title: FGF2 Mediated USP42-PPAR𝜸 Axis Activation Ameliorates Liver Oxidative Damage and Promotes Regeneration

status: Public on Jan 15 2025

city: nanjing

first: qiang

last: tian

address: School of Life Sciences, Nanjing University, Nanjing, 210023, China.

department: the school of life sciences

institute: nanjing university

summary: Liver regeneration is critical for maintaining whole-body homeostasis, especially under the exposure to deadly chemical toxins. Understanding the molecular mechanisms underlying liver repair is critical for the development of intervention strategies to treat liver diseases. In this study, we identified ubiquitin-specific Proteases 42 (USP42) as a novel deubiquitinases (DUB) of peroxisome proliferators-activated receptor γ (PPARγ) in hepatocytes. This DUB interacted, deubiquitinated and stabilized PPARγ, and increased PPAR targeted proliferative and anti-oxidative gene expressions, which protects liver from carbon tetrachloride (CCL4) induced oxidative injury and promotes liver regeneration. In addition, fibroblast growth factor 2 (FGF2) initiated USP42 expression and enhanced the interaction between USP42 and PPARduring liver regeneration process. Moreover, the PPARfull agonist, rosiglitazone (RSG), possesses the ability to further reinforce the USP42-PPARinterplay, which enlightens us to construct an extracellular vesicle-based targeting strategy to activate liver USP42-PPAR axis and promote liver regeneration. In summary, our work uncovers the importance of USP42-PPAR axis mediated liver tissue homeostasis, and provides a promising regimen to target this protein-protein interplay for liver regeneration.

overall_design: considering the complex processes involved in liver regeneration, we performed the RNA-seq to explore the potential mechanism of EV@FGF2-RSG on liver repair. The Saline, EV and EV@FGF2-RSG were injected into mice after CCL4 treatment, and the liver tissue were subjected to RNA-seq.

first: Nanfei

last: Yang

first: Qiang

last: Tian

first: Zhenli

last: Lei

first: Shuxin

last: Wang

last: Cheng

first: Zhen

first: Xianqin

last: Jiang

first: Xuqun

first: Wenjing

first: Minyan

last: Ye

first: Longwei

last: Zhao

first: Meiyun

last: Wen

first: Jianlou

last: Niu

first: Weijian

last: Sun

first: Pingping

last: Shen

first: Zhifeng

last: Huang

first: Xiaokun


title: Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq]

status: Public on Jan 16 2025

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

type: Expression profiling by high throughput sequencing

summary: During early mammalian development, the endoderm layer undergoes complex patterning to form the foundations of the respiratory and digestive systems. This intricate process, guided by a series of cell fate decisions, remains only partially understood. Our research introduces a pioneering genetic tracing code across 14 distinct endodermal regions by developing a group of mouse strains. By integrating high-throughput and high-precision single-cell RNA sequencing with sophisticated imaging techniques across various mouse models, we comprehensively resolve the spatiotemporal and genetic lineage differentiation processes of the endoderm at a single-cell resolution. Our findings reveal a previously unrecognized multipotentiality within early endodermal regions for differentiation into diverse organ primordia. Furthermore, this research illuminates the complex and underestimated phenomenon of multiple origins in the development of endodermal organs, prompting a reevaluation of differentiation models for these organs. This work not only advances our understanding of developmental biology, but also has significant implications for regenerative medicine and the development of organoid models, providing new insights into the intricate mechanisms that guide organogenesis.

overall_design:
scRNA-seq of tracing linegae for the development of endoderm

Please note that total 25,847 samples (represented in 140 condensed sample records) were included in the current study.
The individual sample and raw file information is included in the sample_information.txt, SRR_filenames.txt.

first: Keran

last: Li

first: Peilong

last: Yu

first: Qiqi

last: Zheng

first: Xin

first: Xuan

last: Fang

first: Linchen

first: Chengran


title: Control of plasma membrane-associated actin polymerization specifies the pattern of the cell wall in xylem vessels.

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

department: Department of Biological Sciences

country: Japan

institute: Graduate School of Science, The University of Tokyo

summary: Cell wall patterning is central to determining the shape and function of plant cells. Protoxylem and metaxylem vessel cells deposit banded and pitted cell walls, respectively, which enable their distinctive water transport capabilities, but the mechanisms that specify which cell wall pattern is laid down remain unknown. Here, we show that the pitted cell wall pattern in metaxylem vessels is specified by transcriptional control of actin polymerization. A newly isolated allele of KNOTTED-like homeobox transcription factor 7 (KNAT7) was associated with the formation of banded cell walls in metaxylem vessels. To identify the genes responsible for altering the cell wall pattern in knat7 xylem vessels, we performed an RNA-seq analysis of knat7. We used in vitro cultures of hypocotyls and cotyledons because the population of differentiating xylem cells in intact roots is tiny and these methods efficiently induce ectopic differentiation of xylem vessel elements. Formin Homology Domain-Containing Protein 11 (FH11) was upregulated in knat7 metaxylem, but expressed only in protoxylem vessels in wild-type plants. Loss of FH11 suppressed the knat7 phenotype. Conversely, ectopic overexpression of FH11 in metaxylems mimicked the knat7 phenotype. FH11 function required its plasma membrane anchoring and the actin polymerization activity. Actin polymerization by FH11 at the plasma membrane caused the dispersion of activated ROP GTPases, the determinant of pit formation. These results suggest that decontrol of actin polymerization at the plasma membrane abolishes the pitted cell wall formation and promotes the formation of banded cell walls in metaxylem vessels. This study unveils the importance of the proper control of actin polymerization on cell wall pattern specification.

overall_design: RNAseq profiling of knat7 mutant and the complementation line of Arabidopsis cultured tissues differentiating into xylem vessel elements.

first: Saku

middle: T

last: Kijima

first: Takema

last: Sasaki

first: Yuichiro

last: Kikushima

first: Daisuke

last: Inoue

first: Shingo

last: Sakamoto

first: Yuki

last: Kondo

first: Masatoshi

last: Yamaguchi

first: Nobutaka

last: Mitsuda

first: Yoshihisa

last: Oda


title: BRD4 inhibition rewires cardiac macrophages toward a protective phenotype marked by low MHC class II expression

city: Aurora

first: Timothy

last: McKinsey

state: CO

department: Medicine

country: USA

institute: University of Colorado Anschutz Medical Campus

summary: Bromodomain and extra-terminal domain (BET) proteins, including BRD4, bind acetylated chromatin and co-activate gene transcription.  A BET inhibitor, JQ1, prevents and reverses pathological cardiac remodeling in preclinical models of heart failure.  However, the underlying cellular mechanisms by which JQ1 improves cardiac structure and function remain poorly defined.  Here, we demonstrate that BRD4 knockdown reduced expression of genes encoding CC chemokines in cardiac fibroblasts, suggesting a role for this epigenetic reader in controlling fibroblast-immune cell crosstalk.  Consistent with this, JQ1 dramatically suppressed recruitment of monocytes to the heart in response to stress.  Normal mouse hearts were found to have approximately equivalent numbers of major histocompatibility complex (MHC-II)high and MHC-IIlow resident macrophages, while MHC-IIlow macrophages predominated following JQ1 treatment.  Single-cell RNA-seq data confirmed that JQ1 treatment or BRD4 knockout in CX3CR1+ cells reduced MHC-II gene expression in cardiac macrophages, and studies with cultured macrophages further illustrated a cell autonomous role for BET proteins in controlling the MHC-II axis. Bulk RNA-seq analysis demonstrated that JQ1 blocked proinflammatory macrophage gene expression through a mechanism that likely involves repression of NF-kB signaling. JQ1 treatment reduced cardiac infarct size in mice subjected to ischemia/reperfusion.  Our findings illustrate that BET inhibition affords a powerful pharmacological approach to manipulate monocyte-derived and resident macrophages in the heart.  Such an approach has the potential to enhance the reparative phenotype of macrophages to promote wound healing and limit infarct expansion following myocardial ischemia.

overall_design: To address the impact of BRD4 inhibition on resident macrophage phenotypes in the heart, transcriptomic profiling by bulk RNA-seq was performed using purified cardiac macrophages from mice treated with JQ1 or vehicle control for three days.

first: Katherine

last: Schuetze

first: Matthew

last: Stratton

first: Rushita

last: Bagchi

first: Alexander

last: Hobby

first: Marina

last: Felisbino

first: Marcello

last: Rubino

first: Lee

last: Toni

first: Reges

last: Caroline

first: Maria

last: Cavasin

first: Rachel

last: McMahan

first: Michael

last: Alexanian

first: Ronald

last: Vagnozzi


title: Fucosylated haptoglobin promotes inflammation via Mincle in sepsis: an observational study

city: Daejeon

first: Taylor

last: Roh

address: 266, Munhwa-ro

department: Microbiology

country: South Korea

institute: Chungnam National University

summary: Haptoglobin (Hp) scavenges cell-free hemoglobin and correlates with the prognosis of human sepsis, a life-threatening systemic inflammatory condition. Despite extensive research on Hp glycosylation as a glyco-biomarker for cancers, understanding glycosylated modifications of Hp in sepsis patients (SPs) remains limited. Our study reveals elevated levels of terminal fucosylation at Asn207 and Asn211 of Hp in SP plasma, along with heightened inflammatory responses, compared to healthy controls (trial registration NCT05911711). Fucosylated (Fu)-Hp purified from SPs upregulates inflammatory cytokines and chemokines, along with NLRP3 inflammasome activation. Single-cell RNA sequencing identifies a distinct macrophage-like cell population with increased expressions of inflammatory mediators and FUT4 in response to Fu-Hp. Additionally, Mincle, a C-type lectin receptor, interacts with Fu-Hp to amplify the inflammatory responses and signaling. Moreover, the Hp fucosylation (AAL) level significantly correlates with the levels of inflammatory cytokines in sepsis patients, suggesting that Fu-Hp is clinically relevant. Finally, Fu-Hp treatment significantly enhances the levels of inflammatory cytokines in the plasma and various tissues of mice. Together, our findings reveal a role of Fu-Hp, derived from sepsis patients, in driving inflammation, and suggest that targeting Fu-Hp could serve as a promising intervention for combating sepsis. Trial registration NCT05911711

overall_design: Total RNA of Fu-Hp-treated human primary PBMCs (derived from 2 healthy donors)

first: Eun-Kyeong

last: Jo

first: So Young

last: Park


title: The meninges host a unique compartment of regulatory T cells that bulwarks adult hippocampal neurogenesis [RNA-Seq]

