROD1 antibodies

first: Takumida

last: Hiroshi

first: Tanaka

last: Hidenori

first: Suzuki

last: Masami

first: Horie

last: Masafumi


title: Characterization of RPE subpopulation gene expression and cell surface protein composition using single cell sequencing

city: Rensselaer

first: Farhad

last: Farjood

state: NY

address: 1 Discovery Drive

institute: Neural Stem Cell Institute

summary: The retinal pigment epithelium (RPE) has traditionally been considered a homogenous monolayer, however differences in morphology, gene expression and disease susceptibility of RPE cells in different retinal regions has recently been described. To further catalog RPE subpopulation diversity, we have isolated RPE cells from both donated adult human eyes and RPE derived from RPE stem cells (RPESC) to characterize transcriptomic and cell surface differences within the native and clinically relevant cultured RPE subpopulations using CITE-Seq.

overall_design: Using the ICELL8 well-based single cell system, we undertook deep single cell RNA-sequencing (median library size ~130,000 reads) and CITE-Seq with 154 antibodies (median library size ~225,000 reads) to investigate RPE subpopulation identity using ~12,000 cells from six donors. Approximately half of the cells were isolated directly from primary tissue, while the remainder came from RPESC-RPE cultures. scRNA-seq data was analyzed with the Seurat package and the Cite-seq was analyzed by in-house scripts.

first: Sally

last: Temple

first: Jeffrey

last: Stern

first: Nathan

last: Boles


title: Multi-omic characterization of human sural nerves across polyneuropathies [snRNA-seq]


title: Single-cell Sequencing Analysis Identifies Intratumoral Immune Cell Population in Head and Neck Squamous Cell Carcinoma from 4NQO-induced Mice upon JQ1 treatment

first: Cheng

address: 56 Lingyuan Road West

institute: Sun Yat-sen University

summary: In this study, we aimed to identify the landscape alterations of the subpopulations of the tumor-infiltrating immune cells in HNSCC from 4NQO-induced mice upon JQ1 treatment; by using single cell sequencing analysis, we characterized the alterations of intratumoral T cell subpopulations by separating T cells and yielded 9 distinct T cell subpopulations defined by the distribution of classical marker genes, including Tregs, naïve-like cell, γδ T cells 1, IFNG+ HSP+ T cell, CD8+ cytotoxic T cell, CD4+ T effector cell, γδ T cells 2, Xcl1+ T cells and ILC2. In comparison with mice treated with control, JQ1 treatment resulted in an increase of the percentage of CD8+ T cells and Xcl1+ T cells, indicating an activated tumor immune microenvironment in primary HNSCC upon JQ1 treatment.

overall_design: Single-cell transcriptomic analysis of murine HNSCC from 4NQO-induced mice treated with JQ1 and control.

first: Ming

last: Zhang


title: Immunogenicity and protective efficacy of Marburg virus glycoprotein and virus-like particle-forming mRNA-based vaccines.

status: Public on Jun 27 2025

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

summary: Mounting evidence suggests the high immunogenicity of virus-like particle (VLPs) based vaccines. Although VLP vaccines can be effective, they have not been compared to an envelope glycoprotein (GP)-only vaccine for filoviruses. We  conducted a detailed side-by-side comparison of the immunogenicity and protective efficacy of mRNA vaccines encoding for the Marburg virus (MARV) full length GP delivered alone or as a VLP. As expected, co-formulation of the MARV GP and matrix protein VP40 resulted in the formation of VLPs readily detected by electron microscopy after purification from cell supernatants. We vaccinated guinea pigs with a two-component mRNA vaccine  encoding for GP and VP40  (from now on referred as VLP vaccine) or a monovalent mRNA vaccine encoding for GP alone. At high vaccine doses, the VLP group demonstrated reduced humoral response as compared to the GP-only group, but both mRNA vaccines fully protected guinea pigs against lethal MARV infection. However, at low doses, GP-only mRNA conferred a 100% protection, whereas the VLP exhibited only a partial protection. In mice the VLP mRNA vaccine was more efficient at inducing GP-specific CD8+ T cells co-expressing IFN-γ and TNF-α, whereas the GP-only mRNA vaccine better induced CD4+ T cells expressing IFN-γ, IL-2 and TNF-α. In addition, in guinea pigs, the VLP vaccine was associated with down-regulation of  genes associated with various biological and metabolic processes, including the NF-κB signaling pathway, post-transcriptional silencing of small RNAs, and upregulation of genes involved in the mitochondrial respiratory chain complex. In contrast, the GP-only vaccine upregulated genes involved in interferon signaling. Overall, the VLP mRNA vaccine was less immunogenic and protective, whereas the GP-only mRNA vaccine conferred a robust protection by as little as one µg dose in guinea pigs.

overall_design: To understand transcriptional changes in the GP and VLP mRNA vaccinated groups, we performed bulk RNA sequencing (RNA-seq) of guinea pig whole blood for day 54 post-vaccination and day three post-challenge of Marburg virus (day 59 post-vaccination).

