title: Tumor context dictates reliance on Tcf1 for response to immunotherapy

city: London

first: Luca

last: Biasco

address: 30 Guilford St, Holborn

institute: UCL

summary: Stem-like CD8 + T cells are regulated by the transcription factor TCF1 and are key players in the  response to immune checkpoint blockade (ICB). However, recent findings indicate that reliance  on TCF1 + CD8 + stem-like T cells for ICB efficacy may not be equal across patients or tumor  contexts. Here, we uncovered that TCF1-deficient CD8 + T cells showed defective priming in the  tumor-draining lymph node of mice bearing poorly immunogenic tumors and that TCF1  regulates optimal T cell responsiveness to low TCR triggering. Importantly, we found that TCF1  was dispensable for therapy response in settings where ICB expanded intra-tumoral transitory  effector-like cells. Conversely, TCF1 was required for ICB response in tumors that failed to  expand cytotoxic effectors and accumulated Tox + dysfunctional T cells. In the absence of TCF1,  dysfunctional T cells became destabilized and shared features with CD8 + T cells found in  patients that fail ICB. Our study highlights a role for TCF1 in the early stages of the anti-tumor  CD8 + T cell response with important implications for guiding optimal therapeutic interventions  in cancers with low frequency of TCF1 + CD8 + T cells and low neoantigen levels.

overall_design: We combined cell sorting with high-throughput single-cell RNA (scRNA) sequencing to characterize endogenous tumor-infiltrating wild-type (WT) or TCF1-knock out (KO) CD8+ T cells in the tumor microenvironment of mice challenged with either the colorectal MC38-OVA or the B16-OVA melanoma tumors and treated with isotype or immune checkpoint blockade (ICB) antibodies (anti TIM3 + anti-PDL1). Endogenous CD8+ T cells were sorted from tumors treated with two doses of isotype or ICB at 12 days post tumor injection. In a separate set of experiments we combined cell sorting with high-throughput single-cell RNA (scRNA) sequencing to characterize adoptively transferred tumor-specific WT or TCF1-KO OTI T cells present in the tumor-draining lymph node (TDLN) of B16-OVA or MC38-OVA-bearing mice, three days post T cell transfer and after one dose of isotype or ICB treatment.


title: Bulk RNA-seq of whole biopsies and enteroids/colonoids from terminal ileum and rectum of inflammatory bowel disease patients or control subjects

status: Public on Aug 22 2023

city: Philadelphia

first: Yusen

last: Zhou

state: PA

address: 3615 Civic Center Blvd

department: Department of Biomedical and Health Informatics

country: USA

institute: Children's hospital of Philadelphia

type: Expression profiling by high throughput sequencing

summary: The study was design to compare transcriptomic profiles of whole biopsies to enteroid/colonoid lines derived from them. In the accompanying publication, we observed substantial overlap of pathways upregulated in Crohn’s disease in enteroids and ileal biopsies, as well as colonoids and rectal biopsies. Our data support the use of patient enteroids and colonoids as critical translational tools for the study of inflammatory bowel disease.

overall_design: The biopsies were subjected to RNA extraction (Trizol) whole and subsequent library preparation and RNA-seq. To establish enteroids and colonoids, we first isolated crypts from matching biopsies, then seeded these crypts in Matrigel domes. We used complete human IntestiCult OGM to enteroid/colonoid growth. The cultures were passaged once, and then harvested for RNA isolation, library prep and RNA-seq.

first: Kathryn

middle: E

last: Hamilton

first: Tatiana

last: Karakasheva


title: Use of High-plex Data Provides Novel Insights into the Temporal Artery Processes of Giant Cell Arteritis

status: Public on Aug 24 2023

city: Limoges

first: Simon

last: Parreau

state: Haute-Vienne

address: 16 rue Bernard Descottes

country: France

institute: Dupuytren hospital

summary: To identify the key coding genes underlying the biomarkers and pathways associated with giant cell arteritis (GCA), we performed in situ spatial profiling of molecules involved in the temporal arteries of GCA patients and controls

overall_design: Using human formalin-fixed paraffin-embedded temporal artery biopsy samples (GCA, n = 9; controls, n = 7), we performed whole transcriptome analysis using NanoString GeoMx Digital Spatial Profiler

first: Elsa

last: Molina


title: chemical ac4C sequencing (ac4C-seq) to identify mRNA ac4C sites

status: Public on Aug 25 2023

city: Beijing

first: Yuan

address: 38 college road

country: China

institute: Peking University

summary:
NAT10-catalyzed N4-acetylcytidine (ac4C) has emerged as a vital post-transcriptional modulator on the coding transcriptome by promoting mRNA stability.
To explore the transcriptome-wide profile of ac4C modification, we mapped the locations of ac4C modification on wild-type (WT) hESCs and NAT10 KD hESCs by NaCNBH3-based chemical ac4C sequencing (ac4C-seq).

overall_design: Both NAT10 KD hESCs and wild-type (WT) hESCs were analyzed with 2 duplications for chemical ac4C sequencing (ac4C-seq).

first: Rucong

last: Liu

first: Zibaguli

last: Wubulikasimu

first: Runze

last: Cai

first: Fanyi

last: Meng

first: Qinghua

last: Cui

first: Yang

last: Li


title: Low Glucose Culture Environment Can Enhance the Wound Healing Capability of Diabetic Adipose-derived Stem Cells

status: Public on Aug 23 2023

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: Application of autologous adipose-derived stem cells (ASC) for diabetic chronic wounds has become an emerging treatment option. However, ASCs from diabetic individuals showed impaired cell function and suboptimal wound healing effects. We proposed that adopting a low glucose level in the culture medium for diabetic ASCs may restore their pro-healing capabilities. ASCs from diabetic humans and mice were retrieved and cultured in high-glucose (HG, 4.5 g/L) or low-glucose (LG, 1.0 g/L) conditions. Cell characteristics and functions were investigated in vitro. Moreover, we applied diabetic murine ASCs cultured in HG or LG condition to a wound healing model in diabetic mice to compare their healing capabilities in vivo. Human ASCs exhibited decreased cell proliferation and migration with enhanced senescence when cultured in HG condition in vitro. Similar findings were noted in ASCs derived from diabetic mice. The inferior cellular functions could be partially recovered when they were cultured in LG condition. In the animal study, wounds healed faster when treated with HG or LG-cultured diabetic ASCs relative to the control group. Moreover, higher collagen density, more angiogenesis and cellular retention of applied ASCs were found in wound tissues treated with diabetic ASCs cultured in LG condition. In line with the literature, our study showed that a diabetic milieu exerts an adverse effect on ASCs. Adopting LG culture condition is a simple and effective approach to enhance the wound healing capabilities of diabetic ASCs, which is valuable for the clinical application of autologous ASCs from diabetic patients.

overall_design: Human adipose-derived stem cells (hASCs) were extracted from two non-diabetic and two diabetic female donors for the scRNA-seq processing.

first: M

middle: H

last: Wang

first: N

middle: C

last: Cheng


title: EpiGe: A cytosine methyl-genotyping PCR-based machine-learning tool for rapid classification of medulloblastoma

city: Esplugues de Llobregat

first: Soledad

last: Gómez-González

state: Barcelona

address: Santa Rosa, 39-57, 4a planta

department: Oncology

country: Spain

institute: Hospital Sant Joan de Déu

summary: Molecular classification of medulloblastoma is critical for the correct treatment of this malignant paediatric brain tumour. The analysis of genome-wide DNA methylation patterns has profoundly improved diagnostic precision and classification of brain tumours. However, the implementation of DNA methylation microarrays in daily clinical practice can be time-consuming, costly and inaccessible for many centres worldwide. We aimed to develop a machine-learning decision support system for rapid and cost-effective prediction of medulloblastoma methylation class directly from quantitative PCR data.

overall_design: Bisulphite converted DNA from 74 samples was hybridized to the Illumina InfiniumMethylation Epic array

first: Cinzia

last: Lavarino


title: A Cytotoxic T Cell Inspired Oncolytic Nanosystem Promotes Lytic Cell Death by Lipid Peroxidation And Elicits Antitumor Immune Responses

city: Wenzhou

first: hao

last: yin

address: Chashan Higher Education Park, Wenzhou, Zhejiang Province, China

institute: Wenzhou Medical University

summary: Lytic cell death, such as pyroptosis, can trigger antitumour immune response. However, cancerous cells avoid lytic cell death by various escape mechanisms acquired through evolution. Moreover, persistent uncontrolled lytic cell death may inversely cause hyperactive immune response or T-cell exhaustion. Therefore, an oncolytic system capable of breaking through natural restrictions to dissolve cancer cells in a catalytic and controllable manner is needed. Here, we established a microscale cytotoxic T-cell-inspired oncolytic system (TIOs) by which the NIR light-generated reactive oxygen species could precisely rupture the plasma membrane of cancer cells by direct lipids peroxidation. Similar as cytotoxic T cells, TIOs present antigen-based cell recognition and catalytic cell-lysis ability; thus, the TIOs can trigger significant oncolysis and immune response in vivo. The TIOs exhibited exceptional tumour targeting and penetration without any inflammatory risk. We applied TIOs to antitumour therapies, which showed kinds of tumour models could be cleared efficiently with negligible injuries to major organs. Tumour regression was correlated with oncolysis-mediated inflammation and T-cell-based antitumor immune response. Owing to the tuneability of TIOs-mediated oncolysis, we further revealed that though the T-cell recruitment was comparable, the high-intense oncolysis induced acute inflammation in initial stage was crucial for potent antitumour immunity and immune memory effects, and low-intense oncolysis resulted in T-cell exhaustion and tumour progression. To the mice received low-intense oncolysis, although synergizing with anti-PD-1 therapies or STING activation rescued the immune dysfunction, STING activation released a more powerful boost to durative antitumour immunity by reshaping the stemness of CD8+ T cells. Our study provides new insights to design the oncolytic systems for antitumour immunity. Moreover, our application suggests that the intensity of initial inflammation plays a decisive role in maintaining oncolysis-induced antitumour immune function and STING activation holds promise for reversal of immune dysfunction due to T-cell exhaustion.

