title: Hypoxia Inducible Factor 2α promotes tolerogenic macrophage development during cardiac transplantation through transcriptional regulation of colony stimulating factor 1 receptor

first: Samantha

last: Schroth

state: IL

address: 320 E Superior St

institute: Northwestern University Feinberg School of Medicine

summary: Solid organ transplantation mobilizes myeloid cells, including monocytes and macrophages, which are central protagonists of allograft rejection. However, myeloid cells can also be functionally reprogrammed by perioperative costimulatory blockade to promote a state of transplantation tolerance. Transplantation tolerance holds promise to reduce complications from chronic immunosuppression and promote long-term survival in transplant recipients. We sought to identify novel mediators of transplantation tolerance by performing single cell RNA sequencing of acute rejecting or tolerized cardiac allografts. This led to the unbiased identification of the transcription factor, Hypoxia Inducible Factor (HIF)-2α, in a subset of tolerogenic monocytes. Using flow cytometric analyses and mice with conditional loss or gain of function, we uncovered that myeloid cell expression of HIF-2α was required for costimulatory blockade induced transplantation tolerance. While HIF-2α was dispensable for mobilization of tolerogenic monocytes, which were sourced in part from the spleen, it promoted the expression of colony stimulating factor 1 receptor (CSF1R). CSF1R mediates monocyte differentiation into tolerogenic macrophages and was found to be a direct transcriptional target of HIF-2α in splenic monocytes. Administration of the HIF stabilizer, roxadustat, within micelles to target myeloid cells, increased HIF-2α in splenic monocytes, which was associated with increased CSF1R expression and enhanced cardiac allograft survival. These data support further exploration of HIF-2α activation in myeloid cells as a therapeutic strategy for transplantation tolerance.

overall_design: Mice of B6 background were subjected to full MHC-mismatch abdominal heart transplantation with sex matched BALB/c donors. For AR (acute rejecting) group, no additional treatment was given to mice aside from standard analgesics. For Tol (tolerized) group, mice received intravenous infusions of anti-CD40L antibody (CoB, 500 μg per mouse) and donor BALB/c splenocytes (DST, 2 x 10^7 cells) on day 0 prior to transplantation), followed by intraperitoneal injections of anti-CD40L (CoB, 500μg per mouse) on days 7 and 14 post-transplantation. AR allografts were harvested day 8 post transplnatation and day 40 for Tol allografts. Groups were performed in biological replicates (n = 4 mice/group) and pooled together by condition. Each condition was independently enriched utilizing StemCell magnetic enrichment kit for CD45+ cells or Pan-DC and enriched cells were re-pooled at a ratio of 1:1 for processing in the 10x Genomics Chromium System.

first: DeBerge

last: Matthew

first: Schroth

last: Samantha

first: Thorp

last: Edward


title: Dysfunction of infiltrating cytotoxic CD8+ T cells within the graft promotes murine kidney allotransplant tolerance

status: Public on Jun 20 2024

city: Boston

first: Alessandro

last: Alessandrini

state: MA

address: 55 Fruit Street , WEL 807

country: USA

institute: Massachusetts General Hospital

type: Expression profiling by high throughput sequencing

summary: Tolerance of mouse kidney allografts arises in grafts that develop regulatory Tertiary Lymphoid Organs (rTLOs). scRNAseq data and adoptive transfer of alloreactive T cells post-transplant showed that cytotoxic CD8+ T cells are reprogrammed within the accepted graft to an exhausted/regulatory-like phenotype. Establishment of rTLOs was required since adoptive transfer of alloreactive T cells prior to transplantation results in kidney allograft rejection. Despite intragraft CD8+ cells with a regulatory phenotype, they were not essential for the induction and maintenance of kidney allograft tolerance. Analysis of scRNAseq data from allograft kidneys and malignant tumors identified similar regulatory-like cell types within the T cell clusters. Induction of cytotoxic CD8+ T cell dysfunction of infiltrating cells appears to be a beneficial mechanistic pathway that protects the kidney allotransplant from rejection through a process we call “defensive tolerance.” This pathway has implications for our understanding of allotransplant tolerance and tumor resistance to host immunity.

overall_design: Isolated kidney or spleen cells were sorted for viable CD45+ cells via flow cytometry using an anti-CD45+ antibody and a fixable viability dye. These cells were used to construct single-cell RNA-seq libraries at Chromium 10x instrument using Chromium Next GEM Single Cell 3’ kit, which were sequenced in paired-end fashion on Illumina HiSeq 2500 instrument to the depth of approximately 100 million read pairs per sample.

first: Yokose

last: Takahiro

first: Szuter

first: Liss

last: Andrew

first: Baba

last: Taisuke

first: Ruddy

last: David

first: Piquet

last: Michelle

first: Alessandrini

last: Alessadnro


title: Cellular and functional characterization of aging-independent senescent-like cells that modulate tissue repair

city: Rochester

first: Dominik

last: Saul

state: Minnesota

address: 200 First Street SW Rochester

institute: Mayo Clinic

summary: Cells expressing features of cellular senescence, including upregulation of p21 and p16, appear transiently following tissue injury, yet the properties of these cells or how they contrast with age-induced senescent cells remains unclear. Using skeletal fracture as a model of acute injury, we identified rapidly-appearing senescent-like cells, marked by p21 expression, that negatively affected fracture healing. p21+ callus cells, which consisted predominantly of neutrophils and osteochondroprogenitors, existed as transient cells specific to injury and expressed high levels of senescence-associated factors known to impair bone formation and induce paracrine senescence. Targeted genetic clearance of p21+ cells suppressed senescence-associated signatures within the fracture callus and accelerated fracture healing. By contrast, p21+ cell clearance did not alter bone loss due to aging; conversely, p16+ cell clearance, known to alleviate skeletal aging, did not affect fracture healing. Together, our findings establish contextual roles of senescent/senescent-like cells that may be leveraged for therapeutic opportunities.

overall_design: 2 Male, 2 Female p21-LOX-ATTAC mice were used and a  closed diaphyseal tibial fracture introduced. The callus was harvested on day 14. Subsequently, GFP+ and GFP- cells were FACS-sorted.

first: Madison

middle: L

last: Doolittle

first: Jennifer

last: Rowsey

first: Mitchell

middle: N

last: Froemming

first: Robyn

last: Kosinsky

first: Stephanie

middle: J

last: Vos

first: Ming

last: Ruan

first: Nathan

last: LeBrasseur

first: Abhishek

last: Chandra

first: Robert

last: Pignolo

first: Joao

middle: F

last: Passos

first: Joshua

last: Farr

first: David

middle: G

last: Monroe

first: Sundeep

last: Khosla


title: CPYPP induces paraptosis in MDA-MB-231 and MDA-MB-435 melanoma cells

city: Taichung

first: Ling-Chu

last: Chang

state: -- select state --

address: 6F, No. 350, Jingmao 1st Road, Beitun Dist.,

department: Center for Molecular Medicine

country: Taiwan

institute: China Medical University Hospital

summary:
Background:
Paraptosis is a programmed cell death characterized by cytoplasmic vacuolation, which has been used as an alternative cell death method for cancer treatment and is associated with cancer resistance. However, the mechanisms underlying the progression of paraptosis in cancer cells are largely unknown.
Methods:
Paraptosis-inducing agents, CPYPP, cyclosporin, and curcumin, were utilized to investigate the underlying mechanism of paraptosis. Next-generation sequencing and liquid chromatography-mass spectrometry analysis revealed significant changes in gene and protein expressions. Pharmacological and genetic approaches were employed to elucidate the transcriptional events related to paraptosis. The xenograft mouse models were employed to evaluate the potential of paraptosis as an anti-cancer strategy.
Results:
CPYPP, cyclosporin A, and curcumin induced cytoplasmic vacuolization and triggered paraptosis in cancer cells. The paraptotic program involved reactive oxygen species (ROS) provocation and the activation of proteostatic dynamics, leading to transcriptional activation associated with redox homeostasis and proteostasis. Both pharmacological and genetic approaches suggested that cyclin-dependent kinase (CDK) 7/9 drive paraptotic progression in a mutually-dependent manner with heat shock proteins (HSPs). Proteostatic stress, such as accumulated cysteine-thiols, HSPs, ubiquitin-proteasome system, endoplasmic reticulum stress, and unfolded protein response, as well as ROS provocation primarily within the nucleus, enforced CDK7/CDK9–Rpb1 (RNAPII subunit B1) activation by potentiating its interaction with HSPs and protein kinase R (PKR) in a forward loop, amplifying transcriptional regulation and thereby exacerbating proteotoxicity leading to initiate paraptosis. A xenograft mouse model with OECM-1 cells further confirmed the induction of paraptosis against tumor growth.
Conclusions
We propose a novel regulatory paradigm in which the activation of CDK7/CDK9–Rpb1 by nuclear proteostatic stress mediates transcriptional regulation to prime cancer cell paraptosis.

overall_design: MDA-MB-435 and MDA-MB-231 cancer cells were treated with CPYPP for 6 hours, followed by next-generation sequencing to detect alterations in gene expression.

first: Shih-Kai

last: Chiang

first: Wei-Chao

first: Shuen-Ei

last: Chen


title: miR-452-5p mediates SCN5A dependent fibrosis via TGF-beta/SMAD4 axis

city: Taipei

first: Iqra

last: Mushtaq

state: Taipei

address: Wuxing street

institute: Taipei Medical Univ-3014874 - Taipei

type: Non-coding RNA profiling by high throughput sequencing

summary: SCN5A coding for sodium channels in the heart and its reduced activity implicated various biological processes including fibrogenesis.  However, the mechanistic interplay between loss of SCN5A activity and cardiac fibrosis pertinence remains elusive.  In-vitro knockdown of the SCN5A gene activates fibroblasts and increases TGF-β signaling with small-RNA sequencing indicating its impact on miR-452-5P expression in human cardiac fibroblasts (HCF). Mechanistically, miR-452-5p acts as a direct regulator of TGF-β signaling by inhibiting SMAD4 expression, maintaining cellular homeostasis in normal physiological conditions. SCN5A knockdown limits miR-452-5p regulatory function on SMAD4, which further promotes cardiac fibrosis (CF). These results clarify the significant involvement of miR-452-5p in CF development and propose a promising target for potential therapeutic intervention.

overall_design: To investigate the role of SCN5A in CF, we established SCN5A-knockdown cell model by shRNA. We then performed a small RNA-seq to analyze the microRNA expression profiles affected by SCN5A knockdown in human cardiac fibroblasts.

first: Tsung

middle: H

last: Hsieh

first: Yu-Hsun

last: Kao

first: Yi-Jen


title: qPCR panels for plasma microRNAs of responders versus non responders metastatic castration resistant prostate cancer patients to abiraterone acetate

city: Trento

first: Simone

last: Detassis

address: Via Sommarive 9

department: CIBIO

country: Italy

institute: University of Trento

summary:
Abiraterone acetate (AA) serves as a medication for managing persistent testosterone production in patients with metastatic castration-resistant prostate cancer (mCRPC). However, its efficacy varies among individuals, thus the identification of biomarkers to predict and follow treatment response is required. In this pilot study, we explored the potential of circulating miRNAs (c-miRNAs) to stratify patients based on their responsiveness to AA. We conducted a miRNA candidate analysis on 9 responders versus 9 non-responders mCRPC patients via Exiqon qPCR panels
The patients were considered responders to AA if they either achieved a radiological response without PSA progression and performance status deterioration, or in the presence of PSA reduction ≥ 50% compared to the baseline values without radiological progression and performance status deterioration.

