title: Braf-mutant Schwann cells divert to a repair phenotype to induce congenital demyelinating neuropathy [ScN]

city: Marseille

first: Heather

middle: C

last: Etchevers

address: 27 boulevard Jean Moulin

department: INSERM U1251

country: France

institute: INSERM/Aix-Marseille Univ

summary: RASopathies are a diverse group of developmental disorders associated with germline or somatic mutations in genes of the Mitogen Activated Protein Kinase (MAPK) signaling pathway. We characterized in this dataset a mosaic mouse model, in which a constitutively active form of the MAPK effector Braf (V600E) is expressed in the embryonic progenitors of myelin-forming Schwann cells of peripheral nerves under the control of the MpZ(P0)-Cre recombinase. These mice develop an early, fully penetrant degenerative peripheral neuropathy. The RNAseq experiment compares total RNA extracted from whole sciatic nerves between spinal cord and knee between mutant and control pairs of littermates from six distinct outbred litters at postnatal day 21.

overall_design: We performed RNA-seq to compare four mutant whole sciatic nerves to four control littermate sciatic nerves at two different postnatal stages. After aligning sequences to the mouse genome, we undertook differential gene expression analysis.

first: Elise

last: Maréchal

first: Valérie

last: Delague


title: CircRNA Expression Profiling of the Rat Thalamus In Temporomandibular Joint Chronic Inflammatory Pain

status: Public on Dec 31 2024

city: Chongqing

first: Haixia

last: Deng

state: Chongqing

address: No. 426, Songshi North Road, Yubei District, Chongqing, China

department: Department of Anesthesiology

country: China

institute: Stomatological Hospital of Chongqing Medical University, Chongqing, China.

type: Expression profiling by high throughput sequencing

summary: Differential expression of circular RNAs (DEcircRNAs) in the thalamus, a relay station of the orofacial pain transmission pathway, may play an important role in inflammation and inflammatory pain progression in TMJOA and serve as a potential marker for its targeting. In this study, we obtained the expression profile of circRNAs from the thalamus of the rat TMJOA model by high-throughput sequencing to explore the potential role of circRNA in TMJOA inflammation and chronic inflammatory pain progression and their potential as new targeted molecular markers. Additionally, providing new clues to unravel the molecular mechanisms of chronic orofacial pain, providing insights into the potential roles of circRNAs in pain modulation, and paving the way for future research in this area.

overall_design: To explore the mechanisms of chronic orofacial pain, we established a 14-day TMJOA chronic inflammatory pain model in rats and tested their orofacial mechanical pain thresholds. Six rats were randomly divided into CFA and CON groups and injected bilaterally into the temporomandibular joints with 50uL CFA and saline (n=3),Injections twice a week to maintain chronic inflammatory pain states. Thalamus was obtained for circRNA high-throughput sequencing to obtain expression profiles after 14 days, and KEGG and GO analyses of DEcircRNAs were performed, and miRanda software was used to predict the binding sites of the sheared circRNAs. miRNA binding sites were predicted by miRanda software, and it was determined that thalamic DEcircRNAs broadly regulate TMJOA inflammation and chronic inflammatory pain through several potential mechanisms.

first: Jing

last: Wang

first: Jie

last: Zeng

first: Cong

last: Yu


title: Microenvironmental acidification by pneumococcal sugar consumption fosters barrier disruption and immune suppression in the human alveolus

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: Streptococcus pneumoniae (S.p.) is the most common causative agent of community-acquired pneumonia worldwide. A key pathogenic mechanism that exacerbates severity of disease is the disruption of the alveolar-capillary barrier. However, the specific virulence mechanisms responsible for this in the human lung are not yet fully understood. In this study, we infected living human lung tissue with S.p. and observed a significant degradation of the central junctional proteins occludin and VE-cadherin, indicating barrier disruption. Surprisingly, neither pneumolysin, bacterial hydrogen peroxide nor pro-inflammatory activation were sufficient to cause this junctional degradation. Instead, pneumococcal infection led to a significant decrease of pH (approximately 6), resulting in acidification of the alveolar microenvironment, which was linked to junctional degradation. Stabilizing the pH at physiological levels during infection reversed this effect, even in a therapeutic-like approach. Further analysis of bacterial metabolites and RNA sequencing revealed sugar consumption and subsequent lactate production were the major factors contributing to bacterially induced alveolar acidification, which also hindered the release of critical immune factors. Our findings highlight bacterial metabolite-induced acidification as an independent virulence mechanism for barrier disruption and inflammatory dysregulation in pneumonia. Thus, our data suggest that strictly monitoring and buffering alveolar pH during infections caused by fermentative bacteria could serve as an adjunctive therapeutic strategy for sustaining barrier integrity and immune response.

overall_design:
Lung tissue explants were obtained from 7 patients primarily diagnosed with bronchial carcinoma, who had undergone lung resection at local thoracic surgery centres. The study was approved by the ethic committee at the Charité clinic (protocol number EA2/079/13) and the written informed consent was obtained from all patients. Tumour-free peripheral lung tissue was dissected into small pieces by scalpel (5 x 5 x 5 mm, 80 - 200 mg) and incubated overnight in RPMI 1640 medium (PAN-Biotech) at 37°C with 5 % CO2 to wash off clinically applied antibiotics as described. The following infection experiments were carried out in RPMI 1640 medium supplemented (volume-controlled) with 10 % fetal calf serum at 37°C with 5 % CO2. For infection, tumour-free normal lung tissue was inoculated with culture medium as control (mock infection) or 106 CFU/mL S.p. D39 wt in the presence and absence of 25 mmol/L HEPES (volume-controlled) or exposed to pH 6 titrated with HCl for 24 h .

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Diana

last: Fatykhova

first: Stefan

last: Hippenstiel

first: Andreas

last: Hocke


title: A randomized double-blind Phase IIb trial to evaluate the efficacy of ChAd63-KH for the treatment of post kala-azar dermal leishmaniasis

city: Siena

first: Maria

last: Novedrati

address: Viale Bracci, 16

country: Italy

institute: University of Siena

summary: Purpose: The goals of this study were to identify molecular patterns activated by the vaccine and potential predictors of clinical success.

overall_design: Methods: Whole blood samples (2.5 ml) were collected into PAXGene tubes immediately prior to vaccination and at 0 and 1 days post vaccination from 102 patients with persistent PKDL

first: Santoro

last: Francesco

first: Novedrati

last: Maria

first: Sonnati

last: Chiara


title: Braf-mutant Schwann cells divert to a repair phenotype to induce congenital demyelinating neuropathy [SCP]

summary: RASopathies are a diverse group of developmental disorders associated with germline or somatic mutations in genes of the Mitogen Activated Protein Kinase (MAPK) signaling pathway. We characterized in this dataset a model of Schwann cell differentiation in vitro (Hörner et al. 2021, PMID: 34943800), in which a constitutively active form of the MAPK effector BRAF (Q257R) is endogenously expressed in two patient-derived human induced pluripotent stem cell lines from distinct individuals RMK0056C and RMK0138C, patients with cardio-facio-cutaneous syndrome (OMIM #115150) as previously described (Yeh E, et al. 2018, PMID: 29158583). Two additional healthy donor hiPSC cell lines derived locally from commercially available fibroblasts, AG08H and hFF15, were also used as controls. The RNAseq experiment compares total RNA extracted from the four cell lines of cultures on day 18 (uncommitted Schwann cell precursor[SCP]-like phenotype) and day 31 (engaged SCP-like phenotype) of culture to find differentially expressed genes in the presence of continuous activation of MAPK signaling during early development and differentiation.

overall_design: We performed RNA-seq analysis to compare the Schwann cell maturation potential derived from wild-type human induced pluripotent stem cells (HFF15 and AG08H lines) and two mutant lines carrying the Q257R mutation associated with cardio-facio-cutaneous syndrome. The analysis was conducted at two different stages of the differentiation protocol: J18 (precursor Schwann cells) and J31 (immature Schwann cells). After aligning the sequences to the human genome, we conducted a differential gene expression analysis.

first: Lauren

last: Weiss


title: Mechanomemory of pulmonary fibroblasts demonstrates reversibility of transcriptomics and contraction phenotypes

city: Dearborn

first: Caymen

last: Novak

state: MI

address: HPEC 1296, 4901 Evergreen Rd

department: Mechanical Engineering

country: USA

institute: University of Michigan Dearborn

summary: Fibroblasts are cells responsible for producing extracellular matrix (ECM) components, which provides physical support for organs. Although these mesenchymal cells are responsive to mechanical cues in their environment, the permanence of these mechano-phenotypes is not well defined. We investigated the mechano-memory of lung fibroblasts and determined how switching culture conditions modulate cell responses and function. Primary murine lung fibroblasts were isolated and cultured on 2D tissue culture plates or within 3D collagen hydrogels and were then passaged within the same or opposite culture condition to assess changes in gene expression, protein production, fibroblast subpopulation, contractile behavior, and traction forces. Compared to fibroblasts isolated on 2D tissue culture plates, fibroblasts within 3D hydrogels exhibited a decreased activation phenotype including reduced contraction profiles, diminished cell traction forces and decreased αSMA gene expression. Cells initially isolated via 2D culture and then cultured in 3D hydrogels exhibited a reversal in activation phenotype as measured by gene expression and contraction profiles. Bulk RNAseq identified groups of genes that exhibit reversible and non-reversable expression patterns. Overall, these findings indicate that lung fibroblasts have a mechanical memory that is altered by culture condition and can be reversible through precondition of cells within a softer 3D microenvironment.

overall_design: To investigate the impact of culture dimension on primary murine fibroblast profiles we isolated primary murine fibroblasts from lung tissue using collagenase digestion. These cells were then separated into the following conditions: 1) sorted for fibroblast populations using Paramagnetic particles to eliminate CD45+, EpCam+, and CD31+ cells. The flow through was then collected for RNAseq and labeled with Sort_Fib 1-4.  2) collagenase digests were placed onto 2D tissue culture plates for 4 days, and 3) collagenase digests were encapsulated into 3D collagen hydrogels for 4 days. After 4 days of culture, the cells were then passaged into the same or alternative culture conditions for 2 days prior to collection for RNAseq, giving rise to the following 4 sample conditions: 1) 2D-2D, 2) 2D-3D, 3) 3D-2D, and 4) 3D-3D.