overall_design: FACS analysis of tumour-infiltrating lymphocytes and tumour-infiltrating lymphocytes isolated in tumour models was performed after staining with a PE-conjugated anti- mouse CD45 antibody (clone 30-F11, Biolegend). CD45+ immune cells were then enriched using a BD FACS Aria III flow cytometer. Cell viability was monitored in real time during the preparation of single CD45+ immune cell suspensions. Ten thousand cells (~600 single cells per microlitre) from each experimental group were barcoded and pooled using a 10x Genomics device. Samples were prepared according to the manufacturer's protocol and sequenced on an Illumina NextSeq sequencer. The Cell Ranger Analysis Pipeline (v.3.0.2) was used for sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of sequencing runs. For quality control of the single-cell RNA-sequencing process, cells with fewer than 300 genes detected and cells with mitochondrial-encoding gene transcript counts exceeding 15% of total transcript counts were removed from subsequent analyses. Genes detected in less than three cells in the entire dataset were also excluded, resulting in a preliminary expression matrix of 15603 cells. After obtaining the digital gene expression data matrix, dimensionality reduction, clustering and differential gene expression analysis were performed using Seurat (v.3.0.0.9000)

first: Zhigui

last: Zuo

first: Hao

last: Yin

first: Yu

last: Zhang


title: Cardiomyocyte-Restricted Expression of IL11 Causes Cardiac Fibrosis, Inflammation, and Dysfunction

status: Public on Aug 21 2023

first: Mark

last: Sweeney

address: Du Cane Road

department: London Institute of Medical Science

country: United Kingdom

institute: Imperial College London

summary: Background: Cardiac fibrosis is a common pathological process in heart disease and represents a therapeutic target. TGFβ is the canonical driver of cardiac fibrosis and was recently shown to be dependent on IL11 for its profibrotic effects in fibroblasts. In the opposite direction, recombinant human IL11 has been reported as anti-fibrotic and also anti-inflammatory in the mouse heart. Objectives: In this study, we determined the effects of IL11 expression in cardiomyocytes on cardiac pathobiology and function. Methods: We used the Cre-loxP system to generate a tamoxifen-inducible mouse with cardiomyocyte-restricted murine Il11 expression. Using protein assays, bulk RNA-sequencing and in vivo imaging we analysed the effects of IL11 on myocardial fibrosis, inflammation and cardiac function and challenge previous reports suggesting cardioprotective potential of IL11. Results: TGFβ stimulation of cardiomyocytes caused Il11 upregulation. As compared to wild-type controls, Il11 expressing hearts demonstrated severe cardiac fibrosis and inflammation that was associated with the upregulation of cytokines, chemokines, complement factors and increased inflammatory cells. IL11 expression also activated a programme of endothelial-to-mesenchymal transition and resulted in left ventricular dysfunction. Conclusion: Our data define species-matched IL11 as strongly profibrotic and proinflammatory when secreted from cardiomyocytes and further establish IL11 as a disease factor.

overall_design: We extracted RNA and performed RNA-sequencing on myocardial samples from male and female tamoxifen inducible cardiomyocyte specific Il11 expressing mice and compared this to control samples  1, 3 and 6 weeks after induction of Il11 expression.

first: Stuart

middle: A

last: Cook

first: Michael

last: Lee


title: VDR is an essential regulatory factor in the stage of hair follicle regression through the progression of cell death

city: Tokushima

first: Yudai

last: Joko

address: 3-18-15 Kuramoto-cho

country: Japan

institute: Tokushima University

summary: The Vitamin D receptor (VDR) is essential for hair follicle homeostasis as its deficiency leads to hair loss. However, the mechanism behind this relationship is unknown. Our research shows that in VDR knockout mice, the hair cycle is halted during the catagen stage, preceding alopecia. Additionally, in VDR knockout hair follicles, epithelial strands that normally regress during the catagen phase persist as "surviving epithelial strands." Analysis using single cell RNA sequencing suggests these surviving epithelial strands are formed by cells in the lower part of the hair follicle. These findings emphasize the importance of the regression phase in hair follicle regeneration and establish the VDR as a regulator of the catagen stage.

overall_design: Epidermis cells of the Vdr flox/flox mice and Vdr flox/flox; Krt14cre mice were isolated by  0.25% trypsin and analyzed using scRNAseq.

first: Shun

last: Sawatsubashi


title: Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [single-cell RNA-seq]

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Lymphoid tissue inducer (LTi) cells, known to be critical for the generation of secondary lymphoid tissues, are the founding member of innate lymphoid cells (ILCs). However, how the development and functions of this ILC subset are regulated is far from clear. In this study, we discovered a striking role of the transcription factor TCF-1 in the development of Peyer’s patches (PPs) but not lymph nodes (LNs). Despite TCF-1 is critical for ILC development at multiple stages, we found normal development of LTi cells in TCF-1-deficient mice indicating that dysfunction of these LTi cells led to the deficiency in Peyer’s patches formation. Through bulk and single cell RNA-Seq, we found differential gene expression patterns between LTi cells from the PPs, LNs and the small intestine laminal propria (siLP), and an important role of TCF-1 in regulating the expression of lymphotoxin (LT) specifically in PP LTi cells. Mechanistically, TCF-1 may regulate Lta indirectly through promoting the expression of GATA3, a critical transcription factor in regulating LTi functions. LTβR agonist injection during the embryonic stage partially rescued the formation of PPs in the TCF-1-deficient mice. Thus, a dose effect of LT expression in LTi cells regulated by TCF-1 contributes to a differential regulation of organogenesis of distinct secondary lymphoid structures.

overall_design: ILC inducers from bone marrow of WT and Tcf7flox;Vav-Cre mice were collected for Single-cell RNA-Seq.

first: Mingzhu

last: Zheng

first: Chen

last: Yao

first: Gang

last: Ren

first: Kairui

last: Mao

first: Xi

last: Chen

first: Difeng

last: Fang

first: Dan

first: Chao

last: Zhong

first: Hyunwoo

last: Chung

first: Xiaoxiao

last: Lu

first: Nikki

last: Cannon

first: Lei

first: Mingxu

first: Bhandoola

last: Avinash

first: Keji

last: Zhao

first: John

middle: J

last: O'Shea

first: Jinfang

last: Zhu


title: Identification and subsequent validation of transcriptomic signature associated with metabolic status in endometrial cancer

city: Bialystok

first: Iwona

last: Sidorkiewicz

address: Sklodowska-Curie Street 24a

department: Clinical Research Centre

country: Poland

institute: Medical University of Bialystok

summary:
Metabolic status was successfully evaluated through Nanostring expression profiling of a total of 768 genes in 87 endometrial cancer (EC) cases.
The study revealed that 11 genes were deregulated in EC samples. Validation by qRT-PCR confirmed our findings. The results suggest that metabolic profiling can potentially be used as predictive biomarkers of EC.

overall_design:
In the study presented here, a consecutively operated, well-defined cohort of 87 EC cases was used to acquire expression profiles of a total of 768 unique metabolic-related genes.

** The submitter noted that the normalized data for the following samples are identical due to low expression of miRNA panel:
GSM5858294 Patient_229_FFPE
GSM5858297 Patient_250_FFPE

first: Maciej

last: Jóźwik

first: Adam

last: Krętowski

first: Magdalena

last: Niemira


title: Nanostring of 3D hiPSC-derived neurons infected with rabies virus-wild type-thai strain (WT-TH) and rabies virus-challenge virus standard 11 (CVS-11) against uninfected controls at 8 and 24 hours post-infection

city: Pathum Thani

first: Papon

last: Muangsanit

state: Pathum Thani

address: 113 Thailand Science Park Phahonyothin Road Khlong Nueng, Khlong Luang, BIOTEC building, Room 345

department: BIOTEC

country: Thailand

institute: NSTDA

summary: This experiment is part of the project that primarily aims to utilize 3D hydrogel-based hiPSC-derived neuronal model to study rabies virus infection in the central nervous system. Having established the optimal 3D neuronal model, we then investigated the growth kinetics of two strains of rabies virus (TH and CVS-11) and comparatively analyzed the 2D and 3D culture models. We performed a gene expression analysis using NanoString to determine whether changes in gene expression could explain the differences in virus growth kinetics of two strains of rabies virus observed between the 2D and 3D neuronal culture models. Gene expression analysis of the neuropathological pathway observed during rabies virus infection demonstrated a vast number of differentially expressed genes in the 3D model as compared to the 2D model.

overall_design: In this study, 36 samples in total were analyzed including the 2D and 3D samples infected with two strains of rabies virus (WT-TH and CVS-11) over 0, 8, and 24 hours post-infection with three replicates. These also include mock-infected controls at each time point.

first: Thanathom

last: Chailangkarn

first: Nathiphat

last: Tanwattana

first: Ratjika

last: Wongwanakul

first: Porntippa

last: Lekcharoensuk

first: Challika

last: Kaewborisuth


title: Activation of AKT induces EZH2-mediated β-catenin trimethylation in colorectal cancer.

city: Bloomington

first: Ahmed

last: Ghobashi

state: IN

institute: Indiana University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues

first: Gangqing

last: Hu


title: Effect of colonic epithelial knockout of tumor necrosis factor receptor 2 (TNFR2) in dextran sulfate sodium (DSS)-induced colitis

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

summary: Colonic epithelial repair is a key determinant of health. After injury, repair initiates through phenotypic reprogramming of wounded epithelium to a regenerative state permissive for the activation of alternative stem cell populations and healing. Although cytokine signals such as interferons may help induce regenerative reprogramming, the signals that modify this state as the wound resolves remain largely unknown. Here we examined whether cytokine signaling mediated by tumor necrosis factor receptor 2 (TNFR2) influenced the wound repair process. We examined mice with targeted deletion of the Tnfrsf1b (TNFR2) gene in intestinal/colonic epithelium (Vil1::Cre;Tnfr2-f/f) and compared their transcriptional profiles to control (Tnfr2-f/f) mice. We sorted EpCAM+ (epithelial) cells from Vil1::Cre;Tnfr2-f/f and control DSS-treated mice and performed bulk RNA-Seq. Comparison of transcript expression profile before and after DSS-induced colitis in control (Tnfr2-f/f) mice revealed upregulation of pathways associated with metabolic regulation, ribosomal function, oxidative stress, TNF signaling, and focal adhesions after DSS treatment. Pathway enrichment analysis demonstrated elevated regenerative (“fetal”) intestinal signaling, reduced inflammation, and increased proliferative signaling in Vil1::Cre;Tnfr2-f/f colonic epithelium after DSS treatment. The knockout epithelium also showed reduced expression of markers of differentiated colonic epithelium and elevated expression of progenitor cell signaling. Thus, the transcriptional data were consistent with increased regenerative signaling in TNFR2-knockout epithelium, suggesting that TNFR2 has a role in restraining the relatively undifferentiated regenerative state.

overall_design: Comparison of distal colonic epithelial gene expression across conditions of health and DSS-induced colitis, in wildtype mice and in mice with epithelial-targeted knockout of TNFR2

first: Zohreh

last: Sharifkhodaei

middle: Y

first: D

middle: B

last: Polk


title: Activation of AKT induces EZH2-mediated β-catenin trimethylation in colorectal cancer. [ChIP-Seq]

summary: The lysine methyltransferase EZH2 is overexpressed in colorectal cancer (CRC) and has been found to be positively and negatively correlated with CRC patient survival depending on the study suggesting that EZH2 has a complex role in CRC. Here, we demonstrate that AKT-mediated EZH2 S21 phosphorylation induced EZH2 to trimethylate β-catenin at K49, which increased β-catenin’s binding to the chromatin. Additionally, EZH2-mediated β-catenin trimethylation induced β-catenin’s interaction with TCF1 and RNA polymerase II and resulted in a dramatic gain in genomic regions with β-catenin occupancy. Interestingly, EZH2 catalytic inhibition decreased stemness but increased migratory phenotypes of CRC cells with active AKT. Overall, we demonstrated that EZH2 modulates AKT-induced changes in gene expression through the AKT/EZH2/β-catenin axis in CRC. Our results suggest that EZH2 inhibitors have tumor-inhibiting and promoting effects in CRC as they inhibit EZH2-mediated methylation of histone and non-histone targets like β-catenin.

