title: Single Cell Analysis of Peripheral TB-Associated Granulomatous Lymphadenitis

summary: We employed a single cell RNA sequencing (scRNA-seq) approach to describe the cells and communication networks characterizing granulomatous lymph nodes of TB patients. When mapping cells from individual patient samples, we uniformly identify several cell types that characterize granulomas. Whether high or low Mtb burden, overall we find the T cell cluster to be the most abundant. Other cell clusters that are uniformly detected, but that vary dramatically in abundance amongst the individual patient samples, are the B cell, plasma cell and macrophage/dendrocyte and NK cell clusters. When we combine all our scRNA-seq data from our current 23 patients (to gain greater n), we distinguish T, macrophage, dendrocyte and plasma cell subclusters. The sizes of these subclusters also varies dramatically amongst the individual patients. In comparing FNA composition we noted trends in which T cell populations and macrophage/dendrocyte populations were negatively or positively correlated with NK cell populations. In addition, we discovered that the scRNA-seq pipeline detects Mtb RNA transcripts and associates them with their host cell’s transcriptome, thus identifying individual infected cells. The number of infected cells also varies dramatically in abundance amongst the patient samples. CellChat analysis identified predominating signaling pathways amongst the cells comprising the various granulomas.


title: Genetic description of isopod species, Livoneca redmanii, at Lake Qarun, Egypt, under the pressure of low salinity and low temperature

status: Public on Mar 03 2025

city: Cairo

first: Hosam

last: Elsaied

address: 101 Kasr ELAiny St.

department: Aquaculture

country: Egypt

institute: National Institute of Oceanography and Fisheries

type: Expression profiling by high throughput sequencing

summary: This study examines the impact of low salinity and temperature on L. redmanii parasitism in Lake Qarun, Egypt, with an emphasis on analyzing the functional gene expression of the parasite, based on RNA sequencing (RNA-Seq). Through the use of de novo transcriptome assembly, this research seeks to identify genes with differential expression in the parasite under different environmental conditions. Thereby, uncovering molecular pathways associated with stress adaptation, metabolism, and virulence.

overall_design:
RNA-Seq profiling of Livoneca redmanii under control, low salinity, and low temperature stress conditions
*** All samples were replaced on Sept. 11, 2025.

first: Engy

middle: T

last: Megahed

first: Mahmoud

last: Saied

first: Adel

last: Abdelmageed


title: Characterisation of an autochthonous mouse ccRCC model of immune checkpoint inhibitor therapy resistance

status: Public on Feb 27 2025

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Hospital Freiburg

summary: Many metastatic clear cell renal cell carcinomas (ccRCC) are resistant to immune checkpoint inhibitor therapies, however the mechanisms underlying sensitivity or resistance remain incompletely characterised. We demonstrate that ccRCCs in the Vhl/Trp53/Rb1 mutant mouse model are resistant to combined anti-PD-1/anti-CTLA-4 therapy alone and in combination with additional therapeutic agents that reflect current ccRCC clinical trials. However, in some animals in vivo checkpoint therapy allowed isolated splenic T cells to recognise cultured ccRCC cells from the same animal, implicating the tumour microenvironment in suppression of T cell activation. We identified putative immunosuppressive myeloid cell populations with features similar to myeloid cells in the microenvironment of human ccRCC. The expression patterns of immune checkpoint ligands in both the mouse model and in human ccRCC suggests that several checkpoint systems other than PD-1 and CTLA-4 are likely to represent the dominant T cell suppressive forces in ccRCC. Our findings characterise an autochthonous mouse ccRCC model of immune checkpoint inhibitor therapy resistance and pave the way for a systematic functional dissection of the identified potential molecular barriers to effective immune therapy of ccRCC.

overall_design: scRNA-seq analysis of a normal kidney and of 3 Vhl/Trp53/Rb1 mutant mouse ccRCC tumours, cells were sorted for CD45.1 and mixed in the ratio of 3:1 positive to negative prior to preparation for scRNA-seq to enrich for immune cells

first: Asin

last: Peighambari

first: Hsin

last: Huang

first: Mojca

last: Adlesic

first: Kyra

last: Zodel

first: Rouven

last: Hoefflin

first: Silvia

last: Schäfer

first: Philipp

last: Seidel

first: Lukas

last: Braun

first: Jan

last: Hülsdünker

first: Wolfgang

last: Melchinger

first: Marie

last: Follo

first: Manching

last: Ku

first: Stefan

last: Haug

first: Yong

last: Li

first: Anna

last: Köttgen

first: Christoph

last: Schell

first: Dominik

last: von Elverfeldt

first: Wilfried

last: Reichardt

first: Robert

last: Zeiser

first: Mathias

last: Heikenwalder

first: Melanie

last: Boerries

first: Ian

middle: J

last: Frew


title: Elucidation of the mechanisms underlying the therapeutic effects of cell therapy using hiPSC-NPCs

status: Public on Feb 26 2025

city: Kyoto

first: Kenji

last: Osafune

address: Shogoin-Kawahara-cho 53

department: Center for iPS Cell Research and Application (CiRA)

country: Japan

institute: Kyoto University

summary: To identify factors contributing to the therapeutic efficacy of hiPSC-NPCs in a cisplatin-induced AKI mouse model, we performed RNA-seq on three samples each of human iPS cell-derived nephron progenitor cells (hiPSC-NPCs) that showed therapeutic efficacy and fate-specific hiPSC-NPCs (hiPSC-FS-NPCs) that showed reduced therapeutic efficacy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from 4A6 cell line-derived hiPSC-NPCs and hiPSC-FS-NPCs (three biological replicates per group).

first: Toshikazu

last: Araoka

first: Kosuke

last: Toyohara

first: Makoto

last: Ryosaka

first: Chihiro

last: Inui

first: Maasa

last: Matsuura

first: Chen

last: Ma

first: Ryuji

last: Yokokawa

first: Mio

last: Iwasaki

first: Jun

last: Watahiki

first: Zhongwei

first: Akira

last: Watanabe

first: Yasuhiko

last: Tabata

first: Juan

middle: C

last: Izpisua Belmonte


title: Preventing CpG hypermethylation in oocytes safeguards mouse development [RNA-seq]

status: Public on Mar 27 2025

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary: DNA methylation (DNAme) controls gene expression, genome stability and cell identity in many mammalian organisms. Genomes of most somatic cells and spermatozoa are largely methylated, apart from CpG-dense sequences including gene promoters1. In mouse oocytes, DNAme is mostly limited to transcribed regions2,3. The mechanisms restricting global DNAme acquisition in developing oocytes and the relevance thereof for regulating gene expression and embryo development after fertilization are unknown. Here we show that the histone H3 lysine 36 dimethyl (H3K36me2) demethylases KDM2A and KDM2B redundantly execute multiple chromatin functions during oocyte development, which are vital to pre- and post-implantation development. Firstly, by serving as recruitment factors of variant Polycomb Repressive Complex 1 (vPRC1), they control genome-wide H2A mono-ubiquitination deposition (H2AK119u1) and PRC1-dependent gene repression4. Secondly, as demethylases, KDM2A/KDM2B prevent global H3K36me2 accumulation, thereby impeding DNMT3A-catalyzed de novo DNAme within PRC1-controlled promoter, genic, and intergenic regions, and even at non-PRC1-controlled CpG-dense gene promoters5. Decisively, we demonstrate that aberrant Dnmt3a-dependent DNAme established in Kdm2a/Kdm2b double mutant oocytes represses transcription from maternal loci in two-cell embryos and impairs pre-implantation development. Hence, KDM2A/KDM2B are essential for defining the appropriate oocyte DNA methylome which in turn conveys competence for early embryonic development. Our research implies that the reprogramming capacity eminent to early embryos is insufficient to erase aberrant DNAme from maternal chromatin. Lastly, our work shows that early development is vulnerable to gene dosage haplo-insufficiency effects, possibly in a parental-specific manner.

overall_design:
To study the transcriptional regulatory function of KDM2A and KDM2B in oocytes and pre-implantation embryos, we conditionally altered their expression in growing oocytes in several ways:
First, by using Zp3-driven CRE recombinase-mediated excision, we removed exons encoding the histone demethylase JmjC domains of Kdm2a or Kdm2b, which fully abrogated expression of either protein.
We also generated mice expressing a KDM2B protein lacking its CxxC domain, unable to be recruited to CpG island regions of the mouse genome.
To address possible combinatorial roles of both proteins, we generated oocytes conditionally deficient for Kdm2a in combination with either Kdm2b mutation.
To compare Kdm2a and Kdm2b function to PRC1 function we generated oocytes deficient for Ring1 and Rnf2 (as described previously by Posfai et al., 2012).
We profiled transcriptomes of single growing oocytes at day 9 and day 14 as well as of fully grown germinal vesicle oocytes for combinations of Kdm2a and Kdm2b mutants (as indicated) as well as for Ring1; Rnf2 double mutants using Smart-Seq2 protocol. In addition, we profiled transcriptomes using bulk total-RNA random primed protocol from day 14 growing oocytes, either wildtype or double deficient for Kdm2a and Kdm2b expression.
We also profiled expression in 2-cell embryos, control or maternally deficient for different Kdm2a; Kdm2b mutations as indicated.

first: Yumiko

middle: K

last: Kawamura

first: Panagiotis

last: Papasaikas

first: Evgeniy

middle: A

last: Ozonov

middle: H


title: Imiquimod-Loaded Phospholipid-Free Unilamellar Vesicles Activate the Tumor Immune Microenvironment to Treat Liver Cancer and Liver Metastases

status: Public on Mar 01 2025

city: Hsinchu

first: Hsin mei

last: Lee

address: Guangfu Rd.

country: Taiwan

institute: National Tsing Hua University

summary: Liver cancers are often diagnosed at advanced stages and the fourth most common cause of cancer death globally. Addition to primary tumours, liver metastases are also common from other cancer sites like colorectal cancers, where 66% of patients develop this condition. Immunotherapies for these diseases have been hindered by the immunosuppressive microenvironment. Our lab has developed phospholipid-free unilamellar vesicles (PFSUV) to localize a toll-like receptor 7 agonist Imiquimod (IMQ), to the hepatocytes. PFSUV is composed of 83 mol% cholesterol and 17 mol% Tween80 and IMQ was loaded inside the aqueous core of these 75-nm particles. When administered intravenously (i.v.), PFSUV-IMQ was found to sustain IFN-α levels in the liver over 24 hours, with significantly lower plasma IFN-α levels compared to free IMQ. In a mouse model of liver metastasis from a colorectal cancer origin generated with CT26 cells, mice treated with PFSUV-IMQ in combination with Oxaliplatin showed a significant reduction in tumour size, with increases in CD8+ T cell and a higher percentage of apoptotic cells in the tumour compared to controls. In a mouse model of primary liver cancer using HCA-1 cells, the same treatment combination also showed a significant decrease in tumour burden, increased apoptotic cell percentage in the tumour, and significantly reduced lung metastasis from the liver compared to controls. Flow cytometry analysis showed tumours treated with PFSUV-IMQ had increased infiltration of CD86+/MHC-II+ dendritic cells and IFN-y+ CD8+ T cells. RNA-seq showed an enrichment of innate immune activation genes after a single dose of PFSUV-IMQ. Overall, these data suggest that the activation of the tumour immune microenvironment through this targeted delivery of IMQ resulted in a decrease in tumour burden across both liver tumour models.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine HCC tumors with or without treatment of IMQ-NP.

