title: Cardiomyocyte-specific ADGRF5 mediates cardiac homeostasis via Gαq coupling

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

summary: G-Protein Coupled Receptors (GPCRs) represent one of the most targeted drug classes in the human genome, accounting for greater than 40% of all FDA-approved drugs, including gold-standard heart failure (HF) therapeutics. However, the second-largest family of GPCRs, known as Adhesion GPCRs (aGPCR), have yet to serve as a clinical target despite increasing evidence of their pathophysiological contributions, representing an area of highly unexplored druggable potential. We identified an aGPCR, known as ADGRF5, to be highly expressed in the left ventricle (LV) of C57BL/6, which we also found increases in response to transaortic constriction (TAC) surgery. To determine the impact of ADGRF5 on cardiac parameters normally or during HF, we generated constitutive cardiomyocyte-specific (αMHC-Cre-driven) ADGRF5 knockout mice (CM-ADGRF5-KO), which displayed normal cardiac structure and function at 12 weeks of age, as assessed via echocardiography, gravimetrics and immunohistochemistry.  However, over time CM-ADGRF5-KO mice developed worsened cardiac function and remodeling with increased mortality, even in the absence of pathologic insult, suggesting ADGRF5 provides a homeostatic regulatory function in the heart. We assessed changes in cardiac gene expression at 12 weeks of age, a timepoint prior to the onset of the eccentric remodeling on the CM-ADGRF5-KO mice. We identified 58 differentially expressed genes, with 31 downregulated and 27 upregulated.

overall_design: Four biological replicates were analyzed for each of 2 genotypes at 12 weeks of age (two genotypes; 4 replicates, 2 per sex)

first: Jeanette

last: Einspahr

first: Douglas

middle: G

last: Tilley


title: Chromatin architecture and cis-regulatory landscape of the DACT2-SMOC2 locus in the developing synovial joint.

status: Public on Jul 01 2024

city: Rotterdam

first: Karol

last: Nowosad

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

summary: We report the 3D chromatin organization of the 3.4Mb DACT2-SMOC2 locus generated for interphalangeal interzone and phalange, tissues collected during synovial joint formation. The interzone and phalange samples have been dissected from developing hindlimb digits of the chicken embryo at Hamilton Hamburger stage 32 (HH32). Collected material has been processed using the Targeted Chromatin Capture protocol optimized for the 1mln cell. Generation of the T2C-interaction maps has revealed the 3D chromatin architecture of the DACT2-SMOC2 locus in the interzone and phalange tissues as well as identified potential candidate enhancers located in spatial proximity of DACT2 and SMOC2 gene promoters. We report the ChIPseq derived Candidate Enhancer (CE) atlas generated for interphalangeal interzone and phalange, tissues collected during synovial joint formation. Three replicates for interzone and three replicated for phalange were immunoprecipitated (IP) with the H3K27ac antibodies. Also, two replicates for interzone and two replicates for phalange were immunoprecipitated with H3K4me1 antibodies. The IP samples for both histone marks were sequenced and used for annotation of CEs. Further, the CEs were functionally annotated. In parallel, the total RNA for three interzone and three phalange replicates was isolated and mRNA sequencing libraries were constructed. Next the identification of differentially expressed genes (DEGs) and integrative analysis of DEGs and CEs was performed.

overall_design: Analysis of 3D chromatin architecture of the 3.4Mb DACT2-SMOC2 locus using low-input Targeted Chromatin Capture (low-T2C) in dissected interdigital interzone and phalange samples.

first: Ewa

last: Hordyjewska-Kowalczyk

first: Aneta

last: Malesa

first: Rutger

middle: W

last: Brouwer

first: Petros

last: Kolovos

first: Adrian

last: Odrzywolski

first: Ilias

last: Boltsis

first: Judith

middle: C

last: Birkhoff

first: Wilfred

middle: F

last: van IJcken

first: Frank

last: Grosveld

first: Andrea

last: Conidi

first: Danny

last: Huylebroeck

first: Przemko

last: Tylzanowski


title: Therapeutic Activation of G Protein-Coupled Estrogen Receptor 1 in Waldenström Macroglobulinemia

city: Milan

first: Antonino

middle: of

last: Neri

address: Via Festa del Perdono 7

country: Italy

institute: University of Milan

summary: Activation of G protein-coupled estrogen receptor 1 (GPER1) is an attractive therapeutic strategy to treat a variety of human diseases, including cancer. Here, we show that GPER1 is remarkably upregulated in tumor cells derived from different cohorts of Waldenström Macroglobulinemia (WM) patients respect to normal B cells. Using the clinically relevant GPER1-selective small-molecule agonist G-1 (also named Tespria), we demonstrate that pharmacological activation of GPER1 leads to G2/M cell cycle arrest and apoptosis both in vitro and in vivo in animal model, even in the context of the protective bone marrow milieu. We report that activation of GPER1 triggers the TP53 pathway, which remains actionable during WM progression. This study identifies a novel druggable target in WM and paves the way for the clinical development of the GPER1 agonist G-1.

overall_design: To investigate the activity of GPER1 in Waldenström Macroglobulinemia,  we performed gene expression profiling using Affymetrix GeneChip analysis in BCWM-1 WM cell line treated with GPER1 selective agonist (G-1) compared to untreated cell line. Duplicate samples were analyzed for each condition.

first: Eugenio

last: Morelli

first: Zachery

middle: R

last: Hunter

first: Mariateresa

last: Fulciniti

first: Annamaria

last: Gullà

first: Ida

middle: D

last: Perrotta

first: Valeria

last: Zuccalà

first: Giada

last: Juli

first: Domenica

last: Ronchetti

first: Martina

last: Manzoni

first: Cinzia

last: Federico

first: Enrica

last: Romeo

first: Maria

middle: E

last: Cantafio

first: Luca

last: Mastracci

first: Lorenza

last: Maltese

first: Aldo

middle: M

last: Roccaro

first: Nmichele

last: Cea

first: Pierfrancesco

last: Tassone

first: Steven

last: Treon

first: Nikhil

last: Munshi

first: Giuseppe

last: Viglietto

first: Nicola

last: Amodio


title: RNA Sequencing Analysis of Peripheral Blood Mononuclear Cells Associated with COVID-19 Deterioration

city: Kobe

first: Kazuya

last: Miyagawa

address: 5-7-1 Koji-dai, Nishi

country: Japan

institute: Kobe City Nishi-Kobe Medical Center

type: Expression profiling by high throughput sequencing

summary: To explore gene expression profiles that is predictive of COVID-19 deterioration, PBMC were collected from early stage non-severe COVID-19 patients and analyzed by grouping patients into 2 groups, deteriorated and non-deteriorated, based on the subsequent clinical courses.

overall_design: We performed gene expression profiling analysis using data from RNA-seq of PBMC from 12 patient grouping into 2 groups.

first: Mami

last: Ikemachi


title: SEMA3E-PLXND1 induced transcriptional changes in B16 melanocytes

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

summary: Exposure to SEMA3E cause an immediate but transient collapse in F-actin of B16 melanocytes expressing the receptor PLXND1. Concomitant signal transduction by activated PLXND1 receptor mediated via its GTPase activating domain has a role in adapting the melanocytes to its micro-environment. To analyse these adaptive transcriptional responses B16 melanocytes were treated with SEMA3E for 2h to study early responses and for 8h to study prolonged responses. Cytochalasin D (8h) was used to distinguish the effects brough about by cytoskeletal collapse alone.

overall_design: Total RNA was extracted from Control, SEMA3E treated (2 hrs and 8hrs) and cytochalasin D treated (8hrs) B16 cells. The RNA was quality controlled and quantified using agilent bioanalyzer. The samples were analyzed by Agilent_mouse_GXP_8X60K array. Two biological replicates of each sample were analyzed. We acknowledge Genotypic Technology Private Limited Bangalore for the microarray processing and data analysis reported in this publication.

first: Yogaspoorthi

middle: J

last: Subramaniam


title: Gene expression profiling of sigmoid colonic tissue form patients with ulcerative colitis and healthy controls

city: Herlev

first: Lauge

last: Kellermann

state: --- Select ---

address: Borgmester Ib Juuls Vej 1

department: Department of Gastroenterology

country: Denmark

institute: Herlev Hospital

summary: To assess mRNA gene expression levels in patients with ulcerative colitis (UC) and healthy controls.

overall_design: Two sigmoid colonic biopsies in close proximity were collected from patients with ulcerative colitis (n=59) and controls (n=19) during endoscopy. RNA from each biopsy was purified and analysed seprately using the Affymetrix HGU219 arrays on 96-PEG plates where 100 ng of RNA was labelled using the 3-IVT expression kit and hybridized to the HGU219 chip. Disease activity was assed by the Mayoscore (Schroeder et.al Coated Oral 5-Aminosalicylic Acid Therapy for Mildly to Moderately Active Ulcerative Colitis. N Engl J Med 1987;317:1625–1629.) at time of biopsy collection. Data has been published in: "Soendergaard C, Kvist PH, Thygesen P, et al. Characterization of Growth Hormone Resistance in Experimental and Ulcerative Colitis. Int J Mol Sci. 2017;18(10):2046."

first: Christoffer

last: Soendergaard


title: Identifying the binding sites for miRSome on miR-9 genomic locus with ChIP-seq

city: Melbourne

first: Diji

last: Kuriakose

state: Victoria

address: Wellington road

country: Australia

institute: Monash University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Recent studies have attributed multiple etiological factors for NDDs. miR-9/29a/107 is a key regulator in NDD. Therefore, understanding the upstream regulation of miR-9/29a/107 is critical for NDDs. We have used a unique multi-animal model-CC line that gives greater genetic diversity because miR upstream regulators could involve single or multiple factors. Using mirQTL mapping of CC we identified three candidates-Panx2/Polr1c/Mgea5. We showed that they modulate neuronal differentiation through miR-9. Next, we determined by ChIP that these genes are recruited to the regulatory region of the miR-9 locus. We showed that Panx2 is cleaved by RIP and translocated to the nucleus to interact with Polr1c and Mgea5. ChIP-combined-loop and 3C assays established the interaction on the miR-9 genomic locus through chromatin loops and histone modifications. We also proved that Panx2/Polr1c/Mgea5-miR-9 crosstalk to alter neuronal differentiation. Overall, we established a miRSome complex that govern transcriptional events during adult hippocampal neurogenesis.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Panx2, Polr1c and Mgea5 in duplicates with treatment and control files


title: Time-course gene expression analysis of melanocyte development

summary: Specification and differentiation of melanocytes is closely associated with their temporal localization. Melanocyte stem cells migrate extensively within defined trajectories before they undergo terminal differentiation to produce the photo-protective pigment, melanin. Cells adapt to the evolving developmental micro-environment via specialized cell surface receptors. To understand the responsive states and distinctive transcriptional states, fluorescently labeled melanocyte stem cells (24hpf and 34 hpf) or pigmented melanophores at 72hpf were isolated and their expression profiles were analysed as described below.

overall_design: Total RNA was extracted from mitfa:GFP positive cells at 24hpf and 34hpf and 72hpf pigmented melanophores. The RNA was quality controlled and quantified using agilent bioanalyzer. The samples were analyzed by Agilent_zebrafish_GXP_8X60K array. Two biological replicates of each sample were analyzed. We acknowledge Genotypic Technology Private Limited Bangalore for the microarray processing and data analysis reported in this publication.

