title: Omics analysis combined with experiments provides insights into ovulation [II]

city: Wuhan

first: changjiu

last: he

state: Hubei

address: 1 Shizishan street, Hongshan District

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

summary:
Running title: More insights into ovulation
Purpose:Ovulation is the process by which mature follicles release fertilized oocytes under the stimulation of gonadotropin. This involves the precise interaction and destiny of various cells in the follicle. Granulosa cells (GCs) are the only cells that recognize and respond to ovulation LH (or HCG) signals. Therefore, the classification and deep interpretation of genes in GCs under LH surge stimulation is the key to understand ovulation.
Methods: In this study, RNA-seq, Q-PCR, Western blot, gene knockout, gene knockout and other experimental techniques were used to conduct trend and classification analysis of the genes regulated by ovulation signal of LH at the cellular and individual levels. Genes that may be involved in ovulation were screened, identified and were selected for functional verification.
Results:(1) Firstly, 7104 and 347 mRNA and Long noncoding RNA (LncRNA) that may be involved in ovulation activity were screened at the gene level by transcriptome sequencing technology, respectively. According to gene expression, they were divided into activated, inhibited and transient activated gene expression patterns. 44 secreted proteins, 62 transcription factors, 22 periodic expression characteristic genes, 10 ovulation process unknown genes, 16 LncRNA-target gene cis pair combinations and 41 highly expressed LncRNA were identified and listed in the three models;(2) The functions of LncRNA Gm12840 and Gm20186 were studied at the cellular level. The results showed that knockdown Gm12840/20186 not only inhibited the proliferation and hormone synthesis of GCs, but also induced cell apoptosis;(3) The function of LncRNA Gm12840 was further studied in mice, and Gm12840 knockout mice were constructed by CRISPR/CAS9 technology: Results It was found that Gm12840 knockout significantly increased the number of antral follicles and ovulation, and significantly inhibited the number of atretic follicles and antral follicles not discharged after ovulation. Gm12840 knockout significantly increased litter size at 2-3 months of age, but also significantly inhibited litter size at 7-9 months of age. Meanwhile, Gm12840 knockout also significantly inhibited the number of follicles growing in the ovary of 11-month-old mice;(4) Finally, transcriptomic sequencing analysis of wilt-type and Gm12840-/- mouse GCs showed 349 genes were differentially expressed. KEGG enrichment analysis and WB results showed that Gm12840 knockout enhanced mTOR and MAPK signals.
Conclusions:The above results screened and identified genes with potential research value during ovulation process, and took LncRNA Gm12840 as an example to verify their functions at the cell and individual levels, providing reference for further revealing the ovulation process.

overall_design: Granulosa cell RNA  profiles of  gonadotropin-induced ovulation in mice.There are 9 samples represented three time points 0h (n=3), 1h (n=3) and 6h (n=3)

first: Qinghua

first: Yingjun

first: Xiaodong

last: Wang

first: Changjiu

last: He


title: LncRNA expression profile is associated with neoadjuvant chemotherapy resistance in luminal B breast cancer

status: Public on Aug 27 2024

city: TLALPAN

first: Cristian

last: Arriaga

state: Federal District

address: AV. SAN FERNANDO, COL. SECCIÓN XVI

country: Mexico

institute: Mexican National Cancer Institute

type: Expression profiling by high throughput sequencing

summary:
Purpose: Identified the expression profile of lncRNAs associated to neoadjuvant chemotherapy response in 47 luminal B tumors of locally advanced breast cancer patients
Methods: We implemented the transcriptomic analysis from 47 luminal B breast cancer samples by paired-end RNA-Seq, as a case-control study (responders vs nonresponders group). Differential expression analysis for lncRNA and mRNA were made to identify lncRNA as predictive biomarkers.
Results: We identified a signature of lncRNAs associated with nonresponders group. Additionally, we identified the pathways were differentially expressed lncRNA and mRNA are associated in neoadjuvant chemotherapy response. Additionally, we proposed the clinical application of lncRNA GATA3-AS1 as a predictive biomarker to neoadjuvant chemotherapy response in luminal B breast cancer patients detected by RNA-ISH.
Conclusion: we propose the clinical utility of lncRNA GATA3-AS1 detected by RNA-ISH to identify luminal B breast cancer patients that will not respond to neoadjuvant chemotherapy.

overall_design: Transcriptomic analysis of 47 tumor samples from luminal B breast cancer mexican patients in a case-control study (responders vs nonresponders group), in order to identify lncRNA associated to neoadjuvant chemotherapy response.

first: Miguel

last: González-Woge

first: Laura

last: Contreras-Espinosa

first: José

last: Antonio García-Gordillo

first: Sergio

last: Aguilar-Villanueva

first: Enrique

last: Bargallo-Rocha

first: Paula

last: Cabrera-Galeana

first: Tania

last: Vasquez-Mata

first: Ximena

last: Cervantes-López

first: Diana

last: Sofía Vargas-Lías

first: Rogelio

last: Montiel-Manríquez

first: Luis

last: Bautista-Hinojosa

first: Rosa

last: Rebollar-Vega

first: Clementina

last: Castro-Hernández

last: María Álvarez-Gómez

first: Inti

last: Alberto De La Rosa-Velázquez

first: Francisco

last: Jiménez-Trejo

last: Arriaga-Canon

last: Alonso Herrera


title: Endocrine cell type sorting and mature architecture in the islets of Langerhans require expression of Roundabout receptors in β cells

status: Public on Aug 26 2024

city: Madison

first: Barak

last: Blum

state: Wisconsin

address: 4551 WIMR II, 1111 Highland Ave.

country: USA

institute: University of Wisconsin-Madison

summary: The spatial architecture of the islets of Langerhans is hypothesized to facilitate synchronized insulin secretion among β cells, yet testing this in vivo in the intact pancreas is challenging. Robo βKO mice, in which the genes Robo1 and Robo2 are deleted selectively in β cells, provide a unique model of altered islet spatial architecture without loss of β cell differentiation or islet damage from diabetes. Combining Robo βKO mice with intravital microscopy, we show here that Robo βKO islets have reduced synchronized intra-islet Ca2+ oscillations among β cells in vivo. We provide evidence that this loss is not due to a β cell-intrinsic function of Robo, mis-expression or mis-localization of Cx36 gap junctions, or changes in islet vascularization or innervation, suggesting that the islet architecture itself is required for synchronized Ca2+ oscillations. These results have implications for understanding structure-function relationships in the islets during progression to diabetes as well as engineering islets from stem cells.

overall_design: Mouse β cell mRNA profiles of P13 Robo1∆; Robo2-flx; Rosa26-H2B-mCherry; Ucn3-Cre neonates

first: Melissa

middle: T

last: Adams

first: Sutichot

middle: D

last: Nimkulrat


title: Early detection of food safety and spoilage incidents based on live microbiome profiling and qPCR-based monitoring of indicators

city: Haifa

first: May

last: Cohen Hakmon

address: Shikago

country: Israel

institute: Technion

summary: Early detection of spoilage microorganisms and food pathogens is of major importance in preventing food recalls and foodborne outbreaks. Although constant effort is invested in developing sensitive methods for rapid microbial detection, none of the current methods enables the detection of food pathogens within a few hours; therefore, development of innovative early-warning food-testing strategies are needed. Herein, we assessed a novel strategy that harnesses the microbiome signature of a food product to determine deviations in the abundance of particular community members and detect production defects. Employing the production process of barbecued (BarBQ) pastrami as a model, we characterized the microbiome profiles of the product along the production line using next-generation sequencing of the 16S rRNA gene, concentrating on the live microbiota. Following the establishment of a microbiome dataset representing a properly produced product, we were able to identify shifts in the microbiome profile of a defective batch produced under potassium lactate deficiency. With the identification of Vibrio and Lactobacillus as potential indicator bacteria for potassium lactate deficiency, rapid qPCR assays were designed for their quantification. Aligned with the microbiome profiling results, these qPCR assays were effective for rapid identification of a defective production event. This implies the use of rapid quantification targeting microbiome profile-derived indicator bacteria for in-house detection of defective batches and identification of food-safety and quality events with results obtained on the same day. The suggested strategy should pave the way toward safer and more efficient food-production systems.

overall_design: Samples of 16S V3 and V4 region DNA from pastrami production process were sequenced using the Illumina MiSeq platform

first: Keren

last: Buhnik-Rosenblau

first: Hila

last: Hanani

last: Korach-Rechtmana

first: Dagan

last: Mor

first: Erez

last: Etkin

first: Yechezkel

last: Kashi


title: The hepatic overexpression of C2-AKT ameliorates obesity-induced insulin resistance

city: Incheon

first: Byung-Chul

last: Oh

address: 155 Gaetbeol-ro, Yeonsu-gu

department: Physiology

country: South Korea

institute: Lee Gil Ya Cancer and Diabetes Institute,Gachon University

summary: Metabolic disorders, such as obesity and diabetes, have become increasingly prevalent worldwide, posing significant challenges to public health. Insulin resistance, a hallmark of these disorders, is characterized by an impaired response to insulin in target tissues, leading to dysregulated glucose and lipid metabolism. Although the pathogenesis of insulin resistance is complex and multifactorial, mounting evidence suggests that disrupted intracellular calcium (Ca2+) homeostasis plays a crucial role in its development. To elucidate the molecular mechanisms underlying the improved metabolic profiles in C2-AKT overexpression mice, we performed RNA-seq on liver tissues from both control and C2-AKT mice

overall_design: To examine the effects of C2-AKT specifically in hepatocytes, we crossed ROSA26-C2-AKT mice with Alb-Cre mice. In this cross, Cre recombinase, driven by the liver-specific albumin (Alb) promoter, enables targeted C2-AKT expression in hepatocytes, providing a valuable tool for studying its function and regulation in liver physiology. At 8 weeks of age, we fed 8-week-old male C2-AKT mice or control mice with a high-fat diet (HFD) for 10 weeks.

first: OK-HEE

last: KIM

first: Jin

middle: W

last: Lee


title: Spatial analysis reveals distinct immune phenotypes and tertiary lymphoid structure-like aggregates in pediatric acute myeloid leukemia [Nanostring PanCancer IO 360]

city: Utrecht

first: Joost

last: Koedijk

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

summary: Comparison of immune-infiltrated  bone marrow samples (n=6) with immune-depleted bone marrow samples (n=17) of pediatric acute myeloid leukemia patients using the Nanostring PanCancer IO 360 panel.

overall_design:
6 immune-infiltrated and 17 immune-depleted FFPE bone biopsies (the non-leukemic controls’ median value of cytotoxic T cells was used as the cut-off value) from a cytogenetically representative cohort of pediatric AML patients were used for this experiment. After passing quality control, raw data were normalized using ROSALIND® according to Nanostring’s recommendations (https://rosalind.bio/; San Diego, CA, USA). Normalized data were uploaded to the online iDEP platform and differentially expressed genes between immune-infiltrated and immune-depleted samples were identified using DEseq2 with a false-discovery rate (FDR) cut-off of 0.05 and a minimum fold change of 2 (integrative Differential Expression and Pathway analysis; http://bioinformatics.sdstate.edu/idep96/; V.0.96; Ge, Son & Yao, 2018). Pathway analysis was performed using parametric gene set enrichment analysis with the GO Biological Processes gene set with an FDR of 0.05 (Ashburner et al., 2000; The Gene Ontology Consortium, 2020). The abundance of M2-like macrophages was estimated using a published gene signature of M2-like macrophages compared to M1-like macrophages, inside the TIDE environment (tide.dfci.harvard.edu/; Beyer et al., 2020; Jiang et al., 2018). Similarly, the T cell inflamed gene expression profile, the CD8-, IFN-γ-, and TIDE scores were all calculated using TIDE.