first: Yunching

last: Chen

first: Hsin-Mei


title: Defects in nephrogenesis result in an expansion of the Foxd1+ stromal progenitor population

status: Public on Feb 22 2025

city: Dallas

first: Keri

last: Drake

state: Texas

address: 5323 Harry Hines Boulevard

department: Pediatric Nephrology

country: USA

institute: UTSW

summary: Reciprocal signaling interactions coordinate multiple aspects of kidney development. While signals from the stroma have been shown to regulate nephron progenitor cell (NPC) differentiation, much less is known about regulation of the stromal progenitor population. We sought to further examine how defects in the nephron lineage may non-autonomously affect stromal development. To aid in this analysis, we generated single nuclei RNA-seq using 10x genomics from paired E15.5 control kidneys (cre-negative and Six2creTGC) and mutant kidneys (Six2cre;Wt1c/c) to identify additional markers and gene expression changes of the Foxd1+ stromal progenitor population at this timepoint, and validated the expression of early B cell factor 3 (Ebf3), aldehyde oxidase 3 (Aox3), fibroblast activation protein (Fap), insulin growth factor 1 (Igf1), and glutamate ionotropic receptor AMPA type subunit 1 (Gria1) in control and mutant kidneys.

overall_design: Kidneys were harvested from E15.5 mouse embryos by timed pregnant matings. Nuclei isolation was performed for 10x genomics single nuclei RNA-seq, targeting 5000 nuclei with 50K reads/nuclei from Six2creTGC and mutant samples and 5000 nuclei with 90K reads/nuclei from one cre-negative and mutant sample.

first: Drake

last: Keri

first: Ma

last: Yanru


title: Copper-induced stress mechanisms in Erwinia amylovora: a comparative phenotypic and transcriptomic study using copper-sensitive and -tolerant strains

status: Public on Feb 28 2025

city: Prosser

first: Ricardo

last: Delgado Santander

address: 24106 N Bunn Rd

institute: Washington State University

summary: Erwinia amylovora causes fire blight. Copper is widely used for fire blight management but there is limited information on the pathogen’s copper homeostasis mechanisms. Upon identifyingE. amylovora strains with unusually high (EaR2, Ea17) and intermediate (Ea19) copper sensitivity, we characterized them phenotypically to find potential correlations with other traits.The highly copper-sensitive strains EaR2 and Ea17 grew slower, showed increased sensitivity to paraquat and cadmium, and developed a characteristic copper-dependent overproduction of amylovoran and levan, with patterns not observed in strain, Ea273, with regular copper tolerance. Copper sensitivity was also associated with higher copper-shock death rates after copper pre-exposure during growth. RNA-Seq analysis revealed similar responses to copper-shock in EaR2 and Ea273 but very different transcriptomic responses during copper adaptation(prolonged growth with copper). EaR2 responded to copper adaptation with earlier activation ofstress responses, exopolysaccharide biosynthesis pathways, and protein quality control systems, while reducing the expression of genes linked to iron uptake. Ea273 mostly displayed an activation of copper homeostasis-related genes, with a characteristic downregulation of histidine catabolism.

overall_design: RNA-seq profiling of copper shock and copper adaptation responses in Erwinia amylovora strains with regular and hypersensitive copper tolerance

first: Awais

last: Khan

first: Paul

last: Stodghill

first: Srðan

last: Aćimović


title: HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy [RNA-Seq_QJ8080]

status: Public on Feb 20 2025

city: Boston

first: Qinqin

last: Jiang

state: Ma

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Clear cell renal cell carcinoma (ccRCC), despite having a low mutational burden, is considered immunogenic because it occasionally undergoes spontaneous regressions and often responds to immunotherapies. The signature lesion in ccRCC is inactivation of the VHL tumor suppressor gene and consequent upregulation of the HIF transcription factor. An earlier case report described a ccRCC patient who was cured by an allogeneic stem cell transplant and later found to have donor-derived T cells that recognized a ccRCC-specific peptide encoded by a HIF-responsive endogenous retrovirus (ERVE-4). We report that ERVE-4 is one of many ERVs that are induced by HIF, translated into HLA-bound peptides in ccRCCs, and capable of generating antigen-specific T cell responses. Moreover, ERV expression can be induced in non-ccRCC tumors with clinical-grade HIF stabilizers. These findings have implications for leveraging ERVs for cancer immunotherapy.

overall_design: We aim to systematically identify HIF-responsive ERVs by RNA-Seq in 786-O cells. We generated three isogenic comparisons to create HIF2 high and low status, for which cells 1) were stably infected with a virus encoding pVHL (VHL) or the empty vector (EV), 2) were treated with 2 uM PT2399 (PT) or vehicle (Veh) for 72 hours, 3) underwent CRISPR-based gene editing with a HIF2a sgRNA or a contrl sgRNA (sgCtrl). We then performed RNA-Seq experiments to quantify ERV amount for each condition in triplicates.

first: David

last: Braun

first: Cleo

last: Forman

first: Zachary

last: Herbert

first: Sachet

last: Shukla

first: Catherine

last: Wu

first: William

middle: G

last: Kaelin Jr


title: HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We aim to systematically identify HIF2α binding sites genome-wide by ChIP-Seq. We performed ChIP-Seq experiments using an anti-HIF2α antibody and isogenic 786-O cells in which HIF2α was or was not eliminated using CRISPR/Cas9. To further enhance our ability to detect HIF2α-binding sites, we also performed ChIP-Seq using an anti-FLAG antibody and ccRCC cells (786-O, OS-RC-2, and RCC4) cells in which CRISPR/Cas9 was used to append a FLAG-HA epitope tag to the N-terminus of HIF2α expressed from the endogenous HIF2α locus. In order to identify additional HIF2α binding sites upon DNMT1i treatment, we also treated isogenic 786-O cells cells that underwent CRISPR-based gene editing with a HIF2α sgRNA or a control sgRNA (sgCtrl) with 0.5 uM GSK3685032 (DNMT1i) for 9 days.

first: Nitin

last: Shirole

first: Ashwin

middle: V

last: Kammula

first: Yijia

first: Rong

last: Li

first: Sudeepa

last: Syamala

first: Xintao

last: Qiu

first: Paloma

last: Cejas

first: Henry

middle: W

last: Long


title: Epigenetic signatures of intergenerational exposure to violence during pregnancy

city: GAINESVILLE

first: Edward

last: Quinn

state: FL

address: 2033 Mowry Road

department: Anthropology

institute: University of Florida

summary: There is substantial evidence for intergenerational health effects of trauma. The biological mechanisms linking traumatic exposures with intergenerational health effects remain unclear, but epigenetics represent a candidate mechanism. We measured DNA methyation to test for intergenerational epigenetic signatures of exposure to violence during pregnancy. Participating families were recruited based on generational exposure to violence trauma. There were four groups: unexposed controls, directly exposed to violence, prenatally exposed to violence, and germline exposed to violence. Three separate epigenome-wide association studies compared direct, prenatal, and germline exposure to unexposed controls to test for differentially methylated positions.

overall_design: Bisulphite converted DNA from the 160 samples were hybridised to the Illumina Infinium MethylationEPIC v1.0 Beadchip

middle: B

first: Connie

last: Mulligan


title: HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy [PRO-seq]

first: Qinqin

overall_design: We aim to systematically identify direct transcriptional target of HIF2a by PRO-Seq in OS-RC-2 cells. OS-RC-2 cells were treated with 2 uM PT2399 (PT) or vehicle (Veh) for 2 hours, we then performed PRO-Seq experiments to quantify ERV amount for each condition in triplicates.


title: Leptin Receptor Ablation in Anterior Pituitary Somatotropes Reveals Broad Transcriptomic Changes and Sex-Specific Signaling Pathways

status: Public on Feb 19 2025

city: LITTLE ROCK

first: Melanie

last: MacNicol

state: Arkansas

address: 4301 W Markham St

department: Neuroscience

institute: UAMS

summary: Anterior pituitary somatotropes utilize metabolic signals from the adipokine leptin to optimize responses to the body’s nutritional state via expression of growth hormone (GH), growth hormone releasing hormone receptors (GHRHR) and their transcriptional regulator POU1F1.  To identify the mechanism underlying leptin action upon somatotropes, we analyzed single cell transcriptomes of pituitaries from somatotropes lacking leptin receptors (LEPR-null) compared with control pituitaries. Computational clustering of results identified all common pituitay cell types plus 5 undefined (UND) clusters. Differentially expressed genes (DEGs) (Log2FC0.58; adjusted p<0.055 thresholds) in mutant males revealed effects upon both transcriptional and mRNA translation regulators, but not direct effects upon hormone mRNA expression.  Dysfunction in the male mutant LEPR-null somatotrope cluster was indicated by down-regulated genes in key transcriptional and second messenger signaling pathways, which were  mostly upregulated in mutant females. Furthermore, mutant female somatotrope dysfunction was indicataed by an increase in markers for pituitary stem and/or progenitor cells (e.g.Sox9) and also increases (0.67-2.6-fold) in non-somatotrope hormone DEGs, e.g. Pomc, Lhb, Tshb, Cga, and/or Prl in female somatotrope, lactotrope, thyrotrope, corticotrope, and the UND3 clusters. Gh mRNA was decreased in mutant female somatotrope, UND2 and UND3 clusters.  Collectively the increases in multihormonal expression did not coincide with increased expression of receptors for their releasing hormones. This and the presence of Sox9 suggested that the female somatotropes presented an immature gene signature.  Collectively, these data point to a trophic role for leptin in the differentiation and/or maturation of somatotropes through regulatory pathways that are unique to each sex.

overall_design: Cre plus (somatotrope LEPR-null) mutants were compared to CRE minus controls in both males and females.

first: Tiffany

last: Miles

first: Angela

last: Odle

first: Stephanie

middle: D

last: Byrum

first: Alex

last: Lagasse

first: Anessa

last: Haney

first: Victoria

last: Ortega

first: Ashley

last: Herdman

first: Angus

middle: M

first: Gwen

last: Childs


title: Genome-wide tongue epithelia transcriptomic profiles from K14-rtTA;TRE-FLBmi-1 (KrTB), KrTB+Doxycycline (KrTB-D), KrTB+4-nitroquinoline 1-oxide (KrTB-N), and KrTB+Doxycycline+4-nitroquinoline 1-oxide (KrTB-DN).

status: Public on Mar 19 2025

city: New York City

first: Jorge

last: Baquero

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

summary: We developed a transgenic mouse model (truncated K14-rtTA; TRE/Bmi1, KrTB) containing a doxycycline- (dox) controlled, Tet-responsive element system to selectively overexpress BMI1 only in the basal epithelial SCs of the tongue. Here, we used this model to delineate BMI1 actions in tongue epithelia during oral tumorigenesis (as induced by 4-nitroquinoline 1-oxide, 4-NQO). Genome-wide transcriptomics indicated that mRNAs associated with human OSCC, including SOX9, HIF1A, MMP9, INHBB, and MYOF, were further increased by ectopic BMI1 expression in murine tongue epithelia. mRNAs encoding multiple metabolic targets, such as SLC2A1 (GLUT1), PKM, LDHA, and HK2, were also increased upon BMI1 overexpression in 4-NQO-treated tongue epithelia.

overall_design: Examination of genome-wide transcript levels in mouse tongue epithelia samples. 16 samples were analyzed, 4 biological replicates per condition (KrTB vs. KrTB-D and KrTB-N vs. KrTB-DN).