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Our knowledge about the meningeal immune system has recently burgeoned, particularly how innate and adaptive effector cells are mobilized in response to brain challenges. However, information on how meningeal immunocytes guard brain homeostasis in healthy individuals remains sparse. This study highlights the heterogeneous and polyfunctional regulatory T (Treg) cell compartment in mouse meninges. A Treg subtype specialized in controlling Th1-cell responses and another subtype devoted to controlling responses in B-cell follicles were substantial components of this compartment, foretelling the finding that punctual Treg-cell ablation rapidly unleashed interferon-gamma production by meningeal lymphocytes, unlocked their access to the brain parenchyma, and altered meningeal B-cell profiles. Distally, the hippocampus took on a reactive state, with activation of multiple glial-cell types; within the dentate gyrus, neural stem cells showed exacerbated death and desisted from further differentiation, associated with inhibition of spatial-reference memory. Thus, meningeal Treg cells are a multifaceted bulwark to brain homeostasis at steady-state.

overall_design: For characterizing meningeal Treg cell identity and changes upon physiological variations (sex, age), and anatomical location we double sorted Treg cells from the meninges, spleen and skull bone marrow at different ages. To study how Tregs regulate the meningeal niche, Tregs were punctually depleted in two different ways: via diphtheria toxin (DT) injections into Foxp3-DTR+ and littermate Foxp3-DTR- controls, or via intra-cisterna magna injection of Ultra-LEAF™ purified mouse anti-CD25 mAb (BioLegend, clone PC61) or the recommended rat IgG1λ isotype control mAb (BioLegend); then  the meninges were digested in QIAzol for RNA extraction, and followed whole-tissue RNA-seq. performed. To study how microglia responded upon punctual Treg depletion (DTR- and DTR+ littermates), we double sorted microglia from the hippocampus. To understand how different brain regions responded upon punctual Treg depletion, we isolated the hippocampus, cortex, thalamus and hypothalamus, and cerebellum, digested using QIAzol for RNA extraction, and followed whole-tissue RNA-seq.

first: Miguel

last: Marin-Rodero

first: Diane

last: Mathis


title: Title: Microarray analysis of transgenic mice specifically overexpressing Dnmt3a in skeletal muscle (Dnmt3a Tg mice, young and old)

city: Kyoto

first: Yasutomi

last: Kamei

address: 1-5 Shimogamo-Hangicho, Sakyo-ku

institute: Kyoto Prefectural University

summary: DNA methylation occurs as 5-methylcytosines mainly at cytosine-guanine dinucleotides, so-called CpG sites, and such methylation is a well-studied epigenetic mechanism for transcriptional regulation. Genomic DNA methylation patterns are established by the actions of the de novo methyltransferases Dnmt3a and Dnmt3b, and are maintained by the methyltransferase Dnmt1. Expression of Dnmt3a mRNA is relatively high in skeletal muscle, suggesting a major role in transcriptional regulation. Thus, we created transgenic mice specifically overexpressing Dnmt3a in skeletal muscle (Dnmt3a Tg mice). In this study, we performed a microarray analysis of skeletal muscle in wild-type control and Dnmt3a Tg mice (young: 3 months of age, female, and old: 26 months of age, female). The microarray data shows upregulation of a set of slow-twitch myofiber-specific genes and downregulation of fast-twitch myofiber-specific genes in Dnmt3a-Tg muscle compared with WT muscle.

overall_design: For microarray analysis, RNA was isolated from the gastrocnemius skeletal muscle of control young mice (3 months of age, female, N=4), control old mice (26 months of age, female, N=8), Dnmt3a Tg young mice (3 months of age, female, N=4), and Dnmt3a Tg old mice (26 months of age, female, N=8).

first: Mamoru

last: Oyabu


overall_design: Total RNA of human primary PBMCs (derived from 2 healthy donors and 2 sepsis patients)


overall_design: Total RNA of Fu-Hp-treated human primary PBMCs (derived from 3 healthy donors)


title: Gene expression and mutation profiles in advanced-stage epithelial ovarian cancer (EOC)

city: Seongnam-si

first: Je-Gun

last: Joung

address: 335, Pangyo-ro, Bundang-gu

institute: CHA University

summary:
Purpose: This open-label, investigator-initiated, phase II study was conducted to evaluate the safety, survival and neoadjuvant outcomes of NAC combined with dual immune checkpoint inhibitors in advanced-stage EOC.

Patients and methods: Between June 2019 and July 2021, 45 patients with unresectable stage III-IV EOC were enrolled. The patients received three cycles of NAC combined with durvalumab and tremelimumab. All patients underwent interval debulking surgery and received three cycles of durvalumab and adjuvant chemotherapy, followed by 12 cycles of durvalumab as maintenance therapy. The primary endpoint was the 12-month progression-free survival (PFS) rate; the secondary endpoints were the objective response rate (ORR) after NAC, a chemotherapy response score (CRS), pathologic complete response (pCR), overall survival (OS), and safety. The pre-planned exploratory analyses assessed the lymphocyte infiltration, PD-L1 expression, and genomic profiles of pre-treatment tumors.

overall_design:
Pretreatment tumors samples from fresh-frozen tissue were obtained for whole-transcriptome sequencing and whole-exome sequencing. RNA and DNA samples were sequenced on HiSeq 2500 sequencing platform. For RNA-seq, sequencing reads were aligned to the human reference genome (GRCh37) by using STAR aligner. Expected counts of reads mapped into genes were estimated and transformed into TPM values by RSEM. For whole exome sequencing, sequenced reads were aligned to the reference human genome (GRCh37) using the Burrows-Wheeler Aligner (BWA). After pre-processing using the Genome Analysis Toolkit (GATK), variants were called by Mutect2.

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

last: Lee


title: Coactivation of innate immune suppressive cells induces acquired resistance against cancer immunotherapy targeting the innate immune system [TIICs RNA-seq]

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

institute: National Cancer Center

summary: Immune checkpoint blockade therapy has been successfully applied in clinical settings as a standard therapy for many cancer types, but its clinical efficacy is restricted to patients with immunologically hot tumors. Various strategies to modify the tumor microenvironment (TME), such as Toll-like receptor (TLR) agonists, have been explored but have not been successful. Here, we identified a mechanism of acquired resistance to combination treatment consisting of an agonist for multiple TLRs, OK-432 (Picibanil), and PD-1 blockade. Adding the TLR agonist failed to convert the TME from immunogenically cold to hot. The combination treatment did not augment antitumor immunity, particularly CD8+ T cell responses, in multiple animal models. The failure was attributed to the coactivation of innate suppressive cells, such as CD11b+ Gr1+ Ly6C- Ly6G+ myeloid-derived suppressor cells (MDSCs) expressing CXCR2, through high CXCL1 production by macrophages in the TME upon OK-432 treatment. Thus, a triple combination treatment with OK-432, PD-1 blockade, and a CXCR2 neutralizing antibody overcame the resistance induced by MDSCs, resulting in a far stronger antitumor effect than that of any dual combination or single treatment. The accumulation of MDSCs was similarly observed in the pleural effusion of lung cancer patients after OK-432 administration. We propose that successful combination cancer immunotherapy stimulating innate immunity against immunologically cold tumors requires modulation of unwanted activation of innate immune suppressive cells, including MDSCs.

overall_design: To investigate cancer types suitable for OK-432 treatment, we performed a comprehensive analysis of CD45+ tumor-infiltrating immune cells across 10 different cancer cell lines using bulk RNA-seq.

first: Hitomi

last: Nishinakamura

first: Sayoko

last: Shinya

first: Takuma

last: Irie


title: Coactivation of innate immune suppressive cells induces acquired resistance against cancer immunotherapy targeting the innate immune system [TME RNA-seq]

overall_design: To further explore  the influence of OK-432 treatment, RNA-seq analysis was conducted on tumor tissues from CT26, CT26-NY-ESO-1 or LL/2 cells treated with or without OK-432, providing comprehensive insights into the immunological landscape within the tumor microenvironment.


title: PKD1 mutation perturbs morphogenesis in tubular epithelial organoids derived from human pluripotent stem cells

city: Bergamo

first: Susanna

last: Tomasoni

state: BG

address: Via Stezzano 87

department: Molecular Medicine

country: Italy

institute: Istituto di Ricerche Farmacologiche Mario Negri IRCCS

summary: Autosomal dominant polycystic kidney disease (ADPKD) is the most common renal genetic disease, with most patients carrying mutations in PKD1. The main feature is the formation of bilateral renal cysts, leading to end stage renal failure in a significant proportion of those affected. Despite recent advances made in understanding ADPKD, there are currently no effective curative therapies. The emergence of human induced pluripotent stem cell (hiPSC)-derived kidney disease models has led to renewed hope that more physiological systems will allow for the development of novel treatments. hiPSC-derived organoid models have been used to recapitulate ADPKD, however they present numerous limitations which remain to be addressed. In the present study, we report an efficient method for generating organoids containing a network of polarised and ciliated epithelial tubules. PKD1 null (PKD1-/-) organoids spontaneously develop dilated tubules, recapitulating early ADPKD cystogenesis. Furthermore, PKD1-/- tubules present primary cilia defects when dilated. Our model could therefore serve as a valuable tool to study early ADPKD cystogenesis and to develop novel therapies.

overall_design: Day 10 and day 24 renal spheroids/organoids differentiated from hiPSCs were analysed with poly A enriched RNA sequencing.

first: Alexandru

last: Scarlat


title: Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation in arabidopsis total RNA [BID-seq]

city: Chicago

first: CHUAN

last: HE

state: Illinois

address: 929 East 57th Street, GCIS E313

institute: University of Chicago

summary: Pseudouridine (Ψ) is the most abundant RNA modification, yet studies of Ψ has been hindered by the lack of robust methods to profile Ψ and comprehensive Ψ maps. In this study, we utilize BID-seq, a newly developed Ψ sequencing method, to generate transcriptome-wide Ψ maps at single-base resolution across various plant species and tissues

overall_design: "Input" and "Treated" samples in BID-seq to detect pseudouridine in  total RNA.


title: Arabidopsis polysome sequencing in nine tissues

summary: We performed the polysome profiling sequencing in nine arabidopsis tissues across its life cycle to reveal the correlations of translation efficiency to RNA modifications.

overall_design: Tissues in polysome profiling sequencing were prepared with two biological replicates.


title: Ubc9 auto-sumoylation-associated changes in the genome-wide pattern of SUMO enrichment.