>>>Submitter states: Patients did not provide consent for open access of raw data. Therefore, raw data are made available in a controlled manner via the EGA platform (https://ega-archive.org/). <<<

middle: B

first: Olaf

last: Heidenreich


title: ST2+ T-regulatory Cells in Renal Inflammation and Fibrosis following Ischemic Kidney Injury

city: Charlottesville

first: Vikram

last: Sabapathy

state: Virginia

address: 1340 Jefferson Park Ave., Pinn Hall, Room No: 4043

department: Center for Immunity, Inflammation and Regenerative Medicine

institute: University of Virginia

summary: Here, we delineated the role of the ST2 specifically in Treg cells, using murine renal injury models and kidney organoids.

overall_design: Differentially expressed gene analysis in sorted ST2-high, ST2-low and ST2KO Tregs was performed

first: Rahul

last: Sharma


title: MYC and p53 cooperate through VEGF signaling to repress cytotoxic T cell and immunotherapy responses in prostate cancer

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: To study the genetic factors that influence the immune landscape of castration-resistant prostate cancer (CRPC), we utilized a flexible, electroporation-based system to introduce genetic alterations relevant to human disease directly into the prostate glands of mice. These electroporation-based genetically engineered mouse models (EPO-GEMM) recapitulate features of traditional models, and allow us to investigate distinct genetic subtypes of prostate cancer within an intact tumor-immune microenvironment. We observed differences between genetic subtypes of CRPC, with MYC-driven subtypes exhibiting a "cold" immune landscape compared to others. Interestingly, we found that the compound loss of different tumor suppressors such as Pten or p53 with MYC further impacts the inflammatory profile of prostate cancer, with MYC and p53  (MP) alterations cooperating to drive VEGF expression and immune suppression. VEGF signaling blockade resulted in re-activation of cytotoxic T cell anti-tumor immunity and restored sensitivity to immunotherapy in MP CRPC. Thus, by leveraging the power of EPO-GEMMs to generate distinct subtypes of CRPC, our studies reveal a functional role for VEGF signaling in driving prostate cancer immune evasion and validate the VEGF pathway as an actionable therapeutic target in MYC and p53 altered prostate cancer.

overall_design: For RNA-seq analysis of the transcriptional profiles of PtPRb EPO-GEMM prostate tumors, total RNA was extracted from bulk tissue using the RNeasy Mini Kit (Qiagen). Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.

first: Katherine

middle: C

last: Murphy

first: Kelly

last: DeMarco

first: Lin

last: Zhou

first: Yvette

last: Lopez

first: Yu-jui

first: Junhui

last: Li

first: Shi

last: Bai

first: Karl

last: Simin

first: Lihua

last: Zhu

first: Arthur

middle: M

last: Mercurio

first: Marcus

last: Ruscetti


title: Secretome from iPSC-derived MSCs exerts proangiogenic and immunosuppressive effects to alleviate radiation-induced vascular endothelial cell damage

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: Background: Radiation therapy is the standard of care for central nervous system tumours. Despite the success of radiation therapy in reducing tumour mass, irradiation (IR)-induced vasculopathies and neuroinflammation contribute to late-delayed complications, neurodegeneration, andpremature ageing in long-term cancer survivors. Mesenchymal stromal cells (MSCs) are adult stem cells that facilitate tissue integrity, homeostasis, and repair. Here, we investigated the potential of the iPSC-derived MSC(iMSC) secretome in immunomodulation and vasculature repair in response to radiation injury utilizing human cell lines. Methods: We generated iPSC-derived iMSC lines and evaluated the potential of their conditioned media (iMSC CM) to treat IR-induced injuries in human monocytes (THP1) and brain vascular endothelial cells (hCMEC/D3). We further assessed factors in the iMSC secretome, their modulation, and the molecular pathways they elicit. Results: Increasing doses of IR disturbed endothelial tube and spheroid formation in hCMEC/D3. When IR-injured hCMEC/D3 (IR ≤ 5 Gy) were treated with iMSC CM, endothelial cell viability, adherence, spheroid compactness, and proangiogenic sprout formation were significantly ameliorated, and IR-induced ROS levels were reduced. iMSC CM augmented tube formation in cocultures of hCMEC/D3 and iMSCs. Consistently, iMSC CM facilitated angiogenesis in a zebrafish model in vivo. Furthermore, iMSC CM suppressed IR-induced NFκB activation, TNF-α release, and ROS production in THP1 cells. Additionally, iMSC CM diminished NF-kB activation in THP1 cells cocultured with irradiated hCMEC/D3, iMSCs, or HMC3 microglial lines. The cytokine array revealed that iMSC CM contains the proangiogenic and immunosuppressive factors MCP1/CCL2, IL6, IL8/CXCL8, ANG (Angiogenin), GROα/CXCL1, and RANTES/CCL5. Common promoter regulatory elements were enriched in TF-binding motifs such as androgen receptor (ANDR) and GATA2. hCMEC/D3 phosphokinome profiling revealed increased expression of pro-survival factors, the PI3K/AKT/mTOR modulator PRAS40 and β-catenin in response to CM. The transcriptome analysis revealed increased expression of GATA2 in iMSCs and the enrichment of pathways involved in RNA metabolism, translation, mitochondrial respiration, DNA damage repair, and neurodevelopment. Conclusions: The iMSC secretome is a comodulated composite of proangiogenic and immunosuppressive factors that has the potential to alleviate radiation-induced vascular endothelial cell damage and immune activation.

overall_design: We generated iPSC-derived iMSC lines and evaluated the potential of their conditioned media (iMSC CM) to treat IR-induced injuries in human monocytes (THP1) and brain vascular endothelial cells (hCMEC/D3). We further used bulk RNA sequencing to assess factors in the iMSC secretome, their modulation, and the molecular pathways they elicit

first: Kshama

last: Gupta

first: Takahisa

last: Kanekiyo


title: Defining the mechanism of systemic NK cell dysfunction associated with melanoma lung metastasis in spontaneous and experimental models

city: Seoul

first: Jinju

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu

institute: University of Ulsan

summary: We isolated dysfunctional splenic NK cells in mice with melanoma metastasis and performed bulk RNA-seq with the NK cells to explore the mechanism of NK cell dysfunction with a special focus on signaling pathway linked to NK cell cytotoxicity.

overall_design: Mice were subcutaneously injected with B16F10 melanoma cells and monitored for primary tumor growth, splenic NK cell dysfunction and spontaneous lung metastasis. After confirmed metastatic tumor progression, dysfunctional splenic NK cells were isolated, subjected to bulk RNA-seq, and analyzed with differential expressed genes linked to NK cell dysfunction.

first: WooSeon

last: Choi

first: Eunbi

last: Yi

first: HunSik

last: Kim


title: Epigenome-wide DNA methylation analysis in inflammatory breast cancer

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation analysis (Infinium Human Methylation EPIC BeadChip platform, Illumina) performed in 24 IBCs and six normal breast tissues.

overall_design: Genomic DNA was isolated from 24 fresh frozen macrodissected IBC tissue biopsies and six surrounding normal breast frozen tissues using the QIAsymphony kit (Qiagen, Valencia, CA, USA). The genome-wide DNA methylation profiling of 24 IBC and six normal breast samples was evaluated using the Infinium Human Methylation EPIC BeadChip platform (Illumina, USA), according to the manufacturer recommendations.

first: Flavia

middle: L

last: Faldoni

middle: A

first: Silvia

middle: R

last: Rogatto


title: Temporal and spatial frameworks supporting plant responses to vegetation proximity

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

country: Spain

institute: IBMCP, CSIC

summary: After perception of vegetation proximity by the phytochrome photoreceptors, shade-avoider plants initiate a set of responses known as the Shade Avoidance Syndrome (SAS). Shade perception by the phytochrome B (phyB) photoreceptor unleashes the PHYTOCHROME INTERACTING FACTORs (PIFs) and initiates SAS responses. In Arabidopsis thaliana seedlings, shade perception involves rapid and massive changes in gene expression, increases auxin production and promotes hypocotyl elongation. Other components, such as phyA and ELONGATED HYPOCOTYL 5 (HY5), also participate in the shade regulation of the hypocotyl elongation response by repressing it. However, it remains unclear why and how so many regulators with either positive or negative activities modulate the same response. Our physiological, genetic, cellular and transcriptomic analyses showed that (1) these components are organized in two main branches or modules (phyA/HY5 and PIFs/HFR1/SAV3) and (2) the connection between them is dynamic and changes with the time of shade exposure. We propose a model for the regulation of shade-induced hypocotyl elongation in which the temporal and spatial functional importance of the various SAS regulators analyzed in here helps to explain the co-existence of differentiated regulatory branches with overlapping activities. Despite the temporal differences observed between phyA, HY5 and PIFs/HFR1/SAV3, their activities overlap and eventually converge in controlling hypocotyl elongation. Hence, we aimed to further investigate possible convergence points between these two groups of regulators.To expand our understanding of the role and interaction of HY5 and PIF4, PIF5 and PIF7 (PIF457) activities, we carried out RNA sequencing (RNA-seq) of seedlings exposed to different times of shade exposure of four genotypes: wild-type (Col-0), the single mutant hy5, the triple pif457 and the quadruple hy5 pif457.

overall_design: Seedlings of wild-type (Col-0), hy5, pif457 and hy5 pif457 were grown from the day of germination under continuous white light (W). On day seven, seedlings were transferred to W enriched in far-red light (W+FR). Three biological replicas of seedlings were harvested at 0, 1 and 8 h of W+FR (about 35 mg per sample) and frozen in liquid nitrogen (FOUR genotypes x THREE time points x THREE biological replicas = 36 samples). RNA was extracted using commercial kits. Total RNA libraries were prepared for each biological replicate, genotypes and treatments (36 samples s and sequenced at the Centre Nacional d’Anàlisi Genòmica (CNAG-CRG) on an Illumina NovaSeq6000 in paired-end 50 bp read length.

