title: Longitudinal epigenome analysis of IDH-wildtype glioblastomas from initial and recurrent surgical specimens

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

institute: Stanford University School of Medicine

summary: Genome-wide DNA methylation profiling of 226 longitudinally collected IDH-wildtype glioblastoma tumor specimens from 106 patients, consisting of 99 initial treatment-naive resection specimens prior to any radiation or chemotherapy and 127 recurrent post-treatment resection specimens at time of recurrence/progression usually following radiation and/or chemotherapy.  These 127 recurrent post-treatment resection specimens were composed of 106 first surgically-treated recurrent specimens, 19 second surgically-treated recurrent specimens, and 2 third surgically-treated recurrent specimens. The Illumina Infinium EPIC 850k version 1.0 Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of the 226 IDH-wildtype glioblastomas.

overall_design: Bisulfite converted genomic DNA extracted from the 226 IDH-wildtype glioblastoma tumor samples was hybridized to Illumina Infinium EPIC 850k version 1.0 Human DNA Methylation Beadchips


title: Differentially expressed miRNAs between the ovaries of Wolbachia-infected and Wolbachia-uninfected Laodelphax striatellus

status: Public on Nov 18 2024

city: Guangzhou

first: Yan

last: Guo

address: Jinying road

country: China

institute: Guangdong ProvincPlant Protection Research Institute, Guangdong academy of Agricultural Science

type: Non-coding RNA profiling by high throughput sequencing

summary: Laodelphax striatellus is naturally infected with the Wolbachia strain wStri, which significantly increase the fecundity of its host. Wolbachia-infected females produce 30%–40% more eggs than Wolbachia-uninfected females. MicroRNAs (miRNAs) are a class of endogenous non-coding small RNAs that play critical roles in the regulation of gene expression at post-transcriptional level. Here we report the differentially expressed miRNAs between Wolbachia-infected and Wolbachia-uninfected strains of L. striatellus ovaries. Our data may be helpful to explore the molecular mechanisms by which Wolbachia increase the fecundity of Laodelphax striatellus.

overall_design: To investigate the differentially expressed miRNAs, we dissected the ovaries of approximately 600 pairs of 3-day-old Wolbachia-infected and Wolbachia-uninfected Laodelphax striatellus. We then preformed miRNAs expression profiling analysis using data obtained from Hiseq data for ovaries of Wolbachia-infected and Wolbachia-uninfected Laodelphax striatellus. Comparative miRNAs expression profiling analysis of Hiseq data for ovaries of Wolbachia-infected and Wolbachia-uninfected Laodelphax striatellus.

first: Qi

middle: X

last: Zhang

first: Bing

middle: B

last: Shi


title: Dcp1a, a novel Mek substrate, regulates the self-renewal and differentiation of mouse embryonic stem cells

status: Public on Nov 19 2024

city: Tianjing

first: Jiayu

last: Yu

address: Weijin street

institute: Nankai university

summary: Mek inhibitor is widely applied to maintain pluripotency, while prolonged Mek inhibition compromises the developmental potential of mouse embryonic stem cells (ESCs). To better understand the mechanism of Mek in pluripotency maintenance, we first demonstrated that Mek regulates gene expression at post-transcriptional steps. Consistently, many of the 66 Mek substrates identified by quantitative phosphoproteomic analysis are involved in RNA processing. We further confirmed that S563 of Dcp1a, a mRNA decapping cofactor and P-body component, is phosphorylated by Mek1. Dcp1a, as well as two other P-body components Edc4 and Dcp2, are required for the proper self-renewal and differentiation of ESCs, indicating the role of P-bodies in ESCs. Dephosphorylation of Dcp1a S563 facilitates both self-renewal and differentiation of ESCs, through promoting P-body formation and RNA storage. In summary, our study identified 66 Mek substrates supporting the Erk-independent function of Mek, and revealed that Dcp1a, phosphorylated by Mek, regulates ESC self-renewal and differentiation, through modulating P-body formation.

overall_design: In Dcp1a KO cells, overexpressing different forms of mutants including Dcp1a WT, S563A, and S563D, to detect the differences in Dcp1 binding to mRNA of different forms.

first: Nannan

last: Zhao

first: Changzhen

last: Ding

first: Zichan

last: He

first: Qingye

first: Jingai

first: Yuying

last: Wang


title: Endothelial FUNDC1 Deficiency Drives Pulmonary Hypertension [bulk RNA-seq]

city: Tianjin

first: yandong

last: pei

address: 94 Weijin Rd.,

institute: Nankai University

type: Expression profiling by high throughput sequencing

summary:
FUNDC1 protein levels were reduced in PH lung vessels from clinical subjects and animal models. Global Fundc1 deficiency exacerbated PH, while its overexpression is protective. The effect of FUNDC1 was mediated by endothelial cells rather than smooth muscle cells. Further, inducible loss of endothelial Fundc1 in postnatal mice was sufficient to cause PH spontaneously, whereas augmenting endothelial Fundc1 protected against PH before and after the onset of disease. Mechanistically, Fundc1 deficiency impaired basal mitophagy in endothelial cells, leading to accumulation of dysfunctional mitochondria, metabolic reprogramming towards aerobic glycolysis, pseudohypoxia and senescence, likely via a mtROS-HIF2α signaling pathway. Subsequently, Fundc1-deficient endothelial cells increased IGFBP2 secretion that drove pulmonary arterial remodeling to instigate PH. Finally, proof-of-principle in vivo studies showed significant efficacy on PH amelioration by targeting endothelial mitophagy, pseudohypoxia, senescence or IGFBP2.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells .

overall_design: Comparative gene expression profiling analysis of RNA-seq data for endothelial cells (FL,EC-KO).

first: Yandong

last: Pei

first: Dongfeng

last: Ren


title: Feed restriction during the suckling period of ewe Assaf lambs (F0) modifies milk quality and milk exosomal miRNAome of the filial generation (F1)

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: Feed restriction during the early life of ewe lambs (F0) triggers the transfer of epigenetic marks to the next generation, thus impairing the reproductive performance of F1. However, the effects of this factor on milk production and composition, including its abundance in regulatory miRNA (many of which are contained in exosomes, small vesicles of endocytic origin that play a role in the modulation of immune response of the offspring), has not been tested so far. Therefore, in this study, the replacement ewe lambs (F0) obtained in a previous project (a group of ewes fed milk replacer ad libitum –ADL– vs. a group of ewes restricted –RES– to 62.5% the intake level of milk replacer during the suckling period) were raised under similar post-weaning conditions and mated to obtain the progeny (F1). The F1 dairy ewes were also mated, and six of these F1 dairy ewes were selected and divided into two groups: the F1-ADL group (n=3) born from F0-ADL and the F1-RES group (n=3), born from F0-RES animals. Milk production was controlled during the peak lactation period, and milk samples were obtained for each gland separately to measure chemical composition, somatic cell counts, and bacteriology. Exosomes were also isolated for each gland separately to define the miRNA content. The miRNAome was determined following a Next Generation Sequencing approach. The first preliminary results indicate significant differences in the abundance of five miRNAs in the milk obtained during the peak of lactation. Thus, oar-miR-150, oar-miR-221, oar-miR-23a, oar-miR-27a, oar-miR-376c were all down modulated in F1-RES when compared to F0-ADL. Most of these miRNAs have been found to play a role in biological functions such as development, apoptosis, muscle differentiation, reproduction, or milk production. Moreover, somatic cell count (SCC) was reduced significantly in milk samples during the peak of lactation of F1-RES dairy sheep. No significant differences were found in milk production, the chemical composition of milk (fat, protein, lactase), or bacteriology (colony forming units, CFU). This study's results provide some evidence of the effects of nutritional programming events on the milk's bioactive components.

overall_design: F1-ADL (4 samples) versus F1-RES (4 samples)

first: Alba

last: Martin

first: Carlos

last: Garcia-Estrada

first: Estela

last: Melcon-Fernandez

first: Maddalena

last: Arigoni

first: Fabrizio

last: Ceciliano

first: Cristina

last: Lecchi

first: Mahsa

last: Dehnavi

first: Javier

last: Giraldez

first: Sonia

last: Andres


title: An mRNA treatment for human skin rejuvenation

city: Boston

first: George

last: Church

address: 77 Avenue Louis Pasteur

country: USA

institute: Harvard Medical School

summary: Aging is characterized by a gradual decline in function, partly due to molecular damage that accumulates over time. Human skin is highly susceptible to both chronological aging and environmental damage in the form of UV photoaging. This results in detrimental structural and physiological changes with age. In this study we sought to comprehensively address both chronological and photoaging at the single-cell level, and to explore genetic and environmental factors, revealing their influences on the aging process. We included samples from young, middle-aged, and old individuals, and with these samples, we compared chronological aging and photoaging. Utilizing single-cell RNA sequencing, we created a comprehensive human skin cell atlas, that offers insights into the cellular composition and functions. We investigated the renewal ability of epidermis stem cells as they age and extended the study to fibroblasts, hair follicles, and endothelial cells. Examining the genetic landscape of aging in keratinocytes, we identified two distinct "gene modules" with altered gene expression during aging. Furthermore, we uncovered that skin aging involves interactions between epidermal keratinocytes and dermal fibroblasts, as well as extensive communication of keratinocytes with various other skin cell types as revealed through ligand-receptor pairs. Interactions, such as COL17A1-A1b1complex, highlighted a direct link between keratinocytes and fibroblast stimulation for collagen production. Most importantly, A key gene, MYO1, associated with skin aging was identified, leading to the development of an innovative mRNA treatment aimed at promoting skin rejuvenation by targeting this gene. Experimental results demonstrated that the mRNA treatment reduces basal stem cell senescence, increases basal stem cell proliferation, and enhances collagen production in fibroblasts via keratinocyte-fibroblast communication. The MYO1-targeted treatment is validated as an effective strategy for reversing skin aging by targeting cellular mechanisms.

overall_design: This study compared skin transcriptomics between skin samples from the arm and back of donors at three ages: young individuals aged 23, middle-aged individuals aged 53, and elderly individuals aged 85.

first: Li

last: Li


title: The methyltransferase MLL4 promotes non-alcoholic steatohepatitis by enhancing NF-κB signaling

city: Gwanak-gu

first: Chong-Su

last: Kim

state: --- Select One ---

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Dongduk Women's University

summary: Non-alcoholic fatty liver disease (NAFLD) is a growing health problem worldwide, ranging from non-alcoholic fatty liver (NAFL) to the more severe metabolic non-alcoholic steatohepatitis (NASH). Although many studies have elucidated the pathogenesis of NAFLD, the epigenetic regulatory mechanism from NAFL to NASH remains incompletely understood. The histone H3 lysine 4 methyltransferase, MLL4 (also called KMT2D), is a critical epigenetic transcriptional coactivator that mediates overnutrition-induced steatosis in mice, but its potential role in the progression of NASH remains largely unknown. Here, we show that mice lacking the one allele of the Mll4 gene are resistant to hepatic steatosis, inflammation, and fibrosis in NASH conditions compared to wild-type controls. Transcriptome analysis of the livers of control and Mll4+/- mice identified pro-inflammatory genes regulated by the nuclear factor kappa B (NF-κB) signaling pathway as major target genes of MLL4. We show that MLL4 binds to p65 and that MLL4 is required for NF-κB transactivation. Myeloid-specific Mll4 knockout mice showed an almost complete block of NASH, while hepatocyte-specific Mll4 knockout mice showed mild inhibition of steatosis. Pro-inflammatory M1 polarization is decreased and anti-inflammatory M2 polarization is increased in liver macrophages from myeloid-specific Mll4 knockout mice. Importantly, we show that histone H3-lysine 4 methylation mediated by the MLL4-complex plays a critical role in promoting the expression of Ccl2 in hepatocytes and M1 marker genes in macrophages. Our results demonstrate that MLL4, through the NF-κB-MLL4 regulatory axis, exacerbates steatohepatitis in the context of an inflammatory response and represents a potential therapeutic target for NASH.