first: Xiao-Han

last: Tang

first: Daniel

last: Galke

first: Theresa

last: Scognamiglio

first: Tuo

last: Zhang

first: Dawson

last: Miller

first: Qiuying

last: Chen

first: Steven

last: Gross

first: Lorraine

last: Gudas


title: Impact of Life Adversity and Gene Expression on Psychiatric Symptoms in Children and Adolescents: Findings from the Brazilian High Risk Cohort Study

status: Public on Feb 18 2025

city: Sao Paulo

first: Sintia

last: Belangero

address: Rua Botucatu

department: Morphology and Genetics

country: Brazil

institute: UNIFESP

summary: While the influence of both genetic and environmental factors on the development of psychiatric symptoms is well-recognized, the precise nature of their interaction throughout development remains a subject of ongoing debate. This study investigated the association between the expression of 78 candidate genes, previously associated with psychiatric phenotypes, in peripheral blood and both adversity and psychopathology in a sample of 298 young individuals assessed at two time points from the Brazilian High Risk Cohort Study for Mental Conditions (BHRCS). Psychopathology was assessed using the Child Behavior Checklist (CBCL), considering the total CBCL, p-factor (i.e. general factor of psychopathology), and internalizing and externalizing symptoms as clinical variables. The life adversities considered in this study includes four composite variables: child maltreatment, stressful life events, threat and deprivation.Gene expression was measured using next-generation sequencing for target genes and differential gene expression was analyzed with the DESeq2 package. Mixed models revealed six genes associated with internalizing symptoms: NR3C1, HSPBP1, SIN3A, SMAD4, and CRLF3 genes exhibited a negative correlation with these symptoms, while FAR1 gene showed a positive correlation. Additionally, we also found a negative association between USP38 gene expression and externalizing symptoms. Finally, DENND11 and PRRC1 genes were negatively associated with deprivation, a latent factor characterized by neglect, parental absence, and measures of material forms of deprivation. No mediation or moderation effect was observed of gene expression on the association between life adversities and psychiatric symptoms, meaning that they might influence distinct pathways. Among these nine genes, NR3C1, which encodes a glucocorticoid receptor, is by far the most investigated, being associated with depressive symptoms, early life adversity, and stress. While further research is needed to fully understand the complex relationship between gene expression, life adversities, and psychopathology, our findings provide valuable insights into the molecular mechanisms underlying mental disorders.

overall_design: Target RNA sequencing of 78 candidate genes was performed on blood samples from 298 young individuals participating in the Brazilian High Risk Cohort study.  Gene expression was assessed at two time points (baseline and follow-up)

first: Vanessa

last: Ota

first: Adrielle

last: Oliveira

first: Amanda

last: Bugiga

first: Helena

last: Conceição

first: Pedro

last: Galante

first: Paula

last: Asprino

first: Julia

middle: L

last: Schafer

first: Mauricio

last: Hoffmann

first: Rodrigo

last: Bressan

first: Elisa

last: Brietzke

first: Gisele

last: Manfro

last: Grassi-Oliveira

first: Ary

last: Gadelha

first: Luis

last: Rohde

first: Euripedes

last: Miguel

last: Pan

first: Marcos

last: Santoro

first: Giovanni

last: Salum

first: Carolina

last: Carvalho

middle: I


title: Pt-seq unveils the genomic binding pattern of platinum-based drugs [Target-seq and RNA-seq]

status: Public on Feb 13 2025

city: Beijing

first: Mingyang

last: Li

address: Yanyuan Subdistrict, Haidian District

country: China

institute: Peking University

summary: Platinum-based drugs (Pt drugs) are widely used in cancer chemotherapy, yet their genome-wide DNA binding patterns remain incompletely understood. Here, we present Pt-seq, an antibody-assisted, genome-wide method for mapping Pt-DNA adducts at single-base resolution. By employing exo- and endo- nucleases to remove background DNA, Pt-seq enables highly robust and sensitive profiling of binding sites for cisplatin, oxaliplatin, lobaplatin, and a Pt(IV) complex. Using Pt-seq, we identified hundreds to a few thousand binding clusters that are 10-20 kb in length and highly consistent among different Pt drugs. Notably, these binding clusters predominantly localize to centromeric and rDNA regions. In cisplatin-resistant cells, we found significantly reduced binding within these regions, suggesting a potential role in drug resistance. Moreover, we found that de novo mutations in cancer cells can create novel binding sites for Pt drugs. Based on this, we demonstrated that ICR-191, an acridine orange compound capable of inducing G insertions, enhances cisplatin-DNA crosslinking and sensitizes cells to Pt drugs. Collectively, Pt-seq sensitively profiles Pt drug-DNA interactions and deepens our understanding of the genome-wide effect of chemotherapeutic drugs.

overall_design: This dataset includes Pt-drugs treatment on HeLa cells, including cisplatin, oxaliplatin, lobaplatin and Pt-Bio-I, also includes cisplatin treatment on A549 wildtype and cisplatin-resistant cell lines (all Pt-seq libraries). Besides, this dataset includes Pt-seq of cisplatin treatment on CHO cell lines, with or without ICR-191 treatment as well. Target-seq libraries on HGPRT gene of CHO with or without ICR-191 treatment are also included.

first: Chuyun

last: Shao


title: Restoring Mitochondrial Quantity and Quality to Reverse Warburg Effect and Drive Tumor Differentiation

status: Public on Jan 31 2025

city: palo alto

first: Jiangbin

last: ye

state: California

address: 269 Campus Drive CCSR-South 1245

institute: Stanford university

summary: Reduced mitochondrial quality and quantity in tumors is associated with dedifferentiation and increased malignancy. However, it remains unclear how to restore mitochondrial quantity and quality in tumors, and whether mitochondrial restoration can drive tumor differentiation. Our study shows that restoring mitochondrial function using retinoic acid (RA) to boost mitochondrial biogenesis and a mitochondrial uncoupler to enhance respiration synergistically drives neuroblastoma differentiation and inhibits proliferation. U-13C-glucose/glutamine isotope tracing revealed a metabolic shift from the pentose phosphate pathway to oxidative phosphorylation, accelerating the TCA cycle and switching substrate preference from glutamine to glucose. These effects were reversed by ETC inhibitors or in ρ0 cells lacking mtDNA, emphasizing the necessity of mitochondrial function for differentiation. Dietary RA and uncoupler treatment promoted tumor differentiation in an orthotopic neuroblastoma xenograft model, evidenced by neuropil production and Schwann cell recruitment. Single-cell RNA sequencing analysis of the orthotopic xenografts revealed that this strategy effectively eliminated the stem cell population, promoted differentiation, and increased mitochondrial gene signatures along the differentiation trajectory, which could potentially significantly improve patient outcomes. Collectively, our findings establish a mitochondria-centric therapeutic strategy for inducing tumor differentiation, suggesting that maintaining/driving differentiation in tumor requires not only ATP production but also continuous ATP consumption and sustained ETC activity.

overall_design: Proper number of cells were plate in 10cm dishes before  treatment by 1µM RA or 1µM RA and RA+ NEN for 24h.  Each group contain 3 biological replicates.

first: Haowen

last: Jiang

first: JIangbin

last: Ye


title: Quorum sensing by Streptococcus pyogenes induces global inflammatory suppression in host macrophages

status: Public on Feb 08 2025

city: Chicago

first: Michael

last: Federle

state: IL

address: 900 S. Ashland Avenue

department: Pharmaceutical Sciences

institute: Universiry of Illinois - Chicago

summary: Streptococcus pyogenes or Group A Streptococcus (GAS), a significant human pathogen, employs quorum sensing (QS) systems to coordinate its behavior and genetic regulation to enhance survival. Our previous research established that one such QS system, the Rgg2/3 system, can suppress macrophage NFκB activity and production of pro-inflammatory cytokines. Yet, the scope of suppression and the mechanism by which it occurs remain unknown. In this study, transcriptomic and phosphoproteomic approaches were used to address these unanswered questions. It was found that QS-ON GAS broadly suppressed most inflammatory transcriptional pathways, including those of NFκB, type I and type II interferon responses, and intracellular stress responses. Yet, we found that no alternative transcriptional programs were activated after QS-ON GAS infection. Additionally, phosphoproteomics showed no disruption in typical inflammatory pathways such as those related to NFκB and MAPK activation, which was confirmed by western blotting and translocation assays. Instead, the proteomic data highlighted a potential role for epigenetic mechanisms of inflammatory regulation. A role for epigenetic regulation in QS-mediated immunomodulation was validated using pharmacological inhibitors of histone and chromatin modifiers. These findings expand our understanding of QS-mediated suppression and of GAS virulence strategies that appear to employ atypical methods of restricting inflammation. Uncovering this mechanism will offer invaluable insight into GAS itself, as well as into understudied immunological pathways.

overall_design: RNAseq profiling the response of RAW264.7 cells to Δrgg2 (QS-OFF), Δrgg3 (QS-ON), Δrgg2 +Δrgg3 (MIXED) Group A Strep infections at 2h-, 4h-, and 8h- post infection as well as uninfected cells.

first: Kate

last: Rahbari

first: Trevor

middle: R

last: Leonardo

first: Sam

middle: F

last: Feldstein


title: Novel insights into the genetic basis and proteotranscriptomic elucidation of virulence attenuation in Pseudomonas syringae pv. actinidiae  variants

city: Guiyang

first: Muhammad

last: Asif

state: Guizhou

address: college of agriculture, Guizhou university

department: Plant Pathology

institute: Guizhou University

summary: Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of kiwifruit bacterial canker, but the factors affecting its pathogenicity in natural settings remain poorly explored. In this study, we isolated two Psa strains, G126 and G282 from infected kiwifruit orchards in Guizhou Province of China. Both isolates, categorized as Psa-biovar 3, were confirmed through Psa3-specific primers and phylogenomic analysis. Pathogenicity assays on kiwifruit cultivar ‘Hongyang’ leaves and branches showed significantly reduced numbers of necrotic spots and reduced lesions sizes upon infection with G282 compared to the G1 positive control strain, while G126 showed nonpathogenic phenotype. Additionally, both strains failed to induce a hypersensitive response in nonhost Nicotiana tabacum plants, and exhibited significantly reduced promoter activity of the hrpR/S, hrpL, and hrpA genes, which are crucial for the type III secretion system (T3SS). Genomic sequencing revealed that the T3SS of G126 was defective due to a single-nucleotide polymorphism in the hrpR gene, while G282 was entirely deficient in the type VI secretion system (T6SS), which potentially regulates the expression of T3SS genes. Transcriptomic analysis showed widespread alterations in key aspects of the secretion system, protein transport, and signal transduction, further supporting the phenotype characteristics exhibited by the strains. This study enhances our understanding of the genetic basis of nonpathogenic and partially pathogenic Psa isolates, highlighting the functional interdependencies between T3SS and T6SS.

overall_design:
RNA-seq profiling of wild-type strain G1， non-pathogenic strain G126 and Pathogenetic deficiency mutant G282 after 6-hour induction in HDM (hrp-derepressing medium) culture medium

