title: Spatiotemporal orchestration of phytohormones determines the organization pattern of aerenchyma in S. polyrhiza

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

summary: Aerenchyma is crucial for plant adaptation to stresses like hypoxia, drought, and nutritional deficiency. Although ethylene-mediated signaling cascades are known to regulate aerenchyma formation under hypoxic conditions, the precise mechanisms are still unclear. Moreover, cellular dynamics underlying the process of aerenchyma formation are still not well understood. We investigated the stage-dependent structural dynamics of aerenchyma in Spirodela polyrhiza (S. polyrhiza), a fast-growing aquatic herb with well-developed aerenchyma in its floating fronds. Using X-ray micro-computed tomography and histological analysis, we found that the spatial framework of aerenchyma was established before frond volume increased, driven by cell division and expansion. Additionally, the substomatal cavity connecting aerenchyma to stomata is formed via programmed cell death (PCD) closely associated with guard cell development. Transcriptome analysis and pharmacological studies further revealed that the organization of aerenchyma in S. polyrhiza is determined by the interplay between PCD and proliferation. This balance was governed by the spatiotemporal regulation of phytohormone signaling, including ethylene, abscisic acid, and salicylic acid. Our study sheds light on the structural dynamics and hormonal regulation of aerenchyma development in duckweeds, improving understanding of plant responses to environmental stresses and providing potential avenues for enhancing crop resilience under climate change.

overall_design: RNA sequencing of frond tissues of Spirodela polyrhiza plants at development stages 2-6 (n=3 for stages 2-4 and n=2 for stages 5-6)

first: Yuree

last: Lee

first: Daehee

last: Hwang


title: Effect of Transcriptional-like Effector  (TALE) on Nicotiana benthamiana leaves

status: Public on Aug 08 2024

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

country: Spain

institute: IBMCP

type: Expression profiling by high throughput sequencing

summary: To investigate gene expression upon inoculation of Nicotiana benthamiana leaves with a TALE inducing cell death

overall_design: Comparative gene expression profiling between TALE26 (inducing cell death) and TALE9 (not inducing cell death) at 36h after infiltration

first: J


title: Immune Editing Roles of SIGLEC15 in Tumor Microenvironment of Hepatocellular Carcinoma

city: Shanghai

first: Zheng

last: Chen

state: Shanghai

address: No.180 Fenglin Road, Xuhui District

department: Department of Liver Surgery and Transplantation, Liver Cancer Institute

country: China

institute: Zhongshan Hospital Fudan University

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

overall_design: Refer to individual Series


title: The DNA-damage response triggered by the caspase-activated DNAse contributes to inflammation and immune response

city: Freiburg

first: Elham

last: Bavafaye Haghighi

address: Breisacherstr. 153

department: Institut für Medizinische Bioinformatik und Systemmedizin

country: Germany

institute: University Hospital of Freiburg

summary: A DNA-damage response (DDR) occurs upon physical and chemical insults to genomic DNA and drives inflammation. The caspase-activated DNAse (CAD) is a nuclear enzyme that degrades DNA during apoptosis but that can also be activated by sub-lethal signals in the mitochondrial apoptosis pathway. Viral and bacterial agents of disease trigger such sub-lethal signals in infected cells and cause the activation of CAD. We report that activation of CAD causes transient genomic DNA-breaks and a DDR that involves activation of major pro-inflammatory signaling pathways and induction of a gene-expression profile typical of the host response to viral and bacterial infection. Cells deficient in CAD had a reduced inflammatory response to sub-lethal mitochondrial signals and to infection with DNA- and RNA-viruses. CAD-deficient mice infected with influenza A virus showed a reduced inflammatory gene-expression profile in lung tissue, accompanied by an increase in viral titers, changes in pathology and higher weight loss. The results identify CAD as a contributor to host defense to infection and the initiation of the immune response. They further suggest that the induction of genomic DNA-damage is a physiological event in the defense against pathogens.

overall_design: HaCaT iCAD knock out cells (expressing Tir1) reconstituted with a minimal auxin inducible degron (mAID) of human ICAD fused to GFP were stimulated for the indicated time points with auxin (IAA) or DMSO (solvent control) and total RNA was isolated. Four replicates were used for "Sequencing"

first: Abdul

last: Moeed

first: Nico

last: Thilmany

first: Frederic

last: Beck

first: Noemi

middle: S

last: Ortmann

middle: B

last: Haghighi

first: Melanie

last: Börries

first: Rupert

last: Öllinger

first: Roland

last: Rad

first: Susanne

last: Kirschnek

first: Philipp

last: Petric

first: Jonas

last: Hummel

first: Christoph

last: Schell

first: Martin

last: Schwemmle

first: Arnim

last: Weber

first: Georg

last: Häcker


title: UVB Irradiation Differential Regulate miRNAs Expression in Acute Skin Injury

city: chang sha

first: yuan

last: fang

address: 138 TongZiPo road

institute: The Third Xiangya Hospital of Central South Uniiversity

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: to explore the function and mechanism of skin damage induced by ultraviolet irradiation.
The mouse model of UVB irradiation was established. Using miRNA Sequence analysis, the miRNA expression profile of the mouse skin model exposed to UVB radiation and the normal skin mice. GO and Pathway analysis were employed for the prediction of miRNA targets.
Results:Compared with normal skin, a total of 23 miRNAs were screened for significantly different expressions. Among them, 7 miRNAs were up-regulated and 16 were down-regulated in the skin wound tissue of mice exposed to UVB irradiation. The differential expression of miRNA is related to a variety of signal transduction pathways, among which mmu-miR-195a-5p and mitogen-activated protein kinase (MAPK) signal pathway is worthy of attention.
Conclusion: There was significant difference expression of miRNA in the skin tissue of normal mice and the skin injury induced by UVB irradiation. Differential expression of miRNA can be used in the diagnosis and treatment of UVB-induced acute skin injury.

overall_design: miRNA profiles of normal skin and UV damage skin mice. Skin of mice in the experimental groups was irradiated using the SS-03B Ultraviolet Phototherapy Instrument. The irradiation dose used for the groups was 0mJ/cm2    (control), 90 mJ/cm 2   (U90), 180mJ/cm 2    (U180) and 360 mJ/cm 2    (U360) based on results from a preliminary experiment.

first: Yuan

last: Fang

first: Jianda

last: Zhou

first: Ke

last: Cao


title: Functional Changes of CD8+ T Cells in Tumor Microenvironment after SIGLEC15 Blockade [bulk RNA-seq]

first: Zheng

last: Chen

summary: To understand how SIGLEC15 regulates CD8+ T cells in tumor microenvironment, we enriched CD8+ T cells using magnetic beads after tumor digestion. Collected CD8+ T cells were examined with flowcytometry analysis and were further loaded for sequencing analysis.

overall_design: IgG (n=6) and anti-SIGLEC15 (n=6) treated percutaneous tumor grafts were constructed in C57 mice and collected in day19 after 2 weeks of intraperitoneal injection. Collected CD8+ T cells were stained for further examination in flowcytometry analysis. After confirmation, 3 samples of collected cell pelletes were mixed together and loaded for sequencing analysis.


title: Gene expression in primed and chemically reset (cR) naïve human iPSCs, and naïve-converted cells after co-culture with mouse embryonic stem cells

city: Cincinnati

first: Kentaro

last: Iwasawa

state: OH

address: 3333 BURNET AVENUE

department: Division of Gastroenterology, Hepatology and Nutrition

country: USA

institute: Cincinnati Children's Hospital Medical Center

summary: We compared the global transcriptome between mESC co-culture-mediated naïve-like hiPSCs and cR cells together with their parental primed cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSCs cultured in different protocols.

first: Masaki

last: Hideki

first: Yoneyama

last: Yosuke

first: Mizuno

last: Naoaki

first: Bhadury

last: Joydeep

first: Iwasawa

last: Kentaro

first: Takebe

last: Takanori


title: RNA sequencing of mouse sciatic nerve to characterize blood-nerve-barrier gene expression in Nf1 deficient mice

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

summary: The goals of this study is to compare blood-nerve-barrier transcriptome profiling (RNAseq) of wildtype; P2RY14-/-;  Nf1fl/f Dhh Cre and P2RY14-/- Nf1fl/f Dhh Cre mouse sciatic nerves (n=2) per genotype.

overall_design: Sciatic nerves from wildtype; P2RY14-/-;  Nf1fl/f Dhh Cre and P2RY14-/-  Nf1fl/f Dhh Cre were dissected from 4-month old mice. RNA was isolated and submitted for RNA  sequencing at the CCHMC.

first: Jennifer

last: Patritti Cram

first: Nancy

last: Ratner


title: Alternative Splicing of bunched Confers a Dual Role in Hippo Pathway-dependent Growth and Tumorigenesis

status: Public on Aug 07 2024

city: Hangzhou

first: Yanxiao

last: Zhang

state: Zhejiang

address: N0.600, Dunyu Road

department: School of Life Sciences

institute: Westlake University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Alternative splicing is a fundamental mechanism that generates functionally distinct proteins from individual genes, contributing to gene regulation and proteomic diversity. In Drosophila, the bunched (bun) gene, a member of the TSC-22 domain gene family, undergoes alternative splicing, yielding diverse protein isoforms involved in crucial biological processes. Nevertheless, the specific roles and regulatory mechanisms of each isoform remain elusive. Here, we employed CRISPR/Cas9 technology to introduce targeted deletions within the endogenous locus of the bun gene, resulting in the removal of either long or short isoforms. We discovered that the short isoforms demonstrated a growth-suppressive role, whereas the long isoforms exhibited a growth-promoting effect. Surprisingly, the long isoforms exhibited a remarkable dual functionality, as both deletion and amplification of long isoform expression impede the excess growth induced by Hippo pathway inactivation. Mechanistically, ectopically expressed Bun long isoforms act as the transcriptional suppressor by competitively binding to targets' promoter regions in conjunction with Yorkie/Scalloped (Yki/Sd), thereby inhibiting its transcriptional outputs and ultimately leading to the growth suppression. These findings unveil the intricate interaction between distinct spliced isoforms of Bun and oncogenic outcomes, highlighting Bun long isoforms as the critical transcription suppressor regulating Hippo pathway inactivation-mediated growth and tumorigenesis in Drosophila.

overall_design: BunA with HA tag was ectopically expressed under the promotor of nub-Gal4, and the anti-HA antibody was used to enrich the DNA fragments bound by BunA

first: Pengjuan

last: Guo

first: Yuxiao

last: Niu

first: Xianjue

last: Ma


title: Effects in gene expression of human induced pluripotent stem cells (hiPSCs) co-cultured with mouse embryonic stem cells (mESC)

summary: To investigate the mechanism of naïve-conversion in the neighboring hiPSCs via mRNA transfer from mESCs, the hiPSCs were cultured with or without mESCs. We then performed gene expression profiling analysis using RNA-seq data obtained from two different hiPSCs co-cultured with mESCs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSCs co-cultured with mESCs.

