title: Loss of adaptive DNA breaks in Alzheimer’s disease brains

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Background: DNA breaks accumulate in Alzheimer’s disease (AD) brains. While their role as true genomic lesions is recognized, DNA breaks also support cognitive function by facilitating the expression of activity-dependent immediate early genes. This process involves TOP2B, a DNA topoisomerase that catalyzes the formation of DNA double-strand breaks. Objective: To characterize how AD impacts adaptive DNA breaks at nervous system genes. Methods: We leveraged the ability of DNA single-and double-strand breaks to activate poly (ADP-ribose) polymerases (PARPs) that conjugate poly (ADP-ribose)(PAR) to adjacent proteins. To characterize the genomic sites harboring DNA breaks in AD brains, nuclei extracted from 3 AD and 3 non-demented autopsy brains (frontal cortex, all male donors, age 78 to 91 years of age) were analyzed through CUT&RUN in which we targeted PAR with subsequent DNA sequencing. Results:Although the AD brains contained 19.9 times more PAR peaks than the non-demented brains, PAR peaks at nervous system genes were profoundly lost in AD brains, and the expression of these genes was downregulated. This result is consistent with our previous CUT&RUN targeting γH2AX, which marks DNA double-strand breaks. In addition, TOP2B expression was significantly decreased in the AD brains.Conclusions:Although AD brains contain a net increase in DNA breaks, adaptive DNA breaks at nervous system genes are lost in AD brains. This could potentially reflect diminished TOP2B expression and contribute to impaired neuron function and cognition in AD patients.

overall_design: Methods: We obtained autopsy brain tissue from 3 AD and 3 age-matched control individuals. The donors were men between the ages of 78 to 91. Nuclei extracted from frontal cortex tissue were subjected to Cleavage Under Targets & Release UsingNuclease (CUT&RUN) assay with an antibody against PARP, a marker of DSBformation. PARP-enriched chromatins were purified and analyzed via high-throughput genomic sequencing.

first: Xiaoyu

last: Zhang

first: Yan

last: Liu

first: Ning

last: Wang


title: RNA polymerase I transcription is essential for establishing the chromatin architecture in mouse but not in human embryos

status: Public on Apr 11 2025

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

type: Expression profiling by high throughput sequencing

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: Isolation of human monoclonal antibodies from 4CMenB vaccinees reveals PorB and LOS as the main OMV components inducing cross-strain protection [E. coli OMV]

status: Public on Apr 09 2025

city: Siena

first: Viola

last: Viviani

address: Via Fiorentina, 1

country: Italy

institute: GSK

summary: In this study, we describe the development and use of an ad hoc protein microarray to characterize the target of HumAbs isolated from 4CMenB vaccinated subjects and induced by the OMV component of the vaccine

overall_design: A panel of 26 recombinant E. coli Outer Membrene Vesicles (hereafter called GMMA) expressing meningococcal antigens and two GMMA empty were printed randomly in replicates on a not-commercial protein microarray. All the proteins expressed in E.coli GMMA were  FLAG- and His-tagged fusions. Recombinant GMMA were obtained from the supernatant of a late-exponential growth of E. coli. The supernatants were subjected to high-speed centrifugation and the pellets containing the GMMA were washed with PBS. Controls consisted of 8 serial 2-fold dilutions of Human IgG and PBS + 40% glycerol spots.

first: Giacomo

last: Vezzani


title: Isolation of human monoclonal antibodies from 4CMenB vaccinees reveals PorB and LOS as the main OMV components inducing cross-strain protection [ Recombinant Chip]

overall_design: A panel of recombinant meningococcal proteins were printed randomly in replicates on a not-commercial protein microarray. With the expection of NadA, GNA2091-fHbp and NHBA-GNA1030 (that are tagless), all the proteins were expressed as FLAG- and His-tagged fusions. Recombinant antigens were expressed in E. coli and then purified either from the cytoplasmic fraction as soluble proteins or resolubilized from the inclusions bodies as insoluble forms. Controls consisted of 8 serial 2-fold dilutions of human IgG, proteins expressed and purified from E. coli following the same expression and purification protocol, but originating from different pathogens other than MenB and PBS + 40% glycerol spots.


title: DFFB suppresses interferon to enable cancer persister cell regrowth

status: Public on Apr 10 2025

city: La Jolla

first: August

last: Williams

state: CA

address: 9500 Gilman Dr.

department: Dermatology

country: USA

institute: UC San Diego

summary: Oncogene targeted cancer therapies can provide deep responses but frequently suffer from acquired resistance. Therapeutic approaches to treat tumours which have acquired drug resistance are complicated by continual tumour evolution and multiple co-occurring resistance mechanisms. Rather than treating resistance after it emerges, it may possible to prevent it by inhibiting the adaptive processes which initiate resistance but these are poorly understood. Here we report that residual cancer persister cells that survive oncogene targeted therapy are growth arrested by drug stress-induced intrinsic Type I interferon (IFN) signaling. To escape growth arrest, persister cells leverage apoptotic machinery to transcriptionally suppress interferon-stimulated genes (ISGs). Mechanistically, persister cells sublethally engage apoptotic caspases to activate DNA endonuclease DNA Fragmentation Factor B (DFFB, also known as Caspase-Activated DNase (CAD)) which induces DNA damage, mutagenesis, and stress response factor Activating Transcription Factor 3 (ATF3). ATF3 limits Activator Protein-1 (AP1)-mediated ISG expression sufficiently to allow persister cell regrowth. Persister cells deficient in DFFB or ATF3 exhibit high ISG expression and are consequently unable to regrow. Therefore, sublethal apoptotic stress paradoxically promotes regrowth of residual cancer cells that survive drug treatment.

overall_design: Bulk and single cell RNA sequencing data. Bulk RNA sequencing with Illumina Stranded mRNA. A375 WT, DFFB KO, and ATF3 KO cells in triplicate were untreated (parental), treated for 14 days with 250 nM dabrafenib and 25 nM trametinib (persister), or persisters were co-treated with 20 uM AP-1 inhibitor T-5224 for the duration of persister formation. Single cell RNA sequencing of PC9 and A375 cells with 10X Genomics. For single cell RNA sequencing, PC9 WT lung cancer cells were untreated (parental) or treated with 2.5 µM erlotinib for 14 days (persister cells). A375 WT or DFFB KO cells were untreated (parental) or treated with 250 nM dabrafenib and 25 nM trametinib in combination for 14 days (persister cells). A375 WT and DFFB KO drug tolerant expanded persister cells (DTEPs) were treated with 250 nM dabrafenib and 25 nM trametinib for 9 weeks.

first: Matthew

last: Hangauer


title: Isolation of human monoclonal antibodies from 4CMenB vaccinees reveals PorB and LOS as the main OMV components inducing cross-strain protection [OMV MenB]

summary: In this study, we describe the development and use of an ad hoc protein microarray to characterize the meningococccal cross-binding of HumAbs isolated from 4CMenB vaccinated subjects and induced by the OMV component of the vaccine

overall_design: A panel of meningococcall Outer Membrane Vesicles (OMV) were printed randomly in replicates on a not-commercial protein microarray. The species-specific N.meningitidis OMV array was printed with different OMV in 20% glycerol. Controls consisted of 8 serial 2-fold dilutions of human IgG.


title: Gfi1 controls the formation of effector CD8+ T cells during chronic infection and cancer [ATAC]

city: Birmingham

first: Oluwagbemiga

last: Ojo

state: Alabama

department: Radiation Oncology

institute: University of Alabama, at Birmingham

summary: During chronic infection and tumor progression, CD8+ T cells gradually lose their cytotoxic effector function and become “exhausted”. These “exhausted” CD8+ T cells are highly heterogenous and comprised of various subsets, including a self-renewing progenitor subset that gives rise to Ly108-CX3CR1+ effector cells with some cytotoxic capabilities. Generation of these effectors is essential for the control (although limited) of chronic infection and tumor. However, the precise cues and mechanisms directing their formation and maintenance remains incompletely understood. In this study, using genetic mouse models challenged with the LCMV clone 13 infection and syngeneic MB49 urothelial adenocarcinoma, we show that the expression of a transcriptional repressor, growth factor independent 1 (Gfi1) is dynamically regulated in “exhausted” CD8+ T cells. By controlling chromatin accessibility and transcriptomic programs, Gfi1 governs the generation of the effector cells. Deletion of Gfi1 in T cells arrests the progenies from progenitors in a Ly108+CX3CR1+ Transitional state, without further differentiation into effector cells. Given the programmable chromatin profile of these transitional cells, we reason that they are a better target than the highly irreprogrammable terminally differentiated cells for therapeutic interventions to combat chronic infection and cancer. Our results show that Gfi1 is a novel epigenetic and transcriptional regulator of CD8+ T cell exhaustion.

overall_design: Gfi1fl/fl CD4cre-/- (Wildtype) or Gfi1fl/fl CD4cre-/- (Gfi1cKO) mice were infected with LCMV clone 13. GP33+ antigen specific CD8+ T cell subsets from wildtype (Progenitor, Effector, Transitional, Terminally Exhausted) and Gfi1cKO (Progenitor and Transitional) mice were FACS sorted 30 days post infection. Assay for transposase-accessible chromatin with sequencing(ATAC-Seq) was used to investigate the chromatin accessibility in FACS sorted antigen specific GP33+ cells. Samples are pooled biological replicates. Naive CD8+ T cells from uninfected wildtype and Gfi1cKO mice were included as controls.

middle: A

first: Hongxing

last: Shen

first: Jennifer

middle: T

last: Ingram

first: Robert

last: Welner

first: Georges

last: Lacaud

first: Allan

middle: J

last: Zajac

first: Lewis

middle: Z

last: Shi


title: Robust differentiation of NK cells from MSLN.CAR-IL-15-engineered human iPSCs with enhanced anti-tumor efficacy against solid tumors [scRNA-seq]

city: Bethesda

first: Mingming

last: Zhao

address: 9000 Rockville Pike

institute: national institutes of health

summary: Human induced pluripotent stem cells (iPSCs) offer a promising source for producing standardized, off-the-shelf CAR-NK products. However, the complex and time-consuming iPSC-NK (iNK) manufacturing challenges clinical use. Here, we identified LiPSC-GR1.1 as a superior iPSC line for iNK production. By engineering LiPSC-GR1.1 with a mesothelin (MSLN)-targeting CAR and IL-15, we achieved efficient robust differentiation of iPSCs into mature and activated iNKs, which demonstrated enhanced tumor-killing efficacy, superior tumor-homing, and vigorous proliferation. Single-cell transcriptomic analysis revealed that TGF-β-producing tumor cells upregulated MHC molecules and downregulated MSLN expression post-CAR-IL-15 iNK treatment. Tumor-infiltrating CAR-IL-15 iNKs exhibited high levels of CAR, IL-15, and NK-activating receptors, negligible checkpoint exhaustion markers, and extremely low levels of NK suppressive factors CISH, TGFBR2, and BATF, enabling them to sustain activation, metabolic fitness, and effective tumor killing within the TGF-β-rich hypoxic tumor microenvironment. Overall, we developed a MSLN.CAR-IL-15-engineered GR1.1-iNK product with enhanced anti-tumor efficacy for solid tumor treatment.

