title: Xenium In Situ Gene Expression of healthy and asthmatic lung endobronchial biopsies

first: Regis

last: Joulia

address: South Kensington, SAF 3rd floor

department: NHLI

institute: Imperial College

summary: We applied single-cell spatial transcriptomics (Xenium, 10X genomics) to reveal the lung wall landscape from healthy donors, patients with asthma undergoing anti-inflammatory therapies and historical clinical trial samples.

overall_design: We detected 106,304 cells across the 2 slides with 3,566,174 transcripts with a median of 31 and 15 transcripts per cell for the samples collected at Imperial College and KIA samples respectively. Samples were processed as recommended by the manufacturer protocol.

first: Régis

first: Clare

last: Lloyd


title: Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_RNA_without_blocking]

status: Public on Apr 10 2025

city: Heidelberg

first: Mikael

last: Marttinen

address: Meyerhofstraße 1

country: Germany

institute: EMBL

type: Expression profiling by high throughput sequencing

summary: Enhancers and transcription factors (TFs) are crucial in regulating cellular processes, including disease-associated cell states. Current technologies to study these elements in gene regulatory mechanisms lack multiplexing capability and scalability. Here, we present SUM-seq, a cost-effective, scalable Single-cell Ultra-high-throughput Multiomic sequencing method for co-assaying chromatin accessibility and gene expression in single nuclei - enabling experiments at the million cell and hundreds of samples scale. SUM-seq outperforms current high-throughput single cell methods in sensitivity. We applied SUM-seq to dissect the gene regulatory mechanisms governing macrophage polarization, and explored their link to traits from genome-wide association studies (GWAS). Our analyses confirmed known TFs orchestrating M1 and M2 macrophage programs, unveiled new regulators, and suggested extensive enhancer rewiring. Integration with GWAS data further pinpointed the impact of specific TFs on a set of immune traits. Notably, enhancers regulated by the STAT1/STAT2/IRF9 (ISGF3) complex were enriched for rheumatoid arthritis (RA)-associated genetic variants, with the strongest link pointing to the CD40 gene, an emerging drug target for RA. This highlights the potential of SUM-seq for dissecting molecular disease mechanisms. In summary, SUM-seq provides a simple workflow for cost-effective, scalable single-cell ultra-high-throughput multiomic sequencing. It is particularly adept at elucidating complex gene regulatory networks in cell differentiation, response to perturbations, and disease contexts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To optimise and evaluate performance and quality, we performed SUM-seq on an equal mixture of human leukemia (K562) and mouse fibroblast (NIH-3T3) cell lines

first: Sara

last: Lobato-Moreno

first: Umut

last: Yildiz

first: Annique

last: Claringbould

first: Nila

middle: H

last: Servas

first: Evi

middle: P

last: Vlachou

first: Christian

last: Arnold

first: Hanke

middle: G

last: Bauersachs

first: Victor

last: Campos-Fornés

first: Karin

middle: D

last: Prummel

first: Kyung

middle: M

last: Noh

first: Judith

last: Zaugg


title: Investigate the functions of core pluripotency transcription factors in embryonic stem cells

status: Public on Apr 08 2025

city: Nanjing

first: Bowen

last: Wang

address: 12 Xue-fu Road, Pukou District

country: China

institute: Nanjing University

summary: Purpose: The goals of this study are to compare control and Sox2-deficient embryonic stem cells transcriptome profiling (RNA-seq) to evaluate the target genes regulated by Sox2.

overall_design: mRNA profiles of Sox2F/F and Sox2-/- embryonic stem cells were generated by deep sequencing, in triplicate, using Illumina Novaseq6000.

first: Jinzhong

last: Qin


title: Understanding and reversing mammary tumour-driven reprogramming of myelopoieisis to reduce metastatic spread [scRNA-seq]

city: Amsterdam

first: Elzo

last: de Wit

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Tumour-induced systemic accumulation and polarisation of neutrophils to an immunosuppressive phenotype is a potent driver of metastasis formation. Yet how mammary tumours reprogram granulopoiesis at the molecular level and when tumour imprinting occurs during neutrophil development remains underexplored. Here we combined single cell, chromatin and functional analyses to unravel the tumour-driven reprogramming of granulopoiesis, along with intervention studies aimed at reversing this process. We observe that mammary tumours accelerate commitment to the neutrophil lineage at the expense of lymphopoiesis and erythropoiesis without stimulating the development of a novel myeloid lineage. Moreover, tumour-directed immunosuppressive imprinting of neutrophils starts early in haematopoiesis. Treatment with anti-IL-1β normalised tumour-induced granulopoiesis, reduced neutrophil production of T cell suppressive superoxides and mitigated metastatic spread. Together, these data provide molecular insights into the aberrant tumour-driven neutrophil differentiation pathway leading to metastasis-promoting chronic inflammation and how it can be reversed to reduce metastatic spread.

overall_design: Single-cell RNA sequencing of CD34+/cKIT+ hematopoietic stem and progenitor cells from bone marrows of wild-type (WT) and K14cre;Cdh1F/F;Trp53F/F tumour-bearing mice (KEP).

first: Hannah

last: Garner

first: Moreno

last: Martinovic

last: de Visser


title: Understanding and reversing mammary tumour-driven reprogramming of myelopoieisis to reduce metastatic spread

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: CHD7 marks TAD boundaries during neuronal differentiation [Cut & Tag]

status: Public on Apr 07 2025

city: Piscataway

first: Kelvin

middle: Y.

last: Kwan

state: NJ

address: 604 Allison Rd.

department: Cell Biology & Neuroscience

country: USA

institute: Rutgers University

summary: The chromodomain helicase DNA binding protein 7 (CHD7) is a nucleosome repositioner implicated in multiple cellular processes, including neuronal differentiation. We identified CHD7 marked sites at TAD boundaries that regulate neuronal differentiation in an otic stem cell line.  We showed that CHD7 co-occupied CTCF sites genome-wide. We identified CTCF+ CHD7+ sites near an essential transcription factor, Sox11, required for otic neuronal differentiation. The Sox11 promoter and  3’ untranslated region (UTR) showed CHD7 enrichment.  The CHD7-marked sites at the 3’UTR displayed histone marks corresponding to active transcription that resulted in Sox11 antisense transcripts.  Blocking the singular CHD7-marked site with CRISPRi decreased neurite lengths, reduced neuronal marker expression (TUBB3), and attenuated Sox11 antisense transcripts. Sox11 antisense transcripts were previously suggested to form double-stranded RNA and degrade the Sox11 transcript. Surprisingly, the level of the Sox11 sense transcripts remained unaffected after CRISPRi.  We propose that CHD7 at TAD boundaries modulate the chromatin accessibility of CTCF-marked insulators, altering the 3D chromatin organization and ultimately affecting gene expression. Our results implicate a general mechanism of CHD7 in facilitating neuronal differentiation and provide insight into CHD7 dysfunction in CHARGE syndrome, an intellectual developmental disability disorder.

overall_design: CUT&Tag for CHD7, H3K4me3, p300, CTCF, H3K36me3, and IgG control from proliferating iMOPs (immortablized multipotent otic progenitors) and iMOP-derived neurons.

first: Edward

last: Martinez

first: Azadeh

last: Jadali

first: Jingyun

last: Qiu

first: Anna-Marie

last: Hinman

first: Zhouli

last: Ni

first: Jihyun

last: Kim

middle: Y


title: Stage-specific phenotypic and transcriptional alterations in HaCaT keratinocytes exposed to acute and chronic blue light

city: Lübeck

first: Leonardo

last: de Assis

address: Marie Curie

institute: University of Lübeck

summary: Despite evidence that visible light (VL) has similar effects on human skin as those of UVA, VL is often viewed as harmless. High SPF sunscreen prevents erythema but can lead to overexposure to UVA and VL, with unknown consequences. To explore the impact of chronic blue light exposure, we irradiated (50 J/cm², λ= 408 nm, three times a week) human immortalized keratinocytes under acute (3 irradiations), intermediate (14 irradiations), and chronic (42 irradiations) blue-light exposure, monitoring phenotypic and gene expression changes. Chronically exposed keratinocytes exhibit increased nuclei area, chromatin alterations, higher proliferation, and apoptosis resistance, mirroring the consequences of chronic UVA exposure. While acute exposure upregulated keratinization and downregulated tissue repair and apoptosis genes, chronically exposed cells had upregulated genes involved with energy metabolism and oxidative phosphorylation and downregulated genes were enriched for immune and inflammatory responses. Specific transcription factors were identified in both the acute and chronic stages, some of which have been associated with UVB exposure. In the acute stage, IRF1, EGR1, ELF3, and FOSL1 were noted, while in the chronic stage, CENPX, SRF, CEBPB, and KLF4 were identified. We identified some changes in chronically irradiated keratinocytes similar to the malignant transformation, emphasizing the need for further research on the long-term impacts of blue light exposure on human skin.

overall_design: HaCaT cells (5 x 10⁵ cells per 100 mm plate) were exposed to a blue light LED source (λ = 408 nm, irradiance = 4.6 mW.cm-2) developed by the Optics and Photonics Research Center at the Institute of Physics, University of São Paulo. The cells were irradiated in phosphate-buffered saline at an irradiation of 50 J/cm² three times a week for up to 14 weeks. Light dose was constant through the experiment and chosen to provide 50% cell death in HaCaT cells. After each irradiation, the culture medium was reintroduced until the next session. Cells were passaged every 3-5 days.

first: Paulo

last: Tonolli

first: Suely

last: Marie

first: Sueli

last: Oba-Shinjo

first: Maurício

last: Baptista


title: The mouse model with Foxg1 frameshift mutation uncovers the pathophysiology of FOXG1 syndrome

city: Buffalo

first: Soo-Kyung

last: Lee

state: NY

address: 109 Cooke Hall, University at Buffalo, North Campus

department: Biological Sciences

institute: University at Buffalo

summary: To investigate the gene expression patterns in Foxg1 frameshift mutation, we performed RNAseq in P1 cortices of Q84Pfs heterozygote and littermate wild type control mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse cortices in wt and FoxG1 KI mutant Q84Pfs.

first: Shin

last: Jeon

first: Jaein

last: Park

first: Ji Hwan

last: Moon

first: Jae

middle: W


title: Understanding and reversing mammary tumour-driven reprogramming of myelopoieisis to reduce metastatic spread [ATAC-seq]

first: Elzo

last: de Wit

overall_design: Bulk ATAC sequencing of sorted cell types within the neutrophil differentiation trajectory (LT-HSCs, MPPs, CMPs, GMPs, pre-neutrophils, immature neutrophils and mature neutrophils) from bone marrows of wild-type (WT) and K14cre;Cdh1F/F;Trp53F/F tumour-bearing mice (KEP) treated with either control antibody or anti-IL-1β.