first: Pedro

last: Pastor-Andreu

first: Jordi

last: Moreno-Romero

first: Anna

last: Esteve-Codina

first: Beatriz

last: Martín-Mur

first: Jaume

middle: F

last: Martinez-Garcia


title: Aluminum-induced terminal differentiation in Arabidopsis roots requires the stem cell niche transcription factor ETHYLENE RESPONSE FACTOR 115

city: Riverside

first: Shiyang

last: He

state: CA

address: 3401 Watkins Drive, Boyce Hall

department: Biochemistry

institute: UCR

summary: Aluminum-dependent stoppage of root growth and terminal differentiation depend on a functional DNA damage response pathway comprised of the master cell cycle checkpoint ATR (ATAXIA TELANGIECTASIA-MUTATED AND RAD3-RELATED) and p53-like transcription factor SOG1 (SUPPRESSOR OF GAMMA RADIATION 1). Mutational loss of either results in failure to trigger endoreduplication following Al treatment even in the Al-hypersensitive mutant, als3-1. Transcriptome analyses were used to identify several Al-induced SOG1-regulated targets as candidate mediators of Al-dependent growth arrest including SMR5, SMR7, ERF114 and ERF115. Analysis of these factors either as loss-of-function/silenced mutants or by overexpression in the als3-1 background indicates ERF115, a key transcription factor involved in stem cell niche restoration, is important for the switch from an actively growing root to one that has terminally differentiated. Consistent with this, a putative ERF115 ortholog and other DDR factors from barley are also upregulated following Al exposure, suggesting a conserved role for this ATR-dependent pathway in response to Al. In contrast to other ts show that ERF115 and related family members are important determinants for the switch to endoreduplication in the root tip following Al exposure and a central output of the ATR-mediated pathway in Al response.

overall_design: SOG1 is a transcription factor that is part of the Al-triggered DDR and is required for terminal differentiation of the root, it is expected that one or more transcriptional target(s) of SOG1 mediate this developmental switch from normal cell cycle progression to endocycling. In order to identify this type of SOG1 targets, an RNAseq approach was undertaken to compare transcript profiles of Al-treated Columbia-0 (Col-0) wt, als3-1 and sog1-7, which is a previously documented loss-of-function mutant for SOG1 that is Al tolerant (Sjogren et al., 2015). Comparison of transcript profiles for als3-1 and sog1-7 following Al treatment has allowed us to greatly reduce the number of potential genes related to stoppage of root growth following Al exposure.

first: Taylor

middle: J

last: Meyer

first: Jernej

last: Murn

first: Paul

last: Larsen


title: Omics analysis combined with experiments provides insights into ovulation [I]

first: changjiu

last: he

country: China

overall_design: Granulosa cell RNA profiles of 21-day old wild type (WT) and knockout (Gm12840-/-) mice. There are 6 samples, namely WT (n=3), Gm12840-/- (n=3)

first: Qinghua

last: Liu

first: Yingjun

last: Chen

first: Xiaodong

last: Wang

first: Changjiu


title: Omics analysis combined with experiments provides insights into ovulation

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

overall_design: Refer to individual Series


title: G9a/GLP Inhibition Promotes Derivation of Functional CAR T cells from Pluripotent Stem Cells

city: Boston

first: Marcelo

last: Falchetti

state: Massachusetts

address: 300 Longwood Ave Karp Family Building, 7th Floor

institute: Boston Children's Hospital

summary: Elucidating mechanisms of T cell development can guide in vitro T cell differentiation from Induced Pluripotent Stem Cells (iPSCs) and facilitate off-the-shelf T cell-based immunotherapies. Using a stroma-free human iPSC-T cell differentiation platform, we screened for epigenetic modulators that influence T cell specification and identified the H3K9-directed histone methyltransferases G9a/GLP as repressors of T cell fate. We show that G9a/GLP inhibition during specific time windows of differentiation of hematopoietic stem and progenitor cells (HSPCs) skews cell fates towards lymphoid lineages. Inhibition of G9a/GLP promotes the production of lymphoid cells during zebrafish embryonic hematopoiesis, demonstrating the evolutionary conservation of G9a/GLP function. Importantly, G9a/GLP inhibition facilitates the generation of robust iPSC-T cells that bear transcriptional similarity to peripheral blood αβ T cells. When engineered to express chimeric antigen receptors, the epigenetically engineered iPSC-T cells exhibit enhanced effector functions in vitro and durable antitumor activity in a xenograft mouse model.

overall_design: Human iPSCs were differentiated into T cells and treated with DMSO or UNC0224 at different time windows (week 0-2 or week 0-4). Cell were collected on multiple time points (week2, week4, before and after T cell activation) and scRNA-seq experiments were performed.


title: Evaluation of anti-vector immune responses to adenovirus mediated lung gene therapy and modulation by αCD20

city: New Orleans

first: Jay

middle: K

last: Kolls

state: LA

address: 333 S Liberty St

department: Medicine

institute: Tulane University

summary: Although the last decade has seen tremendous progress in drugs that treat cystic fibrosis (CF) due to mutations that lead to protein misfolding, there are approximately 8-10% of subjects with mutations that result in no significant CFTR protein expression demonstrating the need for gene editing or gene replacement with mRNA or vector-based approaches.  A limitation for vector-based approaches is the limitation of neutralizing humoral responses. Given that αCD20 has been used to manage post-transplant lymphoproliferative disease in CF subjects with lung transplants, we studied the ability of αCD20 to module both T and B cell responses in the lung to one of the most immunogenic vectors, E1-deleted adenovirus serotype 5. We found that αCD20 significantly blocked luminal antibody responses and efficiently permitted re-dosing. αCD20 had more limited impacts in the T-cell compartment, but reduced tissue resident memory T cell responses in bronchoalveolar lavage fluid.  Taken together, these pre-clinical studies suggest that αCD20 could be re-purposed for lung gene therapy protocols to permit re-dosing.

overall_design: For our scRNA-seq experiment, we compared naïve spleen cells from a publicly available database to interstitial T-cells isolated from mouse lung 4 weeks after lung-directed delivery of a human Adenovirus type 5 (HAdV) vector. To isolate mouse lung cells, mice were injected with anti-CD45.2-PE 2 minutes prior to euthanasia to label intravascular blood cells. Lungs were dissociated by mechanical disruption and digestion with collagenase I + DNAse. After filtration and RBC lysis, cells were subjected to magnetic negative selection using anti-PE microbeads and positive selection using anti-CD3 microbeads (Miltenyi). The resulting cells were analyzed by scRNA-seq, using a 5' VDJ and Gene Expression Profiling assay.

first: Robert

last: Clark

first: Felix

last: Rabito

first: Ferris

last: Munyonho

first: Remcho

last: Parks

first: Shamima

last: Khatun

first: Kejing

last: Song


title: Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler

city: Ithaca

first: Justin

middle: Sungsoo

last: Cha

state: NY

address: 526 Campus Rd

department: Computational Biology

institute: Cornell University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The SWR1 chromatin remodeling complex (SRCAP in humans) is recruited to +1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. Here we use cryo-EM to resolve the structural basis of the SWR1 interaction with free DNA, revealing a distinct open conformation of the Swr1 ATPase that enables sliding from accessible DNA to nucleosomes. A complete structural model of the SWR1-nucleosome complex illustrates critical structure-function roles for Swc2 and Swc3 subunits in oriented nucleosome engagement by SWR1. Moreover, an extended DNA-binding α -helix within the Swc3 subunit enables sensing of nucleosome linker length and is essential for SWR1 promoter-specific recruitment and activity. The previously unresolved N-SWR1 subcomplex forms a flexible extended structure enabling multivalent recognition of acetylated histone tails by reader domains to further direct SWR1 towards the +1 nucleosome. Altogether, our findings provide a generalizable mechanism for promoter-specific targeting of chromatin and transcription complexes.

overall_design: Chromatin Immunoprecipitation DNA-sequencing with exonuclease treatment (ChIP-exo) for histone variant H2A.Z and chromatin remodeler Swr1 in S. Cerevisiae with genetic modifications in the SWR1 complex

first: Louder

last: Robert

first: Park

last: Giho

first: Ye

last: Ziyang

first: Cha

last: Justin

first: Gardner

last: Anne

first: Lei

last: Qin

first: Ranjan

last: Anand

first: Höllmüller

last: Eva

first: Stengel

last: Florian

first: Pugh

last: B Franklin

first: Wu

last: Carl


title: Transcriptomic analysis and high throughput functional characterization of human induced pluripotent stem cell derived sensory neurons  (scRNA-Seq)

city: Minneapolis

first: Vincent

last: Truong

state: MINNESOTA

address: 2112 Broadway ST NE, STE 135

institute: Anatomic Incorporated

summary: Peripheral sensory neurons are a primary effector in pain neurotransmission, and have become a useful cellular model for the study of pain. While rodent tissue has historically served as a source of these neurons, it has become increasingly clear that pain mechanisms in rodents and humans are substantially divergent. Sensory neurons harvested from cadaveric human tissue serve as a superior translational model for studying pain mechanisms, however their relative paucity limits their widespread utility. Theoretically, sensory neurons manufactured from human pluripotent stem cells (hPSCs) could help bridge this translational gap given their relative abundance and potential similarity to primary human tissue. However, hPSC-derived sensory neurons manufactured with the most common methodologies correlate poorly to human tissue both transcriptionally and functionally. In the present work, we compare a novel population of hPSC-derived sensory neurons to previously published datasets and find this novel population to more closely resemble human primary dorsal root ganglia transcriptionally. Furthermore, we evaluate the heterogeneity of this novel population via single nucleus RNA sequencing and find it resembles specific nociceptor and mechanoreceptor subsets found in vivo. Finally, we assay the functionality of this population with high throughput automated patch clamp electrophysiology with respect to voltage-gated sodium (Nav) and potassium channels (Kv), and ligand-gated ionotropic GABA and P2X receptors. Overall, we find this population of hPSC-derived sensory neurons to be of relatively high fidelity, and suitable for interrogating numerous potential pain targets on a fully humanized platform.

overall_design: Three lots of RealDRG manufactured from the same hiPSC line were thawed in Senso-MM (Anatomic Incorporated, #1030) at 100,000 neurons/cm2 in T25 format. Total RNA was collected at weekly timepoints for each line through four weeks.

first: Patrick

last: Walsh

first: Jackson

last: Brougher

first: Dale

last: George


title: Transcriptomic analysis and high throughput functional characterization of human induced pluripotent stem cell derived sensory neurons (bulk RNA-Seq)


title: Blocking YY1 in adipocytes decouples thermogenic capacity from metabolic benefits by generating spermidine

city: Nanjing

first: Kai

last: Li

address: #818, East Tianyuan Road

institute: Nanjing Medical University

summary: Traditional ideas hold that the accumulation of mitochondria in thermogenic adipose tissue, namely brown and beige fat, helps to increase energy expenditure (EE), thereby alleviating obesity and metabolic disorders. However, recent studies in mice have shown that knocking out key proteins that maintain mitochondrial function can inhibit the activation of thermogenic fat while somehow protecting the mice from high-fat diet (HFD)–induced metabolic disorders. Therefore, the specific role of adipose mitochondria in metabolic benefits needs further analysis. Here, our use of non-biased sequencing-based screening identified YY1 as a key player in maintaining mitochondrial function in thermogenic adipose tissue. YY1 promotes the transcription of electron transport chain (ETC) genes during thermogenesis; thus, YY1 adipose knockout (YAKO) mice showed reduced body temperature and EE under cold stress. Interestingly, YAKO mice showed alleviation of HFD-induced obesity and insulin resistance, which can be attributed to a repression of adipose tissue inflammation. Metabolomic analysis revealed that blocking YY1 in adipocytes directs glucose metabolism toward lactate, enhances the uptake of glutamine, and promotes the production of anti-inflammatory spermidine. Blocking spermidine production can reverse the beneficial metabolic effects observed in YAKO mice. In summary, our findings reveal a metabolic reprogramming pathway centered on adipose mitochondria; that is, although blocking YY1 reduced the mitochondria content, it generated spermidine and alleviated adipose inflammation, therefore leads to a thermogenic capacity-metabolic benefits uncoupling phenomenon.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for YY11 in mature adipocytes seperated from iWAT of wild type C57 mice, either after 7 days cold stress or not.