first: Jana

last: Wheat

first: Samir

last: Ghadiali

first: Megan

last: Balliner


title: Study on the Molecular Mechanism of Endometrial Fibrosis Mediated by Oxidative Stress Injury in Breast Cancer

city: Guangzhou

first: HUI

last: CHEN

state: Guangdong

address: Guangzhou Huangpu Road

department: medicine

institute: Jinan University School of Medicine

summary: we used the MDA-MB-231 breast cancer cell line to construct a breast tumor xenograft mouse model, and compared the volume and weight of the uterus of mice in the normal group with those of mice in the tumor group, and found that the uterine body of the tumor group became thinner and narrower, suggesting that the uterine tissue of the tumor group was subjected to certain pathological damage changes. By transcriptome sequencing analysis, it was found that the differential genes focused on fibrosis-related pathways, oxidative stress function, oxidative phosphorylation (OXPHOS), mitochondrial ATP synthesis and so on. By means of immunohistochemical staining of uterine tissues and various molecular experiments to detect the degree of fibrosis in the endometrium, it was found that the endometrium of mice in the tumor group produced fibrotic deposition and the thickness of the endometrium became thinner compared with that of mice in the normal group. Meanwhile, SOD, GSH and MDA tests revealed that antioxidant enzymes were reduced, oxidation products were increased, ROS aggregation occurred and oxidative stress was generated in the tumor group mice. Excessive ROS caused changes in the microenvironment, activated the TGFβ-p38MAPK pathway, and led to phosphorylation of p38 protein, which triggered the Epithelial-Mesenchymal Transition (EMT) reaction in the endometrium, resulting in endometrial fibrosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for endometrium of normal mice and breast cancer tumor mice.

first: Ping

last: Li

first: Hui

last: Chen


title: Gene expression data from human adipose derived stem cell (hASC) treated with 20 uM oleocanthal

city: Tsukuba

first: Rui

last: Wang

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

summary:
Gene expression profiling reveals oleocanthal functionality on adipocyte.
We investigated the effects of oleocanthal on human adipose-derived stem cells. We conducted an untargeted whole-genome transcriptome study to investigate the functioning of oleocanthal on adipocytes.

overall_design: According to the manufacturer's guide, the RNA was extracted using Isogen kit (Nip-pon Gene Co. Ltd., Japan). Then, RNA quantity and quality were determined using the NanoDrop 2000 spectrophotometer (ThermoScientific, USA). DNA microarray analysis was conducted on control and CA-treated hAESC samples using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer's instructions. In brief, complementary DNA (cDNA) was synthesized from 100 ng of RNA solutions. cRNA was synthesized from in vitro transcription of cDNA and then purified and reverse transcribed. Finally, single-stranded cDNA (ss-cDNA) was synthesized, purified, fragmented, and labeled following the manufacturer's instructions. Cartridge Array Hybridization was performed using the Clariom S array (Human; ThermoFisher Scientific) on the GeneChip™ Fluidics Station (ThermoFisher Scientific). Scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data obtained after scanning were analyzed using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific). The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value < 0.05 (one-way between-subjects ANOVA) and fold change > 2 (in linear space) were considered as differentially expressed genes (DEGs). The GeneChip Scanner (Thermo Fisher Scientific) was used for scanning. The raw image data collected after scanning were processed using the Transcriptome Analysis Console (TAC) software (ThermoFisher Scientific, version 4.0.2). The raw data was normalized using the signal space transformation robust multi-chip analysis (SST-RMA) technique. The Limma Bioconductor tool was then used to undertake gene-level analysis. For differential expression analysis, a one-way ANOVA was used, followed by an empirical Bayes correction. The detected above background (DABG) limit was set at 0.05. The positive and negative area under the curve (AUC) values were set to be larger than or equal to 0.7. Genes with a p value < 0.05 (one-way between-subjects ANOVA) and a fold change > 2 (in linear space) were identified as differentially expressed (DEG).

first: Wang

last: Rui


title: Transcriptional response to latrunculin B treatment in WT and sid2 mutants

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: To investigate the role of salicylic acid biosynthesis in transcriptional response to cytoskeleton disruption, we treated WT and sid2 plants (mutant deficient in ICS1) by latrunculin B for 24 h. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 biological replicates.

overall_design: Fully expanded mature rosette leaves (three  per plant) of Col-0 or sid2, were treated by infiltration of 1 µM of latrunculin B (Sigma) or 0.01% DMSO (Sigma) by needleless syringe. After 24h, leaves were detached and were fixed in liquid nitrogen and total RNA was extracted using RNAeasy Mini kit (Qiagen).

first: Tetiana

last: Kalachova

first: Hana

last: Lentovyčová

first: Oksana

last: Iakovenko

first: Lenka

last: Burketová


title: Gene expression data from human adipose derived stem cell (hASC) treated with 20 uM oleuropein

summary:
Gene expression profiling reveals oleuropein functionality on adipocyte.
We investigated the effects of oleuropein on human adipose-derived stem cells. We conducted an untargeted whole-genome transcriptome study to investigate the functioning of oleuropein on adipocytes.


title: Sequencing of salivary exosomal small RNA from patients with ovarian tumor

city: Jinan

first: Yao

last: Liu

state: Shandong

address: Wenhuaxi Road 107#

institute: Qilu Hospital of Shandong University

type: Non-coding RNA profiling by high throughput sequencing

summary: Salivary exosomes were collected from healthy people and patients with benign and malignant tumors, and small RNA sequencing was performed to screen differential small Rnas for tumor screening

overall_design: We collected saliva from 4 healthy volunteers, 4 patients with benign ovarian tumors and 4 patients with malignant ovarian tumors. Exosomes were isolated by ultracentricentrifugation and identified by electron microscopy and particle size. RNA was extracted by abs60263 exosome RNA extraction kit. RNA purity (OD260/280,OD260/230 ratio) was detected by NanoDrop™ One/OneC. The Qubit™ RNA HS Assay Kit was used for accurate quantification using a Life Invitrogen Qubit® 3.0 fluorescence quantizer. Kapa qPCR was used to quantify the library concentration accurately. The Agilent 4200 TapeStation system was used: RNA integrity (RIN value) and library fragment size were precisely determined.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform.

first: Shourong


title: Accessible Homeostatic Gastric Organoids Reveal Secondary Cell Type-Specific Host-Pathogen Interactions in Helicobacter Pylori Infections

city: Lausanne

first: Matthias

last: Lutolf

address: Route Cantonale

country: Switzerland

institute: EPFL

summary: Despite the high prevalence of gastric diseases like gastric cancer and peptic ulcer disease, largely attributed to Helicobacter pylori infections, an understanding of the underlying mechanisms remains limited. Current in vitro models suffer from poor physiological relevance and limitations in live, long-term observations and experimental access. In this study, we introduce a homeostatic human gastric organoid-on-a-chip system with bilateral access, capable of modelling H. pylori niche establishment and persistent colonization of the gastric epithelium.We show that in physiological apical acidic conditions, the model is able to generate mature pit cells, which are absent in traditionally grown organoids. Upon infection with H. pylori for up to 6 days, these mature pit cells exhibit a distinctive response, contrary to existing paradigms. Beyond its immediate relevance for studying H. pylori infection, this model with structurally and functionally increased relevance holds broader significance by providing a versatile platform to advance our understanding of gastric epithelial cell interactions as well as gastric mucosal immunity and host-pathogen interactions.

overall_design: Human gastric epithelial cells from organoids were grown in a Transgel chip in either apically acidic, neutral or air-liquid interface and analyzed with scRNAseq. Secondly, H. pylori-infected samples were analyzed at two different timepoints.

first: Moritz

last: Hofer

first: Youlim

last: Kim

first: Nicolas

last: Broguiere

first: François

last: Gorostidi

first: Manuel

middle: R

last: Amieva

middle: P


title: HVEM in Acute Lymphocytic Leukemia Facilitates Tumor Immune Escape by Inhibiting CD8+ T Cell Function

city: Guang Zhou

first: Yujia

address: 4, Zhongshan Second Road, Yuexiu District, Guangzhou City

institute: sysu

summary: Our research uncovered that the genetic deletion of HVEM in EL4 can markedly inhibit tumor progress thus prolong survival prognosis of tumor-bearing mouse. Additional experiments also verified that HVEM exerted its oncogenous-effect by constraining the anti-tumor function of T cells in vivo and in vitro.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Vec-EL4 and HVEM-KO EL4 tumors.

first: Lixiang

first: Cheng

last: Zhong

first: Yiyi

first: Xiumei

first: Xinyu

first: Jing

last: Liao

first: Zijin

last: Xia

first: Chunliu

last: Huang

first: Chengzhou

last: Mao

first: Yongyi

last: Feng

first: Congzhou

last: Luo

first: Wenhao

last: Mai

first: Hongrui

last: Song

first: Yue

last: Sheng

last: Zhang

first: Xiaolei

last: Wei

first: Jun

first: Wei

last: Yi


title: Non-senescent, conventional marker-negative geriatric muscle stem cells identified by new CD63/CD200 markers [scRNA-seq]

city: Seoul

first: Young-Woo

last: Jo

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: During aging, the accumulation of senescent cells has a pivotal role in age-related dysfunctions. At geriatric age, the emergence of muscle stem cells (MuSCs) exhibiting senescence markers identified in vitro studies have been reported. However, whether they are in cellular senescence and thus have lost their function is unclear, due to the lack of specific marker for senescent cells. Here, by tracing genetically labeled MuSCs throughout life, we found an unknown MuSC population termed GERI-MuSCs that lost conventional MuSC markers at geriatric age. Although they have several known senescence features, they retain considerable functionalities of in vitro proliferation and in vivo myogenesis, suggesting they are not in cellular senescence. These results highlight the potential discrepancies between aging process in vivo and cellular senescence characterized in vitro. Importantly, we found new markers, CD63 and CD200, inclusive of GERI-MuSCs, which provide a crucial tool for a deeper investigation on in vivo senescence.

overall_design: Single-cell RNA-sequencing analysis was performed using isolated YFP-positive cells of the limb skeletal muscle of Pax7-CreERT2;Rosa-YFP mice by FACS. 10 to 14 months old mice are used as middle-aged for control and more than 28 months old mice are used as geriatric-aged. DHT (dihydrotestosterone) comtained silastic tube was implanted to geriatric mice for 1 and 4 weeks and vehicle implanted mice for 4 weeks was used as control.

first: YeLynne

last: Kim

first: Takwon

last: Yoo

first: Young-Yun

last: Kong


title: Genome-wide studies identify the role of PML/RARα phase separation in PML/RARα-driven transcriptional dysregulation.