first: Ayyappa

last: Raja


title: Whole-genome profiling of human HAP1 cells after the genetic and pharmacological inactivation of TRPM7

city: Munich

first: Vladimir

last: Chubanov

state: Non-US/Canada

address: Goethestraße 33

department: Walther-Straub-Institut

country: Germany

institute: Ludwig-Maximilians-Universität München

summary:
The project aims to attain deeper insight into the role of TRPM7 in the regulation of cellular pathways.
We identified a set of differently expressed genes in HAP1 cells after the genetic or pharmacological inactivation of TRPM7.

overall_design: Total RNA was extracted from wild-type HAP1 cells, wild-type HAP1 cells treated with NS8593 and two clones of TRPM7 KO HAP1 cells (n=1).

first: Miyuki

last: Egawa

first: Thomas

last: Gudermann


title: Human lung cancer cell line A549 +/- CD43 knockdown

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: The human lung cancer cell line A549 with high CD43 expression was stably trasfected with a vector expressing a non-functional shRNA or 3 of these same vectors each expressing a different shRNA targeting human CD43 mRNA. The transcriptomes of these two daughter lines were then compared by differential microarray analysis. The generation and functional characteristics of these two daughter cell lines are described by Fu et al., in the International Journal of Cancer, volume 132, pages 1761-1770, published in 2013.

overall_design: Differential microarray analysis of the human lung cancer cell line A549 +/- CD43 knockdown

first: Carl

middle: S

last: Shelley


title: Mutation in FKBP10 causes early onset of scoliosis

city: Shenzhen

first: Peikai

last: Chen

state: GD

address: 1 Haiyuan 1st Rd, Futian District

department: Pediatric Orthopedics

country: China

institute: The University of Hong Kong - Shenzhen Hospital

summary: Scoliosis is a three-dimensional structural deformity of the spine, while the underlying pathogenesis is not fully uncovered. Osteogenesis imperfecta (OI), known as brittle bone disease, is a group of rare genetic disorder associated with osteopenia, deformity and scoliosis. Here we found the mutation in FKBP10 resulted in early onset of scoliosis via deleterious effects on collagen processing and osteoblast differentiation.

overall_design: We sequenced 6 bulk RNAseq samples. Osteoblasts isolated from patients with osteogenesis imperfecta or polidactyly were collected for RNAseq.

first: Zhijia

last: TAN

last: CHEN

first: Hiu

last: SHEK

first: Michael

middle: K

last: TO


title: Clonal diversity of peripheral B cell receptor repertoire for prediction of relapse risk after autologous stem cell transplant in DLBCL patients

city: Beijing

first: Jing

last: Zhang

address: 38 Life Science Park Road

institute: Beijing Institute of Lifeomics

summary: The goal of this study is to analysis the gene expression alterations along the time of hiGC culture. We established a hiGC model by following the protocol previously reported by Kitamura et al. Naïve B cells purified from human PBMC pools underwent two phases of growth under the activation of CD40L, BAFF, IL-4 and subsequently IL-21.

overall_design: There are 5 samples on different culturing time.

first: Yi

last: Wang


title: Ethylene Responsive Factor 34 (ERF34) negatively mediates salt stress-induced leaf senescence by regulating the expression of salt stress-responsive genes in Arabidopsis

city: Hyeonpung-eup

first: Hyunsu

last: Park

state: Dalseong-gun, Daegu

address: E4-620, 333, Techno jungang-daero

department: New biology

country: South Korea

institute: DGIST

summary: Leaf senescence, the last step of leaf development which is important for plant’s fitness, proceeds with age but is modulated by various environmental stresses and hormones. Salt stress is one of the well-known environmental stresses that accelerate leaf senescence. However, the molecular mechanisms how the signal of salt stress is integrated into leaf senescence programs are still elusive. In this study, we characterized the function of an Arabidopsis APETALA 2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) family transcription factor, ERF34, in salt stress-induced leaf senescence. ERF34 was differentially expressed under leaf senescence-inducing conditions including age, dark, and high salt. ERF34 negatively regulated salt stress-induced leaf senescence as well as promoted salt stress tolerance at diverse developmental stages. Analysis of genome-wide targets of ERF34 revealed that the overexpression of ERF34 could alter salt-responsive gene expression. Moreover, ERF34 directly bound to the promoters of EARLY RESPONSIVE TO DEHYDRATION 10  and RESPONSE TO DESICCATION 29A and activated their expression. Our findings imply that ERF34 is a key regulator in the convergence of salt stress response with the regulatory programs of leaf senescence and is a potential candidate for crop improvement, particularly by enhancing salt stress tolerance.

overall_design: mRNA profiling from ERF34 in Shoot leaf samples in arabisopsis

first: Yongmin

last: Kim

first: Sanghoon

first: Hyunsoo

first: Sung-Jin

first: Yeong

last: Yoon

first: Daesang

last: You

first: Uk

last: Jeong

first: Junmin

last: Kwak

first: Do

middle: Y

last: Hyeon

first: Daehee

last: Hwang

first: Hye

last: Woo


title: A novel model to study deficiency of RORγt+ Tregs reveals net suppressive function and dependency on the CCR6/CCL20 axis for expansion and activation

city: Hamburg

first: Georg

last: Herrnstadt

address: Martininstraße 52

department: III. Department of Medicine

institute: University clinic Hamburg-Eppendorf

summary:
Background: Recently, Tregs expressing the Th17 characteristic transcription factor RORγt were identified (biTregs). Both, pro- and anti-inflammatory functions have been described and the sum effect of biTreg deficiency in inflammation remains unknown. Furthermore, it is unclear, whether biTregs are specialized for the control of a defined type of immune response, as in particular Th2 or Th17 immunity.
Methods: FACsorted CD4+ T-cells from fluorescence reporter mice, containing or lacking biTregs, were transferred into RAG1-/- recipients and the nephrotoxic nephritis model of glomerulonephritis was studied. Interactions of biTregs with various leukocyte populations were assessed by multicolor immunofluorescence. Furthermore, biTregs were compared to other Treg subtypes including suppression assays and RNAseq analyses. Finally, the role of the CCR6/CCL20 axis for biTreg biology was characterized.
Results: Lack of endogenous biTregs resulted in aggravation of glomerulonephritis, demonstrating net immunosuppressive functions. However, contrary to our hypothesis, biTreg deficiency did not result in selectively overshooting Th2 or Th17 responses.  Comprehensive analysis instead revealed a unique functional and transcriptional biTreg profile, including high production of IL-10 and dependency on IL-6R, cMAF and IKZF3 activation. Interestingly, we found that expression of the chemokine receptor CCR6 marked a particularly activated biTreg subset, whose absence significantly worsened glomerulonephritis. Unexpectedly, we found that signaling via the CCR6/CCL20 axis mediates biTreg expansion, rather than trafficking.
Our data indicate net immunosuppressive effects of endogenous biTregs, with no preference for regulation of Th2 or Th17 responses. Surprisingly, signaling via the Conclusion: CCR6/CCL20 axis was integral for biTreg expansion and activation, which offers novel therapeutic options.

overall_design: 500,000 naïve splenic RORγt+ Tregs and RORγtnegCCR6+ Tregs were purified by FACSorting and RNA bulk sequencing was conducted

first: Daniela

last: Indenbirken

first: Christoph

last: Niehus

first: Oliver

last: Steinmetz


title: DNA methylation of adenomas from Apc-Min mice with additional Tet1 and Tdg mutations

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

country: USA

institute: Coriell Institute for Medical Research

type: Methylation profiling by high throughput sequencing

summary: Aberrant DNA methylation is frequent in colorectal cancer (CRC), but the underlying mechanisms and pathological consequences are poorly understood.  Ten-Eleven Translocation (TET) dioxygenases and Thymine DNA Glycosylase (TDG) mediate active DNA demethylation by generating and removing oxidized cytosine species. TET1 and TDG mutations, and altered levels of oxidized cytosines have been identified in human CRC. To investigate the TET-TDG demethylation axis in intestinal tumorigenesis, we generated ApcMin mice that are devoid of Tet1 and/or Tdg, and characterized the methylome and transcriptome of intestinal adenomas. There were increased numbers (>30) of adenomas in ApcMin mice expressing the dominant-negative TdgN151A allele, whereas Tet1-deficient and Tet1/Tdg-double heterozygous ApcMin adenomas were larger and displayed features of erosion and invasion. Methylome analysis revealed reduction in global DNA hypomethylation in colonic adenomas from Tet1- and Tdg-mutant ApcMin mice, and hypermethylation of CpG islands in Tet1-mutant ApcMin mice.  In addition, RNA sequencing showed upregulation of inflammatory, immune and interferon response genes in Tet1- and Tdg-mutant colonic adenomas compared to control ApcMin adenomas. The corresponding 127-gene inflammatory signature separated human colonic adenocarcinomas in four groups, closely aligned with their microsatellite or chromosomal instability, and characterized by different levels of DNA methylation and DNMT1 expression that anti-correlated with TET1 expression. These findings demonstrate a novel mechanism of epigenetic regulation during intestinal tumorigenesis by which TET1-TDG-mediated DNA demethylation may decrease methylation levels and inflammatory/interferon/immune responses, and is linked to the type of genomic instability.

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of adenomas (triplicates) from four-genotype groups: Tet1-/- Tdg+/+ ApcMin/+; Tet1+/- TdgN151A/+ ApcMin/+ ; Tet1+/+ TdgN151A/+ ApcMin/+; and Tet1+/+ Tdg+/+ ApcMin/+.  Briefly, genomic DNA was sequentially digested by SmaI and XmaI, which both recognize the sequence CCCGGG. SmaI is methylation sensitive, where XmaI is methylation insensitive. Distinct signatures, 5’-GGG at unmethylated sites or 5’-CCGGG at methylated sites were created by enzyme digestion and ultimately high througput sequencing was used to map these sites to the genome. Methylation ratios for each individual CCCGGG site were calculated as a proportion of methylated counts to the sum of unmethylated and methylated counts, and subsequently adjusted for differences in restriction enzyme efficiency using values obtained from spiked in standards.

first: Rossella

last: Tricarico

first: Jozef

last: Madzo

first: Gabrielle

last: Scher

first: Shinji

last: Maegawa

first: Rajeswari

last: Nagarathinam

first: Carly

first: Wen-Chi

last: Chang

first: Emmanuelle

last: Nicolas

first: Yan

last: Zhou

first: Michael

last: Slifker

first: Karthik

last: Devarajan

first: Kathy

middle: Q

last: Cai

first: Pamela

last: Nakajima

first: Jinfei

last: Xu

first: Pietro

last: Mancuso

first: Valentina

last: Doneddu

first: Luigi

last: Bagella

first: Siddharth

last: Balachandran

first: Sergei

last: Grivennikov

first: Iuliia

last: Peshkova

first: Natalia

last: Kurilenko

first: Aleksandra

last: Mazitova

first: Ekaterina

last: Koltsova

first: Timothy

last: Yen

first: Jean-Pierre

last: Issa

first: Alfonso

last: Bellacosa


title: Genome-wide binding sites of transcription factor 21 in chicken preadipocytes

city: Harbin

first: Xinyang

last: Zhang

state: Heilongjiang

address: No.600 Changjiang street

department: Animal Science and Technology

institute: Northeast Agricultural University

summary: The object of this study is to find the genome-wide TCF21 binding sites and its downstream target genes in chicken adipogenesis

overall_design: Examination of TCF21 binding sites in chicken preadipocytes

first: Hui

last: Li

first: Bohan

last: Cheng


title: WNT-driven PRMT1 Nuclear Localization Generates Synthetic Lethality in Colorectal Cancers

