title: PFKFB3 drives renal fibrosis through promoting histone lactylation-mediated NF-𝜅B activation [CUT&Tag]

status: Public on May 01 2024

first: yating

last: wang

address: 58th Zhongshan Road II  The First Affiliated Hospital ,Sun Yat-Sen University

department: Department of Nephrology

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

summary: Persistently elevated glycolysis in kidney has been demonstrated to promote chronic kidney disease. However, the underlying mechanism remains largely unclear. Here, we observed that PFKFB3, a key glycolytic enzyme, was remarkably induced in kidney proximal tubular cells following ischemia-reperfusion injury in mice, as well as in multiple etiologies of chronic kidney disease patients. Proximal tubular epithelial-specific deletion of PFKFB3 significantly reduced renal lactate levels, mitigated inflammation and fibrosis, and preserved renal function in the IRI mouse model. To explore the mechanism of PFKFB3 in renal fibrosis, we performed RNA-sequencing (RNA-seq) on the kidney cortices from IRI mice. Of note, we found that PFKFB3-mediated kidney tubular glycolytic reprogramming markedly enhanced H4K12la lactylation. To further explore the potential functional significance of H4K12la in renal fibrosis, we performed genome-wide cleavage under targets and tagmentation (CUT&Tag) analysis to identify candidate genes regulated by H4K12la in sham and IRI kidney. Following CUT&Tag, H4K12la-associated DNAs were amplified using non-biased conditions, labeled, and sequenced with Illumina NovaSeq 6000.

overall_design: To identify the transcriptional targets for H4K12la in the kidney of sham and IRI mice.

first: Yating

last: Wang

first: Hongyu

last: Li

first: Wei

last: Chen

first: Qinghua

last: Liu

first: Haiping

last: Mao


title: Multi-omics integration reveals the dynamic impacts of stock enhancement on the intestinal health condition in kaluga sturgeon (Huso dauricus)

city: Changchun

first: Yutao

address: Jingyue Street

country: China

institute: Northeast Normal University

type: Expression profiling by high throughput sequencing

summary: On October 6th,2023, one thousand kaluga sturgeon were released to Songhua River  (119°52′-132°31′ E,11°12′-51°38′ N) after 2 h adaptive domestication to eliminate the physiological response caused by transport stress. Before wild reintroduction to river, non-toxic fluorescent dye was injected into the snout of kaluga sturgeon, which was beneficial to catch them again. On the 0 d (Ori), 7 d (D7FL), 14 d(D14FL) and 30 d (D30FL), three kaluga sturgeon individuals were recaptured randomly using seine nets. We performed a series of experiment to assess the dynamic effects of stock enhancement on the gut health conditions.

overall_design: On October 6th,2023, one thousand kaluga sturgeon were released to Songhua River  (119°52′-132°31′ E,11°12′-51°38′ N) after 2 h adaptive domestication to eliminate the physiological response caused by transport stress. Before wild reintroduction to river, non-toxic fluorescent dye was injected into the snout of kaluga sturgeon, which was beneficial to catch them again. On the 0 d (Ori), 7 d (D7FL), 14 d(D14FL) and 30 d (D30FL), three kaluga sturgeon individuals were recaptured randomly using seine nets. All subject individuals were anesthetized by the intake of tricaine methane sulfonate (MS-222, BIOZYM, China) after the body weight and length were recorded. Blood sample was collected from caudal vein and stored into sterile blood-collecting vessel with coagulant to separate serum at 4 ℃. Finally, intestine tissue samples and gut content were collected into RNase-free centrifuge tubes for the following molecular biology detection and morphology observation. Additionally, residual food debris in stomach also were fixed in anhydrous ethanol to identify feeding habits of kaluga sturgeon during the re-stocking period.


title: Genomic profiles and survival prognosticators in African-American patients with acute myeloid leukemia

city: COLUMBUS

first: Deedra

middle: R

last: Nicolet

state: OH

address: 1800 Cannon Drive, Rm 1250H

department: CCC

country: USA

institute: The Ohio State University

summary: Genomic profiles and prognostic biomarkers in patients with acute myeloid leukemia (AML) from ancestry diverse populations are underexplored. We analyzed the exomes and transcriptomes of 100 Black patients with AML (Alliance) and compared somatic mutation frequencies with those of 323 White patients (BeatAML). Seventy-three percent of 162 recurrent gene mutations identified in Black patients, including a novel PHIP alteration detected in 7% of patients, were found in only ≤1 White patient. Black patients with myelodysplasia-related AML were younger than White patients suggesting intrinsic and/or extrinsic dysplasia-causing stressors. On multivariable outcome analyses of Black patients, NPM1 and NRAS mutations associated with inferior disease-free and IDH1/2 mutations with reduced overall survival. Inflammatory profiles, cell type distributions and transcriptional profiles differed between Black and White NPM1-mutated patients. Incorporation of ancestry-specific risk markers into the 2022 European LeukemiaNet genetic-risk stratification changed risk-group assignment for one-third of Black patients and improved their outcome prediction.

overall_design: Gene expression profiling at time of AML diagnosis

first: Ann-Kathrin

last: Eisfeld

first: Elaine

last: Mardis


title: Aged skin exacerbates experimental osteoarthritis via enhanced IL-36R signaling

city: Guangzhou

first: Dalin

address: 295 Changxing Road

institute: Guangdong Institute of Orthopedics

summary: To investigate  skin aging is an important driver of experimental osteoarthritis(OA) progression in mice via enhanced IL-36 receptor (IL-36R) signaling. The supernatants from the co-culture of UV-aged mouse primary keratinocytes with synovial fibroblasts were collected to induce mouse primary articular chondrocytes (CCs) to become aging SNL CCs. On this basis, Spesolimab (100ng/ml) was added to culture aging SNL CCs to study the drug's effect on OA. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 groups: control CCs, aging SNL CCs, aging SNL CCs+Spesolimab.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control CCs, aging SNL CCs and aging SNL CCs+Spesolimab.

first: Chong

first: Changsheng

last: Yang

first: Liangyu

first: Panpan

first: Zilin

last: Zou

first: Honghao

first: Yun

last: Xiao

first: Junfeng

last: Wu

first: Qinwei

last: Cheng

first: Chengliang

first: Ee

last: Ke

first: Bin

last: Huang

first: Xiaochun

last: Bai

first: Kai


title: Molecular characterization and differential expression profiles of transcription factor Sox gene family between ovaries and testes from golden pompano （Trachinotus ovatus）

first: Honghua

address: Haizhu District - 6-7/F, Xinhai Building, No. 231 Xingang West Road

institute: Chinese Academy of Fishery Sciences

summary: The SRY-related HMG-box (Sox) is a transcription factor related to the testis-determining gene SRY (Sex determination Region of Y chromosome), which plays an important role in the sexual development of Osteichthyes. In order to understand the characteristics of Sox gene family members in Trachinotus ovatus（ToSox）, this study used bioinformatics methods to systematically analyze the physicochemical properties, phylogenetic tree, chromosomal localization, and prediction of interacting proteins of the ToSsxs. The expressions of the ToSoxs were analyzed using transcriptomics data from ovary and testis of T. ovatus. The results showed that 18 members of Sox gene family were identified, and the members of the family were hydrophilic proteins with large differences in amino acid number, molecular weight and isoelectric point. The evolutionary tree analysis showed that the Sox family genes were divided into seven branches (B1, B2, C, D, E, F, H) The chromosomal localization analysis showed that these genes of the family were scattered on 15 chromosomes. The structure of Sox genes was simple and relatively conserved. Intraspecific covariance analysis revealed that one pair of ToSox gene covariance, and interspecific covariance analysis revealed 14 pairs of collinearities between T. ovatus and zebrafish and 20 pairs of collinearities between T. ovatus and tilapia. The members of ToSox proteins had close interactions with one another, and with other proteins as well. The results of transcriptome analysis showed that the genes ToSox30, ToSox1a, ToSox17, ToSox11, ToSox9b, and ToSox9b are likely to regulate the testicular development of oviparous jacks, which is related to male sex determination. This study preliminarily investigated the characterization of Sox genes in the T. ovatus genome and provided theoretical references for the study of the effects of Sox transcription factors on sex determination in T. ovatus.

overall_design: The testes of three male golden pompano and the ovaries of three female golden pompano were taken from the Shenzhen Experimental Base of the South China Sea Fisheries Research Institute (SCFRRI) for transcriptome data determination.

first: RongHua

first: JinMin

last: Pan

first: HuaYang

last: Guo

first: DianChang

last: Zhang


title: Transcriptome Profiles of Mycobacterium marinum sRNA B11-Deleted and -Completed Strains

city: Shanghai

first: Chuan

last: Wang

address: 131 # Dong An Road

institute: Fudan University

summary: Understanding the regulatory roles of small RNAs (sRNAs) in Mycobacterium marinum is crucial for elucidating its pathogenesis. Here, we present transcriptome profiles of M. marinum strains with deletions and completions of sRNA B11. Through RNA sequencing analysis, we identified significant alterations in gene expression patterns between the B11-deleted and completed strains.

overall_design: Wild-type (WT + pCtr), B11-deleted (ΔB11 + pCtr), and B11-deletion complemented with over-expressed B11 (ΔB11 + pPb11-B11) strains of Mycobacterium marinum were cultivated in 7H9-OADC medium until reaching the early exponential phase (OD600 ~ 1.0). At this stage, B11 expression in WT strains stabilizes. Bacterial cultures (4 mL) were mixed with 0.2 volumes of stop solution (95% ethanol and 5% phenol) and immediately frozen in liquid nitrogen. Total RNA was isolated using the Trizol method.


title: RNA sequencing analysis of Ovch2 knockout initial segment-caput epididymis.

