title: Recurrent Implantation Failure: Bioinformatic Discovery of Biomarkers and Identification of Metabolic Subtypes

city: Beijing

first: Cheng

last: Shi

address: NO.11, Xizhimen Southern Street

institute: Peking University People's Hospital

summary: Recurrent implantation failure (RIF) is a challenging scenario from different standpoints. This study aimed to investigate its correlation with the endometrial metabolic characteristics. Transcriptomics data of 70 RIF and 99 normal endometrium tissues were retrieved from the Gene Expression Omnibus database. Common differentially expressed metabolism-related genes were extracted and various enrichment analyses were applied. Then, RIF was classified using a consensus clustering approach. Three machine learning methods were employed for screening key genes, and they were validated through the RT-qPCR experiment in the endometrium of 10 RIF and 10 healthy individuals. Receiver operator characteristic (ROC) curves were generated and validated by 20 RIF and 20 healthy individuals from Peking University People’s Hospital. We uncovered 109 RIF-related metabolic genes and proposed a novel two-subtype RIF classification according to their metabolic features. Eight characteristic genes (SRD5A1, POLR3E, PPA2, PAPSS1, PRUNE, CA12, PDE6D, and RBKS) were identified, and the area under curve (AUC) was 0.902 and the external validated AUC was 0.867. Higher immune cell infiltration levels were found in RIF patients and a metabolism-related regulatory network was constructed. Our work has explored the metabolic and immune characteristics of RIF, which paves a new road to future investigation of the related pathogenic mechanisms.

overall_design: The diagnostic value of the eight gene expression signatures was evaluated by receiver operator characteristic analysis. This model was validated by an external clinical patient cohort. All samples were surplus tissue from endometrial biopsies obtained from patients for diagnostic purposes. The timing of the endometrial biopsy was 5 days after ovulation (evaluated by ultrasonography), which is equivalent to LH + 7 in a natural cycle.

first: Yuan

first: Nannan

last: Huang

first: Fang

last: Fang

first: Li

last: Tian

first: Jianliu


title: RNA Surveillance Maintained by the RNA Helicase MTR4 Determines the Large Volume of Mouse Oocytes [ATAC-seq]

status: Public on Sep 09 2024

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

country: China

institute: Life Sciences  Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Exosome is the main RNA surveillance and degradation pathway during oocyte growth. To figure out specific roles of RNA surveillance in oocyte growth, the pathway was destroied by deleting MTR4, the only known RNA helicase in exosome pathway. Accumulation of waste RNAs in nucleus seriously effect chromatin status and NSN-SN transition. Thus ATAC-seq experiments were performed to get a better review for chromatin status.

overall_design: The ATAC-seq was performed with 50 oocytes per sample. WT and MTR4-null oocytes were extracted and duplicates were conducted. Each sample was sequenced 8G.

first: Yunwen

last: Wu

first: Zuoqi

last: Deng

first: Hengyu


title: The use of ectopic volar fibroblasts to modify skin identity III

city: Baltimore

first: Sam

last: Lee

state: MD

address: 1550 Orleans Street

country: USA

institute: Johns Hopkins University School of Medicine

type: Expression profiling by high throughput sequencing

summary: The modification of skin identity, such as the conversion of residual limb/stump (non-volar) skin of amputees to pressure-resistant palmoplantar skin to enhance prosthesis use and minimize skin breakdown, has tremendous clinical potential. Recognizing the capacity of fibroblasts to modify keratinocyte differentiation, we hypothesized that volar fibroblast injections might induce ectopic volar characteristics. First, we observed pressure-responsive volar fibroblast resulting in increased limb development after pressure treatment, then we confirmed this in using a bioprinted skin construct, and later in a clinical trial that showed increased volar measures in non-volar skin after volar fibroblast injections. Bulk and single cell RNA seq demonstrate gene ontology categories of cornified envelope, keratinization and morphogenic pathways. Thus, the long-term engraftment of volar fibroblasts creates a platform for the therapeutic development

overall_design: Scalp or sole dermal skin fibroblasts from patients were treated with 0.025 Hz dynamic pressure (20s on and 20s off) for 30 min to investigate effect of pressure on the fibroblast.


title: Transcriptome and acetylome profiling identify crucial steps of neuronal differentiation in Rubinstein-Taybi syndrome

city: Bordeaux

first: Slim

last: Karkar

address: Rue Leao Saignat

department: CBiB

country: France

institute: U. Bordeaux

summary: Rubinstein-Taybi syndrome (RTS) is a rare and severe genetic developmental disorder characterized by multiple congenital anomalies and intellectual disability. CREBBP and EP300, the two genes known to cause RTS encode transcriptional coactivators with a catalytic lysine acetyltransferase (KAT) activity. Loss of CBP or p300 function results in a deficit in protein acetylation, in particular at histones. In RTS, nothing is known on the consequences of the loss of histone acetylation on the transcriptomic profiles during neuronal differentiation. To address this question, we differentiated induced pluripotent stem cells from RTS patients carrying a recurrent CREBBP mutation that inactivates the KAT domain into cortical and pyramidal neurons. By comparing their acetylome and their transcriptome at different neuronal differentiation timepoints, we identified 25 specific acetylated histone residues altered in RTS. We also identified the transition between neural progenitors and immature neurons as a critical step of the differentiation process, with a delayed neuronal maturation in RTS.

overall_design: To address our objectives of studying the consequences of acetylation alteration during neuronal differentiation, the first phase of this work will be the generation of iPSCs-derived neurons from fibroblasts of RSTS patients carrying the same CREBBP mutation. The second phase will concern the characterization of acetylation profiles in cells from patients in comparison with control cases. This second step will allow us to characterize the proteins whose acetylation profile is specifically altered in RSTS and the associated biological pathways. In the 3rd phase of the work, we will study the functional impact of these epigenetic alterations on neuronal differentiation by analysing the transcriptome by RNA-Seq.

first: Julien

last: Van Gils

first: Aurelien

last: Barre

first: Seyta

last: Ley-Ngardigal

first: Sophie

last: Nothof

first: Stephane

last: Claverol

first: Caroline

last: Tokarski

first: Jean-Philippe

last: Trani

first: Raphael

last: Chevalier

first: Natacha

last: Broucqsault

first: Claire

last: El Yazidi

first: Didier

last: Lacombe

first: Patricia

last: Fergelot

first: Frederique

last: Magdinier


title: RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes

first: Heng-yu

last: Fan

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

overall_design: Refer to individual Series


title: Gut-Derived Metabolite Trimethylamine N-Oxide Promotes Inflammation and Fibrosis Following Ischemia/Reperfusion through CCR2-Mediated Macrophage Infiltration

city: Shanghai

first: Yuan

last: Ren

state: Shanghai

address: 12 Wulumuqi Middle Road, Jing'an District, Shanghai, China.

institute: Fudan University

summary: Inflammation plays a crucial role in the development of acute kidney injury (AKI) and subsequent chronic kidney disease (CKD) following renal ischemia-reperfusion (IR). It has been demonstrated that metabolites from the gut microbiota can trigger inflammatory responses and modulate renal damage induced by IR. However, the exact driving factors and underlying mechanisms of this process remain unclear. Trimethylamine N-oxide (TMAO), a choline metabolite derived from the gut, has been observed to increase in AKI and CKD patients. Our study reveals that glycyrrhizic acid (GA) exacerbates IR-induced AKI and subsequent CKD through TMAO. To delve into the underlying mechanisms, we employed single-cell sequencing to construct a molecular map of kidney cells.

overall_design: To investigate the effect of TMAO on renal injury development after IR, we used conventionally reared C57BL/6J mice. These mice were pre-fed either a control diet with 0.14% choline or a choline-supplemented diet with 1.4% choline for a period of 14 days. Subsequently, the mice received left renal artery clamping for 45 minutes to induce unilateral renal IR injury. Throughout the experiment, the mice remained on their respective diets and were administered glycyrrhizic acid via gastric gavage. They were then sacrificed on postoperative days 3, 14, and 21 (representing AKI, AKI-to-CKD transition, and CKD respectively)

first: Zuoyuan

last: Wang

first: Li

last: You

first: Jun

last: Xue


title: The use of ectopic volar fibroblasts to modify skin identity II

first: Sam

last: Lee

overall_design: Autologous scalp or sole fibroblasts were injected into the non-volar dermis with various doses (3.33 million or 10 million cells) or equivalent volume of media per injection at 3 visits spanning up to one week. A total of 10 million cells were injected. Skin biopsies from the injected sites were collected at 5-month post-injection time point. 136-26, 27, and28 received single dose of 10 million cells, while 136-43, 45, and 46 received three doses of 3.3 million cells.


title: Administration of the HMGB1 fragment suppresses expression of collagen-related genes

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

summary: To analyze cell profiles in pancreatic tissue, single-cell RNA-seq of CD45-negative cells was performed using pancreatic tissue obtained in the eighth week after HMGB1 fragment injection was begun. After conventional quality check and filtering, we recovered pancreas cells from normal pancreas, control group pancreas, and HMGB1 group pancreas. The UMAP plots depicted 11 distinct cell clusters from the three groups, PDGFRα＋ cells had the most significant number of clusters, which exhibited a high level of Col1α1 gene expression in the bubble plot.Compared with the control and HMGB1 groups, the distribution of the PDGFRα＋ cell cluster was skewed in the normal group. We focused on PDGFRα＋ cell clusters that secrete large amounts of collagen and extracellular matrix components, which are central to the pathogenesis of CP. Many genes were significantly expressed in contrasting ways, gene clusters that were upregulated in the control compared with the normal group were downregulated in the HMGB1 compared with the control group. In contrast, gene groups that were downregulated in the control compared with the normal group were upregulated in the HMGB1 compared with the control group. HMGB1 fragment exposure was associated with a shift in the gene expression pattern of CP toward that of the normal pancreas. Expression of Ccn2 and Ccn1 was upregulated in the control group compared with the normal group but downregulated in the HMGB1 group compared with the control group. Pten expression was downregulated in the control versus normal group but upregulated in the HMGB1 group compared with the controls. Extracellular matrix–related genes in the pancreas were altered with HMGB1 fragment administration.

overall_design: Single-cell RNA-seq analysis was performed on pancreatic tissue obtained from normal mice, and from chronic pancreatitis mice 8 weeks after the start of HMGB1 fragment or saline injection. Chronic pancreatitis model mice were induced by repetitive intraperitoneal injections of caerulein (50 μg/kg body weight/h) six times a day, three times a week, for 4 weeks, as previously described.  Normal mice were given saline intraperitoneal injections. At the same time as caerulein administration, normal saline (control group; 5 μl/g) or HMGB1 fragment treatment (HMGB1 group; 5 mg/kg) was administered via the tail vein three times a week for 8 weeks. Three days after the final HMGB1 fragment or saline administration, pancreatic tissues were collected.