first: Suyang

last: Wu


title: Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State

first: Jason

middle: Paul

last: Smith

state: VA

address: 409 Lane Rd

department: Pediatrics


title: High-Throughput Transcriptomics Toxicity Assessment of Eleven Data-Poor Bisphenol A Alternatives

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

summary: Bisphenol A (BPA), a widely used chemical in the production of plastics and epoxy resins, has garnered significant attention due to its association with adverse health effects, particularly its endocrine-disrupting properties. Regulatory measures aimed at reducing human exposure to BPA have led to a proliferation of alternative chemicals used in various consumer products. While these alternatives serve to reduce BPA exposure, concerns have arisen regarding their safety and potential toxicity as regrettable substitutes. Previous efforts have demonstrated that in vitro high-throughput transcriptomics (HTTr) studies can be used to assess the endocrine-disrupting potential of BPA alternatives, and this strategy produces transcriptomic points-of-departure (tPoDs) that are protective of human health when compared to the PODs from traditional rodent studies. In this study, we leveraged in vitro HTTr advancements to assess the toxicity of eleven data-poor legacy chemicals sharing structural similarities to BPA. Human breast cancer MCF-7 cells were exposed to BPA and 11 alternatives at concentrations ranging from (0.1 - 25 µM) to assess toxicity. Analysis of global transcriptomic changes and a previously characterized estrogen receptor alpha (ERα) biomarker signature revealed that 9/11 chemicals were bioactive. One of the chemicals (2,4’-Bisphenol A) activated the ERα biomarker at the same concentration as BPA (i.e., 4,4’-BPA) but was deemed to be more potent as it induced global transcriptomic changes at lower concentrations. These results are addressing data gaps in ongoing screening assessments to identify BPA alternatives with hazard potential and are helping to identify potential candidates to serve as safer alternatives.

overall_design: Three TempO-Seq plates were sequenced for this study to investigate the gene expression changes of BPA and 11 BPA alternatives on MCF-7 cells. Five concentrations of each chemical were tested in quadruplicate. In addition, technical controls (reference RNA; media only; cells with no treatment), solvent controls (dimethylsulfoxide, methanol), negatives controls (dexamethasone, Bis(4-chlorophenyl) sulfone), and positive controls (estradiol) were sequenced.

first: Marc

last: Beal

first: Melanie

last: Coughlan

first: Andrée

last: Nunnikhoven

last: Gagné

first: Tara

middle: S

last: Barton-Maclaren

first: Lauren

last: Bradford

first: Andrea

last: Rowan-Carroll

first: Andrew

last: Williams


title: The axillary lymphoid organ - an external, experimentally accessible immune organ in the zebrafish

city: Bethesda

first: James

last: Iben

state: MD

address: 10 CENTER DR

department: NICHD

institute: NIH

summary: Lymph nodes and other secondary lymphoid organs play critical roles in immune surveillance and immune activation in mammals, but the deep internal locations of these organs makes it challenging to study dynamic cellular mechanisms of immune cell interaction with pathogens or other host tissues such as the vasculature in living animals.  Here, we describe a previously uncharacterized external immune organ located near the base of the zebrafish pectoral fin, the pectoral axillary lobe (PAL), with a variety of features that make it ideally suited for studying immune cell dynamics in vivo.   This small, transparent organ consists of an outer cortex teeming with immune cells and an inner medulla with a mesh-like network of fibroblastic reticular cells along which immune cells migrate, and a network of lymphatic vessels draining to a large adjacent lymph sac.  Noninvasive high-resolution imaging of transgenically marked immune cells can be carried out in the lobes of living animals, and the PAL is readily accessible to external treatment with antigens or pathogens.  This newly discovered tissue provides a superb model for dynamic live imaging of immune cells and their interaction with pathogens and surrounding tissues, including blood and lymphatic vessels.

overall_design: Single cell expression profiling by high throughput sequencing

first: Daniel

last: Castranova

first: Madeleine

last: Kenton

first: Aurora

last: Kraus

first: Christopher

last: Dell

first: Marina

middle: G

last: Venero

first: Jong

last: Park

first: Gilseung

first: Brant

last: Weinstein


title: the effect of UMI-77 on HGPS-MSCs gene expression during cellular senescence

city: changchun

first: yingying

last: sun

state: jilin

address: 5268 Renmin Street

department: school of life science

institute: northeast normal university

summary: Hutchinson-Gilford progeria syndrome (HGPS) is a rare and fatal disease manifested by premature aging and aging-related phenotypes, making it a disease model for physiological aging. The cellular machinery mediating age-associated hallmarks in HGPS remains largely unknown, resulting in limited therapeutic targets for HGPS treatment. In this study, we showed that deficiencies in mitophagy impaired mitochondrial quality and contributed to cellular phenotypes associated with aging in mesenchymal stem cells derived from HGPS patients (HGPS-MSCs). Mechanistically, we discovered that mitophagy affected the aging-related phenotypes of HGPS-MSCs by inhibiting the cGAS-STING-NF-ĸB pathway and the downstream transcription of senescence-associated secretory phenotype (SASP). Furthermore, by utilizing UMI-77, an effective inducer of mitophagy, we showed that mitophagy induction can alleviate aging-associated phenotypes in both HGPS mice and naturally aged mice. In summary, our results uncover that mitophagy defects mediate mitochondrial dysfunction and aging-associated phenotypes in HGPS models, highlight the function of mitochondrial homeostasis in HGPS progression, and suggest that mitophagy could be exploited as a promising therapeutic target for both HGPS and aging.

overall_design: To further elucidate how mitochondrial homeostasis affects aging phenotypes in HGPS-MSCs, we perform transcriptomic analysis on early-passage HGPS-MSCs (P3), late-passage HGPS-MSCs (P7), and UMI-77-treated late-passage (P7) HGPS-MSCs.


title: The Loss of an orphan Nuclear Receptor augments Wnt/β-Catenin signaling via epigenetic dysregulation that promotes Sp1 and Myc interactions in Hepatocellular Carcinoma Development [RNA-seq]

city: Little Rock

first: Kyounghyun

last: Kim

state: AR

address: Rm 318 CI.3329 4104 Outpatient Circle

department: Pharmacology & Toxicology

institute: University of Arkansas Medical Sciences

summary:
We previously reported that the nuclear receptor NR2E3 activates the tumor suppressor gene p53 by modulating chromatin accessibility. In this study, we further investigated the impact of NR2E3 deficiency on chromatin accessibility. We used FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements) analysis to find that NR2E3 loss increased chromatin accessibility in genomic regions interacting with various transcription factors, including Sp1. Additionally, NR2E3 loss enhanced chromatin accessibility and expression of crucial genes, such as JAK1 and PPARD, essential for WNT-β-catenin signaling pathway activation by facilitating interactions between Sp1 and Myc transcription factors at their promoters. Gene set enrichment analysis (GSEA) on mouse liver tumor tissues from wild-type and NR2E3 knockout mice confirmed that NR2E3 ablation activated WNT-β-catenin signaling pathways in vivo. Kaplan-Meier survival analysis using liver cancer patient data from two clinical datasets confirmed that patients with low NR2E3 expression exhibited increased WNT-β-catenin signaling activation, associated with adverse clinical outcomes. These findings highlight NR2E3 as a crucial tumor suppressor gene in hepatocellular carcinoma (HCC), primarily restraining WNT-β-catenin signaling pathway activation to maintain epigenetic homeostasis and contribute to HCC development. Our results prove NR2E3's critical role in liver cancer pathogenesis by regulating WNT-β-catenin signaling pathways and epigenetic equilibrium maintenance.
RNA-seq with WT and NR2E3 KO Liver Tumors

overall_design: Sung-Gwon,Lee

first: Chungoo


title: The loss of an orphan nuclear receptor NR2E3 augments Wnt/β-Catenin signaling via epigenetic dysregulation that promotes the Sp1-β catenin-p300 interactions in hepatocellular carcinoma.

summary: The orphan nuclear receptor NR2E3 (Nuclear receptor subfamily 2 group E, Member 3) is an epigenetic player essential for p53 activation during liver injuries through its modulation of chromatin accessibility. Nonetheless, a precise tumor suppressive and epigenetic role of NR2E3 in hepatocellular carcinoma (HCC) remains unclear. HCC patients expressing low NR2E3 exhibit unfavorable clinical outcomes, aligning with heightened activation of the WNT/β-catenin signaling pathway. The murine HCC models utilizing NR2E3 knockout mice consistently exhibits accelerated liver tumor formation and progression accompanied by enhanced activation of WNT/β-catenin signaling pathway and inactivation of p53 signaling pathway. At cellular level, the loss of NR2E3 increases the acquisition of aggressive cancer cell phenotype and tumorigenicity and upregulates key genes in the WNT/β-catenin pathway with enhanced chromatin accessibility. This event is mediated through increased formation of active transcription complex involving Sp1, β-catenin, and p300, a histone acetyltransferase, on the promoters of target genes. These findings demonstrate that the loss of NR2E3 promotes WNT/β-catenin signaling activation at cellular, organismal, and clinical levels. In summary, NR2E3 is a novel tumor suppressor that maintains epigenetic homeostasis, thereby preventing activation of WNT/β-catenin signaling that promotes HCC formation and progression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene expression profile at single cell level of OP patient and healthy control

first: Hongmei

last: Wang

state: (None)

address: Ding jia qiao 87, gulou region

institute: Southeast University

summary: To characterize the cellular composition of the lung tissues of OP patient, we collected lung samples for scRNA-seq from one patient with OP, one healthy control

overall_design: single-cell suspensions were produced and libraries were prepared according to the manufacturer’s protocol (10x Genomics, CG000086_RevM). After quality checks, single-cell RNA-seq libraries were pooled and sequenced on a NovaSeq 6000 instrument.

