title: Transcriptome network analysis of inflammation and fibrosis in keloids

first: Jiayi

last: Mao

address: Zhi Zao Ju road

institute: shanghai ninth people's hospital


title: Transcriptome network analysis of inflammation and fibrosis in keloids [miRNA-seq]

status: Public on Sep 30 2024

city: Shanghai

country: China

type: Non-coding RNA profiling by high throughput sequencing

summary: Background:Keloid (KL) is a common benign skin tumor. KL is typically characterized by significant fibrosis and an intensive inflammatory response. Therefore, a comprehensive understanding of the interactions between cellular inflammation and fibrotic cells is essential to elucidate the mechanisms driving the progression of KL and to develop therapeutics. Objective: Investigate the transcriptome landscape of inflammation and fibrosis in keloid scars. Methods: In this paper, we performed transcriptome sequencing and microRNA (miRNA) sequencing on unselected live cells from six human keloid tissues and normal skin tissues to elucidate a comprehensive transcriptome landscape. In addition, we used single-cell RNA sequencing (scRNA-seq) analysis to analyze intercellular communication networks and enrich fibroblast populations in two additional keloid and normal skin samples to study fibroblast diversity. Results: By RNA sequencing and a miRNA-mRNA-PPI network analysis, we identified miR-615-5p and miR-122b-3p as possible miRNAs associated with keloids, as they differed most significantly in keloids. Similarly, COL3A1, COL1A2, THBS2, TNC, IGTA, THBS4, TGFB3 as genes with significant differences in keloid may be associated with keloid development. Using single-cell RNA sequencing data from 24086 cells collected from normal or keloid, we report reconstructed intercellular signaling network analysis and aggregation to modules associated with specific cell subpopulations at the cellular level for keloid alterations. Conclusions: Our multitranscriptomic dataset delineates inflammatory and fibro heterogeneity of human keloids, underlining the importance of intercellular crosstalk between inflammatory cells and fibro cells and revealing potential therapeutic targets.

overall_design: We performed transcriptome sequencing and microRNA (miRNA) sequencing on unselected live cells from six human keloid tissues and normal skin tissues to elucidate a comprehensive transcriptome landscape. In addition, we used single-cell RNA sequencing (scRNA-seq) analysis to analyze intercellular communication networks and enrich fibroblast populations in two additional keloid and normal skin samples to study fibroblast diversity.

first: Lu

last: Chen

first: Shutong

last: Qian

first: Yuhuan

last: Wanga

first: Binfan

last: Zhao

first: Qiuyu

first: Bolun

last: Lu

first: Xiyuan

first: Peisong

last: Zhai

first: Yuguang

last: Zhang

first: Liucheng

first: Xiaoming

last: Sun


title: Transcriptome network analysis of inflammation and fibrosis in keloids [scRNA-seq]

type: Expression profiling by high throughput sequencing


title: Transcriptome network analysis of inflammation and fibrosis in keloids [mRNA-seq]


title: The copepod Eurytemora affinis as a relevant species to assess estuarine sediment toxicity by combining sub-individual and individual endpoints: effects on gene expression and swimming behavior

city: Le Havre

first: Caroline

last: Arcanjo

address: 25, rue Philippe Lebon

country: France

institute: UMR-I02 SEBIO

summary: Compared to freshwater ecosystems, the health status of estuarine waters remains little studied despite their importance for many species. They also represent a zone of interest for Human settlements that make them the final sink of pollution in both the water column and sediment. Once in sediments, pollutants could represent a threat to benthic as well as pelagic estuarine species through resuspension events. In the Seine estuary, the copepod Eurytemora affinis has been previously presented as a relevant species to assess resuspended sediment contamination through the use of fitness-related effects at the individual level. The aim of the present study was to use E. affinis copepods to assess estuarine sediment-derived elutriates toxicity using both a molecular (i.e. transcriptomics) and a behavioral approach. Two sites along the Seine estuary were sampled. They were both under anthropic pressures from the industrial-port activities or wastewater treatment plants (i.e. Tancarville) or agricultural pressure from freshwater affluent (i.e. Fatouville). The analysis of sediments used to prepare elutriates reveals that both sites have close contamination profiles. The transcriptomic analysis reveals that exposure to both sites triggers the dysregulation of genes involved in biological function as defense response, immunity, ecdysone pathway or neurotoxicity. This analysis also reveals a higher count of dysregulated genes in the Fatouville site compared to the Tancarville despite their close contamination profile. These results emphasize the sensitivity of this molecular approach to assess environmental matrix toxicity with E. affinis. The analysis of the swimming behavior of E. affinis did not highlight significant effects after both sites elutriate exposure. However, our strategy to assess E. affinis swimming behavior (i.e the combination of the DanioVision observation chamber and the EthoVision analysis software) allows the discrimination of basal swimming behavior in this species. Thus, it represents a promising standardized tool to assess copepods swimming behavior in ecotoxicological studies.

overall_design: Adult copepods (Eurytemora affinis) sampled from the Seine estuary were exposed to sediment-derived elutriates (2500 mg/L and 350 mg/L) sampled from two sites (i.e. Tancarville and Fatouville). Exposures were performed in biological triplicates for each conditions (Control, Tancarville 350 mg/L, Tancarville 2500 mg/L, Fatouville 350 mg/L and Fatouville mg/L). After 72 h of exposure, pools of 30 males per biological triplicates were sorted, placed in microtubes with ceramic beads (CK14, Bertin, France), washed with RNA-free water, quickly dry frozen in liquid nitrogen and stored at -80 °C before the RNA extraction.

first: Céline

last: Boulangé-Lecomte


title: Metformin enhanced the effect of a Ketogenic diet in MYCN amplified Neuroblastoma xenografts

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

country: Austria

summary: Neuroblastoma (NB) is a childhood cancer in which the MYCN amplification is the most acknowledged marker of poor prognosis. MYCN-amplified NB cells showed to rely on both glycolysis and oxidative phosphorylation system (OXPHOS) for energy production . Previously, we revealed that a ketogenic diet (KD) slowed the tumor growth in MYCN NB xenografts, when combined with classical cytotoxic therapy cyclophosphamide (CP). Metformin (MET) is a compound that targets complex I of the OXPHOS system. Therefore, the aim of this study was to elucidate whether MET can enhance the anti-tumorigenic effects of a KD in NB. Our result indicated that MET decreasedcell proliferation andrespiration in NB cells in vitro. The combination of KD, MET and low dose of chemotherapyreduced also the tumor growth and improved survival in NB xenografts. GO enrichment analysis revealed fatty acid ß-oxidation as the most upregulated process resulting from the addition of MET to KD. The differential expression of CPT1A and of its direct regulator ACC might determine an unbalanced redox state and dictate the anti-tumor effect of the combination therapy in MYCN-amplified xenografts.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for different treatment groups (KD + MET + CP), KD alone (KD + CP), MET alone (MET + CP), control (CP), and control without CP

first: Luca

last: Catalano

first: Daniela

last: Weber

first: Sophia

last: Derdak

first: Martin

last: Bilban

first: Barbara

last: Kofler


title: BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels

city: Nashville

first: Jared

last: Nordman

state: TN

address: 465 21st Ave S

department: Biological Sciences

country: USA

institute: Vanderbilt University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone modifications are critical for regulating chromatin structure and gene expression. Dysregulation of histone modifications likely contributes to disease states and cancer. Depletion of the chromatin-binding protein BRWD3, a known substrate-specificity factor of the Cul4-DDB1 E3 ubiquitin ligase complex, results in increased in H3K4me1 levels. The underlying mechanism linking BRWD3 and H3K4 methylation, however, has yet to be defined. Here, we show that depleting BRWD3 not only causes an increase in H3K4me1 levels, but also causes a decrease in H3K4me3 levels, indicating that BRWD3 influences H3K4 methylation more broadly. Using immunoprecipitation coupled to quantitative mass spectrometry, we identified an interaction between BRWD3 and the H3K4-specific demethylase 5 (KDM5/Lid), an enzyme that removes tri- and di- methyl marks from H3K4. Moreover, analysis of ChIP-seq data revealed that BRWD3 and KDM5 are significantly co-localized throughout the genome and that sites of H3K4me3 are highly enriched at BRWD3 binding sites. We show that BRWD3 promotes K48-linked polyubiquitination and degradation of KDM5 and that KDM5 degradation is dependent on both BRWD3 and Cul4. Critically, depleting KDM5 fully restores altered H3K4me3 levels and partially restores H3K4me1 levels upon BRWD3 depletion. Together, our results demonstrate that BRWD3 regulates KDM5 activity to balance H3K4 methylation levels.

overall_design: Chromatin Immunoprecipitation using Active_motif anti-H3K4me3 antibody was performed in Drosophila S2 cells, with SNAP synthetic nucleosomes spiked-in sequencing.

first: Han

last: Dongsheng

first: Schaffner

middle: H

last: Samantha

first: Davies

middle: P

last: Jonathan

first: Benton

last: Mary Lauren

first: Plate

last: Lars

first: Nordman

middle: T

last: Jared


title: Deconvolution of the mechanisms of T cell drug response in multiple myeloma induction therapy

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: In this study, we characterize the effect of bortezomib, lenalidomide, and dexamethasone on T cells, with the help of high-quality datasets generated using the trimodal single-cell genomics method TEA-seq, which captures mRNA transcripts, cell surface epitopes, and chromatin accessibility. We describe alterations to T cell receptor signaling pathways, metabolism, and cell signaling that have important implications for T cell function, survival, and localization.

overall_design:
Multimodal characterization of bortezomib, lenalidomide, dexamethasone, and DMSO-only control treaments on healthy T cells, studied at three different treatment time-points (0h, 24h, 72h).
**RAW data will be submitted to dbGAP**

first: Lauren

last: Okada

first: Wei-Ling

last: Chang

first: Morgan

last: Weiss

first: Jessica

last: Garber

first: Upaasana

last: Krishnan

first: Mackenzie

last: Kopp

first: Veronica

last: Hernandez

first: Tao

last: Peng

first: Anthony

last: Cicalo

first: Ziyuan

last: He

first: Priya

last: Ravisankar

first: Samir

middle: R

last: Zaim

first: Gregory

last: Szeto

first: Julian

last: Reading

first: Lucas

last: Graybuck

first: Troy

last: Torgerson

first: Peter

middle: J

last: Skene

first: Xiao-jun

last: Li

first: Ernest

last: Coffey

first: Thomas

middle: F

last: Bumol


title: MAFB permits differentiation by permitting WT1 binding to podocyte specific promoters

city: Nice

first: Filippo

last: Massa

state: Provence-Alpes-Cote d'Azur

address: 28, Avenue de Valombrose

institute: CNRS

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

overall_design: Refer to individual Series


title: MAFB permits differentiation by permitting WT1 binding to podocyte specific promoters [Histons modifications ChIP-seq]

summary: Podocytes are highly specialized cells, but their chromatin status and the precise molecular events leading to their differentiation remain poorly defined. Here we used ChIP-Seq analysis for H3K4me3, H3K4me1 and H3K27me3 to establish the histone methylation map in adult.Loss of MafB led to the deposition of extracellular matrix, progressive foot process effacement, and kidney disease.  mouse podocytes. Our data demonstrate open chromatin across podocyte specific genes and reveals that genes expressed in the mesoderm lineage become actively repressed upon podocyte differentiation. To better understand the transcriptional control of podocyte differentiation, we studied the role of transcription factor MAFB.