first: Daiki

last: Hokkoku

first: Kazuki

last: Sasaki

first: Shogo

last: Kobayashi

first: Tomomi

last: Kitayama

first: Sho

last: Yamazaki

first: Yukari

last: Yamamoto

first: Yuya

last: Ouchi

first: Katsuto

last: Tamai


title: The role of activator protein-1 (AP-1) complex in diabetes associated atherosclerosis: Insights from single cell RNA sequencing

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

summary: Despite unprecedented advances in the treatment of atherosclerotic cardiovascular diseases (CVD), it remains the leading cause of death in patients with diabetes worldwide. Lipid-laden atherosclerotic plaque development within the arterial vessel wall is initiated with endothelial cell activation, monocyte adhesion and foam cell formation. Although the current focus has been on mitigation of risk factors, the disease continues to progress, and thus newer approaches and druggable targets need to be identified that can directly inhibit the underlying pathobiology of atherosclerosis. We utilised a single cell RNA sequencing (scRNA-seq) approach to distinguish the proatherogenic transcriptional profile of aortic cells in diabetes.

overall_design: Control and diabetic (streptozotocin induced) Apoe-/- mice were monitored over a 10 week study period, follwed by scRNA-seq analysis of dissociated aortae using the 10X genomics platform and reagents.

first: Abdul

middle: W

last: Khan

first: Man

middle: K

first: Aozhi

last: Dai

first: Anna

last: Watson

first: Scott

last: Maxwell

first: Misbah

last: Aziz

first: Arpeeta

last: Sharma

first: Mark

middle: E

last: Cooper

first: Andrew

last: Murphy

first: Sara

last: Baratchi

first: Karin

middle: A

last: Janeleit-Dahm


title: AIRE drives early life thymic interferons and changes thymic self-antigen expression [bulk RNA-seq]

city: Minneapolis

first: Christine

middle: H

last: O'Connor

address: 117 Pleasant St. SE

department: Minnesota Supercomputer Institute

institute: University of Minnesota

summary: Type I interferons (IFN-I) are transiently induced during infections, but were reported to be produced in the thymus at steady state. We found that developing thymocytes displayed an IFN-I signature that was mainly dependent on IFN-β. Using Ifnb1 reporter mouse strains, we observed IFN-β expression in a small population of medullary thymic epithelial cells (mTEC), which was AIRE-dependent and peaked at 2-3 weeks of age. To study the cellular response to thymic IFN, we used a Mx1gfp reporter mouse strain and found that the IFN response in T cells and myeloid cells was abrogated by IFNaR deficiency, whereas the response in B cells and dendritic cells was dependent on both IFNaR and IFNlR. Furthermore, single-cell RNAseq analysis revealed dramatic transcriptional changes in all thymic APCs in IFNaR/IFNlR deficient mice, and a loss of CCR7+ cDC1 cells. Together, these results show that steady state IFN-I and IFN-III signaling drives a gene-expression program in thymic APCs that shapes the thymic microenvironment.

overall_design: Bulk RNA-seq of thymocytes in WT, IFNAR1-KO, IFNB-KO, IFNAR1-KO IFNLR-KO, STAT1-KO, and IFNLR-KO mice.

first: Oscar

middle: C

last: Salgado

first: S

middle: T

last: Lee

first: Ryan

last: Martinez

first: Elise

middle: R

last: Breed

first: Dan

last: Stetson

first: Kristin

last: Hogquist


title: Small RNA sequencing of 50 laryngeal squamous cell carcinoma and paired adjacent normal tissues

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer with poor prognosis. However, the mechanism underlying the pathogenesis of LSCC remains unclear. We performed high throughout sequencing to identify miRNA that associated with LSCC progression.Small RNA libraries were constructed followed by sequencing on a cohort of LSCC tissues (50 samples) and paired adjacent normal mucosa tissues (50 samples).

overall_design: Expression of miRNA in 50 LSCC and 50 paired adjacent normal mucosa tissues was examination by high throughout sequencing.

first: Wei

last: Gao

first: Binquan

last: Wang

first: Xiwang

last: Zheng


title: The use of ectopic volar fibroblasts to modify skin identity

first: Sam


title: The use of ectopic volar fibroblasts to modify skin identity I

overall_design: Autologous scalp or sole fibroblasts were injected into the non-volar dermis. A total of 10 million cells were injected. Skin biopsies from the injected sites were collected at 2-week, 2-month, 5-month, or 17-month post-injection time points.


title: Gene Expression Profiles Associated with Mφ Spatial Aggregation for HCC

status: Public on Sep 08 2024

city: Guangzhou

first: Yulan

last: Weng

state: No State

address: Guangzhou

institute: Sun Yat-sen University

summary: To validate that the aggregation pattern identifies a pro-tumoral Mφ subset in HCC, we have employed microarray expression profiling as a discovery platform to identify the molecular and functional implications of Mφ spatial distribution in HCC. Gene ontology (GO) and gene-set enrichment analyses (GSEA) revealed that tissues rich in aggregated Mφs significantly upregulated tissue remodeling pathways and “M2” Mφ-associated genes, while pro-inflammatory “M1” gene sets were more pronounced in HCCs with predominantly scattered Mφs. These results indicate that Mφ aggregation signifies a transition to a multifaceted, pro-tumoral phenotype, highlighting the intricate relationship between spatial distribution and function of Mφs in the tumor milieu.

overall_design: To elucidate the molecular and functional implications of Mφ spatial distribution in HCCs, RNA samples from 19 HCC tumors, classified based on Mφ spatial distributions as determined by IHC staining, were subjected to a gene expression microarray assay (Mφ-Agg, n = 3; Mφ-Sca, n = 16).

first: Chong

first: Limin


title: scRNA-seq of B16F10 infiltrating CD45+ immune cells from Kcnj2f/f and Kcnj2CKO mice

first: Di

address: Yuhgang Tang Rd No.866

department: School of Medicine

institute: Zhejiang University

summary: The tumor microenvironment (TME) is a unique niche governed by constant crosstalk within and across all intratumoral cellular compartments.We sorted CD45+ immune cells from Kcnj2f/f and Kcnj2CKO mice and performed 10X single cell sequencing to illustrate the impact of Kcnj2 on TME.

overall_design: Examine the impact of Kir2.1 on TME

first: Sheng

last: Chen

first: Wenyu

last: Cui


title: Atypical Teratoid Rhabdoid Tumours Are Susceptible to Panobinostat-Mediated Differentiation Therapy

city: Clayton

first: Vijesh

last: Vaghjiani

state: Victoria

address: 27-31 Wright Street

institute: Hudson Institute of Medical Reaserch

summary: Atypical teratoid rhabdoid tumour (ATRT) is a rare but highly aggressive undifferentiated solid tumour arising in the central nervous system and predominantly affecting infants and young children. ATRT is exclusively characterised by the inactivation of SMARCB1, a member of the SWI/SNF chromatin remodelling complex that is essential for the regulation of large sets of genes required for normal development and differentiation. Histone deacetylase inhibitors (HDACi) are a promising anticancer therapy and are able to mimic the normal acetylation functions of SMARCB1 in SMARCB1-deficient cells and drive multilineage differentiation in extracranial rhabdoid tumours. However, the potential efficacy of HDACi in ATRT is unknown. Here, we show that human ATRT cells are highly responsive to the HDACi panobinostat and that sustained treatment leads to growth arrest, increased cell senescence, decreased clonogenicity and induction of a neurogenesis gene expression profile. Furthermore, in an orthotopic ATRT xenograft model, continuous panobinostat treatment inhibits tumour growth, increases survival and drives neuronal differentiation as shown by the expression of the neuronal marker, TUJ1. Collectively, this preclinical study supports the therapeutic potential of panobinostat-mediated differentiation therapy for ATRT.

overall_design: to investigate the role of SWI/SNF in ATRT, we compared gene expression profile of three ATRT cell lines treated with vehicle or panobinostat using RNA-seq

first: Wai

last: Chong

first: Samantha

last: Jayasekara

middle: G

first: Jason

last: Cain


title: Single-Cell Transcriptomic Analysis of Astrocytes 12 Hours after Ischemic Stroke.

city: Xi'an

first: Yonghong

address: Xinwang Rd, Weiyang District

institute: Xi'an Medical University

summary: Reactive astrocytes are detrimental or protective in ischemic stroke. However, the mechanisms of these effects are not entirely clear. We investigated the heterogeneity of mice astrocytes 12 h after cerebral ischemia-reperfusion via Single-cell RNA sequencing. We acquired astrocyte subclusters’ transcriptional characteristics involving diversified functions. We identified 9 genes as potential therapeutic targets and 6 genes were specific to astrocyte subcluster 2. Additionally, we explored the effects of melatonin and stattic on the transformation of astrocytes to the A2 phenotype. TTC stain, grip strength test and immunofluorescence were used. We revealed melatonin promoted the transformation of astrocytes to the A2 phenotype, the effect was related to STAT3 and inhibited by Stattic. Our study may lay a foundation for untangling the difference between astrocyte subclusters 12 h after stroke and elucidating the mechanisms of A2 astrocyte transformation 3 d after stroke.

overall_design: Single-cell transcriptome analysis of two samples:one was a mixture of ischemic brain tissue from three MCAO model mice, the other was a mixture of  brain tissue in the same area as the former from three sham mice.

first: Xingchun

last: Gou


title: Wnt signaling activation confers a syncytiotrophoblast progenitor state on trophoblast stem cells of cynomolgus monkey.

city: Otsu

first: Shoma

last: Matsumoto

state: Shiga

address: Setatsukinowa-cho

department: Research Center for Animal Life Science

institute: Shiga University of Medical Science

summary: Trophoblast stem cells (TSCs), derived from the trophectoderm of the blastocyst, are used as an in vitro model to reveal the underlying mechanisms of placentation in the mammal. In humans, suitable culture conditions for TSC derivation have been recently discovered. The established human TSCs differentiate efficiently toward two trophoblast subtypes, i.e., syncytiotrophoblast (STB) and extravillous trophoblast. On the other hand, the differentiation efficiencies were lower in macaque TSCs compared to human TSCs. Here, we demonstrate that the activation of Wnt signaling induced trophoblastic lineage switching to STB progenitor state. macTSCs highly expressed STB progenitor markers and obtained forskolin responsiveness by CHIR99021 treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for two macTSC lines cultured with/without CHIR99021 (duplication).

first: Satoshi

last: Tanaka


title: Effect of BMP4 overexpression in MycCaP cells on TAMs in ostegenic prostate tumors

city: Houston

first: Guocan

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

summary: Tumor-associated macrophages (TAMs) play an important role in cancer progression and have been implicated to play a role in prostate cancer. However, TAMs in osteogenic prostate cancer bone metastasis have not been characterized. Here we used a novel osteogenic MycCaP-BMP4 model to study the unique cellular and molecular mechanisms in driving the tumor progression in osteogenic prostate cancer metastasis.

overall_design: MycCaP and MycCaP-BMP4 cells were injected subcutaneiously into FVB mice.  Bulk tumors were dissociated into single cells and subjected FACS sorting for CD45+, CD11b+, GR1- and F4/80+ macrophages. Total RNA was isolated from sorted macrophages and subjected to RNA-seq.