first: Ying

last: Tang

first: Cuilin

last: Chu

first: Siyuan

last: Bu

first: Qin

last: Sun

first: Airan

last: Liu

first: Lingyan

last: Huang


title: NAT10-mediated mRNA N4-acetylcytidine is Essential for the Translational Regulation of Oocyte Meiotic Maturation in Mice

city: Nanning

first: liu

last: shaoyuan

address: Guangxi province of china

institute: Guangxi university

summary: Mammalian oocyte maturation is driven by strictly translational regulation of maternal mRNAs stored in the cytoplasm. However, the function and mechanism of post-transcriptional chemical modifications especially the newly identified N4-acetylcytidine (ac4C) catalyzed by N-acetyltransferase 10 (NAT10) in this process are previously unknown. In this study, we developed a low-input ac4C sequencing technology - ac4C LACE-seq and mapped 8241 ac4C peaks at the whole transcriptome level using 50 mouse oocytes at the germinal vesicle (GV) stage. We profiled the mRNA landscapes of NAT10-interactions and ac4C modifications. The NAT10-interacted and ac4C modified transcripts displayed association with high translation efficiency in oocytes. Oocyte-specific Nat10 knockout wiped out ac4C signals in oocytes and caused severe defects in meiotic maturation and female infertility. ac4C LACE-seq results indicated that Nat10 deletion led to a failure of ac4C deposition on mRNAs encoding key maternal factors such as MAY2, ZAR1, BTG4 and cyclin B1 that regulate transcriptome stability and maternal-to-zygotic transition. Nat10-deleted oocytes had decreased mRNA translation efficiencies during meiotic maturation, partially due to the direct inhibition ac4C sites on specific transcripts. In sum, we developed low-input, high-sensitivity mRNA ac4C profiling approach and highlighted the important physiological function of ac4C in precise regulation of the oocyte meiotic maturation by enhancing translation efficiency.

overall_design: We developed a low-input ac4C sequencing technology - ac4C LACE-seq and mapped 8241 ac4C peaks at the whole transcriptome level using 50 mouse GV oocyte. In order to study the impact of Nat10 deletion on ac4C modification, we used ac4C LACE-seq technology to detect changes in ac4C modification in wild type and Nat10-GKO.

first: Lu

last: Chen

first: Shao-Yuan

first: Rui-Bao

last: Su

first: Yu-Ke

last: Wu


title: Aging-associated increase in Golgi stress disturbs cellular signaling and epigenetic regulation

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

institute: Kangwon National University

summary: The process of aging is associated with disturbed mineral homeostasis, such as zinc deficiency. Simultaneously, cellular response to external stimuli, including receptor signaling and DNA repair response diminishes, and epigenetic dysregulation occurs.  The Golgi apparatus plays various roles in the cell; however, the effect of aging on the morphology and function of the Golgi apparatus and the impact of Golgi senescence in cellular activity remains unknown. In the present study, we found that Golgi stress is associated with senescent cell irresponsiveness to external stimuli. The senescent Golgi was associated with a disassembled microtubule network in the Golgi and perinuclear areas. These effects could be reproduced by disruption of the Golgi-associated microtubules or zinc depletion. To clarify the importance of Golgi-zinc homeostasis in more detail, the implications of the Golgi-zinc transporter ZIP13 were analyzed; Zip13-deficient mice Golgi exhibited morphology similar to that of senescent Golgi. Additionally, fibroblasts from Zip13-deficient mice showed dysregulation of DNA repair and cellular acetylation with downregulated nuclear translocation of p300, HDAC1/2, and p53 proteins, which are reminiscent characteristics of senescent cells. Our findings demonstrate the underlying reason for senescent cell irresponsiveness to various stimuli and highlight the importance of a zinc-rich diet during aging.

overall_design: To investigate the influence of local zinc homeostasis on the structures of the Golgi and perinuclear region, we performed gene expression profiling of fibroblasts from wildtype and Zip13-/- mice. Gene expression profiles of wildtype and Zip13-/- cells were generated using the Affymetrix GeneChip Mouse Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA).

first: Sofia

last: Brito

first: Bum-Ho

last: Bin


title: Protein local synthesis at synapse is required for neuromuscular transmission

city: Hangzhou

first: Chengyong

last: Shen

address: 268 Kaiquan Rd.

department: Institute of Translational medicine

institute: Zhejiang University

summary:
To profile the local translatome at the neuromuscular junction during various developmental stages
We conducted RNA sequencing of synapse-enriched regions in the mouse diaphragms of both cre- and cre+ mice to investigate the local translatome at motor neuron terminals

overall_design: Comparative profiling analysis of RNA-seq data for ChAT-Cre positive and negative synapse-enriched diaphragms


title: scRNA-seq for analyzing the characteristics of PBMC in patients with autoimmune hepatitis

city: Fukushima

first: Kazumichi

last: Abe

state: Fukushima

address: 1 Hikarigaoka

country: Japan

institute: Fukushima Medical University

summary: Autoimmune hepatitis (AIH) is caused by an immune disorder that is characterized by hypergammaglobulinemia, autoantibodies, and chronic active hepatitis on liver histology. This present study was designed to analyze the characteristics of AIH peripheral blood mononuclear cells (PBMCs) through single-cell RNA sequencing (scRNA-seq, 10x Genomics Gene Expression 3' Chromium V 2.0) and to explore the potential molecular mechanism of AIH.

overall_design: We generated single-cell transcriptomes of PBMCs that were pooled from 4 healthy volunteers and 4 AIH patients by scRNA-seq. PBMCs were used to scRNA-seq for cell clusters identification and differently expressed gene (DEG) determination.


title: CPT1A-mediated MFF succinylation promotes stemness maintenance in ovarian cancer stem cells by enhancing mitochondria-associated membranes formation

city: xian

first: yaqin

last: zhu

address: xi changan street, 620

institute: Shaanxi normal university

summary: Cancer stem cells (CSCs) are key players in cancer progression, immune evasion, drug resistance, and recurrence, particularly in ovarian cancer. Mitochondria-associated membranes (MAMs) are dynamic structures linking mitochondria and the endoplasmic reticulum, essential for cellular processes. Whether MAMs supports CSCs and the underlying mechanisms remain largely unknown. Here, we unveil that CPT1A is highly expressed in ovarian cancer stem cells (OCSCs) and is essential for stemness maintenance. CPT1A facilitates stemness maintenance by regulating lipid desaturation in ovarian cancer. Further studies confirmed that CPT1A enhances SREBP1 cleavage and nuclear translocation, thereby upregulating SCD1 expression and promoting lipid desaturation in OCSCs. Furthermore, MAMs are found to be critical for SREBP1 activation. Mechanistic studies have shown that CPT1A promotes mitochondrial fission factor (MFF) succinylation (succK-MFF) through its lysine succinyltransferase (LSTase) activity, with succK-MFF being crucial for MAMs formation and SREBP1 activation. Additionally, inhibiting the LSTase activity of CPT1A with Glyburide reduced OCSCs' stemness and enhanced cisplatin's anti-tumor effects against ovarian cancer both in vitro and in vivo. Together, our studies reveal the importance of CPT1A's LSTase activity in MAMs formation and OCSCs' stemness maintenance, providing potential targets and therapeutic strategies for ovarian cancer treatment.

overall_design: To investigate the function of CPT1A in lipid metabolism, we established the SKOV3 cell line and knocked down the CPT1A target gene with shRNA.

first: Yaqin

last: Zhu

first: Shuting

first: Hong

first: Yaning

last: Meng


title: Converged Epitranscriptomic Co-regulation of TGFβ Signaling Components Suppresses the Quiescence Transition of Early Postnatal Hippocampal Neural Stem Cells

city: Philadelphia

first: Feng

last: Zhang

state: PA

address: 415 Curie Boulevard

department: Department of Neuroscience and Mahoney Institute for Neurosciences

institute: Perelman School for Medicine, University of Pennsylvania

type: Methylation profiling by high throughput sequencing

summary: Quiescence acquisition of proliferating neural stem cells (NSCs) is required to establish the adult NSC pool yet the underlying molecular mechanisms are not well-understood. Here we showed that conditional deletion of the m6A reader Ythdf2, which promotes mRNA decay, in proliferating NSCs in the early postnatal mouse hippocampus led to elevated quiescence acquisition with decreased neurogenesis. Multimodal profiling of m6A modification, YTHDF2 binding, and mRNA decay in hippocampal NSCs identified shared targets in multiple TGFβ signaling pathway components, including TGFβ ligands, maturation factors, receptors, transcription regulators, and signaling regulators. Functionally, Ythdf2 deletion led to TGFβ signaling activation in NSCs, suppression of which rescued elevated quiescence acquisition of proliferating hippocampal NSCs. Our study reveals the dynamic nature and critical roles of mRNA decay in establishing the quiescent adult hippocampal NSC pool and uncovers a novel mode of epitranscriptomic control via co-regulation of multiple components of the same signaling pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq and Decay-seq data for wild-type (WT) and Ythdf2-conditional-knockout (cKO) hippocampal neural stem cells (NSCs) cultured in vitro, as well as m6A-IP-Seq and YTHDF2-RIP-seq analysis of cultured WT NSCs.

first: Yao

last: Fu

first: Dennisse

last: Jimenez

first: Ting

last: Zhao

first: Yachen

first: Yusha

first: Zhijian

first: Qing

last: Wang

first: Riki

last: Kawaguchi

first: Daniel

middle: H

last: Geschwind

first: Chuan

last: He

first: Guo-li

last: Ming

first: Hongjun

last: Song


title: ARNT2 Controls Prefrontal Somatostatin Interneurons Mediating Affective Empathy

first: Sehyun

last: Chae

summary: Empathy is crucial for our social lives, and its disruption is a prominent characteristic of various psychiatric conditions. However, the specific genes and neurobiological mechanisms underlying empathy deficits remain elusive. By combining forward genetic mapping with transcriptome analysis, we discovered that the Arnt2 gene encoding a basic-helix-loop-helix (bHLH)-PAS transcription factor is a key driver of significant alteration in observational fear, a basic form of affective empathy. Selective deletion of Arnt2 in somatostatin (SST)-expressing inhibitory neurons resulted in reduced excitability of pyramidal cells, an increase in spontaneous firing, and alteration in in vivo Ca2+ dynamics in SST neurons in the anterior cingulate cortex (ACC), leading to deficits in observational fear and affective state discrimination. Together, our findings provide the first direct evidence that ARNT2 regulates emotion recognition and affect sharing through its functional actions in the cortical inhibitory circuit and highlight the neural substrates underlying social affective dysfunctions in psychiatric disorders.

overall_design: RNA profiles of anterior cingulate cortex (ACC) tissues of AKR and B6N mice under naïve and post-observational fear conditioning.

first: Sehoon

last: Keum

first: Jiye

last: Choi

first: Seungmoon

last: Jung


title: Trained immunity is facilitated by T cell-induced CD40-TRAF6 signaling

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

institute: Radboud University

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

overall_design: Refer to individual Series


title: High-grade NF2 mutant meningiomas downregulate oncogenic YAP signaling.