overall_design: CAR-IL15 iNK pre-infusion product were harvested from 7 day expansion culture for pre-infusion product analysis. For tumor tissue analysis, NSG mice were i.p. inoculated with human mesothelioma NCI-Meso63 cells and treated with CAR-IL15 iNKs. The intraperitoneal formed xenograft tumors were harvested from CAR-IL15 iNK-treated and untreated NSG mice. The total cells from tumors were isolated and perform scRNA-seq profiling. Total 8 samples included CAR-IL-15 iNK product cells (2 samples), total cells isolated from untreated NCI-Meso63 tumor tissues (3 samples), and total cells isolated from CAR-IL-15 iNK-treated NCI-Meso63 tumor tissues (3 samples).

first: Qun

last: Jiang

first: Weiming

last: Yu

first: James

last: Ma

first: Jizhong

last: Zou

first: Sameer

last: Mir

first: Jingli

first: Ronald

last: Germain

first: Raffit

last: Hassan


title: Robust differentiation of NK cells from MSLN.CAR-IL-15-engineered human iPSCs with enhanced anti-tumor efficacy against solid tumors [bulk RNA-seq]

overall_design: RNAseq profiling of PBNK, Mock iNK, CAR-IL-15 iNK (3 samples for each group).

last: Zhang


title: Prenatally androgenized PCOS mice have ovary-independent uterine dysfunction and placental inflammation aggravated by high-fat diet

city: Oulu

first: Terhi

last: Piltonen

address: Aapistie 5a

department: Department of Obstetrics and Gynecology

country: Finland

institute: University of Oulu

summary: Polycystic ovary syndrome (PCOS) is a common hyperandrogenic and metabolic condition in women. The syndrome is linked to subfertility and pregnancy complications, yet the independent effects of exposure to hyperandrogenism and obesity on endometrial function remain unclear. Here, PCOS-like mice were generated using prenatal androgenization (PNA) with dihydrotestosterone, followed by a prepubertal high-fat (HF) or standard diet. In ovariectomized mice, PNA impaired uterine closure during the implantation window, disrupted decidualization, and altered extracellular matrix- and inflammation-related gene expression. The effects were aggravated by HF diet. In naturally mated, ovary-intact mice, PNA and HF diet affected decidual and placental gene expression, suggestive of placental dysfunction and inflammation, and induced fetal growth restriction. This study underlines the role of the uterus in adverse pregnancy outcomes in PCOS and identifies possible underlying mechanisms for future studies. Pre-pregnancy interventions targeting metabolic health and hyperandrogenism should be the next steps to optimize PCOS pregnancy outcomes.

overall_design: We sought to examine how prenatal androgenization (PNA) and/or excessive body weight affect uterine function during the pre-pregnancy phase and throughout pregnancy in mice. To achieve this, we conducted three experimental scenarios: the window of implantation, artificial decidualization, and natural pregnancy. Uterine and placental tissues were collected from PNA and control mice, both on high-fat and normal diets. RNA sequencing (RNAseq) was performed on the samples, after which the impact of PNA was assessed by comparing PNA-affected tissues to controls, and the influence of diet evaluated by comparing tissues from mice on high-fat versus normal diets.

first: Lena

last: Luyckx

first: Milena

last: Myllykangas

first: Ulla

last: Saarela

first: Nikke

last: Virtanen

first: Elisa

last: Hurskainen

first: Audrey

last: Savolainen

first: Nadja

last: Ollikainen

first: Anna-Karin

last: Norlén

first: Claes

last: Ohlsson

first: Matti

last: Poutanen

first: Greetje

last: Vande Velde

first: Riikka

middle: K

last: Arffman

first: Renata

last: Prunskaite-Hyyryläinen

first: Joris

last: Vriens


title: Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti [ncRNA-seq]

city: Paris

first: Hélène

last: Lopez-Maestre

address: 25-28 rue du Dr Roux

country: France

institute: Institut Pasteur

type: Non-coding RNA profiling by high throughput sequencing

summary: Transposable elements (TEs) are DNA sequences that can change their position within a genome. In the germline of arthropods, post-transcriptional regulation of TE expression is mainly mediated by the Piwi-interacting RNA (piRNA) pathway. piRNAs are small RNAs of 24-30 nucleotides (nt) in length produced from genomic precursor transcripts as well as through a ‘ping-pong’ amplification cycle. In somatic tissues, certain insects, such as Drosophila, instead rely on the small interfering RNA (siRNA) pathway as a key regulator of TE expression. siRNAs are 21nt small RNAs produced from double-stranded RNA by the endonuclease Dicer2, which guides an RNA-induced silencing complex to degrade a complementary RNA. However, whether the siRNA pathway also regulates TE expression in the mosquito Aedes aegypti, a medically significant vector species with abundant somatic piRNAs, is unknown. To address this question, we investigated the expression of TEs and small RNAs in both somatic and gonadal tissues of a Dicer2 mutant line of Ae. aegypti and its wild-type counterpart. Our results show a modified pattern of TE expression and a decrease in TE-derived 21nt small RNAs in the Dicer2 mutant, but no major shift of TE transcript abundance. The lack of a functional siRNA pathway also causes perturbations in piRNA ping-pong signatures and the expression of certain piRNA-associated genes, but without clear evidence for compensation by increased piRNA pathway activity. We conclude that the mosquito Ae. aegypti produces siRNAs targeting TEs but these lack a critical role in the regulation of TE expression both in somatic and in gonadal tissues.

overall_design: To investigate the role of Dcr2 in the regulation of transposable elements in different tissues of the mosquito Aedes aegypti, we did paired RNA-seq and small RNA-seq on a Dcr2-deficient mutant line of mosquitoes and its sister control wild-type counterpart

first: Alexander

last: Bergman

first: Anna

middle: B

last: Crist

first: Mauro

last: Castelló-Sanjuán

first: Lionel

last: Frangeul

first: Hugo

last: Varet

first: Josquin

last: Daron

first: Sarah

middle: H

last: Merkling

first: Maria-Carla

last: Saleh

first: Louis

last: Lambrechts


title: ALFIN-LIKE proteins bind H3K4me3 and recruit SWR1 to repress responsive genes [RNA-Seq]

city: Cambridge

last: Harris

address: Downing Street

department: Department of Plant Sciences

country: United Kingdom

institute: University of Cambridge

summary: In eukaryotes, the canonical histones deposited during S-Phase are often replaced by histone variants at discrete loci after replication. This function is facilitated by histone chaperones and chromatin remodeling complexes. The chromatin remodeler SWR1 incorporates H2A.Z into chromatin in exchange for its canonical counterpart H2A. Despite its importance, the mechanisms by which SWR1 is recruited to its target loci are not yet fully understood. Here, we show that ALFIN-LIKE (AL) proteins direct the SWR1 complex to H3K4me3 loci, facilitating the deposition of H2A.Z. Simultaneous mutation of the seven AL genes (al7m) leads to severe developmental effects and aberrant upregulation of responsive genes. This geneset exhibits high levels of H3K4me3, which is recognized by AL5. Furthermore, al7m shows a decrease in H2A.Z occupancy, particularly at AL5-bound loci. Our data suggests that AL5, through its interaction with SWR1, guides its activity towards inducible genes.

overall_design: Simultaneous mutation of the seven ALFIN-LIKE (AL) genes (al7m) leads to severe developmental effects. To better understand AL function, we performed RNA-seq in the al7m and the wild-type control (WT, Col-0) in Arabidopsis.

first: Linhao

last: Xu

first: Yafei

last: Wang

first: Xueying

last: Li

first: Qin

last: Hu

first: Vanda

last: Adamkova

first: Junjie

first: Israel

last: Ausin


title: Identification of Leukemia-Enriched Signature Through the Development of a Comprehensive Pediatric Single-Cell Atlas

city: Atlanta

first: Hope

last: Mumme

address: 1760 Haygood Dr NE

institute: Emory University

summary: Single-cell transcriptome profiling enables unparalleled characterization of the heterogeneous microenvironment of pediatric leukemias. To facilitate comparative analyses and generate pediatric leukemia signatures, we collect, process, and annotate single-cell data comprising over 540,000 cells from 159 different pediatric acute leukemia (myeloid, lymphoid, mixed phenotype lineages) and healthy bone marrow (BM) samples, profiled in our lab and curated from publicly available studies. The analysis identifies a leukemia-enriched signature of nine genes with over-expression in leukemic blast as compared to healthy BM cells. The signature is also consistently over-expressed in leukemia samples compared to normal BM in bulk RNA-seq data from the TARGET initiative. Outcome-based analysis using measurable residual disease (MRD) status depicts the enrichment of oncogene-induced senescence and g-protein activation pathways in leukemia patients at diagnosis who achieve MRD positivity at the end of induction. MRD positivity across pediatric leukemias is associated with significant depletion of CD8+ and CD4+ naïve T-cells and M1-macrophages at diagnosis. To enable easy access to this uniformly integrated pediatric leukemia single-cell atlas, we develop the Pediatric Single-cell Cancer Atlas (PedSCAtlas, https://bhasinlab.bmi.emory.edu/PediatricSCAtlas/) resource. The atlas allows for quick exploration of single-cell data based on genes, cell types, and clinical outcomes to understand the cellular landscape of pediatric leukemias.

overall_design:
Single-cell RNA sequencing performed on two healthy pediatric bone marrow samples, with 10x Genomics 3'V2 kit.

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

first: Hope L

first: Chenbin

last: Huang

first: Denis

last: Ohlstrom

first: Mojtaba

last: Bakhtiari

first: Sunil S

last: Raikar

first: Deborah

last: DeRyckere

first: Muna

last: Qayed

first: Sharon M

last: Castellino

first: Daniel S

last: Wechsler

first: Christopher C

last: Porter

first: Douglas K

last: Graham

first: Swati S

last: Bhasin

first: Manoj


title: ALFIN-LIKE proteins bind H3K4me3 and recruit SWR1 to repress responsive genes [ChIP-Seq]

last: Harris

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for FLAG, histone H3 and H2A.Z as well as histone modifications H3K4me3 in Arabidopsis

first: Linhao

last: Xu

first: Yafei

last: Wang

first: Xueying

first: Qin

first: Vanda


title: Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti [RNA-seq]

first: Hélène

last: Lopez-Maestre

first: Alexander

last: Bergman

first: Anna

last: Crist

first: Mauro

last: Castelló-Sanjuán

first: Lionel

last: Frangeul

first: Hugo

last: Varet

first: Josquin

last: Daron

first: Sarah

last: Merkling

first: Maria-Carla

last: Saleh

first: Louis

last: Lambrechts


title: TIE-2 expressing monocytic myeloid-derived suppressor cells are involved in resistance to anti-PD-1 mediates by angiopoietin 2 in melanoma patients

status: Public on Apr 08 2025

city: Besançon

first: Olivier

last: Adotévi

state: Franche-Comté

address: 8 rue du Dr JFX Girod

department: Oncology

institute: Université de Franche-Comté

summary: Immunotherapy using immune checkpoint inhibitors (ICI) has revolutionized the management of melanoma. Although the anti-PD-1 antibodies induce a 40% objective response rate (ORR) in advanced melanoma patients, the majority of patients have a primary resistance or develop a secondary resistance (Robert et al. 2015). Many resistance mechanisms have been described including the loss of the expression of class I MHC, the alteration of antigen presentation, JAK/STAT pathway mutation, or the overexpression of another inhibitory molecule (LAG-3, TIM-3, …). It was also known that immunosuppressive cells such as myeloid-derived Suppressor Cells (MDSC) can negatively impact the efficacy of anti-PD-1 therapy (Limagne et al. 2019). MDSCs are a group of immunosuppressive heterogenous cells found in many cancers that inhibit antitumor T cell functions by several mechanisms. We previously described in lung cancer a novel subpopulation of monocytic MDSC (M-MDSC) overexpressing TIE-2 that mediate inhibition of antitumor T cell responses after angiopoietin-2 (ANGPT2) exposure. Furthermore, we found, that a high level of circulating TIE-2+ M-MDSC and ANGPT2 in melanoma patients is associated with a poor prognosis by inhibiting anti-melanoma T-cell responses (Marguier et al. 2022).TIE-2 is a tyrosine kinase with immunoglobulin and EGF homology domains. This receptor was mainly expressed by endothelial cells but can be expressed by tumor cells and some immune cells such as monocytes. TIE-2 binds to the pro-angiogenic factor ANGPT2 which is involved in tumor neo-angiogenesis. Recent findings in melanoma also showed the implication of ANGPT2 in resistance to anti-PD-1 therapy by promoting the exclusion of T cells (Park et al. 2023). Thus, we assumed that TIE-2+ M-MDSC would be involved in this negative impact of ANGPT2 on anti-PD-1 therapy.