overall_design: We performed RNA-seq analysis on the livers of eight-week-old WT and Mll4+/- mice fed the methionine and choline-deficient diet (MCDD) for eight weeks.


title: Taurine ameliorates radiation-induced oxidative stress in bone marrow mesenchymal stromal cells and promotes osteogenesis

city: Shanghai

first: Heng

last: Chen

address: 639 Zhizaoju Road

institute: Shanghai Jiao Tong University

summary: Osteoradionecrosis of the jaw (ORNJ) is a severe complication following head and neck radiotherapy that significantly impacts the quality of life of patients. Currently, there is a lack of comprehensive understanding of the microenvironmental factors involved in ORNJ. In this study, we reveal the activation of taurine metabolism in irradiated mandibular stromal cells using scRNA-Seq and demonstrate a decrease in taurine levels in irradiated bone marrow mesenchymal stromal cells (BMSCs) through metabolomics. Compared with unirradiated BMSCs, taurine uptake in irradiated BMSCs increases. Taurine concentrations in the peripheral blood and jaws of irradiated mice are significantly lower than those in unirradiated mice (P = 0.0064 and 0.0249 respectively). Supplementation with taurine promotes osteogenic differentiation, reduces oxidative stress, and decreases DNA damage in irradiated BMSCs. Oral administration of taurine significantly improves the survival rate of irradiated mice and enhances osteogenesis in irradiated jaws. Our study highlights the role of taurine in the recovery from radiation-induced jaw injury, and suggests its potential as a non-invasive therapeutic option for combating ORNJ.

overall_design: Twenty-four 10-week-old male C57BL/6 wild-type mice were equally divided into three groups: Ctrl (control), 1d (day 1 post-radiation) and 7d (day 7 post-radiation). Mice in group 1d and 7d were given 10 Gy head and neck irradiation and were sacrificed 1 and 7 days after irradiation respectively. Mice in each group were combined to extract single-cell suspensions. The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits.


title: The Follicular Lymphoma and Chronic Lymphocytic Leukemia Proliferative Microenvironment at Single-Cell Resolution

first: Antonio

last: Ferreira

state: Massachusetts

address: 77 Avenue Louis Pasteur, NRB-652

department: Pathology

institute: Brigham and Women’s Hospital

summary: Human B cell lymphomas such as Follicular Lymphoma (FL) and Chronic Lymphocytic Leukemia/Small lymphocytic lymphoma (CLL) grow in lymph nodes in areas defined as malignant follicles, and proliferation centers, respectively. We used single-cell RNA-sequencing to study the tumor microenvironment of human lymph nodes involved by FL and CLL.

overall_design: CD45+ and CD45- cells derived from single cell suspension of lymph node patient samples (Immune reactive (control), FL and CLL) were sorted, processed and analyzed by scRNA-seq.


title: Longitudinal epigenome analysis of IDH-mutant astrocytomas from initial and recurrent surgical specimens

first: David

last: Solomon

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of 31 IDH-mutant astrocytoma tumor specimens, of which 14 are from initial surgical resections prior to any radiation or chemotherapy and 17 of which are from a second surgical resection at time of recurrence/progression usually following radiation and/or chemotherapy. For 7 patients (#201-#207), there are paired initial and recurrent tumor samples that were analyzed. For the remaining 17 patients, there are 7 (#208-#214) with only an initial tumor sample analyzed and 10 (#215-#224) with only a recurrent tumor sample analyzed. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of the 31 IDH-mutant astrocytomas.

overall_design: Bisulfite converted genomic DNA extracted from the 31 IDH-mutant astrocytoma tumor samples was hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips


title: Transcriptome profiling of human myogenic progenitors following treatment with nicotinamide (NAM) or pyridoxine (PN)  or the combination (NAM/PN).

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

summary: Working with primary human myogenic progenitors (hMPs), we developed a high-content screen to discover molecules that enhanced myogenic function and identified NAM and PN as modulators of myogenic proliferation and differentiation. We characterized genome-wide expression profiles of NAM-, PN-treated and NAM/PN-treated hMPs with the goal to uncover the mechanisms of action of NAM and PN and the potential additivity from the combination at the molecular level in hMPs.

overall_design: hMPs (commercially available from Lonza) were treated with either 1% DMSO (vehicle), 1mM of nicotinamide, or 1mM of pyridoxine or the combination for 72 hours in growth medium (AmsBio). We performed biological replicates on 5 different donors for each treatment condition.

first: Joris

last: Michaud

first: Pascal

last: Stuelsatz

first: Metairon

last: Sylviane

first: Eugenia

last: Migliavaccca

middle: N


title: Time-restricted feeding prevents memory impairments induced by obesogenic diet consumption in mice, in part through hippocampal thyroid hormone signaling.

city: BORDEAUX

first: jean-christophe

last: Helbling

state: --None--

address: Université de Bordeaux - INRAE, Rue Leo Saignat, 146

department: Alimentation humaine

country: France

institute: INRAE

summary:
Objective: The early consumption of calorie-rich diet disrupts circadian rhythms and has adverse effects on memory, yet the effects of timerestricted
feeding (TRF) and the underlying molecular mechanisms are unknown. Here, we set out to identify the behavioral and molecular
circadian rhythms disruptions generated by juvenile obesogenic diet consumption and their restoration by TRF in male mice.
Methods: Metabolic rhythms were measured by indirect calorimetry and memory performances by behavioral tasks. Hippocampal translatome
(pS6_TRAP), enrichment and co-regulated gene network analyses were conducted to identify the molecular pathways involved in memory
impairments and their restoration by TRF. Differential exon usage analyses, mass spectrometry and pharmacological intervention were used to
confirm thyroid hormone signaling involvement.
Results: We show that four weeks of TRF restore the rhythmicity of metabolic parameters and prevents memory impairments in mice fed a high
fat-high sucrose (HFS) diet since weaning, independently of body fat levels. Hippocampal translatome and differential exon usage analyses
indicate that impaired memory of mice under ad libitum HFS diet is accompanied by reduced thyroid hormone signaling and altered expression of
astrocytic genes regulating glutamate neurotransmission. TRF restored the diurnal expression variation of part of these genes and intrahippocampal
infusion of T3, the active form of thyroid hormone, rescues memory performances and astrocytic gene expression of ad libitum
HFS diet-fed mice.
Conclusions: Thus, thyroid hormones contribute to the TRF positive effects on both metabolism and memory in mice fed an obesogenic diet,
highlighting this nutritional approach as a powerful tool in addressing obesity brain comorbidities and paving the way for further mechanistic
studies on hippocampal thyroid signaling.

overall_design:
To investigate translatome in our groups we applied pS6-TRAP mRNA purification for each C57Bl6J mouse sample
We then performed RNA sequencing at basal condition zt3 and zt15. To evaluate translatome during memory formation, we performed RNA sequencing 1h and 12h post 10 minutes Object Recognition Memory task training

first: Jean-Christophe

first: Rachel

last: Ginieis

first: Pierre

last: Mortessagne

first: Mariano

last: Ruiz-Gayo

first: Eva

middle: G

last: Ducourneau

first: Dominique

last: Ciocca

first: Illona-Marie

last: Boulete

first: Alexandre

last: Favereaux

first: Aurélia

last: Ces

first: Enrica

last: Montalban

first: Lucile

last: Capuron

first: Freddy

last: Jeanneteau

first: Guillaume

first: Etienne

last: Challet

first: Marie-Pierre

last: Moisan


title: Whole transcriptome sequencing identifies key lncRNAs,circRNAs, and mRNAs for exploring the pathogenesis and therapeutic target of mouse pneumoconiosis

city: Taiyuan

first: ting

last: liu

address: NO.85 Jiefang South Road, Yingze District

institute: The First Clinical Medical College of Shanxi Medical University

summary: The purpose of this study was to characterize the lncRNA, circRNA, and mRNA profile of silica-treated pneumoconiosis mice model and to analyze the changes in differential expression genes, biological processes, and signaling pathways based on the differently expressed genes. Lung tissues from 12 mice, 6 silicosis mice, and 6 normal saline were collected and analyzed for their lncRNA, circRNA, and mRNA profile profiles. After qualified library inspection, Illumina PE150 sequencing was performed after pooling according to the effective concentration of the library and data output requirements. Differentially expressed mRNAs/lncRNAs/circRNAs (DEMs) were identified between the different groups, the target miRNAs (co-pre-miRNAs) were obtained by intersecting the miRNAs predicted by DElncRNA and DEcircRNA, respectively, and the target mRNAs (co-mRNA) were obtained by intersecting the mRNAs predicted by target miRNA and DEGs. Then, the lncRNA/circRNA-miRNA-mRNA networks were constructed by Cytoscape. Next, the key mRNAs were obtained by protein-protein interaction (PPI) analysis, and the key lncRNAs/circRNAs were selected by correlation analysis. Moreover, the expression of the key lncRNAs, circRNAs and mRNAs on chromosome were studied by the “circlize” package. Furthermore, the TFs-miRNA-mRNA network was constructed and the function of DEGs were explored by Ingenuity Pathway Analysis (IPA). Finally, We used the Drug-Gene Interaction database to predict potential drugs that could interfere with key genes,which may help to find promising treatment. This study constructed the lncRNA/circRNA-miRNA-mRNA and TFs-miRNA-mRNA networks, which could deepen the potential molecular regulatory mechanism of pneumoconiosis/silicosis.

overall_design: RNA-sequence of circRNA,lncRNA and mRNA in the silica-treated silicosis mice model and sterile normal saline sample were performed and analysed by Novogene (Beijing, China)

first: Chen

last: Wang

first: Ting

last: Liu

first: Xuesen

last: Su

first: Xiaomei

last: Kong

first: Hantian

last: Dong

first: Yangyang

last: Wei

first: Yan


title: Transcriptional regulation by the stringent response-associated alarmone (p)ppGpp in Pseudomonas putida

city: Sevilla

first: Marta

last: Pulido-Sánchez

state: Sevilla

address: Ctra. de Utrera Km.1, Sevilla

country: Spain

institute: Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide

summary: The stringent response is an adaptive physiological response triggered by different conditions of nutritional or environmental stress and aimed at increasing survival under harsh conditions. This response is mediated the signalling nucleotides guanosine tetraphosphate (ppGpp) and pentaphospate (pppGpp), collectively known as (p)ppGpp. In this study we aim to identify genome-wide targets of regulation by the stringent-response associated alarmone (p)ppGpp in Pseudomonas putida by performing RNA-seq experiments using the wild-type KT2440tel strain and a KT2440tel-derivative bearing deletions of the (p)ppGpp synthetase-encoding genes relA and spoT (ppGpp0 mutant).

