title: Isoliensinine induces vasorelaxation by regulating Calcium Channel in Hypertension：An in vitro and in vivo approach [vascular tissue]

status: Public on Aug 08 2025

city: Fuzhou

first: Jun

last: Peng

address: 1 Qiuyang Road, Minhou Shangjie

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of this study is to compare the differently expressed genes in abdominal aortaof WKY and SHR with or without isoliensinine treatment. The SHRs (n=10) were randomly divided into 2 groups: SHR, and SHR + isoliensinine (5mg/kg/d) groups (n=5 for each group). WKY rats (n=5) were set as control. Rats in WKY and SHR groups were  intragastrically with double distilled water (dd H2O), while rats in  SHR + isoliensinine (5mg/kg/d) group were intragastrically with 5mg/kg/d of  isoliensinine for 10 weeks.  Then the vascular vessel tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with abdominal aortaof rats in 3 groups: WKY, SHR, SHR + isoliensinine (5mg/kg/d) treated (n=5 for each group) to identify the differently expressed genes and related pathway.

first: Aling

first: Yuting

last: Zhou

first: Dawei

last: Lian

first: Meizhu

last: Wu


title: Single nucleus analysis of post-mortem brain tissues from Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) patients

status: Public on Aug 13 2025

city: Saint Louis

first: Siling

last: Du

address: 4515 Mckinley Ave

country: USA

institute: Washington University in St. Louis

type: Expression profiling by high throughput sequencing

summary: Microglia, the brain's resident macrophages, depend on interleukin 34 (IL-34) and colony-stimulating factor 1 (CSF1) for their development and maintenance, engaging the CSF1 receptor (CSF1R). Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP), a neurodegenerative disorder affecting the brain's white matter, is caused by heterozygous pathogenic mutations in the CSF1R gene. Neuropathological studies of postmortem ALSP brains have shown widespread depletion of microglia, demyelination of cerebral white matter, axonal swellings, and pigmented glial cells. In this study, we investigated how individual brain cell populations respond to microglia depletion and contribute to ALSP progression. To do this, we analyzed post-mortem specimens from patients wirth ALSP using single-nucleus RNA-seq (snRNA-seq).

overall_design: Compare the transcriptomics of occipital cortex of ALSP patients with controls

first: Yingyue

first: Marco

last: Colonna


title: Response of collecting duct cells to hypertonic stress

city: Nashville

first: Juan

middle: Pablo

last: Arroyo

state: TN

address: 1161 21st Ave South MCN C3111

department: Medicine

institute: Vanderbilt University Medical Center

summary: Transcriptional profile of inner medullary collecting duct cells in response to overnight NaCl hypertonic stress

overall_design: To study the transcriptional response of inner medullary collecting duct cells to hypertonic stress, we treated 90% confluent inner medullary collecting duct cells with 100 mmol NaCl for 12 hrs and then extracted RNA for bulq RNA sequencing.

middle: P

first: Joshua

middle: S

last: Carty


title: Xenium Spatial Transcriptomics of Head and Neck Single Cell Carcinoma

status: Public on Aug 06 2025

city: Houston

first: Kelli

last: McCord

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

summary: Recent work has shown that the spatial organization of immune responses is a critical determinant of anti-tumor immunity. Here, we profiled ten head and neck squamous cell carcinoma (HNSCC) patient tumors and one ameloblastoma tumor using Xenium V1 spatial transcriptomics. The 10X genomics human multi-tissue and cancer gene expression panel targeting 377 genes was used in combination with 100 custom Xenium probes targeting patient-specific CDR3 regions of T cell receptors (TCRs) in T cells, additoinal T cell specific genes, HPV oncoprotein genes, and tumor genes of interest. This enabled the detection of 477 transcripts within each tumor sample at a single-cell resolution. For seven of the ten HNSCC samples, different tissue sections run on different days were analyzed as technical replicates. Together, these findings introduce a scalable platform for spatial clonal T cell analysis and provide new insight into the spatial relationship of cells within the HNSCC tumor microenvironment.

overall_design: Ten fresh-frozen HNSCC tumors, five of which were HPV+, were used for analysis. Seven of the ten tumors were run in replicate on different slides on different days for a total of 17 HNSCC tumor sections analyzed via Xenium spatial transcriptomics. One ameloblastoma tumor was also analysised via Xenium spatial transcriptomics.

middle: A

first: William

middle: H

last: Hudson


title: T cell receptor sequencing of HNSCC patient and healthy donor peripheral blood

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

summary: This dataset comprises TCR-seq data from peripheral blood CD4+ and CD8+ T cells of head and neck squamous cell carcinoma (HNSCC) patients and healthy donors. Viable peripheral blood mononuclear cells (PBMCs) were sorted into CD45+CD3+CD4+ (CD4+ T cells) and CD45+CD3+CD8+ (CD8+ T cells) subsets, and RNA was isolated using the Qiagen AllPrep DNA/RNA Micro kit. TCR libraries were prepared with the SMART-Seq Human TCR-seq with UMIs kit (Takara Bio) and sequenced on an Illumina NovaSeq X Plus platform. This dataset includes samples from 27 tumor patients and five healthy donors (HDs).  The study aims to investigate the phenotype, function, and spatial localization of T cells in HNSCC patients. This peripheral blood dataset focuses on characterizing circulating immune determinants of anti-HNSCC immunity and linking circulating T cell clones to those identified in patient-matched tumor scRNA-seq data.

overall_design: CD4+ and CD8+ T cells were sorted from PBMCs of 27 HNSCC patients and 5 healthy donors (HDs). RNA was isolated and TCRs were sequenced using the SMART-Seq Human TCR-seq with UMIs kit from Takara Bio.

first: Sean

last: Hyslop


title: Single-cell RNA-sequencing of HNSCC-infiltrating T cells

summary: This study examines the T cell landscape in head and neck squamous cell carcinoma (HNSCC) using single-cell RNA sequencing combined with T cell receptor and protein profiling. By analyzing tumor-infiltrating T cells from 28 patients, we identified diverse T cell subsets, characterized their transcriptional states, and mapped their clonal dynamics. These findings provide a detailed view of the immune microenvironment in HNSCC and offer insights into T cell-mediated immunity and potential targets for immunotherapy and are patient-matched to PBMC TCR sequencing and Xenium spatial transcriptomics in separate GEO submissions.

overall_design: T cells (CD45+CD3+) were sorted from 28 patients with head and neck and squamous cell carcinoma (HNSCC) using a Cytek Aurora Cell Sorter. Cells originating from each patient were labeled with one Totalseq-C human hashtag antibody (BioLegend). Four patient samples with distinct hashtags were pooled and loaded into one well of a GEM-X microfluidics chip (10x Genomics). 16 GEM-X reactions were performed, run on two independent GEM-X microfluidics chips. Pools 1-7 were replicated on both chips, and two pools (pool 8 and pool 16) were each run on one chip. Hashes used for each patient and the patient composition of each pool are described in the patient_matrix.txt supplementary file. Hashtag sequences are as follows:  Hashing antibody sequences: hashtag 1 - GTCAACTCTTTAGCG; hashtag 2 - TGATGGCCTATTGGG; hashtag 3 - TTCCGCCTCTCTTTG; hashtag 4 - AGTAAGTTCAGCGTA.  Gene expression (GEX), T cell receptor (TCR), and CITE-seq libraries were generated for each pool according to the manufacturer's instructions.  For gene expression libraries, processed files include the aggregated gene expression and CITE-seq matrix from CellRanger. aggregation.csv lists the order of aggregation. A cloupe file of processed gene expression data for use in 10x Genomics' Loupe Browser software is also included. For T cell receptor (TCR) libraries, processed files for each sample are the folder output by cellranger vdj for each sample.  After completion of the study, one patient (patient #10) received a final diagnosis of ameloblastoma.

first: Hudson

last: William

first: McCord

last: Kelli


title: Molecular signatures and lineage diversification of neurogenic and gliogenic radial glia in the gyrencephalic ferret cortex

status: Public on Aug 07 2025

city: Shanghai

first: TongYe

last: Fu

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan University

summary: Human exceptional cognition stems from evolutionarily derived cortical adaptations that drive expansive neurogenesis. Deciphering these mechanisms is crucial for understanding mammalian cortical evolution. In this study, we employ the ferret model to comprehensively map molecular profiles and lineage dynamics of cortical radial glia (RGs). By applying scRNA-Seq to ferret and human cortices, we identify conserved regulatory programs underlying cortical neurogenesis and gliogenesis in mammals. Through integrated scRNA-Seq, BrdU pulse-chase labeling, and immunohistochemical approaches, we demonstrate that, similar to their human counterparts, ferret cortical outer radial glia (oRGs), exhibit enhanced ERK and PKA signaling. ERK and PKA act in a mutually reinforcing manner to boost oRG self-renewal and neurogenesis, while inhibiting gliogenesis and prolonging the neurogenic period. Furthermore, we identify regional specialization within cortical gliogenic RGs: YAP/TAZ activation drives ventricular zone truncated radial glia (tRGs) toward ependymal fate in medial cortex, whereas SHH signaling instructs lateral cortical tRGs to generate tripotential intermediate progenitor cells, which serve as a shared source of astrocytes, oligodendrocytes, and olfactory bulb interneurons. Our data support a model in which mammalian cortical neurogenesis, gliogenesis, and evolutionary expansion are co-regulated through an integrated signaling network involving ERK, PKA, YAP/TAZ, and SHH. These findings provide key insights into the molecular and cellular mechanisms driving cortical development and evolution.

overall_design: P3 ferret pups were deeply anesthetized, and their brains were immediately harvested and immersed in ice-cold Hanks' Balanced Salt Solution (Gibco 14175-095). The dorsal cortices were dissected into small pieces and dissociated into a single-cell suspension using the Papain Cell Dissociation Kit, following the manufacturer’s instructions (Miltenyi Biotec, catalog no. 130-092-628). Single-cell RNA sequencing (scRNA-Seq) libraries were prepared using the Chromium droplet-based sequencing platform (10X Genomics), in accordance with the manufacturer’s guidelines (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina HiSeq 4000.