Grant awarded to Zhao Zhibo: National Key Research and Development Program of China (Grant No. 2022YFD1400200)
Grant awarded to Zhao Zhibo: National Natural Science Foundation of China (Grant No. 31860486, 32001864)
Grant awarded to Zhao Zhibo: Fund for the China Agriculture Research System (Grant No. CARS-26-04A)

first: Renjian

last: Hu

first: Ting

last: Xie

first: Zhibo

last: Zhao


title: restoring mitochondrial quantity and quality to reverse warburg effect and drive neuroblastoma differentiation

status: Public on Jan 29 2025

city: Palo Alto

state: CA

address: 269 Campus Dr

institute: Stanford University

overall_design: Tumors with volumes ranging from 500 to 800 mm³ were collected from each group (CTRL, RA, NEN, and RA+NEN diet) within approximately 2 weeks of treatment. Two tumors per group were harvested for single cell RNA seq.


title: Cannabinoid Receptor 2 Agonists Attenuate HIV Replication and Inflammatory Activation in HIV-infected Myeloid Cells

status: Public on Jan 22 2025

city: Philadelphia

first: Kelly

last: Jordan-Sciutto

state: PA

address: 240 S. 40th St, Levy Building, Room 312

department: Oral Medicine

institute: University of Pennsylvania, School of Dental Medicine

summary: Emerging evidence suggests brain-resident myeloid cells, including macrophages and microglia, provide a reservoir for HIV infection in the central nervous system (CNS), and their inflammatory activation is a proposed pathogenic mechanism in HIV-associated neurocognitive disorders (HAND). We investigated whether cannabinoid receptor 2 (CB2), an immunomodulatory receptor expressed in myeloid cells, regulates viral replication and inflammation in HIV-infected macrophages and microglia. Using the synthetic CB2-specific agonist, JWH-133, we found that CB2 activation reduces HIV replication in primary human monocyte-derived macrophages (MDMs) and human iPSC-derived microglia (iMg) at differing doses, corresponding to the basal expression of CNR2 and related endocannabinoid transcripts in each cell type. Direct CB2 agonism via JWH-133 broadly reduced cytokine release from HIV-infected MDMs, but not iMg. RNA-seq revealed that CB2 agonism primarily altered interferon and integrated stress response pathways in MDMs; homeostatic pathways, including synapse maintenance and phagocytosis, were altered in iMg. Further investigation in iMg found NLRP3 inflammasome activation, but not priming, was reduced by CB2 activation. This study identifies key discrepancies in CB2 response between myeloid cell types and implicates CB2-specific agonists as promising candidates for regulation of HIV-associated neuroinflammation.

overall_design: Human primary monocyte-derived macrophages (MDM) and iPSC-derived microglia (iMg) underwent true or mock infection with HIV-ADA. 24 hours after HIV infection, samples were treated with vehicle (DMSO) or 1 uM JWH-133, a cannabinoid receptor 2-specific agonist. Infected cultures were maintained for 9 days,with cannabinoids replaced during media change every 48 hours. RNA was extracted on day post infection 9 to assess the myeloid cell-type specific responses to HIV infection and concurrent CB2 activation.

first: Alexander

last: Starr

first: Sara

last: Rathore

first: Peter

last: Gaskill

first: Cagla

middle: E

last: Akay-Espinoza


title: cPRC1.2 and CTCF-Mediated Transition from Poised to Active Chromatin Loops Drives Bivalent Gene Activation

status: Public on Jan 28 2025

city: Hershey

first: Zhonghua

last: Gao

address: 700 HMC Cres Rd

department: Biochemistry

institute: Pennsylvania State University

summary: Polycomb Repressive Complex 1 (PRC1) and CCCTC-binding factor (CTCF) are critical regulators of 3D chromatin architecture that influence cellular transcriptional programs. Spatial chromatin structures comprise conserved compartments, topologically associating domains (TADs), and dynamic, cell-type-specific chromatin loops. Although the role of CTCF in chromatin organization is well-known, the involvement of PRC1 is less understood. In this study, we identified an unexpected, essential role for the canonical Pcgf2-containing PRC1 complex (cPRC1.2), a known transcriptional repressor, in activating bivalent genes during differentiation. Our Hi-C analysis revealed that cPRC1.2 forms chromatin loops at bivalent promoters, rendering them silent yet poised for activation. Using mouse embryonic stem cells (ESCs) with CRISPR/Cas9-mediated gene editing, we found that the loss of Pcgf2, though not affecting the global level of H2AK119ub1, disrupts these cPRC1.2 loops in ESCs and impairs the transcriptional induction of crucial target genes necessary for neuronal differentiation. Furthermore, we identified CTCF enrichment at cPRC1.2 loop anchors and at Polycomb group (PcG) bodies, nuclear foci with concentrated PRC1 and its tethered chromatin domains, suggesting that PRC1 and CTCF cooperatively shape chromatin loop structures. Through virtual 4C and other genomic analyses, we discovered that establishing neuronal progenitor cell (NPC) identity involves a switch from cPRC1.2-mediated chromatin loops to CTCF-mediated active loops, enabling the expression of critical lineage-specific factors. This study uncovers a novel mechanism by which pre-formed PRC1 and CTCF loops at lineage-specific genes maintain a poised state for subsequent gene activation, advancing our understanding of the role of chromatin architecture in controlling cell fate transitions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We aim to investigate how PRC1 regulates chromatin organization during neuronal differentiation by targeting Pcgf2, an important PRC1 component. We generated Pcgf2 knock-out (KO), Pcgf4 KO, Phc1 KO, Phc1-SAM-domain KO, and Irx3-anchor KO mESC lines via the CRISPR/Cas9 system. Triplicate WT and knock-out mESC lines were differentiated first into embryonic bodies (EBs) and then into neuro-progenitor cells (NPCs). Duplicated samples were subjected to RNA-seq. WT, Pcgf2 KO, Irx3-anchor KO ESC and NPC; and U2OS samples were subjected to ChIP-seq. WT and Pcgf2 KO ESC and Pcgf2 KO NPC samples were subjected to Hi-C.


title: Role of Cathepsin K in Bone Invasion of Pituitary Adenomas: A Dual Mechanism Involving Cell Proliferation and Osteoclastogenesis

city: beijing

first: Hongyan

last: Liu

address: No. 28 Fuxing Road, Haidian District, Beijing 100853, P.R. China

institute: Department of Endocrinology, Chinese PLA General Hospital

summary: Purpose: This study aimed to investigate the regulation and underlying mechanism of Cathepsin K (CTSK) in bone-invasive pituitary adenomas (BIPAs). Experimental Design: A total of 1437 patients with pituitary adenomas were included and followed up. RNA sequencing, immunohistochemistry, and RT-PCR were used to analyze to detect CTSK expression. The effects of CTSK on cellular proliferation, bone matrix degradation, and osteoclast differentiation were determined by gain/loss of function experiments in vitro and in vivo. The exploration of signaling pathways was determined by molecular biology experiments. Results: Here, we reported a significant fraction (~10%) of pituitary adenoma patients developed bone invasion, which was correlated with tumor recurrence. Patients with BIPAs had shorter recurrence-free survival. CTSK expression was increased in BIPA patients and was strongly associated with a worse prognosis. Increased CTSK expression enhanced pituitary adenoma cell proliferation through the activation of the mammalian target of rapamycin (mTOR) signaling pathway and promoted bone invasion by increasing osteoclast differentiation both in vitro and in vivo. Treatment with the CTSK inhibitor odanacatib effectively inhibited pituitary adenoma cell proliferation and bone invasion in these models. Additionally, CTSK facilitated osteoclast differentiation by promoting RANKL expression in MC3T3-E1 cells via interaction with TLR4. Conclusion: CTSK has the potential to become a novel predictive biomarker and therapeutic target for BIPAs.

overall_design: 10 frozen pituittary adenoma tissue samples were subjected to mRNA sequencing analysis

first: Peng

last: Wang

first: Jie

last: Li

first: Jian

first: Yiming

last: Mu

first: Weijun

last: Gu


title: Structural and Functional Characterization of TgGSK3, a Druggable Kinase in Toxoplasma gondii

status: Public on Jan 20 2025

city: La Tronche

first: Alexandre

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

country: France

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

summary: Toxoplasma gondii and Cryptosporidium species are apicomplexan parasites of significant medical and veterinary importance. Although current therapeutic options for toxoplasmosis and cryptosporidiosis demonstrate notable efficacy, their clinical efficacy is often limited by suboptimal efficacy and frequent adverse effects. Moreover, therapeutic alternatives remain limited or nonexistent, particularly for cryptosporidiosis, for which nitazoxanide is currently the only approved medication to treat diarrhea in adults and children older than 1 year of age. To identify alternative therapeutic options for addressing these health challenges, we performe a phenotypic screening of an FDA-approved drug repurposing library against Toxoplasma. This screening identifies LY2090314 as a potent inhibitor of T. gondii and Cryptosporidium growth in mammalian cells. Through a target deconvolution strategy combining forward genetics, transcriptome sequencing, and computational mutation analysis, we elucidate the parasiticidal mechanism of LY2090314 and demonstrate that TgGSK3 kinase is its primary molecular target. We also report the first X-ray crystal structure of LY2090314 bound to TgGSK3, resolved at 2.1 Å, which reveals an interaction mode characteristic of type I ATP-competitive inhibitors. Furthermore, interactome analysis uncovers functional connections between TgGSK3 and key cytoskeletal and signaling regulators, providing insights into compound’s effects. Collectively, these findings validate TgGSK3 as a promising therapeutic target for toxoplasmosis and offer mechanistic insights into apicomplexan GSK3 biology.

overall_design: Methods: RNA profiles were generated from HFF cells infected by RH wild-type or L2090314-resistant T. gondii strains. Total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA-sequencing was performed by Novogene (Munich, Germany).RNA quantity, integrity, and purity were determined using the Agilent 5400 Fragment Analyzer System (Agilent Technologies, Palo Alto, California, USA). The integrity values or RIN ranged from 9.1 to 10 for all samples, which was considered sufficient. Messenger RNAs (mRNA) were purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. For directional libraries, the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The samples were sequenced using the Illumina NovaSeq platform, employing both non-stranded (for variant calling analysis) and strand-specific sequencing (for gene expression analysis) with 2 x 150 bp reads and generated ~40 million paired-end reads for each sample.

first: Silvia

last: Diaz-Martin

first: Christopher

last: Swale

first: Valeria

last: Bellini

first: Irina

last: Dobrescu

first: Janine

last: Wenker

first: Marie-Pierre

last: Brenier-Pinchart

first: Laurence

last: Braun

first: Alwéna

last: Tollec

first: Charlotte

last: Corrao

first: Yohann

last: Couté

first: Caroline

last: Mas

first: Fabrice

last: Laurent

first: Matthew

last: Bowler

first: Mohamed-Ali

last: Hakimi


title: HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy [RNA-Seq_QJ10472]

first: Qinqin

last: Jiang

overall_design: We aim to systematically identify ERVs that transcriptionally become HIF2 dependent upon DNMTi treatment. 786-O cells first underwent CRISPR-based gene editing with a HIF2a sgRNA or a control sgRNA (sgCtrl) and then treated with 0.5 uM GSK3685032 (DNMT1i) or vehicle (Veh) for 9 days.

first: David

first: Cleo

last: Forman

first: Zachary

middle: T

last: Herbert

first: Sachet

last: Shukla

first: Catherine

last: Wu

first: William

last: Kaelin Jr


title: LATERAL FLORET 2 encoding a SNF2 chromatin remodeling factor regulates axillary meristem of spikelet development in rice (Oryza sativa)

status: Public on Jan 17 2025

city: Chongqing

first: Zhongcheng

last: Li

address: Chongqing

institute: Southwest University

summary: Compared with the wild type, in the lf2 mutant, 835 upregulated genes and 832 downregulated genes were detected, including a large number of genes that regulate the development of rice floral/panicle organs and are involved in the auxin regulation pathway.

overall_design: rice panicles (<2 cm) mRNA profiles of XD1B and lf2 mutant

first: Yunfeng

first: Xiaoqin

last: Zeng


title: NOTCH3 Mutation Causes Glymphatic Impairment and Promotes Brain Senescence in CADASIL

city: Guangzhou

first: Chunyi

state: Guangdong

address: 600 Tianhe Road

department: Department of Neurology, Mental and Neurological Disease Research Center

institute: the Third Affiliated Hospital of Sun Yat-sen University

summary:
NOTCH3 mutation results in development of cerebral autosomal dominant arteriopathy, subcortical infarcts, and leukoencephalopathy (CADASIL), the most common monogenic small vessel disease. Up to date, specific treatment against CADASIL is scarce. Here, we report that both glymphatic influx and efflux are impaired in CADASIL mouse models (Notch3R170C), which impedes waste clearance and promotes brain senescence. In accordance, brain atrophy in CADASIL patients is associated with perivascular space enlargement, indicating that glymphatic impairment contributes to advanced brain senescence in CADASIL. The glymphatic malfunction in CADASIL is attributed to diminished AQP4 expression in astrocytic endfeet, which is the core mediator of glymphatic activity. Mechanistically, AQP4 expression is regulated by RUNX1-CMYB signaling whose activation is suppressed as a result of NOTCH3 mutation. Reinforcing AQP4 expression in astrocytes by AAV-based therapy resumes the glymphatic functions in CADASIL mice, which further prevents brain senescence. Therefore, we propose that to improve glymphatic function by reinforcing AQP4 expression is a promising therapeutic strategy in CADASIL.