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Meningiomas are the most common primary brain tumors in adults. Although generally benign, a subset is of higher grade, recurs even after multiple surgeries, and frequently fatal. Around half of meningiomas harbor inactivating mutations in NF2. While low-grade NF2 mutant meningiomas harbor few additional mutations in addition to NF2 inactivation, high-grade NF2 mutant tumors frequently harbor a highly aberrant genome. We and others have previously shown that NF2 inactivation leads to YAP1 activation and that YAP1 acts as an oncogene in NF2 mutant meningiomas. Here, we show that high-grade NF2 mutant meningiomas downregulate YAP1 signaling, in part through upregulating the expression of the YAP1 competitor VGLL4 and the YAP1 upstream regulators FAT3/4. Overexpression of VGLL4 resulted in the downregulation of YAP activity and the growth inhibition of low-grade NF2 mutant meningioma cells. Our results have important implications for the efficacy of therapies targeting oncogenic YAP1 in high-grade NF2 mutant meningiomas.

overall_design: Ben-Men-1 cells grown in DMEM (11995-073), 20% FBS, 1% PenStrep were lentivirally transduced with pLJM1-GFP or pLJM1-VGLL4. RNASeq was done on positive clones. We then performed gene expression profiling analysis using data obtained from RNASeq of 3 GFP and 3 VGLL4 replicates

first: Frank

last: Szulzewsky

first: Eric

last: Holland


title: Cerebrovasculature in brain malignancies from 13 surgical resected samples

city: Xi’an

first: Lei

last: Zhang

address: No. 620, West Chang'an Avenue

institute: Shaanxi Normal University

summary: Dysfunction in human cerebrovasculature contribute to pathogenesis of multiple neurological diseases, and the blood brain barrier (BBB), an organotypic specialization of the cerebrovasculature, impedes the delivery of systemic therapies for nearly all brain disorders.Here we developed a novel methodology to isolate fresh cells from the human cerebrovasculature with high capture efficiency and cell viability, and performed single-cell mRNA sequencing (scRNAseq) for human cerebrovascular cells from 13 surgical resected samples, including normal human brain tissue and gliomas, the most common brain malignancy. We profiled the transcriptome of 103,230 single cells, including 57,324 endothelial cells and 27,703 mural cells.We molecular defined the principle vascular cell types in the BBB, and uncovered molecular underpinning of heterogeneity in endothelial cells, mural cells and perivascular fibroblasts along the arteriovenous axis.

overall_design: We profiled freshly isolated cells from the cerebrovasculature in brain malignancies from 13 surgical resected samples, including tumor core and paired neighboring non-malignant tissue, in 3 individuals with IDH-mutant LGG and 4 individuals with IDH-wildtype GBM. Single cell suspension, magnetic-activated cell sorting (MACS) depletion of CD45+ leukocytes and enrichment of CD31+ endothelial cells as well as PDGFRβ+ mural cells, were subjected to scRNA-seq using a 10X genomics-based single-cell protocol.

first: Fan

last: Yang

first: Yuan

last: Xie

first: Yanyu


title: AOS10-FMT could rescure the adverse effects induced by STZ on the testis

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We report the side-effects of STZ on the testis, and foud that the AOS10-FMT could rescure the side-effect of STZ in many factors,such as spermatogenesis,lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged testis induced by STZ

first: Yanan

last: Hao


title: Gene expression profile at single cell level of microglia sorted from rats brain with chronic cerebral hypoperfusion

city: Chongqing

first: Yuhan

last: Wang

address: Xinqiao Central Street, Shapingba District

institute: Army Medical University (Third Military Medical University)

summary: Microglia are considered as a heterogenous population in the brain tissues. We used single-cell RNA sequencing (scRNA-seq) to analyze the diversity of microglia in the rats with chronic cerebral hypoperfusion.

overall_design: Young male Sprague-Dawley rats (300-350g, 8 weeks old) were obtained, and bilateral common carotid artery occlusion (BCCAO) method was adopted to establish CCH model and mimic vascular dementia. We split brain tissues of sham and CCH rats into gray matters and white matters after 4 and 8 weeks of modeling (abbreviated to 4W/8W SG, SW, CG and CW). Microglia were sorted by magnetic activated cell sorting (MACS) using CD11b/c microbeads and analyzed using scRNAseq. Gray or white matter single-cell suspensions sorted by MACS in each group were derived from 3 different rats and mixed into 1 sample.

first: Wenchao

last: Cheng

first: Chang

first: Xiuying

last: Chen

first: Lan

first: Kaiyuan

last: Dong

first: Wen

last: Huang


title: Expression data of genes in proliferative and differentiated NSCs derived from brain and spinal cord

city: Beijing

first: Sumei

last: Liu

address: Nanyitiao 3, zhongguancun

institute: Chinese Academy of Sciences

summary: We compared the proliferative and differentiated NSCs derived from brain and spinal cord to investigate the mechanisms of promoting proliferation and differentiation.

overall_design: We selected the proliferative NSCs and differentiated NSCs of brain and spinal cord and extracted the RNA, with hubridization on Affymetrix microarrays.


title: Genome engineering of primary and pluripotent stem cell-derived hepatocytes for modeling liver tumor formation

status: Public on Aug 25 2024

city: Shanghai

first: Yijia

last: Chi

state: 上海

address: No. 555 Zuchongzhi Road, Pudong New District, Shanghai, China

institute: Shanghai Institute of Material Medica

summary: Genome editing has demonstrated its utility in generating isogenic cell-based disease models, enabling the precise introduction of genetic alterations into wildtype cells to mimic disease phenotypes and explore underlying mechanisms. However, its application in liver-related diseases has been limited by challenges in genetic modification of mature hepatocytes in a dish. Here we conducted a systematic comparison of various methods for primary hepatocyte culture and gene delivery to achieve robust genome editing of hepatocytes ex vivo. Our efforts yielded editing efficiencies of up to 80% in primary murine hepatocytes cultured in monolayer and 20% in organoids. To model human hepatic tumorigenesis, we utilized hepatocytes differentiated from human pluripotent stem cells (hPSCs) as an alternative human hepatocyte source. We developed a series of cellular models by introducing various single or combined oncogenic alterations into hPSC-derived hepatocytes. Our findings demonstrated that distinct mutational patterns led to phenotypic variances, affecting both overgrowth and transcriptional profiles. Notably, we discovered that the PI3KCA E542K mutant, whether alone or in combination with exogenous c-MYC, significantly impaired hepatocyte functions and facilitated cancer metabolic reprogramming. In conclusion, our study demonstrates genome-engineered hepatocytes as valuable cellular models for understanding hepatocarcinoma (HCC), especially highlighting PIK3CA and c-MYC—key oncogenes often amplified or upregulated in HCC—and providing insights into early tumorigenesis mechanisms.

overall_design: To test whether genome engineered hepatocytes resemble distinct tumor subtypes, we carried out transcriptome analysis of genetically manipulated cells isolated by FACS.

first: Lulu

first: Xunting

first: Xuelian

first: Yihang

last: Chu

first: Yi

first: Yufan

last: Gong

first: Fei

first: Qiao

first: Dongxin


title: RNAseq of melanoma cells treated with the p300 inhibitor A-485

city: Boston

first: Marianne

last: Collard

state: MA

address: 609 Albany Street, Department of Dermatology, 5th Floor, J508

department: Dermatology

institute: Boston University

summary: SOX10 is a lineage-specific transcription factor critical for melanoma tumor growth, while SOX10 loss-of-function drives the emergence of therapy-resistant, invasive melanoma phenotypes. A major challenge has been developing therapeutic strategies targeting SOX10’s role in melanoma proliferation, while preventing a concomitant increase in tumor cell invasion. We found that the lysine acetyltransferase (KAT) EP300 and SOX10 gene loci on Chromosome 22 are frequently co-amplified in melanomas, including UV-associated and acral tumors. We further show that p300 KAT activity mediates SOX10 protein stability and that the p300 inhibitor, A-485, downregulates SOX10 protein levels in melanoma cells via proteasome-mediated degradation. Additionally, A-485 potently inhibits proliferation of SOX10+ melanoma cells while decreasing invasion in AXLhigh/MITFlow melanoma cells through downregulation of metastasis-related genes.  We conclude that the SOX10/p300 axis is critical to melanoma growth and invasion, and that inhibition of p300 KAT activity through A-485 may be a worthwhile therapeutic approach for SOX10-reliant tumors.

overall_design: RNA sequencing was performed on three melanoma cell lines (A375, CO79, IPC-298) treated with DMSO or 5 uM A-485 for 24 h.

first: Aaron

last: Waddell

first: Rhoda

last: Alani


title: Functional responses of coral microbial communities to ocean acidification

city: Fuzhou

first: Zhenyue

last: Lin

address: Minjiang university

institute: Minjiang university

summary: DNA samples of G. fascicularis were used to investigate the GeoChip 5.0 based functional gene arrays, which contains 57,000 probes and covered over 144,000 gene sequences from 393 functional gene families associated with a variety of microbial functional traits, such as carbon, nitrogen, phosphorus, sulfur cycling, pathogenicity and secondary metabolism.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: In the study presented here, we tested the effect of OA exposure (PH7.85, PH8.15 and PH8.45) on the coral bacterial community and function, using the microarray analyses


title: Loss of homeostatic functions in microglia from a murine model of Friedreich’s ataxia

city: Rome

first: Savina

last: Apolloni

address: Via della Ricerca Scientifica, 1

department: Department of Biology

country: Italy

institute: University of Rome Tor Vergata

summary: Background Friedreich’s ataxia (FRDA) is a rare genetic disorder characterized by motor discoordination and predominant cerebellar involvement. It is caused by mutations leading to decreased transcription of frataxin (FXN), a gene encoding for a mitochondrial protein involved in the biogenesis of iron-sulfur clusters and iron handling. Many advances have been achieved in understanding the pathophysiology of FRDA and the mechanisms whereby FXN deficiency causes cerebellar degeneration. However, the issue concerning the contribution of central nervous system-resident non-neuronal cells to the pathogenesis of FRDA is still poorly explored. In this work, we set out to verify if specific vulnerabilities of cerebellar microglia could be involved in the pathogenesis of FRDA. Methods Primary cerebellar microglia were obtained from the KIKO mouse model of FRDA. We analyzed their phenotype and functions by a multilayer study, encompassing morphological analysis, migration and phagocytosis assays, gene expression by RNA-seq, RT-PCR, western blot, and immunofluorescence. Mitochondria functionality was evaluated by flow cytometry and real-time metabolic analysis. We assessed the effect of FRDA microglia on cell viability and neurite length in primary neurons. We analyzed in vivo microglia phenotype in the cerebellum of KIKO miceduring an early developmental stage by means of morphology analysis, RT-PCR and immunofluorescence. Results We demonstrated that FRDA microglia exhibit traceable morphological, transcriptional and functional changes, particularly regarding inflammatory pathways and mitochondria functionality. In addition, we found that FRDA microglia impair neuron survival and neurite length in vitro. Finally, we showed that cerebellar microglia in vivo exhibit dysregulations at early postnatal age of FRDA mice. Conclusions These results indicate that FRDA microglia display aberrant features and may participate in neuron dysfunction, evidencing a non-cell-autonomous mechanism in FRDA. Therefore, microglia targeting could be a valuable strategy in ameliorating cerebellar degeneration in the disease.

overall_design: Gene expression analysis of primary microglia from cerebellum of KIKO (B6.Cg-Fxntm1MknFxntm1Pand/J ) and control WT (C57BL/6) mice. A total of n=8 sample were analysed by RNA seq: n=4 KIKO and n=4 control WT samples.

