title: Class II KNOX and BELL TALE-class HD genes give insights into the evolution of secondary cell wall development and pectin biosynthesis during land plant evolution

city: Clayton

first: Tom

last: Dierschke

state: VIc

address: Wellington Road

institute: Monash University

summary: Land plants evolved from an ancestral alga around 470 million years ago, evolving complex multicellularity in both haploid gametophyte and diploid sporophyte generations. The evolution of water conducting tissues in the sporophyte generation was crucial for the success of land plants, paving the way for the colonization of a variety of terrestrial habitats. Class II KNOX (KNOX2) genes are major regulators of secondary cell wall formation and seed mucilage (pectin) deposition in flowering plants. Here we show that in the liverwort Marchantia polymorpha loss-of-function alleles of the KNOX2 ortholog, MpKNOX2, or its dimerization partner MpBELL1, have defects in capsule wall secondary cell wall and spore pectin biosynthesis. Both genes are expressed in the gametophytic calyptra surrounding the sporophyte and exhibits maternal effects, suggesting an intergenerational regulation from the maternal gametophyte to the sporophyte generation. These findings also suggest the presence of a “vascular-like” program in the non-vascular liverwort capsule wall.

overall_design: We generated inducible co-overexpression alleles of MpKNOX2 and MpBELL1. M. polymorpha spores were doubly transformed using one construct in cis and one in trans, resulting in lines constitutively expressing MpKNOX2 coding sequence with an estrogen inducible MpBELL1 coding sequence (proEF1:MpKNOX2; proEF1:XVE>>MpBELL1). Gemmae were grown under normal growth conditions (23°C, 24h white light) on ½ B5 Gamborg’s media for 10 days, and then transferred to plates containing 5μM 17-β-estradiol or mock. Plants were sampled at 0h (not induced) and 72h.

first: John

last: Bowman


title: Endothelial cells differentiated from patient dermal fibroblast-derived induced pluripotent stem cells resemble vascular malformations of Port Wine Birthmark

status: Public on Sep 14 2023

city: Columbia

first: Wenbin

last: Tan

state: SC

address: 6311 Garners Ferry Road

department: Cell Biology and Anatomy

country: USA

institute: University of South Carolina School of Medicine

type: Expression profiling by high throughput sequencing

summary: Background:Port wine birthmark (PWB) is a congenital vascular malformation resulting from developmentally defective endothelial cells (ECs). Developing clinically relevant disease models for PWB studies is currently an unmet need. Objective: Our study aims to generate PWB-derived induced pluripotent stem cells (iPSCs) and iPSC-derived ECs that preserve disease-related phenotypes. Methods: PWB iPSCs were generated by reprogramming lesional dermal fibroblasts and differentiated into ECs. RNA-seq was performed to identify differentially expressed genes (DEGs) and enriched pathways. The functional phenotypes of iPSC-derived ECs were characterized by capillary-like structure (CLS) formation in vitro and Geltrex plug-in assay in vivo. Results: Human PWB and control iPSC lines were generated through reprogramming of dermal fibroblasts by introducing the “Yamanaka factors” (Oct3/4, Sox2, Klf4, c-Myc) into them; the iPSCs were successfully differentiated into ECs. These iPSCs and their derived ECs were validated by expression of a series of stem cell and EC biomarkers, respectively. PWB iPSC-derived ECs showed impaired CLS in vitro with larger perimeters and thicker branches as compared to control iPSC-derived ECs. In the plug-in assay, perfused human vasculature formed by PWB iPSC-derived ECs showed bigger perimeters and greater densities than those formed by control iPSC-derived ECs in severe combined immune deficient (SCID) mice. The transcriptome analysis showed that dysregulated pathways of stem cell differentiation, Hippo, Wnt, and focal adhesion persisted through differentiation of PWB iPSCs to ECs. Functional enrichment analysis showed that Hippo and Wnt pathway-related PWB DEGs are enriched for vasculature development, tube morphology, endothelium development, and EC differentiation. Further, members of the zinc finger (ZNF) gene family were overrepresented among the DEGs in PWB iPSCs. ZNF DEGs confer significant functions in transcriptional regulation, chromatin remodeling, protein ubiquitination, and retinoic acid receptor signaling. Furthermore, NF-kappa B, TNF, MAPK, and cholesterol metabolism pathways were dysregulated in PWB ECs as readouts of impaired differentiation. Conclusions: PWB iPSC-derived ECs render a novel and clinically-relevant disease model by retaining pathological phenotypes. Our data demonstrate multiple pathways, such as Hippo and Wnt, NF-kappa B, TNF, MAPK, and cholesterol metabolism, are dysregulated, which may contribute to the development of differentiation-defective ECs in PWB.

overall_design:
To investigate the molecular and pathway signatures in PWB iPSCs and their-derived MSCs and ECs as compared with controls during differentiation
Grant information:
Department of Defense (HT9425-23-10008), PI: Wenbin Tan
Grant title: Targeting of Photodynamic Therapy-Resistant Port Wine Birthmarks Affiliation: UNIVERSITY OF SOUTH CAROLINA

first: Vi

last: Nguyen

first: Chao

last: Gao

first: Marcelo

middle: L

last: Hochman

first: Jacob

last: Kravitz

first: Elliott

middle: H

last: Chen

first: Harold

middle: I

last: Friedman

first: Camilla

middle: F

last: Wenceslau

first: Dongbao

first: Yunguan

last: Wang

first: J

middle: S

last: Nelson

first: Anil

middle: G

last: Jegga


title: Nrf2 alleviates spaceflight-induced immunosuppression and thrombotic microangiopathy

city: Sendai-shi

first: IKUO

last: HIRANO

state: Miyagi

address: 2-1 Seiryou-machi, Aoba-ku

department: Graduate School of Medicine

country: Japan

institute: Tohoku university

summary: Spaceflight-related stresses impact health via various body systems, including the hematopoietic and immune systems, with effects ranging from moderate alterations of homeostasis to serious illness. Oxidative stress appears to be involved in these changes, and the transcription factor Nrf2, which regulates expression of a set of cytoprotective and antioxidative stress response genes, has been implicated in the response to spaceflight-induced stresses. Here, we show through analyses of mice from the MHU-3 project, in which Nrf2-knockout mice travelled in space for 31 days, that mice lacking Nrf2 suffer more seriously from spaceflight-induced immunosuppression than wild-type mice. We discovered that a one-month spaceflight triggered the expression of tissue inflammatory marker genes in wild-type mice, an effect that was even more pronounced in the absence of Nrf2. Concomitant with induction of inflammatory conditions, the consumption of coagulation-fibrinolytic factors and platelets was elevated by spaceflight and further accelerated by Nrf2 deficiency. These results highlight that Nrf2 mitigates spaceflight-induced inflammation, subsequent immunosuppression, and thrombotic microangiopathy. These observations reveal a new strategy to relieve health problems encountered during spaceflight.

overall_design: In the MHU-3 project, we prepared wild-type (WT) male mice and Nrf2-KO male mice, and these mice went to spaceflight for 31 days. After spaceflight, we obtained samples, including bone marrow cells as cryopreserved cells in CELLBANKER2 (Nippon Zenyaku Kougyo). We prepared the RNA samples from the cryopreserved bone marrow cells of space-flew WT mice (FW, n = 6), space-flew Nrf2-KO mice (FN, n = 6), ground-control WT mice (GW, n = 6) and ground-control Nrf2-KO mice by ISOGEN-LS (NIPPON GENE). The cDNA libraries for RNA-sequencing were prepared by MGIEasy RNA Directional Library Prep Set (MGI). The libraries were sequenced using DNBSEQ-G400 (MGI).

first: Ritsuko

last: Shimizu

first: Ikuo

last: Hirano

first: Atsushi

last: Hasegawa

first: Mikiko

last: Suzuki

first: Akihito

last: Otsuki

first: Keiko

last: Taguchi

first: Fumiki

last: Katsuoka

first: Akira

last: Uruno

first: Norio

first: Akane

last: Yumoto

first: Risa

last: Okada

first: Masaki

last: Shirakawa

first: Dai

last: Shiba

first: Satoru

last: Takahashi

first: Takafumi

first: Masayuki

last: Yamamoto


title: Dual scRNA-Seq analysis reveals rare and uncommon parasitized cell populations in chronic L. donovani infection

city: Silver Spring

first: Luis

middle: V

last: Santana-Quintero

state: MD

address: 1627 Whitehall Dr

department: CBER

institute: US FDA

summary: Although phagocytic cells are documented targets of Leishmania parasites, it is unclear whether other cell types can be infected. Here, we use unbiased scRNA-seq to simultaneously analyze host cell and Leishmania donovani transcriptomes to identify and annotate parasitized cells in spleen and bone marrow in chronically infected mice. Our dual-scRNA-seq methodology allows the detection of heterogenous parasitized populations. In the spleen, monocytes and macrophages are the dominant parasitized cells, while megakaryocytes, basophils and NK cells are found unexpectedly infected. In the bone marrow, the Hematopoietic Stem Cells (HSCs) expressing phagocytic receptors FcγR and CD93 are the main parasitized cells. Additionally, we also detect parasitized cycling basal cells, eosinophils, and macrophages in chronically infected mice. Flow cytometric analysis confirms the presence of parasitized HSCs. Ourunbiased dual scRNA-seq method identifies rare, parasitized cells, possibly implicated in pathogenesis, persistence, and protective immunity using a non-targeted approach.

overall_design: Spleen and bone marrow were aseptically harvested from the mice and a single cell suspension was prepared from spleen by gentle mechanical disruption and passed through a 70µm cell strainer. For the bone marrow cells, femur and tibias were isolated and cut at both ends with scissors, and cells were flushed out from the cavity into RPMI medium-1640  supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin , and 0.1% β-mercaptoethanol . Cells were passed through a MACS-LS column to remove the non-targeted cells by using monocyte isolation kit . Monocyte enrichment was achieved by depletion of magnetically labeled non-targeted T cells, B cells, NK cells, dendritic cells, erythroid cells, and granulocytes.

first: Konstantinos

last: Karagiannis

first: Sreenivas

last: Gannavaram

first: Chaitenya

last: Verma

first: Thalia

last: Pacheco-Fernandez

first: Parna

last: Bhattacharya

first: Hira

last: Nakhasi

first: Abhay

last: Satoskar


title: Genetic Variants of Phospholipase C-γ2 Confer Altered Microglial Phenotypes and Differential Risk for Alzheimer’s Disease

city: Stanford

first: Andy

middle: P

last: Tsai

state: California

address: 290 Jane Stanford Way E365

institute: Stanford University

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

overall_design: Refer to individual Series


title: Genetic Variants of Phospholipase C-γ2 Confer Altered Microglial Phenotypes and Differential Risk for Alzheimer’s Disease [snRNA-seq]

summary: The PLCG2 variants bidirectionally modulate disease pathology by inducing distinct transcriptional programs that identify microglial subpopulations associated with protective or detrimental phenotypes

overall_design: Nuclei from 7.5-month-old 5xFAD, 5xFAD;M28L, and 5xFAD;P522R mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of NeuN and analyzed using scRNAseq.