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

summary:
Purpose: The purpose of this study is to characterize gene expression in the Ovch2-ablated mouse initial segment (IS)-caput epididymis.
Methods: Ovch2-/- mice were used when they were 14-week-old. IS-caput epididymal mRNA profiles were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000.
Results: RNA-seq data identified differentially expressed transcripts.
Conclusions: Our results show that the expression of many genes was not critically affected by Ovch2 ablation.

overall_design: IS-caput epididymal mRNA profiles of mice with experimental treatments were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000.


title: RKIP regulates bone homeostasis by mediating the differentiation fate of bone niche macrophages.

city: Hangzhou

first: Fengdong

last: Zhao

state: Zhejiang

address: No. 3, Qingchun Road East

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine

summary: As central cells involved in osteoimmunology, bone niche macrophages possess diverse functions, and their differentiation fate regulates bone homeostasis. Elucidation of the underlying mechanism involved in macrophage differentiation is important for developing new therapeutic targets for osteoporosis. Our RNA-seq data showed that the differentially expressed genes  in BMMs after RKIP knockout were involved in the pathways of cell adhesion and osteoclast differentiation.

overall_design: To investigate RKIP in the regulation of macrophage differentiation, we isolated BMMs from RKIP+/+ and RKIP-/- mice and performed transcriptome sequencing (RNA-seq). We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.


title: Dissecting the respective role of microbiota and host genetics in the susceptibility of Card9-/- mice to colitis

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

summary:
Background: The etiology of Inflammatory Bowel Disease (IBD) is unclear but involves both genetics and environmental factors, including the gut microbiota. Indeed, exacerbated activation of the gastrointestinal immune system toward the gut microbiota occurs in genetically susceptible hosts and under the influence of the environment. For instance, a majority of IBD susceptibility loci lie within genes involved in immune responses, such as caspase recruitment domain member 9 (Card9). However, the relative impacts of genotype versus microbiota on colitis susceptibility in the context of CARD9 deficiency remain unknown.
Results: Card9 gene directly contributes to recovery from dextran sodium sulfate (DSS)-induced colitis by inducing the colonic expression of the cytokine IL-22 and the antimicrobial peptides Reg3 and Reg3 independently of the microbiota. On the other hand, Card9 is required for regulating the microbiota capacity to produce AhR ligands, which leads to the production of IL-22 in the colon, promoting recovery after colitis. In addition, cross-fostering experiments showed that five weeks after weaning, the microbiota transmitted from the nursing mother before weaning had a stronger impact on the tryptophan metabolism of the pups than the pups' own genotype.
Conclusions: These results show the role of CARD9 and its effector IL-22 in mediating recovery from DSS-induced colitis in both microbiota-independent and microbiota-dependent manners. Card9 genotype modulates the microbiota metabolic capacity to produce AhR ligands, but this effect can be overridden by the implantation of a WT or healthy microbiota before weaning. It highlights the importance of the weaning reaction occurring between the immune system and microbiota for the host metabolism and immune functions throughout life. A better understanding of the impact of genetics on microbiota metabolism is key to developing efficient therapeutic strategies for patients suffering from complex inflammatory disorders.

overall_design: Microarray analysis was performed by using total tissue from colon of mice on day 0 and day 7

first: Camille

last: Danne

first: Bruno

last: Lamas

first: Aonghus

last: Lavelle

first: Marie-Laure

last: Michel

first: Gregory

last: da Costa

first: Hang

middle: P

last: Pham

first: Antoine

last: Lefevre

first: Chantal

last: Bridonneau

first: Marius

last: Bredon

first: Julien

last: Planchais

first: Marjolène

last: Straube

first: Patrick

last: Edmond

first: Philippe

last: Langella

first: Harry

last: Sokol


title: Single cell transcriptome profiling of kidney cell populations and the effect of liraglutide in diabetes

status: Public on May 02 2024

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

summary: While incretin-based therapies are known to improve glucose control in diabetes, growing evidence suggests a glucose-independent mechanism in protection against kidney disease. To further investigate incretin effects in kidney, we examined long-term therapy with liraglutide, a Glucagon-like peptide 1 receptor (GLP1R) agonist, in diabetic (Ins2Akita) and control mice and profiled renal cell transcriptomes using single-cell sequencing.

overall_design: Control and diabetic (C57BL/6 - Ins2Akita/J ) mice treated with liraglutide were monitored over a 20 week study period, followed by scRNA-seq analysis of dissociated aortae using the Drop-Seq platform from Dolomite Bio.

first: Karly

middle: C

last: Sourris

first: Scott

middle: S

last: Maxwell

first: Phillip

last: Kantharidis

first: Anil

last: Karihaloo

first: Lotte

middle: B

last: Knudsen

first: Mark

middle: E

last: Cooper

first: Melinda

middle: T

last: Coughlan


title: Bidirection activation of stem-like programs in metastatic cancer and alveolar type II cells within the niche [RNA-seq]

city: London

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

country: United Kingdom

institute: The Francis Crick Institute

summary: A key step for metastatic outgrowth involves the generation of a deeply altered microenvironment (niche) that supports the malignant behavior of cancer cells. However, it is unclear whether a fundamental program driving the generation of this de novo cellular environment can be identified. Here, by focusing on breast cancer metastasis to the lung, we describe a cancer-dependent chromatin remodeling and activation of developmental programs in alveolar type II (AT2) cells. We have identified a relationship linking high metastatic competency in the lung with the induction of a multilineage state in AT2 cells in the niche. In turn, this cancer-induced reprogramming of AT2 cells promoted stem-like features in the cancer cells. In conclusion, we propose the concept of “reflected stemness” during metastatic niche initiation, whereby metastatic cells reprogram the local tissue into a stem-like state that enhance intrinsic cancer-initiating potential, creating a positive feedback loop where tumorigenic programs may be amplified.

overall_design: To investigate the transcriptional changes that occurs in cancer cells during outgrowth in the lung, we compared the RNA of 4T1 cancer cells growing in the dish (in vitro) and 4T1 cancer cells isolated from the lungs of BALB/c mice (in vivo) 7 days after tail vein injection. For isolation of lung epithelial cells, we injected 0.8x10^6 labeling-4T1 cancer cells and collected the lungs 7 days after tail vein injection for FACS sorting. For each biological replicate, we pooled a total of 5 lungs to obtain enough niche lung epithelial cells.

first: F

last: Rodrigues

first: I

first: M

last: Llorian


title: Melanization of fungal necromass drives the upregulation of multiple chitinase, protease, and laccase genes when being degraded by Trichoderma reesei

city: Saint Paul

first: Jonathan

last: Schilling

state: Minnesota

address: 1445 Gortner Avenue

department: Plant and Microbial Biology

institute: University of Minnesota

summary: Fungal necromass in soil represents the stable carbon pools. While fungi are known to decompose fungal necromass, how fungi decomopose melanin, remains poorly understood.  Recently, Trichoderma species was found to be one of the most commonly associated fungi in soil, we have used a relevant fungal species, Trichoderma reesei, to characterized  Genes involved in the decomposition of melanized and non-melanized necromass from Hyaloscypha bicolor.

overall_design: We grew Trichoderma reesei RUT-C30 in liquid cultures with low- and high-melanin necromass and  Determined gene expression patterns relative to each other. We also compared the expression pattern to that on glucose carbon source.

first: Irshad

middle: U

last: Haq

first: Peter

last: Kennedy


title: Exploring the effect of XingNaoKaiQiao acupuncture stimulation in rats with cerebral ischemia injury

city: Nanjing

first: Zhihui

last: Zhang

state: Jiangsu

address: 138 Xianlin Rd

institute: Nanjing University of Chinese Medicine

summary: To reveal the molecular signatures of XingNaoKaiQiao acupuncture on the Cerebral cortex of rats with cerebral ischemia/reperfusion injury, we performed bulk RNA sequencing.

overall_design: The rats were randomly divided into sham group, model group, rt-PA group and acupuncture + thrombolytic group. The model was middle cerebral artery occlusion (MCAO) thromboembolism model, in which the thrombolytic group underwent thrombolytic intervention at 6 hours post model establishment and the acupuncture + thrombolytic group underwent acupuncture intervention at 2 hours, Xingnaokaiqiao acupuncture stimulation was performed at the Shuigou (GV26) and left Neiguan (PC6) acupoints.

first: Guangxia

last: Ni


title: FOG2 modulates a TBX5/GATA4-co-ocupied atrial gene regulatory network linking heart failure to atrial fibrillation risk [RNA-Seq]

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago

summary: The transcription factor FOG2 (ZFPM2) is upregulated in human heart failure and increased FOG2 expression causes heart failure in mice.  We found that FOG2 directly intersects a gene regulatory network driven by the atrial-enriched TF TBX5 and required for atrial cardiomyocyte rhythm control gene expression

overall_design: Transcriptomic and epigenomic analyses of FOG2-TBX5I dependent-networks in cardiac  rhythm

first: Carlos

last: Perez-Cervantes

first: Rangarajan

middle: D

last: Nadadur

first: Michael

last: Broman


title: Obesogenic diet in mice leads to inflammation and oxidative stress in the mother in association with sex-specific changes in fetal development, inflammatory markers and placental transcriptome

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: Obesity during pregnancy is related to adverse maternal and neonatal outcomes. Factors involved in these outcomes may include increased maternal insulin resistance, inflammation, oxidative stress and nutrient mishandling. The placenta is the primary determinant of fetal outcomes, and its function can be impacted by maternal obesity. The aim of this study in mice was to determine the effect of obesity on maternal lipid handling, inflammatory and redox state, and placental oxidative stress, inflammatory signalling, and gene expression relative to female and male fetal growth. Here we showed that HFHS diet induced, in the dams, hepatic steatosis, oxidative stress (reduced catalase, elevated protein oxidation) and activation of pro-inflammatory pathways (p38-MAPK) along with imbalanced circulating cytokine concentrations (increased IL-6 and decreased IL-5 and IL-17A). HFHS fetuses were asymmetrically growth-restricted, showing sex-specific changes in circulating cytokines (GM-CSF, TNF-a, IL-6 and IFN-g). Morphology of the placenta Lz was modified by a HFHS diet, in association with sex-specific alterations in the expression of genes and proteins implicated in oxidative stress, inflammation, and stress signalling. Placental gene expression changes were comparable to that seen in models of intrauterine inflammation and were related to a transcriptional network involving transcription factors, LYL1 and PLAG1. In summary, this study shows that fetal growth restriction with maternal obesity is related to elevated oxidative stress, inflammatory pathways, and sex-specific placental changes. Our data are important given the marked consequences and the rising rates of obesity worldwide.

overall_design: Female mice were fed control or obesogenic high-fat/high-sugar diet (HFHS) from 9 weeks prior to and during pregnancy. On day 18.5 of pregnancy, maternal plasma, and liver, placenta, and fetal serum were collected to examine the immune and redox state. The placental labyrinth zone (Lz) was dissected for RNA-sequencing analysis of gene expression changes.

first: Alejandro

middle: A

last: Candia

first: Samantha

last: Lean

first: Cindy

middle: X

first: Daniel

last: McKeating

first: Anna

last: Cochrane

first: Edina

last: Gulacsi

first: Emilio

last: Herrera

first: Bernardo

middle: J

last: Krause

first: Amanda

middle: N

last: Sferruzzi-Perri


title: Plasmacytoid dendritic cells regulate tissue homeostasis of megakaryocytes

city: Munich

first: Bhavishya

last: Nelakuditi

address: Marchioninistraße 15, 81377 München

country: Germany

institute: LMU Klinikum

summary: Platelet homeostasis is essential for vascular integrity and immune defense. While the process of platelet formation by fragmenting megakaryocytes (thrombopoiesis) has been extensively studied, the cellular and molecular mechanisms required to constantly replenish the pool of megakaryocytes (MKs) by their progenitor cells (megakaryopoiesis) remains unclear. Here we use intravital imaging to track the cellular dynamics of megakaryopoiesis over days. We identify plasmacytoid dendritic cells (pDCs) as homeostatic sensors that monitor the bone marrow for apoptotic MKs and deliver IFN- to the MK niche triggering local on-demand proliferation and maturation of MK progenitors. This fine-tuned coordination between thrombopoiesis and megakaryopoiesis is crucial for MK and platelet homeostasis in steady state and stress. However, excessive activation of pDCs, such as by viral infections, can disturb this homeostatic circuit. Accordingly, we show that pDCs activated by SARS-CoV2 drive inappropriate megakaryopoiesis. Together, we uncover a hitherto unknown pDC-dependent homeostatic circuit that involves innate immune sensing and demand-adapted release of inflammatory mediators to maintain tissue homeostasis of the megakaryocytic lineage.

