title: The Carbohydrate-Active Enzymes (CAZymes) required for cellulose deconstruction in Cellvibrio japonicus are part of an efficient cellodextrin uptake system

status: Public on Jan 21 2025

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

summary: Microbial deconstruction of plant polysaccharides is important for environmental nutrient cycling, and bacteria proficient at this process have extensive suites of polysaccharide-specific enzymes. In the Gram-negative saprophyte Cellvibrio japonicus, genome annotation suggests that 17 genes are predicted to encode Carbohydrate-Active enZymes (CAZymes) with roles in cellulose degradation, however previous work suggested that only a subset of these genes is essential. Building upon that work, here we identify the required and minimally sufficient set of enzymes for complete degradation of cellulose using a combination of transcriptomics, gene deletion analysis, heterologous expression studies, and metabolite analysis. We identified six CAZyme-encoding required for cellulose deconstruction in C. japonicus, which are cel3B, cel5B, cel6A, lpmo10B, cbp2D, and cbp2E. These genes encode for a β-glucosidase, an endoglucanase, a cellbiohydrolase, a lytic polysaccharide mono-oxygenase, and two carbohydrate-binding proteins, respectively. These CAZyme-encoding genes are essential for growth using insoluble cellulose by C. japonicus, and sufficient using soluble cellulose when heterologously expressed in Escherichia coli. Moreover, during C. japonicus grow using insoluble cellulose we detected no cellodextrins in the medium, which suggests that cello-oligosaccharide uptake is highly efficient. RNAseq analysis corroborates these results, as we observed several genes significantly up-regulated during growth on cellulose that encode TonB-dependent and ABC transporters. Our revised model of cellulose utilization by C. japonicus suggests a greater importance for the Cbp2D and Cbp2E proteins than previously thought and that rapid cellodextrin update by C. japonicus is a mechanism to maximize the energetic return on investment for the production and secretion of CAZymes.

overall_design: RNAseq profiling of wild-type Cellvibrio japonicus grown using insoluble filter paper under biomass containment with sampling during exponential growth and during stationary phase

middle: G


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

country: USA

institute: University of Pennsylvania, School of Dental Medicine

type: Expression profiling by high throughput sequencing

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

middle: J

last: Gaskill

first: Cagla

middle: E

last: Akay-Espinoza

middle: L


title: snRNA-seq of murine tarsal plates

city: New York

first: Sarah

last: Millar

state: NY

address: Icahn Building, Floor 13 Room 020C, 1425 Madison Ave

department: Developmental, Cell and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

summary: The eyelid is a complex environment containing, containing epidermal, hair follicles, and conjunctival cells closely adjacent to the Meibomian glands (MGs), making it challenging to isolate pure MG cells or to identify MG contributions in bulk RNA-seq analyses. To analyze transcription in MG subpopulations, and to overcome difficulties in isolating cytoplasmic mRNAs from lipid-rich acinar cells, we utilized snRNA-seq which allows for identification of cell sub-populations within a complex mix.

overall_design: The dorsal portion of the eyelids and the surrounding tissues near the tarsal plates were removed using a scalpel. The tarsal plates were digested with collagenase A and the MGs were dissected using forceps. Nuclei were analyzed from the pooled samples of four 8-week-old and four 21-month-old male mice using two replicates for each age (16 mice analyzed in total).

first: Xuming

last: Zhu

first: Mingang

last: Xu


title: H3K4 methylation-promoted transcriptional memory supports faithful zygotic genome activation and development [RNA-seq-Auxin]

status: Public on Jan 20 2025

city: Munich

first: Eva

last: Hoermanseder

state: Bavaria

address: Feodor-Lynen-Str. 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Center Munich

summary: Accurately established transcriptional programs are paramount for successful embryonic development. At zygotic genome activation, gene expression is initiated for the first time in the life of an embryo. Pioneer transcription factors present in the embryo are essential for this process, however, the role of active chromatin modifications is less clear. It is unknown if active chromatin modifications established in the gamete are propagated in the embryo as epigenetic memory to support zygotic genome activation and development. Here, we provide evidence that in Xenopus laevis, H3K4 methylation contributes to epigenetic memory of active chromatin states, which is required for faithful zygotic genome activation and successful embryonic development. We find that chromatin configurations of promoters displaying high H3K4me3 intensity and breadth, alongside DNA hypomethylation and increased GC content, are maintained from the gametes to the embryo across multiple cell divisions and a transcriptionally quiescent phase in early development. We show that this maintenance of H3K4 methylation is essential for precise zygotic genome activation. Finally, we demonstrate that Kmt2b and Cxxc1 facilitate transcription-independent maintenance of H3K4me3 and proper zygotic gene expression. In summary, our study establishes a role for H3K4 methylation for memory of active chromatin states in embryos and reveals its importance for successful embryonic development.

overall_design: RNA-seq profiling of H4K4me3-depleted Xenopus laevis embryos at ZGA stages using Kdm5b-wt and H3.3-K4M mRNA mutant overexpression. Kdm5b-ci (catalytically inactive) plus H3.3-wt were overexpressed as the respective control conditions. Treatments were performed either in a developmental "window" from zygote to ZGA, or "persistently" from zygote onwards.

first: Meghana

middle: S

last: Oak

first: Marco

last: Stock

first: Matthias

last: Mezes

first: Tobias

last: Straub

first: Antony

middle: M

last: Hynes-Allen

first: Jelle

last: van den Ameele

first: Ignasi

last: Forne

first: Andreas

last: Ettinger

first: Axel

last: Imhof

first: Antonio

last: Scialdone

last: Hörmanseder


title: The SLC1A1/EAAT3 Dicarboxylic Amino Acid Transporter is an Epigenetically Dysregulated Nutrient Carrier that Sustains Oncogenic Metabolic Programs

status: Public on Jan 31 2025

city: Cleveland

first: Abhishek

last: Chakraborty

state: OH

address: 9620 Carnegie Ave NB4-120

department: Cancer Biology

institute: Cleveland Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Inactivation of pVHL tumor suppressor in clear cell Renal Cell Carcinoma (ccRCC) increases the abundance of Histone H3 lysine 27 acetylation (H3K27ac). We hypothesized that H3K27ac, a marker of transcriptional activation, drives the expression of critical oncogenes in ccRCC. Using H3K27ac ChIP-Seq; RNA-Seq; an in vivo positive selection screen; cell-based functional studies; and clinical validations; here, we report the identification of the SLC1A1/EAAT3 aspartate (Asp) and glutamate (Glu) transporter as a ccRCC oncogene. pVHL loss promotes SLC1A1 expression in a HIF-independent manner. SLC1A1 inactivation impedes ccRCC growth both in vitro and in vivo via depletion of Asp/Glu-derived metabolites, and sensitizes ccRCCs to metabolic therapeutics (e.g., glutaminase blockers). In human ccRCC biospecimens, higher SLC1A1 expression is associated with metastatic disease and clusters with elevated expression of other solute careers, but not HIF/Hypoxia pathways. Altogether, our studies identify a HIF-independent metabolic hub in ccRCC and credential SLC1A1 as an actionable ccRCC oncogene.

overall_design: RNA-Seq and H3K27ac ChIP-Seq of UM-RC-2 and 786-O cells expressing VEC or VHL.

first: David

middle: A

last: Orlando

first: Matthew

last: Guenther

first: Treg

last: Grubb


title: Teamwork of clustered low-affinity κB sites and accessory factors regulates transcriptional strength of NF-κB RelA dimers [RNA-seq]

city: La Jolla

first: Shandy

last: Shahabi

state: CA

address: 9500 Gilman Dr

department: Chemistry

institute: UCSD

summary: Non-consensus binding sites of transcription factors are often observed within the promoters and enhancers of various genes; however, their effect on transcriptional strength is unclear. Within the promoters and enhancers of NF-κB-responsive genes, we identified clusters of non-consensus κB DNA sites, many exhibiting low affinity for NF-κB in vitro. Deletion of these sites demonstrated their collective critical role in transcription. We explored how these “weak” κB sites exert their influence, especially given the typically low nuclear concentration of NF-κB. Using proteomics approaches, we identified additional nuclear factors, including other DNA-binding TFs, that could interact with κB site-bound NF-κB RelA without binding to DNA directly. ChIP-seq and RNA-seq analyses suggest that these accessory TFs, referred to as the cofactors of NF-κB, facilitate dynamic recruitment of NF-κB to the clustered κB sites. Overall, the occupancy of NF-κB at promoters and enhancers appears to be defined by a collective contribution from all κB sites, both weak and strong, in association with specific cofactors. This congregation of multiple factors within dynamic transcriptional complexes is likely a common feature of transcriptional programs.

overall_design: Gene expression and RelA genome binding/occupancy profiling by high-throughput sequencing in control and knockdown mouse embryonic cell lines.

