title: RNA-seq identified GLI1 as the target gene for GABP

city: Xuzhou

first: Yinfei

last: Lu

state: Jiangsu

address: No. 209 Tongshan Road, Xuzhou City

institute: Xuzhou Medical University

summary: We performed RNA-seq based transcriptomic analysis to evaluate differential protein expression in the kidneys of GABP overexpressing mice in db/m and GABP knockdown mice in db/db. The cluster analysis heat map shows the genetic changes . Compared with db/m mice, 734 differentially expressed genes, 525 upregulated genes and 209 upregulated genes . Compared with db/db mice, 82 genes were up-regulated and 82 genes were down-regulated in the kidneys of mice with GABP knockdown in db/db . Further, the classical pathway map in IPA database found that cell growth, proliferation, organ development and other pathways were activated after GABP overexpression. Cell growth, proliferation, organ development and other pathways were inhibited . It was further confirmed that GABP was associated with proliferation. Among differentially expressed genes, there were 9 differentially expressed genes up-regulated by GABP overexpression and down-regulated by GABP knockdown . Through the analysis of Ingenuity Pathway Analysis database, GABP and GLI1 were most closely related .

overall_design: The kidney samples of mice were divided into four groups for test: normal control group (db/m-veh), diabetes nephropathy group (db/db veh), GABP overexpression group (db/m-GABP-OE), and GABP knockdown group (db/db GABP-KD). Each group selected 6 different mouse kidney tissues, and 3 tissues were mixed together for testing.

first: Lei

last: Du

first: Xiujuan

last: Yu

first: Sijie

last: Liu

first: Yue

last: Hu

first: Tingting

last: Yang

first: Dongxue

first: Qun

first: Jingxian

last: Ming

first: Jiawei

last: Zhang

first: Xiaoxing

last: Yin

first: Qian


title: Selective Mitochondrial Respiratory Complex I Subunit Deficiency Causes Tumor Immunogenicity

status: Public on Oct 05 2024

city: Boston

first: Tevis

last: Vitale

state: Massachusetts

address: 50 Industrial Drive, LC6201

country: USA

institute: Dana-Farber Cancer Institute

type: Expression profiling by high throughput sequencing

summary: Targeting of specific metabolic pathways in tumor cells has the potential to sensitize them to immune-mediated attack. Here we provide evidence for a specific means of mitochondrial respiratory Complex I (CI) inhibition that improves tumor immunogenicity and sensitivity to immune checkpoint blockade (ICB). Targeted genetic deletion of the CI subunits Ndufs4 and Ndufs6, but not other subunits, induces an immune-dependent tumor growth attenuation in mouse melanoma models. We show that deletion of Ndufs4 induces expression of the transcription factor Nlrc5 and genes in the MHC class-I antigen presentation and processing pathway. This induction of MHC-related genes is driven by an accumulation of pyruvate dehydrogenase-dependent mitochondrial acetyl-CoA downstream of CI subunit deletion. This work provides a novel functional modality by which selective CI inhibition restricts tumor growth, suggesting that specific targeting of Ndufs4, or related CI subunits, increases T-cell mediated immunity and sensitivity to ICB.

overall_design: To investeigate the transcriptional changes that lead to the observed immunogenicity of the sgNdufs4 cells, we performed gene expression profiling using data obtained from RNA-seq of the sgControl and sgNdufs4 cell lines under standard culture conditions.

first: Jiaxin

last: Liang

first: Xixi

first: Thomas

middle: D

last: Jackson

first: Deyang

first: Mark

last: Jedrychowski

first: Steve

middle: P

last: Gygi

first: Hans

middle: R

last: Widlund

first: Kai

middle: W

last: Wucherpfennig

first: Pere

last: Puigserver


title: Role of SIRT5 in Inhibition of Myocardial Hypertrophy

city: Guangzhou

first: Li

last: Ma

state: Guangdong

address: Sun-Yat university

department: Heart Center

country: China

institute: Guangzhou Women and Children's Medical Center, Guangzhou Medical University

summary: SIRT5 is one of the seven members of the NAD+-dependent sirtuin family of protein deacylase that is mainly present in mitochondria and regulates metabolism. In heart, SIRT5 is highly expressed and responsible for succinylation on metabolic enzymes. Although the role of SIRT5 in maintaining cardiac homeostasis under physiological stress and few potential substrates of SIRT5 have been preliminarily revealed, the regulatory network and key cellular signaling pathways involving SIRT5 in myocardial hypertrophy remain largely unknown. Here, we used an established murine model of pressure overload-induced myocardial hypertrophy caused by transverse aortic constriction (TAC) to outline the network and pathway involving SIRT5 in cardiac stress responses. Remarkably, SIRT5 KO mice had enhanced myocardial hypertrophy after TAC surgery compared with wild-type mice.

overall_design: The 5 weeks old conventional SIRT5 knockout (SIRT5 KO), basing on the clustered regularly interspaced short palindromic repeat (CRISPR)/ CRISPR-associated protein 9 (Cas9) methods, male mice (C57BL/6N) and wild-type (WT) male mice using the tamoxifen-inducible Cre-ERT2 system. Each mouse was intraperitoneally injected with 1 mg tamoxifen every 24 h for a total of 10 consecutive days. There is a 4-week waiting period between the final injection of tamoxifen and the establishment of TAC model. After the mice were weighed, TAC surgery was performed under general anesthesia intraperitoneally injected with 50 mg/kg pentobarbital sodium. Mice were fixed on a constant-temperature operating table in the supine position for a trans-sternal thoracotomy. After the aortic arch appeared clearly, a 27-gauge needle was placed along the thoracic aorta, followed by a tight banding between the aorta and the needle with a 6-0 suture. Then, the needle was withdrawn and the chest was closed. The mice were monitored on the operating table until completely recovered. Sham-operated mice underwent the same procedure but without banding. Intraperitoneal injection of 1×104 U penicillin was performed to prevent infection for a total of 3 consecutive days after surgery.          The left ventricular myocardial samples were collected from TAC-induced cardiac hypertrophy mice. 2.0g tissue per samples were used for total RNA extraction.Ribosomal RNA (rRNA) was removed from Total RNA using QIAseq FastSelect RNA Removal Kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s instructions. The enriched mRNAs and non-coding RNAs were fragmented into short fragments (approximately 300 bp) using a fragmentation buffer and reverse-transcribed to cDNA with random primers, and this first-strand cDNA was used as the template for second-strand cDNA synthesis. Then, the cDNA fragments were end-repaired and ligated to Illumina sequencing adapters. The second-strand cDNA was digested using Uracil-DNA Glycosylase (UDG). The digested products were size selected (approximately 450 bp), PCR amplified, and quality assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). After cDNA library construction, a paired-end sequencing was performed using Illumina Hiseq 4000 systems (Illumina, San Diego, CA, USA). The raw data were filtered, and the clean data were mapped to the reference genome Mus_musculus. GRCm38. RNA sequencing libraries were constructed using Illumina TruSeq RNA Preparation kit and Illumina Ribo-Zero GoldrRNA Removal Kit according to the manufacturer’s instructions, and subsequently sequencing was performed via Illumina NextSeq 500 with the 300bp paired-end reads. The filtered RNA reads alignment and map on reference genome (GRCm38) via HISAT2 software (http://ccb.jhu.edu/software/hisat2/index.shtml). Consequently, the raw read counts were quantified by HTSeq software (https://htseq.readthedocs.io,version 0.6.1) based on BAM files. Fragments Per Kilo bases per Million fragments (FPKM), quantified by Stringtie (https://ccb.jhu.edu/software/stringtie/, version 1.2.0) software, was applied normalizing for gene expressional differential analysis.


title: Temporal regulation of gene expression through integration of dynamics and modifications

first: Dan

last: Lu

state: MA

address: 210 Longwood Avenue

department: Department of Systems Biology

institute: Harvard Medical School

summary: The master regulator of the DNA damage response, the transcription factor p53, orchestrates multiple downstream responses and coordinates repair processes. In response to double-strand DNA breaks, p53 exhibits pulses of expression, but how it achieves temporal coordination of downstream responses remains unclear. Here, we show that p53's post-translational modification state is altered between its first and second pulses of expression. We show that acetylations at two sites, K373 and K382, reduced in the second pulse and these acetylations differentially affected p53 target genes, resulting in changes in gene expression programs over time. This interplay between dynamics and modification may offer a strategy for cellular hubs like p53 to temporally organize multiple processes in individual cells.

overall_design: To assess the effect of the temporal changes in p53 acetylation on gene expression systematically, we performed time-series RNA-Sequencing at hourly intervals for 9 hours following 10Gy X-ray irradiation in cells expressing either WT or 2KR p53 along with endogenous p53. Response were compared to untreated cells (0h after treatment). We used MCF7 breast carcinoma cell lines and performed the experiment in duplicates.

first: Lu

last: Dan

first: Faizi

last: Marjan


title: Novel Blood-Based RNA Profiles can Predict Human Degenerative Cervical Myelopathy

city: Changsha, Hunan

first: Bing

last: Wang

address: Renminzhong Road

department: Department of Spine Surgery

institute: The Second Xiangya Hospital, Central South University

summary: In this study, we aim to identify and explore the diagnostic value of differentially expressed genes (DEGs) in the blood of patients with degenerative cervical myelopathy (DCM), cervical spondylotic radiculopathy (CSR), and healthy controls (HC).

overall_design: A total of 46 participants were enrolled in the study, and peripheral blood was collected for subsequent analysis. Further, differentially expressed genes (DEGs) in healthy controls (HCs) and patients with cervical spondylotic radiculopathy (CSR, as DCM mimics) were identified. Gene Ontology (GO) enrichment analysis was performed on DEGs. DEGs enriched in neurological disabilities by DisGeNET ontology category were used to diagnosis DCM and predict severity. Proportions of immune cell types were selected to predict injury levels in DCM.


title: Extracellular vesicles derived from synovial inflammatory macrophages induce the onset of osteoarthritis in a FMRP-selectively sorted manner [RNA-seq]

status: Public on Oct 04 2024

city: shanghai

first: shu

middle: I

last: zhao

address: Road siping 1239

institute: Tongji University

summary: Purpose:Next Generation Sequencing has revolutionized the effect of EVs secreted by synovial inflammatory macrophages on the cartilage of OA progression. The goals of this study are to compare NGS-derived cartilages transcriptome profiling (RNA-seq) between exosomes derived from synovial inflammatory macrophages and PBS treated OA rats model. The key biological processes and siginaling pathway were identified with immunofluorescence (IF), Transmission electron microscopy (TEM) and to evaluate protocols for optimal high-throughput data analysis.

overall_design: Methods: 8-week old SD rats undergoing DMM+ACLT operations allocated into two distinct categories: OA + PBS group; OA + PBS-EVsM1 group. Three weeks after the surgery, rats received several injections of 50 μl PBS or 50 μl PBS-EVsM1 (1×1010 particles/mL) intra-articularly throughout the next 6 weeks (twice a week). After 10 weeks of surgery, the rats’ anesthesia was kept up with isoflurane, and the specimens were collected. Cartilages mRNA profiles of OA rats treated with PBS or EVs derived from synovial inflammatory macrophages (EVsM1) were generated by deep sequencing, in replicate, using illumina NovaseqTM 6000 platform. The bioinformatics examination, comprising genes differentially expressed (DEGs), KEGG and GSEA enrichment. Immunofluorescence (IF), Transmission electron microscopy (TEM) were performed to evaluate the optimal high-throughput data analysis.