overall_design:
We evaluated TIE-2+ M-MDSC by flow cytometry and ANGPT2 levels  by ELISA in peripheral blood collected at baseline in 40 patients with advanced melanoma treated with anti-PD-1 therapy (ITHER cohort NCT02840058). Three main groups were distinguished according to the median rate of TIE-2+ M-MDSC (5%) and median level of ANGPT2 (1000 pg/mL) at baseline:  group 1 with ANGPT2high/ TIE-2high M-MDSC (n= 8), group 2 with ANGPT2low/ TIE-2low M-MDSC  (n=8) and third composite group (group 3) with ANGPT2high /TIE-2Low M-MDSC (n=14) and ANGPT2Low /TIE-2high M-MDSC (n=7). Antitumor T cell responses against melanoma antigens were also evaluated at baseline by IFN-y ELISpot in patients from group 1 and 2.
Next, preliminary transcriptomic analysis was performed using bulk RNA sequencing of TIE-2+ and TIE-2- M-MDSC cells isolated from patients in group 1 (ANGPT2high/ TIE-2high M-MDSC) based on CD14+ HLA-DR-/low and TIE2 expression. PBMC from three patients were pooled and TIE-2+ and TIE-2- M-MDSC were sorted to form two paired samples

first: Amélie

last: Marguier

first: Jessica

last: Mathiot

first: Babacar

last: Ndao

first: Mylène

last: Wespiser

first: Victor

last: Pereira

first: Benoît

last: Lecoester

first: Laura

last: Boullerot

first: Marine

last: Malfroy

first: Caroline

last: Laheurte

first: François

last: Aubin

last: Adotevi

first: Charlée

last: Nardin


title: Elevated levels of UDP-Glucuronic acid mitigate drug resistance and stress response through a protease and a nucleotide sugar transporter in Cryptococcus gattii

first: Sujiraphong

last: Pharkjaksu

state: MD

address: 10 Center Dr

department: NIAID

institute: NIH

summary: UDP-glucuronic acid (UDP-GlcUA) is a nucleotide sugar that plays important roles in many organisms and excessive UDP-GlcUA in the cell causes many defects in the cellular processes. In Cryptococcus spp., mutations in the UXS1 gene which encodes an enzyme that converts UDP-GlcUA into UDP-xylose trigger high level accumulation of UDP-GlcUA and effectuate resistance to the antifungal drug 5-fluorocytosine. Here, we show that elevation of UDP-GlcUA affects several cellular processes including growth rate, ability to grow at various stress conditions, and resistance to fluorine containing analogs. RNA-seq analyses reveal that UXS1 deletion leads to the identification of three differentially expressed endopeptidase genes, notably PEP401. Lack of PEP401 from the uxs1 mutant background reduces the UDP-GlcUA levels and reverts all the phenotypes of the uxs1 mutant toward the wild-type characteristics. Particularly, high levels of UDP-GlcUA not only regulate expression of PEP401 at RNA and protein levels, but it also enhances the proteolytic activity of total protein extracts in a PEP401-dependent manner, establishing a functional link between nucleotide sugar metabolism and proteolytic regulation. Moreover, the UDP-GlcUA transporter gene, UUT1, can further modulate the levels of UDP-GlcUA in the uxs1 pep401 double mutant and manifests the drug resistance phenotypes observed in the uxs1 mutant. Taken together, these findings reveal a previously unrecognized regulatory network that connects UDP-GlcUA metabolism to protease-mediated cellular processes and to the transportation of UDP-GlcUA. This newly identified interplay provides a foundation for targeting nucleotide sugar metabolism and protease regulation in the development of improved therapeutic strategies against cryptococcosis.

overall_design:
WM276 = WT strain
C2053 = UXS1 deletion mutant
C2104 = UXS1 deletion mutant with UGD1 (G19A)
C2061 = UGD1 (G19A) strain
Total RNAs were isolated by the Trizol reagent (Invitrogen, Carlsbad, CA) and RNAeasy mini kit (Qiagen). RNAs were treated with Turbo RNase-free DNase (Ambion) to remove genomic DNA. polyA-RNA was purified from total RNA, processed, and paired-end directional libraries (150 bp) were prepared and sequenced using an Illumina HiSeq 4000 platform (Novogene, Davis, CA).

first: Hongyi

last: Cai

first: Peter

last: Walter

first: Yun

middle: C

last: Chang

first: Kyung

last: Kwon-Chung


title: Anti-Müllerian hormone signalling sustains circadian homeostasis in zebrafish [scRNA-seq]

city: Wuhan

first: Jie

last: Mei

state: Hubei

address: No.7, Donghu South Road, Wuchang District

department: Institute of Hydrobiology

institute: Chinese Academy of Sciences

summary: Circadian clocks temporally orchestrate the behavioural and physiological rhythms. The core molecules establishing the circadian clock are clear; however, the critical signalling pathways that cause or favour the homeostasis are poorly understood. Here, we report that anti-Müllerian hormone (Amh)-mediated signalling plays an important role in sustaining circadian homeostasis in zebrafish. Remarkably, amh knockout dampens molecular clock oscillations and disrupts both behavioural and hormonal circadian rhythms, which were recapitulated in bmpr2a null mutants. Somatotropes and gonadotropes were identified as Amh-positive pituitary cell populations. Single-cell transcriptome analysis further revealed a lineage-specific regulation of pituitary clock by Amh. Moreover, Amh-induced effect on clock gene expression could be abolished by blocking Smad1/5/9 phosphorylation and bmpr2a knockout. Mechanistically, Amh binds to its receptors, Bmpr2a/Bmpr1bb, which in turn activate Smad1/5/9 by phosphorylation and promote circadian gene expression. Our findings reveal a key hormone signalling pathway for circadian homeostasis in zebrafish with implications for rhythmic organ functions and circadian health.

overall_design: Molecular components of the circadian clock are known; however, the mechanisms by which long-term circadian homeostasis and oscillation are achieved throughout complex systems and anatomical regions are poorly understood. We performed CUT&Tag and single-cell RNA sequencing of wildtype, amh or bmpr2a knockout zebrafish pituitary to investigate the molecular mechanism by which Amh signaling sustains circadian homeostasis.

first: Qiaohong

last: Lin

first: Xian

last: Du

first: Fan

last: Ren


title: PANCREATIC DUCTAL ADENOCARCINOMAS RESISTANT TO KRAS INHIBITION ARE DRUGGABLE WITH AN ANTI-MUC1-C ADC

city: Brookline

first: Hiroki

last: Ozawa

address: 450 Brookline

institute: Dana-Farber Cancer Institute

summary: Treatment of pancreatic ductal carcinomas (PDACs) has been advanced by the development of KRAS mutant inhibitors. Despite this progress, PDACs invariably develop resistance to these agents by mechanisms that largely remain unclear. The MUC1 gene, which encodes an oncogenic MUC1-C protein, is upregulated in PDAC KRAS G12D tumors. We report that treatment of PDAC cells with the selective KRAS G12D MRTX1133 inhibitor is associated with induction of MUC1-C expression. We show that KRAS G12D inhibition activates a MUC1-C/NF-B p65 auto-inductive pathway. Our results further demonstrate that MUC1-C drives resistance to MRTX1133 by activating the inflammatory IFN type I and II pathways. Of clinical relevance, targeting MUC1-C genetically and pharmacologically reverses MRTX1133 resistance and is synergistic in combination with MRTX1133 treatment. In leveraging MRTX1133-induced upregulation of MUC1-C expression, an anti-MUC1-C (M1C) antibody-drug conjugate (ADC) is highly effective against MRTX1133-resistant PDAC KRAS G12D cell lines, patient-derived organoids and PDX tumor xenograft models. These findings demonstrate that MUC1-C confers resistance of PDAC KRAS G12D mutant cells to MRTX1133 and identify MUC1-C as a target for M1C ADC treatment of PDAC patients who are refractory to MRTX1133 treatment.

overall_design: RNA Seq in PDAC Cell line with MUC1-C shRNA silencing. We conpared DMSO and DOX treatment cells for differential gene expression analysis. MUC1shRNA (MISSION shRNA TRCN0000122938; Sigma, St. Louis, MO, USA)  was inserted into the pLKO-tet-puro vector (Plasmid #21915; Addgene, Cambridge, MA, USA) . Vector-transduced cells were selected for growth in 1–2 μg/ml puromycin. Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).


title: Anti-Müllerian hormone signalling sustains circadian homeostasis in zebrafish

first: Qiaohon


title: CHD7 binds to insulators 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

institute: Rutgers University

summary: Spiral ganglion neurons (SGNs) are crucial for hearing, and the loss of SGNs causes hearing loss. Stem cell-based therapies offer a promising approach for SGN regeneration and require understanding the mechanisms governing SGN differentiation. We investigated the chromatin remodeler CHD7 in SGN differentiation using immortalized multipotent otic progenitor (iMOP) cells. We demonstrate that CHD7 knockdown significantly impairs neuronal differentiation. Genome-wide analysis reveals CHD7 enrichment at diverse cis-regulatory elements, with notable enrichment at sites marked by the insulator-binding protein CTCF between topologically associating domains (TADs). Insulators marked by the enrichment of CHD7 and CTCF resided near genes critical for neuronal differentiation, including Mir9-2. Targeting these regulatory regions in iMOPs with CRISPR interference (CRISPRi) and activation (CRISPRa) increased miR9 transcription, irrespective of the method. The occlusion of the regulatory elements suggested that the insulators function to regulate gene expression. The study highlights CHD7 activity at insulators and underscores its importance in promoting neuronal differentiation.

overall_design: CUT&Tag for CHD7, CTCF, H3K4me3, EP300, and secondary antibody only (no primary antibody) control from proliferating iMOPs (immortablized mutipotent otic progenitors) and iMOP-derived neurons.

first: Jingyun

last: Qiu

first: Azadeh

last: Jadali

first: Julie

last: Ni

first: Edward

last: Martinez

first: Zhichao

last: Song


title: Form follows function: Nuclear morphology as a quantifiable predictor of cellular senescence

city: Vienna

first: Alexis

middle: J.