first: Ilaria

last: Della Valle

first: Martina

last: Milani

first: Simona

last: Rossi

first: Mauro

last: Cozzolino

first: Nadia

last: D’Ambrosi


title: Effect of Col1a2 mutation in the gene expression of immature and mature osteoblasts in a mouse model of osteognesis imperfecta (OI)

city: London

first: Michelangelo

last: Corcelli

state: London

address: Zayed Centre for Research, 20 Guilford Street, London,

country: United Kingdom

institute: UCL

summary: In Europe, approximately 85-90% of individuals with Osteogenesis Imperfecta (OI) have dominant pathogenic variants in the COL1A1 or COL1A2 genes whilst for Asian, especially Indian and Chinese cohorts, this ratio is much lower. This leads to decreased or abnormal Collagen type I production. Subsequently, bone formation is strongly reduced, causing bone fragility and liability to fractures throughout life. OI is clinically classified in 5 types with the severity ranging from mild to lethal depending on the gene and the type and location of the OI-causative variant and the subsequent effect on (pro) collagen type I synthesis. However, the specific effects on the phenotype and function of osteoblasts are not fully understood. To investigate this, the OI murine model was used, with the oim/oim (OIM) mice closest resembling severely deforming OI type 3 in humans. We showed that in OIM, COL1 mutation results in a multifactorial inhibition of the osteogenic differentiation and maturation as well as inhibition of osteoclastogenesis. The phenotype of differentiated OIM osteoblasts also differs from that of wild type mature osteoblasts, with upregulated oxidative cell stress and autophagy pathways, possibly in response to the intracellular accumulation of type I collagen mRNA. The extracellular accumulation of defective type I collagen fibres contributes to activation of the TGF- signalling pathway and activates the inflammatory pathway. These effects combine to destabilise the balance of bone turnover, increasing bone fragility. Together, these findings identify the complex mechanisms underlying OI bone fragility in the OIM model of severe OI and can potentially enable identification of clinically relevant endpoints to assess the efficacy of innovative pro-osteogenic treatment for patients with OI.

overall_design: To propose a theoretical model of OI bone fragility, we used primary pre-osteoblasts isolated from the calvaria of homozygous OIM and wild type (WT) neonatal mice to determine the genetic impact of the recessive variant of Col1a2 on osteoblast phenotype during the process of osteogenic differentiation. The WT and OIM pre-osteoblasts were cultured for 21 days under osteogenic conditions and then RNA was isolated for transcriptomic analysis by RNAseq. 5 different groups of samples were compared: Group A (WT preosteoblasts or WTd0), Group B (WT differentiated osteoblast or WTd21); Group C (OIM pre-osteoblasts or OIMd0) and Group D (OIM differentiated osteoblast OIMd21). DEGs from sveral comparisons were Comparisons

first: Pascale

last: V Guillot


title: Cannabinoid receptor type 2 expression in mouse brain: from mapping to regulation in microglia under inflammatory conditions [snRNA-seq]

city: Lyon

first: Guillaume

last: Marcy

address: 8 avenue Rockefeller

country: France

institute: Universite Lyon 1

summary: Since its detection in the brain, the cannabinoid receptor type 2 (CB2) has been considered a promising therapeutic target for various neurological and psychiatric disorders. However, precise brain mapping of its expression is still lacking. Using magnetic cell sorting, calibrated RT-qPCR and single-nucleus RNAseq, we show that CB2 is expressed at a low level in all brain regions studied, mainly by few microglial cells, and by neurons in an even lower proportion. Upon lipopolysaccharide stimulation, modeling neuroinflammation in non-sterile conditions, we demonstrate that the inflammatory response is associated with a transient reduction in CB2 mRNA levels in brain tissue, particularly in microglial cells. This result, confirmed in the BV2 microglial cell line, contrasts with the positive correlation observed between CB2 mRNA levels and the inflammatory response upon stimulation by interferon-gamma, modeling neuroinflammation in sterile condition. Discrete brain CB2 expression might thus be up- or down-regulated depending on the inflammatory context.

overall_design: Nuclei of postnatal day 10 mouse cortex were isolated and then selected using Fluorescence-activated nuclei sorting (FANS) based on high DAPI intensity for analysis using snRNA-seq. Nuclei were individually captured by the iX Chromium (10x Genomics) and libraries were prepared according to 10x Genomics protocol.

first: Cyril

last: Dégletagne

first: Wanda

last: Grabon

first: Laurent

last: Bezin


title: Toxoplasma gondii transcription factor AP2XII-8 is a key regulator for the G1 phase progression and parasite division

city: Nanning

first: Dandan

last: Hu

state: China

address: Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.

institute: Guangxi University

summary: The apicomplexan parasite Toxoplasma gondii can infect humans and almost all warm-blooded animals worldwide, poses significant threat to the public health and of veterinary importance. The acute infection was characterized by fast replication of tachyzoites inside the host cells. During this fast amplification process, the gene expression is highly regulated by series of regulator networks. The G1 phase is usually conserved across species and responsible for the preparation of materials for the next replication cell cycle, but seldom regulators were identified in this stage. Here, we functionally characterized the C/G1 phase expressed ApiAP2 transcription factor TgAP2XII-8 in T. gondii tachyzoite. Conditionally knockdown of TgAP2XII-8 leads to significant growth defects and asexual division disorder. Additionally, the parasite cell cycle progression was also disrupted after TgAP2XII-8 depletion, which is characterized by G1 phase arrest. RNA-seq and CUT&Tag experiments revealed that TgAP2XII-8 played as an activator for the ribosomal proteins expressed in G1 phase. Moreover, TgAP2XII-8 bind to a specific DNA motif ([T/C]GCATGCA), which is abundant and conserved in the intergenic region of several other apicomplexans, which may suggest a broad and conserved role for this ApiAP2 in the Phylum of Apicomplexa. These data provide important knowledge for the understanding of transcriptional regulation of parasite cell cycle in T. gondii.

overall_design:
To assess the functions of TgAP2XII-8 in T. gondii, an indole-3-acetic acid (IAA) degradation (mAID) system was used to generate an inducible knockdown (iKD) of TgAP2XII-9 parasites (iKD TgAP2XII-9). Potentially regulated genes of the transcription factor TgAP2XII-8 were investigated by RNA-seq using TgAP2XII-8 iKD parasites with or without IAA treatment for 12 or 24 hours. Three biological replicates were employed.
To further characterize the direct target genes of TgAP2XII-8, CUT&Tag experiments were performed using the endogenously 3xHA tagged parasite and RH strain.

first: Yuehong

last: Shi

first: Xuan

last: Li

first: Yue

last: He

first: Xingju

last: Song


title: Elucidating the Effects of the Environmental Pollutant Benzo[a]pyrene [BaP] on Cardiac Arrhythmogenicity

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: Benzo[a]pyrene (BaP) is a product of combustion and is an abundant constituent of wildfire derived smoke and particulate matter 2.5 (PM2.5). Although arrythmias are associated with wildfire, the mechanism remains unclear. We hypothesized that BaP might predispose individuals to arrhythmias and possibly sudden cardiac death. Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) from healthy donors (n=3) were used to investigate the cardiovascular toxicity of BaP. Across a broad concentration range, BaP did not affect iPSC-CM viability, and a 4-day exposure of BaP at 50 M did not affect contractility. After exposure to BaP at 50 M for 5 days, iPSC-CMs were subjected to bulk RNA sequencing, and analysis revealed markers of inflammation were upregulated, and ion channel expression was modulated. Because inflammation is associated with reactive oxygen species (ROS) production, iPSC-CMs exposed to BaP had a concentration-dependent increase in ROS production. Mitotracker fluorescent imaging revealed decreased mitochondrial membrane potentials after iPSC-CMs treatment with 50 μM BaP. Seahorse assays revealed that BaP exposure decreased oxygen consumption rate, basal respiration, and maximal respiration in a dose-dependent manner. Using multiple electrode array (MEA) assays, iPSC-CMs exposed to 50 M BaP for 3 days, had prolonged field potential duration (FPD) and increased beat period (BP). However, co-treatment with N-acetyl cysteine (NAC), a nucleophile that scavenges ROS and preserves glutathione, attenuated the effect of BaP on FPD and BP (p<0.001). In summary, BaP exposure upregulated inflammatory cytokines and increased ROS production by impairing mitochondrial function. BaP had proarrhythmic effects of increased BP and FPD and was abrogated by NAC. Thus, BaP inhalation from wildfire smoke may predispose individuals to QT prolongation, arrhythmia, and sudden cardiac death.

overall_design: We exposed three healthy lines (273, 951, 100) to vehicle or 50 micromolar BaP.

first: Mark

last: Chandy

first: Johnson

last: Yang


title: Pericytes contribute to pulmonary vascular remodeling via HIF2α signaling

summary: Using a combination of single-cell RNAseq methods and murine pulmonary hypertension models, we show HIF2α overexpressing pericytes’ transformation into SMC-like cells, confirming HIF2α as a major molecular regulator in hypoxia-induced pulmonary hypertension (PH) and vascular remodeling. We demonstrate that HIF2α overexpression in pericyte-dominant transgenic mice exacerbates PH and right ventricular hypertrophy (RVH), whereas disruption of HIF2α expression attenuates the development of PH.

overall_design: NG2-CreERTM (Jax strain 008538) bred with Ai14 tdTomato lines in order to get NG2 cell labeled with tdTomato color. After 2mg/30g body weight tamoxifen injection, NG2tdT mice rested for 7 days followed by exposure to FiO2 10% for 21 days. The hypoxic and normoxic lung lobes were harvested and digested to single cell suspension using Collagenase and Dnase. From the single cell suspension, tdT positive cells were sorted and enriched using FACS and immediately loaded into the Chromium Single cell controller (10x Genomics). Single cell RNA-seq libraries were generated using 10X provided reagents.

first: Ke

last: Yuan


title: single cell RNA sequecing of Gene epxressions and TCR clones in late-onset EAE

city: Fort Worth

first: Weikan

last: Wang

state: TX

address: 3500 Camp Bowie Blv

department: Dept. of Microbiology, Immunology and Genetics

institute: University of North Texas Health Science Center

summary: Aged patients with multiple sclerosis (MS) have more progressive and severe symptoms, even though aged people have increased frequency of peripheral Treg (pTreg) cells which inhibit this disease. Our goal is to how aged pTreg cells with changes in their frequency and functionality contribute to increased severity of late-onset MS using mouse model experimental autoimmune encephalomyelitis (EAE). For this purpose, we reported the Treg cell plasticities and T cell clonalities in the CNS infiltrated T cells in the late-onset EAE mouse model.

overall_design: single cell RNA-seq was performed on the the analysis of CNS infiltrated T cells in young and aged mouse.Treg plasticity was deterimined by the expression levels of il17a and ifng mRNA in Foxp3+ CD4 T cells. Clonality was deterimined by the frequency of clones in the whole TCR repertoire.

first: Rachel

last: Thomas

first: Jiyoung

last: Oh

first: Dong-Ming

last: Su


title: Granulosa cells provide transcriptomic information on ovarian follicle dynamics in southern white rhinoceros

city: Escondido

first: Elena

last: Ruggeri

address: 15600 San Paqual Valley Rd.