first: Hannah

last: Garner

first: Moreno

last: Martinovic

first: Ning

middle: Q

last: Liu

first: Karin

last: de Visser


title: Heterochromatin de novo formation and maintenance in Plasmodium falciparum

city: Barcelona

first: Alba

last: Pérez-Cantero

state: Barcelona

address: Rosselló, 153

country: Spain

institute: Barcelona Institute for Global Health (ISGlobal)

summary: In the malaria parasite Plasmodium falciparum, the expression of many genes is regulated by heterochromatin (HC) based on the histone mark tri-methylation of histone H3 lysine 9 (H3K9me3). HC assembly involves three distinct steps: de novo nucleation, spreading and maintenance. Nucleation, which consists in formation of HC in a previously euchromatic region, determines at which specific regions of the genome HC occurs, but this process is not well understood in malaria parasites. Here we investigated the DNA sequence cis determinants of HC nucleation in P. falciparum, using a screening approach based on integration of fragments from different heterochromatic genes into an euchromatic locus, followed by chromatin immunoprecipitation (ChIP). We found that fragments of var gene upstream regions nucleated HC efficiently, whereas fragments from the pfap2-g upstream region or from the mspdbl2 locus did not nucleate HC. Fragments from the beginning of the coding sequence (CDS) of pfap2-g nucleated HC with low efficiency, as evidenced by nucleation requiring long fragments of ~2 kb and occurring only in a fraction of the parasites. These results demonstrate that the primary DNA sequence is a main determinant of HC nucleation in P. falciparum. We also studied HC maintenance at the pfap2-g locus, which demonstrated that specific parts of the upstream region, different from the regions competent for HC nucleation, are required for maintenance. Together, our results provide initial insight into how HC is directed to specific loci and maintained in P. falciparum.

overall_design: ChIP-seq of the histone modification H3K9me3 or H3K9ac in different Plasmodium falciparum strains and transgenic lines at the trophozoite/schizont stage

first: Oriol

last: Llorà-Batlle

first: Ingrid

last: Pelaez-Conde

first: César

last: Martínez-Guardiola

first: Alfred

last: Cortés


title: Understanding and reversing mammary tumour-driven reprogramming of myelopoieisis to reduce metastatic spread [bulk RNA-seq]

overall_design: Bulk RNA sequencing of sorted cell types within the neutrophil differentiation trajectory (LT-HSCs, MPPs, CMPs, GMPs, pre-neutrophils, immature neutrophils and mature neutrophils) from bone marrows of wild-type (WT) and K14cre;Cdh1F/F;Trp53F/F tumour-bearing mice (KEP) treated with either control antibody or anti-IL-1β, as well as cKit- neutrophils from blood and lung tissues of untreated WT and KEP mice.


title: B cell receptor sequences from germinal center (-like) B cells and plasmablasts from inflamed lung and lung-draining lymph node

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

summary: Germinal center (GC) like B cells can be generated in unstructured non-ectopic T and B cell infiltrates in the in inflamed lung. We used heavy chain B cell receptor (BCR) RNA sequencing to compare antigen-specific B cells from lung to those from the lung-draining lymph node.

overall_design: Antigen-specific B cells from B1-8i and T cells from Smarta mice were adoptively transferred into C57BL/6 recipients, which were repeatedly challenged intranasally with cognate antigen and LPS. On day 18, cells from lung (enzymatically digested) and the tracheal lymph node (Ln) were isolated and further purified for antigen-specific germinal center (like) B cells and plasmablasts.

first: Andreas

last: Hutloff

first: Laura

last: Bauer

first: Annette

last: Siracusa

first: Pawel

last: Durek

first: Mir-Farzin

last: Mashreghi


title: Chromogranin A (CgA) Deficiency Attenuates Tauopathy by Altering Epinephrine–Alpha-Adrenergic Receptor Signaling

city: La Jolla

first: Shandy

last: Shahabi

state: CA

address: 9500 Gilman Dr

department: Chemistry

institute: UCSD

summary: Our previous studies have indicated that insulin resistance, hyperglycemia, and hypertension in aged wild-type (WT) mice can be reversed in mice lacking chromogranin-A (CgA-KO mice). These health conditions are associated with a higher risk of Alzheimer’s disease (AD). CgA, a neuroendocrine secretory protein has been detected in protein aggregates in the brains of AD patients. Here, we determined the role of CgA in tauopathies, including AD (secondary tauopathy) and corticobasal degeneration (CBD, primary tauopathy). We found elevated levels of CgA in both AD and CBD brains, which were positively correlated with increased phosphorylated tau in the frontal cortex. Furthermore, CgA ablation in a human P301S tau (hTau) transgenic mice (CgA-KO/hTau) exhibited reduced tau aggregation, resistance to tau spreading, and an extended lifespan, coupled with improved cognitive function. Transcriptomic analysis of mice cortices highlighted altered levels of alpha-adrenergic receptors (Adra) in hTau mice compared to WT mice, akin to AD patients. Since CgA regulates the release of the Adra ligands epinephrine (EPI) and norepinephrine (NE), we determined their levels and found elevated EPI levels in the cortices of hTau mice, AD and CBD patients. CgA-KO/hTau mice exhibited reversal of EPI levels in the cortex and the expression of several affected genes, including Adra1 and 2, nearly returning them to WT levels. Treatment of hippocampal slice cultures with EPI or an Adra1 agonist intensified, while an Adra1 antagonist inhibited, tau hyperphosphorylation and aggregation. These findings reveal a critical role of CgA in regulation of tau pathogenesis via the EPI-Adra signaling axis.

overall_design: Comparative gene expression profiling of WT, hTau, and CgA-KO/hTau mouse prefrontal cortex tissue by high throughput sequencing.

first: Suborno

last: Jati

first: Matthew

last: Munoz-Mayorga

first: Kechun

last: Tang

first: Yuren

last: Tao

first: Dennis

last: Dickson

first: Irene

last: Litvan

first: Gourisankar

last: Ghosh

first: Sushil

middle: K

last: Mahata

first: Xu

last: Chen


title: Duplication of autism-related gene Chd8 leads to behavioral hyperactivity and neurodevelopmental defects in mice [cortex]

status: Public on Apr 05 2025

city: Kanazawa

first: Atsuki

last: Kawamura

state: Ishikawa

address: 13-1 Takaramachi

department: Department of Histology and Cell Biology

country: Japan

institute: Graduate School of Medical Sciences, Kanazawa University

summary: Mutations in the gene encoding the chromodomain helicase DNA-binding protein 8 (CHD8) are strongly associated with autism spectrum disorder (ASD). Although duplications of the locus spanning CHD8 are also found in individuals with neurodevelopmental disorders, the role of CHD8 duplication in clinical phenotypes and the underlying mechanisms have remained unknown. Here we show that mice with Chd8 overexpression modeling human CHD8 duplication manifest growth retardation, microcephaly, and behavioral abnormalities including hyperactivity and reduced anxiety-like behavior. Chd8 overexpression results in alterations of transcription and chromatin accessibility of genes involved in neurogenesis that are associated with aberrant binding of CHD8 to enhancer regions and impairs differentiation of deep-layer neurons. Furthermore, genetic and pharmacological interventions rescue hyperactive behavior of Chd8 overexpression mice. Our results thus indicate that Chd8 overexpression mice recapitulate key features of CHD8 duplication syndrome, and they provide insight into cellular and molecular pathogenesis underlying neurodevelopmental disorders.

overall_design: RNA-seq analysis in the cortex from mice at 8 weeks of age (quintuplicate; Chd8 WT vs. KI)


title: Metabolic and proteomic profiling identifies stress response and impaired neural stem cell functions associated with sleep restriction in women

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Adequate sleep (AS) is essential for maintaining many behavioral and physiological functions; however, a third of adults in the United States sleep less than the recommended 7-9 h/night. The circadian rhythm controls tissue homeostasis, in part, through adult stem cell functions. However, little is known about the mechanistic interactions between insufficient sleep and stem cell functions. Using plasma collected from healthy women with adequate habitual sleep duration (7-9 h/night) who were randomized in a crossover design to a 6-week objectively monitored AS or mildly restricted sleep (RS; 1.5 h less than their AS), we identified metabolites and proteins differentially enriched after RS compared to AS. RS induced a stress-like state dominated by the ATF6 interactome, heat shock, and ubiquitination proteins. Joint network pathway analysis highlights a strong link between RS and neuronal development phenotypes. Using neural stem cells (NSCs) differentiated from human embryonic stem cells, we found treatment with metabolic candidates enriched in restricted sleep led to aberrant G1 phase of the cell cycle and defective differentiation of NSCs into neurons, astrocytes, and oligodendrocytes. Thus, restricted sleep that mimics “life-like” conditions can influence the daily dynamics of NSC divisions and differentiation, shedding light on how sleep can shape adult stem cell functions in neural development.

overall_design: RNA-seq of untreated and  glutamic acid or methionine treated FUCCI-hNSCs for 30 days in neural expansion medium.

first: Vikas

last: Malik

first: Xin

last: Huang


title: FOXC2 pH-dependent genome wide binding profile

status: Public on Apr 04 2025

city: San Francisco

first: Kyle

last: Kisor

address: 505 parnassus Ave

institute: UC San Francisco

summary: Intracellular pH (pHi) dynamics regulates diverse cell processes such as proliferation, dysplasia, and differentiation, often mediated by the protonation state of a functionally critical histidine residue in endogenous pH sensing proteins. How pHi dynamics can directly regulate gene expression and whether transcription factors can function as pH sensors has received limited attention. We tested the prediction that transcription factors with a histidine in their DNA binding domain (DBD) that forms hydrogen bonds with nucleotides can have pH-regulated activity, which is relevant to more than 85 transcription factors in distinct families, including FOX, KLF, SOX and MITF/Myc. Focusing on FOX family transcription factors, we used unbiased SELEX-seq to identify pH-dependent DNA binding motif preferences, then confirm pH-regulated binding affinities for FOXC2, FOXM1, and FOXN1 to a canonical FkhP DNA motif that are 2.5 to 7.5 greater at pH 7.0 compared with pH 7.5. For FOXC2, we also find greater activity for an FkhP motif at lower pHi in cells and that pH-regulated binding and activity are dependent on a conserved histidine (His122) in the DBD. RNA-seq with FOXC2 also reveals pH-dependent differences in enriched promoter motifs. Our findings identify pH-regulated transcription factor-DNA binding selectivity with relevance to how pHi dynamics can regulate gene expression for myriad cell behaviours.

overall_design: To investigate which genomic loci FOXC2 binds pH-dependently we established control (high pH) and clonal NHE1-KO (low pH) MDA-MB-436 cells. Next, we fixed, sheared, and immunoprecipitated FLAG-FOXC2 transfected in both control and NHE1-KO cells. Library design, seqeuncing, and peak calling was performed by Azenta. Peaks in each condition were analyzed for differences in binding motifs.

first: Diego

last: Ruiz

last: Jacobson

first: Diane

last: Barber


title: Duplication of autism-related gene Chd8 leads to behavioral hyperactivity and neurodevelopmental defects in mice

overall_design: RNA-seq analysis in the forebrain from mice at E14.5 and E18.5 (quintuplicate; Chd8 WT vs. KI), ChIP-seq analysis with antibody to CHD8 in the forebrain from mice at E14.5 (triplicate; Chd8 WT vs. KI), ATAC-seq analysis in the forebrain from mice at E14.5 (quadruplicate; Chd8 WT vs. KI).


