title: Hybrid capture RNA-seq defines temporal gene expression in Rickettsia

city: Cambridge

first: Allison

middle: T

last: Scott

address: 31 Ames St

department: Biology

institute: Massachusetts Institute of Technology

summary: Pathogenic Rickettsia species are obligate intracellular bacteria that must reside in a mammalian host or arthropod vector cell to survive. Although these bacteria transition between different intracellular environments during infection, they encode few putative transcription factors, and their gene regulatory networks are largely unknown. Because of their inextricable relationship with eukaryotic cells, transcriptional profiling of the pathogen is complicated by the abundance of contaminating host RNA, especially in infection conditions or stages where the bacterial burden is inherently low. Here, we employ a hybrid capture technique (PatH-Cap) to improve library preparation by enriching bacterial transcripts while depleting host and rRNA molecules. Using PatH-Cap, we explored transcriptional changes throughout the first 24 hours of infection, including infection initiation – an infection stage which has been difficult to profile with standard library preparation methods. We then clustered genes based on their temporal trends, revealing cohorts of genes whose expression is up- or downregulated at different stages of infection. We also highlighted the diverse temporal expression trends of genes with known roles in growth and pathogenesis, including translation and cell division genes, secreted effectors, and secretion system components. Lastly, we identified 310 antisense RNA molecules, many of which also showed strong temporal trends. This work demonstrates that sensitive transcriptional profiling approaches like PatH-Cap hold great promise for dissecting gene expression networks driving infection in intracellular pathogens that have historically posed significant technical challenges.

overall_design: Hybrid capture (PatH-Cap) proof of concept with the intracellular bacterium, R. parkeri, at 0, 24, and 48 hours post infection (Samples 1-32). Time course PatH-Cap RNA-seq of R. parkeri during the first 24 hours of infection (Samples 33-86)

first: Vincent

last: Butty

first: Stuart

last: Levine

first: Rebecca

last: Lamason


title: SMAD nucleocytoplasmic shuttling relies on nucleoporin RanBP2 and VIM-AS1 long non-coding RNA during TGF-β signaling

status: Public on Dec 22 2025

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

country: Sweden

institute: Uppsala University

type: Expression profiling by high throughput sequencing

summary: Activation of the transforming growth factor β (TGF-β) signaling leads to established hallmarks of cancer such as the epithelial-to-mesenchymal transition (EMT), initiating cancer dissemination and increasing chemoresistance. TGF-β signal by binding to its type I and II receptors, leading to parallel activation of SMAD proteins, ubiquitin ligases and protein kinases. Here, using a panel of tumor cells we show that TGF-β activation induces the expression of the mammalian nuclear long non-coding RNA (lncRNA) VIM-AS1 (Vimentin antisense RNA 1) variant 2 (v.2) via the formation of a complex among the transcriptional factors GATA6-SMAD-SPI1. Furthermore, transcriptomic analysis indicated VIM-AS1 enhancing TGF-β signaling and EMT, as further validated by functional gain or loss assays. Mechanistically, the TGF-β-induced VIM-AS1 v.2 enhanced SMAD nucleocytoplasmic shuttling by interacting with the N-terminus domain of the nucleoporin RanBP2 (Nup358), whereby acting as a scaffold molecule, facilitates the binding of RanBP2 with SMAD2/3 and its further nuclear import. Finally, VIM-AS1 increases invasion and motility of tumor cells and emerges as a promising therapeutic target to sensitize cancer cells to chemotherapeutic drugs. Hence, we delineated a novel signaling mechanism for VIM-AS1 v.2 facilitating TGF-β response in tumor cells via SMAD nucleocytoplasmic shuttling.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A549 lung adenocarcinoma cells trasfected with scrambled siRNA in the presence or absebce of TGFβ stimulation in comparison to cells transfected with siRNAs against the long noncoding RNA VIM-AS1 in the presence or absence of TGFβ stimulation.

first: Dorival

middle: M

last: Rodrigues-Junior

first: Carl-Henrik

last: Heldin

first: Aristidis

last: Moustakas


title: Spatial transcriptomic profiling (Visium) of meningioma

status: Public on Dec 23 2025

city: Heidelberg

first: Tang

last: Yiheng

address: Im Neuenheimer Feld 224

department: Department of Neuropathology

country: Germany

institute: Heidelberg University Hospital

summary: We applied spatial transcriptomic profiling (10x Genomics Visium) to meningioma samples across grades and methylation classes, in order to characterize features of meningioma heterogeneity across subgroups. We identified an overall decrease in myeloid cell proportions from grade 1 to grade 3 meningiomas, as well as a phenotypic shift from microglia-like cells towards a myeloid-derived proliferative macrophage phenotype.

overall_design: Spatial transcriptomic profiling (10x Genomics Visium) was performed on 42 meningioma samples across WHO grades and methylation classes.

first: Sybren

middle: N

last: Maas

first: Yiheng

last: Tang

first: Eric

last: Stutheit-Zhao

first: Ramin

last: Rahmanzade

first: Felix

last: Sahm


title: Impact of maternal compensation on developmental phenotypes in a zebrafish model of severe congenital muscular dystrophy

city: New Brunswick

first: M. Chiara

last: Manzini

state: NJ

address: 89 French Street, Child Health Institute of New Jersey

department: Neuroscience and Cell Biology

country: USA

institute: Rutgers Robert Wood Johnson Me

summary: Genetic compensation is a common phenomenon in zebrafish in response to genetic alterations. Differences between genetic and morpholino-mediated zebrafish models of human diseases have led to significant difficulties in phenotypic interpretation and translatability. One form of compensation is the maternal deposit of mRNAs and proteins to the oocyte that supports developmental processes before zygotic genome activation. In this study, we generated a zebrafish model of severe congenital muscular dystrophy (CMD) by targeting protein O-mannose N-Acetylglucosaminyltransferase 2 (pomgnt2), a maternally provided gene that maintains cell-extracellular matrix interactions through glycosylation and leads to congenital muscular dystrophy when mutated. Zygotic knockouts (ZKOs) retain protein function in the first week post fertilization and survive to adulthood, only developing muscle disease later in life. In contrast, maternal-zygotic KOs (MZKOs) generated from ZKO females develop early-onset muscle disease, reduced motor function, neuronal axon guidance deficits, and retinal synapse disruptions recapitulating features of the human presentation. While assessing transcriptional changes linked to disease progression, the availability of embryos obtained from different breeding strategies also allowed for a direct comparison of ZKOs and MZKOs to define the impact of having a KO mother. We found that offspring from a ZKO mother, independently of genotype, show distinct expression patterns from animals obtained from heterozygous breedings. Some of these changes reflect changes in metabolic function, possibly stemming from maternal metabolic disruption. These findings will not only be applicable for other CMD models targeting maternally provided genes, but also provide new insight into modeling disease using maternal-zygotic mutants.

overall_design: RNA seq profiling of 5 days and 10 days post-fertilization zebrafish larvae with frameshift mutations in pomgnt2 generated from pomgnt2+/- and pomgnt2-/- female breeders

first: Kyle

middle: P

last: Flannery

first: Shorbon

last: Mowla

first: Namarata

last: Battula

first: L. Rose

last: Clark

first: Callista

middle: D

last: Oliveira

first: Lillian

last: Simhon

first: Deze

last: Liu

first: Cynthia

last: Venkatesan

first: Brittany

middle: F

last: Karas

first: Kristin

middle: R

last: Terez

first: Daniel

last: Burbano


title: Transcriptomic changes upon doxorubicin treatment in the brain of ApoE3 and ApoE4 rats

first: Chadni

last: Patel

address: 195 Little Albany Street

institute: Rutgers Cancer Institute

summary: Many pediatric cancer survivors experience chemotherapy-induced cognitive impairment (CICI), which negatively impacts the quality of life and the interpatient variability in susceptibility to CICI is not well understood. Among pediatric cancer survivors, those with the E4 allele of Apolipoprotein E (ApoE) are more likely to exhibit cognitive dysfunction than those with the more prevalent ApoE3 allele, suggesting the ApoE4 allele increases susceptibility to CICI. To mimic a curative pediatric treatment regimen, in our experimental model, five-week-old rats homozygous for either human ApoE3 or ApoE4 allele were treated with doxorubicin (2mg/kg/week for 4 weeks) or PBS (saline). This study aims to investigate transcriptomic changes in different regions of brain to determine the impact of doxorubicin treatment in ApoE3 and ApoE4 rats.

overall_design: RNA-Sequencing was performed to characterize changes in different regions of the brain (cortex and hippocampus) of ApoE3 and ApoE4 rats after doxorubicin treatment. Rats were treated with doxorubicin (2 mg/kg/week for 4 weeks) starting at the age of 5 weeeks. 5-6 weeks after the last doxorubicin treatment, the hippocampus and cortex regions of the brains were collected for RNA-seq.

first: Peter

last: Cole


title: Single-nuclei RNA-seq of meningioma

first: Tang

last: Yiheng

summary: We applied single-nuclei RNA-seq to meningioma samples across grades and methylation classes, in order to characterize features of meningioma heterogeneity across subgroups. We identified an overall decrease in myeloid cell proportions from grade 1 to grade 3 meningiomas, as well as a phenotypic shift from microglia-like cells towards a myeloid-derived proliferative macrophage phenotype.

overall_design: Single-nuclei RNA-seq was performed on 26 meningioma samples across WHO grades and methylation classes.

first: Sybren

last: Maas

first: Yiheng

last: Tang

first: Eric

last: Stutheit-Zhao


title: Human tolerogenic dendritic cell subtypes exert divergent effects on induction of cytotoxic CD4+ T cells

status: Public on Dec 20 2025

city: Newcastle upon Tyne

first: Catharien

middle: MU

last: Hilkens

state: Tyne & Wear

address: Framlington Place

department: Translational and Clinical Research

country: United Kingdom

institute: Newcastle University

summary: Tolerogenic dendritic cells (tolDC) are currently in clinical trials for the treatment of autoimmune diseases such as rheumatoid arthritis and multiple sclerosis. The methods for producing therapeutic tolDC vary widely, with little being known about the commonalities and differences of distinct cell products in terms of their regulatory actions on CD4+ T cells. We compared human monocyte-derived tolDC generated with vitamin D3 alone or in combination with dexamethasone. We found marked differences in the surface expression of HLA-DR and immune regulatory molecules, but also found commonalities, e.g. a strongly reduced capacity to produce interleukin-12 and a concomitant decreased ability to induce interferon- secretion by allogeneic CD4+ T cells. To gain a deeper understanding of how these tolDC types exert their regulatory effects, we co-cultured them with CD4+ T cells from rheumatoid arthritis patients or healthy controls and analysed the gene expression profile and function of the responding T cells. We found that tolDC generated with vitamin D3 alone, but not in combination with dexamethasone, induced potent cytotoxic activity in the responding CD4+ T cells as demonstrated by an enhanced cytotoxic gene signature, increased levels of intracellular granzyme B, and superior cytotoxic activity towards myeloid and B cells. These data identify cytotoxicity as an atypical CD4+ T helper cell effector function induced by some but not all tolDC types, with implications for their individual clinical applications.