overall_design: ChIP experiment was perfomed on purified primary mouse podocytes, using antibodies against known histon epigenetic markers (H3K4me3, H3K4me1, H27me3)

middle: M

first: Andreas

last: Schedl


title: Effects of the conditioned medium derived from human adipose-derived mesenchymal stem cells (hAdMSC-CM) on Benzalkonium Chloride (BAC)-treated human corneal epithelial cells.

city: Kizugawa

first: Tsutomu

last: Imaizumi

state: Kyoto

address: 6-5-4 Kunimidai

department: Basic Research Development Division

country: Japan

institute: Rohto Pharmaceutical Co., Ltd

summary:
To investigate the mechanism underlying effects of hAdMSC-CM on BAC-induced cytotoxicity, inflammation, and barrier dysfunction in human corneal epithelial cells.
We confirmed that the the effects of hAdMSC-CM were associated  with the TGFβ and JAK-STAT signalling pathways.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BAC-treated  human corneal epithelial cells with or without hAdMSCs-CM.

first: Ryuhei

last: Hayashi


title: MAFB permits differentiation by permitting WT1 binding to podocyte specific promoters [MAFb KO RNA-seq]

overall_design: Whole RNA was extracted from isolated podocytes 72 hours after conditional gene deletion. 4 controls and 4 KO animals were used for comparative analysis


title: MAFB permits differentiation by permitting WT1 binding to podocyte specific promoters [WT1-MAFB_ChIP-seq]


title: Physiological and transcriptome analysis provide new insights into the mechanism of enhanced tolerance to high temperature in Rhododendron by melatonin

city: Zhuji

first: Yanxia

last: Xu

state: Zhejiang

address: 66 Puyang Road

institute: Jiyang College, Zhejiang A&F University

summary: Rhododendron is well known woody plant, as having high ornamental and economic values. Heat stress is one of the important environmental stresses that effects Rhododendron growth. Recently, melatonin was reported to alleviate abiotic stress in plants. However, the role of melatonin in Rhododendron is still unknown. In the present study, the effect of melatonin on Rhododendron under heat stress and the potential mechanism was investigated. Through morphological characterization and chlorophyll a fluorescence analysis, 200µM was selected for the best melatonin concentration to mitigate heat stress in Rhododendron. To reveal the mechanism of melatonin priming alleviating the heat stress, the photosynthesis indexes, Rubisco activity and ATP content were detected in 25 ℃, 35 ℃ and 40 ℃. The results showed that melatonin improves electron transport rate (ETR), PSII and PSI activity, Rubisco activity and ATP content under high temperature stress. Furthermore, transcriptome analysis showed that a significant enrichment of differentially expressed genes in the photosynthesis pathway, and most of genes in photosynthesis pathway displayed a more significantly slight down-regulation under high temperature stress in melatonin-treatment plants, compared with melatonin-free plants. We identified PGR5……Together, these results demonstrate that melatonin could promote the photosynthetic electron transport, improve the enzymes activities in Calvin cycle and the production of ATP, and thereby increase photosynthetic efficiency and CO2 assimilation capacity under heat stress, through regulating the expression of some key genes, such as PGR5…Therefore, melatonin application displayed great potential to cope with the heat stress in Rhododendron.

overall_design: 25 ℃ melatonin-free as CK, 35 ℃ melatonin-free，35 ℃ melatonin-applied，40℃ melatonin-free，40 ℃ melatonin-applied

first: Yan-Xia

first: Jing

last: Zhang

first: Zi-Yun

last: Wan

first: Songheng

last: Jin


title: E7820, an Anti-Cancer Sulfonamide, Degrades RBM39 in Patients with Splicing Factor Mutant Myeloid Malignancies: A Phase II Clinical Trial

city: South San Francisco

first: Simon

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

summary: Mutations in RNA splicing factor genes (SF3B1, SRSF2, and U2AF1) are common in AML and MDS and recent studies demonstrate pharmacologic degradation of the RNA splicing factor RBM39 results in preferential killing of splicing factor mutant cells. We therefore conducted a phase II clinical trial (NCT05024994) of the oral RBM39 degrader E7820 at the recommended phase II dose in patients with R/R MDS/AML and a splicing factor mutation. No patients met the primary endpoint of overall response rate in the first 12 patients enrolled, leading to study termination. However, E7820 was well-tolerated and achieved >50% RBM39 degradation in blood and disruption of splicing. At the same time, the degree of splicing disruption was far less than seen with in vitro doses exhibiting preclinical efficacy, providing potential explanation for limited clinical efficacy. Overall, this study demonstrates on-target safety and feasibility of RBM39 degradation in patients and supports future combination therapies with E7820.

overall_design: Differential RNA splicing analysis by RNA-sequencing on human K562 or NKM1 cell lines (comparing treatment with E7820 or DMSO vehicle control) or cells derived from splicing factor mutated patients (comparing prior to initiation of E7820 clinical trial or on-trial) using single-replicates.

first: Omar

last: Abdel-Wahab


title: The alterations of gene expression profiling induced by ALKBH5 knockdown in HCT116 cells

city: Guangzhou

first: Dingcheng

last: Shen

address: 26 Yuancun Erheng Road

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

summary: ALKBH5 is one of the important m6A demethylases and is reported to be closely associated with tumorigenesis.In this study, we report gene expression profiles of HCT116 cells treated with ALKBH5 shRNA. This study reveals a novel role of ALKBH5 in downstream gene regulation and provides a new explanation ofALKBH5’ s function in colorectal cancer. Samples included 2 HCT1116 shNC and 2 HCT116 shALKBH5.

overall_design: RNA-seq after knockdown of ALKBH5 in HCT116 cells.

first: Yanxin

last: Luo

first: Huichuan

last: Yu


title: Integrating CRISPR knockout, interference, and activation to dissect the functional role and underlying signaling of microRNA-23a-27a-24-2 cluster in hepatocellular carcinoma

city: Birmingham

first: Lizhong

last: Wang

address: 720 20th St S

institute: University of Alabama at Birmingham

summary: The miR-23a-27a-24-2 cluster is overexpressed in human cancers, including hepatocellular carcinoma (HCC). However, the role of three mature miRNAs of the miR-23a-27a-24-2 cluster in HCC is still controversial. Also, the integrative role of the miR-23a-27a-24-2 cluster in HCC remains elusive. In the present study, using CRISPR knockout (KO), CRISPR interference (CRISPRi), and CRISPR activation (CRISPRa) technologies, we established an endogenous miR-23a-27a-24-2 controllable and various knockout (KO) cell models, which were used to dissect the functional role and underlying signaling of the miR-23a-27a-24-2 cluster. Either miR-23a KO or miR-27a KO reduced cell growth in vitro and in vivo. Of particular note, endogenous miRNAs in the miR-23a-27a-24-2 cluster were effectively regulated by CRISPRi/a, identifying an integrated oncogenic role of the miR-23a-27a-24-2 cluster in HCC cells. Functional analysis showed that miR-23a KO and miR-27a KO led the cell cycle arrest, especially at the G2/M phase, by reducing CDK1/cyclin B activation in HCC cells. Furthermore, a high-throughput RNA-seq approach with miRNA target prediction identified the miR-23a/miR-27a-regulated gene network, further validated by various technologies. In addition, miR-23a and miR-27a have opposite roles in cell migration and mesenchymal-epithelial transition. However, an integrated analysis by CRISPRi/a suggested an oncogenic role of the miR-23a-27a-24-2 cluster in cell migration, which may require a miR-23a-BMPR2-Smad-Snail axis in HCC cells. Thus, our CRISPRi/a study offers a valuable research tool for dissecting the integrated role and underlying mechanism of an endogenous miRNA cluster. Also, this CRISPR approach may provide new routes of miRNA intervention for miRNA targeted therapy.

overall_design: total RNA expression by deep-sequencing in HepG2 sorted for different levels of miR-23a and miR-27a activity

first: Mengying

last: Cui

first: Runhua

last: Liu


title: Transcriptomic profiling of blood mTreg and mTeff from healthy control (HC) and multiple sclerosis (MS) [RNA-Seq]

city: New Haven

first: Tomokazu

middle: S

last: Sumida

state: CT

address: 300 George St,, 3rd floor room349

department: Neurology

institute: Neurology, Yale School of Medicine

summary: Autoimmune diseases, among the most common disorders of young adults, are mediated by genetic and environmental factors. While CD4+Foxp3+ regulatory T cells (Tregs) play a central role in preventing autoimmunity, the molecular mechanism underlying their dysfunction is unknown. Here, we performed comprehensive transcriptional and epigenetic profiling of Tregs in multiple sclerosis (MS) to identify central transcriptional programs regulating human autoimmunity.

overall_design:
CD4+CD25hiCD127loCD45RO+ memory Tregs and CD4+CD25low/negCD127hiCD45RO+ memory Teffectors are sorted by FACS and subjected to mRNA-seq

>>>Submitter states that raw data will be submitted to dbGaP due to patient privacy concerns<<<

first: David

middle: A

last: Hafler


title: Genome-wide transcriptome analysis of human cell models exposed to Borrelia burgdorferi

city: Sackville

first: Anne

last: Berthold

state: New Brunswick

address: 62 York Street

department: Biology

country: Canada

institute: Mount Allison University

summary: We used high-throughput sequencing to investigate the genome-wide transcriptional response in human cells to treatment with Borrelia burgdorferi. We chose a time point of 72 h as ticks feed on their host for several days and at the same time the early response in Lyme disease is expected to occur at this time period at a cellular level. We found that the two cell models studied (HUVEC and HEK-293 cells) had significantly different responses. More significantly differentially expressed genes (69 in total) were found in HUVEC cells than in HEK-293 cells (8 in total). Functional analysis indicated induction of the immune response in HUVEC and suggest changes in the extracellular matrix in HEK-293.

overall_design: Examination of gene expression with RNA-seq in HUVEC and HEK-293 cells in response to Borrelia burgdorferi.