first: Chuanpeng

last: Dong

first: Peter

middle: B

last: Lin

first: Adrian

last: Oblak

first: Gonzalo

last: Di Prisco

first: Nian

last: Wang

first: Nicole

last: Hajicek

first: Adam

middle: J

last: Carr

first: Emma

middle: K

last: Lendy

first: Oliver

last: Hahn

first: Micaiah

last: Atkins

first: Aulden

last: Foltz

first: Jheel

last: Patel

first: Guixiang

last: Xu

first: Miguel

last: Moutinho

first: John

last: Sondek

first: Qisheng

last: Zhang

first: Andrew

middle: D

last: Mesecar

first: Yunlong

last: Liu

first: Brady

last: Atwood

first: Tony

last: Wyss-Coray

first: Kwangsik

last: Nho

first: Stephanie

last: Bissel

first: Bruce

middle: T

last: Lamb

first: Gary

middle: E

last: Landreth


title: Genetic Variants of Phospholipase C-γ2 Confer Altered Microglial Phenotypes and Differential Risk for Alzheimer’s Disease [bulk RNA-seq]

first: Andy

last: Tsai

overall_design: We performed RNAseq using cortex samples from 7.5-month-old 5xFAD, 5xFADM28L, and 5xFADP522R mice

first: Chuanpeng

last: Dong

first: Peter

last: Lin

first: Adrian

last: Oblak

first: Gonzalo

last: Di Prisco

first: Nian

last: Wang

first: Nicole

last: Hajicek

first: Adam

last: Carr

first: Emma

last: Lendy


title: Genetic Variants of Phospholipase C-γ2 Confer Altered Microglial Phenotypes and Differential Risk for Alzheimer’s Disease.


title: Phenotypic and transcriptional analysis of the antimicrobial effect of lactic acid bacteria on carbapenem-resistant Acinetobacter baumannii: Lacticaseibacillus rhamnosus CRL 2244 an alternative strategy to fight it

city: Buenos Aires

first: Sieira

last: Rodrigo

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

summary: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a recognized nosocomial pathogen with limited therapeutics options. Lactic acid bacteria (LAB) constitute a promising therapeutic alternative. Here we aimed to study the antibacterial properties of a collection of LAB strains using phenotypic and transcriptomic analysis against A. baumannii clinical strains. One strain, Lacticaseibacillus rhamnosus CRL 2244, exerts a strong inhibitory capacity on A. baumannii with a strong killing activity. Scanning electron microscopy images showed changes in the morphology of A. baumannii with an increase formation of outer membrane vesicles. Significant changes in the expression levels a wide variety of genes were observed. Interestingly, most of the modified genes were involved in metabolic pathway known to be associated with bacterial survival. The paa operon, Hut system, and fatty acid degradation were some of the pathways that have been induced. The data reveals the impact of Lcb. rhamnosus CRL 2244 on A. baumannii response, resulting in bacterial stress and subsequent cell death. These findings highlight the antibacterial properties of Lcb. rhamnosus CRL 2244 and its potential as an alternative or complementary strategy for treating infections. Further exploration and development of this LAB as a treatment option could provide valuable alternatives for combating CRAB infections.

sample_organism:
Acinetobacter baumannii
Lacticaseibacillus rhamnosus

overall_design: Overnight cultures of Acinetobacter baumannii AB5075 and Lacticaseibacillus rhamnosus CRL 2244 with OD adjusted to 600 nm at 4.0 were centrifuged and resuspended in 3 mL of BHI broth and incubated for 90 min at 37°C. Total RNA extractions of Acinetobacter baumannii AB5075 or Acinetobacter baumannii AB5075  coincubated with Lacticaseibacillus rhamnosus CRL 2244 were performed in three biological replicates for each condition. RNA-seq reads corresponding to A. baumannii AB5075 exposed to CRL 2244 were analyzed.

first: Maria

last: Ramirez

first: Rodrigo

last: Sieira


title: DNA methylation patterns in CD4+ T cells separate psoriasis patients from healthy controls, and skin psoriasis from psoriatic arthritis II

city: Liverpool

first: Christian

last: Hedrich

state: Please select...

address: Department of Women's & Children's Health,University of Liverpool, Alder Hey Children's NHS Foundation Trust,Eaton Road,

country: United Kingdom

summary:
Background: Psoriasis is a systemic inflammatory disease primarily affecting the skin. Approximately one-third of psoriasis patients develop joint involvement and are diagnosed with psoriatic arthritis (PsA). While, inIn adult-onset disease,  adults, the development of arthritis usually follows skin psoriasis, but approximately 15% experience arthritis first,  which can delay diagnosis.  While the pathophysiology of psoriasis and PsA is incompletely understood, epigenetic dysregulation affecting CD4+ and CD8+ T-cells has been suggested.  Objectives: This project aimed to identify disease-associated DNA methylation signatures in CD4+ T-cells from psoriasis and PsA patients that may be used as diagnostic and/or prognostic biomarkers.   Methods: PBMCs were collected from 12 patients with chronic plaque skin psoriasis and 8 PsA patients, and 8 healthy controls. CD4+ T-cells were separated through FACS sorting, and DNA methylation profiling was performed (Illumina EPIC850K arrays). Bioinformatic analyses, including gene ontology (GO) and KEGG pathway analysis, were performed using R software. To identify genes under the control of interferon (IFN), the Interferome database was consulted, and DNA Methylation Scores were calculated.  Results: Numbers and proportions of CD4+ T-cell subsets (naïve, central memory, effector memory, CD45RA re-expressing effector memory cells) did not vary between controls, skin psoriasis and PsA patients. 883 differentially methylated positions (DMPs) affecting 548 genes were identified between healthy controls and “all” psoriasis patients. Principal component and partial least-squares discriminant analysis separated controls from skin psoriasis and PsA patients. GO analysis considering promoter DMPs delivered hypermethylation of genes involved in “regulation of wound healing, spreading of epidermal cells”, “negative regulation of cell-substrate junction organization” and “negative regulation of focal adhesion assembly”. Comparing controls and “all” psoriasis, a majority of DMPs mapped to IFN-related genes (69.2%). Notably, DNA methylation profiles also distinguished skin psoriasis from PsA patients (2,949 DMPs/1,084 genes) through genes affecting “cAMP-dependent protein kinase inhibitor activity” and “cAMP-dependent protein kinase regulator activity” (GO analysis). Treatment with cytokine inhibitors (IL-17/TNF) corrected DNA methylation patterns of IL-17/TNF-associated genes, and methylation scores correlated with skin disease activity scores (PASI).  Conclusion: DNA methylation profiles in CD4+ T-cells discriminate between skin psoriasis and PsA. DNA methylation signatures may be applied for quantification of disease activity and patient stratification towards individualized treatment.
The aim of this study was to identify disease-associated DNA methylation signatures in CD4+ T-cells from patients with psoriasis and PsA that may be used as diagnostic and/or prognostic biomarkers to inform treatment and care.

overall_design: Genome wide DNA methylation were analyzed in CD4+T cells from patients with Psoriatic Arthritis (PsA), psoriasis and Healthy Control (HC) before and after  patients start treatment.

first: Valentina

last: Natoli

first: Amandine

last: Charras

first: Sigrun

middle: R

last: Hofmann

first: Sarah

last: Northey

first: Susanne

last: Russ

first: Felix

last: Schulze

first: Liza

last: McCann

last: Abraham

middle: M


title: Genetic Ablation of Prorenin Receptor in the Rostral Ventrolateral Medulla Influences Blood Pressure and Hydromineral Balance in Deoxycorticosterone-Salt Hypertension

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

institute: Medical College of Wisconsin

summary: Non-enzymatic activation of renin via its interaction with prorenin receptor (PRR) has been proposed as a key mechanism of local renin-angiotensin system (RAS) activation. The presence of renin and angiotensinogen has been reported in the rostral ventrolateral nucleus (RVLM). Overactivation of bulbospinal neurons RVLM is linked to hypertension (HTN). Previous studies have shown that the brain RAS plays a role in the pathogenesis of the deoxycorticosterone (DOCA)-salt HTN model. Thus, we hypothesized that PRR in the RVLM is involved in the local activation of the RAS, facilitating the development of DOCA-salt HTN. Selective PRR ablation targeting the RVLM (PRRRVLM-Null mice) resulted in an unexpected sex-dependent and biphasic phenotype in DOCA-salt HTN. That is, PRRRVLM-Null females (but not males) exhibited a significant delay in achieving maximal pressor responses during the initial stage of DOCA-salt HTN. Female PRRRVLM-Null subsequently showed exacerbated DOCA-salt-induced pressor responses during the “maintenance” phase with a maximal peak at 13 days on DOCA-salt. This exacerbated response was associated with an increased sympathetic drive to the resistance arterioles and the kidney, exacerbated fluid and sodium intake and output in response to DOCA-salt, and induced mobilization of fluids from the intracellular to extracellular space concomitant with elevated vasopressin. Ablation of PRR suppressed genes involved in RAS activation and catecholamine synthesis in the RVLM but also induced expression of genes involved in inflammatory responses. This study illustrates complex and sex-dependent roles of PRR in the neural control of BP and hydromineral balance through autonomic and neuroendocrine systems.

overall_design: 14 samples

first: Natalia

last: Mathieu

first: Eva

last: Fekete

first: Patricia

middle: C

last: Muskus

first: Daniel

last: Brozoski

first: Ko-Ting

last: Lu

first: Kelsey

last: Wackman

first: Javier

last: Gomez

first: Shi

last: Fang

first: John

last: Reho

first: Connie

last: Grobe

first: Gary

last: Mouradian Jr

first: Matthew

last: Hodges

first: Jeffrey

last: Segar

first: Justin

first: Curt

last: Sigmund

first: Pablo

last: Nakagawa


title: LIN28B promotes cell invasion and colorectal cancer metastasis via CLDN1 and NOTCH3

city: New York

first: Spyros

last: Karaiskos

state: NY

department: Herbert Irving Cancer Center

institute: Columbia University

summary: The RNA-binding protein LIN28B is overexpressed in over 30% of patients with colorectal cancer (CRC) and is associated with poor prognosis. In the present study, we unravel a novel mechanism by which LIN28B regulates colonic epithelial cell-cell junctions and CRC metastasis. Using human CRC cells (DLD-1, Caco-2 and LoVo) with either knockdown or overexpression of LIN28B, we identified Claudin 1 (CLDN1) tight junction protein as a direct downstream target and effector of LIN28B. RNA immunoprecipitation revealed that LIN28B directly binds to and post-transcriptionally regulates CLDN1 mRNA. Furthermore, using in vitro assays and a novel murine model of metastatic CRC, we show that LIN28B-mediated CLDN1 expression enhances collective invasion, cell migration, and metastatic liver tumor formation. Bulk RNA-sequencing of the metastatic liver tumors identified NOTCH3 as a downstream effector of the LIN28B-CLDN1 axis. Additionally, genetic and pharmacologic manipulation of NOTCH3 signaling revealed that NOTCH3 was necessary for invasion and metastatic liver tumor formation. In summary, our results suggest that LIN28B promotes invasion and liver metastasis of CRC by post-transcriptionally regulating CLDN1 and activating NOTCH3 signaling. This discovery offers a promising new therapeutic option for metastatic CRC to the liver, an area where therapeutic advancements have been relatively scarce.

overall_design: Bulk RNA sequencing was performed on the liver tumors generated from portal vein injection of DLD-1 LIN28Bhigh and LoVo LIN28Bhigh cells with (shCLDN1) or without (shNTC) CLDN1 depletion.