Senescence-associated Migrasomes (SAM) Promote Brain Ageing through Apoptosis Inhibitor of Macrophage (AIM)
Aging is a major risk factor for various neurological disorders, including Alzheimer's disease (AD). During aging, senescent cells produce pro-aging factors that disseminate aging signals and reinforce the senescence process. Migrasomes, newly discovered organelles formed during cellular migration, detach from parent cells and mediate intercellular communication. In this study, we identify border-associated macrophages (BAMs) as the primary cells that acquire pro-senescent properties during brain aging, likely due to prolonged exposure to amyloid beta (A?). In pro-senescent BAMs, migrasome production is elevated, conveying pro-aging signals to neighboring cells. Mechanistically, the apoptosis inhibitor of macrophage (AIM) is packaged into migrasomes. Upon activation of CD16 in recipient cells, AIM protects them from apoptosis, thereby inducing senescence. Treatment with Tspan4-siRNA-encapsulated liposomes in 18-month-old mice suppresses migrasome production in pro-senescent BAMs, slows brain aging, and ameliorates cognitive deficits. Our findings suggest that migrasomes are potent carriers of pro-aging signals and represent a promising target for senomorphic therapy.

Parenchymal border macrophages (PBMs) reside at the interface between the central nervous system and the periphery and are known to mediate the accessibility of the substances to the brain. Here, we report that amyloid-beta (A?) accumulates along brain blood vessels after stroke in both the ipsilateral and contralateral hemispheres. When PBMs were depleted, glymphatic drainage of A? was markedly reduced and this was accompanied by deterioration of cognitive function, highlighting a critical role for PBMs in post-stroke A? disposal. A possible mechanism relates to mesencephalic astrocyte-derived neurotrophic factor (MANF), which is known to impede glymphatic clearance of A?. MANF derived from PBMs suppressed astrocytic stress and maintained glymphatic drainage when supplemented into the cerebral spinal fluid. In the chronic phase of stroke, MANF production in PBMs was down-regulated and consequently, glymphatic impairments were exacerbated, which lead to on-going A? accumulation and cognitive decline. In summary, supplementation of MANF not only mitigates the adverse impacts of PBM depletion, but also exerts therapeutic effects that improve glymphatic system function. We thus propose that this represents a promising strategy to prevent post-stroke cognitive impairment.

overall_design:
Brain of NOTCH3-WT or NOTCH3-R170C mice (16w of age) were isolated and digested, myelin was removed, and single cell suspension were prepared for single cell sequencing.
4 samples; Raw data is multiplexed.
sample 1: NOTCH3-WT4m, replicate 1, scRNAseq
sample 2: NOTCH3-WT4m, replicate 2, scRNAseq
sample 3: NOTCH3-R170C, replicate 1, scRNAseq
sample 4: NOTCH3-R170C, replicate 2, scRNAseq

*** The records have been updated with the additional "WT6m, brain, male" processed data (generated from the GSM8108141 multiplexed raw data) on Jul 30, 2025:

scRNA-seq profiling of wildtype (WT) 6-month-old male mice with two biological replicates:
WT6m, brain, male, rep1
WT6m, brain, male, rep2

*** The records have been updated with the following data (generated from the GSM8108141 multiplexed raw data) on Sep 24, 2025:

Brain of Wildtype, NOTCH3-R170C or transient middle cerebral artery occlusion mice were isolated and digested, myelin was removed, and single cell suspension were prepared for single cell sequencing.
7 samples; Raw data is multiplexed.
sample 1: Wildtype 4m, replicate 1, brain, male
sample 2: Wildtype 4m, replicate 2, brain, male,q
sample 3: NOTCH3-R170C 4m, replicate 1, brain, male
sample 4: NOTCH3-R170C 4m, replicate 2, brain, male
sample 5: Wildtype 6m, replicate 1, brain, male
sample 6: Wildtype 6m, replicate 1, brain, male
sample 7: MCAO3d, brain, male

processed data files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz (detailed in the readme_09242025.txt)

first: Wei

last: Cai

first: Zhengqi

last: Lu

first: Mengyan

last: Hu


title: HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy [RNA-Seq_QJ9511]

overall_design: We aim to systematically identify HIF-responsive ERVs by RNA-Seq in A-498 cells. We generated three isogenic comparisons to create HIF2 high and low status, for which cells 1) were stably infected with a virus encoding pVHL (VHL) or the empty vector (EV), 2) were treated with 2 uM PT2399 (PT) or vehicle (Veh) for 72 hours, 3) underwent CRISPR-based gene editing with a HIF2a sgRNA or a contrl sgRNA (sgCtrl). We then performed RNA-Seq experiments to quantify ERV amount for each condition in triplicates.

last: Braun

middle: J


title: EHMT2 represses totipotency- and differentiation-associated genes in pluripotent stem cells through distinct regulatory modes [ChIP-exo]

status: Public on Jan 15 2025

city: New York

first: Christopher

middle: Mitsuo

last: Uyehara

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

summary: Mouse embryonic stem cells (mESCs) and other naïve pluripotent stem cells, under specific conditions, can reverse typical developmental trajectories and de-differentiate into 2-cell-like cells (2CLCs) that resemble the mammalian embryo during zygotic genome activation (ZGA). We implemented a multipurpose allele for acute protein depletion and efficient immunoprecipitation to dissect the molecular functions of EHMT2 in mESCs. This approach allowed us to define different types of EHMT2 target genes and distinct modes of chromatin engagement and repression. Most notably, EHMT2 directly represses large clusters of co-regulated gene loci that comprise a significant fraction of the 2CLC-specific transcriptome by initiating H3K9me2 spreading from distal LINE-1 elements. Conversely, the loss of EHMT2 allows the recruitment of the activator DPPA2/4 to promoter-proximal ERVs in 2CLCs, thus facilitating the mESC-to-2CLC transition. Repression of germ layer-associated transcripts by EHMT2 occurs outside of gene clusters in collaboration with ZFP462 and entails binding to non-repeat enhancers. Our data suggests that EHMT2 functions as an attenuator of the bidirectional differentiation potential of mouse naïve pluripotent stem cells and define molecular models for the gene-specific repressive activity of this essential histone methyltransferase.

overall_design: EHMT-dTAG lines were treated with DMSO for 24 hours. HA tag was used to probe for genomic occupancy of EHMT by CHIP-exo.

first: Kaushiki

last: Chatterjee

first: Kritika

last: Kasliwal

first: Effie

last: Apostolou

first: Matthias

last: Stadtfeld


title: EHMT2 represses totipotency- and differentiation-associated genes in pluripotent stem cells through distinct regulatory modes [ChIP]

overall_design: EHMT2-HA-dTAG lines were treated with DMSO  or dTAG13 for 24 hours. Cells were harvested using trypsin. CHIP-Seq using HA antibody performed to determine chromatin occupancy of EHMT2


title: EHMT2 represses totipotency- and differentiation-associated genes in pluripotent stem cells through distinct regulatory modes [Cut & Run]

overall_design: MERVL GFP- EHMT dTAG lines were treated with DMSO/dTAG for 72hrs , Sorted for gfp positive and negative population. Cut and Run performed using anti-DPPA4 antibody (AF3730)


title: Transcriptomics of FFPE-derived primary brain tumours

city: Alicante

first: Luis

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

summary: Primary brain cancers are highly heterogeneous and include the most prevalent and aggressive glioblastomas. To understand the key factors underlying brain tumourigenesis, we have built our own database based on RNA sequencing from FFPE-derived biomaterial.

overall_design: We performed RNA-seq to obtain the gene expression profiles of a variety of primary brain tumours subtypes.

first: Anabel

last: García-Heredia


title: Pharmacological or genetic inhibition of LTCC promotes cardiomyocyte proliferation through inhibition of calcineurin activity

city: Brisbane

first: James

last: Hudson

state: Queensland

address: 300 Herston Rd, Herston QLD 4006

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: Cardiomyocytes (CMs) lost during ischemic cardiac injury cannot be replaced due to their limited proliferative capacity. Ca2+ is an important signal transducer that regulates key cellular processes, but its role in regulating CM proliferation is incompletely understood. A drug screen targeting proteins involved in CM Ca2+ cycling in human embryonic stem cell-derived cardiac organoids (hCOs) revealed that only the inhibition of L-Type Calcium Channel (LTCC) using nifedipine induced the CM cell cycle. Overexpression of Ras-related associated with Diabetes (RRAD), an endogenous inhibitor of LTCC, induced CM cell cycle activity in vitro, in human cardiac slices, and in vivo. Mechanistically, LTCC inhibition by RRAD or nifedipine induced CM cell cycle by modulating calcineurin activity and Hoxb13 nuclear translocation. Moreover, ectopic expression of RRAD/CDK4/CCND in combination induced CM proliferation in vitro and in vivo, improved cardiac function and reduced scar size post-myocardial infarction. Together, these findings represent a robust pathway for new  Ca2+ signaling-based cardiac regenerative strategies.

overall_design: To gain insights into the mechanism of action of LTCC-induced cardiac proliferation in hCOs, bulk RNA sequencing was performed after 8 h of treatment with nifedipine or DMSO control

first: Lynn

last: Devilée

first: Janice

last: Reid


title: Human Immune Gene Expression Profile in activated and expanded NK cells, TIGITKO NK cells, GD2.CAR NK cells and TIGITKOGD2.CAR NK cells

status: Public on Feb 17 2025

city: Houston

first: Robin

last: Parihar

address: 1102 Bates Avenue

department: Immunology

institute: Baylor College of Medicine

summary: The purpose of this experiment to examine how the gene expression profile and differential gene expression in NK cells, TIGITKO NK cells, TIGITKOGD2.CAR NK cells or GD2.CAR NK cells changes after 72 hours of neuroblastoma tumor exposure.