title: IL-7-mediated expansion of autologous lymphocytes increases CD8+ T Cell VLA-4 expression and accumulation within glioblastoma

status: Public on Apr 03 2025

city: Durham

first: Kirit

last: Singh

state: NC

address: Room 215, Sands Building, 303 Research Drive

department: Biomedical Engineering

institute: Duke University

summary: The efficacy of T cell-activating therapies against glioma is limited by an immunosuppressive tumor microenvironment and tumor-induced T cell sequestration. We investigated whether peripherally infused non-antigen specific autologous lymphocytes (ALT) could accumulate in intracranial tumors. We observed that non-specific autologous CD8+ ALT cells can indeed accumulate in this context, despite endogenous T cell sequestration in bone marrow. Rates of intratumoral accumulation were significantly increased when expanding lymphocytes with IL-7 compared to IL-2. Pre-treatment with IL-7 ALT also enhanced the efficacy of multiple tumor-specific and non-tumor-specific T cell-dependent immunotherapies against orthotopic murine and human xenograft gliomas. Mechanistically, we detected increased VLA-4 on mouse and human CD8+ T cells following IL-7 expansion, with increased transcription of genes associated with migratory integrin expression (CD9). We also observed that IL-7 increases S1PR1 transcription in human CD8+ T cells, which we have shown to be protective against tumor-induced T cell sequestration. These observations demonstrate that expansion with IL-7 enhances the capacity of ALT to accumulate within intracranial tumors, and that pre-treatment with IL-7 ALT can boost the efficacy of subsequent T cell-activating therapies against glioma. Our findings will inform the development of future clinical trials where ALT pre-treatment can be combined with T cell-activating therapies.

overall_design:
To evaluate IL-7’s effect on migratory integrin expression, we performed bulk RNA sequencing using  glioblastoma donor hPBMC samples. CD8+ T cells were sorted from naïve (pre-expansion), IL-2-expanded, or IL-7-expanded products.

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Processed individual files are included within this repository per Duke IRB institutional certification requirements.
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first: Kelly

last: Hotchkiss

first: Sarah

middle: L

last: Cook

first: Pamy

last: Noldner

first: Ying

last: Zhou

first: Eliese

last: Moelker

first: Chelsea

middle: O

last: Railton

first: Emily

middle: E

last: Blandford

first: Bhairavy

middle: J

last: Puviindran

first: Shannon

last: Wallace

first: Pamela

last: Norberg

first: Gary

last: Archer

first: Beth

last: Shaz

first: Katayoun

last: Ayasoufi

first: John

last: Sampson

first: Mustafa

last: Khasraw

first: Peter

last: Fecci


title: Peritoneal tumor spread in serous ovarian cancer-epithelial mesenchymal status and outcome

city: Vienna

first: Dietmar

last: Pils

address: Spitalgasse 23

department: Dept. of General Surgery

country: Austria

institute: Medical Univ. of Vienna

summary: In this study we aimed to analyze the biological mechanisms underlying apparently different modes of peritoneal tumor spread in serous ovarian cancer: miliary (widespread, millet-like lesions) versus non-miliary (bigger, exophytically growing implants). Tumor tissues and ascites from 23 chemotherapy naive patients were analyzed by RNA-sequencing and flow cytometry. On the basis of differential gene expression between miliary and non-miliary, gene signatures were developed. A calculated tumor spread factor revealed a significant independent negative impact of miliary spread on overall survival (HR 3.77; CI95 1.14–12.39; p = 0.029) in an independent cohort of 165 serous ovarian cancer patients. Comparing previously published epithelial-mesenchymal transition (EMT) gene signatures, non-miliary spread correlated significantly with a reduced epithelial status. We conclude that serous ovarian cancer is a heterogeneous disease with distinct modes of peritoneal tumor spread, differing not only in clinical appearance, but also in molecular characteristics and outcome. EMT, peritoneal inflammation status, and therapeutic options are discussed. Significance: More than half of serous epithelial ovarian cancer patients present with a newly described type of intraperitoneal tumor spread, associated with differences in the inflammation status, activated oncogenic pathways, lack of EMT, and thus reduced overall survival. Both, the diminished immune reaction and the enhanced epithelial and malignant characteristics of the tumor cells open new avenues for therapeutic options and strategies, like Catumaxomab, already in clinical use.

overall_design: From 42 EpCAM-enriched tumor cells of High-Grade Serous Ovarian cancer patients total RNA was isolated and RNA-sequencing performed.


title: Androgens inhibit protective CD8+ T cell responses against pre-erythrocytic malaria parasites

city: Seattle

first: Sean

middle: C

last: Murphy

state: WA

address: 750 Republican St

institute: University of Washington

summary: Attenuated whole organism vaccines targeting the malaria liver stage reliably confer sterile immunity. These vaccines can completely protect female mice from infection, but protection in male mice remains unproven. We discovered that male BALB/cJ mice vaccinated with prime-and-trap, a whole organism-based vaccine strategy, exhibit poorer protection against Plasmodium yoelii sporozoite challenge than females. We investigated this sex difference, and identified vaccinated males have fewer hepatic memory CD8+ T cells than females when scaling for differences in liver biomass, and reduced acute inflammatory responses post-vaccination. Surgical hormone manipulation clarified that the presence of testicular hormones, not the absence of ovarian hormones, hindered protection in male mice. The presence of androgens did not affect memory CD8+ T cells quantity nor quality of, but inhibited protective cellular responses during sporozoite challenge. Thus, both males and females form functional memory responses following prime-and-trap vaccination, but androgens during sporozoite challenge impair protection in male mice.

overall_design: To evaluate the impact of biological sex on response to prime-and-trap vaccination, we conducted bulk RNAseq on whole livers of BALB/cJ male and female mice at two time point (44 hours and 6 days) post-immunization. Each group contain n=4 mice and two immunization conditions were considered (prime-and-trap, and RAS only)

first: Caroline

last: Duncombe


title: Transcriptomic insights into fate choice of pallial versus subpallial GABAergic neurons

first: Zhao

last: Chunjie

state: Jiangsu

address: Hunan Road Street

department: School of Medicine

institute: Southeast University

summary: The connectivity, activity, and plasticity of the telencephalon are shaped by pallial and subpallial GABAergic neurons, two large populations that are produced in the embryonic medial, caudal and lateral ganglionic eminences in a highly complicated manner. Dysregulated development of GABAergic neurons is associated with neuropsychiatric disorders. However, knowledge about the specification of GABAergic neuron subtypes is limited. Here, using single-cell RNA sequencing combined with loss-of-function we delineated developmental trajectories and revealed transcriptional programs that specify GABAergic neuron subtypes in each GE lineage and transcription factors that direct lineage bifurcation decisions. Our study illuminates the control of production between pallial and subpallial populations and offers transcriptomic insights into the pathogenesis of GABAergic neuron-related disorders.

overall_design: The CUT&Tag assay was performed using E16.5 GEs dissected from Dlx5/6-Cre;Foxg1 cKO mice and a FOXG1 rabbit polyclonal antibody. The sample was referred to as Foxg1 cKO.

first: Chunjie

last: Zhao

first: Lijuan

last: Sun

first: Pengfei

last: Jiang


title: Arachidonic acid triggers spermidine synthase secretion from primary tumor to induce skeletal muscle weakness upon irradiation

city: Wuhan

first: Xiaohui

last: Zhang

address: Bayi Road, Wuchang District

institute: Wuhan University

summary: Radiotherapy (RT) reduces the risk of cancer recurrence and death, while accompanied by multiple side effects including muscle weakness, seriously affects the life quality of patients. However, the underlying mechanism is not well defined. Here, we identify cancer cells secrete more spermidine synthase (SRM) protein through small extracellular vesicles (sEVs) to trigger skeletal muscle weakness upon RT. Mechanistically, RT-triggered arachidonic acid (ArA) accumulation elevates the ISGylation of SRM protein, facilitating SRM package into EVs from primary tumor. Circulating SRM proteins enhance spermidine accumulation in skeletal muscle and type I collagen fibers biosynthesis in an eIF5A-dependent manner. Deposition of randomly aligned collogen fibers induced by SRM+ EVs results in skeletal muscle fibrosis and weakness, as well as bone matrix loss. However, losartan treatment blocks the ISGylation of SRM and its subsequent secretion. Collectively, our findings determine that ArA functions in concert for circulating SRM secretion upon RT, which aggravates skeletal muscle fibrosis through rewiring polyamine metabolism, shedding light on the alleviation of RT-mediated muscle weakness when combined with losartan treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ArA-treated and non-treated MDA-MB-231 cells

first: Wei

last: Yan


title: Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [PRO-Seq]

city: Boston

first: Alexis

last: Caulier

state: Massachusetts

address: 1 Blackfan street

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: We developed a strategy to couple highly-efficient pooled CRISPR-mediated perturbation of key master hematopoietic transcription factors in differentiating primary human hematopoietic cells with joint single-cell gene expression and chromatin accessibility profiling to enable the reconstruction of transcription factor-dependent gene regulatory networks throughout primary hematopoietic differentiation.

overall_design: CRISPR/Cas9-mediated editing of AAVS1 or GATA1 locus in primary erythroblasts at day 8 of differentiation. 24h after editing, cells underwent precision nuclear run-on (PRO-seq).

first: Jorge

last: Martin-Rufino

first: Vijay

last: Sankaran

first: Seth

middle: R

last: Goldman

first: Marcus

last: Jones


title: Transcriptomic insights into fate choice of pallial versus subpallial GABAergic neurons (scRNA-Seq)

overall_design: We conducted scRNA-seq of 20640 cells sampled from the ganglionic eminences of Foxg1fl/fl and Dlx5/6-Cre-IRES-EGFP; Foxg1fl/fl mice at E16.5


title: High-Fat Diet-Induced Liver-Gut Crosstalk Suppresses Autophagy and Exacerbates Colitis [liver]

city: Beijing

first: Tian

last: Xu

state: Beijing

address: No.1 Shuaifuyuan, Dongcheng District, Beijing,China

institute: Peking Union Medical College Hospital

summary: The goal of this project is to investigate the mechanisms through which high fat diet (HFD) exacerbates colitis via the liver-gut axis, particularly focusing on liver dysregulated lipid metabolism and intestinal autophagy. We examined liver transcriptomes of C57BL6/J mice fed a control diet (CD) or HFD with or without dextran sulfate sodium (DSS) by RNA seq analysis.

overall_design: The liver mRNA profile of DSS-induced mice  treated with CD and HFD by RNA sequencing.