overall_design: Periphertal blood mononuclear cells from four RA patients were co-cultured with mature DC or two types of tolerogenic DC (DexVD3DC and VD3DC) for 6 days. Expanded CD4+ T cells were sorted and their gene expression was analysed on the NanoString nCounter® platform using the Immune Exhaustion panel.

first: Gabrielle

last: Barran

first: Najib

last: Naamane

first: Abdul

last: Mannan Baru

first: Amy

middle: E

last: Anderson

first: Jane

last: Falconer


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [FC-18mo]

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating aging effects on the epigenomic features of brain is critical to understand brain functional decline and neurodegeneration. Single nucleus methylation sequencing was applied to brain regions of both male and female mouse at the age of 2, 9 and 18 months. We use these data to identify the epigenomic changes with aging in mouse brains.

overall_design:
Apply snmC-seq3 to mouse brain regions to identify aging effects on epigenomics

Processed data for these samples are available at:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE313770

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Huaming

last: Chen

first: M

last: Behrens


title: The intrinsic impact of mechanical stress on the maintenance of oocyte dormancy

status: Public on Dec 30 2025

city: Suita

first: Katsuhiko

last: Hayashi

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

country: Japan

institute: The University of Osaka

summary: In the mammalian ovary, most oocytes remain dormant, and their dormant status plays a central role in maintaining the reservoir population of the female germ line. The equilibrium between the dormant and active states, the latter of which is responsible for producing mature oocytes, is therefore crucial for ensuring the sustained reproductive capability of females. We have previously reported that mechanical stress in the ovary plays a crucial role in oocyte dormancy. However, the mechanism underlying this relation remains unclear. Here we demonstrated that the mechanical stress is directly transduced into the oocytes, rather than to surrounding granulosa cells. Culture experiments and live-imaging analysis revealed the nuclear localization of FOXO3, a hallmark of oocyte dormancy, within oocytes cultured alone in response to mechanical stress. Interestingly, we discovered that the cytological response to mechanical stress was accompanied by ligand-independent internalization of the c-kit receptor, which dampens intracellular signaling and prevents oocyte activation. These results shed light on the relation between mechanical stress and oocyte dormancy and provide clues toward a greater understanding of female reproductive capability.

overall_design:
After culturing female mouse embryonic ovary under an external pressure (33.3 kPa), Stella-CFP- positive cells were isolated by fluorescence-activated cell sorting (FACS) and analyzed using RNA sequencing (RNA-seq).

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Nagamatsu

last: Go

first: Shirane

last: Kenjiro

first: Hayashi

last: Katsuhiko


title: Chemotherapy triggers immune evasion by fostering LEPR+ Kupffer cell differentiation in liver metastases

status: Public on Dec 25 2025

city: Shanghai

first: Xuege

last: Wang

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

first: Qiang

last: Pan


title: Molecular basis of NFIB-Mediated Regulation of Oncogenic Transcription

city: Taipa

first: He

last: Song

state: Macau

address: Avenida da Universidade Research Building N22

department: Institute of Chinese Medical Sciences

country: Macau

institute: University of Macau

summary: The Nuclear Factor I (NFI) family of transcription factors orchestrates key regulatory programs in development, differentiation, and metabolism, with dysregulation implicated in various pathological conditions, including cancer. Among them, NFIB displays significant context-dependent roles, functioning either as an oncogene or a tumor suppressor depending on cancer type. Despite its emerging clinical relevance, the molecular basis of NFIB-mediated DNA recognition and transcriptional regulation in cancer remains poorly understood. Using HeLa cells as a model, we demonstrate that NFIB promotes oncogenic phenotypes, as CRISPR-Cas9-mediated knockout significantly impairs cell proliferation, migration, and invasion. Transcriptomic analysis reveals that NFIB regulates a cohort of cancer-associated genes, including FGFR3 and PDGFRB. To elucidate the underlying mechanism, we performed biochemical characterization and found that both full-length NFIB and its DNA-binding domain (DBD) exist as monomers in solution and bind DNA with 1:1 stoichiometry, challenging long-standing models proposing DBD-mediated dimerization. High-resolution crystal structures of NFIBDBD bound to ChIP-seq-derived DNA motifs reveal a monomeric binding mode driven by base-specific recognition of the TGGCA sequence. Mutational disruption of key DNA-contacting residues abolishes both DNA binding and transcriptional activation in luciferase reporter assays. Together, these findings define the molecular mechanism underlying NFIB-dependent gene regulation and establish a structural framework for its oncogenic activity, providing insights with potential therapeutic implications for targeting NFIB-driven cancers.

overall_design: RNA-seq profiling of wild-type HeLa cells and NFIB knockout cells, with four biological replicates included for each condition.

first: Ci

last: Zhu

first: Ding

last: Xiao

first: Yueyu


title: Examining the effect of oxLDL on CD4+ T cell H3K27ac epigenetic marks

city: Headington

first: Toby

last: Brown

state: Oxfordshire

address: Nuffield Department of Medicine, Roosevelt Dr

institute: Centre for Human Genetics

summary: Elevated circulating low-density lipoprotein cholesterol (LDL-C) is a key risk factor for coronary artery disease (CAD). The pathogenesis of CAD is multifactorial, driven by heritable and lifestyle-related risk factors. Although CD4+ T cells are one of the main cell types in atherosclerotic lesions, their interaction with atherogenic oxidised LDL (ox-LDL) remains poorly understood. Therefore, we sought to characterise the transcriptomic and epigenomic consequences of ox-LDL on CD4+ T cells. We find that ox-LDL causes a shift towards a pro-inflammatory, cytokine-producing CD4+ T cell transcriptomic state. Concurrently, ox-LDL induces genome-wide changes in chromatin accessibility, notably in promoter regions. Multiomic data integration identifies a likely role for NRF1 and SP1 transcription factors in mediating ox-LDL-induced changes in gene expression. In contrast, the influence of AP-1 related factors over CD4+ T cell gene expression decreases following ox-LDL stimulation. We leveraged our multiomic data to investigate the disease-relevance of ox-LDL exposure, by investigating genomic locations where  CAD-associated single nucleotide polymorphisms were found within dynamic ox-LDL-regulated accessible chromatin regions. Together, we demonstrate a disease-relevant role for ox-LDL in atherogenic conditioning of CD4+ T cells. Understanding such cell-type specific interactions with CAD risk factors may facilitate the development of targeted therapies for CAD.

overall_design: Cells were treated for 48 hours with 50 µg/ml ox-LDL or an equivalent volume of control buffer. For ChIP-sequencing the MAGnify Chromatin Immunoprecipitation System (ThermoFisher, Waltham, Massachusetts, USA) was used in accordance with the manufacturer’s instructions with 2µl of antibody [total rabbit IgG or anti-H3K27ac (Abcam (Cambridge, UK) ab472)]. Sonicated but untreated lysates were used as an input control. DNA was purified with a Qiagen (Venlo, Netherlands) MinElute kit prior to TruSeq adaptor ligation.

first: Anil

last: Chalisey

first: Chris

last: O'Callaghan


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [DHC-18mo-m-002]

first: Joseph

last: Ecker

summary: Illustrating aging effects on the epigenomic features of brain is critical to understand brain functional decline and neurodegeneration. Single nucleus methylation sequencing was applied to brain regions of mouse at the age of 2, 9 and 18 months. We use these data to identify the epigenomic changes with aging in mouse brains.

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Jacinta


title: Influenza hijacks circulating myeloid cells to inflict Type-I Interferon-fueled damage in the heart

city: New York

first: Filip

last: Swirski

state: NY

address: 1470 Madison Avenue, 7th Floor

department: Cardiovascular Research Institute

institute: Icahn School of Medicine at Mount Sinai

summary: Infections by influenza A viruses remain a threat to human health. Although much of the virus’s pathogenesis is confined to the lung, there is evidence that IAV inflames and damages other organs, including the heart. Our understanding of how this occurs, however, is lacking. Here, we identify a hijacked heart-lung axis, whereby influenza infects a relatively minor and ontologically unusual monocyte which preferentially migrates to the heart, differentiates into a cardiac macrophage, and disseminate the virus exclusively to cardiomyocytes, which then support active viral replication. The arrival of influenza in the heart initiates TLR3-dependent IFN-I production by myeloid cells, which signal through the IFN-I receptor (IFNAR1) on cardiomyocytes to cause damage and compromise heart function. Therapeutically dampening IFNAR1 on cardiomyocytes or limiting monocyte accumulation protects the heart while allowing for anti-viral immunity in the lung. Our results uncover an axis for intervention to mitigate cardiovascular risk following influenza infection.

sample_organism: Influenza A virus (A/Puerto Rico/8/34/Mount Sinai(H1N1))

overall_design: All experiments were performed on sex- and age-matched mice between the ages of 5 and 12 weeks. In certain experiments, where indicated, aged mice were used. A group of mice were infected with Influenza A virus. Heart tissues from a group of infected and uninfected mice were extracted and single-nuclear RNA-seq (10X Genomics) was performed.

first: Jeffrey

last: Downey

first: Ana

last: Oliviera-Coelho

first: Mate

middle: G

last: Kiss

first: Emir

last: Radkevich

first: Darwin

last: D'Souza

first: Zhihong

last: Chen

first: Seunghee

last: Kim-Schulze


title: Examining the effect of oxLDL on CD4+ T cell chromatin accessibility

first: Toby

last: Brown

overall_design: Cells were treated for 48 hours with 50 g/ml OxLDL or similar volume of buffer solution. For ATAC-sequencing, samples were repeatedly centrifuged before nuclear pellets were suspended in a transposition reaction mix (25 l 2x TD buffer (from Illumina DNA sample preparation kit), 2.5 l hyperactive Tn5 transposase (from Illumina DNA sample preparation kit), and 22.5 l nuclease-free water) and incubated for 30 minutes at 37C. Transposed DNA was purified with the Qiagen MinElute kit and amplified by PCR.


