title: Mitochondrial DNA quantity Counteracts ROS damage in oocytes during female reproductive aging

city: Hangzhou

first: Xiaoling

last: Deng

address: Xihu District

institute: Westlake university

summary: We investigated the contentious role of mitochondrial reactive oxygen species (ROS) on mitochondrial DNA (mtDNA) quality and quantity in female reproductive aging. By conditionally knocking out the Sod2 gene in female mouse germline, we observed increased mitochondrial ROS and decreased oocyte quality, primarily due to impacts on OXPHOS complex II and mtDNA encoded mRNA levels. Interestingly, we found no increased mtDNA mutations, but alterations in mtDNA quantity, indicating the susceptibility of mtDNA to the mitochondrial ROS during reproductive aging. Notably, when we further decreased the basal level of mtDNA quantity by deactivating the mtSSB protein in Sod2 conditional knockout females, we observed an exacerbation of reproductive aging effects. This highlights the crucial role of mtDNA quantity in mitigating the impact of oxidative stress on fertility.

overall_design: To examine the molecular alterations in oocytes caused by elevated levels of mitochondrial matrix ROS, we employed the Smart seq2 method to study the transcriptomic alterations in mature oocytes from approximately six-month-old females between L/L cre mice and L/L mice.

first: Shiyun

last: Long


title: Assessment of Diet and Stress Effects on Ocular Vulnerability in Rodent Models of Traumatic Brain Insults using a Multi-Omics Approach

status: Public on Sep 08 2024

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

summary: Ocular injuries and visual deterioration occur in a large percentage of Warfighters sustaining physical and psychological trauma. From 2000 through the end of 2017, more than 275,000 Service-members have suffered from eye injuries, as shown by Surveillance data from the Department of Defense (DOD). Exposure to blast overpressure (BOP) also directly affects the brain visual signal processing centers (e.g., optic tracts). Likewise, traumatic brain injury (TBI)-induced impairments of vision are commonly seen among Military Veterans even when there is no direct injury to the eye, e.g., retina. Hence, these traumatic insults can influence the regulation of the visual and nonvisual retinal signaling pathways. The ocular system could be directly injured or could degenerate secondary to injury induced by psychological stress. Despite the lifelong disservice that vision losses exhibit, there are only few studies demonstrating the effect of these insults on retinal transcriptomics and the signaling mechanisms underlying the eye damage. Studies have shown that docosahexaenoic acid (DHA) is the most abundant ω-3 PUFA (polyunsaturated fatty acid) in the central nervous system and especially the retina and plays an important role in neuronal membrane structure integrity and neural dendritic connectivity. Hence, inclusion of ω-3s as dietary supplements could possibly be a vital therapeutic approach in alleviating stress-related ocular impairments. The objective of this study is to study the role of essential nutrients i.e., dietary ω-3 fatty acids on the ocular vulnerability to TBI and psychological stress. The retina was collected at 14 days post-insult, and gene expression changes were assessed by analyzing extracted total RNA on whole rat genome microarrays. Our findings in rats showed that TBI exposure significantly impaired the expression of retinal genes in all the diet groups, with highest change observed in the ω-3 rich house chow (HC) group. Psychological stress had a greater effect on retinal gene expression, particularly in rats fed with ω-3 deficient 1% LA diet (2249 genes downregulated and 1256 genes upregulated). The network clusters like neurovascular coupling and synaptic signaling were affected by TBI in ω-3 rich HC diet group while chemokine and actin cytoskeleton signaling were shown to be disrupted in ω-3 deficient 8% LA diet. Together, the results showed that these two diets (i.e., house chow and 8% LA) had opposing effects on some of the signaling pathways including endocannabinoid pathway and neuronal plasticity. For the UWT (underwater trauma) study, exposure to psychological stress significantly altered CREB (cAMP response element-binding protein) and opioid signaling in rodents fed with ω-3 deficient diets (i.e., 8% LA and 1% LA). Additionally, ephrin receptor and calcium signaling were differentially regulated by psychological stress in 1% LA versus 8% LA diet. Overall, the findings of our study suggest that poor dietary conditions can greatly influence the resilience to TBI and psychological stress. This work was intramurally funded by the USAMRDC/MOMRP.

first: Mital

middle: Y

last: Patel

first: Routing

last: Yang

first: Nabarun

last: Chakraborty

first: Stacy

middle: A

last: Miller

first: James

middle: C

last: DeMar

first: Andrew

last: Batuure

first: Donna

last: Wilder

first: Joseph

first: Rasha

last: Hammamieh


title: The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [TT-Seq]

status: Public on Sep 19 2024

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: H3K9me3-heterochromatin, compacted by HP1 proteins, restricts transcription factor binding and functions as a barrier to cell fate changes in development and reprogramming1,2. To investigate principles underlying H3K9me3-heterochromatin maintenance in mammalian cells, we applied degron engineering3,4 on mouse ESCs to conditionally deplete all three H3K9me3-methyltransferases within one hour and found an unexpectedly dynamic nature of heterochromatin maintenance. Following H3K9me3 methyltransferases degradation, HP1β dissociates from heterochromatin within three hours, and transcription factors quickly access the de-compacted heterochromatin, activating transcription of their targets, which then promotes H3K9me3 decay. Both passive dilution and active removal contribute to the H3K9me3 decay. Mathematical modeling reveals distinct H3K9me3 heterochromatin states with diverse chromatin features which influence initial H3K9me3 levels and the stability of H3K9me3 domains, thereby expanding our understanding of distinct heterochromatin domains. Rampant transposable element de-repression interferes with transcription of poised early developmental and signaling genes outside H3K9me3-domains, highlighting the intricate roles of dynamic H3K9me3-heterochromatin maintenance in safeguarding developmental programs. Our findings deconvolve the hierarchical relationships between H3K9me3 marks, methyltransferases, HP1 and transcription factors to reveal principles of H3K9me3-heterochromatin maintenance and how its remodeling enables transcription and cell fate change.

overall_design: A time-course experiment in which histone lysine 9 methyltransferases are ablated in mESCs and the expression of genes, repeats, and other transcriptional units is examined genome-wide by nascent RNA TT-seq. The time-course runs 48hrs with collection points at 0hrs, 3hrs, 12hrs, 24hrs, and 48hrs. Three biological repeats were sequenced in two separate sequencing runs (of the same libraries) for additional genome coverage at each time point. The 0hrs time point is taken to be the baseline against which decay is measured. A S. cerevisiae total RNA spike-in is employed to properly adjust sample signal between different time points.

first: Jingchao

last: Zhang

first: Greg

first: Tomer

last: Lapidot

first: Dario

last: Nicetto

first: Kenneth

last: Zaret


title: Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition [RNA-Seq 2]

status: Public on Sep 06 2024

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

country: China

institute: Westlake University

summary: This study aimed at investigating the transciptional changes during transition. What is more, we could look for key metabolic genes regulating transitions.

overall_design: We analyzed the transcriptome expression with perturbation by knockingout, overexpression of Cpt1a for identification of how Cpt1a impacts on PNT. Then we add HAT(A485) into the samples for investigating whether the PNT is susceptible to the H3K27ac originated from Cpt1a OE.

first: Zhaoyi

last: Ma


title: Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition [CUT&Tag]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We analyzed the H3K27ac to  determine how the Cpt1a influences PNT by histone modification.


title: C2H2-zinc finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes [RNA-seq]

status: Public on Sep 09 2024

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: With over 700 members, the Cys2-His2 zinc finger proteins (C2H2-ZNFs) constitute the largest class of DNA-binding transcription factors (TFs), yet remain largely uncharacterized1. Although certain family members, including GTF3A, WT1 and CTCF, have been shown to bind both DNA and RNA2,3, the extent to which C2H2-ZNFs interact with – and regulate – RNA-associated processes is not known. Here, we utilized UV crosslinking and immunoprecipitation (CLIP) and found that 148 of 150 C2H2-ZNFs that we analyzed bound directly to RNA in human cells. By integrating data from new individual nucleotide resolution RNA-binding maps for 50 of these C2H2-ZNFs with data from chromatin immunoprecipitation sequencing (ChIP-seq), protein-protein interaction, and RNA-seq experiments4, we observe that the RNA-binding profiles of C2H2-ZNFs are generally distinct from their DNA-binding preferences and that they regulate a variety of post-transcriptional processes, including pre-mRNA splicing, cleavage and polyadenylation, and m6A modification of mRNA. Our results thus substantially expand the cellular repertoire of RBPs by systematically defining RNA targets and regulatory roles of C2H2-ZNFs, and they provide a valuable resource for elucidating crosstalk between transcriptional and post-transcriptional regulatory programs.

overall_design: RNA-seq of HEK293 cells upon knockdown of ZNF784, ZBTB7A, or control non-targeting knockdown, and upon overexpression of CBLL1, ZNF654, or GFP control, in duplicate except for CBLL1 overexpression in a single replicate.

first: Syed

last: Nabeel-Shah

first: Shuye

last: Pu

middle: D

last: Burns

first: Nujhat

last: Ahmed

first: Giovanni

middle: L

last: Burke

first: Ernest

last: Radovani

first: Hyunmin

last: Lee

first: Guoqing

last: Zhong

first: Hua

last: Tang

first: Edyta

last: Marcon

first: Zhaolei

first: Timothy

middle: R

last: Hughes

first: Benjamin

middle: J

last: Blencowe

first: Jack

middle: F

last: Greenblatt


title: C2H2-zinc finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes.