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

institute: European Institute of Oncology

summary: Colorectal cancer (CRC) arises from multi-step accumulation of genetic and epigenetic mutations that deregulate intestinal homeostasis leading to neoplastic transformation and metastases. Constitutive activation of WNT signaling is considered the initial driver oncogenic event to which CRCs remain addicted, also in their most aggressive metastatic forms. WNT activation provokes an aberrant signaling that converges into the nucleus where transcription and chromatin-remodeling factors cooperate to regulate cell identity. This leads to deregulated proliferation, block of differentiation and evasion from cell death pathways. We found that the protein arginine methyltransferase 1 (PRMT1) is synthetic lethal with WNT oncogenic activation in both genetically-defined mouse models and patient-derived metastatic CRC organoids.  WNT activation regulates the subcellular localization of PRMT1, inducing its complete nuclear translocation. This makes CRCs specifically dependent on PRMT1 enzymatic activity to sustain WNT-dependent proliferation regardless of the mutational landscape carried by distinct patients. Together these data uncover a new molecular crosstalk between WNT activation and PRMT1 activity and place PRMT1 inhibition as a potential strategy to counteract CRC addiction to WNT oncogenic activation.

overall_design: 2 RNA-seq experiments of intestinal organoids. WT vs Ctnnb1-ex3 organoids (2 replicates each) and sh-scramble vs sh-Prmt1 intestinal organoids (2 replicates each)

first: Daniel

last: Fernandez-Perez


title: HDGF ChIP-Seq in Ewing sarcoma cell line RD-ES

city: Guangzhou

first: yang

last: yang

address: 58, Zhongshan Road II, Guangzhou

institute: Sun Yat-sen University

summary: HDGF is implicated in Ewing sarcoma. We used HDGF ChIP-Seq in combination with gene expression profiling to identify genes and pathways it regulates in Ewing sarcoma.

overall_design: Chromatin was immunoprecipitated by anti-HDGF antibody in Ewing sacoma cell line RD-ES with high basal HDGF expression and submitted for high throughput sequencing.

first: Yang

last: Yang

first: Anjia

last: Han


title: Epigenome analysis of muscle tissue and paired cultured myoblasts from the Hertfordshire Sarcopenia Study extension

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

country: United Kingdom

institute: University of Oxford

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of paired muscle tissue and cultured myoblast genomic DNA. The Illumina Infinium Methylation450 array was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Samples were male, taken from the Hertfordshire Sarcoepnia Study exension (HSSe), to determine prelimnary associations measures of muscle mass, function and insulin/glucose levels and DNA methylation in muscle tissue. Furthermore, we sought to determine whether DNA methylation in the muscle tissue is conserved in cultured myoblasts from the muscle biopsies and whether association differed between the two tissues.

overall_design: Bisulphite converted DNA from the 37 samples were hybridised to the Illumina Human Infinium Methylation450 array


title: RNA-sequencing of peripheral blood in FOP patients

city: Yangzhou

first: Dunmin

last: She

state: CHINA

address: 98，Western Nantong

department: Endocrinology

institute: Northern Jiangsu People’s Hospital

summary: We combined the results of scRNA-seq of PBMCs with total RNA sequencing of peripheral blood to find out the most remarkable different subgroup and the corresponding DEGs.

overall_design: We evaluated the total RNA sequence of peripheral blood (PB) and combined the results with single cell transcriptome of PBMCs to find out the most remarkable subgroup in PBMCs and the corresponding differentially expressed genes (DEGs).

first: Keqin

first: Kunshan

first: Ying

last: Xue


title: Single cell RNA-sequencing of PBMCs in FOP patients

summary: We described a genetic map of PBMCs in FOP patients by using single-cell RNA sequencing for the first time.

overall_design: PBMCs from 3 FOP patients and 3 controls were analyzed by using scRNA-seq.


title: RNA-Seq of peripheral blood in FOP patients

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

overall_design: Refer to individual Series


title: Transcriptomic and proteomic multi-model global gene expression analysis reveals regulatory signatures during ischemia stroke (photothrombotic internal ischemia stroke)

city: Not Hispanic or Latino

first: Sheng

last: Zhao

address: #87, Dingjiaqiao, Gulouqu

department: Biochemistry and Molecular biology

institute: Southeast University

summary: The transcriptomes of focal region in C57BL/6 mice after photothrombotic internal ischemia stroke generated by RNA-sequencing, using Illumina

overall_design: mRNA profiles of the micro-punched focal/sham regions from the caudate putamen in photothrombotic internal ischemia mice (9 week, male)

first: Chunqiang

last: Lu

first: Defeng

last: Wang

first: Meijuan

last: Yu

first: Yi

last: Xu

first: Jun

first: Shenghong

last: Ju


title: Identification of differential expressed genes after SP1 or SP3 knockdown in colorectal cancer cells

city: Shanghai

first: Zhehui

last: Zhu

state: Shanghai

address: Kongjiang Road 1665, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

summary: SP1 and SP3 have been reported to play an critical role in the pregression of tumors. In order to elucidate the molecular mechanism of SP1 and SP3 in colorectal cancer, RNA-seq analysis was performed on SP1 and SP3 knockdown and control HCT116 cells.

overall_design: HCT116 cells with SP1 or SP3  knockdown were generated by siRNAs.

first: Yuegui

last: Guo

first: Long

last: Cui

first: Chen-ying

last: Liu


title: Transcriptomic and proteomic multi-model global gene expression analysis reveals regulatory signatures during ischemia stroke (photothrombotic cerebral ischemia stroke)

summary: The transcriptomes of focal region in C57BL/6 mice after photothrombotic cerebral ischemia stroke generated by RNA-sequencing, using Illumina

overall_design: mRNA profiles of the micro-punched focal/sham regions from the cerebral in photothrombotic cerebral ischemia mice (9 week, male)


title: Activation-induced cytidine deaminase induces DNA demethylation and expression of Ninjurin-2 gene

status: Public on Jun 30 2024

city: Kurume City

first: Toshiyuki

last: Okada

address: 67 Asahi-machi

department: Department of Immunology,

institute: Kurume University School of Medicine

summary: This study investigated the epigenetic role of AID induced by inflammation. AID, which binds to the promoter region of NINJ2, induces DNA demethylation. Thus, these findings suggest physiological roles of AID expression in colonic epithelial cells.

overall_design: DLD-1 cell line was transfected with a pEGFP-N1 empty vector (control#2) or an AID-Myc/his tag vector (AID-OP#1) to identified AID-induced genes.

first: Toshyuki

first: Yusuke

last: Toyoda

first: Atsushi

last: Mizoguchi

first: Shigeaki

last: Saitoh


title: Glycosphingolipid synthesis mediates immune evasion in Kras-driven cancer

city: Cold Spring Harbor

first: Vyom

last: Shah

state: New York

address: 1 bungtown road

department: Beyaz Lab

institute: Cold Spring Harbor Laboratory

summary: Cancer cells frequently alter their lipids to grow and adapt to their environment1–3. Despite the critical functions of lipid metabolism in membrane physiology, signaling, and energy production, how specific lipids contribute to tumorigenesis is incompletely understood. Here, using functional genomics and lipidomic approaches, we identified de novo sphingolipid synthesis as an essential pathway for cancer immune evasion. Synthesis of sphingolipids is surprisingly dispensable for cancer cell proliferation in culture or in immunodeficient mice but required for tumor growth in multiple syngeneic models. Blocking sphingolipid production in cancer cells enhances the anti-proliferative effects of natural killer (NK) and CD8+ T cells partly via interferon gamma (IFNg) signaling. Mechanistically, depletion of glycosphingolipids increases surface levels of IFNg receptor subunit 1 (Ifngr1), mediating IFNg-induced growth arrest and proinflammatory signaling. Finally, pharmacological inhibition of glycosphingolipid synthesis synergizes with checkpoint blockade therapy to enhance anti-tumor immune response. Altogether, our work identifies glycosphingolipids as necessary and limiting metabolites for cancer immune evasion.

overall_design: Tumors were removed from mice 12-13 days after injection and placed into DMEM+ media (DMEM/F-12 (Gibco #11320033, 10% FBS) and kept on ice. Once all tumors were removed, they were washed once with ice cold PBS and placed into a 1.5 mL tube containing dissociation buffer (DMEM+, 1 mg/mL Collagenase D (Sigma-Aldrich #11088858001), 25 ug/mL DNAse (NEB #M0303S)). Tumors were briefly dissociated using scissors and then incubated on a shaking heat block for 35 minutes at 37°C. Each sample was then passed through a 70 µm cell trainer which was rinsed with 5 mL of DMEM+. Cell suspensions were centrifuged at 300 X g for 5 minutes at 4°C. Cells were resuspended in 3 mL of ACK buffer and incubated at room temperature for 4 minutes. Then, 7 mL of DMEM+ was added before centrifuging again at 300 X g for 5 minutes at 4°C. For isolation of CD45+ tumor-infiltrating immune cells, cells were resuspended in 30 µL of FACS buffer containing Fc-block (1:200, BD BioSciences #553141) and incubated on ice for 10 minutes. 30 µL of CD45 antibody in FACS buffer was added to cells (1:10 final concentration) and incubated on ice for 20 minutes. Cells were washed by adding 1 mL of FACS buffer prior to centrifugation at 1000 X g for 5 minutes at 4°C. Cells were resuspended in 200 µL of DAPI-containing FACS buffer. 10,000 CD45+/ DAPI negative cells/ mouse were sorted into a pre-coated Eppendorf tube for a total of 60,000 cells/ condition. 5,000 cells/ condition were targeted for single-cell RNA-sequencing on a Chromium Single Cell System (10x Genomics). Samples were processed as/ the manufacturer’s instructions (Chromium single cell 3’ reagents, v3.1 chemistry) and libraries were sequenced using Illumina NovaSeq. Single cell datasets for each experiment were independently assessed for data quality following the guidelines described in Luecken and Theis, 2019 and Amezquita et al., 202048,49. Cells with more than 10% mitochondrial transcripts as well as cells that had fewer than 250 feature counts or expressed fewer than 500 genes were removed. After QC, Seurat (v4.0.3) was used for normalization, graph-based clustering and differential expression analysis50. Each dataset was normalized using SCTransform and the 5000 most variable genes were identified with SelectIntegrationFeatures. Both PMXS and AB datasets were integrated into a singular dataset via using the PrepSCTIntegration, FindIntegrationAnchors, and IntegrateData function51. MAGIC imputation was conducted on integrated data to impute missing values and account for technical noise52. RunPCA was implemented on the integrated datasets to identify the top 50 principal components (PCs) that were used for UMAP analysis and clustering. Louvain clustering at a resolution of 1 was implemented. Clusters were labeled in accordance with expression levels of CD45 tumor infiltrating lymphocyte subtype signatures . Differential expression analysis was conducted between PMXS vs AB using the FindMarkers function with the MAST method to evaluate differences within the transcriptome54. Wilcoxon rank-sum tests to determine if gene expression was significant was conducted using the wilcox.test function in stats (v4.1.0, R Core Team 2021). For the density map of the differential expression of Ifng, cells were binned based on proximity in the uniform manifold approximation and Projection (UMAP). Log fold change of Ifng expression (KO versus AB) was calculated using the cells in each bin and transposed back onto the UMAP at the generalized location of the cells.