first: Jialin

last: Li

first: Zhengang

last: Yang


title: A high-fidelity RNA-targeting Cas13X downregulates connexin43 in astrocytes: A novel neuroprotective strategy for glaucoma

status: Public on Aug 01 2025

first: Guoli

last: Zhao

address: 131 Dongan Road

summary: Glaucoma is a neurodegenerative disease characterized by the progressive degeneration of retinal ganglion cells (RGCs) and their axons, ultimately leading to irreversible vision loss. Elevated intraocular pressure (IOP) is the primary risk factor; however, neurodegeneration continues even after effective IOP management, underscoring the need for neuroprotective therapies. This study investigates the role of connexin43 (Cx43), which is extensively expressed in retinal macroglia, in regulating microglial activation and optic nerve degeneration in glaucoma. We employed a high-fidelity CRISPR-Cas13 (hfCas13X) system to selectively target and knock down Cx43 expression in astrocytes. Our findings reveal that Cx43-mediated ATP release through hemichannels exacerbates microglial activation and neuroinflammation, thereby contributing to RGC loss. Notably, in a mouse model of chronic ocular hypertension (COH) glaucoma, knocking down Cx43 in astrocytes using the hfCas13X system significantly promoted the survival of RGCs and the integrity of the optic nerve, and improved visual function. The hfCas13X system, which offers high-fidelity RNA editing with minimal off-target effects, represents a novel and promising therapeutic strategy for glaucoma, highlighting the potential of gene editing technologies in the management of neurodegenerative diseases.

overall_design: RNA-seq from retinal cells of control and WT-G3w and Cx43ko-G3w mice to investigate the neuroprotective mechanisms of conditional astrocyte Cx43 knockout in glaucoma.

first: Zhen

first: Mingjie

first: Shuying

first: Qing

last: Xia

first: Shuoyu

last: Xu

first: Yu

last: Zhang

first: Yi

last: Wang

first: Fang

first: Yuling

last: Liu

first: Yunhui

last: Guo

first: Ruoxi

first: Han

first: Hong

first: Wenwen

last: Ding

first: Yongchen

first: Yanying

last: Miao

first: Zhongfeng


title: A kidney specific fasting-mimicking diet induces podocyte reprogramming and restores renal function in glomerulopathy

status: Public on Jul 30 2025

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: Cycles of a fasting-mimicking diet (FMD) promote regeneration and reduce damage in the pancreas, blood, gut, and nervous systems of mice but its effect on kidney disease is unknown, and the FMD has not been tested in rats. Here we show that cycles of a newly developed low-salt FMD (LS-FMD) restore normal proteinuria, nephron structure and function in rats with puromycin-induced nephrosis in the long term. LS-FMD induces expression of nephrogenic markers, resembling renal developmental processes in multiple kidney structures, and activates podocyte-lineage reprogramming pathways, in addition to promoting a quiescent state in mature podocytes.

overall_design: Sprague-Dawley rats were injected with puromycin aminonucleoside. Rats were either fed ad libitum, or a low salts fasting mimicking diet (LS-FMD). A group of healhty rats was used as control. Rats were fed a total of 6 cycles of diet and analyzed 6 weeks post treatment after 5 months from the PAN injection. Another healthy rat was fed one cycle of LS-FMD and analyzed at 72 hours post refeeding.  Kidneys were harvested, embedded in OCT and frozen. 10 um sections were cut and laid on a gene expression slide for Visium spatial transcriptomics.


summary: Cycles of a fasting-mimicking diet (FMD) promote regeneration and reduce damage in the pancreas, blood, gut, and nervous systems of mice but its effect on kidney disease is unknown, and the FMD has not been tested in rats. Here we show that cycles of a newly developed low-salt FMD (LS-FMD) restore normal proteinuria, nephron structure and function in rats with puromycin-induced nephrosis in the long term. LS-FMD induces expression of nephrogenic markers, resembling renal developmental processes in multiple kidney structures, and activates podocyte-lineage reprogramming pathways, in addition to promoting a quiescent state in mature podocytes.  In a pilot randomized cross-over study in patients with chronic kidney disease, FMD cycles promote renoprotection by reducing proteinuria and improving endothelial function. These results show that LS-FMD cycles, which promote the reprogramming of multiple renal cell types, leading to glomerular damage reversal, should be tested further in the treatment of progressive kidney diseases.

overall_design: Sprague-Dawley rats were injected with puromycin aminonucleoside. A group of rats (N=3) were analyzed at 14 days (PAN), another group were subjected to one cycle (4 days) of low salts fasting-mimicking diet (LS-FMD) and analyzed at end of diet (EoD, and at 24 hours and 72 hours after re-feeding with regular chow (N=3 each group). A group of N=4 halthy rats were included as baseline controls in the analysis.


title: Signaling Induced Plasticity Enables Transgene-Free Generation of Mouse Post-Gastrulation Whole Embryo Models Solely from Naïve ESCs and iPSCs (i)

status: Public on Jul 29 2025

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: The ability to generate synthetic mouse embryo models (SEMs) that can grow beyond gastrulation and early organogenesis has proven the plasticity of naïve Pluripotent stem cells (nPSC) to fully recapitulate the developmental dynamics of the mouse embryo. Existing protocols rely on  the induction of extraembryonic lineages by ectopically expressing master transcription factors that induce their differentiation to trophoblast (TE) or primitive endoderm (PrE) that latter will form the placenta and yolk sac, respectively. However, this approach brings technical difficulties related to the required genetic manipulation, separate lineage induction and mixing of different cell lines. While several works have suggested efficient priming to extraembryonic lineages without the need of transgenes, they have not proven the capability of this cells to contribute to the formation of SEMs. In this study, we demonstrate that naive ESCs can be co-induced in a single transgene free condition to give rise to both embryonic and extraembryonic lineages present in the preimplantation mouse embryo while preserving an epiblast compartment. Furthermore, this condition can be aggregated and cultured, resembling post-implantation egg cylinders, and by applying ex-utero growth technologies they progress to mimic features corresponding to E8.5 in-utero growth embryos. Moreover, by optimization of a  media termed Alternative Condition (AC), we provide ready to use condition that can be maintained long term and directly aggregated to generate TF-SEMs, eliminating the need of cell preinductions before aggregation.

overall_design: Following iterative tests and optimizations, we formulated the following regimen and media compositions as most optimal to obtain Epi, PrE and TE cells within 4 days from 2i/LIF naïve ESCs (sample A). Our 4 day regimen consists of 24h treatment of Multilineage Promoting Media 1 (MLPM1) which contains N2B27 based media with CHIR – REPSOX – AM580 and NaB (sample B),  followed by 24h treatment of MLPM2 which is MLPM1 that lacks NaB, and has CHIR concentration reduced from 6 μM to 3 μM, and in which LIF is reintroduced (sample C). Next, the cells were then harvested and aggregated in AggreWell plates, with 30 cells per microwell as employed on previous transgene mediated SEM protocols, for 2 days in Multilineage Maturation Media (MLMM – N2B27 with FGF4, ACTIVIN A, XAV and TRULI) (sample D). Using the AC media, we maintained PrE, TE and Epi-like cells for 12 passages on mouse embryonic fibroblast layers and harvested these cells for sequencing.

first: Alperen

last: Yilmaz

first: Gulben

last: Gurhan

first: Alejandro

last: Aguilera-Castrejon

first: Bernardo

last: Oldak

first: Jacob

last: Hanna


title: Expression of IMPACT curtails metabolic plasticity and augments NK cell killing to abrogate metastatic growth [RNA-Seq 2]

status: Public on Jul 25 2025

city: Bethesda

first: Jonathan

last: Hernandez

state: MD

address: Building 37

institute: NCI/NIH

summary: To form overt metastases, disseminated tumor cells must simultaneously acquire nutrients, circumvent oxidative stress, and evade organ-specific innate immune surveillance upon arrival. Given the propensity of aggressive epithelial tumors to form hepatic metastases, we performed an in vivo cDNA screen using the mouse liver and KRASG12D/TP53R273H pancreatic cells to identify the RNA binding protein general control of amino acid synthesis 1-like 1 (GCN1) as integral component of hepatic outgrowth. RNAi experiments reveal that GCN1 triggers the integrated stress response (ISR) to activate serine, folate, and methionine biosynthetic pathways together with amino acid transporters, which act in concert to facilitate acquisition of critical metabolites and to restore redox homeostasis. Alongside activation of the ISR, we found that GCN1 also functions in the nucleus where it interacts with an RNA binding protein (HNRNPK) to suppress the expression of MHC-I, antigen-presentation pathway molecules, and natural killer (NK) ligands. Intriguingly, we identified IMPACT as an endogenous competitive inhibitor of GCN1 that blocks both ISR-dependent metabolic control and disrupts HNRNPK interaction. In doing so, IMPACT enhances tumor immunogenicity to unleash robust NK cell killing, in addition to sensitizing metastatic tumor cells to immune checkpoint blockade (ICB). Analysis of patient tumors demonstrates that elevated expression of GCN1 and HNRNPK with concomitant loss of IMPACT correlates with poor immunogenicity, aggressive behavior, and abbreviated survival. These studies provide novel insights linking tumor metabolism, immunity, and metastasis.

overall_design: KPC177669 cells with and without GCN1 knockdown were grown in DMEM containing either 4mM or 0pt5mM Glutamine for 24 hr and RNA isolated from the cells were subjected to bulk RNAseq.

first: Surajit

last: Sinha

first: Vishal

last: Koparde


title: Expression of IMPACT curtails metabolic plasticity and augments NK cell killing to abrogate metastatic growth

overall_design: RNA isolated from human pancreatic KLM1 control and GCN1 knockdown cells were subjected to RNA sequencing.


title: TGF-β–mediated epithelial–mesenchymal transition of keratinocytes promotes fibrosis in secondary lymphedema

status: Public on Jul 09 2025

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Secondary lymphedema is characterized by fibrosis and impaired lymphatic function. Although TGF-β is a key regulator of fibrosis in this disease, the cellular mechanisms regulating this process remain unknown. Epithelial-mesenchymal transition(EMT), a mechanism by which TGF-β induces fibrosis in other skin diseases, is characterized by loss of epithelial cell markers and cellular polarity, upregulation of fibrotic gene expression, and gain of migratory capacity. Using clinical lymphedema biopsy specimens and animal models, we show that keratinocytes in the basal layer of epidermis undergo EMT in lymphedematous skin, migrate into the dermis, and contribute to dermal fibrosis. In vitro studies using cultured primary human keratinocytes treated with lymphatic fluid from the affected limbs of patients with secondary lymphedema resulted in a TGF-β-mediated increased expression of EMT markers. We show for the first time that EMT is activated by TGF-β in secondary lymphedema and that this process plays an important role in regulating skin fibrosis in this disease.

overall_design: RNAseq profiling of four pairs of frozen clinical lymphedema biopsy specimens. The ribodepletion method was used for RNAseq. mRNA expression was standardized and analyzed. Standardized expression for each molecule was assessed and data are presented as Z-scores.

first: Hyeung Ju

last: Park

first: Jinyeon

last: Shin

first: Ananta

last: Sarker

first: Mark

last: Klang

first: Elyn

last: Riedel

first: Michelle

last: Coriddi

first: Joseph

last: Dayan

first: Sarit

last: Pal

first: Babak

last: Mehrara

first: Raghu

last: Kataru


title: RNAseq of CD4 T cells treated with Insulin for 48 hours

status: Public on Jul 16 2025

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

summary: RNAseq of CD4 cells from 6 healthy men. Cells were activated with anti-CD3 and treated with Insulin, 10 nM, for 48 hours.