first: Shu

last: Zhao

first: Jun

last: Xu


title: Cellular and Transcriptomic Analyses Identify the Source and Lineage of Regenerated Neurons in the Adult Zebrafish Telencephalon following Blunt-Force Traumatic Brain Injury

city: Baltimore

first: Yang

last: Jin

state: MARYLAND

address: 1800 Orleans St

institute: Johns Hopkins University

summary: Traumatic brain injuries (TBIs) represent a large global disease burden and can result in several short- and long-term deficits. Treatment for TBIs are limited, however stem cell therapies involving either transplantation of exogenous stem cells or stimulation of endogenous stem cells have been proposed. These approaches possess issues with survival and differentiation of stem/progenitor cells, which highlights the need to elucidate mechanisms necessary for complete regeneration. Zebrafish exhibit a robust neuronal regenerative capacity following damage in various parts of the central nervous system. In this study, we use a modified blunt-force TBI (bfTBI) model, the most common type of TBI seen in the human population, to damage the adult zebrafish telencephalon and examine cellular and molecular consequences. This model induces a variety of TBI-related phenotypes across different injury severities, which mimic the pathologies observed following bfTBI in humans. Additionally, we show that after bfTBI, cells in the zebrafish telencephalon, including radial glia (RGC), non-glial neural progenitors (NPs), and neuroblasts, proliferate and differentiate into various neural cell types. We performed a snRNA-Seq analysis of the damaged and regenerating telencephalon, which revealed heterogeneity among the progenitor cells. Further, the snRNA-Seq demonstrated that quiescent radial glia became activated upon injury and yielded neural progenitor cells. To functionally assess how the regenerative process is regulated, we knocked down the expression of PdgfrB and demonstrated that it played a role in maintaining RGC quiescence. Collectively, this study provides a foundation for future studies of neuronal regeneration in the adult zebrafish telencephalon following a bfTBI.

overall_design: Telencephalons of undamaged and severe bfTBI damaged fish at 5, 12, 18, 24, 48, 72, 96, 120, 144, and 168 hpi were dissected as described above. Six telencephalons per group were placed in a Low-Bind Tube (Eppendorf) and snap frozen using liquid nitrogen. Nuclei were extracted using the Frankenstein Protocol as previously described (Martelotto et al. 2020) with some modification. Briefly 500 µL of Lysis buffer (1% Tris-HCl/0.2% NaCl/0.3%MgCl/0.1% NP40 in nuclease-free water) was added to brains. Brains were homogenized using a dounce homogenizer (10-20 times). Homogenate was passed through a 70 µm mesh strainer (Miltenyi Biotech, Auburn, CA, USA) and spun down at 500 xg at 4˚C for 5 minutes. Supernatant was discarded and the nuclear pellet was resuspended in Nuclei Wash Buffer (1% BSA in PBS with 0.2U/µL RNase inhibitors (Roche)). Nuclei were washed and resuspended 2 additional times as described above, and cells were resuspended to a concentration of ~1,000-1,500 nuclei/µL. Nuclei samples were passed through a 35 µm mesh strainer (Miltenyi Biotech). Cell suspension concentration and percent viability were determined by staining with Trypan Blue Stain (0.4%) (Thermo-Fisher Scientific) and Countess II Automated Cell Countess. Nuclei were loaded into Chromium Next GEM Chip G (10X Genomics, Pleasanton, CA, USA) with a targeted recovery of 10,000 nuclei per well and processed with Chromium Controller or Chromium iX (10X Genomics). Single-nuclei RNA-Seq libraries were prepared with Chromium Single Cell 3' Reagent Kit (v3.1 - Dual Index; 10X Genomics PN-1000269 | PN-1000215) at the Genomics and Bioinformatics Core Facility at the University of Notre Dame, following the standard throughput manual workflow and pooled at equal molar ratios. Libraries were sequenced on NovaSeq 6000 System at Center for Medical Genomics at Indiana University.

first: Kaylee

last: Cloghessy

first: Jiang

last: Qian

first: David

last: Hyde


title: Global organelle profiling reveals subcellular localization and remodeling at proteome scale

city: Vienna

first: Marco

middle: Yannic

last: Hein

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs

country: Austria

institute: Medical University of Vienna

summary: Defining the subcellular distribution of all human proteins and its remodeling across cellular states remains a central goal in cell biology. Here, we present a high-resolution strategy to map subcellular organization using organelle immuno-capture coupled to mass spectrometry. We apply this workflow to a cell-wide collection of membranous and membrane-less compartments. A graph-based analysis reveals the subcellular localization of over 7,600 proteins, defines spatial networks, and uncovers interconnections between cellular compartments. Our approach can be deployed to comprehensively profile proteome remodeling during cellular perturbation. By characterizing the cellular landscape following hCoV-OC43 viral infection, we discover that many proteins are regulated by changes in their spatial distribution rather than by changes in abundance. Our results establish that proteome-wide analysis of subcellular remodeling provides unique insights for the elucidation of cellular responses, uncovering an essential role for ferroptosis in OC43 infection. Our dataset can be explored at organelles.czbiohub.org.

sample_organism:
Homo sapiens
Human coronavirus OC43

platform_organism:
Homo sapiens
Human coronavirus OC43

overall_design: HEK293T cells were infected with hCoV-OC43 for 16, 24, and 48 hours at a multiplicity of infection (MOI) of 1.0, and subjected to single-cell transcriptomics processing on the 10x Genomics platform, along with uninfected control cells. MultiSeq was used to barcode the experimental condition before pooling all cells. We used the NextGEM Single-Cell V(D)J Reagents Kit v1.1, following a 5' workflow.

middle: Y

first: Manuel

last: Leonetti


title: Comprehensive transcriptome characterization deciphers mechanisms underpinning the positive selection of B cells in germinal centers.  [mouse; short-read]

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

summary: Alternative splicing (AS) and translational regulation play major roles in the activation and differentiation of immune cells. Previous studies using short-read sequencing linked individual AS events in germinal center (GC) B cells to proliferation and survival. To establish a more comprehensive understanding of transcript isoform changes that accompany B cell selection in the GC we developed a workflow for long-read nanopore sequencing. MYC expression by GC B cells marks cells undergoing a programme of AS which includes the removal of poison exons (PE) in splicing factors SRSF3 and SRSF7. These are crucial for B cell expansion and regulate transcripts encoding the translation machinery which is markedly increased upon positive selection of the GC B cell.

overall_design: Short-read (Illumina) RNA-seq data from naïve and subsets of germinal centre B cells, from mouse. A total of 5 replicates were included for each cell type; however, note that mouse LZ GFP-cMYCneg rep3, and LZ GFP-cMYCpos rep 1 and rep 2 library preparation initially failed, and the repeated libraries were found to be low quality. These samples were therefore excluded from downstream analysis for the short-read data, leaving a total of 3-5 replicates for each cell type.

first: Ozge

last: Gizlenci

middle: S

first: Martin

last: Turner


title: Transcriptome analysis of differentially expressed genes (DEGs) induced by Sporisorium reilianum between the two lines of ZmWRKY-KO and B73

city: Beijing

first: Qianqian

last: Zhang

address: 2 West, Yuanmingyuan Road, Haidian District

institute: China Agricultural University

summary: The 7d-mesocotyls of wild type B73 and its ZmWRKY53-KO counterparts were treated with or without S. reilianum for RNA sequencing.The differentially expressed genes (DEGs) were identified based on the criteria of fold-change > 2 and P < 0.05. Under normal conditions, we found 1,025 downregulated and 599 upregulated differentially expressed genes (DEGs) in the ZmWRKY53-KO plant compared to its wild-type B73 counterpart. Under S. reilianum-infected conditions, 1,041 downregulated and 1,268 upregulated DEGs were identified in the ZmWRKY53-KO plant.

overall_design: To invesigate the ZmWRKY53 mediated  resistance to maize head smut disease, we performed RNA-Seq between ZmWRKY-KO and B73.


title: Effects of methotrexate and tofacitinib on gene expression of activated rheumatoid arthritis fibroblast-like synoviocytes

city: Gothenburg

first: Anna-Karin

middle: Hultgård

last: Ekwall

address: Guldhedsgatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: University of Gothenburg

summary: Activated fibroblast-like synoviocytes (FLS) are drivers of synovitis and structural joint damage in rheumatoid arthritis (RA). Despite the use of disease-modifying drugs, only about 50% of RA patients reach remission in real-world settings. We used an unbiased approach to investigate the effects of standard-of-care methotrexate (MTX) and a Janus kinase inhibitor, tofacitinib (TOFA), on gene expression in RA-FLS, in order to identify untargeted disease mediators.

overall_design: Primary RA-FLS (n = 3 biological replicates) were pre-treated with MTX or TOFA for 24 h, then activated by stimulation with interleukin-1b and platelet-derived growth factor in the presence or absence of MTX or TOFA for 48 h prior to RNA-seq.

first: Beatrice

last: Bergström

last: Hultgård Ekwall


title: Proximity-dependent labeling identifies dendritic cells that prime the antitumor CD4+ T cell response

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: Dendritic cells (DCs) are uniquely capable of transporting tumoral antigens to tumor-draining lymph nodes (tdLNs), and also interact with effector T cells within the tumors themselves, mediating both natural antitumor immunity and the response to checkpoint blockade immunotherapy. Using LIPSTIC (Labeling Immune Partnerships by SorTagging Intercellular Contacts)-based single-cell transcriptomics, we identify individual DCs capable of presenting antigen to CD4+ T cells in the tdLN as well as inside tumors. These represent only a fraction of all DCs present and display a distinctive activated phenotype that in the LN includes production of cytokine IL-27, required for efficient T cell priming and tumor rejection. Tumor progression results in loss of effective priming of naïve CD4+ T cells, downstream of transcriptional changes in DCs that are manifested already when they arrive at the tdLN, which can be rescued by CTLA4 checkpoint blockade.

overall_design: Proximity-dependent labeling and subsequent RNA sequencing (Plate-based scRNA-seq, 10x Genomics, and bulk RNA-seq) were used to analyze dendritic cells (DCs) from tumor-draining lymph nodes (tdLNs) and tumor microenvironments (TME) in mice. The dataset includes RNA profiles of DCs involved in tumor-specific CD4+ T cell interactions, captured via photoactivation and LIPSTIC labeling, under steady-state and checkpoint blockade conditions.

first: Aleksey

last: Chudnovskiy

first: Sandra

last: Nakandakari-Higa

first: Ang

last: Cui

first: Chia-Hao

last: Lin

first: Moshe

last: Sade-Feldman

first: Brooke

middle: K

last: Phillips

first: Juhee

last: Pae

first: Luka

last: Mesin

first: Juliana

last: Bortolatto

first: Lawrence

last: Schweitzer

first: Giulia

last: Pasqual

first: Li-Fan

last: Lu

first: Nir

last: Hacohen

first: Gabriel

last: Victora


title: Hypoxic stabilization of RIPOR3 mRNA via METTL3-mediated m6A RNA methylation drives breast tumor growth and metastasis [m6A-seq-T47D]

city: wuhan

first: Jingjing

last: Xiong

state: Hubei

address: Shuiguohu Street

institute: Wuhan University

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) modification is the most abundant internal mRNA modification in eukaryotes. Hypoxia induces reprogramming of m6A epitranscriptome, but the detail underlying regulator mechanism remains elusive in breast cancer. Here we reported that hypoxia induced elevated m6A modification involved in tumor progression. m6A- sequencing (m6A-seq) combined with RNA sequencing (RNA-seq) identified RIPOR3 as a key target gene of m6A modification under hypoxic stress. Hypoxia-induced increased of RIPOR3 m6A levels promoted its mRNA stability and expression, thereby facilitating the progression and metastasis of breast cancer. Besides, RIPOR3 was overexpressed in breast cancer cells and breast tumor tissues, and elevation of RIPOR3 expression was associated with poor prognosis. Mechanistically, RIPOR3 bound to EGFR and the interaction was enhanced under hypoxia, promoting the activation of the EGFR downstream PI3K-AKT signaling pathway. Altogether, our studies reveal that RIPOR3 responds to hypoxic stress to promote EGFR-PI3K-AKT signal pathway, facilitating breast cancer progression and metastasis, thus presenting itself as a potential therapeutic target.