first: Zhang

last: RanRan

first: Adam

last: Mike


title: Distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes of Mycoplasma pneumoniae

city: Guangzhou

first: Bingxue

last: Hu

state: China Mainland (PRC)

address: Guangzhou 510700

institute: Vision MedicalsCo., Ltd.

summary: To unravel distinct pattern of metagenomic surveillance and respiratory microbiota between Mycoplasma pneumoniae (M. pneumoniae) P1-1 and P1-2 and explore the impact of COVID-19 pandemic on epidemiological features

overall_design: In this study, we analyzed metatranscriptomics 174 M. pneumoniae positive cases with P1-1 or P1-2 genotype.

first: Hailong

last: You

first: Bin

last: Yang

first: Huifang

last: Liu

first: Wenjiao

first: Wencai

last: Wu

first: Yong

first: Hongyan

last: Zou

first: Sijia

last: Hao

first: Yunping

last: Xiao

first: Teng

last: Xu

first: Yanfang

last: Jiang


title: CD4+ CAR-T cell exhaustion associated with early relapse of multiple myeloma after BCMA CAR-T cell therapy II

city: Seattle

first: Lawrence

last: Fong

state: Washington

address: 1100 Fairview Ave N

department: Immunotherapy Integrated Research Center, Translational Science and Therapeutics Division

institute: Fred Hutch Cancer Center

summary: Multiple myeloma is characterized by frequent clinical relapses following conventional therapy. Recently, chimeric antigen receptor T (CAR-T) cells targeting B-cell maturation antigen (BCMA) has been established as a treatment for patients with relapsed or refractory disease. However, while >70% of patients initially respond to this treatment, clinical relapse and disease progression occurs in most cases. Recent studies showed persistent expression of BCMA at the time of relapse, indicating that immune intrinsic mechanisms may contribute to this resistance. While there were no pre-existing T cell features associated with clinical outcomes, we found that patients with a durable response to CAR-T cell treatment had greater persistence of their CAR-T cells compared to patients with transient clinical responses.  They also possessed a significantly higher proportion of CD8+ T effector memory cells. In contrast, patients with short-lived responses to treatment have increased frequencies of cytotoxic CD4+ CAR-T cells. These cells expand in vivo early after infusion but express exhaustion markers (HAVCR2 and TIGIT) and remain polyclonal. Finally, we demonstrate that non-classical monocytes are enriched in the myeloma niche and may induce CAR-T cell dysfunction through mechanisms that include TGFβ. These findings shed new light on the role of cytotoxic CD4+ T cells in disease progression after CAR-T cell therapy.

overall_design: Bone marrow aspirates and peripheral blood samples were obtained from multiple myeloma patients pre- and post- anti-BCMA CAR T treatment and from healthy donors undergoing hip replacement surgery. Multiple myeloma patients were enrolled in clinical trials NCT02658929, NCT03274219 and NCT03430011. Bone marrow and PBMC samples were harvested prior to CAR T infusion and at 14days, 30days, 90days, 180days, 270days and 360days post infusion for analysis when available.

first: Guy

last: Ledergor

first: Zenghua

last: Fan

first: Kai

first: Elizabeth

last: McCarthy

first: Axel

last: Hyrenius Wittsten

first: Alec

last: Starzinski

first: Hewitt

last: Chang

first: Serena

last: Kwek

first: Alexander

last: Cheung

first: Sophia

last: Bylsma

first: Erik

last: Hansen

first: Jeffrey

last: Wolf

first: Sandy

middle: W

last: Wong

first: Nina

last: Shah

first: Kole

last: Roybal

first: Thomas

last: Martin

first: Jimmie

last: Ye


title: Evaluating the toxicity of two endocrine disrupting chemicals, BPA and TBBPA using a larval zebrafish transcriptomic approach

city: Saskatoon

first: Morgan

last: Kirzinger

state: Saskatchewan

address: 110 Gymnasium Place

country: Canada

institute: National Research Council Canada

summary: We use a larval zebrafish model to assess the transcriptomic alterations caused by sub-phenotypic concentrations of two endocrine disrupting drugs: BPA and TBBPA.

overall_design: We use two approaches to evaluate potential toxicological mechanisms; we determine differentially expressed genes, and compare serial dilutions of each drug to the vehicle control and we determine the Point of Departure (POD) for each drug by modelling gene expression changes as continuous systems.

first: Michael

middle: G

last: Morash

first: Lee

middle: D

last: Ellis


title: Voluntary exercise sensitizes cancer immunotherapy via collagen degradation-orchestrated inflammatory tumor immune microenvironment

city: Nanjing

first: Jie

last: Mei

state: Jiangsu

address: No. 101, Longmian Road

institute: Nanjing Medical University

summary: Physical activity reduces cancer-associated mortality through multiple mechanisms, including tumor immune microenvironment (TIME) reprogramming. However, whether and how physiological interventions promote anti-tumor immunity and immunotherapy remains elusive. Here we report that clinically relevant voluntary exercise promotes muscle-derived exosomal miR-29a-3p for extracellular matrix (ECM) degradation in patients and mouse models with multiple types of cancer, thereby permitting immune cell infiltration and immunotherapy. Mechanistically, an unbiased screening identified exercise-responsive exosomal miR-29a-3p that targets tumor cell and cancer associated fibroblasts to downregulate COL1A1 and reduce ECM. State-of-the-art techniques including cytometry by time-of-flight (CyTOF) demonstrated miR-29a-3p-induced TIME remodeling and immune cell infiltration. Combining immunotherapy with voluntary exercise or miR-29a-3p further increased the anti-tumor efficacy in preclinical models. Clinically, miR-29a-3p was correlated with degraded ECM and T-cell infiltration in various cancer types in patients, and correlated with immunotherapy responders. Our work reveals the novel predictive value of miR-29a-3p for immunotherapy, provides mechanistic insights into exercise-promoted anti-cancer immunity, and highlights the therapeutic potential of voluntary exercise in immunotherapy.

overall_design: To identity differentially expressed miRNAs in circulating extracellular vesicles in serum from NSCLC patients with and without exercise habit, total RNA of circulating extracellular vesicles were submitted for miRNA-seq .

first: Yaying

last: Sun


title: HuPSA and MoPSA Atlases Reveal Novel Cell Populations and Lineage Plasticity in Prostate Cancer at Single-Cell Level

city: New Orleans

last: Lan

state: LA

address: 533 Bolivar Street, CSRB Room 623E

department: School of Medicine

institute: LSUHSC

summary: Androgen deprivation therapy has improved patient survival. Nevertheless, treatment resistance inevitably emerges due to the complex interplay of tumor heterogeneity and lineage plasticity. We integrated scRNAseq data from multiple studies, comprising both publicly available cohorts and data generated by our research team, and established the HuPSA (Human Prostate Single cell Atlas) and MoPSA (Mouse Prostate Single cell Atlas) datasets. Through unsupervised clustering and manual annotation, we found that both atlases consisted of previously known cell clusters including prostate adenocarcinoma (AdPCa), neuroendocrine prostate cancer (NEPCa), stromal, and immune cell populations. Our analysis also unearthed the less described populations including MMP7+ prostate club cells and two novel lineage plastic cancerous populations, namely Progenitor-like and KRT7. Immunohistochemical staining analysis confirmed the presence of these populations in both human and mouse PCa tissues, reinforcing their significance in PCa pathobiology. Furthermore, employing HuPSA based deconvolution, we scrutinized 877 high-quality human PCa bulk RNAseq samples and reclassified them into different molecular subtypes, including the newly discovered KRT7 and Progenitor-like categories. Moreover, employing supervised dimensional reduction and label transferring techniques, we projected the scRNAseq data derived from C4-2B xenograft tumors onto HuPSA. Our analysis effectively identified the diverse subpopulations within the tumor, including C4-2B derived AdPCa and NEPCa cells as well as the murine cells in the tumor microenvironment. We launched the “PCaAtlas” app (https://pcatools.shinyapps.io/ProAtlas_dev/) for users to visualize genes expression in re-classified human prostatic tissue samples. In conclusion, our study has successfully integrated multiple scRNAseq datasets and made these data easily accessible to researchers. Our results elucidate a roadmap of PCa progression, showcasing the development of heterogeneous populations and the involvement of lineage plasticity. This understanding holds promise for guiding the development of precision medicine in PCa field. Additionally, the HuPSA and MoPSA provide invaluable blueprints for analyzing and interpreting user-generated PCa single-cell RNAseq data.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: C4-2B xenograft and TRAMP tumor tissues were harvested and dissociated using “Tumor Dissociation Kit, human, #130-095-929” and “Tumor Dissociation Kit, mouse, #130-096-730” from Miltenyi Biotec. The dead cells were removed by “Dead Cell Removal Kit, #130-090-101” from Miltenyi Biotec. The red blood cells were removed by “Red Blood Cell Lysis Solution, # 130-094-183” from Miltenyi Biotec. The cDNA libraries were constructed using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1. The resulting cDNA was fragmented, processed, and size selected. Adaptors were ligated and dual indexes were attached via PCR. The libraries were cleaned up and assessed for quality with the Agilent TapeStation D5000 High Sensitivity Kit. The libraries were quantitated with qPCR (NEBNext Library Quant Kit for Illumina, Bio-rad CFX96 Touch Real-Time PCR) and normalized to 1.5 pM and pooled. The library pool was denatured and diluted to approximately 300 pM. A library of 1.5 pM PhiX was spiked in as an internal control. Paired-end sequencing was performed on an Illumina NovaSeq 6000.

first: Cheng

last: Siyuan

first: Li

last: Lin

first: Yu

last: Xiuping


title: CD4+ CAR-T cell exhaustion associated with early relapse of multiple myeloma after BCMA CAR-T cell therapy

first: Lawrence

last: Fong


title: GOLM1 dictates acquired Lenvatinib resistance by a GOLM1-CSN5 positive feedback loop upon EGFR signaling activation in hepatocellular carcinoma

first: Mengyuan

last: Wu

address: 180 Fenglin Road

institute: Zhongshan hospital, Fudan university

summary: Lenvatinib is a multiple receptor tyrosine kinases inhibitor (TKI) authorized for first-line treatment of hepatocellular carcinoma (HCC). However, Lenvatinib resistance is common in HCC clinical treatment, highlighting the urgent need to understand mechanisms of resistance. Here, we identified Golgi membrane protein 1 (GOLM1), a type II transmembrane protein originally located in the Golgi apparatus, as a novel regulator of Lenvatinib resistance. We established Lenvatinib resistance in human HCC cell lines PLC/PRF/5. Through RNA-seq, we found that GOLM1 was significantly upregulated, which was further validated in patients derived tumor tissue and peripheral blood. GOLM1 overexpression contributes to Lenvatinib resistance and HCC progression in vitro and in vivo. Mechanistically, GOLM1 upregulates CSN5 expression through EGFR-STAT3 pathway. Reversely, CSN5 deubiquitinates and stabilizes GOLM1 protein by inhibiting ubiquitin-proteasome pathway of GOLM1. Collectively, our data demonstrate that GOLM1 is one of the key driver of Lenvatinib resistance in HCC and depicts a molecular network in Lenvatininb resistant HCC cells.