city: Daegu

first: Hong-Yeoul

last: Ryu

state: Buk-Gu

address: Daehak-ro 80

department: Biotechnology

institute: Kyungpook National University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Calorie restriction (CR) provides anti-aging benefits through diverse processes, such as reduced metabolism and growth and increased mitochondrial activity. Although controversy still exists regarding CR-mediated lifespan effects, many researchers are seeking interventions that mimic the effects of CR. Yeast has proven to be a useful model system for aging studies, including CR effects. We report here that yeast adapted through in vitro evolution to the severe cellular stress caused by loss of the Ulp2 SUMO-specific protease exhibit both enhanced growth rates and replicative lifespan, and they have altered gene expression profiles similar to those observed in CR. Notably, in certain evolved ulp2Δ lines, a dramatic increase in the auto-sumoylation of Ubc9 E2 SUMO-conjugating enzyme results in altered regulation of multiple targets involved in energy metabolism and translation at both transcriptional and post-translational levels. This increase is essential for the survival of aged cells and CR-mediated lifespan extension. Thus, we suggest that high Ubc9 auto-sumoylation exerts potent anti-aging effects by promoting efficient energy metabolism-driven improvements in cell replication abilities. This potential could be therapeutically explored for the development of novel CR-mimetic strategies.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-Seq) for HisFlag tagged Smt3 in Saccharomyces cerevisiae.

first: Dong-Won

last: Jeong

first: Seung-Yeon

last: Kim

first: Seok-Won

last: Jeoung

first: Dejian

last: Zhao

first: James

last: Knight

first: TuKiet

last: Lam

first: Jong-Hwa

last: Jin

first: Hyun-Shik

first: Mark

last: Hochstrasser


title: Single cell RNA sequencing of Ewing sarcoma tumors demonstrate transcriptional heterogeneity and clonal evolution

first: Andrew

last: Goodspeed

address: 12801 E 17th Ave, Mail Stop 8303

summary: Ewing sarcoma (ES) is the second most common bone cancer in children, accounting for 2% of pediatric cancer diagnoses. Patients who present with metastatic disease at the time of diagnosis have a dismal prognosis, compared to the >70% 5-year survival of those with localized disease. Here, we utilized single-cell RNA sequencing (scRNA-seq) to characterize the transcriptional landscape of primary ES tumors and surrounding tumor microenvironment (TME). Copy-number analysis identified subclonal evolution within patients even prior to treatment. Primary tumor samples demonstrate a heterogenous transcriptional landscape with several conserved gene expression programs composed of gene related to proliferation and EWS targets. We also were able to identify the composition of the tumor microenvironment and molecularly dissect the transcriptional profile of circulating tumor cells (CTCs) in peripheral blood at the time of diagnosis.

first: Masanori

last: Hayashi


title: Single-cell Transcriptomics Reveals Inter-ethnic Variation in Immune Response to Falciparum Malaria [Batch2]

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

summary: Africa’s environmental, cultural and genetic diversity can significantlygreatly influences how the populations’ respondse to infectious diseases, including malaria, caused by Plasmodium falciparum. Differences in susceptibility to malaria between populations are documented but the underlying mechanisms are poorly understood. The Fulani ethnic group in Africa was reported to be less susceptible to malaria compared to other sympatric groups, such as the Mossi., They exhibit with lower disease rates and parasite load, as well as higher levels of serological protection. Unraveling the underlying genetic, molecular and cellularimmunological basis of this protection remains challenging, in part due to a lack of in-depth immunological characterization at the cellular level. Therefore, to address this question, we performed single cell transcriptomic RNA sequencing analysis ofon peripheral blood mononuclear cells from 126 infected and non-infected Fulani and Mossi children in rural Burkina Faso., This analysis generateding > 70,000 single-cell RNA-Seq profiles and identifiedying 30 cell subtypes. By performing cell subtype proportion analysis, we report an increased abundance of γδ T cells in infected Fulani samples compared to the Mossi counterpart. Moreover, cell-type specific differential expression analysis revealed ethnic-specific immune signatures in both infection states, and highlighted lower pro-inflammatory responses in the monocytes and T cell subtypes of the Fulani in both infection states, with a stronger activation and inflammatory profile in their B cell subtypes. Single-cell expression quantitative trait loci (eQTL) analysis in monocytes of infected samples revealed several significant regulatory variants with ethnic-specific effects. Overall, the results demonstrate the power of single cell transcriptomics in identifying ethnic, cell-type specific and genetic regulatory effects in the host immune response to malaria and provide valuable single-cell eQTL and transcriptomic data from populations underrepresented in genomic studies.

overall_design: Expression profiling by high throughput sequencing

first: Y

first: MM

last: Dieng

first: T

last: Shahin


title: Single-cell Transcriptomics Reveals Inter-ethnic Variation in Immune Response to Falciparum Malaria. [Batch1]

overall_design: Expression profiling by high throughput sequencing.


title: Molecular and physiological characterization of brassinosteroid receptor BRI1 mutants in Sorghum bicolor

city: Cerdanyola del Vallès

first: Andrés

last: Rico-Medina

state: Barcelona

address: C/ de la Vall Moronta SN

country: Spain

institute: CRAG

summary:
* The high sequence and structural similarities between BRI1 brassinosteroid receptors of Arabidopsis (AtBRI1) and sorghum (SbBRI1) prompted us to study the functionally conserved roles of BRI in both organisms.
* Introducing sorghum SbBRI1 in Arabidopsis bri1 mutants restores defective growth and complements developmental phenotypes to WT levels.
* Sorghum mutants for SbBRI1 receptors show defective BR sensitivity and results in impaired growth and development throughout the entire sorghum life cycle. Embryonic analysis of sorghum primary roots traced the root growth and development at the early stages, revealing the role of SbBRI1 in BR perception during cell division and BR sensing. RNA-seq of SbBRI1 mutants support the roles of SbBRI1 in cell wall biosynthesis and remodeling.
* Together, these results uncover that sorghum SbBRI1 receptor protein play functionally conserved roles in plant growth and development.

overall_design: To study the role of BRI1 in sorghum in more molecular detail, RNA-seq analysis was used to investigate which processes are transcriptionally regulated by SbBRI1 in bri1-ems72 roots against their sibling WT-ems72 using BC2F2 plants (ko vs wt). For each biological replicate, a minimum of 6 bri1-ems72 and WT-ems72 roots were pooled to homogeneize as much as possible the genetic background of the samples. RNA was extracted using Maxwell 16 LEV PLANT RNA KIT (PROMEGA) and quality checked using Bioanalyzer. A total of 3 biological replicates were taken for each genotype.

first: Ana

middle: I

last: Caño-Delgado


title: Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

summary:
Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is a crucial first step towards engineering improved drought resilience.
However, the molecular responses to drought are complex as they depend on multiple factors including the severity of drought, the profiled organ, its developmental stage or even the cell types therein. Thus, deciphering the transcriptional responses to drought is specially challenging.
In this study, we investigated tissue-specific responses to mild drought in young Arabidopsis thaliana (Arabidopsis) leaves using single-cell RNA sequencing (scRNA-seq). To preserve transcriptional integrity during cell isolation, we inhibited RNA synthesis using the transcription inhibitor actinomycin D, demonstrating the benefits of transcriptome fixation for studying mild stress responses at single-cell level.
We present a curated and validated single-cell atlas comprising 50,797 high-quality cells from almost all known cell types present in the leaf. All cell types were validated with a new library of reporter lines.

overall_design: Single-cell RNA-seq experiments were performed on protoplasts extracted from leaves of Arabidopsis thaliana.

first: Rubén

last: Tenorio Berrío

first: Eline

last: Verhelst

first: Thomas

last: Eekhout

first: Carolin

last: Grones

first: Lieven

last: De Veylder

first: Marieke

last: Dubois


title: Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (maize)

first: Chang

last: Ye

overall_design: "Input" and "Treated" samples in BID-seq to detect pseudouridine in  polyA+ RNA.


title: Fucosylated haptoglobin drives inflammation via Mincle in sepsis: an observational study

first: Taylor

last: Roh

overall_design: RNA sequencing was performed on PBMCs from HC and SP to examine the different gene expression and ontology pathway analysis. Briefly, RNA-seq libraries were prepared using a SureSelect RNA Direct_Human Library Construction Kit (Agilent Technologies). Total RNA was extracted from PBMCs using TRIzol® Reagent (Thermo Fisher, 15596026) according to the manufacturer’s instructions. Transcriptome library sequencing was carried out using the 101-bp paired-end mode with Illumina NovaSeq 6000. The data integrity of the raw sequences was evaluated with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The raw read data were trimmed using Trimmomatic (version 0.38) and the following criteria: first trimming: base quality < 3, window size = 4, and mean quality = 15; second trimming: min length = 36 bp. The trimmed reads were mapped against the reference genome GRCh38 using HISAT2 version 2.1.0 (https://ccb.jhu.edu/software/hisat2/index.shtml) and Bowtie2 aligner. After the read mapping, StringTie (version 2.1.3b) was used for transcript assembly. The expression profile was calculated for each sample and transcript/gene as read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million). DEG (Differentially Expressed Genes) analysis was performed on a comparison pair (Sepsis patients_vs_Healthy control) using DESeq2. The statistical method used was calculated based on fold change, nbinomWaldTest using DESeq2, and Hierarchical Clustering. Using each sample’s normalized value, the high expression similarities were grouped together. The significant results are selected on conditions of the absolute value of |log2(fold change)|  >= 2 & nbinomWaldTest raw p-value < 0.05. Normalized gene expression values were utilized to generate a heatmap using the pheatmap package (version 1.0.12) and a volcano plot employing the ggplot2 package (version 3.4.4) within the R programming environment (version 4.1.3). Pathway enrichment analysis was conducted using the clusterProfiler package (version 4.10.0) in R and the Gene Set Enrichment Analysis (GSEA) software (version 4.3.2).

first: Eun-Kyeong

last: Jo

first: So Young

last: Park


title: Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (Arabidopsis)


title: Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (soybean)


title: Quantitative RNA pseudouridine maps reveal multi-layered translation control through plant rRNA, tRNA and mRNA pseudouridylation (rice)


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy

first: Wesley

last: Nogueira Brandao

state: Massachusetts

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Oncogenic Potential of Truncated-Gli3 via the Gsk3β/Gli3/AR-V7 Axis in Castration-Resistant Prostate Cancer

city: OMAHA

first: Jyoti

middle: Bala

last: Kaushal

state: NE

address: 42nd and Emile

institute: UNMC

summary: The functional activation of the androgen receptor (AR) and its interplay with the aberrant Hh/Gli cascade are pivotal in the progression of castration-resistant prostate cancer (CRPC) and resistance to AR-targeted therapies. Our study unveils a novel role of the truncated form of Gli (t-Gli3) in advancing CRPC. Investigation into Gli3 regulation revealed a Smo-independent mechanism for its activation. Despite lacking a transactivation domain, t-Gli3 relies on androgen receptor variant 7 (AR-V7) for its action. Mechanistically, Gsk3β activation leads to the t-Gli3 generation, and inhibition of Gsk3β supports the accumulation of full-length Gli3 through a non-canonical mechanism. Knockdown of Gsk3β (Gsk3β KD) reduces CRPC cell proliferation, induces apoptosis via mitochondrial fragmentation, and triggers metabolomic reprogramming. Orthotropic implantation of Gsk3β KD cells in the mouse prostate results in tumor growth retardation compared to scramble control cells. RNA-seq analysis of Gsk3β KD reveals upregulation of pathways associated with apoptosis, tumor suppressor pathway, and downregulation of oncogenic pathway relative to control. Furthermore, combinational use of a Gsk3β inhibitor with anti-Smo or Gli1 significantly inhibits the growth of CRPC cells, which are resistant to individual Smo or Gli1 inhibitor targeting. Intriguingly, solely targeting Gli3 proves effective in inhibiting CRPC cell growth. Overall, our study underscores the clinical significance of Gli3, emphasizing t-Gli3, and provides novel insights into the interplay of the Gsk3β/t-Gli3/AR-V7 axis in CRPC.

