title: Characterization of IL-6R-expressing monocytes in the lung of patients with chronic obstructive pulmonary disease [THP1]

city: Sendai

first: Takuya

last: Saito

state: Miyagi

address: 1-1 Seiryomachi, Aobaku

department: Department of Respiratory Medicine

institute: Tohoku University Graduate School of Medicine

summary: Background: Monocytes play a crucial role in innate immune responses for host defense, yet their involvement in chronic obstructive pulmonary disease (COPD) remains poorly understood. We previously identified a subset of monocytes in COPD lung tissues characterized by high interleukin-6 receptor (IL-6R) expression. This study aimed to characterize the phenotypes of IL-6Rhi monocytes in the lung of COPD patients.  Methods: Using flow cytometry, we assessed the abundance of pulmonary CD14+IL-6Rhi cells in never smokers (CNS), control ex-smokers (CES) and COPD patients. IL-6 expression in CD14+ monocytes from peripheral blood of patients with COPD was also examined. CD45+CD206–CD14+IL-6Rhi and CD45+CD206–CD14+IL-6R– cells were isolated from COPD lung tissues for transcriptome analysis. A monocyte line THP1 cell with constitutive IL-6R expression was stimulated with recombinant IL-6, followed by RNA sequencing to evaluate IL-6 responsiveness of IL-6R+ monocytes.   Results: The number of pulmonary CD14+IL-6Rhi monocytes was elevated in COPD patients compared to CNS, while CD14+ monocytes in the peripheral blood of COPD patients did not express IL-6R. Upregulated mRNA expression in CD14+IL-6Rhi monocytes was associated with chemotaxis, monocyte differentiation, fatty acid metabolism and integrin-mediated signaling pathway. Stimulation of THP1 cells with recombinant IL-6 induced gene expression changes linked to chemotaxis and organism development.  Conclusion: In patients with COPD, CD14+IL-6Rhi monocytes increase in lung tissues compared to CNS and exhibit a different transcriptome profile from CD14+IL-6R– monocytes.

overall_design: To investigate the changes in the gene expression profile of THP1 cells driven by IL-6, we treated THP1 cells with human recombinant (hr) IL-6 and collected total RNA at 6 hours (THP1-IL6-6h), 24 hours (THP1-IL6-24h), and 48 hours (THP1-IL6-48h) post-treatment.

first: Yoshinao

last: Ono

first: Naoya

last: Fujino

first: Mitsuhiro

last: Yamada

first: Hisatoshi

last: Sugiura


title: Characterization of IL-6R-expressing monocytes in the lung of patients with chronic obstructive pulmonary disease [IL-6 mono]

status: Public on Aug 21 2024

country: Japan

type: Expression profiling by high throughput sequencing

overall_design: We compared the global gene expression patterns between CD14+IL-6Rhi and CD14+IL-6R− monocyte subsets isolated from lung tissues of COPD patients (n=3)


title: Tho2-mediated escort of Nrd1 regulates gene expression for lifespan maintenance

city: Daegu

first: Hong-Yeoul

last: Ryu

state: Buk-Gu

address: Daehak-ro 80

department: Biotechnology

country: South Korea

institute: Kyungpook National University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The relationship between aging and RNA biogenesis and trafficking is attracting growing interest, yet the precise mechanisms are unknown. The THO complex is crucial for mRNA cotranscriptional maturation and export. Herein, we report that the THO complex is closely linked to maintaining a normal lifespan. Deficiencies in Hpr1 and Tho2, components of the THO complex, reduced replicative lifespan (RLS) and are linked to a novel Sir2-independent RLS control pathway. Although transcript sequestration in hpr1Δ or tho2Δ mutants was countered by exosome component Rrp6, loss of this failed to mitigate RLS defects in hpr1Δ. However, RLS impairment in tho2Δ was counteracted by Nrd1-specific mutants that interacted with Rrp6. This effect relied on the interaction of Nrd1, a transcriptional regulator of aging-related genes, including ribosome biogenesis or RNA metabolism genes, with RNA polymerase II. Nrd1 overexpression reduced RLS in a Tho2-dependent pathway. Intriguingly, THO2 deletion mirrored Nrd1 overexpression effects by inducing arbitrary Nrd1 chromatin binding. Taken together, these findings underscore the importance of Tho2-mediated Nrd1 escorting in maintaining a normal lifespan by transcriptional regulation of aging-related genes.

overall_design: Chromatin immunoprecipiation sequencing (ChIP-seq) for recruitment of Nrd1 by tho2Δ


title: Maternal obesity induces the meiotic defects and epigenetic alterations during fetal oocyte development [RNA-seq]

city: Nanjing

first: Qiuzhen

last: Chen

address: 101 Longmian Rd, Nanjing, Jiangsu, 211166 China

country: China

institute: Nanjing Medical University

summary: It has been widely reported that obesity adversely impacts reproductive performance of females. However, the effects of maternal obesity on fetal germ cells remain poorly understood. In the present study, by employing a high-fat diet (HFD)-based mouse model, we found that maternal obesity disrupts the chromosomal synapsis and homologous recombination during fetal oogenesis. Moreover, transcriptomic profiling revealed the potential molecular network controlling this process. Of note, the global hypermethylation of genomic DNA in fetal oocytes from obese mouse was detected. Importantly, time-restricted feeding (TRF) of obese mice not only ameliorated the meiotic defects, but also partly restored the epigenetic remodeling in fetal oocytes. In sum, we provide the evidence showing the deficit fetal oogenesis in obese mother, implicating a mechanism underlying the intergenerational effects of environmental insults. TRF may represent a potentially effective approach for mitigating fertility issues in obese patients.

overall_design: RNA-seq was used for transcriptome profiling. Fetal oocytes from both ND and HFD mice were collected at E18.5.

first: Shoubin

last: Tang

first: Jiashuo

last: Li

first: Xi

last: Wang

first: Qiang


title: The RPD3L deacetylation complex is required for facultative heterochromatin repression in Neurospora crassa [Mnase-seq]

city: Sapporo

first: Hideki

last: Tanizawa

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

institute: Hokkaido University

summary: Repression of facultative heterochromatin is essential for developmental processes in numerous organisms.  Methylation of histone H3 lysine 27 (H3K27) by Polycomb repressive complex 2 is a prominent feature of facultative heterochromatin in both fungi and higher eukaryotes.  Although this methylation is frequently crucial for silencing, the detailed mechanism of repression remains poorly understood.  We utilized a forward genetics approach to identify three previously uncharacterized genes required to maintain silencing at facultative heterochromatin genes in Neurospora crassa: sds3 (NCU01599), rlp1 (RPD3L protein 1; NCU09007) and rlp2 (RPD3L protein 2; NCU02898).  We found that SDS3, RLP1, and RLP2 associate with N. crassa homologs of the Saccharomyces cerevisiae RPD3L complex and are required for repression of a subset of H3K27-methylated genes.  Loss of these genes does not lead to loss of H3K27 methylation but increases acetylation of histone H3 lysine 14 at upregulated genes, and SDS3 binding levels are highest at genes derepressed upon loss of sds3, rlp1, and rlp2, implying that RPD3L-driven deacetylation is a previously undescribed factor required for silencing of facultative heterochromatin in N. crassa.

overall_design: To check the position of the +1 nucleosome, we performed MNase-seq in wild type, ∆sds3, ∆rlp1, and ∆rlp2.

first: Colleen

middle: C

last: Mumford

first: Elizabeth

middle: T

last: Wiles

first: Kevin

middle: J

last: McNaught

first: Kirsty

last: Jamieson

first: Kenta

last: Tsukamoto

first: Eric

middle: U

last: Selker


title: Antibiotic use during influenza infection augments lung eosinophils that impair lung immunity against secondary bacterial pneumonia

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

country: USA

institute: cedars-sinai medical center

summary: A leading cause of morbidity and mortality during influenza infection is the development of a secondary bacterial pneumonia, which is appropriately treated with antibiotics. In the absence of a bacterial superinfection, prescribing antibiotics is not indicated but has nevertheless become a common clinical practice for those presenting with a respiratory viral illness. We found that antibiotic use during an antecedent influenza infection impaired the lung innate immunologic defenses toward a secondary challenge with methicillin-resistantStaphylococcus aureus(MRSA). The antibiotics perturbed the gut microbiome causing a fungal dysbiosis that drives an increase in lung eosinophils. We also demonstrate eosinophils, through the release of major basic protein, impair macrophage ability to clear MRSA. Moreover, we provide clinical evidence that eosinophils positively correlate with antibiotic use and worsened outcomes in patients hospitalized for viral infections. Altogether, our work establishes a counterproductive effect of antibiotic treatment during influenza infection that have negative immunologic consequences in the lungs thereby increasing the risk of developing a secondary bacterial infection.

overall_design: We have four groups Macrophage cultures with different conditions, three replicates for each group.

first: Peter

first: Tanyalak

last: Parimon

first: Stephanie

last: Bora

first: Marilia

last: Zuttion


title: Identification of retinal cell types within the ageing African turquoise killifish retina and their respective age-related transcriptional changes using scRNA-seq

city: Leuven

first: Lieve

last: Moons

address: Naamsestraat 61

department: Biology

country: Belgium

institute: KU Leuven

summary: The mammalian central nervous system (CNS) and its retina are susceptible to age-related patholgoies, resulting in progressive, irreversible diseases like glaucoma and age-related macular degeneration (AMD), which are increasingly prevalent with rising life expectancy. Currently, there are no targeted long-term therapies to prevent vision loss. The short lived African turquoise killifsh (Nothobranchius furzeri, GRZ-AD) is a valuable genetic model for ageing studies, displaying rapid ageing phenotypes within its four to six-month lifespan. Our investigation on the molecular consequences of ageing in the retina, employing scRNA-sequencing, shows a a comprehensive overview of the cellular heterogeneity of the killifish retina, uncovering age-related gene expression changes specific to certain retinal cell populations.

overall_design: The investigate the cellular heterogeneity of the killifish retina and age-related cell type specific gene expression changes, we performed scRNA-sequencing on the retinas of young (6 weeks), middle-aged (12 weeks) and old (18 weeks) killifish. Per condition (age group), we included two biological replicates containing retinas from 3 (young) or 2 (middle-aged and old) female killifish.