overall_design: To investigate the petential molecule reponsible for Lenvatinib resistance,  PLC/PRF/5 cells were cultured with increasing doses of Lenvatinib (Selleck) at 20 μmol/L initially.The cell culture media was replaced every 48 h until the cells have occupied 90% of the culture dish, at which point they were passaged and replated. After passage, the concentration of Lenvatinib was increased by 0.5 mmol/L until PLC/PRF/5 cells proliferated rapidly at 40 mmol/L. The resistant cell strains were named PLC/PRF/5 LR.

first: Peiyi

last: Xie


title: Impact of yihO/Q deletion in O-Antigen capsule formation, environmental stress mitigation, and intracellular virulence, survival and replication of Salmonella Typhimurium

city: Iksan

first: Khristine Kaith

middle: Sison

last: Lloren

address: 79 Gobong-ro

country: South Korea

institute: Jeonbuk National University

summary: This study characterized the involvement of yihO and yihQ of yih operon associated with O-antigen capsule formation, in phenotypic characteristics, intracellular survival, and virulence in Salmonella Typhimurium (ST). Bacterial fitness screening of the ∆yihO, ∆yihQ, and ∆yihO/Q ST mutants showed impairment in biofilm formation, motility, starvation, and stress survival. In vitro studies using phagocytic and non-phagocytic cells revealed a significant decrease in bacterial invasion and intracellular replication, particularly by the ∆yihO and ∆yihO/Q ST which correlated with the lack of proliferation ability in vivo as observed in the liver and spleen colonization. Transcriptome analysis of the ∆yihO mutant further revealed the downregulation of several genes associated with key processes such as flagellar assembly, Salmonella infection, and T3SS protein secretion such as SPI-1 and SPI-2. This evidence expands the role of yihO as an essential gene for maintaining Salmonella’s environmental resilience and virulence.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: To investigate the possible regulatory role of yihO in Salmonella Typhimurium, the gene was deleted by lambda red recombination method; differentially expressed gene analysis was performed against the Salmonella Typhimurium wild-type using data obtained from RNA-seq

first: John Hwa

last: Lee


title: Effect of pH modulation on cardiomyocyte differentiation

city: Taipa

first: Guokai

last: Chen

address: University of Macau E12-3060

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

summary: To investigate the impact of pH modulation on cell fate determination during mesendoderm differentiation using RNA-Seq data.

overall_design: Gene expression profiles on day 0, 3, 5, 7, 11 of mesendoderm spontaneous differentiation or WNT inhibitor-driven cardiac differentiation under pH modulation

first: Weiwei

last: Liu


title: Transcriptome modulation by long duration giredestrant treatment and the effect of GPX4 CRISPR KO in MCF7 cells

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

summary: In the giredestrant resistance/sensitization CRISPR Ko whole genome screen in MCF7 cells, ferroptosis regulator GPX4 comes out as top sensitization hits. We like to see how GPX4 KO changes gene expression profiles, and how giredestrant alone and the combination of GPX4 KO and giredestrant long duration treatment modulate the transcriptome

overall_design: Bulk RNA-Seq

first: Ciara

last: Metcalfe

first: Jane

last: Guan

first: Jinchu

last: Vijay


title: LAG3 and PD1 synergize on CD8+ T cells to drive T cell exhaustion and hinder autocrine IFN gamma-dependent anti-tumor immunity

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: 5051 Centre Avenue

department: Immunology

institute: University of Pittsburgh

summary: Combined nivolumab (anti-PD1) and relatlimab (anti-LAG3) have shown enhanced effectiveness in melanoma patients. However, how these two receptors work together to hinder anti-tumor immunity remains unclear. Our study demonstrates that PD1/LAG3-deficient CD8+ T cells with more effectively clearing tumors  and survive longer in melanoma mouse models. These PD1/LAG3-deficient CD8+ T cells have unique transcriptional profiles, broad TCR clonality, and enriched effector-like and interferon-responsive genes, leading to increased IFN gamma release indicating functionality. PD1 and LAG3 together drive T cell exhaustion, with a significant impact on TOX modulation. Mechanistically, autocrine IFN gamma signaling is crucial for enhancing anti-tumor immunity in PD1/LAG3-deficient CD8+ T cells, providing insights into the enhanced efficacy of combined PD1 and LAG3 targeting.

overall_design: We employed single-cell RNA sequencing to profile CD8 cells from polyclonal/pMEL mice, both with and without single or double deficiencies of PD1 or LAG3. This comprehensive approach aimed to gain a deeper understanding of the enhanced efficacy observed in the melanoma model.

middle: P

last: Andrews

first: Dario

middle: A

last: Vignali


title: Tumoral Interferon Beta Induces an Immune-Stimulatory Phenotype in Tumor-Associated Macrophages in Melanoma Brain Metastases

city: Heidelberg

first: Julia

last: Gellert

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

summary: Type I interferons (IFNs) are immune-stimulatory cytokines involved in antiviral and antitumor immune responses. They enhance the efficacy of immunogenic anticancer therapies by activating both innate and adaptive intratumoral immune cell populations. Macrophages are one of the most abundant innate immune cells in the immune microenvironment of melanoma brain metastases (MBMs) and can exert potent immune-suppressive functions. Here, we investigate the potential of tumoral type I IFNs to re-polarize tumor-associated macrophages (TAMs) in a murine melanoma mouse model. We describe a pro-inflammatory and M1-like TAM phenotype induced by tumoral IFNβ and identify a myeloid type I interferon-response signature associated with a high M1/M2 TAM ratio and an increased overall survival in previously irradiated patients with MBMs. We provide evidence that tumoral IFNβ supports an effective antitumor immune response by re-educating immune-regulatory TAMs. These findings uncover type I interferon-dependent therapies as a potential macrophage-targeting therapeutic approach and provide a rationale for combining radiotherapy with concomitant immunotherapy to improve treatment response in patients with MBM.

overall_design:
To investigate the effects of tumoral IFNβ on the phenotype of M2-like TAMs in a murine MBM model, we generated bone marrow-derived macrophages (BMDMs) and polarized them into a M2-like polarization state (n=3 mice per condition).
M2-like BMDMs were treated with cell culture supernatant containing tumoral IFNβ from Dox-treated YUMM5.2 Ifnb1eGFP cells, recombinant IFNβ, cell culture supernatant from Doxycycline (Dox)-treated YUMM5.2 eGFP control cells or left untreated. Cell culture supernatant was obtained from the YUMM5.2 cell line which was transduced with a lentiviral vector containing a tetracycline response promotor followed by the Ifnb1 and eGFP (or only the eGFP gene as control) allowing Dox-dependent tumoral IFNβ secretion.
After 72h, we performed bulk RNA sequencing analysis of the BMDMs (4 conditions, 3 biological replicates each).

first: Theresa

last: Bunse


title: eIF4E-independent translation is largely eIF3d-dependent

first: Mykola

last: Roiuk

address: Im Neuenheimer Feld 580

institute: DKFZ

summary: We study here how mRNAs are translated in an eIF4E1-independent manner by blocking eIF4E1 using a constitutively active version of eIF4E-binding protein (4E-BP). Via ribosome profiling we identify a subset of mRNAs that are still efficiently translated when eIF4E1 is inactive. We find that these mRNAs preferentially release eIF4E1 when eIF4E1 is inactive and bind instead to eIF3D via its cap-binding pocket. eIF3D then enables these mRNAs to be efficiently translated due to its cap-binding activity.

overall_design:
To see which transcripts are translated in an eIF4E-independent manner, we performed ribosome profiling in HeLa wt cells overexpressing either the empty vector or constitutively-active form of 4E-BP1. The experiment was performed in duplicates. Ribosome-protected footprints as well as total RNA were sequenced.
To see if resistant transcripts are released from eIF4E upon 4E-BP1 overexpression, we performed RIP experiment with antibodies specific to eIF4E1. The IP-ed and total input fractions were sequenced. The experiment was performed in duplicates.

first: Aurelio

last: Teleman


title: Transcriptome analysis of differentially expressed genes (DEGs) induced by RBSDV between the two NILs (NIL-R and NIL-S

city: Beijing

first: Suining

last: Deng

address: 2 West Yuanmingyuan r.d.

institute: China Agricultural Univesity

summary: In the study, RBSDV accumulation was detected in NIL-S starting from 16 days post inoculation (dpi) and increased linearly thereafter to reach a high level. Concurrently, the viral S10 encoding the coat protein exhibited a dramatic accumulation in NIL-S but not in NIL-R, as did the viral S7-1. We performed RNA-seq analysis at 16 dpi between NIL-S and NIL-R. The differentially expressed genes (DEGs) were identified based on the criteria of fold-change > 2 and P < 0.05. Compared to NIL-R, NIL-S exhibited 24 downregulated and 21 upregulated DEGs. Gene Ontology (GO) term analysis revealed that these DEGs are mainly enriched in one molecular process: oxidoreductase activity, and in three biological processes: biology, oxidation-reduction, and single-organism. KEGG analysis demonstrated significant DEG enrichment in three pathways: photosynthesis-antenna proteins, fatty acid elongation, and diterpenoid biosynthesis.

overall_design: To invesigate the ZmGDIα-hel mediated  recessive resistant to maize rough dwarf disease, we performed RNA-Seq between NIL-S (with ZmGDIα) and NIL-R (with ZmGDIα-hel).

first: Mingliang

last: Xu

first: Siqi

last: Jiang


title: The transcriptional regulator oxtR and its involvement in oxygen stress response in T. denticola

city: Tokyo

first: Kazuyuki

last: Ishihara

address: 2-1-14 Kanda-Misakicho, Chiyoda-ku

department: Microbiology

country: Japan

institute: Tokyo Dental College

summary:
Treponema denticola has been strongly implicated in the pathogenesis of chronic periodontitis. Previously, we reported increased expression of TDE_0259 (oxtR), which exhibits similarities with the multiple-antibiotic resistance regulator (marR)-like gene in the bacteriocin ABC transporter gene-deficient mutant, which altered susceptibility to antimicrobial agents. Therefore, we investigated the function of oxtR in T. denticola using an oxtR-deficient mutant.
We observed increased OxtR expression upon oxygen exposure. The growth rate of the bacterium was unaffected by the inactivation of oxtR. We observed a relative increase in the expression of genes associated with iron-sulfur cluster-binding proteins, flavodoxin, oligopeptide/dipeptide ABC transporters, heat shock proteins, DNA helicase, iron compounds, ABC transporters, and lipoproteins. The oxtR mutant exhibited an increased minimum inhibitory concentration against ofloxacin. In addition, the mutant showed a slightly faster growth rate than that of the wild type under oxygen stress. Our findings also suggested that OxtR may regulate the operon by binding to a potential promoter region. The oxygen-sensing regulator oxtR plays a role in regulating the expression of a potential ferredoxin, which may contribute to the response to oxygen-induced stress in T. denticola.