last: LOMAKIN

address: Währinger Straße 10

department: Center for Pathobiochemistry & Genetics

country: Austria

institute: Medical University of Vienna

summary: Enlarged or irregularly shaped nuclei are frequently observed in tissue cells undergoing senescence. However, it remained unclear whether this peculiar morphology is a cause or a consequence of senescence and how informative it is in distinguishing between proliferative and senescent cells. Recent research reveals that nuclear morphology can act as a predictive biomarker of senescence, suggesting an active role for the nucleus in driving senescence phenotypes. By employing deep learning algorithms to analyze nuclear morphology, accurate classification of cells as proliferative or senescent is achievable across various cell types and species both in vitro and in vivo. This quantitative imaging-based approach can be employed to establish links between senescence burden and clinical data, aiding in the understanding of age-related diseases, as well as assisting in disease prognosis and treatment response.

overall_design: The goal of this RNA sequencing experiment was to test in an unbiased manner whether changes in nuclear shape, size, and abundance—induced by exposing cells to subsaturating concentrations of the microtubule-targeting agent Docetaxel (DTX)—would trigger an adaptive transcriptional program consistent with a senescence-like phenotype. To this end, RNA was isolated and sequenced from HeLa Kyoto cells that were either untreated (Control, Day 0) or treated with 10 nM DTX for 72 hours (Day 3). The experiment was performed in triplicate, with replicate numbers indicated next to each sample name. The main conclusion from this experiment is that the cellular transcriptome undergoes global changes in response to DTX-induced perturbations in nuclear morphogenesis (and potentially chromatin organization). Many of the observed transcriptomic alterations are consistent with the activation of a stress-induced, senescence-like program. The resulting transcriptomic dataset will be of broad interest to researchers studying drug resistance mechanisms, cellular stress responses, senescence and senescence-like states, as well as nuclear architecture and cytoskeletal biology.

first: Jakub

last: Belhadj

first: Surina

last: Surina

first: Markus

last: Hengstschläger

last: Lomakin


title: HERPES SIMPLEX VIRUS TYPE 1 IMPAIRS DENDRITIC CELL FUNCTION BY REMODELLING NEUTRAL LIPID METABOLISM AND INDUCING LIPID DROPLET ACCUMULATION

city: Santiago

first: Pablo

middle: González

last: Muñoz

state: Santiago

address: Avenida Libertador Bernardo O Higgins 340

country: Chile

institute: Pontifical Catholic University of Chile

summary: Herpes simplex virus type 1 (HSV-1) infects dendritic cells (DCs), professional antigen-presenting cells that initiate and regulate host antiviral responses. HSV-1 infects DCs limiting their maturation, migration to draining lymph nodes and T cell activation capacity, ultimately promotes their apoptosis. Here, we investigated the impact of HSV-1 infection over neutral lipid metabolism in DCs and their function. We found that HSV-1 significantly alters neutral lipid metabolism in infected DCs and promotes LD accumulation. Pharmacological inhibition of cholesterol ester synthesis, or fatty acid transporter proteins in infected DCs reduced LD accumulation and viral replication, enhanced DC viability and DC migration to draining lymph nodes and promoted DC priming of virus-specific CD8+ T cells. These findings highlight the role of neutral lipid metabolism in HSV-1-infected DCs and its impact over host immunity against this virus, underscoring lipid metabolism in DCs as a potential therapeutical target for triggering antiviral immunity against HSV-1.

overall_design:
To investigated the impact of HSV-1 infection over neutral lipid metabolism in DCs and their function. We have 2 experimental groups, which were treated with MOCK or infected with HSV-1 (F) at MOI: 3 and at a time of 12 hours post-infection. n=4
We then performed gene expression analysis of MOCK treated and HSV-1 (F) infected bone marrow dendritic cells using data from RNA-seq

first: Mónica

last: Farías

first: Felipe

last: Cancino

first: Areli

last: Navarro

first: Luisa

middle: F

last: Duarte

first: Abel

last: Soto

first: Eduardo

middle: I

last: Tognarelli

first: Maximiliano

last: Ramm

first: Barbara

middle: N

last: Alarcón

first: José

last: Cordero

first: Sergio

last: San Martín

first: Cristian

last: Agurto-Muñoz

first: Angello

last: Retamal-Díaz

first: William

middle: R

last: Jacobs Jr

first: Nelson

middle: P

last: Barrera

first: Luis

last: Bustamante

first: Susan

middle: M

last: Bueno

last: Kalergis

last: González


title: Phospholipid flippase ATP11A brokers uterine epithelial integrity and function

city: Calgary

first: Myriam

last: Hemberger

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

summary: Uterine adaptations driven by the steroid hormones estrogen and progesterone are pivotal for embryo implantation and, ultimately for a successful pregnancy. Here, we show that genetic ablation of the membrane lipid flippase Atp11a in mice causes severe deficits in this hormonal response and profound defects in the morphological organization and transcriptional profile of the uterine epithelial compartment where ATP11A is expressed. Atp11a-null uterine epithelial cells lack tight junctions, and the luminal epithelium exhibits profound disruptions to cellular morphology as it displays a loss of the columnar epithelial architecture and instead acquires a multi-layered morphology of rounded cells resembling a squamous epithelium. Furthermore, the specification of luminal epithelial cells remains incomplete as they maintain expression of the normally gland-restricted marker FOXA2. The uterine glands of Atp11a-null females are depleted for progenitor cells marked by SOX9, PAX8, LGR5 and PROM1. Collectively, these defects likely underpin the frequent early pregnancy losses in Atp11a-depleted females. Most intriguingly, however, loss of only a single functional Atp11a allele causes a higher frequency of abnormal placental trophoblast differentiation as well as a higher incidence of congenital heart defects in wild-type embryos. These data highlight the far-reaching impact of uterine dysfunction on reproductive outcome and highlight the importance of the maternal genotype in the etiology of developmental disorders.

overall_design: To analyze the role of Atp11a-loss in uterine function, we isolated uterine horn sections for RNA-extraction and sequencing. These were collected from Atp11a-KO (n=9) and Atp11a-HET (n=5) as well as Wiildtype controls (n=9). We then performed gene expression analysis comparing thsamples of different genotypes.

first: Alexa

last: Krala

first: Bethany

last: Radford

first: Aleksandra

last: Tsolova

first: Xiang

last: Zhao

first: Wendy

last: Dean


title: Dynamic activation of rAAV transgene expression by a small molecule that recruits endogenous transcriptional machinery

city: Chapel Hill

first: Austin

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: The silencing of adeno-associated virus (AAV) vectors over time poses a challenge to the development of effective gene therapies. Here, we describe a bioorthogonal platform for tuning AAV expression, enabling the controlled activation of viral transgenes after transduction. This platform uses a small, synthetic DNA binding protein embedded in the AAV genome coupled with a heterobifunctional small molecule that recruits endogenous transcriptional machinery to chemically induce transgene expression in a dose-dependent and reversible manner. In human cells, this strategy successfully activates AAV expression across different viral serotypes, cassette configurations, and transgene payloads. Epigenomic analysis reveals that this technology facilitates direct and specific recruitment of the transcriptional regulator BRD4 to AAV genomes. Our results demonstrate that the expression of native AAV genomes can be tuned through chemically induced proximity (CIP), opening the possibility of a new class of AAV vectors that can be dynamically potentiated.

overall_design: CUT&RUN in AAV-infected U2OS cells for BRD4, H3K27ac, and H3K9ac with and without treatment of C207.

first: Sara

last: Wasserman

first: Savannah

last: Muron

first: Deena

last: Scoville

first: Avery

last: Huber

first: Jessica

middle: D

last: Umana

first: Nicole

middle: E

last: Pereira

first: Caroline

middle: A

last: Foley

first: Lindsey

last: James

first: Nathaniel

last: Hathaway


title: The SAS-Chromatin Remodeling Complex Mediates Inflorecence-Specific Chromatin Accessibility for Transcription Factor Binding

status: Public on Apr 06 2025

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: The SAS-type SWI/SNF complex regulates inflorescence-specific chromatin accessibility at distal promoter and upstream intergenic regions, thereby facilitating the binding of transcription factors involved in flower development.

overall_design: Examination of the mRNA expression of wild type and six SWI/SNF mutants in Arabidopsis.

first: Xin

middle: J


title: The SAS-Chromatin Remodeling Complex Mediates Inflorecence-Specific Chromatin Accessibility for Transcription Factor Binding [ChIP-Seq]

overall_design: Examination of the genome-wide binding sites of SWI/SNF subunits and AP1 in Arabidopsis.


title: Quantseq 3'mRNA-seq in Ctrl and TXNIP OE BMOL cells

city: Daejeon

first: Eun Bok

last: Baek

address: 99 Daehak-ro

country: South Korea

institute: Chungnam National University

summary: RNA samples were collected from Ctrl and TXNIP OE BMOL cells. High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 550.

overall_design: High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 550 in Ctrl and TXNIP OE BMOL cells

first: EunBok

first: Young-Suk

last: Won

first: Hyo-Jung

last: Kwon


title: CAN-Scan: a multi-omic phenotype-driven precision oncology platform identifies prognostic biomarkers of therapy response for colorectal cancer

status: Public on Apr 04 2025

city: Glasgow

first: Niranjan

last: Shirgaonkar

state: East Dunbartonshire

address: Switchback Rd, Garscube Estate

institute: Cancer Research UK

summary: Application of machine learning (ML) on cancer-specific pharmacogenomic datasets shows immense promise for identifying predictive response-biomarkers to enable personalized treatment. We introduce CAN-Scan, a precision oncology platform, that applies ML on next-generation pharmacogenomic datasets generated from a freeze-viable biobank of patient-derived primary cell lines (PDCs). These PDCs are screened against 84 FDA-approved drugs at clinically relevant doses (Cmax), focusing on colorectal cancer (CRC) as a model system. CAN-Scan uncovers prognostic biomarkers and alternative treatment strategies, particularly for patients unresponsive to first-line chemotherapy. Specifically, it identifies gene expression signatures linked to resistance against 5-Fluorouracil (5FU)-based drugs and a focal copy number gain on chromosome 7q, harbouring critical resistance-associated genes. CAN-Scan-derived response signatures accurately predict clinical outcomes across four independent, ethnically-diverse CRC cohorts. Notably, drug-specific ML models reveal Regorafenib and Vemurafenib as alternative treatments for BRAF-expressing, 5FU-insensitive CRC. Altogether, this approach demonstrates significant potential in improving biomarker-discovery and guiding personalized treatments.

overall_design: Patient derived cells (PDC) were generated from resected samples. Baseline gene expression profiles of these samples were generated.

first: Shumei

last: Chia

first: Ramanuj

last: Dasgupta


title: The SAS-Chromatin Remodeling Complex Mediates Inflorecence-Specific Chromatin Accessibility for Transcription Factor Binding [ATAC-Seq]

overall_design: Examination of the chromatin accessibility in Arabidopsis inflorescences or seedlings of the wild type and mutants


title: Selective interactions at pre-replication complexes categorize baseline and dormant origins

first: Mirit

last: Aladjem

address: 37 convent drive

department: DTB

institute: NCI/NIH

summary: The initiation of DNA synthesis in metazoans is restricted to a group of baseline replication origins, whereas other (dormant) origins do not initiate replication despite recruiting apparently indistinguishable pre-replication complexes. Dormant origins are activated as backups when DNA synthesis stalls. We report that dormant origins selectively bind CDK-phosphorylated RecQL4 (pRecQL4), a helicase mutated in Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes. In unperturbed cells, pRecQL4 restricts replication initiation to baseline origins by preventing dormant origins from binding the essential initiation factor MTBP. When cells encounter replication stress, pRecQL4 first promotes the dissociation of MTBP from chromatin, and then enables its redistribution to both baseline and dormant origins, facilitating compensatory initiation to complete genome duplication. Thus, MTBP-pRecQL4 interactions modulate replication origin choice and facilitate recovery from replication stress.