first: Vett

last: Lloyd

first: Gabriel

last: Wajnberg


title: PAC1 constrains type II inflammation through promotion of CGRP signaling in ILC2s [scRNA-seq]

status: Public on Sep 29 2024

city: Beijing

first: Yuan

address: 38 Xueyuan Road

institute: Peking University Health Science Center

summary: Dysfunction of group II innate lymphoid cells (ILC2s) plays an important role in the development of type II inflammation-related diseases such as asthma and pulmonary fibrosis. Notably, neural signals are increasingly recognized as pivotal regulators of ILC2s. However, how ILC2s intrinsically modulate their responsiveness to these neural signals is still largely unknown. Here, using single-cell RNA sequencing and bulk mRNA sequencing, we report that the immune regulatory molecule PAC1 (phosphatase of activated cells 1) selectively promotes the signaling of neuropeptide CGRP (calcitonin gene-related peptide) in ILC2s. Moreover, PAC1 is necessary for ensuring the expression of CGRP-response genes by influencing chromatin accessibility. In summary, our study demonstrates that PAC1 is an important regulator of ILC2 responses and we propose that PAC1 is a potential target for therapeutic interventions of type II inflammation-related diseases.

overall_design: Transcriptome and epigenome data from wild-type and Pac1-/- murine lung ILC2s in steady or activated conditions.

first: Bowen

first: Yuxin

last: Yin


title: Effects of vitamin D on VDR binding in THP-1 cells

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: Three independent repeats of ChIP-seq or ChIPmentation with THP-1 cells after treatment with either 1,25(OH)2D3 (VD) or control (EtOH) using antibody against VDR.

overall_design: THP-1 cells were treated with vitamin D (1,25(OH)2D3) or solvent (EtOH) for 8h before performing ChIP-seq or ChIPmentation with antibody against VDR.

first: Sabine

last: Seuter

first: Antonio

last: Neme

first: Veijo

last: Nurminen


title: Interactions between pituitary cell lineages direct tissue architecture and size

city: Montreal

first: Arthur

middle: Jules

last: Gouhier

state: Quebec

address: 110 Avenue des Pins

institute: IRCM

summary: Organ architecture is established during development through specific cell:cell contacts. The mechanisms responsible for these specific cell interactions remain poorly understood. In order to address this question, we used the anterior pituitary gland that harbors five different and interdigitated hormone-secreting homotypic cell networks. We now report that blocking differentiation of the first lineage to arise during pituitary development, the corticotrope cells, leads to pituitary hypoplasia with a major effect on the somatotrope cells that are fewer, with less secretory granules and a loss of cell polarity. These somatotrope cell phenotypes are dependent on gene dosage for the corticotrope-restricted transcription factor Tpit. In addition, the Tpit-deficient pituitary is hyper-vascularized. Single cell transcriptomics identifiy corticotrope and somatotrope regulatory and signaling pathways that may underlie cell:cell communications responsible for these phenotypes. Collectively, the results indicate that the corticotrope cell network is an important paracrine signalling center regulating pituitary architecture and size.

overall_design: scRNA-seq in mouse pituitary

first: Konstantin

last: Khetchoumian

first: Kevin

last: Sochodolsky

first: Chrystel

last: Lafont

first: Amandine

last: Bemmo

first: Paul

last: LeTissier

first: Patrice

last: Mollard

first: Helen

last: Christian

first: Jacques

last: Drouin


title: PAC1 constrains type II inflammation through promotion of CGRP signaling in ILC2s [RNA-seq]

last: Jin

last: Liu


title: Co-culture of iAT2  with fibroblast isolated from healthy and COPD lung in alveosphere culture system

city: gaithersburg

first: Xiaotao

last: Qu

state: md

address: 1 medimmune way

institute: Astrazeneca

summary: transciptomic approach applied to our sophisticated in vitro model of iPSC-alveospheres with fibroblasts, we explored epithelial-mesenchymal cross-talk in alveolar niche in COPD.

overall_design: iAT2 epithelial cells were co-cultured with fibroblast in 3D alveosphere to study the impact of fibroblast on epithelial cells

first: Rania

last: Dagher

first: Aigul

last: Moldobaeva

first: Pradip

last: Shahi

first: Peter

last: Byrne

first: Chia

middle: C

last: Chiang

first: Mahboobe

last: Ghaedi


title: SREBP2 restricts osteoclast differentiation and activity by regulating IRF7 and limits inflammatory bone erosion.

city: New York

first: Kyung-Hyun

last: Park-Min

email: ParkminK@HSS.EDU, parkmink@gmail.com

state: NY

address: 535 East 70th Street

institute: Hospital for Special Surgery

summary: Osteoclasts are multinucleated bone resorbing cells, and their dysregulation leads to pathological bone destruction. Osteoclast formation must be tightly regulated to prevent excessive bone loss and to minimize bone damage. SREBP2 is a key transcription factor for cholesterol biosynthesis and a sensor for intracellular lipids. However, how the crosstalk between SREBP2 and lipid metabolism contributes to osteoclasts has not been determined. Here, we reveal that SREBP2 is a negative regulator of osteoclastogenesis. Targeted deletion of SREBP2 in myeloid cells result in low bone mass and accelerates inflammatory bone destruction. SREBP2-mediated regulation of osteoclastogenesis is independent of its canonical function in cholesterol biosynthesis but is mediated, in part, by its downstream target, interferon regulatory factor (IRF)7. Taken together, our study highlights the SREBP2-IRF7 regulatory circuit forms as a negative feedback inhibitory loop in osteoclast differentiation that represents a novel mechanism to restrain deleterious pathological bone destruction.

overall_design: Each condition has two biological replicates.


title: Stimulation of neuronal stress signaling in optic nerve crush

city: San Francisco

first: Trent

middle: A.

last: Watkins

state: CA

address: 675 Nelson Rising Lane, Rm 214A

institute: University of California at San Francisco

summary: Dual Leucine-zipper Kinase (DLK)-dependent stress signaling is a critical determinant of neuronal survival and regenerative potential following axon damage, but it remains uncertain whether injury-activated DLK is adequate to initiate and maintain a pro-regenerative transcriptional response in the CNS. Using a drug-activatable DLK construct, we stimulated stress signaling for comparison of the retinal transcriptional response to, and in addition to, the response stimulated by mouse optic nerve injury in wildtype mice and in the context of partial axon regeneration enabled by disruption of the tumor suppressor PTEN.

overall_design: In a study to understand how augmenting stress signaling influences gene expression under conditions in which retinal ganglion cells (RGCs) undergo apoptosis in response to optic nerve. crush, mice were intravitreally injected with AAV2-hSyn1-mTagBFP2-ires-Cre and either a vector for the expression of drug-activatable DLK (AAV2-hSyn1-mTagBFP2-2A-ddDLK) or a control vector (AAV2-hSyn1-mTagBFP2-2A-ddYFP). Following optic nerve crush and repeated stimulation of ddDLK activity by systemic trimethoprim (TMP) injection, retinas were harvested 3 days post-crush for RNA-seq. In a parallel study to understand how augmenting stress signaling influences gene expression under conditions in which RGCs exhibit limited axon regeneration, PTEN conditional knockout mice were intravitreally injected with AAV2-hSyn1-mTagBFP2-ires-Cre and either a vector for the expression of drug-activatable DLK (AAV2-hSyn1-mTagBFP2-2A-ddDLK) or a control vector (AAV2-hSyn1-mTagBFP2-2A-ddYFP). Following optic nerve crush and repeated stimulation of ddDLK activity by systemic trimethoprim (TMP) injection, retinas were harvested at two time points (7 days post-crush and 10 days post-crush) for RNA-seq.


title: PAC1 constrains type II inflammation through promotion of CGRP signaling in ILC2s [FastATAC-seq]

first: Yuan

first: Bowen

first: Yuxin

last: Yin


title: Spatially resolved multi-bait mapping of stress granule and processing body transcriptome

first: Ziqi

last: Ren

address: Chengfu Road No.292

department: College of Chemistry and Molecular Engineering

institute: Peking University

summary: Stress granules (SGs) are dynamic, membrane-less organelles containing complex RNA-protein networks. The RNA components of SGs have been profiled through various approaches, characterized as long, translation-repressed, and highly epigenetically modified. However, it remains unclear whether these RNAs are uniformly distributed within SGs. In this study, we used multiple SG core proteins to genetically target the photocatalyst protein miniSOG, which allows for comprehensive CAP-seq profiling of RNA components within SGs. We discovered that RNAs associated with different SG core proteins exhibit heterogeneous distribution and distinct intrinsic features. Furthermore, we applied CAP-seq to map the RNA components in processing bodies (PBs) under both unstressed conditions and arsenite stimulation. By comparing the SG and PB transcriptomes, our data revealed that m6A modification may promote the localization of RNAs to SGs, while higher AU content may facilitate the targeting of mRNAs to PBs. This suggests potential regulatory roles in determining the subcellular localization of mRNAs within membrane-less organelles.

overall_design: Expression profiling by next-generation sequencing form stress granule or p-bodies CAP-seq libraries from different treatment with TIA1, G3BP2 and DDX6 as bait

first: Songrui

last: Zhao

first: Peng

last: Zou


title: Ythdf2 deficiency in microglia induces retinal inflammation and microvascular anomalies to aggravate ischemic retinopathy

city: nanjing

first: Zhu

last: Hongjing

address: hanzhong road

institute: nanjing medical university

summary: We used RNA-Seq to annotate aberrantly changed biological processes and signaling pathways induced by Ythdf2 loss in microglia isolated from the Ythdf2-/- and the Ythdf2fl/fl mice at P7

overall_design: To annotate aberrantly changed biological processes and signaling pathways induced by Ythdf2 loss in microglia

first: Hong-Jing

last: Zhu

first: Ye-Ran

last: Zhang

first: Yi-Chen

first: Xue

last: Chen


title: Single cell RNA sequencing reveals a shift in cell function and maturation of endogenous and infiltrating cell types in response to acute intervertebral disc injury

city: St. Louis

first: Simon

last: Tang

state: MO

address: 425 S. Euclid Ave, Campus Box 8233, Tang Lab, Washington University School of Medicine

department: Orthopaedic Surgery

institute: Washington University in St. Louis

summary: The intervertebral disc (IVD) is a spinal joint that accumulates damage with age but has limited tissue repair capabilities. IVD damage progresses into degeneration, and IVD degeneration is a leading cause of lower back pain. There are no effective therapies to treat IVD degeneration, but understanding the cell populations that change and respond to injury will uncover targets to restore IVD function. Mesenchymal stem cells (MSCs) are cells within the IVD that can potentially replenish the cells lost after IVD damage. To identify the cell populations of the IVD and how they change with injury, we performed single cell RNA sequencing of IVD tissue 7 days post injury and analyzed the differences in gene regulation. We identified diverse cells populations such as IVD specific tissues, immune cells, vascular cells, and MSCs. We discovered the presence of Saa2 and Grem1 expressing MSCs that become less stem cell-like and express higher levels of IVD gene markers after injury. We also determined that Saa2 and Grem1 have slightly different expression patterns in IVD tissues, and this expression becomes reduced after injury. These MSCs could be used in future stem cell therapies to prevent IVD degeneration.