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

overall_design: Refer to individual Series


title: Selenium supplementation induces changes in body composition, increases CD4+ T cells frequency and is associated with the expression of genes responsible of naïve and memory CD8+ T cells function on treated HIV-infected individuals.

city: Mexico City

first: Marti

last: Wilson-Verdugo

state: Mexico City

address: Ciudad Universitaria

country: Mexico

institute: Instituto de Fisiologia Celular

summary: Background & aim: Micronutrient deficiencies, particularly those of zinc and selenium, are common in persons living with human immunodeficiency virus (PLWHIV), and have been associated with the development of non-AIDS related comorbidities, impaired immune system function, HIV disease progression and mortality. The implementation of intervention strategies on clinically stable long-term-treated PLWHIV could bring potential benefits on impeding or delaying the onset of non-AIDS associated comorbidities, improving their health status and overall quality of life. The aim of the present study is to analyze the effect of zinc and selenium supplementation on body composition, bone mineral density (BMD), lipids profile, glucose and immune system activation and function on PLWHIV on antiretroviral therapy (ART) without metabolic diseases. Methods: This pilot trial was composed of 60 PLWHIV on ART who were randomly assigned to either zinc, selenium, zinc + selenium supplementation or to a control group. Daily supplementation was prescribed during 6 months as follows: the zinc group received 30 mg of zinc gluconate, the selenium group received 200 mcg of selenium yeast and the zinc + selenium group received both micronutrients at the same doses and presentations. Individuals in the control group were followed during the same time without any nutritional supplementation. Body composition (weight, body mass index [BMI], fat mass and muscle mass), BMD, blood pressure, blood biochemical parameters (cholesterol, glucose and triglycerides), serum zinc and selenium concentrations, CD4+ T cell count and CD4+ and CD8+ T cells immune activation were assessed before and after supplementation. One individual of each supplementation group and one of the control group were analyzed for single cell transcriptomics before and after supplementation. Results: BMI (p=0.03), fat mass in kg (p=0.03) and percentage (p=0.02), as well as trunk fat (p=0.01), were significantly decreased after selenium supplementation. No changes were observed for body composition, BMD, biochemical determinations or blood pressure on the other intervention groups after supplementation (p>0.05 in all cases). The CD4+ T cells frequency and count significantly increased after selenium and zinc supplementation (p=0.03, p=0.05 respectively). CD4+ and CD8+ T-cell immune activation did not change after supplementation (p>0.05 in both cases). On the single cell transcriptome analysis, zinc and selenium supplementation significantly change de expression of genes associated with the function of naive and memory CD8+ T cells (adjusted p<0.05 in all cases). Conclusions: Selenium supplementation have beneficial effects on the body composition, while zinc and selenium supplementation increased CD4+ T cell replenishment of PLWHIV on long-term ART without metabolic diseases. Additionally, zinc and selenium supplementation modified the expression of genes associated with the function of naive and memory CD8+ T cells. Zinc and selenium supplementation are a simple, low-cost, and safe nutritional treatment that represents a complementary intervention to improve the health status and increase the quality of life of clinically stable PLWHIV  without metabolic diseases. Registered: Under ClinicalTrails.gov identifier NCT03421314

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated from EDTA-anticoagulated peripheral blood by density gradient centrifugation. Vials with 25 million PBMCs were cryopreserved until used. Blood samples taken at baseline and after six months of treatment were used for targeted scRNA-seq library preparation; the samples came from a control patient (with no supplementation) and three patients that had received zinc, selenium, or zinc plus selenium supplementation, respectively.

first: I

last: Osuna-Padilla

first: N

last: Rodríguez-Moguel

first: A

last: Aguilar-Vargas

first: M

last: Tolentino-Dolores

first: O

last: Perichart-Perera

first: V

last: Ahumada-Topete

first: S

last: Ávila-Ríos

last: Soto-Nava

first: D

last: Díaz-Rivera

first: E

last: De León-Lara

first: G

last: Reyes-Terán

last: Briseño


title: scNanoSeq-CUT&Tag: a long-read single-cell CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells

city: BeiJing

first: Yuqing

last: Guo

state: BeiJing

address: Peking University, No.5 Yiheyuan Road, Haidian District, Beijing, China

department: Biomedical Pioneering Innovation Center

institute: Peking University

summary: We developed scNanoSeq-CUT&Tag, a streamlined method by adapting a modified CUT&Tag protocol to Oxford Nanopore sequencing platform for efficient chromatin modification profiling at single-cell resolution. We firstly tested the performance of scNanoSeq-CUT&Tag on six human cell lines: K562, 293T, GM12878, HG002, H9, HFF1 and adult mouse blood cells, it showed that scNanoSeq-CUT&Tag can accurately distinguish different cell types in vitro and in vivo. Moreover, scNanoSeq-CUT&Tag enables to effectively map the allele-specific epigenomic modifications in the human genome andallows to analyze co-occupancy of histone modifications. Taking advantage of long-read sequencing,scNanoSeq-CUT&Tag can sensitively detect epigenomic state of repetitive elements. In addition, by applying scNanoSeq-CUT&Tag to testicular cells of adult mouse B6D2F1, we demonstrated that scNanoSeq-CUT&Tag maps dynamic epigenetic state changes during mouse spermatogenesis. Finally, we exploited the epigenetic changes of human leukemia cell line K562 during DNA demethylation, it showed that NanoSeq-CUT&Tag can capture H3K27ac signals changes along DNA demethylation. Overall, we prove that scNanoSeq-CUT&Tag is a valuable tool for efficiently probing chromatin state changes within individual cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: scNanoSeq-CUT&Tag for chromatin midifications on six human cell lines (K562, 293T, GM12878, HG002, H9, HFF1), adult mouse blood cells and adult mouse testicular cells.

first: Qingqing

last: Li

first: Zixin

last: Wu


title: Computational modeling integrating transcriptomic and vulnerability responses can predict suppressors of cell death as candidate targets for cancer therapy

status: Public on Sep 05 2024

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: Identification of novel target genes for cancer therapy is a significant challenge of biomedical research. Here, we describe a computational pipeline, which integrates transcriptomic and vulnerability responses to cell-death inducing drugs, to predict repressors of cell-death as candidate targets for cancer therapy. The candidate target genes were predicted based on two modules: the transcriptomic similarity and the correlation modules. The transcriptomic similarity module identified genes whose targeting results in similar transcriptomic responses of the death-inducing drugs, while the correlation module identified candidate genes whose expression was correlated to the vulnerability to the death-inducing drugs. The combined predictors generated by these two modules were integrated into a single ranked metric. As a proof-of-concept, we selected ferroptosis inducers as death-inducing drugs, and triple negative breast cancer as a cancer model. The pipeline could predict candidate genes as ferroptosis repressors, as demonstrated by computational and experimental validation, including experimental data of 9 representative genes, thus, highlighting the robustness and power of this pipeline. The described pipeline can be used to identify repressors of different cell-death pathways as potential therapeutic targets for various cancer types.

overall_design: In this study, 3 triple negative breast cancer lines (HS578, BT549, SUM159) were treated with the ferroptosis inducers erastin and RSL3, with DMSO serving as vehicle control. Experiment was done in duplicates. RNA was extracted, and RNAseq was performed in order to study the transcriptomal response to the ferroptosis inducers.

first: Yaron

last: Vinik


title: Inflammatory intracellular signaling in neurons is influenced by glial soluble factors in iPSC-based cell model of PARK2-associated Parkinson’s disease

city: Moscow

first: Daniil

last: Poberezhniy

address: Kurchatov sq. 2

country: Russia

institute: National Research Centre "Kurchatov Institute"

summary: Neuroinflammation is considered one of the driving factors in Parkinson’s disease (PD). Astrocytes affect the function of neurons in different ways, of which humoral interactions are very important. Here, we used neuronal and glial cell cultures differentiated from iPSC of healthy donors (HD) and PD patients with different PARK2 mutations (PD) in order to evaluate the influence of glial secretome on inflammatory gene network in neurons and to estimate the impact of the lack of Parkin to this interaction.

overall_design: iPSCs obtained from HD and from PD patient with PARK2-mutation (hom EX8 del PARK2) underwent the full course of differentiation into mature neurons. iPSCs obtained from 2 healthy donors and 2 patients with PARK2-associated PD underwent the full course of differentiation in glial direction. Further, neurons were cultivated in conditioned media obtained from glial cultures in four possible combinations: HD neurons in the conditioned medium from HD astrocytes (HD2), PD neurons in the conditioned medium from HD astrocytes (PD2), HD neurons in the conditioned medium from PD astrocytes (HD3), and PD neurons in the conditioned medium from PD astrocytes (PD3). The HD and PD neurons in the base neuronal culture medium (HD0, PD0), and HD and PD neurons in the base glial culture medium (HD1, PD1) were used as a control.

first: Tatiana

last: Gerasimova

first: Valentina

last: Nenasheva

first: Ekaterina

last: Novosadova


title: Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition

first: Xingnan

last: Huang

first: Zhaoyi

last: Ma


title: Deficiency of Tlr7 and Irf7 increases the severity of COVID-19 through the reduced interferon production

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: Toll-like receptor 7 (Tlr7) deficiency-accelerated severe COVID-19 is associated with reduced production of interferons (IFNs). However, the underlying mechanisms remain elusive. Here, we demonstrate that the deficiency of Tlr7 and Irf7 globally and/or in immune cells in mice increases the severity of COVID-19 via impaired IFN activation in both immune and/or non-immune cells, leading to increased lung viral loads. These effects are associated with reduced IFN alpha and gamma production. The deficiency of Tlr7 in the infected mice tends to cause the reduced production and nuclear translocation of Interferon regulatory factor 7 (IRF7), indicative of reduced IRF7 activation. Despite higher amounts of lung viral antigen, Tlr7 or Irf7 deficiency resulted in substantially reduced production of antibodies against SARS-CoV-2, thereby delaying the viral clearance. These results highlight the importance of the activation of TLR7 and IRF7, leading to IFN production on the development of innate and adaptive immunity against COVID-19.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Irf7 KO mice at 2DPI and non infected B6 mice.

first: Chenxiao

last: Wang

first: Mst

middle: S

last: Khatun

first: Calder

last: Ellsworth

first: Zheng

last: Chen

first: Mohammad

last: Islamuddin

first: Ana

last: Karina

first: Nisperuza

last: Vidal

last: Alam

first: Shumei

last: Liu

first: Nicholas

last: Maness

first: Robert

middle: V

last: Blair

middle: K

first: Xuebin

last: Qin


title: Loss of synovial tissue macrophage homeostasis precedes Rheumatoid Arthritis clinical onset

status: Public on Sep 10 2024

city: Dublin 2

first: Megan

middle: Mary

last: Hanlon

state: Dublin

address: Trinity biomedical sciences institute, trinity college dublin

department: School of Medicine

country: Ireland

institute: Molecular Rheumatology research group

summary:
To investigate the transcriptional profiles of distinct macrophage subsets residing within the inflammed RA synovium.
RNA sequencing was perfomed on FACS sorted CD206+CD163+ and CD206-CD163- synovial tissue macrophages from RA synovial tissue and fluid samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD206+CD163+ and CD206-CD163- synovial tissue macrophages from RA synovial tissue and fluid.

first: Ursula

last: Fearon


title: IBR1: A Novel Endogenous dsRNA Binding to the Helicase Domain of IFIH1 and Its Role in LPS-induced IFIH1 Activation and Macrophage M1 Polarization in ARDS [RNA-seq]

city: Jinan

first: zhang

last: shi

address: handong First Medical University

institute: handong First Medical University

summary: Uncontrolled inflammatory responses driven by macrophages and monocytes play a crucial role in perpetuating lung injury and the severity of acute respiratory distress syndrome (ARDS). Previous studies have identified IFIH1 as a key regulator of macrophage M1 polarization in pneumonia-induced ARDS. IFIH1 is a cytosolic receptor responsible for recognizing viral double-stranded RNA (dsRNA) and activating inflammatory and antiviral signaling pathways. Interestingly, our observations indicate that IFIH1 can also be activated by lipopolysaccharide (LPS), a component of bacterial cell walls. However, the precise molecular mechanism underlying LPS-induced IFIH1 activation remains unclear. In our preliminary investigations, we have discovered a novel transcript, named IFIH1-binding RNA1 (IBR1), which is upregulated by LPS and gram-negative bacilli in monocytes and macrophages. We have confirmed that IBR1 interacts with the IFIH1 protein, forming a complex. Further experiments have revealed that IBR1, acting as an endogenous dsRNA, binds to the helicase domain of IFIH1 due to its local double-stranded structure. This specific interaction serves as the underlying molecular mechanism responsible for LPS-induced IFIH1 activation and subsequent macrophage M1 polarization in ARDS. Importantly, our observations indicate a significant upregulation of IBR1 expression in ARDS patients with gram-negative bacilli-induced pneumonia. Understanding the molecular mechanisms driving IFIH1 activation and macrophage M1 polarization in ARDS is of great importance for developing new therapeutic strategies to alleviate lung inflammation and improve patient outcomes. Further research is warranted to elucidate the precise roles of IBR1 and its potential as a therapeutic target in the management of ARDS.