overall_design: FACS-sorted bone marrow MKPs from control mice (C57Bl6), platelet-depleted mice (C57Bl6+R300) and platelet depleted plus pDCs depleted mice (BDCA2-DTR+R300) were analyzed. 6 mice were pooled per condition and labeled with hashtag antibodies.

first: Florian

last: Gaertner


title: Perfluorooctanesulfonic acid alters pro-cancer phenotypes and metabolic and transcriptional signatures in testicula germ cell tumors

city: Urbana

last: Spinella

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

summary: The potential effects of poly- and perfluoroalkyl substances (PFAS) are a recent human and environmental health concern. There is a persistent link between PFAS exposure and cancer, but the mechanisms are poorly understood. Although epidemiological evidence supporting PFAS exposure and cancer in general is conflicting, there is a relatively strong evidence linking PFAS and testicular germ cell tumors (TGCTs). However, there have been no mechanistic studies to date cancerning PFAS and TGCTs. In this report, the effects of the legacy PFAS, perfluorooctanesulfonic acid (PFOS) and the newer "clean energy" PFAS, lithium bis(trifluoromethylsulfonyl)imide (LiTFSi and called HQ-115) on TGCT tumorigenicity, survival, metabolism, and gene regulation were investigated. In vitro, proliferation and survival of both chemo-sensitive and -resistant TGCT cells were minimally affected by a wide concentration range of PFOS and HQ-115. However, both chemicals promoted the growth of TGCT cells in mouse xenografts at doses consistenet with human exposure but had minimal acute toxicity, as assessed by total body, kidney, and testis weight. PFOS, but not HQ-115, increased liver weight. Transcriptiomic alterations of PFOS-exposed normal mouse testes were dominated by cancer-related pathways and gene expression altersations associated with the H3K27me3 polycomb pathway and DNA methylation, epigenetic pathways were previously shown to be critical for the survival of TGCT cells after cisplatin-based chemotherapy. Similar pattersn of PFOS-mediated gene expression occured in PFOS-exposed cells in vitro. Metabolomic studies revealed that PFOS also altered metabolites associiated with steroid biosynthesis and fatty acid metabolism in TGCT cells, consistent with the proposed ability of PFAS to mimic fatty acied based ligands controlling lipid metabolism and the proposed role of PFAS as endocrine disrupters. Our data, this first cell and animal based study on PFAS in TGCTs, support a pro-tumorigenic effect of PFAS on TGCT biology and suggests epigenetic, metabolic, and endocrine disruption as potential mechanisms of action that are consistent with the non-mutagenic nature of the PFAS class.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: gene expression of Control or PFAS treated testicular cell line or mouse testis.

first: Zeeshan

last: Fazal

first: Doha

last: Shokry


title: Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

city: Stockholm

first: Christian

last: Oertlin

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institutet

summary: We compare effects platform characteristics  on differential translation, i.e. differences between DNA- microarray and RNAsequencing. Using both DNA- microarray and RNAsequencing data we want to elucidate whether mTOR independent insulin induced translation exists.

overall_design: 12h serum starved MCF7 cells treated for 4h with DMSO (control), insulin, insulin + torin1.

first: Ola

last: Larsson

first: Ivan

last: topisirovic

first: Luc

last: Furic

first: Valentina

last: Gandin

first: Laia

last: Masvidal Sanz

first: Julie

last: Lorent

first: Carl

last: Murie


title: Integrative Omics reveals changes in the cellular landscape of yeast without peroxisomes

city: Groningen

first: Marc Pilegaard

last: Pedersen

address: Nijenborgh 7

country: Netherlands

institute: University of Groningen

summary: Peroxisomes are organelles that are crucial for cellular metabolism. However, these organelles play also important roles in non-metabolic processes, such as signalling. To uncover the consequences of peroxisome deficiency, we compared two extremes, namely Saccharomyces cerevisiae wild-type and pex3 cells, which lack functional peroxisomes, employing transcriptomics and quantitative proteomics technology. Cells were grown on acetate, a carbon source that involves peroxisomal enzymes of the glyoxylate cycle and does not repress peroxisomal proteins. Transcripts of peroxisomal β-oxidation genes and the corresponding proteins were enhanced in pex3 cells. Peroxisome-deficiency also caused reduced levels of membrane bound peroxins, while the soluble receptors Pex5 and Pex7 were enhanced at the protein level. In addition, we observed alterations in non-peroxisomal transcripts and proteins, especially mitochondrial proteins involved in respiration or import processes. Our results not only reveal the impact of the absence of peroxisomes in yeast, but also represent a rich resource of candidate genes/proteins that are relevant in peroxisome biology.

overall_design: Deletion of pex3 obstruct formation of functional peroxisomes. Will deletion of pex3 have an effect on the overall transcriptome? We compared transcriptomes of S. cerevisiae BY4741 wild type as control strain to the S. cerevisiae BY4741 pex3 deletion strain. These strains were cultivated on acetate because it derepresses the expression of many peroxisomal proteins.

first: Tjasa

last: Kosir

first: Hirak

last: Das

first: Marc

first: Marco

last: Anteghini

first: Silke

last: Oeljeklaus

first: Vitor

last: Martins dos Santos

first: Ida

last: van der Klei

first: Bettina

last: Warscheid


title: Expression data from Saccharomyces cerevisiae

city: Richmond

first: chunjun

last: zhan

state: CA

address: 2131 NAPA St

institute: JEBI

summary: Reprogramming a non-methylotrophic industrial host, such as Saccharomyces cerevisiae, to a synthetic methylotroph reprents a huge challenge due to the complex regulation in yeast. Through TMC strategy together with ALE strategy, we completed a strict synthetic methylotrophic yeast that could use methanol as the sole carbon source. However, how cells respond to methanol and remodel cellular metabolic network on methanol were not clear. Therefore, genome-scale transcriptional analysis was performed to unravel the cellular reprograming mechanisms underlying the improved growth phenotype.

overall_design: To understand how cells reprogram cellular metabolism to adapt growth on methanol,the evolved strain CX01F (B1-3) was compared with its parental strain CX01 (Sample1-3).

first: Chunjun

last: Zhan

first: Xiaowei

last: Li

first: Jay

last: Keasling

first: Yun

last: Chen

first: Jens

last: Nielsen


title: PFKFB3 drives renal fibrosis through promoting histone lactylation-mediated NF-𝜅B activation [RNA-seq]

first: yating

last: wang

state: Guangdong

address: 58th Zhongshan Road II  The First Affiliated Hospital ,Sun Yat-Sen University

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

summary: Persistently elevated glycolysis in kidney has been demonstrated to promote chronic kidney disease. However, the underlying mechanism remains largely unclear. Here, we observed that PFKFB3, a key glycolytic enzyme, was remarkably induced in kidney proximal tubular cells following ischemia-reperfusion injury in mice, as well as in multiple etiologies of chronic kidney disease patients. Proximal tubular epithelial-specific deletion of PFKFB3 significantly reduced renal lactate levels, mitigated inflammation and fibrosis, and preserved renal function in the IRI mouse model. To explore the mechanism of PFKFB3 in renal fibrosis, we performed RNA-sequencing (RNA-seq) on the kidney cortices from IRI mice. Of note, we found that PFKFB3-mediated kidney tubular glycolytic reprogramming markedly enhanced H4K12la lactylation. To further explore the potential functional significance of H4K12la in renal fibrosis, we performed genome-wide cleavage under targets and tagmentation (CUT&Tag) analysis to identify candidate genes regulated by H4K12la in sham and IRI kidney. Following CUT&Tag, H4K12la-associated DNAs were amplified using non-biased conditions, labeled, and sequenced with Illumina NovaSeq 6000.

overall_design: To investigate the role of PFKFB3 in the renal fibrosis, proximal tubular cell conditional Pfkfb3 knockout mice  and their littermate controls  were used and followed by ischemia kidney injury . Total RNA isolated from IRI kidney tissues  was used as input material for the RNA sequence.

first: Yating

last: Wang

first: Hongyu

first: Wei

first: Qinghua

last: Liu

first: Haiping

last: Mao


title: TAX1BP1 deficiency impair initiation of autophagic flow in HK-2 cells through downregulate AMPK-ULK1 pathway

city: Zhanjiang

first: Ji-Xin

last: Tang

address: No.57, Renmin Avenue

institute: Affiliated Hospital of Guangdong Medical University

summary: Selective autophagy receptor can combine with substrate in cells to degrade them and maintain cellular homeostasis. TAX1BP1, a kind of selective autophagy receptor, has N-terminal SKIP carboxyl homology (SKICH) domain (LC3-Interacting Region) and a C-terminal ubiquitin binding domain (UBD).TAX1BP1 can also be a potential regulatory factor to influence macroautophagy initiation. In order to research the function of TAX1BP1in renal tubular epithelial cells, we knockout and over expressive TAX1BP1 in HK-2 cells and research the state of autophagy flow and senescence. We found that TAX1BP1 knockout could impair initiation of autophagic flow, causing obstruction in LC3 lipidation. Farther, TAX1BP1 knockout could bring senescence and sensitivity in damage factor.

overall_design: Bulk RNA-seq between WT HK-2 cells and TAX1BP1-KO HK-2 cells, each group has three biological duplication

first: Jun-hao

last: Wen

first: Ze-Sen

last: Feng

first: Hua-Feng


title: Mutant IDH inhibitors induce lineage differentiation in IDH-mutant Oligodendroglioma II

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

institute: Massachusetts General Hospital

type: Methylation profiling by high throughput sequencing

summary: A subset of patients with IDH-mutant glioma respond to inhibitors of mutant IDH (IDHi), yet the molecular underpinnings of such responses are not understood. Here, we profiled by single-cell or single-nucleus RNA-sequencing three IDH-mutant oligodendrogliomas from patients who derived clinical benefit from IDHi. Importantly, the tissues were sampled on-drug, four weeks from treatment initiation. We further integrate our findings with analysis of single-cell and bulk transcriptomes from independent cohorts and experimental models. We find that IDHi treatment induces a robust differentiation towards the astrocytic lineage, accompanied by a depletion of stem-like cells and a reduction of cell proliferation. Furthermore, mutations in NOTCH1 are associated with decreased astrocytic differentiation and may limit the response to IDHi. Our study highlights the differentiating potential of IDHi on the cellular hierarchies that drive oligodendrogliomas and suggests a genetic modifier that may improve patient stratification.