overall_design:
To investigate the impact of functional blockage of Gsk3β on Hh/Gli pathway, particularly regarding the posttranslational modification of Gli-family proteins. In addition to understand Gsk3β -mediated other regulatory signaling elements involved in oncogenesis in castration-resistant prostate cancer (CRPC). To achieve this, we have developed 22Rv1 cells with Gsk3β knockdown using shRNA.
We performed differential gene expression analysis (DEGs) and HALLMARK of Gene Set Enrichment Analysis (GSEA) of RNA seq data obtained from 22Rv1-Scramble vs. 22Rv1 Gsk3β-shRNA cells

middle: B

first: Pratima

last: Raut

first: Sushanta

last: Halder

first: Zahraa

middle: W

last: Alsafwani

first: Seema

last: Parte

first: Gunjan

last: Sharma

first: K

middle: M

last: Abdullah

first: Parthasarathy

last: Seshacharyulu

first: Subodh

last: Lele

first: Surinder

middle: K

last: Batra

first: Jawed

middle: A

last: Siddiqui


title: TLN468 changes the pattern of tRNA used to read through premature termination codons in CFTR

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

type: Non-coding RNA profiling by high throughput sequencing

summary: Nonsense mutations account for 12% of cystic fibrosis (CF) cases. The presence of a premature termination codon (PTC) leads to gene inactivation, which can be countered by the use of drugs stimulating PTC readthrough, restoring production of the full-length protein. We recently identified a new readthrough inducer, TLN468, more efficient than gentamicin. We measured the readthrough induced by these two drugs with different cystic fibrosis transmembrane conductance regulator (CFTR) PTCs. We then determined the amino acids inserted at the S1196X, G542X, W846X and E1417X PTCs of CFTR during readthrough induced by gentamicin or TLN468. TLN468 significantly promoted the incorporation of one specific amino acid, whereas gentamicin did not greatly modify the proportions of the various amino acids incorporated relative to basal conditions. The function of the engineered missense CFTR channels corresponding to these four PTCs was assessed with and without potentiator. For the recoded CFTR, except for E1417Q and G542W, the PTC readthrough induced by TLN468 allowed the expression of CFTR variants that were correctly processed and had significant activity that was enhanced by CFTR modulators. These results suggest that it would be relevant to assess the therapeutic benefit of TLN468 PTC suppression in combination with CFTR modulators in preclinical assays.

overall_design: tRNAseq from Expi293 cell line in presence or absence of the readthrough-inducing drug TLN468. Each experiment has been done in triplicate.

first: Sabrina

last: Karri

first: Laure

last: Bidou

first: David

last: Cornu

first: Claudia

last: Serot

first: Iwona

last: Pranke

first: Alexandre

last: Hinzpeter

first: Isabelle

last: Sermet-Gaudelus


title: EMILIN1 suppresses cell proliferation by inactivating Aurora Kinase and cell cycle regulator in head and neck squamous cell carcinoma

city: Bangkok

first: Pichaya

last: Chanpanitkitchote

address: Phayathai

country: Thailand

institute: Mahidol University

summary: The extracellular matrix (ECM) proteins play an important role in the physiological and pathological processes of tumor development and progression. EMILIN1 (Elastic Microfibril Interface Located ProteIN-1), a homotrimeric ECM glycoprotein, has been reported to be associated with cell adhesion and migration. We previously identified downregulated-EMILIN1 as a prognostic biomarker for secondary primary malignancy in head and neck squamous cell carcinoma (HNSCC). We hypothesized that EMILIN1 functions as a tumor suppressor in HNSCC. In this study, we overexpressed exogenous EMILIN1 expression in the FaDu and CAL27 cell lines and knockdown EMILIN1 expression in both HNSCC Cancer-Associated Fibroblast (CAF) and normal fibroblast cells. Our results showed that EMILIN1 overexpression decreased cell proliferation, cell migration, and cell invasion in FaDu and CAL27 cells. Knockdown EMILIN1 in CAFs also induced cell proliferation and migration. RNA-sequencing analysis revealed the cell cycle and Aurora kinase signaling as the most significant enrichment pathways, and we then confirmed this finding at the protein level. Furthermore, we studied the effect of EMILIN1 on tumor development in vivo using chick chorioallantoic membrane (CAM) assay. EMILIN1overexpression reduced tumor area, Ki67-positive cells, and increased cleaved caspase-3 apoptotic cells. These findings suggest the tumor suppressing role of EMILIN1 in HNSCC through the inactivation of cell cycle pathway and Aurora kinase signaling. To the best of our knowledge, this is the first study to show that Aurora kinases are the key players in EMILIN1 tumor suppressive functions in head and neck cancer cells.

overall_design: We created FADU and CAL27 cell lines with EMILIN1 overexpress and primary fibroblast with EMILIN1 knockdown  by lentiviral transfection. We then performed the RNA-sequencing and differiential gene expression analysis of 6 different cells with control sample.

first: Natini

last: Jinawath


title: Retrograde mitochondrial signaling governs the identity and maturity of metabolic tissues

city: Ann Arbor

first: Emily

last: Walker

state: MI

address: 1000 Wall Street

institute: University of Michigan

summary: Mitochondrial damage is a hallmark of metabolic diseases, including diabetes and metabolic dysfunction-associated steatotic liver disease, yet the consequences of impaired mitochondria in metabolic tissues are often unclear. Here, we report that dysfunctional mitochondrial quality control engages a retrograde (mitonuclear) signaling program that impairs cellular identity and maturity across multiple metabolic tissues. Surprisingly, we demonstrate that defects in the mitochondrial quality control machinery, which we observe in pancreatic β cells of humans with diabetes, cause reductions of β cell mass due to dedifferentiation, rather than apoptosis. Utilizing transcriptomic profiling, lineage tracing, and assessments of chromatin accessibility, we find that targeted deficiency anywhere in the mitochondrial quality control pathway (e.g., genome integrity, dynamics, or turnover) activate the mitochondrial integrated stress response and promote cellular immaturity in β cells, hepatocytes, and brown adipocytes. Intriguingly, pharmacologic blockade of mitochondrial retrograde signaling in vivo restores β cell mass and identity to ameliorate hyperglycemia following mitochondrial damage. Thus, we observe that a shared mitochondrial retrograde response controls cellular identity across metabolic tissues and may be a promising target to treat or prevent metabolic disorders.

overall_design: Islets were isolated from TfamKO and controls, Clec16aKO and controls on RFD and HFD, RNA was isolated and submitted for sequencing, both males and females were used


title: Effect of the simulated shade on reproductive tissues (floral buds) of Arabidopsis thaliana

city: Valencia

first: jaume

middle: f

last: martinez-garcia

state: Valencia

address: CPI, Edifici 8E, Campus UPV, Carrer Enginyer Fausto Elio s/n

department: Development and Hormonal Action in Plants

institute: IBMCP, CSIC

summary: To investigate the effect of simulated shade on the genetic network regulating ovule development, we treated Arabidopsis adult plants with W or simulated shade (W+FR) for up to 24 h. After extracting total RNA from floral buds we performed gene expression profiling analysis using data from RNA-seq of two different treatments at different time points

overall_design: Wild-type (Col-0) and mutant (MB2 line, an inducible transgenic line expressing pAP1:AP1-GR in an ap1 cal background) Arabidopsis plants were grown under LD conditions (W; high R:FR) until they started to flower. Then, plants were treated with simulated shade (W enriched with FR, W+FR; low R:FR) and floral buds were harvested at 0, 1, 3 and 24h. Samples were also harvested from control plants grown for 24 h under W. In the case of MB2 line, inflorescences were induced treating the plants with 2 μM dexamethasone 3 days before the simulated shade treatment

first: Irma

last: Roig-Villanova

first: Salvador

last: Torres-Montilla

first: Estefanía

last: López-García

first: Anna

last: Esteve-Codina

first: Jaume

last: Martínez-García


title: Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: B304 TIFR Homi Bhabha road

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

summary: In the developing vertebrate central nervous system, neurons and glia typically arise sequentially from common progenitors. Here, we report that the transcription factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and in postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, that is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic ligand FGF18 in newborn neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons increases Fgf18 expression and enhances gliogenesis in the progenitors. These results fit well with the model that newborn neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex.

overall_design: To assess the implications of the loss of Foxg1 in the neuron-glia cell fate decisions in the developing cerebral cortex,  hGFAPCreERT2; Foxg1lox/lox; Ai9 (Progenitor Control) mice were administered Tamoxifen at E15.5 to delete Foxg1 from the progenitors. Brains were isolated, and the fluorescently labelled mutant cells were FACS-purified at E17.5. The corresponding Controls were obtained by administering FlashTag at E15.5 in WT brains and FACS purifying the cells at E17.5. For postmitotic neuron-specific deletion of Foxg1, cortical plate were collected at P1 from NexCre/+; Foxg1lox/lox; FR/FRT (postmitotic mutant) or their littermate controls Foxg1lox/lox; FRT/FRT.

first: Mahima

last: Bose

first: Varun

last: Suresh

first: Ishita

last: Talwar

first: Urvi

last: Mishra


title: Safety profile of sikamat virus and its oncolytic potential in leukemic cells and cancer stem cells

status: Public on Jan 14 2025

city: Semenyih

first: Zhen Yun

last: Siew

state: Selangor

address: University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.