first: Guoyu

last: Yu

first: Sue-Hwa

last: Lin


title: Subtype-selective agonists of COI1-JAZ co-receptors screened from the stereochemical-isomers of jasmonate mimic

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

summary: We report the development of subtype selective ligands into plant hormone jasmonate co-receptor COI1-JAZ. Plant hormone jasmonoyl isoleucine and the structural mimic natural product coronatine has non-selective affinity with 13 species of COI1-JAZ co-receptors in Arabidopsis thaliana to cause bath of bacterial defense and growth inhibition. Some subtype selective ligands were developed by our chemical screening and activated the part of whole jasmonate signaling. To examine the mode-of-action of the subtype selective ligand, gene expression profiles of WT and jaz9 mutant treated with mock or with coronatine (2) and subtype selective ligands (2e and 12) was performed using the RNA-seq. The subtype selective ligand induced partial activation of jasmonate signaling to cause defense responses against bacterial pathogen without growth inhibition.

overall_design: Gene expression by the treatment of 1 µM of natural product coronatine (2) and the derivatives (2e and 12) for 8 h in A. thaliana WT seedlings. Gene expression by the treatment of 1 µM of natural product coronatine (2) and the derivatives (2e and 12) for 8 h in A. thaliana jaz9 mutant seedlings

first: Kengo

last: Hayashi

first: Nobuki

last: Kato

first: Haruna

last: Nomoto

first: Misuzu

last: Nakayama

first: Kuhrram

last: Bashir

last: Takahashi

first: Andrea

last: Chini

first: Yousuke

last: Takaoka

first: Hiroaki

last: Saito

first: Raku

last: Watanabe

first: Maho

first: Atsushi

middle: J

last: Nagano

first: Koji

last: Miyamoto

first: Kazunori

last: Okada

first: Motoaki

last: Seki

first: Minoru

last: Ueda


title: Sleep fragmentation aggravates myocardial infarction through promoting type I interferon-mediated SiglecFhi neutrophil expansion

status: Public on Sep 07 2024

first: Peinan

last: Ju

address: 301 Middle Yanchang Road

department: Department of Cardiology,

institute: Shanghai Tenth People’s Hospital, School of Medicine, Tongji University

summary:
Background: Sustained sleep insufficiency impairs immune system and increases the adverse outcomes of cardiovascular diseases. However, the role and mechanisms prolonged sleep fragmentation (SF) on the outcomes of myocardial infarction (MI) remains elusive.
Methods: Among 497 MI patients with complete sleep data participating in the National Health and Nutrition Examination Survey, the association between different types of sleep disorders and post-MI survivability was evaluated. We then developed a mouse model with 10 weeks of SF followed by MI surgery. Emergency hematopoiesis and neutrophil expansion were analyzed. Potential mechanisms were explored using bone marrow (BM) transplantation, anti-SiglecF neutralizing antibodies and Interferon alpha and beta receptor subunit 1 knockout (Ifnar1-/-) in BM.
Results: Frequent nocturnal awakening independently predicted reduced survival rate of MI patients, with a hazard ratio (HR) of 2.136 (95% CI=1.142-3.995). Increased infarct size, deteriorated cardiac function and lower survival rate were also observed in MI mice pretreated with 10-week SF. SF facilitated post-MI neutrophil expansion and infiltration into infarct area, differentiating into SiglecFhi subset. Inhibition of SiglecFhi neutrophils allowed for the alleviations of post-MI cardiac remodeling. Furthermore, BM progenitors were skewed toward neutrophil lineage concomitant with the clonal expansion of granulocyte-monocyte progenitors (GMPs) in MI mice pretreated with 10-week SF. Transcriptome analysis and functional experiments revealed that activation of type I interferon (IFN) signaling was involved in this process, while depletion of Ifnar1 in BM and administration of IFNAR1-neutralizing antibodies significantly alleviated post-MI cardiac remodeling and neutrophil expansion.
Conclusions: SF aggravates post-MI cardiac remodeling and dysfunction through promoting GMP differentiation and neutrophil expansion. Blockage of type I IFN could alleviate this detrimental influence.

overall_design: To investigate the mechanisms underlying the enhanced proliferation and differentiation of GMPs into neutrophils in SF mice post-MI, we used flow cytometry to sort bone marrow GMPs from both control and SF mice on day 3 after MI and performed RNA-seq analysis to compare their transcriptomic differences.

first: Jianhui

last: Zhuang


title: Ubiquitylation of Pol II controls early stages of the transcription cycle [dxChIP-seq]

city: Cambridge

first: Ana

last: Tufegdzic Vidakovic

state: Cambridge

address: Cambridge Biomedical Campus, Francis Crick Ave

country: United Kingdom

institute: MRC-LMB

summary: Control of RNA Polymerase II (Pol II) through ubiquitylation is essential for the DNA-damage response. Here we reveal a distinct ubiquitylation pathway in human cells that targets excessive and defective Pol II molecules at the initial stages of the transcription cycle. This pathway, mediated by ARMC5CUL3 ubiquitin ligase, drives homeostatic Pol II turnover, and is further enhanced when early stages of transcription - initiation and pausing - are perturbed. Upon ARMC5 loss, Pol II accumulates in the free pool and in the promoter-proximal zone, but is not permitted into elongation. We identify Integrator subunit 8 (INTS8) as a gatekeeper preventing the release of excess Pol II molecules into gene bodies. Combined loss of ARMC5 and INTS8 has strong detrimental effects on cell growth, with ARMC5 loss exacerbating transcriptional defects seen in INTS8-depleted cells. These findings uncover that ARMC5CUL3 and INTS8 form a collaborative checkpoint, monitoring the quantity and quality of transcription complexes before they are licensed into elongation.

overall_design: We aimed to study how ARMC5 loss affects Pol II occupancy on chromatin and how is a partial resistance to XBP inhibition by triptolide achieved in ARMC5 KO cells in HEK293 Trex flp In background. We treated WT and ARMC5 KO cells with triptolide at 300 nM for 2 h. We then performed double cross-linking, first we incubated the washed cells with disuccinimidyl glutarate (DSG) for 15 minutes, followed by washing and incubation with formaldehyde. Immunoprecipitation was performed against total Pol II (D8L4Y Antibody) and Serine 5 phosphorylated Pol II (3E8 Antibody).

first: Andrew

last: Zeller

first: Iván

last: Shlamovitz

last: Tufegdžić Vidaković


title: scRNA-seq of AAV-scramble or AAV-shBicd2 infected mice livers under Con A-induced acute autoimmune hepatitis

first: Wenyu

last: Tian

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

summary: To explore the effect of Bicd2 in Con A-induced acute autoimmune hepatitis, we conducted single cell RNA sequencing of AAV-scramble or AAV-shBicd2 infected  mice livers in response to Con A injection.

overall_design: We infected 4w wild-type C57BL/6J mice with AAV-scramble or AAV-shBicd2. After 3 weeks, mice were injected with 15mg/kg Con A i.v. and 6 hours later livers were collected to perform single cell RNA sequecing.

first: Xin

last: Zhang

first: Dan

last: Lu


title: A critical role for thrombin in regulating chondrocytes catabolism through RNA-Seq and experimental validation

city: shanghai

first: daofang

last: ding

address: 1200 Cai Lun Road,Zhangjiang Hi-TechPark,Pudong New Area

institute: Shanghai University of Traditional Chinese Medicine

summary:
Purpose: To reveal the effects of thrombin on the proliferation, morphology, and gene expression in chondrocytes.
Methods: Rat primary chondrocytes were cultured with RS, RP and RPT for 24hours, and RNA was extracted for sequencing. The chondrocytes’ morphology was investigated under inverted microscope. Chondrocyte’s proliferation was evaluated by Edu staining, CCK8 methods and PPI network of proliferation-associated genes. The differential gene expression was visualized using a volcano plot. The variance in expression levels of the genes was visualized by the heatmap. GO-based functional annotation clustering analysis was performed on the upregulated and downregulated DEGs, which included biological process, cellular component, and molecular function. The endoplasmic reticulum of chondrocytes from three groups were labeled by molecular probes. The expression levels of Col2a1 and proteoglycan synthesis were detected by cellular immunofluorescence and Safranin O staining separately. The expression levels of Lox were determined by immunocytochemistry staining. The following genes including Comp, Eln, P3H1 and Colgalt1 were examined by RT-qPCR. The expression of MMPs and Sox9 were evaluated by Western Blot. Further analysis of PPI network was performed, and the corresponding modules were selected.
Results: As compared with RP group, chondrocytes proliferation was obvious and normal chondrocytes quickly transformed into fibroblast-like chondrocytes in the presence of RS and RPT. we found that 727 genes were up-regulated, and 1162 genes were down-regulated in Venn diagram through analyzing differentially expressed genes (DEGs). The results of GO analyses showed that both the expression of ECM and MMPs were significantly influenced by RS and RPT. Both the labeled endoplasmic reticulum and the expression of representative genes analyzed from the results of RNA sequencing confirmed that chondrocytes were dominated by catabolism. The expression of ECM, MMPs, inflammatory factors and chemokines were verified at the protein level or at the RNA level which agreed with PPI network and functional modules.
Conclusions: Thrombin stimulated the proliferation and promoted the morphology transformation towards fibrotic chondrocytes. Thrombin improved the chondrocytes’ catabolism by regulating the expression of the key enzymes which were responsible for ECM synthesis. Meanwhile thrombin increased the expression of MMPs and chemokines that aimed at extracellular ECM degradation.

overall_design: Rat primary chondrocytes were cultured with Rat Serum (RS  group), Rat Plasma  (RP  group), and Rat plasma plus thrombin (RPT  group) for 24hours, and RNA was extracted for sequencing. Further experiments were performed to verify the results of RNA sequencing.

first: Daofang

last: Ding


title: Toxic Exposure of Pyridostigmine Bromide Chronically Impairs Colonic Motility Via Low Grade Enteric Neuroinflammation

city: College Station

first: Claudia

last: Collier

address: 3120 TAMU

institute: Texas A&M University

summary: Combat veterans from the Persian Gulf War have unexplained yet persistent impairment in colonic motility due to combat-related toxic exposures. Central to Gulf War-related toxic exposures was the unmitigated ingestion of Pyridostigmine bromide (PB). We previously developed a Gulf War Illness (GWI) mouse model, where acute PB exposure led to immediate disruptions in colonic motility. Here, we explore mechanisms by which acute enteric neuroinflammation produces peristent impairment in colonic motility. GWI mice were exposed to PB transiently, and allowed to recover with no exposures for 1 month. GWI mice had significantly increased amplitudes of colonic contraction and diminished nerve-stimulated colonic relaxation, compared to naive controls. Immunohistological characterization demonstrated persistent chronic damage in enteric neuronal network integrity, accompanied by a significant imbalance in excitatory and inhibitory motor neuronal populations. Inflammatory CD40+ tissue- resident macrophages were identified with enteric neural stem cells in GWI colons, with an increase in secreted inflammatory cytokines. Unbiased transcriptomic analysis corroborated peristent low grade enteric neuroinflammation, overall resulting in impaired repair and regeneration of neural circuity in GWI. Our learnings can be leveraged to design new regenerative therapies for Gulf War veterans, and broadly impact our understanding of severeal inflammatory disorders of the gut.