first: Chandru

last: Subramani

first: Michelle

middle: N

last: Meyer

first: Matthew

last: Hyde

first: Margaret

last: Comeaux

first: James

last: Crowe

first: Vsevolod

last: Popov

first: Harshwardhan

last: Thaker

first: Sunny

last: Himansu

first: Andrea

last: Carfi

first: Alexander

last: Bukreyev


title: Elovl1 inhibition reduced very long chain fatty acids in a mouse model of adrenoleukodystrophy

city: Cambridge

first: Jeremy

last: Huang

address: 350 Water Street

department: Research

institute: Sanofi

summary: We used single nuclei RNA seq to identify the pathways altered in the ABCD1-/y mouse, a model for Adrenoleukodystrophy (ALD) and corrected with Elovl1 inhibition via CPD37.

overall_design: 6-month old WT, ABCD1 -/y mice were treated with CPD37 formulated to deliver 100mg/kg/day in feed, with accompanying controls. After treatment, the animals were sacrified and tissue from the brain and the spinal cord were isolated for single nuclei RNA-sequencing.

middle: Y

first: Can

last: Kayatekin


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

city: New York

first: Emily

last: Mace

institute: Columbia University Irving Medical Center

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

overall_design: PBMCs were stained with PE-Cy7 CD34 (RRID:AB_2629726, Biolegend, 343616), APC CD14 (RRID:AB_314190, Biolegend, 301808), Pacific Blue CD19 (RRID:AB_2073118, Biolegend, 302232), Alexa488 CD56 (RRID:AB_2564093, Biolegend, 362518), BUV CD3 BD (RRID:AB_2870222, Biosciences, 612940). T cells, NK cells, CD34+ cells and B cells were isolated and directly processed. 2~10 X 104 cells were lysed, and RNA was collected with NucleoSpin RNA XS kit (Takara, 740902) according to the manufacturer’s protocol. RNA quality control was performed using the Agilent 2100 Bioanalyzer System. Libraries were generated with SMARTer stranded RNA-Seq kit (Takara, 634839) and sequenced on NovaSeq 6000 (Illumina).

first: Seungmae

last: Seo

first: Yong-Oon

last: Ahn

first: Sagar

last: Patil

first: Jacqueline

last: Armetta

first: Madrikha

last: Saturne

first: Everardo

last: Hegewisch-Solloa

first: Nicole

last: Guilz

first: Achchhe

last: Patel

first: Barbara

last: Corneo

first: Malgorzata

last: Borowiak


title: IRF4 promotes immune-evasion and shapes the Tumor Microenvironment in Follicular Lymphoma

city: Rochester

first: Emmanuel

last: Contreras Guzman

state: Minnesota

address: 150 3rd St SW

institute: Mayo Clinic

summary: Twenty percent of follicular lymphoma (FL) patients relapse early with poor outcomes; however, the molecular mechanisms underlying this aggressive behavior are unknown. Using a multiomics approach, we show that FL patients with elevated IRF4 expression (IRF4hi) have increased transformation risk, dysregulated immune signaling, and a suppressive tumor microenvironment. Loss- and gain-of-function experiments in IRF4hi lymphoma cells, along with chromatin profiling, demonstrate that IRF4 impairs their interaction with T cells by repressing antigen presentation and co-receptor gene modules, while promoting the expression of cytokines that antagonize TFH and Treg functions. Additionally, IRF4 rewires tumor metabolism which restricts glucose availability to immune cells. Silencing of IRF4 inhibits tumor cell growth and restores immune surveillance mechanisms, thus representing a promising target for therapy. Our data suggest that IRF4hi lymphoma cells co-opt a developmental mechanism used to exit the germinal center response in promoting a more aggressive cancer via engagement of multiple immune-evasive mechanisms.

overall_design:
Fresh-frozen lymph node samples from 21 FL patients (n=10 IRF4hi, n=11 IRF4lo) were used to single cell RNA-seq/scBCR-seq

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Surendra

last: Dasari

first: Kerstin

last: Wenzl

first: Geoffrey

last: Nelson

first: Zhiquan

last: Wang

first: Loic

last: Chartier

first: Zhi-Zhang

last: Yang

first: Jose

last: Villasboas

first: Joshua

last: Olson

first: Prithviraj

last: Mukherjee

first: Vaishali

last: Bhardwaj

first: Xinyi

last: Tang

first: Brianna

last: Negaard

first: Johannes

last: L Zakrzewski

first: Rebecca

last: King

first: Sara

last: Huet

first: Bruno

last: Tesson

first: Matthew

last: Maurer

first: Franck

last: Morschhauser

first: Grzegorz

last: Nowakowski

first: Karen

last: Adelman

first: Harinder

last: Singh

first: Laura

last: Pasqualucci

first: Mark

last: Shlomchik

first: Anne

last: Novak

first: Stephen

last: Ansell

first: Patrizia

last: Mondello