overall_design: Testing if β-catenin binding to the chromatin is regulated by EZH2-mediated β-catenin methylation. ChIP-seq was performed using FLAG antibody to determine β-catenin's enrichment on the chromatin in EV and PTEN knockdown SW480 cells expressing equal levels of FLAG-β-catenin untreated or treated with EZH2 inhibitor. SW480 cells not transfected with FLAG-expressing plasmid were used as a negative control.

first: Heather

last: O'Hagan


title: Renal pharmacokinetic adaptation to cholestasis leads to increased accumulation of nephrotoxic drugs due to ABCC6 downregulation in mice

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: In hepatic dysfunction, renal pharmacokinetic adaptation can be observed, although information on the changes in drug exposure and the interorgan regulation of membrane transporters in kidney in liver diseases is limited. This study aimed to clarify the effects of renal exposure to nephrotoxic drugs during cholestasis induced by bile duct ligation (BDL). Among the 11 nephrotoxic drugs examined, the tissue accumulation of imatinib and cisplatin in kidney slices obtained from mice 2 weeks after BDL operation was higher than that in sham-operated mice. The uptake of imatinib in the kidney slices of BDL mice was slightly higher, whereas its efflux from the slices was largely decreased compared to that in sham-operated mice. Proteomic analysis revealed a reduction in renal expression of the efflux transporter multidrug resistance-associated protein 6 (Mrp6/Abcc6) in BDL mice, and both imatinib and cisplatin were identified as Mrp6 substrates. Survival probability after cisplatin administration was reduced in BDL mice. In conclusion, the present study demonstrated that BDL-induced cholestasis leads to the downregulation of the renal basolateral efflux transporter Mrp6, resulting in drug accumulation in renal cells and promoting drug-induced renal injury.

overall_design: Comparison between bile duct ligation (BDL) and sham operations. There are two biological replicates for each condition.

first: Hiroshi

last: Arakawa

first: Takumi

last: Kawanishi

first: Dai

last: Shengyu

last: Nishiuchi

first: Makiko

last: Meguro-Horike

first: Masahiro

last: Sugimoto

first: Yukio

last: Kato


title: 10X genomics scRNA-seq of testicular THY1+ cells in adult C57 mice

first: Cheng

last: Jin

state: State...

address: dongdansantiao num5

institute: Chinese Academy of Medical Sciences

overall_design: We performed scRNA-seq on the whole testicular Thy1+ spermatogonia in adult C57 mice using the 10x Genomics Chromium platform.

first: Zhipeng

last: Wang


title: CUT&Tag_Foxc2 for Foxc2+ cells from adult mice testes


title: Self-formation of concentric zones of telencephalic and ocular tissues and directional retinal ganglion cell axons

city: Bronx

first: Wei

state: NEW YORK

address: 1300 Morris Park Avenue, Ullmann 117

institute: Albert Einstein College of Medicine

summary: Telencephalon, optic stalk, and optic-cup in vertebrates are originated from adjacent fields in the anterior neuroplate. How these tissues develop coordinately along the midline-periphery axis is unclear. Here, we report the self-formation of a human telencephalon-eye organoid comprising concentric zones of FOXG1+ telencephalon, PAX2+ optic disc/stalk, VSX2+ neuroretina, and PAX6+ tissues along the center-periphery axis. FGFs and BMPs were expressed starting at early stages and subsequently exhibited concentric gradients, suggesting their involvement in tissue patterning and coordinated cell differentiation. Early differentiated retinal ganglion cells (RGC) grew axons towards and along a path defined by an adjacent PAX2+ cell population. Lens cells were also found. Single-cell RNA sequencing confirmed telencephalic and ocular cell identities, located PAX2+ cell populations mimicking the optic disc/stalk, and identified RGC-specific cell surface protein CNTN2. RGCs were isolated in one step via CNTN2 in a native condition, facilitating therapeutic development for RGC-related retinal diseases such as glaucoma.

overall_design: CONCEPT telencephalon-eye organoids at day 24 from one culture well were dissociated into single cells using activated Papain (Worthington Biochemical Corporation LS003126) following manufacturer’s instructions. Then, 10,000 dissociated cells were captured using Chromium Controller (10x Genomics), followed by library preparation following manufacturer’s instructions. The library was sequenced in one lane of Illumina HiSeq (2x150 bp) in GeneWIZ company.

first: Rupendra

last: Shrestha

first: Albert

last: Lowe

first: Xusheng

last: Zhang


title: Activation of AKT induces EZH2-mediated β-catenin trimethylation in colorectal cancer. [RNA-Seq]

first: Ahmed

last: Ghobashi

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SW480 cells and its PTEN KD and EV KD with and without EZH2 inhibitor.


title: Sinus venosus adaptation models prolonged cardiovascular disease and reveals insights into evolutionary transitions of the vertebrate heart

status: Public on Aug 19 2023

city: Cincinnati

first: Joshua

last: Waxman

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology Division

institute: Cincinnati Children's Hospital Medical Center

summary: How two-chambered hearts in basal vertebrates have evolved from single-chamber hearts found in ancestral chordates remains unclear. Here, we show that the teleost sinus venosus (SV) is a chamber-like vessel comprised of an outer layer of smooth muscle cells. We find that in adult zebrafish nr2f1a mutants, which lack atria, the SV comes to physically resemble the thicker bulbus arteriosus (BA) at the arterial pole of the heart through an adaptive, hypertensive response involving smooth muscle proliferation due to aberrant hemodynamic flow. Single cell transcriptomics show that smooth muscle and endothelial cell populations within the adapting SV also take on arterial signatures. Bulk transcriptomics of the blood sinuses flanking the tunicate heart reinforce a model of greater equivalency in ancestral chordate BA and SV precursors. Our data simultaneously reveal that secondary complications from congenital heart defects can develop in adult zebrafish similar to those in humans and that the foundation of equivalency between flanking auxiliary vessels may remain latent within basal vertebrate hearts.

overall_design: RNA-seq of Ciona robusta heart and blood sinuses

first: Jacob

middle: T

last: Gafranek

first: Enrico

last: D'Aniello

first: Padmapriyadarshini

last: Ravisankar

first: Kairavee

last: Thakkar

first: Ronald

last: Vagnozzi

first: Hee-Woong

last: Lim

first: Nathan

last: Salomonis

middle: S


title: Effects of TNFR2 deletion on the development of mouse colonic epithelial organoids

first: Cambrian

last: Liu

summary: The early phase of colonic epithelial wound healing involves cellular reprogramming to a fetal-like state and reorganization of discrete crypt units into merged wound channels. After re-epithelialization is complete, a latter phase restoring homeostatic signaling and crypt patterning must occur. However, the signals that mediate this regenerative transition are unknown. Here we show that injury-associated upregulation of a cytokine receptor, tumor necrosis factor (TNF) receptor 2 (R2, TNFR2, Tnfrsf1b), suppresses fetal-like signaling and promotes crypt production. We used tissue clearing and whole-mount imaging, RNA-Seq, and organoid cultures to characterize mice with a colonic epithelial-specific deletion of TNFR2. These mice exhibited increased crypt size and reduced fission in adult homeostasis and after colitis, abnormal persistence of fetal-like molecular markers in organoids and after injury, reduced terminal differentiation, and increased proliferative potential. These results demonstrate how epithelial cells can adapt to inflammatory cues to regulate wound healing morphogenesis and signaling.

overall_design: A total of 20 samples were analyzed. Each sample is composed of total RNA isolated from wildtype or Tnfr2-/- mouse colonic organoids grown for either 1, 2, 3, 5, 7 days after passage. Two biological replicates (i.e., mice) per genotype were studied.

first: Zohreh

last: Sharifkhodaei

first: David

last: Polk


overall_design: RNA-seq of zebrafish heart chambers


title: HDCA binding proteins

status: Public on Aug 17 2023

city: Shanghai

first: Jing

last: Zhong

address: 1200,Cailun Road, Shanghai

institute: Shanghai University of Traditional Chinese Medicine

summary: To elucidate the molecular mechanism behind the anti-NAFLD effect of HDCA, we screened for potential HDCA binding proteins using biotin-labeled HDCA and HuProt human proteome microarray.

overall_design: Biotin-HDCA was incubated with human proteome microarray, biotin was as a control.

first: Houkai

last: Li


sample_organism:
Danio rerio
Ciona robusta

platform_organism:
Danio rerio
Ciona robusta


title: Bojungikgi-tang improves skin barrier function and immune response in atopic dermatitis mice fed a low aryl hydrocarbon receptor ligand diet

city: Daejeon

first: You Mee

last: Ahn

address: Yuseong-daero, Yuseong-gu

country: South Korea

institute: KOREA INSTITUTE OF ORIENTAL MEDICINE

summary: To identify the effects of BJIKT on skin homoestasis via skin barrier, AhR target genes and the immune response profile in AD mice fed a low-Ahr ligand diet.

overall_design:
The low Ahr ligand diet (ENVIGO [#TD130959]) group is provided with Ahr ligand free diet paper beddings (#SSP0001, ALPHA-dri, Shepherd Specialty Papers, Watertown, TN). A low Ahr ligand diet was carried out for 12 weeks. After 2 weeks of a low Ahr ligand diet, atopic dermatitis (AD) was induced with 2,4-dinitrochlorobenzene (DNCB), and Bojungikgi-tang (BJIKT, 1g/kg/day in water) was administered by oral gavage daily at the same time. To induce AD, dorsal skin was applied twice a week with 1% DNCB mixed in acetone/olive oil (3:1).
Comparative gene expression profiling analysis of Skin RNA-seq data obtained from C57BL/6 mice in Control group, Low Ahr ligand diet group, the AD mice fed a Low Ahr ligand diet, BJIKT treated  AD mice fed a Low Ahr ligand diet

first: Jeeyoun

last: Jung


title: O304 ameliorates hyperglycemia in mice by dually promoting muscle glucose effectiveness and preserving β-cell function

city: Umeå

first: Stefan

last: Norlin

address: Trastvägen 4F

department: UCMM

country: Sweden

institute: Umeå University

summary: In Type 2 diabetes, insulin resistance elicits compensatory insulin hypersecretion, provoking β-cell stress and eventually compensatory failure. In insulin deficient STZ treated diabetic mice the dual AMPK activator and mitochondrial uncoupler O304  stimulates insulin independent glucose uptake and utilization in skeletal muscle and heart in vivo, thus improving  glucose homeostasis. In obese In type 2 diabetic db/db mice, O304 additionally  preserves β-cell function by preventing decline in insulin secretion, β-cell mass, and pancreatic insulin content.  It remains however unclear whether these  effects of  O304 is mediated by a direct protective effect on β-cells, or indirectly by improving  glucose homeostasis thereby inducing β-cell rest. To investigate the ability of O304 to directly mitigate the detrimental effect of hyperglycemia on β-cell function, we exposed isolated islets ex vivo to normoglycemic and hyperglycemic comdition in the abscence or prescene of O304.