first: Tapan

last: Biswas

first: Yuting

last: Shen

first: Rose

last: Sanahmadi

first: Yaya

last: Zou

first: Gourisankar

last: Ghosh


title: Teamwork of clustered low-affinity κB sites and accessory factors regulates transcriptional strength of NF-κB RelA dimers [ChIP-seq]


title: Combined single-cell RNA-sequencing and single-cell bisulfite-sequencing reveal key regulatory mechanisms associated with oocyte in vitro maturation in pig [scRNA-seq]

status: Public on Jan 29 2025

city: Murcia

first: Francisco

last: Huertas

address: C/ Campus Universitario de Espinardo Nº7 (Edificio CEEIM)

country: Spain

institute: Marbyt - Smart Solutions for Biotechnology

summary: In vitro maturation (IVM) is a critical step in current animal in vitro embryo production protocols. However, in vitro matured oocytes often exhibit lower developmental competence than their in vivo counterparts, and the molecular mechanisms underlying successful maturation remain unclear. In this study, we compared the developmental competence up to the blastocyst stage of IVM and in vivo matured porcine oocytes (N=397) and also analysed simultaneously their gene expression and DNA methylation profiles at single cell resolution (N=40) using RNA sequencing and bisulfite sequencing. Our final aim was to find the associations between the developmental and molecular differences between the two groups of oocytes. All the oocytes were obtained by aspiration of either ovarian follicles between 3-6 mm diameter, and the subsequent IVM, or ovarian follicles from 8-10 mm diameter, with no need of maturation (in vivo matured oocytes). Significant differences were found at day 2 for cleavage rates (58.2 ± 3.0 and 45.7 ± 4.4, P = 0.010) and at day 7 for the blastocyst rates (31.4 ± 3.7 and 47.5 ± 6.6, P = 0.014) for IVM and in vivo groups, respectively, but not for the total cell number per blastocyst (48.1 ± 1.9 and 48.2 ± 2.7). Using the in vivo group as a reference, 1297 and 476 differentially expressed genes (DEGs) were down-regulated and up-regulated, respectively, in the IVM group. The up-regulated DEGs in IVM oocytes were mainly associated with organelle organization, DNA methylation, and cell cycle processes; down-regulated genes were mainly enriched in ribosomal RNA processing, protein synthesis, oxidative phosphorylation and metabolomic processes such as glycosyl and aldehyde compound pathways. The global percentage of methylation was similar between the IVM and in vivo groups, but 321, 344, and 843 differentially methylated regions (DMRs) were detected (P < 0.05) in CpG islands, promoters and coding regions, respectively. Integrative analysis of RNA-sequencing and DNA methylation data identified the main methylated regions and genes that define each group. A total of 236 loci and 296 genes defined the IVM group, while 856 loci and 688 genes were related to the in vivo group. In addition, in the IVM group, we found a higher number of negative correlations between gene expression and DNA methylation, while the in vivo group showed higher number and stronger positive correlations. Taken together, these results indicate a discrete effect of IVM on the DNA methylation landscape in mature porcine oocytes, but these changes seem to have a greater impact on gene expression regulation.

overall_design: Ovaries from Landrace-Large-White gilts were collected at the slaughterhouse and transported to the laboratory (within 60 minutes) in saline solution containing 100 µg/mL kanamycin sulphate at 38.5°C, washed once in 0.04% cetrimide solution (w/v) and then twice in saline. Then, the IVM protocol was the same as in Romero-Aguirregomezcorta et al. (2024). As for the in vivo matured oocytes, the contents of follicles of 8-10 mm diameter were aspirated and washed twice in Dulbecco's PBS supplemented with 1 mg mL-1 PVA. All IVM and in vivo matured COCs were identified under a stereomicroscope and mechanically detached from the cumulus cells using an automatic pipette set to a volume of 200 microlitres. To do this, the COCs were gently aspirated and repeatedly ejected into the Petri dish until the zona pellucida was visualised free of cumulus cells at 50x magnification. Only oocytes with a visible polar body under the stereomicroscope were selected and snap frozen in LN2 and stored at -80°C until use (n = 20 IVM and 20 in vivo matured oocytes).

first: Pilar

last: Fuster Coy

first: Laura

last: Abril-Parreño

first: Gavin

last: Kelsey

last: Galvao

last: Huertas-López

first: Emilio

last: Serrano-López

last: Martínez-Moreno


title: Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus

city: Shanghai

first: Dandan

last: Dong

address: 130 Dongan Road, Xuhui

country: China

institute: Fudan University Shanghai Cancer Center

summary: Genome wide association studies (GWASs) have identified numerous risk loci associated with prostate cancer, yet unraveling their functional significance remains elusive.  Leveraging our high-throughput SNPs-seq method, we pinpointed rs4519489 within the multi-ancestry GWAS-discovered 2p25 locus as a potential functional SNP due to its significant allelic differences in protein binding. Here, we conduct a comprehensive analysis of rs4519489 and its associated gene, NOL10, employing diverse cohort data and experimental models. Clinical findings reveal a synergistic effect between rs4519489 genotype and NOL10 expression on prostate cancer prognosis and severity. Through unbiased proteomics screening, we reveal that the risk allele A of rs4519489 exhibits enhanced binding to USF1, a novel oncogenic transcription factor (TF) implicated in prostate cancer progression and prognosis, resulting in elevated NOL10 expression. Furthermore, we elucidate that NOL10 regulates cell cycle pathways, fostering prostate cancer progression. The concurrent expression of NOL10 and USF1 correlates with aggressive prostate cancer characteristics and poorer prognosis. Collectively, our study offers a robust strategy for functional SNP screening and TF identification through high-throughput SNPs-seq and unbiased proteomics, highlighting the rs4519489-USF1- NOL10 regulatory axis as a promising biomarker or therapeutic target for clinical diagnosis and treatment of prostate cancer.

overall_design: To examine the potential enhancer functionality of the rs4519489 region, we performed chromatin immunoprecipitation sequencing (ChIP-seq) experiments for epigenetic markers in various cell lines and clinical specimens. Expanding ChIP-seq to include histone modifications in both normal and tumor prostate tissues from the CPGEA cohort confirmed enhancer/promoter activity at rs4519489, reinforcing its functional gene regulatory role. Subsequently, to assess the impact of NOL10 or USF1 knockdown on downstream gene expression, we performed RNA sequencing analysis to identify differentially expressed genes (DEGs) in LNCaP,DU145,PC3, and 22Rv1 cells treated with shRNA or siRNA targeting NOL10 or USF1.


title: H3K4 methylation-promoted transcriptional memory supports faithful zygotic genome activation and development [RNA-seq-Morpholino]

first: Eva

last: Hoermanseder

overall_design: RNA-seq profiling of H3K4-demethylated Xenopus laevis embryos at ZGA stages after injection of Cxxc1, Kmt2b or control asMOs (anti-sense morpholinos) into 1-cell embryos.

first: Meghana

last: Oak

first: Marco

last: Stock

first: Matthias

last: Mezes

first: Tobias

last: Straub

first: Antony

last: Hynes-Allen

first: Jelle

last: van den Ameele

first: Ignasi

last: Forne

first: Andreas

last: Ettinger

first: Axel

last: Imhof

first: Antonio

last: Scialdone

last: Hörmanseder


title: FCRL4 and exhausted B cell signature in tumor infiltrating B cells from lung cancer

city: Moscow

first: Ekaterina

last: Serebrovskaya

address: Ostrovityanova st., 1

country: Russia

institute: Russian National Research Medical University

summary: Our understanding of the heterogeneity of tumor-infiltrating B cells (TIBs) evolves in parallel with the advances in high-dimensional flow cytometry and single-cell RNA sequencing (scRNA-seq). Subpopulations of TIBs have been described with diverse and even opposite roles in tumor control, based on surface molecule, cytokine and transcriptional factor expression. Furthermore, recently the predictive role of IgA and IgG expression in tumors was shown for melanoma and KRAS-mutated, but not KRAS wild type, lung adenocarcinoma. This may imply that B cells producing different immunoglobulin isotypes also acquire different functional characteristics that have unequal effects on tumor microenvironment (TME) and differentially affect tumor progression. To address this question, we performed comparative bulk transcriptome analysis of tumor-infiltrating surface-IgA+ (sIgA+) and sIgG+ memory B cells from lung adenocarcinoma (LUAD) tumors. We identified FCRL4, PDCD1 and RUNX2 among genes overexpressed in IgA+ B cells, which suggests exhausted, chronically antigen-stimulated phenotype. Using public scRNA-seq data, we showed that FCRL4-expressing memory TIBs form a distinct cluster of cells with transcriptomic profile characterized by upregulation of genes involved in IFNγ and IFNα responses. sIgG+ B cells, on the other hand, overexpress IL5RA, consistent with the role of IL-5 in class-switch recombination to IgG isotype. Moreover, based on the analysis of the TCGA LUAD cohort, we found that FCRL4 to CD20 expression ratio correlates with lower overall survival, further strengthening the view on FCRL4 as a marker of exhausted dysfunctional TIBs. Our findings support the initial hypothesis that IgA/IgG ratio in tumors is not merely an indication of cytokine environment in the TME, but also reflects the difference in the functional characteristics of the respective B cell populations.

overall_design: bulk RNA sequencing of sorted B cells from primary lung and renal cancer

last: Bryushkova

first: Evgeny

last: Shchoka

first: Daniil

last: Lukyanov

first: Marina

last: Gikalo

first: Dmitry

last: Chudakov


title: Post-transcriptional monoadenylation by TENT2 terminates human RNA polymerase III transcript 3' end processing and promotes 7SL RNA biogenesis [gene_specific_RNAseq]

first: Cody

last: Ocheltree

address: 9500 Gilman Drive

type: Non-coding RNA profiling by high throughput sequencing

summary: Small non-coding RNAs (sncRNAs) are subject to a variety of 3' end trimming and tailing activities during biogenesis, which dictate whether they undergo maturation or are instead subjected to degradation. To investigate the dynamics of human sncRNA 3' end processing at a global level we performed genome-wide 3' end sequencing of nascently-transcribed and steady state sncRNAs. This revealed widespread post-transcriptional adenylation of nascent sncRNAs, which came in two distinct varieties. One is characterized by oligoadenylation, which is transient, promoted by TENT4A/4B polymerases, and observed primarily on unstable sno- and scaRNAs that are not fully processed at their 3' ends. The other is characterized by monoadenylation, which is broadly catalyzed by TENT2 and stably accumulates at the 3’-end  of many RNA Polymerase-III-transcribed (Pol-III) RNAs as well as a subset of small nuclear RNAs. This monoadenylation event terminates 3' end uridylation/deuridylation dynamics characteristic of nascent Pol-III RNAs and, in the case of 7SL RNAs, prevents their accumulation with nuclear La protein and promotes their biogenesis towards assembly into cytoplasmic signal recognition particles.

overall_design: RNAs from control or TENT2-depleted conditions were gene-specifically PCR amplified for 3' end sequencing. RNAs associated with La and SRP54 during IP were PCR amplified for 3' end sequencing. RNAs labeled with s4U (two 3-hour pulses) in control or TENT2 KO conditions were PCR amplified for 3' end sequencing.

first: Blake

last: Skrable

first: Tim

last: Nicholson-Shaw

first: Jens

last: Lykke-Andersen


title: H3K4 methylation-promoted transcriptional memory supports faithful zygotic genome activation and development [MBD-seq]

first: Eva

last: Hoermanseder

type: Methylation profiling by high throughput sequencing

overall_design: Profiling of DNA methylation in pre-ZGA (4.5hpf/256-cell) stage embryos using MBD-sequencing, performed by affinity purification of methylated genomic DNA to the MethylCap protein (H6-GST-MBD).