overall_design: Bone Marrow-Derived Macrophage (BMDM) isolation, differentiation, and identification: Male C57BL/6 mice, aged 8 weeks, were euthanized by cervical dislocation. BMDMs were isolated from the bone marrow using established methods, including density gradient centrifugation and cell differentiation in the presence of M-CSF. The differentiated BMDMs were identified by flow cytometry analysis using macrophage-specific markers.  RIP-seq for IFIH1-bound RNA complexes: RNA extracts from the isolated BMDMs were subjected to RNA-binding protein immunoprecipitation (RIP) using the Magna RIPTM kit. The IFIH1-bound RNA complexes were enriched by incubating the RNA extracts with IFIH1 antibody-bound beads and RIP immunoprecipitation buffer. The purified RNAs from the IFIH1-bound complexes were then sequenced using Illumina Sequencing Technology, with 5% input RNA as a negative control to reduce noise.

first: Shi

last: Zhang


title: IBR1: A Novel Endogenous dsRNA Binding to the Helicase Domain of IFIH1 and Its Role in LPS-induced IFIH1 Activation and Macrophage M1 Polarization in ARDS [ATAC, ChIP]

overall_design: Bone Marrow-Derived Macrophage (BMDM) isolation, differentiation, and identification: Male C57BL/6 mice, aged 8 weeks, were euthanized by cervical dislocation. BMDMs were isolated from the bone marrow using established methods, including density gradient centrifugation and cell differentiation in the presence of M-CSF. The differentiated BMDMs were identified by flow cytometry analysis using macrophage-specific markers. CD14+ mononuclear cell isolation, differentiation, and identification: Peripheral blood samples were collected from healthy donors aged 18-40 years. Mononuclear cells were isolated using density gradient centrifugation and the differential adhesion method. CD14+ monocytes were then isolated from the mononuclear cell population using magnetic cell sorting. The differentiated CD14+ monocytes were identified by flow cytometry analysis using CD14-specific antibodies. RNA extraction and sequencing: Total RNA was extracted from the isolated BMDMs and CD14+ monocytes using TRIzol. After rRNA depletion, the remaining RNA was prepared for library preparation following Illumina's instructions. The resulting libraries were sequenced using Illumina Sequencing Technology on an Illumina Genome Analyzer II. RIP-seq for IFIH1-bound RNA complexes: RNA extracts from the isolated BMDMs were subjected to RNA-binding protein immunoprecipitation (RIP) using the Magna RIPTM kit. The IFIH1-bound RNA complexes were enriched by incubating the RNA extracts with IFIH1 antibody-bound beads and RIP immunoprecipitation buffer. The purified RNAs from the IFIH1-bound complexes were then sequenced using Illumina Sequencing Technology, with 5% input RNA as a negative control to reduce noise.


title: IBR1: A Novel Endogenous dsRNA Binding to the Helicase Domain of IFIH1 and Its Role in LPS-induced IFIH1 Activation and Macrophage M1 Polarization in ARDS


title: Heat Shock Transcription Factor 1 Facilitates Liver Cancer Progression by Driving Super-Enhancer-Mediated Transcription of MYCN

status: Public on Sep 04 2024

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

summary: HSF1–MYCN axis, a transcription-dependent regulatory axis, could be a prognostic indicator and potential therapeutic target in liver cancer.

overall_design: Identify downstream target genes co-regulated by HSF1 and MYCN in Huh7 cells using whole transcriptome sequencing (RNA-Seq). Investigate the binding sites of HSF1 and H3K27ac in Huh7 cells using Cleavage Under Targets and Tagmentation (CUT&Tag) with specific antibodies. Study the H3K27ac status and enhancer changes influenced by HSF1 in Huh7 cells using chromatin immunoprecipitation and sequencing (ChIP-seq) with specific antibodies.

first: Yizhe

first: Qili

last: Shi

first: Shenglin

last: Huang

first: Zhiao


title: mesendoderm differentiation of WT and PHD2 knockout mESCs (scRNA-seq)

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

institute: Anhui Normal University

summary: To study the cell composition and gene expression profile in the mesendoderm differentiation of WT and PHD2 knockout, we performed scRNA-seq on the cells collected from the differentiation of WT and PHD2 knockout AB2.2 mESCs at differentiation day 4. PHD2 knockoutout mESCs were constructed by CRISPR/Cas9. The differentiation was performed using a non-lineage tendency differentiation protocol.

overall_design: scRNA-seq of WT and PHD2 knockout AB2.2 mESCs differentiated for 4 days

first: Meng

last: Li


title: Left ventricular systolic dysfunction in female NBCe1-B/C-knockout mice

city: Buffalo

first: Clayton

middle: Timothy

last: Brady

state: NY

address: 955 Main Street

department: Physiology and Biophysics

institute: University at Buffalo

summary: To investigate the role of NBCe1-B in the heart we performed RNAseq experiments to examine genome-wide transcriptional changes in female NBCe1-B/C knockout (KO) mice compared to female wild-type (WT) mice.

overall_design: Total mRNA via RNA-seq analysis from the hearts of three female NBCe1-B/C KO mice and three WT mice were compared.

middle: T

first: Mark

last: Parker


title: Transcriptomic Analysis Reveals Key Molecular Signatures Across Recovery Phases of Hemorrhagic Fever with Renal Syndrome

city: Xi'an

first: Xuzhao

last: Bian

state: Shaan'xi

address: No.28 Xianning West Road

institute: xi'an jiaotong university

summary: Hemorrhagic fever with renal syndrome (HFRS), a life-threatening zoonosis caused by hantavirus, poses significant mortality risks and lacks specific treatments. Here we employed RNA sequencing to analyze the transcriptomic alterations in peripheral blood mononuclear cells from HFRS patients across the oliguric phase (OP), diuretic phase (DP), and convalescent phase (CP). Our analysis revealed pronounced transcriptomic differences between DP and OP, with 38 differentially expressed genes (DEGs) showing consistent expression changes across all phases. Notably, immune checkpoint genes like CD83 and NR4A1 demonstrated a monotonic increase, in contrast to a monotonic decrease observed in antiviral and immunomodulatory genes, including IFI27 and RNASE2. 12 DEGs were validated using quantitative real-time PCR. Furthermore, this research elucidates a sustained attenuation of immune responses following viral infection, alongside an upregulation of pathways related to tissue repair and regeneration. In conclusion, our research reveals the transcriptomic shifts during the recovery phases of HFRS, illuminating key pathways and genes that may serve as markers for disease progression and recovery.

overall_design: Nine Peripheral blood samples at different phases were collected from three patients

first: Yuanyuan

last: Hu

first: Chao

last: Wu

first: Tuohang

first: Yang

first: Kun

last: Yao

first: Mengtian

first: Pan


title: C2H2-zinc finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes [iCLIP-seq]

first: Ulrich

last: Braunschweig

overall_design: iCLIP-seq of 84 proteins and m6A, in 1-4 replicates (mean 2.3), with 16 inputs size-matched to proteins of different sizes, in HEK293 cells

first: Syed

last: Nabeel-Shah

first: Shuye

last: Pu

first: James

last: Burns

first: Nujhat

last: Ahmed

first: Giovanni

last: Burke

first: Ernest

last: Radovani

first: Hyunmin

last: Lee

first: Guoqing

last: Zhong

first: Hua

last: Tang

first: Edyta

last: Marcon

first: Zhaolei

first: Timothy

last: Hughes

first: Benjamin

last: Blencowe

first: Jack

last: Greenblatt


title: A sexually dimorphic hepatic cycle of very low density lipoprotein uptake and assembly

city: Lausanne

first: Felix

last: Naef

address: EPFL SV IBI

country: Switzerland

institute: EPFL

summary: Single-cell transcriptomes can reveal spatiotemporal programmes of liver function on the sublobular scale. However, how sexual dimorphism affects this space-time logic remains poorly understood. To address this, we performed single-cell RNA-seq in the mouse liver, which allowed us to model how lobular position, circadian time and sex shape the transcriptome.

overall_design: Mice were perfused with collagenase via the inferior vena cava, livers isolated, and cells released into medium and enriched for hepatocytes with a centrifugation step. The cells were then frozen. Upon thawing, sequencing libraries for scRNA-seq were constructed using 10x Genomics Chromium v3.

first: Tomaz

last: Martini

first: Cedric

last: Gobet


title: Droplet Hi-C enables scalable, single-cell profiling of chromatin architecture in heterogeneous tissues

city: La Jolla

first: Yang

last: Xie

state: CA

address: Rm.2071, 9500 Gilman Dr

department: Department of Cellular and Molecular Medicine

institute: UC San Diego

type: Methylation profiling by high throughput sequencing

summary: Current methods for analyzing chromatin architecture are not readily scalable to heterogeneous tissues. Here we introduce Droplet Hi-C, which uses a commercial microfluidic device for high-throughput, single-cell chromatin conformation profiling in droplets. Using Droplet Hi-C, we mapped the chromatin architecture of the mouse cortex and analyzed gene regulatory programs in major cortical cell types. In addition, we used this technique to detect copy number variations, structural variations and extrachromosomal DNA in human glioblastoma, colorectal and blood cancer cells, revealing clonal dynamics and other oncogenic events during treatment. We refined the technique to allow joint profiling of chromatin architecture and transcriptome in single cells, facilitating exploration of the links between chromatin architecture and gene expression in both normal tissues and tumors. Thus, Droplet Hi-C both addresses critical gaps in chromatin analysis of heterogeneous tissues and enhances understanding of gene regulation.

overall_design:
Commercial microfluidic device based high-throughput, single-cell chromatin conformation profiling in droplets