overall_design: Islets of langerhans were isolated from the pancreas of wildtype mice and exposed to normoglycemic (11mM Glucose) or hyperglycemic (22mM Glucose) conditions with or without the addition of 5uM O304 for 48h (i.e 4 conditions). Five (5) independent replicates were analysed for each experimental condition (i.e total 20 samples)


title: Distinctive Interactomes of RNA polymerase II phosphorylation during different stages of transcription

city: Austin

first: Yan

middle: Jessie

last: Zhang

address: 100 E. 24th Street

institute: University of Texas-Austin

summary: We have discovered distinctive protein interactomes for Ser2 and Ser5 phosphorylation of the C-terminal domain (CTD) of RNA Pol II. Calcium Homeostasis Endoplasmic reticulum (CHERP) was identified in our pulldown to directly interact with Ser2 phosphomarks on the CTD of Pol II. As Pol II is a chromatin-associated protein, we sought to identify genomic regions that CHERP, a Pol II binding protein, occupy through ChIP-seq analysis.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HA-tagged CHERP in WT HEK293 cells and for HA-tagged CHERP in HEK293 cells that have decreased levels of Ser2 phosphorylation on the C-terminal domain of Pol II.

first: Rosamaria

last: Moreno


title: Transcriptome-wide Mapping of Internal N7-Methylguanosine Methylome in human oral squamous cell carcinoma

city: Weifang

first: Dongyuan

last: Sun

state: Shandong

address: 7166,BaoTong West Street

institute: Weifang Medical University

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Three pairs of human OSCC tissues and normal tissues were collected. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was used to identify m7G sites on Transcriptome (including lncRNAs, mRNAs and circRNAs) and differences in m7G distribution between OSCC tissues and normal tissues.

overall_design: Transcriptome-m7G modification in human oral squamous cell carcinoma (OSCC) was comprehensively analyzed.

first: Yingying

last: Jiang


title: NEUROD1 reinforces endocrine cell fate acquisition in pancreatic development

city: Vestec by Prague

first: Gabriela

last: Pavlínková

address: Průmyslová 595

department: Laboratory of Molecular Pathogenetics

country: Czech Republic

institute: Institute of Biotechnology, CAS, v.v.i

summary: NEUROD1 is a transcription factor that helps maintain a mature phenotype of pancreatic β cells. Disruption of Neurod1 during pancreatic development causes severe neonatal diabetes; however, the exact role of NEUROD1 in the differentiation programs of endocrine cells is unknown. Here, we report a crucial role of the NEUROD1 regulatory network in endocrine lineage commitment and differentiation. Mechanistically, transcriptome and chromatin landscape analyses demonstrate that Neurod1 inactivation triggers a downregulation of endocrine differentiation transcription factors and upregulation of non-endocrine genes within the Neurod1-deficient endocrine cell population, disturbing endocrine identity acquisition. Neurod1 deficiency altered the H3K27me3 histone modification pattern in promoter regions of differentially expressed genes, which resulted in gene regulatory network changes in the differentiation pathway of endocrine cells, compromising endocrine cell potential, differentiation, and functional properties.

overall_design: Mouse pancreatic islets were isolated (and pooled) from four mice per each genotype (control and Neurod1CKO) by perfusion of the common bile duct with Collagenase. Digestion of islets to single cell was performed with trypsin supplemented with Actinomycin D. Single-cell suspension was used for library preparation:743 Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10 × Genomics, Pleasanton, CA) was sed to prepare the sequencing libraries, according to the manufacturer’s protocols.

first: Romana

last: Bohuslavova

first: Pavel

last: Abaffy

first: Ondrej

last: Smolik

first: Valeria

last: Fabriciova

first: Lukas

last: Valihrach

first: Sarka

last: Benesova

first: Daniel

last: Zucha

first: Zuzana

last: Berkova

first: Frantisek

last: Saudek

last: Pavlinkova


first: Svetlana

last: Panina

state: TX

address: 101 East 21st St.

department: Molecular Biosciences

institute: The University of Texas at Austin

summary:
To investigate the whole-transcriptome effects of Calcium Homeostasis Endoplasmic Reticulum Protein (CHERP)/SCAF6 which specifically binds to the Ser2 of C-terminal domain of RNA Polymerase II, we established HEK293 cell line in which SCAF6 gene was knocked down by shRNA.
We then performed gene expression and alternative splicing profiling using data obtained from RNA-seq of 2 cell lines (HEK293 Control vs HEK293 SCAF6 KD).

overall_design: Comparative gene expression and alternative splicing analysis of RNA-seq data for HEK293 cells and its SCAF6 knockdown (HEK293 shSCAF6), two biological replicates per cell line.

first: Kyle

last: Juetten

first: Jamie

middle: P

last: Butalewicz

first: Brendan

middle: M

last: Floyd

first: Mukesh

middle: K

last: Ramani

first: Edward

last: Marcotte

first: Jennifer

last: Brodbelt

first: Jessie


title: Transcriptomic signature related to welfare of horses housed in individual boxes

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

institute: INRAE

summary: In this new study, we analyzed the blood transcriptome of horses housed individually that were first examined for their behavior, health and microbiota. We performed differential and regression analyzes of gene expression to unveil the molecular pathways related to the behavioural changes associated with housing horses in individual boxes. This study shows that aggressiveness towards humans and stereotypies are behavioural indicators that covary with physiological alterations.

overall_design: The study population consisted of 45 sport horses. RNA was extracted from blood and gene expression profiles were performed using Agilent microarrays (1 sample per animal).

last: Foury

first: Nuria

last: Mach

first: Alice

last: Ruet

first: Léa

last: Lansade

first: Marie-Pierre

last: Moisan


title: NEUROD1 is critical for the initial cell identity determination and differentiation of the endocrine progenitors in the pancreas [RNA-seq]

city: Vestec

first: Šárka

last: Benešová

address: Prumyslova 595

department: Institute of Biotechnology

institute: Czech Academy of Science

summary: While diabetes incidence is gradually rising worldwide, novel therapeutical approaches are required in the search for a replacement of dysfunctional endocrine tissue, especially beta-cells. A promising potential lies in direct cellular reprogramming of similar cell types sharing common multipotent progenitors. With the knowledge of molecular mechanisms determining the endocrine cell fate commitment and endocrine lineage differentiation, other endocrine cells contained within the islets of Langerhans or closely related cells could be trans- or dedifferentiated either in situ or in vitro with their subsequent transplantation into the patient.  NEUROD1 is a transcription factor situated on the base of the gene regulatory network of the developing endocrine precursors, directly downstream of endocrine lineage master regulator NEUROG3. While NEUROG3 initiates a rapid cascade of chromatin reorganization in numerous bivalent promoters resulting in spatiotemporal gene expression leading to differentiation of all endocrine cell subtypes from pancreatic multipotent progenitors, the role of NEUROD1 has yet to be clarified. Notably, NEUROD1 can induce neuronal program through pioneering and chromatin remodelling in other cell types.  In this study, we performed advanced molecular and phenotypic analyses in early endocrine-specific Neurod1-deficient mouse model, including RNA and CUT&Tag sequencing and lightsheet microscopy, to gain insight into the NEUROD1-regulated transcription network driving endocrine lineage cell fate commitment. Besides a postnatal diabetic phenotype, disrupted endocrine differentiation and associated altered islet architecture, we observed an apparent elevation in the non-endocrine gene expression pattern and uncovered alterations in the epigenetic landscape of characteristic genes, specifically in the H3K4me3 and H3K27me3 distribution. Therefore, we provide evidence that NEUROD1 is critical player responsible for the establishment of the endocrine cell identity, which further affects endocrine development and may serve as a potent proendocrine reprogramming driver.

overall_design: 8 samples of 100 FACS-sorted  tdTomato+ endocrine cells were analyzed (4 control samples and 4 mutant samples).

first: Ondrej

last: Smolik

first: Romana

last: Bohuslavova

first: Sarka

last: Benesova

first: Lukas

last: Valihrach

first: Gabriela


title: A R-loop sensing pathway mediates the relocation of transcribed genes to nuclear pore complexes

city: Paris

first: Benoit

last: Palancade

address: 15 rue Helene Brion

institute: Institut Jacques Monod, CNRS

summary: Nuclear organization has emerged as a critical player in the control of genomic processes, including transcription.  In this context, nuclear pore complexes (NPCs) have increasingly recognized interactions with the genome, as exemplified in yeast, where they bind inducible genes and damaged genomic regions, positively impacting their fate. To investigate the pathways fostering chromatin association with NPCs, we have combined genome-wide approaches with live imaging of individually-tagged model loci. Strikingly, ChIP-seq analyses of NPC-bound genes revealed a strong correlation between pore association and the propensity to accumulate co-transcriptional R-loops, which are genotoxic structures forming through hybridization of nascent RNAs with their DNA templates. Manipulating cis- or trans-acting regulators of hybrid formation further demonstrated that R-loop accumulation per se, rather than high transcription or R-loop-associated genetic instability, is the primary trigger for relocation to NPCs. Mechanistically, R-loop-dependent repositioning involves the recognition of displaced ssDNA moieties by the ssDNA-binding protein RPA, and SUMO-dependent interactions between RPA and NPC-associated factors. Preventing R-loop-dependent NPC localization leads to lethality, while permanent NPC tethering of a model hybrid-prone sequence attenuates R-loop-dependent genetic instability. Remarkably, this novel relocation pathway involves similar molecular factors as those required for the association of stalled replication forks or eroded telomeres with NPCs, suggesting the existence of convergent mechanisms for sensing transcriptional and  genotoxic stresses.

overall_design: NPC-bound genes have been assessed in wild-type and R-loop-accumulating mutant (mft1∆) cells by ChIP-seq using a tagged nucleoporin (Nic96-myc) as a bait. Untagged strains were used as controls.

first: Arianna

last: Penzo

first: Marion

last: Dubarry

first: Clémentine

last: Brocas

first: Myriam

last: Zheng

first: Raphaël

last: Mangione

first: Mathieu

last: Rougemaille

first: Coralie

last: Goncalves

first: Ophélie

last: Lautier

first: Domenico

last: Libri

first: Marie-Noëlle

last: Simon

first: Vincent

last: Géli

first: Karine

last: Dubrana


title: Effects of Transcription factor IIB (TFIIB)‑related factor 2 (BRF2) on mRNA expression in hepatocellular carcinoma

status: Public on Aug 16 2023

city: Jinan

first: guangxiao

last: meng

address: 107 West Wen Hua Road, Jinan, 250012, China.

institute: Qilu Hospital of Shandong University

summary: To reveal the potential key molecular mechanisms underlying the effect of BRF2 on the phenotype of HCC cells, we performed RNA-seq on Huh7 cells after BRF2 knockdown.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Huh7-NC (infected with NC-Si) and Huh7-Si (infected with siRNA-BRF2) cells

first: Guangzhen

last: Li

first: Guangxiao

last: Meng

first: Tao


title: Gene expression profile at single cell level of mouse cortical brain cells

status: Public on Aug 20 2023

city: Boston

first: Kashish

last: Chetal

state: MA

address: 55 Fruit St

department: Molecular biology

institute: MGH

summary: We used single cell RNA sequencing (scRNA-seq) to compare cortical brain cells from mast cell wild-type with mast cell knockout mice.

overall_design: Total cotical brain cells of 8-month-old 5XFAD.Cpa3+/+ and 5XFAD.Cpa3Cre/+ mice were isolated by enzymatic digestion and analyzed using scRNA-Seq.