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Acute promyelocytic leukemia (APL) is characterized by a specific t(15;17) chromosome translocation that generates the promyelocytic leukemia/retinoic acid receptor-α (PML/RARα) fusion gene. However, the mechanism underlying PML/RARα mediated transcriptional dysregulation remain unclear. Here, we performed the transcription profiling in NB4, an APL patient-derived cell line.

overall_design: Expression profiling of NB4 cells with endogenous PML/RARα knock-down and replaced with empty vector or full-length PML/RARα or phase separation-imcompetent mutants (F158E or ΔIDR) using RNA-seq.

first: Kankan

last: Wang

first: Yi


title: Genome-wide studies identify the role of PML/RARα phase separation in PML/RARα and BRD4 chromatin occupancy

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Acute promyelocytic leukemia (APL) is characterized by a specific t(15;17) chromosome translocation that generates the promyelocytic leukemia/retinoic acid receptor-α (PML/RARα) fusion gene. However, the global association between PML/RARα and transcriptional co-regulators, and the rules of their association in governing the key processes during the leukemogenesis remain unclear. Here, we performed the genome-wide binding profiling of PML/RARα and BRD4 in NB4, an APL patient-derived cell line. Moreover, we also performed ChIP-seq of PML/RARα and BRD4 upon genetic or pharmacological pertubation of PML/RARα or BRD4 to determine how they target regulatory elements.

overall_design: Genome-wide binding profiling of PML/RARα and BRD4 in NB4 cells with endogenous PML/RARα knock-down and replaced with empty vector or full-length PML/RARα or phase separation-imcompetent mutants (F158E or ΔIDR) using ChIP-seq.


title: Dynamic changes in cellular atlases and communication patterns within yak ovaries across diverse reproductive states unveiled by single-cell analysis [scRNAseq_Yak_Ovary_Pregnancy_2]

city: Lanzhou

first: Jie

last: Pei

state: Gansu

address: No. 335 Jiangouyan ST, Qilihe District

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

summary: Yaks (Bos grunniens) exhibit exceptional adaptation to the challenging high-altitude environment of the Qinghai-Tibetan plateau, making them the sole bovine species capable of thriving in such exreme conditions. Investigating the cellular and molecular characteristics of yak ovaries across different reproductive states is crucial for gaining insight into their ovarian functions. Herein, the cellular atlases of yak ovaries in different reproductive states were depicted by single-cell RNA-sequencing (scRNA-seq). The cellular atlases of the ovaries were established by identifying specific gene expression patterns of various cell types, including granulosa cells, theca cells, stromal cells, smooth muscle cells, endothelial cells, glial cell, macrophages, natural killer cells, and proliferating cells. The cellular compositions of the ovaries vary among different reproductive states. Moreover, a cell-to-cell communication network was constructed among distinct cell types within the ovary, spanning the three reproductive states.

overall_design: We performed scRNA-seq to investigate the cellular atlases of yak ovaries and their communication across different states of the reproductive cycle.

first: Xian

last: Guo


title: The Effects of Complement in a Chronic Murine Model of Inflammatory Erosive Arthritis and Pulmonary Vascular Disease

city: Rochester

first: Benjamin

last: Korman

state: NY

address: 601 Elmwood Avenue, Box 695

institute: AIR

summary: Dysfunction of the complement pathway contributes to diseases such rheumatoid arthritis (RA) and pulmonary hypertension (PH). Here we aim to determine whether complement deficiency has a protective effect on joint and lung disease using the tumor necrosis factor-transgenic (TNF-Tg) mouse model with constitutive human TNF-ɑ expression characterized by spontaneous onset of inflammatory-erosive arthritis and PH.

overall_design: Cells were obtained from the lungs and synovium of TNF-Tg and WT mice and analyzed by using scRNAseq

first: Homaira

last: Rahimi

first: Kiana

middle: L

last: Chen

first: Gaochan


title: Dynamic changes in cellular atlases and communication patterns within yak ovaries across diverse reproductive states unveiled by single-cell analysis [scRNAseq_Yak_Ovary_Estrus_1]


title: Dynamic changes in cellular atlases and communication patterns within yak ovaries across diverse reproductive states unveiled by single-cell analysis [scRNAseq_Yak_Ovary_Pregnancy_1]


title: Transcriptomic profiling of peroxisome-deficient, myelin debris-laden macrophages

city: Houston

first: Jian

last: Hu

state: TX

address: 1881 East Rd, South Campus Research Building 3

department: Cancer Biology

institute: University of Texas MD Anderson Cancer Center

summary: Study objective was to investigate the molecular underpinnings of how Pex5 and peroxisome integrity facilitated the demyelination response in myeloid cells. We investigated the transcriptomic changes related to myelin debris uptake in the context of disrupted peroxisome integrity using Pex5 deficient bone marrow derived macrophages.

overall_design: Cultured bone marrow derived macrophages (BMDM) were derived from control and Pex5KO mice. BMDM were incubated with 0.5 mg/mL of crude myelin debris for 24 hours and 72 hours duration. Resting BMDM that did not receive myelin debris were used as baseline controls. After incubation with myelin debris for the indicated durations, total RNA was extracted from BMDM and submitted to Novogene for high-throughput sequencing.

first: Joseph

middle: A

last: Barnes-Vélez


title: Endothelial Kallikrein-Related Peptidase 8 Promotes Diabetic Nephropathy via Reducing SDC4 Expression and Enhancing LIF Release

first: Jiankui

last: Du

state: State...

address: 800 Xiangyin Road

department: Department of physiology

institute: Navy medical university

summary: The molecular mechanisms underlying diabetic nephropathy (DN) are poorly defined. We sought to investigate the roles of kallikrein-related peptidases (KLKs) in DN pathogenesis. Screening of renal tissue from diabetic mice revealed KLK8 as the most highly induced gene in KLK family. KLK8 expression was greater in glomerular endothelial cells (GECs) than other glomerular cells in DN patients and diabetic mice. The rats with KLK8 overexpression exhibited proteinuria, reduced glomerular filtration rate (GFR), and mesangial expansion, podocytopenia, glomerulosclerosis and interstitial fibrosis in renal tissues. In contrast, global KLK8 deficiency reversed streptozotocin-induced hallmark of DN features including proteinuria, reduced GFR, glomerular hypertrophy, glycocalyx loss in GECs, podocytopenia, leukocyte infiltration, glomerulosclerosis, and interstitial fibrosis in mice. Moreover, endothelial KLK8 ablation also blocked streptozotocin-induced hallmark of DN features. Mechanically, elevated KLK8 in GECs promoted endothelial hyperpermeability, glycocalyx injury, and monocyte recruitment and adhesion through downregulation and shedding of syndecan-4 (SDC4). KLK8 upregulation in GECs stimulated mesangial cell proliferation and activation via increasing leukemia inhibitory factor (LIF) release. Moreover, circulatory KLK8 levels correlated positively with LIF and SDC4 in diabetic nephropathy patients. Our study identifies KLK8 as a novel driver of DN development and progress and highlight potential therapeutic strategies targeting KLK8 for DN.

overall_design: Using a streptozotocin (STZ)-induced diabetic mouse model and screening the KLKs of renal tissue from diabetic mice. Co-immunoprecipitation (Co-IP) combined with mass spectrometry identified that SDC4 was the potential proteins that can be degraded by KLK8 in GECs. HGECs infected with KLK8 OVE with or without SDC4 OVE were subjected for RNA-seq analysis.

first: Ying

last: Jiang

first: Shiping

last: Shen

first: Zhengshan

last: Tang

first: Danhong

last: Xu

first: Hongling

last: Yin

first: Jihong

last: Yuan

first: Xuan

first: Shifang

last: Peng

first: Xiaoyan

last: Zhu

first: Xin

last: Ni


title: Non-senescent, conventional marker-negative geriatric muscle stem cells identified by new CD63/CD200 markers

first: Young-Woo

last: Jo

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

overall_design: Refer to individual Series


title: IGF2BP3 mediates m6A-modified E2F2 stability to affect neuroblastoma progression [m6A-seq]

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: We report a previously unrecognized role of IGF2BP3 in survival of neuroblastoma cells. To explore IGF2BP3-dependent gene regulation and m6A modification, RNA-seq and m6A-seq analysis was conducted and the differently expressed/modified genes were revealed in the IGF2BP3-knockdown SK-N-BE(2) cells in comparison to control group.

overall_design: RIP assay was performed using m6A antibody in SK-N-BE(2) cells transfected with control shRNA (sh-NC) or sh-IGF2BP3, and the enriched RNA was sequenced with input sample.

first: Pengcheng

last: Yang

last: Wang

last: Pan


title: Dynamic changes in cellular atlases and communication patterns within yak ovaries across diverse reproductive states unveiled by single-cell analysis [scRNAseq_Yak_Ovary_Anestrus_1]

first: Jie

last: Pei

first: Xian

last: Guo


title: ITPK4 is critical for root elongation under salt stress in Arabidopsis

first: Yuying

last: Ren

address: chenhua road,No 3888

institute: CAS center for excellence in Molecular plant Sciences

summary: Salt stress is one of the abiotic stresses that adversely affect plant growth and agricultural productivity all over the word. Root is the organ that immediately suffers salt stress in soil, and thus the ability of roots to adapt to high salinity is critical for salt stress tolerance in plants. During a long-term evolution, plants have developed a variety of strategies to respond to salt stress. The mechanisms of salt stress response are complicated and are stilly largely unknown. In this study, through the screening of Arabidopsis mutants that are sensitive to salt stress, we identified a mutant itpk4, that displayed reduced root growth, reduced seeds germination, and increased root hairs under salt stress compared with wild type plants. in future, the molecular mechanism underlying the role of ITPK4 in root elongation under high.

overall_design: mRNA extracting  from wild type (WT)and 6-6,

first: Chunzhao

last: Zhao


title: Transcriptomic changes in a KRASG12C mutant cell line (H358 cells) treated with the allosteric SHP2 inhibitor TNO155 for different times

first: Yi

last: Chen

address: 555 Zuchongzhi Rd.

institute: Shanghai Institute of Materia Medica Chinese Academy of Sciences

summary: Allosteric SHP2 inhibitors have been shown to be effective against RTKs and certain KRAS mutation-driven tumors in preclinical models. However, the comprehensive effects of SHP2 inhibitors on cellular signaling, particularly the inhibition of its phosphatase function, remain unclear.

overall_design: We used the SHP2 inhibitor TNO155 (1 μM) to treat the KRASG12C mutated H358 cells for different times (4, 24, 48 h), with DMSO treatment serving as a control, and then utilized RNA-seq to explore the impact of SHP2 inhibition on gene expression and signaling pathways.

first: Hua

last: Xie


title: CasRx-Based KRASG12D Silencing for In Vivo Tumor Inhibition in Spontaneous Lung Adenocarcinoma

city: Bengbu

first: Xiaojing

state: China

address: No 287, Changhuai Road

institute: The first affiliated hospital of Bengbu Medical college

summary: Lung adenocarcinoma with KRAS mutation represents a formidable challenge in cancer treatment due to its undruggable oncogenic mutation. Here, we explored the CasRx-editing approach on lung adenocarcinoma driven by the KRAS activation and Tp53 loss in vivo, a scenario closely resembling clinical conditions. We screened seven sgRNAs in cultured cells and identified that CasRx combined with sgRNA5 effectively suppressed murine KRASG12D transcript levels by 93.185 ± 4.758%, leading to significant attenuation of cell viability and proliferation. Subsequently, we administered CasRx + sgRNA5 via in vivo Adeno-associated viruses (AAV) delivery at the early tumorigenesis stage, resulting in inhibition of tumor initiation and progression, ultimately enhancing the survival of the mice. Mechanistically, the treatment directly targeted the classic KRAS signal pathways and regulated a potential protein network comprising KRAS, DUSP8, NR4A1, DUSP1, and EGR1. Encouragingly, the CasRx + sgRNA5 treatment in mice bearing the induced lung adenocarcinoma demonstrated an optimistic therapeutic outcome, characterized by reduced mutation burden, diminished tumor size, and seemingly improved overall survival. Remarkably, no obvious off-target events were detected in the treated tissues, highlighting the specificity and safety of CasRx + sgRNA5 therapy. This study establishes the feasibility of CasRx-based-KRASG12D editing for efficient in vivo tumor inhibition and provides insights into the potential role of the KRAS-associated protein network in the early development of lung cancer. These findings hold great promise for the development of novel targeted therapies for this aggressive malignancy.