first: Steven

last: Bergmans

first: Nicole

last: Noel

first: Luca

last: Masin

first: Ellen

last: Harding

first: Aleksandra

middle: M

last: Krzywańska

first: Julie

middle: D

last: De Schutter

first: Ayana

last: Rajagopal

first: Chi-Kuo

last: Hu

first: Lut

last: Arckens

first: Philip

middle: A

last: Ruzycki

first: Ryan

middle: B

last: MacDonald

first: Brians

middle: S

last: Clark


title: Matrix stiffness-dependent regulation of immunomodulatory genes in human MSCs is associated with the lncRNA CYTOR

city: Toronto

first: Justin

middle: Jisu

last: Lim

address: 160 College Street

department: Moleuclar Genetics

country: Canada

institute: University of Toronto

summary: Previous studies have demonstrated that the physical properties of biomaterials can be adjusted to program therapeutically relevant functions in encapsulated mesenchymal stromal cells (MSCs). However, the intracellular pathways affected by mechanical cues in this cell type are not well understood. An understanding of the pertinent factors involved would not only aid in the rational design of substrates but also uncover targetable mechanisms that can facilitate the engineering of MSCs for cell therapies. Here, a bone marrow-mimetic hydrogel is employed to systematically explore the stiffness-responsive transcriptome of MSCs. High matrix rigidity impedes integrin-collagen adhesions which yields changes in cell morphology that are characterized by a contractile network of actin proximal to the cell membrane. This results in a suppression of ECM-regulatory genes involved in the remodeling of collagen fibrils and an upregulation of secreted immunomodulatory factors. Moreover, an investigation of long non-coding RNAs reveals that CYTOR contributes to these stiffness-driven changes in gene abundance. A robust knockdown of CYTOR using antisense oligonucleotides enhances the expression of numerous mechanoresponsive cytokines and chemokines to levels exceeding what is achievable by modulating matrix stiffness alone. Taken together, these findings emphasize the utility in studying previously unexplored mechanisms of mechanotransduction to inform novel strategies for enhancing the efficacy of MSC-based therapies.

overall_design:
To investigate the stiffness-sensitive transcriptome of MSCs and assess the role of intracellular contractility in mechanotransduction, we cultured human mesenchymal stromal cells (MSCs) in a stiffness-tunable hydrogel consisting of an interpenetrating network (IPN) of alginate and rat tail collagen I. The cells were encapsulated in IPNs with storage moduli of 150, 500, and 2000 Pa for 24 or 48 hours with either DMSO or blebbistatin treatment.
We preformed RNA-sequencing on two cDNA libraries: poly(A)-enriched and ribosomal RNA-depleted. The poly(A)-enriched libraries were comprised of 36 samples aquired from three biological replicates of all permutations of stiffness, blebbistatin, and time conditions described above.
The ribosomal RNA-depleted libraries were formed from a second set of 9 samples of MSCs cultured at the three different stiffnesses for 48 hours without any chemical treatment.

first: Kyle

middle: H

last: Vining

first: David

last: Mooney

first: Benjamin

last: Blencowe


title: Transcriptomic profiling reveals histone acetylation-regulated genes involved in somatic embryogenesis in Arabidopsis thaliana

city: Katowice

first: Barbara

middle: Karolina

last: Wójcikowska

state: Silesia

address: Jagiellonska

department: Faculty of Natural Sciences; Institute of Biology, Biotechnology and Environmental Protection

country: Poland

institute: University of Silesia

summary: Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed. To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2,4-dichlorophenoxyacetic acid; 2,4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors TF) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction. The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants.

overall_design: The immature zygotic embryos of Arabidopsis at the cotyledonary stage of development were cultured on two alternative SE-induction media, ET and EA, supplemented with TSA (1 µM) and auxin (5 µM 2,4-D), respectively. The explants that were cultured on a non-embryogenic medium (E0) developed into seedlings. The EA-, ET- and E0-cultured explant tissues were sampled for RNA-seq analysis at two culture points representing the early (5th day) and the advanced (10th day) stage of SE induction.  In total, six experimental combinations in three replicates were used in RNA-seq analysis.

first: Karolina

last: Chwiałkowska

first: Małgorzata

last: Gaj


title: Identification and characterization of metastasis-initiating cells in esophageal squamous cell carcinoma in a pulmonary metastasis mouse model [scRNA-Seq]

city: Hong Kong

first: Ching Ngar

last: Wong

state: Hong Kong

address: Lab Block, 21 Sassoon Road,

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

summary: Background and aims: Cancer metastasis is the biggest obstacle to esophageal squamous cell carcinoma (ESCC) treatment. At present, understanding of its mechanism remains insufficient. Therefore, an in-depth exploration of the mechanisms of metastasis is crucial for early detection and intervention to reduce metastasis-related mortality. Methods: This study applied single-cell RNA sequencing analysis to investigate lung metastatic ESCC cells isolated from a pulmonary metastasis mouse model at multiple timepoints to characterize early metastatic microenvironment. Results: We identified a small population of parental ESCC KYSE30 cell line (Cluster S) resembled metastasis-initiating cells (MICs) because they could survive and colonize at lung metastatic sites. By comparing differential expression profiles between Cluster S and other subpopulations, we identified a panel of 7 metastasis-initiating signature genes (MIS), including CD44 and TACSTD2, to represent MICs of ESCC. Functional studies demonstrated that Cluster S cells (CD44high) exhibited significantly enhanced cell survival (resistances to oxidative stress and apoptosis), cell migration, invasion, stemness, and in vivo lung metastasis capabilities. Multiplex immunohistochemistry (mIHC) staining of 4 MISs (CD44, S100A14, RHOD, and TACSTD2) in ESCC cell lines and clinical samples found that differential MIS expression scores (dMISs) could predict lymph node metastasis, overall survival and risk of carcinothrombosis. GO and KEGG analyses revealed that CD44high cells were enriched in cell migration, organ development, stress responses, and neuron development, which might be related to the establishment of early metastatic microenvironment. Conclusion: This study identified CD44, S100A14, RHOD, and TACSTD2 as MISs to represent the MICs in ESCC populations and predict patient outcomes. Keywords: ESCC, metastasis-initiating cells, metastasis-initiating signatures, biomarker, scRNA-seq.

overall_design: Human origin ESCC cell line labelled with luciferase and GFP (KYSE30-Luc-GFP) at in vitro state and retrieved from metastatic lungs of pulmonary metastasis mouse models at four timepoints (6 hours, 48 hours, 2 months, and 4 months) were collected via flow cytometry cell sorting (FACS), and undergone 10X Genomics single-cell transcriptome sequencing.

first: Ching

last: WONG

first: Yu

last: ZHANG

first: Beibei

last: RU

first: Songna

last: WANG

first: Hongyu

last: ZHOU

first: Jiarun

last: LIN

first: Yingchen

last: Lyu

first: Yanru

last: QIN

first: Peng

last: JIANG

first: Victor

last: LEE

first: Xin-Yuan

last: GUAN


title: A Transcription Factor Functional Atlas of Germline Development in Caenorhabditis elegans

city: Clayton

first: Sandeep

middle: Deveson

last: Gopal

state: Vic

address: 15 Innovation Walk,

department: Department of Anatomy and Developmental Biology

country: Australia

institute: Monash University

summary: Fertility requires the faithful proliferation of germ cells and their differentiation into gametes. Controlling these cellular states demands precise timing and expression of gene networks. Transcription factors (TFs) play critical roles in gene expression networks that influence germ cell development. There has, however, been no functional analysis of the entire TF repertoire in controlling in vivo germ cell development. Here, we analyzed germ cell states and germline architecture to systematically investigate the function of 364 germline-expressed TFs in the Caenorhabditis elegans germ line. Using germline-specific knockdown, automated germ cell counting, and high-content analysis of germ cell nuclei and plasma membrane organization, we identify 156 TFs with discrete autonomous germline functions. By identifying TFs that control the germ cell cycle, proliferation, differentiation, germline structure and fertility, we have created an atlas for mechanistic dissection of germ cell behavior and gamete production.

overall_design: To identify trancription factors expressed in the Caenorhadbditis elegans  germline

first: Wei

last: Cao

first: Qi

last: Fan

first: Gemmarie

last: Amparado

first: Dean

last: Begic

first: Rasoul

last: Godini

first: Roger

last: Pocock


title: Identification and characterization of metastasis-initiating cells in esophageal squamous cell carcinoma in a pulmonary metastasis mouse model [bulk RNA-Seq]

first: Ching Ngar

last: Wong

overall_design: Human origin ESCC cell line labelled with luciferase and GFP (KYSE30-Luc-GFP) underwent flow cytometry cell sorting (FACS) for metastasis-initiating signature enrichment, CD44 high verus CD44 low, and underwent bulk RNA sequencing.

first: Ching

last: WONG

first: Yu

last: ZHANG


title: Fungal Dysbiosis in Post-Influenza MRSA Infection

first: Changfu

last: Yao

overall_design:
Single cells were FACS sorted to gate out dead cells and subject for single cell RNAseq experiments, 4 mouse lungs for each group. Each repilicate was barcoded by Totalseq-A HTO antibody.
Please note that the .h5 data file linked to each sample is also associated with the corresponding HTO sample.

first: Peter

last: Chen

first: Tanyalak

last: Parimon

first: Stephanie

last: Bora


title: The Splicing Factor CCAR1 Regulates the Fanconi Anemia/BRCA Pathway

city: Boston

first: Huy

last: Nguyen

state: MA

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

summary: The twenty-three Fanconi Anemia proteins cooperate in a DNA repair pathway, called the FA/BRCA pathway, required for the monoubiquitination of FANCD2 and the excision of interstrand DNA crosslinks (ICLs). The CCAR1 (cell division cycle and apoptosis regulator 1) protein is also a regulator of ICL repair, though its possible function in the FA/BRCA pathway remains unknown. Here, we demonstrate that CCAR1 plays a unique upstream role in the FA/BRCA pathway and is required for FANCA protein expression and FANCD2 monoubiquitination. Interestingly, loss of CCAR1 results in retention of a poison exon in the FANCA transcript, thereby leading to reduced FANCA protein expression. A unique domain of CCAR1, the so-called EF-hand domain, binds to the spliceosome SF3B complex and is required for its mRNA splicing activity. Taken together, CCAR1 is a unique splicing factor, required for normal splicing of the FANCA mRNA and perhaps other mRNAs involved in various cellular pathways.

overall_design: To evaluate the possible genome-wide effect of CCAR1 knock-out, we performed RNA sequencing using RPE p53-/-  parental and CCAR1 knockout cells.

first: Naoya

last: Harada

first: Shuhei

last: Asada

first: Divya

last: R Iyer

first: Alan

last: D’Andrea


title: Nanos-2 mutant line of the sea anemone Nematostella vectensis

city: Vienna

first: Alison

middle: G

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

summary: CRISPR/Cas9 mediated gene knockout show that nanos2+ progenitor cells are indispensable for male and female germline maintenance in Nematostella. This suggests nanos and piwi genes have a conserved role in somatic and germline stem cells in cnidarians.