overall_design:
ChIP-seq involves crosslinking cells with formaldehyde, extracting and sonicating chromatin, then immunoprecipitating with antibodies against validated ChIP-grade antibodies. After stringent washing, DNA eluted, purified, and sequenced.
Nascent strands were size fractionated (0.5-2kb) and enriched with the lambda exonuclease digestion, purified and sequenced

first: Bhushan

middle: L

last: Thakur

first: Christophe

last: Redon

first: Haiqing

last: Fu

first: Robin

last: Sebastian

first: Nana

last: Kusi

first: Sophie

middle: Z

last: Zhuang

first: Lorinc

middle: S

last: Pongor

first: Vilhelm

last: Bohr


title: Targeting epigenetic regulators to overcome drug resistance in the emerging human fungal pathogen Candida auris

status: Public on Apr 05 2025

city: Shanghai

first: Yuping

last: Zhang

state: Shanghai

department: Shanghai Institute of Immunity and Infection

institute: Chinese acadmy of sciences

summary: The rise of drug-resistant fungal species, such as Candida auris, poses a serious threat to global health, with mortality rates exceeding 40% and resistance rates surpassing 90%. The limited arsenal of effective antifungal agents underscores the urgent need for novel strategies. Here, we systematically evaluate the role of histone H3 post-translational modifications in C. auris drug resistance, focusing on acetylation mediated by Gcn5 and Rtt109, and methylation mediated by Set1, Set2, and Dot1. Mutants deficient in these enzymes exhibit varying degrees of antifungal drug sensitivity. Notably, we discover that GCN5 depletion and the subsequent loss of histone H3 acetylation downregulates key genes involved in ergosterol biosynthesis and drug efflux, resulting in increased susceptibility to azoles and polyenes. Additionally, Gcn5 regulates cell wall integrity and echinocandin resistance through the calcineurin signaling pathway and transcription factor Cas5. In infection models using Galleria mellonella and immunocompromised mice, GCN5 deletion significantly reduces the virulence of C. auris. Furthermore, the Gcn5 inhibitor CPTH2synergizes with caspofungin in vitro and in vivo without notable toxicity. These findings highlight the critical role of Gcn5 in the resistance and pathogenicity of C. auris, positioning it as a promising therapeutic target for combating invasive fungal infections.

overall_design: RNA-Seq profiling of wild-type CBS12767 and gcn5Δ strains after 2-hour treatment with fluconazole or an equal volume of DMSO.

first: Guangsheng

last: Chen

first: Changbin


title: CD55 upregulation in T cells of COVID-19 patients suppresses type-I interferon responses [scRNA-seq]

city: Athens

first: Anastasia

last: Kotanidou

address: 45 Ipsilantou Str

department: 1st Department of Critical Care Medicine and Pulmonary Services

country: Greece

institute: Evangelismos Hospital, National and Kapodistrian University of Athens

summary: Complement overactivation, has been verified in COVID-19 patients. Complement regulatory proteins, including CD55, control complement overactivation thus eliminating complement deposition and cell lysis. We investigated complement regulatory protein expression in COVID-19 for potential deregulated expression patterns driving disease pathogenesis.  Single-cell RNA-seq revealed increased PBMCs CD55 expression in severely and critically ill patients. This increase was also detected upon integrated subclustering analysis of monocyte, T cell and B cell populations. FACS analysis confirmed the significant upregulation of CD55 expression in CD4+ and CD8+ T cell and monocyte populations of severely and critically ill COVID-19 patients. This upregulation was associated with decreased expression of type-I IFN-stimulated genes (ISGs) in patients with severe and critical COVID-19, indicating a suppressor effect of CD55. Silencing of CD55 in T cells from COVID-19 severely ill patients in-vitro and sensitization with SARS-CoV-2 peptides resulted in significantly augmented expression of ISGs and a reversal of their expression to levels similar to control or higher. The present study uncovers, to the best of our knowledge, a novel regulatory effect of CD55 on type-I IFN responses of severely ill COVID-19 patients, thus indicating its contribution to COVID-19 pathogenesis, and identifies a novel mechanistic pathway in the COVID-19 immune response.

overall_design: single cell RNA sequencing of PBMCs from COVID-19 patients and healthy controls used for validation of gene expression data uncovered from scRNA-seq analysis.

first: Maria

middle: G

last: Detsika

last: Sakkou

first: Dimitris

last: Konstantopoulos


title: Exogenous RNA surveillance by proton-sensing TRIM25

city: Seoul

first: Myeonghwan

last: Kim

address: 1, Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: Exogenous mRNAs require cellular machinery for delivery and translation but also encounter inhibitory factors. To investigate their regulation, we performed genome-wide CRISPR screens with in vitro-transcribed mRNAs in lipid nanoparticles (LNPs). Heparan sulfate proteoglycans and vacuolar ATPase were identified as mediators of LNP uptake and endosomal escape, respectively. TRIM25 emerged as a key suppressor inducing turnover of both linear and circular mRNAs. Endoribonucleases, N4BP1 and KHNYN, along with ZAP, act redundantly in TRIM25-dependent surveillance. TRIM25 specifically targets mRNAs delivered via endosomes, and its RNA affinity increases at acidic pH, suggesting activation by protons released from ruptured endosomes. N1-methylpseudouridine (m1Ψ) modification reduces TRIM25’s RNA binding, helping RNAs evade its suppressive effect. This study comprehensively maps cellular pathways regulating LNP-mRNAs, offering insights into RNA immunity and therapeutics.

overall_design: CRISPR-Cas9 knockout screen on in vitro-transcribed mRNAs with or without N1m-pseudouridine modification delivered by LNP. GFP-stably expressing cell line was included as cellular control.

first: Youngjoon

last: Pyo

first: Seong-In

last: Hyun

first: Minseok

last: Jeong

first: Yeon

last: Choi

first: V. Narry


title: METTL14 regulates chondrogenesis through the GDF5–RUNX–extracellular matrix gene axis during limb development [RNA-seq]

status: Public on Apr 03 2025

city: Minneapolis

first: Nobuaki

last: Kikyo

state: MN

address: University of Minnesota, MTRF, Room 2-216, 2001 6th St SE

institute: University of Minnesota

summary: METTL14 forms a protein complex that induces m6A methylation on RNA but its roles in mouse limb development remains elusive. We knocked out Mettl14 in a limb bud-specific manner with the Prx1 promoter-driven Cre. The resulting Prx1-cre;Mettl14 flox/flox (conditional KO or cKO) mice showed shorter limbs with disrupted bone and cartilage development compared with the heterozygous Prx1-cre;Mettl14 wild type/flox (cHet) control mice. To understand the molecular basis for the abnormalities, we analyzed polysome RNA  prepared from day 12.5 (E12.5) embryonic limb buds with RNA-seq.

overall_design: Cytoplasmic fractions were prepared from cKO and cHet limb buds on E12.5 and loaded to sucrose gradient ultracentrifugation to purifiy polysome fractions. Total RNA prepared from the cytoplasmic and polysome fractions were labeled as input and polysome RNA,  respectively and applied to RNA-seq.

first: Nobuko

last: Katoku-Kikyo

first: Hiroko

last: Kawakami

first: Max

last: Cantor

first: Yasuhiko


title: METTL14 regulates chondrogenesis through the GDF5–RUNX–extracellular matrix gene axis during limb development [m6A-seq]

summary: METTL14 forms a protein complex that induces m6A methylation on RNA but its roles in mouse limb development remains elusive. We knocked out Mettl14 in a limb bud-specific manner with the Prx1 promoter-driven Cre. The resulting Prx1-cre;Mettl14 flox/flox (conditional KO or cKO) mice showed shorter limbs with disrupted bone and cartilage development compared with the heterozygous Prx1-cre;Mettl14 wild type/flox (cHet) control mice. To understand the molecular basis for the abnormalities, we applied total RNA from day 12.5 (E12.5) embryonic limb buds to m6A-seq.

overall_design: RNA prepared from cKO and cHet limb buds on E12.5 was applied to m6A-seq as follows. First, a small fraction of the RNA was analyzed with RNA-seq as input. Second, m6A-modified RNA was immunoprecipitated with anti-m6A antibody from the remaining RNA and applied to the second RNA-seq as IP (immunoprecipitated). The sequencing results with a pair of input and IP for six groups (biological triplicates for cKO and cHet each) are uploaded.


title: MicroRNA-371-373 cluster and methylome analysis suggests that a subset of “somatic-type” malignancies arising in germ cell tumors may originate in yolk sac tumor components

city: New York

first: Yiying

last: Yang

state: NY

address: 240 E 38th St

department: Pathology

institute: NYU Langone Health

type: Methylation profiling by genome tiling array

summary: Background: Somatic-type malignancies (SM) arising in germ cell tumors (GCTs) represent aggressive and chemoresistant neoplasms frequently occurring as metastases after chemotherapy. Historically, SM have been interpreted as originating in teratoma; however, recent observations suggest that a subset may derive from yolk sac tumor. In this study, we evaluate the relationship between conventional histologic types of GCT and SM of germ cell origin by assessing expression of miR-371~373 and genomic methylation.  Methods: A cohort of 97 samples (41 SM and 38 conventional GCTs, including paired conventional GCT and SMs from individual tumors) were assessed for miR-371~373 expression (RT-qPCR) and genomic DNA methylation (clinically validated assay).  Results: Expression of miR-371~373 was higher in conventional non-teratomatous GCT than in SM (considered as a single category containing all histologic subtypes). However, miR-371~373 expression was heterogeneous among the latter, with significantly higher levels in  sarcomatoid yolk sac tumor (SYST) and glandular neoplasms than in other SMs. Genomic DNA methylation analysis showed that SMs (considered as a single category) did not form a discrete cluster. Instead, they grouped into subclusters that intercalated with conventional GCTs. Analysis of paired conventional GCT and SM or “SM-like” components (i.e., components with SM histology that did not meet size criteria) from individual tumors demonstrated a clear separation according to histology, suggesting that epigenetic processes play a significant role in the transformation of GCT to SM.   Discussion: A subset of SMs shows molecular similarities to (and may derive from) yolk sac tumor, with SYST and glandular yolk sac tumor possibly representing intermediate phenotypes. The transformation of conventional GCT into SM seems to be driven largely by epigenetic mechanisms, suggesting that trials of targeted treatment with epidrugs may be beneficial in selected patients.

overall_design: FFPE tissues were manually dissected, and DNA was extracted. The DNA was then processed for hybridization and fluorescence staining using the Infinium MethylationEPIC (850k) BeadChip array (Illumina, San Diego, USA) according to the manufacturer’s instructions. The arrays were scanned with the Illumina iScan microarray scanner. Raw idat files were analyzed using R version 4.3.2, and raw intensities were processed with the Bioconductor R package Minfi (23). Each sample’s quality was assessed by mean detection p-value (p < 0.05). Samples were normalized using quantile normalization, and batch effects were corrected using the removeBatchEffect function in the R package limma (24). Probes that failed in one or more samples (detection p < 0.01) and probes with single-nucleotide polymorphisms were removed. Beta-values were calculated using the default offset value of 100 recommended for Illumina assays. Top variable probes were identified by calculating the variance of beta values across all samples, and the top 1000 probes were selected to plot the unsupervised heatmap using the R package ComplexHeatmap (25). PCA was performed based on the top 1000 variable probes using the prcomp function in R.