overall_design: m6A-modified sites in T47D cells which were treated in normoxic incubator or hypoxic work station (5% CO2,1% O2,37°C) for 24 hours.

first: Jing

last: Zhang


title: Hypoxic stabilization of RIPOR3 mRNA via METTL3-mediated m6A RNA methylation drives breast tumor growth and metastasis [m6A-seq-sgControl and sgMETTL3]

overall_design: m6A-modified sites in T47D cells infected sgMETTL3 or sgControl (sgCtrl) which were treated in normoxic incubator or hypoxic work station (5% CO2,1% O2,37°C) for 24 hours.


title: Platelet miRNA expression in NSCLC patients

city: Sao Paulo

first: Patricia

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

summary: Gene expression profile of platelets have been explored due to their stability and abundance in plasma. In this study, we try to address the knowledge gap regarding liquid biopsy markers for early detection of non-small cell lung cancer (NSCLC). For that blood samples were collected in two time points, in the presence and absence of NSCLC. Platelets were isolated and miRNA expression evaluated by microarray technique.

overall_design: 19 platelets samples from patients with NSCLC, in which 10 samples corresponds to pret-treatment samples and 9 corresponds to post-treatment samples.


title: Expression data from platelets from early NSCLC and HNSCC patients in tumour presence and tumor free samples

summary: Gene expression profile of platelets. In this study, we try to address the knowledge gap regarding liquid biopsy markers for early detection of non-small cell lung cancer (NSCLC) and head and neck squamous cell carcinoma (HNSCC). For that blood samples were collected in two time points, in the presence and absence of NSCLC or HNSCC. Platelets were isolated and gene expression evaluated by microarray technique.

overall_design: Sixty nine platelet samples from NSCLC and HNSCC patients. 15 and 21 samples correspond to NSCLC and HNSCC pre-treatment, respectively, while 11 and 22 samples correspond to NSCLC and HNSCC post-treatment samples, respectively.


title: Plasma miRNA data from early NSCLC and HNSCC patients

overall_design: 44 patients with NSCLC and HNSCC with plasma colected in two time points, pre- and post-treatment. 18 patients correspond to NSCLC cases and 26 patients correspond to HNSCC cases.


title: NSCLC and HNSCC patients

type:
Non-coding RNA profiling by array
Expression profiling by array

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Genotyping of hundreds of individuals from Kazakh population in Kazakhstan

city: Astana

first: Ulykbek

last: Kairov

address: Kabanbay batyr ave.53

department: Center for Life Sciences

country: Kazakhstan

institute: National Laboratory Astana, Nazarbayev University

summary: Genotyping of hundreds of healthy individuals with Kazakh ethnicity as a reference cohort for further genetic investigations

overall_design: Control samples without any inherited and severe diseases


title: Comparative Transcriptomics Identifies Differentially Expressed Genes Regulating Gametic Development in Arabidopsis thaliana

city: Zhengzhou

first: Zhaoran

last: Ti an

state: Henan

address: No.100 Science Avenue

institute: Zhengzhou University

summary:
Purpose:Comparative transcriptome analyses was applied to characterize gene expression during gametophytic development in Arabidopsis thaliana.
Methods:  Leaf and immature floral buds (contain the entire developmental progress, > 0.4 mm long floral buds) were collected, then Separated male and female organs were kept in liquid nitrogen immediately until use. Total RNA was extracted using the TRIzol reagent (Invitrogen, Waltham, MA, USA). DNase (Promega, USA) was used to remove potential DNA contamination. For the quantitative real-time polymerase chain reaction (qRT-PCR) analysis
Results: In this study, both male and female gametes had much more similarity in gene expression patterns, particularly the genes involved in cell cycle and DNA repair, were enriched during the gametic development stage, but the differentially expressed genes related to DNA repair, recombination pathway  and genes in RdDM pathway.
Conclusions: Genes encoding proteins associated with the production and modification of pectins and cell wall rearrangements were shown male-preferred implies the dynamic changes of pollen wall during the development of male gametes.   The DEGs, related to BR signaling pathway and BR synthesis pathway were highly enriched in developmental female gametes, suggesting that BR played pivotal roles in female gamete development.

overall_design: mRNA profiles of male and female gametophytes

last: Tian

first: Fang

last: Wei


title: A feedforward loop between STAT1 and YAP1 stimulates lipid biosynthesis, accelerates tumor growth, and promotes chemotherapy resistance in mutant KRAS colorectal cancer.

status: Public on Oct 03 2024

city: Montréal

first: Antonis

last: Koromilas

state: QC

address: 3755 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: Lady Davis Institute - McGill University

summary:
In tumorous conditions, the transcription factor STAT1, traditionally recognized for its anti-tumor role in immunology, exhibits pro-survival characteristics, though the underlying mechanisms remain unclear. Investigating STAT1's function in isogenic colorectal tumor cells with wild-type or mutant KRAS, we found that STAT1 specifically promotes the survival and proliferation of cells with mutant KRAS. Through gene expression profiling, we discovered a previously unknown role of STAT1 in upregulating sterol and lipid biosynthetic genes specifically in mutant KRAS cells. This effect is driven by STAT1’s phosphorylation at serine 727 and its cooperation with STAT3 and STAT5 for the transcriptional upregulation of sterol regulatory element-binding proteins (SREBP) 1 and 2, which boost de novo sterol and lipid biosynthesis. In mutant KRAS cells, STAT1 amplifies the mevalonate pathway, maintaining its serine 727 phosphorylation through the upregulation of RHO GTPase signaling and establishing a positive feedback loop through the transcription factors YAP1 and TEAD4, further driving lipid biosynthesis and tumor growth. Through xenograft tumor assays in mice, we discovered that the STAT1-YAP1 axis plays a role in mutant KRAS tumor cells' resistance to mevalonate pathway inhibitors, which can be overcome by pharmacologically targeting the YAP1-TEAD interaction. Additionally, the STAT1-YAP1 arm is essential for the intrinsic resistance to EGFR-targeting therapy in the mutant KRAS colon cancer cells. These findings indicate that the STAT1-YAP1 pathway plays a significant role in therapy resistance and presents a potential therapeutic target in mutant KRAS colorectal cancer.
We used microarrays to detail the global programme of gene expression underlying genes commonly regulated by STAT1 and YAP1 in HCT116 cells.

overall_design: RNA was extracted from four colon carcinoma HCT116 cell lines containing or lacking STAT1, YAP1 or both. Samples were processed using the Affymetrix Clariom S Human HT Expression platform. A total of 16 samples were processed.

first: Shuo

last: Wang

first: Shiqi

last: Diao

first: Hyungdong

last: Kim

first: Jiayi

last: Zou

first: Keke

last: Li

middle: E


title: Klf9 is essential for cardiac mitochondrial homeostasis

city: Tianjin

first: Lei

address: qixiangtai 22

institute: Tianjin Medical University

summary: Mitochondrial dynamics and mitophagy are intimately linked physiological processes that are essential for cardiac homeostasis. Here we show that cardiac Klf9 is dysregulated in human and rodent cardiomyopathy. Young adult global Klf9-knockout mice displayed hypertrophic cardiomyopathy that was characterized by depressed systolic function, increased left ventricular mass and pulmonary congestion. Klf9 knockout led to mitochondrial disarray and fragmentation in cardiomyocytes. Biochemical analysis confirmed that mitochondrial respiratory function was impaired in Klf9-knockout cardiomyocytes, with reduced myocardial ATP levels and elevated ROS. Furthermore, cardiac-specific Klf9-deficient mice phenocopied global Klf9-knockout mice, suggesting that cardiac Klf9 is essential for mitochondrial homeostasis and heart function. Moreover, cardiac Klf9 deficiency inhibited mitophagy induced by angiotensin II (ANGII), thereby leading to accumulation of dysfunctional mitochondria and acceleration of heart failure in mice in response to ANGII treatment. In contrast, cardiac-specific Klf9 transgene improved cardiac systolic function via promoting mitophagy in mice in response to ANGII treatment. Molecular mechanism studies indicated that Klf9 knockout decreased the expression of PGC-1α and its target genes involved in mitochondrial energy metabolism. Moreover, Klf9 controlled the expression of Mfn2 by directly binding to its promoter region, thereby regulating mitochondrial dynamics and mitophagy. Finally, we performed Mfn2 rescue experiments in Klf9-CKO mice and found that AAV-mediated Mfn2 rescue in heart improved cardiac mitochondrial and systolic function in Klf9-CKO mice treated with or without ANGII. Thus, Klf9 integrates cardiac energy metabolism, mitochondrial dynamics and mitophagy. Modulating Klf9 activity may have therapeutic potential in the treatment of heart failure.

overall_design: To investigate the influence of Klf9 on the cardiac mitochondrial function, we utilized heart tissues from wild-type and Klf9 knockout mice to examine gene expression patterns.

first: Menglin


title: Transcriptomic analysis in brown adipose tissue from the brown adipocytes-specific Crif1 deficiency mice

city: Daejeon

first: Ju Hee

last: Lee

address: Munhwa-ro 266

country: South Korea

institute: Chungnam National University

summary: This study investigates the coordination of thermogenesis between brown and beige adipocytes, with a focus on mitokines induced by mitochondrial stress, and its role in maintaining metabolic homeostasis.

overall_design: To investigate the effects of abnormalities in brown adipocyte-specific mitochondrial proteostasis, we generated a mouse model of mitochondrial dysfunction induced by the genetic inactivation of the Crif1 gene in brown adipocytes.

first: Ji

first: Ju

middle: H


title: The transcriptional response of prostate cells to infection with Trichomonas vaginalis and Mycoplasma hominis

city: Los Angeles

first: Joshua

middle: Andrew

last: Kochanowsky

state: California

address: 619 Charles E Young Dr E

department: Microbiology, Immunology and Molecular Genetics

institute: University of California Los Angeles

summary: The sexually transmitted parasite Trichomonas vaginalis is often found in symbiosis with the obligate intracellular pathogen Mycoplasma hominis. M. hominis is itself an opportunistic pathogen of the female reproductive tract associated with bacterial vaginosis. The goal of this experiment was to identify the effects of each pathogen individually and in symbiosis on host cell gene expression.

overall_design: To investigate the effects of infection with T. vaginalis, M. hominis, and T. vaginalis in symbiosis with M. hominis on host cell gene expression we infected prostate derived cells (BPH-1s) with either T. vaginalis alone, M. hominis alone, the same strain of T. vaginalis (B7RC2) in symbiosis with M. hominis or mock infected for 6 hours (MOI=1) prior to RNA isolation and sequencing.