sample_organism:
Treponema denticola
Treponema denticola ATCC 35405

overall_design: Comparison of 2 strains of T. denticola. Treponema denticola ATCC 35405 and NY-7 were cultured in TYGVS medium for 24-48 h. Profile of gene expression of T. denticola NY-7 was compared to that of ATCC 35405.

first: Yumi

last: Numata

first: Yuichiro

last: Kikuchi

first: Toru

last: Sato

first: Kazuko

last: Okamotro-Shibayama

first: Yutaro

last: Ando

first: Eitoyo

last: Kokubu


title: Deterioration of multi-level 3D genome organization during breast cancer progression

city: Oslo

first: Roberto

last: Rossini

address: Blindernveien 31

country: Norway

institute: University of Oslo

summary: Breast cancer progression entails intricate, multi-level alterations in genome organization and expression. To gain insights into the modifications in chromatin's three-dimensional (3D) structure during breast cancer progression, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) remain largely stable, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observed a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identified a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene becomes inserted into a highly active region on chromosome 10. This insertion event leads to the formation of de novo enhancer contacts and activation of the oncogene, illustrating how structural variants can interact with the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the degradation of genome organization at multiple scales during breast cancer progression revealing the complex interplay between genomic structure and oncogenic processes.

overall_design: We sequenced the transcriptome of MCF10A, MCF10AT1, and MCF10Ca1a cell lines to investigate changes in gene expression during breast cancer progression.

first: Mohammadsaleh

last: Oshaghi

first: Maxim

last: Nekrasov

first: Aurélie

last: Bellanger

first: Renae

last: Domaschenz

first: Yasmin

last: Dijkwel

first: Philippe

last: Collas

first: David

last: Tremethick

first: Jonas

last: Paulsen


title: Reevaluation by CRISPR-Cas9 approach reveals multiple lincRNAs dispensable for pluripotency maintenance and SNORA73 essential for pluripotency exit

first: Jiajian

last: Zhou

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

institute: Southern Medical University

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

overall_design: Refer to individual Series

first: Yangming

last: Wang

first: Huiqing

last: Cao

first: Zhen

last: Li


title: A Repressive Type of TEAD4 Condensation and Engineering a Glue Peptide Therapy Against Cancer [Cut&Tag_T4]

city: shanghai

first: yang

last: tang

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Transcriptional factors (TFs) act as central determinants to coordinate cell death and survival by differentially modulating gene expression. Here, we systematically identified many TFs including TEAD4 forming condensates in stressed cells. In sharp contrast to YAP-induced transcription-activating condensation of TEAD4, we found co-factors such as VGLL4 and RFXANK could alternatively induce repressive condensation of TEAD4 to trigger cell death. Illustrated by VGLL4, we mechanistically revealed that the heterotypic interactions between TEAD4 with VGLL4 favors its oligomerization and assembly of large condensates to manifest a nonclassical inhibitory function of this transcription factor, i.e., causing DNA/chromatin to be aggregated and entangled, which eventually impede gene expression. Based on these findings, we engineered a linker peptide (GLUP) to selectively “glue” TEAD4 molecules together, therefore forcefully driving its repressive condensation against YAP-induced activation. This glue peptide displayed a strong antitumor effect via inhibition of TEAD4-related gene transcription. Collectively, this work revealed a new type of phase separation, i.e., repressive condensation of TFs, and revealed how cofactor-induced differential condensation orchestrate opposite functions of a given TF, and further developed a new class of antitumor strategy by artificially inducing repressive condensation.

overall_design: Cut&Tag assay for H3K27me3 antibody in WT or TEAD4 KO HGC-27 cells treated with or without GLUP peptide

first: Yang

last: Tang

first: Liwei

last: An

first: Hui

last: Zhang


title: Gene expression profiles of human Natural Killer Cells, unstimulated and stimulated with IPH6501, a tetraspecific NK cell engager (NKCE).

city: Marseille

first: Eric

last: Vivier

state: PACA

address: 117 Avenue de Luminy BP 30191

country: France

institute: Innate Pharma

summary: The impact of IPH6501 treatment on the transcriptome of blood NK cells was dissequed using scRNA seq analysis. Unsupervised analysis of human blood NK cells revealed significant transcriptomic changes across NK1, NK2, and NK3 cell subsets following in vitro stimulation by CD20-NKCE-IL2v, indicating that treatment affect all NK cell subsets. Stimulation with the CD20-NKCE-IL2v led to the emergence of another NK cell cluster characterized by a signature resembling cytokine-induced memory-like (CIML) NK cells similar to that found in NK cells activated by IL-2/IL-15/IL-12/IL-18. This population was observed at both 4- and 24-hours post-stimulation.

overall_design: Human NK cells, purified from 4 healthy donor PBMC, were activated for 4h and 24h in the presence of the murine huCD20-B16F10 target cells, with 0.1 μg/mL of CD20-NKCE-IL2v (IPH6501), or without treatment (unstimulated).

first: Olivier

last: Demaria

first: Constance

last: Vagne

first: Justine

last: Galluso


title: Reevaluation by CRISPR-Cas9 approach reveals multiple lincRNAs dispensable for pluripotency maintenance and SNORA73 essential for pluripotency exit (RNA-Seq)

summary: Many lincRNAs have been identified as essential regulators for ESC pluripotency through siRNA-based screening. However, the biological and molecular functions of the large intergenic noncoding RNAs (lincRNAs) remain unclear. Here, we employed CRISPR/Cas9-mediated knockout technology to explore the functions of 8 previously annotated lincRNAs in ESCs. Unexpectedly, it was found that most lincRNAs are dispensable for pluripotency maintenance, cloning formation ability, proliferation and apoptosis in ESCs when we disrupted these lincRNAs individually or in combinations. Single-cell transcriptomic analysis of a set of lncRNA knockout ESCs showed consistent results, indicating that previously observed functions of lincRNAs on ESC pluripotency maintenance may be due to off-targeted effects. Interestingly, deletion and transcriptional repression of linc1343 disrupts embryoid body (EB) differentiation in ESC. Notably, GM17300 and two small RNAs (Snora73a, Snora73b) derived from the lnc1343 locus are highly expressed in ESCs. Further overexpression of Snora73a and Snora73b in linc1343 knockout cells rescue the phenotype, suggesting that snoRNAs derived from linc1343 are the responders for EB differentiation. Taken together, our results demonstrate the divergent effects of lincRNAs on regulating ESC pluripotency and EB differentiation.

overall_design: Comparative gene expression profiling analysis on WT and KO of 8 selected lncRNAs in mES cells.


title: The Interferon γ Pathway Enhances Pluripotency and X-Chromosome Reactivation in iPSC Reprogramming

city: Barcelona

first: Mercedes

last: Barrero

address: Dr. Aiguader, 88

institute: Centre for Genomic Regulation


title: Reevaluation by CRISPR-Cas9 approach reveals multiple lincRNAs dispensable for pluripotency maintenance and SNORA73 essential for pluripotency exit (scRNA-Seq)

overall_design: We pooled 15 KO types and WT ES cells with 8 nt barcodes at the end of GFPs for 16 days co-culture in Lif medium and then subjected to single-cell RNA sequencing.


title: Bulk RNA-seq analysis of PDAC tumor Cells

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

summary: Orthotopic PDAC tumor were established with KPC and KPSC cells, respectively. After about 10-14 days, PDAC cells with Setd2-KO and Setd2-WT were sorted from orthotopic PDAC tumor by DPAI-CD45.2-Pdpn-Epcam+, and used for RNA preparation.

overall_design: For RNA preparation, PDAC tumor cells were sorted and collected. RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit (Illumina) using 5 μg of total RNA, according to manufacturer’s instructions.

first: Niu

last: Ningning

first: Xue

last: Jing


title: Landscape of super-enhancer-associated lncRNAs in hepatocellular carcinoma [lncRNA-seq]

city: Guangzhou

first: Li

last: Peng

address: No. 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital

summary:
Super-enhancer (SE) plays a vital role in the determination of cell identity and cell fate through the control of cell- or tissue-specific gene regulation. Upregulated expression of coding genes is frequently associated with SE. However, the transcription dysregulation driven by SE, from long non-coding RNAs (lncRNAs) viewpoint, remains unclear. Here, SE-associated lncRNAs in HCC were comprehensively screened.
The result shows that pol2-mediated transcription of SE-associated lncRNAs is more sensitive to JQ1 treatment in a genome-wide manner.

overall_design: Examination of lncRNA expression in HCC cells with the treatment of JQ1.

first: Xiao-Qing

last: Yuan


title: Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at the single-cell level

status: Public on Aug 06 2024

city: Napoli

first: Maria Ina

last: Arnone

address: Villa Comunale 1

department: Biology and Evolution of Marine Organisms

country: Italy

institute: Stazione Zoologica Anton Dohrn

summary: We use multi-omics (ATAC-seq, single cell RNA-seq and differential bulk RNA-seq) to increase resolution of the sea urchin posterior gut GRN for the cells expressing the ParaHox gene Sp-Pdx1.

overall_design: Generation, analysis and integration of ATAC-seq,  single cell and bulk RNA-seq data of 2 dpf Strongylocentrotus purpuratus embryo to draft gut GRN. Bulk RNAseq data was published previously and is not included here.

first: Danila

last: Voronov

first: Periklis

last: Paganos

first: Marta

last: Magri

first: Claudia

last: Cuomo

first: Ignacio

last: Maeso

first: Jose

middle: L

last: Gómez-Skarmeta

first: Maria

middle: I


title: Unique structural features of the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex [RNA-seq]

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

summary: The human NuA4/TIP60 co-activator complex, a fusion of the yeast SWR1 and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4/H2A/H2A.Z to play crucial roles regulating gene expression and maintaining genome stability. Our cryo-EM studies show that within the NuA4/TIP60 complex, the EP400 subunit serves as an architectural scaffold holding the different functional modules in specific positions and giving rise to a novel arrangement of the ARP module. EP400 interacts with the TRRAP subunit using a footprint that overlaps with that of the SAGA acetyltransferase complex, thereby preventing the formation of a hybrid complex. Loss of the TRRAP subunit leads to mislocalization of NuA4/TIP60, resulting in the redistribution of H2A.Z and its acetylation across the genome, emphasizing the dual functionality of NuA4/TIP60 as a single macromolecular assembly.

overall_design: To investigate the effect of the Delta-TRRAP mutation in the EP400 subunit of TIP60, we generated clonal K562 cell lines with the inducible acute degradation tag (dTAG) at the endogenous EP400 locus, rescued by stable exogenous expression of either WT (control) or Delta-TRRAP EP400. We degraded the endogenous EP400 and evaluated the effect of the EP400 mutation compared to the WT control on steady-state transcription by RNA-seq (poly-A). We generated 3 biological replicates for each rescue condition, for a total of 6 libraries.

first: Amel

last: Mameri

last: Cattoglio

first: Jacques

last: Côté


title: A Critical Role of KCNQ1 in Human β-Cell Developmen

city: Berlin

first: Zhimin

last: Zhou

address: Robert-Rössle-Straße 10

institute: MDC

summary: We report the KCNQ1 mutation (permant neonatal diabete patient's KCNQ1 homozygous point mutation) negatively affected the expression of the metabolic genes of β-like cells, especially at their late stage.