first: Chih-Chung

last: Lin

first: Ruslan

middle: I

last: Sadreyev

first: Rudolph

last: Tanzi


title: 10X genomics single-cell RNA sequencing of the testicular Thy1+ spermatogonia in Foxc2f/+ and Foxc2f/-;Ddx4-cre mice

city: Beijing

first: Cheng

last: Jin

overall_design: We performed scRNA-seq on the whole testicular Thy1+ spermatogonia in Foxc2f/+ and Foxc2f/-;Ddx4-cre mice using the 10x Genomics Chromium platform.

first: Zhipeng

last: Wang


title: C9orf72-ALS human iPSC microglia are pro-inflammatory and toxic to co-cultured motor neurons via MMP9

city: Oxford

first: Kevin

last: Talbot

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

institute: University of Oxford

summary: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive motor neuron loss, with additional pathophysiological involvement of non-neuronal cells such as microglia. The commonest ALS-associated genetic variant is a hexanucleotide repeat expansion (HRE) mutation in C9orf72. Here, we study its consequences for microglial function using human iPSC-derived microglia. By RNA-sequencing, we identify enrichment of pathways associated with immune cell activation and cyto-/chemokines in C9orf72 HRE mutant microglia versus healthy controls, most prominently after LPS priming. Specifically, LPS-primed C9orf72 HRE mutant microglia show consistently increased expression and release of matrix metalloproteinase-9 (MMP9). LPS-primed C9orf72 HRE mutant microglia are toxic to co-cultured healthy motor neurons, which is ameliorated by concomitant application of an MMP9 inhibitor. Finally, we identify release of dipeptidyl peptidase-4 (DPP4) as a marker for MMP9-dependent microglial dysregulation in co-culture. These results demonstrate cellular dysfunction of C9orf72 HRE mutant microglia, and a non-cell-autonomous role in driving C9orf72-ALS pathophysiology in motor neurons through MMP9 signaling.

overall_design: We sequenced a total of 36 samples, with 2 sequence runs per sample. The samples included 3 technical replicates (differentiations) each for iPSC microglia generated from 3 different healthy control lines and 3 different C9ORF72-ALS patients. For all lines, cells without stimulation ('M0') and with LPS stimulation (100 ng/mL, 48 hours, 'M1') were included. For differential expression analysis, the 3 technical replicates for each line were either merged ("merged" supplementary files) or analysed separately.

first: Björn

middle: F

last: Vahsen

first: Jakub

last: Scaber


title: MLL-AF4 cooperates with PAF1 and FACT to drive high density enhancer interactions in leukemia

city: London

first: Nick

last: Crump

address: Du Cane Road

department: Dept of Immunology and Inflammation

institute: Imperial College London

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

overall_design: Refer to individual Series


title: Age-dependent transcriptome characterization of the rat supraoptic nucleus  (RNA-Seq)

city: Grand Forks

first: John

middle: Andrew

last: Watt

state: North Dakota

address: 504 Nth Hameline St

department: Biomedical Sciences

institute: University of North Dakota

summary:
Our prior studies indicat age-dependent contralateral axonal sprouting following unilateral lesion of magnocellular neurons in the supraoptic nucleus.
To understand the changes in the transcriptome that underlies this phenomenon, we performed RNA-seq and functional analysis of the rat supraoptic nucleus to determine changes in gene expression with age.

overall_design:
Comparative gene expression of the supraoptic nucleus was performed on two age groups, 35 days and 125 days old. Each group consisted of 4 biological replicates.
For each biological replicate, the supraoptic nuclei of 4 rats were pooled.

first: Derick

last: Thompson

first: Abiodun

last: Odufuwa

first: Catherine

last: Brissette


title: Age-dependent DNA methylation characterization of the rat supraoptic nucleus (Methylation)

summary:
Our prior studies indicat age-dependent contralateral axonal sprouting following unilateral lesion of magnocellular neurons in the supraoptic nucleus.
We performed Oxford Nanopore sequencing of the rat supraoptic nucleus to determine changes in DNA methylation with age.

overall_design:
Comparative analysis of DNA CpG methylation was performed on two age groups, 35 days and 125 days old. Each group consisted of 3 biological replicates.
For each biological replicate, the supraoptic nuclei of 4 rats were pooled.


title: Trained immunity of alveolar macrophages promotes injury resolution by enhancing KLF4-MERTK-mediated efferocytosis.

city: Chicago

first: Jalees

last: Rehman

address: 909 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC


title: Trained immunity of alveolar macrophages promotes injury resolution by enhancing KLF4-MERTK-mediated efferocytosis [RNA-seq]

summary: Recent studies suggest that training of innate immune cells such as tissue-resident macrophages by repeated noxious stimuli can heighten host defense responses. However, it remains unclear whether trained immunity of tissue-resident macrophages also comprises enhanced injury resolution capacity to counterbalance the heightened inflammatory responses. Here, we studied lung-resident alveolar macrophages (AMs) pre-challenged with either the bacterial endotoxin or with Pseudomonas aeruginosa and observed that these trained AMs showed greater resilience to pathogen-induced cell death. Transcriptomic analysis, and functional assays showed greater capacity of trained AMs to efferocytosis of cellular- debris, and facilitate injury resolution. Single-cell high-dimensional mass-cytometry analysis and lineage tracing demonstrated that training induces an expansion of a MERTKhiMarcohiCD163+F4/80low lung-resident AMs subset with pro-resolving phenotypes. Training epigenetically reprogrammed AMs to express a higher level of the transcription factor KLF4 which in turn upregulates the efferocytosis receptor MERTK. Adoptive transfer of these trained AMs restricted inflammatory lung injury in recipient mice exposed to lethal Pseudomonas aeruginosa. Thus, our study has identified a unique subset of tissue-resident trained macrophages which prevent hyper-inflammation and restore tissue homeostasis following pathogen challenge.

overall_design: Lung alveolar macrophage were isolated by flow sorting from naïve and LPS treated groups.  Three replicates for each group has been done.

first: Sreeparna

last: Chakraborty

first: Abhalaxmi

last: Singh

first: Li

first: Xinge

first: Mark

last: Sanborn

first: Zijing

last: Ye

last: Maienschein-Cline

first: Amitabha

last: Mukhopadhyay

first: Balaji

last: Ganesh

first: Asrar

last: Malik


title: Transcriptome and Methylome of the Supraoptic Nucleus Provides Insights into the Age-dependent Loss of Neuronal Plasticity


title: Single-cell ATAC seq analysis of peripheral blood CD4+CD26- T cells from Cutaneous T cell Lymphoma patients

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

summary: Purpose: Determine the epigenetic and transciptional landscape of CTCL subtypes

overall_design: We isolated malignant CD4+CD26- T cells from 5 CTCL peripheral blood PBMCs and performed 10X ATAC sequencing

first: Carly

last: Harro

first: Xiaoqing

last: Yu

first: Jose

middle: R

last: Conejo-Garcia


title: Single Nucleus Transcriptomes from the Ventral Midbrain of Opioid Overdose Cases and Controls

status: Public on Aug 18 2023

city: Detroit

first: Roger

last: Pique-Regi

state: Michigan

address: 540 E Canfield (Scott Hall 3309)

institute: Wayne State University

summary: Dynamic interactions of neurons and glia in the ventral midbrain (VM) mediate reward and addiction behavior. We studied gene expression in 212,713 VM single nuclei from 95 human opioid overdose cases and drug-free controls. Chronic exposure to opioids left numerical proportions of VM glial and neuronal subtypes unaltered, while broadly affecting glial transcriptomes, involving 9.5 - 6.2% of expressed genes within microglia, oligodendrocytes, and astrocytes, with prominent activation of the immune response including interferon, NFkB signaling, and cell motility pathways, sharply contrasting with down-regulated expression of synaptic signaling and plasticity genes in VM non-dopaminergic neurons. VM transcriptomic reprogramming in the context of opioid exposure and overdose included 325 genes with genetic variation linked to substance use traits in the broader population, thereby pointing to heritable risk architectures in the genomic organization of the brain’s reward circuitry.

overall_design:
We generated ventral midbrain single nuclei RNA-seq libraries for 95 brain donors, including 45 subjects with documented histories of opioid abuse and overdose, and 50 demographically-matched, opioid-free control subjects, collected from two geographically distinct regions within the U.S. (greater Detroit area, Michigan and Miami, Florida).
Each sample included both substantia nigra and the adjacent ventral tegmental area. Nuclei were processed in pools of 3-4 brains using the 10X Chromium system followed by Illumina sequencing, read alignment and processing by 10X Cellranger.

>>>Raw data fastq.gz files and vcf files with genotypes  have been deposited in dbGaP (phs003260.v1.p1) due to donor privacy concerns.<<<

first: Schahram

last: Akbarian

first: Michael

last: Bannon

first: Francesca

last: Luca

first: Deborah

last: Mash


title: Trained immunity of alveolar macrophages promotes injury resolution by enhancing KLF4-MERTK-mediated efferocytosis

first: Jalees

last: Rehman

overall_design: Lung alveolar macrophage were isolated by flow sorting from naïve and 7day-LPS-trained mouse. Naïve macrophages were used for control and trained AM compared with naïve AMs. Two replicates with 200000 cells for each group has been done.

first: Sreeparna

last: Chakraborty

first: Abhalaxmi

last: Wang


title: NEUROD1 is critical for the initial cell identity determination and differentiation of the endocrine progenitors in the pancreas.

first: Šárka

last: Benešová


title: Profiling of chromatin accessibility across multiple tissues and developmental stages of pig

status: Public on Aug 15 2023

city: Chengdu

first: Jing

last: Li

state: China

address: No. 211 Huimin Road, Wenjiang District

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

relation:
SuperSeries of: GSE229520
SuperSeries of: GSE229521


title: Post-COVID symptoms and endotypes are associated with the inability to modulate the trajectory of immune and hemostatic pathways

city: Vancouver

first: Robert

middle: E W

last: Hancock

state: British Columbia

address: Room 232 – 2259 Lower Mall Research Station

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

summary: Persistent symptoms after COVID-19 infection can affect almost half of COVID-19 survivors, leading to poor quality of life. Despite its prevalence, the pathophysiology of this phenomenon is poorly understood. We analyzed differences in gene expression between patients with and without post-COVID symptoms in hospital, at follow-up, and longitudinally.  As part of the Banque Québécoise de la COVID-19 biobank, 24 adult patients who were hospitalized due to respiratory COVID-19 were enrolled. Whole blood was collected within the first 10 days in hospital and 4-12 weeks after discharge. K-medoids clustering was performed to further separate patients into clusters/endotypes for DE analysis and pathway enrichment. We found that high rates of post-COVID symptoms in hospitalized patients were associated with an inability to mount, and subsequently resolve by 4-12 weeks after discharge, a robust early response involving immune and hemostatic pathways, which was seen in two of three endotypes.

overall_design: To identify gene expression changes associated with post-COVID symptoms longitudinally and identify mechanistic endotypes related to symptoms. Samples were sequenced over three sequencing runs. K-medoid clustering resulted in three endotypes: cluster 1 (resolving), cluster 2 (dampened), and cluster 3 (activated).