first: Meghana

last: Oak

first: Marco

last: Stock

first: Matthias

last: Mezes

last: Straub

last: Hynes-Allen


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

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: H3K4 methylation-promoted transcriptional memory supports faithful zygotic genome activation and development [DamID-seq]

first: Eva

last: Hoermanseder

overall_design: Chromatin Accessibility profiling using Targeted DamID (CATaDa) sequencing performed on pre-ZGA (4.5hpf/256-cell) stage Xenopus laevis embryos. Dam mRNA construct was injected into 1-cell stage embryos and embryos were collected at the stage of interest.

first: Meghana

last: Oak

first: Marco

last: Stock

last: Mezes

first: Tobias

last: Straub

first: Antony

first: Jelle

last: van den Ameele

first: Ignasi

last: Forne

first: Andreas

last: Ettinger

first: Axel

last: Imhof

first: Antonio

last: Scialdone

last: Hörmanseder


title: Single-cell Transcriptome and Crosstalk Analysis Reveals Immune Alterations and Key Pathways in the Bone Marrow of Knee Osteoarthritis Patients

status: Public on Jan 17 2025

city: Atlanta

first: Krishnendu

last: Roy

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

institute: Georgia tech

summary: Knee osteoarthritis (OA) is a significant medical and economic burden. To understand systemic immune effects, we performed deep exploration of bone marrow aspirate concentrates (BMAC) from knee-OA patients via single-cell RNA sequencing and proteomic analyses from a randomized clinical trial (MILES: NCT03818737). We found significant cellular and immune alterations in the bone marrow, specifically in MSCs, T cells and NK cells, along with changes in intra-tissue cellular crosstalk during OA progression. Unlike previous studies focusing on injury sites or peripheral blood, our probe into the bone marrow—an inflammation and immune regulation hub—highlights remote organ impact of OA, identifying cell types and pathways for potential therapeutic targeting. Our findings highlight increased cellular senescence and inflammatory pathways, revealing key upstream genes, transcription factors, and ligands. Additionally, we identified significant enrichment in key biological pathways like PI3-AKT-mTOR signaling and IFN responses, showing their potentially crucial role in OA onset and progression.

overall_design: scRNAseq data genration and analysis to find knee-OA related changes in patient bone marrow

first: Paramita

last: Chatterjee

first: Hazel

last: Stevens

first: Linda

last: Kippner

first: Greg

last: Gibson

first: Krish


title: Microglial Prrc2a regulates microglia-neuron interaction in cerebellum and motor functions in mice

status: Public on Jan 16 2025

city: Beijing

first: Zengqiang

last: yuan

address: No. 27 Taiping Road, Haidian District

institute: Beijing Institute of Basic Medical Sciences

summary: The crosstalk between microglia and neuron has been recognized as a crucial process in the development and disorders of the central nervous system. The present study probes into the role of Prrc2a—a post-transcriptional regulator that binds and stabilizes transcripts pivotal for microglial development—specifically within cerebellar microglia using a microglia-targeted conditional knockout model, identifying it as a crucial regulator of microglial function. Single-cell RNA sequencing underscored a transcriptomic shift in Prrc2a-ablated microglia, revealing an abnormally activated state. Prrc2a deficiency and the consequent alteration of cerebellar microglia were associated with reduced mutual interactions, altered Purkinje cell morphology and electrophysiological activity, decreased molecular layer width, and subsequently defects in motor balance and coordination. Collectively, this study provides insights into the molecular mechanisms underlying microglia-neuron interaction within the cerebellum.

overall_design: To investigate the role of Prrc2a in microglia, we utilized microglia-specific knockout mice and ablated Prrc2a at postnatal day1. In order to gain a more comprehensive understanding of Prrc2a deficiency on microglial transcriptome characteristics and subsequent neuronal changes in cerebellum, we performed single-cell RNA-sequencing of 18658 murine cerebellar cells from Prrc2a cKO (specific deletion of Prrc2a in microglia) and Prrc2a flox/flox (control) mice at postnatal day7.

first: Xiaoheng

last: Li

first: Pin

last: Yang

first: Binbin

last: Dong

first: Lingling

last: Jiang

first: Ruilian

last: Xiu

first: Jia

last: Guo

first: Shuoshuo

first: Ping

last: Zhang

first: Runze

last: Gu

first: Ao

first: Jinyu

first: Rong

last: Wu

first: Fengchao

last: Wang

first: Ying

last: Shen

first: Ningsheng

last: Shao

first: Jinbo

last: Cheng

last: Yuan


title: Transcriptomic Profile of Neuroinflammation in Alzheimer’s Mouse Brain Treated With and Without Extracellular Vesicles

city: Irvine

first: Munjal

last: Acharya

address: 811 Health Sciences Road, MedSci B-149

department: Anatomy and Neurobiology

institute: University of California, Irvine

summary: Expression of 757 genes related to neuroinflammation was analyzed across 4 treatment groups of male mice to investigate the neuroprotective effects of either human neural stem cell (hNSC) or induced pluripotent stem cell microglial-like (iMGL) cell-derived extracellular vesicles (EVs) in 5xFAD mouse model of Alzheimer’s Disease (AD).

overall_design: Samples from 18 male mice, ages 25-26 weeks at the time of perfusion, were analyzed using the commercially available nCounter® Mouse Neuroinflammation Panel from NanoString™, with 4-5 samples for each of the 4 treatment groups. The 5xFAD transgenic mouse line was selected for the rapid neuropathological progression of beta-amyloid plaque deposition and subsequent cognitive dysfunction. 5xFAD mice were randomly assigned to one of three AD treatment groups that would receive 4 weekly retroorbital injections of either: hNSC-derived EVs  or iMGL-derived EVs at a dose concentration of 2.25E+07 EVs/50 ul injection; or vehicle consisting of phosphate buffered saline without calcium or magnesium (PBS -/-). C57BL/6J mice served as WT controls and also received 4 weekly retroorbital injections of vehicle.

first: Robert

last: Krattli

first: Mineh

last: Markarian


title: scRNAseq Data Analysis Code Muscle Inflammation is Regulated by NF-kB From Multiple Cells to Control Distinct States of Wasting in Cancer Cachexia

status: Public on Jan 15 2025

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary: Although cancer cachexia is classically characterized as a systemic inflammatory disorder, emerging evidence indicates that weight loss also associates with local tissue inflammation. We queried the regulation of this inflammation and its causality to cachexia by exploring skeletal muscle, whose atrophy strongly associates with poor outcome. Using multiple mouse models and patient samples, we show that cachectic muscle is marked by enhanced innate immunity. NF-kB activity in multiple cells, including satellite cells, myofibers, and fibro-adipogenic progenitors, promotes macrophage expansion derived equally from infiltrating monocytes and resident tissue. Moreover, NF-kB activated cells and macrophages undergo crosstalk: whereas NF-kB+ cells recruit macrophages to inhibit regeneration and promote atrophy, while interestingly also protecting myofibers, macrophages stimulate NF-kB+ cells in a feed forward loop to sustain inflammation. Together, we propose that NF-kB functions in multiple cells in the muscle microenvironment to stimulate macrophage inflammation that both promotes and protects against muscle wasting in cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: scRNA sequencing was done for 3 datasets, one from Human Pancreatic ductal adenocarcinoma (PDAC) and other two from cachexia in mice induced by C26 colon cancer cells and cachexia in KPP mice(KrasLSL-G12D/+, Ptenf/f, Ptf1aER-Cre/+).For the human  dataset Muscles from human samples were taken at time of pancreatic tumor resection, or time of other abdominal surgery for control patients. Muscle were digested in an enzymatic buffer and CD45 negative and positive cells were separated by MACs beads. Both fractions were sent for single cell RNA sequencing. Samples include CD45-/CD45+ Weight Stable PDAC(Neg_WS_PDAC,Pos_WS_PDAC),CD45-/CD45+ Control(Neg_Control,Pos_Control) and CD45-/CD45+ Cachetic PDAC(Neg_C_PDAC, Pos_C_PDAC). For cachexia in mice we induced  cancer by injecting the C-26 colon cancer cells subcutaneously in CD2F1 mice. At endpoint, hindlimb muscle was extracted and enzymatically digested. MACs beads were used to sort CD45 positive and negative fractions for single cell sequencing.Samples include CD45-/+ Control and CD45-/+ C26 cachexia from two batches(S1 and S2). For cachexia in KPP mice tamoxifen was injected for 5 days to induce pancreatic tumor formation. Mice were euthanized after tumor formation and cachexia development.MACs beads were used to sort CD45 positive and negative fractions for single cell sequencing. Samples include CD45-/+ Control and CD45-/+ Kpp cachexia.

first: Suganya

last: Subramanian

first: Benjamin

last: Pryce

first: Denis

last: Guttridge


title: Limitations in mitochondrial programming restrain the maturation of human stem cell-derived β cells

city: Ann Arbor

first: Anne

last: Lietzke

state: MI

address: 1000 Wall Street

institute: University of Michigan

summary: Pluripotent stem cell-derived (SC) islets offer a renewable source for β cell replacement for type 1 diabetes, yet functional and metabolic immaturity may limit their long-term therapeutic efficacy. Here, we describe that limitations in mitochondrial transcriptional programming prevent the maturation of SC-β cells. We observe several alterations in SC-islet mitochondria compared to human islets, including reductions in mitochondrial respiration, expression of OXPHOS machinery, and mitochondrial lipid metabolism. Surprisingly, these effects were not related to reductions in mitochondrial mass, genome integrity, or structure. Transcriptomic profiling throughout differentiation to SC-islets revealed several unstudied candidates in β cell maturation that regulate programming of mitochondrial oxidative and fatty acid metabolism, including the nuclear receptors PPAR⍺ and PPARγ.  Indeed, treatment of SC-islets with WY14643, a potent PPAR⍺ agonist with PPARγ activity, promoted expression of mitochondrial targets, improved insulin secretion, and increased the presence of β cells both in vitro and upon transplantation into immunodeficient mice. Mitochondria are vital to fuel β cell insulin release; however, our studies here revealed the potential for targeting mitochondrial programming to enhance the differentiation and metabolic maturation of SC-β cells.