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [NACB-9mo-m-012]

last: Lucero

first: Julia

last: Osteen

first: Huaming

first: M

last: Behrens


title: Tractable mouse TNBC models capture the heterogeneous tumor immune microenvironment and adaptation to PD-L1 blockade

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: Triple-negative breast cancer (TNBC) patients exhibit variable responses to programmed death (PD)-ligand (L)1 blockade, largely determined by the ‘hot’ versus ‘cold’ state of the tumor immune microenvironment (TIME). We here characterized 9 mouse TNBC models, relying on intraductal mammary gland inoculation of established mouse TNBC cell lines, with a heterogeneous TIME to study anti-PD-L1 resistance mechanisms. Complementary in vitro and in vivo screening classified the 4T1-hot-based model, a highly inflamed control through its immunogenic luciferase tag expression compared to the untagged 4T1-cold-based model, as displaying the ‘hottest’ TIME. However, both 4T1-based counterparts did not respond to anti-PD-L1, which was attributed to their immunosuppressive myeloid cell content as well as upregulation of cancer-associated fibroblasts in the 4T1-hot and high PD-L1-expressing CXCL10+ tumor-associated macrophages in 4T1-cold primary tumors. These anti-PD-L1 adaptation mechanisms across TIME states as captured by mouse TNBC models highlight specific cellular targets for future studies.

overall_design: 9 Different TNBC models were characterized on different levels, with as a first step genomic characterization of the 9 selected TNBC celllines (4T1-hot, 4T1-cold, EMT6, D2A1, 66CL4, PY230, AT3, MVT1 and MET1) in vitro using single-cell RNA-sequencing. Creating a single-cell ATLAS of these 9 cell lines, analyzing transcriptomic differences between these cell lines identifying their heterogeneity based on their transcriptome on the in vitro level. The scRNAseq was performed in collaboration with the VIB Single-cell core.

first: Robbe

last: Salembier

first: Caro

last: De Haes

first: Kristel

last: Demeyere

first: Steven

last: Van Laere

first: Lucie

last: Cervenkova

first: Nicolaas

last: Van Renne

first: Christos

last: Sotiriou

first: Evelyne

last: Meyer

first: Jonas

last: Steenbrugge


title: Examining the effect of oxLDL on CD4+ T cell gene expression

overall_design: Cells were treated for 48 hours with 50 µg/ml ox-LDL or an equivalent volume of control buffer. For RNA-sequencing, RNA was extracted with TRIzol and the PureLink RNA mini kit (Invitrogen, Waltham, Massachusetts, USA) following the manufacturers’ instructions. Illumina (San Diego, CA, USA) reverse-stranded TruSeq library preparation with polyA selection was performed prior to sequencing.

first: Anil

last: Chalisey

first: Chris

last: O'Callaghan


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [FC-8wk-m-018]

first: Joseph

last: Ecker

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Jacinta

last: Chen


title: Oxidised LDL induces pro-inflammatory transcriptomic and epigenomic responses in human CD4+ T cells

first: Toby

last: Brown

summary: Comprehensive multiomic profiling of the CD4+ T cell response to ox-LDL. Individual experimental design is described in more detail in the subseries.

overall_design: 50ml of peripheral blood was obtained from healthy volunteers by venesection and density centrifugation was used to isolate peripheral blood mononuclear cells (PBMCs). PBMCs were then incubated with CD14 microbeads to isolate and remove the blood monocyte population. Unbound cells were incubated with CD4 microbeads prior to activation with bead-bound anti-CD3 and anti-CD28 at 37⁰C. Ox-LDL was prepared as described previously from fresh human blood. Following activation, cells were treated for 48 hours with 50 µg/ml ox-LDL or an equivalent volume of control buffer. Library preparation was performed as described within the subseries.


title: Systemically inducing trained immunity overcomes solid tumors’ immunosuppressive microenvironment. [scRNA-Seq]

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

summary: scRNAseq on B16F10 tumors of mice.

overall_design: Viable CD45+ cells were isolated from B16F10 tumors of mice by flow cytometry. 10X scRNAseq was performed subsequently.

first: Bram

last: Priem

first: Menno

last: de Winther

first: Willem

last: Mulder


title: Systemically inducing trained immunity overcomes solid tumors’ immunosuppressive microenvironment


title: Systemically inducing trained immunity overcomes solid tumors’ immunosuppressive microenvironment. [scMULTIome]

summary: scATACseq on the bone marrow of mice with and without a B16F10 tumor.

overall_design: Bone marrow was isolated from femurs. scATACseq was performed using 10x Genomics scMULTIome.


title: Interleukin-2 is a potent latency reversal agent in people with treated HIV-1

status: Public on Dec 19 2025

city: Cleveland

first: Konstantin

last: Leskov

state: OHIO

address: 2109 Adelbert Rd, Wood W200

department: Molecular Biology and Microbiology

institute: Case Western Reserve University School of Medicine

summary: Eliciting human immunodeficiency virus type 1 (HIV-1) expression from latently-infected CD4+ T cells allows these rare reservoir cells to become targets of the immune system and may also result in death of reservoir cells via virus-induced cytopathy. We asked whether administration of recombinant interleukin-2 (rIL-2) to people with HIV-1 (PWH) on antiretroviral therapy (ART) would induce HIV-1 replication and activate cellular immunity. Nine men with ART-suppressed HIV-1 completed a single 4-day cycle of rIL-2 administration. Plasma HIV-1 RNA levels rose from <20 copies per milliliter at entry to a mean of 301 copies per milliliter at day 7 (an average increase of 0.82 log10; P=0.008). Additionally, we observed robust natural killer (NK) and T cell activation, with a modest increase in Treg-like cells. Thus, rIL-2 appears to be one of the most potent latency-reversing agents tested in PWH on ART.

overall_design: Single-cell RNAseq results (BD AbSeq) from peripheral blood mononuclear cells (PBMCs) acquired at baseline and day 7 from 4 male participants of a clinical trial of recombinant IL-2 administration (aldesleukin; subcutaneous injections of 5 million international units, twice daily, for four consecutive days) (Clinical Trials[dot]gov #NCT03308786).

first: Michael

middle: L

last: Freeman

first: Brian

last: Clagett

first: Daniela

last: Moisi

first: George

middle: A

last: Yendewa

first: Scott

last: Sieg

first: Gregory

last: Laird

first: Jonathan

last: Karn

first: Jeffrey

last: Jacobson

first: Benigno

last: Rodriguez

last: Lederman


title: Integrin β1 demarks precursors of brain-residing antibody-secreting cells in multiple sclerosis

city: Rotterdam

first: Yifan

last: van Hasselt

state: Zuid holland

address: Dr Molewaterplein 40

department: Immunology

institute: Erasmus MC

summary: Multiple sclerosis (MS) is characterized by B cells that infiltrate the central nervous system (CNS) to mature into antibody-secreting cells (ASCs). To date, it remains to be determined how to benefit from this disease hallmark as a prognostic tool. We aimed to uncover markers that reflect B-cell entry and maturation in the CNS and on that basis explore associations with response to high efficacy therapies in MS. Single-cell RNA sequencing (scRNA-seq) revealed ITGB1 (integrin β1/CD29) as a major discriminator of memory B cells expressing CXCR3, which was validated on protein level by spectral flow cytometry. Functional in vitro assays showed that CD29+CXCR3+ memory B cells preferentially cross a brain microvascular endothelial layer and are more receptive to T-cell help to become ASCs. In MS blood, CD29 and CXCR3 were particularly co-expressed on circulating memory B cells, but not on ASCs. In CNS compartments of MS donors, however, high co-expression of CD29 and CXCR3 was restricted to ex vivo ASCs, which was supported by a stronger upregulation of CD29 on in vitro-differentiated ASCs. In MS, while CD29 was effectively downregulated on CXCR3+ memory B cells that accumulated in the blood of natalizumab-treated patients, CD29 levels were only reduced on CXCR3+ memory B cells that repopulated in cladribine-treated patients without early breakthrough disease activity. Taken together, this study reveals that CD29 defines CXCR3+ B cells with a propensity to infiltrate and develop into ASCs in the CNS, which holds potential to be utilized as a cellular biomarker to predict treatment responses in people with MS.

overall_design: Single-cell RNA-seq profiling of FACS-sorted CD19+ B cells from thawed PBMCs from healthy donors (n=3)

first: Kirsten

last: Kuiper

first: Laurens

last: Bogers

first: Jasper

last: Rip

first: Marie-Jose

last: Melief

first: Annet

last: Wierenga-Wolf

first: Romy

last: Klein-Kranenbarg

first: Eric

last: Bindels

first: Harmen

last: van de Werken

first: Janet

last: de Beukelaar

first: Ide

last: Smets

first: Beatrijs

last: Wokke

first: Joost

last: Smolders

first: Marvin

last: van Luijn


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [DHC-18mo-m-003]

first: Joseph

last: Ecker

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Huaming

last: Chen

first: M

last: Behrens


title: Identification of mRNAs as potential blood based biomarekrs for diagnosis and therapeutic monitoring of active tuberculosis

city: Busan

first: Jungho

last: Kim

address: 57, Oryundae-ro, Geumjeong-gu, Busan, Republic of Korea

department: Department of Clinical Laboratory Science, College of Health Sciences

country: South Korea

institute: Catholic University of Pusan

summary: To identify potential mRNA candidates for biomarkers for using a transcriptome-based approach, we extracted total RNAs from blood samples of study participants, including a complete set from patients with ATB who underwent a six-month treatment course

overall_design: Through mRNA sequencing, we identified potential differentially expressed mRNAs

first: Eunsol

last: Ahn

first: Young Ae

last: Kang

first: Hyejon

last: Lee


title: Identifying membrane-bound transcriptional regulatory proteins from rare but evolutionarily conserved domain combinations

status: Public on Dec 18 2025

city: Austin

first: Muyoung

state: TX

address: 2506 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Transcriptional regulatory proteins, including transcription factors (TFs) and chromatin modifiers, perform their crucial cellular functions inside cell nuclei. However, unlike most TFs, membrane-bound transcription factors (MBTFs) are first anchored in membranes before nuclear translocation. Known MBTFs are vital for processes from myelin expression (MYRF) to cholesterol homeostasis (SREBP), yet their overall diversity remains uncharted. We hypothesized that additional membrane-bound transcriptional regulators (MBTRs) might exist and developed a bioinformatics screen that prioritizes membrane proteins likely to regulate transcription. Our approach leverages domain composition, assuming that surprising domain combinations suggest novel biological functions. We searched for rare but evolutionarily conserved combinations of transmembrane domains paired with domains likely involved in transcriptional regulation. Our method rediscovered known MBTFs and membrane-bound histone kinases, and identified novel MBTR candidates, including histone N-acetyltransferases and the prolactin regulatory element-binding protein PREB. Experimental validation indicates that PREB may undergo cleavage. Without its transmembrane domain, PREB exhibits nuclear localization and chromatin association in mouse embryonic stem cells. Furthermore, we identified a putative class of new MBTFs that share MYRF's DNA-binding domain. These findings underscore the utility of our method and provide a framework for investigating MBTRs that likely facilitate the integration of extracellular signals with transcriptional responses.