department: School of Pharmacy

country: Malaysia

institute: University of Nottingham Malaysia

summary: Myelogenous leukaemia remains a global health concern. The oncotherapy resistance of leukaemia might be due to the existence of cancer stem cells population. This study investigated the therapeutic potential of Sikamat virus (PRV7S), a Pteropine orthoreovirus, as an oncolytic virus against acute myeloid leukaemia (AML) and chronic myeloid leukaemia (CML). Using AML and CML cell lines (THP1 and K562) and an AML-M5-derived cancer stem cell (CSC) model, PRV7S was shown to infect, replicate within, and reduce cell viability in these leukaemic cells. PRV7S-induced cell death was associated with caspase-mediated apoptosis without significant cell cycle arrest. Transcriptomic and proteomic analyses revealed that PRV7S infection altered several cell death pathways, including apoptosis and necroptosis, highlighting its complex cell death mechanisms. PRV7S replicated efficiently in infected cells, though it did not cause persistent infection. An in vivo safety evaluation in immunocompetent mice demonstrated that PRV7S was well-tolerated, showing no adverse effects on survival, body weight, or histopathology, and no evidence of viral persistence. These findings suggest PRV7S as a promising oncolytic candidate for myeloid leukaemia, with potential efficacy against CSCs and a favourable safety profile. The study provides new insights into the cellular pathways involved in PRV7S-mediated oncolysis and supports further exploration of PRV7S in clinical applications for resistant leukaemic and solid tumours.

overall_design: mRNA-seq profiling of PRV7S infected and non-infected wildtype THP-1 (ATCC TIB-202) and K562 (ATCC CCL-243) cells at Day 5 post-infection.

first: Ghee Khang

last: Ong

first: Siew Tung

last: Wong

first: Pooi Pooi

last: Leong

first: Boon Shing

last: Tan

first: Chee-Onn

first: Juita Binti

last: Chupri

first: Chee-Mun

last: Fang

first: Kenny

last: Voon


title: Genome wide STAT3 binding analysis of  primary human hepatocytes-derived organoids [ChIP-seq]

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

summary: To analyze the primary STAT3 binding sites induced by OSM, chromatin immunoprecipitation sequencing (ChIP-seq) was performed using an anti-human STAT3 antibody. HHOs were cultured in EM for 1 week and cultured EM (-OSM) for 24 hrs to deplete OSM before OSM induction, and then incubated with EM(+OSM) for 0.5 hr. HHOs at 0h and 0.5h after OSM induction were subjected to ChIP-seq analysis using ChIPmentation methodology with minor adaptations [Schmidl et al. PMID: 26280331]. Briefly, organoids were dissociated into single cells and fixed for 10 min, and then quenched by glycine. The lysed and sonicated chromatin was transferred to a new tube. The chromatin was reacted with the anti-STAT3 antibody (Cell Signaling Technology: Stat3 (D3Z2G) Rabbit mAb #12640) on a rotator overnight at 4°C. Washed and blocked Dynabeads Protein A/Protein G magnetic beads in RIPA-LS supplemented with 0.1% BSA were added to the lysates and incubated for 2 hr on a rotator at 4°C. Beads were subsequently washed with RIPA-LS, RIPA-HS , RIPA-LiCl, and Tris-Cl pH 8.0. The beads were then resuspended in a tagmentation reaction mix containing 1 μl of TDE1 Tagment DNA Enzyme (Illumina) and incubated at 37°C for 3 min on a thermocycler. The beads were further washed and incubated with Pronase for 1 hr at 42°C and 8 hr at 65°C to revert cross-linking. Finally, DNA was purified with MinElute columns and eluted with elution buffer. The DNA was subsequently amplified with Nextera sequencing primers and NEBNext high fidelity 2x PCR master mix for 5–10 cycles. Enriched libraries were purified, size selected using AMPure XP beads to recover libraries with the fragment length of 200–400 bp, and sequenced by llumina HiSeq 2500 sequencer with 150 bp paired-end reads.

overall_design: Genome wide binding analysis of STAT3 of cytokine-induced HHOs.

first: Ryo

last: Igarashi

first: Kazuhiro

last: Togasaki

first: Toshiro

last: Sato


title: Metformin alters liver metabolism to sustain egg production in the reproductively aging broiler breeder hen

city: University Park

first: Evelyn

middle: Anne

last: Weaver

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

summary: The liver plays a critical role in avian reproduction as it is the primary site of de novo lipogenesis and yolk precursor synthesis. Broiler breeder hens, the parents of commercial broiler chickens, often experience poor reproductive efficiency primarily due to declining egg production beginning around 45 weeks of age. Metformin, an antidiabetic drug, exerts its primary effects in the liver by increasing insulin sensitivity and reducing hepatic glucose production in humans. This study aimed to characterize the liver transcriptomic profile of broiler breeder hens supplemented with metformin in the diet at 0 or 75 mg/kg body weight for 40 weeks (25-65 weeks of age; n=45 hens/treatment). Liver tissue was collected from a subset of hens (n=12 hens/treatment group) at 65 weeks of age, RNA was extracted and sequenced using next-generation sequencing. Differential gene abundance analysis revealed that metformin treatment led to the most significant changes in gene expression, with 552 genes differentially expressed compared to the control group. Further transcriptomic analysis highlighted increased expression of genes related to estrogen-stimulated yolk precursor synthesis, insulin-stimulated de novo lipogenesis, and AMPK-mediated glucose homeostasis. qPCR analysis revealed increased expression of ESR1, APOB, APOV1, VTG2, ADIPOQ, ADIPOR2 and ACACA mRNA and decreased expression of PCK1 mRNA validating the transcriptomic data. Collectively, the present study suggests that metformin supplementation supports prolonged egg production in aging broiler breeder hens by sustaining yolk precursor and fatty acid synthesis that are typically diminished in aging broiler breeder hens.

overall_design: RNA-seq profiling of liver tissue collected from broiler breeder hens supplemented with metformin (0 or 75 mg/kg body weight) in the diet for 40 weeks (25-65 weeks of age).

first: Nathan

middle: P

last: Connolly

first: Tae Hyun

last: Kim

first: Ramesh

last: Ramachandran


title: Maternal Circadian Rhythms during Pregnancy Dictate Metabolic Plasticity in Offspring

city: Irvine

first: Kousha

last: Changizi Ashtiani

state: California

address: Institute for Genomics and Bioinformatics 243, Info & Computer Science Building 2

department: ICS

institute: University of California, Irvine

summary: The circadian gene expression in peripheral tissue displays rhythmicity which is reprogrammed by feeding rhythms and dietary composition in mammals. In this study, circadian transcriptome was performed to investigate how maternal circadian rhythms during pregnancy influences circadian gene regulation in the mouse liver.

overall_design: C57BL/6J pregnant mice were randomly divided and housed under either thecontrol 12h-light/ 12h-dark condition (CON) or chronically phase-shifted condition (CPS) where phase was advanced by 8 hours every 5 days exclusively during pregnancy. 4-week-old, male offspring mice were subjected to ad libitum low-fat diet or to high-fat diet for 12 weeks. Tissues were collected every 6hours over a circadian cycle at ZT0, ZT6, ZT12, and ZT18. Total RNA was extracted from the liver, and used for RNA-seq.

last: Yao

first: Kenichiro

last: Kinouchi

first: Sherif

last: Abdelkarim

first: Pierre

last: Baldi

first: Hiroshi

last: Itoh


title: CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks

city: London

first: Sarah

middle: J

last: Marzi

address: Maurice Wohl Clinical Neuroscience Institute

department: Basic and Clinical Neuroscience

country: United Kingdom

institute: King's College London

summary: We comprehensively benchmarked CUT&Tag for H3K27ac and H3K27me3 against published ChIP-seq profiles from ENCODE in K562 cells. Combining multiple new and published CUT&Tag datasets, there was an average recall of 54% known ENCODE peaks for both histone modifications. To optimize data analysis steps, we tested peak callers MACS2 and SEACR and identified optimal peak calling parameters. Considering both precision and recall of known ENCODE peaks, the peak callers were comparable in their performance, although peaks produced by MACS2 match ENCODE peak width distributions more closely. We found that reducing PCR cycles during library preparation lowered duplication rates at the expense of ENCODE peak recovery. Despite the moderate ENCODE peak recovery, peaks identified by CUT&Tag represent the strongest ENCODE peaks and show the same functional and biological enrichments as ChIP-seq peaks identified by ENCODE. Our workflow systematically evaluates the merits of methodological adjustments, providing a benchmarking framework for the experimental design and analysis of CUT&Tag studies, and will facilitate future efforts to apply CUT&Tag in human tissues and single cells.

overall_design: 8 CUT&Tag experiments profiling H3K27ac and H3K27me3 in the K652 cell line using different antibodies (H3K27ac: Abcam ab177178, Abcam 4729, Diagenode C15410196, and H3K27me3: CST9733).

first: Leyla

last: Abbasova

first: Paulina

last: Urbanaviciute

first: Di

last: Hu

first: Joy

middle: N

last: Ismail

first: Brian

last: Schilder

first: Alexi

last: Nott

middle: G

last: Skene


title: RNA-seq of C4-2 parental and enzalutamide resistant cells

city: Tianjin

first: zhiqun

last: shang

address: Pingjiang road, tianjin

institute: tianjin medical university

summary: To explore the potential drug target candidate in enzalutamide-resistant PCa, the differential abundances of transcripts between enzalutamide-resistant C4-2 Enz-R and C4-2 cells were examined.

first: Shang

last: Zhiqun

first: Zhang

last: Mingpeng

first: Yu

last: Jianpeng

first: Niu

last: Yuanjie


title: Control eCLIP from K562 (ENCSR111UKN)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
eCLIP control experiment on K562 against FXR1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Identification of lens-regulated genes driving anterior eye development and eye size.

city: Aberdeen

first: Lynda

last: Erskine

address: Foresterhill

department: School of Medicine, Medical Sciences and Nutrition

institute: University of Aberdeen

summary: Signals from the lens regulate multiple aspects of eye development, including establishment of eye size, patterning of the presumptive iris and ciliary body in the anterior optic cup and migration and differentiation of neural crest cells. To advance understanding of the molecular regulation of eye development by the lens, we performed transcriptome analysis of lens-removed and contralateral unoperated embryonic chicken eyes. Lens-regulated genes implicated in periocular mesenchyme, cornea and anterior optic cup development were identified. Identified candidates included genes known to be regulated by lens-derived signals and important for anterior eye development, including WNT pathway genes. Factors not previously implicated in eye development also were identified, paving the way for additional research in this area. Genes associated with nervous system development were upregulated in lens-removed eyes, but the presumptive ciliary body and iris region did not adopt a neural retina identity following lens removal. Intriguingly, transcriptomic differences were identified in retinas from male versus female chicken embryos, suggesting sexual dimorphism from early stages. These analyses have identified candidate genes and biological pathways involved in eye development, providing avenues for new research in this area.

overall_design: RNA-seq profiling of operated and contralateral unoperated embryonic chicken retinas 6 hours after lens removal from one eye at Hamburger and Hamilton (HH) 23 (~E4).