first: Mariluz

last: Soula

first: Kivanc

last: Birsoy

first: Semir

last: Beyaz


title: Postnatal fluoxetine evoked gene expression changes in the rat medial prefrontal cortex

city: Mumbai

first: UTKARSHA

last: GHAI

state: Maharashtra

address: Tata Institute Of Fundamental Research, Old Navy Nagar,, Colaba, Mumbai, Maharashtra, India- 400005

department: DEPARTMENT OF BIOLOGICAL SCIENCES

institute: Tata Institute Of Fundamental Research

summary:
To understand the consequences of chronic exposure to fluoxetine during postnatal life on global transcriptional changes withing the rat medial prefrontal cortex in adulthood.
To understand the consequences of chronic exposure to fluoxetine during postnatal life on global transcriptional changes withing the rat medial prefrontal cortex in adulthood.

overall_design: Agilent one-color experiment,Organism: Rattus Norvegicus, Agilent-016352 Genotypic designed Custom Rattus Norvegicus 8x15k, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Parul

last: Chachra

first: Vidita

last: Vaidya


title: Juvenile fluoxetine evoked gene expression changes in the rat medial prefrontal cortex

summary:
To understand the consequences of chronic exposure to fluoxetine during juvenile life on global transcriptional changes withing the rat medial prefrontal cortex in adulthood.
To understand the consequences of chronic exposure to fluoxetine during juvenile life on global transcriptional changes withing the rat medial prefrontal cortex in adulthood.


title: Identification and Validation of Small Molecule Inhibitors Targeting FGFR through Molecular Docking-Based Screening

city: Wenzhou

first: LIjun

last: Chen

state: Other

address: Wenzhou Medical University, Wenzhou City, Zhejiang Rrovince,China

institute: Wen Zhou Medical University

summary: Fibroblast growth factors and their receptors (FGFRs) play important roles in multiple cellular processes. FGFR genetic alterations such as mutations, amplifications, and chromosomal translocations are prevalent in various cancer types, contributing to the initiation and progression of tumors by enhancing FGFR signaling. Identifying effective small molecule inhibitors that selectively target FGFR can advance cancers therapy driven by FGFR abnormalities. Here, we conducted molecular docking and dynamics simulations to discover new small compounds targeting FGFRs. By docking with 2.8 million small molecules, we identified three promising FGFR inhibitors ranked in the top average absolute difference in free energy. By evaluating the binding stability of the docking pose of these three compounds, we found that ZINC000101867325 formed the most stable binding interactions with FGFRs. After treatment with ZINC000101867325, colorectal cancer cell lines showed a decrease in FGFR phosphorylation and early apoptosis. In addition, ZINC000101867325 is also predicted to interact with FGFR2 mutations in colorectal cancer (CRC) patients. This study provides the novel FGFR inhibitors, and enriches treatment strategies for cancers.

overall_design: We docked approximately 2.8 million small molecule drugs to the crystal structure of FGFR1-4 and predicted three small molecules targeting fgfr. Among them, ZINC000101867325 showed superior bond type and stability. The effects of ZINC000101867325 on FGFR phosphorylation and apoptosis induction in two colorectal cancer cell lines were verified by RNA-seq combined with WB and flow cytometry analysis.In the RNA-seq analysis on cells, ~100 cells were used for per reaction and two or three replicates were performed for each group.

first: Ming

last: Zong

first: Jingzhang

last: Ji

first: Lijun

first: Lixin

last: Zhang


title: Exportin 1 governs the immunosuppressive functions of tumor myeloid derived suppressor cells through ERK1/2 nuclear export

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Myeloid derived suppressor cells (MDSCs) are a main driver of immunosuppression in tumors. Understanding the mechanisms that determine the development and immunosuppressive function of these cells could provide new therapeutic targets to improve anti-tumor immunity. Here, we discovered in preclinical murine models, that exportin 1 (XPO1) expression is upregulated in tumor MDSCs and this expression is induced by IL-6 activated STAT3 during MDSC differentiation. XPO1 blockade transforms MDSCs into T cell-activating neutrophil-like cells, enhancing the anti-tumor immune response and restraining tumor growth. Mechanistically, XPO1 inhibition leads to nuclear entrapment of ERK1/2, resulting in prevention of ERK1/2 phosphorylation post-IL-6 activation of the MAPK signaling pathway. Similarly, XPO1 blockade in human MDSCs induces neutrophil-like cells with immunostimulatory functions. Therefore, our findings have revealed a critical role of XPO1 in MDSC differentiation and suppressive function; exploiting these new discoveries reveals new targets to reprogram immunosuppressive MDSCs to improve cancer therapeutic responses.

overall_design: MDSCs were generated in vitro using IL-6 (40 ng/ml) and GM-CSF (40 ng/ml) for 4 days in presence of Selinexor (50 nM) of vehicle (DMSO) and their transcriptomics profile was evaluated by single cell RNA sequencing (scRNA-seq).

first: Saeed

last: Daneshmandi

first: Hemn

last: Mohammadpour


title: A rapid and robust method for Mitochondrial DNA profiling

city: shanghai

first: Guoqiang

last: Zhou

address: Fudan University, Shanghai, 200438, China

institute: Fudan University School of Life Sciences

summary: Human mitochondrial DNA (mtDNA) variations, particularly the presence of both mutated and wild type mtDNA known as mtDNA heteroplasmies, have garnered increasing attention due to their clinical relevance to numerous diseases. Nonetheless, the absence of a feasible and economical approach has hampered large-scale population studies on mtDNA variations. Here, we present a novel human mtDNA sequencing method called 123-seq, which is based on the 123-multiplex PCR and completed in consecutive three-step biochemical reactions, with experimental validation of its reliability. The entire library construction process takes only about 90 minutes, enabling efficient capture, amplification, and library construction of mtDNA at the bulk genomic DNA level or single-cell level in a streamlined workflow. We then applied our method to assess single-cell mtDNA mutations in a human sample, profiling over 286 T lymphocytes from a 79-year-old female. We discovered that over 90% of cells carried at least one mtDNA mutation with variant allele frequencies (VAFs) exceeding 20%. Furthermore, 83.78% of these mutation sites were enriched in the protein-coding regions of mtDNA. Our findings suggest that mtDNA mutations with functional significance may be widespread in advanced age, indicating a potential link to T cell aging. This emphasizes the need for further investigation into the dynamics of age-related mtDNA mutations at the single-cell level.

overall_design: Genomic DNA from bulk cells or the lysate of single cells can serve as the initial template, and the mtDNA library construction process can be completed through a consecutive three-step method. In the 1st step, the entire mitochondrial genome is selectively amplified using 123 multiple primers targeting mtDNA, with each primer pair containing a shared sequence of 20 nucleotides at the 5' end. The first round of PCR involves a low-temperature, low-cycle phase for targeted amplification of mtDNA to address specificity issues between targets, and a high-temperature phase for exponential amplification of the shared sequence to address compatibility issues between targets. In the 2nd step, Exonuclease I (Exo I) is added to the reaction system to remove residual multiple PCR primers from the first round of PCR. In the 3rd step, library construction is completed by adding sequencing adapter primers containing the shared sequence and cell barcode (sample index) into the reaction system, followed by the second round of PCR.

first: Yuanwu

last: Liu

first: Deng

last: Lin

first: Mengying

last: Wu

first: Chengpeng

last: He

first: Yu

last: Yang

first: Yuting

first: Jingjing

last: Du

first: Weilin

last: Pu

first: Zhenglong

last: Gu


title: Effect of IFN-γ on gene expression of bone marrow-derived macrophages

city: Wuhan, China

first: Xiao

state: 湖北省

address: 武汉市江汉区马场路109号协和医院肿瘤中心

institute: Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

summary: Here, we report that IFN-γ derived from CD8+ T cells promotes the transcription of ACOD1 in macrophages and the subsequent production of itaconate. To explore the molecular mechanism by which IFN-γ induces ACOD1 in macrophages, we analysed the transcriptome of IFN-γ-treated BMDMs by RNA-seq. Enrichment analysis of differentially expressed genes (DEGs) revealed that the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway was significantly enriched in IFN-γ-treated BMDMs compared with the control group.

overall_design:
To identify the molecular mechanism by which IFN-γ induces ACOD1 in macrophages, we performed RNA-seq on untreated BMDMs and IFN-γ-stimulated BMDMs.
We then performed gene expression profiling analysis using data obtained from RNA-seq of BMDMs untreated or treated with IFN-γ for 3 h.
Comparative gene expression profiling analysis of RNA-seq data for untreated BMDMs and IFN-γ-stimulated BMDMs.

first: Yue

last: Deng

first: Chao

last: Wan

first: Kunyu


title: The interplay between glucogenic amino acids and carbohydrate metabolisms in regulating the clinical fate of preterm infected newborns

city: Copenhagen

first: tik

last: muk

state: copenhagen

address: Dyrlægevej 68,1870 Frederiksberg C, Dyrlægevej 68, 1870 Frederiksberg C

institute: University of Copenhagen

summary: Early-life sepsis remains one of the leading causes of global morbidity and mortality in the neonatal population, especially preterm infants. Using a preterm piglet model of neonatal sepsis to test nutritional interventions as a therapeutic approach, we demonstrated that high parenteral glucose induced hyperglycemia with severe sepsis, whereas glucose restriction offered protection against infection but led to severe hypoglycemia. Building on this, our current study aims to maintain normoglycemia through galactose metabolism or gluconeogenesis and reduce sepsis risks by substituting glucose with galactose, or supplementing glucogenic amino acids (GAAs).

overall_design: Three experiments were designed with similar setups, 74 cesarean-delivered preterm pigs (90% gestation) were challenged with Staphylococcus epidermidis (SE) or saline control (CON) and nourished with different compositions of PN for 15~20 h. Clinical symptoms, physiological, metabolic, and immunological responses to infection were evaluated across the study. In study 1, animals were randomly allocated to sGAL group: standard galactose (10%, 14.4g/kg/d) or sGLU group: standard glucose (10%, 14.4g/kg/d). In study 2, animals were randomly allocated to rGLU-GAAs group: restricted glucose (1.4%, 2g/kg/d) plus four GAAs (glutamine/valine/aspartate/asparagine, 1g/kg/d each) or sGLU group: standard glucose (10%, 14.4g/kg/d). In study 3, animals were randomly allocated to rGLU-GAAs group: restricted glucose (1.4%, 2g/kg/d) plus four GAAs (glutamine/valine/aspartate/asparagine, 1g/kg/d each) or rGLU group: restricted glucose alone (1.4%, 2g/kg/d). Liver samples at euthanasia were collected and liver RNA was extracted for RNAseq.

first: Ziyuan

last: WU

first: Tik

last: Muk

first: Ole

last: Bæk

first: Duc

middle: N

last: Nguyen


title: Effect of 4-octyl itaconate on gene expression of dendritic cells

address: 武汉市江汉区马场路109号协和医院肿瘤中心

summary: Here, we report that macrophage-derived itaconate exerts a significant suppressive effect on dendritic cell (DC) function. To delve deeper into the impact of itaconate on DCs, we treated bone marrow-derived dendritic cells with 4-OI, a derivative of itaconate, and conducted RNA-seq analysis. Gene-set enrichment analysis (GSEA) of 4-OI-treated DCs showed a general downregulation of innate immunity and immune-response pathways.