first: Margherita

last: Grasso

first: Valerio

last: Del Vescovo

first: Michela

middle: A

last: Denti


title: Single-cell RNAseq of Neurog1-Neurog2-DsRed transduced DRG cells

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

country: Germany

institute: University Hospital Würzburg

summary: Cultured adult mouse dorsal root ganglia (DRG) cells exhibit glial sensory progenitor properties in vitro. Therefore, they might be a good starter cell for reprogramming into sensory neurons. Here, we infected them with the retroviral vector Neurog2-Neurog1-DsRed to induce sensory neuron development and analyzed by scRNAseq at 14 days post infection whether infected cells show properties of sensory neurons such as nociceptors. After 10x Genomics, data analysis of 4,549 individual cells indicated the generation of neurons, but at an immature cell state.

overall_design: Cells from dorsal root ganglia culture of adult mice were infected with Neurog2-Neurog1-DsRed, DsRed-positive cells were isolated with Fluorescence-activated cell sorting (FACS) at 14 days post infection and analyzed using scRNAseq.

first: Annemarie

last: Sodmann

first: Fabian

last: Imdahl


title: Macrophages show unprecedented anti-HIV activity in HIV-infected iHMD-NSG mice

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Very little is known about the role of macrophages as immune mediators during natural HIV infection. Humanized mice are a highly valuable in vivo model to study HIV pathogenesis. Still, the presence of murine mononuclear phagocytes in these models represents a significant limitation for the study of their human counterpart. Therefore, we generated a novel humanized mouse model for the selective depletion of human myeloid cells at a time point of our choosing. These inducible human myeloid cell depletion (iHMD) mice showed specific human myeloid cell depletion with no adverse events for the animals. We used this model to demonstrate that human mononuclear phagocytes restrict HIV replication in vivo by secreting antiviral cytokines and chemokines. These in vivo data were validated by a co-culture assay, showing soluble factors are at the basics of macrophage-mediated restriction of HIV. Transcriptomic data confirmed macrophages restrict HIV replication via upregulation of antiviral cytokines and chemokines. RNA sequencing CD4+ T-cells showed cellular activation, up-regulation of HIV restriction factors and the downregulation of DNA transcription and RNA translation in the presence of macrophages. This work describes a novel role of macrophages as effector cells acting against HIV replication and disease progression.

overall_design: PBMCs were isolated from 3 heathly donors. Mathched PBMCs were split equally for either HIV infection or CD14+ cells isolations (via magnetic beads). CD14+ cells differentiated into pro-inflammatory (M1) macrophages. Upon differentiation of CD14+ monocytes into macrophages (verified via flow cytometry), and succesfull HIV infection of PBMCs (verified via qPCR), co-cucltures (in 3 techincal replicates), were established for the 3 different donors, as well as monocultures of both HIV infected PBMCs and uninfected MDMs, as exprimental controls. Co-cultures were incubated for 48h, after which time cells were processed for RNA isolation. For CD4+ T cells an extra sorting step of these cells from PBMCs was performed prior RNA isolation.

first: Luca

last: Baroncini

first: Roberto

last: Speck


title: Interleukin-1β Induces and Accelerates Human Endometrial Stromal Cell Senescence and Impairs Decidualization via the c-Jun N-Terminal Kinase Pathway

city: Buffalo

first: Jie

last: Yu

state: NY

address: 955 Main Street

department: Department of Obstetrics and Gynecology

institute: SUNY Buffalo

summary: As the mean age of first-time mothers increases in the industrialized world, inquiries into causes of human reproductive senescence have followed. Rates of ovulatory dysfunction and oocyte aneuploidy parallel chronological age, but poor reproductive outcomes in women older than 35 years are also attributed to endometrial senescence. The current studies, using primary human endometrial stromal cell (ESC) cultures as an in vitro model for endometrial aging, characterize the proinflammatory cytokine, IL-1β-mediated and passage number-dependent effects on ESC phenotype. ESC senescence was accelerated by incubation with IL-1β, which was monitored by RNA sequencing, ELISA, immunocytochemistry and Western blotting. Senescence associated secreted phenotype (SASP) proteins, IL-1β, IL-6, IL-8, TNF-α, MMP3, CCL2, CCL5 and other senescence-associated biomarkers of DNA damage (p16, p21, HMGB1, phospho-γ-histone 2A.X) were noted to increase directly in response to 0.1 nM IL-1β stimulation. Production of the corresponding SASP proteins increased further following extended cell passage. Using enzyme inhibitors and siRNA interference, these effects of IL-1β were found to be mediated via the c-Jun N-terminal kinase (JNK) signaling pathway. Hormone-induced ESC decidualization, classical morphological and biochemical endocrine responses to estradiol, progesterone and cAMP stimulation (prolactin, IGFBP-1, IL-11 and VEGF), were attenuated pari passu with prolonged ESC passaging. The kinetics of differentiation responses varied in a biomarker-specific manner, with IGFBP-1 and VEGF secretion showing the largest and smallest reductions, with respect to cell passage number. ESC hormone responsiveness was most robust when limited to the first six cell passages. Hence, investigation of ESC cultures as a decidualization model should respect this limitation of cell aging. The results support the hypotheses that “inflammaging” contributes to endometrial senescence, disruption of decidualization and impairment of fecundity. IL-1β and the JNK signaling pathway are pathogenetic targets amenable to pharmacological correction or mitigation with the potential to reduce endometrial stromal senescence and enhance uterine receptivity.

overall_design: To replicate inflammatory aging, known as "inflammaging", ESC were subjected to a 24-hour incubation with 0.1 nM human recombinant IL-1β. Senescence-associated biomarkers were assessed, and cellular lysates were utilized for mRNA sequencing (RNAseq), which was then compared to untreated ESC cultures.

first: Sarah

last: Berga

first: Eric

last: Zou

first: Brandon

last: Marzullo

first: Indrani

middle: C

last: Bagchi

first: Milan

middle: K

last: Taylor


title: Context-dependent role of type 3 innate lymphoid cells in mucosal protection

city: New York City

first: Yiming

last: Huang

state: New York

address: 3960 Broadway

department: Department of Systems Biology

institute: Columbia University

summary: How group 3 innate lymphoid cells (ILC3) regulate mucosal protection in the presence of T cells remains poorly understood. Here, we examined ILC3 function in intestinal immunity using ILC3-deficient mice that maintain endogenous T cells, Th17 cells, and secondary lymphoid organs. ILC3 were dispensable for generation of Th17 and Th22 cell responses to commensal and pathogenic bacteria, and absence of ILC3 did not affect IL-22-production by CD4 T cells before or during infection. However, despite presence of IL-22-producing T cells, ILC3 and ILC3-derived IL-22 were required for maintaining homeostatic functions of the intestinal epithelium. T cell-sufficient, ILC3-deficient mice were capable of pathogen clearance and survived infection with low dose Citrobacter rodentium. However, ILC3 increased pathogen tolerance at early timepoints of infection by activating tissue-protective immune pathways. Consequently, ILC3 were indispensable for survival of high dose infection. Our results demonstrate a crucial context-dependent role for ILC3 in immune-sufficient animals and provide a blueprint for uncoupling of ILC3 and Th17 cell functions.

overall_design: We performed gene expression profiling anlaysis using data obtained from RNA-seq of isolated CD4 T cell, IEC, small intestine and colon tissue from WT, STOP and dILC3 mice

first: Ivanov

last: Ivaylo

first: Araujo

last: Leandro

first: Edwards

last: Madeline


title: Single-cell profiling reveals the impact of genetic alterations on the differentiation of inflammation-induced colon tumors

city: Bloomington

first: Ahmed

last: Ghobashi

state: IN

institute: Indiana University

summary: Genetic mutations and chronic inflammation of the colon contribute to the development of colorectal cancer (CRC). Using a murine model of inflammation-induced colon tumorigenesis, we determined how genetic mutations alter colon tumor cell differentiation. Inflammation induced by enterotoxigenic Bacteroides fragilis (ETBF) colonization of multiple intestinal neoplasia (MinApcΔ716/+) mice triggers loss of heterozygosity of Apc causing colon tumor formation. Here, we report that the addition of BRAFV600E mutation (BRAFFV600ELgr5tm1(Cre/ERT2)CleMinApcΔ716/+, BLM) or knocking out Msh2 (Msh2LoxP/LoxPVil1-creMinApcΔ716/+, MSH2KO) in the Min model altered colon tumor differentiation. Using single cell RNA-sequencing, we uncovered the differences between BLM, Min, and MSH2KO tumors at a single cell resolution. BLM tumors showed an increase in differentiated tumor epithelial cell lineages and a reduction in the stem cell population. In contrast, MSH2KO tumors were characterized by an increased stem cell population that had higher WNT signaling activity compared to Min tumors. Additionally, comparative analysis of single-cell transcriptomics revealed that BLM tumors had higher expression of transcription factors that drive differentiation, such as Cdx2, than Min tumors. Using RNA velocity, we identified additional potential regulators of BLM tumor differentiation such as NDRG1. The role of CDX2 and NDRG1 as putative regulators for BLM tumor cell differentiation was verified using organoids derived from BLM tumors. Our results demonstrate the critical connections between genetic mutations and cell differentiation in inflammation-induced colon tumorigenesis. Understanding such roles will deepen our understanding of inflammation-associated colon cancer.

overall_design: Investigating cellular heterogeneity of inflammation-induced colon tumors using single-cell RNA sequencing (scRNA-seq)

first: O'Hagan

last: Heahter

first: Ghobashi

last: Heather


title: Basis of gene-specific transcription regulation by the Inegrator Complex (ChIP-Seq II)

city: Zürich

first: Stefanie

last: Jonas

state: Zürich

address: Otto-Stern-Weg 5

department: Biology

institute: ETH Zurich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Integrator (INT) is a multi-subunit modular RNA processing complex, which exhibits both RNA endonuclease and protein phosphatase activity. It is responsible for transcription termination at the 3’ ends of a diverse array of RNA polymerase II (RNAP2) transcribed non-coding RNAs, as well as transcription regulation at a large number of protein coding genes. There, it terminates RNAP2 at promoter proximal pausing sites, cleaves the nascent transcript and competes with elongation factors.This INT-mediated tapering of gene expression attenuates stimulus responsive genes and is essential for cell differentiation. Although INT affects transcription at varying classes of RNAs in diverse biological contexts, how it achieves specificity in a gene- and context-dependent manner has remained elusive. Using a combination of proteomics, interaction studies and structural characterization, we identified a diverse set of transcription factors (TFs) that associate directly with defined surfaces on INT. Stress conditions lead to changes in the types of TFs bound by INT, and quantitative binding studies suggest that TF affinities can be modulated by altering the phosphorylation states of specific residues in their INT-binding motifs. Integrated multi-omics data show that INT and its TF interactors regulate significantly overlapping sets of genes and indicate that these TFs recruit INT to specific genomic loci. Consistently, we find that starvation induced formation of primary cilia, which is a cellular stress response reliant on INT-mediated transcription regulation, depends on intact TF-INT binding. Taken together, our data suggest that TFs lend INT specificity to elicit targeted gene regulation as a transcriptional response in defined biological contexts.