overall_design: HUES8 and H1 cell lines were differentiated to SC-islets in a 6 stage differentiation protocol (Hogrebe et al. 2021, PMID: 34349281). Total RNA was isolated from each stage (n=3-6 per stage). Primary human islets were received and cultured per protocol (Prodo Labs). Total RNA was isolated from 6 human islet donors. Additionally, H1 Stage 6 cells were treated for 7 days starting at stage 6 day 3 with vehicle or WY14643. Total RNA was isolated from both conditions (n=4 per condition).

middle: C

first: Jessica

last: King

first: Kelly

last: Crumley

first: Elizabeth

last: Bealer

first: Ava

last: Stendahl

first: Jie

last: Zhu

first: Gemma

last: Pearson

first: Elena

last: Levi-D'Ancona

first: Belle

last: Henry-Kanarek

first: Emma

last: Reck

first: Manikanta

last: Arnipalli

first: Vaibhav

last: Sidarala

first: Emily

last: Walker

first: Subramaniam

last: Pennathur

first: Lonnie

middle: D

last: Shea

first: Scott

last: Soleimanpour


title: High-resolution whole-genome DNA methylation revealed unique signatures of painful diabetic neuropathy

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

country: Italy

institute: Univeristy of Bologna

type: Methylation profiling by genome tiling array

summary: This work describes the DNA methylation signature and identifies genes associated with neuropathic pain in type 2 diabetes mellitus. Genome-wide methylation data for 315 DNA (WB) samples were generated using Illumina Infinium Methylation EPIC v1.0 BeadChip. Four different selection criteria were used to identify promising pain-related genes. The findings revealed significant differences in methylation patterns between painful and painless diabetic neuropathy and identified a set of individual CpG sites of unique candidate genes associated with the painful phenotype. Several of these genes, including GCH1, MYT1L and MED16, have been previously linked to pain-related phenotypes or diabetes. Through pathway enrichment analysis, we demonstrated that specific epigenetic signatures could contribute to the complex phenotype of diabetic neuropathy and cluster analyses highlighted significant epigenetic dissimilarities between painful and painless phenotypes. Our results uncovered epigenetic differences between painful and painless diabetic neuropathy patients and identified targeted genes linked to neuropathic pain through DNA methylation mechanisms. This approach holds promise for investigating other chronic pain conditions, such as secondary chronic pain from cancer treatment, thoracic surgery, and various transplant settings.

overall_design: Bisulphite converted DNA isolated from 315 whole blood samples were hybridised to the Illumina Infiniun MethylationEPIC BeadChip following manufacture's protocols.

first: Katarzyna M

last: Kwiatkowska


title: TGF-β Signaling Pathway and Cell-Cell Interactions in the Tumor Microenvironment Drive Bladder Cancer Progression after BCG Instillation Treatment: Insights from longitudinal Single-Nucleus RNA-Seq

status: Public on Jan 13 2025

city: Seocho-gu

first: Kim

last: Tae-Min

address: Banpo-daero

country: South Korea

institute: The Catholic University of Korea

summary: In this study, we aimed to characterize cellular subtypes and cognate genetic markers using single nuclear RNA sequencing on 8 NMIBC samples treated with BCG, including 3 cases exhibited disease progression.

overall_design: 14 samples from 9 patients with BCG. 3 cases show progression after BCG treatment; NP = non-progression, P = Progression sample, CF = Cancer Cell Free

first: Tae-Min

last: Kim

first: Seo-Young

last: Lee

first: Yun-Hee

first: Y-Syn

last: Ha


title: Decoding transcriptional identity during Neuron-Astroglia Cell Fate driven by RAR-specific agonists [Spatial transcriptomics]

city: Evry

first: Marco Antonio

last: MENDOZA-PARRA

address: 2 rue Gaston Crémieux

institute: CNRS UMR8030

summary: How cells respond to different signals leading to defined lineages is an open question to understand physiological differentiation leading to the formation of organs and tissues. Among the various morphogens, retinoic acid signaling, via the RXR/RAR nuclear receptors activation, is a key morphogen of nervous system development and brain homeostasis. Here we analyze gene expression in ~80,000 cells covering 16 days of monolayer mouse stem cell differentiation driven by the pan-RAR agonist all-trans retinoic acid, the RAR-alpha agonist BMS753 or the activation of both RAR-beta and RAR-gamma receptors (BMS641+BMS961). Furthermore, we have elucidated the role of these retinoids for driving nervous tissue formation within 90 days of brain organoid cultures, by analyzing > 8,000 distinct spatial regions over 28 brain organoids. Despite a delayed progression in BMS641+BMS961, RAR-specific agonists led to a variety of neuronal subtypes, astrocytes and oligodendrocyte precursors. Spatially-resolved transcriptomics performed in organoids revealed spatially distinct RAR isotype expression leading to specialization signatures associated to matured tissues, including a variety of neuronal subtypes, retina-like tissue structure signatures and even the presence of microglia.

overall_design: mouse embryonic stem cells were cultured in monoloayer in presence of either the pan-RAR agonist ATRA, the RAR-alpha agonist BMS753, or the combination of the RAR-beta and RAR-gamma agonists (BMS641+BMS961). Monolayer cultures driven into differentiation by the action of these RAR ligands were analyzed by single-cell transcriptomics after 4, 8 and 16 days of treatment. Samples collected after 16 days of differentiation were also used for Cut&tag assays for revealing histone modification signatures associated to promoter regions as a way to reveal active, repressed or bivalent promoter chromatin states. To further reveal the role of retinoids action in nervous tissue development, we have cultured mouse stem cells in 3-dimensional conditions. After 3 months of culture, the obtained brain organoid tissues were anlaysed by spatial transcriptomics.

first: Ariel

last: Galindo-Albarrán

first: Aysis

last: Koshy

first: Maria-Grazia

last: Mendoza-Ferri

first: Marco-Antonio

last: Mendoza-Parra


title: Decoding transcriptional identity during Neuron-Astroglia Cell Fate driven by RAR-specific agonists [scRNA-seq]


title: Novel PET/CT Imaging Biomarkers of CB-839 in Combination With Panitumumab and Irinotecan in Patients With Metastatic and Refractory RAS Wildtype Colorectal Cancer

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

summary: In managing patients with rat sarcoma virus (RAS) wild-type (WT) metastatic colorectal cancer (mCRC), monoclonal antibodies against the epidermal growth factor receptor (EGFR) represent a key therapeutic strategy. However, their limited ongoing effectiveness in this setting underscores the importance of elucidating other factors that affect response, including underlying immunological and metabolic repertoires. An emerging therapeutic target, glutamine metabolism is crucial for cancer cell growth; symbiotically, tumor glutamine demand relative to the microenvironment disadvantages potential anti-tumor immunity. We conducted a phase I/II clinical trial in patients with RAS WT mCRC combining panitumumab, an EGFR inhibitor, and CB-839, a glutaminase inhibitor, hypothesizing that antagonizing glutamine-centric tri-carboxylic acid (TCA) cycle metabolism and mitogen-activated pathway kinase (MAPK)-mediated growth would favor response in well-selected patients. Here, we demonstrate that a novel B cell activation signature, ‘Bscore’ was associated with clinical benefit from combined therapy in patients who previously progressed on anti-EGFR therapy. Patient ‘Bscore’ was positively associated with treatment-induced change in lesion size. Furthermore, patients with lower ‘Bscore’ tended to exhibit greater tumor avidity of glutamine by non-invasive positron emission tomography (PET), suggesting the sensitivity of B cell activation to a glutamine-depleted microenvironment and highlighting future opportunities to enhance immune response in the treatment of mCRC and potentially other glutaminolysis-dependent solid tumors.

overall_design: Tumor core biopsies were collected from participants enrolled on the phase II portion of the study. Tissue was collected at baseline prior to treatment. One tumor sample was analyzed per participant.

first: Seong-Woo

last: Bae

first: Kristen

middle: K

last: Ciombor

first: Quanhu

last: Sheng

first: Gregory

last: Ayers

first: Cathy

last: Eng

first: Laura

last: Goff

first: Dana

last: Cardin

first: Jordan

last: Berlin

first: H

last: Manning


title: Endogenous fine-mapping of functional regulatory elements in complex genetic loci in HAP1 [microC]

status: Public on Jan 10 2025

city: Tianjin

first: Ke

last: Zhao

address: Qixiangtai Road, No.22

institute: Tianjin Medical University

summary: The majority of genetic loci linked to polygenic complex traits are found in non-coding regions of the human genome. These loci often exhibit complex gene regulatory relationships and linkage disequilibrium (LD) configurations, making it challenging to accurately identify causal variants and their target genes. We used multiplexed single-cell CRISPR interference and activation perturbations to investigate cis-regulatory element (CRE) and target gene expression relationships within tight LD in the endogenous chromatin context. We demonstrated the prevalence of multiple causality in perfect LD (pLD) for independent expression quantitative trait locus (eQTL) and uncovered fine-grained genetic effects on gene expression within pLD, which are difficult to decipher using traditional eQTL fine-mapping or existing computational methods. We found that over one third of the causal CREs lack classical epigenetic markers, and we functionally validated one of these hidden regulatory mechanisms. Leveraging Multiome single-cell epigenetic and sequence perturbations, we highlighted the regulatory plasticity of the human genome. Our study will guide the exploration of missing causal mechanisms in molecular trait formation and disease development.

overall_design: Nine scRNA-seq datasets under varying multiplicity-of-infection (MOI) conditions, three single-cell multiome datasets (ATAC + Gene Expression) from modified HAP1 clones(dCas9-KRAB-blast, dCAS9-VP64-blast and Cas9-blast stably expressed HAP1 clones), four ATAC-seq datasets from wild-type and CRISPR-edited HAP1 cells(64bp deletion, 17bp deletion and CRISPRi around rs73156934-tagged cis-regulate element(CRE)), six CUT&TAG histone modification datasets and 1 Micro-C dataset from wild-type HAP1 cells, and three 4C-seq datasets for validating CRE-gene regulatory relationships in HAP1 cells.