overall_design: We examine differently expressed genes present in both mutated colonies and were also differently expressed from wild-type (WT) and unmodified-control (UC) of hESCs_H1-derived pancreatic β cell-like organoids.

first: Zsuzsanna

last: Izsvak

first: Amit

last: Pande


title: Unique structural features of the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex [ChIP-seq]

overall_design: To investigate the effect of the Delta-TRRAP mutation in the EP400 subunit of TIP60, we generated clonal K562 cell lines with the inducible acute degradation tag (dTAG) at the endogenous EP400 locus, rescued by stable exogenous expression of either WT (control) or Delta-TRRAP EP400. We degraded the endogenous EP400 and evaluated genome-wide the effect of the EP400 mutation compared to the WT control on H2A.Z incorporation and acetylation by ChIP-seq. We generated a total of 12 libraries, including 2 biological replicates of inputs (controls), H2A.Z and H2A.Zacetyl pull-downs for each rescue condition (WT or Delta-TRRAP EP400).


title: Dynamic methylation and expression of alternative promoters for oestrogen receptor alpha in cell line models of fulvestrant resistance

city: Lund

first: Helena

last: Persson

address: Scheelevagen 2

department: Dept of Clinical Sciences, Oncology

country: Sweden

institute: Lund University

type: Methylation profiling by high throughput sequencing

summary: Oestrogen receptor alpha (ER, gene symbol ESR1) is the most important prognostic and treatment-predictive biomarker in breast cancer. Drugs targeting oestrogen and the ER for endocrine therapy of breast cancer include aromatase inhibitors, the selective ER modulator tamoxifen and the selective ER degrader fulvestrant. Tumours can develop resistance to endocrine therapy through several mechanisms, which is often linked to altered expression of the ER. To investigate the role of promoter methylation in regulation of ER expression, we used bisulfite sequencing to measure methylation at CpG sites in alternative ER promoter regions for six cell line models of fulvestrant resistance. Both CpG methylation and expression of alternative first exons changed dynamically with striking differences between cell lines that had stable or unstable resistance upon fulvestrant withdrawal. Methylation at some CpG sites was strongly negatively correlated with expression of specific first exons. In a breast tumour cohort, higher relative expression of upstream alternative first exons was associated with worse prognosis in post-menopausal women with ER-positive tumours who received endocrine therapy.

overall_design: Bisulfite sequencing of 12 genomic regions near alternative first exons of ESR1 in six cell line models of fulvestrant resistance including sensitive parental cells, resistant sublines and resistant sublines cultured in the absence of fulvestrant.

first: Juliane

last: Albrecht

first: Mirjam

last: Müller

first: Völundur

last: Hafstad


title: A transient brain endothelial translatome response to endotoxin is associated with mild cognitive changes post-shock in young mice

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary: Sepsis-associated encephalopathy (SAE) is associated with increased risk of long-term cognitive impairment. SAE is driven, at least in part, by brain endothelial dysfunction in response to systemic cytokine signaling. However, the mechanisms driving SAE and its consequences remain largely unknown. Here, we performed translating ribosome affinity purification and RNA-sequencing (TRAP-seq) from the brain endothelium to determine the transcriptional changes after an acute endotoxemic (LPS) challenge. LPS induced a strong acute transcriptional response in the brain endothelium that partially correlates with the whole brain transcriptional response and suggested an endothelial-specific hypoxia response. Consistent with a crucial role for IL-6, loss of the main regulator of this pathway, SOCS3, leads to a broadening of the population of genes responsive to LPS, suggesting that an overactivation of the IL-6/JAK/STAT3 pathway leads to an increased transcriptional response that could explain our prior findings of severe brain injury in these mice. To identify any potential sequelae of this acute response, we performed brain TRAP-seq following a battery of behavioral tests in mice after apparent recovery. We found that the transcriptional response returns to baseline within days post-challenge, but reductions in gene expression regulating protein translation and respiratory electron transport remained. We observed that mice that recovered from the endotoxemic shock showed mild, sex-dependent cognitive impairment, suggesting that the acute brain injury led to sustained effects. A better understanding of the transcriptional and non-transcriptional changes in response to shock is needed in order to prevent and/or revert the devastating consequences of septic shock.

overall_design: Performed translating ribosome affinity purification (TRAP) and RNA-sequencing (TRAP-seq) from the brain endothelium to determine the transcriptional changes after an acute endotoxemic (LPS) challenge

first: Alejandro

last: Adam

first: Shuhan

last: Lu


title: Unique structural features of the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex


title: Pseudomonas aeruginosa controls both Caenorhabdtitis elegans attraction and pathogenesis by regulating nitrogen assimilation

city: Princeton

first: Jacob

last: Marogi

state: Nj

address: Lewis Thomas Laboratory

institute: Princeton University

summary: Detecting chemical signals is important for identifying food sources and avoiding harmful agents. Like many animals, C. elegans use olfaction to chemotax towards their main food source, bacteria. However, little is known about the bacterial compounds governing C. elegans attraction to bacteria and the physiological importance of these compounds to bacteria. Here, we address these questions by investigating the function of a small RNA, P11, in the pathogen, Pseudomonas aeruginosa, that was previously shown to mediate learned pathogen avoidance. We discovered that this RNA also affects the attraction of untrained C. elegans to P. aeruginosa and does so by controlling production of ammonia, a volatile odorant produced during nitrogen assimilation. We describe the complex regulation of P. aeruginosa nitrogen assimilation, which is mediated by a partner-switching mechanism involving environmental nitrates, sensor proteins, and P11. In addition to mediating C. elegans attraction, we demonstrate that nitrogen assimilation mutants perturb bacterial fitness and pathogenesis during C. elegans infection by P. aeruginosa. These studies define ammonia as a major mediator of trans-kingdom signaling, implicate nitrogen assimilation as important for both bacteria and host organisms, and highlight how a bacterial metabolic pathway can either benefit or harm a host in different contexts.

overall_design: To investigate total transcriptional changes to PA14 nitrogen assimilation in surface-attached conditions

first: Coleen

middle: T

last: Murphy

first: Cameron

last: Myhrvold

first: Zemer

last: Gitai


title: Deterioration of multi-level 3D genome organization during breast cancer progression

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

overall_design: The aim of this section of the overall project is to deterine the extent to which regions of the genome interacting with lamin B1 (lamina-associated domains, or LADs) vary, and to what extent topologically-associated domains (TADs) interact with lamin B1 in an in vitro model of breast cancer progression. The model consists of MCF10A, MCF10A and MCFCA1 cells cultured under prliferation conditions. LAD data were collected in parallel to chromatin interaction data using Hi-C, and trnascriptomic data using RNA-seq, in each cell type. Hi-C and RNA procedures and datafiles are described in associated GEO metada submissions.

first: Roberto

last: Rossini

first: Mohammadsaleh

last: Oshaghi

first: Maxim

last: Nekrasov

first: Aurélie

last: Bellanger

first: Renae

last: Domaschenz

first: Yasmin

last: Dijkwel

first: Mohamed

last: Abdelhalim

first: David

last: Tremethick

first: Jonas

last: Paulsen


first: Ningning

last: Niu

summary: To gain mechanistic insight into how Setd2 loss reprogramming tumor cell metabolism, we performed CUT&Tag sequencing in PDAC cells with Setd2-KO and Setd2-WT sorted from orthotopic PDAC tumor. Setd2-WT and -KO murine PDAC cells were sorted with DAPI-CD45.2-Pdpn-Epcam+ or cultured, and freshly collected as soon as possible. Hyperactive pA-Tn5 Transposase for CUT&Tag kit from Vazyme (TD901), and antibodies against H3K36me3, H3K27Ac and H3K27me3 were employed. Trueprep index kit v2 and v3 for illumina were used to establish DNA library.

overall_design:
For library preparation, murine PDAC cell lines with Setd2-WT and -KO were first established. CUT&Tag and DNA library were prepared according to manufacturer’s instructions.
antibodies used:
Anti-H3K36me3: Abcam, Ab9050, Lot GR3382010-1
Anti-H3K27me3: Abcam, Ab6002, Lot GR275911-8
Anti-H3K27Ac: Abcam, Ab4729, Lot GR3303559-1

first: Niu

last: Ningning

first: Xue

last: Jing


title: Minimal Residual Disease in Mouse Hepatocellular carcinoma [in vitro]

city: Stanford

first: Renumathy

last: Dhanasekaran

address: 300 Pasteur Drive, Alway M211

institute: Stanford University

summary: Residual tumor cells which remain dormant after MYC inactivation in a primary MYC-HCC derived cell line.

overall_design: MYC-HCC clonal primary celll line treated with doxycyline for one week to inactivate the MYC oncogene. Viable cells used for scRNAseq.


title: Mice are not men: scRNA-sequencing of the human atherosclerotic plaque identifies species-specific immune cell phenotypes that associate with clinical disease

city: Freiburg

first: Hauke

last: Horstmann

address: Hugstetterstraße 55

institute: University Heart Center Freiburg

summary: Local and systemic immunity shapes atherosclerosis, the most frequent cause of cardiovascular disease. The distinct function of immune cells has been mostly defined by preclinical mouse studies, while recent immune cell atlases of human atherosclerosis suggest divergent immune cell mechanisms. Until now, it is not clear whether genetic animal models replicate the immunological complexity of human disease. Here we demonstrate significant variations in the immune cell composition in murine and human atherosclerotic plaques by integrative single-cell RNA-sequencing. In contrast to widely applied mouse models, human plaque leukocytes primarily contained various T-cell phenotypes displaying activation, memory formation, and pro-inflammatory signaling. In a clinical validation cohort, the abundance of activated T cell clusters in human plaques associated with the extend of clinical disease emphasizing the specific role of T-cell-driven immunity in plaque development and instability. Collectively, our study questions the translatability of mouse models for studying the immune system in atherosclerosis.

overall_design: Single cell and gel bead emulsion (GEM) were generated from flow-sorted viable CD45+ cells on a Chromium Controller (10x Genomics). Samples were sequenced on an Illumina NovaSeqsequencer using paired-end sequencing.

first: Nathaly

last: A Miche

first: Dennis

last: Wolf


title: Minimal Residual Disease in Mouse Hepatocellular carcinoma [in vivo]

summary: Transgenic MYC/Twist1 HCC uncergoes tumor regression with persistence of minimal residaul disease (MRD) in the liver upon oncogene deprivation.