overall_design: CD4 cells from PBMC from 6 healthy men, isolated by positive selection on Dynabeads (cat.11331D), stimulated with anti-CD3 (OKT3, Sigma-Aldrich) with addition of Insulin, 10nM or control for 48h

first: Karin

middle: M

last: Andersson

first: Malin

middle: C

last: Erlandsson

first: Eric

last: Malmhäll-Bah


status: Public on Jul 11 2025

first: Jonathan

last: Hernandez

state: Maryland

address: 10 Center Drive

department: Surgical Oncology Program

institute: National Cancer Institute

overall_design: KPC control and IMPACT-overexpressing pancreatic tumor cells (3X105 cells) were injected into the spleen of syngeneic mice and allowed to develop liver lesions for 25 days following which leukocytes were isolated from the liver and analyzed using scRNA-seq.

first: Surajit

last: Sinha

first: Alexei

last: Lobanov

first: Michael

last: Kelly

first: Anna

last: Lee Fong


status: Public on Jul 02 2025

city: Qingdao

first: Yanhai

last: Gong

address: No.189 Songling Road

department: single cell center

institute: qibebt, cas

summary: Transcriptome analysis of NoPAC4 mutants under low light revealed a novel role of PAC4 that enhances carotenoid synthesis in N. oceanica

overall_design: Cells were cultured in flasks for 5 days to reach the logarithmic phase at 23 °C under continuous light (50 μmol photons m-2 sec-1).

first: Qintao

last: Wang

first: Jian

last: Xu


title: Tubular Cell Senescence Disrupts FOXO1-Dependent Renal Gluconeogenesis During Starvation in Chronic Kidney Disease

status: Public on Jun 30 2025

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

summary: Renal gluconeogenesis accounts for a substantial fraction of systemic glucose production during starvation, yet its regulation and pathological disruption in chronic kidney disease (CKD) remain poorly understood. Here, we investigated the mechanisms governing renal gluconeogenesis during starvation and their impairment in CKD. Integrated transcriptome analysis of starved mouse kidneys revealed that starvation robustly induces gluconeogenic gene expression in proximal tubular epithelial cells through activation of FOXO1. Consistently, tubule-specific deletion of FOXO1 (FOXO1^flox/flox^; Ksp-Cre) markedly reduced renal gluconeogenic enzyme expression and resulted in hypoglycemia during starvation, establishing FOXO1 as a critical regulator of renal glucose production. In multiple CKD models, basal serum glucose levels were preserved despite suppressed renal FOXO1 activation and gluconeogenic gene expression, indicating compensatory glucose production under fed conditions. In contrast, during prolonged starvation, CKD mice developed profound hypoglycemia accompanied by impaired FOXO1 activation and insufficient induction of renal gluconeogenesis, a phenotype that was similarly observed in aged mice. In human CKD kidneys, a senescent tubular cell state was associated with coordinated downregulation of gluconeogenesis-related genes. These findings were recapitulated in cisplatin-induced senescence models, which showed diminished FOXO1 activity, reduced gluconeogenic gene expression, and decreased glucose production. Collectively, these findings identify tubular cell senescence as a pathogenic mechanism that disrupts FOXO1-dependent renal gluconeogenesis, thereby compromising glucose homeostasis during starvation in CKD and aging. Targeting tubular senescence or restoring FOXO1 signaling may represent therapeutic strategies to prevent starvation-induced hypoglycemia in these conditions.

overall_design: This study aims to investigate the effects of starvation on the mouse kidney, both with and without kidney damage. Control mice and folic acid-treated mice (250 mg/kg, IP injection) were subjected to starvation, after which their kidneys were collected for analysis.

first: KiWung

last: Chung


title: m6A sequencing of vitreous bodies of diabetic retinopathy patients

city: Wu'xi

first: Yu

last: Xin

state: Jiangsu

address: 1800 Lihu Road

institute: Jiangnan University

summary: As the most prevalent, abundant and conserved internal cotranscriptional modification in eukaryotic RNAs, N6-methyladenosine (m6A) plays vital role in the progression of different types of human diseases, including cancers. m6A RNA methylation have been reported to affects the physiological and pathological progressions of hematopoietic, central nervous and reproductive systems. As diabetic retinopathy is one of the most importent microvascular complication of diabetes, in this work, MeRIP-seq was employed to investigate the RNA m6A levels in the vitreous body samples of diabetic retinopathy and control groups.  A group of mRNAs were suggested with significantly fluctuated transcription and m6A levels, and they would be inverstigated in the further work to understand the mechanisam of the progression of diabetic retinopathy.

overall_design: During pars plana vitrectomy, vitreous bodies of diabetic retinopathy patients (DR group, 90 eyes) and  non-diabetic retinopathy patients (NC group, 90 eyes, including rhegmatogenous retinal detachment, macular hole, epimacular membrane) were collected. To enrich the RNA, samples of each group were combined (30 samples were mixed) as DR_1-3 and NC_1-3.  Comparative gene expression profiling and m6A modification analysis using RNA-Seq data of two groups were performed.

first: Jun

last: Shao

first: Lu

last: Ye

first: Shujing

last: Cui


title: Cross-talk between Cancer-Associated Fibroblasts and Triple Negative Breast Cancer (TNBC) cells in heterotypic clusters

status: Public on Jun 25 2025

city: Minneapolis

first: Angela

middle: K

last: Spartz

state: MN

address: 420 Delaware St SE, MMC480

institute: University of Minnesota

summary: Circulating Cancer-Associated Fibroblasts (cCAFs) have been discovered in circulating tumor cell clusters from all stages of disease progression in breast cancer patients. As the most abundant non-cancerous cell type in the tumor microenvironment (TME), CAFs impart many of the tumor promoting functions defined by the hallmarks of cancer such as: proliferation, invasion, migration, metastasis, stemness, immunosuppression, altered cancer cell metabolism, and drug resistance. Human primary CAF cell lines can form co-clusters in vitro with human breast cancer cells when grown in ultra-low attachment conditions. We have previously used these co-clusters to show that they promote metastasis in the mouse tail vein model. In this study, we seek to understand the cross-talk that occurs between CAFs and TNBC  cells when they are present in heterotypic co-clusters compared to TNBC monoclusters or CAF monoclusters. We created samples of mono-clusters and co-clusters grown in 3D conditions for 48 hrs, then disrupted the clusters into a single cell suspension, and subsequently processed them for Single-cell RNA sequencing. Comparisons of breast cancer cells grown as mono-clusters versus co-clusters revealed differentially expressed genes (DEGs) that are up and down regulated in the presence of CAFs. Integration Pathway Analysis and Gene Ontology analysis revealed that CAFs increase expression of several components of the fibrinolysis pathway in breast cancer cells, such as uPA/PLAU and SERPINE1. Upstream regulators identified included TGFbeta. We also looked at DEGs in CAFs when in co-clusters versus mono-clusters and found that when in co-clusters, CAFs become even more CAF-like with the upregulation of genes such as collagens, integrins, and FN1. This study provided us with candidates to study in the process of CAF-mediated breast cancer cell extravasation, such as uPA/PLAU. Pathways identified support our conclusions that circulating CAFs are important players in the metastatic process.

overall_design: CAF23 cells and TNBC cells were cultured together for 48 hrs under non-adherent conditions in ultra low attachment plates to generate 48 in vitro mono-clusters or co-clusters. Clusters were then broken apart into a single cell suspension and processed for Single-cell RNA sequencing.

first: Dorraya

last: El-Ashry

first: Carol

last: Lange


title: Elementary 3D organization of active and silenced E. coli genome (MicroC)

status: Public on Jun 24 2025

first: Ilya

last: Shamovsky

state: New York

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

summary: Unraveling how genomes are spatially organized and how their 3D architecture drives cellular functions remains a major challenge in biology. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid. Despite progress in characterizing bacterial 3D genome architecture over recent decades, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods like Hi-C. In this study, we developed an enhanced Micro-C chromosome conformation capture, achieving 10 bp resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the E. coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, play key roles in repressing horizontally transferred genes (HTGs). Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, while removing both H-NS and StpA results in their complete disassembly, increased HTGs transcription, and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery.

overall_design: Using the Micro-C technique, we generated contact maps of the E. coli genome at a resolution up to 10 bp. We analyzed wild-type E. coli cells, cells subjected to heat shock, cells treated with different antibiotics and drugs (rifampicin, bleomycin, novobiocin, ciprofloxacin, netropsin), as well as different knockout strains (deltaHNS, deltaStpA, deltaHNSdeltaStpA, deltaFis, deltaMukBEF). We performed gene expression profiling analysis using data obtained from Red-C and RNA-seq. We also performed Hi-C analysis of wild-type E.coli cells.

first: Alexey

last: Gavrilov


title: Elementary 3D organization of active and silenced E. coli genome

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

overall_design: Refer to individual Series


title: Maternal Vitamin C Deficiency and Genetic Risk Factors Contribute to Congenital Malformations through Dysregulation of DNA Methylation.