overall_design: Control IVDs were isolated from female, 12-week old C57BL/6 (#000664) mouse tails in the coccygeal “CC” region CC12/13 through CC16/17. Injured IVDs were conducted using a 30G needle to bilaterally puncture regions CC5/6 through CC9/10. Control and Injured IVDs are from the same animal. Punctures were performed by using digital palpation to identify CC5/6 through CC9/10, puncturing each level with a sterile 30G needle. Control and Injured IVDs from 6 mice were pooled so that there was a total of 30 IVDs per group rendered into a single cell suspension and snap frozen. Snap frozen cells were thawed, and fluorescently activated cell sorting (FACS) was performed to sort out the viable cells from cell debris and dead cells using DAPI and then resuspended in PBS + 0.04% nonacetylated BSA for preparation of scRNASeq using a Chromium Controller (10X Genomics). Library preparation was performed using Chromium Single Cell 30 GEM, Library & Gel Bead Kit v3 (10X Genomics) following the manufacturer’s protocol and sequenced using Illumina NextSeq 500. Alignment of scRNASeq data to the mouse genome (mm10) and gene counting was completed utilizing the 10XGenomics Cell Ranger. Subsequently, output files from the Cell Ranger ‘count’ were read into Seurat v3 for further analysis17. Cells with fewer than 250 detected genes or genes that were expressed by fewer than 5 cells were excluded from the analysis. After normalization of the data and the most variable genes identified, the data were scaled, and the dimensionality of the data was reduced by principal component analysis (PCA). A non-linear dimensional reduction was then performed via uniform manifold approximation and projection (UMAP) and various cell clusters were identified.

first: Sade

middle: W

last: Clayton

first: Aimy

last: Sebastian

first: Stephen

last: Wilson

first: Nicholas

last: Hum

first: Remy

middle: E

last: Walk

first: Garrett

last: Easson

first: Rachana

last: Vaidya

first: Kaitlyn

last: Broz

first: Gabriela

middle: G

last: Loots

middle: Y


title: Large Scale Mapping of the trimethyl Guanosine Cap on Human RNAs

city: Manhasset

first: Sophie

last: Kwon

state: New York

address: 51 Clapham Ave

institute: Saint Mary's High School

summary: Nucleotides on RNA are chemically modified during biogenesis of various mammalian RNA species and RNA modifications have profound effects on RNA function. The 2,2,7-trimethylguanosine modification of the 5′ of RNA molecules is one of the earliest discovered modified nucleotides on mammalian RNAs. Although the TMG cap is one of the most intensively studied RNA modifications, its distribution on a global scale has not been explored. In this study, the locations of the TMG cap on human RNA is determined, using RNA immunoprecipitation coupled with high-throughput sequencing.  Although all prototypical modification sites were supported by this study, modification positions of some RNAs were erroneously annotated. In contrast to prototypic sites, many sites reported later were not validated at all. In addition to annotated modification sites, novel candidate sites were found on small Cajal body-specific RNAs.

overall_design: RNA-seq of RNA fragments enriched by immunoprecipitation with an antibody for 2,2,7-trimethylguanosine.


title: Potential landscape decomposes the cell identity conversion in liver regeneration and tumorigenesis [scRNA-seq]

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: Tumorigenesis, accompanied by tissue regenerative responses, always occurs during mammalian organ injury. In liver, injury context promotes dedifferentiated liver progenitor-like cells (LPLCs) from hepatocytes for regeneration, and also increases the occurrence of hepatocellular carcinoma (HCC). However, little is known about the contribution of injury specific LPLCs to tumorigenesis. Here, by using lineage tracing model, we have demonstrated that LPLCs are highly susceptible to oncogene-induced tumorigenesis. By using quantitative landscape of differentiation dynamics (LDD) model, we have constructed potential landscape of liver regeneration and tumorigenesis via scRNA-seq data, in order to predict distinct regulations of cell fate decisions. Applying this landscape with in vivo validation by transgenic mouse model, we have found blocking Wnt activation not only inhibits tumorigenesis, but also decreases LPLCs. Surprisingly, by using least action pathway analysis, we have decomposed regeneration and tumorigenesis routes, and found EP300 is specifically involved in tumorigenesis, which is further supported by in vivo EP300-knockout model and EP300 inhibitor assays. These findings might be applied as a framework to find tumor-specific regulators and develop strategies specifically inhibiting tumor initiation while leaving tissue regeneration unaffected.

overall_design: Single-cell RNA sequencing of hepatocytes, LPLCs and DDC&cMet induced HCC cells in liver

first: Qiang

last: He

first: Junbo

last: Jia

first: Shijie


title: Targeting Glycomes Sensitizes Ovarian Tumors to Immune Checkpoint Blockade II

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Aberrant glycosylation is a crucial strategy employed by cancer cells to evade cellular immunity. However, homologous recombination (HR) status-dependent glycosylation has never been explored therapeutically. Here, we show that the inhibition of branched N-glycans sensitizes HR-proficient, but not HR-deficient, epithelial ovarian cancers (EOCs) to immune checkpoint blockade (ICB). In contrast to fucosylation whose inhibition sensitizes EOCs to anti-PD-L1 immunotherapy regardless of HR-status, we observe a unique enrichment of branched N-glycans on HR-proficient compared to HR-deficient EOCs. Mechanistically, BRCA1/2 transcriptionally promotes the expression of MGAT5, the enzyme responsible for catalyzing branched N-glycans. The branched N-glycans on HR-proficient tumors augment their resistance to anti-PD-L1 by enhancing its binding with PD-1 on CD8_ T cells. In orthotopic syngeneic EOC mouse models, inhibiting branched N-glycans, using 2-Deoxy-D-glucose, sensitizes HR-proficient, but not HR-deficient EOCs, to anti-PD-L1. These findings indicate branched N-glycans as promising therapeutic targets whose inhibition sensitizes HR-proficient EOCs to ICB by overcoming immune evasion

overall_design: single cell RNA-seq in young and aged treated and naïve mice

first: Hao

last: Nie

first: Rugang


title: Potential landscape decomposes the cell identity conversion in liver regeneration and tumorigenesis

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

overall_design: Refer to individual Series


title: Potential landscape decomposes the cell identity conversion in liver regeneration and tumorigenesis [RNA-seq]

overall_design: Hepatocyte mRNA profiles of normal diet, DDC injury and DDC&cMet treatment mice；EP300 KO vs WT hepatocyte mRNA profiles of DDC&cMet treatment mice.


title: MAX controls meiotic entry in sexually undifferentiated germ cells

city: Hidaka-shi

first: Ayumu

last: Suzuki

state: Saitama

address: 1397-1 Yamane

department: Division of Biomedical Sciences, School of Medicine

institute: Saitama Medical University

summary: In mammals, female, but not male, germ cells onset meiosis physiologically during embryonic stages. We examined whether germ cell-specific disruption of Max gene leads to the activation of meiosis-related genes in embryonic male germ cells by single cell RNA sequencing.

overall_design: Single-cell RNA sequencing was carried out on gonadal cells from 6 Max cKO embryos at E12.5. These embryos included 4 with the Max fl/fl genotype driven by the Oct4-CreERT2 transgene and 2 controls with the Max fl/fl genotype. The pregnant mice from which these embryos were derived had been administered tamoxifen at E8.5. Each set of gonads obtained at E12.5 was individually dissociated using typsin-EDTA into single-cell suspensions. Cells from gonads with the CreERT2 transgene were then combined with those lacking the gene for the sequencing analysis. Library preparation, including the creation of gel beads and barcoding, was done using the Single Cell 3’ Reagent Kits v3 (10X Genomics). Sequencing was performed on an Illumina HiSeq platform, aiming for >50,000 reads per cell across 6,000 cells. The reference genome employed was the Genome Reference Consortium Mouse Build 38 (mm10), supplemented with a general transfer format file (Ensembl 93). Additional sequences for the CreERT2 cDNA and the SV40 genome were incorporated into the reference genome, labeled as ENSG00000N1 and ENSG00000N2, respectively. Data analysis was executed using Cell Ranger (v7.0.1) and the Loupe Browser (6.5.0).

first: Kousuke

last: Uranishi

first: Akihiko

last: Okuda


title: Eosinophils exhibit a unique transcriptional signature and increased sensitivity to IL-3-induced activation in response to colorectal cancer cells

city: Tel Aviv

first: Ariel

last: Munitz

address: Klachkin 35

country: Israel

institute: Tel Aviv University

summary: Identifying mechanisms by which eosinophils interact with tumor cells could lead to the development of new immunotherapies for colorectal cancer and other solid tumors.

overall_design: We characterized the interactions between eosinophils and colorectal cancer cells using an unbiased transcriptomic and proteomic analyses approach. Human eosinophils were stimulated with colorectal cancer cell-conditioned media, containing tumor cell-secreted factors from multiple cancer cell lines.

first: Michal

last: Itan

first: Shai

last: Dulberg

first: Asaf

last: Madi


title: Liver transcriptome of Psoraleae Fructus decoction induced liver damage in mice

city: Nantong

first: YU

last: WU

address: Nantong, 226001, PR China;

institute: Nantong Hospital of Traditional Chinese Medicine

summary: Psoraleae Fructus can cause liver damage, we study its effect on liver transcription,According to the sequence data, a total 6689 mRNAs were identified. Compared with control group, 1814 differential mRNAs were identified in the SPHD group, including 939 upregulated mRNAs and 875 downregulated mRNAs. Top 20 pathways are shown in the result, including “Metabolic pathways”, “NOD−like receptor signaling pathway”, “PI3K−Akt signaling pathway”, “Drug metabolism − other enzymes”, and “Estrogen signaling pathway”. To understand the functions of differential mRNAs, the target genes of differential mRNAs were predicted and were mapped to terms in the GO database and compared with the background (Figure 5C). The GO has 3 ontologies, which are “biological process”, “cellular component”, and “molecular function”. In the “biological process” part, most genes were related to “immune system process”, “oxidation−reduction process”, and “transport”. In the “cellular component” part, most genes were related to the “ribosomal part”, “mitochondrial part” and “membrane part”. In the “molecular function” part, most genes were related with “structural constituent of ribosome part”,  “protein binding ” and “poly(A) RNA binding”.

overall_design: The high-dose Psoraleae Fructus decoction group was compared with the control group, with four in each groups.

first: Yu

last: Wu

first: Zhengying

last: Hua

first: Nong

last: Zhou

first: Chunmei

last: Chun

first: Lingtian

last: Min


title: Potential landscape decomposes the cell identity conversion in liver regeneration and tumorigenesis [ChIP-seq]

first: Lijian

last: Hui

overall_design: We collected primary hepatocytes via perfusion as reported from normal (WT mice for denoting normal liver-derived cells, n=2) and DDC-injured (Sox9-EGFP mice to trace hepatocyte-derived Sox9-positive LPLC, n=2) liver, HCC cells are collected from 5 months of DDC+cMet treatment Sox9-CreERT2:Rosa26-mTmG, and performed ChIP-SEQ

first: Qiang

last: He

first: Junbo

first: Shijie

last: Tang


title: Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [RNA-seq]

status: Public on Sep 28 2024

city: Kyoto

first: Shuh

last: Narumiya

address: Yoshidahonmachi

department: Department of Drug Discovery Medicine

institute: Kyoto University

summary: Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathwaysin these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor.