overall_design: To investigate the effects of PB exposure on C57BL/6 male mice specifically targeting the colon and intestinal motility. Mice were treated with 7 days of PB then allowed 21 days to recover before colon explants were extracted for and prepared for RNA isolation for high throughput analysis. Conditions include controls (water exposed mice)  and GWI (PB exposed mice).

first: Aelita

last: Salikhova

first: Sufiyan

last: Sabir

first: Shreya

last: Raghavan


title: Gene expression profile at single cell level of intestinal lamina propria cells from nulliparous mice and lactating mice

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the differentially expressied genes in lamina propria cells and compare them between nulliparous mice and lactating mice.

overall_design: Immunce cells and mesenchymal cells from lamina propria were enriched by sorting and analyzed using scRNA-seq.

first: Masahiro

last: Onji

first: Josef

middle: M

last: Penninger


title: Predicting Oncology Drug-Induced Cardiotoxicity with  Donor-Specific iPSC-CMs – Model Verification with Doxorubicin

city: Milwaukee

first: Ulrich

last: Broeckel

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Many oncology drugs have been found to induce cardiotoxicity in a subset of patients, which significantly limits their clinical use and impedes the benefit of lifesaving anti-cancer treatments. Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) carry donor-specific genetic information and have been proposed for explore the inter-individual difference in oncology drug-induced cardiotoxicity. Herein, we evaluated the inter- and intra- individual variability of iPSC-CM-related assays and presented a practical approach for using donor-specific iPSC-CMs to predict personalized doxorubicin (DOX)-induced cardiotoxicity (DIC) prior to chemotherapy. Our findings demonstrated that donor-specific iPSC-CMs exhibited greater line-to-line variability than the intra-individual variability in impedance cytotoxicity and transcriptome assays. The variable and dose-dependent cytotoxic responses of iPSC-CMs resembled those observed in clinical practice, and largely replicated the reported mechanisms of DIC. By categorizing iPSC-CMs into DOX-resistant and DOX-sensitive cell lines based on their phenotypic reactions to DOX, we found that the sensitivity of donor-specific iPSC-CMs to DOX may predict in vivo DIC risk. Furthermore, we assessed the limitations of the model for identification of potential genetic/molecular biomarker and pinpointed a differentially expressed gene, DND microRNA-mediated repression inhibitor 1 (DND1), between the DOX-resistant and DOX-sensitive iPSC-CMs. We also discussed the selection of DOX dose and exposure duration for inter-individual variability of DIC assessment. Our results support the utility of donor-specific iPSC-CMs in assessing inter-individual difference and enabling personalized cardiotoxicity prediction. Further studies will encompass a large panel of donor-specific iPSC-CMs to investigate the role of the DND1 and known DIC genetic variants, and to identify potential novel molecular and genetic biomarkers for predicting DOX and other oncology drug-induced cardiotoxicity.

first: Li

last: Pang

first: Chengzhong

last: Cai

first: Praful

last: Aggarwal

first: Dong

last: Wang

first: Vikrant

last: Vijay

first: Prathyusha

last: Bagam

first: Jacob

last: Blamer

first: Andrea

last: Matter

first: Amy

last: Turner

first: Lijun

last: Ren

first: Katy

last: Papineau

first: Vinodh

last: Srinivasasainagendra

first: Hemant

last: Tiwari

first: Xi

last: Yang

first: Laura

last: Schnackenberg

first: William

last: Mattes


title: Fast Low-Input Efficient Hi-C

status: Public on Sep 06 2024

city: Haifa

first: Noam

last: Kaplan

address: Efron 1

country: Israel

institute: Technion - Israel Institute of Technology

summary: We developed FLIE (Fast Low-Input Efficient) Hi-C, a highly optimized and simplified version of Hi-C. Our method shortens the duration of Hi-C from five days to two days and decreases key reagent amounts 5-20 fold, while maintaining experimental controls and data quality. Importantly, the method also reduces the required input material by 100-1000 fold, as we demonstrate by generating detailed high complexity interaction maps from low-input sorted mouse frozen neuron nuclei and from 5,000-10,000 human Hap1 cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: FLIE Hi-C (optimized Hi-C protocol) on Hap1 cells and frozen mouse neuron nuclei

first: Mor

last: Guetta

first: Nili

last: Avidan

first: Hagai

last: Kariti

first: Liron

last: Davis

first: Revital

last: Shemer

first: Evan

last: Elliot


title: The methylarginine reader function of SND1 is oncogenic

first: Bin

last: Liu

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: Staphylococcal nuclease Tudor domain containing 1 (SND1) protein is an oncogene that “reads” methylarginine marks through its Tudor domain. Specifically, it recognizes methylation marks deposited by protein arginine methyltransferase 5 (PRMT5), which is also known to promote tumorigenesis. SND1 is a known driver of hepatocellular carcinoma, but it is unknown if the Tudor domain is needed to drive this disease. We sought to identify the biological role of the SND1 Tudor domain in normal and tumorigenic settings. To do so, we developed two genetically engineered SND1 mouse models, namely a knockout (Snd1 KO) and a Snd1 Tudor domain mutated (Snd1 KI) mouse. Transcriptome analysis of normal KO and KI liver samples reveals a role for the SND1 Tudor domain in regulating expression of major acute phase proteins (APPs) and genes involved in the unfolded protein response (UPR), which could provide mechanistic insight into SND1’s functions in a tumor setting. These processes may provide insight into how SND1 functions as an oncogene.  These results support the use of PRMT5 inhibitors, and the development of small molecule inhibitors that target the SND1 Tudor domain, as novel treatments for HCC.

overall_design: To understand the transcriptional consequences of SND1 Tudor domain, we harvested total RNA from livers of SND1 WT, SND1 KO, and SND1 Tudor domain mutant (SND1 KI) mice to perform RNA-seq.

first: Mark

last: T Bedford

first: Tanner

last: Wright

first: Yalong

last: Wang


title: Transcriptomic Analysis of Identical Twins with Different Onset Ages of ALD

city: Chongqing

first: Yinglian

last: Chen

address: Fengtian Road

institute: Southwest Hospital, Army Medical University (Third Military Medical University)

summary: Adrenoleukodystrophy (ALD) is a rare X-linked neurogenetic disease caused by mutations in the ABCD1 gene. Currently, the molecular mechanisms underlying the onset and severity of ALD still remain unclear. For mining information on candidate genes associated with onset and severity of ALD, RNA-seq had been executed via using whole blood samples from monozygotic twin families with ALD disease. The information on candidate genes of this research had been considered as the crucial for preliminarily exploring the molecular mechanisms relating to the onset and severity of ALD, which offered novel insights and research directions for mitigating and treating the development of ALD.

overall_design: To invesigate the onset and severity of ALD in identical twins, eight whole blood samples from monozygotic twin families with ALD disease had used to divided into five groups according to phenotype. Then, the relevant candidate genes were mined by comparison between different groups.

first: Liang

last: Tan

first: Chuhua

last: Fu

first: Changlin

last: Yin


title: Single-cell RNA-seq of RANKL treated mouse intestinal organoids

first: Maria

last: Novatchkova

summary: We generated intestinal organoids from a C57BL6/J mouse and stimulated them with mouse recombinant RANKL. We dissociated them into single cells and generated single-cell RNA-seq data from them.

overall_design: Single-cell RNA-seq analysis of RANKL treated mouse intestinal organoids

first: Masahiro

last: Onji

first: Josef

last: Penninger


title: The proteomic landscape and temporal dynamics of  mammalian gastruloid development

city: Seattle

first: Riddhiman

last: Garge

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Gastrulation is the highly coordinated process by which the early embryo breaks symmetry, establishes germ layers and a body plan, and sets the stage for organogenesis. As early mammalian development is challenging to study in vivo, stem cell-derived models have emerged as powerful surrogates, e.g. human and mouse gastruloids. However, although single cell RNA-seq (scRNA-seq) and high-resolution imaging have been extensively applied to characterize such in vitro embryo models, a paucity of measurements of protein dynamics and regulation leaves a major gap in our understanding. Here we sought to address this by applying quantitative proteomics to human and mouse gastruloids at four key stages of their differentiation (naïve ESCs, primed ESCs, early gastruloids, late gastruloids). To the resulting data, we perform network analysis to map the dynamics of expression of macromolecular protein complexes and biochemical pathways, including identifying cooperative proteins that associate with them. With matched RNA-seq and phosphosite data from these same stages, we investigate pathway-, stage- and species-specific aspects of translational and post-translational regulation, e.g. finding peri-gastrulation stages of human vs. mice to be discordant with respect to the mitochondrial transcriptome vs. proteome, and nominating novel kinase-substrate relationships based on phosphosite dynamics. Finally, we leverage correlated dynamics to identify conserved protein networks centered around congenital disease genes. Altogether, our study showcases the potential of intersecting proteomics and in vitro embryo models to advance our understanding of early mammalian development in ways that may not be possible through transcriptomics alone.

overall_design: To map the temporal changes underlying gastruloid development, we performed multi-omic phenotyping on 4 stages of gastruloid differentiation namely Naive ESCs, Primed ESCs, Early gastruloids and Late gastruloids.

first: Valerie

last: Lynch

first: Rose

last: Fields

first: Silvia

last: Casadei

first: Sabrina

last: Best

first: Jeremy

last: Stone

first: Chris

middle: D

last: McGann

first: Jay

last: Shendure

first: Lea

last: Starita

first: Nobuhiko

last: Hamazaki

first: Devin

last: Schweppe


title: RNA-seq of intestinal epithelial cells from WT and Rank-knockout mouse at lactation day5

summary: We isolated intestinal epithelial cells from WT and Rank-knockout mouse at lactation day5. We generated bulk RNA-seq data from them.

overall_design: Bulk RNA-seq of intestinal epithelial cells from WT andRank-knockout mouse at lactation day5


title: RNA-seq of intestinal organoids generated from caRANKvil-Tg mice

summary: we generated a transgenic mouse line that conditionally expresses a constitutively active RANK mutant (Rosa26-LSL-caRANK) in the intestinal epithelium using Villin1 promoter-driven Cre (Villin1-Cre) (caRANKvil-Tg) .We generated intestinal organoids from caRANKvil-Tg mice and littermate mice. We generated bulk RNA-seq data from them.