>>>Submitter states: Raw data for GSM8521393, GSM8521394, or GSM8521395 will be submitted to dbGaP due to patient privacy concerns.<<<

first: Lei

last: Chang

first: Bing

last: Ren


title: Maternal dietary antioxidants enrichment regulates weaned piglets’ adipose tissue functionality

status: Public on Sep 02 2024

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

summary: Homeostasis during the perinatal period is critical for the correct development of mammals and unbalances in the redox potential are common in this stage. Thus, enrichment of maternal diets with antioxidants may be useful to improve piglet early development. We have tested the effects of sows’ diet enrichment with different antioxidants on the piglets’ adipose tissue functioning, in comparison to a control diet with a basal antioxidant level, by studying gene expression and cellularity. The maternal diet strongly influenced adipose tissue transcriptome of the offspring post-weaning. Piglets born to sows supplemented with either vitamin E or hydroxytyrosol show improved metabolic and antioxidant status of adipose tissue, while animals from control group show impaired homeostasis and activation of oxidative stress, immune signalling, and inflammation pathways. Moreover, vitamin E, when supplemented alone at a high dose, activated lipid metabolism and increased adipocyte size. When both vitamin E and hydroxytyrosol were combined, the gene expression profile was scarcely affected in comparison to the control, showing a prooxidant/proinflamatory adipose tissue, which is an unexpected result with different potential explanations. Findings deepen in the processes taking place in adipose tissue of genetically fat individuals and highlight the crucial role of antioxidants in fat cells metabolism

overall_design: In total 24 adipose tissue samples were analyzed, 6 coming from each experimental group: -Control group (C): 30 mg of all-rac-α-tocopheryl acetate (Rovimix E-50, DSM)/kg feed. -Vitamin E group (VE): 100 mg of all-rac-α-tocopheryl acetate/kg. -Hydroxytyrosol group (HT): 30 mg all-rac-α-tocopheryl acetate/kg and 1.5 mg hydroxytyrosol/kg -Combined group (VEHT): 100 mg/kg of all-rac-α-tocopheryl acetate/kg and 1.5 mg hydroxytyrosol/kg feed.


title: Modulation of liver cholesterol homeostasis by choline supplementation during fibrosis resolution

city: Bunkyo-ku

first: Eiko

last: SAIJOU

state: Tokyo

address: 1-1-1 Yayoi

department: Institute of Quantitative Bioscience

country: Japan

institute: The University of Tokyo

summary: Liver fibrosis is a critical global health challenge, often leading to severe liver diseases without timely intervention. Choline deficiency has been linked to metabolic dysfunction associated steatohepatitis (MASH) and liver fibrosis, suggesting choline supplementation as a potential therapeutic approach. This study aimed to explore the therapeutic potential of choline supplementation in liver fibrosis resolution and its effects on cholesterol homeostasis using a mouse model with induced liver fibrosis. Our findings reveal that choline supplementation significantly decreases blood lactate dehydrogenase (LDH) and non-high-density lipoprotein cholesterol (non-HDL-C) levels. Transcriptome analysis showed that choline supplementation primarily induces genes related to cholesterol homeostasis, suggesting a significant impact on liver cholesterol synthesis. However, choline supplementation did not significantly alter the expression of fibrosis-related, choline metabolism-related, or epigenetics-related genes. This study provides novel insights into the role of choline in liver health and cholesterol metabolism, potentially informing treatments for liver fibrosis and related conditions.

overall_design: To induce liver fibrosis, mice were administered thioacetamide (TAA) (204-00881; WAKO; 300 mg/L) in drinking water for 8 weeks. Following fibrosis formation, choline chloride (037-09815; WAKO; 3.5 g/L) was dissolved in water and administered in drinking water for 1,2 or 4 weeks.

last: Saijou

first: Yoshiko

last: Kamiya

first: Katsunori

last: Fujiki

first: Katsuhiko

last: Shirahige

first: Ryuichiro

last: Nakato


title: Cathepsin B Promotes Aβ Proteotoxicity by Modulating Aging Regulating Mechanisms

status: Public on Sep 03 2024

city: Jerusalem

first: Atif

last: Ahmed

state: Jerusalem

address: Botnar building, Room 132, First floor, Faculty of medicine, Institute of medical research Israel-Canada (IMRIC), Hebrew University, Ein Kerem campus

department: Biochemistry and Molecular biology

institute: Hebrew University

summary: While the activities of certain proteases promote proteostasis and prevent neurodegeneration-associated phenotypes, the protease cathepsin B (CTSB) enhances proteotoxicity in Alzheimer’s disease (AD) model mice, and its levels are elevated in brains of AD patients. How CTSB exacerbates the toxicity of the AD-causing Amyloid β (Aβ), is controversial. Using an activity based probe, aging-altering interventions and the nematode C. elegans we discovered that the CTSB CPR-6 promotes Aβ proteotoxicity but mitigates the toxicity of polyQ stretches. While the knockdown of cpr-6 does not affect lifespan, it alleviates Aβ toxicity by reducing the expression of swsn-3 and elevating the level of the protein SMK-1, both involved in the regulation of aging. These observations unveil a novel mechanism by which CTSB aggravates Aβ–mediated toxicity, indicate that it plays opposing roles in the face of distinct proteotoxic insults and highlight the importance of tailoring specific remedies for distinct neurodegenerative disorders.

overall_design: Synchronized CL2006 worms (expressing Aβ) were grown from egg onwards on E.Coli K12 strain HT115 (DE3) containing plasmids expressing (i) EV (Empty Vector) RNAi or (ii) cpr-6 RNAi. These worms were collected at Day6 of adulthood to perform RNA sequencing. This data  represents four biological repeats of this experimental design.

last: Siddiqui

first: Emmanuelle

last: Merquiol

first: Hana

last: Boocholez

first: Yonghong

last: Yan

first: Meng

middle: Q

last: Dong

first: Galia

last: Blum

first: Ehud

last: Cohen


title: The transcriptomic landscape of spinal V1 interneurons reveals a role for En1 in specific elements of motor output

city: Memphis

first: Jay

last: Bikoff

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: We present a transcriptomic atlas of spinal V1 interneurons across postnatal development (P0, P14, P28, and P56) in the mouse using single-nucleus RNA sequencing (snRNA-seq). We also present transcriptomic data comparing V1 interneurons in En1 heterozygous and En1 KO mice at age P0 only.

overall_design: V1 nuclei were genetically labeled by crossing En1::Cre mice in either the heterozygous or homozygous (KO) state to RC.lsl.Sun1-sfGFP (INTACT) mice, and GFP+ nuclei were isolated by flourescence activated cell sorting. snRNA-seq was performed on the 10X Genomics Chromium 3' platform  (v3.1).

first: Alexandra

last: Trevisan

first: Katie

last: Han

first: Phillip

last: Chapman

first: Anand

last: Kulkarni

first: Jennifer

middle: M

last: Hinton

first: Cody

last: Ramirez

first: Ines

last: Klein

first: Graziana

last: Gatto

first: Mariano

middle: I

last: Gabitto

first: Vilas

last: Menon

middle: B


title: Integrated analyses reveal two molecularly and clinically distinct subtypes of H3 K27M-mutant diffuse midline gliomas with prognostic significance

city: Regensburg

first: Annika

last: Wefers

address: Franz-Josef-Strauß-Allee 11

department: Neuropathology

country: Germany

institute: Regensburg University Hospital

summary: We identified two subgroups of diffuse midline gliomas (DMGs) with unsupervised hierarchical cluster analyses of DNA methylation data from 149 DMGs derived from different localisations: DMG-A and DMG-B. The two epigenetic DMG-subtypes have different characteristics: DMG-A are enriched for cases with MAPK-signalling-pathway associated mutations, a methylated MGMT-promoter, medullary localisation and adult age, while DMG-B are enriched for cases with TP53-mutations, PDGFRA-amplifications, pontine localisation and paediatric patients. DMG-A have a significantly better overall survival compared to DMG-B (p < 0.001). This effect on survival is larger than that of all other parameters tested, and all other parameters are dependent on the cluster attribution. Hence, the subtype attribution based on two methylation clusters is best suited to predict survival as it integrates different molecular and clinical parameters.

overall_design: Bisulphite converted DNA from 149 samples was hybridised to either Illumina HumanMethylation450 BeadChips or Infinium MethylationEPIC BeadChips.

first: Lotte

last: Stegat


title: Gene Pool Preservation Across Time And Space In Mongolian-speaking Oirats  [Set 2]

status: Public on Sep 01 2024

city: Tartu

first: Alena

last: Kushniarevich

address: Riia 23b

department: Institute of Genomics

country: Estonia

institute: UNIVERSITY OF TARTU

type:
Genome variation profiling by array
Genome variation profiling by SNP array

summary: Genomewide SNP data of the Oirats and related populations has been used to study their origin and migration.

overall_design: 15 samples were analysed with the Illumina InfiniumOmniExpress-24 v1.3 are described herein.

first: Natalia

last: Balinova


title: Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition [RNA-Seq 1]

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

summary: This study aimed at investigating the transciptional changes during transition. What is more, we could look for key metabolic genes regulating transitions.

overall_design: We analyzed the transcriptome expression during mouse primed to naïve transition at D0(EpiSCs), D3, D5, D8 and rESCs, ESCs.

first: Zhaoyi

last: Ma


title: Genome-wide discovery and integrative genomic characterization of insulin resistance loci using serum triglycerides to HDL-cholesterol ratio [bulk RNA-seq]

first: Amit

last: Majithia

address: 9500 Gilman Dr

institute: UCSD

summary: To investigate gene expression differences during the course of human adipocyte differentiation, we performed differentiation on Human Simpson-Golabi-Behmel syndrome (SGBS) preadipocyte cells following standard protocols (PMID: 20054179). Differentiation begins on day 0 by incubating cells in a serum-free differentiation medium (rosiglitazone, dexamethasone, methylisobuthylxantine, cortisol, transferrin, triiodotyronin, and human insulin). The medium is changed to cortisol, transferrin, triiodotyronin, and human insulin after 4 days.

overall_design: RNA was collected and sequenced on day 0, 4, 8, and 15, with three replicates per day.


title: Generation of Human Expandable Limb Bud Cells via Chemically Induced Dedifferentiation Strategy [bulk RNA-seq]

city: Beijing

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.

institute: Peking University

summary: Here, we introduce a novel chemically induced dedifferentiation approach that reverses the cellular development from a differentiated state to progenitor state, conferring the generation of limb bud progenitors from human adult mesenchymal stromal cells and dermal fibroblasts. These chemically induced limb bud cells (hCiLB cells) show a high degree of transcriptomic similarity to human embryonic limb bud cells. We found that hCiLB cells can undergo extensive expansion, while maintaining population homogeneity and long-term self-renewal capacity. Moreover, hCiLB cells exhibit increased osteochondrogenic differentiation ability than their parental cells, providing a new platform for the development of authentic articular cartilage. These results also highlight a potential therapeutic approach for the repair of damaged human tissues through reversal of developmental pathways from mature cells to expandable progenitor cells.

overall_design: we use small-molecule combiantions to induce the dedifferentiation of human somatic cells to progenitors and then characterized the features of the progenitors.


title: Gene Pool Preservation Across Time And Space In Mongolian-speaking Oirats [Set 1]

overall_design: 65 samples were analysed with the Illumina InfiniumOmniExpress-24 v1.2 are described herein.


title: Generation of Human Expandable Progenitors with Limb-Bud Features via Chemically Induced Dedifferentiation

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

overall_design: Refer to individual Series


title: Tracking of donor and recipient immune and leukemia phenotypes after allogeneic stem cell transplantation using mitochondrial DNA mutations. [ASAP-Seq 4]

status: Public on Aug 31 2024

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Mitochondrial DNA mutations (mtDNA) enable deconvolution of donor- and recipient-derived single cell profiles. Here, we provide examples for sensitive donor-recipient deconvolution of peripheral blood and bone marrow ASAP-seq profiles in the context of incipient and overt AML relapse following allogeneic hematopoietic stem cell transplantation. Further, using single cell DNA sequencing (Tapestri), we demonstrate co-evolution of mtDNA and somatic nuclear DNA mutations in relapsed CLL post-HSCT.

overall_design:
Staining of bone marrow or peripheral blood-derived single cells with oligotags for detection of surface marker expression using Total-seq A, B or D followed by single cell ATAC with select antigen profiling by sequencing (ASAP-seq) or single cell DNA sequencing using the Tapestri platform (Mission Bio).