first: Alice

last: Shin

first: Kensuke

last: Sugiura

first: Anil

last: Rustgi


title: Administration of tamoxifen regulates changes in gene expression during the acute phase of traumatic spinal cord injury

city: Ciudad de Mexico

first: Yalbi

middle: Itzel

last: Balderas-Martinez

state: Distrito Federal

address: Calzada de Tlalpan 4502, Sección XVI, Belisario Domínguez

country: Mexico

institute: INER

summary: Traumatic spinal cord injury (SCI) may induce irreversible damage leading to severe incapacity. Molecular mechanisms underlying SCI are not fully understood, preventing the development of novel therapeutic resources. Tamoxifen has demonstrated to be a promising therapy. Our aim was to elucidate the molecular mechanisms involved in the beneficial effect of TMX administered after SCI. We use a rat model of SCI, Tamoxifen was administred intraperitoneal 30 min after injury. Four groups were organized, 1) Non-injured without TMX (Sham/TMX-), 2) Non-injured with TMX (Sham/TMX+), 3) Injured without TMX (SCI/TMX-), and 4) Injured with TMX (SCI/TMX+). From the comparison between Sham/TMX- and SCI/TMX-, 708 genes showed differential expression. Among the relevant genes Anxa1 was upregulated, this gene’s product is a promising marker of injury severity. Enriched pathways were the spinal cord injury pathway and pathways related to inflammatory response. When comparing SCI/TMX- versus SCI/TMX+, only 30 genes showed differential expression. Our results reinforce the key role of inflammatory response in SCI and Tamoxifen seem to be able to regulate this response by suppressing changes in gene expression. Our data also support the potential of previously described severity markers.

overall_design: We use a rat model of SCI, Tamoxifen was administred intraperitoneal 30 min after injury. Four groups were organized, 1) Non-injured without TMX (Sham/TMX-), 2) Non-injured with TMX (Sham/TMX+), 3) Injured without TMX (SCI/TMX-), and 4) Injured with TMX (SCI/TMX+). Trancriptome analysis was performed using the Clariom S Assays Array.

first: Eibar

last: Cabrera-Aldana

first: Rafael

last: Velázquez-Cruz

first: Luis

last: Tovar-Y-Romo

first: Rosalba

last: Sevilla-Montoya

first: Angelina

last: Martínez-Cruz

first: Claudia

last: Martinez-Cordero

first: Margarita

last: Valdes-Flores

first: Monica

last: Santamaria-Olmedo

first: Alberto

last: Hidalgo-Bravo

first: Gabriel

last: Guízar-Sahagún


title: Transcriptomic profiling of peripheral blood cells in HPV-associated carcinoma patients receiving combined valproic acid and avelumab

city: Edmonton

first: Najmeh

last: Bozorgmehr

state: Alberta

address: 11361 87th Ave NW, 7020L Katz Group Centre

department: Dentistry

country: Canada

institute: University of Alberta

summary: We recruited 39 samples of metastatic HPV-associated carcinoma patients before and after immunotherapy (Combined Valproic acid + Avelumab). Based on the best overall response by iRECIST criteria, we stratified patients into Responders (iCCR, iCPR, iSD) and Non-responders (Clinically progressive, iCPD, iUPD). We analyzed the transcript differential expression in two groups (Rs vs. NRs) before (Baseline) and after therapy (EP) to understand the differences between the two groups in each time point and in time points (C1, C2, EP) compared to C0 for each group to check the changes related to therapy.

overall_design: A total 39 samples of isolated Peripheral Blood Mononuclear Cells (PBMCs) from HPV-associated carcinoma patients, including Baseline (Before initiation of treatment), Cycle1 (Valproic acid), Cycle2 (Valproic acid + Avelumab), Cycle6/7 (Valproic acid + Avelumab, End of treatment) were analyzed for differential transcript expression.

first: Shokrollah

last: Elahi

first: John

last: Walker

first: Siavash

last: Mashhouri

first: Hussain

last: Syed


title: Intact mitochondrial function in the setting of telomere-induced senescence

city: Pittsburgh

first: Jonathan

middle: K.

last: Alder

state: PA

address: 3459 Fifth Ave, NW 628

department: Medicine

institute: University of Pittsburgh

summary: We chacterized the transcriptional changes that occur following induction of telomere dysfunction by deletion of Terf2. We analyzed mouse embryonic fibroblasts and primary liver cells following the same genetic intervention (deletion of Terf2).

overall_design: 3 biologic replicates of control MEFs and Terf2-deleted MEFs seven days after deletion of Terf2. 4 biologic replicates of control and Terf2-deleted livers, six weeks after deletion of Terf2.


title: DNA methylation patterns in CD4+ T cells separate psoriasis patients from healthy controls, and skin psoriasis from psoriatic arthritis I

first: Christian

last: Hedrich

department: Department of Women's & Children's Health

overall_design: Genome wide DNA methylation were analyzed in CD4+T cells from patients with Psoriatic Arthritis (PsA), psoriasis and Healthy Control (HC)

first: Valentina

last: Natoli

first: Amandine

last: Charras

first: Sigrun

last: Hofmann

first: Sarah

last: Northey

first: Susanne

last: Russ

first: Felix

last: Schulze

first: Liza

last: McCann

last: Abraham


title: Transcriptomic profile of wheat seed development under progressive drought conditions

city: Yamaguchi

first: Ryosuke

last: Mega

address: 1677-1, Yoshida

institute: Yamaguchi University

summary: To investigate how progressive drought stress affected gene expression during seed development

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TaPYLox and the Null segregant

first: June-Sik

last: Kim

first: Yasuko

last: Watanabe


title: Nanostring gene expresson-based, antibody activation of bone marrow derived macrophages (BMDM)

city: Indianapolis

first: Xavier

last: Taylor

state: Indiana

address: 307 E Merrill St

institute: Eli Lilly and Company

summary: We study immune responses induced by amyloid targeting antibodies and CAA-mediated microhemorrhages using histology and gene expression analyses in AD mouse models and primary culture settings. We cultured and plated primary bone marrow-derived macrophages in wells coated with high Fc receptor activating antibody IgG2a or isotype control antibody harboring the LALAPG mutation, ablating Fc-FcR mediated effector functions

overall_design: To compare the transcriptional profiles for BMDM activated by Fc receptor signaling, isotype control antibody or non-treated.

first: X

first: I

last: Clark


title: Lysine methylation of EHMT1/GLP as a molecular switch to reprogram transcription networks in prostate cancer [RNA-seq UNC0642]

city: Boston

first: Changmeng

last: Cai

state: MA

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

summary: Our studies provide novel molecular insights into the activity and function of EHMT1 during PCa progression and suggest a novel therapeutic strategy to treat CRPC with EHMT1 inhibitors.

overall_design: LNCaP-tet-EHMT1 cells were treated with/out 0.5ug/mL docxycycline and 2uM UNC0642 for two days. LNCaP cells were treated with siNTC, SiEHMT2 at 20nM for two days. All RNA-seq samples contain replications.

first: Anna

last: Besschetnova

first: Wanting

last: Han

first: Mingyu

last: Liu

first: Dong


title: shRNA-mediated knockdown of Clock and Bmal1 genes in a T-cell acute lymphoblastic leukemia (T-ALL) cell line

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary: Here, we report that the disruption of circadian clock obtained through shRNA-mediated knockdown of Clock and Bmal1 genes negatively impacted the in vitro growth of a T-cell acute lymphoblastic leukemia (T-ALL) cell line. We performed gene expression profiling analysis of RPMI-8402 cell line upon knock-down of the circadian genes Clock and Bmal1. We found that circadian clock directly infuences the expression of genes, such as IL20RB, involved in JAK/STAT signaling, making the T-ALL cells more responsive to Interleukin 20 (IL20).

overall_design: A total of six samples were analyzed with three different conditions i.e. shBmal1, shClock and control. Experimental replicates were performed.

first: Gianluigi

last: Mazzoccoli

first: Vincenzo

last: Giambra


title: Directed Evolution of an Adenine Base Editor with Increased Activity and Context Compatibility [RNA-seq data]

city: CHICAGO

first: Yuan

last: Wu

state: Illinois

address: 929 E 57th St, GCIS E535

department: Chemistry

institute: University of Chicago

summary: It is known that current the-art-of-the-state TadA8 and TadA8e which evolved from E. coli TadA. They inherited the 'YA' context from tRNA deaminase. We started with wildtype E. coli TadA and designed an evolution campaign to force TadA variants to deaminate “GA” with fast kinetics. Three rounds of de novo directed evolution followed by DNA shuffling led to TadA8r, a TadA variant of superior “RA” deamination activity. TadA8r acts on a broadened editing window when fused to Streptococcus pyogenes Cas9 (SpCas9) and delivers robust editing at PAM distal positions. While highly active at on-target sites, ABE8r shows off-target DNA and RNA editing much lower than ABE8e. The off-target effects of ABE8r can be further mitigated by introducing a V106W substitution23, a R153 deletion22, or by mRNA delivery. Lastly, we demonstrate ABE8r-mediated correction of G1961E in ABCA4, the most prevalent mutation driving Stargardt disease (STGD1), in a “GA” context. ABE8r, with its superior activity and broadened context compatibility, complements and expands the current ABE family.

overall_design: Twenty HEK293T samples were collected for high-throughput sequencing. Each treatment included two replicates. Targeted gene editing in mammalian cell were quantified by Miseq.

first: Yulan

last: Xiao

first: Weixin

last: Tang


title: SAP30 promotes breast cancer progression and metastasis by gene activation (ChIP-Seq)

city: Dallas

first: Lei

last: Bao

state: TX

address: 5323 Harry Hines Blvd, NB6.126

department: Pathology

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SAP30 recuits MLL1 to induce H3K4 trimethylation, increase chromatin accessobility and enhances Pol II binding on angiogenesis and migration genes to activate their expression, leading to breast cancer progression and metastasis

overall_design: Parental and SAP30 KO MDA-MB-231 cells were subjected to ChIP-seq, and occupancies on subsets of genes were compared.

first: Weibo

last: Luo


title: SAP30 promotes breast cancer progression and metastasis by gene activation

overall_design: Refer to individual Series


title: High-throughput mRNA sequencing and microRNA sequencing analysis of human nasopharyngeal carcinoma cell line (6-10B) transfected with EBV-encoded microRNA BART2-5p mimics

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

country: China

institute: Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using  mRNA and microRNA sequencing analysis to evaluate the effects of EBV-encoded microRNA BART2-5p mimics on the mRNA and microRNA profiles of human nasopharyngeal carcinoma cell line 6-10B.
Methods: 6-10B cells were transfected with either EBV microRNA BART2-5p mimics or negative control (NC) mimics for 48 hours. Cellular RNA was then sequenced at the mRNA and microRNA levels using illumina high-throughput sequencing service (Oebiotech, Shanghai, China). Data were extracted and normalized according to the manufacturer's standard protocol.
Results: Log-fold changes of up- or down-regulated mRNAs and microRNAs between the control and experiment group were selected with a significance threshold of p<0.05.
Conclusions: Our study describes the mRNA and microRNA alterations induced by EBV-miRNA-BART2-5p in 6-10B cells

overall_design: 6-10B cells were transfected with BART2-5p mimics or negative control (NC) mimics for 48 hours. Cellular RNA was then sequenced at the mRNA and microRNA levels to show the gene expression profile and microRNA profile changes induced by BART2-5p transfection.