overall_design: Bulk RNA-seq analysis of intestinal organoids generated from caRANKvil-Tg mice

first: Onji

last: Masahiro


title: High-throughput sequencing Analysis of mouse BMDM cell Transcriptomes after tumor supernatants induction

city: Hangzhou

first: Di

last: Wang

address: Yuhgang Tang Rd No.866

institute: Zhejiang University

summary: The tumor microenvironment (TME) is a unique niche governed by constant crosstalk within and across all intratumoral cellular compartments. In particular, intratumoral high potassium has shown its immune-suppression potency on T cells. However, as a pan-cancer characteristic related to local necrosis, the impact of this ionic disturbance on innate immunity is still unknown. Here, using both murine and human samples, we reveal that intratumoral high potassium leads to profound suppression of the anti-tumor capacity of tumor-associated macrophages (TAMs). We report the high-throughput profiling of the transcriptomes of murine primary BMDMs after tumor conditioned medium (TCM) stimulation.

overall_design: Primary BMDMs from C57B6J mice were treated with B16F10 tumor cells conditioned medium supplemented with/without KCl or NaCl for 6 hours, and the final KCl and NaCl concentration was 40mM.

first: Sheng

last: Chen

first: Wenyu

last: Cui


title: RNA-seq of RANKL treated mouse intestinal organoids

first: Maria

last: Novatchkova

summary: We generated intestinal organoids from a C57BL6/J mouse and stimulated them with mouse recombinant RANKL. We generated bulk RNA-seq data from them.

overall_design: Bulk RNA-seq analysis of RANKL treated mouse intestinal organoids

first: Masahiro

last: Onji


title: Powell-Wiley: The Washington DC Cardiovascular Health and Needs Assessment

city: New York

first: Michael

last: Corley

state: NY

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

institute: Weill Cornell Medicine

type: Methylation profiling by genome tiling array

summary:
Genome-wide DNA methylation profiling of blood of participants from a high CVD risk community-based cohort of African American individuals from Washington D.C.
Chronic stress increases the risk of cardiovascular disease (CVD) and amygdalar activity (AmygA), a known marker of chronic stress which has been associated with subclinical CVD. Previous research suggests a plausible connection between AmygA, hematopoietic tissue activity, arterial inflammation, and cardiovascular events. There is a paucity of data on the relationships between AmygA, hematopoietic activity, and epigenomics modifications through deoxyribonucleic acid (DNA) methylation among racial and ethnic minorities. We investigated the association between AmygA and spleen (SpleenA) and bone marrow activity (BMA) as well as DNA methylation at genes previously associated with stress. Participants included in the study were from a high CVD risk community-based cohort of African American individuals from Washington D.C. AmygA was measured by aortic uptake of 18Fluorodeoxyglucose (FDG) on Positron Emission Tomography/Computed Tomography and calculated as standardized uptake values (SUVs). SpleenA and BMA were calculated as SUVs from regions of interest within the spleen and vertebrae, respectively. Standardized beta coefficients (β ) and p-values were calculated from linear regression models adjusted for body mass index and 10-year predicted atherosclerotic CVD risk.

overall_design: Bisulfite converted DNA from Buffy Coats were hybridized to the Illumina MethylationEPIC Beadchip


title: Extensive modulation of inflammatory and axonal genes led to robust axon regeneration in severe benzalkonium chloride-injured corneas treated with cord blood-derived biologics

first: Ruojing

last: Huang

address: Huangpu Street 613

department: Department of Ophthalmology

institute: The First Affiliated Hospital of Jinan University

summary: Modern ophthalmic solutions contain benzalkonium chloride (BAK), a potent antimicrobial preservative, that chronically damages the ocular apparatus. Umbilical cord blood serum (UCS) and platelet-rich plasma (UCPRP) are promising treatments for BAK-injured corneas. Here, for the first time, the feasibility of using both of these biologics for corneal treatment was demonstrated. Using animal studies and RNA-seq analysis, it was validated that severe BAK injury led to the upregulation of innate and adaptive immune responses, which corresponded to morphological and pathological changes in the cornea. When UCS and UCPRP were administered, besides significant corneal recovery, widespread immune pathways downregulation was observed. Subsequent verification of some of the genes involved in two of the most notable KEGG pathways suggested that the amelioration of inflammation was likely due to the reduction of immune cells, the decrease in chemoattractants, as well as the lessening of pro-inflammatory MMPs. Besides that, regulation of several key axonal genes led to robust axon recovery that correlated to nearly restored corneal sensitivity. Thus, these findings demonstrated the viability of cord blood-derived therapeutics for treating sustained, BAK-induced injuries in the cornea and also provided evidence that an optimal level of inflammatory response is crucial for stimulating axon regeneration.

overall_design: In order to study the effects of BAK on mice cornea, we administered BAK to the cornea, waited for the effects to occur, harvested and sequenced the injured corneas, and compared its gene expression with control corneas. The treatment groups are UCS and UCPRP. Mice cornea that were injured by BAK were applied with UCS and UCPRP, harvested, sequenced and compared with the non-treatment groups. A total of 6 corneas per 3 mice were pooled to form one sample. A total of 3 samples per group (Normal (Control), BAK-injured no treatment (Vehicle), UCS-treated and UCPRP-treated) were obtained.

first: Caiying

last: Su

last: Zhang

first: Wei

last: Wei

first: Jiansu


title: Has-miR-30c-1-3p inhibits macrophage autophagy and pro-motes Mycobacterium tuberculosis survival by targeting ATG4B and ATG9B

city: Wuhan

first: Xianglin

last: Peng

address: No.215, Zhongshan Road, Qiaokou District

department: Department of Orthopedics

institute: Huazhong University of Science and Technology

summary: Autophagy is a widespread physiological process in the body, which also protects the host by degrading invading pathogens and harmful substances during pathological conditions. However, Mycobacterium tuberculosis (MTB) can affect the process of autophagy by regulating the expres-sion of microRNAs (miRNAs), allowing for immune evasion. In this study, we constructed a model of a strong virulent strain (H37Rv) infection in human macrophage cell line. Following H37Rv infection, we screened 14 differentially expressed miRNAs by RNA-seq and bioinformatics. We predicted and demonstrated that miR-30c-1-3p inhibits autophagy and promotes macrophage survival by targeting ATG4B and ATG9B during the infection process.Additionally, the intervention of miR-30c-1-3p mimics resulted in an increased bacterial load in macrophages, suggesting that MTB achieves immune evasion by upregulating miR-30c-1-3p during infection. In conclusion, our study provides a valuable target for the development of host-directed anti-tuberculosis therapy as well as a new diagnostic marker.

overall_design: To investigate the effect of miRNAs expression on macrophage autophagy after macrophages were infected with Mycobacterium tuberculosis.Total RNA was extracted from THP-1 cells infected with H37Rv for 2h and blank control and subjected to RNA-seq to analyze differentially expressed miRNAs associated with autophagy.

first: Feifei

last: Pu

first: Jing

last: Feng

first: Ping

last: Xia


title: Proliferation and differentiation of intestinal stem cells depends on the zinc  finger transcription factor BCL11/Chronophage

city: Heidelberg

first: Nick

last: Hirschmüller

address: Meyerhofstrasse

department: Genome Biology

country: Germany

institute: European Molecular Biology Laboratory

summary: The  molecular  programs  that  drive  proliferation  and  differentiation  of  intestinal  stem  cells (ISCs) are essential for organismal fitness. Notch signalling regulates the binary fate decision of ISCs, favouring enterocyte commitment when Notch activity is high and enteroendocrine cell (EE) fate when activity is low. However, the gene regulatory mechanisms that underlie this process on an organ scale remain poorly understood. Here, we find that the expression of the  C2H2-type  zinc-finger  transcription  factor  Chronophage  (Cph),  homologous  to mammalian  BCL11,  increases  specifically  along  the  ISC-to-EE  lineage  when  Notch  is inactivated. We show that the expression of Cph is regulated by the Achaete-Scute Complex (AS-C) gene, scute, which directly binds to multiple sites within the Cph locus to promote its expression. Our genetic and single-cell RNA sequencing experiments demonstrate that Cph maintains  the  ISC  and  EE  populations  and  is  necessary  to  remodel  the  transcriptome  of progenitor cells with low Notch activity. By identifying and functionally validating Cph target genes, we uncover a novel role for sugar free frosting (sff) in directing proliferative and lineage commitment steps of ISCs. Our findings provide mechanistic insight into how Cph maintains intestinal epithelial homeostasis, and together with our evolutionary analysis of Cph/BCL11, suggests that it may represent a general mechanism used by adult somatic stem cells in other tissues to balance proliferation and differentiation.

overall_design: To gain insights into the function of Chronophage we performed single-cell RNA sequencing of the Drosophila melanogaster intestine under different conditions: knockout of Notch (NotchKO), knockdown of Notch (NotchRNAi) and knockdown of Notch and Chronophage (NotchRNAiCphRNAi). For both the knockout and the knockdown experiments a control exists. All experiments were preformed in duplicates.

first: Siamak

last: Redhai

first: Wolfgang

last: Huber

last: Boutros


title: RNA-Seq analysis of the effect of regorafenib on melanoma cells

city: wuhan

first: xiu

middle: yun

last: xuan

address: 1095 Emancipation Avenue

department: Department of Dermatology

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

summary: Melanoma is a malignant tumor with a terrible prognosis. In this study, we showed regorafenib has the ability to limit the growth, invasion and metastasis of melanoma cells but to upregulate apoptosis-prompting markers (cleaved-PARP and Bax). Moreover, ERK/E2F3 signaling influences regorafenib's ability to suppress melanoma cell growth. Ultimately, regorafenib significantly inhibits tumor growth in a dose-dependent manner in vivo.

overall_design: To investigate the influence of regorafenib for melanoma cell, melanoma cell SK-MEL-2 was treated regorafenib and followed performed RNA-Seq.

first: Xiuyun

last: Xuan

first: Yanqiu

last: Li

first: Changzheng

first: Yong


title: Single-cell multiomic analysis identifies macrophage subpopulations in promoting cardiac repair

city: Guangzhou

first: fu

last: Ai

state: Guangdong

address: Jingxijiedao

institute: Southern Medical University

summary: Our study comprehensively investigated the epigenetic features of cardiac F4/80+CD45+ macrophages after adult mouse MI or Sham sugery at infarct zones of mouse hearts through single cell H3K27ac ChIP-seq. We identified 7 subclusters and analyzed their potential functions, cluster-specific enhancer features.

overall_design: Adult mouse hearts were collected at 3 days and 7 days after MI. The heart tissues from infarct zone were digested with collagenase type II enzyme at 37°C for 30 min to generate single-cell suspension. F4/80+CD45+ cardiac macrophages were collected by FACS sorting and then subjected to single cell H3K27ac CoBATCH profiling.

first: Shanshan

first: Mingzhu

last: Fu

first: Shengtao

last: Jia

first: Longhui

last: Xu


summary: Our study comprehensively investigated the epigenetic features of cardiac F4/80+CD45+ macrophages at 3 and 7 days after P1 and P10  MI at infarct, border, and remote zones of mouse hearts (IZ, BZ, and RZ) through single cell H3K27ac ChIP-seq. we identified 9 subclusters and analyzed their potential functions, cluster-specific enhancer features, and enrichment of cell-type specific transcription factors. Surprisingly, we found intracluster epigenetic heterogeneity exists with biological functions. Moreover, we identified two MI-responsive lineages and targeted one inflammatory lineage exhibiting obvious pre-regenerative function.