overall_design: Microdissected area of residual tumor in mouse HCC subjected to single nuclear RNA sequencing


title: Minimal Residual Disease in Mouse Hepatocellular carcinoma

overall_design: Refer to individual Series


title: Effect of  of RFX1 on regene expression in mouse peritoneal macrophages

city: Nanjing

first: Xiaoli

last: Min

address: No.4 Jiang Wang Temple Street

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: To investigate the function of RFX1 in the regulation of macrophage polarization, we overexpressed RFX1 in mouse peritoneal macrophages(PMAs)  by  lentivirus infections. We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PMAs

first: Shuang

last: Yang

last: Xiao


title: Transcriptome analysis of AoNmd5 in nematode-trapping fungus Arthrobotrys oligospora

city: Kunming City, Yunnan Province

first: Liu

last: Qianqian

address: No.2 Cuihu North Road, Wuhua District

institute: Yunnan University

summary: Transcriptomic analysis revealed that differentially expressed genes in the absence of AoNmd5 were involved in  carbohydrate metabolism, amino acid metabolism, lipid metabolism, transport and catabolism, energy metabolism, and translation.

overall_design: Examination of differential genes in the WT and ΔAonmd5 mutant strains and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

last: Zhao

first: Qianqian

last: Liu

first: Meichen

last: Zhu

first: Jinkui


title: Transcriptional Profile Tumor Evolution in Metastatic and Non Metastatic MYC driven HCC

summary: Comparative transcriptional profiling of MYC driven HCC and MYC/Twist1 driven HCC during tumor progression, regression and recurrence.

overall_design: RNA sequencing of MYC-HCC and MYC/Twist1-HCC was performed.

first: Renu

first: Dean

last: Felsher


title: Transcriptome analysis of Physcomitrium wild type and ppdnmt2 protonemata under Mannitol stress

city: New Delhi

first: Dr. Meenu

last: Kapoor

address: Guru Gobind Singh Indraprastha University, Sector-16C, Dwarka

department: University School of Biotechnology (USBT)

country: India

summary: RNA-seq of 14 day old wild type and ppdnmt2 protonemata exposed to 24 hour mannitol stress

overall_design: Comparison of transcriptome of Wild type and ppdnmt2 plants under mannitol stress

first: Meenu

first: Nikita

last: Wadhwa


city: Oslo

first: Roberto

last: Rossini

address: Blindernveien 31

institute: University of Oslo

summary: Breast cancer progression entails intricate, multi-level alterations in genome organization and expression. To gain insights into the modifications in chromatin's three-dimensional (3D) structure during breast cancer progression, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) remain largely stable, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observed a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identified a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene becomes inserted into a highly active region on chromosome 10. This insertion event leads to the formation of de novo enhancer contacts and activation of the oncogene, illustrating how structural variants can interact with the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the degradation of genome organization at multiple scales during breast cancer progression revealing the complex interplay between genomic structure and oncogenic processes.

overall_design:
We generated Hi-C datasets for MCF10A, MCF10AT1, and MCF10Ca1a cell lines to investigate changes in 3D genome conformation during breast cancer progression.

***Please note that the records have been updated with additional/replacement processed data files on Aug 9, 2024****

first: Mohammadsaleh

last: Oshaghi

first: Maxim

last: Nekrasov

first: Aurélie

last: Bellanger

first: Renae

last: Domaschenz

first: Yasmin

last: Dijkwel

first: Philippe

last: Collas

first: David

last: Tremethick

first: Jonas

last: Paulsen


title: Establishment of constitutive heterochromatin in Drosophila early embryos involves H3K14ac-mediated recruitment of Eggless/SetDB1

city: Changsha

first: Ruijun

last: Tang

address: No. 97 Xiangya Road

institute: Xiangya Hospital Central South University

summary: The establishment of heterochromatin is a crucial process in the early embryonic development. Recent research suggests that SetDB1 is necessary for heterochromatin establishment in the early embryonic development of Drosophila. Additionally, SetDB1 has been found to bind to H3K14ac in mammalian cells. However, the role of the H3K14ac in heterochromatin establishment during embryogenesis remains unknown. Here we discovered that the active modification H3K14ac serves as an intergenerational marker from oocytes to early embryos, and it is recognized by Eggless/SetDB1 through its Tudor domains. Furthermore, we have introduced a point-mutation in the endogenous Eggless/SetDB1 locus, resulting in the loss of H3K14ac-binding. Both H3K14ac attenuation and SetDB1 mutant embryos exhibit abnormal heterochromatin formation and genomic instability. We reveal a novel model of heterochromatin establishment via H3K14ac-mediated recruitment of SetDB1.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K14ac, H3K9me3 and the histone methyltransferase SetDB1 in Drosophila early embryos (stage 4 to 6).

first: Tang

last: Ruijun

first: Jiang

last: Zhenghui

first: Yuan

last: Kai


title: Transcriptome and epigenome in the cortical neurons transfected with Gata1

city: Seoul

first: Koeul

last: Choi

address: 84, Heukseok-ro

institute: Chung-Ang university

summary: Gata1, a member of the GATA transcription factor family, has been considered as an important factor in the hematopoietic system. As a transcriptional regulator, Gata1 has a crucial role in differentiation of blood cells such as erythrocytes, megakaryocytes, eosinophils, and dendritic cells. Recently, a novel function of Gata1 has been demonstrated in the central nervous system. Gata1, a stress-inducible gene in the brain, has been shown to increase the expression in the dorsolateral prefrontal cortex of patients with depression and function as a transcriptional repressor of synapse-related genes. In this study, we investigated the global alteration in gene expression by Gata1 using ChIPseq, mRNAseq, and smallRNAseq. From the result of ChIPseq for histone marks H3K4me3 and H3K27me3, we have identified 1127 and 4881 unique peaks respectively in the gene promoter region in the cultured cortical neurons overexpressed with Gata1 compared to the control. We also identified 113 differentially expressed mRNAs and 82 miRNAs in cultured neurons transfected with Gata1 through the mRNAseq and smallRNAseq. Through the three-sequencing data analysis, we have profiled genes that might be affected by Gata1 in the cultured cortical neurons. Gene ontology (GO) analysis revealed that Gata1 might be associated with the immune-related function. These results will provide a better understanding of the regulatory mechanisms of Gata1 that affects the pathophysiological status, such as depression.

overall_design: Profiles of histone modification, mRNA, and miRNAs in the cultured neuron transfected with Gata1 were generated by ChIPseq, RNAseq, and small RNAseq.

first: Joonhee

last: Lee

first: Gukdo

last: Kim

first: HyoJung

last: Kang


title: Transcriptomic profiling of human alveolar organoids(hALOs)

city: Xianmen

first: Yuchen

last: Liu

address: Xiangan South Road

institute: Xianmen University

summary: We performed global transcriptomic profiling of  hALOs at early (P4), middle (P13) and late (P20) passages and found that the transcripts of the hALOs were similar to that of primary lung progenitor organoids.hALOs highly expressed genes associated with lung development/lung progenitor, AT2 specification and AT1 specification.We found that our hALOs were more similar to pseudoglandular-staged lung.The gene sets associated with alveolar maturation, such as surfactant homeostasis or response to oxygen levels, were upregulated in P20. Besides, genes involved in endoderm development or respiratory tube development were downregulated

overall_design: To determine how similar the transcriptomic identities of hALOs were to primary human lung, we performed RNA-sequencing (RNA-seq) of hALOs at early (P4), middle (P13) and late (P20) passages and compared our data with lung adenocarcinomas cancer cell line A549, H9 hESCs, human fetal lung and primary lung progenitor organoids from publicly available databases

first: Lian

last: Li

first: Ying

last: Lin

first: Zhili

last: Rong


title: Next Generation Sequencing Facilitates Quantitative Analysis of ob/+ and ob/ob pancreatic islet Transcriptomes

city: Hangzhou

first: Meng

last: zhuoxian

address: 866 Yuhangtang Road, Xihu District

department: Department of Pathology and Pathophysiology

institute: Zhejiang University School of Medicine

summary:
Purpose:To identify which genes are differentially expressed in pancreatic islets of the ob/ob mice compared to the control ob/+ mice
Methods: The data were aligned to mm10 reference genome with HISAT2 (V2.1.0).Differential expression analysis was performed using the DESeq2(V 1.2.0).
Results:Library construction, and sequencing were performed by Beijing Genomic Institution (www.genomics.org.cn, BGI) using an optimized data analysis workflow

overall_design: Pancreatic islet mRNA profiles of 12-week old ob/+ and ob/ob mice

first: Xinyuan

last: Qiu

first: R

middle: R

last: Wang


title: Study of the changes on placenta transcriptome in normal pregnacy and preterm birth

city: Wuhan

first: Mi

last: Wu

address: Tongji Medical College, No. 13 Hangzhou Road, Qiaokou District, Wuhan

institute: 华中科技大学

summary: To identify the differential expression genes between Normal placenta and preterm birth placenta.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human placenta tissue in normal pregnancy and preterm birth.

first: Xiufang

last: Weng


title: Early-life thymectomy leads to an increase of granzyme-producing γδ T cells in children with congenital heart disease

city: Hannover

first: Sarina

last: Ravens

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary: Congenital heart disease (CHD) is the most common birth defect in newborns, often requiring cardiac surgery with concomitant thymectomy that is known to increase disease susceptibility later in life. Studies of γδ T cells, which are one of the dominant T cells in the early fetal human thymus, are rare. Here, we provide a comprehensive analysis of the γδ T cell compartment via flow cytometry and next-generation sequencing in children and infants with CHD, who underwent cardiac surgery shortly after birth. A perturbation of the γδ T cell repertoire is evident and Vδ1 T cell numbers are reduced. However, those cells that are present, do retain cytotoxicity. In contrast, GZMA+CD28+CD161hi innate effector Vγ9Vδ2 T cells are found in higher proportions. TCR-seq identifies an increase in TRDJ3+ γδ T cell clones in children with CHD, but not in a confirmatory group of neonates prior to CHD surgery, which overall points to a persistence of fetal-derived effector γδ T cells in children with CHD.

overall_design: We aim to investigate the transcriptional profiles of T cells in children with CHD after thymectomy. To this end, scRNA-seq was performed on peripheral blood T cells from 5-12-year-old children with CHD who received thymectomy early after birth (CHD, n = 4, old_CHD) and control children (ctrl, n = 4, old_Ctrl). Next, to elucidate the impact of congenital heart surgery with concomitant removal of thymic tissue on the postnatal maturation of T cells within the first 6 months of life, we performed scRNA-seq of isolated peripheral blood T cells from two longitudinally followed infants with CHD before (Baseline, BSL, on day 8 and 9 of life, HLM139_1 and HLM140_1) and six months after surgery (Follow-up, FU, at day 188 and 189 of life, HLM139_2 and HLM140_2)

first: Martin

last: Boehne

first: Tao

last: Yang

first: Alexa

last: Cramer


title: Delayed leaf greening involves a major shift in expression of cytosolic and mitochondrial ribosomes to plastid ribosomes in the highly phosphorus-use-efficient Hakea prostrata (Proteaceae)

city: Perth

first: Patrick

middle: Michael

last: Finnegan

state: WA

address: 35 Stirling Hwy

department: School of Biological Sciences

country: Australia

institute: University of Western Australia

summary: Hakea prostrata (Proteaceae) maintains a high photosynthetic rate at low leaf phosphorus and exhibits delayed leaf greening, a convergent adaptation found in many plant families where investment in photosynthetic machinery is delayed until after the leaf structure is built, saving on nutrient investment. To identify the dynamics of gene expression underlying delayed greening, we made a de novo transcriptome assembly for H. prostrata using roots and leaves from hydroponically grown plants, and leaves from five morphologically distinct stages of leaf development from wild plants. Abundance of unique transcripts was compared among the developing leaf stages to identify differentially expressed genes, which were separated into groups based on co-expression patterns. In general, transcripts encoding functions associated with leaf structure decreased in abundance across leaf development, with this concomitant with the decline in foliar P and N concentrations. An enrichment of differentially expressed genes associated with photosynthetic function increased in abundance at or after leaf expansion and much later in development than in species that do not have delayed greening. The abundance of transcripts encoding cytoplasmic and mitochondrial ribosomal subunits generally declined across leaf development, whilst transcripts encoding chloroplast ribosomal subunits increased. Taken together, these results indicate a clear shift in protein synthesis apparatus, moving from a leaf developmental stage and into the photosynthetically-active stage.