middle: A

middle: J

last: Johnson


title: Detection Of Residual iPSCs Following Differentiation of iPSC-Derived Retinal Pigment Epithelial Cells

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: PURPOSE: The goal of this study was to develop a lot release assay for iPSC residuals following directed differentiation of iPSCs to retinal pigment epithelial (RPE) cells. METHODS: RNA Sequencing (RNA Seq) of iPSCs and RPE derived from them was used to identify pluripotency markers downregulated in RPE cells. Quantitative real time PCR (qPCR) was then applied to assess iPSC residuals in iPSC-derived RPE. The limit of detection (LOD) of the assay was determined by performing spike-in assays with known quantities of iPSCs serially diluted into an RPE suspension.  RESULTS: ZSCAN10 and Lin28a were among 8 pluripotency markers identified by RNA Seq as downregulated in RPE. Based on copy number and expression of pseudogenes and lncRNAs ZSCAN10 and Lin28a were chosen for use in qPCR assays for residual iPSCs. Reverse transcription PCR indicated generally uniform expression of ZSCAN10 and Lin28a in 21 clones derived from 8 iPSC donors with no expression of either in RPE cells derived from 5 donor lines. Based on qPCR, ZSCAN10 and Lin28a expression in iPSCs was generally uniform. The LOD for ZSCAN10 and Lin28a in qPCR assays was determined using spike in assays of RPE derived from 2 iPSC lines. Analysis of DDCt found the limit of detection to be <0.01% of cells, equivalent to <1 iPSC / 10,000 RPE cells in both iPSC lines. CONCLUSIONS: qPCR for ZSCAN10 and Lin28a detects <1 in 10,000 residual iPSCs in a population of iPSC-derived RPE providing an adequate LOD of iPSC residuals for lot release testing.

overall_design: RNA Seq and differential gene expression analysis was performed by Azenta Life Sciences (Chelmsford, Massachusetts) on 3 samples each of 22/1 iPSCs and 3 samples of RPE cells derived from them. Reads were aligned and mapped to the HG38 genome assembly.

first: Matthew

last: Hill

first: Cynthia

last: Andrews-Pfannkoch

first: Evan

last: Atherton

first: Travis

last: Knudsen

first: Emma

last: Trncic

first: Alan

last: Marmorstein


title: Human iPSC-derived cardiomyocytes under hypoxia/normoxia, treated with bone marrow or cardiac stromal cell extracellular vesicles

city: Liverpool

first: Richard

last: Barrett-Jolley

address: 6 West Derby Street

institute: University of Liverpool

summary: Effects of cardiac stromal cell extracellular vesicles on human iPSC-derived cardiomyocytes response to hypoxia.

overall_design: There are four groups, with three samples per group: H1,H2,H3. Negative control. Healthy, normoxic iPSC-CMs D1,D2,D3. Positive control. iPSCs cultured under hypoxic (0-1% O2) for 48h with 2% v/v PBS as vehicle control EV1,EV2,EV3. Treatment 1. iPSCs cultured under hypoxic (0-1% O2) for 48h, with cardiac stromal cell derived extracellular vesicles, provided at a dose of 67ng/µl (2% v/v) EV21, EV23, EV24. Treatment 2 iPSCs cultured under hypoxic (0-1% O2) for 48h, with bone marrow mesenchymal stromal cell (BM-MSC) derived extracellular vesicles, provided at a dose of 67ng/µl (2% v/v)

first: David

last: Lundy


title: RNA-seq reveals ultrasound-guided renal parenchymal infusion of mesenchymal stem cells in chronic kidney disease rat model

city: Kunming

first: Shanshan

last: Wan

address: Dianmian 374 Street

department: Department of Radiology

institute: The second affiliated hospital of Kunming Medical University

summary: Chronic kidney disease (CKD) is a disease characterized by normal or reduced proteinuria, glomerular filtration rate, progressive damage to glomeruli, tubules, and interstitium. In this study, we performed RNA-seq reveals ultrasound-guided renal parenchymal infusion of mesenchymal stem cells in SD rats animal model in chronic kidney disease. Our results indicate that differential genes in the normal group(n=3) VS CKD group(n=3) and normal group(n=3) VS MSCs treatment group(n=3).

overall_design: Transcriptome analysis by high throughput sequencing

first: Daiyuan

last: Tang

first: Yinqing

last: Zeng

first: Long

last: Hu


title: The transcriptional response of prostate cells to Trichomonas vaginalis extracellular vehicles

summary: The sexually transmitted parasite Trichomonas vaginalis secretes extracellular vesicles (TvEVs) that are internalized by human host cells. The goal of this experiment was to identify the effects of TvEV uptake on host cell gene expression.

overall_design: To investigate the effects of TvEVs on host cell gene expression we treated prostate derived cells (BPH-1s) with TvEVs (50ug/mL) or mock treated for 6 hours prior to RNA isolation and sequencing.

first: Patricia


title: Drosha loss drives pineoblastoma by upregulating Ccnd2 [RNA-seq of Drosha and Rb1 tumors]

city: Dallas

first: Kenneth

last: Chen

state: TX

address: 5323 Harry Hines Blvd

department: Pediatrics

institute: UT Southwestern

summary: Mutations in the microRNA processing genes DICER1 and DROSHA drive childhood cancers such as pineoblastoma, a brain tumor that resembles undifferentiated precursors of the pineal gland. To understand how microRNAs regulate proliferation of these progenitors, we developed a mouse model of pineoblastoma by ablating Drosha or Dicer1 in the developing pineal gland. The tumors that arise in these models resemble proliferative, undifferentiated embryonic progenitors. They are marked by loss of microRNAs, including the let-7 family, and de-repression of let-7 target genes. One upregulated let-7 target gene is the oncofetal transcription factor Plagl2, which activates expression of key pro-growth genes Igf2 and Ccnd2, and we show that small molecules targeting these two drivers block tumor growth. Thus, our results demonstrate that tumors driven by loss of microRNA processing may be therapeutically targeted by inhibiting downstream drivers of proliferation.

overall_design: We used RNAseq to identify overexpressed genes and enriched pathways in IPDrosha vs IPRb1 tumors.

first: Claudette

last: Fraire

first: Kavita

last: Desai

first: Lindsay

last: Mendyka

first: Uma

last: Obalaparum

first: Teja

last: Sebastian

first: Veena

last: Rajaram


title: Young and Aged Striatal Astrocyte MERFISH Panel

first: Kay

last: Linker

address: 10833 Le Conte Avenue, 53-263 CHS

department: Physiology

institute: UCLA

summary: Given that the striatum is a large, multifunctional nucleus, we next aimed to understand where  astrocyte subtypes exist in the striatum at a single-cell resolution using MERFISH. We reproducibly identified the seven astrocyte subtypes, some of which were dorsal (A1, A7), medial (A3, A6) or ventral dominant (A4).

overall_design: MERFISH was performed according to Vizgen's instructions. Data was initally processed using MERLIN, and cell segmentation completed with Vizgen software.

first: Baljit

last: Khakh


title: Drosha loss drives pineoblastoma by upregulating Ccnd2 [RNAseq of ceritinib treatment]

overall_design: We used RNAseq to identify genes and pathways affected by ceritinib treatment in IPDrosha tumors.


title: Drosha loss drives pineoblastoma by upregulating Ccnd2 [smallRNAseq Drosha and Rb1 tumors]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: We used small RNA sequencing to identify microRNAs expressed in IPRb1 tumors and lost in IPDrosha tumors.


title: Drosha loss drives pineoblastoma by upregulating Ccnd2 [miR-eCLIP]

overall_design: We used miR-eCLIP to identify transcripts targeted by microRNAs in pineal tumor cells (IPRb1).


title: Phosphatidylserine phospholipase A1 enables GPR34-dependent immune cell accumulation in the peritoneal cavity

city: San Francisco

first: Hanson

last: Tam

state: CA

address: 513 Parnassus Ave

institute: UCSF

summary: The peritoneal cavity (PerC) is an important site for immune responses to infection and cancer metastasis. Yet few ligand-receptor axes are known to preferentially govern immune cell accumulation in this compartment. GPR34 is a lysophosphatidylserine (lysoPS)-responsive receptor that frequently harbors gain-of-function mutations in mucosa-associated B cell lymphoma. Here, we set out to test the impact of a GPR34 knock-in (KI) allele in the B-lineage. We report that GPR34 KI promotes the PerC accumulation of plasma cells (PC) and memory B cells (MemB). These KI cells migrate robustly to lysoPS ex vivo, and the KI allele synergizes with a Bcl2 transgene to promote MemB but not PC accumulation. Gene expression and labeling studies reveal that GPR34 KI enhances PerC MemB proliferation. Both KI PC and MemB are specifically enriched at the omentum, a visceral adipose tissue containing fibroblasts that express the lysoPS-generating PLA1A enzyme. Adoptive transfer and chimera experiments revealed that KI PC and MemB maintenance in the PerC is dependent on stromal PLA1A. These findings provide in vivo evidence that PLA1A produces lysoPS that can regulate GPR34-mediated immune cell accumulation at the omentum.

overall_design: To investigate the GPR34 KI allele's effect on gene expression, we performed bulk RNAseq on sorted B2 (IgD+IgM+) and MemB (IgD-IgM-) cells from the PerC of littermate control (n=3) and KI (n=3) mice.

first: Jason

last: Cyster


title: CRISPR-CLEAR: Nucleotide-Resolution Mapping of Regulatory Elements via Allelic Readout of Tiled Base Editing

city: Boston

first: Eric

last: Che

address: 531 Newbury St

institute: Harvard Medical School

summary: CRISPR tiling screens have advanced the identification and characterization of regulatory sequences but are limited by low resolution arising from the indirect readout of editing via guide RNA sequencing. This study introduces CRISPR-CLEAR, an end-to-end experimental assay and computational pipeline, which leverages targeted sequencing of CRISPR-introduced alleles at the endogenous target locus following dense base-editing mutagenesis. This approach enables the dissection of regulatory elements at nucleotide resolution, facilitating a direct assessment of genotype-phenotype effects.

sample_organism:
Homo sapiens
synthetic construct

overall_design: Tiling mutagenesis of the CD19 enhancer in ABE8e-SpRY and evoCDA expressing NALM-6 cell lines. Cells were stained with a fluorescently conjugated antibody used to assess expression of CD19. After staining, cells were sorted using fluorescence-activated cell sorting into a "CD19 positive" and "CD19 negative" population. Genomic DNA was extracted from these populations and split into half – half was used for the traditional guide RNA sequencing approach and in the other half the endogenously targeted region was directly sequenced. A follow-up experiment involving a single guide, sg218, was also performed.

first: Basheer

last: Becerra

first: Sandra

last: Wittibschlager

first: Zain

last: Patel

first: Ana

last: Kutschat

first: Justin

last: Delano

first: Anzhelika

last: Karjalainen

first: Ting

last: Wu

first: Marlena

last: Starrs

first: Martin

last: Jankowiak

first: Daniel

last: Bauer

first: Davide

last: Seruggia

first: Luca

last: Pinello


title: Drosha loss drives pineoblastoma by upregulating Ccnd2 [RNA-seq of palbociclib treatment]

first: Kenneth

last: Chen

overall_design: We used RNAseq to understand the genes and pathways affected by palbociclib therapy in IPDrosha tumors.