overall_design: Three biological replicates of wild-type P. putida KT2440tel and the ppGpp0 mutant were grown to stationary phase (OD600=4.0) in lysogeny broth (LB) at 30ºC and 180 rpm shaking.

first: Aroa

last: López-Sánchez

first: Fernando

last: Govantes


title: Effect of IP6K2-deletion on mRNA expression in mouse spinal cord and duodenum

city: Isehara

first: Masatoshi

last: Ito

state: Kanagawa

address: 143 Shimokasuya

country: Japan

institute: Tokai University

summary: Inositol pyrophosphates (PP-IPs) regulate diverse physiological processes. Mammalian genome encodes three enzymes (IP6K1-3) synthesizing PP-IP diphosphoinositol pentakisphosphate (IP7). The objective of this experiment is to elucidate the physiological roles of IP6K2-dependent PP-IPs metabolism in gene expression of central nervous system and gastrointestinal tract. Mouse GE 4×44K v2 microarray was employed to comprehensively analyze mRNA expression in spinal cord and duodenum. We observed that mRNAs prominently increased or decreased by IP6K2 deletion were different in each organ, suggesting differential regulatory roles of IP6K2-IP7 axis in these two organs.

overall_design: Spinal cord and duodenum were obtained from IP6K2-KO and Littermate WT control mouse. Total RNA extract of mouse duodenum was carefully carried out to minimize RNA degradation by digestive juice.

first: M

first: K

last: Yokoyama

first: S

last: Isaki

last: Tanaka

first: E

last: Nagata


title: Endothelial FUNDC1 Deficiency Drives Pulmonary Hypertension [scRNA-seq]

first: yandong

last: pei

summary: FUNDC1 protein levels were reduced in PH lung vessels from clinical subjects and animal models. Global Fundc1 deficiency exacerbated PH, while its overexpression is protective. The effect of FUNDC1 was mediated by endothelial cells rather than smooth muscle cells. Further, inducible loss of endothelial Fundc1 in postnatal mice was sufficient to cause PH spontaneously, whereas augmenting endothelial Fundc1 protected against PH before and after the onset of disease. Mechanistically, Fundc1 deficiency impaired basal mitophagy in endothelial cells, leading to accumulation of dysfunctional mitochondria, metabolic reprogramming towards aerobic glycolysis, pseudohypoxia and senescence, likely via a mtROS-HIF2α signaling pathway. Subsequently, Fundc1-deficient endothelial cells increased IGFBP2 secretion that drove pulmonary arterial remodeling to instigate PH. Finally, proof-of-principle in vivo studies showed significant efficacy on PH amelioration by targeting endothelial mitophagy, pseudohypoxia, senescence or IGFBP2.

overall_design: Single-cell suspensions from NW,NK,HSW,HSK proup were analyzed using scRNAseq. We use the HySu (hypoxia and SU5416) PH model. The HySu mice received 3 weekly doses of SU5416. SU5416 was resuspended in a carboxymethylcellulose solution (wt/vol: 0.5% carboxymethylcellulose sodium, 0.9% sodium chloride, 0.4% polysorbate 80, and 0.9% benzyl alcohol in water). Control groups were administered with the same volume of vehicle and kept under normoxia.Single lung cell suspensions from Normoxia-WT (NW), Normoxia-FUNDC1-KO (NK), HySu-WT (HSW), HySu-FUNDC1-KO (HSK) group were analyzed using scRNAseq.

first: Yandong

last: Pei

first: Dongfeng

last: Ren


title: Aspergillus nidulans dynamic transcriptome during synchronized conidiation

city: Baltimore

first: Harley

last: Edwards

state: Maryland

address: 1000 Hilltop Circle

department: CBEE

institute: University of Maryland, Baltimore County

summary: The dynamic transcriptome of A. nidulans during synchronized conidiation has over 2500 gene products show differential expression, including transcripts for both brlA and abaA, which increase steadily over time. In contrast, GSE136562, a dynamic transcriptomic response taken during wall-stress induced by the echinocandin micafungin, the brlA transcript is upregulated while the abaA transcript is not. In addition, when mpkA (last protein kinase in the cell wall integrity signaling pathway) is deleted, brlA expression is not upregulated in response to wall stress. Together, these data imply BrlA may play a role in a cellular stress-response which is independent of the canonical BrlA-mediated conidiation pathway.

overall_design:
Synchronous asexual development of Aspergillus nidulans was initiated via growth of mycelia from the air/liquid interface. Samples were taken at 0, 6, 12, 18, 24, 30 and 48 hours after the initiation of asexual development.

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first: Daniel

last: Ebbole

first: Heather

middle: H

last: Wilkinson

first: Brian

middle: D

last: Shaw

first: Steven

last: Harris

first: Mark

middle: R

last: Marten


title: Multidimensional analysis of patient-matched primary and recurrent glioblastoma identifies microglial FCGR1A (CD64) and other FCGRs as contributors of tumor recurrence [NS_Hs_NeuroInflam_v1.0]

city: Basel

first: Sabrina

middle: Annie

last: Hogan

address: Hebelstrasse 20

institute: University of Basel

summary: Introduction: Glioblastoma (GBM) is a lethal brain tumor without effective treatment options. Here, we sought to characterize longitudinal tumor immune microenvironment (iTME) changes in order to find potential actionable targets to prevent GBM-induced immune evasion mechanisms. This study included 15 patient-matched treatment-naïve (primary, pGBM, WHO grade 4) and recurrent (rGBM) IDH1 wild type tumors. Methods: Extracted RNA and proteins from fresh frozen tumor samples from matched pGBM and rGBM were profiled via transcriptomics and proteomics, respectively. Paired formalin-fixed paraffin-embedded tumor samples were processed for spatial transcriptomics analysis. Results: Differentially expressed genes and proteins between pGBM and rGBM were involved in pathways responsible for  synapse development and myelination which have been shown to play a role in GBM recurrence. By categorizing patients into short and long time-to-relapse (STTR vs LTTR), and by correlating TTR with gene expression, we detected genes positively or negatively associated with tumor relapse. Expression of FCG receptor and complement system genes such as FCGR1A (CD64), FCGR3A (CD16a) and the complement C3 were negatively correlated with STTR, whereas high expression of DNMT1/3A, and SMARCA4, involved in DNA methylation, were positively correlated with LTTR. Spatial transcriptomic analysis of the tumor cells compartment defined by GFAP expression showed enrichment in the proportion of oligodendrocytes in recurrent tumors in rGBM, whereas CD64-positive myeloid cell compartment showed a switch of quiescent to activated microglia, appearance of B cells and a reduction in macrophage proportion in recurrent tumors with STTR. Conclusion: Our results uncover a role of CD64-expressing myeloid cells, mostly activated microglia, in GBM recurrence and suggest that interfering with these cells may represent a new therapeutic option for preventing GBM relapse.

overall_design: RNA from 17 patients' matched primary and recurrent GMB tumors was extracted and gene expression was analyzed through hybridization to the NanoString Human nCounter Neuroinflammation panel set probes

first: Tala

last: Shekarian

first: Tomas

last: Martins

first: Philip

last: Schmassmann

first: Alexandra

last: Gerber

first: Julien

last: Roux

first: Deniz

last: Kaymak

first: Célia

last: Durano

first: Bettina

last: Burger

first: Matthias

last: Matter

first: Marie-Françoise

last: Ritz

first: Gregor

last: Hutter


title: Genome-wide transcriptional regulation by the flagellar sigma factor FliA in Pseudomonas putida

first: Marta

last: Pulido-Sánchez

summary: The sigma factor FliA (σ28) has been described to activate the expression of several chemoreceptor-encoding genes and the late flagellar genes in Pseudomonas putida, enabling synthesis of the filament, an stator complex and completion of the flagella-associated chemotaxis machinery. The activity of FliA is repressed in the cytoplasm by the anti-sigma factor FlgM upon completion of the flagellar hook. In this study we aim to identify genome-wide targets of regulation by FliA in P. putida KT2442 (a spontaneous rifampicin-resistant mutant of the reference strain KT2440) by performing RNA-seq experiments using a fliA deletion mutant and a constitutively active strain that combines the deletion of flgM with ectopic production of FliA.

overall_design: We introduced a miniTn7-derivative to express fliA under the salicylate-inducible nahR-Psal system into a P. putida KT2442-derivative ΔflgM mutant (ΔflgM/Psal-fliA), and a control miniTn7 cassette only bearing the nahR-Psal system into the ΔfliA strain. Three biological replicates of the control ΔfliA and ΔflgM/Psal-fliA strains were grown to exponential phase (OD600=0.3) in lysogeny broth (LB) supplemented with 2 mM sodium salicylate at 30ºC and 180 rpm shaking.

first: Aroa

last: López-Sánchez

first: Fernando

last: Govantes


title: Multidimensional analysis of patient-matched primary and recurrent glioblastoma identifies microglial FCGR1A (CD64) and other FCGRs as contributors of tumor recurrence

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

overall_design: Refer to individual Series


title: Multidimensional analysis of patient-matched primary and recurrent glioblastoma identifies microglial FCGR1A (CD64) and other FCGRs as contributors of tumor recurrence [NS_IO_360_v1.0]

overall_design: RNA from 17 patients' matched primary and recurrent GMB tumors was extracted and gene expression was analyzed through hybridization to the NanoString Human nCounter PanCancer IO 360 Panel set probes


title: Comprehensive gene expression analysis of grape-like and other morphologically different organoids in iPSC derived hepatocyte organoids(iHOs).

city: Kamakura

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: iHOs contain morphologically different organoids. Comprehensive gene expression analysis showed grape-like organoids have hepatocyte-like gene expression profiles.

overall_design: Comparative gene expression profiling analysis of microarray data for grape-like and other morphologically different organoids. iHOs were harvested in passage 0. Then grape-like organoids and others were visually sorted and each RNA was extracted respectively.

first: Taro

last: Shimizu

first: Masato

last: Miyoshi

first: Sei

last: Kakinuma


title: Integrated multiomic analysis identifies TRIP13 as a mediator of alveolar  epithelial type II cell dysfunction in idiopathic pulmonary fibrosis

city: Duarte

first: Crystal

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Idiopathic pulmonary fibrosis (IPF) is a lethal progressive lung disease urgently needing new therapies. Current treatments only delay disease progression, leaving lung transplant as the sole remaining option. Recent studies support a model whereby IPF arises because alveolar epithelial type II (AT2) cells, which normally mediate distal lung regeneration, acquire airway and/or mesenchymal characteristics, preventing proper repair. Mechanisms driving this abnormal differentiation remain unclear. We performed integrated transcriptomic and epigenomic analysis of purified AT2 cells which revealed genome-wide alterations in IPF lungs. The most prominent epigenetic alteration was activation of an enhancer in thyroid receptor interactor 13 (TRIP13), coinciding with TRIP13 upregulation. TRIP13 is broadly implicated in epithelial-mesenchymal plasticity and transforming growth factor-beta signaling. In cultured human AT2 cells and lung slices, small molecule TRIP inhibitor DCZ0415 prevented acquisition of the mesenchymal gene signature characteristic of IPF, suggesting TRIP13 inhibition as a potential therapeutic approach to fibrotic disease.