overall_design: Gene expression profiling analysis of RNA-seq data for wild growing leaves of Hakea prostrata . We compared expression of genes over four stages of leaf growth, with three replicates per stage.

first: Benjamin

middle: J

last: Nestor

first: Toby

last: Bird

middle: M

first: Philipp

middle: E

last: Bayer


title: Unraveling Heterogeneity in Tumor Evolution Induced by Diverse Radiation Modes: Insights from Systems Biology

status: Public on Aug 05 2024

city: Suzhou

first: Wanshi

address: 苏州大学

institute: 苏州大学

summary: The biomedical consequences of space radiation pose a significant concern for astronauts engaged in deep space. However, the effects of long-term low dose-rate exposures in space environments remain elusive. In this study, we simulated the space radiation environment by exposing human bronchial epithelial cells to low dose-rate (0.0067 Gy/day) α-particles, and continuously irradiated them multiple times to achieve cumulative total doses of 0.2 Gy, 0.4 Gy, and 0.5 Gy, respectively. At the same time, the cells were irradiated with the same total dose in a single exposure to investigate the potential of low dose-rate alpha particles to induce malignant transformation of human bronchial epithelial cells. A comprehensive suite of assays was employed to assess tumorigenic potential, including tumor formation in NOD/SCID mice, immunohistochemistry, CCK-8 proliferation assay, invasion assay, and the evaluation of multicellular spheroid formation during subsequent passages post-irradiation. Moreover, we dissected differential malignant mechanisms in tumor evolution ecosystem induced by the two distinct irradiation modes from systems biology views based on scRNA-seq technology. Our results showed that exposure to α-particles, whether through a single acute exposure or long-term low dose-rate exposures, induced the occurrence and development of tumors. Long-term low dose-rate exposures to α-particles increase the malignancy of induced tumors, but not the risk of carcinogenesis, compared to a single acute exposure with the same total dose. In addition, through scRNA-seq, we found that long-term low dose-rate exposures triggered more copy number variation (CNV) and epithelial-mesenchymal transition (EMT) events, and the activation of DNA damage repair pathways occurred significantly later than with a single acute exposure and involved more specific changes in cellular communication dynamics. In conclusion, our findings provide emerging yet convincing evidence that not only sheds light on why cells exposed to long-term low dose-rate exposures exhibit heightened malignancy, but also offers valuable insights into the genetic determinants driving tumor evolution and heterogeneity.

overall_design: To elucidate the differential effects between single acute irradiation and long-term low dose-rate irradiation, we developed a series of α-particle exposure models to investigate the oncogenic effects of α-particles on human bronchial epithelial cells (BEAS-2B). Specifically, BEAS-2B cells cultured on cover slides were exposed to α-particles emitted by 241Am isotope at a dose rate of 0.14 Gy/min. The samples were divided into seven groups, Ctrl, sham control; R1_0.2, one acute exposure to 0.2 Gy; R1_0.4, one acute exposure to 0.4 Gy; R1_0.5, one acute exposure to 0.5 Gy; R10_0.2, low dose-rate exposure with a total dose of 0.2 Gy, i.e. one exposure with 0.02 Gy and subculture on the other day followed by another exposure two days later, so that totally 10 exposures in 30 days; R20_0.4, low dose-rate exposure to 0.4 Gy, 20 exposures in 60 days; R25_0.5, low dose-rate exposure to 0.5 Gy, 25 exposures in 75 days. So, the average dose rate of single acute exposures was 0.14 Gy/min while that of long-term low dose-rate exposures 0.0067 Gy/day. The seven groups of cells were treated and divided strictly following the same procedure. Once the exposure of the R25_0.5 group was completed, all the seven groups of cells were subcultured every three days, and cells were partially harvested at various passages for subsequent analysis (e.g., 10th, 30th, and 50th). To repeat the experiments independently, three independent sets of experiments were conducted from the very beginning by different individuals in parallel. To delve into the molecular processes and factors contributing to the disparities in malignancy between two irradiation modes, with a focus on genetic determinants, we performed single-cell RNA sequencing (scRNA-seq) on seven samples. These samples included sham control cells without irradiation (Ctrl), the cells after a single acute irradiation of 0.5 Gy and then subcultured for 10 (R1-10), 30 (R1-30), and 50 passages (R1-50), and the cells subjected to long-term low dose-rate exposures to 0.5 Gy and subcultured for 10 (R25-10), 30 (R25-30), and 50 passages (R25-50), respectively.

first: Weiwei

last: Pei

first: Wenying

last: Yan

first: Yiwei

first: Wentao

last: Hu

first: Guang

first: Guangming

last: Zhou


title: Expression profiling by microarray in breast cancer cells

city: shenyang

first: wen qian

last: chen

address: 77 Puhe Road

department: College of pharmacy

institute: China Medical University

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

summary: Dysregulation of LINCRNAs is closely associated with various cancer types, including breast cancer. Breast cancer stem cells (BCSCs) were characterized by unlimited self-renewal/repopulating potential and contribute to the initiation and progression of the disease, as well as to treatment failure and recurrence of BRCA. To identify the LINCRNAs involved in the maintenance of BCSCs properties, we performed genome-wide microarray on MCF-7 MS along with its parental MCF-7 cells. We identified that LINC00887 is significantly upregulated in BCSCs and serves as a key regulator of BRCA stemness.

overall_design: Our microarray data to comprehensively explore LINCRNA heterogeneity in BCSCs.

first: Xuemei

last: Lu

first: Li

last: Han

first: Minjie

last: Wei

first: Miao

last: He


title: Smart RNA sequencing Facilitates Quantitative Analysis of dermal CD4+ Trm cells between SLE and NC.

first: zhidan

last: zhao

address: #139 Renmin Middle Road, The 2nd Xiangya Hospital

institute: central south university

summary: The goals of this study are to compare  transcriptome of dermis-derived CD4+ Trm cells between SLE and NC.

overall_design: CD4+ Trm cells' mRNA profiles of SLE and NC.

first: Zhidan

last: Zhao


title: Fn14 antagonist L524-0366 exerts protective effect on fibroblasts

city: Xi'an

first: Mei

address: No. 157, West 5th Road, Xincheng District

institute: The Second Affiliated Hospital of Xi'an Jiaotong University

summary: The expression of TWEAK and Fn14 was increased in early skin lesions of SSc patients. Fn14 expression on human dermal fibroblasts is significantly increased after stimulation with serum from patients with systemic sclerosis. The interplay between TWEAK and Fn14 is pivotal in the fibrotic progression of various autoimmune diseases. These observations implicate the TWEAK/Fn14 signaling pathway may as a critical player in the pathological advancement of systemic sclerosis; however, the precise underlying mechanisms require further clarification. Thus, human dermal fibroblasts were stimulated by serum from systemic sclerosis patients, and with or without the addition of Fn14 antagonists. We then assessed the antifibrotic effects of this antagonist through RNA sequencing, and preliminary exploration of possible molecular mechanisms.

overall_design: Human dermal fibroblasts (HDF) were treated with serum derived from patients diagnosed with systemic sclerosis (SSc). This treatment was conducted either in the presence or absence of the Fn14 antagonist, L524-0366, to evaluate its potential regulatory effects.


title: FoxK1 and FoxK2 cooperate with ORF45 to promote late lytic replication of Kaposi’s sarcoma-associated herpesvirus

city: guangzhou

first: Qingyang

last: Chen

address: Zhongshan 2nd Road

institute: Sun Yat-sen University

summary: Lytic replication is essential for persistent infection of Kaposi’s sarcoma-associated herpesvirus (KSHV) and the pathogenesis of related diseases, and many cellular pathways are hijacked by KSHV proteins to initiate and control the lytic replication of this virus. However, the machinery involved in KSHV lytic replication from the early to the late phases remains largely undetermined. We previously revealed that KSHV ORF45 plays important roles in late transcription and translation. In the present study, we reveal that the Forkhead box proteins FoxK1 and FoxK2 are ORF45-binding proteins and are essential for KSHV lytic gene expression and virion production and that depletion of FoxK1 or FoxK2 significantly suppresses the expression of many late viral genes. FoxK1 and FoxK2 directly bind to the promoters of several late viral genes, ORF45 augments the promoter binding and transcriptional activity of FoxK1 and FoxK2, and then FoxK1 or FoxK2 cooperates with ORF45 to promote late viral gene expression. Our findings suggest that ORF45 interacts with FoxK1 and FoxK2 and promotes their occupancy on a cluster of late viral promoters and their subsequent transcriptional activity; consequently FoxK1 and FoxK2 promote late gene expression to facilitate KSHV lytic replication.

overall_design: To further investigate the roles of FoxK1 and FoxK2 in KSHV gene expression during lytic replication, FoxK1 and FoxK2 were separately depleted in iSLK.Bac16 cells by shRNA transduction, and genome-wide gene expression in iSLK.Bac16 cells with induction of lytic replication was analyzed by RNA sequencing.

first: Xiaojuan

last: Li

last: Quan


title: Parental Alcohol Exposures Promote Increased Susceptibility to Hepatocellular Carcinoma in Adult Male Offspring

city: College Station

first: MICHAEL

middle: C.

last: GOLDING

state: Texas

address: 4466 TAMU

department: Physiology

institute: Texas A&M UNiversity

summary: There is a growing interest in understanding how lifestyle choices and social factors affect life expectancy, healthspan, and the onset of chronic age-related diseases, including cancer. Although alcohol is a known carcinogen that accounts for roughly one-third of primary liver cancer cases worldwide, it is not yet known if chronic alcohol consumption by an individual’s parents heritably influences their predisposition to developing liver cancer. Here, we employed our established multiplex mouse model to compare sensitivities of the male offspring of maternal, paternal, and dual-parental alcohol exposures to the potent hepatocellular carcinoma inducer, Diethylnitrosamine (DEN), and determine their predisposition for tumor formation and growth. Our experiments reveal that chronic parental alcohol consumption programs a pro-tumor environment in the liver. This increased cancer susceptibility correlates with increased steatosis, hepatic fibrosis, inflammation, and oxidative stress. Interestingly, some of these changes display accumulative effects and are more pronounced when both parents are exposed to alcohol.