overall_design:
Mouse hearts were collected at 3 days and 7 days after P1 and P10 MI. The heart tissues were roughly divided into three zones and then digested with collagenase type II enzyme at 37°C for 30 min to generate single-cell suspension. F4/80/CD45+ cardiac macrophages were collected by FACS sorting and then subjected to single cell H3K27ac CoBATCH profiling.
Please note that each bw file was genearated from both replicates and is linked to the corresponding *rep1 sample records.


title: Next Generation Sequencing Technologies to Investigate Autosomal  Recessive Polycystic Kidney Disease (ARPKD).

city: Wolverhampton

first: Paraskevi

last: Goggolidou

address: Wulfruna Street

department: Faculty of Science and Engineering

institute: University of Wolverhampton

summary: Autosomal Recessive Polycystic Kidney Disease (ARPKD) is a rare paediatric disease primarily caused by mutations in the gene PKHD1. ARPKD presents with considerably clinical variability which is linked to the type of PKHD1 mutation but not position. Animal models of Polycystic Kidney Disease (PKD) suggest there is a complex genetic landscape with genetic modifiers as a potential cause of disease variability.  Transcriptomic analysis identified a considerable number of genes linked to cellular metabolism and development. Amongst these genes were those linked to WNT signalling. Two individuals in this cohort had the same mutations in PKHD1 but different rates of kidney disease progression. Amongst the transcriptomic differences of these two individuals were differences in the expression changes of WNT genes.

overall_design: To identify transcriptomic changes in ARPKD, four human ARPKD kidney samples between the ages of 9 days and 10 years and were compared to four age-matched normal “healthy” kidney samples collected from the PKD funded biobank hosted by University College London.   RNA was extracted from kidney tissue samples using the Qiagen RNeasy mini kit with library preparation and sequencing performed by the Oxford Genomics Centre using NEBNext Ultra II Directional RNA Library Prep Kit on an Illumina NovaSeq6000.  Sequencing data underwent alignment using the HISAT2 aligner using the GRCH38 genome files provided by Ensembl. Raw count data was determined using StringTie and differential expression analysis was performed using Deseq2.

first: Taylor

last: Richards

first: Patricia

last: Wilson


summary: Our study comprehensively investigated the epigenetic features of cardiac F4/80+CD45+ macrophages at 3 and 7 days after P1 and P10  MI at infarct, border, and remote zones of mouse hearts through single cell H3K27ac ChIP-seq. we identified 9 subclusters and analyzed their potential functions, cluster-specific enhancer features, and enrichment of cell-type specific transcription factors. Surprisingly, we found intracluster epigenetic heterogeneity exists with biological functions. Moreover, we identified two MI-responsive lineages and targeted one inflammatory lineage exhibiting obvious pre-regenerative function.

overall_design: We performed single-cell RNA-seq on CD45+F4/80+ macrophages/monocytes isolated from the IZ and BZ of P10-Sham_Vehicle, P10-MI_Vehicle, and P10-MI_SB225002 hearts at 3 days after P10-MI. The heart tissues were manually divided into three zones (infarct zone, border zone and remote zone) and then digested with collagenase type II enzyme at 37°C for 30 min to generate single-cell suspensions. F4/80/CD45+ cardiac macrophages in infarct zone and border zone were collected and subjected to FACS sorting for CD45+/F4/80+ cells.


title: Gadd45β is critical for regulation of type I interferon signaling by facilitating G3BP-mediated stress granule formation

city: Daejeon

first: Jong-Soo

last: Lee

address: 99 Daehak-ro

department: Veterinary Medicine

country: South Korea

institute: Chungnam National University

summary: Stress granules (SGs) constitute a signaling hub that plays a critical role in type I interferon responses. Here, we report that growth arrest and DNA damage-inducible beta (Gadd45β) act as a novel positive regulator of SGs-mediated interferon signaling by targeting G3BP upon RNA virus infection. Gadd45β deficiency markedly impairs SG formation and SG-mediated activation of interferon signaling in vitro. Gadd45β knockout mice are highly susceptible to RNA virus infection and their ability to produce interferon and cytokines is severely impaired. Specifically, Gadd45β interacts with the RNA-binding domain of G3BP, leading to conformational expansion of G3BP1 via dissolution of its autoinhibitory electrostatic intramolecular interaction. The acidic loop 1- and RNA-binding properties of Gadd45β markedly increase the conformational expansion and RNA-binding affinity of the G3BP1-Gadd45β complex, thereby promoting assembly of SGs. These findings suggest a role for Gadd45β as a new component and critical regulator of G3BP1-mediated SG formation which facilitates RLR-mediated interferon signaling.

overall_design: To elucidate the comprehensive effects of Gadd45β on RNA virus-induced global immune gene signatures, we performed RNA sequencing (RNA-seq) of lung tissues isolated from SeV infected Gadd45β+/+ and Gadd45β-/- mouse lungs at 2 days post-infection.

first: W

last: Chathuranga

first: Chamilani

last: Nikapitiya

first: Jae-Hoon

last: Kim

first: Kiramage

first: Asela

last: Weerawardhana

first: Niranjan

last: Dodantenna

first: Doo-Jin

first: Haryoung

last: Poo

first: Jae

middle: U

last: Jung

first: Chul-Ho


title: RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells.

city: LYON

first: Mathieu

last: GABUT

address: 28 rue laennec

department: Cancer Initiation and Tumor cell Identity

institute: Cancer Research Centre of Lyon, Inserm U1052

summary: Embryonic stem cell (ESC) fate decisions are regulated by a complex molecular circuitry that requires tight and coordinated gene expression regulations at multiple levels from chromatin organization to mRNA processing. Recently, ribosome biogenesis and translation have emerged as key pathways that efficiently control stem cell homeostasis. However, the molecular mechanisms underlying the regulation of these pathways remain largely unknown to date. Here, we analyzed the expression, in mouse ESCs, of over 300 genes involved in ribosome biogenesis and we identified RSL24D1 as the most differentially expressed between self-renewing and differentiated ESCs. RSL24D1 is highly expressed in multiple mouse pluripotent stem cell models and its expression profile is conserved in human ESCs. RSL24D1 is associated with nuclear pre-ribosomes and is required for the maturation and the synthesis of 60S subunits in mouse ESCs. Interestingly, RSL24D1 depletion significantly impairs global translation, particularly of key pluripotency factors, including POU5F1 and NANOG, as well as components of the polycomb repressive complex 2 (PRC2). Consistently, RSL24D1 is required for mouse ESC self-renewal and proliferation. Taken together, we show that RSL24D1-dependant ribosome biogenesis is required to both sustain the expression of pluripotent transcriptional programs and silence developmental programs, which concertedly dictate ESC homeostasis.

overall_design: RSL24D1 was downregulated using a pool of siRNAs. CGR8 mouse ESCs were treated with a pool of non targeting siRNAs (si-CTL) or with si-Rsl24d1 siRNAs for 48h prior to RNA extraction. Si-CTL or siRSL24d1 were divided in two groups, with independant triplicates for each group

first: Sébastien

last: Durand

first: Marion

last: Bruelle

first: Fleur

last: Bourdelais

first: Bigitha

last: Bennychen

first: Juliana

last: Blin-Gonthier

first: Caroline

last: Isaac

first: Aurélia

last: Huyghe

first: Antoine

last: Seyve

first: Christophe

last: Vanbelle

first: David

last: Meyronet

first: Frédéric

last: Catez

first: Jean-Jacques

last: Diaz

first: Fabrice

last: Lavial

first: Emiliano

middle: P

last: Ricci

first: François

last: Ducray

last: Gabut


title: RNA fine-tunes estrogen receptor-alpha binding on low-affinity DNA motifs for transcriptional regulation

city: Bangalore

first: Dimple

last: Notani

address: National Centre for Biological Sciences Tata Institute of Fundamental Research Bellary Road

department: Cellular Organization and Signallinga

country: India

institute: National Centre for Biological Sciences

summary: Transcription factors (TFs) regulate gene expression by binding, with varying strength, to DNA via their DNA-binding domain. Additionally, some TFs also interact with RNA, which modulates transcription factor binding to chromatin. However, whether RNA-mediated TF binding results in differential transcriptional outcomes remains unknown. In this study, we demonstrate that estrogen receptor α (ERα), a ligand-activated TF, interacts with RNA in a ligand-dependent manner. Defects in RNA binding lead to genome-wide loss of ERα recruitment, particularly at weaker ERα-motifs. Furthermore, ERα mobility in the nucleus increases in the absence of its RNA-binding capacity. Unexpectedly, this increased mobility coincides with robust polymerase loading and transcription of ERα-regulated genes that harbor low-strength motifs. However, highly stable binding of ERα on chromatin negatively impacts ligand-dependent transcription. Collectively, our results suggest that RNA interactions spatially confine ERα on low-affinity sites to fine-tune gene transcription.

overall_design: Chromatin Immunoprecipitation (ChIP-seq) for the FLAG tagged  WT and RBM Estrogen receptor-alpha upon 72 hours of hormone deprivation and  1 hour of E2 signaling. RNAseA ChIP-seq of Estrogen receptor- alpha with and without pre-extraction after 72 hours of hormone deprivation and 1 hour  of E2 siganling . ChIP-seq of total PolII upon 1 hour of E2 siganling with expression of either FLAG tagged WT or RBM Estrogen receptor alpha. Paired factor ChIP with antiFLAG and anti-CTCF upon expression of either FLAG tagged WT or RBM Estrogen receptor alpha.

first: D

last: Soota


title: Investigating the regulatory role of KMT2D in neurodeveolopment using organoid and single cell techniques

first: Yingying

last: Zhao

address: Kaiyuan Avenue

department: Chinese Academy of Sciences Guangzhou Branch

institute: Guangzhou Institutes of Biomedicine and Health

summary: Enhancer-mediated gene activation of lineage-specifiers, together with extrinsic niche factors, determines cell fate. Mutations in KMT2D, the H3K4me1-catalyzing enhancer-activator, result in ~70% of the KABUKI syndrome, a neurodevelopmental disorder. Yet the impacted cell-of-origin and the bona fide targets of KMT2D in human neurodevelopment are missing. Here we applied cerebral organoid and single-cell technologies to delineate human-specific distal regulatory elements across heterogeneous cell types.