overall_design: Embryos/animals were dissociated and cell suspensions were processed with a 10X Genomics Chromium Controller

first: Ulrich

last: Technau


title: Cytoglobin overexpression-dependent transcriptomic changes in A375 melanoma cells

city: Antwerpen

first: Joey

last: De Backer

state: Antwerpen

address: Universiteitsplein 1

institute: University of Antwerp

summary: Cytoglobin (CYGB) is a member of the oxygen-binding globin superfamily. In this study, we comprehensively explored the CYGB-dependent transcriptome in A375 melanoma cells overexpressing CYGB. Our findings reveal that CYGB overexpression positively enriches cancer-associated pathways, including the mTORC1 and AKT/mTOR signaling pathways, which are frequently overactivated in tumors. Moreover, several cancer-associated pathways, such as epithelial-mesenchymal transition (EMT) mediated by CSPG4, were downregulated upon CYGB overexpression. Intriguingly, our results indicate that CYGB overexpression leads to a reduction in the inflammatory state of melanoma cells. This anti-inflammatory potential is exemplified by the downregulation of key inflammasome-associated genes, including NLRP1, CASP1, and CD74, which play pivotal roles in cytokine regulation and inflammasome activation. Consistent with established globin functions, CYGB appears to play a crucial role in redox homeostasis. Furthermore, our study highlights CYGB's involvement in DNA repair mechanisms and its regulation of NOX4, reinforcing its versatility in safeguarding genomic integrity. Collectively, our data illuminate the diverse functions of CYGB in melanoma cells, pointing to its roles in cellular protection against oxidative stress, inflammation, and cancer-associated pathways. These findings pave the way for further research into the physiological role of CYGB and its potential as a therapeutic target in melanoma.

overall_design: Differential gene expression analysis of CYGB overexpressing A375 melanoma cells compared to A375 wildtype melanoma cells

first: David

last: Hoogewijs


title: OPTN as a therapeutic target for acetaminophen-induced liver injury by activating mitophagy

city: Hangzhou

first: Jiajia

last: Wang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Acetaminophen (APAP) is a leading cause of acute liver failure in Western countries result from the accumulation of damaged mitochondria. However, there is no related clinically useful therapeutic intervention. Optineurin (OPTN) is a multifunctional protein involved in autophagy, oxidative stress, as well as nuclear factor κB (NF-κB) and IRF3 signaling, and OPTN mutations are associated with several human diseases.Here, to study the role of OPTN in APAP induced liver injury, we performed  RNA-seq analysis of isolated control and Optn-/- mouse liver tissues.

overall_design: RNA-seq analysis was performed on a total of 6 samples extracted from murine liver, post hepatic injury induced by acetaminophen administration. Transcriptional profiles were from replicate samples generated at 6 hours post injury. Replicate samples were generated from 2 individual animals sacrificed at each timepoint, and compared to a control of 2 animals not subjected to acetaminophen treatment.

first: Yueping

last: Qiu

first: Qinjie

last: Weng


title: Transcriptome expression study with chronological aging in human hippocampus

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

country: Spain

institute: Biodonostia Institute

summary: In our study, we performed a transcriptomic analysis from hippocampal samples from human individuals of different ages. We identified a set of genes that were differentially expressed in aged samples. Moreover, we revealed a subset of genes whose expression correlated with chronological aging. Analysis in a validation cohort confirmed some genes having negative correlation with age. Additional immunohistochemistry in another validation cohort confirmed transcriptomic results. In summary, these results identify putative biomarkers and regulators of brain aging.

overall_design: Brain hippocampal samples from human individuals from different ages ranging from 27 to 88 years-old.

first: Ander

last: Saenz-Antoñanzas

first: Manuel

last: Moreno-Valladares

first: Ainhoa

last: Alberro

first: Marian

last: de Pancorbo

last: Otaegui

last: Matheu


title: Regenerative trophoblast models are largely in concordance with trophoblasts from peri-implantation human embryos while maintaining subtle differences

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: The mechanisms controlling trophoblast proliferation and differentiation during embryo implantation are fundamentally important in defining a successful pregnancy, yet poorly understood. Human trophoblast stem cells (TSC) and BMP4/A83-01/PD17034-treated pluripotent stem cell derived trophoblast cells (BAP) are two widely employed, contemporary models to study trophoblast development and function but how faithfully they mimic the identity of early stage trophoblast cells has not been fully examined. Here, we evaluate the transcriptomic profiles of trophoblast cells from these two widely used cell models and directly compare them with trophoblast cells from peri-implantation stage human embryos during extended embryo culture (EEC) between embryonic d 8 to d 12. Cells from BAP and TSC models all grouped closely with trophoblast cells from EEC, with the trophoblast sublineages, including cytotrophoblast (CTB), syncytiotrophoblast (STB), and extravillous-like migratory trophoblast (MTB), clustered together following dimensional analysis and unsupervised hierarchical clustering. However, subtle differences amongst models exist for each trophoblast sublineages. TSC-CTB is more similar to EEC-CTB from d 8 embryos with transcripts associated with increased Wnt signaling activities important for trophoblast stemness. BAP-CTB are more similar to EEC-CTB from d 10 and 12 embryos and upregulate transcripts important for trophoblast differentiation and invasion. For STB, EEC-STB showed enriched GO terms related to oxygen-dependent metabolism, while BAP and TSC-derived STB both prioritize lipid and membrane synthesis as well as actin reorganization and cell spreading. EEC-MTB transcripts indicate an increased level of invasiveness and motility compared to TSC-MTB with increased proliferative capacity. We also provide a pool of novel lineage markers in early trophoblast that were upregulated (>4-fold) across all three models and validate the presence of 11 proteins prominent in peri-implantation human embryos. Together, our comprehensive analysis revealed that both commonly used BAP and TSC models resemble features of peri-implantation trophoblasts, while still maintaining subtle transcriptomic differences in sublineages.

overall_design: We collected human TSC and TSC derived STB and EVT, as well as hESC derived trophoblast cells (separated by cell size, <40um and >70um) by BAP treatment, then total RNA was extracted, followed by RNA-sequencing analysis.

first: Zongliagn

first: Ye

last: Yuan

first: Hao

last: Ming


title: Lactic acid bacteria derived bacteriocin targets purine and histidine metabolisms of gut microbiota to alleviate colitis

status: Public on Aug 20 2024

first: Xiangfeng

last: Chen

address: Xuezheng Street 18

institute: Zhejiang Gongshang University

summary: Gut microbiota is an unignored target in maintaining intestinal homeostasis due to its regulatory effects on intestinal health through multiple mechanisms, including enhancing intestinal barriers, modulating microbial diversity, secreting various metabolites, etc. Bacteriocins produced by probiotics have been gradually proved vital for intestinal diseases intervention, however, the corresponding mechanisms have received less attention and the whole story of their regulative activities are hard to be fully uncovered. The two-peptide Plantaricin NC8 (PLNC8), coded by gene plnc8, is a bacteriocin ubiquitously produced by Lactobacillus plantarum, has been regarded as the potential vital bacteriocin for the anti-inflammatory effects of Lactobacillus plantarum. This study exploited CRISPR-cas9 and prokaryotic gene overexpression techniques to construct the plnc8 strains for the anti-inflammatory mechanism investigation. Based on the metagenomics, transcriptomics and metabolomics analysis, the anti-enteritis mechanism of PLNC8 systematically in DSS-induced enteritis models were comprehensively revealed. PLNC8 induced alterations in the composition of gut microbiota composition, promoting the alterations of multiple probiotics such as Eubacterium plexicaudatum, Doreasp.5-2, Enterococcus cecorum and Prevotella oulorum. Besides, various metabolites produced by the gut microbiota were influenced, and the key metabolites of xanthine, hypoxanthine, and L-histidine were regulated via purine and histidine metabolic pathways. These metabolites further inhibited p38 MAPK phosphorylation of enterocytes induced by DSS. Ultimately, the intestinal barrier repairment and anti- enteritis were achieved, proving the anti-enteritis effects of PLNC8 via microbe-metabolites-enterocyte axis.

overall_design: Besides, the repaired intestinal epithelial damage was also observed; thus, transcriptome analysis was further conducted to ensure the way of differential expressed metabolites to regulate enteritis. Based on the transcriptome, the significant differential expressions of murine colonic genes transcription can be revealed.

first: Qing

last: Gu

first: Ping

last: Li

first: Yonglu


title: Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries [ChIP-Seq1]

city: Miami

first: Danny

last: Reinberg

state: Florida

address: 1501 NW 10th Ave

department: Sylvester Cancer Center/Human Genetics

institute: University of Miami

summary: In this experiment, we sought to identify how the distribution of CTCF, MAZ, PATZ1, RAD21 change in WT and PATZ1 KO mouse embryonic stem cells (ESCs).

overall_design: Examination of CTCF, MAZ, PATZ1, and RAD21 binding in embryonic stem cells using ChIP-seq, by status of WT and PATZ1 KO.


title: Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries

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

overall_design: Refer to individual Series


title: Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries [RNA-Seq2]

summary: In this experiment, we sought to analyze how transcriptome of WT and PATZ1 knock-out (KO) cells change during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

overall_design: Examination of gene expression of cervical MNs differentiated from ESCs using ribo-zero RNAseq, by knock-out status of PATZ1 in duplicates, 2 cell lines (WT and PATZ1 KO)


title: Targeting NTRK1 Enhances Immune Checkpoint Inhibitor Efficacy in NTRK1 Wild-type Non-Small Cell Lung Cancer

city: Winston Salem

first: Fei

last: Xing

state: NC

address: Main Medical center BLVD

department: Cancer Biology

institute: Wake Forest School of Medicine

summary: Treatment of non-small cell lung cancer (NSCLC) has drastically changed in recent years owing to the robust anti-cancer effects of immune-checkpoint inhibitors (ICI). However, only 20% of NSCLC patients benefit from ICIs, highlighting the need to uncover the mechanisms mediating resistance. By analyzing the overall survival (OS) and mutational profiles of 424 NSCLC patients who received ICI treatments between 2015 and 2021, we determined that patients carrying a loss of function mutation in neurotrophic tyrosine kinase receptor 1 (NTRK1) had a prolonged OS compared to patients with wild-type NTRK1. Notably, suppression of the NTRK1 pathway by knockdown or Entrectinib treatment significantly enhanced ICI efficacy in mouse NSCLC models. RNA sequencing of tumors and NTRK1 knockdown cell lines were performed to demonstrates the role for NTRK1 signaling.

overall_design: To investigate the role of NTRK1 in ICI response in NSCLC, we constructed NTRK1 knockdown cell line. Tumors from mice treated by ICI with or without NTRK1 inhibitor were also sequenced.

first: Margaret

middle: R

last: Smith

first: Yin

last: Liu


title: Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries [ChIP-Seq2]

summary: In this experiment, we sought to identify how the distribution of CTCF, MAZ, and RAD21 change in CTCF-degron (no auxin), CTCF-degron (auxin), CTCF-degron MAZ KO (no auxin), and CTCF-degron MAZ KO (auxin) backgrounds in mouse embryonic stem cells (ESCs).

overall_design: Examination of CTCF, MAZ, and RAD21 binding in embryonic stem cells using ChIP-seq, by status of CTCF-degron (no auxin), CTCF-degron (auxin), CTCF-degron MAZ KO (no auxin), and CTCF-degron MAZ KO (auxin).