overall_design: Control Saline, Maternal Saline, Paternal Saline, Dual Saline, Control DEN, Maternal DEN, Paternal DEN, Dual DEN

first: A

last: Basel

first: M

last: Golding


title: Combinatorial tagging generates a multi-purpose knock-in mouse model revealing  phase separation-dependent germ granules in RNA homeostasis and germline development

city: Hefei

first: Caoling

last: Xu

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

institute: University of Science and Technology of China

summary: A large resource of epitope-tagged or Cre/CreERT2-expressing mouse models are available for study of germ granules or germline development. The germ granules are proteinaceous, membraneless organelles implicated in germ cell differentiation and maturation; however, their protein and RNA transcript constituents, and their mechanistic insight remain not fully understood. Herein, we generated a versatile germline mouse model through combinatorial tagging of DDX4 for simultaneous  expression of three cistronic coding products (C-terminal tagged DDX4 - DDX45HA, EGFP, and CreERT2) under the driving control of endogenous Ddx4 promoter. By leveraging the high-affinity HA tag, we optimized an efficient workflow for purification of germ granules (Chromatoid body, CB) from spermatids, and characterized the landscape of protein constituents and RNA transcripts in CB. Moreover, we explored and ascertained that DDX4-mediated, phase-separation dependent CB integrity is functionally important for recruiting distinctive long RNA transcripts and biogenesis of pachytene- and TE-derived piRNAs. Together, our study generated a versatile germline mouse model with a multiplicity of applications for germline study, and provided mechanistic insight into germline development as dictated by germ granules.

overall_design: We have designed a combinatorial tagging knock-in mouse model：Ddx45XHA-EGFP-CreERT2.We found that homozygous knock-in male mice are sterile. Abnormal sperm acrosome and chromatoid body were found in homozygous mice. We want to isolation RNA from round spermatids and chromatoid body for RNA-seq to explore the mechanism of sterility of homozygous knock-in male mice.

first: Jianqiang

last: Bao

first: Lan

last: Meng


title: Whole transcriptomic analysis of uterine fluid exosomes during fresh embryo transfer cycles [lncRNA-seq]

city: beijing

first: Yumeng

last: Ren

state: Beijing

address: Xicheng District

institute: Peking university people’s hospital

summary: By comparing the difference in whole transcriptome of uterine fluid exosomes on embryo transfer day between pregnant and unpregnant groups during IVF cycles, novel biomarkers that may predict embryo implantation were identified. This prospective cohort study included78 cases with infertility who underwent routine in vitro fertilization(IVF) and fresh embryo transfer; they were divided into pregnant group and unpregnant group.

overall_design: In the first step, 38 participants were included, whole transcriptome sequencing was performed. In the second step, 40 patients were included, quantitative real-time PCR (qRT-PCR) were performed to validate the differentially expressed genes (DEGs) by the first step.

first: Hongjing

first: Xi

first: Fumei

last: Gao

first: Min

last: Fu

first: Cheng

last: Shi


title: Whole transcriptomic analysis of uterine fluid exosomes during fresh embryo transfer cycles [miRNA-seq]

last: Han


title: HPV induced R-loop formation represses innate immune gene expression while activating DNA damage repair pathways [H3K36me3 ChIP seq]

city: Chicago

first: Conor

last: Templeton

address: 300 E Superior Street

institute: Northwestern University

summary: R-loops are trimeric nucleic acid structures that form when an RNA molecule hybridizes with its complementary DNA strand, displacing the opposite strand. These structures regulate transcription as well as replication, but aberrant R-loops can form, leading to DNA breaks and genomic instability if unresolved. R-loop levels are elevated in many cancers as well as cells that maintain high-risk human papillomaviruses. We investigated how the distribution as well as function of R-loops changed between normal keratinocytes and HPV positive cells derived from a precancerous lesion of the cervix (CIN I). The levels of R-loops associated with cellular genes were found to be up to 10-fold higher in HPV positive cells than in normal keratinocytes while increases at ALU1 elements increased by up to 500-fold. The presence of enhanced R-loops resulted in altered levels of gene transcription, with equal numbers increased as decreased. While no uniform global effects on transcription due to the enhanced levels of R-loops were detected, genes in several pathways were coordinately increased or decreased in expression only in the HPV positive cells. This included the downregulation of genes in the innate immune pathway, such as DDX58, IL-6, STAT1, IFN-b, and NLRP3. All differentially expressed innate immune genes dependent on R-loops were also associated with H3K36me3 modified histones. Genes that were upregulated by the presence of R-loops in HPV positive cells included those in the DNA damage repair such as ATM, ATRX, and members of the Fanconi Anemia pathway. These genes exhibited a linkage between R-loops and H3K36me3 as well as gH2AX histone marks only in HPV positive cells. These studies identify a potential link in HPV positive cells between DNA damage repair as well as innate immune regulatory pathways with R-loops and gH2AX/H3K36me3 histone marks that may contribute to regulating important functions for HPV pathogenesis

overall_design: Enrichment of H3K36me3 marks was compared between HPV-negative HFKs (samples 2 and 3) and HPV-positive CIN 612 cells (samples 6 and 7). Sample 1 is an input control from the HFKs, and Samples 4 and 5 are input controls from CIN 612 cells. Briefly, formaldehyde was added to 1 × 107 HFKs (samples 1-3) or CIN 612 cells (samples 1-4) to a final concentration of 1% for 10 min at room temperature. Excess formaldehyde was quenched upon adding 0.125M glycine before then washing samples with PBS. Cells were then incubated in collection buffer (0.1M TrisHCl pH 9.4 and 10mM DTT containing Roche Protease Inhibitor Cocktail)  for 10min on ice. Cells were then collected and spun down before being sequentially washed and incubated with NCP1 (10mM EDTA, 0.5mM EGTA, 10mM HEPES pH 6.5, 0.25% Triton X100) and NCP2 (1mM EDTA, 0.5mM EGTA, 10mM HEPES, and 200mM NaCl) before being lysed in 0.5% Empigen BB, 1% SDS, 10mM EDTA, 50mM Tris HCl pH 8.0 containing Roche Protease Inhibitor Cocktail for 30 min on ice. Samples were then sonicated using a Bioruptor (Diagenode) on high power, 30 s on/90 s off cycles for 20 min. After sonication, Input DNA was removed (to create samples 1, 4, and 5) from before loading the samples into preblocked magnetic beads in IP buffer containing 2 ug of the H3K36me3 antibody (Samples 2, 3, 6, and 7). Immunoprecipitations were allowed to incubate overnight at 4 °C while rotating. The next day, samples were washed 8 times with RIPA buffer for 5 min while rotating. One wash in TE buffer was performed before samples 2, 3, 6, and 7 were eluted for 10 min at 65 °C in 10% sodium dodecyl sulfate (SDS), 10 mM Tris pH 7.4, 50 mM ethylenediaminetetraacetic acid (EDTA). DNA was purified from all samples using a PCR purification kit (Qiagen) and stored at ?20 °C.

first: Laimonis

last: Laimins


title: Novel inhibition of central carbon metabolism pathways by Rac and Cdc42 inhibitorMBQ-167 and paclitaxel

city: New York

first: Ilya

last: Shamovsky

state: New York

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

summary: Triple negative breast cancer (TNBC) represents a therapeutic challenge where standard chemotherapy is limited to paclitaxel. MBQ-167, a clinical stage small molecule inhibitor that targets Rac and Cdc42, inhibits tumor growth and metastasis in mouse models of TNBC. Herein, we investigated the efficacy of MBQ-167 in combination with paclitaxel in TNBC pre-clinical models, as a prelude to safety trials of this combination in advanced breast cancer patients. Individual MBQ-167 or combination therapy with paclitaxel was more effective at reducing TNBC cell viability and increasing apoptosis compared to paclitaxel alone. In orthotopic mouse models of human TNBC (MDA-MB-231 and MDA-MB-468), individual MBQ-167, paclitaxel, or the combination reduced mammary tumor growth with similar efficacy, with no apparent liver toxicity. However, paclitaxel single agent treatment significantly increased lung metastasis, while MBQ-167, single or combined, reduced lung metastasis. In the syngeneic 4T1/BALB/c model, combined MBQ-167 and paclitaxel decreased established lung metastases by ~80%. To determine the molecular basis for the improved efficacy of the combined treatment on metastasis, 4T1 tumor extracts from BALB/c mice treated with MBQ-167, paclitaxel, or the combination were subjected to transcriptomic analysis. Gene set enrichment identified specific downregulation of central carbon metabolic pathways by the combination of MBQ-167 and Paclitaxel but not individual compounds. Biochemical validation, by immunoblotting and metabolic Seahorse analysis, shows that combined MBQ-167 and paclitaxel reduces glycolysis. This study provides a strong rationale for the clinical testing of MBQ-167 in combination with paclitaxel as a potential therapeutic for TNBC and identifies a unique mechanism of action.

overall_design: BALB/c mice were injected in the 4th mammary fat pad with 300,000 mouse 4T1 mammary carcinoma cells expressing firefly luciferase on two different occasions. To determine the effect of single or combination agent treatment (under MBQ-167 and paclitaxel treatments) on the established lung metastatic burden and to perform genome wide transcriptomic analyses. For the transcriptomic analysis, BALB/c mice bearing 4T1 mouse tumors were treated on day 14 with 100 mg/kg MBQ-167 5X a week for 2 weeks and 5 mg/kg paclitaxel 1X a week. On day 28, mice were sacrificed, and the tumor extracts subjected to transcriptomic analysis.

first: Olga

last: Katsara

first: Robert

last: Schneider

first: Suranganie

last: Dharmawardhane


title: Contact-based thymidylate transfer promotes collective tumor growth

city: Odense - M

first: Paolo

last: Ceppi

address: Campusej, 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Sustained cell proliferation is a fundamental hallmark of cancer, yet its mechanism remains elusive. While tumor cells often cooperate to enhance survival, the specific molecular forces driving this behavior are unknown. We uncover a novel mechanism of tumor growth, that cancer cells proliferate through a contact-dependent transfer of thymidylate (dTMP) via gap junctions with neighboring cells, bypassing canonical biosynthetic and salvage pathways driven by thymidylate synthase (TS) and thymidine kinase (TK1). Importantly, using a genetic mouse model of lung cancer harboring dual TS/TK1 tumor-specific knockout, we show that cancer cells lacking canonical synthesis maintain proliferation. These findings advance the current dogma of a ubiquitous nucleotide-driven activation in cancer, suggesting that a programmed dTMP re-equilibration sustains tumor growth. This novel mechanism could be exploited in cancer therapy.

overall_design: Differential gene expression analysis for A549 cells with Cas9 mediated KO of TYMS (TS-KO) and TS-KO cells with restored proliferation in presence of parental A549 cells (TS-KO coculture)

first: Mohammad

last: Siddiqui

first: Vignesh

last: Ramesh