overall_design: Chromatin Immunoprecipitation followed by sequencing (ChIPseq) of INTS13 after starvation or depletion of HDGF  was performed to determine whether starvation stress and/or TF relocalization or depletion are associated with INTS13 relocalization on the genome.

first: Kevin

last: Sabath

first: Amena

last: Nabih

first: Christian

last: Arnold

first: Rim

last: Moussa

first: David

last: Domjan

first: Judith

last: Zaugg


title: Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

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

overall_design: Refer to individual Series


title: Inferring secretory and metabolic pathway activity from omic data with secCellFie

city: La Jolla

first: Nathan

last: Lewis

address: 9500 Gilman Dr

institute: UCSD

summary: Understanding protein secretion has considerable importance in the biotechnology industry and important implications in a broad range of normal and pathological conditions including development, immunology, and tissue function. While great progress has been made in studying individual proteins in the secretory pathway, measuring and quantifying mechanistic changes in the pathway's activity remains challenging due to the complexity of the biomolecular systems involved. Systems biology has begun to address this issue with the development of algorithmic tools for analyzing biological pathways; however most of these tools remain accessible only to experts in systems biology with extensive computational experience. Here, we expand upon the user-friendly CellFie tool which quantifies metabolic activity from omic data to include secretory pathway functions, allowing any scientist to infer protein secretion capabilities from omic data. We demonstrate how the secretory expansion of CellFie (secCellFie) can be used to predict metabolic and secretory functions across diverse immune cells, hepatokine secretion in a cell model of NAFLD, and antibody production in Chinese Hamster Ovary cells.

overall_design: Gene expression profiling analysis of RNA-seq data comparing control vs invitro model of NAFLD in Huh7 cells

first: Lewis

last: Nathan


title: Navel Orange Peel Essential Oil Inhibits the Growth and Progression of Triple Negative Breast Cancer

city: nanchang

first: Chao

last: Yang

state: jiangxi

address: 1688 Meiling Avenue

department: cancer center

country: China

institute: Jiangxi University of Traditional Chinese Medicine

summary: Triple Negative Breast Cancer (TNBC) is a particular type of breast cancer with the highest mortality rate and there has been growing concern about the development of essential oils as potential anti-cancer drugs.This investigation explored the bioactivity and molecular mechanisms of navel orange peel oil (NOPEO) against TNBC cells. By initiating cell cycle block and apoptosis, NOPEO demonstrated potent growth suppressive properties on the TNBC cell lines MDA-MB-231 and MDA-MB-453. NOPEO was also effective in inhibiting the motility of MDA-MB-231 cells and in down-regulating the levels of MMP-9 and MMP-2 proteins. Additionally, NOPEO's inhibitory effects on MDA-MB-231 gene expression were analysed by RNA sequencing. In total, 1376 genes were found to be upregulated and 1335 genes were downregulated after NOPEO treatment. According to KEGG and GO pathways, the differentially expressed genes were related to MAPK, Jak/stat and FoxQ signalling pathways.

overall_design: To investigate the mechanism of action of navel orange essential oil against triple-negative breast cancer. The samples were 50ppm NOPEO treated MDA-MB-231 cells for 24 hours , the DMSO  treated  cells as control.

first: Wenwen

last: Zhang

first: Hui

last: Chen


title: The SBP transcription factor SPL10 regulates leaf curvature by promoting REVOLUTA transcription in plants

city: Shanghai

first: Xu

last: Pengfei

state: Shanghai

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

summary: The developmental functions of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) 10 have been extensively studied in Arabidopsis, but SPL10's role in regulating leaf curvature has not been well characterized. In this study, we observed an upward-curling leaf phenotype upon overexpression of a miR156/157-resistant version of SPL10 (rSPL10). DNA affinity purification sequencing (DAP-seq), RNA-seq, and transient transactivation assays revealed that SPL10 binds to the promoter of REVOLUTA (REV). Consistent with binding assays, overexpression of a miR165/166-resistant version of REV (rREV) in WT plants caused an upward-curling leaf phenotype. Conversely, overexpression of rSPL10 in a rev-6 mutant couldn't rescue the downward-curling leaf phenotype of rev-6. Notably, SPL10 physically interacts with REV, attenuating the upward-curling leaf phenotype of rREV mutants, suggesting a role as a molecular rheostat to prevent overamplification of REV transcripts. Furthermore, overexpression of the BrpREV-1 gene caused rosette leaves to change from flat to upward curving and accelerated heading in Chinese cabbage. Taken together, our findings identify the role of the SPL10-REV module in regulating leaf curvature in Arabidopsis and the crucial functions of BrpREV-1 in the heading of Chinese cabbage.

overall_design: DAP-seq to identify the dirctely target genes of SPL10.

first: Pengfei

last: Xu

first: Qihui

last: Wan

first: You

last: Wu

first: Xiang

last: Yu


title: Comparison of two materials effection on mice bone marrow mononuclear cells and cardiac repairing

city: wuxi

first: jiangan

last: li

address: No 68, Zhongshan Road

institute: Wuxi NO.2 People's Hospital of Nanjing Medical University

summary: Biomaterials can improve cardiac repair combined with transplantation of bone marrow mononuclear cells (BMMNCs). In this study, we compare the phenotype and cardiac repair between human heart valve-derived scaffold (hHVS) and nature protein/polycaprolactone (NP/PCL) anchored BMNNCs. Methods and Results: BMMNCs were obtained from mice five days following myocardial infarction. Subsequently, BMMNCs were separately cultured on hHVS and PCL. Proliferation and cardiomyogenic differentiation were detected in vitro. Cardiac function was measured after transplantation of cell-seeded cardiac patch on MI mice. After that, the BMMNCs were collected for mRNA sequencing after culturing on the scaffolds. Upon anchoring onto hHVS or PCL, BMMNCs exhibited an increased capacity for proliferation in vitro, however, the cells on hHVS exhibited superior ability cardiomyogenic differentiation ability. Moreover, both BMMNCs-seeded biomaterials effectively improved cardiac function after 4 weeks of transplantation, with reduced infarction area and restricted LV remodeling. Cell-seeded hHVS was superior to cell-seeded PCL.  Conclusion: BMMNCs on hHVS show better capacity in both cell cardiac repairing and improvement for cardiac function than on PCL. Compared with seeded onto PCL, BMMNCs on hHVS have 253 genes up regulated and 189 genes down regulated. The reason of hHVS is better than PCL for a scaffold for BMMNCs might be the optimized method of decellularization let more cytokines in ECM retained.

overall_design: BMMNCs were separately cultured on hHVS and PCL. Proliferation and cardiomyogenic differentiation were detected in vitro.the BMMNCs were collected for mRNA sequencing after culturing on the scaffolds.

first: Yao

first: Zhanghao

last: Huan

first: Jiahai

last: Shi


title: Dual role of GRHL3 in bladder carcinogenesis is associated with histological subtypes

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

institute: University Hospital Aachen

summary: Grainyhead-like transcription factor 3 (GRHL3) is known to affect cancer development depending on subtypes in various entities. Here, we analyzed the subtype-specific role of GRHL3 in bladder carcinogenesis comparing common urothelial carcinoma (UC) with squamous  bladder cancers (sq-BLCA). We examined GRHL3 mRNA and protein expression in cohorts of patient samples, its prognostic role as well as its functional impact on tumorigeneses in different molecular and histopathological subtypes of bladder cancer. We showed for GRHL3 a reverse expression in squamous and urothelial bladder cancer subtypes. Stably GRHL3 overexpressing EJ28 and SCaBER in vitro models revealed a tumor suppressive function in squamous and a oncogenic role in the urothelial cancer cells affecting cell migratory and invasive capacities. Transcriptomic profiling demonstrated highly subtype specific GRHL3 regulated expression networks coined by enrichment of genes involved in integrin mediated pathways. In SCaBER loss of RhoA GTPase activity was demonstrated associated with co-regulation of EIF4E3, a potential tumor suppressor gene. Thus, our data provide for the first time a detailed insight into the role of the transcription factor GRHL3 in different histopathological subtypes of bladder cancer.

overall_design: To investigate the function of GRHL3 in bladder carcinogenesis comparing different histological subtypes, we generated GRHL3 overexpressing single cell clone models in urothelial cell line EJ28 and squamous-like cell line SCaBER. We used mock clones as references with low (EJ28) and moderate (SCaBER) endogenous GRHL3 expression.

first: Franziska

last: Lammert

first: Julia

last: Pannhausen

first: Erik

last: Noetzel

first: Florian

last: Friedland

first: Yannick

last: Herfs

first: Ralf

last: Weiskirchen

first: Danny

last: Jonigk

first: Michael

last: Rose

first: Nadine

middle: T

last: Gaisa


title: Identification of factors influencing the pattern of polyadenylation site use in Saccharomyces cerevisiae

city: Boston

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

summary: Alternative polyadenylation gives rise to a wide variety of mRNA isoforms with distinct 3' ends; an individual gene can yield many 3' mRNA isoforms and has a typical pattern of poly(A) site use.   To identify possible determinants of polyadenylation site distribution, we have used CRISPR to create Saccharomyces cerevisiae strains harboring precise ORF deletions in candidate genes encoding various factors involved in gene expression.  We have performed 3' READS  to determine the genome-wide pattern of 3' mRNA isoform endpoints in these mutant strains.

overall_design: We have studied poly(A) profiles genome wide using the 3' READS technique in yeast strains harboring precise ORF deletions.

first: Joseph

middle: V

last: Geisberg

first: Kevin

last: Struhl


title: Effect of ZFPM2-AS1 knockdown on gene expression of breast malignant phyllode tumor cells.

city: Guangzhou

first: Shishi

last: He

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: ZFPM2-AS1 can promote the proliferation, migration and invasion of tumor cells, but its mechanism is still unclear.To investigate the molecular mechanism of malignant progression of breast phyllode tumors, we knocked down the expression of ZFPM2-AS1 in malignant phyllode tumor cells, and detected the genes regulated by ZFPM2-AS1 by RNAseq.

overall_design: We performed RNA-seq after knocking down ZFPM2-AS1 with siRNA in malignant phyllode tumor cells. Comparative gene expression profiling analysis of RNA-seq data for ZFPM2-AS1 knockdown cells and its control.