institute: San Diego Zoo Wildlife Alliance

summary: Much remains unknown about the reproductive physiology of southern white rhinoceros (SWR) and the effect of ovarian stimulation prior to ovum pickup (OPU) have not been fully elucidated. Granulosa cells (GC) provide valuable insight into follicle growth and oocyte maturation status. The goals of this study were to evaluate transcriptomic changes in GC from three stages of follicle development and to identify biomarkers possibly associated with follicular growth and maturation as a result of ovarian stimulation. GC collected from SWRs following OPU were assigned stages based upon follicle size. Total RNA was isolated, and cDNA libraries were prepared and sequenced on a NovaSeq 6000. All bioinformatics analyses were performed utilizing the Galaxy web platform. Reads were aligned to CerSimCot1.0, and the manual curation was performed with EquCab3.0. Overall, 39,455 transcripts (21,612 genes) were identified across follicle stages, and manual curation yielded a 61% increase in gene identification from the original annotation. Granulosa cells from preovulatory follicles expressed the highest number of unique transcripts. The following seven biomarkers were determined based upon cluster analysis and patterns of expression: COL1A1, JMY, FBXW11, NRG1, TMPO, MACIR and COL4A1. These data can be used to potentially evaluate the effects of different ovarian stimulation protocols on follicle dynamics, improve OPU results, and support conservation efforts in this species.

overall_design: Transcriptomic of SWR GC from follicles in different stages of development.

first: Kristin

last: Klohonatz

first: Barbara

last: Durrant

first: Sirard

last: Marc-André


title: Isolate specific transcriptome changes exerted by isavuconazole treatment in Candida auris

status: Public on Aug 24 2024

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

summary: Invasive fungal infections are important healthcare associated disease worldwide especially in intensive care units More recently, Candida auris a multidrug and potentially pan-resistant species has globally emerged as a new nosocomial pathogen, which has been already reported from at least 50 countries on six continents. Clinical studies showed that previously well-defined phylogenetic C. auris clades display significant differences regarding their pathogenicity, virulence, metabolism and susceptibility profile to traditional antifungal therapies. Based on epidemiological data, isolates belonging to the South Asian clade show the highest ratio of resistance to fluconazole (97%), amphotericin B (47%) and this clade involves the highest number of multidrug resistant isolates (45%), which compromise the efficacy of applied antifungal therapy. In the past decade, a new broad-spectrum antifungal drug, isavuconazole (ISA), has been introduced into clinical practice. ISA is primarily approved for the treatment of invasive aspergillosis and mucormycosis, and currently, there are no available recommendations for the therapy of invasive Candida infections. In our previous study, we reported different ISA susceptibility profiles between isolates belonging to South Asian lineage. However, the global transcriptional - even isolate specific - response remained unresolved. Therefore, our study aimed to reveal those molecular events, which are associated with ISA exposure using high throughput RNA sequencing (RNAseq).

overall_design: Comparative gene expression profiling analysis of RNA-seq data of isavuconazole treated and untreated Candida auris  cells.

first: Noémi

last: Balla

first: Fruzsina

last: Kovács

first: Zoltán

last: Tóth

first: Andrea

last: Harmath

first: Aliz

last: Bozó

first: László

last: Majoros

first: Renátó

first: Ágnes


title: RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [Oxford Nanopore Technology Direct RNA Sequencing]

city: Onna-son, Kunigami-gun, Okinawa

first: ATSUSHI

last: SHIMADA

address: 1919-1 Tancha

department: Plant Epigenetics Unit

institute: Okinawa Institute of Science and Technology

summary: The centromere is a pivotal chromatin domain that ensures accurate chromosome segregation during cell division. However, the epigenome regulation of the centromere and its impact on centromere function remain largely elusive. Here in the model plant Arabidopsis, we show that CCR4, the catalytic subunit of the RNA deadenylation complex CCR4-NOT, is essential for maintenance of the centromere epigenome and chromosome integrity. We demonstrate that CCR4 is involved in shortening of the poly(A) tails of transcripts originated from centromeric transposons and repeats, thereby promoting the production of small interfering RNAs (siRNAs). The CCR4-dependent siRNAs guide non-CG DNA methylation at centromere repeats, and CCR4 cooperates with canonical DNA methylation pathways to enhance centromeric H3K9 methylation and ensure mitotic chromosome stability. Our study illustrates the crucial role of RNA quality control in RNA interference and reveals the elaborate mechanism that safeguards plant centromeres through epigenomic regulation.

overall_design: Oxford Nanopore Technology Direct RNA Sequencing using 12-day-old seedlings in WT, ccr4a ccr4b, ddm1rdr2, ddm1 rdr2 ccr4a ccr4b.

first: Atsushi

last: Shimada

first: Hidetoshi

last: Saze


title: RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [EM-seq]

overall_design: Enzymatic Methyl-seq samples using 6-week-old leaves in WT, ccr4a ccr4b, ddm1rdr2, ddm1 rdr2 ccr4a ccr4b.


title: RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [RNA-seq]

overall_design: Three biological replicates of RNA-seq samples using 12-day-old seedlings in WT, ccr4a ccr4b, ddm1rdr2, ddm1 rdr2 ccr4a ccr4b, ddm1 rdr2 rdr6.


title: RNA-binding protein IGF2BP1 is required for spermatogenesis in an age-dependent manner

city: shanghai

first: Jiaqiang

last: Luo

address: 85th Wujin Road

institute: Shanghai Jiao Tong University School of Medicine

summary: This study characterizes the in vivo function of RNA-binding protein IGF2BP1 during spermatogenesis, and further identifies ELAVL1 as a novel binding partner, and Lin28a mRNA as a downstream target.

overall_design: RNA immunoprecipitation-sequencing (RIP-Seq) of IGF2BP1 in mouse cultured germ stem cells

first: Chencheng

last: Yao

first: Zheng

last: Li

first: Chao

last: Yang


title: RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [ChIP-seq]

overall_design: Two biological replicates of H3K9me2 ChIP-seq samples using 2-week-old seedlings in WT, ccr4a ccr4b, ddm1rdr2, ddm1 rdr2 ccr4a ccr4b.


title: The human pathome shows sex specific aging patterns post-development

city: Copenhagen N

first: Morten

last: Scheibye-Knudsen

state: Copenhagen N

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

summary: Little is known about tissue specific changes that occur with aging in humans. Using the description of 33 million histological samples we extract thousands of age- and mortality-associated features from text narratives that we call The Human Pathome (pathoage.com). Notably, we can broadly determine when pathological aging starts, indicating a sexual dimorphism with females aging earlier but slower and males aging later but faster. Using machine learning, we employ unsupervised topic-modelling to identify terms and themes that predict age and mortality. As a proof of principle, we cross reference these terms in PubMed to identify nintedanib as a potential aging intervention and show that nintedanib reduces markers of cellular senescence, reduces pro-fibrotic gene pathways in senescent cells and extends the lifespan of fruit flies. Our findings pave the way for expanded exploitation of population datasets towards discovery of novel aging interventions.

overall_design: Examination of transcriptome in ionizing radiation (IR) induced senesecent human dermal fibroblasts treated with varying doses of Nintedanib and Axitinib versus control

first: Michael

last: Ben Ezra

first: Jonas

last: Bach Garbrecht

first: Nasya

last: Rasmussen


title: RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [smallRNA-seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Two biological replicates of small RNA-seq samples using 5-week-old adult plant leaves in WT, ccr4a ccr4b, ddm1rdr2, ddm1 rdr2 ccr4a ccr4b, ddm1 rdr2 rdr6, rdr6.


title: Classical Dendritic Cells Contribute to Hypoxia-Induced Pulmonary Hypertension

city: Aurora

first: Claudia

last: Mickael

state: Colorado

institute: University of Colorado

summary: Pulmonary hypertension (PH) is a chronic and progressive disease with significant morbidity and mortality. It is characterized by remodeled pulmonary vessels associated with perivascular and intravascular accumulation of inflammatory cells. While there is compelling evidence that bone marrow-derived cells, such as macrophages and T cells, cluster in the vicinity of pulmonary vascular lesions in humans and that they contribute to PH development in different animal models, the role of dendritic cells in PH is less clear. Dendritic cells' involvement in PH is likely since they are responsible for coordinating innate and adaptive immune responses. We hypothesized that dendritic cells drive hypoxic PH. We demonstrate that a classical dendritic cell (cDC) subset (cDC2) is increased and activated in wild-type mouse lungs after hypoxia exposure. We observe significant protection after the depletion of cDCs in ZBTB46 DTR chimera mice before hypoxia exposure and after established hypoxic PH. In addition, we find that cDC depletion is associated with a reduced number of two macrophage subsets in the lung (FolR2+ MHCII+ CCR2+ and FolR2+ MHCII+ CCR2-). We found that depleting cDC2s, but not cDC1s, was protective against hypoxic PH. Finally, proof-of-concept studies in human lungs show increased perivascular cDC2s in patients with Idiopathic Pulmonary Arterial Hypertension (IPAH). Our data points to an essential role of cDCs in the pathophysiology of PH.

overall_design: ZBTB46 DTR chimera mice were treated either with a vehicle (PBS) or diphtheria toxin (N=3 in each group). The transcription factor ZBTB46 is controlled by a diphtheria toxin promoter (DTR). Therefore, we deplete classical dendritic cells upon injection of diphtheria toxin. Mice from both groups were exposed to 7 days of hypoxia (FiO2 10%) 1 day before lung collection. RNA was extracted from whole lungs. Our goal was to identify processes related to protection from hypoxia-induced pulmonary hypertension observed in these mice.

first: Rubin

last: Tuder

first: Brian

last: Graham

first: Kurt

last: Stenmark


title: DDX17-regulated alternative splicing that produced a novel oncogenic isoform of PXN-AS1 to promote HCC metastasis [Cells]

city: Chongqing

first: Hongzhong

last: Zhou

institute: ChongQing Medical University/.

summary: The mechanism underlying hepatocellular carcinoma (HCC) metastasis remains unclear, many oncogenes are known to regulate this process. However, the role of alternative splicing (AS) in pro-metastatic HCC is poorly understood.  The current study aimed to explore the function and molecular mechanism of DDX17 in alternative splicing.

overall_design: The expression profiles and clinical value of DDX17 in HCC were analyzed by TCGA database.Subsequently, DDX17 was knockouted to investigate the abilities in proliferation and metastasis in vitro and in vivo.Furthermore, we conducted RNA sequencing to determine the underlying regulatory mechanism of DDX17-mediated HCC progression.

first: Juan

last: Chen

first: Hong-Zhong

first: Sheng-Tao

last: Cheng

first: Hai-Jun

last: Deng

first: Yu-Jiao

first: Min-Li

first: Ji-Hua

last: Ren


title: Real-time quantitative PCR analysis of differentiated U937 cells stimulated with LPS+IFNgamma

status: Public on Aug 23 2024

city: Geesthacht

first: Krathika

last: Bhat

address: Max-Planck-Str. 1

country: Germany

institute: Helmholtz Zentrum Hereon

summary: U937 monocyte cell line was differentiated using PMA.  Differentiated U937 monocytes were exposed to MEM+10% FBS medium (untreated cells) and the same medium containing LPS+IFNgamma.   The changes in the gene expression of cytokines and chemokines were evaluated using RT2 Profiler qPCR array

overall_design: Cells from three wells of 6WP were pooled and RNA was extracted from cells for both conditions. One array plate was used per condition.

first: Heike

last: Helmholz

first: Regine

last: Willumeit-Römer