title: Cancer cell-secreted spermidine synthase induces skeletal muscle fibrosis upon radiotherapy (Gastrocnemius muscle KD)

summary: Radiotherapy (RT) reduces the risk of cancer recurrence and death, while accompanied by multiple side effects including muscle fibrosis and weakness, seriously affects the life quality of patients. However, the underlying mechanism is poorly defined. Here, we identify cancer cells secrete more spermidine synthase (SRM) enzyme through small extracellular vesicles (sEVs) to trigger skeletal muscle weakness upon RT. Mechanistically, RT-triggered arachidonic acid (ArA) accumulation elevates the ISGylation of SRM protein, facilitating SRM packaging into EVs from primary tumor. Circulating SRM results in spermidine accumulation in skeletal muscle and type I collagen fiber biosynthesis in an eIF5A-dependent manner. However, losartan treatment blocks the ISGylation of SRM and its subsequent secretion. Collectively, our findings determine that ArA functions in concert for circulating SRM secretion upon RT, which aggravates skeletal muscle fibrosis through rewiring polyamine metabolism, shedding light on the alleviation of RT-mediated muscle weakness when combined with losartan treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for gastrocnemius muscle (GA) of radiotherapy-treated and non-treated mice bearing MDA-MB-231/Rab27a KD xenograft tumors.


title: Lung germinal center like B-cells

first: Frederik

last: Heinrich

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

overall_design: Refer to individual Series


title: Cancer cell-secreted spermidine synthase induces skeletal muscle fibrosis upon radiotherapy (MDA-MB-231)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RT-treated and non-treated MDA-MB-231 cells


title: USP2 inhibition overcomes CD47-mediated phagocytosis suppression and enhances anti-tumor immunity.

first: panpan

last: Dai

address: 115 Donghu Road, Wuhan, China

summary: USP2 inhibition by ML364 treatment significantlly suppressed tumor growth. We aim to investigate the impact of ML364 treatment on the immune microenvironment of tumor-bearing mice by single-cell sequencing.

overall_design: The subcutaneous LLC tumors from mice treated with ML364 or the control were dissociated into single-cell suspensions, which were then subjected to single-cell sequencing.


title: Cancer cell-secreted spermidine synthase induces skeletal muscle fibrosis upon radiotherapy (Gastrocnemius muscle)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for gastrocnemius muscle (GA) of radiotherapy-treated and non-treated mice bearing MDA-MB-231 xenograft tumors.


title: A Non-Genotoxic Stem Cell Therapy Boosts Lymphopoiesis and Averts Age-Related Blood Diseases in Mice

city: Lund

first: Anna

last: Konturek-Ciesla

state: Skane

address: Klinikgatan 26, BMC B12

department: Laboratory Medicine

country: Sweden

institute: Lund University

summary: Hematopoietic stem cell (HSC) transplantation can potentially cure various blood disorders, which are especially prevalent among the elderly. However, the high toxicity of conventional conditioning often makes elderly patients ineligible for this treatment. In response, we developed and tested low-intensity conditioning protocols based on antibody-mediated HSC depletion in a murine transplantation model. Initially, we identified significant age-related impediments to effective HSC engraftment. By optimizing HSC doses and a combination of non-toxic targeting methods, we significantly enhanced the long-term multilineage activity of the transplanted cells. We demonstrated that young donor HSCs, once transplanted, not only survive but thrive in aged hosts, dramatically improving hematopoietic output and correcting defective lymphopoiesis. This culminated in a strategy that robustly mitigated disease progression in a genetic model of myelodysplastic syndrome. These results suggest that non-invasive HSC transplantation strategies could fundamentally change the clinical management of age-associated hematological disorders, offering a novel, prophylactic tool to delay or even prevent their onset in elderly patients.

overall_design: This study examined how aging bone marrow (BM) environment affects the molecular profiles of lymphoid associated multipotent progenitor (MPP Ly) cells. To this end, we established chimeric animals by transplanting young ex vivo expanded HSCs into young (3 months) and aged (16 months) recipients conditioned with G-CSF/AMD3100. After 20 weeks, mice were additionally treated with CD45.2-saporin to deplete host BM cells. Each experimental group comprised four biological replicates. After 16 weeks of treatment with CD45.2-saporin, 200 donor (young) and host (young or aged) MPP Ly cells were isolated by FACS from each recipient and subjected to bulk transcriptome profiling. Cell isolation was performed in two batches, with each batch containing samples from both young and aged recipients.

first: Qinyu

first: Shabnam

last: Kharazi

first: David

last: Bryder


title: Heat stress response in the cave nectar bat Eonycteris spelaea differs from that of Mus musculus

status: Public on Apr 02 2025

city: Singapore

first: Leon Jia Wei

last: Tang

address: 21 Lower Kent Ridge Rd

country: Singapore

institute: National University of Singapore

summary: Bats as the only flying mammals incur a high metabolic cost during extended powered flight, which results in febrile-like temperatures without injury. Herein, we investigate the in vivo heat shock response (HSR) in the cave nectar bat Eonycteris spelaea. We demonstrate that E. spelaea exhibits enhanced physiological heat resistance, marked by reduced lethality, tissue damage and serum corticosterone levels in comparison to mice upon heat challenge. Additionally, E. spelaea did not exhibit an acute transcriptional response observed heat stress in mice. Instead, bats displayed a delayed and non-canonical HSR that did not involve the activation of classical heat shock related genes and pathways. This altered response in E. spelaea is attributed to the elevated basal expression of heat shock proteins, which we demonstrate to be a common characteristic exhibited by bats from diverse sub-orders, families and diets. Taken together, we demonstrate a distinct HSR in E. spelaea relative to the conventional model organism, mouse, which may provide insights to understand novel regulatory targets and effector proteins that underlie the mammalian heat shock response.

sample_organism:
Mus musculus
Eonycteris spelaea

platform_organism:
Mus musculus
Eonycteris spelaea

overall_design: To characterize the heat shock response of bat against a mammalian proxy mice, in vivo heat shock was performed on animals and subsequent organ was harvested for bulk sequencing at multiple time points. Ctl – Baseline of animals, prior to treatment. Hs – Animals immediately after 1h in vivo heat shock treatment. R - Animals undergone 1h invivo heat shock treatment followed by 4h of recovery.  The following organs were harvested: lung (lg), blood (bl) and muscle (mc).

first: Leon

first: Lin-Fa

last: Wang

first: Akshamal

last: Gamage


title: RNA transcripts regulate G-quadruplex landscapes through G-loop formation (RNA-Seq)

city: Solna

first: Simon

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

summary: G-quadruplexes (G4s) are prevalent DNA structures that regulate transcription but also threaten genome stability. How G4 dynamics is controlled remains poorly understood. Here, we report that RNA transcripts govern G4 landscapes through coordinated ‘G-loop’ assembly and disassembly. G-loop assembly involves activation of the ATM and ATR kinases followed by homology-directed invasion of RNA opposite the G4 strand mediated by BRCA2 and RAD51. Disassembly of the G-loop resolves the G4 structure via DHX36-FANCJ-mediated G4 unwinding that triggers nucleolytic incision and subsequent hybrid strand renewal by DNA synthesis. Inhibition of G-loop disassembly causes global G4 and R-loop accumulation, leading to transcriptome dysregulation, replication stress, and genome instability. These findings establish an intricate G-loop assembly-disassembly mechanism that controls G4 landscapes and is essential for cellular homeostasis and survival.

overall_design: Wild-type, DHX36KO, FANCJKO or DHX36/FANCJKO were subjected to RNA sequencing using the CELseq2 protocol.

first: Koichi

last: Sato

first: Diana

last: Braat

first: Victoria

last: Cruz

first: Puck

last: Knipscheer


title: RNA transcripts regulate G-quadruplex landscapes through G-loop formation (G4 and R-loop CUT&Tag)

overall_design: Wild-type, DHX36KO, FANCJKO or DHX36/FANCJKO, ERCC1 mouse ESC were subjected to G4 CUT&Tag (three biological replicates), and R-loop (S9.6) CUT&Tag (two biological replicates)

first: Jing

last: Lyu

first: Carmen

last: Navarro


title: Durable HTT silencing using non-evolved dCas9 epigenome editors in patient-derived cells

status: Public on Apr 01 2025

city: Sacramento

first: Jennifer

last: Waldo

address: 2921 Stockton Blvd

institute: UC Davis

type: Methylation profiling by high throughput sequencing

summary: Huntington’s disease (HD) is an autosomal dominant neurodegenerative disorder caused by a trinucleotide repeat expansion in exon 1 of the huntingtin (HTT) gene. Nuclease-deficient Cas9 protein (dCas9) epigenetic editing for targeted gene regulation is a promising therapeutic approach for HD through downregulation of the causative gene, HTT. A screen of several dCas9 variants with expanded PAM recognition was fused to KRAB and DNMT3A/L to assess the ability to downregulate total HTT. Surprisingly, only SpdCas9 could significantly downregulate HTT, while expanded PAM recognition variants dxCas9 and dCas9-VQR were less efficient or unable to reduce HTT expression. Using our lead construct with SpdCas9, DNA methylation changes were assessed through reduced representation bisulfite sequencing, showing high on-target increases in DNA methylation and few off-targets. In addition, HTT silencing was mitotically stable for up to 6 weeks in a rapidly dividing cell line. Finally, significant downregulation of HTT was achieved in patient-derived neuronal stem cells, showing the efficacy of this system in a disease-relevant cell type. This approach represents a novel therapeutic pathway for the treatment of HD.

overall_design: cells were treated with either an unguided CRISPRoff or CRISPRoff with gRNA 6 via a transient transfection. Methylation status was assessed 72 hours post transfection to understand methyation changes after treatment.

first: Julian

middle: A

last: Halmai

first: Kyle

last: Fink


title: Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [10x ATAC + GEX Multiome]

first: Alexis

last: Caulier

summary: We developed a strategy (Perturb-Multiome) to couple highly-efficient pooled CRISPR-mediated perturbation of master transcription factors in differentiating primary human hematopoietic cells with joint single-cell gene expression and chromatin accessibility profiling. This approach enabled the reconstruction of transcription factor-dependent gene regulatory networks throughout hematopoietic differentiation. Ultimately, we integrated GWAS datasets to explore the heritability of blood phenotypes explained by these identified transcription-factor regulatory networks.

overall_design:
Pooled CRISPR-mediated perturbation of transcription factors in primary human hematopoietic cells, harvested at day 7, day 9, day 11 and day 14 of in vitro erythroid differentiation with single cell RNA and ATAC readouts.

UPDATE: [June 05, 2025] The Sample titles were updated.

first: Jorge

last: Martin-Rufino

first: Vijay

last: Sankaran


title: Granulysin-high decidual NK cells in macaques and humans share signatures of immune defense and regulation

city: Los Angeles

first: Suhas

last: Kallapur

address: 10833 Le Conte Avenue

institute: UCLA

summary: Decidual NK cells (dNK) are key immune effector cells at the maternal-fetal interface. dNK utilize the anti-microbial peptide granulysin (GNLY) to kill pathogens, without killing trophoblast cells. Since rodents lack the GNLY gene, the in vivo biology of GNLY expression by dNK and their control of microbes is not well-understood. Here we defined dNK GNLY expression in placental membranes of Rhesus macaques and humans. GNLY-high dNK of both species shared conserved transcriptional and protein signatures of anti-microbial defense and immunoregulation. In addition, both human and rhesus GNLY-high dNK responded to inflammation and infection by increasing their cytotoxic, cytokine and inflammatory signatures. Thus high GNLY expression defines a unique dNK type with active roles in innate immune defense in humans and Rhesus macaques. Defining the regulatory networks of GNLY expression by dNK and their mechanism of infection control will open up therapeutic opportunities to enhance immunity and reduce infection-related pregnancy complications

overall_design:
CAMD (chorio-amnion-decidual membranes) from pre-term deliveries (two without inflammation denoted "CTR", two with acute chorioamnionitis denoted "ACA") were formalin-fixed paraffin-embedded and later used for scRNA-seq transcriptomic analysis, in comparison with preterm Rhesus macaque CAMD that had been intra-amnionically injected with saline or LPS (the Rhesus scRNA-seq data are available under a separate GEO entry). The sample numbers 1, 2, 4, 5 below correspond to the sample numbers in Table 1 of the manuscript.