overall_design:
To further investigate the effect of itaconate on DCs, we performed RNA-seq analysis on bone marrow-derived dendritic cells (BMDCs) that were either incubated with IFN-γ alone or co-treated with IFN-γ and 4-OI.
We then performed gene expression profiling analysis using the RNA-seq data obtained from BMDCs of IFN-γ group and IFN-γ+4-OI group.
Comparative gene expression profiling analysis of RNA-seq data for BMDCs of IFN-γ group and IFN-γ+4-OI group.


title: small RNA-sequencing analysis of db/db mice exudate from subcutaneously implanted sponges

city: Boston

first: Nikolaos

last: Kalavros

state: Massachusetts

address: 330 Brookline Avenue

department: Pathology

institute: Beth Israel Deaconess Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Dried polyvinyl alcohol (PVA) sponges were used for subcutaneous implantation in the mice dorsum, and were harvested on days 3, 5, 10, and 16 post-implantation.

overall_design: Male 16-week old db/db mice (stock # 000642) were obtained from Jackson Laboratories and were acclimated to the animal facility for at least one week before surgery. A vertical incision of 2 cm was created on depilated and disinfected dorsum and a pocket was formed by separating the skin from the muscle to insert 4-6 PVA sponges. Once insertions were completed, the incisions were sutured and dermabond was applied. On collection days, PVA sponges containing wound fluids were collected in empty 5 ml syringes, placed in 15 ml falcon tubes and centrifuged for fluid collection at 3,000 rpm for 10 minutes at 4 °C.

first: Georgios

last: Theocharidis


title: A chromatin-driven mechanism of transcription in ammonia-oxidizing archaea under environmental stress

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

institute: Chungbuk National University


title: Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration [ST-seq]

city: Beijing

first: Zhuqing

address: 22 Zhongguancun Avenue South, Haidian District, Beijing

department: Department of Prosthodontics

institute: Peking University School and Hospital of Stomatology

summary: The bone-defect-repair process involves complex interaction between mesenchymal stem cells (MSCs) and immune cells, while the heterogeneity of osteoimmune microenvironment around implanted biomaterials remains elusive. By combining analysis of scRNA-seq and spatial transcriptomics technologies, we revealed that MgphiMSCs subpopulation served as the pioneers during the early stage of biomaterials-mediated bone defect healing process. They performed efficient osteogenic differentiation potential and had close interactions with immune cells. Remarkably, the MgphiMSCs could response to biomaterials-mediated osteoimmune microenvironment, rewired the polarization and osteoclastic differentiation of macrophages via midkine (MDK) signaling pathway. The inhibition of MDK activated the pro-inflammatory programs of macrophages and osteoclastogenesis. Meanwhile, multiple innate and adaptive immune-cell subsets exhibited close crosstalk between MgphiMSCs via SPP1 signaling pathway. These cellular profiles and interactions characterized in this study could broaden our understanding of the functional MSCs subpopulations at the early stage of biomaterial-mediated bone regeneration and provide the basis for the materials-designed strategies that target osteoimmune modulation.

overall_design: The calvarial bone defects were repaired with or without collagen/nHA materials, the tissues within bone defect regions were analyzed via spatial transcriptomics


title: Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration [scRNA-seq]

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for cells harvested from calvarial bone defect regions repaired with or without Col+nHA materials.


title: Isolation, identification and osteogenic capability analysis of mesenchymal stem cells derived from different layers of human maxillary sinus membrane

city: Chang chun

first: huixin

last: Lv

address: 1500 Tsinghua Road

institute: School and Hospital of Stomatology, Jilin University

summary: Mesenchymal stem cells (MSCs) from different tissue sources have different biological processes and differentiation abilities. Although previous studies confirm that MSCs derived from human maxillary sinus membrane (hMSM) can be cultured in vitro, it cannot confirm whether they belong to the same type and possess the same differentiation ability. In this study, lamina propria layer derived MSCs (hLMSCs) and periosteum layer derived MSCs (hPMSCs) from hMSM are isolated and expanded using explant cell culture method and the biological characteristics of hLMSCs and hPMSCs are compared using RNA sequencing. According to RNA sequencing and subsequent functional verification, hLMSCs and hPMSCs are identified as CD171+/CD90+ and CD171-/CD90+ phenotypes separately. This study suggests that two different types of MSCs can be identified and isolated from hMSMs. Both cells serve as good MSCs potential candidates for bone regeneration. It also indicates that hLMSCs and hPMSCs are valuable in vitro tools for preclinical studies and future exploration of the origin osteogenesis machenism in maxillary sinus region.

overall_design:
To discover the biological characteristics of hLMSCs and hPMSCs and evaluate their osteogenic capabilities, we isolated and cultured the two cells in vitro, and processed osteogenic induction on them.
We performed gene expression profiling analysis using data obtained from RNA-seq of hLMSCs and hPMSCs. Each group contained three samples.
We then compared the differential expression genes between the RNA-seq data of hLMSCs and hPMSCs, and their osteogenic induced patterns, respectively. Each group contained three samples.

first: Huixin

first: Jing

last: Xu

first: Yihan

last: Wang

first: Xiuyu

last: Liu

first: Jingjie

last: Zhai

first: Yanmin

last: Zhou


title: Construction of autonomous osteogenic microtissues based on human dental pulp derived mesenchymal stem cells

city: Changchun

first: zhuoran

last: wang

address: Tsinghua Road

institute: Jilin university

summary: Bone regeneration is currently a major clinical challenge. Adult human mesenchymal stem cells (MSCs) possess a unique advantage in organ tissue repair and physiological function recovery. Human dental pulp derived MSCs (hDPSCs) have the dual advantages of proliferation and osteogenic differentiation abilities. They can be induced to secrete bone matrix proteins to form osteogenic microtissues by constructing an appropriate osteogenic three-dimensional microenvironment. The biological characteristics of hDPSCs from microtissues and two-dimensional cultured cells are compared using RNA sequencing. According to RNA sequencing and subsequent functional verification, the osteogenic activations of hDPSCs might be related to cell adhesion related signaling pathways. In this process, cells could sense the tension from the environment to activate related signaling pathways, such as the FAK/RhoA/Rock signaling pathway. Further, the downstream osteogenic transcription factors could be activited into the nucleus, thereby promoting the expression of osteogenic proteins.

overall_design:
To construct human dental pulp derived mesenchymal stem cells (hDPSCs) based osteogenic microtissues (hDOMTs) and evaluate its bioactivity and osteogenic potential.
We performed gene expression profiling analysis using data obtained from RNA-seq of hDPSCs.
We compared the differential expression genes between the RNA-seq data of two-dimensional cultured hDPSCs and hDPSCs from the microtissues, and their osteogenic induced patterns, respectively.

first: Zhuoran

first: Daowei

last: Li


title: MITF perturbation in A2058 Melanoma cell lines

city: Brisbane

first: Brad

last: Balderson

state: QLD

address: Chemistry Bld, 68 Cooper Rd

department: The School of Chemistry and Molecular Bioscience

institute: The University of Queensland

summary: We performed bulk RNA-seq on cultured melanoma with up- and down- regulation of the master regulator MITF in A2058 human melanoma cells.

overall_design: Bulk RNA-Seq analysis was performed with 3 biological replicates on A2058 human melanoma cells with various treatments: overexpression of MITF, MITF siRNA mediated knockdown, an empty vector control and a scrambled siRNA control.

first: Mitchell

last: Fane

first: Tracey

last: Harvey

first: Michael

last: Piper

first: Mikael

last: Boden

first: Aaron

last: Smith


title: Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration

first: Zhuqing

last: Wan

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

overall_design: Refer to individual Series


title: Bisulfite-Free Whole-Genome Mapping of 5-Methylcytosine at Single-Base Resolution by TAD-seq

city: wuhan

first: neng

middle: bin

last: xie

address: 115 donghu road

institute: wuhan university

summary: 5-Methylcytosine (5mC) is a crucial epigenetic modification plays a significant role in the regulation of gene expression. Accurate and quantitative detection of 5mC at single-base resolution is essential for understanding its epigenetic functions within genomes. In this study, we develop a novel nTET-assisted deaminase sequencing (TAD-seq) method for the base-resolution and quantitative detection of 5mC in genomic DNA. The TAD-seq method utilizes a Naegleria TET-like dioxygenase (nTET) to oxidize 5mC, generating 5-methylcytosine oxidation products (5moC). We also engineered a variant of the human apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (A3A), creating an A3A mutant (A3Am). Treatment with A3Am results in the conversion of cytosine to uracil, while 5moC remains unchanged. Consequently, TAD-seq enables the direct deamination of cytosine to uracil by A3Am, which is sequenced as thymine, whereas 5mC, once oxidized to 5moC by nTET, resists deamination and is sequenced as cytosine. Therefore, the cytosines that persist in the sequencing data represent the original 5mC sites. We applied TAD-seq to HEK293T cells, generating a base-resolution map of 5mC that exhibits strong concordance with maps generated by conventional BS-seq. TAD-seq emerges as a powerful, bisulfite-free approach for the single-base resolution mapping of 5mC stoichiometry in genomic DNA.

overall_design: Single-base resolution mapping of 5-methylcytosine in cell line HEK293T by TAD-seq and BS-seq.

first: Nengbin

last: Xie

first: Min

first: Bifeng

last: Yuan


title: Novel RNA-Seq Signatures Post-Methamphetamine and Oxycodone Use in a Model of HIV-Associated Neurocognitive Disorders

city: Omaha

first: Pendyala

last: Gurudutt

state: NE

address: University of Nebraska Medical Center

institute: University of Nebraska Medical Center

summary: In the 21st century, the effects of HIV-associated neurocognitive disorders (HAND) have been significantly reduced in individuals due to the development of antiretroviral therapies (ARTs). However, the growing epidemic of polysubstance use (PSU) has led to concern for the effects of PSU on HIV-seropositive individuals. To effectively treat individuals affected by HAND, it is critical to understand the biological mechanisms affected by PSU including identification of novel markers. To fill this important knowledge gap, we used an in vivo HIV-Transgenic (HIV-Tg) animal model, to investigate the effects of the combined use of chronic methamphetamine (METH) and oxycodone (oxy). RNA-Seq analysis on the striatum - a brain region that is primarily targeted by both HIV and drugs of abuse - identified key differentially expressed markers post-METH and oxy exposure. Furthermore, ClueGO analysis and Ingenuity Pathway Analysis (IPA) revealed crucial molecular and biological functions associated with ATP-activated adenosine receptor, neuropeptide hormone activity, and the oxytocin signaling pathway to be altered between the different treatment groups. The current study further reveals the harmful effects of chronic PSU and HIV infection that can subsequently impact neurological outcomes in polysubstance users with HAND.

overall_design: Gene expression comparison between WT and HIV transgenic rats in the presence or absence of polysubstance (Methamphetamine and Oxycodone combined) use.