first: Claudette

last: Fraire

first: Kavita

last: Desai

first: Lindsay

last: Mendyka

first: Uma

last: Obalaparum

first: Teja

last: Sebastian

first: Veena

last: Rajaram


title: Drosha loss drives pineoblastoma by upregulating Ccnd2 [CUT&RUN]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We used CUT&RUN for histone marks to understand how loss of Rb1 or Drosha affect chromatin regulation.


title: Drosha loss drives pineoblastoma by upregulating Ccnd2 [RNAseq of brain, Drosha tumor, and pineal gland]

overall_design: We used RNA-seq to identify overexpressed genes and enriched pathways in IPDrosha tumors, compared with matched normal brain and age matched normal pineal glands.


title: Drosha loss drives pineoblastoma by upregulating Ccnd2 [ATAC-seq]

overall_design: ATACseq of normal brain and pineal tumors of three genotypes: IPDrosha, IPDicer1, IPRb1


title: T-lymphocyte recruitment and retention in lichen planus

city: Philadelphia

first: Satish

last: Sati

state: Pennsylvania

address: 421 Curie Blvd, BRB 1039

department: Dermatology

institute: University of Pennsylvania

summary: Lichen planus (LP) is a chronic, debilitating, inflammatory disease of the skin and mucous membranes that affects 1-2% of Americans. Its molecular pathogenesis remains poorly understood, and there are no FDA-approved treatments. We performed single cell RNA sequencing on blood and affected and unaffected skin from 7 LP patients. LP affected skin exhibited a robust immune infiltrate primarily composed of CD8 T-cells. These cells were specifically recruited by cytokines secreted by both superficial and dermal layers of skin. Basal keratinocytes and fibroblasts secrete CXCL9 and CXCL10, and fibroblasts secrete CCL19. Molecular analysis of LP skin and blood samples increased our understanding of disease pathogenesis and identified CCL19 as a new therapeutic target for treatment.

overall_design: scRNA-seq of Human PBMCs, Human skin cells

first: Anna

last: Kersh

first: Thomas

last: Leung


title: Identification of tumor-agnostic biomarkers for predicting prostate cancer progression and biochemical recurrence

city: Ribeirão Preto

first: William

last: Lautert Dutra

state: SP

address: Av. Bandeirantes, 3900

department: Genetics Department

institute: Universidade de São Paulo

summary: The diverse clinical outcomes of prostate cancer have led to the development of gene signature assays predicting disease progression. Improved prostate cancer progression biomarkers are needed as current RNA biomarker tests have varying success for high-risk prostate cancer. Interest grows in universal gene signatures for invasive carcinoma progression. Early breast and prostate cancers share characteristics, including hormone dependence and BRCA1/2 mutations. Given the similarities in the pathobiology of breast and prostate cancer, we utilized the NanoString BC360 panel, comprising the validated PAM50 classifier and pathway-specific signatures associated with general tumor progression as well as breast cancer-specific classifiers. This retrospective cohort of primary prostate cancers (n=53) was stratified according to biochemical recurrence status and the CAPRA-S to identify genes related to high-risk disease

overall_design: we utilized the NanoString BC360 panel, comprising the validated PAM50 classifier and pathway-specific signatures associated with general tumor progression as well as breast cancer-specific classifiers. This retrospective cohort of primary prostate cancers (n=53) was stratified according to biochemical recurrence status and the CAPRA-S to identify genes related to high-risk disease.

last: Lautert-Dutra

first: Camila

middle: M

last: Melo

first: Luiz

last: Chaves

first: Fracisco

middle: C

last: Souza

first: Cheryl

last: Crozier

first: Adam

last: Sundby

first: Elizabeth

last: Woroszchuk

first: Fabiano

last: Saggioro

first: Felipe

last: Avante

first: Rodolfo

last: dos Reis

first: Jeremy

last: Squire

first: Jane

last: Bayani


title: CXCR2 knockout promotes skin and hair regeneration without scarring

summary: Mammals heal faster with imperfect fibrotic scars, while amphibians regenerate slower with scarless wound healing. These observations support the prevailing paradigm that speed of wound closure is inversely related to repair quality. Here we find evidence that this is a false trade-off. In multiple injury models, mice lacking CXCR2 (CXCR2-KO) globally improved both speed and quality of skin wound healing, including hair regeneration. We found CXCR2 primarily expressed in neutrophils, and injury induced neutrophils to secrete neutrophil extracellular traps (NETs). Mice engineered to be specifically deficient in myeloid CXCR2 or NET production partially recreated the phenotype with improved early speed of wound closure. Thus, CXCR2+ neutrophils regulate the speed of wound closure.

overall_design: scRNA-seq of Mouse skin cells

first: John

last: Huang

first: Christina

last: Murphy


title: Maternal Biomarker Study for Single Ventricle Heart Defects

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

summary: The goal of this study was to discover novel cell-free molecular signals within the blood of pregnant women that potentially signal abnormal cardiac morphogenesis during gestation. RNA from maternal blood plasma and from a single-ventricle defect iPSC model were extracted and sequenced to identify differentially expressed miRNAs.

overall_design: Blood from pregnant women after 20 weeks of gestation whose fetus was formally diagnosed as healthy, PAIVS, or with HLHS were recruited and their cell-free RNA was sequenced. Furthermore, iPSCs from CHD patients were differentiated into cardiomyocytes and their supernatant RNA was sequenced. Both sequenced datasets were compared to identify any differentially expressed miRNAs that could potentially be used as a biomarker for single-ventricle disease. Pregnant women with healthy babies and iPSC lines from healthy individuals were used as controls.

first: Matthew

last: Alonzo

first: Mingtao

last: Zhao

first: Shiqiao

last: Ye


title: Mouse Striatum 18 months of age

first: Kay

last: Linker

summary: The striatum is a functionally diverse brain region. We investigated aged astrocyte and glia diversity within this brain region.

overall_design: To investigate the functional heterogeneity of astrocytes from a defined brain region, we performed single cell RNA-seq of striatal cells from aged mice 18 months old

first: Linker

last: Kay

first: Khakh

last: Baljit


title: Modulation of m6A RNA Methylation by Death Associated Protein 3 (DAP3) [eCLIP-seq]

city: Singapore

first: jinghe

last: xie

address: 21 Lower Kent Ridge Road

country: Singapore

institute: nuh

summary: eCLIP-seq data of METTL3 binding in shScr control and two shDAP3 knockdown samples

overall_design: We examined METTL3 binding sites on RNA in EC109 cells by eCLIP-seq. Protein-RNA interactions were covalently linked by UV crosslinking and RNase I treatment removed unbound RNA. The crosslinked RNA was immunoprecipitated together with METTL3 using specific antibody targeting METTL3 (Proteintech,15073-1-AP), and converted to double-stranded DNA high-throughput sequencing libraries through adapter ligation and reverse transcription. Two biological replicates of METTL3 eCLIP in shScr control and two shDAP3 knockdown samples were performed and an IgG eCLIP served as a control. Each eCLIP experiment has a corresponding size-matched input control experiment.

first: Jian

last: Han

first: Jinghe

last: Xie

first: Leilei

last: Chen


title: Modulation of m6A RNA Methylation by Death Associated Protein 3 (DAP3)

summary: MeRIP-seq data of m6A signals in shScr control and two shDAP3 knockdown samples

overall_design: RNA was fragmented to around 200nt and purified using RNeasy Mini Kit (Qiagen). Dynabeads™ protein G beads (Invitrogen) were washed twice by IP buffer (150 mM NaCl, 10 mM Tris-HCl [pH 7.5], 0.1% IGEPAL CA-630 in nuclease-free H2O), resuspended in 500 μl of IP buffer with 5μg anti-m6A antibody at 4oC for 4 hours. Following 2 washes in IP buffer, the beads was resuspended in 500μl of the IP reaction mixture containing 10μg fragmented total RNA, 100μl of 5×IP buffer, and 5μl of SUPERase·In™ RNase Inhibitor (Invitrogen) and incubated for 2 hours at 4 oC. A low/high salt-washing method was used: the RNA reaction mixture was washed twice in 1ml IP buffer, twice in 1ml low-salt IP buffer (50 mM NaCl, 10 mM Tris-HCl [pH 7.5], 0.1% IGEPAL CA-630 in nuclease-free H2O), and twice in 1ml high-salt IP buffer (500 mM NaCl, 10 mM Tris-HCl [pH 7.5], 0.1% IGEPAL CA-630 in nuclease-free H2O) for 5 minutes each at 4 oC. After extensive washing, the m6A-enriched fragmented RNA was eluted from the beads in 350 μl of RLT buffer supplied in RNeasy Mini Kit (Qiagen) for 10 minutes at room temperature. A magnetic separation rack was used to pull beads to the side of the tube. Supernatant was collected to a new tube and 350μl 70% ethanol was added to it. RNA was purified following the manufacturer's protocol. Equal volume of m6A-enriched fragmented RNA from control and knockdown samples was used for library construction using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) and sequenced using Hiseq X platform.


title: Effect of TET3 expression in macrophage

city: New Haven

first: Haining

last: Lyu

state: Connecticut

address: 1145 chapel street, 401

institute: Yale

summary:
To identify TET3 downstream target in macropahge, we transfected with siCTL or siTET3 in RAW 264.7 cells
After 48h, we isolated the total RNA and perfomed bulk RNA-sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for siCTL group and siTET3 group in RAW 264.7 cells

first: Yingqun

last: Lv


title: HOT3/eIF5B1 confers Kozak motif-dependent translational control of photosynthesis-associated nuclear genes for chloroplast biogenesis

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

summary: Photosynthesis requires chloroplasts, where most proteins are nucleus-encoded and produced via cytoplasmic translation. The translation initiation factor eIF5B gates the transition from initiation (I) to elongation (E), and the Kozak motif is associated with translation efficiency, but their relationship is previously unknown. Here, with ribosome profiling, we determined the genome-wide I-E transition efficiencies. We discovered that the most prevalent Kozak motif is associated with high I-E transition efficiency in Arabidopsis, rice, and wheat, thus implicating the Kozak motif in facilitating the I-E transition. Indeed, the effects of most Kozak motifs, including the most effective ones, depend on HOT3/eIF5B1 in Arabidopsis. HOT3 preferentially promotes the translation of photosynthesis-associated nuclear genes in a Kozak motif-dependent manner, which explains the chloroplast defects of hot3 mutants. Our study reveals an evolutionarily-conserved link between the Kozak motif and eIF5B-mediated translational I-E efficiency and elucidates a HOT3-mediated translational control of nuclear photosynthesis genes for chloroplast biogenesis.

overall_design: Arabidospsis seedlings and inflorescence. 12 RNA-seq libraries: 3 replicates for seedlings and inflorescence of WT and hot3-2.

first: Runlai

last: Hang

first: Ye

first: Hao

last: Hu

first: Xuemei


overall_design: Arabidospsis seedlings and inflorescence. 12 Ribo-seq libraries: 3 replicates for seedlings and inflorescence of WT and hot3-2.