overall_design: Fresh or frozen IDH-mutant gliomas treated with IDHi were dissociated and profiled by single-cell or single-nucleus RNA sequencing (Smart-seq2 or 10x). In-vitro IDH-mutant glioma models treated with or without IDHi was profiled by single-cell RNA-seq (10x) and single-cell multi-omics protocol (DNA methylome and transcriptome). In-vitro IDH-mutant glioma models that we knock out Notch1 (Notch1-KO) and the control (Notch1-WT) were profiled by single-cell RNA-sequencing (10x).

first: Avishay

last: Spitzer

first: Simon

last: Gritsch

first: Keith

middle: L

last: Ligon

first: Daniel

last: Cahill

first: Mario

last: Suva

first: Itay

last: Tirosh


title: The activity and safety of sintilimab on high-risk ground glass opacity lesions in multiple primary lung cancer patients

city: Guangzhou

first: Yi

address: Jingxiu Road, Panyu District

institute: the First Affiliated Hospital of Guangzhou Medical University

summary: Lung cancer is the second most commonly diagnosed cancer and the leading cause of cancer death worldwide, of which approximately 85% are non-small cell lung cancer (NSCLC). The overall survival (OS) of patients with advanced NSCLC was significantly prolonged with immune checkpoint inhibitors (ICIs) targeting the programmed cell death-1 (PD-1) and programmed death-ligand 1 (PD-L1) axis. For early-stage lung cancer, the 5-year survival rate for patients ranges from 80% in stage IA to 41% in stage IIIA, and many cases relapse after surgical resection. Currently, multiple clinical trials have manifested the encouraging efficacy of neoadjuvant immunotherapy in stage I-IIIA resectable NSCLC. However, the effect of immunotherapy in ultra early-stage NSCLC patients with micro-invasive or even pre-invasive lesions remains unclear. In this study, we aimed to evaluate the activity and safety of sintilimab on high-risk ground glass opacity lesions in multiple primary lung cancer patients.

overall_design: The difference of exosomal RNA in early-stage lung cancer patients who responded to anti-PD-1 antibody or not.

first: Wenhua

last: Liang

first: Bo

last: Cheng


title: The microglial transcriptome of age-associated deep subcortical white matter lesions suggests a neuroprotective response to blood-brain barrier dysfunction

city: SHEFFIELD

first: Rachel

last: Waller

state: South Yorkshire

address: SITraN, 385A Glossop Road

department: Neuroscience

institute: The University of Sheffield

summary: Age-associated deep-subcortical white matter lesions (DSCL) are an independent risk factor for dementia, displaying high levels of CD68+ microglia. This study aimed to characterise the transcriptomic profile of microglia in DSCL and surrounding radiologically normal-appearing white matter (NAWM) compared to non-lesional control white matter.  CD68+ microglia were isolated from white matter groups (n=4 cases per group) from the Cognitive Function and Ageing Study neuropathology cohort by immuno-laser capture microdissection.  Microarray gene expression profiling, but not RNA-sequencing, was found to be compatible with immuno-LCM-ed post-mortem material and identified significantly differentially expressed genes (DEG).  Functional grouping and pathway analysis was assessed using DAVID, and immunohistochemistry was performed to validate gene expression changes at the protein level.  Transcriptomic profiling of microglia in DSCL compared to non-lesional control white matter identified 181 significant DEG (93 upregulated and 88 downregulated).  Functional clustering analysis revealed dysregulation of haptoglobin-hemoglobin binding (Enrichment score 2.15, p=0.017), confirmed by CD163 immunostaining, suggesting a neuroprotective microglial response to blood-brain barrier dysfunction in DSCL.  In NAWM versus control white matter, microglia exhibited 347 DEGs (209 upregulated, 138 downregulated), with significant dysregulation of protein de-ubiquitination (Enrichment score 5.14, p<0.0001), implying an inability to maintain protein homeostasis in NAWM that may contribute to lesion spread. These findings enhance understanding of microglial transcriptomic changes in aging white matter pathology, highlighting a neuroprotective adaptation in DSCL microglia and a potentially lesion-promoting phenotype in NAWM microglia.

overall_design: 1- Isolate microglia from frozen post-mortem cases using immuno-LCM, and Perform transcriptomic profiling of microglia in control, NAWM and DSCL samples using RNA-seq. 2- Perform bioinformatics analysis of the datasets generated by RNA-seq to identify significantly differentially expressed genes and dysregulated pathways, and functional groups.

first: Taghreed

last: Almansouri

first: Racheal

first: Paul

last: Heath

first: Freek

last: van Eden

first: Julie

last: Simpson


title: IRF3 drives replication stress signaling and determines sensitivity to genotoxic agents in triple-negative breast cancer cells

first: Marcel

last: van Vugt

state: Netherlands

address: Hanzeplein 1

institute: University Medical Center Groningen

summary: Interferon-β signaling has been shown to play important roles in anti-virus as well as anti-tumor immunity. We here report that the key transcription factor in type I interferon signaling, IRF3, as well as downstream interferon-β are able to induce replication stress signaling in triple-negative breast cancer cells. IRF3 overexpression sensitizes triple-negative breast cancer cells to several genotoxic agents. Addition of IFN-β, a key downstream cytokine of IRF3,reduced replication fork speed and activated ATR-CHK1 signaling. Conversely, type I interferon-neutralizing antibodies or nucleosides supplementation rescued IRF3-induced replication stress.

overall_design: We treated two triple-negative breast cancer cell lines, HCC38 and MDA-MB-231, with interferon-β (400 IU/mL) for 48 hours. We then performed gene expression profiling analysis using data obtained from RNA-seq of untreated samples and interferon-β-treated samples.

first: Mengting

last: Chen


title: Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions

city: Waltham

first: Melissa

last: Seman

address: 415 South St

institute: Brandeis University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Visualizing and measuring molecular-scale interactions in living cells represents a major challenge, but recent advances in microscopy are bringing us closer to achieving this goal. Single-molecule super-resolution microscopy enables high-resolution and sensitive imaging of the positions and movement of molecules in living cells. HP1 proteins are important regulators of gene expression because they selectively bind and recognize H3K9 methylated (H3K9me) histones to form heterochromatin-associated protein complexes that silence gene expression. Here, we extended live-cell single-molecule tracking studies in fission yeast to determine how HP1 proteins interact with their binding partners in the nucleus. We measured how genetic perturbations that affect H3K9me alter the diffusive properties of HP1 proteins and each of their binding partners based on which we inferred their most likely interaction sites. Our results indicate that H3K9me promotes specific complex formation between HP1 proteins and their interactors in a spatially restricted manner, while attenuating their ability to form off-chromatin complexes. As opposed to being an inert platform or scaffold to direct HP1 binding, our studies propose a novel function for H3K9me as an active participant in enhancing HP1-associated complex formation in living cells.

overall_design: Chromatin immunoprecipitation seqeuencing (ChIP-Seq) for Chp2 tagged with PAmCherry using a mCherry antibody

first: Ziyuan

first: Ali

last: Farhat

first: Yekaterina

last: Fyodorova

first: Saikat

last: Biswas

first: Alexander

last: Levashkevich

first: P

last: Freddolino

last: Biteen

first: Kaushik

last: Ragunathan


title: Effect of glutamine treatment on human brain microvascular endothelial cells

city: Beijing

first: Qiheng

last: He

state: Beijing

address: 119 South Fourth Ring West Road, Fengtai District

department: Neurosurgery

institute: Beijing Tiantan Hospital

summary: We found glutamine levels were positively associated with a greater risk of stroke. After treatment with glutamine, HBMECs exhibited enhanced proliferation, migration, and EndMT, all reversed by ITGB4 knockdown. In ITGB4-transfected HBMECs, the MAPK-ERK-TGF-β/BMP pathway was activated, with Smad4 knockdown reversing the EndMT. Furthermore, atorvastatin suppressed the EndMT by inhibiting Smad1/5 phosphorylation and promoting Smad4 ubiquitination in ITGB4-transfected HBMECs. Finally, ITGB4 upregulation was confirmed in the superficial temporal arteries of patients with moyamoya.

overall_design: To investigate the effect of glutamine on human brain microvascular endothelial cells, we treat cells with glutamine at a concentration of 20 mM.

first: Junsheng

last: Li

first: Zhiyao

last: Zheng

first: Peicong

last: Ge


title: DCAF2 regulates the proliferation and differentiation of mouse progenitor spermatogonia by targeting p21 and thymine DNA glycosylase

city: China

first: hongwei

last: Wei

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: South China University of Technology

summary: DDB1-cullin-4-associated factor-2 (DCAF2, also known as DTL or CDT2), a conserved substrate recognition protein of Cullin-RING E3 ligase 4 (CRL4), recognises and degrades several substrate proteins during the S phase to maintain cell cycle progression and genome stability. Our study found that Dcaf2 was highly expressed in the germ cells of human and mouse testes. To determine whether DCAF2 plays a crucial role in spermatogenesis, we generated germ cell conditional Dcaf2 knockout mice by crossing Dcaf2fl/fl mice with Stra8-Cre mice. The depletion of Dcaf2 in germ cells causes a reduction in progenitor spermatogonia and differentiating spermatogonia, eventually leading to the failure of meiosis initiation and male infertility. Further study showed that depletion of Dcaf2 in germ cells caused abnormal accumulation of the substrate proteins cyclin-dependent kinase inhibitor 1A (p21) and thymine DNA glycosylase (TDG). Overexpression of p21 or TDG attenuates proliferation and increases DNA damage and apoptosis in GC-1 cells. Co-overexpression of p21 and TDG exacerbates DNA damage and apoptosis. These results suggest that DCAF2 maintains the expansion and differentiation of progenitor spermatogonia by targeting the substrate proteins p21 and TDG.


title: Erythromycin mediates co-flocculation between cyanobacterium Synechocystis sp. PCC 6803 and filamentous fungi in liquid cultivation without organic compounds [CE and CEF]

city: Bangkok

first: Jidapa

last: Leksingto

country: Thailand

institute: Chulalongkorn

summary: Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. The fungi in the co-flocculated biomass were isolated and found to consist of five species with the filamentous Purpureocillium lilacinum and Aspergillus protuberus making up 71% of the overall fungal population. The optimal co-cultivation for flocculation was an initial 5 mg (fresh weight) of fungi, an initial cell density of Synechocystis of 0.2 OD730, 10 µM EM, and 14 days of cultivation in 100 mL of BG11 medium with no organic compound. This yielded 248 ± 28 mg/L of the Synechocystis-fungi flocculated biomass from 560 ± 35 mg/L of total biomass, a 44 ± 2 % biomass flocculation efficiency. Furthermore, the EM treated Synechocystis cells in the Synechocystis-fungi flocculate had a normal cell color and morphology, while those in the axenic suspension exhibited strong chlorosis. Thus, the occurrence of the Synechocystis-fungi flocculation was mediated by EM, and the co-flocculation with the fungi helped Synechocystis to alleviate the negative effect of EM. Transcriptomic analysis of suspended and flocculated (with the fungi) Synechocystis cells suggested that the EM-mediated co-flocculation was a result of down-regulation of the minor pilin genes and up-regulation of several genes including the chaperone gene for pilin regulation, the S-layer protein genes, the exopolysaccharide-polymerization gene, and the genes for signaling proteins involved in cell attachment and abiotic-stress responses. The EM treatment may be applied in the co-culture between other cyanobacteria and fungi to mediate cell bio-flocculation.