first: Yao

last: Zhou

first: Mulin

last: JunLi


title: Symmetric DNA Adenine Methylation Plays an Essential Role in Early-Diverging Fungi [RNA-seq]

status: Public on Jan 12 2025

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

institute: University of Murcia

summary: The discovery of N6-methyladenine (6mA), typically found in prokaryotic DNA, in eukaryotic genomes, has revolutionized epigenetics. Here, we show that symmetric 6mA is essential in the early diverging fungus Rhizopus microsporus, as the absence of the MT-A70 complex (MTA1c) responsible for this modification results in a lethal phenotype. 6mA is present in 70% of the genes, correlating with the presence of H3K4me3 and H2A.Z in open euchromatic regions. This modification is found predominantly in nucleosome linker regions, influencing the nucleosome positioning around the transcription start sites of highly expressed genes. Controlled downregulation of MTA1c results in a reduction of symmetric 6mA sites affecting nucleosome positioning and histone modifications, leading to altered gene expression, which is likely the cause of lethality. Our study highlights the indispensable role of the DNA 6mA in a multicellular organism and delineates the mechanisms through which this epigenetic mark regulates gene expression in a eukaryotic genome

overall_design: RNA-seq experiment to analize gene expression of R. microsporus ATCC 11559 growing with Zinc (20mg/L) and withouz Zinc (0mg/L)

first: Stephen

last: Mondo

first: José

middle: F

last: Martínez

first: Anna

last: Muszewska

first: Leo

last: Baumgart

last: Pérez-Ruiz

first: Pablo

last: Carrillo-Marín

first: Kurt

last: LaButti

last: Lipzen

first: Yu

last: Zhang

first: Jie

last: Huo

first: Vivian

last: Ng

first: Eusebio

last: Navarro

first: Teresa

last: Pawlowska

first: Igor

middle: V

last: Grigoriev

first: Francisco

last: Nicolás-Molina

first: Victoriano

last: Garre


title: Endogenous fine-mapping of functional regulatory elements in complex genetic loci in HAP1 [scMulti]

first: Ke

last: Zhao

first: Yao

last: Zhou

last: JunLi


title: CA-125 as a Biomarker in Renal Medullary Carcinoma: Integrated Molecular Profiling, Functional Characterization, and Prospective Clinical Validation [ChIP-Seq cell lines]

status: Public on Jan 07 2025

city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Purpose: Renal medullary carcinoma (RMC) is a highly aggressive malignancy defined by the loss of the SMARCB1 tumor suppressor. It mainly affects young individuals of African descent with sickle cell trait, and it is resistant to conventional therapies used for other renal cell carcinomas. This study aimed to identify potential biomarkers for early detection and disease monitoring of RMC. Experimental Design: Integrated profiling of primary untreated RMC tumor tissues and paired adjacent kidney controls was performed using RNA-sequencing (RNA-seq) and histone Chromatin Immunoprecipitation Sequencing (ChIP-seq). The expression of serum cancer antigen 125 (CA-125), was prospectively evaluated in 47 patients with RMC. Functional studies were conducted in RMC cell lines to assess the effects of SMARCB1 re-expression and MUC16 knockdown. Results: MUC16, encoding for CA-125, was identified as one of the top upregulated genes in RMC tissues, with concomitant enrichment of active histone marks H3K4me3 and H3K27ac at its promoter. Elevated serum CA-125 levels were found in 31 of 47 (66%) RMC patients and correlated significantly with metastatic tumor burden (p = 0.03). SMARCB1 re-expression significantly reduced MUC16 expression in RMC cell lines. Functional studies in RMC cell lines demonstrated that SMARCB1 re-expression significantly reduced MUC16 expression, and that MUC16 knockdown induced apoptosis and reduced cell proliferation. Conclusions: The correlation between serum CA-125 levels and metastatic burden suggests that CA-125 is a clinically relevant biomarker for RMC. These findings support further exploration of CA-125 for disease monitoring and targeted therapeutics in RMC.

overall_design: Cell lines derived from Renal medullary carcinoma (RMC) were transfected with either empty vector or SNF5 (SMARCB1) constructs and treated with doxycycline to express SNF5 (SMARCB1).

first: Pavlos

last: Msaouel

first: Cristian

last: Coarfa

first: Sandra

last: Grimm

first: Menuka

last: Karki


title: Decoding transcriptional identity during Neuron-Astroglia Cell Fate driven by RAR-specific agonists [CUT&Tag]

first: Marco Antonio

last: MENDOZA-PARRA

first: Ariel

last: Galindo-Albarrán

first: Aysis

last: Koshy

first: Maria-Grazia

last: Mendoza-Ferri

first: Marco-Antonio

last: Mendoza-Parra


title: Endogenous fine-mapping of functional regulatory elements in complex genetic loci in HAP1

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

overall_design: Refer to individual Series


title: Endogenous fine-mapping of functional regulatory elements in complex genetic loci in HAP1 [CUT&Tag]

status: Public on Jan 03 2025

first: Mulin


title: CA-125 as a Biomarker in Renal Medullary Carcinoma: Integrated Molecular Profiling, Functional Characterization, and Prospective Clinical Validation

status: Public on Jan 06 2025


title: Lactylated histone promotes rheumatoid arthritis progression by increasing NFATc2 expression and the production of anti-lactylated histone autoantibodies [II]

city: Wenzhou

first: Wu

last: Gan

address: Chashan Street, Ouhai District

institute: Wenzhou Medical University

summary: The elevated lactate in the joint microenvironment of patients with rheumatoid arthritis (RA) is crucial for disease progression, although the underlying mechanism remains to be elucidated. In this study, we observed significantly increased global lactylation levels within fibroblast-like synoviocytes (FLS) of RA patients compared to HC (healthy controls), and lactylated proteins were enriched in histones. Furthermore, we found that anti-lactated histone antibodies were detected in almost RA patients and positively correlated with Disease Activity Score 28 (DAS28). Then we identified NFATc2 as a key target gene regulated by histone H3 lysine 9 lactylation (H3K9la) using CUT&Tag combined with RNA-seq. Functional studies revealed that NFATc2 promotes migration of RA-FLSs. Additionally, using server combined immune-deficiency (SCID) and collagen-induced arthritis (CIA) mouse models, we demonstrated that NFATc2 exacerbates RA disease progression through enhanced FLS cartilage invasion function. Collectively, our findings suggest that upregulated target gene NFATc2 by lactate-dependent histone lactylation, can be used as a potential therapeutic target for intervention, anti-lactated histone autoantibodies is promising as a diagnostic marker for RA.

overall_design: RNA-seq profiling of wildtyp and NFATc2 knockdown fibroblast-like synoviocytes (FLS) from RA patients.


title: A developmentally-inspired hypoxia condition promotes kidney organoids differentiation from human pluripotent stem cells

status: Public on Jan 05 2025

city: Ulsan

first: Tae-Eun

last: Park

address: 50, UNIST-gil, Eonyang-eup, Ulju-gun

department: Biomedical Engineering

institute: Ulsan National Institute of Science and Technology (UNIST)

summary: Kidney organoids derived from human pluripotent stem cells (hPSCs) lack a contiguous network of collecting ducts, which limits their utility in modeling kidney development and disease. Here, we report the generation of kidney organoids containing ureteric bud (UB)-derived collecting ducts connected to metanephric mesenchyme (MM)-derived nephrons using a developmentally-inspired hypoxic differentiation condition. Hypoxia promotes a reiterative process of branching morphogenesis and nephron induction through reciprocal interactions between co-induced MM and UB, which lead to a higher-order kidney organogenesis in vitro. The resulting kidney organoids demonstrate greater maturity, as indicated by higher levels of functional markers and a more realistic micro-anatomy. Additionally, these hypoxic-enhanced kidney organoids show a great potential as in vitro models for renal cystic diseases, as they efficiently generate cystic formations and display high sensitivity to drugs. This hypoxia approach may open new avenues for an enhanced understanding of kidney development and diseases.

overall_design: Single-cell RNA sequencing was conducted to profile the cellular composition of kidney organoids differentiated under normoxic and hypoxic conditions.

first: Hyeonji

last: Lim

first: Dong

last: Kim


title: CA-125 as a Biomarker in Renal Medullary Carcinoma: Integrated Molecular Profiling, Functional Characterization, and Prospective Clinical Validation [ChIP-Seq tumors]

overall_design: Renal medullary carcinoma (RMC) kidney tumors or adjacent normal tissue from untreated patients were used for Chromatin immunoprecipitation against four histone marks (H3K27ac, H3K4me1, H3K4me3, H3K27me3).


title: Lactylated histone promotes rheumatoid arthritis progression by increasing NFATc2 expression and the production of anti-lactylated histone autoantibodies [CUT&Tag]

overall_design: CUT&Tag of the histone modification H3K9la in fibroblast-like synoviocytes (FLS) from RA patients and healthy controls

first: Gan

last: Wu


title: Endogenous fine-mapping of functional regulatory elements in complex genetic loci in HAP1 [4C]

first: Ke

last: Zhao

first: Yao

last: Zhou


title: CA-125 as a Biomarker in Renal Medullary Carcinoma: Integrated Molecular Profiling, Functional Characterization, and Prospective Clinical Validation [RNA-Seq]

first: Amrit

last: Koirala

first: Pavlos


title: Tumor and immune environment changes in EGFR-TKI treated EGFR-mutant non-small cell lung cancer

city: Seoul

first: Soomin

address: 101, Daehak-ro, Jongno-gu

institute: Seoul National University Cancer Research Institute

summary: Patients with EGFR mutations exhibit immunosuppressive microenvironments, limiting responsiveness to immunotherapy. In our analysis, 25 Korean patients diagnosed with NSCLC harboring common EGFR mutations (L858R and exon 19 microdeletion) that received EGFR-TKI treatment was compared before and after treatment. 25 patients were analyzed overall, and 14 patients were analyzed in the paired analysis who received first-line osimertinib. Among 171 ROIs, 68ROIs were used for tumor paired analysis, and 51 ROIs for immune region.

overall_design: In this study, clinical specimens from 25 patients were selected for spatial and whole transcriptome analysis. To decipher the molecular changes that occur with EGFR-TKI (especially, osimertinib) treatment, we conducted DEG analysis by categorizing the patients into pre-treated and post-treated groups. This study was approved by the Institutional Review Board of the Seoul National University Hospital and performed in accordance with the Declaration of Helsinki.