title: Immunogenic Senescence Sensitizes Lung Cancer to LUNX-Targeting Therapy

city: 合肥

first: Defeng

last: Jiao

address: 黄山路443号

institute: USTC

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

overall_design: Refer to individual Series


title: Immunogenic Senescence Sensitizes Lung Cancer to LUNX-Targeting Therapy [NCI-H292]

summary: The higher immunogenicity of tumors usually predicts favorable therapeutic responses. Tumor antigens dominate the immunogenic character within tumors. We investigated if there was a targetable tumor antigen during immunogenic chemotherapy within lung cancer. Chemotherapy-induced immunogenic senescence was demonstrated using a multi-marker, three-step workflow and RNA-sequencing data. The ability of anti-lung-specific X protein (LUNX) antibody to suppress the survival of senescent lung cancer cells was evaluated in vitro and in vivo using real-time cytotoxicity analysis and xenograft mouse models, respectively. The induction of cellular senescence by immunogenic chemotherapy boosted cell-surface shuttling of LUNX and enhanced the immunogenic features of senescent tumor cells, which sensitized lung cancer cells to anti-LUNX antibody-mediated therapy and contributed to tumor suppression. The immunogenic senescence-mediated anti-tumor response was triggered by the direct action of antibody on tumor cells, strengthened by natural-killer cells through an antibody-dependent cell-mediated cytotoxicity response and, ultimately, led to tumor control. Our findings suggest that LUNX is a lung cancer targetable-immunogenic antigen. The proportion of lung cancers responding to LUNX-targeting therapy could be expanded substantially by immunogenic chemotherapy that induces senescence-associated translocation of LUNX to the plasma membrane.

overall_design: Examination of the differences between DMSO-treated NCI-H292 cells and mitoxantrone-treated NCI-H292 cells

first: Jiao

last: Defeng


title: Single Cell RNAseq of the hippocampus after RSD following microglia depletion

status: Public on Oct 02 2024

city: Columbus

first: Ethan

last: Goodman

state: Ohio

address: 460 Medical Center Drive

institute: Ohio State University

summary: Chronic stress is associated with anxiety and cognitive impairment. Repeated social defeat (RSD) in mice induces anxiety-like behavior driven by microglia and the recruitment of inflammatory monocytes to the brain. Nonetheless, it is unclear how microglia communicate with other cells to modulate the physiological and behavioral responses to stress. Using single-cell (sc)RNAseq, novel stress-associated microglia were identified in the hippocampus and defined by RNA profiles of cytokine/chemokine signaling, cellular stress, and phagocytosis. Microglia depletion with a CSF1R antagonist (PLX5622) attenuated the stress-associated profile of leukocytes, endothelia, and astrocytes. Furthermore, RSD-induced social withdrawal and cognitive impairment were microglia dependent, but social avoidance was microglia independent. Furthermore, single-nuclei (sn)RNAseq showed robust responses to RSD in hippocampal neurons that were both microglia dependent and independent. Notably, stress-induced CREB, oxytocin, and glutamatergic signaling in neurons were microglia dependent. Collectively, these stress-associated microglia influenced transcriptional profiles in the hippocampus linked to social and cognitive deficits.

overall_design: control-veh, control-plx, stress-veh, stress-plx, 3 hippocampi pooled, two separate cohorts with two separte 10x barcoding and sequencing


title: Comparison of annulus fibrosus tissue from tails of neonatal mice aged postnatal day 5, day 14, day 21, and day 28

city: Manhattan

first: Danielle

last: D'Erminio

address: 1 Gustave L. Levy Place

department: Orthopaedics

institute: Mount Sinai

summary: Neonatal mouse intervertebral discs lose regenerative potential between postnatal day 14 and  day 28during a period of Intervertebral disc (IVD) defects heal poorly and can cause back pain and disability. We identified that IVD herniation injury heals regeneratively in neonatal mice until postnatal day 14 (p14) and shifts to fibrotic healing by p28. This age coincides with the shift in expansive IVD growth from cell proliferation to matrix elaboration, implicating collagen crosslinking. 𝛽-aminopropionitrile treatment reduced IVD crosslinking and caused fibrotic healing without affecting cell proliferation. Bulk sequencing on naïve IVDs were depleted for matrix structural organization from p14 to p28 to validating the importance of crosslinking in regenerative healing. We conclude that matrix changes are key drivers in the shift to fibrotic healing, and a stably crosslinked matrix is needed for IVD regeneration.

overall_design: 4 samples per age. Each sample consists of AF tissue from 2-3 mice (including both males and females) with each mouse contributing 10 discs

first: James

last: Iatridis

first: Igor

last: Brodsky


title: Identification and analysis of microRNAs responsible for brown planthopper resistance in BPH14/BPH15 pyramiding rice

city: Wuhan

first: Liang

address: 1 Nanhu Yaoyuante, Hongshan District

institute: Hubei Academy of Agricultural Sciences

summary: Background Rice farming faces a serious challenge from the brown planthopper (BPH), with the pyramiding of BPH14 and BPH15 genes delivering effective protection in elite rice strains. However, the molecular basis behind this resistance is still unclear. Results The study investigated miRNA levels in BPH14/BPH15 pyramiding line (B1415) and their recurrent parent (RP) under BPH infestation employing high-throughput sequencing and revealed 136 differentially expressed miRNAs (DEMs) among 550 known miRNAs. An integrated analysis highlighted that 587 miRNA-mRNA pairs linking 95 DEMs to 537 targeted genes were enriched in phenylpropanoid and lignin metabolism, circadian rhythms, and amino acid metabolism. The candidate DEMs, miR172d-3p, and miR396 family members were identified as negative regulators to decrease their target genes Os06g0708700 (encoding a nodulin-like protein) and Os11g0129700 (encoding an AP2 domain transcription factor), suggesting their key roles in rice against BPH. Conclusions Our investigation provides the first insights into miRNA-mediated defense mechanisms in the B1415. Identifying miRNAs and their target mRNAs in BPH resistance opens a new avenue for rice breeding programs, offering potential targets for improving pest resistance. Understanding these molecular interactions paves the way for developing more resistant rice cultivars, thereby contributing to sustainable rice production and food security.

overall_design: To uncover miRNAs responsible for BPH resistance in B1415, we conducted small RNA sequencing and characterized small RNAs in the B1415 and RP plants infested by BPH at onset (B1415_0, RP_0), early infestation stage (B1415_early, RP_early), and late infestation stage (B1415_late, RP_late), revealing key miRNA-mRNA regulatory networks contributing to B1415's BPH resistance. The pyramiding line containing both BPH14/BPH15 genes (B1415) was created using the indica cartivar 'Wushansimiao' as the recurrent parent (RP).

first: Dabing

last: Yang

first: Hongbo

last: Wang

first: Xueshu

last: Du

last: Lu

first: Jinbo

last: Li

first: Mingyuan

last: Xia

first: Huaxiong

last: Qi

first: Wenjun

last: Zha

first: Yan

last: Wu

first: Tongmin

last: Mou

first: Aiqing

first: Bingliang

last: Wan


title: Immunogenic Senescence Sensitizes Lung Cancer to LUNX-Targeting Therapy [A549]

first: Defeng

last: Jiao

overall_design: Examination of the differences between DMSO-treated A549 cells and mitoxantrone-treated A549 cells

first: Jiao


title: OCI-AML22 multiome datasets (scRNA-Seq/scATAC-Seq)

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

institute: University Health Network

summary:
The leukemia stem cell (LSC) compartment is a complex reservoir fuelling disease progression in acute myeloid leukemia (AML). The existence of heterogeneity within this compartment is well documented but prior studies have focused on genetic heterogeneity without being able to address functional heterogeneity. Understanding this heterogeneity is critical for the informed design of therapies targeting LSC, but has been hampered by LSC scarcity and the lack of reliable cell surface markers for viable LSC isolation. To overcome these challenges, we turned to the patient-derived OCI-AML22 cell model. This model includes functionally, transcriptionally and epigenetically characterized LSC broadly representative of LSC found in primary AML samples.
Focusing on the pool of functionally assessed LSC (Boutzen et al, Leukemia, 2022), we performed single cell RNA-Seq/ATAC-Seq analysis. Using an integrated approach combining xenograft assays this single-cell analysis identified two LSC subtypes with distinct transcriptional, epigenetic and functional properties. These LSC subtypes differed in depth of quiescence, differentiation potential, repopulation capacity, sensitivity to chemotherapy and could be isolated based on CD112 expression. A majority of AML patient samples had transcriptional signatures reflective of either LSC subtype, and some even showed coexistence within an individual sample.

overall_design:
The functionally assessed LSC fraction in the OCI-AML22 primary AML derived model was sorted and subjected to multiome (scRNA-Seq/scATAC-Seq)
***Submitters state that raw data will be deposited to a controlled access repository***

first: Alex

first: Helena

last: Boutzen

first: John

last: Dick


title: Therapeutic Single-Cell Landscape: Methotrexate Exacerbates Interstitial Lung Disease by Compromising the Stemness of Alveolar Epithelial Cells under Systemic Inflammation

city: Seoul

first: Jeongjun

last: Chae

address: Irwon-ro 115

department: SAIHST

institute: Sungkyunkwan University

summary: Interstitial lung disease (ILD) poses a serious threat in patients with rheumatoid arthritis (RA). However, the impact of cornerstone drugs, including methotrexate (MTX) and TNF blockade, on RA-associated ILD (RA-ILD) remains controversial. Our study using an SKG mouse model and single-cell transcriptomics revealed that MTX exacerbates pulmonary inflammation by promoting immune cell infiltration, Th17 activation, and fibrosis. In contrast, TNF blockade ameliorates these features and inhibits ILD progression. Analysis of data from a human RA-ILD cohort revealed that patients with ILD progression had persistently higher systemic inflammation than those without progression, particularly among the subgroup undergoing MTX treatment. These findings highlight the need for personalized therapeutic approaches in RA-ILD, given the divergent outcomes of MTX and TNF blockade.

overall_design: At 8-10 weeks of age, male SKG mice received a single intraperitoneal injection of zymosan from Saccharomyces cerevisiae (7.5 mg per 20 g; MilliporeSigma, St. Louis, MO, USA) to induce arthritis and pneumonitis. We then gave them twice-weekly intraperitoneal injections of PBS, MTX (7.5 mg/kg; MilliporeSigma), or TNFα inhibitor (100 μg/kg; R&D Systems, Inc., Minneapolis, MN, USA).

first: Sung-Hae

last: Chang

first: Seyoung

last: Jung

first: Jeong-Jun

first: Jeong-Yeon

last: Kim

first: Seon-Uk

first: Ji-Yong

last: Choi

first: Hye-Jeong

last: Han

first: Hyun-Taek

first: Hak-Jae

first: Hyun-Je

first: Woong-Yang

last: Park

first: Jeffrey

last: Sparks

first: Eun-Young

last: Lee

first: Jeong-Seok


title: Virome of monocotyledonous weeds growing at crop fields revealed infection with several viruses and suggested their virus reservoir role

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

summary: During a proof-of-concept study, virome of millet, grown as weed was determined by small RNA HTS. As a result, from the pools of 20 randomly collected millet samples collected at two locations, we identified the presence of three viruses, two of them first time in Hungary. Based on our results we could only suspect that these viruses: wheat streak mosaic virus (WSMV), barley stripe mosaic virus (BYSMV) and barley virus G (BVG) could have been overwintered in millet or other monocotyledonous weeds growing at these fields. As a follow-up research, in the summer of 2021, we collected symptomatic leaves of several monocotyledonous plants at the same fields. This time the sampling was done in July. From the samples, small RNA HTS was carried out.