title: Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries [RNA-Seq1]

summary: In this experiment, we sought to analyze how transcriptome of WT and PATZ1 knock-out (KO) cells change in mouse embryonic stem cells (ESCs)

overall_design: Examination of gene expression of ESCs using ribo-zero RNAseq, by knock-out status of PATZ1 in triplicates, 2 cell lines (WT and PATZ1 KO)


title: RASD1: a small G protein with a complex role in vasopressin magnocellular neurons

city: Bristol

first: Ghadir

last: ElSamad

address: Whitson St.

country: United Kingdom

institute: University of Bristol

summary: To investigate  the polyadenylated transcriptomes of the Sprague Dawley rat SON following the knockdown (KD) of RASD1 by microRNA.

overall_design:
We then performed gene expression profiling analysis using data obtained from control and RASD1 KD rat in euhydrated condition.
Comparative gene expression profiling analysis of RNA-seq data for the Control and KD SON of rats.

first: Audrys

last: Pauza

first: Michael

last: Greenwood

first: David

last: Murphy


title: Regeneration-specific lncRNA CR40469 is essential for Drosophila regeneration

city: Barcelona

first: Montserrat

last: Corominas

state: Catalonia

address: Diagonal 643

department: Genètica, Microbiologia i estadística

institute: University of Barcelona

summary: The discovery of functional long non-coding RNAs (lncRNAs) changed the initial concept of lncRNAs as transcriptional noise. Since then, a wide array of functions have been associated with lncRNAs, including changes in the chromatin state and gene expression, modulation of splicing, translation or degradation of mRNAs. Also, many lncRNAs are known to be deregulated in multiple diseases, including cancer and neurological disorders. However, functional studies of lncRNAs are hindered by the usual lack of phenotypes upon deletion or inhibition. Here, we used Drosophila imaginal discs as a model system to identify putatively functional lncRNAs involved in development and regeneration. We described the subset of lncRNAs expressed in the wing, eye and leg disc development. Also, we analyzed transcriptomic data from regenerating wing discs to profile the expression pattern of lncRNAs upon damage. Particularly, we focused on the intergenic lncRNA CR40469 whose expression is upregulated in regeneration. We generated fully viable CR40469 mutants that showed no visible developmental defects. However, these mutants experience a remarkable loss of their wing regeneration capacity upon the induction of cell death. Additionally, we describe a duplication of the CR40469 genomic sequence in the Drosophila genome, but it does not seem to be necessary for development or wing regeneration.

overall_design: RNA-seq data for Drosophila wing imaginal discs after cell death induction

first: Carlos

last: Camilleri-Robles

first: Raziel

last: Amador-Rios

last: Corominas-Guiu


title: RNA Interacts with Topoisomerase I to Modulate its Catalytic Activity

city: Chicago

first: Mannan

last: Bhola

state: IL

address: 303 E Superior St

department: BMG

institute: Northwestern university

summary: Topoisomerase I (TOP1) is an essential enzyme that relaxes DNA to prevent and dissipate torsional stress during transcription. However, the mechanisms underlying the regulation of TOP1 activity remain elusive. Using eCLIP and UV-RIP-seq we identify TOP1 as a RNA binding protein (RBP). Using a TOP1 RNA binding mutant and TOP1cc-seq to map TOP1 catalytic activity, we reveal that RNA opposes TOP1 activity as RNAPII commences transcription of active genes. These findings support new insights into the coordinated actions of RNA and TOP1 in regulating DNA topological stress intrinsic to RNAPII-dependent transcription.

overall_design: Examination of TOP1 UV-RIP-seq, TOP1 eCLIP-seq and TOP1cc-seq in SW480 colon cancer cell line.

first: Kouki

last: Abe

first: Paola

last: Orozco

first: Homa

last: Rahnamoun

first: Pedro

last: Avilla-Lopez

first: Elijah

last: Taylor

first: Nefertiti

last: Muhammad

first: Anne

last: Starner

first: Bei

first: Prachi

last: Patel

first: John

last: Marko

first: Chuan

last: He

first: Eric

middle: L

last: Van Nostrand

first: Alfonso

last: Mondragón

first: Shannon

last: Lauberth


title: An unbiased lncRNAs dropout CRISPR-Cas9 screen reveals RP11-350G8.5 as a potential therapeutic target for Multiple Myeloma

city: Milano

first: FRANCESCO

last: IORIO

state: MI

address: Viale Rita Levi-Montalcini, 1 (Area MIND)

country: Italy

institute: Human Technopole

summary: Multiple Myeloma (MM) is an incurable malignancy characterised by alterations of coding and non-coding genes that promote tumour growth and drug resistance. Despite the crucial role of long non-coding-RNAs (lncRNAs) in myeloma genesis is established, the functional role of the non-coding RNAome in MM remains largely unknown. We performed an unbiased CRISPR-Cas9 recessive screen targeting 671 lncRNAs in MM cell lines unvealing and prioritising a list of novel onco-lncRNAs essential for MM cell fitness and associated with high expression and poor prognosis in MM patients. Among them, RP11-350G8.5 emerged as the most promising vulnerability for MM cells, irrespective of their resistance to the standard-of-care bortezomib. We i) validated the oncogenic role of RP11-350G8.5 in vitro and in vivo; ii) characterised its function in relation  to the unfolded protein stress response and induction of immunogenic cell death, and iii) shed light on its sub-cellular localisation, structural and chemical predictions of RNA-G-quadruplex-forming regions to pave the way to the development of novel therapeutics.

overall_design: To reveal the molecular changes induced by RP11-350G8.5 KO in MM cells resistant to bortezomib (ABZB), we profiled the cell line, 7 days post transduction with SCRAMBLE or RP11-350G8.5 KO CRISPR-Cas9 vectors, via RNA-sequencing from two independent biological replicates.


title: Fetal hypoplastic lungs have multilineage inflammation that is reversed by amniotic fluid stem cell extracellular vesicle treatment

first: Lina

last: Antounians

state: Ontario

address: 686 Bay St

institute: The Hospital for Sick Children

summary: We performed single nucleus RNA-seq on rat fetal lungs from: control (normal), hypoplastic (injury), and hypoplastic+ amniotic fluid stem cell extracellular vesicles treated (injury+treatment).

overall_design: Single nucleus RNA-seq on rat fetal lungs at E21.5. Conditions: 1) control (normal), 2) hypoplastic (injury), and 3) hypoplastic+ amniotic fluid stem cell extracellular vesicles treated (injury+treatment)


title: Transcriptome profiling of L02 cells upon Huh7-cell-derived large extracellular vesicles incubation

city: Wenzhou

first: Pei-pei

last: Hou

state: Zhejiang

address: Central North Road, Ou'hai District

department: School of Laboratory Medicine and Life Sciences

institute: Wenzhou Medical University

summary: Analysis of the transcriptome of L02 cells upon Huh7-cell-derived large extracellular vesicles (lEVs) incubation. L02 cells were incubated with or without lEVs (10 μg/ml) derived from control or ACSL4 knocking down (ACSL4 KD) Huh7 cells for 3 days, and the gene expression profiling analysis were then performed. The result provides a new perspective on the crosstalk between Huh7 cells and L02 cells via lEV-mediated ACSL4 transmission.

overall_design: Total RNA was extracted from L02 cells by Trizol method and the gene expression was quantified by RNA-seq analysis.

first: Yong-liang

last: Lou


title: RNA sequencing of bronchial epithelial cells cultured in air-liquid interface for 7 days treated or not with an antibody targeting the sonic hedgehog ligand (AB5E1)

city: Reims

first: Valérian

last: Dormoy

address: 45 rue Cognacq-Jay

country: France

institute: Université de Reims Champagne-Ardenne

summary: The hedgehog pathway is crucial during airway epithelial cell differentiation. To assess the transcriptomic print of airway epithelial cells in absence of hedgehog pathway activation, we performed a comparative transcriptomic analysis on air-liquid interface cell cultures. Bronchial epithelial cells from 5 non-COPD subjects (ex- and current smokers) were isolated from bronchial brushes and cultured in air-liquid interface. The total RNA were extracted after 7 days of culture in air-liquid conditions in presence of an antibody targeting the sonic hedgehog ligand (AB5E1) or not (CTL). The libraries were prepared with NEBNext Ultra II directeional RNA Library Prep Kit and sequenced on Illumina.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bronchial airway epithelial cells

first: Randa

last: Belgacemi

first: Audrey

last: Brisebarre

first: Laure

last: Petit


title: Human microglia carrying an early-onset Parkinson’s disease mutation display cell-autonomous disease-relevant phenotypes that may worsen neuronal damage

city: Leeds

first: Marine

last: Krzisch

state: West Yorkshire

address: Woodhouse Lane

department: School of Biomedical Sciences

institute: University of Leeds

summary: Parkinson’s disease (PD) is characterized by the aggregation of α-synuclein into Lewy bodies and Lewy neurites in the brain. Microglia-driven neuroinflammation may contribute to neuronal death in PD, however the exact role of microglia remains unclear and has been understudied. The A53T mutation in the gene coding for α-synuclein has been linked to early-onset PD, and exposure to A53T-mutant human α-synuclein increases the potential for inflammation of murine microglia. To date, its effect has not been studied in human microglia. We aimed to study the impact of the A53T mutation on human microglia developed in a physiologically relevant context Here, we used 2-dimensional cultures of human iPSC-derived microglia and transplantation of these cells into the mouse brain to assess the effects of the A53T mutation on human microglia. We found that A53T-mutant human microglia had an intrinsically increased propensity towards pro-inflammatory activation upon inflammatory stimulus. Additionally, A53T mutant microglia showed increased oxidative stress, with a strong decrease in catalase expression in non-inflammatory conditions. Together, these results indicate that A53T mutant human microglia display cell-autonomous phenotypes that may worsen neuronal damage in early-onset PD.

overall_design: 3 isogenics pairs of A53-mutant (PD)/control microglia were used in this study. Each cell line was differentiated separately, or transplanted into a separate cohort of mice. The RNA was either extracted directly from the cultured cells, or the transplanted cells were extracted from the mouse brain using GFP labeling and the RNA was subsequently extracted for each cell line.

first: Bingbing

last: Yuan


title: Sigma-1 Receptors Control Neuropathic Pain and Peripheral Neuroinflammation After Nerve Injury in Female Mice: A Transcriptomic Study

city: GRANADA

first: Enrique

middle: José

last: Cobos del Moral

state: Granada

address: Departamento de Farmacología, Facultad de Medicina, Torre B, Planta 11, Despacho. B11-04.