first: Yan

last: Nie

first: Di

last: Huang


title: Colchicine Ameliorates Doxorubicin Cardiotoxicity Via Promoting Autophagic Flux

city: Zhengzhou

first: Ying

last: Peng

address: No.1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: ；The First Affiliated Hospital of Zhengzhou University

summary: Doxorubicin (DOX) cardiotoxicity is an important factor of heart failure. The only clinically approved drug is dexrazoxane, while its side effect of secondary malignancies severely limited its application. It is urgent to find other alternative efficacious molecular for these chemotherapy patients. Colchicine is a safe and well tolerated anti-inflammation drug which also functions in attenuating the reactive oxygen species (ROS) generation. High dose of colchicine was reported block the autophagosome-lysosome fusion in cancer cells due to its destabilization effect to the microtubule system, while how colchicine affects the autophagic flux in cardiomyocytes is largely unknown. Recent years low dose of colchicine administration was reported helpful to the patients with pericarditis, postprocedural atrial fibrillation and coronary artery disease, most of the research attributed it to its anti-inflammation effect. Whether the autophagic flux regulated by colchicine also benefits to DOX induced heart failure remains unclear. Doxorubicin (DOX) administration was used to establish heart failure models in vivo and in vitro. Results showed that DOX blocked the autophagic vacuoles degradation, leading to damaged mitochondria and ROS accumulation. Heart failure characteristics were obviously improved after low dose of colchicine administration. Mechanistically, low dose of colchicine promoted the autolysosome degradation, cleared the damaged mitochondria, and ROS accumulation induced by the DOX and as a result attenuated DOX cardiotoxicity.

overall_design: hiPSc-CMs were treated with PBS or doxorubicin for 48h, and performed with RNA seq

first: Zhonggen

last: Li

first: Jianchao

last: Zhang

first: Xiaowei

first: Jianzeng

last: Dong


title: TNFR2 upregulation-caused loss of cell polarity prevents differentiation of myeloid-derived suppressor cells with ageing

city: ZhengZhou

first: Ming

last: Wang

address: jianshe Road

institute: ZhengZhou university

summary: Differentiation blockage can cause expansion of myeloid-derived suppressor cells (MDSCs) with ageing. Cell polarity loss (apolarity) in old stem or progenitor cells prevents their differentiation; but whether and how cell polarity is lost in old MDSCs, subsequently affecting their mature differentiation remains elusive. Here, we show that TNFR2 upregulation in old MDSCs triggers JNK over-activation, resulting in apolarity, differentiation blockage, and expansion of MDSCs with ageing. We find that TNFR2 expression in MDSCs can be induced by pro-inflammatory factors of senescence-associated secretory phenotype (SASP) and Tnfr2 deficiency in old mice significantly attenuates MDSCs’ differentiation blockage. Elevating TNFR2 expression in young MDSCs can induce apolarity and impair their differentiation; whereas suppressing JNK activity in old MDSCs can partially reverse their polarity and restore their differentiation capability. Therefore, TNFR2 aberrant upregulation represents a general mechanism by which extrinsic SASP signals dysregulate intrinsic cell polarity behaviors to arrest MDSCs’ mature differentiation during ageing.

overall_design: To detect the gene expression of ageing MDSC, the splenic MDSCs were isolated from ageing mice of the WT, Tnfr1-/-, and Tnfr2-/- strains for further RNA-seq analysis.

first: Zihao

first: Zhaoqing

first: Zhihai

last: Qin


title: Mitochondrial anomalies in induced pluripotent stem cells from Alzheimer’s disease cases with Presenilin 1 mutation

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

country: Canada

institute: HMR

summary: Presenilin 1 (PSEN1) is the most frequently mutated gene in early-onset sporadic and familial Alzheimer’s disease (FAD). The PSEN1 complex displays gamma-secretase activity and promotes cleavage of the C99-terminal fragment of the Amyloid Precursor Protein (APP) into the A42 peptide. PSEN1 is also involved in vesicle transport across ER and mitochondria in so called mitochondria associated membranes. We generated induced pluripotent stem cells (iPSCs) from 5 controls and 5 FAD cases carrying the PSEN1 A246E and L286V mutations. Unexpectedly, global gene expression profile analysis of FAD iPSCs revealed profound perturbation of mitochondrial, Golgi apparatus and ER pathways. PSEN1, APP and Nicastrin were highly expressed in iPSCs and PSEN1 localized to membrane-bound organelles. FAD iPSCs grown slower and showed elevated cell death together with abnormally high A42 secretion. Mitochondrial reactive oxygen species (ROS) were elevated in FAD iPSCs and treatment with a ROS scavenger significantly improved cell death, proliferation, and DNA damage. However, it could not improve the severe ATP deficit. Inhibition of gamma-secretase activity further exacerbated the overall FAD iPSC phenotype. Cortical neurons produced from the differentiation of FAD iPSCs showed Alzheimer’s pathology and TGFb pathway hyper-activation. PSEN1-mutant iPSCs may serve as a new model to perform genome-wide genetic screens and to study FAD pathophysiology and PSEN1 cellular function.

overall_design: In order to understand the role in PSEN1 in iPSC and neurons cells we compared the transcriptional background of iPSC or neurons that were affected or not by a mutation of PSEN1.


title: Basis of gene-specific transcription regulation by the Inegrator Complex (RNA-Seq)

first: Stefanie

last: Jonas

overall_design: To assess the functional relationship between INT and its TF factor interactors, we depleted one subunit of INT (INTS13) as well as each TF individually with siPOOLs in HEK293T cells and subjected these samples to total RNA-sequencing. In order to obtain efficient knockdown of each protein, we subjected the cells to double transfections with the first one occurring 24 hours after seeding and the second one occuring 24 hours later. The cells were then left to proliferate for 48 hours, after which RNA was extracted, Dnase treated. In order to determine the role of INTS13 and the TFs in glucose starvation response, we repeated the depletions of INTS13, HDGF and ZMYND8 under starved conditions, where growth medium was changes to glucose-free medium 24 hours after the second transfection. After DNase treatment, ribosomal RNAs were depleted and sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit. Libraries were sequenced on an Illumina NovaSeq 6000 using 100 bp single-end reads at a depth of 40M reads per library.

last: Sabath

first: Amena

last: Nabih

first: Christian

last: Arnold

first: Rim

last: Moussa

first: David

last: Domjan

first: Judith

last: Zaugg


title: Basis of gene-specific transcription regulation by the Inegrator Complex


title: Transcriptional landscape of human keratinocyte models exposed to 60-GHz millimeter-waves

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary:
Purpose: The use of millimeter waves (MMW) will likely grow exponentially in the coming years due to their future utilization in high-speed telecommunications. The question of the possible biological effects of these frequencies has been raised, and in the present study, we aimed to explore, throw an innovating RNA sequencing approach known as Bulk RNA Barcoding sequencing (BRB-seq), the difference in gene expression under exposure.
Methods: Tree main exposure scenario were explored. The first one aim to compare the cellular response of two primary culture of keratinocytes (HEK and NHEK) and one keratinocyte derivate cell line (HaCaT) exposed to MMW. The second scenario explore the dose effect of gradient of incident power density on gene expression in cell line. The last one explore the exposure time at the new exposure limit for the general population.
Results: Our data shows that gene expression is quite different between the cellular models used, which validates the method used. However, the exposure scenarios demonstrates that the main effect was the heat effect associated with high power MMW. Some genes were also altered by exposure. Altered expression of 2 genes was confirmed with qRT–PCR.
Conclusions: These results show that acute exposure to MMW has low effect on gene expression.

overall_design: HEK_3N, NHEK and HaCat cells were exposed 3 hours to 20 mW/cm² or equivalent Heat effect or Sham exposed. For HaCat cell gradient exposure between 0 and 20 mW/cm² was evaluated and long term treatment 14h at 10 MW/cm².

first: Catherine

last: Martin

first: Bertrand

last: Everard

first: Thomas

last: Darde

first: Aurelie

last: Lardenois

first: Frederic

first: Denis

last: Habauzit


title: 0.1 Terahertz irradiation alleviates rheumatoid arthritis and exerts immunomodulatory effects in CIA mice

city: xi'an

first: Qi

last: Zhang

address: No. 28 Xianning West Road

institute: Xi’an Jiaotong University

summary: This study investigated the systemic effects of 0.1 THz irradiation on the inflammatory status of rheumatoid arthritis (RA) in the collagen-induced arthritis (CIA) mouse model. It was found that THz irradiation apparently alleviated the symptoms of arthritis in CIA mice, reducing the joint swelling, mitigating the tissue damage and relieving the expression of pro-inflammatory factors (TNF-, IL-6, RANKL and MMPs) in the swollen joint of the CIA mice. Moreover, the reduction of serum inflammatory cytokines levels together with the reduced CD4+ T cell count and the recovered percentage of regulatory T cells (Treg) indicated that THz irradiation exerted a systemic immunoregulatory activity in CIA mice. The blood leukocyte mRNA-seq GO analysis also enriched several biological processes including the differentiation and adhesion of leukocytes, lymphocyte differentiation and T cell activation, providing additional supporting evidence for the immunoregulatory effects of THz.

overall_design: Total 60 7-week-old male DBA/1 mice were divided into three groups randomly,  the control group (Ctrl, C), the CIA model group (CIA, M) and the CIA with THz irradiation group (CIA+THz, F). when the CIA model established, the swollen joint of mice were treated with 0.1Thz wave for 14 days. leukocyte obtained from blood of mice were performed to RNAseq.


title: Transcriptomics reveals novel molecular features of SLE severity

city: HeFei

first: zhang

middle: xiao

last: jing

state: AnHui

address: 81 Meishan Road

department: dermatology

institute: Anhui Medical University

summary: Complex blood transcriptomes can lead to the clinical heterogeneity of systemic lupus erythematosus (SLE). In the current study, we integrated transcriptomics, public data mining and clinical parameters to reveal whether SLE severity is affected by specific genes or pathways.

overall_design: Blood from SLE patients was collected and divided into two groups according to the severity of disease. Transcriptome data characteristics of the two groups were analyzed

first: Xiaojing

first: Jiali

first: Zhaobing

last: Pan

first: Yuxi

first: Xiaoqing

last: Xu

first: Fusheng

last: Zhou

first: Zhengwei

last: Zhu

first: Leilei

last: Wen


title: Progressive multiple sclerosis

city: Odense

first: Anne

last: Hartebrodt

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark


title: An ex vivo human precision-cut lung slice platform provides insight into SARS-CoV-2 pathogenesis and antiviral drug efficacy

city: Little Rock

first: Stephanie

middle: D

last: Byrum

state: Arkansas

address: 501 Jack Stephens Dr, Jackson T. Stephens Bldg 4th floor

institute: University of Arkansas for Medical Sciences

summary: COVID-19 has claimed millions of lives since the emergence of SARS-CoV-2, and lung disease appears the primary cause of the deaths in COVID-19 patients.  However, the underlying mechanisms of COVID-19 pathogenesis remain elusive and there is no existing model where the disease can be faithfully recapitulated and conditions for the infection process can be experimentally controlled.  Herein we report the establishment of an ex vivo human precision-cut lung slice (hPCLS) platform for studying SARS-CoV-2 pathogenicity and innate immune response, and for evaluating the efficacy of antiviral drugs against SARS-CoV-2.  We show that while SARS-CoV-2 continued to replicate during the course of infection of hPCLS, infectious virus production peaked within 2 days, and rapidly declined thereafter.  Although most proinflammatory cytokines examined were induced by SARS-CoV-2 infection, the degree of induction and types of cytokines varied significantly among hPCLS from individual donors, reflecting the heterogeneity of human populations.  In particular, two cytokines (IP-10 and IL-8) were highly and consistently induced, suggesting a role in the pathogenesis of COVID-19.  Histopathological examination revealed focal cytopathic effects late in the infection.  Transcriptomic and proteomic analyses identified molecular signatures and cellular pathways that are largely consistent with the progression of COVID-19 in patients.  Furthermore, we show that homoherringtonine, a natural plant alkaloid derived from Cephalotoxus fortunei, not only inhibited virus replication but also production of pro-inflammatory cytokines, and ameliorated the histopathological changes of the lungs caused by SARS-CoV-2 infection, demonstrating the usefulness of the hPCLS platform for evaluating antiviral drugs.