overall_design: bioChIP-seq was performed on PREB- and PREBΔTM-expressing ES cells treated with 0.5 µg/mL Dox for 24 hours as previously described (21). Cells were cross-linked with 1% formaldehyde (Fisher Bioreagents, BP531-500) for 7 minutes at room temperature, and the reaction was quenched by adding glycine (Fisher Scientific, BP381-1) to a final concentration of 0.125 M. The chromatin was sheared to an average fragment size of ~200 bp using a Bioruptor sonicator (Diagenode). Cross-linked chromatin was pre-cleared with Protein A agarose beads (Thermofisher, 10008D) and subsequently subjected to immunoprecipitation using Dynabeads MyOne Streptavidin T1 (Invitrogen, 65602). Immunoprecipitated complexes were washed twice with 2% SDS, once with buffer A (0.1% Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 500mM NaCl), once with buffer B (250mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 10mM Tris-Cl pH 8.1), and twice with TE buffer. The crosslinked protein-DNA complexes were reversed with an elution buffer (1% SDS, 10mM EDTA, 50mM Tris-Cl 8) to the washed beads and were incubated at 65°C overnight. RNase A (Thermo Scientific, EN0531) was then treated for 30 minutes, followed by treatment of proteinase K (NEB, P8107S) for 2 hours. DNA was extracted with phenol:chloroform:isoamyl alcohol (Invitrogen, 15593031), then precipitated and re-suspended in the TE buffer. Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit (NEB, 7103L), and sequencing was conducted on an Illumina NovaSeq 6000 platform to generate 50-bp paired-end reads. Comparison of the samples with the BirA-only control allowed identification of target-specific binding sites, and IgG ChIP served as a negative control, providing a background signal.

first: Yeejin

last: Jang

first: Qingqing

last: Guo

first: Jonghwan

first: Edward

last: Marcotte


title: Effect of chronic mechanical compression on immortalized human astrocytes

city: Notre Dame

first: Christopher

last: Patzke

state: IN

address: 109A Galvin Life Sciences Building

department: Department of Biological Sciences

institute: University of Notre Dame

summary: Immortalized human astrocytes were subjected to a controlled in vitro model of chronic mechanical compression to investigate how solid stress—similar to that exerted by growing brain tumors—directly affects astrocyte transcriptional programs. RNA sequencing was performed after 24 hours of compression to measure sustained mechanotransductive responses. Compressed astrocytes showed robust induction of AP-1-associated immediate-early genes and activation of NF-κB–dependent inflammatory pathways. These data define the transcriptional signatures by which human astrocytes detect and respond to mechanical stress, providing a resource for understanding mechanobiology and neuroinflammatory signaling in diseases featuring mass effect, including glioblastoma and traumatic brain injury.

overall_design: RNA-seq profiling of immortalized human astrocytes cultured under control conditions or subjected to 24 hours of chronic mechanical compression equivalent to 0.14 kPa of stress.

first: Maksym

last: Zarodniuk

last: Wenninger

first: Julian

last: Najera

first: Jihaeng

first: Jack

last: Markillie

first: Cameron

last: MacKenzie

first: Jenny

last: Bergqvist-Patzke

first: Bianca

last: Batista

first: Megna

last: Panchbhavi

first: R’nld

last: Rumbach

first: Alice

last: Burchett

first: Charles

last: Sander

first: Meenal

last: Datta


title: Joint single-cell profiling of Cas9 edits and transcriptomes reveals on- and off-target effects on gene expression

first: Graham

last: McVicker

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies


title: Uptake of exogenous phospholipids by Borrelia burgdorferi

city: Boston

first: Peter

last: Gwynne

state: MA

address: 136 Harrison Ave

department: Molecular and Microbiology

institute: Tufts University

summary: The Lyme disease pathogen Borrelia burgdorferi can take up environmental phospholipids for membrane biosynthesis. These phospholipids include those also produced de novo by the bacterium (PC and PG) and some that are mammalian-like. We examined the effect of exogenous phospholipids on gene expression.

overall_design: RNAseq analysis of B. burgdorferi cells grown in standard medium or medium supplemented with extra phospholipids.

first: Jeff

last: Bourgeois

first: Linden

last: Hu


title: Single-cell multi-omic and multi-region atlas of the Aging Male Mouse Brain

first: Joseph

last: Ecker

summary: Aging is the primary risk factor for many neurodegenerative diseases, primarily attributed to progressive changes in cellular epigenomes. Despite this known association, the complexity of the mammalian brain complicates the identification of brain regions and cell types that are most susceptible to aging effects. While alterations in gene expression have been observed in aging neural cells, comprehension of the epigenetic regulatory mechanisms underlying the transcriptomic changes remains largely elusive.  To unveil these complexities in a comprehensive manner, we utilized single-nucleus methylome sequencing (snmC-seq3) and multi-omic sequencing (snm3C-seq) to produce extensive datasets comprising 132,551 methylomes and 72,666 chromatin conformation-methylome joint profiles from eight distinct brain regions of C57BL/6J mice aged 2, 9, and 18 months. These regions include the anterior hippocampus (AHC), posterior hippocampus (PHC), frontal cortex (FC), amygdala (AMY), nucleus accumbens (NACB), PAG/PCG, entorhinal cortex (ENT), and caudate putamen (CP). We utilized this dataset to investigate age-related changes in DNA methylomes and transcription factor motifs potentially affected by methylation alterations. We also examined methylation changes in transposable elements, observing locus-specific retrotransposon activation. At the chromatin conformation level, we analyzed aging-related changes in compartmentalization, topologically associating domains (TADs), and chromatin loops. Furthermore, we explored regional heterogeneity during aging within identical cell types and validated our findings using the MERFISH dataset.

overall_design:
C57BL/6J (males and females) mice of different ages were purchased from Jackson Laboratories and maintained in the Salk animal barrier facility on 12-hour dark-light cycles with food ad-libitum for up to 4 weeks (Housing condition: Temperature: 21-23 °C, relative humidity: 61-63%). Brains were extracted, sliced, and dissected in an ice-cold dissection buffer as previously described (Liu et. al. 2021). Females were synchronized for their estrous cycle by exposing them to male bedding for three days, and collected during diestrus. For snmC-seq3 and snm3C-seq samples, brains were sliced coronally at 600 μm intervals from the frontal pole across the whole brain, yielding 18 slices, and dissected brain regions were obtained according to the Allen Brain Reference Atlas Common Coordinate Framework version 3 (CCFv3) as previously described (Liu et. al. 2023). For nuclei isolation, each region was dissected from 2-7 animals and pooled to make 2-3 biological replicates. No statistical methods were used to predetermine sample size. We empirically determined to use two to three biological experiments for all single-cell epigenomic experiments to achieve minimum reproducibility for this large-scale project. Blinding and randomization is not performed during handling the tissue samples. Additionally, all dissected regions were digitally registered into CCFv3 using ITK-SNAP60 (v4.0.0) at a 25 μm resolution.

Additional raw data for this project are included in the following series:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169182
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169236
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169251
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169273
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169345
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169384
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169467
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE181116
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE181141
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE181359

The file "Additional_GSMs_analyzed.tsv" contains the mapping of the GSM associated with raw data to the GSM in this series that contains the quantified processed data of that raw data.

first: Qiurui

last: Zeng

first: Wei

last: Tian

first: Anna

last: Bartlett

last: Nery

first: Rosa

last: Gomez Castanon

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Nicholas

last: Johnson

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon


title: Effect of chronic mechanical compression on co-cultures of human induced neurons and murine glia

first: Christopher

last: Patzke

summary: Human induced neurons and primary murine glia were subjected to a controlled in vitro model of mechanical compression to determine how solid stress—similar to forces present in glioblastoma—directly alters neuronal and glial transcriptional programs. RNA sequencing was performed after 24 hours of compression, with species-specific alignment enabling independent analysis of neuronal and glial responses. Compressed human neurons showed strong activation of hypoxia-responsive metabolic genes, pro-inflammatory signaling pathways, and intrinsic apoptotic programs. Murine glia exhibited parallel induction of hypoxia and apoptotic pathways, accompanied by robust NF-κB/AP-1-driven inflammatory cytokine expression characteristic of astrocytic and microglial activation. These data define the conserved transcriptional responses by which neurons and glia detect and respond to solid stress, providing a resource for understanding mechanotransduction and neuroinflammatory signaling in diseases characterized by mass effect, including glioblastoma.

overall_design: RNA-seq profiling of human induced neurons and murine glia co-cultures maintained under control conditions or subjected to 24 hours of controlled mechanical compression (0.14 kPa) to model solid stress-induced transcriptional responses in each cell type.

first: Maksym

last: Zarodniuk

last: Wenninger

first: Julian

last: Najera

first: Jihaeng

last: Lee

first: Jack

last: Markillie

first: Cameron

last: MacKenzie

first: Jenny

last: Bergqvist-Patzke

first: Bianca

last: Batista

first: Megna

last: Panchbhavi

first: R’nld

last: Rumbach

first: Alice

last: Burchett

last: Sander


title: Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle

city: Jerusalem

first: Reut

last: Bruner

address: Hadassah Ein Kerem Campus

country: Israel

institute: The Hebrew University of Jerusalem

summary: Bacteriophages (phages) significantly influence bacterial populations in their natural environment. However, one aspect that has not been thoroughly explored in the context of phage-bacteria interactions is the post-transcriptional regulation of gene expression, despite the growing attention it has received for bacterial physiology over the last two decades. Important players in this process are small RNAs (sRNAs) that regulate target mRNAs via base-pairing, typically using RNA chaperones like Hfq to facilitate this regulation. Here, we apply RIL-seq, to map in-vivo the sRNA-RNA network in Escherichia coli upon lambda phage infection. We highlight changes in the bacterial transcriptome and sRNA interactome while uncovering a novel phage-encoded sRNA that regulates key genes in E. coli. We decipher the molecular mechanism of the sRNA-mediated regulation and illustrate how it hijacks the host replication machinery and helps the infection cycle. Overall, we uncover an RNA-level regulatory layer that shapes the E. coli - lambda interactions.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RIL-seq and Total RNA-seq of E. coli MG1655 WT carrying a chromosomal FLAG-tagged Hfq, infected and non-infected with phage lambda, at 30 and 60 minutes after infection. As a control, libraries were similarly generated for WT cells not encoding tagged proteins. Two biological replicates were done for each sample.

first: Aviezer

last: Silverman

first: Raneem

last: Nashef

last: Wasserman

first: Tamar

last: Noy

first: Sahar

last: Melamed


title: Spatially distinct cellular and molecular landscapes define prognosis in triple negative breast cancer

city: Pasadena

first: David

middle: Eugene

last: Frankhouser

address: 1500 E Duarte Rd

department: Population Sciences

institute: City of Hope

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

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: MiR-302 regulates pancreatic progenitor pool and pancreatic size [mRNA-seq]

city: Houston

first: Ziyue

last: Yang

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Disruptions in pancreatic development lead to health issues such as pancreatic agenesis and congenital diabetes mellitus. Understanding pancreatic organogenesis is critical for identifying disease mechanisms and developing regenerative therapies. The pancreas consists of endocrine and exocrine cells, both of which are derived from multipotent progenitor cells (MPCs). MPC proliferation and differentiation are tightly controlled by multiple mechanisms, including post-transcriptional regulation by miRNAs. However, these regulatory factors are not fully understood. Here, we profiled miRNA expression in MPCs and identified that miR-302 was highly enriched during the earliest stages of pancreatic development. Loss of miR-302 resulted in reduced pancreatic size without altering the proportions of endocrine and exocrine cells at E17.5, suggesting that miR-302 regulates MPC number rather than differentiation. Transcriptomic analysis at E10.5 revealed that miR-302 modulates genes involved in the Wnt signaling pathway and cell cycle progression. Notably, miR-302 prolonged S phase in MPCs, leading to slower cell proliferation and a smaller MPC pool at E10.5. These findings provide the first comprehensive miRNA profile during early pancreatic development and establish miR-302 as a critical regulator of MPC number and pancreas size.