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 651

department: Deparment of Human Genetics

country: Belgium

institute: KU Leuven

type: Methylation profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing


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

status: Public on Jun 23 2025

city: Memphis

first: Jasmine

last: Plummer

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

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

PhenoCycler (protein) data is available at https://stjude.app.box.com/s/fg5e5r43heipjh6lchu6m0d612ojwtw1
This is the content within the .tar file: There are 3 STAMPs on the slide i) {PBMC, MCF-7, SK-BR-3}, ii) {MCF-7}, and iii) {SK-BR-3}.You can separate each STAMP by referring to stamp12b_MCF7_new.tsv and stamp12b_SKBR3.tsv - the remaining stamp in the slide will be {PBMC, MCF-7, SK-BR-3}.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus
synthetic construct


title: Enhancer poising enables pathogenic gene activation by noncoding variants [ATAC-seq]

status: Public on Jun 20 2025

city: Irvine

first: Evgeny

last: Kvon

address: 836 Health Sciences Road

institute: University of California, Irvine

summary: Single nucleotide variants within enhancers—non-coding DNA elements that regulate transcription—often lead to aberrant gene activation and contribute to a wide range of genetic disorders (Claussnitzer et al. 2015; Doan et al. 2016; Turner et al. 2017; Yanchus et al. 2022; Lettice et al. 2008). The mechanism by which ectopic gene activation occurs through these gain-of-function enhancer mutations remains poorly understood. Using the ZRS, a benchmark disease-associated enhancer of Sonic hedgehog (Shh), as a model, we demonstrate that poised (i.e., accessible but inactive) chromatin sensitizes Shh to aberrant activation in anterior limb bud, leading to polydactyly. In the anterior limb cells of wild-type mice, Shh is inactive, but the ZRS is accessible and marked by enhancer-associated histone modifications. We demonstrate that this poising signature explains how over 20 independent rare variants within the ZRS cause Shh misexpression in the same anterior limb bud cell population, resulting in similar limb malformations, despite affecting binding sites for different activators and repressors. Disabling pioneer transcription factor binding to the ZRS suppresses its poised state in anterior cells, prevents aberrant activation of the ZRS by rare variants, and fully rescues limb malformations in variant knock-in mice. A thorough examination of other disease-associated enhancers with pathogenic gain-of-function variants revealed that they are all poised in tissues with ectopic activity. We use this poising signature to predict and validate in vivo ectopic forebrain activity of previously uncharacterized autism-associated non-coding variants. Our findings suggest that spatial enhancer poising, likely a byproduct of development, leads to susceptibility to non-coding mutations offering a potential mechanistic explanation for the burden of disease-associated non-coding variants.

overall_design: ATAC-seq was performed on 50-100k fluorescently-sorted cells from anterior, central, and posterior domains of E11.5 mouse hindlimb buds. Sorted cells were lysed in nuclear lysis buffer for 5 min on ice before being spun down for transposition with Tn5 and then library preparation. Omni-ATAC-seq was performed following Corces et al, 2017 protocol.

first: Ethan

last: Hollingsworth


title: Identification of PRMT5 as a therapeutic target in cholangiocarcinoma [RNA-seq II]

status: Public on Jun 17 2025

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

summary: Cholangiocarcinoma is a very aggressive cancer whose incidence is increasing. Moreover, chemotherapies are little effective and the response to immune checkpoint inhibitors is low. We have identified protein arginine-methyltransferase 5 (PRMT5) as a novel therapeutic target in cholangiocarcinoma. Treatment with PRMT5 inhibitor significantly restrains the growth of experimental cholangiocarcinoma model TAZ/AKT without adverse effects. Our findings support the evaluation of PRMT5 inhibitors in clinical trials.

overall_design: To study the effect of PRMT5 inhibition in tumor progression, cholangiocarcinoma (CCA) was induced in C57BL/6J mice by hydrodynamic tail vein injection (HTVI) of plasmids coding for mutant TAZ, myr-AKT and the sleeping beauty transposase (TAZAKT). One group of mice was treated with PRMT5 inhibitor JNJ-64619178 (TAZAKT_JNJ) and control mice received the vehicle (TAZAKT_V). C57BL/6J mice without HTVI injection nor treatment were used as healthy controls (C). We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different mice of each group.

first: Jasmin

last: Elurbide

first: Leticia

last: Colyn

first: Maria

middle: U

last: Latasa

first: Iker

last: Uriarte

first: Amaya

last: Lopez Pascual

first: Emiliana

last: Valbuena Goiricelaya

first: Borja

last: Castello Uribe

last: Fernandez  Barrena

first: Matias

last: Avila


title: Identification of PRMT5 as a therapeutic target in cholangiocarcinoma

platform_organism:
Homo sapiens
Mus musculus


title: A pathogenic CD4 T cell phenotype in experimental uveitis shares common features with other immune mediated inflammatory diseases [EAU]

status: Public on Jun 16 2025

city: Bristol

first: Lindsay

last: Nicholson

address: Biomedical Sciences Building

department: Cellular and Molecular Medicine

country: United Kingdom

institute: University of Bristol

summary: Experimental autoimmune uveoretinitis, a mouse model of ocular autoimmunity, was induced by the transfer of allelically marked T cells. Thirteen days after transfer, CD4 cells were sorted from spleens and individual eyes and processed using the SMART-Seq v4 Ultra Low Input RNA kit. Samples were classified as: transferred cells from the eye, transferred cells from the spleen, endogenous cells from the eye, endogenous cells from the spleen. Analysis of differential gene expression revealed an extended pathogenic phenotype that shared common features with other models of autoimmunity.

overall_design: Data from 24 samples obtained from two experiments (ASS03 & ASS04) and classified as transferred CD4 cells from single eyes (e4T), transferred CD4 cells from the spleen (s4T), endogenous cells from the eye (e4E) and endogenous cells from the spleen (s4E). Cells numbers were in the range 18-100 cells.

first: Amy

last: Ward

first: Oliver

last: Bell

first: Luis

last: Martinez-Robles

first: Phillip

middle: J

last: Lait

first: Colin

last: Chu

first: David

last: Copland

first: Andrew

middle: D

last: Dick

middle: B


title: A pathogenic CD4 T cell phenotype in experimental uveitis shares common features with other immune mediated inflammatory diseases

summary: Experimental autoimmune uveoretinitis, a mouse model of ocular autoimmunity, was induced by immunization with the uveitogenic peptide IRBP1-20. 26 days after disease induction, CD4 T cells were purified by cell sorting for RNAseq.

overall_design: Data from 12  samples obtained from C57BL/6 mice immunised with the uveitogenic peptide IRBP 1-20 and adjuvants. CD4+ T cells were obtained 26 days after disease by sorting from individual eyes (8 samples) or from the spleens of animals with disease (2 mice, A2S&B3S) or naïve (2 mice, A3S&B1S).


title: Metastatic site influences driver gene function in pancreatic cancer [[InVitro ATAC-Seq]]

status: Public on Jun 12 2025

first: Yu-Jui

last: Ho

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: Driver gene mutations can increase the metastatic potential of the primary tumor, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 – a transcriptional effector of TGFβ signaling – which is a hallmark of multiple gastrointestinal malignancies. SMAD4 inactivation mediates TGFβ’s remarkable anti- to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had opposite effects depending on the tumor’s organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis revealed organ-specific differences in the tumor cells’ epigenomic state, whereby the liver and lungs harbored chromatin programs respectively dominated by the KLF and RUNX developmental transcription factors, with Klf4 depletion being sufficient to reverse Smad4’s tumor-suppressive activity in liver metastases. Our results show how epigenetic states favored by the organ of residence can influence the function of driver genes in metastatic tumors. This organ-specific gene–chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.

overall_design: To determine whether organ-biased differences in chromatin accessibility were maintained in vitro, we performed ATAC-seq on the Smad4-OFF primary tumor-derived cell lines used to generate liver and lung metastases, as well as on matched cell lines derived from the respective metastatic sites.

first: Kaloyan

last: Tsanov

first: Scott

middle: W

last: Lowe


title: Metastatic site influences driver gene function in pancreatic cancer [InVitro RNA-Seq]

overall_design: SMAD4 acts as a transcription factor (TF) by forming a complex with the SMAD2/3 TFs to activate gene expression programs downstream of TGFβ receptors. Hence, we performed RNA-seq of the input cells in vitro after Smad4 restoration and TGFb treatment (see Methods), and compared the resulting pathway enrichment to our in vivo data from the pancreas, liver and lungs.


title: Virus-Human Chromatin Interactions Reorganise 3D Genome and Hijack KDM5B for Promoting Metastasis in Nasopharyngeal Carcinoma [ATAC-seq]

status: Public on Jun 06 2025

city: HK

first: Lai Shun Dittman

last: CHUNG

state: HK

address: 21 Sassoon Road, Pokfulam

department: Department of Clinical Oncology

country: Hong Kong

institute: the University of Hong Kong

summary: As the first human DNA tumour virus Epstein-Barr virus (EBV) is detectable in over 90% of nasopharyngeal carcinoma (NPC) patients in the endemic regions. Genome-wide analysis of 3D chromosome conformation revealed the virus-host chromatin interactions induce spatial reorganisation of loops and compartments, exhibiting “enhancer infestation” and “H3K27 bivalency” at EBV interaction regions (EBVIRs). Through this mechanism, EBV hijacks KDM5B, a genome stability gatekeeper, and its binding targets leading to aberrant activation of the EBVIRs-enhancer-KDM5B signature. The cancer cells with this signature had increased MYC activation, DNA damage responses, and epigenetic plasticity for epithelial-immune cell dual features with metastatic potential. Our multi-centre multi-omics study further confirmed that this signature was highly relevant to chromosome instability and could be utilised as a risk factor for distant metastasis. This study highlights a novel paradigm where latent viral episomes could alter host high-order epigenotype, promoting transcriptional rewiring and risk of metastasis in NPC.

overall_design: Two normal epithelial cells (NP69, NP460), three EBV+NPC cells (C17, C666, NPC43), three EBV-NPC cells (NPC53, NPC38 HK1) were conducted ATAC-seq to assess the chromatin accessibility. Each cell line has two replicates.

first: Dittman Lai-Shun

last: Chung

first: Wei

last: Dai


title: Spatiotemporal molecular and cellular dynamics of intratelencephalic neurons in mouse prefrontal cortex during postnatal development

status: Public on May 28 2025

city: Wuhan

first: Hu

last: Zheng

state: Hubei

address: shizishan street No.1

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

summary: In early postnatal brain, the prefrontal cortex (PFC) remains immature and highly plastic, particularly for the intratelencephalic (IT) neurons. However, the spatiotemporal molecular and cellular dynamics of PFC during this period remain poorly characterized. Here, we performed spatiotemporal single-cell RNA analysis on mouse PFC during different postnatal time points and systematically delineated the molecular and cellular dynamics of mouse PFC during early postnatal development, among which IT neurons exhibit most dramatic alterations. Based on these comprehensive spatiotemporal atlases of PFC, we deciphered the time-specific molecular and cellular characteristics during the maturation process of IT neurons in PFC, particularly the dynamic expression programs of genes regulating axon development and synaptic formation, and the risk genes of neurological developmental diseases. Furthermore, we revealed the dynamic neuron-glia interaction patterns and the underlying signaling pathways during early postnatal period. Our study provided a comprehensive resource and important insights for PFC development and PFC-associated neurological diseases.

overall_design: To delineate the molecular trajectories underlying postnatal development of prefrontal cortex (PFC) neurons and investigate the mechanisms governing early neural circuit assembly, we performed high-throughput single-cell RNA sequencing (scRNA-seq) on PFC tissues from mice across key developmental timepoints (postnatal day: P1, P4, P10 and adulthood: P84). Our comprehensive transcriptomic atlas captured dynamic gene expression patterns during critical stages of neuronal maturation.