overall_design:
To assess the expression levels of therapeutic vectors and Kras transcripts, elucidate the underlying mechanisms, and evaluate potential off-target effects of CRISPR/CasRx in the context of lung cancer therapy by targeting the driver KRASG12D, the research was performed on an in vivo spontaneous tumor model.
We then performed gene expresion profiling analysis using data obtained from deep RNA_seq of lungs subjected to CasRx therapy for either two weeks of six weeks at the early stage of tumorigenesis. Additionally, we analyzed tumors that underwent CasRx treatment for a duration of six weeks.
Comparative gene expression profiling analysis of RNA_seq data for tissues between experimental groups (AAV-CasRx + sgNC) and control groups (AAV-CasRx + sgRNA2 and/or AAV-CasRx + sgRNA5), considering diverse time points and experimental designs.

first: Fei

last: Liu

first: Lingling

last: Xu

first: Li

last: Xiang

first: Yan

last: Shi


title: IGF2BP3 mediates m6A-modified E2F2 stability to affect neuroblastoma progression [RNA-seq]

overall_design: mRNA profiles of SK-N-BE(2) cells transfected with control shRNA (sh-NC) or sh-IGF2BP3 were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Jian


title: Epigenetic Modulation to perturb the SYNGAP1 Intellectual Disability (ID) that ameliorates synaptic and behavioural deficits

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Sporadic heterozygous mutations in SYNGAP1 affect social and emotional behaviour that are often observed in intellectual disability (ID) and autism spectrum disorder (ASD).  Although neurophysiological deficits have been extensively studied, the epigenetic landscape of   SYNGAP1 mutation-mediated intellectual disability is unexplored.   Here, we have surprisingly found that the p300/CBP specific acetylation marks of histones are significantly repressed in the adolescent hippocampus of Syngap1+/- mouse.  To establish the causal relationship of Syngap1+/- phenotype and the altered histone acetylation signature we have treated 2-4 months old Syngap1+/- mouse with glucose-derived carbon nanosphere (CSP) conjugated potent small molecule activator (TTK21) of p300/CBP lysine acetyltransferase (CSP-TTK21). The enhancement of the p300/CBP specific acetylation marks of histones by CSP-TTK21 restored deficits in spine density, synaptic function, and social preferences of Syngap1+/- mouse that is very closely comparable to wild type littermates. The hippocampal RNA-Seq analysis of the treated mice revealed that the expression of many critical genes related to the ID/ASD reversed due to the treatment of the specific small molecule activator. This study could be the first demonstration of the reversal of autistic behaviour and neural wiring upon the modulation of altered epigenetic modification (s).

overall_design: To delineate the molecular networks through which this small molecule activator (CSP-TTK21) could be acting, we performed whole hippocampal transcriptome analysis after 4 days of Morris Water Maze training across the 6 treatment groups (1. WT: Saline, 2. Syngap1+/-: Saline, 3. WT: CSP, 4. Syngap1+/-: CSP, 5. WT: CSP-TTK21 and 6. Syngap1+/-: CSP-TTK21).

first: Akash

middle: K

last: Singh

first: Ila

last: Joshi

first: Neeharika

middle: M

last: Reddy

first: S

last: Purushotham

first: M

last: Eswaramoorthy

first: Madavan

last: Vasudevan

first: Sourav

last: Banerjee

first: James

last: Clement

first: Tapas

last: Kundu


title: Non-senescent, conventional marker-negative geriatric muscle stem cells identified by new CD63/CD200 markers [RNA-seq]

first: Young-Woo

last: Jo

overall_design: High-throughput RNA-sequencing analysis was performed using isolated YFP-positive cells of the limb skeletal muscle of Pax7-CreERT2;Rosa-YFP mice by FACS. 10 to 14 months old mice are used as middle-aged for control and more than 28 months old mice are used as geriatric-aged. YFP-positive cells of geriatric mice are devided by the VCAM1 fluorescence intensity as VCAM1-High, VCAM1-Mid, and VCAM1-Low/- based on the intensity of YFP-positive cells of middle aged mice.

first: YeLynne

last: Kim

first: Takwon

last: Yoo

first: Young-Yun

last: Kong


title: SOX4 promotes T cell acute lymphoblastic leukemia progression

first: Zimu

last: Zhang

summary: We report a previously unrecognized role of SOX4 in T cell acute lymphoblastic leukemia (T-ALL). To explore SOX4-dependent gene regulation, RNA-seq analysis was conducted and the differently expressed genes were revealed in the SOX4-knockdown Jurkat cells in comparison to control group.

overall_design: mRNA profiles of Jurkat cells transfected with scramble shRNA (sh-Scb) or sh-SOX4 were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Qian

last: Li

first: Yi

last: Wang


title: IRF3 activates RB to authorize cGAS-STING-induced senescence and mitigate liver fibrosis

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Cytosolic dsDNA surveillance by cGAS-STING signaling triggers autophagy, biased mRNA translation, cellular senescence, and interferon-mediated immune responses. However, detailed mechanisms and physiological relevance of STING-induced senescence are not fully understood. Here, we unexpectedly found that IRF3, activated during innate DNA sensing, forms substantial endogenous complexes in the nucleus with retinoblastoma (RB), a well-known tumor suppressor and key cell cycle regulator. The IRF3-RB interaction attenuates CDK4/6-mediated hyperphosphorylation of RB that mobilizes RB to deactivate E2 family (E2F) transcription factors, thereby driving cells into senescence. STING-IRF3-RB signaling plays a notable role in hepatic stellate cells (HSCs) within CCl4 or bile duct ligation (BDL)-induced murine models, pushing activated HSCs towards senescence. Accordingly, global IRF3 knockout or conditional deletion of IRF3 in HSCs aggravated liver fibrosis, a process mitigated by an FDA-approved CDK4/6 inhibitor. These findings underscore a straightforward yet vital mechanism of cGAS-STING signaling in inducing cellular senescence and unveil its unexpected biology in limiting liver fibrosis.

overall_design: DLD1 wild type (WT) and IRF3 knock out (KO) cells treated with ddH2O or HU for two replicates are performed mRNA sequencing.

first: Qirou

last: Wu

first: Yezhang

last: Zhu

first: Pinglong

last: Xu


title: Transcriptomic differential gene expression in polarized RAW 264.7 cells treated with Hydroprotopine

first: Wenjun

last: Qi

address: Xingfu Temple Street

institute: Shandong First Medical University

summary: The aim was to eluci-date the alterations in key pathways associated with Hydroprotopine treatment and to further ex-plore the underlying mechanism behind Hydroprotopine's impact on the inflammatory phenotype of macrophages.

overall_design: In order to investigate the expression of differential genes in polarized RAW 264.7 cells subjected to Hydroprotopine treatment, a comparison was made between the genomes of cells treated with LPS alone and those treated with both LPS and Hydroprotopine.


title: Lin-sca1+cKit+ cells cultured with or without ILC2 supernatant

city: Bern

first: Pascal

last: Naef

address: Murtenstrasse 35

institute: University of Bern

summary:
To investigate the effect of cytokines secreted by type 2 innate lymphoid cells (ILC2s) on hematopoietic stem cells (LSKs), we cultered LSKs with or without ILC2 conditioned supernatant (ILC2sn)
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3-4 samples per condition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS-sorted BL/6 LSKs with or without IL-33 treatment, or with ILC2sn originating from ILC2s cultured with or without IL-33


title: small RNA sequencing from leaf of Arabidopsis to identify tsRNA

city: Chengdu

first: Lei

state: --- Select One ---

address: No.17 People's South Road

institute: Sichuan University

summary: tsRNA is newly found small non-coding RNA with important biological function. However, the knowlede of diversity, biogeneis and function of tsRNA in plant is still lacking. Here, we selected 10-60 nt small RNA for high-throughput sequencing and uncovered the diversity,biogenesis and potentical function of tsRNA in Arabidopsis.

overall_design: Col-0, rns1 and rns2 were grown under long-day (16h light) condition at 23°C. Leaves of four week old plants were harvested 3 h after wounding, or as control leaves without wounding. As for in vitro tRNAs cleavage assay, 0.5 μg tRNAs were incubated at 20°C in the presence of 15 μL leaf enzymatic extract for 30 min in a 90 μL reaction volume complemented with DEPC-H2O. As negative controls, 0.5 μg tRNAs in the absence of leaf enzymatic extract or 15 μL leaf enzymatic extract without additional tRNAs were incubated under the same conditions, respectively. After incubation, RNAs were extracted by TRIzol regent and separated on a 15% TBE-urea polyacrylamide gel.Total RNA or RNA underwent in vitro cleavage was fractionated by electrophoresis. RNA from 10 to 60 nt was sliced and recovered. The purified small RNA was subjected to adapter ligation, reverse transcription, PCR amplification with NEXTflex Small RNA Sequencing Kit (Bioo Scientific), and the resulting libraries sent for deep sequencing.

first: Yan

last: Chen

first: Xiaobin

last: Liu

first: Weiqiang


title: scRNA-seq and MAS-seq in Eftud2-deficient Purkinje cells

city: Nanjing

first: Yuanlin

last: He

address: 101Longmian Avenue, Jiangning District

institute: Nanjing medical university

summary: Spliceosomal GTPase EFTUD2 (Elongation factor Tu GTP binding domain containing 2) is a causative gene for mandibulofacial dysostosis with microcephaly (MFDM) in humans, a complex syndrome with multiple neurological symptoms including cerebellar hypoplasia and motor dysfunction. How EFTUD2 deficiency contributes to these neurological symptoms remains elusive. In this study, we demonstrate that specific ablation of Eftud2 in cerebellar Purkinje cells (PCs) in mice results in severe ferroptosis, PC degeneration, dyskinesia and cerebellar atrophy, which are similar to phenotypes observed in MFDM patients. Mechanistically, Eftud2 promotes the expression of Scd1 and Gch1, upregulates monounsaturated fatty acids-phospholipids (MUFA-PLs), and enhances systematic antioxidant activity, thereby suppressing ferroptotic cell death of PCs. Importantly, inhibiting ferroptosis efficiently rescues PC loss and motor deficits in Eftud2 cKO mice. Our data reveals a novel role of Eftud2 in maintaining the survival of PCs, and that inhibiting ferroptosis via pharmacological or genetic means may be a promising therapeutic strategy for EFTUD2 deficiency-induced MFDM and related disorders.