first: Andy

last: An

first: Arjun

last: Baghela

first: Peter

last: Zhang

first: Travis

last: Blimkie

first: Jeff

last: Gauthier

first: Daniel

last: Kaufmann

first: Erica

last: Acton

first: Amy

middle: H

last: Lee

last: Levesque

middle: E


title: Profiling of chromatin accessibility across multiple tissues and developmental stages of pig [ATAC-seq]

summary: Landscape of chromatin accessibility across tissues and developmental stages is essential to elucidate the transcriptional regulation in various biological processes and phenotypes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development have been seldomly investigated. Here, we profiled open chromatin maps and transcriptional features of the heart, kidney, liver, lung, skeletal muscle, and spleen tissues in newborn pigs and that of porcine liver tissue at suckling and adult stages using ATAC-seq and rRNA-depleted RNA-seq, respectively. Employing a union set of protein coding genes (PCGs) and two kinds of transcripts (lncRNAs and TUCPs), we obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue or developmental stage. The PCGs with tissue-specific accessible promoters, as expected, had active transcription and were relevant to tissue-specific functions. Other non-coding tissue-specific peaks were involved in both physical activities and morphogenesis in the neonatal tissues. We also characterized stage-specific peaks and observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. Overall, this study expands the understanding of epigenetic regulation in mammalian tissue functions and organ development, which can benefit both economic trait improvement and better biomedical use of pigs.

overall_design: We analyzed the chromatin accessibility and transcriptomic profiles for six tissues (heart, kidney, liver, lung, skeletal muscle [longissimus dorsi muscle], and spleen) of newborn (one-day-old) pigs, and characterized the dynamic chromatin accessibility and concomitant transcriptional changes in liver during development, i.e., from newborn to suckling at postnatal 28 days and adult at postnatal 180 days. We identified tissue-specific and stage-specific accessible regions, and found these segments played important regulatory roles in tissue-specific functions and hepatic function transition during development. Our study not only confirmed the transcriptional regulatory role of chromatin accessibility across promoter and other non-coding regions in tissue-specific physical activities and organ development, but also enriched the epigenetic profiling and genome regulation of pigs regarding diverse tissues and developmental stages.

first: Jingyi

last: Bai

first: Yu

last: Lin

first: Mingzhou


title: CXCR6 orchestrates brain CD8+ T cell residency and limits mouse Alzheimer’s disease pathology

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital


title: Cellular and Molecular Linkage between Diabetic Nephropathy and Diabetic Retinopathy

city: nanjing

first: XU

last: Ying

state: jiangsu

address: xuanwu district

institute: Nanjing university

summary: Diabetic nephropathy and diabetic retinopathy are related. We used scRNA-seq and RNA-seq to analyze the cellular linkage between them.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Glomerular and retinal vascular cells of  mice were isolated and analyzed using scRNAseq. Human mesangial cells (HMC) and retinal pericytes (HRPC) treated with bovine serum albumin (BSA) or advanced glycation end products (AGEs) were subjected to RNA-seq.

first: Ying

last: Xu

first: Zhihong

last: Liu

first: Zhaohong

last: Chen

first: Jingping

last: Yang


title: NEUROD1 is critical for the initial cell identity determination and differentiation of the endocrine progenitors in the pancreas [CUT&Tag]

first: Šárka

last: Benešová

overall_design: 5 biological samples pooled from 3 to 7 pancreata (biological replicates of 2 control, 2 mutant samples, and one pooled-sample from both for IgG antibody) were analyzed at age E15.5. Approximately 5 000 - 20 000 FACS-sorted  tdTomato+ endocrine cells per sample were used for CUT&Tag profiling, determining amplification cycles number. SNAP-CUTANA™ K-MetStat Panel was included as a spike-in component.

first: Ondrej

last: Smolik

first: Romana

last: Bohuslavova

first: Sarka

last: Benesova

first: Lukas

last: Valihrach

first: Gabriela

last: Pavlinkova


title: Sinus venosus adaptation models prolonged cardiovascular disease and reveals insights into evolutionary transitions of the vertebrate heart

city: Cincinnati

first: Nathan

last: Salomonis

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: How two-chambered hearts in basal vertebrates have evolved from single-chamber hearts found in ancestral chordates remains unclear. Here, we show that the teleost sinus venosus (SV) is a chamber-like vessel comprised of an outer layer of smooth muscle cells. We find that in adult zebrafish nr2f1a mutants, which lack atria, the SV comes to physically resemble the thicker bulbus arteriosus (BA) at the arterial pole of the heart through an adaptive, hypertensive response involving smooth muscle proliferation due to aberrant hemodynamic flow. Single cell transcriptomics show that smooth muscle and endothelial cell populations within the adapting SV also take on arterial signatures. Bulk transcriptomics of the blood sinuses flanking the tunicate heart reinforce a model of greater equivalency in ancestral chordate BA and SV precursors. Our data simultaneously reveal that secondary complications from congenital heart defects can develop in adult zebrafish similar to those in humans and that the foundation of equivalency between flanking auxiliary vessels may remain latent within basal vertebrate hearts.

overall_design: Single cell transcriptomic analysis of smooth muscle and endothelial cells within the adapting sinus venosus of nr2f1a mutants of the bulbus arteriosus and sinus venosus.

first: Jacob

last: Gafranek

first: Enrico

last: D’Aniello

first: Padmapriyadarshini

last: Ravisankar

first: Kairavee

last: Thakkar

first: Ronald

last: Vagnozzi

first: Hee-Woong

last: Lim

first: Joshua

last: Waxman


title: Gene expression in gut CD11b+ Ly6G+ myeloid-derived suppressor cells (MDSCs), which arise during long-term chronic infection.

status: Public on Aug 14 2023

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary:
Myeloid-derived suppressor cells (MDSCs) comprise a hetergenous immune cell population that expands within the inflamed microenvironment of the stomach during pre-cancerous and cancerous  lesion development in mouse.
This study consists of 2-day C. difficile infected mouse ceca.

overall_design: Two infected mouse ceca. Two cell types extracted from each (CD11b-Ly6G-, CD11b+Ly6G+)  for a total of 4 samples with two biological replicates.

first: John

last: Kao

first: Mohamad

last: El-Zaatari

first: Helmut

last: Grasberger


title: Characterizing the heterogeneity of the murine gastric granulocytic Myeloid-derived suppressor cells (MDSCs)  in mice

summary:
Myeloid-derived suppressor cells (MDSCs) comprise a hetergenous immune cell population that expands within the inflamed microenvironment of the stomach during pre-cancerous and cancerous  lesion development in mouse.
MDSCs are heterogeneous and this study aims to understand their diverse functions.

overall_design: Two each of non-myeloid (CD11b-Ly6G-), non-granulocytic-MDSC  (CD11b+Ly6G-), granulocytic MDSC (CD11b+Ly6G+), and one non-myeloid control (CD11b+Ly6G+)

first: Kao

last: John


title: The Cxcr2+ subset of the S100A8+ Gastric Granylocytic Myeloid-Derived Suppressor Cell Population Regulates Gastric Pathology


title: Profiling of chromatin accessibility across multiple tissues and developmental stages of pig [RNA-seq]

first: Jing

last: Li

first: Jingyi

last: Bai

first: Yu

last: Lin

first: Mingzhou


title: Maternal Diet During Early Gestation Influences Postnatal Taste Activity-Dependent Pruning By Microglia

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

summary: Microglia aid in refining central gustatory circuits during normal development. This process is arrested by merely restricting their mother’s dietary sodium during a limited, early prenatal period when microglia progenitors migrate from the yolk-sac to the brain.

overall_design: Mothers fed low sodium (Na) or control diet during a defined window. Microglia were isolated using laser tissue microdissection.

first: Chengsan

last: Sun

first: Shuqiu

last: Zheng

first: Geoffrey

last: Norris

first: Mei

last: Cheng

first: Fanzhen

last: Kong

first: Rolf

last: Skyberg

first: Jianhua

last: Cang

first: Alev

last: Erisir

first: Jonathan

last: Kipnis

first: David

last: Hill


title: THE SSBP3 CO-REGULATOR IS REQUIRED FOR GLUCOSE HOMEOSTASIS, PANCREATIC ISLET ARCHITECTURE, AND BETA-CELL IDENTITY

city: Birmingham

first: Chad

last: Hunter

state: AL

address: 1825 University Boulevard

institute: Division of Endocrinology, Diabetes, and Metabolism

summary:
Objective: Transcriptional complex activity drives the development and function of pancreatic islet cells to allow for proper glucose regulation. Our prior work highlighted that the LIM-homeodomain transcription factor (TF), Islet-1 (Isl1), and its interacting co-regulator, Ldb1, are vital effectors of developing and adult β-cells. We further found that a member of the Single Stranded DNA-Binding Protein (SSBP) co-regulator family, SSBP3, interacts with Isl1 and Ldb1 in β-cells and primary islets (mouse and human) to impact β-cell target genes MafA and Glp1R. Members of the SSBP family stabilize TF complexes by binding directly to Ldb1 and protecting the complex from ubiquitin-mediated turnover. In this study, we hypothesized that SSBP3 would have critical roles in pancreatic islet cell development and function in vivo, similar to the Isl1::Ldb1 complex.
Methods: We first generated a novel SSBP3 LoxP allele mouse line, where Cre-mediated recombination imparts a predicted early protein termination. We bred this mouse to constitutive Cre lines (Pdx1- and Pax6-driven) to recombine of SSBP3 in the developing pancreas and islet (SSBP3DeltaPanc and SSBP3DeltaIslet), respectively. We assessed glucose tolerance and used immunofluorescence to detect changes in islet cell abundance and markers of β-cell identity and function. Using an inducible Cre system we also deleted SSBP3 in the adult β-cell, a model termed SSBP3Deltaβ-cell. We measured glucose tolerance as well as glucose-stimulated insulin secretion (GSIS), both in vivo and in isolated islets in vitro. Using islets from control and SSBP3Deltaβ-cell we conducted RNA-Seq and compared our results to published datasets for similar β-cell specific Ldb1 and Isl1 knockouts to identify commonly regulated target genes.
Results: SSBP3DeltaPanc and SSBP3DeltaIslet neonates present with hyperglycemia. SSBP3DeltaIslet mice are glucose intolerant by P21 and exhibit a reduction of β-cell maturity markers MafA, Pdx1, and UCN3. We observe disruptions in islet cell architecture with an increase in glucagon+ α-cells and ghrelin+ ε-cells at P10. Inducible loss of β-cell SSBP3 in SSBP3Deltaβ-cell causes hyperglycemia, glucose intolerance, and reduced GSIS. Transcriptomic analysis of  14-week SSBP3Deltaβ-cell islets revealed a decrease in β-cell function gene expression (Ins, MafA, Ucn3), increased stress and dedifferentiation markers (Neurogenin-3, Aldh1a3, Gastrin), and shared differentially expressed genes between SSBP3, Ldb1, and Isl1 in adult β-cells.
Conclusions: SSBP3 drives proper islet development and identity, where its loss causes altered islet-cell abundance and glucose regulatory function. β-cell SSBP3 is required for GSIS and glucose homeostasis, at least partially through shared regulation of Ldb1 and Isl1 target genes.