title: TEAD1 condensates are transcriptionally inactive storage sites on the pericentromeric heterochromatin

city: Baltimore

first: Danfeng

last: Cai

address: 615 N Wolfe St

institute: Johns Hopkins Bloomberg School of Public Health

summary: TEA domain transcription factor 1 (TEAD1), a Hippo pathway transcription factor important in cellular homeostasis and development, is increasingly implicated in cancer biology. Here, we reveal a novel role for TEAD1 in organizing nuclear condensates, independent of active transcription. Using high-resolution imaging, ChIP-seq, RNA-seq and proximity-based proteomics, we demonstrate that in patient-derived renal cell carcinoma cells, TEAD1 forms micron-sized foci by binding to the heterochromatic pericentromeric regions using its DNA-binding domain. These TEAD1 foci do not mediate transcription but instead serve as depots for excess TEAD1. This contrasts with TEAD1 organization in other genomic regions of both RCC and normal kidney cells, where TEAD1 associates with markers of active transcription. Our findings provide a mechanistic framework for TEAD1’s dual regulatory roles, offering new insights into its contribution to transcriptional dysregulation and tumor progression.

overall_design:
Chromatin immunoprecipitation (Ch-IP) was performed based on previous studies81. In general, 108 cells are used per each ChIP-seq experiment. HK2 and UOK cells were first treated with 1% formaldehyde in UOK media, followed by the addition of 0.125M glycine to halt cross-linking. The cells, washed in ice-cold PBS, were then lysed in cell lysis buffer, with subsequent nutation at 4°C. Cells were treated by dounce homogenization on ice, followed by centrifuge at 500 x g for 10min. The supernatant was discarded, and the pellets was resuspended using nuclear lysis buffer. Nuclear lysates were then sheared by Covaris E220 to achieve average chromatin length of 300-400 bp. The protein/chromatin complexes are captured using antibodies specific to the TEAD1, H3K9me3, YAP1, H3K27ac, and mouse IgG, and the mixtures were incubated overnight on nutator at 4°C.

Please note that the records have been updated with the following files on April 28, 2026:
GSM9011941_HK2-TEAD1-rep1_S8.k50.bw
GSM9011942_HK2-TEAD1-rep2_S24.k50.bw
GSM9011950_UOK121-TEAD1-rep1_S5.k50.bw
GSM9011951_UOK121-TEAD1-rep2_S27.k50.bw
GSM9011958_UOK122-TEAD1-rep1_S6.k50.bw
GSM9011959_UOK122-TEAD1-rep2_S16.k50.bw
GSM9011967_UOK342-TEAD1-rep1_S7.k50.bw
GSM9011968_UOK342-TEAD1-rep2_S19.k50.bw


title: A spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity

status: Public on May 27 2025

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

summary: A molecular understanding of lung organogenesis requires delineation of the timing and drivers of spatial-temporal cellular movements that ultimately form and support a surface capable of gas exchange. While the advent of single-cell transcriptomics has allowed for the discovery and identification of transcriptionally distinct populations present during lung development, the spatiotemporal dynamics of these transcriptional shifts remain undefined.. With imaging-based spatial transcriptomics, we analyzed the gene expression patterns in 17 human infant lungs at varying stages of development and lung injury, creating a spatial transcriptomics atlas of ~1.2 million cells. We applied computational clustering approaches to identify shared molecular similarities among this cohort, establishing a framework that will generate hypotheses about how tissue architecture and molecular spatial relationships are coordinated during normal development and disrupted in disease. Recognizing that all preterm birth represents an injury to the developing lung, we have moved away from the conventional paradigm of classifying an infants as “disease” or “control” in favor of a linear regression approach that accounted for the routinely collected object measures of gestational age, life span, and disease severity. Within this new framework, we have identified cell type patterns across these variables that would likely be overlooked when using a binary conventional “diseased vs. control” comparison. Together, these data represent a resource for the lung research community, supporting discovery-based inquiry and identification of targetable molecular mechanisms in both normal and arrested human lung development.

overall_design:
We profiled 17 infant lung samples that were collected from the Human Infant Lung Repository at Vanderbilt University with a gene probeset of 343 genes using the 10X Genomics Xenium platform. Sample names were generated by appending ‘PDL’ and then ranged from ‘001’ - ‘017’ (ex. PDL001). This dataset is comprised of individuals that range from the canalicular stage of lung development to the alveolar, with variable levels of disease pathologies. We took a 3x3 μ square of each tissue and arranged them in a tissue micro-array. We then took two adjacent serial sections and ran them concurrently, generating two technical replicates per sample.

UPDATE: [Jun-26-2025] The transcript.csv.gz files were replaced.

first: Saahithi

last: Mallapragada

first: Ruqian

last: Lyu

first: Arianna

middle: L

last: Williams-Katek

first: Brandon

last: Fischer

first: Niran

last: Hadad

first: Evan

last: Mee

first: Shawyon

last: Shirazi

first: Anne

last: Hilgendorff

first: Laurie

last: Eldredge

first: Gail

last: Deutsch

first: Davis

last: McCarthy

first: Jonathan

last: Kropski

first: Jennifer

last: Sucre

middle: E


title: The broccoli derivative sulforaphane extends lifespan by slowing the transcriptional aging clock

status: Public on May 22 2025

city: Eugene

first: Patrick

last: Phillips

state: OR

address: 5289 University of Oregon

department: Institute of Ecology and Evolution

institute: University of Oregon

summary: Sulforaphane (SFN), an organosulfur isothiocyanate derived from cruciferous vegetables, has been shown to inhibit inflammation, oxidative stress, and cancer cell growth; it has also been shown to increase the lifespan of the C. elegans nematode strain N2. Here, we tested the lifespan effects of SFN following the standard experimental procedures of the Caenorhabditis Intervention Testing Program (CITP). The CITP, a multi-institute research consortium, aims to identify chemical interventions that can robustly and reproducibly promote health and lifespan. To investigate the functional targets of SFN, we employed bulk RNA-Seq at a variety of ages to create a “transcriptional aging clock” using control individuals and then tested how global patterns of gene expression are altered under SFN treatment. Multi-dimensional scaling analysis of the transcriptome revealed transcriptional age under SFN treatment was similar to control individuals approximately four days younger, representing a nearly 20% shift relative to overall lifespan. These results support the idea that robust longevity-extending interventions can act via global effects across the organism, as revealed at a functional level via changes in gene expression.

overall_design: We performed differential gene expression analysis comparing SFN-treated and DMSO control samples in 2, 4, 8, 12, and 16-day old adult worms in the wildtype N2 strain; and in 4 and 12-day old skn-1 and daf-16 mutant strains.

first: Christine

last: Sedore

first: Erik

last: Segerdell

first: Anna

last: Coleman-Hulbert

first: Stephen

last: Banse

first: Gordon

last: Lithgow

first: Monica

last: Driscoll


title: Androgens mediate sexual dimorphism in Pilarowski-Bjornsson syndrome

city: Reykjavik

first: Kimberley

last: Anderson

address: Sturlugata 8

country: Iceland

institute: University of Iceland

summary: The effect of sex on the penetrance of autosomal dominant Mendelian conditions is an understudied area of research. Variants in CHD1 have previously been identified in females with Pilarowski-Bjornsson syndrome (PILBOS), a recently described cause of developmental delay. We now demonstrate that both sexes can show signs of PILBOS, although males are more likely to display PILBOS phenotypes when carrying more severe variants. A novel mouse model carrying a human-derived missense variant in the Chd1 gene (Chd1R616Q/+) shows female-restricted disease phenotypes including growth retardation, anxiety and hypotonia. Orchiectomy of male mice unmasks a growth retardation phenotype in Chd1R616Q/+ mutants compared to orchiectomized wild type (WT) littermates. Conversely, testosterone supplementation in female Chd1R616Q/+ mice and WT littermates rescues the growth phenotype, suggesting that androgens dictate PILBOS disease penetrance. On the human population level, we demonstrate a significant overrepresentation of healthy males carrying rare missense variants in CHD1 in the gnomAD database, further supporting a male protective effect against CHD1 variants. We further identify 212 other genes that show similar missense variant overrepresentation in males. Together our data suggests androgen-regulated sexual dimorphism in Pilarowski-Bjornsson syndrome and opens up novel avenues to understand the mechanistic basis of sexual dimorphism of autosomal Mendelian disorders.

overall_design: In order to examine the functional impact of the CHD1 R616Q variant, we performed bulk RNA-sequencing (RNAseq) using E18.5 NPCs derived from mouse embryos of both mutant and wild-type genotypes. Futhermore, we treated the cells with DMSO vehicle control or dihydrotestosterone (DHT) in order to assess the impact of androgens on the gene expression of these cells.

first: Sara

middle: T

last: Halldorsdottir

first: Hans

last: Bjornsson


title: Metastatic site influences driver gene function in pancreatic cancer [scRNA-seq]

status: Public on May 14 2025

city: New York

first: Yu-Jui

last: Ho

summary: Driver gene mutations can increase the metastatic potential of the primary tumor, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 – a transcriptional effector of TGFβ signaling – which is a hallmark of multiple gastrointestinal malignancies. SMAD4 inactivation mediates TGFβ’s remarkable anti- to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had strikingly opposite effects depending on the tumor’s organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis and functional perturbations revealed that the divergent effects of Smad4 were underpinned by organ-specific differences in the tumor cells’ chromatin state that emerged in the premalignant pancreas and were distinguished by the dominance of KLF (liver-biased) or RUNX (lung-biased) transcription factors. Our results show how epigenetic states favored by the organ of residence can influence the output of driver gene mutations in metastatic tumors. This organ-specific gene–chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.

overall_design: To explore the origin of liver- and lung metastasis-biased chromatin states, we performed scRNA-seq on premalignant pancreata in the KC-shRen and KC-shSmad4 autochthonous model (at 8 weeks of age) +/– Dox after treatment with PBS or Cerulein (for 2 days). Cerulein treatment induces pancreatitis, which facilitates PDAC development.

first: Kaloyan

last: Tsanov

first: Scott

last: Lowe


title: Transcriptomic atlas of the morphologic development of the fungal pathogen Coccidioides reveals key phase-enriched transcripts

status: Public on May 19 2025

city: San Francisco

first: Christina

middle: M.

last: Homer

department: Biochemistry & Biophysics

institute: UCSF


title: Metastatic site influences driver gene function in pancreatic cancer [RNA-seq]

overall_design: SMAD4 acts as a transcription factor (TF) by forming a complex with the SMAD2/3 TFs to activate gene expression programs downstream of TGFβ receptors. Hence, we performed RNA sequencing (RNA-seq) to explore the transcriptional basis of the observed organ-specific phenotypes. Leveraging the mKate2 reporter in our model, we used fluorescent-activated cell sorting (FACS) to isolate tumor (mKate2+) cells 7 and 14 days after Dox withdrawal, which allowed for assessment of Smad4 output kinetics.