overall_design: Applied RNAseq to compare the transcriptomic profile of ex vivo human precision-cut lung slices (hPCLS) following infection from 24hr to 96hr with SARS-CoV-2, and compared them with those from uninfected hPCLS.

first: Roger

last: Pechous

first: Priyangi

last: Malaviarachchi

first: Srijon

last: Banerjee

first: Duah

last: Alkam

first: Alireza

last: Ghaffarieh

first: Richard

last: Kurten

first: Joshua

last: Kennedy

first: Xuming


title: Gene expression screening using E17.5 mouse nasomaxillary tissue

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: The tissues prepared from both Pth1r f/f and Wnt1-Cre: Pth1r f/f embryos were analysed.

overall_design: Once frozen tissues were subjected to RNA isolation using Trizol.

first: Katsuhiko

last: Amano

last: Okuzaki


title: Human bladder cancer cell line high throughput sequencing - genes regulated by hMSH2 - untreated

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

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

summary: The activation status of some DNA damage repair proteins is closely related to the efficacy of CDDP chemotherapy in MIBC. In this study, we used CRISPR/cas9 gene-editing technology to construct hMSH2-deficient bladder cancer cells and confirmed that loss of hMSH2 decreased the sensitivity of bladder cancer cells to cisplatin. Transcriptome analysis was performed to find the potential genes that could be regulated by hMSH2.

overall_design: In order to screen downstream genes regulated by hMSH2, transcriptome analysis was performed in hMSH2-deficient EJ cells and compaired wild-type EJ cells.

first: Wei

last: Wenjie


title: Human bladder cancer cell line high throughput sequencing - genes regulated by hMSH2

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of peripheral neuropathy in a high-fat diet-induced mouse model of type 2 diabetes

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

summary: Peripheral neuropathy (PN) is the most common microvascular complication of type 2 diabetes mellitus (T2D). However, a thorough understanding of the mechanisms underlying PN pathogenesis is currently lacking. Thus, the goal of the current study was to use system biology approaches to investigate the development and progression of PN in a high-fat diet (HFD)-induced mouse model of T2D. Transcriptomic data sets from sciatic nerve (SCN) and dorsal root ganglia (DRG) tissue were collected from 12- and 36-week-old HFD-fed mice and analyzed using self-organizing map and differentially expressed gene analysis with functional enrichment. Consistent with prior literature, pathways related to immune function and inflammation, mTOR signaling, and lipid metabolism were dysregulated in the SCN and DRG of HFD-fed mice. Additionally, cell-type abundance analysis revealed changes in cell composition in the SCN and DRG of HFD-fed T2D mice over time, particularly in the SCN. Comparison of differentially expressed genes from the SCN of HFD-fed mice to transcriptomic data from human sural nerve further supported the role of inflammation, mTOR signaling, and lipid metabolism in PN. Results from this study provide the basis for mechanistic studies investigating nerve damage in T2D and support the development of mechanism-based treatment options for PN.

overall_design: mRNA of two diabetic complication-prone peripheral nerve tissues (sciatic nerve and dorsal root ganglia) from 12- or 36-week old C57BL/6 mice with 45% fat kcal high-fat-diet-fed or standard-diet-fed were collected. Deep sequencing of five-six biological replicates in each tissue/age-group was performed using Illumina HiSeq 2000.

first: Eva

last: Feldman


title: Depletion of MALAT1-dependent WTAP reduces aggressiveness of hypoxic TNBC cells

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

institute: University of Padova

summary: Numerous studies have identified long non-coding RNAs (lncRNA) as critical players in regulating tumor progression and metastasis formation. Here, we show that MALAT1 in hypoxic conditions, positively regulates WTAP protein expression, which influences the response to hypoxia by favoring the transcription of the master regulators HIF1A and HIF1B. Furthermore,WTAP stimulates BC cell migratory ability and the expression of N-Cadherin and Vimentin, hallmarks of epithelial-to-mesenchymal transition (EMT)

overall_design: RNA samples from 2 biological replicates of ChIRP assays performed in MDA-MB-468 cells to recover lncMALAT1-interacting RNAs have been pulled and subjected to RNAseq, along with relative Input samples used as reference

first: Martina

last: Dragonetti

first: Chiara

last: Turco

first: Anna

last: Benedetti

first: Giulia

last: Fontemaggi


title: lncRNAs differentially expressed in benign and malignant phyllodes tumors [array]

first: Shishi

last: He

summary: To investigate the pathogenesis of malignant phyllodes tumors of the breast, we used lncRNA+mRNA microarray expression profiling as a platform to investigate lncRNAs that play a key role in the malignant progression of phyllodes tumors of the breast.A total of 4 cases of breast fibroadenomas, 6 cases of benign phyllodes tumors and 6 cases of malignant phyllodes tumors were included. Fibroadenomas and benign phyllodes tumors were used as controls to screen out significantly differentially expressed lncrnas in malignant phyllodes tumors.

overall_design: LncRNAs expression in human breast tumors were measured.  Biological replicates: 4 cases of breast fibroadenomas, 6 cases of benign phyllodes tumors and 6 cases of malignant phyllodes tumors.

first: Yan

last: Nie

first: Di

last: Huang


title: Transcriptomes of Norway spruce seedling roots

city: Uppsala

first: Van

last: Nguyen

address: Almas Allé 5

country: Sweden

institute: Uppsala University

summary: We examine the development of the seedling roots based on two sets of data: one includes segments of the roots and one includes laser capture microdissection (LCM) root tissues.

overall_design: Regarding the zone data, we collected 4 segments of the root from the root tip (3 x 1mm each and 1 x 2mm). Regarding the LCM data, we collected the QC area, ground tissues, and steles of the elongation and differentiation zones.

first: Daniel

last: Uddenberg

first: Annelie

last: Carlsbecker


title: miR-seq analysis of nucleus pulposus tissues from compression-induced intervertebral disc degeneration rats

city: Suzhou

first: Jiangbo

last: Guo

state: Jiangsu

address: 899 Pinghai St.

department: Department of Orthopaedics

institute: The First Affiliated Hospital of Soochow University

summary: Intervertebral disc degeneration (IDD) is an important cause of low back pain. And abnormal mechanical factors are an important contributor to IDD. To identify mechanical responsive miRNAs in IDD, we used a custom-made compression device to establish IDD in rats and considered as IDD group, and the Sham group was inserted with K-wires into coccyxes only. After four weeks, rat nucleus pulposus tissues were obtained for miR-seq analysis.

overall_design: To identify mechanical responsive miRNAs in IDD, we examined the miRNA expression profiles with miR-seq on 3 nucleus pulposus tissues from the IDD group vs. 3 nucleus pulposus tissues from the Sham group.

first: Zongping

last: Luo

first: Qin

last: Shi

first: Huilin

last: Yang


title: Basis of gene-specific transcription regulation by the Inegrator Complex (ChIP-Seq I)

city: Zürich

first: Stefanie

last: Jonas

address: Otto-Stern-Weg 5

institute: ETH Zurich

summary: Integrator (INT) is a multi-subunit modular RNA processing complex, which exhibits both RNA endonuclease and protein phosphatase activity. It is responsible for transcription termination at the 3’ ends of a diverse array of RNA polymerase II (RNAP2) transcribed non-coding RNAs, as well as transcription regulation at a large number of protein coding genes. There, it terminates RNAP2 at promoter proximal pausing sites, cleaves the nascent transcript and competes with elongation factors.This INT-mediated tapering of gene expression attenuates stimulus responsive genes and is essential for cell differentiation. Although INT affects transcription at varying classes of RNAs in diverse biological contexts, how it achieves specificity in a gene- and context-dependent manner has remained elusive. Using a combination of proteomics, interaction studies and structural characterization, we identified a diverse set of transcription factors (TFs) that associate directly with defined surfaces on INT. Stress conditions lead to changes in the types of TFs bound by INT, and quantitative binding studies suggest that TF affinities can be modulated by altering the phosphorylation states of specific residues in their INT-binding motifs. Integrated multi-omics data show that INT and its TF interactors regulate significantly overlapping sets of genes and indicate that these TFs recruit INT to specific genomic loci. Consistently, we find that starvation induced formation of primary cilia, which is a cellular stress response reliant on INT-mediated transcription regulation, depends on intact TF-INT binding. Taken together, our data suggest that TFs lend INT specificity to elicit targeted gene regulation as a transcriptional response in defined biological contexts.

overall_design: Chromatin Immunoprecipitation followed by sequencing (ChIPseq) of INTS13 and several of its TF interactors was performed to determine whether they colocalize at genomic loci. Geen-specific antibodies were used for each pulldown

first: Kevin

last: Sabath

first: Amena

last: Nabih

first: Christian

last: Arnold

first: Rim

last: Moussa

first: David

last: Domjan

first: Judith

last: Zaugg


title: Effect of  LPS-MCM and Hemin-MCM on gene expression of astrocytes

city: Shanghai

first: Chang

last: Liu

address: 1954 Hua Shan Road

department: School of Biomedical Engineering

institute: Shanghai Jiao Tong University

summary: To investigate the transcriptional changes occurred in astrocytes after inflammatory or hemorrhagic stroke in vitro, we performed RNA sequencing (RNA-seq) of resting-MCM treated astrocytes, LPS-MCM treated astrocytes, and Hemin-MCM treated astrocytes.

overall_design: Astrocytes were isolated from P0 C57BL/6 mice and were treated with conditioned medium from LPS-stimulated microglial (LPS-MCM) or hemin (the degradation product of hemoglobin)-stimulated microglial (Hemin-MCM). Comparative gene expression profiling analysis of RNA-seq data for resting-MCM treated astrocytes, LPS-MCM treated astrocytes, and Hemin-MCM treated astrocytes, each group has 3 separate duplications.

first: Shiyu

last: Deng

first: Guo-Yuan

first: Yaohui

last: Tang


title: Effects of aflatoxin B1 on metabolism- and immunity-related gene expression in Hermetia illucens L. (Diptera: Stratiomyidae)

status: Public on Jun 18 2024

city: Wageningen

first: Parth

last: Shah

state: Gelderland

address: Droevendaalsesteeg 1

department: Laboratory of Entomology

country: Netherlands

institute: Wageningen University

summary: Contamination of food products with mycotoxins such as aflatoxin B1 (AFB1) poses a severe risk to human health. Larvae of the black soldier fly (BSFL), Hermetia illucens (Diptera: Stratiomyidae), can successfully metabolize AFB1 without any negative consequences on their survival or growth. However, the underlying mechanisms that allow BSFL to metabolize AFB1 are unknown. In this study, five-day-old BSFL were fed with either a control  or an AFB1-spiked (20 µg/kg) diet to elucidate the underlying mechanisms. Larval samples were collected at three timepoints (6 h, 24 h, and 72 h) and subjected to RNA-Seq analysis to determine gene expression patterns. Provision of an AFB1-spiked diet resulted in an up-regulation of 357 and a down-regulation of 929 unique genes. Upregulated genes include multiple genes involved in AFB1 metabolism in other (insect) species. Downregulated genes were generally involved in the insects' growth, development, and immunity. BSFL possesses a diverse genetic arsenal that encodes for enzymes capable of metabolizing AFB1 without trade-offs on larval survival.