overall_design: The entire cerebellum is separated from the entire brain with tweezers and the meninges are removed. The sample was then cut in 1×Hank equilibrium salt solution (HBSS) and digested in 0.25% trypsin solution (Thermo Fisher Scientific) for 15-20 minutes. The dissociated cells were filtered through a 22 μm cell filter (Millipore), centrifuged at 300 g for 3 min, and then suspended in a solution containing 0.04% BSA (Sigma) at a concentration of 2000-3000 cells /ml (without calcium and magnesium). Trypan Blue staining was used to detect cell health status and cell number. The dissociated cells in each sample were segmented into nanoscale gel bead emulsions (GEMs) at limited dilution to reduce the multiplication rate. Single-cell GEMs are then incubated with reverse transcription reagents, including several primers for cell and transcript barcoding in cDNA synthesis, followed by cDNA amplification and library construction. All procedures follow the guidelines provided by 10x Genomics, Inc.

first: Guochao

last: Yang

first: Yinghong

first: Zhihong

last: Song


title: Mechanism underlying long-term visual dysfunction in the mouse model of oxygen-induced retinopathy

city: tianjin

first: siyi

last: liu

state: province

institute: tianjin medical university eye hospital

summary: To investigate the mechanism of long-term visual dysfunction in the mouse model of oxygen-induced retinopathy (OIR) by performing RNA sequencing (RNA-seq) . Then further verify the results in transcriptional, expression and function, to explore the methods to improve its electrophysiological function and provide new ideas for the treatment of retinopathy of prematurity (ROP). 7 days C57BL/6 mice  were placed in a closed hyperoxia chamber. After 5 days, they were raised in the ordinary air environment. On, the 17th day and 25th day, the eyes were removed.  The results of RNA-seq in the retina of the OIR mice at P17 showed that compared with the normal control group, 102 differentially expressed genes were identified, of which 95 were significantly up-regulated and 7 were significantly down-regulated. This study  provides a new idea of neuroprotection for the treatment of patients with mild premature retinopathy.

overall_design: To investigate the mechanism of long-term visual dysfunction in the mouse model of oxygen-induced retinopathy by performing RNA sequencing (RNA-seq). 7 days C57BL/6 mice  were placed in a closed hyperoxia chamber. After 5 days, they were raised in the ordinary air environment. On, the 17th day, the eyes were removed for RNA-seq.


title: BM-resident BL/6 and ST2-/- ILC2s cultured with or without rmIL-33

summary:
To investigate the effect of interleukin (IL-33) on bone marrow (BM) resident type 2 innate lymphoid cells (ILC2s), we treated BL/6 and ST2-knockout (ST2-/-) ILC2s for 24h with recombinant mouse IL-33
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3-4 samples per condition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS-sorted BL/6 ILC2s without IL-33 treatment, BL/6 ILC2s with IL-33 treatment, and ST2-/- ILC2s without IL-33 treatment.


title: Single Cell Sequencing of Prader-Wlli Syndrome Dental Pulp Stem Cell-derived Neurons

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: A major challenge to the study and treatment of neurogenetic syndromes is the difficulty in gaining access to live neurons from individuals with these disorders. Although other sources of stem cells are currently available for differentiation into neurons, these can involve invasive procedures and be difficult or expensive to generate limiting their use on a broad scale, especially for rare syndromes which may not be well represented in the local population.  Dental pulp stem cells (DPSC) are neural crest derived multipotent stem cells that reside deep the pulp of shed (baby) teeth and have the potential for broad use in the study of neurogenetic disease. Here, we use DPSC-derived neurons to investigate the developmental differences between neurotypical controls and Prader-Willi syndrome (PWS) by single cell sequencing using SPLiT-Seq.

overall_design: scRNA-seq analysis of DPSC-derived neurons from 5 neurotypical control and 5 PWS subjects. Libraries were prepared with the Evercode Whole Transcriptome kit from Parse Biosciences which involves barcoding and pooling cells from all samples prior to sequencing. Sequencing reads from all samples are distributed across the library. For demultiplexing information please see the 'README.txt' and 'sample_well_IDs.tsv' file. Note that Sample 104 was dropped from downstream analysis after sequencing due to incorrect genetic signature arising from a technical error in library prep.

first: A

last: Victor

first: David

last: Garmire

first: Lawrence

middle: T

last: Reiter


title: Effect of polystyrene petri dishes modified with small intestinal submucosa on the human umbilical cord-derived mesenchymal stem cells

city: jinan

first: Feifei

address: wenhua West Road

institute: Shandong university

summary: We found that compared to PS, SIS-PS modification increased the stemness, immunomodulatory capacity, and exosome secretion of UC-MSC, but decreased the resistance to stimuli.

overall_design: RNA was extracted from UC-MSCs cultured in PS and SIS-PS groups then sequenced

first: Dong

last: Li

last: Dong

first: Huixian

last: Ma

first: Linghong

first: Qing

last: Shi

first: Xiuli

last: Ju


title: Expression data from allo-stimulated human CD19+ cells

city: Boston

first: Urvashi

last: Bhatia

state: MA

address: 450 Brookline Avenue

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

summary: Allogeneic transplant of cells/tissue/organ from a genetically dissimilar donor can lead to severe complications that are largely immune-mediated. We used gene expression data from microarrays to understand how allo-stimulation provided by irradiated peripheral blood mononuclear cells (PBMC) (stimulators) differentially affect the functionality of CD19+ B cells of responder PBMC across different responder-stimulator donor pairs.

overall_design: Untouched CD19+ B cells were enriched from 6 mixed lymphocyte cultures (day 3) using depletion of magnetically labelled non-B cells. RNA isolated from cells were hybridized on Affymetrix microarrays.

first: Eva

last: Guinan


title: Characterizing preeclamptic developmental lung injury pathways through human placental spatial transcriptomics

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

summary: Bronchopulmonary dysplasia (BPD) continues to impact the health of preterm infants worldwide.  Preeclampsia (PE), a placental-driven pregnancy disorder, has a strong clinical association with BPD risk. We hypothesize that preeclampsia causes a unique type of developmental lung injury that predisposes infants to an increased risk of BPD.   Research on human placental tissues is needed to more clearly define the role of PE in developmental lung injury. A new approach to human placental analysis is spatial transcriptomics (Sp-Tr), a technique which produces spatially oriented gene expression data from cells in their native tissue environment.

overall_design: Placental tissues were collected from pregnant patients with severe PE or gestational hypertension (GHTN).  Samples were matched for mode of delivery and infant gender.   Tissues were evaluated using the 10x Genomics Visium Sp-Tr platform.  Data were analyzed using the Seurat spatial workflow. The counts were normalized using SCTransform, dimensionality reduction and clustering were performed using RunPCA, FindNeighbors, FindClusters, and RunUMAP functions.   Clusters corresponding with cellular niches were annotated using the FindMarkers function to identify placental cell-specific phenotype markers followed by analysis of differential gene expression comparing PE vs GHTN.

first: Chelsea

last: Sheth

first: Elisha

last: Wachman

first: Amir

last: Khan

first: Stephanie

middle: D

last: Byrum

first: Elizabeth

middle: S

last: Taglauer


title: Transcriptome analysis the APS-UCMSC and Normal-UCMSC

first: Haibin

last: Tian

address: 1239 Siping Road

institute: Tongji University

summary: We aim to explore the types and expression of RNA in APS-UCMSC and Normal-UCMSC .

overall_design: The gene expression of four APS-UCMSC cell lines and three Normal-UCMSC cell lines were analysed with RNA sequencing.

first: Qi

last: Shen

first: Xueying

last: Wang


title: GATA2 upregulation restores androgen receptor chromatin association and advances darolutamide resistance in prostate cancer (RNA-Seq)

first: Tianyi

last: Zhou

address: 3517 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: Darolutamide is the latest FDA-approved antiandrogen for the treatment of metastatic prostate cancer. Despite its efficacy in prolonging disease-free survival, drug resistance invariably develops. This study aims to understand the molecular mechanisms underlying darolutamide resistance and identify potential therapeutic targets for overcoming the resistance.

overall_design: To investigate the differential genes expression in the DaroR resistant cells that promote the cell survival and gain resistance

first: Chengtai

last: Yu

first: Yali

last: Han

first: Bin

last: He

first: Qin

last: Feng


title: Bulk RNA-seq of murine lung mesenchymal cells sorted after day 7 and day 14 of sham or pneumonectomy

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: The aim was to investigate the transcriptomic alterations that occur in lung mesenchymal cells during compensatory lung growth following unilateral partial pneumonectomy (PNX). The hypothesis is that during lung re-growth, these cells upregulate the alveolar myofibroblast signature that is active during developmental alveologenesis

overall_design: Lung mesenchymal cells defined as EpCAM- CD45- CD31- (triple negative) were FACS-sorted from sham or pneumonectomized lungs at days 7 or 14 after surgery, and subjected to bulk RNA-seq.

first: Elie

last: El-Agha

first: Ali

last: Khadim


title: Effect of protein kinase D inhibition on the transcriptome of epithelial ovarian cancer cells

city: Noida

first: Adhiraj

last: Roy

state: Uttar Pradesh

address: Sector 125

department: AIMMSCR

institute: Amity University

summary: Epithelial ovarian cancer (EOC) is the most lethal gynaecological malignancy with poor prognosis and high relapse rate. Despite of discovery of several therapeutic approaches including poly-ADP ribose polymerase (PARP) inhibitors, EOC remains highly lethal and warrants early detection and novel therapeutic interventions. Protein kinase D (PKD) isoforms regulate cellular functions associated with tumorigenesis including cell proliferation, migration, invasion but their role in EOC remains unknown. In this study, PKD was inactivated by using pan-PKD inhibitors CRT0066101 and kb-NB142-70 in EOC cell lines OVCAR8 and SKOV3 followed by RNASeq Analysis by Illumina NovaSeq 6000 Sequencing. The data was pooled together to identify differentially expressed genes (DEGs) in each group considered (n=4), filtered with the cut-off of Log2FC +2 for upregulation & -2 for downregulation along with 0.005 of P-value cut off. Our results indicates that PKD abrogation in EOC cells caused differential expression of 4622 genes including KIFC1, KIF22, RAB2A, LAMA5, PLK1, AURKA & PCNA which are majorly involve in cell cycle, membrane trafficking, signal transduction and gene expression. Discovery of these novel PKD-associated proteins\pathways might serve as new therapeutic targets against this lethal pathology.