overall_design: There are 24 experimental samples. Total RNA from NK cells, TIGITKO NK cells, TIGITKOGD2.CAR NK cells or GD2.CAR NK cells is represented at two different timepoints, the day 0 timepoint an day 3 timepoint. Each condition is represented by 3 matched donors.

first: Ishwar

last: Navin


title: EHMT2 represses totipotency- and differentiation-associated genes in pluripotent stem cells through distinct regulatory modes [RNA-seq]

overall_design: Transcriptional activity of EHMT-dTAG ESC's  treated with DMSO or dTAG for 24 hours, 7 days or 15days and  7 days of dTAG treatment followed by 8 days of recovery.  Transcriptional activity of MERVL GFP+ and GFP- population after 72 hours of dTAG treatment and post sorting was assesed using low input RNA-sequencing. Transcriptional activity of WT or Dppa4 KO ESC's  treated with DMSO or UNC0638 for 48 hrs.


title: Effect of Mn2+@Man-phage on gene expression in RAW264.7 macrophages

status: Public on Jan 13 2025

city: hangzhou

first: Zhaoming

last: Ye

address: 88 jiefang road

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

summary: Bacterial infectious diseases have posed a serious challenge to public health, often resulting in treatment failure and infection recurrence due to the emergence of drug-resistant bacteria. Owing to inaccessible binding sites, pathogens can evade attack from host immune cells and traditional antibiotics, leading to local immunosuppressive status. Our study reports a novel bacteriophage-based immune scavenger labeling nanoplatform (Mn2+@Man-phage) to combat immune-evasive bacteria and reverse immunosuppressive status. Our nanosystem utilizes the inherent bacterium-targeting ability of bacteriophages to aggregate at infection sites and mediates mannose-dependent recognition, phagocytosis, and killing of bacteria by macrophages, while the released Mn2+ amplifies the antibacterial immune efficacy. Consequently, macrophages polarize towards M1 and secrete various pro-inflammatory factors, effectively clearing bacteria. Moreover, reprogramming macrophages directly activate T cells at infection sites, eliciting potent adaptive antibacterial immune responses and ultimately achieving bacterial eradication. Overall, we demonstrate a universal strategy for pathogen targeting and immunomodulation of macrophages against bacterial infection.

overall_design: To investigate the effect of Mn2+@Man-phage on gene expression in RAW264.7 macrophages, RAW264.7 macrophages were cultured with Mn2+@Man-phage for 24 h.Then the cells were collected and the total RNA was extracted.

first: Minjun

last: Yao

first: Liang

last: Chen


title: EHMT2 represses totipotency- and differentiation-associated genes in pluripotent stem cells through distinct regulatory modes

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

overall_design: Refer to individual Series


title: EHMT2 represses totipotency- and differentiation-associated genes in pluripotent stem cells through distinct regulatory modes [ATAC-Seq]

overall_design: EHMT-dTAG lines were treated with DMSO  for 24 hours. Cells were harvested using trypsin. Open chromatin regions were mapped by ATAC-seq on three technical replicates per sample.


title: Effect of infected bone marrow suspension on gene expression in RAW264.7 macrophages

status: Public on Jan 11 2025

overall_design: To investigate the effect of infected bone marrow suspension on gene expression in RAW264.7 macrophages, the mouse implant-related skeleton infection model was established on the BALB/c mouse tibiae. After 7 days post E.coli infection, the tibiae were harvested and the bone marrow was flushed out with high-glucose medium to obtain bone marrow suspension. Then the bone marrow suspension was filtrated through a 0.22μm filter to culture RAW264.7 cells for 24 h. After co-cultured with E. coli for 6 h, the cells were collected and the total RNA was extracted.


title: EHMT2 represses totipotency- and differentiation-associated genes in pluripotent stem cells through distinct regulatory modes [ULI-NChIP]

overall_design: Bulk ChIP - 100,000 cells for EHMT2-HA-dTAG targeted lines were counted and flash frozen. Sorted ChIP -  72hr DMSO and dTAG treated EHMT2-dTAG-mCherry MERVL-GFP sorted for (~100,000) mESC and 2CLCs. ULI-NChIP was conducted according to the protocol published by Brind’Amour et al. (PMID 25607992). 1ug H3K9me2 antibody ab1220 was used.


title: Vesicular transplantation of gasdermin pores propagates pyroptosis

status: Public on Jan 07 2025

city: Avon

first: Beiyan

last: Zhou

state: Connecticut

address: 263 Farmington Ave, Immunology

institute: UCONN Health

summary: Pyroptosis—inflammatory cell death mediated by gasdermins (GSDM)—plays crucial roles in antimicrobial defense and inflammatory diseases. Pyroptosis results in the release of proinflammatory molecules, including damage-associated molecular patterns (DAMPs). However, our understanding of the consequences of pyroptosis—especially beyond IL-1 cytokines and DAMPs—that govern inflammation is limited. Here, we show intercellular propagation of pyroptosis from dying cells to bystander cells in vitro and in vivo. We identified extracellular vesicles (EVs) released by pyroptosing cells as the propagator of lytic death to naïve cells, triggering inflammatory responses and tissue damage. Remarkably, DNA-PAINT super-resolution and immunoelectron microscopical analyses revealed the presence of GSDMD nanostructures, such as pores, on EVs released by pyroptotic cells. Importantly, the transplantation of these GSDMD pores on adjacent cells’ plasma membrane by EVs causes cell-extrinsic lysis of bystanders. Overall, our findings demonstrate that cell-to-cell vesicular transplantation of GSDMD pores disseminates pyroptosis, revealing a domino-like effect shaping disease-associated bystander cell death.

overall_design: To assess the biological effects of pyroptotic EVs and explore the physiological importance of bystander pyroptosis, total RNA was extracted from the spleens of Gsdmd-/- mice injected with EVs from pyropototic PBS- or dox-stimulated iBMDM-iGSDMD-NT cells. Reads in .fastq files were trimmed using cutadapt/3.5.

first: Alyssa

last: Matz

first: Vijay

last: Rathinam


title: A genome-wide screen reveals Ints7 deficiency activates endogenous retrovirus MERVL, accompanied by anastasis of embryonic stem cells

status: Public on Jan 01 2025

city: changsha

first: shen

last: yunfan

state: hunan

address: xiangya road

institute: central south university

summary: The murine endogenous retrovirus MERVL is closely associated with the developmental potential of totipotency, manifesting dynamic and reversible activation within a small population of in vitro-cultured mouse embryonic stem cells (mESCs). While numerous regulators have been identified to influence the on and off switches of MERVL, how its activation is linked to the cellular decision-making of mESCs remains poorly understood. In this study, our genome-wide knockout screen uncovered an intimate relationship between MERVL activation and DNA damage response pathways. Specifically, we found that deficiency of Ints7, a backbone subunit of the Integrator complex, resulted in increased DNA damage, stabilization of p53, and hence transcriptional activation of MERVL. Moreover, we revealed that MERVL activation upon Ints7 knockdown was frequently accompanied by the activation of caspase 3. Intriguingly, a proportion of the caspase-activated mESCs were able to switch on MERVL meanwhile circumvent apoptosis and evade cell death, resembling a process known as anastasis. Altogether, our study highlights an association between MERVL activation and the p53-dependent cell fate plasticity in response to DNA damage, suggesting that limited caspase activation can alter developmental potential of stem cells.

overall_design: We used the MERVL-tdTomato reporting system for genome-wide knockout screening to search for activators of MERVL

first: Li

last: Li

first: Shen

last: Yunfan

first: Yuan

last: Kai


title: Effect of STN1 knockdown on gene expression of PDAC cell lines

status: Public on Dec 31 2024

city: Beijing

first: Chengqi

last: Yi

address: Yiheyuan Road

department: School of Life Sciences

institute: Peking University

summary: We aimed to elucidate the mechanistic involvement of STN1 in facilitating the metastatic processes of PDAC. Utilizing RNA-seq profiling, we observed a substantial downregulation of the EMT pathway in PANC-1 cells with stable STN1 knockdown

overall_design: Comparative gene expression profiling analysis of RNA-seq data for knockdown cell lines and controls. Three replicates were included for each group.

first: Zhe

first: Di

last: Dong


title: Therapeutic effects of FGF21 mimetic bFKB1 on MASH and atherosclerosis in Ldlr-/-.Leiden mice

city: Leiden

first: Martine

middle: C

last: Morrison

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

summary: Fibroblast growth factor 21 (FGF21) is a promising target for treatment of obesity-associated diseases including metabolic dysfunction-associated steatohepatitis (MASH) and atherosclerosis. We evaluated the effects of the bispecific anti-FGF21-β klotho (KLB) agonist antibody bFKB1 in a preclinical model of MASH and atherosclerosis. Low-density lipoprotein receptor knockout (Ldlr−/−).Leiden mice received a high-fat diet for 20 weeks, followed by treatment with an isotype control antibody or bFKB1 for 12 weeks. Effects on plasma risk markers and (histo)pathology of liver, adipose tissue, and heart were evaluated alongside hepatic transcriptomics analysis. bFKB1 lowered body weight (−21%) and adipose tissue mass (−22%) without reducing food intake. The treatment also improved plasma insulin (−80%), cholesterol (−48%), triglycerides (−76%), alanine transaminase (ALT: −79%), and liver weight (−43%). Hepatic steatosis and inflammation were strongly reduced (macrovesicular steatosis −34%; microvesicular steatosis −100%; inflammation −74%) and while the total amount of fibrosis was not affected, bFKB1 did decrease new collagen formation (−49%). Correspondingly, hepatic transcriptomics and pathway analysis revealed the mechanistic background underlying these histological improvements, demonstrating broad inactivation of inflammatory and profibrotic transcriptional programs by bFKB1. In epididymal white adipose tissue, bFKB1 reduced adipocyte size (−16%) and inflammation (−52%) and induced browning, signified by increased uncoupling protein-1 (UCP1) protein expression (8.5-fold increase). In the vasculature, bFKB1 had anti-atherogenic effects, lowering total atherosclerotic lesion area (−38%). bFKB1 has strong beneficial metabolic effects associated with a reduction in hepatic steatosis, inflammation, and atherosclerosis. Analysis of new collagen formation and profibrotic transcriptional programs indicate that bFKB1 treatment may have antifibrotic potential in a longer treatment duration as well.

overall_design: Ldlr-/-.Leiden mice were fed a high-fat diet (HFD) for 20 weeks, after which mice were treated with an isotype control antibody or bFKB1 for 12 weeks. Effects on pre-existent MASH and atherosclerosis were assessed histopathologically and biochemically. Underlying mechanisms of bFKB1 treatment were investigated by hepatic transcriptomics analysis (NGS).

first: José

last: Inia

first: Joline

last: Attema

first: Christa

last: de Ruiter

first: Aswin

last: Menke

first: Martien

last: Caspers

first: Lars

last: Verschuren

first: Maria

last: Wilson

first: Hans

last: Brightbill

first: J

last: Jukema

first: Anita

last: van den Hoek

last: Princen

first: Mark


title: Specialized enteric glial cells coordinate intestinal motility

status: Public on Dec 23 2024

city: Cleveland

first: Marissa

last: Scavuzzo

state: OH

address: 2109 Adelbert Rd

department: Genetics

institute: Case Western Reserve University

summary: Enteric glia are the predominant cell type in the enteric nervous system yet their identities and roles in gastrointestinal function are not well classified. Using an optimized single nucleus RNA-sequencing method, we identified distinct molecular classes of enteric glia and defined their morphological and spatial diversity. Our findings revealed a functionally specialized class of enteric glial cells that we call “hub cells.” Hub cells retain dual functionality: they generate neurons and glia and act as force transducers to regulate intestinal physiology. Deletion of the mechanosensory ion channel PIEZO2 from adult enteric glial hub cells, but not other subtypes of enteric glia, led to defects in intestinal motility and gastric emptying in mice. These results provide insight into the multifaceted functions of different enteric glial cell subtypes in gut health and emphasize that therapies targeting enteric glia could advance the treatment of gastrointestinal diseases.