first: João

last: Lobo

first: Nuno

last: Tiago Tavares

first: Diana

last: Fonseca

first: Carmen

last: Jerónimo

first: Rui

last: Henrique

first: Nicolas

last: Wyvekens

first: Matija

last: Snuderl

first: Fiona

last: Maclean

first: Jennifer

last: Gordetsky

first: Christopher

last: Fletcher

first: Michelle

last: Hirsch

first: Jason

last: Hornick

first: Muhammad

last: Idrees

first: Katrina

last: Collins

first: Laura

last: Warmke

first: Thomas

last: Ulbright

first: Andres

last: Acosta


title: PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma [RNA-seq]

city: Badalona

first: Gerard

last: Martinez-Cebrian

state: Barcelona

address: Edifici Josep carreras, Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Institut Josep carreras

summary: Alveolar rhabdomyosarcoma (ARMS) patients harboring PAX3-FOXO1 and PAX7-FOXO1 fusion proteins exhibit a greater incidence of tumor relapse, metastasis, and poor survival outcome, thereby underscoring the urgent need to develop effective therapies to treat this subtype of childhood cancer. To uncover mechanisms that contribute to tumor initiation, we develop a muscle progenitor model and use epigenomic approaches to unravel genome rewiring events mediated by PAX3/7 fusion proteins. Among the key targets of PAX3/7 fusion proteins, we identify a cohort of oncogenes, FGF receptors, tRNA-modifying enzymes, and genes essential for mitochondrial metabolism and protein translation, which we successfully targeted in preclinical trials. We identify leucine usage as a key factor driving the growth of aggressive PAX-fusion tumors, as limiting its bioavailability impaired oxidative phosphorylation and mitochondrial metabolism, delaying tumor progression and improving survival in vivo. Our data provide a compelling list of actionable targets and suggest promising new strategies to treat this tumor.

overall_design:
Human induced pluripotent stem cells (iPS) were differentiated to muscle progenitors through the inducible expression of Pax7 with doxycycline. Next, we introduce the expression of the oncogenic fusion proteins Pax3-FOXO1 or Pax7-FOXO1 (Flag tagged) using lentiviruses and stopped Pax7 expression for 3 days to study the roles of the fusion proteins in gene regulation. We extracted RNA for gene expression analysis by RNA-seq. We performed Cut&Run followed by sequencing using antibodies against Falg, H3K4me1, H3K4me3 and H3K27ac. Finally, we extracted DNA to perform promoter-capture HiC (pcHiC) and HiC to explore the changes in chromatin topology exerted by the expression of the fusion proteins.

**Please note that the records have been updated with new sample titles and additional sample records on May 5, 2025.

first: Bhargab

last: Kalita

first: Brian

last: Dynlacht


title: PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma [pcHiC_HiC]

overall_design: Human induced pluripotent stem cells (iPS) were differentiated to muscle progenitors through the inducible expression of Pax7 with doxycycline. Next, we introduce the expression of the oncogenic fusion proteins Pax3-FOXO1 or Pax7-FOXO1 (Flag tagged) using lentiviruses and stopped Pax7 expression for 3 days to study the roles of the fusion proteins in gene regulation. We extracted RNA for gene expression analysis by RNA-seq. We performed Cut&Run followed by sequencing using antibodies against Falg, H3K4me1, H3K4me3 and H3K27ac. Finally, we extracted DNA to perform promoter-capture HiC (pcHiC) and HiC to explore the changes in chromatin topology exerted by the expression of the fusion proteins.

first: Brian David


title: Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

summary: The identification of sites of DNA replication initiation in mammalian cells has been challenging. Here, we present unbiased detection of replication initiation events in human cells using BrdU incorporation and single-molecule nanopore sequencing. Increases in BrdU incorporation allow us to measure DNA replication dynamics, including identification of replication initiation, fork direction and termination on individual nanopore sequencing reads. Importantly, initiation and termination events are identified on single-molecules with high resolution, throughout S-phase and across the human genome. We find a significant enrichment of initiation sites within the broad initiation zones identified by population level studies. However, these focused sites only account for ~20% of all identified replication initiation events. Most initiation events are dispersed throughout the genome and are missed by cell population approaches. This indicates that most initiation occurs at sites that, individually, are rarely used. These dispersed initiation sites contrast with the focused sites identified by population studies, in that they do not show a strong relationship to transcription or a particular epigenetic signature. Therefore, single-molecule sequencing enables unbiased detection and characterisation of DNA replication initiation events, including the numerous dispersed initiation events that replicate most of the human genome.

overall_design: Nanopore sequencing to detect BrdU (DNAscent) incorporated at the replication fork in cultured human cells (HeLa-S3 and hTERT-RPE1)

first: Jamie

last: Carrington

first: Rosemary

middle: H

last: Wilson

first: Sathish

last: Thiyagarajan

first: Tom

last: Barker

first: Leah

last: Catchpole

first: Alex

last: Durrant

first: Vanda

last: Knitlhoffer

first: Chris

last: Watkins

first: Karim

last: Gharbi


title: PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma

summary:
Alveolar rhabdomyosarcoma (ARMS) patients harboring PAX3-FOXO1 and PAX7-FOXO1 fusion proteins exhibit a greater incidence of tumor relapse, metastasis, and poor survival outcome, thereby underscoring the urgent need to develop effective therapies to treat this subtype of childhood cancer. To uncover mechanisms that contribute to tumor initiation, we develop a muscle progenitor model and use epigenomic approaches to unravel genome rewiring events mediated by PAX3/7 fusion proteins. Among the key targets of PAX3/7 fusion proteins, we identify a cohort of oncogenes, FGF receptors, tRNA-modifying enzymes, and genes essential for mitochondrial metabolism and protein translation, which we successfully targeted in preclinical trials. We identify leucine usage as a key factor driving the growth of aggressive PAX-fusion tumors, as limiting its bioavailability impaired oxidative phosphorylation and mitochondrial metabolism, delaying tumor progression and improving survival in vivo. Our data provide a compelling list of actionable targets and suggest promising new strategies to treat this tumor.
This SuperSeries is composed of the SubSeries listed below.

first: Justina

last: McEvoy

first: Melody

last: Allensworth

first: Michelle

last: Knight

first: Alessandro

last: Magli

first: Rita

last: Perlingeiro

first: Michael

last: Dyer

first: Elizabeth

last: Stewart


title: Viscoelastic Extracellular Matrix Enhances Epigenetic Remodeling and Cellular Plasticity [ATAC-seq]

status: Public on Apr 02 2025

city: Los Angeles

first: Song

last: Li

state: California

address: 404 Westwood Plaza, Eng VI

institute: UCLA

summary: Extracellular matrices of living tissues exhibit viscoelastic properties, yet how these properties regulate chromatin and the epigenome remains unclear. Here, we show that viscoelastic substrates induce changes in nuclear architecture and epigenome, with more pronounced effects on softer surfaces. Fibroblasts on viscoelastic substrates display larger nuclei, lower chromatin compaction, and differential expression of distinct sets of genes related to the cytoskeleton and nuclear function compared to those on purely elastic surfaces. Slow-relaxing viscoelastic substrates reduce lamin A/C expression and enhance nuclear remodeling. These structural changes are accompanied by a global increase in euchromatin marks and local increase in chromatin accessibility at cis-regulatory elements associated with neuronal and pluripotent genes. Consequently, viscoelastic substrates improve the reprogramming efficiency from fibroblasts into neurons and induced pluripotent stem cells. Collectively, our findings unravel the roles of matrix viscoelasticity in epigenetic regulation and cell reprogramming, with implications for designing smart materials for cell fate engineering.

overall_design: To determine whether substrate viscoelasticity influenced genome-wide chromatin accessibility, primary mouse ear fibroblasts isolated from 1-month-old mice were seeded on elastic or viscoelastic alginate-based hydrogels and samples were collected at 48 hours for ATAC-seq.

first: Yifan

last: Wu

first: Yang

last: Song

first: Jennifer

last: Soto


title: METTL14 regulates chondrogenesis through the GDF5–RUNX–extracellular matrix gene axis during limb development [scRNA-seq]

first: Nobuaki

last: Kikyo

summary: Mettl14 forms a protein complex that induces m6A methylation on RNA but its roles in mouse limb development remains elusive. Here, the Mettl14 gene was knocked out in a limb bud-specific manner in Mettl14 flox/flox mice with the Prx1 promoter-driven cre. Dissociated cells from day 12.5 (E12.5) embryonic limb buds were applied to scRNA-seq to identify differentially expressed genes in a cell type-specific manner. Samples prepared from Per1cre;Mettl14 wild type/flox and Per1cre;Mettl14 flox/flox mice were labeled as cHet and cKO, respectively.

overall_design: Single cells prepared from limb buds on E12.5 were applied to scRNA-seq.

first: Nobuko

last: Katoku-Kikyo

first: Hiroko

last: Kawakami

first: Max

last: Cantor

first: Yasuhiko


title: Phase Separation of MRG15 delays cellular senescence [CUT&Tag]

first: Chunyu

last: Yu

address: Xueyuan Road 38#

institute: Peking University

summary: Phase separation, a biophysical process that segregates subcellular environments into condensates, is recognized for its role in regulating transcription. However, the extent of its influence on cellular senescence processes remains to be fully elucidated. Here, we have established that the depletion of MRG15, a conserved chromodomainprotein, leads to cellular senescence in human mesenchymal stem cells (hMSCs). MRG15 is capable of forming phase-separated liquid condensates via its intrinsically disordered region (IDR). Through the utilization of IDR deletion and replacement assays, we have shed light on the pivotal role that MRG15 condensation plays in the senescence of hMSCs. Through epigenomic and transcriptomic analysis, the depletion of MRG15 impacts pathways that are integral to the cell cycle and the senescence process, as evidenced by the diminished binding and the modified expression of key genes, including CDKN1A, LMNB1, CCNB1, NPM1, MYC, and HMGB2. Within a bleomycin-induced model of idiopathic pulmonary fibrosis in mice, hMSCs of the wild-type variety were able to ameliorate inflammation and fibrosis, a stark contrast to the outcomes observed in MSCs where MRG15 was knocked down or its IDR was deleted. Our findings establishes a link between phase separation and senescence regulation and could present a promising new therapeutic target for the alleviation of age-related diseases and the potential extension of lifespan.

overall_design: To investigate the genomic binding sites of MRG15 and its role in cellular senescence, we performed Cleavage Under Targets & Tagmentation (CUT&Tag) of MRG15 in HEK293T cells.