overall_design: To examine the effect of PGE2 on naïve CD8 T cell transcriptome, we stimulated mouse naïve CD8 T cells with anti-CD3/CD28 Dynabeads and 30 u/ml IL2 in the presence or absence of 30nM PGE2 and collected cells on the different time points and subjected the cells to RNA-seq analysis

first: Siwakorn

last: Punyawatthananukool

first: Dean

last: Thumkeo


title: Identifying of a novel RUNX1-RARA fusion in variant acute promyelocytic leukemia

city: shanghai

first: Jia-Cheng

last: Jin

address: 600 Yishan Rd

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

summary: Here we report a novel fusion gene, RUNX1-RARA, in acute promyelocytic leukemia (APL). RUNX1-RARA triggers APL genesis by mediating transcriptional repression of target genes, and it can be potently restrained by all-trans retinoic acid treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary murine hematopoietic cells transduced with either empty vector or RUNX1-RARA.

first: Jiacheng

first: Lingyun

first: Meng

last: Yan

first: Liyu


title: Transcriptomics coupled with Metabonomics for elucidating differences between the components in different varieties Atractylodes

city: Changchun

first: Tao

last: Zhang

address: Key Laboratory of Chinese Medicine Planting and Development. Changchun University of Chinese Medicin

summary: Atractylodes macrocephala is a traditional Chinese medicine in China. It is widely used in clinic and the market demand is great. The quality difference between A. chinensis(Bunge) Koidz and A. japonica Koidz.ex Kitam is great, which seriously affects its clinical curative effect. Determination of Atractylosin by High-performance liquid chromatography. Transcriptomics coupled with Metabonomics for elucidating differences between the components in  A. chinensis(Bunge) Koidz and A. japonica Koidz.ex Kitam. It was found that ACS, ACC, PAL and NOS were the key genes and metabolites related to the synthesis of atractylodes macrocephala. The decrease of salicylic acid content in A. chinensis(Bunge) Koidz may lead to the decrease of its ability to mediate the elicitor of endophytic fungi, resulting in the down-regulation of the expression of TGAL4 transcription factor and the up-regulation of DOGL3 transcription factor in A. chinensis(Bunge) Koidz cells, which may affect the accumulation of Atractylosin. The study above provides a theoretical basis for elucidating the biosynthesis pathway of atractylosin in A. chinensis(Bunge) Koidz.

overall_design: Samples of A. chinensis(Bunge) Koidz and A. japonica Koidz.ex Kitam were collected in the Herb Garden of Changchun University of Traditional Chinese Medicine, Nanguan District, Changchun City, Jilin Province, China (latitude 43°49'N, longitude 125°25'E). Plant samples were collected using a five-point sampling method. After the plant samples are collected, the surface soil and dust are washed off with clean water, and the surface liquid of the material is blotted with absorbent paper. It is divided into 50-100 mg sizes, divided into two aliquots, one into sterile, enzyme-free cryovials with screwed caps and labeled. It was quick-frozen in liquid nitrogen, and then quickly moved to -80°C for storage for transcriptome and metabolome sequencing. Another sample was naturally dried to determine the content of the pharmacodynamic ingredient. All experimental samples were identified by Associate Professor Qi Weichen of the School of Pharmacy of Changchun University of Chinese Medicine.


title: Expression data from liver tissue from Spontaneously hypertensive rat (SHR) and its minimal congenic strain PD5 on standart labaratory chow and after dexamethasone challenge

first: Lukáš

middle: Farhád

last: Mirchi

address: Albertov 4

country: Czech Republic

institute: Charles University PRague

summary:
The dissection of genetic components of metabolic syndrome is currently one of the most important research topics. Plzf gene is a promising candidate gene. Previously, we described minimal congenic strain PD5 derived from spontaneously hypertensive rat (SHR), containing congenic segment of polydactylous (PD/Cub) origin with a 2964bp intronic deletion within Plzf gene and displaying attenuated features of metabolic syndrome.
To unravel the genetic background responsible for the observed of this phenotype in PD5 we compared liver transcriptomes and physiologic parameters between SHR and PD5 strains without intervention and after dexamethasone administration.

overall_design: Only male SHR (n=6) and male PD5 (n=6) were used. Rats were kept under 12h light-dark cycle, fed standard laboratory chow and given access to water ad libitum. After 12 months, half of the SHR rats (n=3) and half of the PD5 rats (n=3) were administered DEX (Dexamed, Medochemie) in drinking water (2.6 µg/ml) for 3 days. After that all rats were anesthetized by ether and decapitated. Organs were snap frozen in liquid nitrogen, livers were used for further analysis.

first: L

first: K

last: Procykova

first: F

last: Liska


title: Potent and selective binders of the E3 ubiquitin ligase ZNRF3 stimulate Wnt signaling and intestinal organoid growth

city: Ottawa

first: Pirunthan

last: Perampalam

state: ON

address: 336 Drumlsih Lane

summary: Selective and precise activation of signaling transduction cascades is key for cellular reprogramming and tissue regeneration. However, the development of small or large molecule agonists for many signaling pathways has remained elusive and is rate limiting to realize the full clinical potential of regenerative medicine. Focusing on the Wnt pathway, here we describe a series of disulfide-constrained peptides (DCPs) that promote Wnt signaling activity by modulating the cell surface levels of ZNRF3, an E3 ubiquitin ligase that controls the abundance of the Wnt receptor complex FZD/LRP at the plasma membrane. Mechanistically, monomeric DCPs induce ZNRF3 ubiquitination, leading to its cell surface clearance, ultimately resulting in FZD stabilization. Furthermore, we engineered multimeric DCPs that induce expansive growth of human intestinal organoids, revealing a dependence between valency and ZNRF3 clearance. Our work highlights a strategy for the development of potent, biologically active Wnt signaling pathway agonists via targeting of ZNRF3.

overall_design: To study the functional relevance of ZNRF3 domains required for DCP activity unbiasely, we generated a SW48 Cas9 cell line and delivered a CRISPR/Cas9 tiling library of gRNA spanning the entire ZNRF3. We treated the cells with DMSO or DCP for 1 h and subjected the cells to FACS sorting. To rule out gRNAs that resulted in premature truncation and loss of ZNRF3 expression, we first filtered out all hits that altered the cell surface abundance of ZNRF3 in DMSO control treated cells. Next, we evaluated the selective enrichment of gRNAs in the top 10% of ZNRF3 expressing cells in the MK1-2.A2.B9.1 DCP treated cells compared to DMSO treatment .

first: Kristel

last: Dorighi

first: Yvonne

last: Kschonsak

first: Felipe

last: de Sousa e Melo


title: Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [scRNA-seq]

first: Shuh

overall_design: Utilizing scRNA-seq (10x Genomics) to examine the transcriptomic signature of PTGER4 hi and PTGER4low immune cell from human cancer tumor microenvironment


title: scRNAseq in human iPSC-derived motor neurons(hiPSC-MNs).

status: Public on Sep 27 2024

city: Niigata

first: Masato

last: Yano

address: 757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,

department: Division of Neurobiology and Anatomy

institute: Niigata University

summary: We sequenced mRNA from hiPSC-derived human motor neurons to confirm gene expression in these cells.

overall_design: Differentiated human motor neurons were dissociated into a single-cell suspension using Accutase (Innovative Cell Technologies).

first: Takahisa

last: Ogasawara

first: Tsuyoshi

last: Matsuo

first: Yoshika

last: Hayakawa-Yano


title: 3D genome topology distinguishes molecular subgroups of medulloblastoma

city: Houston

first: Marco

last: Gallo

state: TX

address: 1102 Bates Avenue

department: Pediatrics

institute: Baylor College of Medicine

summary: Four main medulloblastoma (MB) molecular subtypes have been identified based on transcriptional, DNA methylation and genetic profiles. However, it is currently not known whether MB subtypes have their own specific 3D genome architecture. Hi-C maps were globally stable across MB subtypes. However, among the 3D genome features we tested, boundary strengths of topologically associating domains (TADs) were the best at classifying MB samples – including Group 3 and Group 4 specimens - according to their known molecular subtypes. Although boundary strength was not generally associated with differential gene expression between subtypes, we found that Group 3 and Group 4 specimens had differential TAD boundary strengths near genes that are uniquely expressed in their respective lineages of origin. Accordingly, we provide examples of TAD boundary reorganization that clearly distinguish Group 3 and 4 samples at these developmentally important genomic sites. TAD boundary strength allows classification of MB molecular subtypes, indicating that the shape of the 3D genome is unique to each molecular subtype. Genome topologies of Group 3 and 4 tumors are shaped differently at key lineage genes, but these differences are not strongly predictive of changes in gene expression. 3D genome architecture might be a fossil of the lineages of origin of MB subtypes.

overall_design:
We performed in situ Hi-C to reconstruct the 3D genome architecture of MB subtypes. We generated high-resolution Hi-C data for 28 surgical specimens and one patient-derived xenograft. Additionally, we generated matched transcriptomics data for the 28 surgical specimens for integrative studies.