first: Verónica

last: Murcia-Belmonte

first: Yanlin

last: Liu

first: Sadia

last: Shamsi

first: Sophie

last: Shaw

first: Elaina

last: Collie-Duguid

first: Eloisa

last: Herrera

first: Martin

last: Collinson

first: Neil

last: Vargesson


title: Upregulation of the MBM CTC Signature and CTC:B Cell Clusters Associate with Secondary Liver Metastasis: a Melanoma Brain-Liver Metastasis Axis [Xenium]

city: Albuquerque

first: Kathryn

last: Brayer

state: New Mexico

address: 1 University of New Mexico, MSC07 4025

institute: University of New Mexico

summary: CTC-generated tumor tissues were interrogated at single-cell gene and protein expression levels using 10x Genomics Xenium

overall_design: Tissue sections were processed using the manufacturer?s guidelines for Xenium (10x Genomics; www.10xgenomics.com). Both the standard pre-designed human multi-tissue/cancer panel (10x Genomics, product number 1000626), as well as a custom designed panel of 22 genes were used to generate the 10x Xenium results.!Series_type = Other

first: Tetiana

middle: Y

last: Bowley

first: Mireya

middle: C

last: Ortiz

first: Irina

middle: V

last: Lagutina

first: Mara

last: Steinkamp

first: Bridget

last: Fahy

first: Bernard

last: Tawfik

first: Moises

last: Harari-Turquie

first: Dario

last: Marchetti


title: Upregulation of the MBM CTC Signature and CTC:B Cell Clusters Associate with Secondary Liver Metastasis: a Melanoma Brain-Liver Metastasis Axis [RNA-Seq]

summary: Melanoma brain metastasis (MBM) is linked to dismal prognosis, low overall survival, and is detected in up to 80% of patients at autopsy. Circulating tumor cells (CTCs) are the smallest functional units of cancer and precursors of fatal metastasis. We previously employed an unbiased multilevel approach to discover a unique ribosomal protein large/small subunits (RPL/RPS) CTC gene signature associated with MBM. Here, we hypothesized that CTC-driven MBM secondary metastasis (?metastasis of metastasis? per clinical scenarios), has targeted organ specificity for liver. We injected parallel cohorts of immunodeficient and newly-developed humanized NBSGW (HuNBSGW) mice with cells from CTC-derived MBM to identify secondary metastatic patterns. We found the presence of a melanoma brain-liver metastasis axis in humanized NBSGW mice.  Further, RNA-Seq analyses of tissues showed a significant upregulation of the RPL/RPS CTC gene signature linked to metastatic spread to liver. Additional RNA-Seq of CTCs from HuNBSGW blood revealed extensive CTC clustering with human B cells in these mice. CTC:B cell clusters were also upregulated in blood of primary melanoma patients, and maintained either in CTC-driven MBM or MBM CTC-derived cells promoting liver metastasis.  CTC-generated tumor tissues were interrogated at single-cell gene and protein expression levels (10x Genomics Xenium and HALO spatial biology platforms, respectively). Collectively, our findings suggest that heterotypic CTC:B cell interactions can be critical at multiple stages of metastasis. This study provides important insights for relevance of pro-metastatic CTC:B cell clusters extending from primary metastatic disease, and identifies new targets for therapies of clinical metastasis to improve patient care.

overall_design: Mouse tissues were isolated during necropsies and frozen. They were thawed, homogenized, and RNA was extracted using Qiagen RNA kit. RNA was sent for RNA seq to the ATG core.


title: Heterozygous GAA knockout is nonconsequential on metabolism and the spatial liver transcriptome in high-fat diet induced obese and prediabetic mice

city: Baton Rouge

first: Tim

last: Heden*

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

summary: The liver is composed of periportal and perivenous hepatocytes that have different metabolic profiles. This study used spatial transcritpomics to identify how high-fat diet induced obesity and heterozygous GAA knockout impacted the periportal and perivenous transcriptome. The spatial transcritpomics analysis revealed that heterozygous GAA knockout had no impact on liver transcriptomes. However, the high-fat diet, compared to the low-fat diet, reduced metabolic pathway gene abundance in both zones, while uniquely reducing ribosome gene abundance in perivenous hepatocytes.

overall_design: Four groups of mice were included in the analysis including 1) wildtype low-fat fed mice, 2) heterozygous GAA knockout low-fat diet fed mice, 3) wildtype high-fat diet fed mice, and 4) heterozygous GAA knockout hig-fat diet fed mice. Formalin fixed paraffin embedded liver sections were used for the spatial transcriptomics analysis.

first: Cameron

last: McCall

first: Melina

last: Mancini

first: Jaroslaw

last: Staszkiewicz

first: Douglas

last: Mashek

first: Timothy

last: Heden

first: John

last: Garbe

first: Juan

last: Abrahante

first: Grant

last: Barthel


title: Maternal circadian rhythms and metabolic plasticity in the offspring

first: Kenichiro

last: Kinouchi

address: 35 Shinanomachi, Shinjuku-ku

institute: Keio University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: The impact of maternal circadian disruption during pregnancy on the metabolic outcome in the offspring was explored. To investigate whether epigenetic changes engage in the metabolic plasticity, global patterns of DNA methylation was compared between the control and circadian disruption during pregnancy in the fetal and mouse livers.

overall_design: The fetal livers on E18.5 and mouse livers at four weeks of age from the offspring of the control and CPS (chronic phase shifting condition during pregnancy) mothers were sampled.

first: Ya

last: Nao

first: Hiroshi

last: Itoh


title: Gene expression profile at single cell level of the placenta from pregnant mice undergoing circadian disruption.

city: Bunkyo-ku

first: Manami

last: Katoh

state: Tokyo

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

summary: The placenta is composed of distinct cell types. Single cell RNA sequencing (scRNA-seq) was performed to analyze the diversity of cell types contained in the placenta.

overall_design: C57BL/6J pregnant mice were randomly divided and housed under either the control 12h-light/ 12h-dark condition (CON) or chronically phase-shifted condition (CPS) where phase was advanced by 8 hours every 5 days exclusively during pregnancy. On embryonic day 18.5, the placenta was collected and analyzed using scRNA-seq.


title: hNSCs siRNA BRPF1, DYRK1A et PQBP1

city: Strasbourg

first: Amélie

last: Piton

address: 1 rue Laurent Fries

institute: IGBMC

summary: NOT PROVIDED; REQUESTED

overall_design:
inactivation of BRPF1, DYRK1A and PQBP1 genes in human neural stem cells (hNSCs)
Re-analysis of GSE138766/PRJNA577099:
GEO Sample      SRA Runs        BioSample       Title
==========      ========        =========       =====
GSM4118987      SRR10267209     SAMN13019212    NSC INF_1
GSM4118988      SRR10267210     SAMN13019211    NSC siScr_1
GSM4118990      SRR10267212     SAMN13019209    NSC INF_2
GSM4118991      SRR10267213     SAMN13019208    NSC siScr_2

first: Amelie

first: Courraud

last: Jérémie


title: The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

institute: VIB

summary: During secondary growth, the vascular cambium produces conductive xylem and phloem cells, while the phellogen (cork cambium) deposits phellem (cork) as the outermost protective barrier. Although most of the secondary tissues are made up of parenchyma cells, which are also produced by both cambia, their diversity and function are poorly understood. Here we combined single-cell RNA sequencing analysis with lineage tracing to recreate developmental trajectories of the cell types in the Arabidopsis root undergoing secondary growth. By analysing 93 reporter lines, we were able to identify 20 different cell types or cell states, many of which have not been described before. We additionally observed distinct transcriptome signatures of parenchyma cells depending on their maturation state and proximity to the conductive cell types. Our data show that both xylem and phloem parenchyma tissues are required for normal formation of conductive tissue cell types. Furthermore, we show that mature phloem parenchyma gradually obtains periderm identity, and this transformation can be accelerated by jasmonate treatment or wounding. Our study thus reveals the diversity of parenchyma cells and their capacity to undergo considerable identity changes during secondary growth.

overall_design: A single-cell RNA-seq experiment was performed on protoplasts extracted from secondary root growth of Arabidopsis thaliana.

first: Munan

last: Lyu

first: Hiroyuki

last: Iida

first: Thomas

last: Eekhout

first: Meeri

middle: H

last: Mäkelä

first: Sampo

last: Muranen

first: Lingling

last: Ye

first: Anne

last: Vaten

first: Brecht

last: Wybouw

first: Xin

last: Wang

first: Ykä

last: Helariutta

first: Ari

last: Mähönen


title: Reactivating the phototransduction cascade with a mutation agnostic gene therapy preserves vision in Rod-Cone Dystrophies

status: Public on Jan 13 2025

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

institute: Institut de la Vision

summary: Rod-cone dystrophy (RCD), or retinitis pigmentosa, involves genetic conditions where rod degeneration precedes cone degeneration, resulting in tunnel vision and eventual blindness. Previous studies attempted to restore cone activity and prolong vision by expressing microbial chloride pumps in degenerating cone photoreceptors. However, microbial opsins require high expression and intense light, limiting their effectiveness. In this work, we explored the phototransduction cascade in degenerating cones in two RCD mouse models. We observed that opsin and arrestin expression persists in the soma during outer segment degeneration. This led us to hypothesize that reactivating cones based on cone opsin signaling may be possible by expressing a target channel activated by G proteins recruited by cone opsin. Through adeno-associated viral (AAV) mediated expression of the G protein-coupled inwardly rectifying K (GIRK) channel, we achieved improvements in visual function in two RCD mouse models with mutations in different genes. Importantly, we validated the rationale of GIRK-mediated gene therapy in humans by confirming cone opsin and cone arrestin expression in cones of late-stage RCD patients. Our proposed approach involves GIRK channel expression in cones as a novel method to maintain high acuity, sensitivity, and color vision in RCD, independent of the underlying mutation.

overall_design: Single-cell RNAseq of rd10 retinas from six mice at PND126 and rd1 retinas from five rd1 mice at PND112-PND116. Cells from rd10 and rd1 retinas were pooled into two and three samples, respectively.