first: Yangge


title: Genetic Variants of Phospholipase C-γ2 Confer Altered Microglial Phenotypes and Differential Risk for Alzheimer’s Disease [NanoString]

first: Andy

last: Tsai

summary: Differential expression analysis in Plcg2 variants AD mouse models identified genes and pathways.

overall_design: To investigate the role of PLCG2 variants, Nanostring nCounter Gial Profiling and Neuropathology panels were employed to analyze cortical RNA of 7.5-month-old mice

first: Chuanpeng

last: Dong

first: Peter

last: Lin

first: Adrian

middle: L

last: Oblak

first: Gonzalo

last: Viana Di Prisco

first: Nian

last: Wang

first: Nicole

last: Hajicek

first: Adam

last: Carr

first: Emma

last: Lendy

first: Oliver

last: Hahn

first: Micaiah

last: Atkins

first: Aulden

last: Foltz

first: Jheel

last: Patel

first: Guixiang

last: Xu

first: Miguel

last: Moutinho

first: John

last: Sondek

first: Qisheng

last: Zhang

first: Andrew

last: Mesecar

first: Yunlong

first: Brady

last: Atwood

first: Tony

last: Wyss-Coray

first: Kwangsik

last: Nho

first: Stephanie

last: Bissel

first: Bruce

last: Lamb

first: Gary

last: Landreth


title: Effect of SAP30 in breast cancer progression and metastasis (RNA-Seq)

first: Lei

last: Bao

summary:
To investigate the cooperative function of SAP30/SIN3A(SIN3B)/MLL1 complex in breast cancer progression and metastasis, we established SAP30-KO, SIN3A+SIN3B-DKO and MLL1-KO MDA-MB-231 cells by CRISPR-Cas9.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the parental cells as well as each KO cell line. Two biological repeats were applied for each cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for parental MDA-MB-231 cells and its KO derivatives (SAP30-KO, SIN3A+SIN3B-DKO, MLL1-KO).

first: Weibo

last: Luo


title: Single-cell sequencing reveals the optimal time window and mechanism of anti-inflammatory treatment in spinal cord injury

city: Yiwu

first: jingjia

last: ye

state: zhejiang

address: chouzhoubeilu 1575

institute: zhejiang university

summary: Though the occurrence of neuroinflammation after spinal cord injury (SCI) is essential for antigen clearance and tissue repair, excessive inflammation results in cell death and axon dieback. The effect of anti-inflammatory medicine utilized in clinical treatment remains debatable owing to the inappropriate therapeutic schedule that does not align with the biological process of immune reaction. A better understanding of the immunity process is critical to promote effective anti-inflammatory therapeutics. However, cellular heterogeneity, which results in complex cellular functions, is a major challenge. In this study, we performed single-cell RNA sequencing by profiling the tissue proximity to the injury site at different time points after SCI. Depending on the analysis of single-cell data and histochemistry observation, we proposed an appropriate time window for anti-inflammatory medicine treatment. We also verified the mechanism of typical anti-inflammatory medicine MPSS, which was found attributable to the activation inhibition of cells with pro-inflammatory phenotype through the down-regulation of pathways such as TNF, IL2, and MIF. These pathways could also be provided as targets for anti-inflammatory treatment. Collectively, we provide a therapeutic schedule of 1–3 dpi (days post-injury) to argue against classical early pulse therapy and provide some pathways for target therapy in the future.

overall_design: Spinal cord tissue at 1,3,7 days post-injury and intact tissue was used in single-cell sequency for analysis of immunity reaction through SCI. MPSS and PBS treated spinal cord was used for the analysis of medicine mechanism.

first: Jingjia

last: Ye

first: Wei

last: Wei


title: SAP30 promotes breast cancer progression and metastasis by gene activation (ATAC-Seq)

overall_design: Parental and SAP30 KO MDA-MB-231 cells were subjected to ATAC-seq, and chromatin accessobility on subsets of genes were compared.


title: A Cellular Atlas of the Down Syndrome Brain Identifies Accelerated Oligodendrocyte Precursor Cell Senescence

first: Brian

last: Kalish

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

summary: We performed single nucleus RNA-seq and single nucleus ATAC-seq on the cortex of Ts65Dn mouse model of Down Syndrome and euploid controls (wild types).

overall_design: Single nucleus RNA-seq and ATAC seq from 6 month old mouse cortex under two conditions: 1)Control (wild type), 2)Ts65Dn mouse model for Down Syndrome.


title: Spatial transcriptomics on human dorsal root ganglion (DRG)

city: Chicago

first: Rachel

last: Miller

address: 1735 W Harrison St

institute: Rush University Medical Center

summary: Visium Spatial Gene Expression by the 10X genomics protocol was performed on 2 sections of human DRG tissue to elucidate the spatial transcriptomic organization.

overall_design: 2 Sequential 16µm thick sections of a human female (female; age 96; BMI 22.5) DRG donor were mounted on a slide and then spatially molecularly profiled through the Visium Spatial Gene Expression platform by 10X Genomics.

first: Matthew

last: Wood

first: Anne-Marie

last: Malfait


title: Differential transcriptomic expression of an imprved astaxanthin production

city: Brisbane

first: Carlos

middle: Horacio

last: Luna Flores

state: QLD

address: 2 george st, brisbane city

country: Australia

institute: Queensland University of Technology

summary: The differential expression of the high-yield astaxanthin Phaffia rhodozyma BPAX-A1 with the wild-type Phaffia rhodozyma CBS6938 was obtained and analysed to understand metabolic changes leading to an improved astaxanthin production.

overall_design: We performed fermentations in instrumented fermenters with wild-type and mutant strains (three biological replicates with each strain) and samples were obtained at the late exponential growth phase for RNA-seq analysis- this phase presented the highest astaxanthin production rate suggesting to be the most informative to explain metabolic changes leading to an improved astaxanthin production in the mutant strain.

middle: H

last: Luna-Flores

first: Alexander

last: Wang

first: Juhani

last: von Hellens

first: Robert

last: Speight


title: Transcriptome profile of hepatocellular carcinoma from non-alcoholic fatty liver.

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Non-alcoholic fatty liver disease (NAFLD) is a major global health problem with its high prevalence and risk of developing lethal complications, progressive liver fibrosis and hepatocellular carcinoma (HCC), the only rising cancer mortality in the U.S. Ever after curative surgical resection, HCC can recur at extremely high rate (70% within 5 years); therefore, prediction of recurrent HCC is expected to guide decision of neo/adjuvant therapies currently under active development. Herein, we derived an HCC-transcriptome-based signature to predict disseminative recurrence, which originates from disseminated HCC cells from surgically resected initial tumor, and validated it in an independent cohort.

overall_design: HCC tumor tissues were obtained from 45 patients who underwent surgically curative resection and used for RNA isolation and genome-wide transcriptome profiling by RNA-Seq.

first: Naoto

last: Fujiwara

first: Shijia

last: Zhu


title: Epigenetic regulation of T cell lineages in skin and blood following hematopoietic stem cell transplantation

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary: RNA seq and ATAC seq data of pooled T cells isolated from skin and blood at multiple time points before and after hematopoietic stem cell transplantation

overall_design: Examination of 1 cell type at 4 time points before and after treatment

first: R

last: Pandey

first: J

last: Strobl

first: G


title: Genome-wide coherence between enhancer states and 3D chromosome conformation in mouse T cell differentiation

city: London

first: Ya

last: Guo

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

summary: Complex genomes are intricately organised in 3D nuclear space, yet the extent to which genome form and function are interconnected remains subject to intense debate. To elucidate this relationship, we generated developmental stage-specific maps of enhancer state, gene expression, and chromosome conformation during CD4 T cell differentiation. While progression from the DP to the CD4 SP stage of thymocyte differentiation was accompanied by activation and repression of hundreds of genes and enhancers, Hi-C maps of DP and CD4 SP were visually highly similar, and discrete Hi-C measures such as TADs, contact domains, loops, or compartments failed to unambiguously link genome organisation to gene regulatory activity. At face value, these findings appear to support proposals of a disjoint between genome form and function. By contrast, Twins, a deep learning approach trained to distinguish technical from biological variation in Hi-C data, revealed compelling coherence between gene regulatory changes and genome organisation. Analysis of local Hi-C contacts demonstrated that the strength of Hi-C contacts quantitatively reflected developmental stage-specific enhancer states. These findings demonstrate correspondence between genome form and function in mouse T cell differentiation, and suggest a rationale for the control of gene expression by distal regulatory elements.

overall_design: Chromatin contact profiles in wild type or CTCF/Rad21 double knockout cells were generated by in situ Hi-C. Chromatin contact profiles in control or enhancer insertion cells were generated by capture Hi-C. Examination of enrichment of total H3 and H3K27ac in primary cells by ChIP-seq.

first: Matthias

last: Merkenschlager


title: Resolving fate bifurcation of photoreceptor precursor in human retinal organoid by single-cell transcriptomics

city: Guangzhou

first: xiao

last: yuhua

state: Guangdong

address: No. 7 Jinsui Road

institute: sun yat-sen university

summary: Cone and rod photoreceptors in human enable daytime color and nighttime dark vision respectively and abnormality in photoreceptor  development results in blindness. However, when and how the two photoreceptors are fate-determined during development is largely unknown. Herein, we established a cell atlas for human photoreceptor development, based on single-cell transcriptomic profiling of engineered human retinal organoids engineered to trace the photoreceptor lineages during developmentto monitor the photoreceptor lineages during development. For the first time, we demonstrated the subtypes of photoreceptor precursors based on unsupervised clustering of single-cell transcriptomesbifurcation of cell fate in the photoreceptor precursors, withwith the conespecific expression of molecular marker gene PDE6H ands for cone precursor and rod marker gene NR2E3 differentially expressed among others precursor. Further dissection of transcriptional segregation of the two precursors uncovered PHLDA1 as an intrinsic regulator intrinsic regulator in the fate bifurcation of of the rod-related gene networksphotoreceptor subtypes. Photoreceptor precursors with decreased PHLDA1 yield more cones while reduced the number of rods. The PHLDA1-mediated modification of cell fate can be directed downstream of IGF1 signaling, and exhibited an inhibitory effect on AKT phosphorylation which was associated with cone differentiation.,  which directed the downstream effects of IGF1 to promote the rod differentiation. Collectively, our data identified PHLDA1 as a novel regulator of fate determination of photoreceptors at the precursor stage, andour study shed lights on the cellular and molecular mechanisms of human photoreceptor precursor specification, and provided a framework to study mechanisms of cell fate determination of human retinal cells.

overall_design: scRNA-seq profiles of retinal organoid from D45, D80, and D120.