title: Metastatic site influences driver gene function in pancreatic cancer


title: Metastatic site influences driver gene function in pancreatic cancer [scMultiome]

overall_design: To assess whether chromatin states that pre-exist in the primary tumor are linked to organ-specific metastasis, we performed coupled single-cell multiomics (ATAC/RNA-seq) on three independent KC-shSmad4 primary tumors (on Dox).


title: Metastatic site influences driver gene function in pancreatic cancer [ATAC-seq]

overall_design: Given the organ-specific transcriptional responses, we hypothesized that liver and lung metastases may harbor distinct chromatin states that afford different accessibility to SMAD4’s target genes. To test this, we performed ATAC-seq (assay for transposase-accessible chromatin using sequencing) on FACS-isolated tumor cells from the pancreas, liver, and lungs +/- Smad4 restoration (for 14 days).


title: The RNA-seq of  Ulcerative colitis patients and health

status: Public on May 07 2025

city: Chengdu

first: Ming

last: Chen

state: Sichuan

address: No. 37, GuoXue Xiang, Chengdu, China

institute: West China Hospital of Sichuan University

summary: The RNA extracted from left-sided colonic mucosal biopsy specimens of active UC patients (n=3), remission UC patients (n=3), and healthy controls (n=3) was subjected to RNA-seq.

first: Chengwei

last: Tang

first: Zhiyin

last: Huang


title: Base editing mediated correction of severe β0 IVS2-1 thalassemia mutations.

status: Public on May 05 2025

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: β-thalassemia is a highly prevalent monogenic recessive disease caused by mutations affecting the synthesis of the adult hemoglobin β-chains. Transplantation of autologous, genetically modified hematopoietic stem/progenitor cells (HSPCs) is an attractive therapeutic option. However, current gene therapy strategies based on the use of lentiviral vectors or CRISPR/Cas9 nuclease are not equally effective in all the patients and/or raise safety concerns. Base editing (BE), a new CRISPR/Cas9 derived genome editing tool, allows the effective introduction of point mutations at precise locations within the genome without generating double strand breaks. The two β0 mutations CD39 (CAG>TAG) and IVS2-1 (G>A) are among the most common and severe β-thalassemia mutations in the Mediterranean area and Middle East. We exploited the capacity of BE to correct these mutations in HSPCs from β-thalassemia patients. We demonstrated that red blood cells in vitro derived from edited HSPCs exhibited high β-globin levels and that the delayed erythroid differentiation typically observed in β-thalassemic cell cultures was corrected by our treatment. Finally, xenotransplantation experiments showed base editing in HSCs and correction of the β-thalassemic phenotype in vivo. Overall, our study provides in vitro and in vivo proof of efficacy of a BE approach to treat patients with prevalent and severe β-thalassemia mutations.

overall_design: Human sickle HSPCs  were transfected using an adenine base editor and a gRNA that corrects the IVS2-1  thalassemic mutation to evaluate potential off-targets. As control, each of the 3 donors was mock-transfected with TE buffer. Bulk RNAseq was performed at 48h to evaluate the impact of the editing procedure at the transcriptomic level.

first: Giulia

last: Hardouin

first: Annarita

last: Miccio


title: Base editing mediated correction of severe β0 thalassemia mutations

overall_design: Human beta-thalassemia HSPCs carrying the CD39 mutation were transfected using an adenine base editor to correct the CD39 mutation. As control, each of the 3 donors was mock-transfected with TE buffer. Bulk RNAseq was performed at 48h to evaluate the impact of the editing procedure at the transcriptomic level.


title: The RNA-Seq of PCK1 intestinal epithelial cell-specific knockout mice and their littermate control mice

summary: RNA-Seq was performed on PCK1 intestinal epithelial cell-specific knockout mice and their littermate control mice after 7 days of DSS treatment.


title: In vivo CRISPRi screen reveals lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth [in_vivo_CRISPRi]

status: Public on Apr 28 2025

city: Stanford

first: Luca

last: Ducoli

state: California

address: 269 Campus Drive CCSR 2150

institute: Stanford University

summary: Cutaneous squamous cell carcinoma (cSCC) accounts for 20% of all skin cancer mortality globally, making it the second-highest subtype of skin cancer. The high prevalence of cSCC in humans highlights the need to uncover alternative actors and mechanisms influencing skin cancer development. Significant advances have been made to better understand some key factors in cSCC growth. However, little is known about the role of noncoding RNAs, particularly of a specific subclass termed long noncoding RNA (lncRNA). By performing pseudobulk analysis of single-cell sequencing data from normal and cSCC human skin tissues, we determined a global portfolio of lncRNAs specifically expressed in keratinocyte subpopulations. Integration of CRISPR interference screens in vitro and the xenograft model identified several lncRNAs impacting the growth of cSCC cancer lines both in vitro and in vivo. Among these, we further validated LINC00704 and LINC01116 as proliferation-regulating lncRNAs in cSCC lines and potential biomarkers of cSCC growth. Taken together, our study provides a comprehensive signature of lncRNAs with roles in regulating cSCC growth.

overall_design: In vivo CRISPR-interference (CRISPRi) screen using squamous carcinoma cells (A431, Cal27) grown in nude mice as flank injected tumors harvested after few weeks comparing to week 0 (pre-tumor injection) samples.

first: Gyuhyeon

last: Kim

first: Zurab

last: Siprashvili

first: Xue

first: Paul

middle: A

last: Khavari


title: In vivo CRISPRi screen reveals lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth [s3DRAS_scRNAseq]

overall_design: Single cell RNA-seq of spheroid of transformed human Keratinocyte with CDK4(R24C) and Ras(G12V)

first: Jordan

last: Meyers


title: AGED CD8+ T CELLS DRIVE COGNITIVE DECLINE VIA GZMK [parabiosis]

status: Public on May 02 2025

first: Juliana

last: Sucharov Costa

address: 505 Parnassus Ave

department: Anatomy

summary: Changes in peripheral CD8+ T cells are a prominent hallmark of immune aging. While infiltrating CD8+ T cells are implicated in aging and neurodegenerative disease-related pathology in the brain, the role of aged non-infiltrating CD8+ T cells has yet to be fully defined. Here, we show that targeting activated aged peripheral CD8+ T cells rescues age-related cognitive decline. Using heterochronic parabiosis and single cell transcriptomics analysis we observed that aged peripheral CD8+ T cells maintain properties intrinsic to their age, being refractory to the effects of a young or aged systemic milieu. Systemic exposure of young mice to aged CD8+ T cells elicited synaptic-related aging transcriptional signatures in the hippocampus and impaired cognition. Inhibiting migration of aged peripheral CD8+ T cells to lymph nodes mitigated pro-aging effects on the young hippocampus. Conversely, targeting aged CD8+ T cells restored synaptic-related signatures in the aged hippocampus and ameliorated cognitive impairments. Mechanistically, we identified granzyme k (GZMK) as a secreted age-associated CD8+ T cell-derived factor that impairs cognitive function. Together, our data identify activated aged CD8+ T cells and their secreted factors as potential therapeutic targets to rescue cognition in old age.

overall_design: Considering the pro-aging effects observed in the hippocampus following both heterochronic parabiosis and transplantation of an aged hematopoietic system into young mice, we first assessed changes in peripheral CD8+ T cell trafficking and transcriptional responses to a young and aging systemic milieu using heterochronic parabiosis. Young (4 months) and aged (20 months) mice were surgically joined into isochronic (young-young and old-old) and heterochronic (young-old) parabiotic pairings for 28 days. To distinguish young versus aged cells in heterochronic parabionts, young CD45.1 B6/BoyJ and aged CD45.2 B6 mice were joined. We performed single cell RNA seq analysis on splenocytes of young isochronic, aged isochronic, young heterochronic and aged heterochronic parabionts after separation of CD45.1+ or CD45.2+ cells to analyze donor versus recipient immune cells.

last: Sucharov

first: Karishma

last: Pratt

first: Saul

last: Villeda


title: In vivo CRISPRi screen reveals lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth [RNASeq_knockdown]

overall_design: Bulk RNA-seq in A431 cells after antisense oligonucleotide (ASO) treatment including non-targetin ASO, two different LINC00704-ASO, two different LINC01116-ASO.


title: AGED CD8+ T CELLS DRIVE COGNITIVE DECLINE VIA GZMK [transfer]

overall_design: We sought to investigate functionally how aged CD8+ T exerted their pro-aging effects on the young hippocampus. Activation of memory CD8+ T cells is dependent on G?i/o-coupled G protein-coupled receptor (GPCR)-mediated migration to lymph nodes. Correspondingly, we pre-treated aged CD8+ T cells with pertussis toxin (PTx), a known inhibitor of Gi/o protein signaling, to block migration into lymph nodes following adoptive transfer. Specifically, we performed an adoptive transfer of PTx or vehicle treated aged (26 months) CD8+ T cells into young (5 months) mice, and vehicle treated young CD8+ T cells into age-matched young animals as a baseline control for age-related changes. PTx pre-treatment has been shown to prevent T cell migration to lymph nodes without altering migration to open circulation tissues such as spleen, bone marrow, or liver, Moreover, the timeframe used for our studies was selected in line with previous reports showing minimal entry into the brain parenchyma with no impact on migration to the brain by PTx treatment. To investigate the impact on the young hippocampus, we performed single nucleus RNA seq (snRNAseq) analysis. Having observed pro-aging effects of aged circulating CD8+ T cells in the young hippocampus, we conversely explored the possibility that targeting CD8+ T cells can rescue cognitive function in aged mice. To selectively target aged peripheral CD8+ T cells late in life, aged (22 months) mice were given intraperitoneal injections of a CD8a depleting antibody or IgG2b isotype control. To investigate molecular changes elicited in the aged hippocampus following depletion of aged peripheral CD8+ T cells, we performed snRNAseq.


title: In vivo CRISPRi screen reveals lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth [in_vitro_CRISPRi]

overall_design: In vitro CRISPR-interference (CRISPRi) screen using two sublibraries (KC and TSK) in squamous carcinoma cells (A431, Cal27) at Week 0 and Week 3, and normal Keratinocytes at Week 0 and Week 1.5.