first: Cardillia-Joe

last: Simon

first: Hanen

last: Khabou

first: Antoine

last: Chaffiol

first: Marco

last: Rucli

first: Marion

last: Finzi

first: Nat

last: Norberg

first: Anaïs

last: Grimaud

first: Brix

last: Mücher

first: Mélissa

last: Desrosiers

first: Serge

last: Sancho

first: Vera

middle: L

last: Bonilha

first: Kate

last: Grieve

first: Jens

last: Duebel

first: Michel

last: Paques

last: Picaud

first: José

last: Sahel

first: Isabelle

last: Audo

first: Stefan

last: Herlitze

first: Deniz

last: Dalkara


title: Somatic NAP1L1 p.D349E promotes cardiac hypertrophy through cGAS-STING-IFN signaling

city: Beijing

first: Yibo

last: Wang

state: Beijing

address: 167 Beilishi Rd

institute: National Center for Cardiovascular Diseases

summary: Hypertrophic cardiomyopathy (HCM) is the most common inherited heart disease, often caused by sarcomere gene mutations, though many sporadic cases remain genetically unexplained. Here we show that the somatic variant NAP1L1 p.D349E was involved in cardiac hypertrophy in sporadic HCM patients. Through next generation sequencing, we found that somatic variant NAP1L1 p.D349E was recurrent in the cardiomyocytes of gene elusive sporadic HCM patients. Subsequent in vivo and in vitro functional analysis confirmed that NAP1L1 p.D349E contributes to HCM by triggering an innate immunity response. This mutation destabilizes nucleosome formation, causing DNA to leak into the cytoplasm. This leakage activates a key immune pathway, cGAS-STING, which leads to the release of inflammatory molecules and promotes heart muscle thickening. Our findings reveal a new mechanism driving HCM and suggest that somatic variants could be important in understanding and management of HCM.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Nap1l1 knokcdown and control; Nap1l1 mutation type, overexpression and control group


title: Linear motif specificity in signaling through p38α and ERK2 mitogen–activated protein kinases

city: New Haven

first: Jaylissa

middle: Marie

last: Torres Robles

state: CT

address: 333 Cedar St. Department of Pharmacology, Yale School of Medicine

department: Chemistry and Pharmacology

institute: Yale University

summary: Mitogen-activated protein kinase (MAPK) cascades are essential for eukaryotic cells to integrate and respond to diverse stimuli. Maintaining specificity in signaling through MAPK networks is key to coupling distinct inputs to appropriate cellular responses. Docking sites—short linear motifs found in MAPK substrates, regulators, and scaffolds—can promote signaling specificity through selective interactions, but how they do so remains unresolved. Here, we screened a proteomic library for sequences interacting with the MAPKs extracellular signal-regulated kinase 2 (ERK2) and p38α, identifying selective and promiscuous docking motifs. Sequences specific for p38α had high net charge and lysine content, and selective binding depended on a pair of acidic residues unique to the p38α docking interface. Finally, we validated a set of full-length proteins harboring docking sites selected in our screens to be authentic MAPK interactors and substrates. This study identifies features that help define MAPK signaling networks and explains how specific docking motifs promote signaling integrity.

overall_design: High throughput yeast two hybrid Illumina sequencing to determine the interactions of ERK2 and p38α with a library of the ERK2 substrate ELK1 with a variable docking site sequence. In the library the native MAPK docking sequence in ELK1 is replaced by short linear motifs found in human proteins. Library representation is evaluated after two cycles of competitive selection. Extracted DNA from each aliquot and the D-site coding sequence was PCR-amplified with barcoding primers. Samples were pooled and sequenced on an Illumina HiSeq 4000 instrument with 100-bp paired end reads. Screens with ERK2 and p38α were performed three times independently.

first: Benjamin

middle: E

last: Turk


title: Retinoic acid antagonizes estrogen signaling to maintain adult uterine cell fate

city: Saint Louis

first: Yan

last: Yin

state: MO

address: 660 S. Euclid Ave

department: Medicine

institute: Washington University School of Medicine

summary: Uterine epithelial transformation/metaplasia occurs in Rar tKO mice at a young age. We performed single cell RNA sequencing (scRNA-seq) of isolated uterine cells at two time points during development in order to investigate the origin and charactoristics of these transformed cells.

overall_design: Uterine cells were isolated from postnatal day 21 (PD21) and PD54 Rar tKO and control (CTRL) mice and analyzed using scRNAseq

first: Liang

last: Ma


title: Gene expression analysis of cultures of acinar-enriched explants from KC Fgfr2+/+ and Fgfr2f/f mice in collagen provides insight into mutant Kras-driven trasformation of acinar cells

city: Cold Spring Harbor

first: David

last: Tuveson

state: New York

address: 1 Bungtown Road

department: Cancer Center

institute: Cold Spring Harbor Laboratory

summary: This study used RNA-sequencing of cultures of acinar-enriched epithalial explants from KC Fgfr2+/+ and Fgfr2f/f mice in collagen to study mutant Kras-induced malignant trasformation of acinar cells in the presence and absence of Fgfr2.

overall_design: Strand-specific RNA-sequencing of epithelial organoid cultures of primary cells from KrasLSLG12D/+; Trp53LSLR172H/+; Pdx1-Cre (KPC) mice.

first: Claudia

last: Tonelli

first: Astrid

last: Deschênes


title: ADAR1 Regulates Lipid Remodeling through MDM2 to Dictate Ferroptosis Sensitivity

first: Che-Pei

last: Kung

state: Missouri

address: 1 Brookings Dr.

institute: Washington University in St. Louis

summary: Triple-negative breast cancer (TNBC), lacking expression of estrogen, progesterone, and HER2 receptors, is aggressive and lacks targeted treatment options. An RNA editing enzyme, adenosine deaminase acting on RNA 1 (ADAR1), has been shown to play important roles in TNBC tumorigenesis. We posit that ADAR1 functions as a homeostatic factor protecting TNBC from internal and external pressure, including metabolic stress. We tested the hypothesis that the iron-dependent cell death pathway, ferroptosis, is a ADAR1-protected metabolic vulnerability in TNBC by showing that ADAR1 knockdown sensitizes TNBC cells to GPX4 inhibitors. By performing single-reaction monitoring-based liquid chromatography coupled to mass spectrometry (LC-MS) to measure intracellular lipid contents, we showed that ADAR1 loss increased the abundance of polyunsaturated fatty acid phospholipids (PUFA-PL), of which peroxidation is the primary driver of ferroptosis. Transcriptomic analyses led to the discovery of the proto-oncogene MDM2 contributing to the lipid remodeling in TNBC upon ADAR1 loss. A phenotypic drug screen using a ferroptosis-focused library was performed to identify FDA-approved cobimetinib as a drug-repurposing candidate to synergize with ADAR1 loss to suppress TNBC tumorigenesis. By demonstrating that ADAR1 regulates the metabolic fitness of TNBC through desensitizing ferroptosis, we aim to leverage this metabolic vulnerability to inform basic, pre-clinical, and clinical studies to develop novel therapeutic strategies for TNBC.

overall_design: RNA-seq profiling of TNBC cell lines treated with control (shNT) or ADAR1-targeting (shADAR1) short-hairpin RNAs to assess the effect of ADAR1 knockdown

first: Jason

middle: D

last: Weber


title: Gene expression analysis of pancreatic cancer organoids provides insights in tumor progression mechanisms.

summary: This study used strand-specific RNA-sequencing of epithelial organoid cultures of primary cells from KrasLSLG12D/+; Trp53LSLR172H/+;Pdx1-Cre (KPC) mice to study the pathways that are dysregulated during tumor progression following p53 inactivation. We profiled gene expression in 3 TR172H/+ and TR172H/LOH organoid pairs.


title: Immune checkpoint molecule Tim-3 regulates microglial function and the development of Alzheimer’s disease pathology [scRNA-Seq]

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

summary: Microglia, resident immune cells in the brain, play a critical role in neurodevelopment and neurological diseases. We investigated the role of the immune checkpoint molecule Tim-3 (Havcr2), which was recently identified as a genetic risk factor for late-onset Alzheimer’s disease (LOAD) in microglia. While Tim-3 has been shown to play an important role in inducing T cell exhaustion, it shows high and specific expression in the microglia where its role is unknown. Here we show that Tim-3 expression in microglia was induced by TGFβ signaling. Mechanistically, Tim-3 binds both Smad2 and Tgfbr2 by its C-terminus tail and enhances TGFβ signaling by promoting the phosphorylation of Smad2 by Tgfbr, thereby contributing to microglial homeostasis. Genetic deletion of Tim-3 in microglia resulted in increased phagocytic activity with a gene expression profile skewed towards neurodegenerative microglia (MGnD) phenotype, also known as disease-associated microglia (DAM). Moreover, microglia-targeted deletion of Tim-3 ameliorated AD pathology in 5xFAD mice. Single-nucleus RNA sequencing (snRNA-seq) identified a subpopulation among MGnD/DAM microglia in Havcr2-deficient 5xFAD mice, characterized by increased pro-phagocytic and anti-inflammatory gene expression together with decreased proinflammatory gene expression. Additional single-cell RNAseq confirmed these transcriptomic shifts in Havcr2-deficient 5xFAD mice in most microglial clusters. Our study shows a Tim-3-mediated regulatory mechanism of homeostatic microglia through its interaction with TGFβ signaling and the beneficial role of targeting microglial Tim-3 in AD mice. Our findings promise a potential therapeutic strategy targeting checkpoint molecule Tim-3 in currently intractable AD.

overall_design: Female Tim3 f/f, 5XFAD and Tim3 f/f, CX3CR1 CreERT2, 5XFAD mice were prepared. Tamoxifen (150 mg/kg body weight) was injected intraperitoneally in two consecutive days at the age of 6 weeks. Microglia were isolated from the brain cortex at the age of 5 months. Mice were deeply anesthetized with CO2 and transcardially perfused with cold HBSS (Gibco). The brains were quickly removed from the skull into cold HBSS. The brain cortices were gently separated with forceps on ice under the microscope. The prepared cortices were homogenized gently with Dounce Homogenizer (Bellco Glass) on ice. After centrifugation, the pellet was dissolved in 70% Percoll Plus (GE Healthcare) solution, with 37% Percoll Plus put gently on top of it. After gentle centrifugation, the cell layer in the middle was collected into cold PBS-based flow cytometry (FCM) buffer, including 0.5% BSA and 2mM EDTA. The sorted microglia were then collected into PBS with 1% BSA.