This study was supported by:

. Cincinnati Children's Research Foundation (CCRF) Tilburgs lab startup funds (Tamara Tilburgs)
. CCRF Research Innovation Pilot (RIP) Award (Tamara Tilburgs)
. Fixed RNA Profiling Grant Program  - 10X Genomics (Pietro Presicce)
. March of Dimes Prematurity Research Center Ohio Collaborative (Tamara Tilburgs)
. Burroughs Wellcome Fund Next Gen Pregnancy Award #NGP10115 (Tamara Tilburgs)
. CCHMC Vaccinology Training Program NIH T32 AI165396 (Nina Pransaphanich)
. K12-HD000850 from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (Nina Prasanphanich)

first: Nina

middle: S

last: Prasanphanich

first: Giulia

last: Protti

first: Monica

last: Cappelletti

first: Feiyang

last: Ma

first: Neema

last: Pithia

first: Angel

last: Rapp

first: Jerzy

last: Stanek

first: Claire

last: Chougnet

first: Matteo

last: Pellegrini

first: Tamara

last: Tilburgs

first: Pietro

last: Presicce


title: Transforming growth factor-beta dependent signaling drives tumor growth and aberrant extracellular matrix dynamics in NF1-associated plexiform neurofibroma

city: Indianapolis

first: Steven

last: Rhodes

state: IN

address: 1044 W. Walnut St.; Bldg R4, Rm 325

institute: Indiana University

summary: Plexiform neurofibromas (PNF) are benign tumors of the peripheral nervous system that represent a major source of morbidity in persons with neurofibromatosis type 1 (NF1). A significant proportion of individuals do not respond to current therapies or experience intolerable side effects.  Here, we performed a systematic transcriptomic characterization of murine and human PNF at the bulk and single cell level and identified TGF-beta (TGFβ) signaling as a key upstream regulator in PNF, driving aberrant production of basement membrane (BM) proteins by both neoplastic Schwann cells and fibroblasts.  Furthermore, we show that conditional overexpression of TGFβ1 in Nf1 deficient Schwann cells driven by Hoxb7-Cre promotes PNF growth and malignant transformation in vivo. Conversely, pharmacologic inhibition of the type I TGFβ receptor (TGFβRI) reduced PNF tumor burden in Nf1 mutant mice. Proteomic characterization of the extracellular matrix (ECM) revealed a reduction in BM proteins in response to TGFβRI inhibition. Collectively, these studies implicate the TGFβ pathway as a potential therapeutic target in PNF and provide insights into the role of TGFβ signaling in orchestrating ECM dynamics in the PNF microenvironment.

overall_design: PNF bearing sciatic nerve tissues pooled from five, 11-month-old Nf1flox/flox;PostnCre+ mice were harvested, flash frozen at -80°C and shipped on dry ice to Novogene for single nucleus capture, library preparation and sequencing.  Single nuclei suspensions were loaded onto Chromium Chips (10x Genomics) for 3’ library preparation according to the manufacturer’s recommendations. Library quality control was performed by Qubit 2.0 for preliminary determination of the library concentration, Agilent 2100 to determine the insert size, and Q-PCR to precisely quantify the library effective concentration. The resulting library was sequenced on an Illumina sequencing platform at a depth of 106,831 mean reads per cell across an estimated 6,881 cells with 24,062 total genes detected and a median of 1,654 genes per cell.


title: Transcriptomic insights into fate choice of pallial versus subpallial GABAergic neurons (CUT&Tag)

city: Nanjing

first: Zhao

last: Chunjie

overall_design: The CUT&Tag assay was performed using E16.5 GEs dissected from wild-type mice and a FOXG1 rabbit polyclonal antibody.70 Briefly, the cells were isolated from the GEs, and were evenly divided into three samples; the two samples treated with FOXG1 antibody were referred to as replicate1 and replicate2, respectively, while the sample without FOXG1 antibody was referred to as negative control.

first: Chunjie

last: Zhao

first: Lijuan

last: Sun

first: Baoshen

last: Zhang


title: Naïve CD8 T cell RNA sequencing in C57BL/6 and MD4 mice

city: Aurora

first: Jared

last: Klarquist

state: CO

department: Immunology and Microbiology

institute: University of Colorado, Anschutz

summary: The presence of B cells is essential for the formation of CD8 T cell memory after infection and vaccination. In this study, we investigated whether B cells influence the programming of naïve CD8 T cells prior to their involvement in an immune response. RNA sequencing indicated that B cells are necessary for sustaining the FOXO1-controlled transcriptional program, which is critical for their homeostasis. Without an appropriate B cell repertoire, mouse naïve CD8 T cells exhibit a terminal, effector-skewed phenotype, which significantly impacts their response to vaccination. A similar effector-skewed phenotype with reduced FOXO1 expression was observed in naïve CD8 T cells from human patients undergoing B cell-depleting therapies. Furthermore, we show that patients without B cells have a defect in generating long-lived CD8 T cell memory following COVID vaccination. In summary, we demonstrate that B cells promote the quiescence of naïve CD8 T cells, poising them to become memory cells upon vaccination.

overall_design: The spleens of 5 x 10-week-old female wildtype C57BL/6J mice and 5 x 10-week-old female hemizygous MD4 transgenic mice (originally made on a C57BL/6J background) were harvested and enriched for CD8 T cells using a mangetic enrichment kit (BioLegend). Cells were then stained and sorted using a FACS Aria (BD Biosciences) cell sorter , gating on CD3+CD8+B220−CD44low live single cells.


title: Cancer cell-secreted spermidine synthase induces skeletal muscle fibrosis upon radiotherapy (Xenograft tumor)

first: Xiaohui

overall_design: Comparative gene expression profiling analysis of RNA-seq data for irradiation-treated and non-treated MDA-MB-231 xenografted tumors.

first: Wei

last: Yan


title: Context-specific requirements of Tet enzymes in the modulation of CD8 effector and memory cell fates during acute viral infection [EM-seq]

city: Iowa City

first: Priya

last: Issuree

state: IA

address: 431 Newton Road

department: Internal Medicine

institute: University of Iowa

summary: In response to infections, naïve CD8 T cells give rise effector and memory T cells. However, eliciting long-lived memory CD8T cells remains a challenge for many infections. DNA demethylation of cytosines within CpG dinucleotides by Tet enzymes is a key epigenetic mechanism that regulate transcriptional programs. However, their roles in CD8 T cell memory differentiation is unclear. We report that following viral infection, Tet1/3-deficient CD8 T cells preferentially differentiate into short-lived effectors and effector memory cells. Using genome-wide DNA methylation and mice, in which Tet1/3 were ablated during T cell development and in mature CD8 T cells, respectively, we established that Tet1/3 regulate these cell fates by licensing the chromatin landscape of genes downstream of T cell receptor signaling during thymic T cell maturation. These findings unveil the context-specific roles of DNA demethylation, which is essential for defining pathways that contribute to CD8 memory T cell generation against infectious diseases.

overall_design: To assess changes in methylation following T cell activation, FACs-sorted Naïve CD8 T cells were stimulated with plate-bound anti-cd3/cd28 and 18hrs later, cells were harvested for EM-Seq processing


title: Context-specific requirements of Tet enzymes in the modulation of CD8 effector and memory cell fates during acute viral infection


title: RNA transcripts regulate G-quadruplex landscapes through G-loop formation

first: Simon

last: Elsässer


title: A single-cell genomic atlas for the effects of chronic ethanol exposure in the mouse dorsal striatum

status: Public on Mar 31 2025

city: Baltimore

first: Seth

last: Ament

state: MD

address: 670 W Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: In our study of AUD, we used single-nuclei RNA-sequencing (snRNA-seq; n = 86,715 cells) to examine the impact of chronic intermittent ethanol exposure on the dorsal striatum in C57BL/6 male and female mice. We detected 462 differentially expressed genes at FDR < 0.05, the majority of which were mapped to spiny projection neurons (SPNs), the most prominent cell type in the striatum. Gene co-expression network analysis and functional annotation of differentially expressed genes revealed down-regulation of postsynaptic intracellular signaling cascades specifically in canonical SPNs. Inflammation-related genes were down-regulated across many striatal cell types. Gene set enrichment analyses also pointed to altered states of rare cell types, including the induction of angiogenesis-related genes in vascular cells

overall_design: Chronic Intermittent Ethanol: Mice were exposed to ethanol vapor or air 16 hours/day, 4 days a week for a total of 5 weeks. After 4 days in the inhalation chambers, mice underwent a 72-hour forced abstinence period from ethanol. pyrazole (1 mmol/kg, i.p.) was injected daily in weeks 4- 5 to stabilize blood ethanol concentrations. Male and female mice co-housed with littermates. Dorsal Striatal sections used for snRNAseq. In the discovery dataset, 16 animals total, with one male and one female pooled together. In both replication datasets, 8 animals total, with four males and four females pooled in each sample.

first: Erin

last: Wildermuth

first: Michael

last: Patton

first: Marcia

last: Cortes-Gutierrez

first: Brian

last: Mathur

first: Zeal

last: Jinwala

first: Benjamin

last: Grissom

first: Rianne

last: Campbell

first: Henry

last: Kranzler

first: Mary Kay

last: Lobo


title: A recombinant hybrid provides insights into gene regulation, pathogenesis and tumorigenesis of phytopathogenic smut fungi [3 dpi]

city: Köln

first: Janina

last: Werner

state: NRW

address: Zülpicherstraße 47A

institute: University of Cologne, Terrestrial Microbiology

summary: The maize smut fungi Ustilago maydis and Sporisorium reilianum are closely related and have similar genomes in terms of size and synteny. While U. maydis induces tumors locally at sites of infection, S. reilianum systemically colonizes the host and causes symptoms in the inflorescences. To investigate the genetic basis of these differences, an interspecific recombinant hybrid (rUSH) with the mating type system of S. reilianum was generated. rUSH exhibited extensive in-planta proliferation, showing a S. reilianum-like phenotype at all developmental stages except teliospore formation. Transcriptome profiling revealed that expression of pathogenicity-related effector gene orthologs was induced in rUSH, but not in a wild-type hybrid control. Multiple transcriptome comparisons identified 253 differentially expressed one-to-one effector orthologs with distinct regulatory patterns, including cis-, trans-, and rUSH-specific regulation. Functional analysis via CRISPR/Cas9 mutagenesis uncovered three novel virulence factors among the rUSH-specific regulated effectors. Ultimately, rUSH facilitated to identify the transcription factor UmHdp2 as key regulator of U. maydis-induced tumorigenesis. Together, these findings highlight the utility of a recombinant, interspecific hybrid in unraveling the molecular mechanisms underlying pathogenic differences in closely related fungal pathogens.