overall_design: Pdx1-Cre, miR-302+/- animals were crossed with tdtomato, miR302+/- animals. Embryos were dissected at E10.5 and Pdx1-labelled cells were isolated from trunk region

middle: Z

first: Caroline

last: Snider

first: Ronald

middle: J

last: Parchem


title: Visualize and quantify rDNA instabilities in mammalian cells and mouse models

first: Yu

last: Liang

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

summary: Ribosomal DNA (rDNA) encodes the 18S, 5.8S, and 28S RNA components of ribosomes, accounting for up to 70% of cellular transcription. Despite its central role in cellular function and known association with cancer and aging, quantifying rDNA instability in mammals remains challenging due to its repetitive organization and inherent heterogeneity. In this study, we developed murine rDNA FISH probes and genomic tools tailored for laboratory strains. The results confirmed the locations of rDNA clusters, uncovered marked inter-/intra-strain and inter-cell heterogeneity at rDNA loci in inbred mice and unstressed cells, and identified sources of spontaneous, replication-associated DNA double-strand breaks within rDNA. Focused mini-screens using DNA repair-deficient cells uncovered distinct contributions of homologous recombination, non-homologous end-joining, and the ATM-mediated DNA damage response in safeguarding rDNA stability. Together, these findings and tools provide a robust framework for assessing rDNA instability in mammalian cells and animal models with applications in aging and cancer research.

overall_design: Using RPA ChIP-seq in cytokine-activated B cells to identified recurrent, unidirectional DSBs in rDNA region.

first: Xiaolu

last: Zhu

first: Wenxia

last: Jiang

first: Wei

last: Wu

first: Brian J.

last: Lee

first: Demis

last: Menolfi

first: Anthony

last: Tubbs

first: Olivia

last: Cupo

first: Eli

last: Malkovskiy

first: Mattie

last: Nester

first: Xiaobin S.

last: Wang

first: Peter A.

last: Sims

first: Richard

last: Baer

first: Chyuan-Sheng

last: Lin

first: Lorraine

last: Symington

first: Andre

last: Nussenzweig

first: Brian

last: MsStay

first: Shan

last: Zha


title: Wildtype granuloma cells from M. marinum-infected zebrafish

status: Public on Dec 17 2025

city: Durham

first: David

last: Tobin

state: North Carolina

address: 207 Research Drive

institute: Duke University

summary: We use our previously published single-cell RNA sequencing protocol to interrogate the transcriptional nature of granuloma structures extracted from Mycobacterium marinum-infected zebrafish (Danio rerio).

overall_design: Granulomas were dissected from M. marinum-infected zebrafish adults. Single-cell suspensions were generated by brief digestion with trypsin and sent for 10X Genomics scRNAseq processing.

first: Jacob

last: Lowy

first: Gopinath

last: Viswanathan

first: Erika

last: Hughes

first: Charlie

last: Pyle

first: Simon

last: Gregory


title: Depletion of individual dietary amino acids induces distinct metabolic and chromatin states

city: Madison

first: Cara

last: Green

state: WI

address: 2500 Overlook Terrace

institute: University of Wisconsin-Madison

summary: Reducing dietary levels of protein or specific essential amino acids (EAAs) promotes favorable metabolic reprogramming, including improved glucose tolerance, increased insulin sensitivity and reduced fat mass. However, the extent to which shared or EAA-specific mechanisms facilitate diet-associated phenotypes remains unclear. Here, we compared the physiological and molecular responses to dietary levels of methionine, leucine, and isoleucine by feeding C57BL/6J mice diets in which each of these specific AAs is depleted. Dietary depletion of Met, Leu, or Ile (Met-D, Leu-D, or Ile-D) elicited distinct, AA-specific physiological and hepatic molecular (transcriptome, metabolome, histone proteome) responses that were not phenocopied by mTORC1 inhibition via rapamycin treatment. Ile-D yielded the most distinct and dramatic responses, highlighted by expression of select chromatin modifying and metabolic enzymes that led to a prominent epigenetic state of histone H2A/H4 hypoacetylation and maintained hepatic acetyl-CoA levels despite downregulated β-oxidation. Multi-Omics Factor Analysis of 14,139 data points objectively affirmed Ile-D phenotypes are distinct from Met-D or Leu-D and identified metabolic and chromatin features as primary discriminators. We further demonstrated the metabolic and epigenetic responses to Ile-D can be recapitulated in vitro, suggesting that these responses are cell intrinsic. Together, these results demonstrate that dietary depletion of EAAs induce unique phenotypes and highlight distinct molecular mechanisms by which individual EAAs may control metabolic health.

overall_design: All mice were housed three per cage, maintained at a temperature of approximately 22°C, and health checks were completed on all mice daily. Studies were commenced when the mice were 14 weeks of age. Mice were then randomized to receive the indicated diets from Inotiv either the Control (TD.01084), Met-D (TD.140119), Leu-D (TD.180789) or Ile-D (TD.190879) diets, or the Control diet plus rapamycin (delivered I.P. in 5% Tween 20, 5% PEG40, 0.9% NaCl, 3% ethanol at 4 mg/kg/day). The randomization of mice was performed at the cage level to ensure that all groups had approximately the same initial starting weight and body composition. Mice were housed in a SPF mouse facility in static microisolator cages, except when temporarily housed in a Columbus Instruments Oxymax/CLAMS-HC metabolic chamber system. Mice were housed under a 12:12 h light/dark cycle with free access to food and water. R, L or N indicate mouse ID (within the same cage).

first: Spencer

last: Haws

first: Yang

last: Liu

first: Krittisak

last: Chaiyakul

first: Pragyan

last: Mishra

first: Reji

last: Babygirija

first: Eric

last: Armstrong

first: Anusha

last: Mehendale

first: Irene

last: Ong

first: Dudley

last: Lamming

first: John

last: Denu


title: MiR-302 regulates pancreatic progenitor pool and pancreatic size [miRNA-seq]

first: Ziyue

last: Yang

type: Non-coding RNA profiling by high throughput sequencing

first: Caroline

last: Snider

first: Ronald

last: Parchem


city: Urbana

first: Ido

last: Golding

state: IL

address: 1110 W Green St.

department: Physics

institute: University of Illinois Urbana-Champaign

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Total RNA-seq was performed on E. coli MG1655 wild-type cells infected with phage lambda at high or low multiplicity of infection (MOI), or mock-infected with buffer, at multiple time points post-infection. As controls, libraries were similarly generated from uninfected MG1655 host cells and lambda lysogens. Two biological replicates were done for each condition.

first: Tianyou

last: Yao

first: Yuncong

last: Geng

first: Ehsan

last: Homaee

first: Susan

last: Born


title: MicroRNAs shape mouse age-independent tissue adaptation to spaceflight via ECM and developmental pathways

city: Saarbrücken

first: Friederike

last: Grandke

address: Saarbrücken Campus

institute: Saarland University

summary: As human space exploration accelerates, understanding the organism-wide molecular effects of longer spaceflight in mammals becomes increasingly critical. Non-coding RNAs like miRNAs are key to regulating this landscape. We thus analyzed 686 small RNA samples of mice from 13 solid organs at 3 and 8 months of age, after at least 3 weeks on the ISS and compared them to earth-bound controls. We observed significant spaceflight effects in systemic tissue remodeling pathways along the Fat-Liver-Pancreas axis and in heart, brain, spleen and thymus. The MIR-17/92 and MIR-1/133 families drive distinct molecular changes through specific gene targeting. Age-dependent changes, smaller in magnitude compared to age-independent changes, primarily involved tissue remodeling through MIR-8, MIR-154 and MIR-15 families in MAT, pancreas, and diaphragm. Our findings provide evidence on how spaceflight regulates mammalian gene expression in preparation for interplanetary spaceflight.

overall_design: We sequenced 686 samples across 13 organs of young (3 months) and middle-aged (8 months) mice that were sent to the ISS (Flight). We compared them against mice living in standard conditions (Vivarium Ground Control) and mice living in an environment matched to ISS conditions (Habitat Ground Control). We euthanized mice at two time-points (matching timelines for controls and flight mice), one before returning to earth (TERM) and one after (LAR) in order to distinguish spaceflight-induced effects from the reentry-induced stress

first: Shusruto

last: Rishik

first: Viktoria

last: Wagner

first: Annika

last: Engel

first: Nicole

last: Ludwig

first: Kruti

last: Calcuttawala

first: Fabian

last: Kern

first: Verena

last: Keller

first: Marcin

last: Krawczyk

first: Louis

last: Stodieck

first: Virginia

last: Ferguson

first: Amanda

last: Roberts

first: Eckart

last: Meese

first: Nicholas

last: Schaum

first: Steven

last: Quake

first: Tony

last: Wyss-Coray

first: Andreas


title: Differential nucleosome organization in human interphase and metaphase chromosomes [RNA-Seq]

city: Evanston

first: Xiaozhong

last: Wang

address: 2200 Campus Dr

institute: Northwestern University

summary: Mitosis induces profound changes in chromosome structure, impacting nucleosome organization. Here, we employed chemical mapping to achieve single-base-pair resolution of nucleosome positioning in human interphase and metaphase chromosomes, unveiling distinct organizing principles between the two states. During interphase, we observe greater variability in internucleosome spacing, with a higher abundance of shorter linkers compared to metaphase, reflecting the genome's adaptability in accommodating nucleosome arrays for gene expression. Local analyses further uncover differential nucleosome landscapes at key euchromatin landmarks, including promoters, enhancers, and insulators, in each state. Moreover, we analyzed the relationship between DNA cyclizability and dyad positioning during mitosis. Our results indicate that in metaphase, nucleosomes exhibit significantly higher cyclizability around the dyad, whereas during interphase, nucleosomes more frequently position DNA with higher cyclizability in the nucleosome shoulder near regulatory genomic regions. Together, this study offers novel insights into the intricate interplay between DNA mechanics and nucleosome dynamics during mitosis.