first: Xiying

last: Mao

first: Yuhua

last: Xiao


title: Gene expression data from differentiating 3T3-L1 cells

city: New York

first: Keiichi

last: Ito

address: 1230 York Avenue

institute: The Rockefeller University

summary: The MED1 subunit has been shown to mediate ligand-dependent binding of the Mediator coactivator complex to multiple nuclear receptors, including the adipogenic PPARγ, and to play an essential role in ectopic PPARγ-induced adipogenesis of mouse embryonic fibroblasts. However, the precise roles of MED1, and its various domains, at various stages of adipogenesis and in adipose tissue have been unclear. Here, after establishing requirements for MED1, including specific domains, for differentiation of 3T3L1 cells and both primary white and brown preadipocytes, we used multiple genetic approaches to assess requirements for MED1 in adipocyte formation and function in mice. We show that MED1 is indeed essential for the differentiation and/or function of both brown and white adipocytes, as its absence in these cells leads to, respectively, defective brown fat function and lipodystrophy. This work establishes MED1 as an essential transcriptional coactivator that ensures the formation and homeostatic functions of adipocytes.

overall_design: MED1-KO 3T3-L1 clones were generated using CRISPR/Cas9, and differentiated along with their parental WT 3T3-L1 cells. Pools of RNA fro individual KO clones at Day0 and Day2 of differentiation were subjected to microarray analysis together with the WT 3T3-L1 cells to identify MED1-dependent transcriptional events during early phase of adipogenesis in culture. The role of MED1 in brown adipose tissue formation and function was also examined using microarray in Myf5-Cre as well as AdipoqCre- based Med1 conditional knockout models.

middle: G

last: Roeder


title: Lysine methylation of EHMT1/GLP as a molecular switch to reprogram transcription networks in prostate cancer [ChIP-seq]

first: Changmeng

last: Cai

overall_design: V5 (EHMT1) ChIP-Seq were performed in LNCaP cells with/out treatment of 0.5ug/mL doxycycline for two days. H3K9me2 ChIP-Seq were performed in LNCaP cells with/out treatment of 0.5ug/mL doxycycline for two days. EHMT1 ChiP-Seq was performed in LNCaP cells without treatment. All ChIP-seq samples contain replications.

first: Anna

last: Besschetnova

first: Wanting

last: Han

first: Mingyu

last: Liu

first: Cai

last: Changmeng


title: Bifidobacterium infantis intracellular 2-oxogluturate concentration is inversely related to nitrogen accessibility

first: Shuqi

last: Li

address: 60 Fenwood Rd.

department: Neurology

institute: Harvard Medical School and Brigham and Women's Hospital

summary: Bifidobacterium longum subsp. infantis (B. infantis) resides in the human infant gut and helps with the utilization of human milk-derived nutrient components. While its utilization of various carbohydrate sources has been studied extensively, mechanisms behind utilization of nitrogen components from human milk remain largely unknown. In this study, we present B. infantis growth profiles on the N-containing human milk oligosaccharides (HMO) as nitrogen sources, namely, lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT). Dietary 2-Oxoglutarate (2-OG) in known in mice model for its protective effects against intestinal inflammation and colitis development. In this study, we have shown that B. infantis had increased 2-OG concentration when utilizes LNT or LNnT as a primary nitrogen source. As LNT and LNnT are the isomers of HMO core structures, N-acetyl glucosamine (NAG), the N-containing monosaccharide, was regarded as the nitrogen provider of the HMO core structures. Differentially expressed gene patterns in B. infantis were analyzed under the less efficient nitrogen conditions (HMOs and NAG) relative to the complex nitrogen controls. Proteomics analysis of B. infantis using 15N-labeled NAG revealed that NAG nitrogen was incorporated into B. infantis metabolism. Transcriptomics results of B. infantis in LNT, LNnT and NAG nitrogen were consistent with the proteomics results. This further indicated that B. infantis metabolism was affected by NAG nitrogen in nitrogen assimilation, HMO catabolism, NAD cofactor biosynthesis and regeneration, and peptidoglycan biosynthesis pathways. In summary, B. infantis can use NAG-containing HMO as a nitrogen source and incorporate NAG nitrogen into metabolism pathways.

overall_design: Gene expression of B. infantis ATCC 15697 while growing on NAG, LNT, LNnT, pooled HMO, and complex nitrogen. Gene expression of B. infantis JCM 1260, B. infantis JCM 7009 while growing on NAG as a nitrogen source.

first: Xiaomeng

last: You

first: Asha

last: Rani

first: Ezgi

last: Ozcan

first: David

middle: A

last: Sela


title: RNF8 ubiquitylation of XRN2 facilitates R-loop resolution and restrains genomic instability in BRCA1 mutant cells

city: Toronto

first: Razq

last: Hakem

state: Ontario

address: TMDT, 101 College Street. Rm13-310

department: Princess Margaret Cancer Centre

institute: University Health Network

summary: Breast cancer linked with BRCA1/2 mutations commonly recur and resist current therapies, including PARP inhibitors. Given the lack of effective targeted therapies for BRCA1-mutant cancers, we sought to identify novel targets to selectively kill these cancers. Here, we report that loss of RNF8 significantly protects Brca1-mutant mice against mammary tumorigenesis. RNF8 deficiency in human BRCA1-mutant breast cancer cells was found to promote R-loop accumulation and replication fork instability, leading to increased DNA damage, senescence, and synthetic lethality. Mechanistically, RNF8 interacts with XRN2, which is crucial for transcription termination and R-loop resolution. We report that RNF8 ubiquitylates XRN2 to facilitate its recruitment to R-loop-prone genomic loci and that RNF8 deficiency in BRCA1-mutant breast cancer cells decreases XRN2 occupancy at R-loop-prone sites, thereby promoting R-loop accumulation, transcription-replication collisions, excessive genomic instability, and cancer cell death. Collectively, our work identifies a synthetic lethal interaction between RNF8 and BRCA1, which is mediated by a pathological accumulation of R-loops.

overall_design:
DRIP-seq and RNA-seq in WT (shScr) and RNF8-depleted (shRNF8) MDA MB 436 cells.
Please note that *.mean.bw was generated from all replicates and is linked to the corresponding *rep1 sample records.

first: Rehna

last: Krishnan

first: Anne

first: Kevin

last: Nixon


title: Trunk neural crest gene MOXD1 affects embryonic development

status: Public on Sep 13 2023

city: Lund

first: Stina

last: Andersson

address: Sölvegatan 19

country: Sweden

institute: Lund University

summary: Ectoderm-derived neural crest is a transient structure arising during early embryogenesis in vertebrates. Neural crest consists of four derivatives based on their anterior- to posterior location along the body axis; cranial, vagal, trunk and sacral, respectively. We recently showed that trunk neural crest-specific gene MOXD1 functions as a tumor suppressor in trunk neural crest-derived childhood cancer form neuroblastoma and is essential for proper development of healthy adrenal glands. However, the role of MOXD1 during early embryogenesis is not known. Here, we conditionally knocked out MOXD1 in trunk neural crest cells before they become lineage-committed, using a CRISPR/Cas9 approach in chick embryos. Assessment of embryo growth showed that knockout of MOXD1 delayed development with knockout embryos being smaller. RNA sequencing of trunk-derived neural crest cells from control and knockout embryos showed enrichment of genes connected to gland development, copper ion metabolism and neuroblastoma progression. In conclusion, MOXD1 is important during early and prolonged embryonic development with effects on gland formation, possibly mediated via its role in copper metabolism.

overall_design: We conditionally knocked out MOXD1 in trunk neural crest cells before they become lineage-committed, using a CRISPR/Cas9 approach in chick embryos. We included nice control embryos and twelve MOXD1 knock-out embryos.

first: Elina

last: Fredlund

first: Manon

last: Ferreira

first: Sofie

last: Mohlin


title: Lysine methylation of EHMT1/GLP as a molecular switch to reprogram transcription networks in prostate cancer

first: Changmeng

last: Cai

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

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

overall_design: Refer to individual Series


title: Lysine methylation of EHMT1/GLP as a molecular switch to reprogram transcription networks in prostate cancer [RNA-seq]

summary: Our studies provide novel molecular insights into the activity and function of EHMT1 during PCa progression and suggest a novel therapeutic strategy to treat CRPC with EHMT1 inhibitors.

overall_design: LNCaP-tet-EHMT1 cells were treated with/out 0.25ug/mL doxycycline for two days. LNCaP cells were treated with siNTC, siEHMT1 at 20nM for two days. All RNA-seq samples contain replications.

first: Anna

last: Besschetnova

first: Wanting

first: Dong


title: RNA sequencing of RAW264.7 with or without Sal-B and LPS addition

city: Shanghai

first: Sun

middle: Jia

last: Ming

address: No. 639, Zhi Zao Ju Road,

department: Department of Plastic & Reconstructive Surgery

institute: Shanghai Ninth People’s Hospital

summary: Autologous fat grafting (AFG), although an appealing approach to repair soft tissue defects, has various complications. Excessive inflammation at the transplant site is one of the main reasons for the poor effect of fat transplantation and occurrence of complications. Our previous study proved that Salvia miltiorrhiza can enhance fat graft survival. Salvianolic acid B (Sal-B) is the most abundant and bioactive water-soluble compound in Salvia miltiorrhiza and has anti-inflammatory effects on other diseases. Therefore, we hypothesized that salvianolic acid B could improve the effect of fat grafts by inhibiting inflammation.

overall_design: Examination of R264.7 RNA sequencing comparing the LPS(10ng/ml)+Sal-B addition(50μmol/L) group[LPS+50], LPS(10ng/ml) group[LPS+0] and control group[NC]

first: Jiaming

last: Sun

first: Li

last: Yu


title: Effects of Neolamarckia cadamba essential Oil on microbial transcription

city: guangzhou

first: Wu

last: Shuo

address: wushan

institute: South China Agricultural University

summary: In order to explore the bacteriostatic mechanism of Neolamarckia cadamba essential oil, the effect of Neolamarckia cadamba essential oil on microbial transcription in logarithmic growth phase was determined.

sample_organism:
Niallia circulans
Aspergillus flavus
Nakaseomyces glabratus

overall_design: The transcriptional group of three kinds of microorganisms(Bacillus circulans,Candida glabrata,Aspergillus flavus) treated with Neolamarckia cadamba essential oil for four hours was determined, and the control group was set up.

first: Shuo

last: Wu

first: Qing

last: Zhang


title: Molecular characterization of the sea urchin larva photosensory system: Insights into the evolution of a Go-Opsin positive neuronal population

city: Napoli

first: Maria Ina

last: Arnone

address: Villa Comunale 1

department: Biology and Evolution of Marine Organisms

institute: Stazione Zoologica Anton Dohrn

summary: Sea urchin larvae possess a group of photoreceptor cells (PRCs) deploying a Go-Opsin (Opsin3.2). In this study, we investigate investigate the molecular signature of the Sp-Opsin3.2 cells using single cell transcriptomics.

overall_design: Generation, analysis and integration of single cell RNA-seq data of 5 dpf Strongylocentrotus purpuratus larva.

first: Cocurullo

last: Maria

first: Paganos

last: Periklis

first: Annunziata

last: Rossella

first: Voronov

last: Danila

first: Arnone

last: Maria Ina


title: Effects and mechanism of Neolamarckia cadamba essential oil on the aerobic stability of whole-plant corn silage

summary: The purpose of this study was to explore the mechanism of aerobic decay of whole-plant corn silage and the effect of Neolamarckia cadamba essential oil on aerobic stability of whole-plant corn silage. Firstly, the dynamic changes of temperature, microbial community and metabolite content after aerobic exposure of whole-plant corn silage were determined, and the main microbial species and mechanism leading to aerobic spoilage of whole-plant corn silage were analyzed. The N. cadamba essential oil was extracted from fresh N. cadamba leaves by steam distillation, and the minimal inhibitory concentration, antibacterial stability and bacteriostatic mechanism of N. cadamba essential oil against undesirable microorganisms in whole-plant corn silage were determined. According to the minimum inhibitory concentration of N. cadamba essential oil on undesirable microorganisms in silage, N. cadamba essential oil was added to whole-plant corn silage to explore the effect of N. cadamba essential oil on the aerobic stability of whole-plant corn silage.