overall_design: AT2 cells purified from primary human normal and IPF samples underwent bulk RNAseq and bulk ATACseq profiling and data integration to determine the extent and effect of epigenomic remodeling on AT2 biology in IPF. Bulk ATACseq was also performed on primary proximal lung basal cells.

first: Laurence

last: St. Pierre

first: Asres

last: Berhan

first: Eun

last: Sung

first: Juan

last: Alvarez

first: Hongjun

last: Wang

first: Yanbin

last: Ji

first: Yixin

last: Liu

first: Haoze

last: Yu

first: Angela

last: Meier

first: Kamyar

last: Afshar

first: Eugene

middle: M

last: Golts

first: Grace

middle: Y

last: Lin

first: Alessandra

last: Castaldi

first: Ben

last: Calvert

first: Amy

last: Ryan

first: Beiyun

last: Zhou

first: Ite

last: Offringa

first: Zea

last: Borok


title: Transcriptome Analysis Reveals Organ-Specific Effects of 2-Deoxyglucose Treatment in Healthy Mice

city: Bar Harbor

first: Chih-Hao

last: Chang

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Glycolytic inhibition via 2-deoxy-D-glucose (2DG) has potential therapeutic benefits for a range of diseases, including cancer, epilepsy, systemic lupus erythematosus (SLE), and rheumatoid arthritis (RA), and COVID-19, but the systemic effects of 2DG on gene function across different tissues are unclear. This study analyzed the transcriptional profiles of nine tissues from C57BL/6J mice treated with 2DG to understand how it modulates pathways systemically. Principal component analysis (PCA), weighted gene co-network analysis (WGCNA), analysis of variance, and pathway analysis were all performed to identify modules altered by 2DG treatment. Data analyses, data, and code are available as a data resource website. PCA revealed that samples clustered predominantly by tissue, suggesting that 2DG affects each tissue uniquely. Unsupervised clustering and WGCNA revealed six distinct tissue-specific modules significantly affected by 2DG, each with unique key pathways and genes. 2DG predominantly affected mitochondrial metabolism in the heart, while in the small intestine, it affected immunological pathways. These findings suggest that 2DG has a systemic impact that varies across organs, potentially affecting multiple pathways and functions. The study provides insights into the potential therapeutic benefits of 2DG across different diseases and highlights the importance of understanding its systemic effects for future research and clinical applications.

overall_design: C57BL/6J male mice were treated with 2DG (6g/L) orally for 96 hours or 4 weeks or received control water. At 96 hours or 4 weeks mice were euthanized and heart, hippocampus, hypothalamus, kidney, liver, prefrontal cortex, skeletal muscle, small intestine, and spleen were harvested for bulk RNAseq.

first: Ann

middle: E

last: Wells

first: John

middle: J

last: Wilson

first: Sarah

last: Heuer

last: Sears

first: Jian

last: Wei

first: Raghav

last: Pandey

first: Mauro

middle: W

last: Costa

first: Catherine

middle: C

last: Kaczorwoski

first: Derry

last: Roopenian

first: Gregory

last: Carter


title: Transcriptome profiling of Muscle Stem cells from aged mice following treatment with the combination of nicotinamide (NAM) and pyridoxine (PN) for 3 days.

first: Jerome

last: Feige

summary: Nicotinamide and pyridoxine have been identified as potent modulators of Muscle Stem cell activity. We characterized genome-wide expression profiles of NAM/PN-treated MuSC and Vehicle to verify if NAM/PN supplementation reverses MuSC dysfunction  during Aging.

overall_design: Freshly isolated MuSC from aged mice were seeded and treated with either 1% DMSO (vehicle) or the combination of nicotinamide and pyridoxine for 72 hours in growth medium. From 8 mice, we performed 4 independent biological replicates (pool of 2 mice).

first: Joris

last: Michaud

first: Pascal

last: Stuelsatz

first: Metairon

last: Sylviane

first: Eugenia

last: Migliavaccca


title: Aberrant zonal recycling of germinal center B cells impairs appropriate selection in lupus

city: Newark

first: Arthur

middle: James

last: VanValkenburg

state: NJ

address: 185 S Orange Ave

institute: Rutgers New Jersey Medical School

summary: Systemic autoimmunity is driven by the production of pathogenic autoantibodies that can arise from germinal centers (GCs). Typically, B cells that acquire autoreactivity following somatic hypermutation in the GC die of neglect, but in autoimmunity these autoreactive clones still receive T cell help, driving aberrant selection. GC B cells cycle between the dark zone (DZ), where proliferation and mutation occur, and the light zone (LZ) where selection occurs. Temporal assessment comparing GCs from mice with chronic infection or lupus revealed a shared accumulation of LZ B cells while lupus GC B cells had a unique reduction in proliferation and a progressive loss of MYC and FOXO1 in lupus. This loss in proliferative capacity coincided with a reduction in B cell receptor repertoire diversity and mutational burden. Furthermore, we identified persistent dominant GC B cell clones associated with an expansion in plasma cell differentiation throughout disease. Together, our findings suggest that lupus disease progression is characterized by an inability for proper LZ selection, preventing zonal recycling, thereby driving the permissive selection and differentiation of autoreactive B cells.

overall_design: Germinal center (GC) B cells were sorted from the spleens of 3 B6.SLE1.yaa mice for each timepoint of 2 months (pre-disease), 4 months (disease onset), and 6 months (disease onset). 6000 GC B cells from each mouse were barcoded with hashtag antibodies, pooled, processed through the 10X RNA/V(D)J kit, and sequenced with the 10x Genomics Noavaseq 6000. Data was aligned to mm10 reference genome with cellranger ver.XXX. Output scRNA-seq FASTQ files were processed using Immcantations pipelines from Kleinstein Lab pREST0 and Change-O for BCR alignment and V(D)J alignment respectively, and Seurat (v.5.0.1) was used to analyze gene expression data to determine differences in GC B cell gene expression, V(D)J sequences, and BCR repertoire at different stages of the onset of lupus.

first: Gina

last: Sanchez

first: Eden

middle: S

last: Hirsch

first: Daniel

middle: P

last: Mayer

first: Komi

last: Gbedande

first: Rebecca

middle: L

last: Francis

first: Wenzhi

last: Song

first: Olivia

middle: Q

last: Antao

first: Kyleigh

last: Brimmer

first: Alexander

last: Lemenze

first: Robin

last: Stephens

first: W

last: Johnson

first: Jason

last: Weinstein


title: Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia [scRNA-Seq]

city: Vestec

first: Lukas

last: Valihrach

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science

summary: We performed spatial and single-cell transcriptomics on male mouse brains to map out the molecular and cellular processes governing the response to ischemic stroke during the first week after the injury. Focusing on glial cells, we documented their activation, the formation of the glial scar, and significant changes in cell–cell communication patterns. Interestingly, we identified various activated populations of oligodendrocytes that, while similar in their anti-inflammatory properties, differ in their immunogenic and metabolic characteristics. This challenges the long-held belief that oligodendrocytes play a passive role in neuropathologies. Altogether, we present a major contribution to the current understanding of the role of glial cells in stroke pathobiology, comprehensively mapping their acute response and role in the formation of the glial scar.

overall_design: To invesigate ischemic brain injury, mouse model of permanent middle cerebral artery occlusion was used. Screened timepoints include control, day 1, 3, and 7 post the injury. For each timepoint, three forebrain hemispheres (bregma from ~ +3 to -4 mm) were collected, pooled, FACS-sorted and processed with scRNA-Seq protocol.

last: Zucha

first: Pavel

last: Abaffy

first: Denisa

last: Kirdajova

last: Jirak

first: Mikael

last: Kubista

first: Miroslava

last: Anderova


title: Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia


title: Transcriptome profiling of Gastrocnemius from mice following supplementation with the combination of nicotinamide and pyridoxine (NAM/PN)

first: Jerome

last: Feige

summary: Nicotinamide and pyridoxine have been identified in an in vitro screening as potent modulators of Muscel Stem cell activity. To test the in vivo efficacy (of NAM/PN) on muscle regneration, we used a mouse model of muscle injury and regeneration. Transcriptomic analyses on whole muscles harvested 5 days after muscle injury were performed to better understand the effect of NAM/PN.

overall_design: To induce a muscle injury (Day 0), cardiotoxin was injected into muscles from 1 leg. From Day 0, mice were daily treated by oral gavage either with NAM/PN or a matching placebo. At Day 5 after induction of muscle injury, mice were euthanized and muscle tissue were collected. Young and aged mice were used in this study. Gastrocnemius muscles from both legs (contralateral and injured) were used for transcriptomic analyses.

first: Joris

last: Michaud

first: Pascal

last: Stuelsatz

first: Metairon

last: Sylviane

first: Eugenia

last: Migliavaccca

middle: N


title: Glutathione enhances antitumor activity of NK cells via modulation of mitochondrial metabolism in acute leukemia patients

status: Public on Nov 17 2024

city: hefei

first: Yue

last: Zhao

institute: univerisity of science and techonology of china

summary: Natural killer (NK) cell function is markedly impaired in acute leukemia patients, weakening their antitumor immune response; however, the specific mechanisms underlying these functional deficits remain incompletely understood. Here, we reveal the critical role of glutathione (GSH) metabolism in maintaining NK cell homeostasis and function. Compared with healthy individuals, NK cells from acute leukemia patients exhibit markedly reduced GSH levels. GSH depletion impairs NK cell cytotoxic activity, cytokine production, and proliferative capacity. Notably, supplementation with glutathione reduced ethyl ester (GSHEE) enhances the antileukemic activity of NK cells. Mechanistically, GSH supports optimal NK cell function by improving mitochondrial function and promoting oxidative phosphorylation (OXPHOS). In summary, this study identifies disrupted GSH metabolism as a driver of NK cell dysfunction in acute leukemia and suggests that GSH supplementation may enhance NK cell-mediated antileukemic effects, offering a potential new strategy for NK cell-based immunotherapy.

overall_design: To explore the regulatory effect of BSO on HC-NK cell function, we isolated and purified NK cells from the peripheral blood of 3 healthy donors and treated them with BSO for 72 hours. To explore the effect of GSHEE on AL-NK cells, we isolated and purified NK cells from the peripheral blood of 4 acute leukemia patients and treated them with GSHEE for 12 hours.