overall_design: Nuclei from the whole adult duodenum of C57/Bl6 mice were isolated using CitraPrep and analyzed using snRNAseq

middle: A

first: Paul

last: Tesar


title: GWAS identifies a OsPIF4 gene underlying iWUE under fluctuating light and drought combined stress in rice

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

summary: Fluctuating light (FL) usually occur concomitantly with drought stress (DS); this combined (FL-DS) condition influences intrinsic water use efficiency (iWUE) pattern during FL and DS response. However, the molecular mechanisms governing iWUE during FL-DS combined events in rice remain unexplored. In this study, we quantified iWUE kinetics in 200 rice accessions exposed to a 20-day FL-DS. Using genome-wide association studies (GWAS), we identified a significant gene variation in the phytochrome-interacting factor (OsPIF4) gene which significantly associated with a novel trait, iWUEFL. This gene variation was highly expressed in the high iWUEFL subgroup. Two haplotypes containing nine SNPs of OsPIF4 were classified, where the mutation of v3 SNP at its promoter shows substantially reduced activities of promoter and greatest sensitivity to FL among mutation of other SNPs via protoplast transient transformation approach. Mutation at v3 SNP (PIF4v3m) and overexpression of OsPIF4 resulted in at least 20% reduction and 25% increase in iWUEFL under FL-DS, compared it to WT, respectively. Two genes (OsSAL1 and OsNHX1) were identified with the most significant differences in expression between PIF4v3m and WT based on transcriptome analysis. PIF4v3m displayed an 85% reduction in adenosine 3', 5'-diphosphate (PAP) levels and a 73% increase in OsSAL1 gene expression compared to WT. Moreover, our results revealed that OsPIF4 has a dual role in repressing OsSAL1 transcriptionally and activating OsNHX1 by binding to their G-box motifs. This regulatory mechanism increased by 16% (sal1) and 10% (OsNHX1-OE) in iWUEFL compared to WT under FL-DS. OsPIF4 haplotypic distribution is strongly associated with the local light regime where accessions originated. This study highlights the key role of OsPIF4 in enhancing iWUEFL during FL-DS by regulating chloroplast retrograde signaling pathways and vacuolar ion exchanges.

overall_design: To better identify the key regulatory genes in rice induced by fluctuating light and drought combined stress, we carried out transcriptome deep sequencing of rice leaves from exposed to fluctuating light and drought combined stress condition.

first: Suyang

last: Fang

first: Jemaa

last: Essemine


title: Inducible nitric oxide synthase is repressed by Nuclear Factor Erythroid 2-Related Factor 2 in KRAS-driven pancreatic cancer cells

status: Public on Dec 22 2024

city: Perugia

first: Elisabetta

last: Albi

state: Italy

address: Via Romana

department: Department of Pharmaceutical Sciences

country: Italy

institute: Università degli studi di Perugia

summary: Nitric oxide is a pleiotropic free radical produced by three nitric oxide synthases (NOS1-3), of which the inducible NOS2 is involved in carcinogenesis. In this study, RNA-seq, ChIP-seq, and qRT-PCR experiments combined with bioinformatic analysis showed that NRF2 is a repressor of the NOS2 gene by maintaining a distal enhancer located 22 Kb downstream of the transcription start site (TSS) in a poised state. NRF2 depletion primed the activation of this enhancer, exerting a pioneering activity before achieving full activation. Specifically, NRF2 controls the inducible expression of NOS2 in response to intracellular oxidative stress and extracellular oxygen partial pressure. Abrogation of NOS2 expression using esiRNAs partially reduced or severely impaired the ability to form 3D spheroids respectively of WT and NRF2-depleted Panc-1 cells. Mechanistically, NOS2 and nitric oxide release are required to sustain the epithelial-to- mesenchymal transition (EMT) process. Importantly, silencing of NOS2 blocked 3D Matrigel invasion of NRF2-depleted Panc-1 cells, demonstrating that a short circuit in the reciprocal regulation of NOS2 and NRF2 attenuates PDAC cell malignancy. Overall, our data demonstrate for the first time that: i) NRF2 is a repressor of the NOS2 gene in pancreatic cancer cells; ii) identify a poised enhancer whose priming is triggered in conditions that simulate or stimulate NRF2 depletion; iii) NOS2 activity is required for NRF2-depleted Panc-1 cells to maintain their malignancy and invasiveness.

overall_design: H3K27ac chipped samples from Panc-1 wt, NRF2KO and their input: cells were grown for 7 days in 3D matrix generating 3D spehorids. Cells were fixed with 1% formaldeyde for 15 min at room temperature and then quenched with 5 ml of PBS/GLYCINE for 5 min at room temperature. Matrigel was melted and Cells were lysed in 0.1 ml ChIP lysis buffer (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% deoxycholate with 0.1 mM PMSF and the EDTA-free Protease Inhibitor Cocktail). Samples were incubated on ice for 10 min and then centrifuged at 3,000 rpm for 3 min at 4°C. The pellet was resuspended in 500 µl lysis buffer 2 (10 mM Tris, pH 8.0, 200 mM NaCl with 0.1 mM PMSF and the EDTA-free Protease Inhibitor Cocktail) and incubated at room temperature for 10 min. Samples were centrifuged at 3,000 rpm for 5 min at 4°C. Next, the pellet was resuspended in 300 µl lysis buffer 3 (10 mM Tris, pH 8.0, 100 mM NaCl, 0.5% deoxycholate, and 0.1% SDS with 0.1 mM PMSF and the EDTA-free Protease Inhibitor Cocktail). Cells were sonicated using a Biorupter (Diagenode) for 15 min (30 s on, 1 min off). Next, 30 µl of 10% Triton X-100 was added to each tube, and then samples were centrifuged at max speed for 15 min at 4°C. The supernatant was transferred to new tubes, and the DNA concentration was quantified. Samples were precleared for 1 h at 4°C on a rotator using 8 µl protein A Dynabeads (Zymo) in ChIP lysis buffer. Samples were centrifuged at max speed for 15 min at 4°C, after which the supernatant was transferred to a new tube. 1/100 input was collected. 3 µg Antibodies were added O/N. 8 µl of protein A Dynabeads were added and chromatin was immunoprecipitated for 2h at 4°C. The following washes were performed for 15 min each by rotating for 15 min at 4°C: ChIP lysis buffer (twice), ChIP lysis buffer + 0.65 M NaCl, wash buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 0.5% NP-30, 0.5% DOC, and 1 mM EDTA, pH 8.0), and TE (10 mM Tris-HCl, pH 8.0, and 1 mM EDTA, pH 8.0). Beads were incubated with RNASEA solution (100ul TE/2ul Rnasi A (10mg/ml). DNA was eluted by adding to the beads 100ul of TES (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, pH 8.0, and 1% SDS) for 15 min at 65°C with brief vortexing every 2 min. Reversal of cross-linking was performed by incubating samples overnight at 65°C: transfer into 0.5ml tubes and place in termocycler. Proteins were digested using 150ug of proteinase K (0.5ul proteinase K) by incubating at 37°C for 5h. Finally, the DNA was purified using the Zymo Research Kit and eluted 2 times in 40ul H20.

first: Nicolò

last: Gualandi

first: Ylenia

last: Cortolezzis

first: Eros

last: Di Giorgio

first: Luigi

last: Xodo


title: RNA-seq of TGF-beta1-induced NRK-52E cells after treatment with 2D- and 3D-EVs

status: Public on Dec 18 2024

first: Qiang

last: Guo

address: No. 26, Erheng Road, Yuancun, Tianhe District

institute: Sun-Yat Sen university, The sixth affiliated Hospital

summary: Renal tubular epithelial cells are the main cells affected in the process of renal fibrosis, and it has been shown that mesenchymal stem cell-derived exosomes can treat renal fibrosis, and then the traditional 2D-EVs production method is inefficient. We efficiently extracted 3D-EVs by coaxial bioprinting, but the mechanism of 3D-EVs for treating renal fibrosis is not yet known. Therefore, we used TGF-beta1 to induce a renal fibrosis phenotype in NRK-52E cells and took 2D- and 3D-EVs for treatment in order to explore the possible differential molecular mechanisms of 2D- and 3D-EVs for renal fibrosis. This approach facilitates the discovery of new mechanisms for exosomes to treat renal fibrosis.

overall_design: To compare the difference in efficacy between 2D-EVs of conventional methods and efficiently produced 3D-EVs in the treatment of renal fibrosis. We induced a renal fibrosis phenotype in rat renal tubular epithelial cells NRK-52E by TGF-beta1, followed by treatment with 2D- and 3D-EVs.

first: Jianwei

last: Chen

first: Dejuan

last: Wang


title: Single cell approached deine forebrain neural stem cell niches and identify microglial ligands that enhance precursor-mediated remyelination (Xenium)

status: Public on Dec 20 2024

city: Vancouver

first: Freda

middle: D.

last: Miller

state: BC

department: Michael Smith Laboratories, Department of Medical Genetics

country: Canada

institute: University of British Columbia

summary: Here we used single cell RNA-sequencing and single cell spatial transcriptomics to characterize the forebrain neural stem cell (NSC) niche under homeostatic and injury conditions. We define the dorsal and lateral ventricular-subventricular zones (V-SVZ) as two distinct neighborhoods, and show that following white matter injury, dorsal NSCs are locally activated to make oligodendrocytes for remyelination. This activation is coincident with a robust increase in transcriptionally-distinct microglia in the dorsal V-SVZ niche. We modeled ligand-receptor interactions within this changing niche and identified two remyelination-associated microglial ligands, IGF1 and OSM, that promote precursor proliferation and oligodendrogenesis in culture. Infusion of either ligand into the lateral ventricles also enhanced oligodendrogenesis, even in the lateral V-SVZ, where NSCs normally make neuroblasts. These data support a model where gliogenesis versus neurogenesis is determined by the local NSC neighborhood and where injury-induced niche alterations promote NSC activation, local oligodendrogenesis, and likely contribute to myelin repair.

overall_design:
Multiplexed in situ hybridization-based spatial transcriptomics using the 10X genomics Xenium platform was used to analyze coronal adult (P100) CD-1 mouse forebrain sections containing the V-SVZ and corpus callosum, with a probeset that included marker genes for relevant cell types, ligands and receptors. We analyzed a region of interest that included the V-SVZ and corpus callosum from four different brains from mice which had been exposed to either a control or cuprizone-rapamycin (cup-rap) protocol (2 control, and 2 cup-rap). Replicates are indicated at the end of each sample name (i.e. Adult_Control_Forebrain_Xenium_Biol1, Adult_CupRap_Forebrain_Xenium_Biol1 ).
Multiplexed in situ hybridization-based spatial transcriptomics using the 10X genomics Xenium platform was used to analyze coronal adult (P100) CD-1 mouse forebrain sections containing the V-SVZ and corpus callosum, with a probeset that included marker genes for relevant cell types, ligands and receptors. We analyzed a region of interest that included the V-SVZ and corpus callosum from four different brains from mice which had been exposed to either a control or cuprizone-rapamycin (cup-rap) protocol and were given no recovery after treatment cessation. Replicates are indicated at the end of each sample name (i.e. Adult_Control_NoRecovery_Xenium_Biol1, Adult_CupRap_NoRecovery_Xenium_Biol1 ). We also collected tissue from adult CD1 mice which were fitted with osmotic minipumps to infused ligands into the right lateral ventricle. Animals were then either infused with 0.1% BSA-PBS (control) or 204ng OSM in 0.1% BSA-PBS for 7 days, with a delivery rate of 0.5ul per hour.