first: Yuwen

first: Xinrong

last: Jin

first: Hu

last: Wang


title: Cholesterol biosynthesis and mutant IDH activity are linked to cellular glycogen through PPP1R3C in growth plate chondrocytes and chondrosarcoma

city: Durham

first: Makoto

last: Nakagawa

address: 308 Research Drive

department: Department of Orthopaedic Surgery

institute: Duke University

summary: Enchondromas are common bone tumors composed of chondrocytes originating from growth plate cells, which can progress to malignant chondrosarcoma. Mutations in the genes encoding isocitrate dehydrogenase (IDH1 and IDH2) are identified in a large proportion of these tumors. IDH enzymes convert isocitrate to alpha-ketoglutarate (α-KG), an essential component of the citric acid cycle. The mutant IDH enzymes produce 2-hydroxyglutarate (2-HG), which has epigenetic effects important in tumor initiation. Tumor maintenance and growth rely on additional factors as well. Prior work shows that intracellular cholesterol and glycogen are upregulated in mutant IDH chondrocytes.  Here, we show that Protein Phosphatase 1 Regulatory Subunit 3C (PPP1R3C, previously termed Protein Targeting to Glycogen or PTG) is upregulated in chondrocytes harboring a mutant IDH. PPP1R3C expression correlates with the level of intracellular cholesterol biosynthesis and can be regulated by Sterol Regulatory Element-Binding Proteins (SREBPs), which are transcriptional regulators of enzymes involved in sterol biosynthesis. We found that PPP1R3C regulates glycolysis and glycolytic capacity in chondrocytes. Depletion of PPP1R3C in mouse chondrocytes in vivo suppresses the enchondroma phenotype. The growth plate phenotype associated with the inhibition of cholesterol biosynthesis is partially rescued by PPP1R3C overexpression. Taken together, our data show that PPP1R3C integrates the effects of cholesterol metabolism and isocitrate dehydrogenase on growth plate and neoplastic chondrocyte metabolism by regulating intracellular glycogen levels.

overall_design: HA ChIP in HT1080−HA−SREBF2 cells and parental control cells

first: Eijiro

last: Shimada

first: Ryo

last: Miyamoto

first: Benjamin

last: Alman


title: PROTein Evolution Using Selection (PROTEUS)

city: Camperdown

first: Graham

middle: Gregory

last: Neely

state: NSW

address: John Hopkins Drive

country: Australia

institute: Charles Perkins Centre, The University of Sydney

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

sample_organism:
Homo sapiens
Semliki Forest virus
synthetic construct

overall_design: Refer to individual Series


title: Viscoelastic Extracellular Matrix Enhances Epigenetic Remodeling and Cellular Plasticity [RNA-seq]

first: Song

overall_design: To determine whether substrate viscoelasticity altered gene expression in a stiffness-dependent manner, primary mouse ear fibroblasts isolated from 1-month-old mice were seeded on elastic or viscoelastic alginate-based hydrogels of 2 and 20 kPa and samples were collected at 48 hours for RNA-seq.

first: Yifan


title: Transcriptional regulon under the control of LIMYB protein

city: Vicosa

first: Elizabeth

middle: Pacheco

last: Fontes

state: Minas Gerais

address: Av. PH Rolfs, S/N

department: Biochemistry

country: Brazil

institute: Universidade Federal de Vicosa

summary: Seedlings harboring a YFP-LIMYB transgene from three independently transformed lines were used for ChiP-seq. LIMYB-GFP targets from LIMYB-32-L1 LIMYB-32-L3, and LIMYB-32-L4 isolated nuclei were immunoprecipitated using rabbit polyclonal anti-GFP - IgG antibody   ChIPed-DNA was sequenced using Illumina HiSeq 4000

overall_design: Was showed first that the downstream component of the NIK1/RPL10 antiviral signaling module,  LIMYB, which represses translational machinery-related gene expression and translation, also  suppresses photosynthetic apparatus-related genes leading to inhibition of the photosynthetic  function. The repressing transcriptional activity of LIMYB was the primary determinant for the  decrease in electron transport rate, exchange gas parameters, quantum efficiency, and water-use  efficiency in the LIMYB-overexpressing lines. The decreased photosynthetic activity was linked  to the NIK1 antiviral signaling and stunted growth. Activation of antiviral NIK1 by viral or  bacterial PAMPs, or expressing a constitutively activated NIK1 mutant, T474D, inhibited the  photosynthetic function in control lines but not in lymyb knockout lines.

first: Ruan

last: Teixeira

first: Marco

last: Ferreira

first: Otávio

last: Brustolini


title: Single cell RNA sequencing (scRNAseq) of epithelial cells from untreated and IFNy-treated colon organoids

city: Berlin

first: Michael

last: Sigal

address: Augustenburger Platz 1

department: Dept. Hepatology and Gastroenterology

country: Germany

institute: Charité Universitätsmedizin

summary: The colon epithelium frequently faces environmental toxic influences that can result in injuries. Repair is rapid, mediated by cellular plasticity and acquisition of the highly proliferative regenerative state. The mechanisms that promote this state are not fully understood. Here, we addressed the role of the inflammatory cytokine IFN-y on mucosal reorganization and regeneration after injury by analyzing the colonic epithelium. We reveal that IFN-y drives widespread epithelial remodeling that also involves uninjured compartments.

overall_design: Live epithelial cells from colon organoids were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Julian

last: Heuberger

first: Lichao

last: Liu

first: Hilmar

last: Berger

first: Thomas

last: Conrad


title: Phase Separation of MRG15 delays cellular senescence

first: Chunyu

last: Yu


title: Phase Separation of MRG15 delays cellular senescence [RNA-Seq]

overall_design: To explore MRG15's role in cellular senescence, we performed RNA-seq on HEK293T cells with MRG15 knockdown (shMRG) and control (vector) conditions, using Illumina NovaSeq 6000. The study investigates how MRG15 depletion affects gene expression related to senescence, focusing on phase separation's influence on cellular processes.

first: Yuwen

last: Li

first: Xinrong

last: Jin

first: Hu


title: Cholesterol biosynthesis and mutant IDH activity are linked to cellular glycogen through PPP1R3C in growth plate chondrocytes and chondrosarcoma [RNA-seq]

first: Makoto

last: Nakagawa

overall_design: RNA-sequencing for PPP1R3C overexpressing cells and knockout cells in Chondrosarcoma cell lines (HT1080, JJ012)

first: Eijiro

first: Benjamin


title: PDGFRα signaling regulates cartilage and fibrous tissue differentiation during synovial joint development [scRNA-seq]

status: Public on Apr 01 2025

city: Oklahoma city

first: Lorin

last: Olson

state: OK

department: CVB

institute: OMRF

summary: Limb development begins with limb buds that develop into long appendicular bones separated by joint-forming structures called interzones. Mesenchymal progenitor cells of the interzone differentiate into cartilaginous and fibrous tissues of the synovial joint, including articular cartilage, menisci, and ligaments. Platelet-derived growth factor receptor-α (PDGFRα) is expressed by mesenchymal cells of the limb bud, but it is not known to have a role in limb or joint development. By analyzing PDGFRα expression in single-cell RNA sequencing data, immunofluorescence, and lineage tracing, we observed dynamic PDGFRα expression in the mouse limb bud, interzone, and perichondral mesenchyme. To investigate PDGFRα function, we use Prrx1-Cre to cause mouse limb bud mesenchyme to express mutant PDGFRα with a kinase domain point mutation (D842V) that increases receptor signaling. Overall limb development was unaffected. However, the hind limbs were immobile with knee joints fused by cartilage and lacking ligaments and menisci. The mutant perichondrium exhibited ectopic cartilage matrix and the enthesis of the patellar tendon was enlarged. The interzone marker Gdf5 was initially expressed at E12.5 but was downregulated at E13.5 and thereafter, suggesting a defect in maintenance of the interzone. Spatial transcriptomics of the mutant joint identified co-expression of genes for both cartilage (Sox9, Col2a1) and fibrotic tissue (Postn, Col1a1, Col1a2), suggesting fibrocartilage. These data suggest that elevated PDGFRα signaling corrupts joint tissue differentiation by downregulating Gdf5 and redirecting interzone progenitors into a fibrocartilage fate. These results highlight the need to balance chondrogenic and fibrogenic cell fates during joint development, with tight regulation of PDGFRα signaling as a necessity for the development of the mouse knee joint.

overall_design: Cell were dissociated from E13.5 hindlimbs and E15.5 knees and analyzed via scRNA sequencing

first: John Paul

last: Woods

first: Alex

last: Rackley

first: Hae Ryong

last: Kwon

first: Lorin E


title: A novel compound exhibits potent anti-Candida albicans activity

first: Xiaowei

last: Chai

address: Siping Road

institute: Tongji University

summary: Candida albicans is a prevalent fungal pathogen in humans worldwide, causing life-threatening invasive candidiasis in immunocompromised individuals, largely due to the scarcity and poor efficacy of present antifungals, necessitating the search for novel antifungal medications.By leveraging machine learning methodologies, we have identified a novel compound that demonstrates robust antifungal activity against C. albicans. To explore the mechanisms behind its efficacy, we undertook an extensive study involving transcriptomic profiling of C. albicansexposed to the compound across different cultivation times and doses.The findings of this study not only contribute to our understanding of antifungal mechanisms, but also have great potential to guide the development of innovative therapies against C. albicans for meeting the growing clinical demand for new treatments.

overall_design: A comprehensive analysis of the transcriptome of C. albicans exposed to the compound under varying conditions of exposure time and concentration.

first: Hui

last: Lu

first: Yuanying

last: Jiang

first: Xin

last: Huang


title: Viscoelastic Extracellular Matrix Enhances Epigenetic Remodeling and Cellular Plasticity

first: Song


title: Mitochondrial Hyperactivity and Reactive Oxygen Species Drive Innate Immunity to the Yellow Fever Virus-17D Live-Attenuated Vaccine

city: Bethesda

first: Philip

last: Murphy

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: The yellow fever virus 17D (YFV-17D) live attenuated vaccine is considered one of the successful vaccines ever generated associated with high antiviral immunity, yet the signaling mechanisms that drive the response in infected cells are not understood.  Here, we provide a molecular understanding of how metabolic stress and innate immune responses are linked to drive type I IFN expression in response to YFV-17D infection. Comparison of YFV-17D replication with its parental virus, YFV-Asibi, and a related dengue virus revealed that IFN expression requires RIG-I-like Receptor signaling through MAVS, as expected. However, YFV-17D uniquely induces mitochondrial respiration and major metabolic perturbations, including hyperactivation of electron transport to fuel ATP synthase. Mitochondrial hyperactivity generates reactive oxygen species (ROS) including peroxynitrite, blocking of which abrogated MAVS oligomerization and IFN expression in non-immune cells without reducing YFV-17D replication. Scavenging ROS in YFV-17D-infected human dendritic cells increased cell viability yet globally prevented expression of IFN signaling pathways. Thus, adaptation of YFV-17D for high growth imparts mitochondrial hyperactivity to meet energy demands, resulting in generation of ROS as the critical messengers that convert a blunted IFN response into maximal activation of innate immunity essential for vaccine effectiveness.

overall_design: Human monocyte-derived dendritic cells (DCs) were either mock-infected or infected with YFV-17D at an MOI of 0.1. We added fresh DC medium to the wells to the desired volume and MnTBAP (50 µM) or vehicle control was added to the appropriate wells at 0 and 24 h post-infection. At 48 hpi, we harvested hDCs by centrifugation, and lysed the cells with 1 mL of TRIzol reagent/sample (Thermo Fisher Scientific), and samples were stored at -80˚C before extraction and bulk RNA-seq. Differential expression was performed between infected and mock infected.