overall_design: To investigate the novel downstream tagets of Protein Kinase D (PKD) in epithelial ovarian cancer

first: Komal

last: Tyagi

first: Priyanka

last: Jain


title: Testicular piRNA analysis identified dysregulated piRNAs in non-obstructive azoospermia

city: Hamadan

first: Fahimeh

last: Piryaei

state: Hamadan

address: Shahid Fahmideh

department: Molecular Medicine and Genetics

country: Iran

institute: Hamadan University of Medical Sciences

summary: Male infertility has remained idiopathic in a remarkable proportion of all cases. Gonadal expression of PIWI-interacting RNAs (piRNAs) has been shown to be vital to normal spermatogenesis, as they are expressed in almost all types of testicular germ cells. These molecules and their related Piwi proteins strictly regulate transposable elements’ activity and gene expression. We aimed to identify dysregulated piRNAs in idiopathic non-obstructive azoospermic (NOA) testis by global expression analysis. In the NOA group, 1328 piRNAs were identified to be differentially expressed, of which 1322 were down-regulated and 6 were up-regulated. Bioinformatics analysis corroborated the involvement of dysregulated piRNA in spermatogenesis. We also identified 64 clusters of differentially expressed piRNAs, of which 42 clusters had a minimum of 10 absolute piRNA hits. Our study suggests that piRNAs show significant dysregulation in infertility. Their target genes play a role in their self-biogenesis, probably by regulating their own production through a feedback mechanism. The down-regulated piRNAs may find value as biomarkers for the presence of spermatozoa in the testis of azoospermic individuals, while the up-regulated piRNAs are great candidates for further investigation of their precise functions in spermatogenesis.

overall_design: Testis tissue samples from 18 azoospermic patients (10 NOA and 8 OA) were studied by small RNA sequencing. To validate high-throughput sequencing data, quantitative real-time polymerase chain reactions for two differentially altered piRNAs were performed. Bioinformatics analyses were undertaken to identify pathways affected by piRNA dysregulation.

first: Poonam

last: Mehta

first: Hossein

last: Mozdarani

first: Fatemeh

last: Hamzehlooy

first: Mahmoud

last: Barati

first: Zeynab

first: Mohammad

last: Sadighi Gilani

first: Mohsen

last: Alemi

first: Rajender

last: Singh


title: Enhancer-associated LncRNA-ITGA2 promotes vascular smooth muscle remodeling by mediating ITGA2 promoter-enhancer interactions

city: shanghai

first: Xian

last: Guo

address: changhai road 168

institute: Changhai hospital

summary: In this study, multiomics profiling, including CUT&Tag, promoter capture Hi-C (PCHi-C), and microarray, identified LncRNA-ITGA2 as a novel elncRNA that was highly expressed in PDGF-induced proliferative human VSMCs. Notably, LncRNA-ITGA2 was significantly increased in both plasma and coronary atherosclerotic tissues of patients with coronary artery disease (CAD) compared with control subjects. Loss- and gain-of-function studies revealed that LncRNA-ITGA2 potently increased PDGF-induced VSMC proliferation and migration. Moreover, LncRNA-ITGA2 overexpression enhanced neointimal hyperplasia in vivo in a mouse carotid artery injury model, exhibiting its partial functional conservation. RNA-sequencing and CRISPR-Cas9 gene-editing technology revealed integrin α2 (ITGA2) as a downstream target of LncRNA-ITGA2 in VSMCs. Mechanistically, promoter-enhancer interactions were detected by PCHi-C at the ITGA2 locus after PDGF-BB treatment. Chromatin immunoprecipitation sequencing (ChIP-Seq) and chromatin isolation by RNA purification (ChIRP)-qPCR showed that LncRNA-ITGA2 directly bound to the Enhancer-ITGA2 and increased H3K27 acetylation in both the Enhancer-ITGA2 and Promoter-ITGA2. In addition, we demonstrated, by ChIRP-MS and RNA immunoprecipitation, that LncRNA-ITGA2 interacted with the DNA binding-protein NONO (non-pou domain containing octamer-binding protein), which also bound to the ITGA2 promoter, as verified by the ChIP-qPCR assay. Ultimately, the knockout cell lines of NONO, LncRNA-ITGA2, and its promoter confirmed the above regulatory mechanism.

overall_design: To investigate the DNA chromatin loops in vascular smooth muscle remodeling, promoter capture Hi-C  was performed in human aortic smooth muscle cells treated with PDGF-BB or without PDGF-BB.


title: AB5D mitigates UVB-induced erythema through the modulation of PGE2

city: Singapore

first: Tze Hau

last: Lam

address: 70 Biopolis Street

country: Singapore

institute: Procter and Gamble

summary: Erythema, characterized by the redness of the skin, is a common skin reaction triggered by various endogenous and exogenous factors. This response is often a result of the activation of underlying biological mechanisms within the skin. The objective of this study is to investigate the potential benefits of applying a combination of well-established active ingredients namely Allantoin, Bisabolol, D-Panthenol, and Dipotassium Glycyrrhizinate (AB5D). These ingredients are often incorporated in skincare formulations to deliver specific benefits. Additionally, the study aims to elucidate the mechanisms by which these ingredients exert their combined actions to alleviate erythema. Through in-vitro experiments involving the application of AB5D to UVB-exposed keratinocytes, we have uncovered novel insights into the potential response mechanism of AB5D.  We observed a significant downregulation of gene sets associated with inflammatory responses, highlighting the anti-inflammatory properties of AB5D. Specifically, AB5D effectively reduced the production of PGE2, leading to the downregulation of inflammatory cytokines.  Moreover, our findings indicate that AB5D exhibits antioxidative capabilities, functioning as both an antioxidant agent and a regulator of antioxidant enzyme expression to counteract the detrimental effects of cellular oxidative stress. Overall, it is plausible to suggest that AB5D may alleviate erythema by modulating inflammation via PGE2 and through antioxidation mechanisms.

overall_design: To evaluate the mechanism of action by which the combination of Allantoin, Bisabolol, D-Panthenol, and Dipotassium Glycyrrhizinate (AB5D) may exert benefical effects on UVB-exposed hTERT keratinocytes

first: TzeHau


title: Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation [ChIP-Seq]

city: Stanford

first: Andy

last: Chen

address: 240 Pasteur Rd

institute: Stanford University

summary: 3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of how rapid transcriptional responses, transcriptional memory, and integration of different environmental signals are orchestrated in the 3D genome is limited. Here, we study various aspects of the inflammatory response in macrophages using transcriptomic, epigenomic, and genome conformation mapping technologies, including high-resolution Micro-Capture C. We report that interleukine-4 (IL-4) stably rewires the 3D genome conformation of macrophages and juxtaposes endotoxin-, interferon-gamma-, and dexamethasone-activated enhancers to cognate gene promoters to support enhanced gene expression. IL-4-driven conformational change is indispensable for the integration of IL-4- and endotoxin-induced enhanced and synergistic transcriptional responses, provides short-term transcriptional memory, and can occur in the absence of IL-4-induced epigenetic and transcriptional changes. Our work reveals that IL-4-driven 3D genome conformation is required to shape macrophage plasticity to subsequent immunological responses, integrate distinct inflammatory signals, and provides memory.

overall_design: Examination of TFs binding during macrophage responses to polarizing cytokines.

first: Bence

last: Daniel

middle: Y

first: Katalin

last: Sandor


title: Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation

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

overall_design: Refer to individual Series


title: Cyclical macrophage plasticity provides periodic inflammatory and regenerative gene expression programs in cell cycle[RNA-Seq]

summary: Cell cycle (CC) is a fundamental biological process with robust, cyclical gene expression programs to facilitate cell division. In the immune system, a productive immune response requires the expansion of pathogen-responsive cell types, but whether CC also confers unique gene expression programs that inform the subsequent immunological response remains unclear. Here we demonstrate that single macrophages adopt different plasticity states in CC which is a major source of heterogeneity in response to polarizing cytokines. Specifically, macrophage plasticity to interferon gamma (IFNG) is substantially reduced, while interleukin 4 (IL-4) can induce S-G2/M-biased gene expression. Additionally, IL-4 polarization shifts the CC-phase distribution of the population towards G2/M phase, providing a mechanism for reduced IFNG-induced repolarization. Finally, we show that macrophages express tissue remodeling genes in the S-G2/M-phases of CC, that can be also detected in vivo during muscle regeneration. Therefore, CC defines macrophage inflammatory and regenerative responses in a cyclical, CC-phase-dependent manner.

overall_design: Examination of macrophage responses to polarizing cytokines in the different pases of cell cycle.

first: Julia

last: Belk

first: Stefanie

last: Meier


title: Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation [ATAC-Seq]


title: Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation [Hi-C]


title: EZH2 drives transcriptional repression of trpc5 gene in morphine tolerance

first: Chun-Yi

last: Jiang

institute: Nanjing Medical University

summary: Purpose: To identify differentially expressed genes regulated by morphine in mice. Methods: Mice were intrathecally injected with normal saline or morphine (10 ug/10 uL) for 7 days and then spinal cords L4-L5 were collected and subjected to mRNA-sequencing by geneseeq and data analysis. Results: We identified morphine upregulated 42 genes and downregulated 44 genes compared with saline group. KEGG enrichment analysis showed calcium signaling pathway was downregulated by morphine and we noticed that TRPC5 was one of the most significantly downregulated genes by morphine. We confirmed that intrathecal injection of morphine leads to Trpc5 transcriptional suppression via reducing GABA release, contributing to morphine tolerance.

overall_design: The profiles of spinal cords L4-L5 collected from saline-treated and morphine treated mice respectively were generated for High-throughput sequencing, in triplicate, and analyzed the morphine-regulated transcriptomes.

first: Chun

first: Wan

last: Li


title: Integrated functional ceRNA network analysis reveals that circLIPH promotes pancreatic cancer progression via the miR-769-3p/GOLM1/mTOR pathway

city: Jinshan Distric

first: Jin

last: Wang

state: Shanghai

address: 2901 Caolang Road, Scientific Research Center, RM 319

department: Shanghai Public Health Clinical Center

institute: Fudan University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Pancreatic ductal adenocarcinoma (PDAC) is the most common malignancy of the pancreas with a high mortality rate because of metastasis of advanced tumors and recurrence after treatment. To identify more informative detection, diagnostic, and prognostic markers for improving the clinical therapeutic outcome of PDAC patients, we employed an SBC ceRNA array to screen differentially expressed ceRNAs in PDAC tumors, and circRNA/lncRNA-miRNA-mRNA regulatory networks were constructed. Gain- and loss-of-function experiments were also conducted to verify the biological function of circLIPH in vitro and in vivo. We found that 145 mRNAs and 358 circRNAs were differentially expressed in PDAC tumors. High circLIPH expression was correlated with tumor size and stage, and the inhibition of circLIPH repressed pancreatic cancer progression. We identified that circLIPH promoted pancreatic cancer progression via the miR-769-3p/GOLM1/mTOR pathway and might be a key regulator of tumorigenesis in PDAC.