overall_design: 6 Samples

first: Eliana

last: Toren

first: Jessica

middle: D

last: Kepple

first: Kristen

middle: V

last: Coutinho

first: Sam

last: Poole

first: Iztiba

last: Deeba

first: Tanya

last: Pierre

first: Yanping

last: Liu

first: Maigen

last: Bethea


title: Effects of CXCR2 knockdown in gastric granulocytic myeloid-derived suppressor cells (G-MDSCs) during chronic inflamation.

first: Bioinformatics

last: Core

summary:
Myeloid-derived suppressor cells (MDSCs) comprise a hetergenous immune cell population that expands within the inflamed microenvironment of the stomach during pre-cancerous and cancerous  lesion development in mouse.
This study compares  gastric CD11b+Ly6G+ cells vetween Cxcr2flox/flox and S100A8CreCxcr2flox/flox after 6 month H. felis infection.

overall_design: Two mice and two knockdown conditions for four samples and 2 biological replicates per genotype.

first: John

last: Kai

first: Mohamad

last: El-Zaatari

first: Helmut

last: Grasberger


title: Whole transcriptome analysis of canine pheochromocytoma and paraganglioma

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

summary: Pheochromocytomas and paragangliomas (PPGLs) are neuroendocrine tumors arising from the chromaffin cells in the adrenal medulla and extra-adrenal paraganglia, respectively. Local invasion, concurrent disorders, and in rare occasions metastases  prevent surgical removal, which is the most effective treatment to date. Given the current lack of effective medical treatment, there is a need for novel therapeutic strategies. To identify druggable pathways driving PPGL development, we performed RNA sequencing on PPGLs (n=19) and normal adrenal medullas (NAMs; n=10) of dogs. Principal component analysis (PCA) revealed that PPGLs clearly clustered apart from NAMs. In total, 4,218 genes were differentially expressed between PPGLs and NAMs with a false discovery rate (FDR)-adjusted P value <0.05. Of these, 232 had a log2 fold change of >3 or <-3, of which 149 were upregulated in PPGLs, and 83 were downregulated. Compared with NAMs, PPGLs had increased expression of genes related to the cell cycle, tumor development, progression and metastasis, hypoxia and angiogenesis, and the Wnt signaling pathway, and decreased expression of genes related to adrenal steroidogenesis. Our data revealed several overexpressed genes that could provide targets for novel therapeutics, such as Ret Proto-Oncogene (RET), Dopamine Receptor D2 (DRD2), and Secreted Frizzled Related Protein 2 (SFRP2). Based on the PCA, PPGLs were classified into 2 groups, of which group 1 had significantly higher Ki67 scores (P=0.035) and worse survival times (P=0.04) than group 2. One of the differentially expressed genes (FDR-adjusted P value <0.1)  between PPGL group 1 and 2, pleiotrophin (PTN), was significantly associated with survival (P=0.025).

overall_design: 19 samples of pheochromocytomas and paragangliomas and normal adrenal tissue of 10 individuals

first: Marit

last: van den Berg

first: Hans

last: Kooistra

first: Guy

middle: C

last: Grinwis

first: Stefano

last: Nicoli

first: Stefania

last: Golinelli

first: Lisa

last: Stammeleer

first: Monique

last: van Wolferen

first: Elpetra

last: Timmermans-Sprang

first: Maurice

last: Zandvliet

middle: G

first: Sara

last: Galac


title: miRNA expression from mouse adipose tissues

status: Public on Aug 13 2023

city: Nanjing

first: Xiaohong

last: Jiang

address: 163 Xianlin Rd.

institute: Nanjing University

summary: We used microarrays to detail the global programme of  miRNA expression from different types of 8-week male C57BL/6 mice.

sample_organism:
Mus
Mus musculus

overall_design: Here we tested miRNA expression in interscapular brown adipose tissue, subcutaneous white adipose tissue and visceral white adipose tissue of C57BL/6 mice under room temperature

first: Jinhong

last: Xu


title: Simultaneous identification of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing

city: Solna

first: Maria

last: Needhamsen

address: Solnavagen 1

department: Clinical Neuroscience

institute: Karolinska Institutet

summary: The Human Leukocyte Antigen (HLA) locus associates with a variety of complex diseases, particularly autoimmune and inflammatory conditions. The HLA-DR15 haplotype, for example, confers the major risk for developing Multiple Sclerosis in Caucasians, pinpointing important role in the etiology of this chronic inflammatory disease of the central nervous system. In addition to the protein-coding variants that shape the functional HLA-antigen-T cell interaction, recent studies suggest that the levels of HLA molecule expression, that are epigenetically controlled, also play a role in disease development. However, deciphering the exact molecular mechanisms of the HLA association has been hampered by the tremendous genetic complexity of the locus and a lack of robust approaches to investigate it. Here we developed a method to specifically enrich the genomic DNA from the HLA class II locus (chr6:32,426,802-34,167,129) and proximal promoters of 2,157 immune-relevant genes, utilizing the Agilent RNA-based SureSelect Methyl-Seq Capture method, followed by sequencing to detect genetic and epigenetic variation. We demonstrated successful simultaneous detection of the genetic variation and quantification of DNA methylation levels in the HLA locus. Moreover, by utilizing differentially methylated positions in promoters of immune-related genes, we detected relevant pathways following stimulation of cells. Taken together, we present a method that can be utilized to study the impact of the interplay of genetic and epigenetic regulation in HLA class II region on cellular states in a wide context of HLA haplotypes and diseases.

overall_design: THP-1 (DNA-IFNγ/LPS, DNA- IFNγ), THP-1 (BS-IFNγ/LPS and BS-IFNγ) and THP-1 (EM-IFNγ/LPS and EM-IFNγ)

last: Kalomoiri

first: Chandana

last: Rao Prakash

first: Sonja

last: Lagström

first: Kai

last: Hauschulz

first: Ewoud

last: Ewing

first: Klementy

last: Shchetynsky

first: Lara

last: Kular

first: Maja

last: Jagodic


title: Expression patterns of total stomach cells in 6-month H. felis-infected versus uninfected mice.

status: Public on Aug 11 2023

first: Bioinformatics

last: Core

summary: Stomachs were dissociated into single cells from two groups of mice: 6-month H. felis-infected versus uninfected.

overall_design: Stomachs were dissociated into single cells using EDTA and liberase from 6-month H. felis-infected mice versus uninfected.

first: Mohamad

last: El-Zaatari


title: Elucidating the effect of a new indoline derivative (AN1284) against Non-alcoholic steatohepatitis

city: Jerusalem

first: Rinat

last: Abramovitch

address: Hadassah Ein Kerem

department: Institute for Gene Therapy

country: Israel

institute: Hadassah Medical Organization

summary: The aim of the current study was to check whether chronic treatment with AN1284 could reverse steatosis and fibrosis in a mouse model of NASH. We used a mouse model of dietary induced NASH that was given for 4 month. Treatment with saline or AN1284 was given via implanted minipumps for 2 month. Treatment was started after 2 month feeding. Our results revealed that AN1284 significantly attenuated liver damage, as indicated by a reduced liver/body ratio, decreased ALT serum levels, a significant reduction in liver fat content and hepatic fibrosis. To investigate the underlying mechanism, we performed RNA sequencing on mice fed with normal diet (ND) or high fat diet (HFD; Envigo-Teklad TD.150235).

overall_design: Mice were fed with normal diet (ND) or high fat diet (HFD; Envigo-Teklad TD.150235), and given either saline or AN1284 in two doses, 1mg and 5mg per kg per day. At least 3 replicates were performed for each condition.

first: Adi

middle: S

last: Yehezkel

first: Marta

last: Weinstock


title: Prenatal phenotypes and pregnancy outcomes of fetuses with recurrent 1q21.1 microdeletions and microduplications

city: Changchun

first: Hongguo

last: Zhang

state: Jilin

address: 1 Xinmin Street, Changchun, Jilin 130021, P.R. China

department: Center for Reproductive Medicine and Center for Prenatal Diagnosis

institute: First Hospital, Jilin University, Changchun, China

summary:
Objective: Chromosomal 1q21.1 deletions and duplications are genomic disorders which are usually diagnosed postnatally. However, the genotype-phenotype correlations of 1q21.1 copy number variants (CNVs) during prenatal period are still not clear. This study aimed to provide a systematical summary of prenatal phenotypes for such genomic disorders.  Methods: Twenty-six prenatal amniotic fluid samples diagnosed with 1q21.1 microdeletions/microduplications were obtained from pregnant women who opted for invasive prenatal testing. Karyotypic analysis and chromosomal microarray analysis (CMA) were performed for all cases simultaneously. The pregnancy outcomes and health conditions after birth for all cases were followed up. Meanwhile, prenatal cases with 1q21.1 microdeletions or microduplications in the literature were retrospectively collected.  Results: Eleven pregnancies (11/8252, 0.13%) with 1q21.1 microdeletions and fifteen (15/8252, 0.18%) with 1q21.1 microduplications were identified. Among these 1q21.1 CNVs, four cases covered thrombocytopenia-absent radius (TAR) region, sixteen cases covered 1q21.1 recurrent microdeletion/microduplication region, and six cases covered all regions mentioned above. The prenatal abnormal ultrasound findings were recorded in four participants with 1q21.1 deletions and seven participants with 1q21.1 duplications. Finally, three cases with 1q21.1 deletions and five with 1q21.1 duplications terminated their pregnancies.  Conclusion: 1q21.1 microdeletions were associated with increased nuchal translucency (NT), anomalies of urinary system and cardiovascular abnormalities, and 1q21.1 microduplications were correlated with cardiovascular malformations, nasal bone dysplasia and increased NT in prenatal setting. In addition, cerebral ventriculomegaly might be correlated with 1q21.1 microduplications. Considering the variable expressivity and incomplete penetrance of 1q21.1 CNVs, long term follow up after birth should be carried out for these cases.
We identified 26 fetuses carrying the 1q21.1 microdeletions and microduplications using chromosomal microarray analysis. And diverse prenatal phenotypes and the critical genes involved in the deleted/duplicated regions were described in this study.

overall_design: Eleven pregnancies with 1q21.1 microdeletions and fifteen with 1q21.1 microduplications were included. **Please note that raw data CEL files for ？samples (out of total ？) have been lost and thus are not provided***

first: Fagui

last: Yue


title: A rationally designed dual PI3-kinase (PI3K) and BET-inhibitory chimeric small molecule demonstrates potent anti-neoplastic activity versus MYC-driven haematological cancers in vivo

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

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

overall_design: Refer to individual Series


title: Single cell multi-omics analysis deconstructs diabetes-associated β-cell heterogeneity in human islets

status: Public on Aug 10 2023

city: cleveland

first: Peidong

last: Gao

state: Ohio

address: 10900 Euclid Avenue

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: The functional heterogeneity of β-cells is important for metabolism and diseases, but the nature and mechanism of such variation at molecular level remain elusive. Here we explore this question by comparing both single cell RNA-seq and single cell ATAC-seq maps of healthy and type II diabetic (T2D) human islets. We dissect the T2D-associated single cell trajectory and identified signature genes and enhancers in β-cells. We also map the 3D genome of both α- and β-cells with low-input eHi-C approach to unravel the cell type-specific gene regulatory circuits. Strikingly, more than one third of the T2D signature genes show significant intra-donor heterogeneity at single cell level; these genes are functionally distinct from other signature genes that are largely invariant among cells from the same individual but differentially expressed between donors, suggesting different roles in T2D pathogenesis. Importantly, we identified consistent intra-donor variations at both transcriptomic and epigenomic levels, which strongly support the heterogenous β-cell states and transcription programs. Finally, we construct the disease-signature regulatory networks and pinpointed HNF1A as one of the top transcription factors governing T2D-associated β-cell heterogeneity. Taken together, we provide the first multi-omic characterization of β-cell heterogeneity and reveals its connection to T2D.