first: Yan

last: Wang

first: Changcheng

last: Zheng

first: Fang

last: Ni


title: m6A sequences 2 WT_input vs 2 Ythdf1 KO_input

city: Shenzhen

first: yuan

last: meng

address: College avenue 1066#

department: Department of Medicine

institute: Shenzhen University

summary: Methylated RNA immunoprecipitation(MeRIP) with specific m6A antibody and used for library construction and the next generation sequencing, to identify m6A modified transcripts in WT or Ythdf1 deficiency colon epithelial cells after DSS treatment

overall_design: 2 WT_input vs 2 Ythdf1 KO_input

first: Yuan

last: Meng

first: Chenzhong

last: Xu

first: Baohua

last: Liu


title: m6A modification in Herceptin resistant cells [MeRIP-Seq]

city: nanjing

first: yongfei

last: li

address: No.155 Hanzhong Road

department: Department of Mastopathy

institute: The Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of TCM)

type: Methylation profiling by high throughput sequencing

summary: We report the application of specific antibodies and high-throughput sequencing technologies (methylated RNA immunoprecipitation sequencing, MeRIP-seq) for high-throughput profiling of m6A modifications in breast cancer herceptin resistant cells. We generated maps of m6A modified transcripts in BT474 and BT474.TtzmR cells. We find that the m6A level was significantly increased in BT474.TtzmR cells compared to the BT474 cells. We show that there was a close correlation between the m6A modification and herceptin  resistance.

overall_design: Examination of m6A modifications in 2 cell types

first: Yongfei

last: Li


title: Multidimensional analysis of patient-matched primary and recurrent glioblastoma identifies microglial FCGR1A (CD64) and other FCGRs as contributors of tumor recurrence [seq]

first: Sabrina

last: Hogan

summary: Introduction: Glioblastoma (GBM) is a lethal brain tumor without effective treatment options. Here, we sought to characterize longitudinal tumor immune microenvironment (iTME) changes in order to find potential actionable targets to prevent GBM-induced immune evasion mechanisms. This study included 15 patient-matched treatment-naïve (primary, pGBM, WHO grade 4) and recurrent (rGBM) IDH1 wild type tumors. Methods:Extracted RNA and proteins from fresh frozen tumor samples from matched pGBM and rGBM were profiled via transcriptomics and proteomics, respectively. Paired formalin-fixed paraffin-embedded tumor samples were processed for spatial transcriptomics analysis.Results: Differentially expressed genes and proteins between pGBM and rGBM were involved in pathways responsible for synapse development and myelination which have been shown to play a role in GBM recurrence. By categorizing patients into short and long time-to-relapse (STTR vs LTTR), and by correlating TTR with gene expression, we detected genes positively or negatively associated with tumor relapse. Expression of FCG receptor and complement system genes such as FCGR1A (CD64), FCGR3A (CD16a) and the complement C3 were negatively correlated with STTR, whereas high expression of DNMT1/3A, and SMARCA4, involved in DNA methylation, were positively correlated with LTTR. Spatial transcriptomic analysis of the tumor cells compartment defined by GFAP expression showed enrichment in the proportion of oligodendrocytes in recurrent tumors in rGBM, whereas CD64-positive myeloid cell compartment showed a switch of quiescent to activated microglia, appearance of B cells and a reduction in macrophage proportion in recurrent tumors with STTR. Conclusion: Our results uncover a role of CD64-expressing myeloid cells, mostly activated microglia, in GBM recurrence and suggest that interfering with these cells may represent a new therapeutic option for preventing GBM relapse.

overall_design: This dataset comprises gene expression data from a glioblastoma (GBM) tissue microarray (TMA) constructed with a subset of 7 patient-paired primary and recurrent FFPE GBM samples.  Two molecularly defined compartments were analysed, CD64+ (FCGR1A) myeloid cells and GFAP+ tumor cells. Experiments was performed twice on subsequent slides from the same block. Nanostring GeoMx Digital Spatial Profiling (DSP) Whole Transcriptome Atlas (WTA) Panel (>18,677 target genes) was used per manufacturer’s protocol. 78 ROIs corresponding to 78 AOIs were collected and analysed

first: Tala

last: Shekarian

first: Tomas

middle: A

last: Martins

first: Philip

last: Schmassmann

first: Alexandra

last: Gerber

first: Julien

last: Roux

first: Deniz

last: Kaymak

first: Célia

last: Durano

first: Bettina

last: Burger

first: Matthias

last: Matter

first: Marie-Françoise

last: Ritz

first: Gregor

last: Hutter


title: Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [small RNA-seq]

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

summary: Tomato is a major global crop however its production is limited by Botrytis cinerea. Due to the toxicity of post-harvest pesticide application, alternative control methods such as priming are being investigated. Plants were treated with β-aminobutyric (BABA) at two developmental stages and resistance against B. cinerea was tested in fruit tissue and in progenies. DNA methylation and RNA sequencing were conducted to characterise the (epi)genetic changes associated with long-lasting resistance. Grafting experiments were done to assess the systemic nature of this signal, which was further characterised by small RNA (sRNA) sequencing of scions. Only BABA-treated seedlings displayed induced resistance (IR). DNA methylation analysis revealed seedling-specific changes, which occurred in the context of lower basal methylation. BABA-IR was found to be transmissible from primed rootstock to grafted unprimed scions. In these scions, we identified a subset of mobile 24 nt sRNAs associated with primed genes to infection in fruit. Our results demonstrate the functional association of a systemic signal with long lasting IR and priming. Through integrated omics approaches we have identified markers of long-lasting priming in tomato fruit which could also serve as targets for durable resistance in other crops.

overall_design: Examination of small RNAs from leaves of Solanum lycopersicum (cv. Micro Tom), from scions  grafted on rootstock exposed to β-aminobutyric (BABA), or treated with water, along with self-grafted control plants.

first: Estrella

last: Luna-Diez

first: Katie

last: Stevens


title: Tristraprolin regulates basophil inflammatory responses

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

institute: Institute of Science Tokyo


title: Transcriptomic analysis reveals the importance of Protein Phosphatase 2 regulating the growth of soybean roots

city: Guangzhou

first: Xiaohui

last: Mo

address: 483 WUSHAN ROAD, TIANHE DISTRICT.

institute: South China Agricultural University

summary: We functionally characterized a protein phosphatase, GmHAD1-2, which belongs to haloacid dehalogenase (HAD) family. Suppression of GmHAD1-2 significantly decreased lateral root number and length mainly through affecting naringenin, a kind of flavonoid concentration and auxin accumulation in lateral root primordia and tips. RNA-seq analysis revealed that a total of 726 genes exhibited differential expression patterns between WT and suppression of GmHAD1-2 transgenic soybean plant (Ri). A set of DEGs appeared to be involved in root development, including 16 transcription factors (e.g, GmZATs), 2 cell wall related proteins (i.e, GmEXLB1/2), 29 genes related to auxin and ethylene signaling pathways. The results suggest that a complex transcriptional regulatory network participates in the growth of soybean roots.

overall_design: Soybean wild type (WT) and suppression of GmHAD1-2 transgenic soybean plant (Ri) were used in the experiments. Soybean seedlings were transferred into nutrient solution containing 250 mM KH2PO4 (+P). After 12 days, soybean roots were collected for mRNA library construction and sequencing. Each treatment had two biological replicates.

first: Cuiyue

last: Liang

first: Jiang

last: Tian


title: HuR coordinates systemic aging through platelet infiltration

status: Public on Nov 16 2024

city: Beijing

first: liu

last: cihang

address: Xueyuan Road

institute: Peking University Health Science Center

summary: Aging involves morphological and functional changes across different organs, but how these changes are linked among the different organs remains to be elucidated. Here, we uncover a central role of platelets in sys temic aging. In aged mice, the levels of platelet secreted pro inflammatory factors (PSPF) increased greatly in the serum and platelets, leading to a diffuse increase of platelet infiltration in brain, liver, lung, kidney, and aortic root. The RNA binding protein HuR/ELAVL1, a major regulator of R NA metabolism, promoted the production of PSPF in platelets. Platelet specific deletion of HuR reduced the expression of PSPF in platelets, alleviated platelet infiltration in brain, liver, lung, kidney, and aortic root, and delayed systemic aging. Our findings highlight a role of platelets in coordinating aging traits across organs.

overall_design: To investigate the function of platelet HuR in systemic aging, we generated a conditional platelet-specific HuR knockout (cKO) mouse. We collected three 25 month-old wild type(WT) and cKO mice liver, lung and brain for single-nucleus RNA sequencing. We then performed gene expression profiling analysis using data obtained from sn-RNA-seq of 3 WT and cKO mice. Comparative gene expression profiling analysis of different cell type from different tissue of sn-RNA-seq data for cKO mice and its WT littermates.

first: Cihang

last: Liu

first: Ying

last: Wang

first: Tianjiao

last: Xia

first: Jing

last: Lin


title: Results of RNA-Seq in Mn-treated N2a cells

city: Nanning

first: yunfeng

last: zou

address: Shuangyong road

institute: Guangxi Medical University

summary: In order to study the role of epigenetic changes in manganese-induced neurotoxicity, we used RNA-Seq to detect changes in ncRNA expression profiles, providing new insights for the comprehensive study of the mechanism of manganese-induced neurotoxicity.

overall_design: N2a cells were cultured in  MEM medium containing 300 μM manganese for 48 hours

first: Yunfeng

last: Zou


title: Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia [snRNA-Seq]

first: Lukas

last: Valihrach

overall_design: To invesigate ischemic brain injury, mouse model of permanent middle cerebral artery occlusion was used. Screened timepoints include control, day 1, 3, and 7 post the injury. For each timepoint, three forebrain hemispheres (bregma from ~ +3 to -4 mm) were collected, pooled, and processed with snRNA-Seq protocol.

first: Daniel

last: Zucha

first: Pavel

last: Abaffy

first: Denisa

last: Kirdajova

last: Jirak

first: Mikael

last: Kubista

first: Miroslava

last: Anderova


title: Bulk RNA-seq analysis of WT and tristetraprolin (TTP)-knockout basophils treated with antigen/IgE stimulation

first: Kensuke

last: Miyake

summary: Basophils play crucial roles in type 2 immune responses, such as chronic allergic inflammation and protective immunity against parasites. However, the molecular mechanisms regulating basophil activation and effector molecule production remain poorly understood. To investigate the role of RNA-binding proteins (RBPs), we first analyzed the gene expression of CCCH zinc finger proteins in antigen/IgE-stimulated basophils. Among these proteins, we identified that Zfp36, encoding tristetraprolin (TTP), was the most significantly upregulated gene. Therefore, we focused on the functions of TTP in basophils. We generated TTP-KO mice using the CRISPR-Cas9 method and conducted bulk RNA-seq analysis of antigen/IgE-stimulated basophils from wild-type (WT) and TTP-knockout (TTP-KO) mice. TTP-KO basophils exhibited elevated mRNA expression of pro-inflammatory mediators, such as Il4, Il13, Areg, Ccl3, and Cxcl2, compared to WT basophils. These data suggest that TTP is a key regulator of basophil activation, controlling the mRNA expression of inflammatory mediators.

overall_design: To examine the effect of TTP deficiency on gene expression profiles in antigen/IgE-stimulated basophils, WT and TTP-KO basophils sensitized with hapten TNP-specific IgE were treated with control OVA for 2 hours or TNP-conjugated OVA for 2 and 4 hours and then subjected to bulk RNA-seq analysis.