***************************************************************
Submitter states that missing raw data are being made available for controlled access in dbGaP.
***************************************************************

first: Nicoletta

last: Cieri

first: Katie

last: Maurer

first: Catherine

last: Wu


title: Generation of Human Expandable Limb Bud Cells via Chemically Induced Dedifferentiation Strategy [scRNA-seq]

summary: Here, we introduce a novel chemically induced dedifferentiation approach that reverses the cellular development from a differentiated state to progenitor state with reduced senescence features, conferring the generation of limb bud progenitors from human adult mesenchymal stromal cells and dermal fibroblasts. These chemically induced limb bud cells (hCiLB cells) show a high degree of transcriptomic similarity to human embryonic limb bud cells. We found that hCiLB cells can undergo extensive expansion, while maintaining population homogeneity and long-term self-renewal capacity. Moreover, hCiLB cells exhibit increased osteochondrogenic differentiation ability than their parental cells, providing a new platform for the development of authentic articular cartilage. These results also highlight a potential therapeutic approach for the repair of damaged human tissues through reversal of developmental pathways from mature cells to expandable progenitor cells.


title: CLPTM1L is a putative regulator of tumorigenesis and chemotherapy sensitization in cervical cancer

city: Kunming

first: Weipeng

last: Liu

state: Yunnan

address: Jiao ling road

department: Institute of Medical Biology

institute: Chinese Academy of Medical Sciences

summary: Cervical cancer stands as one of the leading causes of cancer-related mortality in women worldwide, yet the precise functions of host genes implicated in its pathogenesis remain elusive. Genome-wide association studies (GWAS) have revealed a significant association between the CLPTM1L locus and cervical cancer risk in European women, and aberrant expression of CLPTM1L has been noted in various malignant tumors. However, the role of CLPTM1L in cervical cancer remains largely unexplored. This study aimed to explore the biological function of CLPTM1L in cervical cancer. The expression of CLPTM1L in cervical cancer cells and tissues was detected by RT-qPCR. Furthermore, the potential biological functions of CLPTM1L in the context of cervical cancer were explored via RNA sequencing. Cell proliferation rates and the responsiveness of cervical cancer cells to cisplatin were evaluated using the CCK-8 assay, while cell apoptosis was quantified through the utilization of flow cytometry. Nude mouse xenograft models were utilized to explore the impact of CLPTM1L on tumor formation in vivo. Our findings demonstrated a significant increase in CLPTM1L mRNA expression levels in HeLa and C33A cells, as well as in cervical carcinoma tissues, compared to ECT1/E6E7 cells and adjacent normal tissues. Genes related to CLPTM1L were found to be enriched in the Hedgehog signaling pathway. In vitro and in vivo studies showed that reducing CLPTM1L expression markedly inhibited cell proliferation via downstream candidate genes BOC and LRP2. Furthermore, the downregulation of CLPTM1L was found to enhance cisplatin-induced cell apoptosis and increase the susceptibility of cervical cancer cells to cisplatin through DAP1. This investigation has bestowed upon us novel insights into the pathogenesis of cervical cancer, underscoring the potential of CLPTM1L as a promising target for chemotherapeutic sensitization in the management of this malignancy.

overall_design: Total RNA was extracted from a total of 9 samples, comprising three negative control samples, three samples infected with pSicoR-Ef1a-mCh-Puro-CLPTM1L-shRNA1, and three samples infected with pSicoR-Ef1a-mCh-Puro-CLPTM1L-shRNA2. Subsequently, a cDNA library was constructed and sequenced using the BGISEQ-500 platform. Transcriptome data analyses were conducted using an online platform.

first: FengDan

first: Yueting

last: Yao

first: Yufeng


title: Single-cell RNA sequencing analysis of peripheral blood mononuclear cells in PD-1-induced renal toxicity in patients with lung cancer

city: Changzhou

first: Shusu

address: No 185，Juqian Road

department: Department of Nephrology

institute: The Third Affiliated Hospital of Soochow University

summary: The purpose of the study was to investigate the potential role of the immune system in renal irAEs by analyzing the features of peripheral blood mononuclear cells (PBMC) from patients with renal irAEs using single-cell RNA sequencing (scRNA-seq).

overall_design: PBMCs were collected from three patients with renal irAEs induced by anti-PD-1 therapy and three patients without renal irAEs. In order to find cell clusters and differentially expressed genes (DEGs), the PBMCs were submitted to scRNA-seq. KEGG and GO analysis were carried out to investigate the most active biological processes in CD4+ T and CD8+ T cells.

first: Peiyu

last: Lu

first: Bixia

last: Yang

first: Yan

first: Hua

last: Zhou

first: Min


title: Tracking of donor and recipient immune and leukemia phenotypes after allogeneic stem cell transplantation using mitochondrial DNA mutations. [Tapestri]

overall_design:
Staining of bone marrow or peripheral blood-derived single cells with oligotags for detection of surface marker expression using Total-seq A, B or D followed by single cell ATAC with select antigen profiling by sequencing (ASAP-seq) or single cell DNA sequencing using the Tapestri platform (Mission Bio).
Raw data for AML samples are available at dbGap phs003015.v2


title: The alternative splicing landscape of infarcted mouse heart identifies isoform level therapeutic targets

first: Xia

last: Binbin

address: NO.1 Beichen West  Road, Chaoyang District

institute: The Institute of Microbiology of the Chinese Academy of Sciences

summary: Alternative splicing is an important process that contributes to highly diverse transcripts and protein products, which can affect the development of disease in various organisms. Cardiovascular disease (CVD) represents one of the greatest global threats to humans, particularly acute myocardial infarction (MI) and subsequent ischemic reperfusion (IR) injury, which involve complex transcriptomic changes in heart tissues associated with metabolic reshaping and immunological response. In this study, we used a newly developed ONT full-length transcriptomic approach and performed transcript-resolved differential expression profiling in murine models of MI and IR. We built an analytical pipeline to reliably identify and quantify alternative splicing products (isoforms), expanding on the currently available catalog of isoforms described in mice. The updated alternative splicing landscape included transcripts, genes, and pathways that were differentially regulated during IR and MI. Our study establishes a pipeline to profile highly diverse isoforms using state-of-the-art long-read sequencing, builds a landscape of alternative splicing in the mouse heart during MI and IR.

overall_design:
Cardiac tissue was sampled from myocardial infarction and ischemia-reperfusion mice, and sham-operated controls were set up separately. Using different sequencing methods, novel transcripts were identified and pairs of differential transcripts and genes were investigated.

Please note that Nanopore-based long-reads data (GSM8486343-GSM8486346) were used to identify novel transcripts and genes, therefore there is no coresponding data columns in the raw_count_gene.tsv and tpm_transcript.csv files.


title: Tracking of donor and recipient immune and leukemia phenotypes after allogeneic stem cell transplantation using mitochondrial DNA mutations. [ASAP-Seq 2]

overall_design: Staining of bone marrow or peripheral blood-derived single cells with oligotags for detection of surface marker expression using Total-seq A, B or D followed by single cell ATAC with select antigen profiling by sequencing (ASAP-seq) or single cell DNA sequencing using the Tapestri platform (Mission Bio).


title: Tracking of donor and recipient immune and leukemia phenotypes after allogeneic stem cell transplantation using mitochondrial DNA mutations. [ASAP-Seq 1]


title: CITE-seq analysis of SARS-CoV-2 spike-specific nasal T cells

status: Public on Aug 30 2024

city: Seoul

first: Min-Seok

last: Rha

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Otorhinolaryngology

country: South Korea

institute: Yonsei University College of Medicine

summary: We examined the phenotypes and functions of SARS-CoV-2-specific T cells in the nasal mucosa of vaccinated individuals with breakthrough infection (BTI) or without infection.

overall_design: We analysed nasal SARS-CoV-2 spike-reactive AIM+ T cells via CITE-sequencing

first: Gyeongyeob

last: Kim

first: Chang-Hoon

first: Eui-Cheol

last: Shin


title: TET proteins regulate Drosha expression and impact microRNAs in iNKT cells

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: DNA demethylases TET2 and TET3 play a fundamental role in thymic invariant natural killer T (iNKT) cell differentiation by mediating DNA demethylation of genes encoding for lineage specifying factors. Paradoxically, differential gene expression analysis revealed that significant number of genes were upregulated upon TET2 and TET3 loss in iNKT cells. This unexpected finding could be potentially explained if loss of TET proteins was reducing the expression of proteins that suppress gene expression. In this study, we discover that TET2 and TET3 synergistically regulate Drosha expression, by generating 5hmC across the gene body and by impacting chromatin accessibility. As Drosha is involved in microRNA biogenesis, we proceed to investigate the impact of TET2/3 loss on microRNAs in iNKT cells. We report that among the downregulated microRNAs are members of the Let7 family that downregulate in vivo the expression of the iNKT cell lineage specifying factor PLZF. Our data link TET proteins with microRNA expression and reveal an additional layer of TET mediated regulation of gene expression.

overall_design: To assess the impact of TET2 and TET3 loss in small RNA biogenesis, we isolated RNA from wild type and Tet2/3 DKO thymic iNKT cells and we performed small-RNA sequencing to compare small RNA expression.