first: Kimitoshi

last: Kimura

first: Ayshwarya

last: Subramanian

first: Zhuoran

first: Yufan

last: Wu

first: Ahad

last: Khalilnezhad

first: Danyang

last: He

first: Karen

last: Dixon

first: Udbhav

last: Chitta

first: Xiaoming

last: Zhang

first: Ruihan

last: Tang

first: Thomas

last: Pertel

first: Samuel

last: Myers

first: Aastha

last: Aastha

first: Masashi

last: Nomura

first: Vasundhara

last: Singh

first: Lei

last: Liu

first: Conner

last: Lambden

first: Kilian

last: Kleemann

first: Neha

last: Gupta

first: Yiran

last: Cheng

first: Sebastian

last: Silveira

first: Huiyuan

first: Aamir

last: Suhail

first: Toni

last: Delorey

first: Orit

last: Rosenblatt-Rosen

first: Dennis

last: Selkoe

first: Carlos

last: Cruchaga

first: Aviv

last: Regev

first: Mario

last: Suva

first: Oleg

last: Butovsky

first: Vijay

last: Kuchroo


title: Multi-omic spatial atlas shows Deleted inMalignantBrain Tumours 1 (DMBT1) glycoprotein is lost in colonic dysplasia I

city: Nashville

first: Nicholas

last: Markham

state: TN

address: 2213 Garland Ave

institute: VUMC

summary: Colorectal cancer(CRC) is responsible for 50,000 deaths annually in the United States. Emerging evidence supports a causal role for pro-carcinogenic bacteria in the colonic microbiome. We previously showed toxigenic C. difficile from human CRC-associated bacterial biofilms accelerates tumourigenesis in ApcMin/+ mice, both in specific pathogen-free mice and in gnotobiotic mice colonised with a defined consortium of bacteria. To further understand host-microbe interactions during colonic tumourigenesis, we combined single-cell RNA-sequencing (scRNA-seq), spatial transcriptomics, and immunofluorescence to define the molecular spatial organization of colonic dysplasia in our consortium model with or without C. difficile. Our data show a striking bipartite regulation of Deleted in Malignant Brain Tumours 1 (DMBT1) in the inflamed versus dysplastic colon. From scRNA-seq, differential gene expression analysis of normal absorptive colonocytes at 2 weeks post-inoculation showed DMBT1 upregulated by C. difficile compared to colonocytes from mice without C. difficile exposure. In contrast, our spatial transcriptomic analysis showed DMBT1 dramatically downregulated in dysplastic foci compared with normal-adjacent tissue. We further integrated our datasets to generate custom colonic dysplasia scores and ligand-receptor mapping. Validation with immunofluorescence showed DMBT1 protein downregulated in dysplastic foci from three mouse models of colonic tumourigenesis. Finally, we demonstrated downregulation of DMBT1 mRNA and protein in adenomatous dysplasia from human samples. Together, our data reveal cell type-specific regulation of DMBT1, a potential mechanistic link between bacteria and colonic tumourigenesis.

overall_design:
C57Bl/6 mice with the ApcMin/+ (Δ716 Apc) genotype were bred germ-free. At age 8-10 weeks, adult males in the C. difficile experimental group were inoculated with a single gavage of the 29-member bacterial consortium described by Drewes et al, (2022 Cancer Discovery) along with 104 spores of C. difficile strain Cd_3728T. The control group was given a single gavage of the same consortium but without C. difficile (n = 3 mice/group). Two weeks after inoculation, all mice were euthanised humanely for tissue harvesting and scRNA-seq.

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Submitter states that missing raw files are due to file loss.
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first: Emily

last: Green

first: Julia

last: Drewes

middle: O


title: Transcriptional characterization of cocaine withdrawal versus extinction within nucleus accumbens

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Neurobiological alterations seen in addiction amplify during abstinence and compromise relapse prevention. Cocaine use disorder (CUD) exemplifies this phenomenon in which reward regions such as nucleus accumbens (NAc) undergo withdrawal-associated modifications. While genome-wide transcriptional changes in NAc are linked to specific addiction phases, these have not been examined in a context- and NAc-subregion-specific manner during withdrawal vs. extinction. We used cocaine self-administration in rats combined with RNA-sequencing of NAc core and shell to transcriptionally profile withdrawal in the home-cage, in the previous drug context, or after extinction. As expected, home-cage withdrawal maintained drug seeking, whereas extinction reduced it. Conversely, withdrawal involving the drug context increased seeking. Bioinformatic analyses revealed specific gene expression patterns and networks associated with these states. Comparing NAc datasets of CUD patients highlighted conserved transcriptomic signatures with rats experiencing withdrawal in the drug context. Together, this work reveals fundamental mechanisms that can be targeted to attenuate relapse.

overall_design: We used different cocaine abstinence modalities to study withdrawal and extinction conditions and the associated transcriptomic changes in the nucleus accumbens subregions (core/shell) in rats.

first: Freddyson

last: Martínez-Rivera

first: Leanne

middle: M

last: Holt

first: Angélica

last: Minier-Toribio

first: Szu-Ying

last: Yeh

first: Solange

last: Tofani

first: Rita

last: Futamura

first: Caleb

last: Browne

first: Philipp

last: Mews

first: Li

last: Shen

first: Eric

last: Nestler


title: Repetitive transcranial magnetic stimulation induces cortical layer, brain region, and protocol dependent neural plasticity [Bulk RNA-seq]

city: Perth

first: Alexander

last: Tang

state: Western Australia

address: 35 Stirling Highway, University of Western Australia

department: School of Biomedical Science

country: Australia

institute: University of Western Australia

summary: Repetitive transcranial magentic stimulation (rTMS) is a non-invasive toll commonly used to study neural plasticity processes and treat neurological disorders. Despite the popularity of rTMS, it is still unclear what neural plasticity mechanisms are induced in the brain regions at and beyond the stimulation site, and how this varies with different rTMS protocols. Here we used spatial transcriptomics to map the neural plasticity mechanisms induced across cortical and sub-cortical regions following intermittent or continuous theta-burst stimulation protocols to the mouse sensorimotor cortex. Our results revealed that rTMS alters the expression of genes related to several cellular processes and neural plasticity mechanisms across the brain which was both brain region and rTMS protocol dependent. In the cortex, the effect of rTMS was not only dependent on the cortical region, but also the cortical layer within each cortical region. These findings uncover the neural plasticity mechanisms induced across the brain following rTMS and help inform how different stimulation protocols can be used to drive specific neural plasticity mechanisms.

overall_design: Whole transcriptome sequencing data generated from RNA extracted from the sensorimotor cortex of wildtype C57BL/6J mice that received a one-off stimulation session of either intermittent theta-burst (iTBS), continuous theta-burst (cTBS) or sham stimulation. A total of five animals were included in each treatment group. Animals were euthanised three hours post-stimulation, after which the brain was removed and the sensorimotor cortex was dissected and extracted for RNA.

first: Rebecca

last: Ong


title: BmGATA occupation on silkworm genome without BmGATA overexpression

status: Public on Jan 12 2025

city: Hangzhou

first: Shudi

last: Zhao

address: Yuhangtang Road No.866

institute: Zhejiang University

summary: To investigate the genomic occupation of the transcription factor BmGATA, and the impact of BmNPV infection on its genomic occupation

overall_design: NOT PROVIDED; REQUESTED


title: Generation and expansion of induced respiratory airway progenitors (iRAPs) from human pluripotent stem cells.

first: Hans-Willem

last: Snoeck

address: 650 west 168th street

institute: Columbia University Irving Medical Centre

summary: Several novel distal lung populations were recently identified that may be involved in regeneration after injury.1–3 As these are absent in rodents, a deeper understanding of their roles and lineage relations requires availability of equivalent cells in vitro. Here we report the generation of expandable, clonal spheres, called induced respiratory airway progenitors (iRAPs), from human pluripotent stem cells. iRAPs consist mainly of previously identified type 0 alveolar epithelial (AT0) cells, terminal respiratory bronchiole stem cells (TRB-SCs) and distal basal cells (BCs).3 Velocity analysis of single cell RNAseq data suggests that distal BCs are the most undifferentiated progenitors in the iRAPs and give rise to AT0 cells. iRAPs will be an important resource for studies in human lung regeneration, and potentially for regenerative approaches for human lung disease.

overall_design: We performed single cell RNA sequencing on induced respiratory airway progenitors. iRAPs were dissociated to single cells and resuspended at a concentration of 5000 cells/ul for sequencing.

first: Ivana

last: Leko

first: Nadine

last: Schrode

first: Juan

last: Torres

first: Mikael

last: Pezet

first: Tania

middle: A

last: Thimraj

first: Kristin

last: Beaumont


title: Single-cell transcriptomic profling of the aging mouse choroid plexus

city: Shanghai

first: Yidong

address: 320 Yueyang Road

institute: CAS Center for Excellence in Molecular Cell Science (CEMCS)

summary: The blood-cerebrospinal fluid (B-CSF) barrier in the choroid plexus (CP) consists of tight junctions between CP epithelial cells. It is critical to maintaining the environmental homeostasis of the central nervous system and is associated with age-related disorders, such as neurodegenerative diseases. Nevertheless, its ageing is poorly understood. This study collects CP from both young and aged mice for single-cell sequencing, aiming at elucidating the molecular mechanisms driving the age-dependent degeneration of the B-CSF barrier in CP.

overall_design: CPs in lateral ventricles (LV) and the fourth ventricle (4V) from the mice aged 3 and 24 months were isolated and subjected to single-cell RNA sequencing (scRNA-Seq). The CPs from four 3-month-old mice were pooled together as the sample of young CP, whereas the CPs from four 24-month-old mice were pooled together as the sample of old CP.

first: Yifei

last: Zhou

first: Yifan

last: Chen


title: Generation of expandable multipotential distal lung progenitors from human pluripotent stem cells that model idiopathic pulmonary fibrosis [scRNA-Seq]

summary: Human lungs contain unique cell populations in distal respiratory airways and terminal bronchioles (RA/TRB) that accumulate in patients with lung injury and idiopathic pulmonary fibrosis (IPF), a lethal lung disease. As these populations are absent in rodents, deeper understanding requires a human in vitro model. Here we convert human pluripotent stem cells into expandable spheres, called induced respiratory airway progenitors (iRAPs), consisting of  ~99% RA/TRB-associated cell types. One hPSC can give rise to 1010 iRAP cells. We differentiate iRAPs through a stage consistent with transitional AT2 like cells into a population corresponding to mature AT1 cells with 95% purity. iRAPs with deletion of HPS1, which causes pulmonary fibrosis in humans, replicate the aberrant differentiation and recruitment of profibrotic fibroblasts observed in IPF, indicating that intrinsic dysfunction of RA/TRB-associated alveolar progenitors contributes to HPS1-related IPF. iRAPs may provide a system suitable for IPF drug discovery and validation.

overall_design: We performed single cell RNA sequencing on iRAPs, iAT1 and transitional type 2 alveolar epithelial. The samples were dissociated to single cells and resuspended at a concentration of 5000 cells/ul for sequencing.

last: Matkovic Leko

first: John

middle: W

last: Murray


title: Repetitive transcranial magnetic stimulation induces cortical layer, brain region, and protocol dependent neural plasticity [Spatial transcriptomics]

overall_design: Wild-type male C57BL/6J mice were treated with a single session of intermittent theta-burst (iTBS), continuous theta-burst (cTBS), or sham stimulation, with four mice used for each stimulatio group. Animals were euthanised three hours post-stimulation and the brains were removed and dissected along the midline. Coronal sections from the right brain hemisphere, taken approximately 0.26 - 0.74 mm anterior from bregma, were analysed using spatial transcriptomics.


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

city: Murcia

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: ChIP experiments to determine H3K4me3, H3K9me3 and H2A.Z distribution in the R. microsporus genome as well as the binding profile of P1 (mCherry-tagged)

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

last: Grigoriev

first: Franciscos

last: Nicolás-Molina

first: Victoriano

last: Garre