first: Junya

last: Ito

first: Tomoki

last: Chiba

first: Kazufusa

last: Takahashi

first: Yutaro

last: Uchida

first: Hajime

last: Karasuyama

first: Hiroshi

last: Asahara


title: Locus coeruleus vulnerability to tau hyperphosphorylation in a rat model

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

summary: Post-mortem investigations indicate that the locus coeruleus (LC) is the initial site of hyperphosphorylated pretangle tau, a precursor to neurofibrillary tangles (NFTs) found in Alzheimer's disease (AD). The presence of pretangle tau and NFTs in the LC correlates with AD progression. LC neuron integrity and quantity are linked to cognitive states, with degeneration associated with AD. However, the mechanisms of pretangle tau-induced LC degeneration are unclear. This study examined the transcriptomic and mitochondrial profiles of LC noradrenergic neurons after transduction with pseudophosphorylated human tau. Tau hyperphosphorylation increased the somatic expression of the L-type calcium channel (LTCC), impaired mitochondria health, and led to deficits in spatial and olfactory learning. Sex-dependent alterations in gene expression were observed in rats transduced with pretangle tau. Chronic LTCC blockade prevented behavioral deficits and altered mitochondrial mRNA expression, suggesting a potential link between LTCC hyperactivity and mitochondrial dysfunction. Our research provides insights into the consequences of tau pathology in the originating structure of AD.

overall_design: Nuclei were isolated from the locus coeruleus of two experimental groups (AAV-GFP and AAV-htauE14), each with six biological replicates (3 males and 3 females), and analyzed for single nuclei RNA sequencing (snRNA-seq).

first: Zia

last: Hasan

first: Qi

last: Yuan


title: Spatial transcriptome analysis reveals the lymph node atlas of breast cancer metastases

city: Nanjing

first: kun

last: xu

address: 300 Guangzhou Road

institute: Department of Oncology, The First Affiliated Hospital of Nanjing Medical University

summary: To obtain more information about the lymph node metastasis of breast cancer cells, we performed spatial transcriptomics analysis of the positive lymph node (PL) with the 10× Genomics Visium platform, which allows characterization of the spatial topography of gene expression.

overall_design: The positive lymph nodes (PL) were analysed with spatial transcriptome.

first: Kun

last: Xu


title: Redondoviridae infection regulates circRNAome in periodontitis

city: Shanghai

first: Yu

last: Zhang

address: 639 Zhizaoju Road, Shanghai, PR China

institute: Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

summary: Redondoviridae is a recently identified family of DNA viruses associated with periodontitis. Circular RNAs (circRNAs) emerged as a novel endogenous, conserved noncoding RNAs, which contributed to the virus related immune‐inflammatory response. However, the characteristics and function of circRNAs in Redondoviridae related periodontal inflammation are not yet understood. The present study aimed to analyze the expression profiles of circRNAs in gingival tissues in periodontitis patients with and without Redondoviridae-infection and healthy controls using high-throughput RNA sequencing combined with experimental validation. Out of 17819 circRNAs, 175 circRNAs were dysregulated. Functional annotation and enrichment analysis of the differential circRNAs host genes demonstrated the potential alteration in the molecular and cellular components and metabolism in individuals suffering from periodontitis with Redondoviridae infection. Moreover, “axon guidance” (PATH:04360), “lysine biosynthesis” (PATH:00300) and “vascular endothelial growth factor signaling pathways” (PATH:04370) were significantly enriched in Redondoviridae infected gingivitis tissues. Furthermore, the key circRNAs (circCOL1A1, circAASS, circPTK2, circATP2B4, circDOCK1, circTTBK2, and circMCTP2) associated with the pathobiology of Redondoviridae related periodontitis were revealed by constructing circRNA-miRNA-mRNA networks. The bioinformatic analyses demonstrated that several abnormal expression circRNAs may contribute to the etiopathogenesis and development of Redondoviridae-related periodontitis. The findings of the present study have enhanced the current understanding of the mechanism of Redondoviridae-related periodontitis process and provide an insight into further applications for diagnostic markers and therapeutic uses.

overall_design: Analyze the expression profiles of circRNAs in gingival tissues in periodontitis patients with and without Redondoviridae-infection and healthy controls using high-throughput RNA sequencing

first: Chunmei

last: Wang

first: Tongling

last: Shan

first: Wen


title: Nobelitin and Sorafenib Combination Therapy

city: Houston

first: Kristin

last: Mahan

address: 1825 Pressler St

department: MDD

institute: UTHealth science

summary: To enhance hepatocellular carcinoma (HCC) treatment, the combination of Nobelitin (NOB) and Sorafenib (SOR) is being explored. Nobelitin is utilized to induce the expression of BMAL1, a circadian rhythm-related protein, with the goal of improving the effectiveness of SOR in treating HCC. This innovative strategy holds promise for optimizing treatment outcomes for HCC patients.

overall_design: To investigate the effects of NOB and SOR reatments on HCC, the HepG2 cancer cell line was treated with vehicle control, NOB alone, SOR alone, and a combination of NOB and SOR.

first: Baharan

last: Fekry


title: Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia [bulk RNA-Seq]

first: Lukas

last: Valihrach

overall_design: To invesigate ischemic brain injury, mouse model of permanent middle cerebral artery occlusion was used. Screened timepoints include control, day 1, 3, and 7 post the injury. For each timepoint, three forebrain hemispheres (bregma from ~ +3 to -4 mm) were collected and processed using bulk RNA-Seq protocol.

first: Daniel

last: Zucha

first: Pavel

last: Abaffy

first: Denisa

last: Kirdajova

last: Jirak

first: Mikael

last: Kubista

first: Miroslava

last: Anderova


title: Next Generation Sequencing Facilitates Quantitative Analysis of H1299 Wild Type and TTC28-KO Transcriptomes

first: Ge

address: Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Aetiology, Peking University Cancer Hospital and Institute, Beijing 100142, China

institute: Beijing Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education)

summary: Currently, research on the TTC family is still in its early stages. We have generated the H1299 TTC28-KO cell line. The purpose of this study is to utilize next-generation sequencing techniques to investigate the effects of TTC28 knockout on the biological behavior of tumor cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H1299 WT cells and H1299 TTC28-KO cells.

first: Meiyi

last: Xiang

first: Wei

last: Tian

first: Dajun

last: Deng


title: N-acetyl-tryptophan in acute kidney injury after cardiac surgery

status: Public on Nov 15 2024

first: Ning

last: Shi

address: No.639 Longmian Road

institute: State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.

summary: The transcriptome sequencing, surface plasmon resonance and protein mutation were employed to explore the mechanism of N-acetyl-tryptophan on the kidney.

overall_design: To explore the underlying mechanism of N-acetyl-tryptophan in kidney protection, the kidney samples of the 28-day I/R model mice with and without N-acetyl-tryptophan treatment were analyzed by RNA sequencing.


title: Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells

city: New York

first: Wen-Wei

last: Liang

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Mammalian genomes host a diverse array of RNA that includes protein-coding and noncoding transcripts. However, the functional roles of most long noncoding RNAs (lncRNAs) remain elusive. Using massively parallel RNA-targeting CRISPR Cas13 screens, we probed how loss of ~6,200 lncRNAs impacts cell fitness across five human cell lines and identified 778 lncRNAs with either context-specific or broad essentiality. We observe a high level of consistency between distinct guide RNAs targeting the same lncRNA in the pooled screens and confirm their essentiality with individual perturbations. We find that the overwhelming majority of essential lncRNAs operate independently of their nearest protein-coding genes. Using transcriptome profiling in single cells, we discover that essential lncRNAs modulate key cellular pathways for proliferation and that their loss can impair cell cycle progression and drive apoptosis. Many essential lncRNAs demonstrate dynamic expression across tissues during development and, using ~9,000 primary tumors, we pinpoint those lncRNAs whose expression in tumors correlates with survival, yielding new biomarkers and potential therapeutic targets. This transcriptome-wide survey of functional lncRNAs advances our understanding of noncoding transcripts and demonstrates the potential of transcriptome-scale noncoding screens with Cas13.

overall_design: To identify essential lncRNAs, we engineered five human cell lines, HAP1, HEK293FT, K562, MDA-MB-231 and THP1, to express the nuclear-localized RfxCas13d effector under doxycycline-inducible control. Next, we transduced each cell line with the lentiviral gRNA library at a low multiplicity-of-infection to ensure each cell received only a single perturbation and induced Cas13 expression via doxycycline addition. We harvested genomic DNA from these cells at 0, 7, and 14 days post-Cas13 induction and computed changes in gRNA abundance via amplicon sequencing.


title: Identification and comparison of orthologous cell types from primate embryoid bodies shows limits of marker gene transferability

city: Planegg

first: Ines

last: Hellmann

address: Großhaderner Straße 2

department: Anthropology and Human Genomics, Faculty of Biology

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: The foundation of many human-specific traits is likely established during early embryonic development. To understand these molecular processes, we compared gene expression dynamics in embryoid bodies (EBs) differentiated from iPSCs of four primate species: human, orangutan, cynomolgus, and rhesus macaque. We performed scRNA-seq on ∼ 85,000 cells after 8 and 16 days of EB differentiation, identifying diverse cell types across all three germ layers. To accurately compare cell types across species, we developed a semi-automated computational pipeline combining classification and label transfer across clusters to identify orthologous cell types. This approach allowed us to investigate cross-species reproducibility of marker genes, revealing that human markers were less effective in macaques, and vice versa. We found transcription factors to be the most conserved markers, highlighting their potential for cross-species studies. Overall, our study enhances the understanding of conserved and diverged molecular features in early primate development and we provide a well curated cell type reference for future in vitro studies using primates.

sample_organism:
Macaca fascicularis
Macaca mulatta
Pongo abelii
Homo sapiens

overall_design: We generated embryoid bodies (EBs) from iPSCs of two human individuals, two orangutan clones, three cynomolgus clones from two individuals, and three rhesus clones. iPSCs were dissociated to clumps and kept in floating culture for 8 days to form EBs, followed by 8 days of attached culture in gelatin-coated wells. At day 8 and day 16 of the differentiation, we dissociated EBs into single-cells and equally pooled cells from all 4 species, before generating sequencing libraries. We performed the experiment in three independent replicates, generating a total of 4x lanes and 6x lanes of 10x Genomics scRNA-seq at day 8 and day 16, respectively.

first: Jessica

last: Jocher

first: Philipp

last: Janssen

first: Beate

last: Vieth

first: Fiona

last: Edenhofer

first: Tamina

last: Dietl

first: Anita

last: Térmeg

first: Johanna

last: Geuder

first: Wolfgang

last: Enard


title: Methylation cytometric pretreatment blood immune profiles with tumor mutation burden as prognostic indicators for survival outcomes in head and neck cancer patients on anti-PD-1 therapy

city: Boston

first: Ze

last: Zhang

state: MA

address: 375 Longwood Ave

department: Medical Oncology & Population Sciences

institute: Harvard Medical School

summary: Tissue biomarkers for immune checkpoint inhibitor (ICI) response are limited by tumor sample heterogeneity and availability. This study identifies clinically actionable pretreatment blood biomarkers that are associated with ICI treatment response and survival in recurrent/metastatic head and neck squamous cell carcinoma. A prospective multi-center study enrolled 100 patients before standard-of-care immunotherapy. Blood immune profiles, measured by methylation cytometry, were assessed alongside tumor mutational burden (TMB) and PD-L1 combined proportion score (CPS). TMB and PD-L1 CPS were available for 56 and 91 patients, respectively. High neutrophils, monocytes, and neutrophil-to-lymphocyte ratio were associated with worse survival, while high CD4T cells, especially naïve CD4T cells, and lymphocyte-to-monocyte ratio were associated with better survival. Significant interactions between TMB and peripheral immune profiles for both progression-free and overall survival were found. Clinically relevant pretreatment peripheral immune biomarkers were identified, demonstrating the potential of DNA-based immune profiling to predict ICI response before treatment.