title: In vivo transcriptome profiling of control and GANAB-KD UMUC3 bladder carcinoma cells

city: Guangzhou

first: Yuqing

address: North campus of Sun Yat-sen University, No.74 of Zhongshan 2nd road, Yuexiu Distinct, Guangzhou, Guangdong

institute: Sun Yat-sen University

summary: Carcinoma cells achieve malignant progression and therapy resistance through de-differentiation. While differentiation therapy has proven to be highly efficient in acute promyelocytic leukemia, this therapeutic strategy has not been successfully applied in human solid tumors. Here, we identify α-Glucosidase II (GANAB) as a novel driver of bladder cancer de-differentiation using a systemic biology approach and demonstrate its potential to serve as a therapeutic target of solid tumor differentiation therapy. Partial knock-out of GANAB by CRISPR Cas9 differentiates one of the most aggressive bladder carcinoma line into a non-invasive papillary form in vivo and decreases chemotherapy resistance in vitro. As differentiation and de-differentiation program are mostly activated in vivo, we labelled control and GANAB-KD cells with a lentivirus to express a H2B-EGFP localized in the nuclei. After sorting by BD FACS Aria II, cells were lyzed for RNA-sequencing.

overall_design: 11samples were analyzed, including 4 samples for control bladder cancer PDX which are obtained from the seventh day  ,3 samples for control bladder cancer PDX which are obtained from the fourteenth day, and 4 samples for GANAB-KD bladder cancer PDX which are obtained from the fourteenth day.

first: L

last: Yuqing


title: Methyltransferase Setd2 prevents T cell-mediated autoimmune diseases via phospholipid remodeling [V]

first: Yali

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: Purpose: RNA-seq analysis of gene expression patterns in Naïve t, Th0, Treg and Th17 cells of wild-type mice. The goals of this study are to compared the gene expression between Naïve T and other types Th cells by RNA-seq analysise.

overall_design: Naïve T cells were CD4+ T cells directly selected from the spleen. Th0 cells were stimulated with αCD3/CD28 for three days. Th17 cells were collected at 3 days under Th17 differentiation conditions, Treg cells were collected at 3 days under Treg differentiation conditions,and then subjected to RNA seq.

first: Xuetao

last: Cao


title: Microarray identification and characterization of differentially expressed microRNAs in pediatric ovarian immature teratoma

city: Shanghai

first: Kezhe

last: Tan

address: Luding Road 355, Shanghai, China

institute: Shanghai Children's Hospital

summary: Ovarian immature teratoma (IM) is a type of germinal malignant tumor, affecting children, adolescents and young adults. Event-free survival is below 25% in high-grade IM. Pediatric IM is rare and seldom studied, raising controversial issues such as histopathological standard and lack of specific biomarkers. This study aimed to perform microRNA (miRNA) microarray and identify specific differentially expressed miRNAs in IMs than in other types of ovarian tumors. Our work enables practitioners to optimally exploit relevant characteristics for precise diagnostic and therapeutic strategies in IM.

overall_design: We retrospectively reviewed the medical records of 20 patients with ovarian tumors who were treated at Shanghai Children's Hospital between March 2010 and October 2018. The enrolled patients underwent tumor resection and the samples were collected, including 18 cases using the formalin-fixed, paraffin-embedded (FFPE) approach, of which 2 cases of ovarian cyst, 3 cases of mature teratoma, 6 cases of immature teratoma, 3 cases of yolk sac tumor, 3 cases of juvenile granulosa cell tumor, and 1 case of dysgerminoma; 2 cases were fresh frozen tissue samples preserved in -81℃ environment, including one mature teratoma and one yolk sac tumor. All cases were histologically confirmed by two independent pathologists.

first: Jing

last: Xiong


title: Alistipes putredinis protects DSS-induced colitis through mediating immune tolerance

city: Changsha

first: Xing

last: Wu

address: 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China

department: Department of Gastroenterology

institute: The Third Xiangya Hospital of Central South University

summary: Alistipes putredinis can alleviate DSS-induced colitis in mice, but the mechanism is unknown. The aim of this study was to examine the changes in gene expression in the intestinal tissue of mice with colitis following treatment with  Alistipes putredinis by RNA sequencing.

overall_design: To clarify the role of  Alistipes putredinis in colitis, We treated dextran sulfate sodium salt (DSS)-induced mice with  Alistipes putredinis. The body weight, disease activity index (DAI), Colon length and colon tissue H&E staining was used to evaluate the severity of colitis. In mice, we compared the severity of colitis between DSS and DSS+AP groups and randomly selected four mice from each group for RNA sequencing analysis.

first: Jiahao

last: Xu

first: Xiaoyan


title: Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation [MCC]

first: Andy

first: Bence


title: Gene expression profile of CDH17 silenced human colorectal cancer cell lines KM12SM and SW620

city: Madrid

first: Javier

last: Robles

state: Madrid

address: Calle Ramiro de Maetzu 9

department: Biomedicine

country: Spain

institute: Biological Research Centre Margarita Salas

summary: CDH17 is a key protein in the development of hepatic metastasis in colorectal cancer. In this study, stable silencing of CDH17 was achieved in the KM12SM and SW620 cell lines using shRNA technology, with the objective of exploring the cellular functions and  pathways in which CDH17 is implicated.

overall_design: Affymetrix (Clariom S) array-based mRNA expression profiles generated for KM12SM and SW620 colorectal cancer (CRC) cell lines after CDH17 silencing by using shRNA technology.

first: Laura

last: Pintado

first: Rubén

last: Bartolomé

first: Juan

middle: I

last: Imbaud

first: José

last: Casal


title: Effect of Phb2 depletion in retinal photoreceptors on gene expression in the bulk retina of C57BL/6J mice

city: 广州

first: haoyu

last: zuo

address: 天河区金穗路7号

institute: 中山眼科中心

summary: To explore the functions for Phb2 gene in early retinal degeneration, we performed RNA-seq analysis on the bulk retinas from control and photoreceptor-specific knockout Phb2 mice at 6 weeks of age. Compared with control mice, there were 778 differentially expressed genes (log2 |fold change|> 1, log10 adjusted p-values < 0.05) identified to be associated with distinct biological processes. 585 genes were significantly upregulated and 192 genes were significantly downregulated in photoreceptor cell-specific knockout Phb2 mice. The KEGG pathways analysis of up-regulated and down-regulated genes and ranking the enrichment pathways according to the corrected p-value.To explore the critical signaling pathways that might be affected by knockout Phb2 in retinal photoreceptors, we performed RNA-seq analysis on 6-week-old C57BL/6J photoreceptor cell-specific knockout Phb2 mice and control mice. Compared with control mice, there were 778 differentially expressed genes (log2 |fold change|> 1, log10 adjusted p-values < 0.05) identified to be associated with distinct biological processes. 585 genes were significantly upregulated and 192 genes were significantly downregulated in photoreceptor cell-specific knockout Phb2 mice. The KEGG pathways analysis of up-regulated and down-regulated genes and ranking the enrichment pathways according to the corrected p-value.

overall_design: retina were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.RNA libraries were prepared for sequencing using standard Illumina protocols

first: Zhao

last: ling

first: Zuo

last: haoyu

first: Han

last: wenjuan


title: MiR-137 gain of function in the dorsomedial striatum promotes continued cocaine-taking despite punishment in rats

city: Callaghan

first: Dylan

last: Kiltschewskij

state: NSW

address: Room MS616, Level 6, Medical Sciences Building, University Drive

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: The University of Newcastle

summary: Drug addiction is a major public health issue that is characterised by continued drug use despite negative consequences. However, the molecular and cellular mechanisms that underlie this behaviour are not well understood. In this study we investigated the role of miR-137, a microRNA that has been previously shown to control the expression of genes necessary for neuronal development and synapse maturation, with common variants in the MIR137 gene linked to a higher risk of schizophrenia. Previously, we revealed that miR-137 expression in cocaine-trained animals exhibited spatial and temporal variability in the dorsal striatum (DS). Building upon this observation, we hypothesised that augmenting miR-137 function in the DS would impact drug-seeking behavior under punishment conditions by modulating molecular targets involved in synaptic plasticity. Male Sprague-Dawley rats were trained to self-administer cocaine and then randomly assigned to receive either lentiviral-mediated overexpression of hsa-miR-137 (miR-137OE) or an empty pCDH-vector (pCDH-EV) control in the dorsomedial striatum (DMS). Once stable cocaine self-administration was achieved, drug-taking was assessed under conditions in which lever presses were associated with a 0.25 probability of foot shock (0.5 mA). During five days of testing, pCDH-EV control animals showed a significant reduction in responding for cocaine, whereas miR-137OE animals displayed greater resistance to the suppression of cocaine responding across foot shock sessions compared to controls. RNA-sequencing analysis of striatal tissue from miR-137OE animals revealed significant enrichment of genes involved in synaptic plasticity and astrocyte signalling compared to control animals. Taken together, these findings provide insight into the mechanisms underlying addiction risk and and contribute to a better understanding of the neural substrates involved in these disorders.

overall_design: mRNA sequencing of the rat dorsomedial striatum after lentiviral transduction with pre-miR-137 or pCDH empty vector constructs.

last: Greco

first: Simon

last: Fisher

first: Elizabeth

middle: E

last: Manning

middle: J

first: Amy

last: Pearl

first: Isabel

middle: H

last: Sien

first: Paul

last: Kenny

last: Corbit

first: Bernard

middle: W

last: Balleine

first: Murray

last: Cairns

first: Christopher

middle: V

last: Dayas


title: Single cell transcriptomics of cerebrospinal fluid cells from patients with recent-onset narcolepsy

city: Munich

first: Klaus

last: Dornmair

address: Grosshaderner Strasse 9

department: Institute of Clinical Neuroimmunology

institute: University Hospital LMU Munich

summary: Narcolepsy is a rare cause of excessive daytime sleepiness and may be associated or not with cataplexy, i.e. sudden muscle weakness. These forms are designated NAR-type 1 (NT1) and -type 2 (NT2), respectively. Notable characteristics of narcolepsy are that most patients carry the HLA-DQB1*06:02 allele and NT1-patients have highly decreased levels hypocretin-1 (synonym orexin-A) in the cerebrospinal fluid (CSF). The pathogenesis of narcolepsy is still enigmatic but the strung HLA-bias and increased frequencies of CD4+ T cells reactive to hypocretin in the peripheral blood suggest autoimmune processes in the hypothalamus. Here we analyzed the transcriptomes of single CSF-cells from 16 narcoleptic patients by mRNAseq. As controls, we used single cells from patients with multiple sclerosis, radiologically isolated syndrome, and idiopathic intracranial hypertension. We identified 20 clusters of different cell types and >1000 genes that were differentially regulated between the different diseases. Surprisingly, the strongest upregulation in narcolepsy patients as compared to controls were the genome-encoded MTRNR2L12 and MTRNR2L8 peptides, which are homologous to mitochondria-encoded HUMANIN peptide that is known playing a role in other neurological diseases.