overall_design: Five-day-old BSF larvae were fed on control or AFB1-spiked chickenfeed diet. Samples were collected from respective treatment at 6 h, 24 h and 72 h post-treatment respectively. Total RNA was extracted and sequenced. Genes that were differentially expressed due to AFB1 feeding were determined using DESeq2, and the affected biological processes were determined using gene ontology (GO) analysis.

first: Kelly

last: Niermans

first: Elise

last: Hoek-van den Hil

first: Marcel

last: Dicke

first: Joop

last: van Loon


title: Human bladder cancer cell line high throughput sequencing - genes regulated by hMSH2 - CDDP therapy

first: Guosong

last: Jiang

overall_design: In order to screen downstream genes regulated by hMSH2, transcriptome analysis was performed in hMSH2-deficient EJ cells and compaired wild-type EJ cells treated with CDDP.

first: Wei

last: Wenjie


title: Planar cell polarity proteins mediate ketamine-induced restoration of glutamatergic synapses in prefrontal cortical neurons in a mouse model for chronic stress

city: San Diego

first: Andiara

last: Espindola de Freitas

state: California

address: Gilman Drive

department: Biological Sciences

institute: UC San Diego (UCSD)

summary: We performed single cell transcriptomics analyses in medial prefrontal cortical (mPFC) and basolateral amygdala (BLA). Ketamine induced changes in inflammatory pathways reversing corticosterone effects. Cell-cell communication analyses predicted that planar-cell-polarity (PCP) signaling is decreased after corticosterone but increased following ketamine administration in excitatory neurons. Single cell transcriptomics analyses in dorsolateral prefrontal cortical (dl-PFC) neurons of depressed patients also showed decreased PCP signaling in excitatory neurons. Using chemogenetics, we found that the BLA-projecting infra limbic prefrontal cortex (IL PFC) neurons regulate immobility time in the tail suspension test and food consumption. Using RNAScope, we found, in the excitatory neurons in mPFC, Celsrs and Prickle2 were reduced by corticosterone but increased by ketamine. Using CRISPR-Cas9, we conditionally knocked out Celsrs and Prickle2 in the BLA-projecting IL-PFC neurons and found that ketamine-induced synapse restoration and behavioral remission were abolished.  Ketamine affects gene expression and PCP proteins underly long-lasting effects of low-dose ketamine.

overall_design: C57BL/6J mice exposed to 35 µg/ml of CORT in the drinking water for 6 weeks. A control group received regular drinking water without CORT. After chronic CORT treatment, mice were treated with the fast-acting antidepressant Ket (10 mg/kg, i.p.). 24 h after Ket’s treatment, brains were harvested, and the prefrontal cortices were rapidly dissected and processed according to the manufacturer’s instructions.

last: E. Freitas

first: Bo

last: Feng

first: Clayton

last: Baker

first: Shae

last: Galli

first: Yue

last: Ban

first: Yimin

last: Zou


title: Transcriptomic studies on ruxolitinib with or without checkpoint inhibitors as a cancer therapy

first: John

middle: R

last: Teijaro

state: CA

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

institute: The Scripps Research Institute

summary: Unleashing anti-tumor T cell activity by checkpoint inhibition is effective in many cancer patients but clinical response rates remain limited. Myeloid derived suppressor cells erode antitumor lymphocyte numbers and function, and correlate with resistance to checkpoint inhibitors. By screening small molecule libraries, we identified JAK inhibitors’ ability to rescue T cell function. Despite its documented immune suppressive properties, the prototypical JAK inhibitor ruxolitinib enhanced the efficacy of immune checkpoint blockade in cancer. This effect correlated with loss of suppressive gene expression, and acquisition of immunostimulatory molecular markers and T cell stimulatory activity in myeloid cells. In preclinical models, ruxolitinib significantly improved the function and increased the total numbers of activated tumor-infiltrating NK and CD4 T cells compared to checkpoint blockade alone and the efficacy was conditional on granulocytic cells. In addition to myeloid reprogramming in the tumor, ruxolitinib blunts G-CSF signaling in the bone marrow to prevent expression of suppressive and chemotaxis genes in neutrophils.

overall_design: Immunocompetent mice bearing wt MC38, JAK1ko MC38, LLC1 or EL4 tumors were treated with ruxolitinib or vehicle (daily gavage) and anti-PD1 plus anti-CTLA4 (ICB), or isotype control (intraperitoneal injection every 7 d). Treatment was initiated once tumors became palpable. At a pre-selected timepoint tumors were harvested and processed into single-cell suspension. Live single CD45+ cells were sorted and subjected to CITE-seq using a standard protocol for 10X Genomics 3' single-cell transcriptome with antibody-derived protein barcoding. Bone marrow and blood CD45+ were harvested as single-cell suspensions and processed using the same CITE-seq protocol. To test the effect of ruxolitinib on splenocytes during persistent viral infection, mice infected with LCMV Clone 13 (2x10^6 pfu) were treated with ruxolitinib or vehicle by daily gavage from the day of infection and at 10 d post infection single-cell splenocyte suspension sorted by flow cytometry. Live single CD45+ splenocytes were subjected to the same CITE-seq protocol.

first: Jaroslav

last: Zak

first: Isaraphorn

last: Pratumchai


title: Effects of VNS on the NTS

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: Chronic intermittent VNS was applied in sponteneously hypertensive rats.

overall_design: VNS was applied 3x per day, 5x per week, for 7 weeks.

first: Jasenka

last: Zubcevic

first: Elliott

last: Dirr

first: Kevin

last: Otto


title: miRNA expression profiling of human gastric cancer cell lines with or without HDACi vorinostat  treatment

city: Guangzhou，China

first: jide

last: Wang

state: Guangdong ，China

address: 1838 Guangzhou Avenue North

department: Department of Digestive Medicine

institute: Nanfang Hospital, Southern Medical University

summary: To investigate whether microRNAs (miRNAs) were induced by histone deacetylase inhibitors (HDACi) in human gastric cancer cells, the miRNA-seq was used to screen differentially expressed miRNAs in two human gastric cancer cell lines (HGC-27 and AGS) treated with the HDACi vorinostat (SAHA) or vehicle (DMSO).

overall_design: The human gastric cancer cell lines (HGC-27 and AGS) were treated with SAHA (5 µM) or vehicle (DMSO) for 24 hours. Then, we extracted total RNA from the cells and miRNA-seq was performed.

first: Jide


title: A role for histone lysine demethylase 4 in regulating HBV replication

city: Oxford

first: James

last: Harris

state: Oxfordshire

address: Old Road Campus, Roosevelt Drive

country: United Kingdom

institute: University of Oxford

summary: HepG2-NTCP cells were infected with HBV, before being treated with 30uM FG-4592, 5uM QC6352, or cultured in 1% oxygen for 72 hours. The impact of cuture conditions on both the host and viral transcriptome were determined by RNA-sequencing.

overall_design: mRNA expression profiles of HBV infected HepG2-NTCP cells cultured in 18% (control) or 1% Oxygen, or treated with 5uM QC6352 or 30uM FG-4592 for 72 hours.

first: Peter

last: Wing

first: Andrea

last: Magri

last: Balfe

first: Jane

last: McKeating


title: Effect of hormone treatment on Norway spruce seedlings [Hypocotyl]

first: Van

last: Nguyen

summary: We analyze the underlying molecular mechanisms for the observed changes to cambium and xylem differentiation by assessing gene expression changes after hormone applications.

overall_design: Approximately 2-week old seedlings were treated with either cytokinin, auxin or a combination of both hormones using lanolin as the carrier. Lanolin was applied onto the middle region of the hypocotyl.

first: Annelie

last: Carlsbecker


title: FoxM1-Retinoblastoma Interaction Induces Tumor Microenvironment That Drives Metastasis

city: Chicago

first: Maria

middle: Paula

last: Zappia

state: IL

address: 900 S Ashland Ave

department: Biochemistry and Molecular Genetics

institute: University of Illinos at Chicago

summary: A mouse strain expressing an Rb-binding deficient mutant of FoxM1, FoxM1 DD, develops PyMT-driven mammary tumors that are deficient in metastasis. Single-cell RNA-Seq analyses revealed altered tumor microenvironment (TME). Unlike the FoxM1 +/+ tumors, the FoxM1 DD/DD tumors lack tumor-infiltrating cells, resulting from a deficiency in the tumor cell-populations that express factors necessary for their recruitment. Furthermore, FoxM1 DD/DD tumors contain fewer mammary cancer stem/progenitor cells, but more differentiated tumor cells.

overall_design: FoxM1 +/+ PyMT-driven mammary tumors were compared to FoxM1 DD/DD PyMT-driven mammary tumors by single cell RNA-seq (Drop-seq)

middle: P

first: Dragana

last: Kopanja

first: Maxim

last: . Frolov

first: Abul

middle: B

last: Islam

first: Pradip

last: Raychaudhuri


title: Skin transcriptome of non-communicable inflammatory skin diseases

city: Munich

first: Stefanie

last: Eyerich

address: Biedersteinderstrasse 29

institute: Center of Allergy and Environment

summary: This study includes RNAseq data of lesional and autologous non-lesional skin from patients with non-communicable inflammatory skin diseases, including psoriasis, nummular eczema and atopic dermatitis.

overall_design:
RNA from skin biopsies was isolated using the QIAzol Lysis Reagent (Qiagen) and miRNeasy Mini Kit (Qiagen) according to manufacturer’s protocol. RNASeq libraries were generated using the TruSeq Stranded Total RNA Kit (Illumina) according to manufacturer’s high sample protocol. Finally, samples were sequenced on an Illumina HiSeq4000 as paired-end with a read length of 2x 150 bp and an average output of 40 Mio reads per sample and end.