first: Jaemoon

last: Koh

first: Songji

last: Oh

first: Tae Min


title: Inflammatory milieu by crosstalk between podocytes and proximal tubular cells in type 2 diabetic kidney disease

status: Public on Jan 01 2025

first: Yong jun

address: 329, Daehak-ro 103, Jongno-gu, Seoul, Republic of korea

department: biomedical science

institute: Seoul National University

summary: Due to the limited availability of therapeutic agents for type 2 diabetic kidney disease (DKD), there is a need for further knowledge derived from experimental models and innovative techniques. In addressing this issue, single-cell RNA sequencing (scRNA-seq) has been exclusively applied to a genetically modified DKD model, but not an induced model representing type 2 DKD. Herein, we analyzed scRNA-seq and other experiments from an induced type 2 DKD model, and validated the results in human-derived biospecimens. The model was induced by combining a high-fat diet with streptozotocin to simulate induced type 2 DKD. scRNA-seq, histological, and flow cytometric analyses were conducted, and their results were compared with control mice. The findings were then applied to human kidneys exhibiting diabetic glomerulosclerosis associated with type 2 diabetes.

overall_design: single-cell RNAdata for induced type 2 DKD with HFD/STZ

first: Peong

first: Juhyeon

last: Hwang

first: Yongjun

first: Hyunje

first: Seung

last: Han


title: IL-21 Shapes the B Cell Response in a Context-Dependent Manner [RNA-seq

city: New York

first: Jayanta

last: Chaudhuri

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: The cytokine interleukin-21 (IL-21) is a pivotal T cell-derived signal crucial for germinal center (GC) responses, but the precise mechanisms by which IL-21 influences B cell function remain elusive. Here, we investigated the B cell-intrinsic role of IL-21 signaling by employing a novel IL-21 receptor (Il21r) conditional knock-out mouse model and ex vivo culture systems and uncovered a surprising duality of IL-21 signaling in B cells. While IL-21 stimulation of naïve B cells led to Bim-dependent apoptosis, it promoted robust proliferation of pre-activated B cells, particularly class-switched IgG1+ B cells ex vivo. Consistent with this, B cell-specific deletion of Il21r led to a severe defect in IgG1 responses in vivo following immunization. Intriguingly, Il21r-deleted B cells are significantly impaired in their ability to transition from a pre-GC to a GC state following immunization. Although Il21r-deficiency did not affect the proportion of IgG1+ B cells among GC B cells, it greatly diminished the proportion of IgG1+ B cells among the plasmablast/plasma cell population. Collectively, our data suggest that IL-21 serves as a critical regulator of B cell fates, influencing B cell apoptosis and proliferation in a context-dependent manner.

overall_design: To examine the B cell-intrinsic role of IL-21 signaling, we performed RNA-sequencing (RNA-seq) on naïve B cells stimulated ex vivo with combinations of αCD40, IL-4, and IL-21 for 6 or 24 hours

first: Youngjun


title: A single-cell transcriptomic atlas characterizes the kidney in the diabetic kidney disease

city: Jinan

first: jinxiu

last: Hu

address: jingwuweiqi

institute: Shandong Provincial Hospital

summary: Diabetic kidney disease (DKD), a common and devastating microvascular complication of diabetes, is the leading cause of end-stage renal disease (ESRD). Since mechanisms of kidney injury in DKD were largely unknown, we performed single-cell RNA sequencing (scRNA-seq) on human kidneys collected from 3 DKD and 3 normal samples using 10×Genomics. In our study, a total of 51315 cells were enrolled for analyses and nine kidney cell types and seven immune cell types were identified. The cell-type-specific changes in gene expression and signaling pathways of podocyte, mesangial cells, endothelial cells, proximal tubule and macrophages indicate abnormal regulation associated with inflammation, apoptosis, oxidative stress, extracelluar matrix accumulation, and immune activation. In particular, we show that podocytes and renal tubular epithelial cells have a tremendous capacity to regenerate, which is involved in the repairment of injury. And extracellular vesicles, an important mediator of intercellular communication, might play a vital role for this progress. Besides, we identified new candidate transcription factors responsible for the progression of DKD. We also revealed a M1-M2 hybrid pattern, in which M1 and M2 are coupled activation in macrophages of DKD. Furthermore, we demonstrated a complex intercellular interaction between kidney cells and kidney cells or kidney cells and immune cells. Thus, our study will further the understanding of DKD pathogenesis and provide novel therapeutic targets for its treatment in the future.

overall_design: Fresh kidney samples were isolated and sequenced using scRNAseq.

first: L

last: Zhimei

first: Wang

last: Rong


title: Determination of the mechanisms of MCPA resistance in Amaranthus powellii

status: Public on Jan 02 2025

city: Guelph

first: Isabelle

last: Aicklen

address: 50 Stone Road East

country: Canada

institute: University of Guelph

summary: Resistance to synthetic auxin herbicides was recently confirmed in a population of Amaranthus powellii. Following field studies, an RNA-seq experiment was devised to determine the mechanism of resistance to MCPA (a synthetic auxin herbicide) by comparing the level of gene expression of genes in the auxin pathway between the resistant and a susceptible population of Amaranthus powellii. The results identified several differentially expressed genes (DEGs) in the auxin pathway that were significantly downregulated in the resistant samples indicating that the resistance mechanism may be linked to a target site modification.

overall_design: Young leave tissue samples from four treaments were used for RNA extraction. The four treatments were as follows: resistant treated (501T), resistant untreated (501U), susceptible treated (511T), and susceptible untreated (511U). Treated samples were sprayed with 1225 g a.e./ha of MCPA (a synthetic auxin herbicide). At six hours after application, leaf tissue samples from both treated and untreated plants were sampled for RNA extraction. Samples were aligned to both a reference genome (Amaranthus hybridus) and an assembled de novo transcriptome (Amaranthus powellii) and gene count data was compared between all treatments to identify differentially expressed genes DEGs.

first: Mithila

last: Jugulam

first: Todd

last: Gaines

first: William

last: Kramer

first: Martin

last: Laforest

first: Darren

last: Robinson

first: Peter

last: Sikkema

first: Francois

last: Tardif


title: Single-cell sequencing of murine small intestinal dendritic cells

city: Aachen

first: Hieu

middle: Trong

last: Nguyen

address: Pauwelstrasse 30

institute: RWTH Aachen University Hospital

summary: This study was designed to analyse the transcriptomes of dendritic cell populations from the lamina propria of the small intestine in order to identify transcriptomic changes along their maturation towards a migratory phenotype.

overall_design: Transcriptomic profile of dendritic cells isolated from the lamina propria of the murine small intestine

first: Fabian

middle: T

last: Hager

first: Lydia

last: Kopplin

first: Vuk

last: Cerovic

first: Anna

last: Andrusaite


title: Endogenous fine-mapping of functional regulatory elements in complex genetic loci in HAP1 [ATAC-seq]

status: Public on Dec 31 2024

first: Ke

last: Zhao

first: Yao

last: Zhou

first: Mulin

last: JunLi


title: Sex-dependent niche responses modulate steady-state and regenerative hematopoiesis

city: Cleveland

first: Vladimir

last: Makarov

address: 9500 Euclid Ave

department: CITI

institute: CLEVELAND CLINIC LERNER COM-CWRU

summary: Hematopoietic stem cells (HSCs) adapt to organismal blood production needs. While it has been established that sexual dimorphism drives differential hematopoietic function in males vs. females, the mediators responsible for these effects remain unclear. Here, we characterize hematopoiesis in male and female mice at steady state and during regeneration following hematopoietic stem cell transplantation (HST). We found that steady-state males possessed greater bone marrow (BM) hematopoietic stem and progenitor cell (HSPC) populations and varied in frequency for stromal populations. PCR analysis from stromal CD45(-)-purified BM cells demonstrated alterations in niche genes, including Ptn, IL6, Angpt1, Vcam1, and Spp1, together suggesting the male microenvironment is primed for HSC differentiation and mobilization. RNA sequencing of BM lineage(-) cells revealed differential expression of genes, like Hif1a and Aldh1, and corresponding cellular pathways—including those involving reactive oxygen species, oxidative phosphorylation, and Tnf-a signaling via NF-κB—underscoring male lineage(-) cells as more inflammatory and proliferative. To determine the functional outcomes of steady-state transcriptional differences we performed sex-matched and mismatched transplantation studies of lineage(-) donor cells into male and female recipients. We demonstrated a role for TNF-a-driven proliferation of male donor cells and Cxcl12-mediated homing into male recipients during short-term 56-day HST recovery. Serial transplantation of lineage(-) cells suggested the male short-term proliferative advantage may precede long-term disadvantages of inflammation-induced exhaustion. We show that sex-specific cellular and molecular signaling, marked by differing expression of niche factors and inflammatory mediators, shapes normal and regenerative hematopoiesis, with implications for the fundamental and clinical understanding of hematopoietic function.

overall_design: To investigate sexual dimorphism in hematopoiesis, we separated lineage-depleted bone marrow (BM) hematopoietic stem and progenitor (HSPC) populations from male and female C57/BL6 mice at steady state, isolated their RNA, and performed bulk RNA sequencing from samples. N=5 mice/arm.

first: Rahul

last: Chaudhary

first: Julianne

middle: N

last: Smith

first: Riya

last: Tiwari

first: Bailey

middle: R

last: Klein

first: Brittany

last: Cordova

first: Frederick

last: Petroze

first: Brian

last: Richardson

first: Alyssia

last: Broncano

first: Juyeun

last: Lee

first: Prerana

last: Bangalore Parthasarathy

first: Karina

last: Inacio Ladislau De Carvalho

first: Scott

last: Cameron

first: Justin

last: Lathia

first: Wendy

last: Goodman

first: Mark

first: Amar

middle: B

last: Desai


title: Phase separation of RXRγ drives tumor chemoresistance and represents a therapeutic target for small cell lung cancer

city: Guangzhou

first: Hong

last: Wang

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-sen University

summary: Small cell lung cancer (SCLC) is the most lethal type of lung cancer, characterized by limited treatment options and rapid evolution from chemosensitivity to chemoresistance. However, the mechanisms underlying this evolution remain poorly understood. Identifying the druggable drivers and developing pharmacological strategies to overcome chemoresistance are imperative. Here, we show that Retinoid X receptor γ (RXRγ) is uniquely overexpressed in chemo-resistant SCLC tumors, and that RXRγ serves as an essential factor driving chemoresistance in SCLC. RXRγ forms phase-separated droplets with LSD1 in the nucleus, which enhances RXRγ-mediated gene transcription activity and reprograms gene expression, promoting tumor stemness and metastasis, and eventually driving SCLC chemoresistance. In turn, RXRγ antagonist disrupts RXRγ-LSD1 interaction, reducing their binding to the target gene locus, markedly suppressing the expression of the RXRγ target gene network. Finally, RXRγ antagonists strongly suppress tumor growth and metastasis and restore SCLC vulnerability to chemotherapy in multiple preclinical SCLC models, without overt toxicity, in mice. Thus, these results establish RXRγ as a key player in SCLC by phase separation and as a potential therapeutic target for this deadly disease.