first: Ageliki

last: Tsagaratou


title: Transcription regulation by CavA cyclase in Acinetobacter baumannii AB5075

city: Southampton

first: Lyuboslava

last: Harkova

address: Building 85, University Road

department: School of Biological Sciences

country: United Kingdom

institute: University of Southampton

summary: We perform RNA-seq for comparison of deleted cavA wiht empty vector and complemented strains in A. baumannii AB5075 in order to assess the transcription regulation uder the control of this cyclase. A. baumannii AB5075 ΔcavA EV and ΔcavA+cavA cultures were grown in LB medium with 1mM IPTG (3 biological replicates per strain) until reaching mid-exponential phase. At this point, cells were harvested, treated with RNAlate for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample. The results showed 234 differentially expressed genes of which 143 were upregulated and 91 were downregulated in the ΔcavA+cavA complemented strain compared to the deleted cavA mutant harbouring empty vector (ΔcavA EV). The gene functional groups showing the strongest transcriptional alterations were those related to twitching motility (upregulation of genes involves in biogenesis and control of Type IV pili and com genes) as well as biofilm formation, exopolysaccharides production and fimbriae biogenesis (downregulation of csu operon, pga operon and ABUW_2052-2055). Also, genes related to inter- and intracellular signalling were differentially expressed. Cyclic AMP response regulator vfr and genes involved in c-di-GMP synthesis (ABUW_2135) and degradation (ABUW_1138) were upregulated while another gene linked to c-di-GMP degradation (ABUW_2631) and autoinducer synthase encoding gene abaI (part of the quorum sensing signalling system) were downregulated.

overall_design: Three independent replicates of A. baumannii AB5075 ΔcavA EV and ΔcavA+cavA cultures were grown in LB medium with 1mM IPTG (3 biological replicates per strain) until reaching mid-exponential phase. At this point, cells were harvested, treated with RNAlate for preservation of total RNA and stored at -80⁰C. After that, total RNA was extracted from each sample.

middle: G

first: Rubén

last: de Dios

first: Ronan

last: McCarthy


title: Tracking of donor and recipient immune and leukemia phenotypes after allogeneic stem cell transplantation using mitochondrial DNA mutations. [ASAP-Seq 3]

first: Livius

last: Penter

overall_design:
Staining of bone marrow or peripheral blood-derived single cells with oligotags for detection of surface marker expression using Total-seq A, B or D followed by single cell ATAC with select antigen profiling by sequencing (ASAP-seq) or single cell DNA sequencing using the Tapestri platform (Mission Bio).
Raw data are available at dbGap phs003015.v2

first: Nicoletta

last: Cieri

first: Katie

first: Catherine


title: Mutant p53 gain-of-function impact is repressed in the presence of other major oncogenic drivers

city: Warszawa

first: AKANKSHA

last: JAISWAR

address: ul. Adolfa Pawińskiego 5

country: Poland

institute: Mossakowski Medical Research Institute

summary: Mutant TP53, mutant KRAS and hyperactive CMYC are driver oncogenes with no standard clinical protocols for their direct targeting. To identify interplay of mutant TP53, KRAS and hyperactive CMYC, and exploit them in a therapeutic manner, we performed global proteomics and transcriptomics in a panel of 8 cell lines of colorectal and lung cancers 48h post knock-out of the oncogenes with CRISPR/Cas9. In each cancer type the cell lines containing either all, or one, of each of the activated oncogenes were analyzed. Higher numbers of significant protein and transcript level changes were observed upon CMYC and KRAS disruption compared to mutant TP53 disruption. In contrast to mutant KRAS and CMYC downstream programs the number of mutant p53-dependent proteins and transcripts was reduced several-fold in the presence of mutant KRAS and hyperactive CMYC, compared to cell lines with mutant p53 only. We observed a functional repression of the mutant p53 ability to drive phenotype of cancer cells and transcriptional activity in the presence of mutated KRAS and/or overexpressed CMYC, which in such configuration overtake many of the mutant p53 functions. An overlap of pathways regulated by the transcripts and proteins revealed a molecular program shared by the oncogenes as well as pathways lost or retained in the mutant p53 program, when co-present with the other oncogenes. This allowed to exploit the program common to the oncogenes by experimental, pre-clinical drug targeting.   Oncogene cooperation is known to be important in driving cell transformation, however our observations suggest that mutant KRAS and/or overexpressed CMYC compete with mutant p53 for activation of important oncogenic pathways. While the exact mechanism of this competition is under investigation, we hypothesize that mutant p53 is a context-dependent oncogene – whose gain-of-function range of impact heavily depends on the molecular background of neoplastic cells.

overall_design:
Cell lines indicated in the file names were 48h post knock-out of the oncogenes with CRISPR/Cas9 techniques in biological triplicates (numbers 1-3). Total RNA was extracted from cells and subjected to mRNA sequencing.
We then performed gene expression profiling analysis using data obtained from RNA-seq of lung, colon and pancreatic cancer cell lines.

first: Akanksha

last: Jaiswar

first: Maria

last: Grześ

first: Marcin

last: Grochowski

first: Dawid

last: Walerych


title: Morphine-responsive neurons that regulate mechanical antinociception

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

summary: Opioids are widely used, effective analgesics to manage severe acute and chronic pain, although they have recently come under scrutiny because of epidemic levels of abuse. While these compounds act on numerous central and peripheral pain pathways, the neuroanatomical substrate for opioid analgesia is not fully understood. By means of single-cell transcriptomics and manipulation of morphine-responsive neurons, have identified an ensemble of neurons in the rostral ventromedial medulla (RVM) that regulates mechanical nociception in mice. Among these, forced activation or silencing of excitatory RVMBDNF projection neurons mimicked or completely reversed morphine-induced mechanical antinociception, respectively, via a brain-derived neurotrophic factor (BDNF)/tropomyosin receptor kinase B (TrkB)-dependent mechanism and activation of inhibitory spinal galanin-positive neurons. Our results reveal a specific RVM-spinal circuit that scales mechanical nociception whose function confers the antinociceptive properties of morphine.

overall_design: Mouse rostral ventromedial medulla (RVM) and spinal cord neurons isolated and analyzed using scRNA-seq

first: Michael

last: Fatt

first: Ming-Dong

last: Zhang

first: Jussi

last: Kupari

first: Müge

last: Altınkök

first: Yunting

last: Yang

first: Yizhou

last: Hu

first: Per

last: Svenningsson


title: Axolotl mandible regeneration occurs through mechanical gap closure and a shared regenerative program with the limb

status: Public on Aug 29 2024

city: Dresden

first: Tatiana

last: Sandoval-Guzmán

state: Saxony

address: Fetscherstrasse 74

department: Department of Internal Medicine III, Center for Healthy Aging, Medical Faculty Carl Gustav Carus

institute: Technische Universität Dresden

summary: The mandible plays an essential part in human life and, thus, defects in this structure can dramatically impair the quality of life in patients. Axolotls, unlike humans, are capable of regenerating their lower jaws; however, the underlying mechanisms and their similarity to those in limb regeneration are unknown. In this work, we used morphological, histological, and transcriptomic approaches to analyze the regeneration of lateral resection defects in the axolotl mandible. We found that this structure can regenerate all missing tissues in 90 days through gap minimization, blastema formation, and finally tissue growth, differentiation, and integration. Moreover, transcriptomic comparisons of regenerating mandibles and limbs showed that they share molecular phases of regeneration, that these similarities peak during blastema stages, and that mandible regeneration occurs at a slower pacing.  Altogether, our study demonstrates the existence of a shared regenerative program used in two different regenerating body structures with different embryonic origins in the axolotl, and contributes to our understanding of the minimum requirements for a successful regeneration in vertebrates, bringing us closer to understand similar lesions in human mandibles.

overall_design: Bulk RNAseq from paramedially resected axolotl mandibles at intact, 5-, 14-, and 35 days-post injury. 2 biological replicates per time point were used.

first: Rita

last: Aires

first: Julia

last: Kramer

first: Sean

last: Keeley

first: Tom

middle: A

last: Schröder

first: Günter

last: Lauer


title: Deciphering glial contributions to CSF1R-related leukoencephalopathy via single-nuclear transcriptomic profiling: A case study

city: Stanford

first: JAUME

last: FORES MARTOS

state: California

address: 300 Pasteur Drive

department: Pathology

institute: Stanford

summary: Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) is a neurodegenerative disorder resulting from genetic alterations in CSF1R, a gene expressed by microglia. We studied an elderly man with a hereditary progressive dementing and behavioral disorder of unclear etiology. Standard genetic testing for leukodystrophy and other neurodegenerative conditions was negative. Brain autopsy revealed classic features of ALSP, including confluent white matter degeneration with axonal spheroids and pigmented glial cells in the affected white matter. Subsequent long-read sequencing identified a novel deletion in CSF1R. To elucidate mechanisms underlying white matter degeneration in ALSP, we compared multiple brain regions exhibiting varying degrees of white matter pathology. Our analysis revealed markedly decreased CSF1R transcript levels and protein across brain regions, including intact white matter. Single nuclear RNA sequencing (snRNAseq) analysis identified two disease-associated microglial cell states: lipid-laden microglia (expressing GPNMB, ATG7, LGALS1, LGALS3) and inflammatory microglia (expressing IL2RA, ATP2C1, FCGBP, VSIR, SESN3), along with a small population of CD44+ peripheral monocyte-derived macrophages exhibiting migratory and phagocytic signatures. Disease-associated oligodendrocytes exhibited cell stress signatures and dysregulated apoptosis-related genes. Disease-associated oligodendrocyte precursor cells (OPCs) displayed a failure in their differentiation into mature myelin-forming oligodendrocytes, as evidenced by upregulated LRP1, PDGFRA, SOX5, NFIA, and downregulated NKX2-2, NKX6.2, SOX4, SOX8, TCF7L2, YY1, ZNF488. Overall, our findings highlight microglia–oligodendroglia crosstalk in demyelination, with CSF1R dysfunction promoting phagocytic and inflammatory microglia states, resulting in oligodendrocyte depletion, an arrest in OPC differentiation, and lack of remyelination.

overall_design: Fresh-frozen postmortem brain tissue was obtained from an ALSP donor, including white and gray matter from the prefrontal cortex, and white matter from the medial temporal lobe, parietal cortex, and occipital cortex. Additionally, tissue was obtained from seven controls, consisting of white and gray matter from the prefrontal cortex. The tissue was homogenized, and the nuclei were isolated using iodixanol gradient centrifugation. FANS was employed to enrich single nuclei from glia. RNA capture and library preparation were performed using the 10× Genomics Chromium Single Cell 3’ v3 assay. The resulting paired-end libraries were sequenced on an Illumina Novaseq 6000.

first: Cobos

last: Inma

first: Pan

last: Jie

first: Fores

last: Jaume


title: Risk assessment with gene expression markers in sepsis development

city: Jena

first: Alberto

last: Garcia Lopez

state: Thuringia

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute

summary: We investigated the individual phenotypic predisposition to developing uncomplicated infection or sepsis in a large cohort of non-infected patients undergoing major elective surgery. We built machine learning classification models on preoperative transcriptomic signatures to predict postoperative outcomes including sepsis. To test the predictive capability of these models for ongoing infection, whole blood RNA sequencing analysis on 61 independent patients with COVID-19 (10 mild, 51 severe cases) was performed.

overall_design: Whole blood RNA sequencing analysis was performed on 61 affected COVID-19 patients (10 mild, 51 severe cases).