overall_design:
Transcriptomic analysis was performed between the Synechocystis in the suspended Synechocystis cells with EM and the Synechocystis cells in the flocculated (with the fungi) Synechocystis-fungi flocculated biomass.  The results suggested that the presence of fungi did not significantly altered the expression levels of pillin genes. Thus the altered gene expression levels of pillin genes were results from the EM treatment.
Samples include:
No fungi 1: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 1
No fungi 2: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 2
No fungi 3: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 3
with fungi 1: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin and 5 mg of fungi addition_replicated 1
with fungi 2: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin and 5 mg of fungi addition_replicated 2
with fungi 3: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin and 5 mg of fungi addition_replicated 3

first: Tanakarn

last: Monshupanee

first: Panutchaya

last: Pichaiyotinkul


title: Erythromycin mediates co-flocculation between cyanobacterium Synechocystis sp. PCC 6803 and filamentous fungi in liquid cultivation without organic compounds [C and CE]

overall_design:
Transcriptomic analysis of Synechocystis cells with and without EM suggested that EM mediated the up-regulation of several pillin gens. The EM treatment may be applied in the co-culture between Synechocystis cells and other antibiotics.
Samples include:
without EM1: The Synechocystis cultivation under normal BG-11 medium condition_replicated 1
without EM2: The Synechocystis cultivation under normal BG-11 medium condition_replicated 2
without EM3: The Synechocystis cultivation under normal BG-11 medium condition_replicated 3
Cyano EM_1: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 1
Cyano EM_2: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 2
Cyano EM_3: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 3


title: Se Deficiency Exacerbates Hyperoxia-Induced Lung Injury in Newborn C3H/HeN Mice

city: Oklahoma City

first: Abhrajit

last: Ganguly

state: Oklahoma

address: 800 Research Pkwy

department: Pediatrics

institute: University of Oklahoma Health Center

summary: Extremely preterm infants are often treated with supraphysiological oxygen which contributes to the development of bronchopulmonary dysplasia (BPD). These same infants exhibit compromised antioxidant capacities due in part to selenium (Se) deficiency.  The present study was designed to develop a perinatal Se deficiency mouse model, identify the effects of newborn hyperoxia exposure, and explore alternative pathways affected by Se deficiency (SeD) that would contribute to impaired lung development.  Se deficient breeding pairs were generated, once pups were born, they were exposed to room air or 85% O2 for 14 d.  Survival, antioxidant and Nrf2-regulated protein expression, and RNA seq analyses were performed. Greater than 40% mortality was observed in Se deficient (SeD), hyperoxia exposed pups.  Surviving SeD pups had greater lung growth deficits than Se sufficient (SeS) pups exposed to hyperoxia.  Gpx2 and 4 protein and Gpx activity were significantly decreased in SeD pups.  Nrf2-regulated proteins, NQO1 and Gclc were increased in the setting of Se deficiency and hyperoxia exposure.  RNA seq revealed significant decreases in the Wnt/-catenin and Notch pathways. Se is a biologically relevant modulator of perinatal lung development and antioxidant responses, especially in the context of hyperoxia exposure. RNA seq implicates pathways essential for normal lung development are dysregulated by Se deficiency.

overall_design:
Male and female C3H/HeN mice were placed on diets that differ only in Se content (Se-sufficient (SeS) with 0.4 ppm or Se-deficient (SeD) containing <0.01 ppm sodium selenite) at 3 weeks of life and remained on the diets throughout the experiment.
After 3 weeks on respective SeS or SeD diets, mice were bred to create SeS and SeD litters for use in the present studies.
At birth, pups were placed in FiO2 0.85 hyperoxia or remained in room air. Pups were euthanized at PN1 or 3 and lungs were perfused with ice-cold PBS, snap-frozen in Trizol, and stored at –80°C for RNAseq.

first: Lora

last: Bailey-Downs

first: Laura

last: Sherlock

first: Michaela

last: Crossley

first: Aristides

last: Rivera Negron

first: Paul

last: Pierce

first: Shirley

last: Wang

first: Hua

last: Zhong

first: Cynthia

last: Carter

first: Kathryn

last: Burge

first: Jeffrey

last: Eckert

first: Lynette

middle: K

last: Rogers

first: Peter

middle: F

last: Vitiello

first: Trent

last: Tipple


title: Pharmaceutical inhibition of RAS overcomes cytokine mediated resistance to FLT3 inhibition in FLT3-ITD+ AML [ChIP-seq II]

city: Birmingham

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

summary: AML is characterised by a variety of co-occurring driver mutations in genes associated with cell signallingand growth regulationsuch as the FLT3-ITD. Inhibitors targeting FLT3 (FLT3i) are beingused to treat FLT3-ITD+ patients but most relapse.By profiling the gene regulatory networks of samples from patients before and after FLT3i treatment weobservedan increase in AP-1 mediated and a loss of RUNX1 mediated connections in treatment resistant cells. Treatmentinducesupregulation of signalling pathway genesindicatingthat cytokines mediate resistance to FLT3i, with IL-3 playing a major role. IL3 rescues survival by counteracting FLT3i mediated globalRUNX1 degradation and adown-regulationof bindingof RUNX1 in chromatin.To identify inhibitors which bypass the RUNX1 barrier we inhibitedMAPK signalling with a novel pan-RAS inhibitor which overcomes cytokine mediated resistance.Our data show (I) that cytokinesinstructAML maintenance via the stabilisation of transcriptional regulators and (ii)pan-RAS drugs bypass thisbarrier, suggesting a novel approach to treatment of AML.

overall_design: ChIP-Seq for RUNX1 in the FLT3-ITD cell line MV411, transfected with a doxycycline inducible dominant-negative FOS (dnFOS) or empty vector - and with or without doxycycline induction

first: Daniel

last: Coleman

last: Cockerill

first: Constance

last: Bonifer


title: Intestinal NSD2 aggravates hepatic steatosis during obesity through histone modifications [CUT&Tag]

city: 北京市

first: YIJIA

last: ZHANG

address: 和平街道

institute: Beijing University of Chemical Technology

summary: The impairment of the intestinal barrier will lead to the accumulation of fat and harmful substances in the liver, inducing hepatic steatosis or steatohepatitis. Zhang et al. identified NSD2 in the intestine as a novel and essential regulator of hepatic steatosis. NSD2 directly regulates transcriptional activation of ERN1 through the modification of H3 dimethylated on lysine 36 (H3K4me36), thereby activating the ERN1-JNK axis to induce inflammatory response, intestinal barrier impairment, and hepatic steatosis. This functional mechanism of NSD2 provides a potential therapeutic target for this disease.

overall_design: After 16 weeks of HFCD in NSD2fl/fl mouse and NSD2∆IE mouse, colon tissues were taken and subjected to CUT & Tag assays for H3K36me2

first: Yi-jia

last: Zhang

first: Liang

last: Peng


title: Autism patient derived SHANK2BY29X mutation affects ALDH1A1 negative dopamine neuron development

first: Yingying

last: Zhao

address: Kaiyuan Avenue

department: Chinese Academy of Sciences Guangzhou Branch

institute: Guangzhou Institutes of Biomedicine and Health

summary: Autism spectrum disorder (ASD) includes a series of neurodevelopmental conditions. Different mutations on a single ASD gene contribute to heterogeneous disease phenotypes, possibly due to functional diversity of generated isoforms. Increasing evidence indicates such phenomenon in SHANK2, a causative gene in ASD; however, there is a scarcity of tools for studying endogenous SHANK2 proteins in an isoform-specific manner. Here we reported a patient-derived mutation on SHANK2, hitting only the SHANK2B transcript variant (NM_133266.5), hereby SHANK2BY29X.

overall_design:
We conducted an analysis of the transcriptome of an autism patient clone (PC1) and his unaffected father (HC1) during 9 days of neural induction from induced pluripotent stem cells (iPSCs).
***Submitter declares that the RNA-seq raw data is not provided due to patient privacy concerns***
***Submitters state that the result of the scRNA-seq seq bam file viewed in IGV is included in the associated manuscript (i.e. no quantified processed data for scRNA-seq samples).

first: Wanjing

last: Lai

first: Yalan

last: Chen

first: Zhenzhu

last: Dai

first: Yimei

last: Niu

first: Xiaoxia

first: Shuting

first: Guanqun

last: Huang

first: Ziyun

last: Shan

first: Jiajun

last: Zheng

first: Yu

last: Hu

first: Qingpei

first: Siyi

last: Gong

first: Sai

last: Kang

first: Hui

last: Guo

first: Xiaokuang

last: Ma

first: Youqiang

last: Song

first: Kun

last: Xia

first: Jie

first: Kai

first: Shenfeng

last: Qiu

first: Li

first: Jiekai

first: Lingling

last: Shi


title: The gene expression of HUVEC in response to the cytokine stimulations

city: St. Petersburg

first: JUNKO

last: SAWADA

address: 600 5th Street South

institute: Johns Hopkins All Children's Hispital

summary: The response of endothelial cells to the tissue environment has a critical impact on their function in inflammation and tumors. In particular, cytokine stimulation such as TNFa, IL-4, IFNg, and LTbR induces gene expression changes, which significantly impact endothelial cell function and differentiation. To understand the degree of gene expression change, we performed a transcriptome analysis of HUVEC.

overall_design: HUVEC cells were cultured at 2X10(5)/well in the 6-well plate. The next day, the cell medium was replaced with 10 ng/ml TNFa, 10 ng/ml IL-4, 50 ng/ml IFNg, or control (EGM-2 medium only) and cultured 2 days. RNA was isolated and used for the library generation.

first: Sawada

last: Junko

first: Komatsu

last: Masanobu

first: Jiang

last: Lu


title: Transcriptome profiling of Artemia cyst in 30min after embryonic diapause termination

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

institute: College of Life Sciences, Tianjin Normal University

summary: Embryonic diapause is a widely occurring evolutionary adaptation phenomenon in animals. Artemia is one of the classic animal models for diapause research. The current studies of Artemia diapause mainly focus on the induction and maintenance of the embryonic diapause, but there is little research on the molecular regulatory mechanism of Artemia embryonic diapause termination (EDT) and embryonic reactivation. Here the gene expression of Artemia cyst at 30min after embryonic diapause termination (EDT), which is in post-diapause stage were tested by RNA-seq to analyze the mechanism of signal regulation involved in Artemia EDT at the molecular level.

overall_design: The mRNA expression of Artemia cyst at 30min after embryonic diapause termination (EDT) with the Illumina high-throughput sequencing technology by Novogene Inc.The DEGs were analyzed especially the DEGs related to signaling transduction.