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Submitter states that missing raw data are being made available for controlled access in EGA.
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first: Michael

middle: D

last: Taylor


title: Fate induction in CD8 chimeric antigen receptor T-cells through asymmetric cell division

first: Christoph

last: Ellebrecht

address: 421 Curie Blvd, 1005 BRB

department: Dermatology

institute: University of Pennsylvania

summary: Early expansion and long-term persistence predict efficacy of chimeric antigen receptor T-cells (CARTs), but mechanisms governing effector versus memory CART differentiation and whether asymmetric cell division (ACD) induces differential fates in human CARTs remain unclear. We use target-induced proximity labeling to isolate first-division proximal--daughter and distal-daughter CARTs to interrogate TCR clonality, surface proteome, and transcriptome at the single-cell level.

overall_design: First-division proximal (LIPSTIC label positive, first cell division by CTV stain), first-division distal (LIPSTIC label negative, first cell division), activated-undivided (LIPSTIC label positive, zero cell division), and resting (LIPSTIC label negative, zero cell division) CARTs were isolated using fluorescence-activated cell sorting and analyzed by single cell sequencing.

first: Lee

last: Casey

first: Ellebrecht

last: Christoph


title: DNA methylation of postnatal liver development in pig

city: Chengdu

first: Hongling

last: Jin

address: Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

type: Methylation profiling by high throughput sequencing

summary: In this study, BS-seq technology was used to analyze the epigenomic analysis of liver tissues of Rongchang pigs at three important feeding stages. There was little difference in DNA methylation profiles among the neonatal, weaned and adult groups. However, we observed significant changes in DNA methylation in the gene body and promoter regions of metabolic and immune-related genes from neonates to adulthood. Correlation analysis showed that the methylation level of gene promoters was significantly negatively correlated with gene expression. In neonatal Rongchang pigs, most genes related to nutritional metabolism lost DNA methylation and mRNA expression increased. The few fatty acid metabolism-related genes that were hypomethylated and highly expressed in the early development of Rongchang pigs may satisfy the nutritional requirements of Rongchang pig neonates, and their immune-related genes may be related to the establishment of liver immunity.

overall_design: To investigate the changes of 5mC methylation during liver development, we generated 5mC methylation profiles of pigs at three important feeding stages after birth, and compared DNA methylation and gene expression in liver tissues of neonatal piglets (0 days), weanling piglets (21 days) and adult sows (730 days). The developmental transcriptome distribution pattern of 5mC was characterized and the relationship between gene expression and 5mC modification was analyzed.

first: Bo

last: Zeng


title: RNA deep sequencing data of the whole transcriptomes of the aa3 mutant, aa3 mprA double mutant, and aa3 rel double mutant strains of Mycobacterium smegmatis MC2 155

city: Busan 46241, Republic of Korea

first: Yuna

last: Oh

address: Busandaehakro63bun-gil, 2

department: Department of Integrated Biological Science

country: South Korea

institute: Pusan national university

summary: To identify the effect of additional deletion of rel and mprA in the aa3 mutant strain lacking the aa3 cytochrome c oxidase of the respiratory electron transport chain of Mycobacterium smegmatis MC2 155, we constructed the aa3 rel double mutant and aa3 mprA double mutant and profiled the transcriptomes of the aa3 mutant, aa3 mprA double mutant and aa3 rel double mutant strains. Our comparative RNA sequencing analysis revealed that expression of most ribosomal proteins was induced in the aa3 rel double mutant and aa3 mprA double mutant relative to the aa3 mutant.

overall_design: Comparison of gene expression between the aa3 mutant, aa3 mprA double mutant, and aa3 rel double mutant strains of Mycobacterium smegmatis that are aerobically grown.

first: Jeong-Il


title: Trans-generatioanl epigenetic inheritance and resetting of an environmentally-triggered change in gene expression in C. elegans

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

institute: CU Boulder

summary: Transgenerational epigenetic inheritance and resetting of an environmentally-triggered change in gene expression in C. elegans

overall_design: Small RNA sequencing of 3 replicates offspring of worms grown at low temperature, “low worms” and 3 replicates offspring of worms grown at high temperature, “high worms”

first: Adam

last: Klosin

first: Cristina

last: Hidalgo

first: Tanya

last: Vavouri

first: Ben

last: Lehner


title: Molecular Profiling Reveals Immunosuppressive Tumor Immune Microenvironment in Primary versus Paired Asynchronous Metastatic Clear Cell Renal Cell Carcinoma

city: Ann Arbor

first: Simpa

last: Salami

state: MI

address: 1500 E Medical Center Dr

department: Urology

institute: University of Michigan

summary: Clear cell renal cell carcinoma (ccRCC) is a highly immune infiltrated cancer, but how the tumor immune microenvironment (TIME) evolves during disease progression is unknown. Insights into heterogeneity within primary ccRCC raise questions about potential heterogeneity between primary and paired metastatic tumors. This information may improve understanding of immune evasion leading to metastatic disease and response to immunotherapy. In this study, we characterize and compare the TIME of primary ccRCC with paired asynchronous metastases. We demonstrate higher infiltration of immunosuppressive cells in the TIME of primary ccRCC compared with metastatic sites. Further studies are necessary to determine the prognostic and therapeutic significance of these findings. Understanding the heterogeneity of the tumor immune microenvironment in RCC, both intratumorally and between metastatic sites, has important clinical implications for selecting appropriate therapies and developing predictive biomarkers. Future research should focus on elucidating the impact of these findings on immunotherapeutic responses and patient outcomes in ccRCC.

overall_design: Analysis of ccRCC patients who developed recurrence post radical nephrectomy and had both primary and metastatic tissue available. Whole-transcriptome sequencing was performed on formalin-fixed paraffin-embedded (FFPE) specimens using the illumina platform. Differential expression gene (DEG) analysis was performed using R package edgeR. Gene set enrichment analyses (GSEA) to identify hallmark pathway enrichment was performed using R package fgsea. TIME deconvolution was quantified using CIBEROSRT, an in silico flow cytometry tool.

first: Brittney

middle: H

last: Cotta

first: Srinivas

last: Nallandhighal

first: Zayne

last: Knuth

first: Nathan

last: Graham

first: Yuping

last: Zhang

first: Rui

last: Wang

first: Amy

last: Kasputis

first: Xuhong

last: Cao

first: Aaron

last: Udager

first: Saravana

last: Dhanasekaran

first: Ganesh

last: Palapattu

first: Rohit

last: Mehra

first: Marcin

middle: P

last: Cieslik

first: Todd

last: Morgan


title: RNA variant assessment using transactivation and transdifferentiation

city: Adelaide

first: Alison

last: Gardner

state: SA

address: AHMS, Uni of Adelaide, North Terrace

department: Faculty of Health and Medical Sciences

country: Australia

institute: University of Adelaide

summary: Understanding the impact of splicing and nonsense variants on RNA is crucial for the resolution of variant classification as well as their suitability for precision medicine interventions. This is primarily enabled through RNA studies involving transcriptomics followed by targeted assays using RNA isolated from clinically accessible tissues (CATs) such as blood or skin of affected individuals. Insufficient disease gene expression in CATs does however pose a major barrier to RNA based investigations, which we show is relevant to 1,436 Mendelian disease genes. We term these ‘silent’ Mendelian genes (SMGs), the largest portion (36%) of which are associated with neurological disorders. We developed two approaches to induce SMG expression in human dermal fibroblasts (HDFs) to overcome this limitation, including CRISPR-activation based gene transactivation, and fibroblast-to-neuron transdifferentiation. Initial transactivation screens involving 40 SMGs stimulated our development of a highly multiplexed transactivation system culminating in the 6- to 90,000-fold induction of expression of 20/20 (100%) SMGs tested in HDFs. Transdifferentiation of HDFs directly to neurons led to expression of 193/516 (37.4%) of SMGs implicated in neurological disease. The magnitude and isoform diversity of SMG expression following either transactivation or transdifferentiation was comparable to clinically relevant tissues. We apply transdifferentiation and/or gene transactivation combined with short- and long-read RNA sequencing to investigate the impact that variants in USH2A, SCN1A, DMD and PAK3 have on RNA using HDFs derived from affected individuals. Transactivation and transdifferentiation represent rapid, scalable functional genomic solutions to investigate variants impacting SMGs in the patient cell and genomic context.

overall_design: Samples are RNA collected from human dermal fibroblasts (time point day 0) and following transdifferentiation into induced neurons (time points day 10, 20 and 26) in biological quadruplicate.

first: Jolly

last: Lachlan

first: Mark

last: Corbett

first: Jozef

last: Gecz


title: Disease-related AUTS2 disruption causes an imbalance of neuronal/glial lineage specification through the WNT/β-catenin pathway (RNA-Seq).

city: HERSHEY

first: Yen Teng

last: Tai

address: 700 HMC Cres Rd

department: Biochemistry and Molecular Biology

institute: Penn State College of Medicine

summary: Individuals with disruptions in the Autism Susceptibility Candidate 2 (AUTS2) gene frequently exhibit symptoms like intellectual disability, microcephaly, growth retardation, and distinct skeletal and facial differences. The role of AUTS2 in neurodevelopment has been explored using animal models and in vitro embryonic stem cell models. However, the precise molecular mechanisms through which AUTS2 influences neurodevelopment, particularly in humans, are not thoroughly understood. To address this, our study employs a 3D human organoid culture system, in combination with genetic, genomic, cellular, and molecular approaches, to investigate how AUTS2 impacts neurodevelopment through cellular signaling pathways. We used CRISPR/Cas9 technology to create AUTS2-deficient human embryonic stem cells (hESCs), replicating a 190kb genetic deletion observed in a patient. These cells were then differentiated into cerebral organoids. Our single-cell RNA sequencing (scRNA-seq) analysis of these organoids indicates that the absence of AUTS2 results in a significant reduction in neuron-related cells and an increase in choroid plexus (ChP) epithelial cells. Notably, our research reveals that AUTS2 negatively regulates the Wnt/β-catenin signaling pathway, evidenced by the observed overactivation of this pathway in AUTS2-deficient organoids as well as in a luciferase reporter cell line with AUTS2 deletion.  Importantly, treating the AUTS2-deficient cerebral organoids with a Wnt inhibitor ameliorated the abnormalities in neuronal differentiation. This study offers new insights into the role of AUTS2 in neurodevelopment and suggests new potential targeted therapies for NDDs.

overall_design: To understand the role of AUTS2 in human brain development, we utilized a cerebral organoids model system with the CRISPR/Cas9-engineered hESCs with AUTS2 deletion. We then performed bulk RNA-seq on the day 75 WT, AUTS2+/- and AUTS2-/- cerebral organoids.

first: Zhuangzhuang

last: Geng

first: Yen

middle: T

first: Qiang

first: Eric

last: Zhou

first: Zhonghua

last: Gao


title: Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2

city: Aurora

first: Christina

last: Como

state: CO

institute: University of Colorado

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

overall_design: Refer to individual Series


title: Disease-related AUTS2 disruption causes an imbalance of neuronal/glial lineage specification through the WNT/β-catenin pathway


title: A comprehensive analysis of spermatozoal RNA elements in idiopathic infertile males undergoing fertility treatment

city: Detroit

first: Grace

middle: Michelle

last: Swanson

address: 275 E. Hancock, C.S. Mott Center room 271

institute: Wayne State University

summary: Current approaches to diagnosing male infertility inadequately assess the complexity of the male gamete. Beyond the paternal haploid genome, spermatozoa also deliver coding and non-coding RNAs to the oocyte. While sperm-borne RNAs have demonstrated potential involvement in embryo development, the underlying mechanisms remain unclear. In this study, 47 sperm samples from normozoospermic males undergoing fertility treatment using donor oocytes were sequenced and analyzed to evaluate associations between sperm RNA elements (exon-sized sequences) and blastocyst progression. A total of 366 RNA elements (REs) were significantly associated with blastocyst rate (padj<0.05), some of which were linked to genes related to critical developmental processes, including mitotic spindle formation and both ectoderm and mesoderm specification. Of note, 27 RE-associated RNAs are predicted targets of our previously reported list of developmentally significant miRNAs. Inverse RE-miRNA expression patterns were consistent with miRNA-mediated down-regulation. This study provides a comprehensive set of REs which differ by the patient’s ability to produce blastocysts. This knowledge can be leveraged to improve clinical screening of male infertility and ultimately reduce time to pregnancy.