overall_design: According to the minimum inhibitory concentration of Neolamarckia cadamba essential oil, the effect of Neolamarckia cadamba essential oil on the aerobic stability of whole corn silage was studied by adding Neolamarckia cadamba essential oil, inoculating Aspergillus flavus spores, adding Neolamarckia cadamba essential oil and inoculating Aspergillus flavus spores, and blank control.


title: Ets1 and IL17RA cooperate to regulate autoimmune responses as well as skin immunity to Staphylococcus aureus

city: Buffalo

first: Michael

last: Battaglia

address: 955 Main St

department: Microbiology and Immunology

institute: SUNY at Buffalo

summary: Autoimmune diseases display many changes to the immune environment. The lineage-specific transcription factor Ets1 has been associated with autoimmune diseases including SLE. Ets1KO mice develop significant autoimmune disease with an expansion of IL-17 expressing lymphocytes. To ascertain the role of IL-17 in the phenotype of Ets1KO mice, mice lacking both Ets1 and IL17Ra were generated. These double-knockout mice (DKO) were found to develop significant autoimmune disease characterized by development of spontaneous skin lesions. To ascertain the potential causative factors contributing to the lesional skin development, RNA sequencing was conducted on ventral neck skin bulk RNA samples harvested from wild-type, Ets1KO, IL17RaKO, and DKO animals. We report here that Ets1 and IL17Ra deletion results in significant gene expression changes. Among the changes in gene expression reported here is significantly elevated expression of proinflammatory cytokines commonly part of the normal skin immune response to wounding and/or infection. Together these data suggest that Ets1 and Il17Ra signaling interact resulting in significantly altered immune related gene expression in the skin of DKO mice.

overall_design: Ventral neck skin harvested from DKO, single-kncout controls, and wild type mice. Extracted RNA was subjected to bulk RNA sequencing to ascertain differentially expressed genes as a result of Ets1 and/or IL17Ra deletion in comparison to WT skin.

first: Lee

last: Garrett-Sinha


title: Role of cGAS-STING pathway in aging and sexual dimorphism in diabetic kindey disease

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

summary: We investigated the cGAS-STING inflammatory pathway differential activity among both sexes in T2DN rats and its impact on the temporal progression of the diabetic kidney disease. Here we used both male and female old and young T2DN rats. The cGAS-STING pathway presented distinct protein expression profiles between male and female T2DN rats, which significantly intensify with aging. In male T2DN rats, pro-inflammatory genes are particularly heightened in comparison to female rats of similar age, and such levels are further exacerbated with age. Interestingly, a comprehensive RNA-Seq analysis conducted in the kidney cortex of both sexes of T2DN rats, in younger and older ages, disclosed several central molecules, with crucial genes identified within the cGAS-STING pathway. Our study showed the intricate sexual differences in the development and progression of DKD and proposed the fundamental role of cGAS-STING pathway in disease development.

overall_design: Animals used for the current study were young and old male and female. The animals were euthanized by opening thoracic cavity under deep anesthesia (2% (vol/vol) isoflurane), and both kidneys were collected. One kidney was stored in Formalin for histological analyses, and the other was snap-frozen for molecular analyses. Transcriptomics was done using kidney cortex from each time point for both sexes old and young groups.

last: Staruchenko

first: Sherif

last: Khedr

first: Mellowes

last: Center


title: Single cell analysis of PVNS synovium from human

city: beijing

first: fei

last: wu

address: 49 North Garden Rd

institute: Peking university 3rd hospital

summary:
Pseudotime analysis, cytotrace, velocity was used to determine the source of subpopulation. To compare the difference between PVNS and steady state synovium, we conduct collaborated analysis containing both PVNS and OA synovium. Qusage analysis reveal the difference of the subsets between them.
We for the first time using single cell analysis delineating PVNS cell atlas and have deepen understanding toward PVNS Presumed function and source of certain subpopulation might be the future target that worth trying. We also locate major subpopulation that is responsible for its unremitting inflammation, angiogenesis and invasiveness.

overall_design: Single cell analysis to uncover mechanism of PVNS synovium, with osteoarthritis synovium as control.

first: Yingfang

last: Ao

first: Xin

first: Fei


title: A High-Phosphorus Diet Moderately Alters the Lipidome and Transcriptome in the Skeletal Muscle of Adult Mice

city: Giessen

first: Sarah

middle: Maria

last: Grundmann

state: Hesse

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: Justus Liebig University Giessen

summary: A high phosphorus intake has been associated with various metabolic disorders, including chronic kidney disease, cardiovascular disease, and osteoporosis. Recent studies have demonstrated the effects of dietary phosphorus on lipid and glucose metabolism. This study investigated the impact of a high-phosphorus diet on mouse skeletal muscle lipid composition and gene transcription. Adult male mice (n = 12/group) received either a diet with an adequate (0.3%) or a high (1.2%) phosphorus concentration for 6 weeks. The lipidome analysis showed that among the 17 analyzed lipid classes, the concentrations of three classes were reduced in the high phosphorus group compared to the adequate phosphorus group. These classes were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and lysophosphatidylcholine (LPC) (p < 0.05). Out of the three hundred and twenty-three individual lipid species analyzed, forty-nine showed reduced concentrations, while three showed increased concentrations in the high phosphorus group compared to the adequate phosphorus group. The muscle transcriptome analysis identified 142 up- and 222 down-regulated transcripts in the high phosphorus group compared to the adequate phosphorus group. Gene set enrichment analysis identified that genes that were up-regulated in the high phosphorus group were linked to the gene ontology terms “mitochondria” and “Notch signaling pathway”, whereas genes that were down-regulated were linked to the “PI3K-AKT pathway”. Overall, the effects of the high-phosphorus diet on the muscle lipidome and transcriptome were relatively modest, but consistently indicated an impact on lipid metabolism.

overall_design: For microarray analysis, n = 6 RNA samples each of the adequate phosphorus group (P0.3) and high phosphorus group (P1.2) were used for hybridization to the Affymetrix GeneChip Clariom S mouse array.

first: Robert

last: Ringseis

first: Klaus

last: Eder


title: Amino acid availability is a crucial factor for survivability of cancer cells

city: Hannover

first: Laura

last: Hinze

state: Niedersachsen

address: Carl-Neuberg-Straße 1

institute: Hannover Medical School

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Identifying early, intermediate, and late responses to GSK3a inhibition in Jurkat T-ALL cells in the presence or absence of an asparagine depletion

summary: Amino acid availability is a crucial factor for survivability of cancer cells. Leukemia cells have been shown to resist asparagine depletion by utilizing GSK3-dependent proteasomal degradation, termed Wnt-dependent stabilization of proteins (Wnt/STOP), to replenish their amino acid pool. Inhibition of GSK3a halts the sourcing of amino acids, which subsequently leads to cancer cell vulnerability towards asparaginase therapy. Leveraging RNA sequencing we show that GSK3a inhibition leads to temporally dynamic downregulation of distinct ribosomal proteins upon amino acid starvation.

overall_design:
To investigate the early, intermediate, and late responses to GSK3a inhibition in Jurkat T-ALL cells in the presence or absence of an asparagine depletion, a robust GSK3a knockdown was induced in Jurkat T-ALL cells using shRNA.
Subsequently the cells were treated with vehicle or asparaginase, and harvested at 8, 16, 32, and 56 hours of treatment.
Comparative gene expression analysis was performed compairing: timepoints, genotypes and treatment conditions.

first: Lorent

last: Loxha

first: Nurul

last: Ibrahim

first: Anna

middle: S

last: Stasche

first: Büsra

last: Cinar

first: Julia

last: Niessen

first: Sabine

last: Schreek

first: Beate

last: Fehlhaber

last: Forster

first: Martin

last: Stanulla


title: Helicase-like transcription factor (HLTF)-deleted CDX/TME model of colorectal cancer increased transcription of oxidative phosphorylation genes and diverted glycolysis to boost S-glutathionylation in intravascular metastatic niches

city: Lubbock

first: Beverly

last: Chilton

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC


title: GSDMD knockout alleviates hyperoxia-induced hippocampal brain injury in neonatal mice

city: Miami

first: Augusto

middle: F

last: Schmidt

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

summary: Exposure to neonatal hyperoxia is associated with brain injury and poor neurodevelopmental outcomes in preterm infants. Our goal was to determine the pathogenic role of GDMD in hiipocampal in injury in newborn mice

overall_design: Newborn GSDMD knockout mice and their wildtype littermates were randomized within 24 hours of birth to room air or hyperoxia (85%) from postnatal day 1 to 14. Samples were collected on P15.

first: Naga

middle: V

last: Divya Challa

first: Shaoyi

last: Chen

first: Huijin

last: Yun

first: Matthew

last: Duncan

first: William

middle: J

last: Moreno

first: Helen

last: Bramlett

first: W

last: Dietrich

first: Merline

last: Benny

first: Shu

last: Wu


title: Stereotypic persistent B cell receptor clonotypes in Alzheimer’s Disease

city: Seoul

first: Namphil

last: Kim

address: Gwanak-ro 1

department: Electrical and Computer Engineering

country: South Korea

institute: Seoul National University

summary: The growing evidence suggest that the effect of Alzheimer’s Disease (AD) is not solely restricted to the brain. Numerous groups investigated the relation between the central nervous system and peripheral system, whereupon the peripheral system is closely involved in accordance with the progression of disease and systemic immunity. In our previous report, we identified shared B cell receptor (BCR) sequences among 10 AD patients which showed similar class-switching orientation, identical isotypes and high somatic hypermutation rate. For further investigation, we recruited 44 patients with AD at baseline and 37 patients for second follow-up to identify the shared BCR sequences among patients and persistent BCR within an individual patient. We were able to annotate 3983 unique AD specific BCR clonotypes and one of the clonotype showed binding affinity against human Aβ42 peptide. Our finding can provide evidence of common BCRs in AD patients exposed to antigenic stimulus which are related to AD pathogenesis.