first: Anqi

last: Li


title: The microglial transcriptome of age-associated deep subcortical white matter lesions suggests a neuroprotective response to blood-brain barrier dysfunction (microarray)

first: Rachel

last: Waller

overall_design: CD68+ microglia were isolated from white matter groups (n=4 cases per group) from the Cognitive Function and Ageing Study neuropathology cohort by immuno-laser capture microdissection.  Microarray gene expression profiling, but not RNA-sequencing, was found to be compatible with immuno-LCM-ed post-mortem material and identified significantly differentially expressed genes (DEG). Functional grouping and pathway analysis was assessed using DAVID, and immunohistochemistry was performed to validate gene expression changes at the protein level.

first: Taghreed

last: Almansouri

first: Stephen

last: Wharton

first: Paul

middle: R

last: Heath

first: Fiona

last: Matthews

first: Carol

last: Brayne

first: Fredericus

last: van Eeden

first: Julie

last: Simpson


title: Intestinal NSD2 aggravates hepatic steatosis during obesity through histone modifications [RNA-seq]

first: YIJIA

last: ZHANG

overall_design: Intestinal-specific NSD2 disruption mice (NSD2∆IE) and controls (NSD2fl/fl) were treated with a 16-week HFCD diet, and colon tissues were collected for further study, with three replicate samples per group

first: Yi-jia

last: Zhang

first: Liang

last: Peng


title: Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever [scRNA-seq]

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Alcelaphine gammaherpesvirus 1 (AlHV-1) is a member of the Gammaherpesvirinae subfamily and establishes asymptomatic latent infection in its natural host species, the wildebeest. Cross-species transmission to various ruminant species including cattle can occur, resulting in the induction of malignant catarrhal fever (MCF), a deadly peripheral T cell lymphoproliferative disease. Here, we experimentally infected calves to confirm that AlHV-1 latency-associated gene expression is essential for persistent infection of CD8+ T cells and MCF development. Then, deep sequencing of the T cell receptor repertoire revealed an oligoclonal expansion of peripheral CD8+ T cells during bovine MCF, associated with transcriptomic and epigenetic changes identified by (sc)RNA-seq and ATAC-seq analyses which indicated a mixed effector/memory and exhaustion phenotype of infected cells in vivo. Analysis of the viral genome transcription identified viral genomic regions being expressed in infected CD8+ T cells, such as the region predicted to encode the gene A10. A10 encodes a transmembrane signaling protein displaying multiple tyrosine residues, with predicted ITAM and SH3 motifs. We could demonstrate that impaired expression of A10 did not affect AlHV-1 replication in vitro but rendered AlHV-1 unable to induce MCF in the rabbit experimental model, and we showed that A10 is phosphorylated in T lymphocytes in vitro and affects T cell signaling. Finally, while AlHV-1 viruses expressing mutated forms of A10 devoid of ITAM and/or SH3 motifs could induce MCF, an A10 knock-in viral mutant unable to phosphorylate tyrosine residues resulted in the absence of MCF development. Overall, we identified AlHV-1-induced phenotypic changes in CD8+ T cells during MCF and demonstrated that A10 expression in infected CD8+ T lymphocytes results in the dysregulation of T cell signaling and MCF.

overall_design: Bovine PBMC were isolated from veinous blood collected from the jugular vein. PBMCs were subjected to a microbead-based negative selection protocol to isolate CD8 T cells.

first: Meijiao

last: Gong

first: Françoise

last: Myster

last: Azouz

first: Guillem

last: Sanchez Sanchez

first: Jenna

last: Nichols

first: Lucas

last: Lefevre

first: Shifang

first: Benoit

last: Charloteaux

first: Bin

last: Yang

first: Justine

last: Javaux

first: Sylvain

last: Leemans

first: Olivier

last: Nivelles

first: Willem

last: van Campe

first: Stefan

last: Roels

first: Laurent

last: Mostin

first: Thierry

last: van den Bergh

first: Andrew

last: Davison

last: Gillet

first: Tim

last: Connelley

first: David

last: Vermijlen

first: Stanislas

last: Goriely

first: Alain

last: Vanderplasschen

first: Benjamin

middle: G

last: Dewals


title: Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever [RNA-seq]

first: Abdulkader

last: AZOUZ

first: Meijiao

last: Gong

first: Françoise

last: Myster

last: Azouz

first: Guillem

last: Sanchez Sanchez

last: Li

first: Jenna

last: Nichols


title: Mutant IDH inhibitors induce lineage differentiation in IDH-mutant Oligodendroglioma III

first: Masashi

last: Nomura

overall_design:
Fresh or frozen IDH-mutant gliomas treated with IDHi were dissociated and profiled by single-cell or single-nucleus RNA sequencing (Smart-seq2 or 10x). In-vitro IDH-mutant glioma models treated with or without IDHi was profiled by single-cell RNA-seq (10x) and single-cell multi-omics protocol (DNA methylome and transcriptome). In-vitro IDH-mutant glioma models that we knock out Notch1 (Notch1-KO) and the control (Notch1-WT) were profiled by single-cell RNA-sequencing (10x).

***************************************************************
human raw data not deposited due to patient privacy concerns
***************************************************************

first: Avishay

last: Spitzer

first: Simon

last: Gritsch

first: Keith

last: Ligon

first: Daniel

middle: P

last: Cahill

first: Mario

last: Suva

first: Itay

last: Tirosh


title: Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever

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

overall_design: Refer to individual Series


title: 20S Proteasome Hyperactivation enhances translation, lipid metabolism, proteostasis and longevity: a Proteo-transcriptimic analysis

city: Morgantown

middle: Rodrigo

last: Salcedo

state: WV

address: 64 Medical Center Drive

department: Biochemistry and Molecular Medicine

institute: West Virginia University

summary: Our study elucidates the broad-spectrum effects of proteasome hyperactivation on the proteome, demonstrating its substantial influence on the proteostasis network. Through comprehensive analyses, we identified a significant reorganization of the transcriptome, enhanced mRNA processing, and increased translation activity. The study further reveals the hyperactivation's impact on intrinsically disordered proteins, lipid synthesis, and biogenesis, evidenced by major changes in lipid droplets and peroxisome proliferation. Notably, we uncovered protective phenotypes against oxidative stress, primarily mediated by Super Oxide Dismutases (SODs), indicating an elevated stress response readiness. Additionally, our research highlighted the hyperactive proteasome's selective targeting of vitellogenins, crucial for lipid metabolism and implicated in the aging process of C. elegans. Enhanced ERAD-dependent degradation was observed, facilitating the clearance of senescent VIT-2 protein aggregates and promoting healthier aging. The α3ΔN mutant significantly reduced the quantity of human alpha-1 antitrypsin (ATZ) aggregates and delayed their formation in a C. elegans model for ATZ disease, suggesting its potential as an ERAD enhancer. These findings propose proteasome hyperactivation as a promising strategy for treating aggregation-prone diseases, offering novel avenues for drug development and therapeutic interventions against neurodegeneration.

overall_design: Total mRNA was extracted from age synchronized C.elegans populations . In total 5 replicates Wild types and 5 replicates  Hyperactive proteasome mutants from Day 8 adults were used for sequencing.

last: Salcedo Tacuma

first: Nadeem

last: Asad

first: Giovanni

last: Howells

first: Raymond

last: Anderson

middle: M

last: Smith


title: IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma (RNA-Seq human 16).

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

summary: Multiple myeloma (MM) is an incurable malignancy of plasma cells that exploits transcriptional networks underpinning normal plasma cell biology to drive malignant growth and survival. The transcription factor IRF4 serves as the principal architect of plasma cell identity, and MM cells are addicted to IRF4 expression for their survival. To discover unique molecular vulnerabilities in MM, we employ a multi-omics approach integrating functional genomics screening, spatial-proteomics, and global chromatin mapping. We find that ARID1A, a member of the SWI/SNF chromatin remodeling complex, is both required for IRF4 expression and functionally associated with IRF4 protein on chromatin. Conditional deletion of Arid1a in activated murine B cells thwarts subsequent plasma cell differentiation by disrupting IRF4-dependent transcriptional networks, thus defining ARID1A as a novel plasma cell vulnerability. Targeting ARID1A-dependent SWI/SNF activity via SMARCA2/4 inhibition induces a rapid loss of IRF4-target gene expression and quenches global oncogenic amplification of gene expression driven by MYC, resulting in profound toxicity to MM cells. Notably, SWI/SNF-dependent genes are upregulated in MM patients with aggressive disease, and SMARCA2/4 inhibitors retain their activity in immunomodulatory drug (IMiD)-resistant MM cells. To fully harness the potential of these drugs, we use combinatorial drug screens to uncover profound synergistic toxicity between SMARCA2/4 and MEK inhibitors. Thus, targeting SWI/SNF activity potently represses an IRF4-MYC feed forward loop and provides a feasible path forward to effectively treat this incurable disease.

overall_design: RNA sequencing to determine gene expression in NCH929 and SKMM1 multiple myeloma cells treated with control (DMSO) versus 1000 nM AU15330 for 6 and 24 hours.

first: Arnold

last: Bolomsky

first: Ryan

last: Young


title: Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever [ATAC-seq]

first: Abdulkader

last: AZOUZ

first: Meijiao

last: Gong

last: Myster

last: Azouz

last: Sanchez Sanchez

last: Nichols

first: Lucas

last: Lefevre

first: Shifang

last: Li

first: Benoit

last: Charloteaux

first: Bin

last: Yang

first: Justine

last: Javaux

first: Sylvain

last: Leemans

first: Olivier

last: Nivelles

first: Willem

last: van Campe

first: Stefan

last: Roels

first: Laurent

last: Mostin

first: Thierry

last: van den Bergh

first: Andrew

last: Davison

last: Gillet

first: Tim

last: Connelley

last: Vermijlen

first: Stanislas

last: Goriely

first: Alain

last: Vanderplasschen

first: Benjamin

last: Dewals


title: IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma (CUT&RUN mouse 13)

first: David

last: Huang

overall_design: Cut&Run analysis of ARID1A to determine chromatin binding in murine naive B cells, germinal center B cells, and plasma cells.

first: Arnold

last: Bolomsky

first: Ryan

last: Young


title: IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma


title: IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma (CUT&RUN human 8).

overall_design: Cut&Run analysis to determine IRF4 and ARID1A chromatin binding profiles in  SKMM1 multiple myeloma cells treated with control (DMSO) versus 1000 nM AU15330 for 3 hours.


title: ATAC-sequencing of Artemia cyst at 30min after embryonic diapause termination

first: Tong

last: Hao

summary: Embryonic diapause is a widely occurring evolutionary adaptation phenomenon in animals. Artemia is one of the classic animal models for diapause research. The current studies of Artemia diapause mainly focus on the induction and maintenance of the embryonic diapause, but there is little research on the molecular regulatory mechanism of Artemia embryonic diapause termination (EDT) and embryonic reactivation. Here the gene expression of Artemia cyst at 30min after embryonic diapause termination (EDT), which is in post-diapause stage were tested by ATAC-seq to analyze the mechanism of signal regulation involved in Artemia EDT at the molecular level.