overall_design:
We analyzed RNA-seq, CUT&Tag, scRAN-seq, scATAC-seq data of brain organoids differentiated from HN4 cell lines at multiple time points.
*** Raw data not submitted due to patient privacy concerns ***

first: Ziyun

last: Shan

first: Xuejie

last: Yang

first: Ning

last: Guo

first: Xiuyu

last: Chen

first: Fang

last: Wu

first: He

last: Liu

first: Yujian

first: Junju

last: Huang

first: Guodong

last: Zhan

first: Biyuan

first: Kaixin

first: Lihui

last: Lin

first: Yiping

first: Xiaobing

last: Zou

first: Jiangping

last: He

first: Jie

last: Wang

first: Jiekai


title: Multiple Mechanistic Models Reveal the Neuroprotective Effect of Ginkgo Bilobalides for the Treatment of Ischaemic Stroke

city: Jiangsu province

first: Wei

last: Xiao

address: N0.58 Kangyuan Road, Jiangning Industrial town, Economic and development zone, Lianyun District

institute: State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process

summary: To elucidate the potential neuroprotective mechanism of ginkgolides, experiments in seven in vitro cell models that mimic the pathological processes of ischaemic stroke confirmed the antiplatelet properties of ginkgolides and their potential antiapoptotic, anti-inflammatory and neuroprotective activities in the nervous system.

overall_design: The present study assessed the effects of DGMI and its three constituent monomers on seven cell models of pathological processes involved in ischaemic stroke by high-throughput transcriptome sequencing. The seven cell models include PMA-induced platelet secretion model of MEG-01, oxygen-glucose deprivation/reperfusion (OGD/R) model of differentiated SH-SY5Y cells, THP-1-derived foam cell model and inflammatory models of U251, HMC3, HUVEC-T1 and THP-1-derived macrophage.


title: Characterising day 90 human C9ORF72-ALS/FTD cerebral organoids at single cell level

city: Utrecht

first: Ronald Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

summary: A hexanucleotide repeat expansion (HRE) in C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Human imaging and experimental studies hint at early changes in the brain in C9-ALS/FTD, which remain poorly understood. To define these changes, we used cerebral organoid models derived from C9-ALS/FTD patients and controls to create a single cell RNA sequencing dataset at day 90. Together, these dataset will help to shed light on initial pathologies crucial for understanding disease onset and the design of therapeutic strategies.

overall_design: iPSC derive cerebral organoids were generated as reported previously (Lancaster & Knoblich, 2014; Ormel et al., 2018). To study the cell types present in day 90, single cell RNA sequencing (scRNA-seq) was performed on HC (n=3 lines) and C9-ALS/FTD (n=3 lines) organoids

first: Astrid

last: van der Geest

first: R

first: Onur

last: Basak


title: Large-scale manipulation of radial positioning does not affect most aspects of genome organization

first: Noam

last: Kaplan

address: Efron 1

institute: Technion - Israel Institute of Technology

summary: Although the spatial organization of the genome is closely linked to biological function, genome structure is highly stochastic. Within this heterogeneity, specific function-associated structural elements must be maintained, even when the nucleus is deformed due to physiological physical constraints. The radial positioning of genomic loci - their distance from the nuclear periphery - has long been considered an important feature of genome organization which is correlated with both structural elements and genomic activity. In the current study, we developed an experimental system for manipulating the radial positioning of the genome, by expressing the sperm-specific protein Prm1 in somatic cells. By microscopy, we observe that initial Prm1 nuclear foci develop within 72 hours into a large Prm1 focus occupying most of the nuclear interior, while the entire genome is driven towards the nuclear periphery, resulting in a 3-5 fold reduction in the volume that the genome occupies. Noting that this system enables isolation of a pure population of cells with reorganized nuclei, we then used Hi-C to study the effects of this perturbation. Remarkably, we find that interaction patterns are largely robust to this major nuclear reorganization, with minor changes which mostly reflect a strengthening of heterochromatin self-interactions. Our experimental system provides means for manipulating nuclear organization in a reproducible manner, potentially allowing to examine radial positioning decoupled from other features of genome organization. Highlighting the complementary nature of microscopic and genomic methods, our work further suggests a remarkable resilience of genome structure such that large-scale nuclear changes, including chromosome compression and changes in radial positioning, can occur without extensive alteration of functional genome organization.

overall_design: HEK293 cells were transfected with Prm1-mCherry. After 72h, the cells were crosslinked and sorted to isolate Prm1 positive and negative populations, and these were subject to Hi-C (FLIE Hi-C)

first: Mor

last: Guetta

first: Hagai

last: Kariti

first: Liora

last: Sherman

first: Lena

last: Israitel

first: Moran

last: Tel-Paz

first: Nili

last: Avidan

first: Revital

last: Shemer


title: Unveiling the Mechanisms of Mechanical Loading-Induced Knee Osteoarthritis Through Transcriptomics

status: Public on Sep 05 2024

city: changchun

first: Yongji

last: Wu

address: academic article

institute: Jllin hospital of chinese medicine

summary: Aims：To establish a novel model of mechanical loading-induced knee osteoarthritis (KOA) and explore its regulatory mechanisms through transcriptomics. Methods：Knee joints of Sprague-Dawley (SD) rats were mechanically loaded with 13 N, 20 N and 27 N for 2 or 4 weeks to construct mechanically-induced KOA model. Immunohistochemistry (IHC), quantitative real-time polymerase chain reaction (qRT-PCR), Western blot, Safranin O/fast green staining, enzyme-linked immunosorbent assay (ELISA), micro-computed tomography (Micro-CT) and behavioral analysis were used to evaluate damage on the right knee joint. Transcriptomic analysis combined with validation experiments were performed to explore the regulatory mechanism of excessive mechanical loading on KOA development. Results：A vertical load of 27 N resulted in calf fractures, whereas a 13 N load did not cause remarkable pathological alteration in the knee joint. Notably, applying compression at a load of 20 N for 4 weeks (w) significantly promoted the levels of pro-inflammatory factors IL-6, IL-β and TNF-α in serum and joint fluids and markedly minimized the levels of anti-inflammatory factors IL-10 and TGF-β. Immunohistochemistry, qRT-PCR and Western blot analyses suggested that the 20 N load reduced the expression of anabolism markers (ACAN and COL2A1) and escalated the expression of catabolism markers (MMP13 and ADAMTS4). KEGG analysis and validation results showed that the PIEZ1 channel, Ca2+ signaling pathway, PI3K-AKT signaling pathway and NF-κB signaling pathway were significantly activated in the 20N-4 w group. Conclusion：Continuous loading with 20 N for 4 weeks can induce significant OA-like damage to the cartilage of the right knee in rats, which might be induced through the piezo1-Ca2+/PI3K-AKT/ NF-κB signaling pathway.

overall_design: Seventy 6-week-old male SD rats  were randomly classified into 7 groups: Control group ; 13 N - 2 w group; 13 N - 4 w group; 20 N - 2 w group; 20 N - 4 w group; 27 N - 2 w group; 27 N - 4 w group. A ZwickRoell static material testing machine was used for axial compression of the right knee and ankle joints of anaesthetized rats. The compression was done every two days for 2 or 4 weeks. Each compression consisted of 40 cycles and each cycle lasted for 10 seconds (s), with a base load of 5 N for 9 s and peak loads of 13 N, 20 N, or 27 N for 0.5 s. Transcriptome sequencin was performed from the right knee cartilage of rats in the blank group (n=3) and 20N - 4 w group (n=3).

first: Ailin

last: Li

first: Xiangyang

last: Leng

first: Haisi

last: Dong


title: Gene expression profile at single cell level of LMPP (lymphoid-primed multipotent progenitor) cells from CP-CML and BC-CML patients.

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: LMPPs comprise of heterogeneous populations which are progenitors of lymphocytes and myeloid cells. We aim to identify the difference of distribution of the diverse populations from CP-CML versus BC-CML patients.

overall_design: LMPPs from CP-CML and BC-CML were isolatd by Fluorescence-activated cell sorting (FACS) of CD34+CD38-CD45RA+CD90- cells.

first: Fang

last: Chen

first: Bin

last: Zhang

first: Min-Hsuan


title: Liver transcriptome modifications by nutrient restriction in early lactation Holstein cows challenged with intramammary lipopolysaccharide

city: St Genès-Champanelle

first: Christine

last: LEROUX

address: Route de Theix

institute: INRAE

summary:
The objective was to evaluate the effects of nutrient restriction on the liver transcriptomic response after 24 h challenge to intramammary lipopolysaccharide (LPS) in early lactation cows. At 24 ± 3 days of lactation, multiparous cows were fed either an ad libitum lactation diet (CON, n = 6), or a ration diluted with barley straw (48% DM) for 4 days (RES, n = 6). On day 3, one healthy rear mammary quarter from each cow was infused with 50 µg of LPS. Blood and liver biopsies were collected on day 4, corresponding to 24 h after LPS challenge. The liver transcriptome was analyzed using 44K bovine microarrays (Agilent Technologies). Blood and transcriptomic data were analyzed using SAS mixed models and GeneSpring (moderate t-test with Westfall-Young correction, P < 0.05), respectively, and data mining was performed using Panther and Pathway Studio software. The energy balance was no different before the diet change. By experimental design, energy intake was 41 and 97 ± 15 % of NEL requirements in RES and CON, respectively.
Plasma NEFA and BHBA were higher, and glucose was lower in RES than in CON, which is consistent with a 4-day nutrient deficit in RES. Seventy seven differentially expressed genes (DEGs) between CON and RES were identified, with 29 genes downregulated and 48 upregulated in RES. Genes involved in fatty acid synthesis (ACAT2, FASN, SCD), lactate metabolism (LDHC), and cortisol binding (SERPINA6) were downregulated in RES, while those involved in fatty acid oxidation, detoxification, cholesterol synthesis, lipoprotein lipid secretion, and gluconeogenesis (ACADVL, CPT1A, CPT1B, ANGPTL4, CYP4A11, HMGCSA, APOA1, APOA4, GK, PC and PCK2) were upregulated in RES. Overall, DEGs were in agreement with the negative energy balance and plasma metabolite profile, and reflect a state of intense lipomobilization, glucose deficit and ketogenesis in RES. Preliminary results suggest that nutrient restriction did not alter hepatic expression of genes directly involved in immune function 24 h after an intramammary LPS challenge.

overall_design: One-color experiment, two groups of cows, one restricted (n=6) and one control (n=6). All animals were submited to LPS challenge after 3 days since the begining of restriction of restricted group.

first: Karol

last: Pawlowski

first: Yannick

last: Faulconnier

last: Leroux


title: Role of RANKL in mouse intestinal epithelial cells

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

institute: IMP/IMBA

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

overall_design: Refer to individual Series


title: Single-cell multiome uncovers differences in glycogen metabolism underlying species-specific speed of development [scRNAseq and scATACseq]

city: Leiden

first: Max

last: Fernkorn

address: Einsteinweg 55

department: Leiden Academic Centre for Drug Research (LACDR)

institute: University Leiden

summary: Embryos from different mammalian species develop at characteristic timescales. These timescales are recapitulated during the differentiation of pluripotent stem cells in vitro. Specific genes and molecular pathways that modulate cell differentiation speed between mammalian species remain to be identified. Here we use single-cell multi-omic analysis of neural differentiation of mouse, cynomolgus monkey and human pluripotent cells to identify new regulators for differentiation speed. We demonstrate that species-specific differences in transcriptome dynamics are mirrored at the chromatin level, but that, contrary to other developmental contexts, the speed of neural differentiation is insensitive to manipulations of cell growth and cycling. Exploiting the single-cell resolution of our data, we identify glycogen storage levels regulated by UGP2 expression as a new species-specific trait of pluripotent cells, and show that lowered glycogen storage in UGP2 mutant cells is associated with accelerated neural differentiation. The control of energy storage could be a general strategy for the regulation of cell differentiation speed.