department: Pharmacology

institute: University of Granada

summary: To investigate transcriptional changes in the DRG and dorsal spinal cord in wild-type and sigma-1 knockout mice in a well-established model of neuropathic pain (Spared Nerve Injury)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DRG and dorsal spinal cord from wild-type and sigma-1 knockout mice under naive conditions or after spared nerve injury

first: M

last: Ruiz-Cantero

last: Cobos


title: RNA-sequencing of the oxygen induced retinopathy (OIR) model in C57BL/6 mice

city: 上海/上海市/杨浦区

first: 青

last: 李

address: 长海路168号

institute: 中国人民解放军海军军医大学第一附属医院

summary: Pathological retinal angiogenesis is one of the major causes of vision loss worldwide. The breakdown of blood vessels and aberrant vessels growth usually lead to hemorrhage, macular edema, fibrotic scar, and retinal detachment. OIR model serves as a proxy for human pathological retinal neovascularization such as proliferative diabetic retinopathy, retinal vein occlusion and retinopathy of prematurity. C57BL/6 mice were exposed to 75% O2 in a hyperoxic chamber from postnatal day P7 to P12 and then returned to room air. The greatest neovascular response occurred at postnatal 17 days (P17) when the mice are put back to room air condition for 5 days. In order to reveal potential genes that involve in pathological neovascularization, we performed transcriptomic analyses of retina of P17.

overall_design: 12 samples were analyzed: normoxic mice postnatal 17 (6 replicates), OIR mice postnatal 17 (6 replicates)

first: Hongyuan

last: Song

first: Wei

last: Shen

first: Qing

last: Li

first: Xiao

last: Gui


title: YTHDF2 Promotes Cardiac Ferroptosis via Degradation of SLC7A11 in Cardiac Ischemia–reperfusion Injury

city: harbin

first: yu

last: bian

address: baojian road

institute: harbin medical university

summary: Aims: Myocardial ischemia–reperfusion (I/R) injury severely facilitates cardiomyocyte death and endangers human health. RNA N6-methyladenosine (m6A) methylation modification plays a critical role in cardiovascular diseases. M6A reader YTHDF2 could identify m6a-modified RNA and promote target RNA degradation. Hence, we hypothesized that YTHDF2 impacts I/R injury by regulating RNA stability, in turn revealing the potential regulatory mechanism.  Results: Both the mRNA and protein levels of YTHDF2 were upregulated in I/R mice and hypoxia-reoxygenation (H/R)-induced cardiomyocytes. Silencing endogenous YTHDF2 abrogated cardiac dysfunction and lowered infarct size in I/R mice, and forced expression of YTHDF2 aggravated the above-mentioned adverse pathological process. Consistently, the protective effect of silencing YTHDF2 reappeared in cardiomyocytes induced by H/R and erastin. Furthermore, RNA-seq and RIP revealed that YTHDF2 could recognize the m6A modification sites of ferroptosis-related gene SLC7A11 mRNA to promote its degradation both in vivo and in vitro. Inhibition of SLC7A11 also aggravated cardiac function, infarct size and the release of LDH in I/R mice after silencing YTHDF2. The advantageous effect of si-YTHDF2 in H/R injury was reversed by cotransfection with si-SLC7A11, which substantially exacerbated ferroptosis and the production of ROS. Innovation and Conclusion: All of the obtained data demonstrate that the cardioprotective effects of silencing YTHDF2 are accomplished by enhancing SLC7A11 stability and expression and reducing the level of ferroptosis, furnishing novel potential therapeutic targets for treating ischemic cardiac diseases.

overall_design: C57BL/6 mice were injected with the virus solution AAV9 carrying a YTHDF2 shRNA or NC via tail vein injection, and a cTNT promoter conjugated with the GFP gene was constructed. After 4 weeks, I/R surgery was administered.

first: Yu

last: Bian

first: Baofeng

last: Yang

first: Ning

last: Wang

first: Ping

last: Pang


title: Bulk RNA-seq analysis of IFNγ-PD-L1all, IFNγ+PD-L1all and IFNγ+PD-L1hi PDAC 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: For comparison of the transcription profile between IFNγ-PD-L1all and IFNγ+PD-L1all cells, we treated KPC1199 cells with vehicle control or 10 ng/mL recombinant mouse IFNγ for 20 hours and harvested them. For comparison of PD-L1hi with PD-L1all, cells were either sorted with the top 15% PD-L1+ or total of IFNγ+PD-L1all PDAC cells, and freshly collected as soon as possible to be used for RNA preparation.

overall_design: For RNA preparation, PDAC cell were collected by FCM analysis of PD-L1 surface expression after the stimulation of recombinant mouse IFN-γ. 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: Chen

last: Yueyue

first: Niu

last: Ningning


title: Different effects of pre-mRNA splicing inhibitors on RNA polymerase II transcription

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

summary: The production of a mature mRNA in eukaryotes requires both transcription by RNA polymerase (pol) II and co-transcriptional processes, including mRNA capping, splicing, and cleavage and polyadenylation. The pol II complex serves as a hub to coordinate transcription and co-transcriptional processes, especially via the carboxyl terminal domain (CTD) of the large subunit of pol II that is composed in human of 52 repeats of the heptapeptide Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 and that can be modified by several post-translational modifications. To understand better the effects of pre-mRNA splicing on pol II transcription, we investigated the transcriptional effects of two small molecule inhibitors of splicing: Madrasin and Isoginkgetin. We found that while Madrasin can quickly inhibit pre-mRNA splicing, it is not the case of Isoginkgetin, which affects transcription before any visible effect on pre-mRNA splicing. Interestingly, we found that these two small molecules promote a global transcriptional readthrough, including intronless protein-coding genes and histone genes, which is not the case of the splicing inhibitors targeting the splicing factor SF3B1.

overall_design: mNET-seq to determine the effects of the pre-mRNA splicing inhibitors Madrasin (30 minutes, 90 μM) and Pladienolide B (30 minutes, 1 μM), and of the CDK9 inhibitor DRB (15 minutes, 100 μM) with DMSO as control, on nascent transcription (total RNA polymerase II) and pol II Tyr1, Ser2, Thr4, Ser5, and Ser7 phosphorylation.

first: Gilbert

last: Ansa

first: Shona

last: Murphy


title: The effect of Glutamine synthetase on the expression profile in the macrophages with  LPS treatment

first: Jianghong

last: Yu

state: State...

address: Dong'an Road

institute: Fudan University

summary: RNA-seq was analyzed to confirm related genes enrichment in BMDMs transfected with control or overexpressing Glul constructed using lentiviral vectors for 36h, followed by stimulating with LPS (100 ng/ml) for 3h for transcriptome assay.

first: Huilu

last: Zhang

first: Jie

last: Liu


title: TCR beta sequencing in LMP2-positive and LMP2-negative human T cells treated with anti-PD-L1 and anti-TIM3 antibodies.

city: Montreal

first: Jean-Sebastien

last: Delisle

state: Quebec

address: 5415 Boulevard de l'Assomption

institute: Centre de recherche de l'Hôpital Maisonneuve-Rosemont

summary: We report the change in TCR beta profile of LMP2 multimer-positive and multimer-negative human T cells generated following weekly stimulations with antigen-pulsed dendritic cells and subjected or not to PD-L1/TIM3 double blockade.

overall_design: TCR beta (CDR3 region) at day 21 and 28 in LMP2 multimer FACS-sorted negative and positive fractions of human T cells cultured with or without anti-PD-L1 and anti-TIM3 antibodies from 4 healthy donors.

first: Shirin

last: Lak

first: Valérie

last: Janelle

first: Anissa

last: Djedid

first: Gabrielle

last: Boudreau

first: Ann

last: Brasey

first: Véronique

last: Lisi

first: Cédric

last: Carli

first: Lambert

last: Busque

first: Vincent-Philippe

last: Lavallée

first: Jean-Sébastien


title: Parsing digital or analogue TCR performance through piconewton forces

city: BOSTON

first: Aoi

last: Akitsu

address: 35 Binney St., Boston

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: T lymphocytes leverage T-cell receptor (TCR) recognition of aberrant peptides bound to major histocompatibility complex molecules (pMHCs) on altered cells to protect the mammalian host from infectious pathogens and cancerous transformations. While adaptive immunity requires efficient TCR performance, comparison metrics are widely limited to force-free assays. Recent data reveals, however, that mechanical load on the TCR-pMHC bond resulting from cellular motions between a T cell-antigen presenting cell conjugate formed during immune surveillance tunes TCR specificity and sensitivity. Here, we cloned TCRs from lung resident CD8 T cells following influenza A virus (IAV) infection directed against two immunodominant epitopes, the luminous nucleoprotein NP366-374 /Db and sparse acid polymerase PA224-233/Db pMHCs, arrayed at >1000 vs <10 copies/cell, respectively. Using optical tweezers-based methods to apply biologically relevant loads, we observe that certain TCRs belonging to the NP repertoire require many ligands for activation while others only few, functioning in analogue or digital modes, correspondingly. In contrast, prevalent TCRs tested in the PA repertoire all perform digitally. When held at a critical force, moreover, even digital TCRs are distinguishable, exhibiting dramatic increases in bond lifetime and performance relating to their structural transition rate and distance. Digital performance is best for both specificities in vitro and in vivo, but undiscernible using conventional functional avidity or TCR sequence distance metrics. Correlates of optimal biophysical parameters include magnitudes of ERK phosphorylation, CD3 surface loss, and activation marker upregulation.  Our findings underscore the requirement to match TCR performance quality with pMHC copy number, as nature does. Given tumor antigen array paucity, engaging choice digital TCRs appears critical for T-cell adoptive cancer therapies and vaccines.

overall_design:
To determine response of specific TCR-bearing T cells to influenza virus, CD8+ retrogenic T cells bearing unique TCR were adoptively transferred into C57BL/6 mice hosts that were then infected with influenza A virus(IAV).
The transferred retrogenic T cells expressed unique fluorophores permitting their isolation by FACs from dissociated lymph node and lung of mice at 7 days post-IAV infection.
We then performed RNA-Seq and gene expression analysis of the lymph node- and lung-isolated retrogenic T cells for 3 unique TCR on 3 individual mice for each TCR (i.e. 3 replicates of lymph node, and of lung, for 3 TCR: 18 samples).

first: Matthew

last: Booker

first: Jonathan

last: Duke-Cohan

first: Ellis

last: Reinherz


title: CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub and H3K27me3 in treated KPC1199 murine PDAC cell line

first: Ningning

last: Niu

summary: To gain mechanistic insight into how Epigenetic factors reprogramming tumor immune microenvironment in response to IFNγ stimulation. we performed CUT&Tag sequencing in murine PDAC cells.For comparison of the transcription profile between IFNγ-PD-L1all and IFNγ+PD-L1all cells, we treated KPC1199 cells with vehicle control or 10 ng/mL recombinant mouse IFNγ for 20 hours and harvested them. For comparison of PD-L1hi with PD-L1all, cells were either sorted with the top 15% PD-L1+ or total of IFNγ+PD-L1all PDAC cells, and freshly collected as soon as possible. Hyperactive pA-Tn5 Transposase for CUT&Tag kit from Vazyme (TD901), and antibodies against H3K4me3 from Abcam (ab213224), H3K27Ac from Abcam (ab4729),H2A119Ub from Cell Signaling (8240T) and H3K27me3 from Abcam (ab6002) 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 withIFNγ-PD-L1all, IFNγ+PD-L1all and IFNγ+PD-L1hi  were first established. CUT&Tag and DNA library were prepared according to manufacturer’s instructions.