first: Albert

first: Sascha

last: Schaeuble

first: Tongta

last: Sae-Ong

first: Bastian

last: Seelbinder

first: Michael

last: Bauer

first: Evangelos

last: Giamarellos-Bourboulis

first: Mervyn

last: Singer

first: Roman

last: Lukaszewski

first: Gianni

last: Panagiotou


title: Analysis on TME of animals treated with Multilamellar uRNA with or without IFNAR1 mAb and PD-1

city: Gainesville

first: Sadeem

last: Qdaisat

address: 1333 Center Dr.

institute: University of Florida

summary:
Nanostring profiling of animals treated with ML uRNA with or without IFNAR1 and PD-1 verses Untreated animals
UT vs ML uRNA vs ML uRNA with IFNAR1 mAb and PD-1

overall_design: Tumor tissue from mice treated with  ML uRNA vs UT

first: Elias

last: Sayour

first: Hector

last: Mendez-Gomez


title: Single-cell transcriptomics of neuroblastoma tumors

city: Gent

first: Noah

last: Bonine

state: -- SELECT --

address: Technologiepark-Zwijnaarde 75

country: Belgium

institute: Ghent University

summary: Neuroblastoma is a rare embryonic tumor arising from neural crest development and is responsible for 15% of pediatric cancer-related deaths. Over the past years, several single-cell transcriptome studies were performed to investigate the cell-of-origin and tumor heterogeneity. These individual studies typically involved a limited number of neuroblastoma tumors. To overcome this limitation, we integrated seven single-cell or single-nucleus data sets into a harmonized cell atlas covering 362,991 cells across 68 patient samples.  We use this integrated atlas to decipher the transcriptional tumoral landscape of neuroblastoma at single-cell resolution. Notably, within the tumor compartment, we find associations between transcriptomic profiles and clinical outcomes. In addition, we characterize the complex immune cell landscape of neuroblastoma and uncover considerable heterogeneity amongst tumor-associated macrophages. Finally, we showcase the utility of our atlas as a resource by expanding it with new data and using it as a reference for data-driven cell type prediction.

overall_design:
Neuroblastoma tumor samples were disaggregated for single-cell RNA-sequencing, single-nucleus RNA-sequencing or CITE-sequencing with 10X Genomics 3’ gene expression.
Raw data available at EGA: EGAD50000000328

first: Katleen

last: De Preter


title: Tracking rare single donor and recipient immune and leukemia cells after allogeneic hematopoietic cell transplantation using mitochondrial DNA mutations

first: Livius

last: Penter

country: USA

overall_design: Refer to individual Series


summary: We investigated the individual phenotypic predisposition to developing uncomplicated infection or sepsis in a large cohort of non-infected patients undergoing major elective surgery. Whole blood RNA sequencing analysis was performed on preoperative samples taken from 267 patients. These comprised patients who developed postoperative infection with (n=77) or without (n=49) sepsis, non-infectious systemic inflammatory response (n=31), or an uncomplicated postoperative course (n=110). Machine learning classification models built on preoperative transcriptomic signatures predicted postoperative outcomes including sepsis.

overall_design: Whole blood RNA sequencing analysis was performed on preoperative samples taken from 267 patients. These comprised patients who developed postoperatively infection leading to sepsis (n=77) or an uncomplicated infection outcome (n=49), non-infectious systemic inflammatory response (n=31), or an uncomplicated postoperative course (n=110).


title: Effects of wheat germ diet on intestinal antioxidant capacity, immunological function and gut microbiota of Sichuan white geese

city: Chengdu

first: Xin

last: Wang

country: China

institute: Sichuan Agricultural University

summary: Wheat germ is known for its antioxidant, anti-inflammatory, and disease resistance properties in animals. However, its effect on the gut of Sichuan white geese remains unclear. In this study, thirty 250-day-old geese were divided into three equal groups, the control group, LWG group (21.8% wheat germ) and HWG group (43.6% wheat germ), the experiment lasted 12 weeks. We assessed various aspects of geese intestinal health, including barrier function, digestibility, antioxidant capacity, immunity, microbiota, and metabolism.  The study revealed a significant increase in villus height (VH), villus height-to-crypt depth (VH/CD) ratio, amylase, and lipase activities in the duodenum and ileum, increased putrescine levels in the duodenum and jejunum, as well as spermidine levels in the jejunum(P < 0.05). LWG increased the total antioxidant capacity (T-AOC) in the duodenum, while decreasing levels of intestinal malondialdehyde (MDA), serum lipopolysaccharide (LPS), interleukin-6 (IL-6), and diamine oxidase (DAO) activity (P < 0.05). Furthermore, LWG increased the relative abundance of Oscillospiraceae_unclassified, Ligilactobacillus, and Roseburia, as well as increased levels of acetic acid, butyric acid, and valeric acid, while decreasing the relative abundance of Subdoligranulum, Flavonifractor, and Klebsiella. Additionally, we observed 17 up-regulated genes and 25 down-regulated genes in the jejunum, which are associated with the cell cycle and immunity. These genes play roles in pathways such as the p53 signaling pathway, cell cycle regulation, and pathways associated with immune modulation. On the other hand, HWG increased intestinal VH and spermidine content, as well as amylase and lipase activities in the duodenum (P < 0.05). It also elevated ileal T-AOC and sIgA levels ( P <0.05), while reducing intestinal MDA content, serum LPS levels, DAO activity, and propionic acid in cecum contents (P < 0.05). Moreover, HWG increased the relative abundance of Ligilactobacillus, Oscillospiraceae_unclassified, and Roseburia (P < 0.05). Overall, wheat germ diets, particularly the LWG diet demonstrated the ability to enhance antioxidant capacity, digestibility, immunity, and barrier properties of the intestinal tract, while modulating the gut microbiota and metabolism. Therefore, wheat germ diets hold promise in improving intestinal health by preserving barrier function and regulating flora structure.


title: Gene expression profiles in human liver organoid-derived hepatocytes

city: Suita

first: Yukiko

last: Ueyama-Toba

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

summary: Human liver organoids are expected to be a hepatocyte source for preclinical in vitro studies. Although these organoids show long-term proliferation, their hepatic functions remain low. Here, we propose a novel method for two dimensional (2D)-cultured hepatic differentiation from human liver organoids. When cultured under a 2D condition, the single cells from human liver organoids were seeded on collagen type I-coated plates. Then, optimal conditions for hepatic differentiation were screened using several reagents. We determined the 2D-cultured hepatocyte differentiation method from human liver organoids. Hepatic gene expressions in human liver organoids-derived hepatocytes (Org-HEPs) were greatly increased, compared to those in human liver organoids. The metabolic activities of cytochrome P450 (CYP) 1A2, CYP2C8, CYP2E1 and CYP3A4 were at levels comparable to those in primary human hepatocytes (PHHs). These results suggested that human liver organoids could be differentiated into highly functional hepatocytes in 2D culture. We also treated Org-HEPs and PHHs with hepatotoxic drugs. The cell viability of Org-HEPs was almost the same as that of PHHs, suggesting that Org-HEPs could be used for hepatotoxicity tests. Thus, Org-HEPs will be useful for pharmaceutical research.

overall_design: Human liver organoid and human liver organoid-derived hepatocytes were subjected to RNA-sequencing. Data are human liver organoids and human liver organoid-derived hepatocytes,which were established from two different donors.

first: Yanran

last: Tong

first: Jumpei

last: Yokota

first: Kazuhiro

last: Murai

first: Hayato

last: Hikita

first: Hidetoshi

last: Eguchi

first: Tetsuo

last: Takehara

first: Hiroyuki

last: Mizuguchi


title: Therapeutic efficacy of intracerebral hematopoietic stem cell gene therapy in an Alzheimer’s disease mouse model

status: Public on Aug 28 2024

first: Danilo

last: Pellin

address: 300 Longwood Ave

institute: Boston Childrens Hospital

summary: The conditions supporting the generation of microglia-like cells in the central nervous system (CNS) after transplantation of hematopoietic stem/progenitor cells (HSPC) have been extensively studied to advance the treatment of neurodegenerative disorders. Here, we challenge the HSPC transplantation paradigm by exploring different cell subsets and delivery routes with the goal of favoring the establishment of a robust and exclusive engraftment of HSPCs and their progeny in the CNS of transplant recipients. In this setting, we show that the CNS environment uniquely drives the expansion, distribution and myeloid differentiation of the locally transplanted cells towards a microglia-like phenotype. Importantly, intra-CNS transplantation of engineered HSPCs benefit 5xFAD Alzheimer’s disease mice, a finding that provides not only the first example of efficacy of HSPC gene therapy in this indication, but also a proof of the therapeutic potential of this novel approach that determines a CNS-restricted engraftment of the transplant progeny cells.

overall_design: The experimental design involved assessing the effects of different delivery methods and hematopoietic cell subsets on competitive transplantation outcomes in mice. CD34+-equivalent lineage-negative (Lin-) murine hematopoietic stem and progenitor cells (HSPCs) were delivered into the cerebroventricular space (ICV), followed by intravenous (IV) administration of various hematopoietic cell subsets, including total bone marrow (BM), Lin- cells, and c-kit+ Sca-1+ stem cell-enriched Lin- (KSL) cells. The IV delivery was either simultaneous with or delayed by 5 days after the ICV delivery. Additionally, the study explored a novel intrathecal lumbar (ITL) delivery method as an alternative to the ICV route. The outcomes were evaluated based on hematopoietic reconstitution and competitive transplantation efficiency.


title: Transcriptomics of varying strength and timing of specific activation of the Integrated Stress Response

city: South San Francisco

first: Carmela

last: Sidrauski

address: 1170 Veterans Blvd

institute: Calico Life Sciences

summary: The integrated stress response (ISR) is a central signaling pathway induced by a variety of insults, but how its outputs contribute to downstream physiological effects across diverse cellular contexts remains unclear. Using a synthetic tool, we specifically and tunably activated the ISR and performed multi-omics profiling to define the core modules elicited by this response in the absence of co-activation of parallel pathways commonly induced by pleiotropic stressors. We found that the ISR can elicit time- and dose-dependent gene expression changes that cluster into four modules with ATF4 driving only a small but fast and sensitive module that includes many amino acid metabolic enzymes. We showed that ATF4 was required to reroute carbon utilization towards amino acid synthesis derived both from glucose and reductive carboxylation of glutamine and away from the tricarboxylic acid cycle and fatty acid biogenesis revealing a new role for ATF4 in modulating cellular energetics. We also discovered an ATF4-independent reorganization of cellular lipids that promotes triglycerides synthesis and accumulation of lipid droplets that was essential for cell survival. Together, we demonstrate that a minimal ISR-inducing system is sufficient to trigger formation of two distinct cellular structures, stress granules and lipid droplets, and a previously unappreciated metabolic state.