sample_organism:
Panicum miliaceum
Setaria viridis
Sorghum halepense
Zea mays
Cynodon dactylon
Echinochloa crus-galli

overall_design: virome was determined by sRNA HTS in pools of individuals originating from the same plant species

first: Zsuzsanna

middle: N

last: Galbacs

first: Evans

last: Duah Agyemang

first: Gyorgy

last: Pásztor

first: András

middle: P

last: Takács

first: Éva

last: Várallyay


title: A novel noninvasive murine model of neonatal hypoxic ischemic encephalopathy demonstrates developmental delay and motor deficits with activation of inflammatory pathways in monocytes [scRNA-seq]

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

summary: Neonatal hypoxic ischemic encephalopathy (HIE) occurs in 1.5 per 1000 live births, leaving affected children with long-term motor and cognitive deficits. Few animal models of HIE incorporate maternal immune activation (MIA) despite the significant risk MIA poses to HIE incidence and diagnosis. Our non-invasive model of HIE pairs late gestation MIA with postnatal hypoxia. HIE pups exhibited a trend toward smaller overall brain size and delays in the ontogeny of several developmental milestones. In adulthood, HIE animals had reduced strength and gait deficits, but no difference in speed. Surprisingly, HIE animals performed better on the rotarod, an assessment of motor coordination. There was significant upregulation of inflammatory genes in microglia 24 hours after hypoxia, which were largely downregulated one week later. Single cell RNAseq revealed upregulation of epigenetic machinery in macrophages invading the brain following HIE. These results support a two-hit noninvasive model pairing MIA and hypoxia as a model for HIE in humans. This model results in a mild phenotype compared to established HIE models; however, HIE is a clinically heterogeneous injury resulting in a variety of outcomes in humans. The pathways identified in our model of HIE may yield novel targets for therapy for neonates with HIE.

overall_design: scRNA-seq libraries were constructed from 24 mouse brain tissue samples, which are either CONTROL or HIE treated from P8 and P10 to timepoints

first: Lemanski

last: Elise

first: Zheng

last: Qi

first: Franke

last: Karl

first: Wright-Jin

last: Elizabeth


title: A novel noninvasive murine model of neonatal hypoxic ischemic encephalopathy demonstrates developmental delay and motor deficits with activation of inflammatory pathways in monocytes


title: A novel noninvasive murine model of neonatal hypoxic ischemic encephalopathy demonstrates developmental delay and motor deficits with activation of inflammatory pathways in monocytes [bulkRNA-seq]

overall_design: bulk RNA-seq libraries were constructed from 22 mouse brain tissue samples, which are either CONTROL, HIE, or Hypoxia treated from 6 different timepoints (P7, P8, P9, P10, P11, P14)

first: Elise

last: Lemanski

first: Karl

last: Franke

first: Elizabeth

last: Wright-Jin


title: Untargeted and targeted transcriptome analysis to decipher the impact of exogenous fatty acids in cold stress adaptation of Listeria monocytogenes

city: Jouy En Josas

first: Maud

last: Darsonval

state: State/Province

address: Domaine de Vilvert, bâtiment 440

department: Institue Micalis

country: France

institute: Université Paris-Saclay, INRAE, AgroParisTech

summary: Listeria monocytogenes is a ubiquitous and psychrophilic foodborne pathogen commonly found in raw materials, ready to eat products and food environments. It was previously demonstrated that L. monocytogenes can grow faster at low temperature when unsaturated fatty acids (UFA) are present in its environment. In this study, we used comparative gene expression profiling of RNA-sequencing data to understand the impact of UFA on the behavior and cold adaptation of L. monocytogenes. We demonstrate that the incorporation of UFA into the membrane induces changes in the regulation of overall fatty acid biosynthesis, which prompts us to propose two hypotheses for UFA synthesis in L. monocytogenes. The general stress response is also highly impacted by the incorporation of UFA into the membrane at low temperature. In particular, we hypothesize that transcriptional regulation of cspB is not a temperature dependent mechanism, but could be related to a membrane fluidity stimulus. Furthermore, when UFA are incorporated into the membrane at low temperature, we observed overexpression of genes involved in flagella assembly. This study sheds light on the cold adaptation of L. monocytogenes in the presence of exogenous FA and on potential concerns for controlling these bacteria in food environments.

overall_design:
To investigate the impact of the presence of exogenous unsaturated fatty acid (18:1) at low temperature on gene expression profile of Listeria monocytogenes Lm208, we performed gene expression profile analysis using data obtained from RNA sequencing of L. monocytogenes grown in four growth conditions at one time point (mid-exponential phase).
Comparative gene expression profiling of RNA-seq data for L. moncotyogenes Lm208 strain grown without (C) or with fatty acid supplementation (FA) at two temperature 37°C (C37 and FA37) or 5°C (C5 or FA5) in tritplicates.

first: Aurore

last: Quilleré

first: Angelos

last: Papadochristopoulos

first: Alban

last: Amoros

first: Pierre

last: Nicolas

first: Florence

last: Dubois-Brissonnet


title: Compensatory electron transfer from the ubiquinol pool circumvents cytochrome c oxidase deficiency and restores effector and memory T cell function

city: Bethesda

first: Peter

last: McGuire

state: MD

address: 10 Center Dr, Building 10, Room 7N260A

department: NHGRI

institute: NIH

summary: The ultimate goal of immunometabolism is to modulate metabolic pathways to enhance immunity. Here, we investigate the potential of an alternative oxidase (AOX) to counteract cytochrome c oxidase (COX) deficiency in T cells. COX is vital for oxidative phosphorylation (OXPHOS), and its deficiency leads to redox imbalances, impaired metabolism, reactive oxygen species (ROS), and apoptosis, resulting in T cell immunodeficiency. We introduced an AOX into COX-deficient T cells, which revealed a normalization of genes involved in redox balance, apoptosis, and metabolic pathways. Mitochondrial function, glycolysis and TCA cycle function were also restored. AOX-enhanced T cells showed improved activation, proliferation, differentiation, and memory formation, resulting in better immune responses against viral challenges. These findings suggest that targeting the ubiquinol pool could be a promising therapeutic strategy for enhancing T cell function in conditions characterized by COX dysfunction and compromised immune responses.

overall_design:
This study includes read counts from two RNAseq experiments. In the first experiment, RNA was derived from T cells from four groups of mice on a C57Bl/6J background: wildtype (WT), Cox10fl/fl;Cd4-Cre (TCox10-/-), Rosa26-targeted Ciona intestinalis alternative oxidase expressing (Aox), and TCox10-/-/Aox double mutants. The goal of this experiment was to evaluate the ability of AOX to compensate for COX deficiencies in T cells. In the second experiment, RNA is derived from T cells from two groups of mice on a C57BL/6-Tg(TcraTcrb)1100Mjb/J (OT-1) background: wildtype (WT_IL15), and TCox10-/-/Aox double mutants (TCox10-/-/Aox_IL15). The goal of this experiment was to evaluate the ability of AOX to compensate for COX deficiencies in memory T cells.

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

last: Tarasenko

first: Emily

middle: B

last: Warren

first: Amanda

middle: L

last: Fuchs

first: Bharati

last: Singh

first: Jose

last: Marin Franco


title: Targeting epigenetic regulation and post-translational modification with 5-Aza-2’ deoxycytidine and SUMO E1 inhibition Augments T Cell Receptor Therapy

city: Leiden

first: Jessica

last: Roelands

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

summary: Cellular immunotherapy using modified T cells offers new avenues for cancer treatment. T cell receptor (TCR) engineering of CD8 T cells enables these cells to recognize tumor associated antigens (TAA) and tumor specific neo-antigens. Improving TCR T cell therapy through increased potency and in vivo persistence will be critical for clinical success. We evaluated a novel drug combination to enhance TCR therapy in mouse models for acute myeloid leukemia (AML) and multiple myeloma (MM). Combining TCR therapy with the SUMO E1 inhibitor TAK981 and the DNA methylation inhibitor 5-Aza-2’ deoxycytidine resulted in strong anti-tumor activity in a persistent manner against two in vivo tumor models of established AML and MM. We uncovered that the drug combination caused strong T cell proliferation, increased cytokine signaling in T cells, improved persistence of T cells, and reduced differentiation towards exhausted phenotype. Simultaneously the drug combination enhanced immunogenicity of the tumor by increasing HLA and costimulation and surprisingly reducing inhibitory ligand expression. Combining T cell therapy with TAK981 and 5-Aza-2’ deoxycytidine may be an important step towards improved clinical outcome.

overall_design: This study utilizes in vivo tumor models in NSG mice to investigate the efficacy of TAK981 and/or 5-Aza-2’ treatment on OCI-AML3 and U266 tumors. Luciferase-tdTomato tagged cells enable real-time monitoring of tumor growth and T cell dynamics. Ex vivo analysis involves the isolation of bone marrow and tumors for comprehensive molecular profiling, including flow cytometry and single-cell RNA sequencing using the 10x Genomics Chromium X platform. Samples were collected from both bone marrow and tumor tissues. For each mouse, bone marrow from both paws was combined to ensure representative sampling. The bone marrow samples underwent negative MACS enrichment to isolate human cells, using anti-human CD45 (APC) antibodies and APC-beads. This process specifically targeted human cells within the mouse bone marrow population. To further purify the enriched human cell population, positive selection was performed using anti-human CD45 antibodies, sorting for cells expressing this marker. This ensured a high level of purity in the final cell population. Subsequently, the purified human cells were labeled with unique hashtags, allowing for individual sample identification and tracking throughout downstream analyses. Following cell isolation and labeling, a single run of 10x Genomics 3’ v3.1 chemistry was conducted. This involved the preparation of single-cell gene expression libraries using the 10x Genomics Chromium X platform, following the manufacturer's instructions.

first: Jessie

last: Kroonen

first: Anne

last: Wouters

first: Ilona

last: de Graaf

first: Dennis

middle: G

last: Remst

first: Sumit

last: Kumar

first: Tassilo

last: Wachsmann

first: Amina

last: Teunisse

first: Noel

last: de Miranda

first: Marieke

last: Griffioen

first: Mirjam

last: Heemskerk

first: Alfred

middle: O

last: Vertegaal


title: Gene expression profiling at the single nuclei level of channel catfish spleen

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: Channel catfish, Ictalurus punctatus, is an important model U.S. aquaculutre species. Given its role in food production, the catfish immune response to industry-relevant pathogens has been extensively studied and has provided crucial information on innate and adaptive immune function during disease progression. To further examine the channel catfish immune system, single-nuclei RNA sequencing on whole spleens from three adult individuals was performed. Spleen cell suspensions were prepared by passing tissues through cell sieves. Single-cell RNAseq libraries were then prepared using the 10X Genomics Chromium X with the Next GEM Single Cell 3’ Reagents and sequenced 2x150bp on an Illumina sequencer. Each demultiplexed library was aligned to the CoCo_2.0 channel catfish reference assembly, filtered, and counted to generate feature-barcode matrices. Cluster analysis allowed for the identification of multiple cell types including erythrocytes, hematopoietic stem cells, B cells, T/NK cells, myeloid lineage derivatives, plasma cells and endothelial cells. The majority of cells detected were erythrocytes, which are nucleated in teleost fish.

overall_design: Whole spleen samples from three adult catfish were collected to generate a channel catfish spleen cell atlas.

first: Johanna

last: Aldersey

first: Miles

middle: D

last: Lange

first: Benjamin

last: Beck

middle: W


title: Perturbation of healthy iPSC-CM with hsa-miR-134, hsa--433, and hsa-487b mimic and inhibitor