first: Chen

last: Yueyue

first: Niu

last: Ningning


title: Characterization of aberrant splicing reveals CLK1 as a candidate oncogenic dependency in pediatric high-grade gliomas

city: Philadelphia

first: Jo Lynne

last: Rokita

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: Pediatric brain cancer is the leading cause of disease-related mortality in children, and many aggressive tumors still lack effective treatment strategies. Despite extensive studies characterizing these tumor genomes, alternative transcriptional splicing patterns remain underexplored. Here, we systematically characterized aberrant alternative splicing across pediatric brain tumors, identifying pediatric high-grade gliomas (HGGs) among the most heterogeneous. Through integration with UniProt Knowledgebase annotations, we identified 12,145 splice events in 5,424 genes, leading to functional changes in protein activation, folding, and localization. We discovered that the master splicing factor and cell-cycle modulator, CDC-like kinase 1 (CLK1), is aberrantly spliced in HGGs to include exon 4, resulting in a gain of two phosphorylation sites and subsequent activation of CLK1. Inhibition of CLK1 with Cirtuvivint in the pediatric HGG KNS-42 cell line significantly decreased both cell viability and proliferation in a dose-dependent manner. Morpholino-mediated depletion of CLK1 exon 4 splicing reduced RNA expression, protein abundance, and cell viability. Notably, KNS-42 cells treated with the CLK1 exon 4 morpholino demonstrated differential expression impacting 173 cancer genes and differential splicing with loss or gain of a functional site in 529 cancer genes. These genes were enriched for cancer-associated pathways, with 20 identified as significant gene dependencies in pediatric HGGs. Our findings highlight a dependency of pediatric HGGs on CLK1 and its roles contributing to tumor splicing heterogeneity through transcriptional dysregulation of splicing factors and direct transcriptional modulation of oncogenes. Overall, aberrant splicing in HGGs and other pediatric brain tumors represents a potentially targetable oncogenic pathway contributing to tumor growth and maintenance. Continued investigation of these mechanisms is essential for developing new effective treatment strategies for these patients.

overall_design: We investigated the impact of CLK1 exon 4 splicing by treating KNS-42 cell lines with morpholino oligomers targeting exon 4 to force exon 4 skipping.

first: Naqvi

last: Ammar

first: Rokita

last: Jo Lynne


title: Single-cell RNA sequencing of mesoderm cells derived from hESCs during hematopoietic differentiation

city: 288 Nanjing Rd, Heping

first: Jingjing

last: Zhao

state: TianJin

address: Nanjing Road

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

summary: Purpose: The goal of this study is to identify and characterize human hematopoietic mesoderm. Methods: APLNR+ mesoderm cells  derived from hESCs (H1) were sorted and collected for single cell RNA sequencing after hematopoietic differentiation.

overall_design: APLNR+ mesoderm cells derived from hESC were sorted by fluorescence-activated cell sorting (FACS)  after hematopoietic differentiation. After cell number counting with TC20™ Automated Cell Counter Approximately Number (5000, etc.), cells were subjected to the 10XGenomics Chromium Controller machine for Gel Beads-in-Emulsion (GEM) generation.

first: Yuqi

last: Wen

first: Hongtao

last: Wang

first: Jiaxi

last: Zhou


title: MiR-221/222 suppression induced by activation of the cAMP/PKA/CREB1 pathway is required for cAMP-induced bidirectional differentiation of glioma cells.

first: Minfeng

last: Shu

address: No.131 Dongan Road II Xuhui district

summary: Factors that increase cAMP levels can induce lineage-specific differentiation of glioma cells into astrocyte-like cells. However, the differentiation pattern and underlying mechanisms remain unclear. Here, we find that cAMP/PKA/CREB1-induced miR-221/222 suppression contributes to the neuron-like differentiation of gliomas. cAMP agonists selectively induced neuron- and astrocyte-like but not oligodendrocyte-like differentiation of C6 glioma cells. PKA inhibitors and CREB1 knockout blocked neuron-like differentiation of glioma cells. cAMP inhibited miR-221/222 in a PKA/CREB1 dependent manner. Importantly, both in vitro and in vivo assays demonstrated that transcriptional suppression of miR-221/222 is required for neuronal differentiation of glioma cells. Our findings suggest that increasing cAMP levels can induce bidirectional differentiation of glioma cells. Furthermore, the miR-221/222 cluster acts as an epigenetic brake during glioma differentiation.

overall_design: Examination of mRNAs in C6 glioma cells treated with or without forskolin.

first: Qian

last: Liu

first: Ruotong

last: Tian

first: Panpan

last: Yu


title: Recording morphogen signals reveals mechanisms underlying gastruloid symmetry breaking

status: Public on Aug 19 2024

city: Princeton

first: Harold

middle: Michael

last: McNamara

state: NJ

address: Carl Icahn Laboratory, South Drive

department: Lewis-Sigler Institute

institute: Princeton University

summary: We engineered mouse embryonic stem cells to express reporters and recorders developmental signals, and traced how early signaling states predict cell fates.

overall_design: For single cell sequencing analysis, we collected and dissociated gastruloids at both 96 hours after aggregate ("t96") and 120 hours after aggregation ("t120"). For the 120 h sample, we also recording Wnt signaling activity earlier at 96 h, and used fluorescence activated cell sorting (FACS) to separate Wnt-recorded cells based on a GFP signal ("G") from those in which Wnt was not recorded ("R")


title: Transcriptomic analysis of liver lymphatic endothelial cell isolated from sham or ischemia/reperfusion (I/R) mouse model

city: New haven

first: Yilin

last: Yang

state: CONNECTICUT

address: 300 Cedar street, S220

institute: yale university

summary: This study aims to determine changes in transcriptomic profiles in lymphatic vessels in response to ischemia-reperfusion injury, which mimics conditions in liver transplantation. This experiment will determine the potential role of lymphatic vessels during the ischemia-reperfusion injury in the liver.

overall_design: Samples are hepatic lymphatic endothelial cells isolated from IL7-GFP reporter mice with or without ischemia-perfusion injury.

first: Iwakiri

last: Yasuko


title: Functional maps of a genomic locus reveal confinement of an enhancer by its target gene [ChIP-seq]

city: Amsterdam

first: Christina

last: Moene

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Genes are often activated by enhancers located at large genomic distances. The importance of this positioning is poorly understood. Here, by relocating different promoter-reporter constructs into >1,000 alternative positions within a single locus, we dissected the positional relationship between the mouse Sox2 gene and its distal enhancer. This revealed an intricate, sharply confined activation landscape, in which the native Sox2 gene occupies an optimal position for its activation. Deletion of the gene relaxes this confinement and broadly increases reporter activity. Surprisingly, this confining effect of the Sox2 gene on reporter activity is partially conferred by its ~1 kb coding region. Our local relocation approach provides high-resolution functional maps of a genomic locus and reveals that a gene can strongly constrain its enhancer’s realm of influence.

overall_design: Chromatin immunoprecipitation DNA-seqeuncing (ChIP-seq) for the transcription factor CTCF.

first: Mathias

last: Eder

first: Lise

last: Dauban

first: Christ

last: Leemans

first: Bas

last: van Steensel


title: Time-course scRNA-seq of definitive endoderm directed differentiation

city: Worcester

first: Rene

last: Maehr

state: MA

address: 55 Lake Ave N

department: Program in Molecular Medicine

institute: UMass Medical School

summary: As part of a benchmarking study aiming to infer gene regulatory network models and transcription factor effects from time-series data, we took daily samples of pluripotent stem cells during in vitro differentiation to definitive endoderm.

overall_design:
PSC culture and endoderm induction follow Genga et al. 2019 (Genga, R. M., Kernfeld, E. M., Parsi, K. M., Parsons, T. J., Ziller, M. J., & Maehr, R. (2019). Single-cell RNA-sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development.Cell reports,27(3), 708-718.)
Fixation, tagging, and library prep follow Gehring et al. 2018 (Gehring, J., Park, J. H., Chen, S., Thomson, M., & Pachter, L. (2018). Highly multiplexed single-cell RNA-seq for defining cell population and transcriptional spaces. BioRxiv, 315333.)

first: Tran

last: Tran

first: Eric

last: Kernfeld


title: Gene expression profile at single cell level of CD4+ T cells from the lymph nodes of young and old DBA/1 mice with or without glucose-6-phosphate isomerase (GPI)-induced arthritis (GIA)

city: Tsukuba

first: Isao

last: Matsumoto

state: Ibaraki

address: 1-1-1 Tennodai

department: Department of Rheumatology

institute: University of Tsukuba

summary: It has been suggested that CD4+ T cell senescence is involved in the pathogenesis of elderly-onset rheumatoid arthritis (EORA). We performed scRNA-seq analysis using CD4+ T cells collected from inguinal lymph nodes of young and old DBA/1 mice to investigate the association between aging CD4+ T cells and elderly-onset arthritis.

overall_design: Inguinal lymph nodes (LNs) were harvested from young (8 weeks) and old (14-15 months) DBA/1 mice 14 days after GIA induction (GIA groups) or PBS injection (control groups). CD4+ T cells were isolated by cell sorting system equally from four mice in each of the four groups, each with 10,000 cells, and analyzed using scRNAseq.


title: testosterone application induced H3K27 deacetylation

city: HangZhou

first: JIAMIN

last: JIN

address: QingChun East Road

institute: ZheJiang University

summary: Decreased H3K27 deacetylation after KGN cell was treated with 10 um testosterone for 24 h.

overall_design: KGN cell was treated with 10 um testosterone for 24 h and collected for chip-seq.

first: ZHANHONG

last: HU


title: Dietary folate and cofactors accelerate age-dependent p16 epimutation to promote intestinal tumorigenesis

city: Houston

first: Lanlan

last: Shen

state: Texas

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

summary: We use a mouse model of age-dependent p16 epimutation, in which the p16 gene activity is directly controlled by promoter DNA methylation. We show p16 epimutation is modulated by folate and cofactors in dietary supplementation, which leads to increased colon cancer risk. Importantly, our findings provide functional evidence concerning the safety of folate fortification in the general population.

overall_design: As a control, we analyzed cells from adjacent normal colonic mucosa.

first: Li


title: Gene expression profile at single cell level of mouse heart  from control diet (CD),  high fat diet (HFD) and Western diet (WD)

city: Nanjing

first: Lai

last: Zhang

state: Jiangsu

address: Hushan Road, Jiangning District, Nanjing

institute: The Affiliated Jiangning Hospital of Nanjing Medical University

summary: Macrophages are considered as a homogeneous population in the heart. We used single cell RNA sequencing (scRNA-seq) to analyze thediversity of macrophages in control diet (CD) mouse,  high fat diet (HFD) mouse and Western diet (WD) mouse heart.

overall_design: CD45+F4/80+CD11b+ macrophages of the diet mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Hanwen

first: Adwait

last: Sathe

first: Andi

last: Xu


title: Endogenous glucocorticoids are required for normal macrophage activation and gastric Helicobacter pylori immunity [RNA-seq]