**Please note that the records have been updated on June 28, 2024**

first: Richa

last: Batra

first: Natalie

last: Garzorz-Stark

first: Felix

last: Lauffer

first: Manja

last: Jargosch

first: Nikola

last: Müller

first: Kilian


title: Brain mRNA expression profiling of Atlantic salmon (Salmo salar) age-at-maturity-associated genes during different maturation stages

status: Public on Jun 17 2024

city: Helsinki

first: Ehsan

middle: Pashay

last: Ahi

address: Biocenter 1, Viikinkaari 9

country: Finland

institute: University of Helsinki

summary: Study revealed new information about molecular functions of the vgll3 and six6 genes associated with age-at-maturity in the brain of Atlantic salmon

overall_design: In the study presented here, expression patterns of two genes associated with age-at-maturity in Atlantic salmon, their paralogs and 340 additional genes were studied in whole hatchery-derived individuals of three maturation stages, immature-1 and immature-2, and mature, in the brain of two vgll3 genotypes (early and late maturation genotypes).

first: Craig

last: Primmer

first: Johanna

last: Kurko


title: A nucleosome switch primes Hepatitis B Virus infection [ChIP-Seq]

status: Public on Jun 19 2024

city: New York

first: Andres

last: Mansisidor

state: NY

address: 1230 York Ave Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: Rockefeller University

summary: Chronic hepatitis B virus (HBV) infection is an incurable global health threat responsible for causing liver disease and hepatocellular carcinoma. During the genesis of infection, HBV establishes an independent minichromosome consisting of the viral covalently closed circular DNA (cccDNA) genome and host histones. The viral X gene must be expressed immediately upon infection to induce degradation of the host silencing factor, Smc5/6. However, the relationship between cccDNA chromatinization and X gene transcription remains poorly understood. Establishing a reconstituted viral minichromosome platform, we found that nucleosome occupancy in cccDNA drives X transcription. We corroborated these findings in cells and further showed that the chromatin destabilizing molecule CBL137 inhibits X transcription and HBV infection in hepatocytes. Our results shed light on a long-standing paradox and represent a potential new therapeutic avenue for the treatment of chronic HBV infection.

overall_design: We performed RNA-seq and MNase-seq on HEK293T cells that were transfected with hepatitis B virus (HBV) cccDNA over different timepoitns post transfection. We also performed MNase-seq on HBV cccDNA that was reconstituted with nucleosomes at different levels of saturation. Finally, we performed ChIP-seq on cells either constitutively modeling HBV infection (HepAD38) or that were transfected with HBV cccDNA (HepG2).

first: Nicholas

last: Prescott

first: Andrés

first: Yaron

last: Bram

first: Tracy

last: Biaco

first: Justin

last: Rendleman

first: Sarah

last: Faulkner

first: Abigail

last: Lemmon

first: Christine

last: Lim

first: Pierre-Jacques

last: Hamard

first: Richard

last: Koche

first: Viviana

middle: I

last: Risca

first: Robert

middle: E

last: Schwartz

first: Yael

last: David


title: Gene expression in shoot and root tissues (wild-type, oshho3-KO)

city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

state: Tokyo

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

institute: The University of Tokyo

summary: To examine differential effect of the mutation of rice OsHHO3 on the gene exoression in shoot and root tissues, we performed microarray analysis using shoot and root tissues of wild-type and oshho3-KO mutant.

overall_design: Shoot and root tissues from 27 day-old wild-type and oshho3-KO seedlings grown under nitrogen-sufficient conditions

first: Shuichi

last: Yanagisawa


title: Tryptophan 2, 3-dioxygenase positive matrix fibroblasts fuel breast cancer lung metastasis via kynurenine-mediated ferroptosis resistance of metastatic cells and T cell dysfunction

city: Chongqing

first: yong

middle: can

last: liu

address: No.1, Yi-Xue-Yuan Road, Yu-zhong District, Chongqing 400016, China.

institute: Chongqing medical university

summary: Background: Tumor metastasis is a major threat to cancer patient survival. The organ-specific niche plays a pivotal role in tumor organotropic metastasis. Fibroblasts serve as a vital component of the metastatic microenvironment, but how heterogeneous metastasis-associated fibroblasts (MAFs) promote organotropic metastasis is poorly characterized. Here, we aimed to decipher the heterogeneity of MAFs and elucidate the distinct roles of these fibroblasts in pulmonary metastasis formation in breast cancer. Methods: Mouse models of breast cancer pulmonary metastasis were established using an in vivo selection method of repeated injections of metastatic cells purified from the mouse lung. Single-cell RNA sequencing (scRNA-seq) was employed to investigate the heterogeneity of MAFs. Transgenic mice were used to examine the contribution of tryptophan 2, 3-dioxygenase positive matrix fibroblasts (TDO2+ MFs) in lung metastasis.. Results:  We uncovered three subtypes of MAFs in the lung metastatic microenvironment and their transcriptome profiles changed dynamically as lung metastasis evolves. As the predominant subtype, matrix fibroblasts (MFs) were exclusively marked by platelet-derived growth factor receptor alpha (PDGFRA) and mainly located on the edge of the metastasis, and T cells were enriched around MFs. Notably, high MFs signatures were significantly associated with poor survival in breast cancer patients. Lung metastases were markedly diminished and the suppression of T cells was dramatically attenuated in MF-depleted experimental metastatic mouse models. We found that TDO2+ MFs control pulmonary metastasis by producing kynurenine (KYN), which upregulated FTH1 level in disseminated tumor cells (DTCs), enabling DTCs to resist ferroptosis. Moreover, TDO2+ MFs-secreted chemokines CCL8 and CCL11 recruited T cells. TDO2+ MF-derived KYN induced T cell dysfunction. Conditional knockout of Tdo2 in MFs diminished lung metastasis and enhanced immune activation. Conclusions: Our study reveals crucial roles of TDO2+ MFs in promoting lung metastasis and DTCs' immune evasion in the metastatic niche. It suggests that targeting the metabolism of lung-specific stromal cells may be an effective treatment strategy for breast cancer patients with lung metastasis.

overall_design: To further understand how Tdo2high MFs affected the fate of disseminated tumor cells, we performed unbiased RNA sequencing in Tdo2high MFs CM-treated 4T1-LM3 cells (Control CM-treated 4T1-LM3 cells as control). Gene expression profiling  was compared using the bulk RNA-seq data.

first: Yongcan

last: Liu

first: Shanchun

last: Chen

first: Manran


title: DPF2 reads histone lactylation to drive transcription and tumorigenesis [CUT&TAG]

city: Tianjin

first: 爱源

last: 王

state: —Please choose an option—

address: No. 22, Meteorological Observatory Road, Heping District, Tianjin

department: Department of Biochemistry and Molecular Biology

institute: TianjinMedical University

summary: Lysine lactylation (Kla) is a new type of histone mark implicated in the regulation of various functional processes such as transcription. However, how this histone mark acts in cancers remains unexplored due in part to a lack of knowledge about its reader proteins. Here, we observe that cervical cancer (CC) cells undergo metabolic reprogram by which lactate accumulation and thereby boost histone lactylation, particularly H3K14la. Utilizing a multivalent photoaffinity probe in combination with quantitative proteomics approach, we identify DPF2 as a candidate target of H3K14la. Biochemical studies as well as CUT&Tag analysis reveal that DPF2 is capable of binding to H3K14la, and co-localizes with it on promoters of oncogenic genes. Notably, disrupting the association between DPF2 and histone lactylation through structure-guided mutation blunts those cancer-related gene expression along with cell survival. Together, our findings reveal DPF2 as a bona fide H3K14la effector that couples histone lactylation to gene transcription and cell survival, offering insight into how histone Kla engages in transcription and tumorigenesis.

overall_design: We  implemented CUT&Tag assays in Hela cells to test whether DPF2 links H3K14la in the native chromatin context. To this end, the cells were  immunoprecipitated by H3K14la or H3K14ac antibodies, respectively, followed by high-throughput sequencing. Furthermore, to test whether DPF2-occupied peaks are enriched in a DPF-domain-dependent manner, cells stably expressing Flag-tagged DPF2 or its mutants were immunoprecipitated using Flag antibodies and analyzed by sequencing.


title: Fate-mapping and functional dissection reveal perilous influence of type I interferon signaling in mouse brain aging

city: Houston

first: Ethan

last: Roy

state: TX

address: 7000 Fannin St

institute: UT Health Science Center Houston

summary: Aging significantly elevates the risk of developing neurodegenerative diseases. Neuroinflammation is a universal hallmark of neurodegeneration as well as normal brain aging. Which branches of age-related neuroinflammation, and how they precondition the brain toward pathological progression, remain ill-understood. The presence of elevated type I interferon (IFN-I) has been documented in the aged brain, but its role in promoting degenerative processes, such as the loss of neurons in vulnerable regions, has not been studied in depth. To comprehend the scope of IFN-I activity in the aging brain, we surveyed IFN-I-responsive reporter mice at multiple ages. We also examined 5- and 24-month-old mice harboring selective ablation of Ifnar1 in microglia to observe the effects of manipulating this pathway during the aging process using bulk RNA sequencing and histological parameters. We detected age-dependent IFN-I signal escalation in multiple brain cell types from various regions, especially in microglia. Selective ablation of Ifnar1 from microglia in aged mice significantly reduced overall brain IFN-I signature, dampened microglial reactivity, lessened neuronal loss, restored expression of key neuronal genes and pathways, and diminished the accumulation of lipofuscin, a core hallmark of cellular aging in the brain. Overall, our study demonstrates pervasive IFN-I activity during normal mouse brain aging and reveals a pathogenic, pro-degenerative role played by microglial IFN-I signaling in perpetuating neuroinflammation, neuronal dysfunction, and molecular aggregation. These findings extend the understanding of a principal axis of age-related inflammation in the brain, one likely shared with multiple neurological disorders, and provide a rationale to modulate aberrant immune activation to mitigate neurodegenerative process at all stages.

overall_design: Mice of various genotypes were aged to stated time points and harvested. Bulk cortical tissues were used for RNA-seq analysis.

first: Sanming

last: Li

first: Sepideh

last: Saroukhani

first: Yanyu

last: Wang

first: Wei

last: Cao


title: DPF2 reads histone lactylation to drive transcription and tumorigenesis [RNA-seq]

overall_design: On the basis of our findings that the correlation between DPF2 and H3K14la at promoter regions and lactate boosts H3K14la instead of H3K14ac, we propose that DPF2-H3K14la recognition confer transcription, and the genes modulated by this recognition could be obtained through a quantitative RNA-Seq analysis of cells expressing WT-DPF2 and Mut-DPF2 prior to lactate supplementation. To assess this, we performed RNA-Seq detection from WT-DPF2 or Mut-DPF2 expressed cells upon lactate pre-treatment.


title: SASH1 S519N variant links skin hyperpigmentation and premature hair graying to dysfunction of melanocyte lineage

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary: A better understanding of human melanocyte and melanocyte stem cell (McSC) biology is essential for treating melanocyte-related diseases. This study employed an inherited pigmentation disorder carrying the SASH1S519N variant in a Hispanic family to investigate the SASH1 function in melanocyte lineage and the underlying mechanism for this disorder. We used a multidisciplinary approach, including clinical exams, human cell assays, yeast two-hybrid screening, and biochemical techniques. Results linked early hair graying to the SASH1S519N variant, a previously unrecognized clinical phenotype in hyperpigmentation disorders. We identified SASH1 as a novel regulator in McSC maintenance and discovered that TNKS2 is crucial for SASH1’s role in vitro. Additionally, the S519N variant is located in one of multiple tankyrase binding motifs and alters the binding kinetics and affinity of the interaction. In summary, this disorder showcases accelerated aging in human McSC, linking both gain and loss of pigmentation to McSC dysfunction in the same individuals. The findings offer new insights into the roles of SASH1 and TNKS2 in McSC maintenance and the molecular mechanisms of pigmentation disorders. We propose that a comprehensive clinical evaluation of patients with skin disorders should include an assessment and history of hair pigmentation loss.

overall_design: We knocked down SASH1 in primary melanocyte cells using nucleofection, and cultured cells in sphere conditions. The sphere assay enriches for stem-like cells. Results showed that SASH1 is involved in mitotis in stem-like melanocyte cells.