overall_design: Human spermatozoal RNA

first: Matthew

last: Hamilton

first: Stewart

last: Russell

first: Stephen

last: Krawetz

first: Karen

last: Menezes

first: Sergey

middle: I

last: Moskovtsev

first: Clifford

last: Librach


title: Disease-related AUTS2 disruption causes an imbalance of neuronal/glial lineage specification through the WNT/β-catenin pathway (scRNA-Seq).

overall_design: To understand the role of AUTS2 in human brain development, we utilized a cerebral organoids model system with the CRISPR/Cas9-engineered hESCs with AUTS2 deletion. We then performed scRNA-seq on the day 75 AUTS2+/- and AUTS2-/- cerebral organoids.

last: Wang


title: Abberant neuronal Wnt activation causes defective TDP43 localization

city: Baltimore

first: Shanthini

last: Sockanathan

state: Maryland

address: PCTB1004, 725 North Wolfe Street

department: Neuroscience

institute: The Johns Hopkins University School of Medicine

summary: Conserved neuropathologies across multiple neurodegenerative diseases have identified shared causal pathways for neurodegeneration. One pathway involves the RNA-binding protein TDP-43, whose nuclear exclusion and cytoplasmic accumulation are established drivers of neurodegeneration. TDP-43 mislocalization is attributed to defective nucleocytoplasmic transport (NCT), but the underlying mechanisms are unclear. The vertebrate-specific six-transmembrane enzyme, Glycerophosphodiester phosphodiesterase 2 (GDE2 or GDPD5), cleaves the glycosylphosphatidylinositol (GPI)-anchor that tethers some proteins to the membrane. Here, we show that loss of GDE2 leads to aberrant sustained activation of canonical Wnt signaling in adult neurons, which is sufficient to cause NCT and nuclear pore abnormalities and the nuclear exclusion of TDP-43. GDE2 disruption coincides with TDP-43 nuclear exclusion in postmortem tissue from patients with Amyotrophic Lateral Sclerosis (ALS), and neuronal Wnt signaling is erroneously activated in Drosophila and induced human spinal neuronal (iSN) models of ALS. Wnt knockdown in Drosophila ALS models mitigates cell death, while pharmacological inhibition of Wnt activation in iSNs from ALS patients rescues mRNA levels of known TDP-43 splicing targets. Our study identifies GDE2 as a critical regulator of Wnt signaling in adult neurons and highlights Wnt pathway activation as a previously unappreciated mechanism contributing to NCT and TDP-43 abnormalities in disease.

overall_design: We carried out RNA-seq comapring cortices from 19-month WT and Gde2KO animals to evaluate splicing defects due to TDP43 pathology. To look for pathways initiating changes in TDP43 trafficking, we performed RNAseq analyzing cortices from 4-month old WT and Gde2KO animals.

last: Zhang

first: Loyal

last: Goff


title: Transcriptional effects of SARS-CoV-2 E protein and altered BET function

city: Sevilla

first: Elena

last: Gómez Marín

address: Av. Américo Vespucio, 24

country: Spain

institute: CSIC

summary: BET proteins are chromatin adaptors involved in gene transcription control, which recently were reported to interact with the SARS-CoV-2 envelope (E) protein, raising the question of whether the interaction constitutes a hijacking mechanism of the virus in the host cell. To evaluate this possibility, we have compared the effects on cell transcriptome of E overexpression with those of BET inhibition by the JQ1 drug. We have found that effects are quite different, and specially in relation to gene categories related to natural immunity and the interferon response we find opposite effects, being E overexpression a strong inductor of these genes. We have also identified a C-terminal fragment of BET proteins interacting with E. However, co-expression of this fragment with E is not altering the main transcriptional effects of E alone on immunity-related genes.

overall_design: We transfected hek293T cells with a plasmid expressing the SARS-CoV-2 E protein and compared the transcriptional changes produced with cells treated with the BET protein inhibitor JQ1, to observe whether the changes were similar or opposite. In addition, we also transfected HEK293T cells with the plasmid expressing the E protein together with a plasmid expressing the fraction of BET proteins with which it interacts to study whether the interaction inhibits the effect of E protein overexpression.

first: Nieves

middle: L

last: Ureña

first: José

last: Reyes

first: Mario

last: García Domínguez


title: Ago2 protects against diabetic cardiomyopathy via activating mitochondrial gene translation [Ribo-seq]

city: Wuhan

first: zhan

last: jiabing

address: Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Diabetes is associated with cardiovascular complications. microRNAs translocate into subcellular organelles to modify genes involved in diabetic cardiomyopathy. However, functional properties of subcellular Ago2, a core microRNA, remain elusive. We elucidated the function and mechanism of subcellular localized Ago2 on mouse models for diabetes mellitus and diabetic cardiomyopathy. Ago2 decreased in cardiomyocyte mitochondria in both models. Overexpression of mitochondrial Ago2 attenuated diabetes-induced cardiac dysfunction. Ago2 recruited TUFM, a mitochondria translation elongation factor, to activate translation of electron transport chain (ETC) subunits and decrease reactive oxygen species. Malonylation, a post-translational modification of Ago2, reduced the importing of Ago2 into mitochondria in diabetic cardiomyopathy. Ago2 malonylation was regulated by a cytoplasmic-localized short isoform of SIRT3 through a previously unknown demalonylase function. Our results reveal that the SIRT3–Ago2–CYTB axis links glucotoxicity to cardiac ETC imbalance, providing new mechanistic insights and the basis to develop mitochondria targeting therapies for diabetic cardiomyopathy.

overall_design: Comparative Translational profiling analysis of Ribosome-seq data for  RNA extracted from cox8-AGO2 overexpression mice heart and its control.

first: Jiabing

last: Zhan

first: Kunying

last: Jin

first: Rong

last: Xie

first: Chen

last: Chen

first: Huaping

last: Li

first: Dao


title: Ago2 protects against diabetic cardiomyopathy via activating mitochondrial gene translation II

overall_design: Comparative mRNA profiling analysis of RNA-seq data for polyA RNA extracted from rAAV-COX8-Ago2 treated mice and its control.


title: The effects of HSP60 chaperone deficiency on zebrafish larvae

city: Research Unit for Molecular Medicine (MMF)

first: Peter

last: Bross

state: Region Midt

address: Palle Juul-Jensens Boulevard 99

department: Department of Clinical Medicine

country: Denmark

institute: Aarhus University and Aarhus University Hospital

summary: To understand the effects of Hsp60 deficiency in developing vertebrates, we generated CRISPR/Cas9-mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf .

overall_design: Wildtype control and hspd1-/- larvae at 5dpf,  were analyzed by RNASeq. For this purpose, 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.


title: Transcriptomic analysis of Per2-deficient neutrophils compared WT neutrophils following infection.

city: Auckland

first: Chris

last: Hall

address: 85 Park Road, Grafton

country: New Zealand

institute: The University of Auckland

summary: Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils.

overall_design: Differential gene expression analysis of RNA-seq data from Per2-deficient neutrophils and WT neutrophils after Salmonella typhimurium infection in biological quadruplet.

first: Christopher

middle: J


title: The upregulation of K+ and HCN channels in developing spiral ganglion neurons is mediated by cochlear inner hair cells

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

institute: Sorbonne Universite

summary: Spiral ganglion neurons (SGNs) are primary sensory afferent neurons that relay acoustic information from the cochlear inner hair cells (IHCs) to the brainstem. The response properties of different SGNs diverge to represent a wide range of sound intensities in an action-potential code. This biophysical heterogeneity is established during pre-hearing stages of development, a time when IHCs fire spontaneous Ca2+ action potentials that drive glutamate release from their ribbon synapses onto the SGN terminals. The role of spontaneous IHC activity in the refinement of SGN characteristics is still largely unknown. Using pre-hearing otoferlin knockout mice (Otof-/-), in which Ca2+-dependent exocytosis in IHCs is abolished, we found that developing SGNs fail to upregulate low-voltage-activated K+-channels and hyperpolarisation-activated cyclic-nucleotide-gated channels. This delayed maturation resulted in hyperexcitable SGNs with immature firing characteristics. We have also shown that SGNs that synapse with the pillar side of the IHCs selectively express a resurgent K+ current, highlighting a novel biophysical marker for these neurons. RNA-sequencing showed that several K+ channels are downregulated in Otof-/- mice, further supporting the electrophysiological recordings. Our data demonstrate that spontaneous Ca2+-dependent activity in pre-hearing IHCs regulates some of the key biophysical and molecular features of the developing SGNs. KEY POINTS: Ca2+-dependent exocytosis in inner hair cells (IHCs) is otoferlin-dependent as early as postnatal day 1. A lack of otoferlin in IHCs affects potassium channel expression in SGNs. The absence of otoferlin is associated with SGN hyperexcitability. We propose that type I spiral ganglion neuron functional maturation depends on IHC exocytosis.

overall_design: Cochlear Tissue was dissected from heterzygous and homozygous otof KO mice and submitted for RNA-sequencing. Both pairs of cochleas from 2-3 P7 pups were pooled for each genotype.  (n=2 pools per genotype). Sampels were dissected in the same manner as used for all patching experiments. RNA-seq data was analyzed using the nf-core pipeline and differential expression testing was performed using DeSEQ2.

first: Mirna

last: Mustapha


title: mRNAseq in control and siQKI in human iPSC-derived motor neurons(hiPSC-MNs).

first: Masato

last: Yano

institute: Niigata University

summary: We sequenced mRNA from hiPSC-MNs to compare gene expression level and alternative splicing events between 3 control and 3 siQKI.

overall_design: mRNA profiles obtained from 3 different control and 3 siQKI were generated by deep sequencing using Illumina NextSeq.

first: Yoshika

last: Hayakawa-Yano


title: Modelling HSP60 deficiency using an inducible transgenic HSP60 ATPase deficient mutant

summary: To investigate the immediate effect of HSP60 dysfunction on mitochondrial functions, we induced the expression of a dominant-negative ATPase-deficient HSP60 mutant (HSP60-D423A) in HEK293 cells using tetracycline . Incorporation of HSP60-D423A subunits into HSP60 heptamer rings leads to dysfunction of the chaperonin complex. We titrated tetracycline levels to have a biologically relevant cellular model that can be monitored over time. Expression of the HSP60-D432A protein resulted in significantly reduced cell counts at 72 hours induction compared to uninduced and HSP60-WT co-expressing cells. To study the effects of onset of HSP60 deficiency, we monitored transcriptional changes using RNASeq.

overall_design: HEK293-HSP60_D423A Flp-in cells were induced with 50µg/ml tetracyclin for 48h or 72h. As controls/reference, uninduced cells were used. 3 biological replicates for each condition were prepared.


title: Effect of SCN5A depletion on gene expression in xenograft tumours of MDA-MB-231 breast cancer cells