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Glucocorticoids are steroid hormones well-known for their potent anti-inflammatory effects. However, their immunomodulatory properties are multifaceted. Increasing evidence suggests that glucocorticoid signaling promotes effective immunity and that disruption of glucocorticoid signaling impairs immune function. In this study, we conditionally deleted the glucocorticoid receptor (GR) in the myeloid lineage using theLysM-Credriver (myGRKO). We examined the impact on macrophage activation and gastric immune responses toHelicobacter pylori, the best-known risk factor of gastric cancer. Our results indicate that compared to WT, GRKO macrophages exhibited higher expression of proinflammatory genes in steroid-free conditions. However, when challenged in vivo, GRKO macrophages exhibited aberrant chromatin landscapes and impaired proinflammatory gene expression profiles. Moreover, gastric colonization withHelicobacterrevealed impaired gastric immune responses and reduced T cell recruitment in myGRKO mice. As a result, myGRKO mice were protected from atrophic gastritis and pyloric metaplasia development. These results demonstrate a dual role for glucocorticoid signaling in preparing macrophages to respond to bacterial infection but limiting their pathogenic activation. In addition, our results support that macrophages are critical for gastric anti-Helicobacterimmunity.

overall_design: RNAseq of freshly isolated thioglycollate-induced peritoneal macrophages isolated from vehicle-treated WT mice, vehicle-treated mice with Nr3c1 deletion with the Lysm Cre driver or the same genotypes treated in vivo for 3 hours with Helicobacter pylori. There are 4 replicates per group.

first: Stuti

last: Khadka

first: Sebastian

last: Dziadowicz

first: Xiaojiang

first: Lei

last: Wang

first: Jonathan

middle: T

last: Busada


title: Exploring the Dynamics and Consequences of Differential Transcript Usage in Cardiomyocyte Fate Specification

status: Public on Aug 18 2024

city: Poznan

first: Ireneusz

last: Stolarek

address: Z. Noskowskiego 12/14

institute: Institute of Bioorganic Chemistry Polish Academy of Sciences

summary: Cardiovascular research often relies on in vitro models using induced pluripotent stem cells (iPSCs) differentiating into induced cardiomyocytes (iCM). Little is known about the changes in transcript variants, termed differential transcript usage (DTU), which greatly influence cellular programs. In this study, we explored the DTU landscape during the iPSC-to-iCM differentiation and its relation to iCM fate. We found that DTU is consistently displayed by a subset of genes during iCM differentiation. DTU largely operates on a distinct set of genes than DGE, and both impact different biological processes. The DTU is used more often by protein coding in the late stage of iCM differentiation. The DTU-displaying genes are linked with functions specific to CMs, including ion signaling and cell junction organization, and their expression is cell-type specific. The RNA binding proteins (RBPs) involved in shaping the alternative splicing during the iCM differentiation experience early directed gene expression changes in their expression. Our research emphasizes that analyzing transcript variant expression levels is crucial for uncovering novel genes and functions, and for mapping fine-tuning gene expression and cardiomyocyte-specific functions during cell differentiation.

overall_design: To investigate the DTU in iCM differentiation we have establlished iPSC-to-iCM differentiation and sampled the cells at subsequent stages of differentiation.

first: Joanna

last: Delimata-Raczek

first: Natalia

last: Koralewska

first: Magdalena

last: Rakoczy

first: Marek

last: Figlerowicz


title: G3BP1 translocates into mitochondria to impair MCU complex function and promotes NASH progression [G3bp1-HKO and G3bp1-Flox mice with BSA or PA treatment]

first: ying

last: zheng

address: 639 Longmian Avenue, Chunhua Street, Jiangning District,

institute: China Pharmaceutical University

summary: Mitochondrial calcium signaling plays a critical role in mitochondrial homeostasis during non-alcoholic steatohepatitis (NASH) progression. Here, we report Ras‐GTPase activating protein SH3 domain‐binding protein 1 (G3BP1), a core protein of stress granule (SG), significantly upregulated in NAFLD/NASH patients, mouse models and palmitic acid-stimulated hepatocytes. Hepatocyte-specific G3BP1 deficiency attenuates NASH in two dietary mouse models. SG and the mitochondrial import protein TOM70 collaboratively mediate the translocation of G3BP1 to the mitochondria. G3BP1 interacts and stabilizes mitochondrial calcium uptake 1 (MICU1) via inhibiting YME1L1-mediated degradation of MICU1, and also impedes MCU complex activity and assembly, leading to mitochondrial calcium overload. Moreover, metabolic stress suppresses TRIM25-mediated K63-ubiquitination of G3BP1 and subsequent SG disassembly. Pharmacological inhibition of G3BP1 impairs the G3BP1-MICU1 interaction and prevents mitochondrial homeostasis imbalance and NASH progression. Collectively, we uncover the significant role of mitochondrial G3BP1 in mitochondrial homeostasis and NASH progression, which provides a potential target for therapeutic interventions.

overall_design: To investigate how G3BP1 affects NASH, we conducted RNA sequencing (RNA-seq) on the primary hepatocytes of  G3bp1-HKO and G3bp1-Flox mice with BSA or PA treatment

first: Yang

last: Cheng

first: Jingyi

first: Shengtao

last: Ye

first: Yanqiu

first: Mengmeng

last: He

first: Enyi

last: Wu

first: Yingrong

last: Leng

first: Ying

last: Zheng

first: Lingyi

last: Kong

first: Hao


title: Single-organism multimodal characterisation of eukaryotic plankton with Ukiyo-e-Seq

city: Sydney

first: Catherine

middle: Rose

last: Gatt

state: NSW

address: UNSW Sydney High St Kensington

department: School of Clinical Medicine

institute: University of New South Wales

summary: We used single-cell sequencing data and imaging to investigate Eukaryotic plankton from environmental marine samples collected from Coogee, NSW, Australia.

overall_design: Water was collected from the ocean, filtered and centrifuged to remove particles larger 1mm and smaller than 25um. A microscope-mounted cell picker was then used to image an organism in the sample and then transfer it to a well of a microtiter plate. Organisms were then analysed using single-cell rna seq.

first: Yike

last: Xie

first: Kanu

last: Wahi

first: Emma

last: Johansson Beves

first: Fabio

last: Zanini


title: Self-organised pattern formation in the developing dorsal neural tube by a temporal relay of BMP signalling

city: Klosterneuburg

first: Anna

last: Kicheva

address: Am Campus 1

institute: Institute of Science and Technology Austria

summary: Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study BMP signalling dynamicsin the vertebrateneural tube, we developed a new ES cell differentiation systemtailored for growing tissues. Differentiating cellsform strikingself-organised pattern of dorsal neural tube cell typesdriven by sequential phases of BMP signalling that are observed both in vitro and in vivo.Data-driven biophysical modelling showed that thesedynamics result from coupling fast negative feedbackwithslow positive regulation of signalling bythe specification of an endogenousBMP source.Thus, in contrast to relays that propagate morphogen signalling in space, we uncover a BMP signallingrelay that operates intime. This mechanism allows rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation.Altogether, our study provides an experimental and theoretical framework to understand how signalling dynamicsis exploited indeveloping tissues.

overall_design: The differentaition protocol is described in detail in Lehr et al. Cells were treated with bFGF for 48h, followed by bFGF + CHIR for 24h, followed by treatment with RA and the indicated concentration of BMP4. Note that in Lehr et al t=0 denotes the beginning of the treatment with RA+BMP4, which corresponds to 72h after the beginning of the differentiation. Treatment conditions are abbreviated as follows according to the BMP4 concentration that was added: 0ng/ml BMP4 (RA), 0.5ng/ml (RAplus0.5ngB4),1.5ng/ml (RAplus1.5ngB4), 3.0ng/ml (RAplus3ngB4) or 5ng/ml (RAplus5ngB4).

first: Stefanie

last: Lehr

first: David

last: Brückner

first: Thomas

last: Minchington

first: Martina

last: Greunz-Schindler

first: Jack

last: Merrin

first: Edouard

last: Hannezo


title: Differentiation fate of a stem-like CD4 T cell controls immunity to cancer

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

summary: The goals of this study were to gain a better understanding of the heterogeneity and transcriptional profile of bulk PD1+CD45RA- CD4 T cells in kidney cancer primary tumors and activated PD1+ CD4  and CD8 T cells from tumor draining lymph nodes of TRAMPC1-GP bearing mice before and after Treg depletion.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Activated CD4 T cells (live CD3+ CD19- CD8- CD4+PD1+CD45RA-) from 2 primary kidney cancer patients were FACS-purified. Additionally Activated CD4 T cells (live CD3+ CD19- B220- MHCII-CD8-CD4+) from tumor draining lymph nodes of 5-week TRAMPC1-GP bearing mice before and 5-days after Treg depletion were FACS purified. Naive CD4 T cells (PD1-CD44-CD62L+) were FACS purified as a control and spiked in from every sample. Single-cell suspensions of FACS-purified cells were loaded onto the 10X Genomics Chromium Controller. Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit followed by sequencing on a HiSeq3000.

first: Maria

last: Cardenas


title: Dynamics of the thymic transcriptome at stages of acute thymic involution in Japanese Black calves with a poor prognosis.

city: Miyazaki

first: Shoichi

last: Wakitani

address: 1-1 Gakuenkibanadai-nishi

department: Faculty of Agriculture

institute: University of Miyazaki

summary: Transcriptome analysis was performed on the thymus of necropsied Japanese Black calves with a poor prognosis, to clarify the pathology of acute thymic involution, which often happens in farmed calves with a poor prognosis. Gene expression profiles obtained by DNA microarray analysis of eight calf thymuses were grouped into three patterns associated with the histopathological classification of acute thymic involution. Three clusters were arranged by the stage of acute thymic involution based on the first principal component score, suggesting that histopathological conditions have the most significant impact on changes in gene expression profile.

overall_design: 8 specimens covering all stages of acute thymic involution were selected for transcriptome analysis. No replicates were included. No control samples.

first: Ryogo

last: Furukawa


title: Identification of SIRT3 as an eraser for H3K9 lactylation by antibody-mediated proximity labeling strategy

city: Tianjin

first: zilong

last: fan

address: 22 Weidai Road, Heping District

institute: Tianjin Medical University

summary: As a novel post-translational modification of histone derived from lactate, lysine lactylation (Kla) links lactate metabolism to epigenetic regulation, playing a role in modulation of gene expression in tumor and immune microenvironment. Evidence so far indicates that HDAC1-3 can catalyze the removal of Kla. However, the regulated targets of HDACs for Kla and functional consequence remain elusive. Herein, we used an antibody-based proximity labeling approach to identify SIRT3 binding to histone H3K9la and catalytic removal of the lactylationoup. The molecular docking results further revealed the mechanism of the binding of Kla peptide to SIRT3. More importantly, SIRT3 can specifically modulate the gene transcription by regulating H3K9la, inhibiting the progression of esophageal cancer cells (ESCC). In conclusion, our work identifies the delactylase of H3K9la and reveal an H3K9la-mediated molecular mechanism catalyzed by SIRT3 for gene transcription regulation in ESCC, and our findings provide an opportunity to investigate the physiological significance of Kla and shed light on the unknown cellular mechanisms controlled by SIRT3.