first: Yiqun

last: Shellman

first: Jennifer

last: Hintzsche

first: Aik-choon

first: Karoline

last: Lambert


title: CoMtb alters the immune landscape following Mtb infection [B6 scSCRNAseq]

city: Seattle

first: Kevin

last: Urdahl

state: Washington

address: 307 Westlake Ave N #500

department: Global Infectious Disease

institute: Seattle Children's Research Institute

summary: To characterize the influence of CoMtb on immune responses during infection, we performed single-cell RNA sequencing (scRNAseq) and flow cytometry analysis of lungs from Mtb-infected C57Bl/6 mice with and without CoMtb immediately pre-infection and at 10, 17 and 34 days after conventional dose (50-100 CFU) Mtb infection. We found that CoMtb induces rapid recruitment and activation of T cells, macrophage, and diminished late neutrophil responses.

overall_design: Single-cell RNA sequencing (scRNAseq) and flow cytometry analysis of lungs from Mtb-infected B6 mice with and without CoMtb immediately pre-infection and at 10. 17 and 34 days after CD infection. Variables tested including comparing timepoints to each other. and CoMtb vs non-CoMtb

first: Fergal

middle: J

last: Duffy

first: Maxwell

middle: L

last: Neal

first: Alan

middle: H

last: Diercks

first: Sara

last: Cohen

first: Courtney

last: Plumlee

first: Benjamin

last: Gern

last: Aderem

first: John

last: Aitchison

first: Michael

middle: Y

last: Gerner


title: Transcriptome Profiling of Ewing Sarcomas

city: Solna

first: Felix

last: Haglund de Flon

state: Stockholm

address: Solnavägen 1

department: Oncology-Pathology

institute: Karolinska Institute

summary: Ewing sarcomas (ESs) are aggressive sarcomas driven by EWS fusion genes. We sought to investigate whether whole-transcriptome sequencing (RNA-seq) could be used to detect patterns associated with chemotherapy response or tumor progression after first-line treatment. Transcriptome sequencing (RNA-seq) of 13 ES cases was performed. Among the differen- tially expressed pathways, we identified IGF2 expression as a potential dri- ver of chemotherapy response and progression. We investigated the effect of IGF2 on proliferation, radioresistance, apoptosis, and the transcriptome pattern in four ES cell lines and the effect of IGF2 expression in a valida- tion series of 14 patients. Transcriptome analysis identified differentially expressed genes (adj. P < 0.005) and pathways associated with chemother- apy response (285 genes), short overall survival (662 genes), and progres- sion after treatment (447 genes). Imprinting independent promoter P3- mediated IGF2 expression was identified in a subset of cases with aggres- sive clinical course. In ES cell lines, IGF2 induced proliferation, but pro- moted radioresistance only in CADO cells. High IGF2 expression was also significantly associated with shorter overall survival in patients with ES. Transcriptome analysis of the clinical samples and the cell lines revealed an IGF-dependent signature, potentially related to a stem cell-like phenotype. Transcriptome analysis is a potentially powerful complementary tool to predict the clinical behavior of ES and may be utilized for clinical trial stratification strategies and personalized oncology. Certain gene signatures, for example, IGF-related pathways, are coupled to biological functions that could be of clinical importance. Finally, our results indicate that IGF inhibition may be successful as a first-line therapy in conjunction with conventional radiochemotherapy for a subset of patients.

overall_design: Gene expression profiling by RNA-seq from fresh frozen diagnostic fine-needle aspiration cytology specimens from patients with Ewing Sarcoma

first: Yi

last: Chen


title: Impact of Spore Forming (SF) Community of bacteria on the small intestine

first: W. Zac

last: Stephens

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

department: Pathology

institute: University of Utah

summary: To investigate the impact transcription that the Spore Forming (SF) Community of bacteria have on the small intestine, B6 mice on a autoclaved diet that were germfree (GF) or colonized with the SF community were investigated. Using laser capture microdissection the intestinal epithelial cells on the villi and the crypts were dissected out and bulk RNA seq was performed.

overall_design: The duodenum of the small intestines from male B6 mice with different mictobiotas (GF, and SF) were dissected out, cleaned, and flushed with OCT and placed in cryo mold, and embed in OCT. Frozen sections 9 um thick were cut from the blocks and mounted on PEN slides. Working one slide at a time, slides were taken out of the freezer, fixed with 70% EtOH, stained with Methyl Green and Eosin Y, dehydrated in xylene, and then within 1 hour of being taken out of the freezer, villi intestinal epithelial cells were dissected out using a Laser Capture Microdissection scope. After tissue was collected 350uL of Qiagen buffer RLT+ beta mercaptone ethonal was added and incubated at room temperature for 30 min for lysis before being stored in the -80C. RNA was extracted with the RNeasy micro kit from Qiagen with on column DNase I digest and eluted in 14uL RNAse free H2O. Samples have been stored at -80C.

first: Kendra

last: Klag

first: Zac

first: June

last: Round


title: CoMtb alters the immune landscape following Mtb infection [B6 Sp140-/- scRNA-Seq]

summary: To gain further insights into lesion development and effects of CoMtb on immune responses during infection. we performed single-cell RNA sequencing (scRNAseq) and flow cytometry analysis of lungs from Mtb-infected B6 Sp140-/- mice  with and without CoMtb  at 10 days after CD infection. We found that CoMtb induces rapid recruitment and activation of T cells. macrophage activation. and diminished late neutrophil responses.

overall_design: Single-cell RNA sequencing (scRNAseq) and flow cytometry analysis of lungs from Mtb-infected B6 Sp140-/- mice with and without CoMtb immediately  at 10days after CD infection.


title: Identification of Differential Expression Genes of Blood Leukocytes for Schizophrenia

city: nanjing

first: feifan

last: wang

address: No. 818 Tianyuan East Road

institute: Nanjing Medical University

summary: Schizophrenia (SCZ) is a severe neurodevelopmental disorder with brain dysfunction. This study aimed to use bioinformatic analysis to identify candidate blood biomarkers for SCZ. Our study identified 1205 statistically significant DEGs, of which 623 genes were upregulated and 582 genes were downregulated. Functional enrichment analysis showed that DEGs were mainly enriched in cell chemotaxis, cell surface, and serine peptidase activity, as well as involved in Natural killer cell-mediated cytotoxicity. WGCNA identified 16 gene co-expression modules, and 5 modules were significantly correlated with SCZ (P < 0.05). There were 106 upregulated genes and 90 downregulated genes in the 5 modules. The top ten genes sorted by the Degree algorithm were RPS28, BRD4, FUS, PABPC1, PCBP1, PCBP2, RPL27A, RPS21, RAG1, and RPL27. RAG1 and the other 9 genes belonged to the turquoise and pink module respectively. Pathway enrichment analysis indicated that these 10 genes were mainly involved in processes such as Ribosome, cytoplasmic translation, RNA binding, and protein binding.

overall_design: To identify candidate blood biomarkers for SCZ by bioinformatic analysis, we collected peripheral blood leukocyte samples of 9 SCZ patients and 20 healthy controls for RNA sequencing analysis.

first: Feifan

last: Wang

first: Yao

last: Fan

first: Chong

last: Shen

first: Yong

last: Xue


title: Cellular and axonal transport phenotypes due to the C9ORF72 HRE in iPSC motor and sensory neurons

first: Kevin

last: Talbot

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

summary: Transcriptomic signature of the C9orf72 hexonucleotide repeat expansion in induced pluripotent stem cell derived motor and sensory neurons.

overall_design: iPSC-MNs for RNA sequencing were harvested on DIV 62 and iPSC-SNs were havested on DIV 45  from 3 control lines and 3 patient lines from ALS patients carrying the C9orf72 hexonucleotide repeat expansion.

first: Jakub

last: Scaber

first: Yinyan

last: Xu


title: Characterization of human iPSC-derived fibroblasts

city: Nagakute

first: Takashi

last: Kobayashi

state: Aichi

address: 1-1 Yazakokarimata

department: Institute for Molecular Science of Medicine

institute: Aichi Medical University

summary: Fibroblasts are known to be a heterogeneous population, but the characteristics of subpopulations in different tissues and their relationship to pathological conditions such as fibrosis have not been fully elucidated. We induced the differentiation of human iPS cells into FBs of different organ types and performed transcriptome analysis of these cells.

overall_design: We analyzed the expression profiles of human iPSC-derived dermal fibroblasts (DFB), cardiac fibroblasts (CFB), and hepatic fibroblasts (HFB).

first: Hideto

last: Watanabe


title: Effect of depletion of PRR33 on gene expression during myoblast differentiation

city: Hangzhou

first: Xuyang

last: Fu

address: Kaixuan Road NO.258

institute: Zhejiang University

summary: Coordinated cytoskeleton-mitochondria organization during myogenesis is very essential for muscle development and function. Currently, our understanding of the underlying regulatory mechanisms is still inadequate. Here, we identified a novel muscle specific protein PRR33, which is up-regulated during myogenesis and acts as a promyogenic factor. Depletion of PRR33 in C2C12 represses myoblast differentiation. Interactome and transcriptome analyze reveal that PRR33 regulates cytoskeleton and mitochondrial function. Remarkably, PRR33 interacts with DESMIN, a key regulator of cytoskeleton-mitochondria organization in muscle cells. Abrogation of PRR33 in myocytes substantially abolishes the interaction of DESMIN filaments with mitochondria and can result in abnormal intracellular accumulation of DESMIN and mitochondrial disorganization/dysfunction in myofibers. Together, our study shows that PRR33 and DESMIN constitute an important regulatory module coordinating mitochondrial organization with muscle differentiation.

overall_design: To investigate the function of PRR33 in regulation of myoblast differentiation, we established C2C12 cell line which PRR33 has been knocked down  through CRISPR/CAS9 gRNA. Then, we performed gene expression profiling analysis using data obtained from RNA-seq of ctrl-gRNA and Prr33-gRNA C2C12 at differentiation medium 3 days.

first: Feng

last: Zhang

first: Xiaoxuan

last: Dong

first: Jian

last: Ding


title: Single-cell sequencing analysis reveals the tissue architecture and empowers clinical trial in advanced conjunctival melanoma

city: Shanghai

first: Hanhan

last: Shi

address: Zhizhaoju road

institute: Shanghai Ninth People’s Hospital

summary: Single-cell sequencing analysis empowers clinical decision

overall_design: 10 conjunctive tissues respectively from nonmalignant conjunctive and metastatic CoM patients were collected and performed deep scRNA-seq on individual cells to systematically interrogate the origin and tumor micro-environment of CoM

first: Shi

last: Hanhan


title: RNA sequencing for wild type and shENO1 Daudi cells.

city: Dalian

first: Jinsong

last: Yan

state: Liaoning

address: 467 Zhongshan Road, Dalian 116027, Liaoning, P. R. China

department: Department of Hematology

institute: the Second Hospital of Dalian Medical University

summary: We systematically evaluated the expression pattern and function of ENO1 in BL and clarified that ENO1, regulated by cMyc, can promote BL cell proliferation and metastasis by activating TGFβ1 signaling pathways in a plasmin-mediated manner. Through structure-based virtual screening, we successfully discovered Ciwujianoside E (L-06) as a novel ENO1 inhibitor which can limit BL cell proliferation and dissemination in vitro and in vivo.

overall_design: Examination of drug sensitivity for ENO1 knockdown in Burkitt’s lymphoma cell line Daudi