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

summary: In this study, healthy iPSC-CM were transfected with hsa-miR-134, hsa--433, and hsa-487b mimic and inhibitor to study their effects on human cardiac proliferation after it was found that these miRNAs were enriched in maternal blood plasma within SVHD pregnancies. Mock and scramble were used as controls. Overall, it was found that miR134 and miR487b influenced human iPSC-CM proliferation.

overall_design: iPSCs were differentiated in to iPSC-CM via small-chemical modulation of Wnt. D15 iPSC-CM were passaged onto a 24-well plate and then transfected with miRNA mimic, mock, scramble, or inhibitor in experimental triplicates. Four wells were pooled for each group and lysed with Qiazol. Total RNA was extracted four days after transfection, with the results of each being the subject of this RNA-seq data.

first: Matthew

last: Alonzo

first: Mingtao

last: Zhao


title: Cattle Cleavage Under Targets & Release Using Nuclease (CUT&RUN)  for CENP-A locus identification

city: Moscow

first: Brenda

last: Murdoch

state: Idaho

address: 875 Perimeter Dr.

department: Department of Animal, Veterinary & Food Sciences

institute: University of Idaho

summary: CUT&RUN experiment was carried out on bovine semeimbranosous muscle satellite cells to identify the locus of the accumulation of the centromeric protein A (CENP-A) on the cattle Y-chromosome. This was carried out to support the annotation of the DNA signal comprising tandem array of a centromeric satellite signal which characterizes the centromere on the Y-chromosome.

overall_design: To identify the locus of CENP-A signal accumulation with the pull down assay from the bovine satellite cells, the GeneTex CENP-A antibody with catalog number GTX13939 was used in this study. The antibody is monoclonal and of the isotype IgG1

first: Temitayo

last: Olagunju

last: Rosen

first: Holly

last: Neibergs

first: Gabrielle

last: Becker

first: Kimberly

last: Davenport

first: Christine

last: Elsik

first: Tracy

middle: S

last: Hadfield

first: Sergey

last: Koren

first: Kristen

last: Kuhn

first: Arang

last: Rhie

first: Katie

last: Shira

first: Amy

last: Skibiel

first: Morgan

middle: R

last: Stegemiller

first: Jacob

last: Thorne

first: Patricia

last: Villamediana

first: Noelle

last: Cockett

first: Timothy

last: Smith


title: PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation [RNA-Seq]

city: Guangzhou

first: Liang

last: Zhenwei

state: Guangdong

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen University

summary: Nucleation and spreading of H3K27me3 are critical steps for the initiation and maintenance, respectively, of mitotically inheritable Polycomb-mediated repressive chromatin states in cell identity memory, in both animals and plants. Although a semiconservative read-and-write mechanism is proposed to play a key role in H3K27me3 propagation, the specific determinant and underlying mechanism by which the Polycomb Repressive Complex 2 (PRC2) accesses unmodified nucleosomes for propagating H3K27me3 remain enigmatic. Using Arabidopsis thaliana as a model, we show that the chromatin remodeling activity of PICKLE (PKL) has a specialized role in H3K27me3 spreading to safeguard cell identity during differentiation. PKL specifically binds to H3K27me3 spreading regions but not nucleation sites of Polycomb target genes and physically interacts with the MSI1 subunit of PRC2. Loss of PKL abolishes the occupancy of the PRC2 catalytic subunit CLF in spreading regions and leads to aberrant differentiation. Nucleosome condensing endowed by the ATPase function of PKL ensures that unmodified nucleosomes are accessible to PRC2 catalytic activity. Our findings highlight that PKL-dependent nucleosome compaction is critical for PRC2-mediated H3K27me3 read-and-write functions in H3K27me3 spreading, thus revealing a mechanism by which repressive chromatin domains are established and propagated.

overall_design: Examination of global RNA expression in 14-day-old wt and various mutants seedlings.

first: Zhenwei

last: Liang


title: Sheep Y-chromosome methylation profile from long reads sequencing data

first: Brenda

last: Murdoch

summary: The methylation landscape of the sheep Y-chromosome was characterized using methylated cytosine data produced from PacBio and ONT long reads sequencing platforms. The study aimed to corroborate the presumptive locus of the sheep Y-chromosome centromere.

overall_design: The annotation of the centromere was based on the identification of a characteristic centromeric dip in methylation signal associated with the locus of the kinetochore assembly.

first: Temitayo

last: Olagunju

first: Benjamin

last: Rosen

first: Holly

last: Neibergs

middle: E

first: Timoth


title: Cattle Y-chromosome methylation profile from long reads sequencing data

summary: The methylation landscape of the cattle Y-chromosome was characterized using methylated cytosine data produced from PacBio and ONT long reads sequencing platforms.

first: Gabrielle

last: Becker

first: Kimberly

last: Davenport

first: Christine

last: Elsik

first: Tracy

last: Hadfield

first: Sergey


title: PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation [Mnase-Seq]

overall_design: 14-day-old seedlings were used to extract chromatin


title: Gene expression changes in response to tead degrader HC278

city: Stony Brook

first: Jyoti

last: Misra

address: 101 Nicolls Rd

institute: Stony Brook University

summary: TEAD transcription factors associate with the hippo pathway effectors YAP/TAZ and mediate their oncogenic effect. To inhibit YAP activity, we developed a TEAD degrading PROTAC HC278. Here we treated NCI-H226 mesothelioma cells with DMSO or 500nM HC278 for 24 hours and examined the change in gene expression in response to HC278 treatment.

overall_design: NCI-H226 cells were treated with DMSO or 500nM HC278 for 24 hours and RNA was extracted an equenced.


title: Identifying SETBP1 haploinsufficiency molecular pathways to improve patient diagnosis using induced pluripotent stem cells and neural disease modelling.

city: Nedlands

first: Kevin

middle: Guangxing

last: Chen

address: Hospital Avenue

country: Australia

institute: The Kids Research Institute Australia

summary: Background: SETBP1 Haploinsufficiency Disorder (SETBP1-HD) is characterised by mild to moderate intellectual disability, speech and language impairment, mild motor developmental delay, behavioural issues, hypotonia, mild facial dysmorphisms, and vision impairment. Despite a clear link between SETBP1 mutations and neurodevelopmental disorders the precise role of SETBP1 in neural development remains elusive. We investigate three SETBP1 genetic variants including two pathogenic mutations p.Glu545Ter and SETBP1 p.Tyr1066Ter, resulting in removal of SKI and/or SET domains, and a point mutation p.Thr1387Met in the SET domain. Methods: Genetic variants were introduced into induced pluripotent stem cells (iPSCs) and subsequently differentiated into neurons to model the disease. We measured changes in cellular differentiation, SETBP1 protein localisation, and gene expression changes. Results: The data indicated a change in the WNT pathway, RNA polymerase II pathway and identified GATA2 as a central transcription factor in disease perturbation. In addition, the genetic variants altered the expression of gene sets related to neural forebrain development matching characteristics typical of the SETBP1-HD phenotype. Limitations: The study investigates changes in cellular function in differentiation of iPSC to neural progenitor cells as a human model of SETBP1 HD disorder. Future studies may provide additional information relevant to disease on further neural cell specification, to derive mature neurons, neural forebrain cells, or brain organoids. Conclusions: We developed a human SETBP1-HD model and identified perturbations to the WNT and POL2RA pathway, genes regulated by GATA2.  Strikingly neural cells for both the SETBP1 truncation mutations and the single nucleotide variant displayed a SETBP1-HD-like phenotype.

overall_design: To investigate the role of a variant of unknown signifiance (VUS) in SETBP1 Haploinsufficiency Disorder, genetic variants (known pathogenic variants or the VUS) were introduced into KOLF2 cells, and induced into NPCs. Some KOLF2 cells were left as WT. We collected RNAseq data at days 0 and 24 for comparative gene expression analysis among the variants.

first: Nicole

last: Shaw

first: Kathryn

last: Farley

first: Mitchell

last: Hedges

first: Catherine

last: Forbes

first: Garth

last: Baynam

first: Timo

last: Lassmann

first: Vanessa

last: Fear


title: The Candida auris Hog1 MAP kinase is essential for the colonization of murine skin and systemic infection

city: Nutley

first: Neeraj

last: Chauhan

state: New Jersey

address: 111 ideation way

institute: Center for Discovery and Innovation, Hackensack Meridian Health

summary: Candida auris, a multidrug-resistant human fungal pathogen, was first identified in 2009 in Japan. Since then, systemic C. auris infections have now been reported in more than 50 countries, with mortality rates of 30-60%. A major contributing factor to its high inter- and intrahospital clonal transmission is that C. auris, unlike most Candida species, displays unique skin tropism and can stay on human skin for a prolonged period. However, the molecular mechanisms responsible for C. auris skin colonization, intradermal persistence, and systemic virulence are poorly understood. Here, we report that C. auris Hog1 mitogen-activated protein kinase (MAPK) is essential for efficient skin colonization, intradermal persistence, as well as, systemic virulence. RNA-seq analysis of wildtype parental and hog1D mutant strains from YPD-grown cultures revealed marked down-regulation of genes involved in processes such as cell adhesion, cell-wall rearrangement, and pathogenesis in hog1D mutant compared to the wildtype parent. In agreement, we found a prominent role for Hog1 in maintaining cell-wall architecture, as the hog1D mutant demonstrated a significant increase in cell-surface b-glucan exposure and a concomitant reduction in chitin content. Additionally, we observed that Hog1 was required for biofilm formation in vitro and fungal survival when challenged with primary murine macrophages and neutrophils ex vivo. Collectively, these findings have important implications for understanding the C. auris skin adherence mechanisms and penetration of skin epithelial layers preceding bloodstream infections.

overall_design: We performed RNA-seq analysis of logarithmically growing Candida auris isolates in the Yeast Extract Peptone Dextrose broth medium (YPD; 1% yeast extract, 2% peptone, and 2% dextrose) at 30°C. We sequenced parent and HOG1 deletion strain in biological triplicates

first: Shivarathri

last: Raju

first: Jenull

last: Sabrina

first: Desai

last: Jigar

first: Chauhan

last: Neeraj


title: Mitochondrial Calcium Uniporter Promotes Kidney Aging through Inducing Mitochondrial Calcium-Mediated Renal Tubular Cell Senescence

city: guangzhou

first: yabing

last: xiong

address: 1838 North Guangzhou Avenue

institute: southern medical university

summary: Kidney is a vital organ responsible for homeostasis in the body. To retard kidney aging is of great importance for maintaining body health. Whereas the therapeutic strategies targeting against kidney aging are not elucidated. Recent studies show mitochondrial dysfunction is critical for renal tubular cell senescence and kidney aging, however, the underlying mechanisms of mitochondrial dysfunction in kidney aging have not been demonstrated. Herein, we found calcium overload, and the mitochondrial calcium uniporter (MCU) was induced in renal tubular cells and aged kidney. To activate MCU not only triggered mitochondrial calcium overload, but also induced reactive oxygen species (ROS) production and cellular senescence and age-related kidney fibrosis. Inversely, to block MCU or chelate calcium diminished ROS generation, restored mitochondrial homeostasis, and retarded cell senescence and protected against kidney aging. These results demonstrate MCU plays a key role in promote renal tubular cell senescence, which provides a new insight on the therapeutic strategy for fighting against kidney aging.

overall_design: To explore the potential mechanism about kidney aging, we established  natural aging models and performed RNA-seq in 2M and 24M mice. We compared the gene expression differences between the two groups and performed heatmap and GO enrichment analysis.

first: Yabing

last: Xiong

first: Wenyan

last: Huang