first: Ashleigh

last: Willis

first: Danielle

last: Jeong

first: Yunlong

last: Liu

last: Lithopoulos

first: Scott

last: Yuzwa

last: Frankland

first: David

last: Kaplan


title: Single cell approaches define neural stem cell niches and identify microglial ligands that enhance precursor-mediated remyelination

status: Public on Dec 19 2024

platform_organism:
Mus musculus
synthetic construct


title: In vivo DNA replication dynamics unveil aging-dependent replication stress

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

institute: University of Geneva

summary: The genome duplication program is affected by multiple factors in vivo, including developmental cues, genotoxic stress, and aging. Here, we monitored DNA replication initiation dynamics in regenerating livers of young and old mice after partial hepatectomy to investigate the impact of aging. In young mice, the origin firing sites were well defined; the majority were located 10-50 kb upstream or downstream of expressed genes, and their position on the genome was conserved in human cells. Old mice displayed the same replication initiation sites, but origin firing was inefficient and accompanied by a replication stress response. Inhibitors of the ATR checkpoint kinase fully restored origin firing efficiency in the old mice but at the expense of an inflammatory response and without significantly enhancing the fraction of hepatocytes entering the cell cycle. These findings unveil aging-dependent replication stress and a crucial role of ATR in mitigating the stress-associated inflammation, a hallmark of aging.

overall_design: Monitor gene expression in mouse livers before and at 48 and 72 h after PH upon treatment or not with ATRi by RNAseq

first: Giacomo

middle: G

last: Rossetti

first: Noëlle

last: Dommann

first: Angeliki

last: Karamichal

middle: S

first: Ainhoa

last: Aldave

first: Adrian

last: Keogh

first: Daniel

last: Candinas

first: Deborah

last: Stroka

first: Thanos

last: Halazonetis


title: Microbacterium diet rich in branched chain fatty acids promotes lipid droplet enlargement and impacts organismal health in C. elegans

status: Public on Dec 12 2024

city: HK

first: Chaogu

last: Zheng

address: The University of Hong Kong, Pokfulam Road

department: School of Biological Science

country: Hong Kong

institute: University of Hong Kong

summary: Understanding how dietary nutrients alter lipid metabolism in the host is important in deciphering the physiological mechanisms that regulate organismal health. Using the nematode Caenorhabditis elegans as a model organism, I found that a novel gram-positive monomethyl branched-chain fatty acid (mmBCFA) rich bacteria, Microbacterium sp., isolated from C. elegans natural habit can induce supersized lipid droplets (LDs) up to 30 μm in diameter in older animals and adversely affect their lifespan, development rate and brood size. Lipidomic analysis indicated that Microbacterium sp.-fed worms primarily accumulate dietary mmBCFAs in the triacylglycerides stored within LDs. Transcriptomic analysis discovered that the mmBCFA-rich bacteria diet would enhance fatty acid desaturase fat-7 expression and therefore polyunsaturated fatty acids (PUFAs) production to support LD biosynthesis and fusion processes. Additionally, the diet from Microbacterium sp. significantly inhibits creatine kinase argk-1, which results in the suppression of the AMP-activated protein kinase pathway, leading to a halt in mitochondrial beta-oxidation, enhanced lipid de novo synthesis and activation of a mitochondrial unfolded protein response (UPRmt) in C. elegans. Furthermore, using this enlarged LD-inducing bacteria diet, a gain-of-function missense mutation in scav-4 is identified to exacerbate the LD expansion phenotype while the loss of scav-4 results in diminished lipid storage in the worms. Lipidomic analysis showed that the L462F missense mutation nearly doubles the uptake of dietary mmBCFAs, whereas deletion mutants exhibit a reduced proportion of dietary mmBCFAs in total lipids. The localization of SCAV-4 on the intestinal apical membrane and its phylogenetic similarity to the human CD36 fatty acid transporter suggest that SCAV-4 is a homolog of CD36. Structural analysis indicates that the missense mutation is likely located within the transport tunnel, potentially affecting lipid transport. Among the six SCAV family members in C. elegans, SCAV-6 appears to be a less critical paralog compared to SCAV-4, sharing similar expression patterns and showing reduced lipid storage upon deletion. Notably, the transcriptomic analysis reveals that the SCAV-4 missense mutation does not cause much transcriptomic changes under the E. coli OP50 diet but affects over 3,000 genes in response to the Microbacterium sp. diet, suggesting that animals with SCAV-4(L462F) mutation is much more sensitive to the mmBCFAs-rich diet than the wild-type animals. This finding highlights the influence of host genetic variations in the interactions with dietary nutrients, which has strong impact on host metabolism.

overall_design: To study the gene expression changes of different strain of scav-4 mutants under E. coli OP50 diet and Microbacterium sp. JUb74 diet

first: Kam Ue Roy

last: Li

first: Wing Ka

last: Lo

first: Chenyin

last: Wang

first: Chun Yin

last: Lau

first: Jetty Chung-Yung

last: Lee


title: Somatic hypermutation generates antibody specificities beyond the primary repertoire

status: Public on Dec 04 2024

city: Boston

first: Duane

middle: R.

last: Wesemann

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine, Division of Allergy and Clinical Immunology

institute: Brigham and Women's Hospital

summary: B cell somatic hypermutation (SHM) and selection in germinal centers (GCs) enhance antibody affinity for antigen. Here, we investigated whether SHM-based antibody evolution is restricted to specificities established through V(D)J recombination in the primary repertoire. Tracking pre-defined non-specific B cells across multiple immunization models revealed that non-cognate B cells within GCs undergo SHM. Under conditions of limited B cell competition, these B cells generated de novo antigen recognition to multiple epitopes across diverse model antigens. Phylogenetic analyses identified diverse mutational pathways leading to new antigen affinities, and enhanced T cell co-stimulation further promoted new antigen recognition. Our data support a model in which B cell competition-rather than an intrinsic requirement for specific affinity-limits the emergence of new affinities through SHM, highlighting the mammalian adaptive immune system's ability to explore antibody-antigen interactions beyond those encoded by the V(D)J-dependent primary repertoire, demonstrating the flexibility of SHM in not only ripening but also reshaping specificity.

overall_design: Different tissues (spleen, mesenteric lymph node and peyer’s patches) of unimmunized mice were harvested, processed and cells were counted. 1-2 x 106 cells, whenever possible, were aliquoted and stained with 0.5 ug of cell hashing antibodies (BioLegend Total-Seq C antibodies, Hashtag 1-9, different hashtag antibodies per tissue sample) after blocking with TruStain FcX™ PLUS (anti-mouse CD16/32, BioLegend, Cat# 156604) according to manufacturer’s protocol. After incubating with hashing antibodies, cells were washed and stained with FACS staining panel as mentioned above - DAPI, Dump (CD4, CD8, F4/80 and Gr1), B220. Total B cells were sorted (upto 50,000 cells per tissue and cells from all three tissues of one mouse were pooled) and proceeded for scRNA-seq library preparation using Chromium GEM-X Single Cell 5' Reagent Kits v3 (10X Genomics) according to the manufacturer’s protocol. Briefly, sorted B cells were pooled, counted, and 33,000 to 50,000 cells were loaded on the GEM-X Chip to run on Chromium X for gel-beads in emulsion (GEMs) generation. Thereafter RT-PCR, cDNA amplification, fragmentation, end repair, A-tailing and sample indexing were performed. Libraries were quantitated and analysed at Tape station (Agilent Bioanalyzer) during intermediate steps of library preparation. Final libraries were quantified by qPCR (KAPA Library Quantification Kit Illumina® Platforms, Kapa Biosystems # KR0405), diluted to 2 nM and pooled. 650 pM of pooled libraries were mixed with 15% of PhiX control library and loaded on NextSeq™ 2000 P4 XLEAP-SBS™ Reagent Kit (100 Cycles, Illumina # 20100994. Libraries were sequenced on Illumina NextSeq™ 2000 sequencer with paired-end reads for 28 cycles of read 1, 10 cycles of i7 index, 10 cycles of i5 index, and 90 cycles of read 2, targeting a median depth of 10,000 reads per cell (5,000 reads per cell for BCR libraries and 5,000 reads per cell for hashtag libraries).

first: Teng

last: Zuo

first: Avneesh

last: Gautam

first: Shahab

last: Saghaei

first: Sweta

middle: N

last: Khobragade

first: Rahaman

last: Ahmed

first: Azadeh

last: Mahdavinia

first: Mehrdad

last: Zarghami

first: Gaspar

last: Pacheco

first: Kenneth

last: Green

first: Meghan

last: Travers

first: Nicholas

last: Garcia

first: Vishal

last: Rao

first: Zahra

last: Allahyari

first: Sachin

last: Kumar

first: Robert

last: Novak

first: Joyce

middle: K

last: Hwang


title: Human cytomegalovirus infection coopts chromatin organization to modulate TEAD1 transcription factor activity

status: Public on Dec 06 2024

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center


title: Eosinophils restrict CRC metastasis by inhibiting pro-tumorigenic Spp1+ macrophage differentiation.

status: Public on Dec 17 2024

city: Zürich

first: Kristina

last: Handler

address: Winterthurerstrasse

department: Institute of Experimental Immunology

institute: University of Zürich

summary: Eosinophils, traditionally associated with allergic responses, have emerged as critical immune modulators in colorectal cancer (CRC). Here, we reveal that eosinophils actively shape the tumor microenvironment and influence metastatic progression. Using comprehensive transcriptomics analysis of human CRC and a murine orthotopic tumor model, we identify a conserved tumor-specific eosinophil signature and activation profile. Despite their declining presence in advanced CRC, eosinophils suppress metastatic dissemination by counteracting the pro-tumorigenic functions of SPP1+ macrophages – a subset linked to immune exclusion and tumor metastasis. Mechanistically, eosinophils respond to tumor-derived signals and inhibit macrophage differentiation into SPP1+ cells. Eosinophil depletion exacerbates peritoneal tumor spread. These findings highlight the pivotal role of eosinophils in restraining late-stage CRC progression and unveil a novel eosinophil–macrophage axis as potential therapeutic targets.

overall_design:
Immune cells from biopsies of late-stage CRC patients were collected and analysed using the BD Rhapsody pipeline with a specific interest in eosinophils. To validate our findings and to conduct further testing scRNASeq was also performed from mouse models of late stage CRC with and without eosinophil depletion.

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

first: Deeksha

last: Raju

first: Alessandra

last: Gurtner

first: Tosca

last: Dalessi

first: Michael

middle: D

last: Brügger

first: Daniel

last: Crepaz

first: Cinzia

last: Esposito

first: Zlatko

last: Trajanoski

first: Christian

last: Münz

last: Scharl

first: Tomas

last: Valenta

first: Salvatore

last: Piscuglio

first: Hassan

last: Fazilaty

first: Isabelle

last: Arnold