overall_design: H128 cells were treated with HX531 (10 μM) for 48 h.

first: Jie

last: Huang

first: Zhenhua

last: Zhang

first: Yana

last: An


title: Case study of a neuroendocrine tumor of uncertain origin: single-cell transcriptomics unravels potential primary source

city: Moscow

first: Alesya

last: Maluchenko

address: Kulakova str. 20

institute: Moscow Center for Advanced Studies

summary: In this study, we present a clinical case of a patient with a retroperitoneal non-functional non-organ-confined neuroendocrine tumor, as determined by routine testing. The histogenesis of the tumor was assessed based on bulk and single-cell RNA sequencing (bulk RNA-seq and scRNA-seq) data, as standard diagnostic procedures proved ineffective. The use of publicly accessible bulk and single-cell RNA-seq data from pancreatic and small intestinal NETs allowed for the development and validation of gene signatures tailored to each specific localization of origin. Additionally, it enabled the prediction of the primary origin of the previously described NET,  indicating that ectopic pancreatic tissue is the most probable source.

overall_design: Neuroendocrine tumor sample from one patient was analyzed using single-cell RNA-seq

first: Frolova

last: Tatyana

first: Ekaterina

last: Avsievich

first: Diana

last: Salimgereeva

first: Zoia

last: Antysheva

first: Alesia

first: Denis

last: Maksimov

first: Ilia

last: Feidorov

last: Voloshin

first: Olga

last: Glazova

first: Natalia

last: Bodunova

first: Nikolay

last: Karnaukhov

first: Pavel

last: Volchkov

first: Julia

last: Krupinova


title: Manganese homeostasis modulates glucan and chitin unmasking in Candida albicans

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

institute: Universite de Montreal

summary: In our previous work, we generated a mutant of the Mn NRAMP transporter, smf12, to investigate the impact of Mn scarcity on the biology of C. albicans. We found that inactivation of SMF12 resulted in attenuated virulence, increased sensitivity to azoles, and activation of the unfolded protein response (UPR). To investigate further cellular processes affected in smf12, we carried out RNA-seq profiling under manganese (Mn) starvation. The transcriptional profile of smf12 growing in the Mn-free SC medium (SC-Mn) was compared to that of the WT strain growing under similar conditions. Upregulated transcripts in smf12 were mainly enriched in processes related to the synthesis and the processing of the three core polysaccharides of the fungal cell wall namely chitin (CHS2, 7, CDA2, CHT4), glucan (KRE1, 9, UTR2, PNG2) and phosphomannan (MNN1, 15, 41, 42, 43, 45, 47, BMT3, 4, 6, 7, KTR4, DFG5, FAV3). Transcripts related to cell wall signaling proteins and transcriptional control including the Cek1 MAP kinase, the histidine kinase Chk1 and the transcription factor Crz1 were also upregulated. This transcriptional signature is reminiscent of a situation in which the cell wall is undergoing remodeling in response to a specific perturbation.

overall_design: In this study, we identified transcripts that were modulated in the Candida albicans mutant of the manganese NRAMP transporter, smf12. The transcriptional profile of smf12 grown in Mn-free SC (SC-Mn) or Mn-supplemented medium (SC+Mn) was compared to that of the wild-type (WT) strain grown under similar conditions

first: Manon

last: Henry

first: Antony

last: Vincent


title: Endogenous fine-mapping of functional regulatory elements in complex genetic loci in HAP1 [scRNA-seq]

first: Ke

last: Zhao

overall_design: Nine scRNA-seq datasets under varying multiplicity-of-infection (MOI) conditions, three single-cell multiome datasets (ATAC + Gene Expression) from modified HAP1 clones(dCas9-KRAB-blast, dCAS9-VP64-blast and Cas9-blast stably expressed HAP1 clones), four ATAC-seq datasets from wild-type and CRISPR-edited HAP1 cells(64bp deletion, 17bp deletion and CRISPRi around rs73156934-tagged cis-regulate element(CRE)), six CUT&TAG histone modification datasets and 1 Micro-C dataset from wild-type HAP1 cells, and three 4C-seq datasets for validating CRE-gene regulatory relationships in HAP1 cells.

first: Yao

last: Zhou

first: Mulin

last: JunLi


title: Human astrocyte encapsulation for delivery of cytokines to modulate neuroinflammation

first: Robert

last: Krencik

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

summary: RNAsequencing for comparison of human pluripotent stem cell-derived astrocyte response to inflammatory cytokine treatment (Interleukin 1 alpha, TNFalpha, and Complement C1q; aka ITC) while encapsulated within alginate capsules (aka AstroCapsules).

overall_design: Three separate batches of AstroCapsules were generated and subdivided into two group. One group received treatment with vehicle-only (AstroCapsules) while the other group received treatment with a combination of inflammatory cytokines (AstroCapsuleITC). RNAsequencing was performed with samples 48 hours after treatment.

first: Samira

last: Aghlara-Fotovat


title: RNA-seq analysis of bead-purified B cells of wild-type BALB/c mice stimulated in vitro with TLR9 agonists (CpG ODN 1826, Hokkaido System Science) or left unstimulated.

city: Pittsburgh

first: Mark

last: Shlomchik

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary: The goal of this study was to develop a B-cell specific gene signature to catalog induced genes after short term in vitro TLR9 stimulation of wild-type BALB/c B cells. B cells were bead purified from splenocytes (two spleens combined for one replicate) of 7-11-week-old wild-type BALB/c mice. The bead purified B cells (10 million (M) per replicate) were stimulated for 4 hours at 10M/ml with TLR9 agonist CpG (CpG ODN 1826, Hokkaido System Science) at 10µg/ml or left unstimulated. RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN). Samples were sequenced on an NextSeq500 (Illumina, Inc) with 2 x 75 bp paired-end reads (20 million reads per sample).  B-cell specific gene signature of induced genes after short term in vitro TLR9 stimulation was cataloged.

overall_design: mRNA profiles of  B cells of wild-type BALB/c mice stimulated in vitro with TLR9 agonists (CpG ODN 1826, Hokkaido System Science) or unstimulated, were generated in three replicates, by sequencing on an Illumina NextSeq500 using PE 150 Cycles High Output flowcell.

first: Claire

last: Leibler

first: Shuchi

last: Smita


summary:
RNA-seq analysis of bead-purified B cells of (i) 5-7-week-old Tlr779 or Tlr7WT (all Tlr9-/-) MRL/lpr mice,stimulated or not with TLR7 agonists (CL097, invivogen) and of (ii) 5-7-week-old Tlr997 or Tlr9+/- (all Tlr7-/-) MRL/lpr mice, stimulated or not with CpG (ODN 1826, Hokkaido System Science) .
The goal of this study was to evaluate if CL097 or CpG induced qualitatively different responses in Tlr7WT or Tlr779 (all Tlr9-/-) B cells and in Tlr9+/- or Tlr997 (all Tlr7-/-) B cells, respectively.

overall_design: mRNA profiles of (i) Tlr779 or Tlr7WT (all Tlr9-/-) B cells stimulated  with CL097 or unstimulated  and of (ii)  Tlr997 or Tlr9+/- (all Tlr7-/-) B cells stimulated with CpG or unstimulated,  were generated in three replicates, by sequencing on an Illumina NextSeq500 using PE 150 Cycles High Output flowcell.


title: Transcriptome comparison of tobacco cell cultures to address mechanism of auxin autonomous cell proliferation

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: The response to auxin is regulated by spatiotemporally specific expression of the auxin signalling machinery and by precise regulation of auxin concentration through multiple biosynthetic and metabolite pathways supported by auxin transport involving influx, efflux, and intracellular transport. The rapid and steady proliferation of cells in plant cell cultures presents unique model for studying mechanisms involved in cell cycle regulation. Here we present transcriptome analyses in the habituated auxin-autonomous BY-2H and VBI-2 cell lines.

overall_design: To compare transcriptomic profiles of tobacco cell cultures, we isolated total RNA from cells harvested at the exponential (3 day old) and stationary (10 day old) stages of their growth cycle, three replicas for eas sample group.

last: Müller

first: Jan

last: Petrášek

last: Jelínek


title: Transcriptomic profiling of peroxisome-deficient, myelin debris-laden macrophages

first: Jian

last: Hu

address: 1881 East Rd, South Campus Research Building 3

institute: University of Texas MD Anderson Cancer Center

summary: Study objective was to investigate the molecular underpinnings of how Pex5 and peroxisome integrity facilitated the demyelination response in myeloid cells. We investigated the transcriptomic changes related to myelin debris uptake in the context of disrupted peroxisome integrity using Pex5 deficient bone marrow derived macrophages.

overall_design: Cultured bone marrow derived macrophages (BMDM) were derived from control and Pex5KO mice. BMDM were incubated with 0.5 mg/mL of crude myelin debris for 24 hours and 72 hours duration. Resting BMDM that did not receive myelin debris were used as baseline controls. After incubation with myelin debris for the indicated durations, total RNA was extracted from BMDM and submitted to Novogene for high-throughput sequencing.

first: Joseph

last: Barnes-Vélez


title: Transcriptomics Unveil Canonical and Non-Canonical Heat Shock-Induced Pathways in Human Cell Lines

city: Fullerton

first: Nikolas

last: Nikolaidis

address: 800 N. State College Blvd

department: Biological Science

institute: California State Univeristy Fullerton

summary: The cellular stress response (CSR) is a conserved mechanism that protects cells from environmental and physiological stressors. The heat shock response (HSR), a critical component of the CSR, utilizes molecular chaperones to mitigate proteotoxic stress caused by elevated temperatures. We hypothesized that while the canonical HSR pathways are conserved across cell types, specific cell lines may exhibit unique transcriptional responses to heat shock. To test this, we compared the transcriptomic responses of HEK293, HepG2, and HeLa cells under control conditions immediately following heat shock and after an 8-hour recovery period. RNA sequencing revealed conserved activation of canonical HSR pathways, including the unfolded protein response, alongside enrichment of the non-canonical “Receptor Ligand Activity” pathway across all cell lines. Cell line-specific variations were also observed, with HepG2 cells displaying higher transcriptional activity under stress conditions. Validation by qPCR confirmed the activation of key genes within the “Receptor Ligand Activity” pathway across time points. These findings provide insights into conserved and context-specific aspects of the HSR, contributing to a more comprehensive understanding of stress response mechanisms a cross mammalian cells.