overall_design: For a period of 75 weeks, peripheral blood (PB) samples were collected from 44 Alzheimer patients with a median age of 75 years (standard deviation; 7.04) and sex ratio of 34% and 66% (male vs female). Except for seven patients (Patient ID 3, 5, 8, 19, 28, 30, and 37), PB samples were collected twice with interval between 14 and 53 weeks. The duration for the first and second PB sampling was 61 and 34 weeks, respectively. From these 81 PB samples, cDNA was prepared and subjected to the amplification of a gene fragment encoding variable domain (VH) and N-terminal part of constant domain 1 (CH1) of B cell receptor (BCR) heavy chain using a specific primer set (Extended Table 2), which were analyzed in next generation sequencing with a median read of 245,033 (standard deviation of 184,462, Extended Table 3). For the analysis of BCR repertoire, we first removed naïve BCR sequences, which we define as those with IgM or ID isotype containing less than 1 somatic hypermutation (SHM). Then we  grouped the remaining sequences into clonotypes, which was defined as a collection of sequences sharing the same CDR3 sequence at the amino acid level as well as encoded by identical IGHV and IGHJ genes15. Among these BCR clonotypes, AD patient-specific clonotypes were selected by excluding clonotypes found in a control group (CG) established in our prior studies, which was constituted with 55 vaccinees (285 PB samples obtained chronologically) injected three times with COVID-19 vaccine14.Control group specific non-naïve BCR clonotypes were also obtained following the same procedures. Before further analysis, we tried to remove any possibility of aerosol molecular contamination during NGS library preparation and index switching during sequencing15. For this, we excluded all the stereotypic clonotypes in which each patient or control did not show unique BCR sequences at the nucleotide level. After all these selection processes we could select 3,983 and 83,821 BCR clonotypes specific to AD patient group or control group, respectively


title: Helicase-like transcription factor (HLTF)-deleted CDX/TME model of colorectal cancer increased transcription of oxidative phosphorylation genes and diverted glycolysis to boost S-glutathionylation in intravascular metastatic niches [RNA-Seq]

summary: The tumor suppressor, helicase-like transcription factor (HLTF), is expressed in tumor cells but not in the tumor microenvironment (TME) in early stage colorectal cancer (CRC). With disease progression, epigenetic silencing of HLTF in primary CRC tumors coincides with negligible HLTF expression in the TME. Cell line-derived xenograft (CDX) models were developed to test the hypothesis that HLTF-deletion in cancer cells with resultant metabolic reprogramming—a hallmark of metastasis—is a prototypical example of cancer cells modifying their metabolic requirements in response to HLTF-deletion in the TME. The two metabolic pathways that derive energy from glucose—glycolysis and oxidative phosphorylation (OXPHOS)—are variously utilized by cancer cells depending upon the TME. HIF-1α, a master regulator of glycolysis, was eliminated from a role in reprogramming metabolism to satisfy CDX energetic requirements by RNAseq and spatial transcriptomics. Variability in the gut microbiome, with a putative role in altered metabolism, was also eliminated. In contrast, HLTF-deleted cancer cells recovered from DNA damage at a transcriptomic level induction of DNA repair and OXPHOS genes linked to an amoeboid-associated phenotype at the tumor border (confocal microscopy).  HLTF-deleted cancer and endothelial cells of the intravascular niche in the TME share a site-specific protein S-glutathionylation signature (2D DIGE, MALDI-TOF/TOF mass spectrometry) for three glycolytic enzymes (PGK1 Cys379/380, PGAM1 Cys55, ENOA1 Cys119) that diverted glycolysis in support of continued glutathione biosynthesis. The collective absence of HLTF/Hltf from tumor and TME maintained redox homeostasis throughout the CDX and promoted metastasis.

overall_design:
HLTF-/-CDX tumors (1 per ID Hltf KO mouse x 3 biological replicates) were flash frozen and sent to Genewiz, the next generation sequencing (NGS) division of Azenta Life Sciences (South Plainfield, NJ) RNA-sequencing. Briefly, total RNA was isolated, and evaluated for its integrity and purity with an Agilent Bioanalyzer. RNA was polyA selected prior to library preparation followed by Illumina HiSeq, 2x150 configuration, single index per lane with 350 million raw paired-end (PE) reads per lane, i.e. 40-60 million PE reads per sample (>80% of bases >Q30).
Re-analysed Samples PRJNA680156:
GSM4928827 Index5OtC3511+cells-mice SAMN16870870 SRX9552230
GSM4928828 Index6OtC3512+cells-mice SAMN16870869 SRX9552231
GSM4928829 Index7OtC3513+cells-mice SAMN16870868  SRX9552232

first: Dalia

last: Martinez-Marin

first: Rebecca

last: Helmer

first: Gurvinder

last: Kaur

first: Rachel

last: Washburn

first: Raul

last: Martinez-Zaguilan

first: Souad

last: Sennone

first: Jannette

last: Dufour


title: Global transcriptome analysis of colonic tissue during Clostridioides difficile infection

city: Blacksburg

first: Raquel

last: Hontecillas

address: 1800 Kraft dr suite 100

institute: NIMML

summary: Clostridioides difficile can cause severe infections in the gastrointestinal tract and affects almost half a million people in the U.S every year. Upon establishment of infection, a strong immune response is induced. We sought to investigate the dynamics of the mucosal host response during C. difficile infection.

overall_design: C57BL/6 WT mice were pretreated with a cocktail of antibiotics and then were infected with C. difficile VPI 10463 in brucella broth through orogastric gavage. Uninfected mice were administered brucella broth without the inoculum. Colonic tissue samples were collected at day post infection 0, 3, 4, 5, 8 and 10 to investigate the whole transcriptome differential gene expression during infection during the acute and recovery phases.


title: Transcriptomic profiling of differentially expressed mRNA, lncRNA and circRNA in lean and obese individuals

city: Changzhou

first: Shuai

last: Chen

state: Jiangsu

address: 68 Gehu Rd, Wujin District

institute: The Affiliated Changzhou NO.2 People’s Hospital of Nanjing Medical University

summary: Fat accumulation is the main manifestation of obesity. Obesity forms the largest fat pool because white adipocytes primarily store energy, whereas larger adipocytes may encounter hypoxia and mechanical stress and have higher levels of inflammatory cytokines and lipolysis release. In this study, we performed high-throughput sequencing to analyze the differentially expressed circRNAs in visceral adipose tissue between lean and obese individuals, and searched for the important mechanisms involved in the regulation of adipogenesis

overall_design: Visceral adipose tissue from four lean individuals and four obese individuals was sequenced to search for differentially expressed RNA.

first: S

first: P

last: Song

first: L

last: Tang


title: Effect of asparagine depletion on Rspo3 fusion positive colorectal cancer cell organoid transcriptomes

first: Laura

last: Hinze

summary: Amino acid availability is a crucial factor for survivability of cancer cells. Colorectal cancer cells have been shown to resist asparagine depletion by utilizing GSK3-dependent proteasomal degradation, termed Wnt-dependent stabilization of proteins (Wnt/STOP), to replenish their amino acid pool. Inhibition of GSK3a halts the sourcing of amino acids, which subsequently leads to cancer cell vulnerability towards asparaginase therapy. Leveraging RNA sequencing we show that GSK3a inhibition leads to a significant enrichment of ribosomal transcripts amongst transcripts that are differentially downregulated in asparaginase treated Rspo3 fusion positive colorectal cancer cell organoids.

overall_design:
The effect of asparagine depletion on gene expression in Rspo3 fusion positive colorectal cancer cell organoids was investigated.
Transcriptomes of vehicle and asparaginase treated organoids were sequenced and gene expression levels compaired.

first: Lorent

last: Loxha

first: Nurul

middle: K

last: Ibrahim

first: Anna

last: Stasche

first: Büsra

last: Cinar

first: Julia

last: Niessen

first: Sabine

last: Schreek

first: Beate

last: Fehlhaber

first: Michael

last: Forster

first: Martin

last: Stanulla


title: Brain cell-specific origin of circulating microRNA biomarkers in experimental temporal lobe epilepsy

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

summary: The diagnosis of epilepsy is complex and challenging and would benefit from the availability of molecular biomarkers, ideally measurable in a biofluid such as blood. Experimental and human epilepsy are associated with altered brain and blood levels of various microRNAs (miRNAs). Evidence is lacking, however, as to whether any of the circulating pool of miRNAs originates from the brain. To explore the link between circulating miRNAs and the pathophysiology of epilepsy, we first sequenced Ago2-bound miRNAs in plasma samples collected from mice subject to status epilepticus (SE) induced by intraamygdala microinjection of kainic acid. This identified time-dependent changes in plasma levels of miRNAs with known neuronal and microglial-cell origins. To explore whether the circulating miRNAs had originated from the brain, we generated mice expressing FLAG-Ago2 in neurons or microglia using tamoxifen-inducible Thy1 or Cx3cr1 promoters, respectively. FLAG immunoprecipitates from the plasma of these mice after seizures contained miRNAs, including let-7i-5p and miR-19b-3p. Taken together, these studies confirm that a portion of the circulating pool of miRNAs in experimental epilepsy originates from the brain, increasing support for miRNAs as mechanistic biomarkers of epilepsy.

overall_design: 8 groups: c57 mice were subjected to status epilepticus using intra-amygdala injection of kainic acid. Plasma was collected from 10 mice and pooled in equal proportions for an n of 1 for each of 4 timepoints four, eight, twenty-four hours and 2 weeks. Small RNA sequencing using the Illumina HiSeq was performed on microRNAs bound to eluted Ago2 from plasma samples. Control mice were injected with PBS in the same manner.

first: Elizabeth

last: Brindley

first: Mona

last: Heiland

first: Catherine

last: Mooney

first: Mairead

last: Diviney

first: Omar

last: Mamad

first: Thomas

last: Hill

first: Yan

last: Yan

last: Venø

first: Cristina

last: Reschke

first: Aasia

last: Batool

first: Elena

last: Langa

first: Amaya

last: Rodriguez

first: Janosch

middle: P

last: Heller

first: Gareth

last: Morris

first: Karen

last: Conboy

first: Jørgen

last: Kjems

first: Gary

last: Brennan

first: David

last: Henshall


title: Spaceflight-induced gene expression profiles in the mouse brain are attenuated by treatment with the antioxidant BuOE

city: Loma Linda

first: Isaac

middle: Jacob

last: Kremsky

state: CA

address: 11175 Campus St., Chan Shun Pavilion, Room A1022

department: Basic Sciences

institute: Loma Linda University

summary: The demands of deep-space pose a health risk to the central nervous system that has long been a concern when sending humans to space. While little is known about how spaceflight affects transcription spatially in the brain, understanding this has the potential to aid strategies that mitigate the effects of spaceflight on the brain. Therefore, we performed GeoMx Digital Spatial Profiling of mouse brains subjected to either space flight, or grounded controls. Four brain regions were selected: Cortex, Frontal Cortex, Corunu Ammonis I, and Dentate Gyrus. Antioxidants have emerged as a potential means of attenuating the effects of spaceflight, so we treated a subset of the mice with a superoxide dismutase mimic, MnTnBuOE-2-PyP 5+ (BuOE). Our analysis revealed hundreds of differentially expressed genes due to spaceflight in each of the four brain regions. Both common and region-specific transcriptomic responses were observed. Pathways sensitive to oxidative stress, and metabolic pathways, were enriched in the four brain regions due to spaceflight. These findings enhance our understanding of brain regional variation in susceptibility to spaceflight conditions. BuOE reduced the transcriptomic effects of spaceflight at a large number of genes, suggesting that this compound may attenuate oxidative stress-induced brain damage by the spaceflight environment.