first: Samantha

last: Muccilli

last: Schwartz

first: Byron

last: Shue

first: Forrest

last: Jessop

first: Jeffrey

last: Shannon

first: Charles

last: Larson

first: Adam

last: Hage

first: Eric

last: Bohrnsen

first: Seon-Hui

last: Hong

first: Thomas

last: Hsu

first: Alison

middle: W

last: Ashbrook

first: Gail

last: Sturdevant

first: Joseph

last: Guarnieri

first: Justin

last: Lack

first: Douglas

middle: C

last: Wallace

first: Catharine

last: Bosio

first: Margaret

last: MacDonald

last: Rice

first: Jonathan

last: Yewdell

first: Sonja

last: Best


title: PDGFRα signaling regulates cartilage and fibrous tissue differentiation during synovial joint development

first: Lorin

last: Olson

overall_design: E14.5 knees were sectioned in a coronal orientation and processed for NanoString GeoMX RNA sequencing analysis.

first: John Paul

last: Woods

first: Alex

last: Rackley

first: Hae Ryong

last: Kwon

first: Lorin E


title: Induced pluripotent stem cell-derived mesenchymal stem cells (iMSCs) inhibit M1 macrophage polarization and reduce alveolar bone loss associated with periodontitis

city: Beijing

first: Liang

last: Chen

address: No.22, Zhongguancun South Avenue, Haidian District

department: Department of Periodontology

institute: Peking University School and Hospital of Stomatology

summary: Background: Periodontitis is a chronic inflammatory disease and macrophages play a pivotal role in the progression of periodontitis. Mesenchymal stem cells (MSCs) have emerged as potential therapeutic agents for the treatment of periodontitis due to their immunomodulatory properties and capacity for tissue regeneration. Compared to conventionally derived MSCs, induced pluripotent stem cell-derived MSCs (iMSCs) offer distinct advantages as promising candidates for MSC-based therapies, owing to their non-invasive acquisition methods and virtually unlimited availability. This study aims to investigate the effects and mechanisms of iMSCs in modulating macrophage polarization and alleviating periodontitis-related alveolar bone loss. Methods: iMSCs were generated from iPSCs and characterized for differentiation potential. The effects of iMSCs on macrophage polarization were evaluated using THP-1-derived macrophages under inflammatory conditions (LPS and IFN-γ stimulation). Co-culture assays, cytokine analysis, reactive oxygen species (ROS) detection, transcriptomic analysis, flow cytometry, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and western blot analysis were performed to elucidate the underlying mechanisms. The therapeutic potential of iMSCs was assessed in a ligature-induced periodontitis mouse model using micro-CT, histological analysis, and immunofluorescence staining. Results: iMSCs inhibit M1 macrophage polarization through the suppression of the NF-κB signaling pathway. Additionally, iMSCs reduce the production of pro-inflammatory cytokines (IL-1β, IL-17) and reactive oxygen species (ROS), while enhancing the secretion of anti-inflammatory cytokines (IL-10) and growth factors (VEGF), thereby improving the inflammatory microenvironment. Under inflammatory conditions, iMSCs preserve the osteogenic potential of periodontal ligament stem cells (PDLSCs) and alleviate alveolar bone loss in mice with periodontitis. In vivo, iMSCs reduce the number of M1 macrophages and inhibit the activation of NF-κB in periodontal tissues, supporting their anti-inflammatory and immunomodulatory effects. Conclusion: iMSCs demonstrate significant therapeutic potential in periodontitis by modulating macrophage polarization, reducing oxidative stress, and mitigating alveolar bone loss associated with the disease. These findings provide new insights into the mechanisms of iMSCs and their application as cell-based therapies for periodontal diseases.

overall_design: RNA-seq profile analysis of macrophages with or without LPS+IFN-γ stimulation and with or without co-culture with iMSCs at 48 hours. THP-1-derived macrophages were divided into four groups: M0 macrophages, M0 macrophages co-cultured with iMSCs (M0+iMSCs), M0 macrophages stimulated with LPS+IFN-γ (M0+LPS+IFN-γ), and M0 macrophages co-cultured with iMSCs under LPS+IFN-γ stimulation (M0+LPS+IFN-γ+iMSCs).

first: Yuanqing

last: Liu

first: Chenhao

last: Yu

first: Pei

last: Cao

first: Qingxian

last: Luan


title: PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma [Cut&Run]

first: Gerard

last: Martinez-Cebrian

overall_design: Human induced pluripotent stem cells (iPS) were differentiated to muscle progenitors through the inducible expression of Pax7 with doxycycline. Next, we introduce the expression of the oncogenic fusion proteins Pax3-FOXO1 or Pax7-FOXO1 (Flag tagged) using lentiviruses and stopped Pax7 expression for 3 days to study the roles of the fusion proteins in gene regulation. We extracted RNA for gene expression analysis by RNA-seq. We performed Cut&Run followed by sequencing using antibodies against Falg, H3K4me1, H3K4me3 and H3K27ac. Finally, we extracted DNA to perform promoter-capture HiC (pcHiC) and HiC to explore the changes in chromatin topology exerted by the expression of the fusion proteins.

first: Bhargab

last: Kalita

first: Brian David

last: Dynlacht


title: Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs [Bisulfite-Seq]

city: Randwick

first: Julie

last: Thoms

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

department: Adult Cancer Program

institute: UNSW Sydney

type: Methylation profiling by high throughput sequencing

summary: Hypomethylating agents are used as frontline therapy for myelodysplastic neoplasms (MDS), but clinical response is unpredictable. To determine whether response was associated with in vivo dynamics of DNA hypomethylation, we conducted a phase 2 trial for MDS using both injection and oral azacitidine (AZA). We established that global DNA methylation levels in peripheral blood and bone marrow mononuclear cells were comparable in AZA responders and non-responders during their course of treatment. However, there were distinct baseline and early drug induced differences in CpG methylation in haematopoietic stem and progenitor cells (HSPCs) in responders compared to non-responders that overlapped with regulatory regions of genes associated with tissue patterning, cell migration and myeloid differentiation. Following six cycles of therapy when clinical response typically manifests, differential hypomethylation in responder HSPCs pointed to marrow adaptation as a driver of enhanced haematopoiesis. Taken together, CpG methylation differences in HSPCs may explain variable response to AZA.

overall_design: Patients were treated with 6 cycles of injected azacitidine, where a cycle consists of 7 days of treatment followed by 21 days rest. Response assessment was done following 6 cycles. Patients then received an additional cycle of oral azacitidine where a cycle consists of 21 days of treatment.

first: Thoms

last: Julie

first: Saw

last: Jesslyn

first: Yan

last: Feng

first: Pimanda

last: John


title: Two-Stage CAR T-Cell Differentiation in Patients with Large B-Cell Lymphoma

city: Chicago

first: Jun

last: Huang

state: IL

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

summary: To investigate the CAR T-cell differentiation in vivo, we performed single-cell, multi-omics analyses of CD28-costimulated CAR T cells from patients with DLBCL who were successfully treated with axicabtagene ciloleucel. Our data shows that CAR T cells undergo two distinct stages of post-infusion clonal expansion.

overall_design: Data includes CAR T cells from infusion products and peripheral blood mononuclear cells from three patients with diffuse large B-cell lymphoma who achieved a complete response to axicabtagene ciloleucel. CAR T cells were sorted from peripheral blood using CD19-tetramers. Peripheral blood CAR T cells were analyzed at multiple timepoints within 90 days following administration of the infusion product to capture the CAR T-cell expansion, peak, and contraction phases.

first: Justin

last: Kline

first: Guoshuai

first: Yifei

last: Hu

first: Tony

last: Pan


title: Isolation of human monoclonal antibodies from 4CMenB vaccinees reveals PorB and LOS as the main OMV components inducing cross-strain protection [OMV Gono]

city: Siena

first: Viola

last: Viviani

address: Via Fiorentina, 1

institute: GSK

summary: In this study, we describe the development and use of an ad hoc protein microarray to characterize the gonococcal cross-binding of HumAbs isolated from 4CMenB vaccinated subjects and induced by the OMV component of the vaccine

overall_design: A panel of gonococcal Outer Membrane Vesicles (OMV) were printed randomly in replicates on a not-commercial protein microarray. The species-specific N.gonorrhoeae OMV array was printed with different OMV in 20% glycerol. Controls consisted of 8 serial 2-fold dilutions of human IgG.

first: Giacomo

last: Vezzani


title: Auricular Malformations Driven by Copy Number Variations in a Hierarchical Enhancer Cluster and Dominant Enhancer Recapitulates Human Pathogenesis

status: Public on Mar 31 2025

city: Guangzhou

first: Xu

last: Xiaopeng

address: 96 Xingdao South Road, Guangzhou International Bio Island, Haizhu District

institute: Guangzhou National Laboratory

summary: Enhancers, through the combinatorial action of transcription factors (TFs), dictate both the spatial specificity and the levels of gene expression, and their aberrations can result in diseases. While HMX1 downstream enhancer is associated to ear malformations, the mechanisms underlying bilateral constricted ear (BCE) remain unclear. Here, we identify a copy number variation (CNV) containing three enhancers—collectively termed the positional identity hierarchical enhancer cluster (PI-HEC)—that drives BCE by coordinately regulating HMX1 expression. Each enhancer exhibits distinct activity-location-structure features, and the dominant enhancer with high mobility group (HMG)-box and homeodomain TF motifs modulating its activity and specificity, respectively. Mouse models demonstrate that neural crest-derived fibroblasts with aberrant Hmx1 expression in the basal pinna, along with ectopic distal pinna expression, disrupt outer ear development, affecting cartilage, muscle, and epidermis. Our findings elucidate mammalian ear morphogenesis and underscore the complexity of synergistic regulation among enhancers and between enhancers and transcription factors.

overall_design: Using of scRNA-seq compare transcriptional difference bewteen wild type and mEC1 knock-in transgenic mouse models.

first: Xiaopeng

last: Xu

first: Qi

last: Chen

first: Qingpei

first: Timothy

last: C. Cox

first: Hao

last: Zhu

first: Jintian

first: Xi

last: Han

first: Ziqiu

last: Meng

first: Bingqing

last: Wang

first: Zhiying

last: Liao

first: Wenxin

first: Baichuan

last: Xiao

first: Ruirui

last: Lang

first: Jiqiang

last: Liu

first: Jian

first: Xiaokai

last: Tang

first: Jinmo

first: Qiang

last: Li

first: Ting

first: Qingguo

last: Zhang

first: Stylianos

last: E. Antonarakis

first: Jiao

first: Xiaoying

last: Fan

first: Huisheng

first: Yong-Biao


title: Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs

first: Julie

last: Thoms


title: Melatonin Synergizes with Prostaglandin E2 to Enhance YAP-mediated Regenerative Epithelial Cell Emergence During Intestinal Repair

city: Yangsan

first: Hansong

last: Lee

address: 49 Busandaehak-ro

institute: Pusan National University

summary: In this study, we explore the role of melatonin, abundantly secreted by enteroendocrine cells (EECs) yet overlooked beyond its circadian regulation, in promoting intestinal regeneration. Our findings demonstrate that melatonin can be integrated into the PGE2-EP4-YAP signaling axis to facilitate injury-responsive reprogramming and RSC induction in the intestinal epithelium both in vitro and in vivo. This work uncovers a novel function of melatonin, opening new therapeutic possibilities in regenerative medicine.

overall_design: The scRNAseq profiles were derived from two groups of mouse small intestinal organoids, treated and untreated melatonin using the 10x Genomics platform.

first: Yoojin

last: Seo

first: Ji-Su

last: Ahn

first: Yun Hak

last: Kim

first: Hyung-Sik