overall_design: Total RNA was extracted from maize leaves infected with hybrid FB1+SRZ2, rUSH or rUSH_OE_Umhdp2 at 3 dpi.

first: Weiliang

last: Zuo

first: Winkler

last: Tom

first: Gunther

last: Doehlemann


title: Altering metabolism to program cell identity via NAD+ dependent deacetylation [ATAC-seq]

city: Copenhagen

first: Josh

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

summary: Cells change their metabolic profiles in response to an underling gene regulatory network, but how can alterations in metabolism encode specific transcriptional instructions?  Here we show that forcing metabolic change in embryonic stem cells (ESCs) promotes a developmental identity that better approximates the inner cell mass (ICM) of the mammalian blastocyst in cultures we refer to as enhanced metabolic ESCs (EMESCs).  The creation of EMESCs depends on the inhibition of glycolysis and stimulation of oxidative phosphorylation (OXPHOS), that in turns activates NAD+-dependent deacetlylases of the Sirtuin family.  The activation of this pathway leads to the deacetylation of histones and key transcription factors leading to a revised ICM-like gene regulatory network.  The exploitation of the NAD+/NADH coenzyme normally coupled to elevated OXPHOS to program lineage specific transcription suggests new paradigms for how cells respond to alterations in their environment.

overall_design: ATAC-seq of mESCs cultured in EMM for 0h (Serum/LIF), 3h, 9h, and 24h

first: Joshua

first: Robert

last: Bone


title: Altering metabolism to program cell identity via NAD+ dependent deacetylation [RNA-seq]

overall_design: RNA-seq of mESCs cultured in EMM for 0h (Serum/LIF), 3h, 9h, and 24h. RNA-seq of mESCs cultured in SL, EMM, , or Serum/LIF for 10 or 20 passages.


title: METTL14-induced m6A methylation increases G6pc biosynthesis, hepatic glucose production and metabolic disorders in obesity

city: Ann Arbor

first: Qiantao

last: Zheng

state: MI

address: 2800 Plymouth Road

department: Department of Molecular & Integrative Physiology

institute: University of Michigan

summary: RNA N6-methyladenosine (m6A) modification emerges as a pivotal mechanism underpinning numerous intracellular processes. METTL14 dimerizes with METTL3 as a m6A writer to install m6A on mRNA. Subsequently, m6A readers bind to m6A-marked RNAs to influence their metabolism/fate. However, there is a knowledge gap in m6A writers and readers governing liver metabolism. Glucose-6-phosphatase catalytic subunit (G6pc) is the gatekeeper of glycogenolysis and gluconeogenesis, determining hepatic glucose production (HGP); however, posttranscriptional regulation of G6pc is poorly understood. Here, we identify METTL14 as a posttranscriptional regulator of G6pc synthesis. Deletion of Mettl14 decreased, whereas overexpression of METTL14 increased, G6pc mRNA m6A methylation in hepatocytes. We mapped five m6A sites, and mutating the 5 sites (G6pcΔ5A) blocked METTL14-induced m6A methylation of G6pcΔ5A mRNA. METTL14 increased G6pc but not G6pcΔ5A mRNA stability and translation. YTHDF1 and YTHDF3 acted as m6A readers for G6pc mRNA to increase G6pc synthesis. Deletion of Mettl14 decreased gluconeogenesis in primary hepatocytes,  liver slices, and mice. Liver METTL14, METTL3, and m6A-methylated G6pc mRNA were upregulated in mice with diet-induced obesity. Deletion of hepatic Mettl14 decreased HGP and mitigated diet-induced metabolic disorders. Collectively, these results unveil a previously-unrecognized METTL14/G6pc mRNA m6A/G6pc biosynthesis/HGP axis guiding glucose metabolism in health and disease.

overall_design: Mettl14f/f mice (8 weeks) were fed HFD for 10 weeks and injected with AAV8-TBG-Cre or AAV8-TBG-GFP (control) vector via tail vein. Eight weeks later, total RNA was extracted by RNeasy Mini Kit for RNA-seq.

first: Xiao

last: Zhong

first: Liangyou

last: Rui


title: A recombinant hybrid provides insights into gene regulation, pathogenesis and tumorigenesis of phytopathogenic smut fungi

overall_design: Total RNA was extracted from maize leaves infected with U. maydis WT, S. reilianum WT or the hybrid at 20 hpi, 3 dpi and 6 dpi. For the 20h timepoint, liquid latex was applied to the leave surface to enrich the fungal material in the mixed sample.


title: Multigenerational cell tracking of DNA replication and heritable DNA damage

city: Zurich

first: Matthias

last: Altmeyer

address: Winterthurerstrasse 190

department: Department of Molecular Mechanisms of Disease

country: Switzerland

institute: University of Zurich

summary: The goal of this project was to analyze gene expression changes upon polyploidization. To this end, human U-2 OS cells were exposed to the NEDD8-activating enzyme (NAE) inhibitor Pevonedistat (MLN4924), a first-in-class anticancer drug that induces DNA re-replication, or to oncogenic H-RAS V12 (HRAS) over-expression. Untreated U-2 OS cells served as control. Cells with 2N-4N DNA content were separated from cells with >4N DNA content by FACS and single cells were sorted into 384 well plates for scRNA-seq analysis.

overall_design:
For SORT-Seq, cells were sorted on a FACS Aria III 3L system equipped with a 488 nm laser line. Pevonedistat-treated cells were treated for 24 h with 175 nM Pevonedistat. Prior to sorting, cells were incubated for 1 h with a final concentration of 5 µg/ml Hoechst 33342 (Thermo Fisher). Cells were sorted into 384-well plates that were acquired from Single Cell Discoveries. Cells with increased ploidy were gated according to their Hoechst signal and as a reference for the whole population the gate was adjusted in the same sample.
Note: The processed files "barcodes.tsv", "features.tsv" and "matrix.mtx" are poisson-corrected data from the raw count tables.

first: Andreas

last: Panagopoulos

first: Merula

last: Stout

first: Sinan

last: Kilic

first: Peter

last: Leary

first: Julia

last: Vornberger

first: Virginia

last: Pasti

first: Antonio

last: Galarreta

first: Aleksandra

last: Lezaja

first: Kyra

last: Kirschenbühler

first: Ralph

last: Imhof

first: Hubert

last: Rehrauer

first: Urs

last: Ziegler


title: Metabolic dysfunction mediated by HIF-1α contributes to epithelial differentiation defects in eosinophilic esophagitis. [DMOG-ALI]

city: Maynooth

first: Joanne

middle: Carol

last: Masterson

address: Biomedical Sciences Building, Maynooth University

department: Biology

country: Ireland

institute: Maynooth University

summary: Investigating the contributory role that epithelial cell metabolism plays in allergic inflammation is a key factor to understanding what influences dysfunction and the pathogenesis of the allergic disease eosinophilic esophagitis (EoE). Herein, we sought to define the role of HIF-1α-mediated metabolic dysfunction in esophageal epithelial differentiation processes and barrier function in EoE. In RNA-sequencing derived from EoE patient biopsies, we observed the expression pattern of key genes involved in mitochondrial metabolism/oxidative phosphorylation (OXPHOS) and glycolysis. Bioenergetics analysis using Seahorse was performed on EPC2-hTERT cells to decipher the metabolic processes involved in epithelial differentiation processes. In addition, air-liquid interface cultures were employed to delineate metabolic dependency mechanisms required for epithelial differentiation. Transcriptomic analysis identified an increase in genes associated with OXPHOS in patients with EoE. Bioenergetic analysis in vitro revealed thatdifferentiated epithelium was less reliant on OXPHOS compared withundifferentiated epithelium. Increased OXPHOS potential and reduced glycolytic capacity was mirrored in HIF1A-knockdown EPC2-hTERT cells which portray a significant absence of terminal markers of epithelial differentiation, including involucrin. Pharmacological glucose transport inhibition phenocopied this, while rescue of the HIF-1α-deficient phenotype using the pan-prolyl hydroxylase inhibitor DMOG resulted in restored expression of epithelial differentiation markers. An OXPHOS-dominated metabolic pattern in EoE patients, brought about largely by the absence of HIF-1α-mediated glycolysis, is linked with the deficit in esophageal epithelial differentiation.

overall_design:
EPC2-hTERT esophageal epithelial cells cultured at ALI were treated with the pan-prolyl hydroxylase inhibitor Dimethyloxalylglycine (DMOG) for 18hr before harvest.
Vehicle- and DMOG-treated ALI samples were subjected to RNA-sequencing for comparative gene expression profiling.

first: Sinéad

last: Ryan


title: An enriched circulating extracellular vesicle microRNA, miR-451a, attenuates the RORγt expression in T cells in secondary lymphoid tissues, thereby ameliorating IL-17A-mediated allergic responses

city: Kumamoto

first: Ken

last: Takashima

state: Kumamoto

address: 1-1-1, Honjo, Chuo-ku

department: Department of Immunology

institute: Kumamoto University

summary: The miRNAs contained in extracellular vesicles play a vital role in intercellular communication, and miR-451a, which is particularly enriched in circulating extracellular vesicles, contributes to various physiological events, including immune responses. We investigated the impact of miR-451a on IL-17-producing cell-dependent allergic responses using a DNFB-mediated delayed-type hypersensitivity (DTH) induction mouse model. In miR-451a knockout (KO) mice, an increase in IL-17-producing cells was observed in the ear and its associated mandibular lymph nodes following DNFB sensitization. Furthermore, we performed transcriptome analysis using RNA-seq on the mandibular lymph nodes of mice subjected to DNFB sensitization and challenge, evaluating changes and differences in gene expression. This study provides a new mechanism by which miR-451a controls the number and characteristics of IL-17-producing cells, shedding light on new mechanisms in allergies and immune responses.

overall_design: To investigate the impact of miR-451 on DNFB-mediated DTH response, we induced DTH on WT or miR-451a mice. DNFB-mediated DTH response were induced by sensitization on day 0, 1, 2 and challenge on day 9. We harvested mandibular lymph nodes following DNFB sensitization (se; at day9) and/or challenge (DTH; at day10) from WT or miR-451a mice. We obtained gene expression profiling using RNA-seq data of 4 different group (WT_se, WT_DTH, miR-451a KO_se, KO_DTH) which had triplicate samples.