overall_design: Cells were fixed with 1% formaldehyde at RT for 10 min, and the fixation was stopped by 125 mM glycine at RT for 5 min. The chromatin pellets were extracted from cells by lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40), and resuspended with 0.8 ml of RIPA buffer. The genomic DNA was fragmented by sonication at 25% amplitude for a total of 8 min with intervals. Sonicated chromatin was incubated with 2 μg of anti-H3K9la antibody, or control IgG pre-coated on Dynabeads protein G at 4℃ overnight.


title: Exploring the impact of energy metabolism in periosteal cells transcriptional profile.

city: Philadelphia

first: Ernestina

last: Schipani

address: 310A Stemmler Hall, 3450 Hamilton Walk

department: McKay Orthopaedic Research Laboratory

institute: University of Pennsylvania

summary: Glycolytic metabolism, once considered merely a consequence of cellular function, has emerged as a crucial regulator of cellular differentiation. Both glycolysis and oxidative phosphorylation (OXPhos) are vital for osteoblastogenesis. Osteoblasts are the cells that make bone. To deepen our understanding of OXPhos's role in bone mass accrual, we engineered a mutant mouse model deficient in Mitochondrial Transcription Factor A (TFAM) specifically in mesenchymal progenitors within the limb bud and their descendants, using the PRX1-Cre driver system. TFAM is essential for transcription of the mitochondrial genes that encode critical components of the electron transport chain, thereby governing OXPhos. Our TFAM mutant mice exhibit marked shortening of long bones, evident at birth and progressing with age, accompanied by growth plate abnormalities and bone deformities. Critically, these mice develop spontaneous fractures in long bone mid-shafts by three weeks of age, indicating significant compromise in bone integrity. Comparative analyses using MicroCT and histomorphometry reveal drastic cortical bone thinning in mutants due to severely impaired osteoid deposition and bone formation, especially in the diaphyseal periosteum. Furthermore, an increased number of osteoclasts at this site suggests that an elevated bone resorption contributes to the phenotype. Acknowledging the active role of energy metabolism in cell differentiation and function, we measured ATP production in PRX1 lineage periosteal cells. TFAM deletion led to a substantial decrease in steady-state intracellular ATP levels, highlighting a critical metabolic deficit. To rectify this metabolic defect and potentially correct the resultant phenotype, we bred TFAM mice with another mouse line expressing mutated, oxygen-independent Hypoxia Inducible Factor 1alpha (HIF1dPA) within PRX1 lineage cells (yielding TFAM/HIF1dPA mice). These double mutants did not experience spontaneous fractures, and their cortical bone thickness and the ability of periosteal cells to accumulate osteoid was fully restored. Therefore, by examining the transcriptional profile of periosteal cells, our aim is to determine whether TFAM deficiency alters their genetic landscape and if HIF1 activation can reverse these changes. Our goal is to provide new insights into the role of energy metabolism in shaping the transcriptome landscape, thereby influencing cell differentiation and activity.

overall_design: To investigate the impact of energy metabolism on the transcriptional profile of periosteal cells, we established two mouse lines: one with a mutant phenotype characterized by a lack of mitochondrial transcription factor A (TFAM) in PRX1 lineage cells. We conditionally knocked out TFAM in uncommitted mesenchymal progenitors and their descendants using PRX1-Cre drivers and a mouse line homozygous for a floxed Tfam allele (TFAMfl/fl). PRX1-Cre mice express Cre recombinase in mesenchymal cells that give rise to chondrocytes and osteoblasts in long bones and calvaria. Subsequently, we generated double mutants lacking TFAM and expressing a constitutively stabilized form of HIF1α protein in mesenchymal progenitors and their descendants (referred to as PRX1;TFAM;HIF1dPA or TFAM;HIF1dPA). scRNA-seq was performed on periosteal cells isolated from the long bones hindlimbs of three-week-old mice. The resulting data were utilized to identify distinct cell clusters within the periosteum and to conduct differential gene expression analysis between control mice and their mutant counterparts for each line.

first: Elena

last: Sabini

first: Mohd

middle: P

last: Khan


title: Targeting the splicing factor SRSF10 in mouse HCC tumors shapes tumor immunity and immunotherapy

city: shanghai

first: JL

last: CAI

address: shanghai

institute: fudan university

summary: The efficacy of immune checkpoint blockade (ICB) therapy in hepatocellular carcinoma (HCC) patients remains poor. This article aims to uncover the role and mechanism of SRSF10 in HCC immunotherapy. SRSF10 is upregulated in a variety of tumors and is associated with poor prognosis. SRSF10 binds to the 3’UTR region of MYB and enhances the stability of MYB RNA levels. This activation leads to increased transcriptional expression of key enzymes associated with glycolysis, such as GLUT1, HK1, and LDHA, resulting in higher lactate content in tumor cells. The lactate in tumor cells inside can increase histone lactylation so as to upregulated the expression of SRSF10. Besides, the lactate produced by tumors promotes lactylation of the histone H3K18la site upon transport into macrophages, which could activate transcription of M2 macrophage genes and increase protumour macrophage activity, so as to creating a suppressive immune microenvironment. Clinically, SRSF10 can be utilized as a biomarker to assess the resistance to immunotherapy in different types of solid tumors. The pharmacological targeting of SRSF10 with 1C8 has been shown to be effective in both murine and human preclinical models. In conclusion, we prove that the SRSF10/MYB/glycolysis/lactate axis is critical for triggering immune evasion and anti-PD-1 resistance.

overall_design: Tumors from WT or shSrsf10 mice were extracted and digested with collagenase type IV (1 mg/ml) and DNase type I (30 U/ml) for 30 min at 37 °C. The cells were filtered through the 70 μm cell strainers, washed with phosphate-buffered saline (PBS), lysed in red blood cell buffer, and resuspended in PBS. Cells were sorted by FACSAria Fusion Flow Cytometer (BD Biosciences). The cell suspension (300-600 living cells per microliter) was loaded onto the Chromium single cell controller (10 x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Libraries were subsequently prepared sing Single Cell 5’Library and Gel Bead Kit and sequenced on an Illumina NovaSeq 6000 instrument with pair-end 100 bp (PE100) reading strategy.

first: J

last: Cai

first: L

middle: N

last: song

first: Z

last: Dai


title: Chronic subanesthetic ketamine induces schizophrenic-like social deficits and alters translatome in the lateral septum

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: Schizophrenia is often marked by poor social functioning that can have a severe impact on quality of life and independence, but the underlying neural circuity is not well understood. Here we used a translational model of subanesthetic ketamine mice to delineate neural pathways in the brain linked to social deficits in schizophrenia. Mice treated with chronic ketamine exhibit profound social and sensorimotor deficits as previously reported. Using three-dimensional c-Fos immunolabeling and volume imaging (iDISCO), we show that ketamine treatment resulted in hypoactivation of the lateral septum (LS) in response to social stimuli. Chemogenetic activation of the LS rescued social deficits after ketamine treatment, while chemogenetic inhibition of previously active populations in the LS (i.e. social engram neurons) recapitulated social deficits in ketamine-naïve mice. We then examined the translatome of LS engram neurons and found upregulation of genes encoding potassium inwardly-rectifying channels and solute transporters as well as dysregulation of genes implicated in apoptotic processes, all of which could contribute to the hypoactivation of LS social engram neurons after chronic ketamine exposure. A number of ketamine-induced differentially expressed genes (DEGs), including those involved in mitochondrial function and neuroinflammatory pathways, were shared with human schizophrenia and mouse models of neurodevelopmental disorders.

overall_design: To isolate differentially translating mRNAs from social interaction-activated neurons in the lateral septum (LS), we employed the ribo-TRAP approach, which allowed us to selectively isolate translating mRNAs in activated neurons using Cre-dependent expression of EGFP-tagged L10a ribosomal subunits in Fos-iCreER mice. After TRAPing activated neurons, we administered saline or ketamine (30 mg/kg/day, i.p.) for 10 days. Because the expected number of activated neurons was relatively low, we pooled five LS tissue punches into one tube. Consequently, we processed 10 ketamine and 10 saline LS tissue punches to create 2 ketamine and 2 saline pooled samples, respectively, for ribo-TRAP.

first: Nagalakshmi

last: Balasubramanian

first: Ruixiang

last: Wang

first: Catherine

last: Marcinkiewcz


title: Regional Differences in Progenitor Consumption Dynamics Shape Brain Growth during Development

city: Genève

first: Natalia

last: Baumann

state: Genève

address: Michel-Servet 1

department: Fundamental Neuroscience

country: Switzerland

institute: Université de Genève

summary: The structure of vertebrate brains emerges from a shared template where three primary regions — the hindbrain, midbrain, and forebrain — develop during embryogenesis to establish the circuits responsible for distinct functions. While the molecular mechanisms underlying the segmentation of the neural tube into these regions are relatively well understood, how their relative expansion is regulated during embryogenesis remains largely unknown. To address this question, we first generated a single-cell resolution atlas of birthdate across the entire mouse brain (https://www.neurobirth.org), which we next leveraged to identify brain-region-specific neurogenic patterns and investigate underlying molecular mechanisms. We show that in brain regions that expand, such as the neocortex, neurogenesis is sustained (sustained neurogenic regions), while it is limited to the first few days of brain development in hindbrain regions that are comparatively less developed (transient neurogenic regions). We demonstrate that sustained cortical neurogenesis is made possible by a progressive lengthening of the cell cycle and associated lower levels of consumptive divisions in apical progenitors (AP), which preserve the progenitor pool for longer periods. Finally, using single-cell RNA sequencing of AP across the developing brain, we identify spatio-temporal molecular determinants of AP cycling behavior and demonstrate a critical role for the mitochondrial membrane protein Fam210b in regulating region-specific cycling properties. These results identify a parsimonious mechanism to regulate neuronal production in different parts of the brain, in which the time window during which neurons are generated appears to be a critical determinant of a region’s expansion during development and evolution.

overall_design: Mouse single-cell RNAseq of FAC-sorted FT+1H whole brain embryonic sample at E10, E12, E14 and E16.


title: RNA-Seq analysis of prostate cancer cells after morsuin treatment

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

country: Taiwan

institute: China Medical University

summary: We performed RNA-seq analysis using different prostate cancer cell lines (PC3 and 22Rv1) after morusin treatment. We reported that morusin regulates Akt/mTOR pathway-associated genes in PC3 and 22Rv1 cells. Morusin induces apoptosis and suppresses cell cycle progression, cell migration and invasion in PC3 and 22Rv1 cells.

overall_design: Examination of mRNA profile of different prostate cancer cell lines (PC3 and 22Rv1) under morusin treatment.

first: Chia-Yang

last: Li