overall_design: HNF1A CUT&RUN in EndoC-BH3 cell line, 600k cell in total, antibody is abcam cat#:ab204306

first: Chen

last: Weng

first: Anniya

last: Gu

first: Shanshan

first: Fulai

last: Jin

first: Yan

last: Li


title: Increased hyaluronan by naked mole-rat HAS2 extends healthspan in mice

city: Rochester

first: JINLONG

middle: Yuyang

last: LU

state: NY

address: Hutchison Rd

institute: University of Rochester

summary: Abundant high molecular weight hyaluronic acid (HMW-HA) contributes to cancer resistance and possibly longevity of the longest-lived rodent, the naked mole-rat1,2. To study whether the benefits of increased HMW-HA could be transferred to other animal species, we generated a transgenic mouse overexpressing naked mole-rat hyaluronic acid synthase 2 gene (nmrHAS2). nmrHAS2 mice showed increase in hyaluronan levels in several tissues, and lower incidence of spontaneous and induced cancer, extended lifespan and improved healthspan. The transcriptome signature of nmrHAS2 mice shifted towards that of longer-lived species. The most striking change observed in nmrHAS2 mice was attenuated inflammation across multiple tissues. HMW-HA reduced inflammation via several pathways including direct immunoregulatory effect on immune cells, protection from oxidative stress, and improved gut barrier function during aging. These findings demonstrate that the longevity mechanism that evolved in the naked mole-rat can be exploited to other species, and open new avenues for using HMW-HA to improve lifespan and healthspan.

overall_design: To investigate the mechanism responsible for increased lifespan and improved healthspan of nmrHAS2 mice, RNAseq analysis was performed on liver, muscle, white adipose tissue, kidney, small intestine, and spleen of 6- and 24-months old nmrHAS2 and control CreER animals

first: Zhihui

first: J

middle: Y

last: Lu

first: Andrei

last: Seluanov

first: Vera

last: Gorbunova


title: Single-cell transcriptome profiling of mouse bone marrow-derived immune cells in response to trypanosome infection

city: Incheon

first: Magdalena

last: Radwanska

address: 119-5, Songdomunhwa-ro

institute: Ghent University Global Campus

summary: Bone marrow is an extremely important organ as a primary hematopoietic organ where new red blood cells and immune cells are produced. Parasitic infections showed disruption of red blood cell production and changes in immune responses in bone marrow. Therefore, we generated single-cell RNA sequencing (scRNA-seq) data to reveal transcriptomic profile changes to parasitic infection by trypanosomes. These data will ultimately help us understand the mechanisms of the host immune response to trypanosomosis.

overall_design: Bone marrow cells in femur were harvested from 3 non-infected mice and 3 trypanosome-infected mice for scRNA-seq analysis.

first: Boyoon

last: Choi

first: Stefan

last: Magez


title: RNA-seq analysis of Entamoeba histolytica glycerol 3-phosphate dehydrogenase (G3PDH) and glycerol kinase (EhGK) gene silencing strain

city: BUNKYO

first: Ghulam

last: Jeelani

state: Tokyo

department: BIOMEDICAL CHEMISTRY

institute: University of Tokyo

summary: Amebiasis is caused by the protozoan parasite Entamoeba histolytica. Treatment options other than metronidazole and its derivatives are few, and their low efficacy against asymptomatic cyst carriers, and experimental evidence of resistance in vitro justify the discovery/repurposing campaign for new drugs against amebiasis. To better understand the role of glycerol metabolism in this parasite, we focused on characterizing two important enzymes, glycerol kinase (GK) and glycerol 3-phosphate dehydrogenase (G3PDH). Recombinant GK was biochemically characterized in detail, while G3PDH was not due to failure of protein expression and purification. GK revealed novel characteristics and unprecedented kinetic properties in reverse reaction. Gene silencing revealed that GK is essential for optimum growth, whereas G3PDH is not. Gene silencing of G3PDH caused upregulated GK expression, while that of GK resulted in upregulation of antioxidant enzymes as shown by RNA-seq analysis. Although the precise molecular link between GK and the upregulation of antioxidant enzymes was not demonstrated, the observed increase in antioxidant enzyme expression upon GK gene silencing suggests a potential connection between GK and the cellular response to oxidative stress. Together, these results provide the first direct evidence of the biological importance and coordinated regulation of the glycerol metabolic pathways for proliferation and antioxidative defense in E. histolytica, justifying the exploitation of these enzymes as future drug targets.

overall_design:
To investigate the effects of gene silencing we established cells lines in which target gene has been gene silenced by epigenetic silencing.
We then performed gene expression analysis using the data obtained from the RNA-seq of pSAP (mock transfected), GK and G3PDH gene silenced strains (n=3)

first: Tomoyoshi

last: Nozaki


title: Clariom S Microarray Expression Data from Human Eosinophilic Esophagitis and Control Esophageal Biopsies

city: Blacksburg

first: Irving

middle: Coy

last: Allen

state: VA

address: 205 Duck Pond Dr.

department: Biomedical Sciences and Pathobiology

institute: Virginia-Maryland College of Veterinary Medicine

summary:
This study sought to evaluate the diffferential gene expression of human Eosinophilic Esophagitis (EoE) patients compared to control patients.
Abstract from associated publication: Eosinophilic Esophagitis (EoE) is a chronic allergic disease characterized by progressive inflammation of the esophageal mucosa. While the transcriptome of EoE has been reported, few studies have examined the genetics among both adult and pediatric EoE populations. Here, we use microarray analysis to interrogate gene expression using esophageal biopsies from EoE and Control subjects with a wide age distribution. Analysis of differential gene expression and prediction of impaired pathways was compared using conventional transcriptome analysis programs and an artificial intelligence-based ADVAITA program. Principal Components Analysis revealed samples cluster by disease status (EoE and Control) irrespective of clinical features like sex, age, and disease severity. Global transcriptomic analysis revealed differential expression of several genes previously reported in EoE (CCL26, CPA3, POSTN, CTSC, ANO1, CRISP3, SPINK7). In addition, we identified differential expression of several genes from the MUC and SPRR families, which has not been previously reported. Our findings suggest their involvement in impaired barrier integrity and loss of epidermal cell differentiation in EoE patients. These findings present two new gene families that are differentially expressed in EoE patients in both adult and pediatric populations, which presents an opportunity for a future therapeutic targets that would be useful in a large demographic of patients.

overall_design: Biopsies were collected from endoscopically visible areas of active inflammation and healthy mucosa in subjects and controls, respectively. RNA extractions were collected from each biopsy using a Qiagen AllPrep Kit. Groups include Eosinophilic Esophagitis (EoE) (n=12) and control biopsies (n=12), totaling 24 samples. 1 HeLa MRSL, provided by the manufacturer, was included.

first: Holly

middle: A

last: Morrison


title: Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation

city: Boston

first: Jiehui

last: Chen

state: MA

address: 320 Longwood Ave

institute: Boston Children’s Hospital

summary: The blueprint of lineage segregation of early mouse embryo is established during gastrulation in which progenitors of various cell fates are regionalized and patterned in specific embryo locations. Despite the central importance of this period of mammalian development, we currently lack a comprehensive understanding of the underlying developmental trajectories and molecular processes, principally because research efforts either employed in vitro systems, focused on small numbers of genes, or limited the number of developmental stages or cell types that were studied. Here, we study the regulatory landscape of gastrulation by combining single-cell RNA-seq (A total of ~35,000 single cells isolated at E6.5, E6.75, E7.0, E7.25, E7.5) and geographical position sequencing (Geo-seq) technique, and we report a de novo identification of spatial signatures and a method to enable retrospective locating of single cells to their origins. Our work provides insights into the exit from pluripotency and priming for differentiation, and the emergence of regulatory networks associated with cell fate decisions. Finally, we reconstruct the spatio-temporal roadmap of gastrula mouse embryo in single-cell resolution. This result uncovers the cell migration trajectories and molecular processes associated with lineage segregation.

overall_design:
By using spatial transcriptome of Geo-seq , we carried out transcriptome profiling on embryo locations at a high resolution of 20-40 cells per sample. We then constructed a comprehensive spatio-temporal transcriptome map from the pre-gastrulation to late-gastrulation embryos. Combining single-cell RNA-seq data generated using 10x Genomics Chromium system, we visualized the spatio-temporal map in a 3D embryonic model.

Definitions:
region AP: region of 1st section of epiblast
region EAP: region of 1st section of endoderm
region Aregion of anterior epiblast/ectoderm
region EP: region of posterior endoderm
region P: region of posterior epiblast/ectoderm
region EA: region of anterior endoderm
region M: region of mesoderm
region L: region of left lateral epiblast/ectoderm
region R: region of right lateral epiblast/ectoderm
region L1: region of left anterior lateral epiblast/ectoderm
region L2: region of left posterior lateral epiblast/ectoderm
region MA: region of anterior mesoderm
region MP: region of posterior mesoderm
region R1: region of right anterior lateral epiblast/ectoderm
region R2: region of right posterior lateral epiblast/ectoderm
region Epi: region of epiblast
region VE: region of visceral endoderm
region MAR: region of anterior right lateral mesoderm
region MPL: region of posterior left lateral mesoderm
region MPR: region of posterior right lateral mesoderm
region MAL: region of anterior left lateral mesoderm

first: Ran

last: Wang

first: Xianfa

last: Yang

first: Guizhong

last: Cui

first: Naihe

last: Jing


title: Non-invasive assessment of normal and impaired iron homeostasis in living human brains

first: Miriam

last: Adam

state: Israel

address: Givat Ram

institute: The Hebrew University of Jerusalem

summary: Strict iron regulation is essential for normal brain function. The iron homeostasis, determined by the milieu of available iron compounds, is impaired in aging, neurodegenerative diseases and cancer. However, non-invasive assessment of different molecular iron environments implicating brain tissue's iron homeostasis remains a challenge. We present a novel magnetic resonance imaging (MRI) technology sensitive to the iron homeostasis of the living brain (the r1-r2*relaxivity). In vitro, our MRI approach reveals the distinct paramagnetic properties of ferritin, transferrin and ferrous iron. In the in vivo human brain, we validate our approach against ex vivo iron compounds quantification and gene expression. Our approach varies with the iron mobilization capacity across brain regions and in aging. It reveals brain tumors’ iron homeostasis, and enhances the distinction between tumor tissue and non- pathological tissue without contrast agents. Therefore, our approach may allow for non-invasive research and diagnosis of iron homeostasis in living human brains.

overall_design: RNA-seq of 17 human meningioma tumor samples was used to validate our MRI based predictions of iron homeostasis.

first: Shir

last: Filo

first: Daniel

last: Bar Hanin

first: Rona

last: Shaharabani