overall_design: Total RNA-seq of 2 clones of Hela S3 cells were performed as a complimentary data for the analysis of nuclesome mapped by chemical mapping

first: Keren

last: Li

first: Irem

last: Unlu

first: Lilien

last: Voong

first: Xiaotian

last: Ma

first: Yiren

last: Tu

first: Ji-ping


title: Differential nucleosome organization in human interphase and metaphase chromosomes [ChemMap]

overall_design: Through PiggyBac transgenic expression of an shRNA directed against a shared DNA sequence present in all human H4 genes and RNAi-resistant H4S47C cDNA, we generated H4S47C-substituted HeLa S3 stable cell lines suitable for efficient chemical cleavage of nucleosomes. Using these cells, we performed chemical nucleosome mapping experiments in both interphase and synchronized mitotic cells, with two replicates for each condition.


title: ALFQ Adjuvanted HIV-1 Envelope Protein Vaccination Elicits Durable Functional Antibody and Cellular Responses in Nonhuman Primates

city: Silver Spring

first: Rasmi

last: Thomas

state: MD

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

summary: Adjuvants play an important role in modulating antigen-specific immune responses. We conducted a comparative adjuvant immunogenicity study in Rhesus macaques using HIV-1 subtype B gp120 envelope protein, B.63521 formulated with aluminum hydroxide gel (AH), or a family of liposomal adjuvants known as Army Liposome Formulation (ALF) to determine their effect on immune responses. ALF comprises saturated phospholipids, cholesterol, and an immunostimulant, monophosphoryl lipid A. Inclusion of a second immunostimulant, a saponin QS-21, or adsorption of the antigen to AH, followed by the addition of ALF generates ALFQ and ALFA, respectively, while the presence of both immunostimulants generates ALFQA. Priming with canarypox vector ALVAC, followed by boosting with ALVAC and gp120 formulated with AH, ALFA, ALFQ or ALFQA resulted in the QS-21-containing liposomal vaccine formulations (ALFQ and ALFQA) outperforming AH-based vaccine formulations (AH, ALFA) by inducing (i) binding antibodies of higher magnitude, durability, and avidity; (ii) higher neutralizing and Fc effector functional antibodies; (iii) higher frequency of durable antigen-specific plasma cells in the bone marrow; (iv) robust Env-specific polyfunctional CD4+ and CD8+ T cell responses and IL-21 producing T follicular helper cells. Transcriptomic analyses revealed that ALFQ and ALFQA vaccine formulations upregulated antiviral and innate immune pathways, including interferon signaling genes. These findings highlight that ALFQ is a highly potent adjuvant that facilitates multifaceted strong durable immune responses in nonhuman primates. Based on these data, an HIV vaccine containing B.63521 and CRF01_AE proteins formulated in ALFQ is currently being evaluated for safety and immunogenicity in a phase 1 clinical trial (NCT05423418).

overall_design: Bulk RNA-seq profiling of peripheral blood cells at week 12 and week 24 from Rhesus macaques given different adjuvants.

first: Daina

last: Eiser

first: Gautam

last: Kundu

first: Jiae

last: Kim

first: Mangala

last: Rao


title: Differential nucleosome organization in human interphase and metaphase chromosomes [Mnase-seq]

overall_design: MNase digestion of nucleosomal DNA in interphase and metaphase HeLa S3 cells was performed as described previously.


title: Differential nucleosome organization in human interphase and metaphase chromosomes [Chemical Mapping]


title: Immune imbalance in the human hippocampus in PTSD revealed by single-nucleus transcriptomics

city: Charleston

first: Liu

last: Liu

state: South Carolina

address: 173 Ashley Ave. CRI 610

institute: Medical University of South Carolina

summary: Post-traumatic stress disorder (PTSD) is increasingly recognized as a neuroimmune disorder in which disrupted neuron–glia interactions contribute to long-term cognitive and emotional dysfunction. However, the cellular and molecular basis of immune imbalance in the human hippocampus remains unclear.We performed single-nucleus RNA sequencing on postmortem hippocampal tissues from donors with PTSD and matched controls, identifying 10 major cell types, with particular emphasis on neurovascular and glial populations. Differential expression, pathway enrichment, pseudotime trajectory, and cell–cell communication analyses were applied to characterize cellular and molecular alterations.PTSD samples showed prominent activation of stress-response and inflammatory signaling across astrocytes, microglia, endothelial cells, and mural cells. Microglia and astrocytes underwent robust transcriptional reprogramming with enrichment of immune-related pathways, while endothelial and mural cells exhibited inflammation and impaired blood–brain barrier homeostasis. Trajectory analyses revealed altered state transitions in astrocytes and microglia, indicating dysregulated responses to stress. Furthermore, cell–cell communication analysis uncovered markedly reduced interactions between astrocytes or microglia with excitatory neurons and oligodendrocyte lineage cells, particularly involving stress- and inflammation-related ligand–receptor pairs.These findings demonstrate that PTSD is characterized by immune imbalance at both cellular and intercellular levels, driven by maladaptive glial activation and disrupted neuron–glia communication. Our study provides a comprehensive single-cell atlas of the hippocampal neuroimmune landscape in PTSD and highlights dysfunctional glial–neuronal interactions as a central mechanism underlying disease pathogenesis.

overall_design: Frozen hippocampal tissue samples from three PTSD patients and three age-matched controls were processed for single-nucleus RNA sequencing. Nuclei were isolated at Novogene (San Jose, CA) by tissue homogenization, debris removal, and centrifugation. Single-nucleus 3′ RNA libraries were prepared using the 10x Genomics Chromium Single Cell 3′ v3.1 platform and sequenced on an Illumina NovaSeq X Plus system at a target depth of ~50,000 read pairs per nucleus. Sequencing reads were aligned to the human reference genome (GRCh38), and gene expression matrices were generated using Cell Ranger (10x Genomics) with default parameters.

first: Pengfei

first: Hongkuan

last: Fan


title: Differential nucleosome organization in human interphase and metaphase chromosomes [MNase-Seq]


title: Dis3l2-Mediated RNA Surveillance and Extracellular Vesicle Packaging Prevent Innate Immune Activation by Aberrant Cellular RNAs [TGIRT-seq]

status: Public on Dec 16 2025

city: Frederick

first: Sandra

last: Wolin

address: FDC 560 BG RM 11-82C / 560 CHANDLER STREET

institute: NCI

summary: Although most efforts to understand the functions of RNAs packaged in extracellular vesicles (EVs) have focused on mRNAs and miRNAs, recent studies using less-biased sequencing techniques have revealed that tRNAs and other noncoding RNAs (ncRNAs) are far more abundant. However, the extent to which EV ncRNAs resemble overall cellular RNAs and the benefits to host cells of packaging them into EVs remain unknown. Here, we purified EVs from the culture media of mouse and human cells and characterized their RNA components using high throughput sequencing and Northern blotting. We report that EVs are enriched for numerous aberrant ncRNAs, many of which contain oligouridine tails, a modification associated with degradation by Dis3l2, a cytosolic exoribonuclease that degrades defective structured ncRNAs. Both the numbers of EVs released and the fractions of tailed RNAs in EVs increase on Dis3l2 depletion, indicating that packaging of aberrant ncRNAs into EVs occurs in competition with Dis3l2 decay. Upregulation of multiple type I interferon stimulated genes (ISGs) occurs on Dis3l2 depletion, and cells treated with a neutral sphingomyelinase inhibitor that reduces exosome biogenesis also show moderate ISG upregulation, an effect that is enhanced in Dis3l2-depleted cells and accompanied by the accumulation of aberrant ncRNAs in cellular RNA. Thus, Dis3l2 degradation and packaging of aberrant RNAs into vesicles may prevent these RNAs from activating innate immune sensors and triggering an interferon response.

overall_design: TGIRT-sequencing profiling of total RNA purified from RAW 264.7 whole cells expressing a non-silencing shRNA (shNS) and Dis3l2 KD cells (shDis3l2), as well as extracellular vesicles derived from these cells and shDis3l2 cells also expressing an shRNA-resistant Dis3l2 transgene (Dis3l2r), catalytically inacitve Dis3l2 transgene (Dis3l2 D389N), and an empty vector (vector).

last: Williams

first: Soyeong

last: Sim

first: Wilfired

last: Guiblet

first: Jubin

last: George

first: Jennifer

middle: C

last: Jones


title: Inhibition of Wnt signaling in primary human hepatocytes promotes Plasmodium falciparum liver stage development

city: Nijmegen

first: Richard

last: Bartfai

state: Gelderland

address: Geert Grooteplein Zuid 28

department: Molecular Biology

institute: Radboud Institute for Molecular Life Sciences

summary: After infection of the human host, the first stage of the Plasmodium falciparum (Pf) lifecycle takes place in the liver. However, understanding of host-parasite interactions in this stage has been limited by the rapid loss of functionality in cultured primary human hepatocytes (PHHs), the natural host source for Pf liver stage parasites. Here, we link loss of hepatic functionality to a drastic loss in Pf permissiveness, which we can effectively prevent by using a novel medium containing serum-replacement and signal transduction inhibitors. Integrating transcriptomic analysis and phenotypic assessment of infection outcome, we identified several host signaling pathways that influence Pf liver stage development via modulating the host cell environment. Inhibition of the Wnt pathway in particular has a major impact on the size and maturity of Pf liver stage schizonts, by retaining the metabolic activity and epithelial nature of PHHs. Understanding how alteration of the host cellular state via signalling pathways determine Pf liver stage permissiveness provides insight into host-parasite interactions and may accelerate development of novel therapeutic strategies via improved in vitro liver stage models.

sample_organism:
Plasmodium falciparum
Homo sapiens

platform_organism:
Plasmodium falciparum
Homo sapiens

overall_design:
In vitro cultured primary human hepatocytes (either uninfected and infected with NF135/NF54 strain of Plasmodium falciparum) were kept under mock/IWP2/5C treatment till harvest at day 5 post-infection cognate timepoints. All samples, including freshly isolated hepatocytes, were preserved in TRIzol reagent for RNA isolation.
Total RNA was isolated using the Zymo Research RNA extraction kit. Stranded mRNA sequencing library was prepared with the Kapa mRNA HyperPrep Kit. 36bp paired-ended sequencing was performed on the Illumina NextSeq 550 platform.
Differential gene expression analysis was performed between freshly isolated and mock vs IWP2 treated hepatocytes.

first: Abhishek

last: Kanyal

first: Geert-Jan

last: van Gemert

first: Haoyu

last: Wu

first: Alex

last: van der Starre

first: Johannes

middle: H

last: de Wilt

first: Teun

last: Bousema

first: Robert

middle: W

last: Sauerwein

first: Annie

middle: S

last: Yang


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [CP-9mo-m-023]

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating aging effects on the epigenomic features of brain is critical to understand brain functional decline and neurodegeneration. Single nucleus methylation sequencing was applied to brain regions of both male and female mouse at the age of 2, 9 and 18 months. We use these data to identify the epigenomic changes with aging in mouse brains.