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design: Neural differentiation of a UGP2 KO lines was performed with sequencing samples collected at 0 hours and 7 days post-induction.

first: Alexandra

last: de la Porte

first: Julia

last: Schröder

first: Moritz

last: Thomas

first: Johanna

last: Geuder

first: Michael

last: Sterr

first: Wolfgang

last: Enard

first: Christian

last: Schröter

first: Carsten

last: Marr

first: Micha

last: Drukker


title: Single-cell multiome uncovers differences in glycogen metabolism underlying species-specific speed of development [mTORi]

platform_organism:
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design: Neural differentiation of mouse, cynomolgus and human cells was assessed at day 0 (pluripotency), day 2 and day4. Upon the start of neural induction, 50 nM INK128 was added to half of the cells.  To minimize batch effects, samples were multiplexed and pooled before mRNA capture and library preparation for each timepoint.


title: Effect of depletion of Drosophila Hepatocyte Nuclear Factor 4 (dHNF4) in enterocytes on gene expression in the adult midgut

city: Cologne

first: Gilles

last: Storelli

address: Joseph Stelzmannstrasse 26

department: CECAD Research Center

institute: University of Cologne

summary: The main objective of the sudy was to characterize the functions of Drosophila Hepatocyte Nuclear Factor 4 (dHNF4) in midgut enterocytes. For this, we expressed a UAS-dHNF4 RNAi transgene under the control of mex-GAL4, which is active specifically in midgut enterocytes. We then collected adult male midguts, extracted total RNA and performed mRNA-seq. Our data demonstrate that dHNF4 acts as a master regulator of intestinal lipid metabolism in Drosophila.

overall_design: Total RNA was extracted from 20 midguts of adult male flies ( controls - genotype: w1118/Y ; ; UAS-dHNF4 RNAi NIG9310-R2/+), and of adut male flies expressing a UAS-dHNF4 RNAi transgene under the control of the enterocyte-specific mex-GAL4 driver (genotype: w/Y ; mex-GAL4/+; UAS-dHNF4 RNAi NIG9310-R2/+). mRNA sequencing was performed on 5 biological replicates per genotype. Adult male flies were fed a yeast only diet and dissected 7 days after eclosion.

first: Maximilian

last: Vonolfen

first: Akos

last: Gyenis


title: Immunzition of Salp14-C mRNA and lipid nanoparticles elicited multiple immune response to tick challenge in guinea pig skin

city: New Haven

first: Yingjun

last: Cui

state: CT

address: 300 Cedar St, New Haven, CT, TAC S410/Erol Fikrig

department: Internal Medicine

institute: Yale University

summary: In this study, we immunized guinea pigs with mRNA of Salp14 C terminus and lipid nanoparticles (LNP), the animals produced high titers of IgG, and developed moderate erythema during tick challenge, the transcriptomes of skin at tick bite sites enriched multiple immune response pathways, which might be involved in erythema development.

overall_design: we immunized two guinea pigs with Salp14-C mRNA-LNP and two guinea pigs with luciferase mRNA-LNP (control) for three times with 3-week interval, then performed tick challenge with 30 nymph/animal, then did skin biopsies at tick biste sites after all ticks detached. Total RNAs were extracted, and cDNA libraries were consructed, and bulk RNA sequencing performed.


title: Transcriptomic analysis reveals the heterogeneous role of conducting films upon electrical stimulation

city: Perth

first: Nicholas

last: Lawler

state: Western Australia

address: 35 Stirling Hwy

institute: University of Western Australia

summary: Central nervous system (CNS) injuries and neurodegenerative diseases have markedly poor prognoses and can result in permanent dysfunction due to the general inability of CNS neurons to regenerate. Differentiation of transplanted stem cells has emerged as a therapeutic avenue to regenerate tissue architecture in damaged areas. Electrical stimulation is a promising approach for directing the differentiation outcomes and pattern of outgrowth of transplanted stem cells, however traditional inorganic bio-electrodes can induce adverse effects such as inflammation. Here, we demonstrate the implementation of two organic thin films, a polymer/reduced graphene oxide nanocomposite (P(rGO)) and PEDOT:PSS, that have favorable properties for implementation as conductive materials for electrical stimulation, as well as an inorganic indium tin oxide (ITO) conductive film. Transcriptomic analysis revealed that electrical stimulation improved neuronal differentiation of SH-SY5Y cells on all three films, with the greatest effect for P(rGO). Unique material- and electrical stimuli-mediated effects were observed, associated with differentiation, cell-substrate adhesion, and translation. Our work demonstrates that P(rGO) and PEDOT:PSS are highly promising organic materials for the development of biocompatible, conductive scaffolds that will enhance electrically-aided stem cell therapeutics for CNS injuries and neurodegenerative diseases.

overall_design: We implemented three classes of materials, a polymer/reduced graphene oxide nanocomposite (P(rGO)), poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS), and indium tin oxide (ITO) as conductive films for electrical stimulation of SH-SY5Y cells during differentiation. RNA-seq was performed to examine the effects due to both the conductive materials and electrical stimulation.

middle: B

first: Uditi

last: Bhatt

first: Vipul

last: Agarwal

first: Cameron

last: Evans

first: Priya

last: Kaluskar

first: Sebastian

last: Amos

first: Kai

last: Chen

first: Yin

last: Yao

first: Haibo

last: Jiang

first: Yu-Suk

last: Choi

first: Minghao

last: Zheng

first: Dino

last: Spagnoli

first: Irene

last: Suarez-Martinez

first: Per

last: Zetterlund

first: Vincent

last: Wallace

first: Alan

last: Harvey

first: Stuart

middle: I

last: Hodgetts

first: K

middle: S

last: Iyer


title: Integrated multi-omics analysis identification of genetic and epigenetic features that predict human pluripotent stem cell-derived progenitor differentiation to cardiomyocytes [ATAC-Seq]

city: Madison

first: Aaron

last: Simmons

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin

summary: Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are advancing cardiovascular development and disease modeling, drug testing, and regenerative therapies. However, hPSC-CM production is hindered by significant variability in the differentiation process. Establishment of early quality markers to monitor lineage progression and predict terminal differentiation outcomes would address this robustness and reproducibility roadblock in hPSC-CM production. We performed an integrated transcriptomic and epigenomic analysis to assess how attributes of the cardiac progenitor cell (CPC) affect CM differentiation outcome. Our analysis identified predictive markers of CPCs that give rise to high purity CM batches, including TTN, TRIM55, DUSP5, DUSP6, GIPR, RHOBTB3, CRIP2, SLC7A11, MAB21L2, and CALD1.  We also gained insight into mechanisms of batch failure and dominant non-CM cell types generated in failed batches.  This study demonstrates how integrated multi-omic analysis of progenitor cells can identify quality attributes of that progenitor and predict differentiation outcomes, thereby improving differentiation protocols and increasing process robustness.

overall_design: We sought to identify molecular markers at the CPC stage of differentiation of hIPSCs which are predictive of (or correlate with) high terminal purity of cardiomyoytes (i.e. markers at the CPC stage which are enriched in CPCs which have been validate to result in high CM purity batches vs low purity ones). To this end, we performed multi-omic analyses (in this submission, RNA-seq and ATAC-seq) on high efficiency CPCs (those resulting in high CM purity outcomes) and low efficiency CPCs (those resulting in low CM purity outcomes)

first: Claudia

last: Baumann

first: Xiangyu

last: Zhang

first: Timothy

last: Kamp

first: Rabindranath

last: De La Fuente

first: Sean

last: Palecek


title: Integrated multi-omics analysis


title: Integrated multi-omics analysis identifies features that predict human pluripotent stem cell-derived progenitor differentiation to cardiomyocytes [RNA-Seq]


title: METTL3 restricts RIPK1-dependent cell death via the ATF3-cFLIP axis in the intestinal epithelium

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

summary: Intestinal epithelial cells (IECs) are pivotal for maintaining intestinal homeostasis through self-renewal, proliferation, differentiation, and regulated cell death. While apoptosis and necroptosis are recognized as distinct pathways, their intricate interplay remains elusive. In this study, we report that Mettl3-mediated m6A modification maintains intestinal homeostasis by impeding epithelial cell death. Mettl3 knockout induces both apoptosis and necroptosis in IECs. Targeting different modes of cell death with specific inhibitors unveils that RIPK1 kinase activity is critical for the cell death triggered by Mettl3 knockout. Mechanistically, this occurs via the m6A-mediated transcriptional regulation of Atf3, a transcription factor that directly binds to Cflar, the gene encoding the anti-cell death protein cFLIP. cFLIP inhibits RIPK1 activity, thereby suppressing downstream apoptotic and necroptotic signaling. Together, these findings delineate the essential role of the METTL3-ATF3-cFLIP axis in homeostatic regulation of the intestinal epithelium by blocking RIPK1 activity.

overall_design: bulk RNA-seq of control and Mettl3-KO organoids treated with DMSO and Nec-1; DNA profile of Atf3 overexpressed organoids.

first: Meimei

last: Huang

first: Yuan

last: Liu

first: Xiaodan

last: Wang


title: Evaluating the impact that Arid1a deletion has on the transcriptional differences between two murine models of osteosarcoma

city: Provo

first: Jared

last: Barrott

state: UT

address: 701 E University Pkwy, 4005 LSB

department: Cell Biology and Physiology

institute: Brigham Young University

summary: Transgenic mouse models of osteosarcoma originate from osteoblast cells with a baseline deletion of Tp53 and Rb1; however, the model is not 100% penetrant in osteosarcomagenesis and demonstrates no visible evidence of the metastatic disease. To enhance the current model, a fourth allele was added so that Arid1a, Tp53, and Rb1 are all conditionally deleted in osteoblast cells upon tamoxifen-induced, CreERT2-mediated recombination. Mice from both cohorts, with and without Arid1a were compared at the transcriptional level to identify the consequences of Arid1a deletion and the pathways associated with the more aggressive and metastatic mouse model without Arid1a.

overall_design: We compared murine osteosarcomas from two genetic cohorts: OsxCreERT2+/-;p53fl/fl;Rb1fl/fl (non-metastatic) and OsxCreERT2+/-;p53fl/fl;Rb1fl/fl;Arid1afl/fl (metastatic) and performed RNA-seq to identify differences in gene expression

first: Kaniz

last: Fatema

first: Kevin

last: Jones