first: Pranavi

last: Athota

first: Nghi

last: Nguyen

first: Victoria

middle: L

last: Schaal

first: Sankarasubramanian

last: Jagadesan

first: Chittibabu

last: Guda

first: Sowmya

middle: V

last: Yelamanchili

first: Gurudutt

last: Pendyala


title: Specific silencing of pathogenic mRNA by a novel compact RNA-targeting tool TaqTth-hpRNA

city: Nanjing

first: Shu

last: Xu

state: Jiangsu Province

address: China Pharmaceutical University

institute: China Pharmaceutical University

summary: Pathogenic allele silencing is a promising treatment for genetic hereditary diseases. However, the concern about the specificity of present RNA-knockdown strategies has limited their in vivo applications. Here a TaqTth-hpRNA system consisting of a small, chimeric protein (TaqTth) and hairpin-RNA probe (hpRNA) is provided. The TaqTth-hpRNA showed a high-specific knockdown against targeted mRNA with minimal flanking sequence-motif requirement and less cell viability damage, then was applied to mutant APPswe mRNA silencing without altering the wild-type APP mRNA in Alzheimer’s disease. Notably, the combination of the TaqTth and human apolipoprotein E 2 (APOE2) overexpression encoded in a single AAV vector is available due to the compact size of TaqTth, and showed stronger inhibition of pathologies in the mouse model. Altogether, we provided the basis for a small RNA-targeting tool with high selectivity, minimal flanking sequence-motif requirement, less cell viability damage and potentially being an alternative in therapeutic applications.

overall_design: To examine the intensity of the collateral effects of the TaqTth-hpRNA, we performed total RNA integrity analysis and transcriptome-wide RNA-seq of HepG2 cells treated with TaqTth-hpRNA or siRNA. Similar to previous findings , a significant reduction in RNA integrity was observed in the siRNA-treated cells. We also observed off-target degradation of transcripts in cells treated with PPIB siRNA. Data showed that ~ 1084 and 1110 genes were significantly up-regulated and down-regulated in siRNA group compared with the NT control, respectively . Further analysis showed that these off-targeted genes were distributed in many biological processes, including cell growth, cell locomotion, metabolic process and so on . These results are consistent with previous reports that host transcript degradation induced by siRNA results in retarded growth of cells. Unlike siRNA treatment, the TaqTth-hpRNA sharply reduced the number of off-target genes when targeting PPIB (26 vs 2194) , indicating that TaqTth mainly reduced collateral off-target degradation.


title: Nitric oxide inhibits FTO demethylase activity to regulate N6-methyladenosine mRNA methylation [MDA-MB-231-RNASeq]

city: Chicago

first: Douglas

last: Thomas

state: IL

address: 833 S. Wood Street, MC 781

department: Pharmaceutical Sciences

institute: University of Illinois at Chicago

summary: Here we show that nitric oxide (NO) is a potent inhibitor of FTO demethylase activity by directly binding to the catalytic iron center, which causes global m6A hypermethylation of mRNA in cells and results in gene-specific enrichment of m6A on mRNA of NO-regulated transcripts. Both cell culture and tumor xenograft models demonstrated that endogenous NO synthesis can regulate m6A-mRNA levels and transcriptional changes of m6A-associated genes. These results build a direct link between NO and m6A-mRNA regulation and reveal a novel signaling mechanism of NO as an endogenous regulator of the epitranscriptome.

overall_design: With the observation that NO directly inhibits FTO demethylase activity and globally increases m6A-mRNA, we sought to decipher whether this was functionally associated with transcriptional changes in NO-regulated genes. First, we quantified changes in transcription by performing RNA-sequencing on samples from two cell lines treated chronically (10 days) with NO.


title: Nitric oxide inhibits FTO demethylase activity to regulate N6-methyladenosine mRNA methylation [MDA-MB-468-RNASeq]


title: RpS19a depletion alters the haematopoietic translatome to directly drive tissue overgrowth II

city: Canberra

first: Olga

last: Zaytseva

state: ACT

address: 131 Garran Road

institute: John Curtin School of Medical Research

summary: Counterintuitively, increased tumour predisposition is associated with ribosomal protein (RP) loss. Here, we provide the first evidence that RP depletion can directly drive tissue overgrowth. Haematopoietic compartment-specific knockdown (KD) of RpS19a in the Drosophila lymph gland not only results in haematopoietic stem and progenitor cell (HSPC) loss but also drives excess proliferation and tissue overgrowth. In accordance with continued ribosome assembly and protein synthesis, actively translating ribosomes (polysomes) are detected in RpS19a KD Drosophila S2 cells. The RpS19a KD ribosomes do, however, display heterogeneity and significantly altered stoichiometry of the associated translation initiation factors eIF4A and eIF5. Consistent with altered translation, in addition to increased association between polysomes and mRNA encoding growth promoting genes (e.g. Ras), we observe increased abundance of the ortholog of ribosomal (r)RNA small subunit methyltransferase NEP1. Although uncharacterised in Drosophila, in yeast and human NEP1 is implicated in methylation of 18S rRNA and, thus, 40S assembly and 80S ribosome stability. Moreover, NEP1 (EMG1) mutations in humans underpin Bowen-Conradi syndrome, a ribosomopathy associated with developmental defects, growth failure, and infantile death. Remarkably, NEP1 depletion suppresses the RpS19a KD phenotype, restoring both stem and progenitor cells and suppressing lymph gland overgrowth. We further demonstrate NEP1 depletion significantly decreases methylation of the 18S rRNA residue (Ψ1,279) that is implicated in ribosome assembly. Together, these data suggest the increased NEP1 expression associated with RpS19a KD promotes assembly of pro-proliferative “onco-ribosomes” to drive haematopoietic compartment overgrowth.

overall_design: We investigated the effect of RpS19a knockdown driven via RNAi expression by Hemese-GAL4 on the transcriptome in Drosophila lymph glands when compared to control (Hemese-GAL4 crossed to W1118). 3 biological replicates of pooled lymph glands were collected for each condition.

first: Leonie

last: Quinn


title: Nitric oxide inhibits FTO demethylase activity to regulate N6-methyladenosine mRNA methylation [MDA-MB-231-meRIPSeq]


title: Nitric oxide inhibits FTO demethylase activity to regulate N6-methyladenosine mRNA methylation


title: Single-cell analysis reveals the immune heterogeneity and interactions in lungs undergoing hepatic ischemia-reperfusion

city: Tianjin

first: Chen

last: Zhang

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

institute: Tianjin Medical University

summary: Hepatic ischemia-reperfusion IR (HIR) is an unavoidable pathophysiological process during liver transplantation, resulting in systematic sterile inflammation and remote organ injury. Acute lung injury (ALI) is a serious complication after liver transplantation with high postoperative morbidity and mortality. However, the underlying mechanism is still unclear. To assess the phenotype and plasticity of various cell types in the lung tissue microenvironment after HIR at the single-cell level, single-cell RNA sequencing (scRNA-seq) was performed using the lungs from HIR-induced mice.

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for sham and hepatic ischemia-reperfusion (HIR) mice

first: Mingwei

last: Sheng

first: Wenli

last: Yu


title: Uniparental disomy: expanding the clinical and molecular phenotypes of whole chromosomes

city: Zhenjiang

first: Qi

last: Chen

address: 20 ZHENDONG ROAD

institute: Fourth affiliated hospital of Jiangsu University

summary: Uniparental disomy (UPD) refers to as both homologous chromosomes inherited from only one parent without identical copies from the other parent. Current knowledge of the phenotypes is associated with imprinting disorders or autosomal recessive mutations. Recent studies had reported that UPD for chromosomes 6, 7, 11, 14, 15, and 20 accompanied with definite imprinted disorders. However, the phenotypes and outcomes of UPD with other chromosomes have not been completely identified. Herein, we combined three remarkable UPD patients involving different chromosomes and presented their phenotypes. The chromosomal microarray (CMA) demonstrated a whole homozygous region on chromosome 2 in patient A, on chromosome 9 in patient B, accompanied by a gain mosaic region (ratio:22%) of 19.18Mb in 9p22.2p13.2, and a LOH region on 14q23.2q32.12 and several genes with compound heterozygous mutation were detected in patient C

overall_design: Chromosomal microarray analysis (CMA) were performed using amniotic fluids in prenatal

first: Wenlin


title: Murine testis: control vs. prenatally testosterone treated

city: NANJING

first: YU

last: ZHOU

address: NO. 169, HUSHAN ROAD

institute: THE AFFILIATED JIANGNING HOSPITAL OF NANJING MEDICAL UNIVERSITY

summary: mRNA m6A methylation level of mouse testis comparing control group with prenatally testosterone treated group

overall_design: Two-condition experiment, control vs. prenatally testosterone treated , Biological replicates: 5 control replicates, 5 prenatally testosterone treated replicates.

first: Ju

last: Rong

first: Zhou


title: Development of gene expression signatures for high glucose-induced renal tubular fibrosis

city: guangzhou

first: Chun-Min

last: Kang

state: guangdong

address: No. 111, Dade Road, Yuexiu District

institute: The Second Clinical College of Guangzhou University of Chinese Medicine

summary: To further explore differentially expressed genes in high glucose-induced renal tubular fibrosis cells, we used whole transcriptome microarray expression profiling as a discovery platform to identify genes with a potential role in the high glucose-induced renal fibrosis process. Low-glucose stimulation (5.5 mM glucose) and high-glucose stimulation (25 mM glucose) of human renal tubular HK2 cells identified a consensus profile of 644 highly expressed genes to distinguish high-glucose fibrotic renal tubules from control samples.

overall_design: Gene expression was measured in fibrotic kidney tubules after exposure to 25 mM glucose for 72 hours. Three independent experiments were performed, each using a different batch.

first: Chun-min

first: Xian-Zhang

last: Huang


title: RpS19a depletion alters the haematopoietic translatome to directly drive tissue overgrowth I

overall_design: We investigated the effect of RpS19a knockdown driven via shRNA transfection in Drosophila S2 cells on the translated mRNA isolated from polysome when compared to control. We also collected total cellular mRNA to serve as input. 3 biological replicates were collected for each condition.


title: Transplantation of human iPSC-derived cone photoreceptor sheets in the sub-retinal space of a minipig model of severe photoreceptor degeneration

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

country: Canada

institute: HMR

summary: We used single cell  RNA sequencing to investigate the cell diversity in our in vitro differentiation from iPSC to Retinal sheets culture and the development of our culture.

overall_design: In vitro differentiated cells were collected and resuspended then sequenced.

first: Andrea

last: Barabino

first: Katia

last: Mellal

first: Rimi

last: Hamam

first: Anna

last: Polosa

first: May

last: Griffith

first: Jean-François

last: Bouchard

first: Ananda

last: Kalevar

first: Roy

last: Hanna


title: Estrogen receptor β affects hypoxia response in colorectal cancer cells

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary: Our study identifies pathwyas related to tumour suppressor fuunction of estrogen receptor beta in colon cancer cells under hypoxic conditions.

overall_design: Estrogen receptor β, encoded by ESR2, was overexpressed using lentivrial system in HCT116, colon cell line, obtained from ATCC.

first: Agnieszka

middle: A

last: Rawłuszko-Wieczorek

first: Julia

last: Lipowicz

first: Marta

last: Nowacka

first: Paulina

last: Pietras

first: Kamila

last: Ostrowska

first: Małgorzata

last: Blatkiewicz

last: Ruciński

first: Paweł

middle: P

last: Jagodziński

first: Michał

last: Nowicki


title: Paternal exposure alone induces alcohol-related birth defects in a mouse model: Implications of paternal drinking in FAS birth defects.