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

country: United Kingdom

institute: University of York

summary: To investigate the function of SCN5A in tumour progression, we previously established an MDA-MB-231 cell line in which the target gene has been stably knocked down using lentiviral shRNA. The cell line (or equivalent cells expressing control shRNA) was orthotopically implanted into the 4th inguinal mammary fat pad of 6-week old immunodeficient Rag2−/− Il2rg−/− female mice and tumours allowed to form. We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 tumours derived from control and shRNA SCN5A cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDA-MB-231 cell xenograft tumours (shRNA control vs shRNA SCN5A).

first: Theresa

middle: K

last: Leslie

first: Sangeeta

last: Chawla

middle: N

first: William

last: Brackenbury


title: Ago2 protects against diabetic cardiomyopathy via activating mitochondrial gene translation [Ribosome-seq]

first: zhan

overall_design: Comparative Translational profiling analysis of Ribosome-seq data for  RNA extracted from AGO2-KO AC16 cells and its control.

first: Jiabing

last: Wang


title: mRNAseq in control and siQk in NSC34 cells

city: Niigata

address: 757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,

summary: We sequenced mRNA from mouse NSC34 cells to compare gene expression level and alternative splicing events between 3 control and 3 siQk.

overall_design: mRNA profiles obtained from 3 different control and 3 siQk were generated by deep sequencing using Illumina NextSeq.


title: Ago2 protects against diabetic cardiomyopathy via activating mitochondrial gene translation [mRNA-seq]

last: jiabing

overall_design: Comparative mRNA profiling analysis of RNA-seq data for polyA RNA extracted from AGO2-KO AC16 cells and its control.

first: Kunying

first: Rong


title: Single cell RNA-seq analysis of TBX18-driven reprogramming of ventricular myocytes to cardiac pacemaker cells

first: Hee Cheol

last: Cho

state: MD

address: 600 N Wolfe St. Blalock 1257

institute: Johns Hopkins University

summary:
Background: Embryonic trancription factor TBX18 re-expression has been demonstrated to be capable of converting ventricular myocytes to pacemakers cells. The goals of this study are to investigate the effects of TBX18 on myocytes and non-myocytes at day 3, day 6 and day 14, as well as tracking the key node of reprogramming process and mechanism.

Methods: Neonatal rat ventricular myocytes (NRVC) were treated by adeno-TBX18 or GFP for 3 days to investigate the early effects of TBX18 on myocytes and non-myocytes. Except for these 2 treatments, Adeno-TBX18 with one specific Tgfβ inhibitor, A83-01 (0.2uM) was treated for NRVC for 14 days for explore the effects of Tgfβ inhibition on fibroblast activation and myocyte reprogramming process. Attached NRVC monolayers were digested with 0.25% trypsin (Cat# LS003707, Corning, NY) for 5 min at 37 °C, and filtered through a 100-μm cell strainer (Fischer Scientific, Waltham, MA) to generate a single-cell suspension. Single cells were resuspended to a concentration of 700-2,000 cells per microliter. Gel beads-in-emulsion (GEMs) were generated with Chromium X (10X Genomics, Pleasanton, CA) and RNA libraries were prepared using the Chromium Next GEM Single Cell 3' GEM kit, v3.1 (10X Genomics Inc., Pleasanton, CA) with a targeted cell recovery of 4,000-10,000 cells per reaction. Quality control of cDNA and scRNA-seq libraries were performed using the Bioanalyzer High Sensitivity kit (Agilent Technologies Inc., CA). Libraries were sequenced using Novaseq 6000 (Illumina Inc., CA) with a minimum depth of 50,000–65,000 read pairs per cell.

Result: Upon QA/QC filtering, 13,437 cells met the quality thresholds for subsequent analysis. We focused on three cell types: cardiomyocytes (CMs, Tnni3-positive), total FBs (Pdgfrb and Tcf21-positive) with 2 subpopulations, including myoFBs (Pdgfrb, Tcf21, Acta2-high) and quiescent FBs (Pdgfrb, Tcf21, Acta2-low). Pathway analysis further revealed that upregulated DEGs by TBX18 are involved in fibroblast activation and ECM remodeling. Among those, Tgfβ signaling, which is one of the major molecular mediators of fibrosis in the heart, figured prominently in TBX18-transduced CMs and FBs. This was evidenced by upregulated expression of Tgfβ ligands and profibrotic genes such as Tgfb1, Tgfb2, and Acta2 in TBX18-NRVCs. Accordingly, higher proportion of activated myofibroblasts (39.3% vs. 25.4%) and lower proportion of quiescent FBs were observed in TBX18-NRVCs compared to control (Fig. 2F). To test the causative role of Tgfβ signaling in triggering fibrosis upon TBX18 re-expression, monolayers of NRVCs were treated with a small molecule inhibitor of type I Tgfβ receptors, A83-01. Treatment with A83-01 significantly decreased the population of myoFBs from 68.0% in TBX18-NRVC to 49.5% of total cell population at d14. Heat map analysis of all genes indicated that TBX18-CMs show upregulation of fibroblast-related genes, which is mitigated with A83-01 treatment. The upregulated DEGs in TBX18-FBs pointed to ECM remodeling as well as inflammatory response involving Tgfβ and other cytokines. Again, treatment with A83-01 abrogated the rise of these pathways. Profibrotic genes such as Tgfb2, Tgfb3, Acta2, and inflammatory genes were upregulated in FBs transduced with Ad-TBX18, which was mitigated by A83-01 treatment. The upregulated gene clusters in TBX18-FBs were also upregulated in TBX18-CMs, particularly, interferon signaling, interleukin-4 regulation of apoptosis, which may have led to the loss of TBX18-CMs over time. The inflammatory and profibrotic pathways were suppressed by treatment with A83-01 and may explain the higher population of TBX18-CMs with A83-01 at d14.We also quantified the number of de novo iPMs based on: Tnni3high, Hcn4+, Nkx2-5low, Gja1low through our scRNA-seq analysis and demonstrated the proportions of Hcn4+ iPMs was similar in TBX18-CMs regardless of Tgfβ inhibition but was higher compared to control.

Conclusion: Tgfβ signaling inhibition with a83-01 prevents against myofibroblast activation, cardiomyocytes apoptosis and inflammatory response induced by TBX18, and short term treatment of A8301 does not strongly interfere the reprogramming process and efficiency.

overall_design: Single cell transcriptomic profile neonatal rat ventricular cardiomyocytes treated with Adeno-TBX18 or Adeno-GFP with or without Tgf-beta inhibitor A83-01 at day 3 and 14.

first: Jinqi

last: Fan


title: THUMPD3 regulates alternative splicing of ECM transcripts in human lung cancer cells and promotes proliferation and migration

status: Public on Sep 26 2024

city: Cambridge

first: Tony

last: Kouzarides

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: RNA-modifying enzymes have recently garnered considerable attention due to their relevance in cancer biology, identifying them as potential targets for novel therapeutic intervention. THUMPD3 was recently identified as an RNA methyltransferase catalysing N2-methylguanosine (m2G) within certain tRNAs. In this study, we unveil a novel role for THUMPD3 in lung cancer cells. Depletion of the enzyme from lung cancer cells significantly impairs their fitness, negatively impacting key cellular processes such as proliferation and migration. Notably, exogenous expression of THUMPD3 in normal lung fibroblasts stimulates their proliferation rate. Additionally, transcriptome-wide analyses reveal that depletion of THUMPD3 from lung cancer cells induces substantial changes in the expression of cell surface proteins, including those comprising the extracellular matrix (ECM). We further demonstrate that THUMPD3 maintains expression of an extra-domain B (EDB) containing pro-tumour isoform of Fibronectin-1 mRNA, encoding FN1, an important ECM protein. Crucially, depletion of THUMPD3 promotes an alternative splicing event that removes the EDB-encoding exon from Fibronectin-1. This is consistent with THUMPD3 depletion reducing cellular proliferation and migration. Moreover, depletion of THUMPD3 selectively and preferentially affects the alternative splicing of ECM and cell adhesion molecule encoding transcripts, as well as those encoding neurodevelopmental proteins. Overall, these findings highlight THUMPD3 as an important player in regulating cancer-relevant alternative splicing and they provide a rationale for further investigations into THUMPD3 as a candidate target in anti-cancer therapy.

overall_design:
To investigate the function of THUMPD3 in key cellular processes such as prolideration and migration in lung cancer cells, we extablished A549 cell line in which THUMPD3 has been knocked down by shRNA and siRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq data for A549 cells from three different types of KD (shD3 #1, shD3 #4, siD3 #3).
Alternative splicing analysis was performed using another set of deep RNA-seq of A549 cells with THUMPD3 knockdown (shD3 #1).

first: Marie

last: Klimontova

first: Han

last: Zhang

last: Bannister


title: Differentiation Protocol-Dependent Variability in hiPSC-Derived Endothelial Progenitor Functionality

city: Austin

first: Brett

last: Stern

state: Texas

address: 2515 Speedway

institute: The University of Texas at Austin

summary: With multiple groups generating methods for differentiating induced pluripotent stem cells (hiPSCs) into endothelial cells/endothelial progenitors (ECs/EPs), there is a need to better understand the specific endothelial subtypes that different differentiation protocols produce. This is especially important for accurate tissue modeling as researchers continue to incorporate the endothelium into engineered tissues. We illustrated the heterogeneity of cells produced from different differentiation protocols by focusing on two selected protocols, one driving differentiation exclusively using small molecules (SM Protocol) and one driving differentiation primarily using growth factors (GF Protocol). We characterized the cells through a combination of vasculogenic computational analysis following encapsulation in 3D hydrogels, RNA sequencing, and measurement of soluble factor release. Vasculogenic computational analysis indicates that cells from the GF protocol formed more dense and interconnected vasculature compared to cells from the SM protocol. Likewise, RNA-seq analysis showed GF-derived cell enrichment in pathways involved in cell migration and angiogenesis. In addition, GF-derived cells favor differentiation to arterial endothelial cells as well as predisposition to undergoing a partial endothelial-to-mesenchymal transition, whereas SM-derived cells resemble immature progenitors based on higher proliferation rates as well as ECM remodeling. These trends also persisted following extended 3D culture. The results demonstrate that despite using the same starting hiPSC population and isolating EPs using the same surface marker, the two differentiation protocols yield highly distinct cell populations. This work highlights the importance of understanding the specific endothelial subtypes produced by different differentiation protocols for the creation of more accurate tissue models.

overall_design: TagSeq was performed on mRNA isolated from hiPSC-derived endothelial progenitors from differentiation protocols that utilize either exclusively small molecules or a combination of small molecules and growth factors. Each condition has 4 biological replicates.

first: Stern

last: Brett

first: Meng

last: Sarah

first: Larsen

last: Bryce

first: Brock

last: Amy

first: Zoldan

last: Janet