overall_design:
Apply snmC-seq3 to mouse brain regions to identify aging effects on epigenomics

Processed data for these samples are available at:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE313770

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Huaming

last: Chen

first: M

middle: M

last: Behrens


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [DHC-9mo-m-001]

summary: Illustrating aging effects on the epigenomic features of brain is critical to understand brain functional decline and neurodegeneration. Single nucleus methylation sequencing was applied to brain regions of mouse at the age of 2, 9 and 18 months. We use these data to identify the epigenomic changes with aging in mouse brains.

middle: D


title: Dis3l2-Mediated RNA Surveillance and Extracellular Vesicle Packaging Prevent Innate Immune Activation by Aberrant Cellular RNAs [THP TGIRT-seq]

first: Sandra

last: Wolin

overall_design: TGIRT-sequencing profiling of total RNA purified from THP1 whole cells expressing a non-silencing shRNA (shNS) and Dis3l2 KD cells (shDis3l2), as well as extracellular vesicles derived from these cells and shDis3l2 cells.

last: Williams

first: Soyeong

last: Sim

first: Wilfired

last: Guiblet

first: Jubin

last: George

first: Jennifer

last: Jones


title: Dis3l2-Mediated RNA Surveillance and Extracellular Vesicle Packaging Prevent Innate Immune Activation by Aberrant Cellular RNAs [miRNA-Seq]

overall_design: miRNA profiling of total RNA purified from RAW 264.7 whole cells expressing a non-silencing shRNA (shNS) and Dis3l2 KD cells (shDis3l2)


title: Dis3l2-Mediated RNA Surveillance and Extracellular Vesicle Packaging Prevent Innate Immune Activation by Aberrant Cellular RNAs [RNA-seq]

overall_design: Total RNA-seq profiling of  RNA purified from RAW 264.7 cells expressing a non-silencing shRNA (shNS) and Dis3l2 KD cells (shDis3l2).


title: Differential nucleosome organization in human interphase and metaphase chromosomes [RNA-seq]

first: Xiaozhong

last: Wang

overall_design: Total RNA-seq of Hela S3 cells were performed as a complimentary data for the analysis of nuclesome mapped by chemical mapping

first: Keren

last: Li

first: Irem

last: Unlu

first: Lilien

middle: N

last: Voong

first: Xiaotian

last: Ma

first: Yiren

last: Tu

first: Ji-ping


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [CP-9mo-m-022]

first: Joseph

middle: R

last: Ecker

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery


title: Temporal modulation of gene expression in a controlled Schistosoma mansoni human infection model

city: Lubbock

first: Aravindan

last: Kalyanasundaram

state: Texas

address: 3601 4th Street

department: Immunology and Molecular Microbiology

institute: Texas Tech University Health Sciences Center

summary: Background Schistosomiasis is caused by parasitic blood flukes of the genus Schistosoma. Despite ongoing mass drug administration efforts, the disease remains a major public health burden in endemic regions. A better understanding of early host responses to schistosomiasis is critical for developing effective vaccines and therapeutics. Methods We conducted a longitudinal transcriptomic study of peripheral blood samples from 30 Schistosoma-naïve volunteers participating in two controlled human infection trials with male-or female-only S. mansoni cercariae. Blood was collected at six time points over 20 weeks post-infection. Whole-transcriptome RNA sequencing and integrative analyses, including differential gene expression, gene set enrichment, protein interaction networks, co-expression clustering, and immune module profiling, were employed to characterize temporal modulation of genes related to immune responses. Results Robust and highly time-dependent transcriptional responses were observed, peaking at Week 4 post-infection. Differential gene expression and pathway analyses revealed activation of immune responses, including type I and II interferon signaling, chemokine-mediated pathways, and antigen presentation. Notably, both Th1 and Th2 signatures were evident at Week 4. Key immune hubs included IFNG, TNF, and IL1B, along with transcriptional regulators such as STAT1 and IRF7. Blood transcription module analysis further highlighted transient activation of interferon and plasma cell-related responses. Conclusions This study provides a comprehensive transcriptional map of early host responses to S. mansoni infection in humans. The findings underscore the central role of interferon pathways, early mixed Th1/Th2 polarization, and inflammation-associated gene signatures in shaping host response to S. mansoni infection. These insights may inform the rational design of vaccines and biomarkers for schistosomiasis.

overall_design: The two controlled human Schistosoma infection dose escalation trials was performed at Leiden University Medical Center. Total RNA was extracted and purified from whole blood collected in PAXgene® Blood RNA tubes from 30 participants at six time points, including baseline (prior to exposure, Week 0) and every four weeks thereafter until Week 20 post-exposure (i.e.,Weeks 0, 4, 8, 12, 16, and 20). Paired-end whole-transcriptome sequencing (100 base pairs) was performed on the NovaSeq 6000 platform (Illumina,Inc., San Diego, CA).

first: Dawei

first: Chuan

last: Jiang

first: Wenyu

last: Zhu

first: Emma

last: Houlder

first: Koen

last: Stam

first: Jan Pieter

last: Koopman

first: Marijke

last: Langenberg

first: Ranmali

last: Kavishna

first: Sarah

last: Torkzadeh

first: Björn

last: Andersson

first: Josefine

last: Persson

first: Mumtaz

middle: Y

last: Balkhi

first: Desalegn

last: Kifle

first: Aryandra

last: Arya

first: Hyon

last: Jeon

first: Birkneh

middle: T

last: Tadesse

first: Sean

last: Gray

first: Darrick

last: Carter

first: Alison

last: Elliott

first: Florian

last: Marks

first: Ali

last: Harandi

first: Meta

last: Roestenberg

first: Afzal

last: Siddiqui


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types

city: Iowa City

first: Jon

last: Resch

state: Iowa

address: 51 Newton Rd

institute: University of Iowa

overall_design: Refer to individual Series


title: Mouse digit fibroblast AAV gene delivery platform regulates regenerative outcome

first: Jessica

last: Lehoczky

address: 60 Fenwood Rd.

department: Orthopedic Surgery

institute: Brigham and Women's Hospital

summary: The mouse digit tip robustly regenerates post-amputation, a process facilitated by the formation of a blastema. Fibroblasts constitute most of this structure, with specific subtypes contributing significantly more to the blastema. However, it remains unclear whether these fibroblast subpopulations and their associated genes are unique to regeneration or part of a broader wound-healing response. In this study, we performed single-cell RNA sequencing of non-regenerating digits to computationally identify fibroblast subpopulations and genes associated with regeneration and fibrosis. Furthermore, we developed a robust adeno-associated virus (AAV)-based gene delivery system to functionally assess the impact of newly identified candidate pro-fibrotic and pro-regenerative genes on wound healing outcomes.

overall_design: Cohorts of adult wildtype FVB/NJ mice underwent P2 mid-digital (non-regenerative) digit amputation; 12, 17, and 28 days post-amputation, fibrosing digit tissues were collected and used for single cell RNA sequencing and analysis. An unamputated, homeostatic mid-digital sample was also collected.


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (Smart-Seq2)

summary: The paraventricular hypothalamus (PVH) controls many behavioral and physiologic processes, including appetite, social behavior, autonomic outflow, and pituitary hormone secretion. However, molecular markers for functionally-specific PVH neuron projections remain largely undefined, and a complete census of PVH cell types has not been established. Therefore, we performed extensive single-cell/nucleus RNA sequencing to identify unique neuronal subtypes and multiplexed error-robust fluorescence in situ hybridization (MERFISH) to validate and map them spatially. Our spatial transcriptomic atlas resolved 26 Sim1+ and 29 GABAergic neuron populations from the PVH and surrounding areas, revealing multiple subtypes not described previously and distinct transcriptional programs between neuroendocrine and centrally-projecting neurons. Additionally, projection-based profiling determined neuronal subtypes that project to the parabrachial region (PB) and spinal cord, helping to identify PVH populations that regulate satiety and sympathetic nervous system activity, respectively. Notably, PB-projecting PVH neurons expressing bombesin-like receptor 3 (Brs3) induce satiety, and their silencing causes obesity. Together, this atlas fills a critical gap by contributing high-resolution PVH spatial and circuit-based gene expression profiles, representing a valuable resource for the field of homeostasis.

overall_design: Single cells and single nuclei were isolated from dissections of mouse PVH tissue from 1mm-thick coronal brain slices. The transcriptional profile of individual cells and nuclei were then measured using a combination of Drop-seq, DroNc-seq, and 10X Chromium v3 assays. Data were collected from both male and female mice aged 6-12 weeks across 11 batches (Drop-seq = 7 batches, DroNc-seq = 2 batches, and 10X Chromium-v3 = 2 batches). Additionally, we completed targeted projection-specific sequencing of PVH nuclei fluorescently-labeled with retrograde AAV-cre injections into either the spinal cord or parabrachial region of H2B-TRAP mice. Fluorescently-labeled nuclei were then sequenced with either 10X Chromium v3 or Smart-Seq2 sequencing technologies.

first: Yuxi

last: Li

first: Trevor

last: Butler

first: Stefano

last: Nardone

first: Christopher

last: Jacobs

first: Amelia

last: Douglass

first: Joseph

last: Madara

first: Miriam

last: McDonough

first: Jenkang

last: Tao

first: Elijah

last: Lowenstein

first: Luhong

last: Wang

first: Deepti

last: Pant

first: Samuel

last: Walker

first: Annette

first: Harini

last: Srinivasan

first: Zongfang

last: Yang

first: John

last: Campbell

first: Linus

last: Tsai

first: Bradford

middle: B

last: Lowell


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (10X Chromium v3)

first: Jon

last: Resch

first: Yuxi

last: Li

first: Trevor


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (10X Chromium v3 multiplexed)

last: Butler

first: Stefano

last: Nardone

first: Christopher

first: Amelia


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [snATAC-seq]

city: Yuseong-gu, Daejeon-si

first: Taejun

last: Seol

address: 291, Daehak-ro

institute: Korea Advanced Institute of Science and Technology (KAIST)

summary: The transcriptional coregulators YAP and TAZ control tissue homeostasis as downstream effectors of the Hippo signaling pathway. The molecular mechanisms by which they regulate cell differentiation or dedifferentiation have remained unclear, however. Here we reveal how YAP/TAZ regulates the transcription and genomic activity of the adipocyte lineage-specification factor PPARγ at the chromatin level. TAZ binds to the Pparg2 genomic region and to PPARγ target gene enhancers, thereby inducing chromatin reprogramming and transcriptional repression. Binding to TEAD transcription factors is essential for this repressive action of TAZ, but direct protein interaction with PPARγ via the WW domain of TAZ is not. Single-nucleus genomic analyses of mouse adipose tissue revealed that YAP/TAZ hyperactivation drives extensive epigenetic changes and the dedifferentiation of adipocytes. Collectively, our findings indicate that YAP/TAZ determine adipocyte fate by modulating the expression of a key transcription factor and the enhancer landscape of its target genes.