first: Takanobu

last: Yoshida

first: Yohana

last: Mtali

first: Hiroyuki

last: Oshiumi


title: Adaptation to Volumetric Compression Drives an Apoptosis-Resistant and Invasive Phenotype in Liver Cancer

city: New Haven

first: Michael

last: Mak

state: CT

address: 55 Prospect St

institute: Yale University

summary: Physical constraints like compression influence cancer cell invasion and transcriptional dynamics in various tumors. Liver cancer is characterized by the rapid proliferation of tumor cells within a densely packed tissue matrix, subjecting the cancer cells to crowding and compression. The highly dysregulated mechanical environment highlights the need to elucidate the broader impact of compression on liver cancer development and evolution. In this study, we investigated and described a unique adaptive response of liver cells to prolonged compression. Liver cells presented significant transcriptional changes due to compression, including the loss of liver-specific markers and enrichment of epithelial-to-mesenchymal transition genes. Compression elevated Rac1 activity, which promoted cellular protrusions and YAP nuclear translocation and maintained cell viability under mechanical stress. Furthermore, compression disrupted intracellular calcium signaling, leading to resistance to apoptosis. Counteracting the effects of compression by inhibiting Rac1 or manipulating intracellular calcium facilitated death of compression-adapted cells. This study highlights compression as a critical biophysical signal in the tissue microenvironment that can induce cell state transitions and disease-driving phenotypes in the liver.

overall_design:
We cultured HepG2 cells on 2D culture plates with FBS supplemented DMEM. We used 4% (v/v) polyethylene glycol 300 (PEG300)-induced hyperosmolarity in the medium to compress cells for five days. The control group is the cell population cultured in the regular, isotonic medium.
RNA-seq profiling of liver cancer cell lines HepG2 and Hep3B cultured on 2D plates (or transwell membranes) in the regular isotonic culture medium, under osmotic compression induced by 4% or 3%polyethylene glycol (PEG 300) in culture medium, and under mechanical compression induced by weights applied on cells. For HepG2, conditions are Isotonic on dish, 4% PEG on dish, non-compressed on transmembranes, and mechanically compressed on transmembranes. For Hep3B, conditions are non-compressed, mechanically compressed, and 3% PEG (all on transmembranes).

first: Xiangyu

last: Gong


title: Calcitonin gene-related peptide sustains CD8 T cell inflammatory reactions in drug -induced reactions

city: Guangzhou

first: Xiaobao

last: Huang

state: Guangdong

address: No. 58 Zhongshan Second Road, Guangzhou, Guangdong, China

institute: The First Affiliated Hospital, Sun Yat-sen University

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

overall_design: Refer to individual Series


title: Altering metabolism to program cell identity via NAD+ dependent deacetylation

first: Josh

last: Brickman


title: The Immune Landscape of Tumor-Associated Macrophage Reprogramming.

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Tumor-associated macrophages (TAMs) generally acquire an immunosuppressive and tumor-promoting phenotype, which may contribute to tumor resistance to immunotherapy. We previously showed that suppression of microRNA activity through genetic Dicer1 inactivation rewires TAM’s transcriptomes and prompts their immunostimulatory activation. This phenotypic switch enhanced recruitment and activation of CD8+ cytotoxic T cells (CTLs) and improved the efficacy of immunotherapy in mouse cancer models. Here, we performed single-cell RNA sequencing of whole tumors grown in either wild-type mice or mice with macrophage-specific Dicer1 deletion. The analysis of multiple cell populations, including several discrete monocyte and macrophage subsets, indicated broad and convergent immunostimulatory programming of the tumor microenvironment (TME), which was dependent on CTL-derived interferon-gamma (IFNγ), in mice with DICER-deficient macrophages. Intriguingly, dynamic inferences on monocyte/macrophage ontogeny and differentiation by pseudotime analysis revealed trajectories associated with progression into cell cycle, monocyte-to-macrophage differentiation, and transition from an immunostimulatory to an immunosuppressive phenotype in tumors with DICER-proficient macrophages. Dicer1 deficiency interfered with this trajectory and stalled TAMs at an intermediate state between immature monocytes and macrophages with T cell-stimulatory capacity, thereby impeding immunosuppressive TAM development. This translated into enhanced response to antiangiogenic immunotherapy in an immunotherapy-resistant model of non-small cell lung cancer. Cycling/M2-like macrophages were conserved in human melanoma and hepatocellular carcinoma and should represent a more promising therapeutic target than the bulk of TAMs.

overall_design: Comparative gene expression profiling of mouse MC38 tumors with Dicer know-out or wild type.

first: Florent

last: Duval

first: Nahal

last: Mansouri

first: Michele

last: De Palma


title: Calcitonin gene-related peptide sustains CD8+ T cell inflammatory reactions in drug -induced reactions [scRNA-Seq]

summary: We investigated the differentiation pattern of CD8+ T cells from healthy controls and patients with SJS/TEN.

overall_design: The cells for scRNAseq analysis had viability greater than 88% with concentration ranges from ~700-–1200 cells/μL. We selected two representative patients from SJS/TEN as well as two normal donors for normal reference. Cell preparation, library preparation, and sequencing were carried out according to Chromium product-based manufacturer protocols (10X Genomics).Cells from patients were compared to the healthy individuals to identify differentially expressed genes.

first: Suiting

last: Ao

first: Fang

last: Wang


title: Ciliary marginal zone of the developing human retina maintains retinal progenitor cells until late gestational stages

status: Public on Mar 30 2025

city: Seattle

first: Joshua

middle: William

last: Hahn

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

summary: Non-mammalian vertebrates maintain a proliferative stem cell population at the far periphery of their retina called the ciliary marginal zone (CMZ), which gives rise to all retinal cell types and contributes to retinal regeneration upon injury. Humans do not maintain a proliferative CMZ into adulthood; however, it is not known how long in development this region continues to generate new neurons. Here, we identify a population of cells in the far peripheral retina of the fetal human that continues to proliferate long after the rest of the retina is quiescent. Single cell RNA-sequencing and EdU tracing at late time points in development reveal that this region has features of the non-mammalian CMZ, including the capacity to produce both early and late born cell types at late developmental stages, and a longer cell cycle than more centrally located retinal progenitor cells (RPCs). Moreover, while more central RPCs exit the cell cycle with the addition of a TGFb-inhibitor, we show that early RPCs within the CMZ do not. These findings define the late stages of neurogenesis in human retinal development, and present a unique model system to study the fetal CMZ in humans.

overall_design: Retinospheres were generated from day 137 human fetal tissues. Retinospheres were sorted into CMZ containing retinospheres vs. those derived from the far periphery. Retinospheres from both groups were cultured for an additional 48 days, to an equivalent of 185 days fetal gestation. The CMZ of far-peripheral retinospheres was dissected and dissociated, and far peripheral retinospheres were also dissociated for comparison. An equivalent number of cells from each sample were then processed with the 10x Genomics single cell RNA-sequencing platform.

first: Kiara

last: Eldred

first: Sierra

last: Edgerton

first: Isabel

last: Ortuño-Lizarán

first: Juliette

last: Wohlschlegel

first: Stephanie

last: Sherman

first: Sidnee

last: Petter

first: Gracious

last: Wyatt-Draher

first: Dawn

last: Hoffer

first: Ian

last: Glass

first: Anna

last: La Torre

first: Thomas

last: Reh


title: Context-specific requirements of Tet enzymes in the modulation of CD8 effector and memory cell fates during acute viral infection [Cut&Tag]

first: Priya

middle: D

last: Issuree

overall_design: To assess changes in JunB binding following T cell activation, FACs-sorted Naïve CD8 T cells were stimulated with plate-bound anti-cd3/cd28 and 18hrs later, cells were harvested for Cut and Tag processing


title: Context-specific requirements of Tet enzymes in the modulation of CD8 effector and memory cell fates during acute viral infection [ATAC-seq]

overall_design: To assess changes in chormatin accessibility following T cell activation, FACs-sorted Naïve CD8 T cells were stimulated with plate-bound anti-cd3/cd28 and 18hrs later, cells were harvested for ATAC-Seq processing. We also FACS-sorted P14 WT and Tet1/3 T cells from day5 LCMV-infected mice and processed for ATAC-Seq


title: Altering metabolism programs cell identity via NAD+-dependent deacetylation [CUT&Tag]

first: Josh

middle: M

last: Brickman

summary: Cells change their metabolic profiles in response to underlying gene regulatory networks, but how can alterations in metabolism encode specific transcriptional instructions? Here, we show that forcing a metabolic change in embryonic stem cells (ESCs) promotes a developmental identity that better approximates the inner cell mass (ICM) of the early mammalian blastocyst in cultures we refer to as enhanced metabolic ESCs (EMESCs). The creation of EMESCs depends on inhibition of glycolysis and stimulation of oxidative phosphorylation (OXPHOS), that in turns activates NAD+-dependent deacetylases of the Sirtuin family, resulting in the deacetylation of histones and key transcription factors to focus enhancer activity while reducing transcriptional noise, that result in a robust enhanced ESC phenotype. This exploitation of a NAD+/NADH coenzyme coupled to OXPHOS as a means of programming lineage specific transcription suggests new paradigms for how cells respond to alterations in their environment, and implies cellular rejuvenation exploits enzymatic activities to for simultaneous activation of a discrete enhancer set alongside silencing genome-wide transcriptional noise.

overall_design: CUT&Tag of mESCs cultures in Serum/LIF, EMM, or EMM plus NAM. Sirt1 mutants were cultured in Serum/LIF and EMM

first: Robert

last: Bone


title: NGN3 oscillatory expression controls the timing of human pancreatic endocrine differentiation

city: Manchester

first: Anzy

last: Miller

address: Oxford Road

country: United Kingdom

institute: University of Manchester

summary: Understanding protein expression dynamics is crucial for the mechanistic understanding of cell differentiation. We investigate the dynamics and decoding of NGN3, a transcription factor critical for pancreatic endocrine development. A knock-in endogenous reporter shows that NGN3 protein oscillates with a 13-hour periodicity in human iPS-derived endocrine progenitors and is switched off as cells differentiate to β-like and pre-alpha cells. Increasing NGN3 protein stability results in one broad peak of expression instead of oscillations, with a larger peak to trough fold-change. This leads to precocious endocrine differentiation and earlier expression of key NGN3 target genes. Single-cell analysis of dynamics, mathematical modelling and experimental validation suggest that NGN3 oscillations are decoded by fold-change detection (FCD) rather than the level of expression via an incoherent feedforward loop motif (IFFL) that explains both normal and precocious differentiation. Our findings suggest that oscillatory NGN3 dynamics control the timing of differentiation, but not fate specification.

overall_design: We performed gene expression analysis in WT cells every 3 days of the pancreatic differentiation

first: Veronica

last: Biga

first: Andrew

last: Rowntree

first: Mariya

last: Chhatriwala

first: Florence

last: Woods

first: Benjamin

last: Noble

first: Elli

last: Marinopoulou

first: Anoushka

last: Kamath

first: Ludovic

last: Vallier

first: Nancy

last: Papalopulu


title: Protease-activated receptor 2 links protease activity with calcium waves during egg activation and blastomere cleavage

status: Public on Mar 29 2025

city: Singapore

first: Tom

middle: James

last: Carney

address: 59 Nanyang Drive

department: Cancer Discovery & Regenerative Medicine Programme

institute: Lee Kong Chian School of Medicine

summary: Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa, this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1,4,5-trisphosphate (IP3) receptors. Only a subset of the mechanisms employed to generate IP3 during vertebrate egg activation are defined, with strong evidence that other critical mechanisms exist. Serine proteases have been long implicated in egg activation and fertilisation. Here we report that treatment of zebrafish eggs with serine protease inhibitors leads to defective calcium wave propagation and failed egg activation. We further show that mutation of zebrafish Protease-activated receptor 2a (Par2a) also results in severe disruption of egg activation, leading to failed chorion elevation and ooplasmic segregation. Milder par2a mutants progress further, but then show abnormal blastomere cleavage. We observed that par2a mutants show decreased amplitude and duration of calcium transients. Restoring Ca++ or direct injection of IP3 ligand rescues egg activation aborted by either serine protease inhibitor treatment or by mutation of Par2a. We thus show that serine protease activity is a critical regulator of IP3 and subsequent calcium wave amplification during zebrafish egg activation, and link this to intracellular calcium release via the protease receptor, Par2a.  This constitutes a novel signalling pathway critical for successful fertilisation.