title: DNGR-1 regulates proliferation and migration of bone marrow dendritic cell progenitors

status: Public on Apr 26 2025

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

institute: Francis Crick

summary: Conventional dendritic cells (cDCs) are sentinel cells that play a crucial role in both innate and adaptive immune responses. cDCs originate from a common progenitor (pre-cDC) in the bone marrow (BM) that travels via the blood to seed peripheral tissues before locally differentiating into functional cDC1 and cDC2 cells, a process known as cDCpoiesis. We show that DNGR-1, an innate immune receptor expressed by cDC progenitors and type 1 cDCs, functionally regulates cDCpoiesis in mice. In a competitive chimera setting, cDC progenitors lacking DNGR-1 exhibit increased proliferation and tissue migratory potential. Compared to their wildtype counterparts, DNGR-1-deficient cDC progenitor cells display superior colonization of peripheral tissues but an altered distribution. These findings suggest that cDCpoiesis can be regulated in part by cell-intrinsic processes driven by signals from innate immune receptors such as DNGR-1 that may respond to alterations in the BM milieu

overall_design: Transcriptome analysis was performed in bone marrow and spleen pre-cDCs population from DNGR1 KO CD42.2 and BL/6 CD45.1 mice (bone marrow chimeras)

first: Ana

last: Cardoso

first: Caetano

last: Reis-e-Sousa


title: RNA-seq profiling transcriptome of liver endothelial cells of conventionally raised (CONV-R) and germ-free (GF) mice.

status: Public on Apr 23 2025

city: Mainz

first: Hristo

last: Todorov

address: Duesbergweg 6

country: Germany

institute: University Medical Center Mainz


title: Metabolic adaptations direct cell fate during tissue regeneration [crypts RNA-seq]

status: Public on Apr 10 2025

first: Yu-Jui

last: Ho

summary: Although cell fate specification is generally attributed to transcriptional regulation, emerging data also indicate a role for molecules linked with intermediary metabolism. For example, α-ketoglutarate (αKG), which fuels energy production and biosynthetic pathways in the tricarboxylic acid (TCA) cycle, is also a co-factor for chromatin-modifying enzymes1-3. Nevertheless, whether TCA cycle metabolites regulate cell fate during tissue homeostasis and regeneration remains unexplored. In the intestine, we discovered unexpectedly heterogeneous expression of TCA cycle enzymes, with αKG dehydrogenase complex components4-6 upregulated in the absorptive lineage and downregulated in the secretory lineage. Using genetically modified mouse models and organoids, we demonstrated a dual, lineage-specific role for 2-oxoglutarate dehydrogenase (OGDH), the enzymatic subunit of αKG dehydrogenase complex. In the absorptive lineage, OGDH is upregulated by Hnf4 transcription factors to maintain the bioenergetic and biosynthetic needs of enterocytes. In the secretory lineage, OGDH is downregulated through a process that, when modeled, increases αKG levels and stimulates secretory cell differentiation. Consistent with this, in murine colitis models with impaired secretory cell number and maturation, OGDH inhibition or αKG supplementation reversed these impairments and promoted tissue healing. Hence, OGDH dependency is lineage-specific, and its regulation helps direct cell fate, offering insights for targeted therapies in regenerative medicine.

overall_design: RNA sequencing of murine isolated crypts from C57Bl/6 mice, treated or not with 500 mg/Kg of 2DG

first: Almudena

last: Chaves-Perez

first: Scott

last: Millman

first: Sudha

last: Janaki-Raman

first: Clemens

last: Hinterleitner

first: Valentin

last: A. Barthet

first: John

middle: P

last: Morris IV

first: Francisco

last: Barriga

first: Jose

last: Reyes

first: Aye

last: Kyaw

first: H. Amalia

last: Pasolli

first: Dana

last: Pe’er

first: Craig

last: Thompson

first: Lydia

last: S. Finley

first: Justin

middle: R

last: Cross

last: Lowe


title: Interplay between m6A modification and transcripts quantity:  Impacts on mRNA composition in plant stress granules

status: Public on Apr 08 2025

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

summary:
Stress granules (SGs) are cytoplasmic structures that emerge in response to unfavorable environmental conditions. The mechanisms governing the accumulation of transcripts in SGs are only partially understood. Despite the recognized role of m6A in plant transcriptome regulation, its impact on SGs' composition and assembly remains elusive. In L. angustifolius, SGs display a distinctive bi-zonal structure comprising of a ring and a central area with differences in ultrastructure and composition. Subsequent to the transcriptome analysis, specific mRNA were chosen for investigating their localization within SGs and assessing m6A levels. Transcripts of hypoxia-responsive genes (ADH1 and HUP7) showed significantly lower levels of m6A compared to housekeeping genes, but only ADH1 was absent in SGs. HUP7 mRNA, characterized by a low quantity of m6A, is present both in the SGs and cytoplasm, probably due to extremely high expression level. The high amount of m6A was observed only during the assembly of SGs. In mutants of A. thaliana with reduced levels of m6A, ECT2 was not observed in SGs, and poly(A) RNA levels and the number  of SGs were slightly reduced. In summary, our findings demonstrate a limited impact of m6A modification on SGs assembly. However, the interplay between m6A modification and the overall transcript quantity in the cytoplasm appears to play a regulatory role in mRNA partitioning and assembly of SGs
Funding sources that supported the collection of the data: Polish National Science Center, grant PRELUDIUM; 2022/45/N/NZ9/04015

overall_design: Gene expression profiling analysis using data obtained from RNA-seq of narrow-leafed lupin (L.angustifolius) roots grown under physiological conditions, 15-hour submergence, 15 hour submergence followed by 6 hour reoxygenation

first: Dawid

last: Kubiak

first: Michal

last: Szczesniak

first: Janusz

last: Niedojadlo


title: Metabolic adaptations direct cell fate during tissue regeneration [shOGDH_Mice_RNA-seq]

status: Public on Apr 02 2025

first: Yu-Jui

last: Ho

overall_design: RNA sequencing of murine isolated crypts at day 3 after induction of the indicated GFP-linked shRNAs with doxycycline. Two independent shRNAs targeting Ogdh (shOgdh346 and shOgdh2081) and a control shRNA (shRen713) were used.

first: Almudena

last: Chaves-Perez

first: Scott

last: Millman

last: Janaki-Raman

middle: M


title: Metabolic adaptations direct cell fate during tissue regeneration [Organoids_RNA-seq]

overall_design: RNA sequencing of organoids enriched for ISCs treated with 600 mg/ Kg of DM-aKG or doxycycline

first: Sudha

first: Clemens

last: Hinterleitner

first: Valentin

last: A. Barthet

last: Morris IV

last: Barriga


title: Metabolic adaptations direct cell fate during tissue regeneration [DMaKG_Mice_RNA-seq]

overall_design: RNA sequencing of murine isolated crypts from C57Bl/6 mice, treated or not with 600 mg/ Kg of DM-aKG.

first: John

first: Francisco

first: Jose

last: Reyes

last: Kyaw

last: Pasolli

last: Pe’er


title: In vitro pMos have similar gene expression profiles to their blood and bone marrow counterparts; In vitro BM-derived pMos in OP9-DLL1 cell cultures are distinct from classical BM-derived macrophages.

status: Public on Mar 24 2025

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

summary: Patrolling monocytes (pMos) scavenge debris from vessel walls and mediate antibody-dependent cellular phagocytosis, making them attractive cell therapy candidates for cancer, atherosclerosis, and Alzheimer’s disease. However, methods togenerate enhanced numbers of pMos are not available. To address this, we developed a two-step procedure to produce pMos in vitro from murine bone-marrow (BM). First, myeloid progenitors were expanded and enriched from BM using cytokines for four days. Second, expanded progenitors were differentiated into pMos on DLL1-expressing monolayers for eight days. We confirmed that in vitro grown pMos expressed the transcription factor Nr4a1 (Nur77) and other canonical pMos surface proteins, and depended on Notch signalling for their development. RNA sequencing revealed that in vitro pMos expressed hallmark pMos genes, including Cx3cr1, Itgax (CD11c), CD43, Fcgr4, and Cd274 (PD-L1), and their gene signatures clustered closely with in vivo blood and BM pMos. Transcriptomic and phenotypic analyses further demonstrated that in vitro pMos were distinct from classical BM macrophages. Phagocytosis assays demonstrated the function of in vitro pMos in cancer cell uptake. Adoptive transfer studies demonstrated that in vitro pMos persisted within the circulation and lung vasculature during the early post-transfer period compared with BM-derived macrophages, consistent with the vascular-patrolling properties of pMos. Adoptive transfer of pMos reduced lung tumour burden in a metastatic model, supporting an anti-tumoural role for pMos and their ability to mediate immune surveillance in vivo. These findings demonstrate that the DLL1 culture system allows for propagation of functional pMos, enabling studies of pMos biology and their therapeutic potential.

overall_design: RNA-seq study of mouse in vitro monocyte subsets (cMos, intMos, cMos) with 3 replicates per subset.

first: Jessica

last: Silva

first: Kenneth

last: Harder

first: Ashina

last: Nagra


title: Insulin-like growth factor 2 (IGF2) as a Foxn1-independent driving force of exponential expansion in neonatal thymus

status: Public on Mar 19 2025

city: Nashville

first: Qi

last: Liu

state: Tennessee

address: 2525 WEST END AVE

institute: Vanderbilt University Medical Center

summary: Like all organs, the thymus grows in size and function rapidly during development, which comes to a halt after birth. However, the molecular mechanisms behind such a transition in the thymus remain obscure. Using single-cell RNA sequencing (scRNA-seq) of the murine thymic stroma, we identified that major transcriptomic changes occur in the endothelium and mesenchyme across the transition to homeostasis. Differentially expressed gene and intercellular network analyses of temporally resolved scRNA-seq data revealed fibroblast-derived insulin-like growth factor 2 (IGF2) as a candidate driving neonatal thymic expansion. We demonstrated IGF2 activity promotes a cortical TEC-specific proliferation and is tightly regulated at the thymic growth transition. Bulk RNA-seq of human thymi across the transition also revealed IGF2 to drive thymic expansion, suggesting an evolutionarily conserved role. Our study highlights the role of a fibroblast-derived IGF2 in promoting cTEC proliferation, resulting in early thymic expansion that is followed by down-regulation to establish homeostasis.

overall_design: Bulk RNA sequencing was performed on thymus tissues from human donors aged 3 days to 14 years.

first: Kang

last: Seung Woo

first: Helm

last: Bryan R.

first: Wang

last: Yu

first: Liu

last: Qi

first: Lau

last: Ken S.

first: Richie

last: Ellen R.

first: Hale

last: Laura P.

first: Manley

last: Nancy R.


title: The complete molecular atlas of adult C. elegans glia across sexes

status: Public on Feb 21 2025

city: Seattle

first: Manu

last: Setty

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

summary: A comprehensive understanding of nervous system function requires molecular insight into the diversity and sex dimorphism of both its component cell types, glia and neurons. Here, we present a single-nuclear RNA sequencing (RNA-seq) census of all neuroectoderm-derived glia in the adult C. elegans nervous system, across sexes. By iteratively coupling computational modeling and custom analytics with in vivo validations, we uncovered molecular markers for all glia, as well as class-specific and pan-glial molecular signatures. These identified that each glia is functionally heterogeneous across the nervous system and variably sex dimorphic between sexes. Thus, this glial transcriptome (wormglia.org) offers deep mechanistic insights into glial biology brain wide. Complementing the existing C. elegans neuronal transcriptome and mapped connectome, it also enables single-cell and molecular resolution insight into the entire nervous system of an adult metazoan.