overall_design: single nucleus ATAC-seq data obtained from ingunal white adipose of Lats1/2-floxed (Control) or Lats1/2-floxed; Adipoq-Cre (LAKO) mice

first: Ju-Gyeong

last: Kang

first: Dae-Sik

last: Lim


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [CUT&Tag]

overall_design: CUT&Tag data obtained from ingunal white adipose of Lats1/2-floxed (Control) or Lats1/2-floxed; Adipoq-Cre (LAKO) mice


title: Chromatin stability safeguards mitochondrial homeostasis and prevents mTORC1 hyperactivation

status: Public on Dec 15 2025

city: Memphis

first: R.

middle: Nicholas

last: Laribee

state: TN

address: 19 South Manassas

department: Pathology

institute: University of Tennessee Health Science Center

summary: Cells dynamically regulate chromatin in response to nutrient flux that promotes the transcriptional changes necessary for adaptation. The mechanistic target of rapamycin complex 1 (mTORC1) kinase integrates nutrient signaling with chromatin regulation, yet whether chromatin stability feeds back to mTORC1 activation and stress adaption remains unknown. We previously identified histone H3 at lysine 37 (H3K37) as essential for the cellular response to mTORC1 stress where mutation of H3K37 to alanine (H3K37A) causes cell death upon mTORC1 inhibition. Herein, we show that H3K37-dependent chromatin stability prevents proteasome-mediated histone degradation, restricts mTORC1 signaling, and safeguards mitochondrial homeostasis during mTORC1 stress. Genetic interaction analyses reveal that H3K37A combined with mutants that destabilize chromatin, including loss of the Set2 H3K36 methyltransferase, Rpd3S histone deacetylase, or multiple histone deposition pathways, causes synthetic lethality when mTORC1 is inhibited. Transcriptome analysis indicates that H3K37A misregulates the mitochondrial transcriptome during mTORC1 stress, which increases mitochondrial reactive oxygen species (ROS) and triggers lethal mitochondrial retrograde signaling. Inactivation of retrograde signaling, or ROS neutralization, rescues viability of H3K37A and chromatin stability mutants during mTORC1 stress. These findings establish chromatin stability as a key safeguard that restrains mTORC1 signaling and prevents toxic mitochondrial stress during metabolic adaptation.

overall_design: RNA seq profiling of H3WT and H3K37A mutant cells treated with mock or 20 nM rapamycin for 1 hour.

first: Vinoth

last: Sigamani

first: Mohd

last: Yousuf

first: Daniel

last: Johnson

first: Brian

last: Strahl

first: Ronald


title: Chronic compression recapitulates transcriptional, metabolic, and functional state changes in macrophages associated with pro-tumor phenotypes

city: Notre Dame

first: Alice

last: Burchett

address: 2030 McCourtney Hall East

institute: University of Notre Dame

summary: Macrophages comprise a significant portion of the glioblastoma tumor microenvironment and are essential in promoting immunosuppression and tumor progression. Solid tumors such as glioblastoma generate solid stress as they expand, creating a compressive microenvironment for mechanosensitive immune cells including macrophages. Macrophages are known to respond to various mechanical stimuli but have not yet been studied in the context of chronic compression observed in growing tumors. Here, we used a custom in vitro compression system to elucidate the effects of compressive solid stress on murine macrophages. We found that macrophages have significant morphological, transcriptional, metabolic, and functional responses to compression. These changes corresponded to both canonical pro- and anti-inflammatory macrophage states. The gene expression signatures of compressed macrophages more closely resembled those of glioma-associated macrophages known to be associated with worse patient outcomes. These results indicate that compression alone, independent from tumor cell-derived biochemical factors, may contribute to the pathological tumor-associated macrophage phenotype. This could represent a vicious cycle of tumor immunomechanics and mechano-immunology. Targeting solid stress in tumors or the response to solid stress by macrophages may interrupt this feedback loop to help normalize the tumor immune microenvironment and improve glioblastoma response to immunotherapy.

overall_design: RNA-seq profiling of RAW264.7 macrophages under 24 hours of statioc compressive solid stress (weighted) compared to uncompressed controls (agarose).

first: Hao

last: Chen

first: Julian

last: Najera

first: Sc ott

last: Howard

first: Meenal

last: Datta


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [ChIP-seq]

overall_design: ChIP-seq data obtained from C3H10T1/2 cell during adipogenic cocktail treatment.


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [RNA-Seq]

overall_design: RNA-seq data obtained from C3H10T1/2 cell during adipogenic cocktail treatment


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (DroNc-Seq)

first: Jon

last: Resch

first: Yuxi

first: Trevor

first: Stefano

last: Jacobs

last: Douglass

first: Joseph

last: Madara

first: Miriam

last: McDonough

first: Jenkang

last: Tao

first: Elijah

last: Lowenstein

first: Luhong

last: Wang

first: Deepti

last: Pant

first: Samuel

last: Walker

first: Annette

first: Harini

last: Srinivasan

first: Zongfang

last: Yang

first: John

last: Campbell

first: Linus

last: Tsai

first: Bradford

last: Lowell


title: A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (Drop-Seq)

first: Jon

last: Li

last: Butler

last: Nardone

first: Christopher

first: Amelia


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [snRNA-seq]

first: Taejun

last: Seol

overall_design: single nucleus RNA-seq data obtained from ingunal white adipose of Lats1/2-floxed (Control) or Lats1/2-floxed; Adipoq-Cre (LAKO) mice

first: Ju-Gyeong

last: Kang

first: Dae-Sik

last: Lim


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation

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


title: Cross-platform comparison of gene expression-based cancer molecular subtyping reveals discrepancies with exome capture methods

city: Chapel Hill

first: Jen Jen

last: Yeh

state: NC

address: 450 West Dr, CB7295

institute: University of North Carolina at Chapel Hill

summary: Gene expression profiling assays in precision oncology is increasing with uncertain validity across platforms. In this study, we examined the application of PurIST, a molecular subtyping algorithm for pancreatic ductal adenocarcinoma (PDAC), across different platforms. We compared PurIST calls between matched samples processed by whole transcriptome and commercial exome capture RNA-seq. In parallel, we compared subtypes between matched samples processed by NanoString and whole transcriptome RNA-seq from the PANCREAS trial (NCT04683315). Between whole transcriptome and exome capture, subtype agreement was 81% with significant increase in basal-like subtype with exome capture. Differences in overall survival in patients with basal-like tumors compared to classical tumors did not reach statistical significance using exome capture (log-rank P = 0.061), whereas with whole transcriptome it was significantly shorter (log-rank P < 0.0001). Subtype agreement between whole transcriptome RNA-seq and NanoString was higher at 95%. PurIST results should be interpreted with caution when using exome capture method.

overall_design:
For patients with pancreatic cancer who had their tumors sequenced with a commercial assay (Tempus xT/xR), matched tumors were also sequenced with whole-transcriptome RNA-seq in parallel.

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

first: Jaewon

last: Lee


title: Decoding the YAP/TAZ–PPARγ Regulatory Axis in Adipocyte Differentiation and Dedifferentiation [ATAC-Seq]

overall_design: ATAC-seq data obtained from C3H10T1/2 cell during adipogenic cocktail treatment


title: Free-floating Long-term Vascularized Mesenchymal Organoids [scRNA-seq]

city: Atlanta

first: Alejandro

last: de Janon

state: GA

address: 225 North Ave NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

summary: The vasculature is essential for tissue function and pathology. Spheroid co-cultures of endothelial and mesenchymal stem/stromal cells (MSCs) form consistent structures, but the vascular components are short-lived. iPSC-derived  vascular organoids can establish complex vasculature but often have cell heterogeneous variable maturation and low reproducibility. We presents consistently-formed, free-floating, long-term Vascularized Mesenchymal Organoids (VMOs), formed by co-culturing human umbilical vein endothelial cells (HUVECs) and MSCs in a pre-gelled minimal Matrigel scaffold.  We studied, MSC heterogeneity, vascular biology and system dynamics.

overall_design: Samples are cells extracted and pooled from digested organoids cultured for 3 days and 14 days respectively

first: Shuichi

last: Takayama


title: Free-floating Long-term Vascularized Mesenchymal Organoids [RNA-seq]

summary: The vasculature is essential for tissue function and pathology. Spheroid co-cultures of endothelial and mesenchymal stem/stromal cells (MSCs) form consistent structures, but the vascular components are short-lived. iPSC-derived  vascular organoids can establish complex vasculature but often have cell heterogeneous variable maturation and low reproducibility. We presents consistently-formed, free-floating, long-term Vascularized Mesenchymal Organoids (VMOs), formed by co-culturing human umbilical vein endothelial cells (HUVECs) and MSCs in a pre-gelled minimal Matrigel scaffold.  We studied organoid dynamics over 60 days culture time and used spheroids cultured for 14 days as control.

overall_design: RNA was extracted from pooled samples (organoids) cultured for 3, 14, 28  and 60 days respectively. RNA was also extracted from day 14 spheroids (HUVEC + MSC no ECM scaffold)


title: A role for the cholinergic neuron circadian clock in RNA metabolism and mediating neurodegeneration [timecourse]

city: Chicago

first: Sharon

last: Tam

address: 303 E Chicago Ave, Rm 13-270

summary: Circadian clocks are encoded by a transcription-translation feedback loop that aligns physiological processes with the solar cycle. Previous work linking the circadian clock to the regulation of RNA-binding proteins (RBPs) provides a foundation for the vital examination of their mechanistic connections in the context of amyotrophic lateral sclerosis (ALS)—a fatal neurodegenerative disease commonly marked by disrupted RBP function. Here, we reveal that the spinal cord cholinergic neuron rhythmic transcriptome is enriched for genes associated with ALS and other neurodegenerative diseases. We show that there is time-of-day-dependent expression of ALS-linked RBP transcripts and rhythmic alternative splicing of genes involved in microtubule cytoskeleton organization, intracellular trafficking, and synaptic function. Through in silico analysis of RNA sequencing data from sporadic ALS patients, we find that gene expression profiles altered in disease correspond with rhythmic gene networks. Finally, we report that clock disruption through cholinergic neuron-specific deletion of clock activator BMAL1 increases neurodegeneration and drives time-of-day-dependent alternative splicing of RNA processing genes. Our results establish a role for the cholinergic neuron circadian clock in RNA metabolism and mediating neurodegeneration.

overall_design: Timecourse RNA-seq profiling of wild-type mouse spinal cord cholinergic neurons collected every 4 hours across the 24-hr day

first: Nathan

last: Waldeck

first: Matthew

last: Wright

first: Erin

last: Baker

first: Evangelos

last: Kiskinis

first: Joseph

last: Bass

first: Robert

middle: G

last: Kalb

first: Jelena

last: Mojsilovic-Petrovic