overall_design: ATAC-seq profiling of Artemia cyst at 30min after embryonic diapause termination (EDT) with the Illumina high-throughput sequencing technology by Novogene Inc.

first: Anqi

last: Li


title: DUSP1 and SOX2 expression determine Squamous cell carcinoma of the salivary gland progression.

city: Madrid

first: Ana

last: Sastre-Perona

state: Madrid

address: Calle Paseo de la Castellana 261, INGEMM, Laboratorio de Epigenética, Hospital Universitario La Paz

country: Spain

institute: IdiPAZ

summary: Salivary gland squamous cell carcinomas (SG-SCCs) are a rare type of head and neck cancers which are linked to poor prognosis. Due to their low frequencies, the molecular mechanisms responsible for their aggressiveness are poorly understood. In this work we studied the function of the phosphatase DUSP1, a negative regulator of MAPK activity, in controlling the progression of SG-SCCs. We generated DUSP1 KO clones in A253 human cells. These clones showed a reduced ability to grow in 2D, self-renew in ECM matrices and grow tumors in immunodeficient mice. This was caused by an overactivation of the stress and apoptosis kinase JNK1/2 in DUSP1-KO clones. Interestingly, RNAseq analysis revealed that the expression of SOX2, a well know self-renewal gene was decreased at the mRNA and protein level. Unexpectedly, CRISPR-KO of SOX2 did not recapitulate DUSP1-KO phenotype, and SOX2-null cells had an enhanced ability to self-renew and grow tumors in mice. Gene expression analysis demonstrated that SOX2-null cells have a decreased squamous differentiation profile -losing TP63 expression- and an increased migratory phenotype, with an enhanced epithelial to mesenchymal transition signature. In summary, our data indicates that DUSP1 and SOX2 have opposite functions in SG-SCC, being DUSP1 necessary for tumor growth and SOX2 dispensable, and with a tumor suppressor function. Our data will suggest that the expression SOX2 and DUSP1 could be a useful biomarker to predict the progression of patients with SG-SCCs.

overall_design: Compared control A253 cells with DUSP1 or SOX2 KO cells to identify differentially expressed genes.

first: Lucía

last: Acero-Riaguas


title: Transcriptomic analysis of plasma extracellular vesicles from patients with ischemic stroke of different etiologies undergoing mechanical thrombectomy

city: Pamplona

first: Josune

last: Orbe

address: Avenida Pio XII 55

institute: CIMA

summary: INTRODUCTION: Accurate ischemic stroke (IS) etiologic diagnosis provides an appropriate secondary prevention strategy and better outcome. Currently, 45% of IS are cryptogenic urging to find novel approaches to enhance diagnostic precision and secondary stroke prevention. OBJETIVE: To study the transcriptomic content of circulating extracellular vesicles (EVs) to delineate the molecular profile and potential biomarkers of IS etiologies. RESULTS:21 consecutive patients with moderate or severe ischemic stroke (IS) and different IS etiologies were included to perform the transcriptomic analysis of plasma EVs comprising:  atherothrombotic (AT, n=6), Cardioembolic (CE, n=10), and embolic stroke of undetermined source (ESUS, n=5). The RNASeq analysis of EVs detected clusters of differentially expressed genes (DEGs) related to IS etiologies.

overall_design: Transcriptome of patients with ischemic stroke of atherothrombotic (AT, n=6), cardioembolic (CE, n=10) or undetermined etiology (ESUS, n=5) were compared  in circulating extracellular vesicles .


title: KMT9 is an actionable target in muscle-invasive bladder cancer

city: Freiburg

first: Sainab

last: Totonji

address: Breisacherstraße 66

institute: Uniklinik Freiburg

summary: Novel treatment modalities are imperative for the challenging management of muscle-invasive and metastatic BC to improve patient survival rates. The recently identified lysine methyltransferase (KMT) 9, an obligate heterodimer composed of KMT9α and KMT9β, regulates the growth of various types of tumors such as prostate, lung and colon cancer. While overexpression of KMT9α was previously observed to be associated with aggressive basal-like MIBC in an analysis of patients’ tissue samples, a potential functional role of KMT9 in this type of cancer has not been investigated to date. In this study, we show that KMT9 regulates proliferation and migration of various MIBC cell lines with different genetic mutations. KMT9α depletion results in differential expression of genes involved in the regulation of the cell cycle, cell adhesion and migration. Reduced cell proliferation upon KMT9α depletion is also observed in Pten/Trp53 knockout bladder tumor organoids, which cannot be rescued with an enzymatically inactive KMT9α mutant. In accordance with the idea that the catalytic activity of KMT9 is required for the control of cellular processes in MIBC, a recently developed small molecule inhibitor of KMT9 (KMI169) also impairs cancer cell proliferation. Since KMT9α depletion also restricts the growth of xenografts in mice, our data suggest that KMT9 is an actionable novel therapeutic target for the treatment of MIBC.

overall_design:
To investigate the role of KMT9 on BC cell transcriptome, we treated 5637 and CAL-29 cells with an siRNA for KMT9α depletion (siRNA) and a control siRNA (siCT).
We then performed gene expression profiling analysis using data obtained from RNA-seq of the cells treated as described.
Comparative gene expression profiling analysis of RNA-seq data for samples from siCT and siRNA treated cells.

first: Roland

last: Schüle

first: Dominica

last: Willmann


title: IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma (ATAC-Seq human 8)

overall_design: ATAC sequencing to determine open chromatin profiles in NCH929 and SKMM1 multiple myeloma cells treated with control (DMSO) versus 1000 nM AU15330 for 4 hours.


title: The Pkm duet: Coordinating C2C12 myoblast proliferation and differentiation through Histone 3 phosphorylation and cBAF complex dynamics

city: Worcester

first: Tapan

last: Sharma

address: 368 Plantation Street

department: Gene Therapy Centre

institute: University of Massachusetts Medical School

summary: Pkm1 and Pkm2 kinases are expressed in differentiating skeletal myoblasts. Knockdown of Pkm1 or Pkm2, therefore, can affect myoblast differentiation, by two independent regulatory mechanisms involving histone phosphorylation and chromatin remodeling complexes. Pkm2 KD in C2C12 cells reduced the chromatin marks of phosphorylated H3-T6,  H3-T11 and H3-T45 into several essential myogenic promoters, and consequently, prevented their expression. Also, the transcriptional analysis demonstrated that Pkm2 is required for the expression of the cBAF-specific subunits Dpf2 and Baf250a, which we have previously demonstrated are essential for myogenesis. In contrast, Pkm1 KD alters the localization of nuclear Dpf2 into the cytoplasm as well. Mechanistically, Pkm KD resulted in decreased binding of cBAF components to their myogenic target genes, which also suggested a positive regulation between the cBaf complex and the H3 phosphorylation marks.

overall_design: To investigate the role of Pkm1 or Pkm2 in the regulation for myoblast differentiation, we have performed RNA-seq analysis for C2C12 myoblast stably KD for these kinases targeted using specific shRNA. C2C12 cells stably transfected with non-targeting scrambled shRNA construct were used as controls. Myoblasts were differentiated for 48 h.

first: Monserrat

last: Olea-Flores

first: Anthony

last: Imbalzano

first: Teresita

last: Padilla-Benavides

first: Odette

last: Verdejo-Torres

first: Imaru

last: DiBartolomeo


title: High-resolution CRISPR/Cas9 screens identify PAK2 as a suppressor of macrophage proliferation and macropinocytosis.

city: Brookings

first: Natalie

middle: W

last: Thiex

state: SD

address: 1390 College Ave

department: Biology & Microbiology

institute: South Dakota State University

summary: Macrophages play critical roles in immune function and are implicated as etiological agents in disease states such as cardiovascular disease and cancer. However, there is limited understanding of macrophage fitness molecular regulators, including survival, proliferation, and adhesion. This work identifies positive and negative regulators of macrophage fitness by harnessing the power of CRISPR/Cas9 whole genome screening technology. Here, we identified loss-of-function gene disruptions that caused mutant bone marrow-derived macrophages (BMDM) to decrease in culture abundance as supporters of macrophage fitness. Similarly, we identified genes that limit or suppress macrophage fitness by identifying those gene disruptions that caused BMDM to increase in abundance in cell culture. To do this, we analyzed the difference in frequency of sgRNA between the purified plasmid library used for lentiviral transfection versus the amplified sgRNA inserts from the DNA of BMDM following a 14-day post-viral transduction culture. With this approach, we identified gene disruptions to canonical essential genes, including previously described macrophage-specific essential genes such as Csf1r, as well as novel genes required for macrophage growth and survival. In addition, we also identified gene disruptions that increased macrophage abundance in culture, including canonical tumor suppressors such as p53 (Trp53) and cell cycle regulators (Cdkn1a/2a). Interestingly, targeting p21-activated kinase-2 (Pak2) led to those mutants becoming more productive, suggesting a novel role for Pak2 in suppressing macrophage fitness. Using targeted knockouts of PAK2, we show that PAK2 protein depletion affects NF2/Merlin-mediated downregulation of cyclin-d1. Further, this work indicates that PAK2 suppresses macropinocytic uptake in macrophages by modulating actin dynamics impacting pro-mitogenic signaling pathways downstream of macropinocytosis. Overall, this work shows how multiple pathways impact macrophage fitness and highlights the central role of PAK2 in macrophage fitness and macropinocytosis.

overall_design: Transgenic mice with a Rosa26-Cas9 knock-in on a C57BL/6J background were received from Jackson Laboratories (Stock No. 026179, Bar Harbor, ME). Mice were euthanized using CO2 inhalation and cervical dislocation, femurs were dissected from the mice, and bone marrow was harvested (Swanson, 1989) by flushing Dulbecco’s phosphate buffer saline (DPBS) without calcium or magnesium (GE Healthcare Life Sciences, Pittsburgh, PA) through the bone using a needle and syringe. Cells were plated in culture media containing 20% HI-FBS and 30% L-cell supernatant in high glucose DMEM in non-tissue culture-treated sterile dishes and incubated at 37°C with 5% CO2. Additional culture media was added to the cells on day two post-isolation. Following cell adherence to the dish, on day 4, the medium was removed entirely, and fresh BMM was added to the culture. On day five cells were treated with 10 mM Cyclosporin A for 20 minutes before adding lentivirus with Brie library to the cells. Multiplicity of infection (MOI) ~ 0.3-0.1. Library coverage was around 100-200-fold representation of each sgRNA. Transduced cells were antibiotic-selected two days after transduction with 5mg/mL puromycin. Cells were cultured for at least 14 days for protein depletion (post-culture). Genomic DNA was extracted from post-culture cells using the GeneJET genomic DNA extraction kit (#K0721 Thermofisher). The sgRNA inserts from genomic DNA (Post-culture) and library plasmid DNA (Input) were PCR amplified by a single-step PCR protocol (Broad Institute). Barcoded primers with staggered sequences are used for next-generation sequencing (NGS). Sequencing of 75 base reads was conducted on Illumina Nextseq 500. Following quality control analysis using FASTQC, reads were mapped to the sgRNA library to identify genes, and read frequency tables were generated using Model-based Analysis of Genome-wide CRISPR-Cas9 Knockouts (MAGeCK), version 0.5.9 (Li et al., 2014a).