overall_design: Ten-week-old C57BL/6 male mice were launched at the Kennedy Space Center (KSC) and spent 35 days aboard the international space station (ISS). All mice were maintained at an ambient temperature of 26–28 °C with a 12-hour light/dark cycle during the flight. All mice were provided NASA Nutrient-upgraded Rodent Food Bar (NuRFB) and autoclaved deionized water ad libitum. MnTnBuOE-2-PyP5+ (BuOE) at 1 mg/kg (0.2 mL) was administrated subcutaneously 7 days prior to the flight launch and weekly aboard the ISS. All mice were subdivided into saline or BuOE treated groups. Upon return to the Earth, spaceflight mice were transported to the research laboratory at Roskamp Institute, Sarasota, Florida within 20 hours of splashdown. Mice were exsanguinated by closed-cardiac blood collection under deep Ketamine/Xylazine (150/45 mg/kg) anesthesia, followed by cervical dislocation as a secondary euthanasia method to ensure death. Ground control mice were maintained on Earth for 35 days in flight hardware cages under similar environmental conditions as the flight groups, including the same food, light/dark, temperature, treatment (SAL or BuOE), and euthanasia regimens. The protocol for GC mice commenced three days subsequent to the commencement of the protocol for spaceflight mice.

first: Samir

last: Ali

first: Seta

last: Stanbouly

first: Jacob

last: Holley

first: Stephen

last: Justinen

first: Michael

last: Pecaut

first: James

last: Crapo

first: XiaoWen

last: Mao


title: Helicase-like transcription factor (HLTF)-deleted CDX/TME model of colorectal cancer increased transcription of oxidative phosphorylation genes and diverted glycolysis to boost S-glutathionylation in intravascular metastatic niches [Spatial]

first: Beverly

last: Chilton

overall_design: HLTF-/-CDX tumors (1 per ID Hltf KO mouse x 3 biological replicates) were flash frozen and sent to Genewiz, the next generation sequencing (NGS) division of Azenta Life Sciences (South Plainfield, NJ) RNA-sequencing. Briefly, total RNA was isolated, and evaluated for its integrity and purity with an Agilent Bioanalyzer. RNA was polyA selected prior to library preparation followed by Illumina HiSeq, 2x150 configuration, single index per lane with 350 million raw paired-end (PE) reads per lane, i.e. 40-60 million PE reads per sample (>80% of bases >Q30).

first: Dalia

last: Martinez-Marin

first: Rebecca

last: Helmer

first: Gurvinder

last: Kaur

first: Rachel

last: Washburn

first: Raul

last: Martinez-Zaguilan

first: Souad

middle: R

last: Sennone

first: Jannette

middle: M

last: Dufour


title: Effects of AEBP1 knockdown on gene expression profiles in cancer-associated fibroblasts

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

summary: We identified adipocyte enhancer binding protein 1 (AEBP1) as a novel cancer-associated fibroblast (CAF) marker in oral squamous cell carcinoma (OSCC). To study the function of AEBP1 in CAFs, we knocked down AEBP1 in CAFs isolated from surgically resected primary OSCCs. We found that genes associated with cell cycle were significantly affected by AEBP1 knockdown in CAFs.

overall_design: CAFs (1^10E6 cells) were transfected with 100 pmol Silencer Select Pre-designed siRNA (AEBP1 siRNA1, s1145; AEBP1 siRNA2, s1146; Thermo Fisher Scientific) or a Silencer Select Negative Control No. 1 siRNA (Thermo Fisher Scientific) using a TransIT-X2 Dynamic Delivery System (Mirus Bio) and were incubated for 72h.

first: Shohei

last: Sekiguchi


title: Effect of overexpression of FNDC5 on gene expression upon hypoxia 24 h of  bone marrow-mesenchymal stem cells (BMSCs).

city: Guangzhou

first: Huan

last: Wei

address: Zhongshan Road 58

institute: The First Affiliated Hospital of SUMS

summary: To investigate the function of FNDC5 in the regulation of autophagy, we established BMSCs-OE-FNDC5 in which the target gene FNDC5 has been overexpressed by lentivirus transfection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMSCs-OE-FNDC5 and BMSCs-OE-NC.

first: Shuaiye

last: Liu

first: Tingting

last: Wang


title: Knockdown of PGC-1α suppresses dysplastic oral keratinocyte cells proliferation through reprogramming energy metabolism

city: chengdu

first: Liu

last: Yunkun

address: Sichuan

institute: sichuan university

summary: To investigate the effects of knockdown PGC1α on human dysplastic oral keratinocyte (DOK) cell proliferation, cell cycle, apoptosis, xenograft tumor, mitochondrial DNA (mtDNA), mitochondrial electron transport chain complexes (ECT), ROS, oxygen consumption rate (OCR), extracellular acidification rate (ECAR), and glucose uptake

overall_design: Compared gene expression profiling analysis of RNA-seq data for DOK cells after being infected with PGC1α knockdown or control lentivirus.

first: Yunkun

first: Nengwen

last: Huang

first: Xianghe

last: Qiao

first: Zhiyu

last: Gu

first: Jinjin

last: Li

first: Chengzhou

last: Wu

first: Bo

first: Longjiang


title: Zebrafish functional xenograft vasculature platform identifies PF-502 as a durable vasculature normalization drug

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Tumor vasculature are structurally chaotic and functionally inefficient. Restoring aberrant tumor blood vessels, or “normalize” the tumor vasculature can alleviate hypoxia and enhance intra-tumoral drug delivery. However, identifying tumor vascular normalizing drugs are currently hampered by an absence of efficient screening platform. We aimed to develop a robust method to visualize, digitalize and evaluate the structural and functional changes of tumor vasculature in batch: zebrafish functional xenograft vasculature platform (zFXVP). As proof of principle, we applied zFXVP to a small compound library which has been implicated in affecting the morphology of tumor vasculature. zFXVP identified PF-502 as a durable tumor vascular normalization agent. Further molecular analysis using RNA-Seq, pharmaceutical inhibition and gene knockout indicate PF-502 can induce endothelial cell cycle arrest and simplify redundant tumor vasculature by blocking PI3K/mTOR signaling and stabilize the vessel lumen and stimulate the blood function by activating Notch1 signaling with mediating S3 cleavage. Last, in mouse tumor xenograft model, PF-502 reproduced a potent vascular normalizing effect at a sub MTD (maximum tolerated dose) and showed its ability to improve intra-tumoral drug delivery and synergize chemotherapy, which confirms the reliability of zFXVP and implicates the potential application of PF-502 in clinical practice as an adjuvant vascular normalization drug.

overall_design: RNA-seq was performed in HUVEC cells treated the following day with either vehicle(DMSO) or PF-502(0.15μM) for 12hrs

first: Xiangyu

first: Jian

last: Zhong

first: Chaoxin

last: Xiao

first: Chengjian

last: Zhao


title: Exploration of the activation process of Group 2 innate lymphoid cell (ILC2) isolated from mouse fat tissues to produce type 2 cytokine [mouse]

city: Bunkyo-ku

first: Yoshitaka

last: Shirasaki

state: Tokyo

address: Hongo 7-3-1

department: Graduate School of Pharmaceutical Science

institute: The University of Tokyo

summary:
To investigate the gene expression underlying the activation process of ILC2, we performed time-series measurements of type 2 cytokine secretion activity (IL-5 or IL-13) of ILC2 from mouse fat tissues after IL-2/IL-33 stimulation .
Single cells were collected separately before stimulation (Pre-stimulation), just after exhibiting type 2 cytokine secretion (Transition state), and secretion-positive (Activated state) or secretion-negative (Silent state) after sufficient time from stimulation, and performed RNA-seq on each cell for gene expression profiling analysis.

overall_design: Comparative gene expression profiling analysis of single-cell RNA-seq data of mouse ILC2.

first: Mai

last: Yamagishi

first: Yumiko

last: Tanaka

first: Kaede

last: Miyata

first: Sotaro

last: Uemura

first: Takashi

last: Kamatani

first: Kazuyo

last: Moro


title: Exploration of specific gene expression behind the intercellular heterogeneity of type 2 cytokine secretion activity of Group 2 innate lymphoid cell (ILC2) isolated from human peripheral blood

summary:
To investigate the gene expression underlying the intercellular diversity in type 2 cytokine secretion activity of ILC2, we performed time-series measurements of type 2 cytokine secretion activity  of ILC2 from human peripheral blood after IL-2/IL-33/TSLP stimulation .
Single cells were collected separately before stimulation, in transition state or activated cells after stimulation, and performed RNA-seq on each cell for gene expression profiling analysis.

overall_design: Comparative gene expression profiling analysis of single-cell RNA-seq data of human peripheral blood ILC2.

first: Hiroki

last: Kabata

first: Rie

last: Baba

first: Satomi

last: Irie

first: Koichi

last: Fukunaga


title: Exosomal circEZH2_005, an intestinal injury biomarker, alleviates intestinal ischemia/reperfusion injury by mediating hnRNPA1/Gprc5a signaling

first: Wen-Juan

last: Zhang

address: Guangzhou, 1838 Guangzhou Avenue North, Guangzhou 510515, China

institute: Nanfang Hospital, Southern Medical University

summary: Although plasma exosomal circular RNAs (circRNAs) are valuable biomarkers and therapeutic targets for various diseases, their role in intestinal I/R injury remains unknown. This study screens the expression profile of circRNAs in intestinal tissue exosomes collected from intestinal I/R mice.

overall_design: We performed high-throughput sequencing of circRNA to characterize differential expression profiles of circRNA in intestinal tissue exosomes after I/R injury from four mice with intestinal I/R (1 h of ischemia and 2 h of reperfusion) and sham.

first: Wenjuan

first: Bowei

last: Zhou

first: Xiao

last: Yang

first: Cai

last: Li

first: Kexuan

last: Liu


title: Lem2 is essential for cardiac development by maintaining nuclear integrity

city: London

first: Matthew

last: Stroud

address: James Black Centre

institute: King's College London

summary: Importantly, mutations in nuclear envelope-encoding genes are the second-highest cause of familial dilated cardiomyopathy. One such nuclear envelope protein that causes cardiomyopathy in humans and affects mouse heart development is Lem2. However, its role in mechanically active tissue such as heart remains poorly understood.

overall_design: RNA-Seq on XMLC2V-Cre Lem2 cKO and littermate control whole ventricle at embryonic day 14.5 (E14.5)


title: Differential midgut transcriptomics comparing nutritional status reveals a crucial role for V-ATPase subunit a and Niemann-pick 1b protein in the digestive physiology of the desert locust.

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

summary: The main objective of this study was to analyze the general midgut transcript profile of Schiustocerca gregaria as well as changes in midgut gene expression during different stages of feeding. We compared three different time points of the digestive process: no active digestion (24 h after feeding), the initial stages of feeding (10 min after feeding) and active digestion in the midgut (2 h after feeding).

overall_design: Samples are RNA extracts of the desert locust midgut. We compared 3 timepoints. Each timepoint consists of 6 biological replicates.

first: Joachim

last: Van Lommel

first: Michiel

last: Holtof

first: Dorien

last: Cools

first: Seppe

last: Vansteenkiste

first: Daria

last: Polgun

first: Fillip

last: Van Nieuwerburgh

first: Jozef

last: Vanden Broeck


title: Exosomal circEZH2_005, an intestinal injury biomarker, alleviates intestinal  ischemia/reperfusion injury by mediating hnRNPA1/Gprc5a signaling

summary: To investigate the critical role of circEZH2_005 in regulating mRNA synthesis, stability, and translation, we evaluated intestinal crypt cells overexpressing circEZH2_005 by  transcriptome sequencing.

overall_design: We then performed gene expression profiling analysis using data obtained from ranscriptome sequencing of vector and  circEZH2_005 overexpressed cells at three times.