overall_design:
We analyzed the transcriptome of single cells isolated from cerebrospinal fluid (CSF) from patients with NT1 and NT2 with recent disease onset. As controls, we used CSF cells from patients with multiple sclerosis (MS) and radiologically isolated syndrome (RIS) and idiopathic intracranial hypertension (IIH), i.e. from patients with a chronic inflammatory and a non-inflammatory neurological disease, respectively. Author statement: Fastq raw data files from patients are not uploaded due to data protection concerns.
ADT barcode sequence
TotalSeq™-C0072 anti-human CD4 Antibody TGTTCCCGCTCAACT
TotalSeq™-C0046 anti-human CD8 Antibody  GCGCAACTTGATGAT
----------------------------
Submitters state "Due to data protection concerns, our institution does not permit the upload of raw sequencing files generated from human samples.

first: Alina

last: Huth

first: Ikram

last: Ayoub

first: Eduardo

last: Beltrán

first: Roland

last: Liblau

first: Yves

last: Dauvilliers


title: SET-9 and SET-26 impact transgenerational epigenetic inheritance and germline mortality through their PHD finger and SET domains [RNA-Seq ]

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: Transgenerational epigenetic inheritance (TEI), the transmission of epigenetic states between generations, has been observed in complex organisms ranging from plants to nematode worms, insects and mammals. One form of TEI that has been robustly studied is the inheritance of gene silencing. In Caenorhabditis elegans transgenerational gene silencing can be partitioned into three phases: the initiation of silencing, establishment of a heritable silencing signal within the parent individuals, and maintenance of this silencing signal within subsequent generations. Silencing involves nuclear and cytoplasmic components, and most genes involved in the process are linked to small RNA processing pathways. To date, two predicted histone methyltransferases have been implicated in the establishment of TEI, set-25 and set-32. Here, we demonstrate that the closely related paralogues set-9 and set-26 function in establishment and maintenance of TEI. We also identify a third related gene that lacks any predicted ordered domains; we name this gene intrinsically disordered protein-1 (idp-1). Strikingly, idp-1 also plays a role in establishment of TEI. SET-9 and SET-26 each contain a PHD finger and a SET domain. We show that the SET domains of SET-9 and SET-26 likely have no histone lysine methyltransferase activity, but that the PHD fingers bind trimethylated histone 3 lysine 4 (H3K4me3) in the absence of adjacent histone marks. We demonstrate that despite modelling data that suggests that set-9 and set-26 lack histone lysine methyltransferase activity, the function of both genes in TEI requires their PHD finger and SET domains. Our data confirm that the SET domain is functional and identifies three new chromatin factors required for epigenetic inheritance.

overall_design: RNA-seq libaries were prepared from gonads dissected from adult hermaphrodite C. elegans strains that carry set-9, set-26, and set-9;set-26 mutations, as well as the wild type (N2) strain.

middle: G

first: Julie

middle: N

last: Ni

first: Alyson

last: Ash


title: Quantitative Analysis of erythroblast  cells Transcriptomes treated with Carbon Dots(CDs) derived from Codonopsis pilosula or not

city: Jinan

first: Zhiyuan

last: Lu

state: Shandong

address: 6699 Qingdao road

department: School of Pharmaceutical Sciences & Institute of Materia Medica

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

summary: In this study, distinctive biological CDs derived from Codonopsis pilosula were designed and synthesized. In traditional Chinese medicine, Codonopsis pilosula is considered to be a good blood tonic. The synthesized CDs comprise sp2/sp3 carbon atoms and oxygen/nitrogen-based groups and exhibit good biocompatibility and membrane permeability. The in vitro and in vivo experiments were conducted using an erythroid differentiation system and a mouse model, respectively, and showed that the CDs significantly promote the proliferation of erythroid cells. To reveal the detailed mechanisms of CDs in stimulating erythroblast proliferation, we performed RNA sequencing to analyze the gene expression profile change between untreated andmCDs treated erythroblasts.

overall_design: TER119-negative fetal liver erythroblasts were purified and cultured in Epo containing medium for 30 h supplemented with or without CDs (1 ug/ml), and total RNA was extracted using the TRIzol reagent. RNA sequencing was conducted using the BGIseq500 platform (Shenzhen, China) in triplicate.


title: Transcriptomic analysis of tomato plants subjected to multifactorial stress combination

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: Climate change and industrial pollution are responsible for major losses in crop yield worldwide. Tomato plants are subjected to multiple stress conditions in combination when growing in the natural field. In this work, we analyzed the transcriptomic response of tomato plants to the combination of salinity and heat stress, when plants were or were not inoculated with the beneficial bacteria Pseudomonas Putida. The results suggest that specific transcripts are regulated only under stress combination in plants inoculated with the bacteria. These transcripts could be related with the enhanced tolerance of inoculated plants under conditions of stress combination.

overall_design: Moneymaker tomato plants were grown in seedling trays filled with peat moss, perlite, and vermiculite (80:10:10). After germination, seedlings were transplanted to 10-cm diameter pots filled with a mix of sterile autoclaved peat moss and perlite (2:1) and maintained under greenhouse conditions (70% relative humidity, 200 µmol photons m-2· s-1 light intensity, natural photoperiod day/night cycle with temperatures averaging 25.0°C and 18.0°C, respectively). 3-week-old plants were inoculated with Pseudomonas putida KT2240 (OD660 =0.05) through the roots and the rest of the plants were watered with the same amount of M8 buffer 10 days before starting stress treatments. Then, plants were subjected to four different conditions: control (CT), heat stress (37ºC; HS), salinity (150 mM NaCl; S), and the combination of salinity and heat stress (150 mM NaCl + 37ºC; S+HS).  Plants were watered three times a week for 15 days with Hoagland solution or salinity stressor in a half-strength Hoagland solution. For stress combinations that included HS, plants watered in the presence or absence of salinity were subjected to a 3-day treatment of HS (37ºC) in growth chambers. Therefore, eight experimental groups were designed (CT, Pp, HS, HS+Pp, S, S+Pp, HS+S, HS+S+Pp).

first: Lidia

last: Pascual

first: Aurelio

last: Gómez-Cadenas

first: Ron

last: Mittler

first: Sara

last: Zandalinas


title: Type III interferons induce pyroptosis in gut epithelial cells and delay tissue restitution  upon intestinal injury

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

institute: CNRS

summary: To investigate the transcriptional program within the intestinal epithelial cells (IECs) controlling the impact of type III interferons (IFN-λ) on intestinal recovery, we performed a single-cell RNA sequencing (scRNA-seq) on murine IECs following irradiation.

overall_design: Mice deficient for the IFN-λ receptor in IECs and wild-type mice underwent targeted irradiation. 96h after irradiation, IECs were isolated by fluorescence-activated cell sorting (FACS) based on the expression of EPCAM and analyzed using scRNA-seq.

first: Kautilya

last: Jena

first: Julien

last: Mambu

first: Benedetta

last: Sposito

first: Daniel

last: Boehmer

first: Virginie

last: Millet

first: Lionel

last: Spinelli

first: Chloe

last: Riquier

first: Sarah

last: Wurbel

first: Franck

last: Galland

first: Philippe

last: Naquet

first: Vanessa

last: Mitsialis

first: Natália

last: Ketelut-Carneiro

first: Katlynn

last: Bugda Gwilt

first: Jay

middle: R

last: Thiagarajah

first: Katherine

middle: A

last: Fitzgerald

first: Scott

middle: B

last: Snapper

first: Achille

last: Broggi

first: Ivan

last: Zanoni


title: mRNA sequencing data of liver tumor tissues

city: Seongnam

first: Sung Hwan

last: Lee

address: 59 Yatap-ro

department: Department of Surgery

institute: CHA Bundang Medical Center

summary: HCC tissue data to explore biomarkers and mechanisms of therapeutic resistance in patients with advanced HCC involved in immunotherapy.

overall_design: Explore the gene expression pattern of 138 liver cancer tumor tissues

first: Sung

first: Hong

last: Chon


title: Coxiella burnetii type IV secretion-mediated activation of host cell Nrf2 signaling

city: Little Rock

first: Allen

last: Gies

address: 4301 W. Markham

institute: University of Arkansas for Medical Sciences

summary: Coxiella burnetii is the causative agent of human Q fever, which presents with either acute flu-like symptoms or progresses to chronic endocarditis.  Alveolar macrophages engulf C. burnetii after human inhalation, and the pathogen transitions through the phagolysosomal maturation pathway to form a parasitophorous vacuole (PV) for intracellular replication.  PV generation requires a type IV secretion system (T4SS) that serves as a critical C. burnetii modulator of host cell activity.  We previously showed C. burnetii infection activates the antioxidant Nrf2-Keap1 pathway, stabilizing Nrf2, a transcription factor that translocates to the nucleus.  Here, we further investigated the role of Nrf2 during C. burnetii infection of human macrophage-like cells and potential important downstream events that influence infection.  We show Nrf2 is activated in a T4SS-dependent manner and that inhibition of Nrf2 activity negatively impacts PV formation and C. burnetii replication.  Assessment of oxidative stress-related gene expression revealed that nox4, nqo1, sod1, and sod2 expression increase during infection.  Nrf2 inhibition also increases levels of the autophagic proteins LC3, p62, and phosphorylated p62, suggesting dysregulated autophagy is deleterious to infection.  Additionally, RNA sequencing analysis determined that Nrf2 inhibition has a significant impact on gene expression involving multiple pathways including oxidative stress, the unfolded protein response, and cell survival signaling.  Overall, this study advances understanding of Nrf2 importance during C. burnetii infection and the cellular signaling pathways controlled by Nrf2 in response to an intracellular bacterial pathogen.

overall_design: we predict that C. burnetii also usurps Nrf2 activity to regulate autophagy and survival signaling.  To investigate our hypotheses, we used chemical inhibitors to reduce Nrf2 stability in human macrophages [27, 28].  We then assessed the effect of Nrf2 on two major signaling events during macrophage infection by C. burnetii: oxidative stress and autophagy.

first: Amanda

middle: L

last: Dragan

first: Richard

middle: C

last: Kurten

first: Daniel

last: Voth


title: Assessment of the effect of nutrition level on metylome of mammary gland structural components (parenchyma (PAR) and fat pad (MFP)) and liver in dairy calves

city: Balice

first: Ewelina

last: Semik-Gurgul

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

type: Methylation profiling by high throughput sequencing

summary: The aim of this study was to identify changes in metylome of parenchyma (PAR),  fat pad (MFP) and liver in dairy calves. Our earlier results showed that feeding management regulates the dynamics of organ growth in preweaned heifers. We observed that a daily dose of 5.3 kg of milk replacer inhibits mammary gland development. Therefore, this research aims at evaluation of the influence of the nutritional level in the early life period of calves on the biological processes related to the development of the mammary gland through transcriptomic alterations.

overall_design: Comparative DNA methylation profiling analysis of RRBS data for 14 parenchyma, 16 fat pad and 15 liver samples was performed using the Illumina Nextseq 550 platform.

first: Tomasz

last: Szmatoła

first: Artur

last: Gurgul

first: Barbara

last: Niwińska