first: Kevin

last: Wanniarachchi

first: Astha

last: Neupane

first: Bidhi

last: Kasu

first: Bijaya

last: Pradhan

first: Jason

last: Kerkvliet

first: Xijin

last: Ge

first: Adam

last: Hoppe


title: Preclinical study on safety and efficacy of GMP human umbilical cord mesenchymal stem cells in knee osteoarthritis

city: Kunming

first: Yang

last: Naixue

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

institute: LPBR

summary: Clinical trials of MSCs in the treatment of OA have been carried out and good results have been obtained. However, these data on the dose of transplanted cells, the number of transplants, the therapeutic effect especially cartilage regeneration and safety are incomplete. Therefore, we constructed a cynomolgus macaque model consistent with the pathogenesis of OA. We have also established clinical-grade human umbilical cord-derived mesenchymal stem cell line. We selected two cell doses (2.5*10e7 cells per knee and 5*10e6 cells per knee, respectively) to assess differences in treatment effects and to assess the systemic safety of MSC therapy. High-dose hUC-MSCs can regenerate cartilage, increase joint space, and improve bone condition by ultrasound and MRI scans. But low-dose hUC-MSCs simply prevented further deterioration of the joint

overall_design: First, we constructed a cynomolgus macaque model consistent with the pathogenesis of OA. We have also established clinical-grade human umbilical cord-derived mesenchymal stem cell line. Then we selected two cell doses (2.5*10e7 cells per knee and 5*10e6 cells per knee, respectively) to assess differences in treatment effects and to assess the systemic safety of MSC therapy. Evaluate the effectiveness of cell transplantation through ultrasound, MRI, pathology. Evaluate the safety of cell transplantation through hematological tests and CT scans. Finally, collect the joint cartilage and synovium of the higher dose transplant group, model group, and normal group of cynomolgus macaque, and analyze the treatment mechanism through 10X single-cell sequencing.


title: RNA-sequence analysis of human iPSC-derived qHSCs, aHSCs and deactivated HSCs

city: Bunkyo-ku

first: Taketomo

last: Kido

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

summary: Hepatic stellate cells (HSCs) are the major driver of fibrosis by expressing extracellular matrices (ECM). HSCs, in the normal liver, are quiescent and activated by liver injury to become myofibroblasts that proliferate and produce ECM. It has been shown that activated HSCs can be deactivated by removal of liver insults. In order to evaluate the changes of gene expression profiles, we induced quiescent HSCs (qHSCs), activated HSCs (aHSCs) and deactivated HSCs (daHSCs) from human induced pluripotent stem cells and performed RNA-sequence analysis.

overall_design: Total RNA was extracted from qHSCs (day 0), aHSCs (day 7, day 10) and daHSCs (day 10) using the NucleoSpin RNA XS (MACHEREY-NAGAL, Duren, Germany), according to the manufacture’s protocol. Libraries were prepared using the Optimal Dual-mode mRNA Library Prep Kit (BGI). All libraries were sequenced using the DNBSEQ-G400 (MGI).

first: Yasuhiro

last: Nakano


title: Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors [RNA-seq]

city: Seattle

first: Jeff

last: Vierstra

state: WA

address: 2211 Elliot Ave

institute: Altius Institute for Biomedical Sciences

summary: Regulation of gene expression during cell development and differentiation is chiefly orchestrated by distal noncoding regulatory elements that precisely modulate cell selective gene activity. Gene therapy vectors rely on the cellular and context specificity of regulatory DNA elements to express therapeutic transgenes in the correct location and time. Here, we develop a straight-forward, one-shot approach to screen putative regulatory sequences identified in large-scale epigenomics profiling experiments for precise and programmable control of transgenes encoded within gene therapy viral vectors. We designed a library of 15,000 short sequences (~200bp) derived from a set of developmentally active DHS elements during human ex vivo erythropoiesis and cloned them into a GFP reporter lentiviral vector. In an erythroid progenitor cell line, these elements display a gradient of transcriptional enhancer activity, with some demonstrating equivalent activity to the canonical β-globin μLCR despite a 9-fold smaller size. We show that these elements are both highly cell type restricted and developmental stage specific both in vitro and in vivo. Finally, we replace the μLCR element with one of the novel short enhancers in a β-thalassemia lentiviral therapeutic vector and efficiently correct the thalassemic phenotype in patient-derived HSPCs. More broadly, our approach provides further insights into enhancer biology with wider implications into the development of highly cell type specific and efficacious viral vectors for human gene therapy.

overall_design:
DNAseq of  HUDEP-2 cells transduced with a library of 15,000 short DNA sequences cloned in a GFP-reporter lentiviral vector for assaying transcriptional enhancers. Additionally,
We then performed DNase I seq as well as CUT&RUN experiments targeting GATA1, TAL1, H3K27ac and H3K9me3 to identify chromatin features associated with transcriptional enhancer acrivity
Finally we performed genetic deletion experiments of two identified enhancer elements and performed DNaseI and RNA-seq to validate deletion of the hypersensitive sites and identify gene expression changes in cis as a result of the element deletion.

first: Nikoletta

last: Psatha

first: Pavel

last: Sova

first: Grigorios

last: Georgolopoulos

first: Kiriaki

last: Paschoudi

first: Mineo

last: Iwata

first: Jordan

last: Bloom

first: Tatyana

last: Ulyanova

first: Hao

last: Wang

first: Alexandra

last: Kirtsou

first: Ninos-Ioannis

last: Vasiloudis

first: Matthew

middle: S

last: Wilken

first: John

last: Stamatoyannopoulos

first: Evangelia

last: Yannaki

first: Thalia

last: Papayanopoulou

first: George


title: N6-methyladenosine RNA modification is associated with enzalutamide resistance in prostate cancer

city: Los Angeles

first: Emmanuelle

last: Hodara

address: 1450 Biggy Street

institute: Keck School of Medicine of USC


title: IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma (CUT&RUN human 6)

first: David

last: Huang

overall_design: CUT&RUN analysis of ARID1A in SKMM1 multiple myeloma cells 3 days after indcution of CRISPR/Cas9 mediated IRF4 knockout.

first: Arnold

last: Bolomsky

first: Ryan

last: Young


title: N6-methyladenosine RNA modification is associated with enzalutamide resistance in prostate cancer (RNA-seq)

summary: Our study examines the role of m6A RNA modification in regulating gene expression of transcripts promoting enzalutamide resistance in prostate cancer.

overall_design: RNA-seq of C4-2B vs MDVR PC cell lines in 4 replicates (includes input ctrl and MeRIP samples)

first: Aubree

last: Mades

first: Tong

last: Xu

first: Daniel

last: Bsteh

first: Lisa

last: Swartz

first: Suhn

last: Rhie

first: Peggy

last: Farnham

first: Amir

last: Goldkorn


title: Single cell gene and protein expression of 2W:I-Ab specific cells from effector and memory T cells after aLm infection.

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Single-cell gene expression of CD4+ tetramer+ cells from WT B6 animals was determined by sRNAseq after aLm infection.

overall_design: B6 mice were infected with aLm for 6, 10, 15, 19, 22, 25, 30 or 60 days, treated wth an anti-ARTC2 nanobody before harvest, and sorted for CD4+ Tetramer+ cells. Post sort cells were hashtagged for each timepoint and feature barcoded for cell surface proteins and immune receptor mapping. Gene expression was determined by scRNAseq.

first: Marc

last: Jenkins

first: Kevin

middle: C

last: Osum

first: Ian

last: Magill


title: RORγt -expressing FOXP3+ skin-resident Treg cells derived from the periphery in Allergen-Specific Immunotherapy

city: Seoul

first: Kelun

last: Zhang

state: Seoul

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

department: Dermatology

country: South Korea

institute: Yonsei university

summary: The study explored the impact of Specific Immunotherapy on patients with Atopic Dermatitis sensitized to house dust mites by analyzing the transcriptomes of T regulatory cells before and after treatment. Result found that effective SIT is associated with distinct gene expression changes in Treg cells, particularly increased expression of Treg markers and RORC, a gene linked to immune regulation.   These results indicate that successful SIT may enhance the function of Treg cells expressed RORC and help restore immune balance in these patients.

overall_design: Patients with Atopic Dermatitis (AD) sensitized to house dust mites are divided into two groups based on their response to Specific Immunotherapy (SIT): those who showed an effective response (R) and those who did not respond (Non-R).   Results identified differentially expressed genes before and after SIT in R and Non-R groups.

first: Chang

middle: O

last: Park


title: N6-methyladenosine RNA modification is associated with enzalutamide resistance in prostate cancer (MeRIP-Seq)

first: Emmanuelle

last: Hodara

overall_design: MeRIP-seq of C4-2B vs MVR BC cell lines in 4 replicates (includes input ctrl and MeRIP samples)


title: IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma (CUT&RUN human 32)

first: David

last: Huang

overall_design: Cut&Run analysis of IRF4, MYC, ARID1A, BRG1, SMARCB1, H3K4me3, H3K27ac, and isotype control in NCH929 and SKMM1 multiple myeloma cells.


title: Stem Cell-derived Microglia Exhibit HAND Gene Expression Signature Early Upon Infection with HIV-1 [iPSCMG_TFS]

city: Cincinnati

first: Jason

last: Hammonds

state: Ohio

address: 3333 Burnet Ave

department: Infectious Diseases

institute: Cincinnati Children's Hospital Medical Center

summary: HIV-associated neurocognitive disorders (HAND) persist as a notable cause of illness among individuals with HIV. Despite significant progress in antiretroviral therapy (ART), HAND continues to be a major concern, impacting approximately one-third of those infected with HIV. Recent research underscores the pivotal role of microglia, the primary immune cells in the central nervous system (CNS), in the development and progression of HAND. The infection and activation of microglia by HIV leads to the release of pro-inflammatory markers, cytokines, chemokines, secondary messengers, and reactive oxygen species (ROS). These factors collectively initiate signalling pathways that contribute to neuroinflammation, a central process in the development of HAND. In order to validate stem cell-derived microglia (iMGL) as a viable model system for HAND investigation, we infected iMGLs and human monocyte-derived macrophages (MDMs) with the primary HIV-1 isolate Ba-L at an MOI of 0.25. Total RNA was extracted from cell populations on days 1, 2, 4, 6, and 8 following infection. Subsequently, we conducted bulk RNA sequencing to examine the longitudinal transcriptomic alterations induced by the virus over this time frame

overall_design: To demonstrate the effect of an HIV-1 infection time course on the gene expression profile of iPSC-derived microglia-like cells (iMGLs).

first: Roy

last: Moscona

first: Kathleen

last: Candor

first: Thomas

last: Hagan

first: Paul

last: Spearman