overall_design: A comprehensive RNA sequencing (RNA-seq) analysis was conducted comparing cancerous (HeLa, HepG2) and non-cancerous (HEK293) cell lines exposed to heat stress.

first: Andrew

last: Reinschmidt

first: Luis

last: Solano

first: Yonny

last: Chavez

first: William

last: Hulsy


title: Suppressor of cytokine signaling 2 is induced in Huntington’s Disease and involved in autophagy

city: Suwon

first: Kyoung

last: Cho

state: Gyeonggi-do (41)

address: 154-2 Gwanggyosanro, Youngtong-gu

department: Life Science

institute: Kyonggi University

summary: Suppressor of cytokine signaling (SOCS) proteins are primarily feedback inhibitors of cytokine signaling. The two conserved domains of SOCS proteins have distinct functions. Src homology 2 (SH2) domain inhibits cytokine receptor, while SOCS box acts as an E3 ubiquitin ligase. SOCS2, a cytokine signaling suppressor, has been primarily implicated in regulating inflammatory conditions in neuronal diseases. However, SOCS proteins have been suggested to play diverse roles in healthy and diseased nervous system including neurodegenerative disorders. In this study, SOCS2 was found to be upregulated in Huntington’s disease and was substantially induced in extended polyglutamine (polyQ)-expressing striatal cells. The induced level was augmented under aging conditions. In extended polyQ-expressing cells, downregulated SOCS2 improved autophagic dysfunction rather than altered inflammatory conditions. Overall, we suggest that SOCS2 involves in regulating autophagy by functioning as an E3 ligase in extended polyQ conditions, and consequently regulates cell damage and cell death type.

overall_design: To examine gene expression changes in subregions of the brain (striatum and cortex) according to age (before and after the onset of disease symptoms) in Huntington's disease mice, total mRNA was isolated from tissues of striatal and cortical subregions of the brain of HD mice (R6/2) and WT mice (normal R6/2 littermate) of the same age, and RNA-seq was performed.  Gene expression profiling analysis of RAN-seq data from each mouse brain tissue.

first: KyoungJoo


title: Genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA as noninvasive diagnostic markers for gastric cancer

status: Public on Dec 30 2024

city: Changchun

first: Jing

last: Jiang

state: Jilin

address: No.1 Xinmin Street

department: Division of Clinical Epidemiology

institute: First Hospital of Jilin University

summary: Background: Gastric cancer (GC) remains the third leading cause of cancer death worldwide due to the absence of sensitive and specific biomarkers for its early detection. 5-hydroxymethylcytosine (5hmC)-enriched gene profiles and regions show tissue-specific and tumor specific, and cell-free DNA (cfDNA) 5hmC modification feature sequencing provides a robust tool for gastric cancer detection.Methods: A matched case‒control study design with 50 gastric cancer patients and 50 controls was performed to sequence the 5hmC modification of cfDNA. Significantly differential 5hmC modification genes were identified to construct a gastric cancer diagnostic model. The data set from Gene Expression Omnibus consisted of 61 gastric cancer patients, 90 healthy individuals and 22 benign gastric disease controls was used as an external testing set to test the robustness of the diagnostic model. Results: The vast majority of 5hmC peaks were distributed in the gene body, accounting for more than 90% of the total 5hmC peaks in both the GC and control groups. The diagnostic model was developed based on five different 5hmC modification genes, FBXL7, PDE3A, TPO, SNTG2 and SXBP5. The model could clearly distinguish gastric cancer patients from controls in the training (AUC=0.95, sensitivity=88.6%, specificity=94.3%), validation (AUC=0.87, sensitivity=73.3%, specificity=93.3%) and testing (AUC=0.90, sensitivity=81.9%, specificity=90.2%) sets. The predicted risk scores of the controls were significantly lower than those of GC patients in our own data (P<0.001) or GEO external testing data (P<0.001), but no significant difference was observed between different TNM stage groups (P=0.09 and 0.66). Furthermore, the risk scores of healthy and benign gastric disease controls in the testing set were also not different (P=0.10). Conclusions: The characteristics of 5hmC in cfDNA are specific to GC patients, and the diagnostic model constructed by the 5hmC features of five genes could effectively identify GC patients.

first: Yingli

last: Fu

first: Donghui

last: Cao

first: Yanhua

last: Wu

first: Zhifang

last: Jia

first: Yangyu

last: Zhang

first: Dongming

last: Li

first: Yingnan

last: Cui

first: Yuzheng

first: Xueyuan


first: Hong

last: Wang

overall_design: H128 cells were treated with HX531 for 48 h. (Control group, we named Con-2; treated group, we named H10-2)

first: Jie

last: Huang

first: Zhenhua

first: Yana

last: An


title: Laser capture-microdissected islet transcriptomics

city: Gainesville

first: Alexandra

middle: E.

last: Cuaycal

state: FL

address: 1275 Center Drive

department: Infectious Diseases and Immunology/Biomedical Engineering

institute: University of Florida

summary: Type 1 Diabetes (T1D) is an autoimmune disease characterized by T cell-mediated destruction of insulin-producing pancreatic β-cells. The pathogenesis of T1D is not fully understood but involves development of autoantibodies (AAbs) followed by a progressive decline in first phase insulin response. Live imaging of T1D pancreatic slices has revealed β cell dysfunction irrespective of the acute presence or absence of CD3+ T cells. However, the mechanisms that drive this dysfunction in the prediabetic period remain unclear. In-situ longitudinal studies of human islet cell biology in the context of T1D are essentially impossible. Hence, we leveraged the availability of pancreas tissues from the Network for Pancreatic Organ donors with Diabetes (nPOD) program to phenotypically and transcriptionally characterize laser capture-microdissected islets across the natural history of T1D.

overall_design: Fresh frozen pancreas sections were obtained from donors with no diabetes (ND, n=16), single autoantibody positive (sAAb, n=6), multiple autoantibody positive (mAAb, n=5) and patients with Type 1 Diabetes (T1D, n=16). Blocks were selected based on immunohistochemistry staining and contained INS+ islets and/or T cell infiltration as defined by six or more CD3+ cells immediately touching the islet endocrine cells. Blocks were cut into thick (10 μm) serial (3-4) sections and placed onto PEN-slides (Leica) along with thin (4 μm) sections placed onto Superfrost slides (Thermofisher) before and after the thick sections. Thin pancreas sections were immunostained for insulin (INS), CD3, HLA class I and ATP5B to delineate islets with residual beta cells, T cell infiltration, antigen presentation and mitochondrial function. Thick sections were used to laser-microdissect single islets from dehydrated slides. Laser microdissections yielded 3-4 sections per islet captured into 0.6 mL RNAse-free tubes. Sets of 7-25 islets were laser-captured per donor. A total of 260 islets were obtained across the four different clinical phenotypes (ND=73, sAAb=40, mAAb=37, T1D=110). Microarray gene expression profiling of single islets was performed using the Affymetrix Human Gene 2.0 ST arrays.


title: Phase separation of RXRγ drives tumor chemoresistance and represents a therapeutic target for small cell lung cancer [RNA-Seq]

overall_design: RNA-Seq


title: Comparative gene expression profiling of parental A375 melanoma cells and a panel of spontaneously vemurafenib-resistant  derivative cell lines

status: Public on Dec 26 2024

city: Iowa City

first: Jesse

last: Riordan

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: The use of selective BRAF inhibitors (BRAFi) has produced remarkable outcomes for patients with advanced cutaneous melanoma harboring a BRAFV600E mutation. Unfortunately, the majority of patients eventually develop drug-resistant disease through a variety of mechanisms. We previously described the creation of a panel of spontaneously BRAFi/MEKi-resistant A375 melanoma cells that displayed multiple different resistance mechanisms arising within the same parental cell population. These resistance mechanisms include (i) rearrangements in the BRAF gene resulting in truncation of the N-terminal regulatory domain or tandem duplication of the BRAF kinase domain, (ii) loss of Ras-GAP NF1, and (iii) a slower arising form of drug resistance associated with a more spread cell morphology and increased phospho-MEK S298, a characteristic of cells with increased Rac1 signaling. We provide here comprehensive gene expression profiling for this panel of cell lines. Rac1 mutation, particularly the P29S variant, is common in melanoma patients, where it is associated with BRAFi/MEKi resistance and worse clinical outcomes. Here we delineate mechanisms of Rac1-driven MAPKi-resistance and identify strategies to inhibit the growth of this class of cutaneous melanomas. We find that Rac1-driven melanomas manifest pleiotropic resistance mechanisms including (i) reduced dependence on BRAF/MEK, (ii) activation of alternative MAPK pathways utilizing Jun kinase and p38 MAP kinase, and (iii) a partial reliance on YAP/TAZ signaling. Importantly, although Rac1-driven melanoma cells display reduced dependence on BRAF/MEK, they are not completely ERK-independent. Moreover, the presence of activated Rac1 appears to create a dependency on focal adhesion kinase (FAK) signaling in undifferentiated melanoma cells. As a result, we find that, despite the pleiotropic mechanisms of Rac1-driven MAPKi resistance, combined inhibition of MEK and FAK with avutometinib plus defactinib is a promising approach for suppressing the growth of Rac1-driven cells. Thus, the avutometinib plus defactinib combination, which is currently being investigated for brain metastatic cutaneous melanoma may also have utility against Rac1-driven MAPKi-resistance in heavily pre-treated, advanced disease.

overall_design: RNAseq profiling of parental A375 cells, A735 cells treated with vemurafenib for 24 or 96 hours, and a panel of 8 spontaneously vemurafenib-resistant A375 derivative cell lines

first: Adam

middle: J

last: Dupuy

first: Christopher

last: Stipp