overall_design: Bisulphite converted DNA from peripheral whole blood cells were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0 and v2.0

first: Kartik

last: Sehgal

first: Devin

last: Koestler

first: Rondi

last: Butler

first: Lucas

last: Salas

first: Annette

last: Molinaro

first: John

middle: K

last: Wiencke

first: Robert

middle: I

last: Haddad

first: Brock

last: Christensen

first: Karl

middle: T

last: Kelsey


title: Single-cell RNA sequencing defines the interplay between tumor cells, virus and microenvironment in nasopharyngeal carcinoma

first: ruoyan

last: Li

address: Yiheyuan street

institute: Peking University

summary:
Purpose: While viruses play critival roles in many human malignancies, the influence of virus infection on the tumor microenviroment(TME) and how this impacts disease progression are poorly characterized.
Methods:  we applied both Smart-seq2  and 10X Genomics chemistry to ~104000 cells from 19 EBV+ NPC patients and 7 nonmalignant nasopharyngeal biopsies.
Results:
1. We have defined the complex interplay between tumor cells, virus infection, and the TME at single-cell resolution. 2. An epithelial-immune dual feature of malignant cells was discovered and associated with poor prognosis. 3. Stromal and immune cells in the TME were remodeled by tumor cells and virus infection. 4. EBV gene expression was found to correlate with complement factor expression in malignant cells, which, in turn, mediated T cell modulation and recruitment. 5. We subtyped NPC patients into 5 groups with different prognoses according to their respective TME compositions.
Conclusion: Our results provide new insights into the multicellular ecosystem of NPC and offer important clinical implications.

overall_design: NPC single-cell mRNA profiles of primary and lymph node metatstesis were generated through Smart-seq2 and 10X genomic chemistry ,using Illumina Hiseq-X ten.

first: Shanzhao

last: Jin

first: Ruoyan


title: Bioenergetic programs of cancellous and cortical bone are distinct and differ with age and mechanical loading

city: Ithaca

first: Carolyn

last: Chlebek

address: 110 Hoy Road

department: Biomedical Engineering

institute: Cornell University

summary: Mechanical loading induces bone formation in young rodents, but mechanoresponsiveness is reduced with age. Glycolytic activity and mitochondrial dysfunction increase with age and may change bone mechanotransduction. To evaluate load-induced changes to bioenergetic activity in young and adult animals, we loaded the tibia of 10-wk and 26-wk female mice and examined transcriptomic responses at the mid-diaphysis, metaphyseal cortical shell, and cancellous core. Across all biological processes, oxidative phosphorylation and mitochondrial pathways were most often enriched with loading and had opposite enrichment in young and adult animals. Following loading, young animals had temporally-coordinated differential expression of mitochondrial-associated genes, with greatest expression at the mid-diaphysis. In adults, bioenergetic gene expression was lower compared to young animals.

overall_design: Comparative gene expression profiling of RNA-seq data for bone samples from loaded limbs and contralateral control limbs of 10wk and 26 wk old female C57Bl6 mice. At various time points following tibial loading, the cancellous core and 2 cortical segments (metaphyseal cortical shell and mid-diaphysis) were collected. Differential expression was assessed at each cortical location at 1-h, 3-h, and 24-h following a single loading session. To evaluate long term time points, a final group received 5 consecutive days of loading with euthanasia on the eighth day following the first loading session.

first: Tyler

last: McNeill

first: Muyin

last: Huang

first: Maia

last: Raynor

first: Marjolein

last: van der Meulen


title: TSC22D, WNK and NRBP gene families exhibit functional buffering and evolved with Metazoa for cell volume regulation

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

institute: Hospital for Sick Children

summary: The ability to sense and respond to osmotic fluctuations is critical for the maintenance of cellular integrity. We used gene co-essentiality analysis to identify an unappreciated relationship between TSC22D2, WNK1 and NRBP1 in regulating cell volume homeostasis. Each of these genes have paralogs and are functionally buffered for osmo-sensing and cell volume control. Within seconds of hyperosmotic stress, TSC22D, WNK and NRBP family members physically associate into biomolecular condensates, a process that is dependent on intrinsically disordered regions (IDRs). A close examination of these protein families across metazoans revealed that TSC22D genes evolved alongside a domain in NRBPs that specifically binds to TSC22D proteins, which we have termed NbrT (NRBP binding region with TSC22D), and this co-evolution is accompanied by rapid IDR length expansion in WNK family kinases. Our study reveals that TSC22D, WNK and NRBP genes evolved in metazoans to co-regulate rapid cell volume changes in response to osmolarity.

overall_design: Genome-wide CRISPR gene knockout screens were performed in human HAP1 cells across TWN body component knockout queries. Genetic interactions were identified by comparison of each query's fitness profile to screens in HAP1 WT cells documented from Aregger et. al. 2020. WNK463 drug screen were performed in human HAP1 cells and treated with 2.5uM WNK463. The drug screen is compared with DMSO vehicle control to look for sensitizers and maskers.

first: Yu-Xi

last: Xiao

first: Kevin

middle: R

last: Brown


title: Transcriptional response of the cacao pathogen Moniliophthora perniciosa to a strobilurin fungicide

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

department: Biology

country: Brazil

institute: University of São Paulo (ESALQ/USP)

summary: Witches' broom disease (WBD) is a major constraint for cacao production in the Americas. The severe socioeconomic impact of WBD encouraged the evaluation of different control strategies, including the use of strobilurin fungicides. These molecules inhibit mitochondrial respiration, thus impairing ATP generation and leading to oxidative stress. These chemicals, however, have proven ineffective against the WBD pathogen Moniliophthora perniciosa. Here, we demonstrate that M. perniciosa tolerates high concentrations of strobilurins under in vitro conditions and highlight a set of molecular alterations that correlate with strobilurin tolerance in this fungus. Short-term exposure of M. perniciosa to the commercial strobilurin azoxystrobin led to the up-regulation of genes encoding enzymes of the glyoxylate cycle, gluconeogenesis, and fatty acid and amino acid catabolism, indicating that the fungal metabolism is remodeled to compensate for reduced ATP production. Furthermore, cell division, ribosome biogenesis, and sterol metabolism were repressed, which agrees with the impaired mycelial growth on azoxystrobin. Genes associated with cellular detoxification and response to oxidative stress (e.g., cytochrome P450s, membrane transporters and glutathione s-transferases) were strongly induced by the drug and represent potential strategies used by the pathogen to mitigate the toxic effects of the fungicide. Remarkably, exposure of M. perniciosa to azoxystrobin resulted in the spontaneous generation of a mutant with increased resistance to strobilurin. Comparative genomics and transcriptomics revealed alterations that may explain the resistance phenotype, including a large deletion in a putative transcriptional regulator and significant changes in the mutant transcriptome. Overall, this work provides important advances towards a comprehensive understanding of the molecular basis of strobilurin resistance in a tropical fungal pathogen. This is a fundamental step to efficiently employ these fungicides in agriculture and to prevent the emergence of strobilurin resistance.

overall_design: We evaluated the early effects of azoxystrobin on the M. perniciosa transcriptome through a time-course experiment spanning the first eight hours of exposure to the fungicide. Three biological replicates of each M. perniciosa isolate (FA553 and its derivatives FDS01 and FDS02) were cultivated separately in MYEA medium for 28 days. Fungal mycelia were then transferred to liquid cultures and incubated at 28oC under 150 rpm agitation. After seven days, two grams of wet mycelium were transferred to 20 mL of Malt light liquid medium, either without fungicide (control condition) or supplemented with 50 mg/L azoxystrobin (treated condition). Samples were harvested for RNA extraction at five time points: 0 minutes (i.e., immediately after fungal inoculation into the culture media), 30 minutes, 2 hours, 4 hours, and 8 hours.

first: Paula

last: Prado

first: Daniela

last: Thomazella


title: The co-receptor Neuropilin-1 enhances proliferation in inv(16) acute myeloid leukemia via VEGF signaling

city: Worcester

first: Rui

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

summary: Oncogenic programs regulate the proliferation and maintenance of cancer stem cells, and can define pharmacologic dependencies. In acute myeloid leukemia (AML) with the chromosome inversion 16 (inv(16)), the fusion CBF::MYH11 oncoprotein regulates pathways associated with leukemia stem cell activity. Here we demonstrate that expression of Neuropilin-1 (NRP1) is regulated by the fusion oncoprotein, and promotes AML expansion.  Mechanistically, we show that the NRP1 locus has open chromatin in inv(16) AML, and that CBF::MYH11 modulates the local function of the transcription factors ERG, GATA2 and RUNX1 to sustain NRP1 levels. We found that ERG activates NRP1 expression, and that CBF::MYH11 knockdown represses ERG expression, thereby allowing the repressive activity of GATA2/RUNX1 at three NRP1 enhancers. Functionally, we demonstrate that NRP1 enhances the expansion of leukemic cells in vitro and in mice, and that this activity is dependent on its VEGFR-associated FV/FVIII domain. Finally, we show that treatment with VEGF inhibitor axitinib reduces AML cell growth and delays median leukemia latency in vivo. Our findings reveal that the NRP1/VEGF axis mediates proliferation in inv(16) AML blasts, and suggest that targeting NRP1 function could be promising in combination AML therapy.

overall_design: ME-1 cells were transduced with lentiviruses expressing Scramble- or MYH11sh4-RNA in triplicates, cultured for 2 days, and replaced with media supplemented with 5μg/mL Puromycin between days 3 and 6. On day 7, live cells were isolated using Ficoll-gradient centrifugation, and total RNA was isolated with Monarch Total RNA Miniprep kit (New England Biolabs, cat. # T2010S). The RNA concentration was determined using a NanoDrop spectrophotometer (Thermo Fisher Scientific) and the RNA integrity was evaluated with RNA 6000 kit (Agilent Technologies) using a 2100 Bioanalyzer. The sequencing libraries were prepared and sequenced utilizing DNBseq™ Technology (BGI Genomics). The transcriptome profiling of NRP1-shRNA treated ME-1 cells was performed using a similar procedure on day 7 of culture, using Scramble- or NRP1sh3-RNA transduced ME-1 cells, in triplicates.