overall_design: RNA-seq from 1 hour post fertilisation zygotes of severe and mild par2a mutant zebrafish and sibling controls


title: The spatial organization of cDC1 with CD8+ T cells is critical for the response to immune checkpoint inhibitors in melanoma patients

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

summary: Dendritic cells (DCs) are promising targets for cancer immunotherapies because of their central role in the initiation and control of immune responses. The type 1 conventional DC (cDC1) population is of particular interest because of its ability to cross-present antigens to CD8+ T cells, to promote Th1 cell polarization and NK cell activation and recruitment. However, the spatial organization and specific functions of cDC1s in response to immunotherapy remain to be clearly characterized in human tumors. In this study, we used a multiplexed immunofluorescence analysis pipeline coupled with computational image analysis to determine the spatial organization of cDC1s in skin lesions from a cohort of advanced melanoma patients treated with immune checkpoint inhibitors (ICI). For this, we performed a whole-slide image analysis of cDC1 infiltration, distribution, and spatial interaction with key immune partners such as CD8+ T cells and plasmacytoid DCs (pDC). We also analyzed LAMP3+-DC, which correspond to a mature subset of tumor-infiltrating DCs. Distance and cell network analyses demonstrated that cDC1s exhibited a scattered distribution compared to tumor-infiltrating pDCs and LAMP3+-DCs, which were preferentially organized in dense areas with high homotypic connections. The proximity and interactions between CD8+ T cells and cDC1s were positively associated with the response to ICI. In conclusion, our study unravels the complex spatial organization of cDC1s and their interactions with CD8+ T cells in melanoma patient lesions, shedding light on the pivotal role of these cells in shaping the response to ICI.

overall_design: NanoString GeoMx Digital Spatial Profiler (Human Immuno-Oncology Protein Assay) was used on FFPE tissues from eight representative patients. Tissue sections were incubated with a cocktail of oligonucleotide-conjugated antibodies (immuno-oncology panel kit) and counterstained with a nuclear stain.

first: Elisa

last: Gobbini

first: Margaux

last: Hubert

first: Anne-Claire

last: Doffin

first: Anais

last: Eberhardt

first: Leo

last: Hermet

first: Danlin

last: Li

first: Pierre

last: Duplouye

first: Sarah

last: Barrin

first: Justine

last: Berthet

first: Valentin

last: Benboubker

first: Maxime

last: Grimont

first: Candice

last: Sakref

first: Jimmy

last: Perrot

first: Garance

last: Tondeur

first: Olivier

last: Harou

first: Jonathan

last: Lopez

first: Bertrand

last: Dubois

first: Stephane

last: Dalle

first: Christophe

last: Caux

last: Caramel

first: Jenny

last: Valladeau-Guilemond


title: In vivo structure profiling reveals human tRNA structurome and interactions in response to stress

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: Transfer RNAs (tRNAs) are the most abundant RNA family in copy numbers in a cell. It not only folds into defined structures, but also has complex interaction networks in cells involving aminoacyl-tRNA synthetases, translation factors, and ribosomes. The human tRNAome is comprised of chromosomal-encoded tRNAs with a large sequence diversity, and mitochondrial-encoded tRNAs that have A/U-rich sequences and many with non-canonical tertiary interactions. How tRNA folding and interaction in a eukaryotic cell respond to stress is poorly understood. Here, we develop DM-DMS-MaPseq, which utilizes in vivo dimethyl-sulfate (DMS) chemical probing and mutational profiling (MaP) coupled with demethylase (DM) treatment in transcriptome-wide tRNA sequencing to profile tRNA structures and their cellular interactions for human chromosomal and mitochondrial-encoded tRNAs. We found that tRNAs maintain stable structures in vivo, but the in vivo DMS profiles are vastly different from in vitro, which can be explained by their interactions with cellular proteins and the ribosome. We also identify tRNA structure and interaction changes upon arsenite treatment, an oxidative stress that induces translational reprogramming, that are consistent with enhancing reductions of translation. Our results reveal variations of tRNA structurome and dynamic interactome that have functional consequences in translational regulation.

overall_design: To investigate the structure and RNA-protein interactions of human cytosolic and mitochondrial tRNA in vivo. RNA from HEK293T cells were treated with DMS, either following deprotenation or on the live cells, and underwent multiplex small RNA-seq (MSRseq). Generated libraries were sequenced using Illumina. Following quality control processing and demultiplexing, libraries were aligned to hg38 tRNA genes. Mutation profile and abundance were calculated using custom Python and R scripts.

first: Noah

last: Escareño Peña

first: Yichen

last: Hou

first: Christopher

middle: P

last: Watkins

first: Sihao

last: Huang

first: Wen

last: Zhang

last: Katanski


title: Gene expression profile at single cell level of Braf-mutant mouse melanoma tumor and skin

city: Irvine

first: Anand

last: Ganesan

state: CA

address: 839 Health Science Rd

department: Dermatology

institute: University of California, Irvine

summary: Melanomas are genetically heterogeneous, displaying mitogen-activated protein kinase mutations and homozygous loss of tumor suppressor genes.  Mouse models combining such mutations produce fast-growing, pigmented tumors. In contrast, rare, slow-growing, lowly-pigmented tumors arise in mice combining Braf activation with heterozygous loss of Pten or, as we show here, in albino mice bearing only a Braf mutation. Incidence kinetics suggest a stochastic event underlies tumorigenesis, but responsible de novo mutations or structural variants were not found.  Single-cell transcriptomics of tumors identified a cell type resembling “neural crest-like” cells in human and mouse melanomas.  These exist in normal mouse skin, expand upon Braf activation, and persist through serial transplantation; analyses of gene expression suggest they serve as precursors of malignant cells.  This state may serve as an intermediate on a slow path to malignancy that, while not abundant in fast-growing, heavily-mutated tumors, may provide a diagnostically and therapeutically important source of cellular heterogeneity.

overall_design: For the 4-OHT-induced mouse nevi and tumor experiment, a total of 47 skin and tumor samples were collected from 36 animals, including wildtype skin (n=15), black BrafCA/+ skin (n=10, which contain only nevi), albino BrafCA/+ tumors (n=3), albino BrafCA/+ PtenΔ/+ tumors (n=4), black BrafCA/+ PtenΔ/+ tumors (n=4), of which 11 sample-matched tumor-adjacent-skin samples were also collected alongside each of the 11 tumor samples. For the tumor transplantation experiment, tumors derived from BrafCA/+ and BrafCA/+; PtenΔ/+ mouse models were passaged by transplantation onto NSG (immune deficient, n=2 for each round) mice. These samples were subjected to scRNA-seq using the 10x Genomics Chromium Single Cell 3’ v2 protocol.

first: Hui

last: Xiao

first: Jessica

last: Shiu

first: Chi-Fen

last: Chen

first: Jie

last: Wu

first: Peijie

last: Zhou

first: Sahil

last: Telang

first: Rolando

last: Ruiz-Vega

first: Robert

last: Edwards

first: Qing

last: Nie

first: Arthur

last: Lander


title: Somatic development of Wilms tumour via normal kidneys in predisposed children

status: Public on Mar 28 2025

city: Saffron Walden

first: Sam

last: Behjati

address: Hinxton

institute: Wellcome Sanger Institute

type: Methylation profiling by genome tiling array

summary: Ten percent of children with cancer harbour a mutation in a predisposition gene. In children with the kidney cancer, Wilms tumour, the prevalence is as high as 30%. Certain predispositions are associated with defined histological and clinical features, suggesting differences in tumourigenesis. To investigate this, we assembled a cohort of 137 children with Wilms tumour, of whom 71 had a pathogenic germline or mosaic variant. We examined 237 neoplasms (including two secondary leukaemias) from the cohort, utilising whole genome sequencing, RNA sequencing and genome wide methylation, validating our findings in an independent cohort of 21 children. The development of tumours differed between children with sporadic disease and amongst those with a predisposition, depending on the variant gene and its developmental timing. Differences pervaded the repertoire of driver events, including high risk mutations, the clonal architecture of normal kidneys, and the relatedness of neoplasms from the same individual. Predisposition constrains Wilms tumourigenesis, suggesting a variant specific approach to managing these children merits consideration.

overall_design: We analysed methylation data from 455 samples (normal kidney tissue, blood and tumour) from 137 children with Wilms tumour as part of a study to investigate how tumour development differs between chldren predisposed to Wilms tumour and chidlren with sporadic disease.


title: Global transcription factors analyses reveal hierarchy and synergism of regulatory networks and master virulence regulators in Pseudomonas aeruginosa

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: The transcription factor regulatory network (TRN) in Pseudomonas aeruginosa is complicated and involves multiple regulators responding to various environmental signals and physiological cues by regulating gene expression. P. aeruginosa utilizes versatile virulent determinants to exert its virulence, including biofilm formation, quorum sensing (QS), Type III (T3SS) and Type IV (T6SS) secretion system, motility, siderophore production, oxidative stress resistance, and antibiotic resistance, which under the control of TRN. Herein, ChIP-seq was applied to investigate the binding sites of 158 TFs in P. aeruginosa PAO1 strain. The results revealed a total of 30,481 significant binding peaks in the genome, more than half of which were located in the promoter regions. To furthermore decode diverse regulatory relationships among TFs, the hierarchical network was assembled into three levels: top, middle, and bottom. Thirteen ternary regulatory motifs revealed flexible relations of TFs in small hubs, and a comprehensive co-association atlas was established and enriched three high-associated clusters. A total of 32 TFs were identified as master regulators in regulating virulence-related pathways, and 34 TFs were involved in four metabolism pathways significantly. These results will provide significant insight into understanding the pathogenesis mechanisms of P. aeruginosa and relevant bacteria and contributing to developing effective therapies for diseases caused by infection.

overall_design: ChIP-seq analyses of genomic regulators in Pseudomonas aeruginosa

first: X

last: Deng


title: Epigenomic Landscapes Define Differential JAK Inhibitor Sensitivity in IFN-γ-Primed Human Macrophages

city: Cheongju-si

first: Geunho

last: Kwon

state: Chungcheongbuk-do

address: 1, Chungdae-ro, Seowon-gu, 310, S1-5

country: South Korea

institute: Chungbuk National University