city: College Station

first: Michael

last: Golding

state: TX

address: 588 Raymond Stotzer Pkwy

institute: Texas A&M University

summary: Prevailing  dogma  maintains  that  Fetal  Alcohol  Syndrome  (FAS)  craniofacial  and   neurological  birth  defects  are  the  sole  consequence  of  maternal  alcohol  use  during   pregnancy. Using a physiologically relevant mouse model, we contrasted the incidence   of  alcohol-related  growth  and  craniofacial  defects  between  offspring  derived  from   maternal,  paternal,  and  dual  parental  alcohol  exposures.  Geometric  morphometric   analyses reveal that maternal, paternal, and dual parental exposures each induce unique   craniofacial  malformations  and  program  dose-dependent  increases  in  microcephaly,   particularly in male offspring. Notably, dual parental exposures do not exhibit additive or   synergistic effects; instead, our transcriptomic analyses demonstrate that each treatment   programs distinct sex-specific changes in gene expression within the developing brain.   Our data are the first to demonstrate that male drinking is a plausible driver of alcohol-  related birth defects and that epidemiological examination of male alcohol consumption   may help explain the enormous variation in FAS clinical presentations and severity.

overall_design: We isolated total RNA from GD16 fetal cortices using the Qiagen AllPrep Kit (catalog# 80284, Qiagen, Germantown, MD, USA) according to the manufacturer’s instructions. We assessed  RNA  concentration  and  purity  using  a  NanoDrop  2000  Spectrophotometer (Thermo Scientific, Waltham, MA, USA). RNA sequencing was conducted by Quick Biology (Pasadena, CA, USA). Samples were randomized,  and  sequencing  libraries  were  generated  by  the  Illumina  mouse  TruSeq Standard Total RNA kit (catalog# RS-122-2202, Illumina, San Diego, CA, USA). Reads were demultiplexed using Illumina bcl2fastq2 v2.20 with default settings. Read quality was assessed using FastQC.

first: Kara

last: Thomas

first: Nimisha

last: Srikanth

first: Sanat

last: Bhadsavle

first: Kelly

first: Katherine

last: Zimmel

first: Alison

last: Basel

first: Alexis

last: Roach

first: Nicole

last: Mehta

first: Yudishtar

last: Bedi

middle: C


title: Glutamine inhibition combined with CD47 blockade enhances radiotherapy-induced ferroptosis in head and neck squamous cell carcinoma [ChIP-Seq IRF-1]

city: Wuhan

first: An

last: Song

address: Luoyu Road 237

institute: Wuhan University

summary:
To investigate the glutamine inhibition combined with CD47 blockade regulation of ferroptosis in HNSCC.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SCC7 cells and cells received radiotherapy.

first: Lei

last: Wu

first: Bo-Xin

last: Zhang

first: Qi-Chao

last: Yang

first: Yuan-Tong

last: Liu

first: Hao

last: Li

first: Liang

last: Mao

first: Dian

last: Xiong

first: Hai-Jun

last: Yu

first: Zhi-Jun

last: Sun


title: Glutamine inhibition combined with CD47 blockade enhances radiotherapy-induced ferroptosis in head and neck squamous cell carcinoma [ChIP-Seq Stat1]


title: Glutamine inhibition combined with CD47 blockade enhances radiotherapy-induced ferroptosis in head and neck squamous cell carcinoma

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus


title: Transcriptome analysis of CDAN1 deficiency in human erythroleukemic K562 cells.

city: Hong Kong

first: Margaret HL

last: Ng

address: Prince of Wales Hospital

department: Department of Anatomical and Cellular Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Congenital dyserythropoietic anemia Type 1 (CDA1) is a rare macrocytic anemia caused by loss-of-function mutation of CDAN1. To investigate the functional role of CDAN1, we performed RNA-sequencing on human erythroleukemic K562 cells with CDAN1 shRNA knockdown using a doxycycline inducible system

overall_design: Differential gene expression analysis comparing CDAN1 shRNA knockdown clones versus control samples including the respective uninduced clones together with both induced and uninduced cells expressing non-targeting (NT) shRNA

first: Margaret

first: Chi-Keung

last: Cheng

first: Yuk-Lin

last: Yung


title: RpS19a depletion alters the haematopoietic translatome to directly drive tissue overgrowth

first: Olga

last: Zaytseva


title: GPR158 Activates Cellular Stress Responses in Trabecular Meshwork Cells of the Eye’s Aqueous Outflow Pathways: Implications for Ocular Hypertension

city: Córdoba

first: Jose

last: Echenique

state: Córdoba

address: Edificio Integrador, Medina Allende S/N, Ciudad Universitaria

department: Clinical Biochemistry

country: Argentina

institute: School of Chemistry Sciences, National University of Cordoba

summary:
Background: the major risk factor for glaucoma is ocular hypertension, a disorder caused by reduced outflow of aqueous humor through the trabecular meshwork. In a previous pharmacogenomic screen for genes associated with ocular hypertension, we identified the novel G protein-coupled receptor, GPR158, and showed it protects against age-related ocular hypertension in mice. Here we show that the glucocorticoid, dexamethasone, increases the level of accumulated GPR158 protein in the trabecular meshwork of the human eye, ex vivo.
Methods: we performed gene expression microarray profiling of TM-1 cells thar overexpress GPR158
Results: we show that the glucocorticoid, dexamethasone, increases the level of accumulated GPR158 protein in the trabecular meshwork of the human eye, ex vivo. Gene sets controlled by dexamethasone, TGFB1 and TP53 were identified, as well as genes asso-ciated with ossification. GPR158 over-expression in cells of the immortalized trabecular meshwork cell line TM-1 did not affect the fibrotic response to dexamethasone or cause ossification, and loss of GPR158 in knockout mice did not affect the development of glucocorticoid-induced ocular hypertension. However, GPR158 over-expression was cytoprotective.
Discussion:  Our findings suggest that GPR158 activated the cytoprotective branch of the unfolded protein response and bound the TP53-inducible protein PPP1R10, a regulatory subunit of PPI regulatory subunit of PPI. Our data support the idea that GPR158 protects the trabecular meshwork, and suggest possible mechanisms.

overall_design: Microarray analysis of transcripts extracted from HTM cells treated with doxycycline for 24, 72 and 96 hs  to overexpress GPR158. No antibiotic treatment and cells transfected with only lentivector were used as controls,

first: Maria

middle: F

last: Suarez

first: Tatsuo

last: Itakura

first: Satyabrata

last: Pany

first: Shinwu

last: Jeong

first: Shravan

last: Chintala

first: Michael

middle: B

last: Raizman

first: Steven

last: Riesinger

first: Tsvetelina

last: Lazarova

first: Horacio

last: Serra

first: W

last: Stamer

first: Kirill

last: Martemyanov

first: M

last: Fini


title: Effect of L. infantum infection in microtranscriptome of human neutrophils in vitro [Expression]

status: Public on Jun 27 2024

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

summary: To understand the expression patterns of miRNAs expression during acute in vitro infection of human neutrophils by L. infantum we performed a microarray.

overall_design: We isolated neutrophils from whole blood of healthy male donors; cells from each subject (n=5) were split into groups: 1) infected with L. infantum (MOI = 5:1), and 2) uninfected controls. After 3 hours of exposure of infected group to promastigotes of L. infantum, followed by 17 hours of incubation, total RNA was extracted miRNA microarray were performed.

first: Natalia

last: Scaramele

first: Jessica

last: Troiano

first: Juliana

last: Felix

first: Sidnei

last: Costa

first: Mariana

last: Almeida

first: Flavia Regina

last: Athayde

first: Matheus

last: Soares

first: Maria Fernanda

first: Amanda

middle: O

last: Furlan

first: Valeria

last: Lima


title: Augmenting fibronectin levels in injured adult CNS promotes axon regeneration in vivo [bulk RNA-seq]

status: Public on Jun 28 2024

city: Farmington

first: Ephraim

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

summary: In an attempt to repair injured central nervous system (CNS) nerves/tracts, immune cells are recruited into the injury site, but endogenous response in adult mammals is insufficient for promoting regeneration of severed axons. Here, we found that a portion of retinal ganglion cell (RGC) CNS projection neurons that survive after optic nerve crush (ONC) injury are enriched for and upregulate fibronectin (Fn)-interacting integrins Itga5 and ItgaV, and that Fn promotes long-term survival and long-distance axon regeneration of a portion of axotomized adult RGCs in culture. We then show that, Fn is developmentally downregulated in the axonal tracts of optic nerve and spinal cord, but injury-activated macrophages/microglia upregulate Fn while axon regeneration-promoting zymosan augments their recruitment (and thereby increases Fn levels) in the injured optic nerve. Finally, we found that Fn’s RGD motif, established to interact with Itga5 and ItgaV, promotes long-term survival and long-distance axon regeneration of adult RGCs after ONC in vivo, with some axons reaching the optic chiasm when co-treated with Rpl7a gene therapy. Thus, experimentally augmenting Fn levels in the injured CNS is a promising approach for therapeutic neuroprotection and axon regeneration of at least a portion of neurons.

overall_design:
Adult uninjured or ONC-injured RGCs transduced with AAV2 expressing mCherry were Thy1-immunopanned from single cell retinal suspension (from 10 retinas per condition) and FACS’ed for mCherry+ cells. Approximately, 5,000 RGCs (per condition) were collected by FACS. RNA was isolated immediately using the Zymo QuickRNA microprep kit. Total RNA with RNA Integrity Number (RIN) ≥ 9 (by Bioanalyzer 2100 using the Nano 6000 kit, Agilent) was extracted using Direct-zol RNA MiniPrep kit (R2050, Zymo Research). cDNA libraries were prepared using polyA-selected RNA (TruSeq RNA Library Prep Kit, Illumina), paired reads sequenced 100 bp from each end on HiSeq 2000 Sequencer (Illumina), passed QC filters, mapped to the mm10 genome and transcriptome by Hisat2, gene expression was normalized as fragments per kilobase of transcript per million mapped reads (FPKM), and analyzed by Cufflinks/CuffDiff.