overall_design:
Single-nuclear RNA-seq of C. elegans glia from hermaphrodite and male animals with the pan-glial promoter PmiR-228 .  Worms were grown on 10 cm, standard 1% NGM agar plates seeded with E.coli strain OP50.  To obtain synchronized day 1 adult worms, we first obtained embryos by performing hypochlorite treatment (1M NaOH + 4% NaOCl freshly made) on adult hermaphrodites. The embryos hatched overnight (16-20 hours) on unseeded NGM agar plates and starved L1 arrested worms were recovered. All male data was acquired in him-5 mutant background. Single nuclei suspensions were obtained after lysing worms. The nuclei were sorted with a Sony SH800S cell sorter fitted with the 100µm nozzle running at a speed of 10-12k events per second using the PE filter set. For the hermaphrodite samples, age matched N2 worms were used as negative control to set FACS gates. For male samples, him-5 males were used as negative controls. The negative controls were taken through identical dissociation protocols. The nuclei were then loaded into a hemocytometer and counted to determine the final concentration. We targeted 10,000 cells per sample and used the 10X Chromium platform using 10X NextGem v3.1 chemistry. cDNA was amplified for 12 cycles and the index PCR was cycled 12 times. Final libraries were brought to 10 nM concentration and processed on an Illumina HiSeq2500 sequencer. Male and hermaphrodite samples were prepared and sequenced on different days, for a total of 2 biological replicates for hermaphrodites and 2 for males.

Please note that both raw and processed data for GSM8092237, GSM8092238 samples have been updated on Jun 25, 2025.

first: Maria

last: Purice

first: Elgene

last: Quitevis

first: R

middle: S

last: Manning

first: Liza

last: Severs

first: Nina-Tuyen

last: Tran

first: Violet

last: Sorrentino

first: Fienan

last: Wu

first: Aakanksha

last: Singhvi


title: Segment specific loss of NFAT5 function in the kidneys

status: Public on Feb 05 2025

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

institute: University Hospital Halle (Saale)

summary: Nuclear factor of activated T-cells 5 (NFAT5) is a transcription factor known for its role in osmotic stress adaptation in the renal inner medulla, due to osmotic gradient that is generated between renal cortex and renal inner medulla. However, its broader implications in kidney injury and chronic kidney disease (CKD) are less understood. Here we used two different Cre deleter mice (Ksp1.3-Cre and Aqp2-Cre) to generate tubule segment and even cell type specific NFAT5 deficient mice in the principal cells of the collecting duct (CD) and in the distal nephron starting in the TAL up to the CD and performed extensive gene expression profiling. In both Nfat5 knockout models, we observed massive changes in gene expression pattern, with heightened inflammatory responses and renal injury, culminating in renal fibrosis. Interestingly, inflammatory responses and fibrosis were much more prominent in the Aqp2Cre+/-Nfat5fl/fl mice that lack NFAT5 only in the collecting duct. By analyzing gene expression in the medullary and cortical regions of the kidney separately, we confirmed that the loss of NFAT5 results in kidney injury that extends beyond hypertonic areas. The correlation between the levels of inflammatory response, injury severity, and fibrosis indicates that cytokines are key mediators of stress signals in the kidney. Thus, NFAT5 is essential not only for adapting to osmotic stress but also for regulating cytokine signaling.

overall_design:
To explore the impact of spatial Nfat5-KO, we compared transcriptomic data from two different Nfat5-KO mouse models and distinguished between cortex and inner medulla. The first transgenic model involved a knockout driven by the Aqp2-promoter, causing Nfat5-KO in the principal cells of the collecting duct (CD). The second model used a knockout driven by the Ksp-promoter, leading to Nfat5-KO in the distal nephron starting in the TAL up to the CD.
We performed differentially expression analyses using data from RNA-seq of renal cortex (CTX) and inner medulla (IM) of control mice (4 from Aqp2-Cre+/-; 4 from  Nfat5fl/fl, 4 from WT) and 6 from the  in the distal nephron (TAL up to the CD) Nfat5-KO mice (KspCre+/-Nfat5fl/fl). The RNA-seq data from Nfat5-KO in the principal cells of the CD (Aqp2Cre+/-Nfat5fl/fl) and control (Aqp2-Cre+/-) were collected in a previous study (GSE195881).

first: Kristina

last: Engel

first: Vera

last: Kulow

first: Dmitry

last: Chernyakov

first: Edith

last: Willscher

first: Michael

last: Fähling


title: Transcriptional profiling of lungs from SARS-CoV-2-infected K18-hACE2 mice

status: Public on Feb 01 2025

city: Galveston

first: Shailendra

last: Chauhan

state: Texas

address: UTMB Health - Galveston Campus 301 University Boulevard

department: Pathology

institute: UTMB

summary: To explore the effects of SARS-CoV-2 proteins on expression of host genes in lung of infected mice, 4 groups of K18-hACE2 mice (4 mice per group) were mock-infected or infected cells with SARS-CoV-2 WT or its NPS1, or NSP15 mutants respectively.The mice were euthanized at  4 days post-infection to collect the lungs to isolate RNA for RNA sequencing.

overall_design:
4 groups of K18-hACE2 mice (4 mice per group) were mock-infected or infected cells with SARS-CoV-2 WT or its NPS1, or NSP15 mutants respectively.The mice were euthanized at  4 days post-infection to collect the lungs to isolate RNA for RNA sequencing.
L, R, N and RR were used to label the 4 different mice for each group. They are the animal IDs in the same cage.

first: Alexander

last: Bukreyev

first: Fuchun

last: Zhou


title: irCLIP-RNP reveals patterns of dynamic protein associations on RNA [RNA-seq]

status: Public on Jan 28 2025

first: Luca

last: Ducoli

summary: RNA binding proteins (RBPs) control varied processes, including RNA splicing, stability, transport, and translation. Dysfunctional RNA-RBP interactions contribute to the pathogenesis of human disease, however, characterizing the nature and dynamics of multiprotein assemblies on RNA has been challenging. To address this, non-isotopic ligation-based ultraviolet crosslinking immunoprecipitation was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with any RBP of interest. irCLIP-RNP defined landscapes of multimeric protein assemblies on RNA, uncovering previously unknown patterns of RBP-RNA associations, including cell-type-selective combinatorial relationships between RDAPs and primary RBPs. irCLIP-RNP also defined dynamic RDAP remodeling in response to epidermal growth factor (EGF), uncovering EGF-induced recruitment of UPF1 adjacent to HNRNPC to effect splicing surveillance of cell proliferation mRNAs. To identify the RNAs simultaneously co-bound by multiple studied RBPs, a sequential immunoprecipitation irCLIP (Re-CLIP) method was also developed. Re-CLIP confirmed binding relationships seen in irCLIP-RNP and identified HNRNPC and UPF1 RBP co-binding on RND3 and DDX3X mRNAs. irCLIP-RNP and Re-CLIP provide a framework to identify and characterize dynamic RNA-protein assemblies in living cells.

overall_design: RNA sequencing experiments  for the analysis of splicing , mRNA stability after the knockdown of HNRNPC and UPF1 as well as the effect EGF stimulation in A431 cells.

first: Leandra

middle: V

last: Jackrazi

first: Douglas

middle: F

last: Porter


title: High throughput sequencing of small cell lung cancer chemosensitive H69 and corresponding chemoresistant H69AR

city: Guangzhou

first: Qiong

last: Lyu

state: Guang Dong

address: 253 GongYe Road

department: Oncology

institute: Zhujiang Hospital, Southern Medical University

summary: Small cell lung cancer (SCLC) is the most aggressive subtype of lung cancer. Although most patients are initially sensitive to first-line chemotherapy with combined cisplatin and etoposide, chemotherapy drugs resistance easily develops and quickly leads to tumor progression. Therefore, understanding mechanisms of chemotherapy drugs resistance and how to reverse it is key to improving the prognosis of patients with SCLC. The parental SCLC cell lines H69 and corresponding doxorubicin-induced multidrug resistant variant (H69AR)  were used to explore the mechanism of chemoresistance in SCLC.

overall_design: RNA was extracted from SCLC cells (H69 and H69AR). The RNA quality was assessed with a Bioanalyzer 2100 DNA Chip 7500 (Agilent Technologies), and samples with an RNA integrity number (RIN) of over 7 were further analyzed by RNA-seq. All sequencing reactions were performed on an Illumina HiSeq 2000 instrument (Illumina, San Diego, CA, USA). We used HISAT2 (version 2.1.0) with the default setting to map the RNA-seq data to the human reference genome (NCBI38/hg38).We aggregated the read counts at the gene level using HTSeq.

first: Yueqin

last: Sun

first: Weitao

last: Shen

first: Shulu

last: Hu


title: CAR-T cell therapy for chronic kidney disease

status: Public on Jan 19 2025

city: Jinan

first: Fan

last: Yi

address: Wenhua Road

institute: Shandong University

summary: Kidney fibrosis is a hallmark of chronic kidney disease (CKD) and a potential therapeutic target. However, clinical interventions and therapies targeting kidney fibrosis remain conceptual and practical challenges due to the complex origin, functional heterogeneity and regulation of scar-forming cells. Here, we used single cell sequencing technology to identify cell-surface antigens that are broadly and specifically expressed at high levels in kidney cell types that produce extracellular matrix (ECM) during CKD, and study the therapeutic effect of CART therapy targeting the major ECM-producing cell types on kidney fibrosis, which provides a comprehensive treatment strategy for multi-organ fibrosis and its cardiovascular complications in CKD mice.

overall_design: Mouse kidney cells treated with CART cells and each control group were isolated, and single-cell sequencing was used to investigate the effects of CART therapy on renal fibrosis targeting primarily ECM-producing cell types


title: Transcriptional profiling of mammalian preimplantation embryos

city: München

first: Marlies

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: We developed an adapted version of Smart-seq2, which we call Smart-seq+5', to capture both internal transcript fragments, as well as 5' transcript information, in mammalian preimplantation stages on a single-embryo level. Focussing specifically on transposable elements, we find many conserved patterns and features shared between mouse, pig, cow, rabbit and rhesus.

sample_organism:
Macaca mulatta
Sus scrofa
Bos taurus
Oryctolagus cuniculus
Mus musculus

overall_design: Transcriptional profiling using an adapted version of the Smart-seq2 protocol during preimplantation stages of mouse, pig, cow, rabbit and rhesus

first: Diego

last: Rodriguez-Terrones

first: Maria-Elena

last: Torres-Padilla