first: Mahesh

last: Hegde

first: Hafiz

last: Ahmad

first: Roger

middle: M

last: Lazaro

first: Mayumi

last: Sugita

first: Kai

last: Hu

first: Claudia

last: Gebhard

first: Monica

last: Guzman

first: John

middle: H

last: Bushweller

first: Lihua

last: Zhu

first: Michael

last: Brehm

first: Scot

last: Wolfe

first: Ruud

last: Delwel

first: Lucio

last: Castilla


title: RNA-seq to identify differentially expressed mRNAs after cKO of Ybx1 in DRG [RNA-seq]

city: Shenzhen

first: Jun

last: Yu

state: Guangdong

address: Xue Yuan, Nanshan

department: Department of Neuroscience

institute: SUSTech

summary: To identify the target mRNAs of Ybx1 in mouse DRG, we first performed RNAseq to screen differentially expressed mRNAs after knockout of Ybx1. We generated Wnt1-cre+/-;Ybx1fl/fl cKO mice to specifically knockout Ybx1 in DRG. Then we collected E13.5 DRG from cKO mice and litermate Ybx1fl/fl control mice. After RNA extraction and library construction, RNA sequcencing was performed. Finally, we identified 1638 differentially expressed mRNAs. This study provides a gene list which shows mRNA that can be regulated by Ybx1 in mouse DRG.

overall_design: To identify target mRNAs of Ybx1 in mouse DRG, we generated Wnt1-cre+/-;Ybx1fl/fl cKO mice to specifically knockout Ybx1 in DRGs. Then we collected E13.5 DRG from cKO mice and litermate  Ybx1fl/fl control mice. Each group has three biological male samples.

first: Sheng-Jian

last: Ji

first: Yanbo

last: Zhang


title: SLAM-seq analysis of WT and TTP-KO basophils treated with antigen/IgE stimulation

first: Kensuke

last: Miyake

address: 1-5-45, Yushima

institute: Institute of Science Tokyo

summary: Basophils play crucial roles in type 2 immune responses, such as chronic allergic inflammation and protective immunity against parasites. However, the molecular mechanisms underlying the regulation of proinflammatory molecule production by basophils remain unclear. To investigate the role of RNA-binding proteins (RBPs), we first analyzed the gene expression of CCCH zinc finger proteins in antigen/IgE-stimulated basophils and identified that Zfp36, encoding tristetraprolin (TTP), was the most significantly upregulated gene encoding a CCCH zinc finger protein. To explore the functions of TTP in basophils, we generated TTP-knockout (TTP-KO) mice using the CRISPR-Cas9 method and conducted bulk RNA-seq analysis of antigen/IgE-stimulated basophils from wild-type (WT) and TTP-KO mice. TTP-KO basophils exhibited elevated mRNA expression of pro-inflammatory mediators, such as Il4, Il13, Areg, Ccl3, and Cxcl2, compared to WT basophils, suggesting the key role of TTP in the expression of mRNAs encoding proinflammatory mediators. Since TTP is known to regulate mRNA stability in other immune cell types, we evaluated the mRNA stability of WT and TTP-KO basophils under antigen/IgE stimulation using SLAM-seq [thiol (SH)-Linked Alkylation for the Metabolic sequencing of RNA] analysis. SLAM-seq analysis revealed that the mRNA half-lives of proinflammatory molecules, such as Il4, Il13, Areg, Ccl3, and Cxcl2, were prolonged by TTP deficiency, suggesting the importance of TTP in regulating the stability of mRNAs encoding inflammatory molecules in basophils.

overall_design: To examine the effect of TTP deficiency on mRNA stability in antigen/IgE-stimulated basophils, WT and TTP-KO basophils sensitized with hapten TNP-specific IgE were first treated with TNP-conjugated OVA for 1.5 hours in the presence of 4-thiouridine (s4U), then incubated for 0, 1, 2, and 4 hours in the absence of TNP-OVA and s4U, and subjected to alkylation reaction and RNA-seq analysis. The half-life of each mRNA in WT and TTP-KO basophils was calculated using the GRAND-SLAM and grandR packages.

first: Junya

last: Ito

first: Tomoki

last: Chiba

first: Kazufusa

last: Takahashi

first: Yutaro

last: Uchida

first: Hajime

last: Karasuyama

first: Hiroshi

last: Asahara


title: Anti-Ybx1 RIP-seq to identify target mRNAs of Ybx1 in E13.5 DRG [RIP-seq]

summary: In order to identify the target mRNAs of the m5C reader protein Ybx1, we carried out anti-Ybx1 RNA Immunoprecipitation(RIP) followed by RNA-sequencing to find out mRNAs that can directly bind by Ybx1. Using EZ-Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from E13.5 wildtype mouse DRGs was pulled down by rabbit monoclonal anti-Ybx1 (abcam) and sequenced on IIIumina HiSeq3000 platform. The filtered reads were mapped to the mouse reference genome (GRCm39) using BWA mem (v 0.7.12). After peak calling using MACS2 (version 2.1.0) software, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed. Fold enrichment greater than 2 was considered to be enriched. Finally, 2 biological repilicates of anti-Ybx1 RIP-seq identified 2487 transcripts. This study provides a gene list which shows mRNA binding with Ybx1 in mouse DRGs.

overall_design: Anti-Ybx1 RNA immunoprecipitation was performed after lysing dissociated DRGs from E13.5 wildtype mice. Two biological replicates were used, each containing input and IP samples.


title: Transcriptomic analysis of melanoma cells reveals an association of α-synuclein with regulation of the inflammatory response

city: Shreveport

first: Stephan

middle: N.

last: Witt

state: Louisiana

address: 1501 Kings Highway

department: Biochemistry & Molecular Biology

institute: LSUHSC

summary: The Parkinson’s disease protein, alpha-synuclein (α-syn/SNCA), is highly expressed in neurons and melanomas. The goal of this study was to reveal the mechanism(s) of α-syn’s involvement in melanoma pathogenesis. To decipher the genes and pathways affected by α-syn, we conducted an RNA sequencing analysis of human SK-MEL-28 cells and several SK-MEL-28 SNCA-KO clones. We identified 1098 significantly up-regulated genes and 660 significantly down-regulated genes. Several of the upregulated genes are related to the immune system, i.e., the inflammatory response and the matrisome. We validated five upregulated genes (IL-1ý, SAA1, IGFBP5, CXCL8, and CXCL10) by RT-qPCR and detected IGFBP5 and IL-1ý in spent media of control and SNCA-KO cells. The levels of each of these secreted proteins were significantly higher in the spent media of the SNCA-KO clones than control cells. We suggest that the loss of α-syn expression unleashes chemokine/cytokine secretion, which could help melanoma cells evade the immune system.

overall_design: SKMEL28 WT vs SNCA-KO

first: Santhanasabapathy

last: Rajasekaran

first: Siyuan

last: Cheng

first: Nithya

last: Gajendran

first: Sahar

last: Shekoohi

first: Liudmila

last: Chesnokova

first: Xiuping


title: Mechanism of quercetin in the treatment of endometriosis based on network pharmacology and transcriptome sequencing

city: shanghai

first: D

last: Jie

state: shanghai

address: yangpu

institute: Changhai Hospital

summary: This study explores how quercetin may treat endometriosis (EMs) by combining network pharmacology and transcriptome sequencing approaches. Through network pharmacology, 132 shared targets between quercetin and EMs were identified, with KEGG pathway analysis suggesting that the MAPK signaling pathway could be a significant therapeutic target. Transcriptome sequencing revealed that PDGFRB was highly expressed in ectopic endometrial tissue, a finding confirmed by immunohistochemistry (IHC) showing elevated levels of PDGFRB, RAS, RAF1, and ERK1/2 in ectopic lesions. In an EMs mouse model, quercetin treatment led to a marked reduction in ectopic lesion volume, lowered adhesion scores, and decreased expression of PDGFRB, RAS, RAF1, and ERK1/2 in endometrial tissues. Additionally, the knockdown of PDGFRB in endometriosis cells inhibited their proliferation, invasion, and migration, processes critical to EMs pathology. Quercetin treatment further suppressed cell viability and downregulated the protein expression of RAS, phosphorylated RAF1, RAF1, phosphorylated ERK, and ERK1/2. These findings collectively suggest that quercetin exerts its therapeutic effect in endometriosis by regulating the MAPK signaling pathway via PDGFRB, thereby reducing EMs cell proliferation, invasion, and migration. This study provides insights into quercetin’s multi-targeted mechanism of action in endometriosis treatment.

overall_design: Ectopic endometrial tissue and endometrial tissue were obtained from patients undergoing ovarian endometriosis resection in Shanghai Hospital of Traditional Chinese Medicine Affiliated to Shanghai University of Traditional Chinese Medicine from 2019 to 2020. The inclusion criteria were: endometriosis confirmed by pathological diagnosis. This study was approved by the Research Ethics Committee of Shanghai Hospital of Traditional Chinese Medicine, and all patients signed written informed consent. Statement: (1) The experiments were approved by the Ethics Committee of the Shanghai Hospital of Traditional Chinese Medicine (Approval No: 2020SHL-KYYS-102) and registered under clinical trial number SHDC2020CR4056 at the China Clinical Research Trial Registration Center (Registration No: ChiCTR2000036994). (1) All experiments were conducted in strict accordance with relevant guidelines and regulations. Patients for the study were recruited from the Shanghai Hospital of Traditional Chinese Medicine.Transcriptome sequencing was performed using 6 human ectopic endometrial tissue as well as endometrial tissue.  poly (A)+ mRNA in total rna was enriched by oligo (dt) magnetic beads, and the library was purified and constructed.  next generation sequencing (NGS) technology was used, and the library was paired-end based on Illumina sequencing platform, PE sequencing.

first: Jiami

last: Huang


title: BPDCN MYB Fusions Regulate Cell Cycle Genes, Impair Differentiation and Induce Myeloid-Dendritic Cell Leukemia

first: Christopher

last: Booth

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Functional Genomics of Human Skeletal Development and the Patterning of Height Heritability [ATAC-Seq]

city: Stanford

first: Daniel

last: Richard

state: CA

address: 290 Jane Stanford Way

department: Genetics

institute: Stanford University

summary: High-resolution profiling of epigenetic/transcriptomic behaviours of chondrocytes during skeletal development suggest the importance of generalized growth to adult height patterning

overall_design: Epigenetic and transcriptomic profiling of in-vivo chondrocyte populations

first: Pushpanathan

last: Muthuirulan

first: Mariel

last: Young

first: Terence

middle: D

last: Capellini


title: Gene expression in bone marrow-derived dendritic cells obtained from wild-type mice or 3BP2 DL/DL mice stimulated with or without curdlan

city: Yoshida-gun

first: Kazuyasu

last: Chihara

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki, Eiheiji

department: Genome Science and Microbiology

institute: University of Fukui

summary:
C-type lectin dectin-1 is known to recognize beta-glucans such as curdlan and propagate intracellular signaling for activation of NF-kappa B to induce anti-fungal immunity. Recently, we found that adaptor protein 3BP2 is required for the dectin-1-induced activation of NF-kappa B.
In this study, we performed microarray analysis to identify genes of which expression is regulated by dectin-1 and 3BP2.

overall_design: Bone marrow-derived dendritic cells obtained from wild-type mice (WT cells) or 3BP2 DL/DL mice (DL cells) were stimulated with (Cd+) or without (Cd-) curdlan for 4 h. After cells were washed with PBS, total RNA was extracted and subjected to microarray analysis.

first: Ayumi

last: Tsubokawa


title: Functional Genomics of Human Skeletal Development and the Patterning of Height Heritability