overall_design:
We generated a cell line expressing a synthetic construct that allowed us to selectively initiate the ISR in a tunable fashion. We harnessed this system to quantitatively explore the transcriptome over time and define ISR-specific and -sufficient responses.
To specifically profile the cellular effects of ISR signaling, we generated a U2OS cell line stably expressing a synthetic construct, dimerizable PERK (Dmr-PERK), consisting of the eIF2ɑ kinase domain of mouse PERK fused to a chemically inducible DmrB dimerization domain. Upon addition of ligand AP20187 (dimerizer), the fusion protein dimerizes, leading to its activation and phosphorylation of eIF2ɑ. To determine how the transcriptional outputs of the ISR vary with time (duration) and input strength (stress level), we performed RNA-seq on cells treated for 1, 2, 4, 8, 16, or 24 hours with one of three doses of dimerizer. We chose a low dose of dimerizer (0.01 nM) where protein synthesis inhibition would be minimal (<15%) but ATF4 protein expression was still induced, an intermediate dose (0.2 nM) that caused a partial (50%) reduction in protein synthesis, and a high dose (3 nM) that led to the strongest (75%) reduction in protein synthesis and accumulation of stress granules.

first: Lauren

last: LeBon

first: Katherine

last: Labbé

first: Bryan

last: King

first: Ngoc

last: Vu

first: Emily

last: Stoops

first: Nina

last: Ly

first: Austin

last: Lefebvre

first: Phillip

last: Seitzer

first: Swathi

last: Krishnan

first: Jin-Mi

last: Heo

first: Bryson

last: Bennett


title: Transcriptomics of specific activation of the Integrated Stress Response activation in ATF4 WT and ATF4 KO cells

overall_design:
We generated a cell line expressing a synthetic construct that allowed us to selectively initiate the ISR in a tunable fashion. We harnessed this system to quantitatively explore the transcriptome over time and define ISR-specific and -sufficient responses.
To specifically profile the cellular effects of ISR signaling, we generated a U2OS cell line stably expressing a synthetic construct, dimerizable PERK (Dmr-PERK), consisting of the eIF2ɑ kinase domain of mouse PERK fused to a chemically inducible DmrB dimerization domain. Upon addition of ligand AP20187 (dimerizer), the fusion protein dimerizes, leading to its activation and phosphorylation of eIF2ɑ. To specifically profile the cellular effects of ISR signaling, we generated a U2OS cell line stably expressing a synthetic construct, dimerizable PERK (Dmr-PERK), consisting of the eIF2ɑ kinase domain of mouse PERK fused to a chemically inducible DmrB dimerization domain. Upon addition of ligand AP20187 (dimerizer), the fusion protein dimerizes, leading to its activation and phosphorylation of eIF2ɑ.

last: Krishan


title: ZNF750 plays an important role in skin inflammation induced by POLY IC treatment

city: La Jolla

first: Ye

last: Liu

address: 9452 Medical Center Drive, Room L1W106

department: Dermatology

institute: University of California, San Diego

summary: Loss of ZNF750 increased the inflammatory gene expression of differentiated human keratinocytes treated with POLY IC

overall_design: ZNF750 knockdown RNA-Seq in polyIC treated differentiated primary human keratinocytes.

first: George

last: Sen


title: Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [scRNA-seq 2]

status: Public on Aug 27 2024

city: Mexico City

first: Mayra

last: Furlan-Magaril

state: Mexico City

address: Circuito exterior s/n

department: Molecular Genetics

institute: IFC-UNAM

summary: Molecular and cellular characterization of tumors has become essential due to the complex and heterogeneous nature of cancer disease. In recent decades, many bioinformatic tools and experimental techniques have been developed to achieve personalized characterization of tumors. However, sample handling continues to be a major challenge as limitations such as prior treatments before sample acquisition, the amount of tissue obtained, transportation, or the inability to process fresh samples pose a challenge for experimental strategies that require viable cell suspensions. Here, we present an optimized protocol that allows recovery of highly viable cell suspensions from breast cancer biopsies. Using these cell suspensions we successfully characterized genome architecture through Hi-C. Also, we evaluated single-cell gene expression and the tumor cellular microenvironment through single cell RNAseq. Both technologies are key in the detailed and personalized molecular characterization of tumor samples. The protocol described here opens the possibility to obtain viable cell suspensions from biopsies in a simple and efficient manner

overall_design: The cell suspension was derived from a Tru-Cut biopsy specimen obtained from adjacent tissue from a Mexican female patient diagnosed with untreated triple-negative breast cancer. The adjacent tissue was collected at least 1 cm away from the tumor-affected area and presented a macroscopically healthy appearance.

first: Aura

last: Stephenson-Gussinye

first: Luis

last: Rendón-Bautista

first: Blanca

middle: E

last: Ruiz-Medina

first: Eduardo

last: Blanco-Olais

first: Rosario

last: Pérez-Molina

first: Cleofas

last: Marcial-Medina

first: Yanin

last: Chavarri-Guerra

first: Enrique

last: Soto-Perez-de-Celis

first: Andrea

last: Morales-Alfaro

first: Ayerim

last: Esquivel-López

first: Fernando

last: Candanedo-Gonzalez

first: Armando

last: Gamboa-Domínguez

first: Ruben

last: Cortes-González

first: Alejandro

last: Alfaro-Goldaracena

first: Sara

last: Vazquez-Manjarrez

first: Guido

last: Grajales-Figueroa

first: Beatriz

last: Astudillo-Romero

first: Jesus

last: Ruiz-Mariquez

first: A

middle: C

last: Poot-Hernández

first: Paula

last: Licona-Limón


title: Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [Hi-C]

first: Mayra

last: Furlan-Magaril

overall_design: The cell suspension was derived from a Tru-Cut biopsy sample obtained from a Mexican female patient diagnosed with untreated triple-negative breast cancer.

first: Aura

last: Stephenson-Gussinye

first: Luis

last: Rendón-Bautista

first: Blanca

last: Ruiz-Medina

first: Eduardo

last: Blanco-Olais


title: Transcriptomics of specific activation of the Integrated Stress Response compared to Arsenite and Thapsigargin treatment

first: Carmela

last: Sidrauski

overall_design:
We generated a cell line expressing a synthetic construct that allowed us to selectively initiate the ISR in a tunable fashion. We harnessed this system to quantitatively explore the transcriptome over time and define ISR-specific and -sufficient responses.
To specifically profile the cellular effects of ISR signaling, we generated a U2OS cell line stably expressing a synthetic construct, dimerizable PERK (Dmr-PERK), consisting of the eIF2ɑ kinase domain of mouse PERK fused to a chemically inducible DmrB dimerization domain. Upon addition of ligand AP20187 (dimerizer), the fusion protein dimerizes, leading to its activation and phosphorylation of eIF2ɑ. To evaluate how the transcriptional response elicited by this minimal system compared to that of commonly used pleiotropic ISR-inducing agents, we performed RNA-seq on Dmr-PERK cells treated with a time course of dimerizer (0.2nM), thapsigargin (100nM), a SERCA inhibitor that induces ER stress by depleting its Ca++ stores, or sodium arsenite (0.05mM), which generates ROS and causes oxidative stress. For each compound, we chose a dose that elicited comparable levels of phospho-eIF2ɑ. In parallel, we performed transcriptomics measurements on the parental U2OS cell line that did not express the Dmr-PERK construct to confirm that dimerizer treatment did not have any significant transcriptional effects.

first: Lauren

last: LeBon

first: Katherine

last: Labbé

first: Bryan

last: King

first: Ngoc

last: Vu

first: Emily

last: Stoops

first: Nina

last: Ly

first: Austin

last: Lefebvre

first: Phillip

last: Seitzer

first: Swathi

last: Krishan

first: Jin-Mi

last: Heo

first: Bryson

last: Bennett


title: Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [scRNA-seq1]

first: Mayra

last: Furlan-Magaril

overall_design: The cell suspension was derived from a Tru-Cut biopsy specimen obtained from a mexican female patient diagnosed with untreated triple-negative breast cancer

first: Rosario

last: Pérez-Molina

first: Cleofas

last: Marcial-Medina

first: Yanin

last: Chavarri-Guerra

first: Enrique

last: Soto-Perez-de-Celis

first: Andrea

last: Morales-Alfaro

first: Ayerim

last: Esquivel-López

first: Fernando

last: Candanedo-Gonzalez

first: Armando

last: Gamboa-Domínguez

first: Ruben

last: Cortes-González

first: Alejandro

last: Alfaro-Goldaracena

first: Sara

last: Vazquez-Manjarrez

first: Guido

last: Grajales-Figueroa

first: Beatriz

last: Astudillo-Romero

first: Jesus

last: Ruiz-Mariquez

first: A

last: Poot-Hernández

first: Paula

last: Licona-Limón


title: Effect of androgen receptor signaling on H3K27 trimethylation in Th17 cells

city: Nashville

first: Dawn

last: Newcomb

address: 1161 21st Ave South, T-1218 MCN

department: Medicine

institute: Vanderbilt University Medical Center

summary: Females have increased prevalence of many Th17-mediated diseases, including asthma. Androgen signaling decreases Th17-mediated airway inflammation, and Th17 cells rely on glutaminolysis. However, it remains unclear whether androgen receptor (AR) signaling modifies glutamine metabolism to suppress Th17-mediated inflammation. In this experiment, we conducted a CUT & RUN to determine how AR signaling modified histone 3 lysine 27 trimethylation in Th17 cells from WT males, WT females, and ArTfm male mice (n=3 from each group).

overall_design: Naïve T cells were isolated from spleens of WT male, WT female, and ArTfm male mice. ArTfm mice have a mutation in the androgen receptor (AR) that makes it non-functional.  Th17 cells were differentiated in culture for 4 days. Cells were isolated and using a H3K27me3 antibody or IgG isotype control and DNA was extracted using the KAPA Hyper Prep kit protocol. Sequencing libraries were constructed adn sequenced for 150 cycles in paired-end mode on Ilumina Nova-Seq 6000 platform.

first: N

middle: U

last: Chowdhury

first: X

last: Ye

first: J

last: Rathmell


title: Tlr7 mediates tissue-specific disease manifestations in primary Sjogren’s disease in a sex-biased manner

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary: The goal of this study was to determine whether male and female mice with primary Sjogren's disease (pSD) displayed differences in autoreactive IgM and IgG in sera. We also sought to determine whether this reactivity was dependent on the expression of Tlr7.

sample_organism:
Mus musculus
synthetic construct

overall_design: We analyzed sera from female and male NOD.B10H2b (NOD.B10) mice, referred to as NOD in the dataset. We also collected sera from age and sex-matched NOD.B10 Tlr7+/-  females (Het), and NOD.B10 Tlr7-/- females (KO) that lacked Tlr7 expression systemically. Finally, we harvested sera from NOD.B10 Tlr7-/y males that lacked systemic expression of Tlr7 (KO). All animals were at aged to the clinical disease stage (6 - 7 months old). IgM and IgG autoantigen arrays were performed on 6 animals from each group.

first: Jill

last: Kramer


title: Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis

first: Mayra

last: Furlan-Magaril

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