Please note: This series contains raw and processed data for two genes which is atypical for GEO studies.

first: Agnieszka

last: Lukomska

first: Matthew

last: Frost

first: Bruce

last: Rheaume


title: Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

city: Moscow

first: Anna

last: Kononkova

address: Nobel st., Building 1

department: Skoltech Center of Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: Transport of macromolecules through the nuclear envelope (NE) is mediated by nuclear pore complexes (NPCs) consisting of nucleoporins (Nups). Elys/Mel-28 is the Nup that binds and connects the decondensing chromatin with the reassembled NPCs at the end of mitosis. Whether Elys links chromatin with the NE during interphase is unknown. Using DamID-seq, we identified Elys binding sites in Drosophila late embryos and divided them into those associated with nucleoplasmic or with NPC-linked Elys. These Elys binding sites are located within active or inactive chromatin, respectively. Strikingly, Elys knockdown in S2 cells results in peripheral chromatin displacement from the NE, in decondensation of NE-attached chromatin, and in derepression of genes within. It also leads to slightly more compact active chromatin regions. Our findings indicate that NPC-linked Elys, together with the nuclear lamina, anchors peripheral chromatin to the NE, whereas nucleoplasmic Elys decompacts active chromatin.

overall_design: Comparative Hi-C analysis of chromatin spatial organization in control Drosophila S2 cell line and upon nucleoporin Elys knockdown

middle: D


title: Exercise training attenuated the muscle mitochondria genomic response to 70 day bedrest (RNA-Seq)

city: Irvine

first: Fadia

last: Haddad

state: CA

address: 101 Academy Way, Suite 150

department: Pediatrics/Exercise Medicine Division

institute: University of California Irvine

summary: The purpose of this study was to characterize the vastus lateralis (VL) gene and microRNA responses to 70 day bed rest with and without exercise countermeasures to mitigate the negative consequences of weightlessness.

overall_design: Gene expression profiling was determined in vastus lateralis muscle at baseline before bedrest and after ~70 days bedrest in 3 groups: a) Control group (CON), bedrest without exercise intervention; b) Exercise group (EX), bedrest and traditional exercise intervention; c) Flywheel group (FLY), bedrest and flywheel exercise intervention

first: Shlomit

middle: R

last: Aizik

first: Abel

last: Florido

first: Gregory

last: Adams

first: Joshua

last: Cotter


title: Exercise training attenuated the muscle mitochondria genomic response to 70 day bedrest (miRNA-Seq)

overall_design: microRNA profiling was determined in vastus lateralis muscle at baseline before bedrest and after ~70 days bedrest in 3 groups: a) Control group (CON), bedrest without exercise intervention; b) Exercise group (EX), bedrest and traditional exercise intervention; c) Flywheel group (FLY), bedrest and flywheel exercise intervention


title: Effect of L. infantum infection in transcriptome of human neutrophils in vitro [RNA-seq]

first: Flavia

last: Lopes

summary:
To understand the expression patterns of coding and non-coding transcripts during acute in vitro infection of human neutrophils by L. infantum we performed a differential gene expression analysis of RNA-Seq data.
We isolated neutrophils from whole blood of healthy male donors; cells from each subject (n=5) were split into groups: 1) infected with L. infantum (MOI = 5:1), and 2) uninfected controls. After 3 hours of exposure of infected group to promastigotes of L. infantum, followed by 17 hours of incubation, total RNA was extracted and total RNA-Seq were performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human neutrophils after L. infantum in vitro infetion.

first: Natalia

last: Scaramele

first: Jessica

last: Troiano

first: Juliana

middle: S

last: Felix

first: Sidnei

middle: M


title: PI3Kg in B cells promotes antibody responses and generation of antibody-secreting cells [scRNA-seq]

status: Public on Jun 26 2024

city: New Haven

first: Anis

last: Barmada

address: 300 Cedar Street

department: Department of Immunobiology

institute: Yale University

summary: The differentiation of naïve and memory B cells into antibody-secreting cells (ASCs) is a key feature of adaptive immunity. The requirement for phosphoinositide 3-kinase delta (PI3Kδ) to support B cell biology has been investigated intensively; however, specific functions of the related phosphoinositide 3-kinase-gamma (PI3Kγ) complex in B-lineage cells have not. Here we report that PI3Kγ promotes robust antibody responses induced by T cell-dependent antigens. The inborn error of immunity caused by human deficiency in PI3Kγ results in broad humoral defects, prompting our investigation of roles for this kinase in antibody responses using mouse models with bulk and single-cell transcriptome as well as B cell receptor repertoire sequencing.

overall_design: For single-cell RNA and B cell receptor sequencing, lymph node cells were analyzed after enrichment for B cell subsets from either wild-type or Pik3cg knockout mice (n = 3 each) immunized three times with NP-Ova emulsified in alum (Day 34). Cells from the different mice were barcoded with mouse TotalSeqTM-C (BioLegend) before mixing and sequencing using two identical lanes.

first: Stephen

last: Lanahan

first: Anjali

last: Ramaswamy

first: Gisela

last: Gabernet

first: Carrie

last: Lucas


title: Extracellular vesicles from type-2 macrophages increase the survival of chronic lymphocytic leukemia cells ex vivo

status: Public on Jun 29 2024

city: LIMOGES

first: Stéphanie

last: DURAND

address: 2 rue du Dr Marcland

department: UMR 1308 INSERM

institute: University of Limoges / INSERM

summary: The resistance of Chronic Lymphocytic Leukemia (CLL) B-cells to cell death is mainly attributed to interactions within their microenvironment, where they interact with various types of cells. Within this microenvironment, CLL-B-cells produce and bind cytokines, growth factors, and extracellular vesicles (EVs). In the present study, EVs purified from nurse-like cells and M2-polarized THP1 cell (M2-THP1) cultures were added to CLL-B-cells cultures. EVs were rapidly internalized by B-cells, leading to a decrease in apoptosis (P=0.0162 and 0.0469 respectively) and an increased proliferation (P=0.0335 and 0.0109). Additionally, they induced an increase in the resistance of CLL-B-cells to Ibrutinib, the Bruton kinase inhibitor in vitro (P=0.0344). A transcriptomic analysis showed an increase in the expression of anti-apoptotic gene BCL-2 (P=0.0286) but not MCL-1 and an increase in the expression of proliferation-inducing gene APRIL (P=0.0286) following treatment with EVs. Meanwhile, an analysis of apoptotic protein markers revealed increased amounts of IGFBP-2 (P=0.0338), CD40 (P=0.0338), p53 (P=0.0219) and BCL-2 (P=0.0338). Finally, exploration of EVs protein content by mass spectrometry revealed they carry various proteins involved in known oncogenic pathways and the RNAseq analysis of CLL-B-cells treated or not with NLCs EVs show various differentially expressed genes.

overall_design: mRNA from B-cells from three CLL patients that were either treated with extracellular vesicles produced by nurse-like cells or left untreated (paired control samples) were sequenced using the Illumina platform.

first: Léa

last: Ikhlef

last: Durand

first: Marie-Odile

last: Jauberteau

first: Paul-François

last: Gallet


title: Epigenetic control of myogenic identity of human muscle stem cells in Duchenne Muscular Dystrophy

city: La Jolla

first: Jimmy

last: Massenet

address: 10901 N Torrey Pines Rd, Building 12

institute: Sanford Burnham Prebys Medical Discovery Institute, Puri laboratory

summary: In Duchenne Muscular Dystrophy (DMD), the absence of the subsarcolemmal dystrophin protein leads to repeated myofiber damages inducing cycles of muscle regeneration that is driven by muscle stem cells (MuSCs). With time, MuSC regenerative capacities are overwhelmed, leading to fibrosis and muscle atrophy. Whether MuSCs from DMD muscle have intrinsic alterations or are primed by their degenerative/regenerative environment is still debated. We investigated cell behavior and gene expression in human using MuSCs derived from DMD or healthy muscles. We found that proliferation, differentiation and fusion were not altered in DMD-MuSCs, but with time, they lost the expression of the myogenic marker CD56 twice as fast as healthy MuSCs. The rapid drift towards a fibroblast-like cell identity was observed at the clonal level, and resulted from the altered expression of epigenetic enzymes required to maintain the myogenic cell fate. Indeed, the reexpression of CBX3, SMC3, H2AFV and H3F3B prevented the MuSC identity drift. Amongst the epigenetic changes, a closing of chromatin at the gene encoding the transcription factor MEF2B caused a down-regulation of its expression and a loss of the myogenic fate. Thus, MEF2B is a key mediator of the myogenic identity in human MuSCs, that is altered in DMD pathology.

overall_design: To identify potential targets of CBX3, H2A.Z2, H3.3 and SMC3 in MuSCs, ATAC sequencing was performed before and after lentiviral transduction of DMD human CD56pos MuSCs (Muscle Stem Cells). Five conditions were analyzed: (1) pure DMD-CD56pos cells harvested before the infection (Day 0); (2) empty-CD56pos and (3) empty-CD56neg cells resulting from DMD-CD56pos cells transfected empty lentivirus and cultured for 15,20 and 25 days (for about 10 population doublings at 25 days); (4) 4V-CD56pos and (5) 4V-CD56neg cells resulting from DMD-CD56pos cells transfected with CBX3, H2AZ2, H3F3B and SMC3 lentiviruses and cultured for 25 days (10 population doublings).

first: Bénédicte

last: Chazaud

first: Jeffrey

last: Dilworth


title: PI3Kg in B cells promotes antibody responses and generation of antibody-secreting cells [RNA-seq]

overall_design: For bulk RNA sequencing, we immunized mice (3 wild-type and 4 Pik3cg knockout) with sheeps red blood cells via IP injection. At day 28 we harvested various tissues and sorted cells via FACS. Total RNA was submitted to the Yale Center for Genome Analysis for sequencing.


title: Inhibition of JNK ameliorates rod photoreceptor degeneration in a mouse model of retinitis pigmentosa

status: Public on Jun 23 2024

city: Shenzhen

first: Chunyan

last: Liao

address: 1068 Xueyuan Avenue, Shenzhen University Town

department: BCBDI

institute: SIAT

summary: Retinitis pigmentosa (RP) is an inherited eye disease that causes progressive vision loss.To investigate the biological processes and molecular changes that occur in different cell types in the retinas in rd1 mice, a mouse model of retinitis pigmentosa, we performed single-cell RNA-seq to examine the transcriptomes of various retinal cells.

overall_design: We dissected the retinas from WT and rd1 mice, and obtained retinal single-cell suspensions using Papain Dissociation System Source according to the manufacturer’s instructions.

first: Shuai

last: Chen

first: Wanying

last: Yi


title: Adenosine triggers early astrocyte reactivity that provokes microglial reaction and drives the pathogenesis of sepsis-associated encephalopathy

city: Homburg

first: QILIN

last: GUO

address: Kirrberger Str. 100, CIPMM, Geb.48

department: Department of physiology

institute: Saarland University

summary: Molecular pathways mediating systemic inflammation entering the brain parenchyma to induce sepsis-associated encephalopathy (SAE) remain elusive. Here, we report that in mice during the first 6 hours of peripheral lipopolysaccharide (LPS)-evoked systemic inflammation (6 hpi), the plasma level of adenosine quickly increased and enhanced the tone of central extracellular adenosine which then provoked neuroinflammation by triggering early astrocyte reactivity. Specific ablation of astrocytic A1 adenosine receptors (A1ARs) prevented this early reactivity and reduced the levels of inflammatory factors (e.g., CCL2, CCL5, and CXCL1) in astrocytes, thereby alleviating microglial reaction, ameliorating blood-brain barrier disruption, peripheral immune cell infiltration, neuronal dysfunction, and depression-like behaviour in the mice. Chemogenetic stimulation of Gi signaling in A1AR-deficent astrocytes at 2 and 4 hpi of LPS injection could restore neuroinflammation and depression-like behaviour, highlighting astrocytes rather than microglia as early drivers of neuroinflammation. Our results identify early astrocyte reactivity towards peripheral and central levels of adenosine as a novel pathway driving SAE and highlight the potential of targeting A1ARs for therapeutic intervention.

overall_design: To determine the contribution of astrocyte-specific A1ARs to LPS-induced neuroinflammation, we cross-bred GLAST-CreERT2 mice with temporal control of astrocyte-specific gene recombination to floxed A1AR mice, thereby generating inducible astrocytic A1AR cKO mice. In addition, we crossbred RiboTag mice enabling specific and direct purification of mRNAs from Cre-expressing cells in cerebral cortices to avoid pitfalls inherent to cell-sorting procedures. mRNA from astrocyte was purified at 0, 6, 24 hpi by Ribotag strategy and sent to sequencing.

first: Qilin

last: Guo

first: Frank

last: Kirchhoff

first: Wenhui

last: Huang