title: Forebrain neuronal Smc3 regulates weight and metabolic parameters associated with regulation of hypothalamic Melanocortin 4 receptor

status: Public on Jan 04 2024

city: Safed

first: Evan

last: Elliott

address: Henrietta Szold Street, P.O. Box 1589

department: The Azrieli Faculty of Medicine

institute: Bar-Ilan University

summary: SMC3 is a major component of the cohesin complex that regulates higher-order chromatin organization and gene expression. Mutations in SMC3 gene are found in patients with Cornelia de Lange syndrome (CdLs). This syndrome is characterized by intellectual disabilities, behavioral patterns as self-injury, as well as metabolic dysregulation. Nonetheless, little is known about the role of neuronal SMC3 in gene expression and physiology in adulthood. This study determined the role of SMC3 in adulthood brain, by knocking out Smc3 specifically in adulthood forebrain excitatory neurons. Neuron-specific SMC3 knockout mice displayed a very strong metabolic phenotype in both male and female mice, including a robust overweight phenotype, loss of muscle mass, increased food consumption, lower respiratory exchange ratio, lower energy expenditure and hormonal changes. The hypothalamus of these mice displayed dysregulated morphology and RNA-seq in the hypothalamus reveals dysregulation in multiple cellular pathways, including decrease of Melanocortin 4 receptor (Mc4r) expression level, a main regulator of appetite. Treatment of these mice with Setmelanotide, a MC4r agonist, induced a decrease of weight and food consumption in these mice. Therefore, we have identified specific and reversable metabolic parameters that are regulated by neuronal Smc3 in adulthood.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for SMC3 in Wild type and conditional knockout (cKO) of SMC3 in excitatory forebrain-cells mice

first: Natalia

last: Saleev

first: Dmitriy

last: Getselter

first: Joanna

last: Bartman

first: Roee

last: Gutman

first: Assaf

last: Marco


title: ABCC4 impacts megakaryopoiesis and protects megakaryocytes against 6-mercaptopurine induced cytotoxicity

status: Public on Jan 05 2024

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

type: Expression profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Modulation of tumor microenvironment by targeting histone acetylation in bladder cancer

city: Madrid

first: Sandra

middle: Isabel

last: Nunes

state: Madrid

address: Av. Complutense, 40

country: Spain

institute: CIEMAT

summary: Alterations in the epigenetic machinery in both tumor and immune cells contribute to bladder cancer (BC) development, constituting a promising target as an alternative therapeutic option. Here, we have explored the effects of a novel histone deacetylase (HDAC) inhibitor CM-1758, alone or in combination with immune checkpoint inhibitors (ICI) in BC. We determined the antitumor effects of CM-1758 in various BC cell lines together with the induction of broad transcriptional changes, with focus on the epigenetic regulation of PD-L1. Using an immunocompetent syngeneic mouse model of metastatic BC, we studied the effects of CM-1758 alone or in combination with anti-PD-L1 not only on tumor cells, but also in the tumor microenvironment. In vitro, we found that CM-1758 has cytotoxic and cytostatic effects either by inducing apoptosis or cell cycle arrest in BC cells at low micromolar levels. PD-L1 is epigenetically regulated by histone acetylation marks and is induced after treatment with CM-1758. We also observed that treatment with CM-1758 led to an important delay in tumor growth and a higher CD8+ T cell tumor infiltration. Moreover, anti-PD-L1 alone or in combination with CM-1758 reprogramed macrophage differentiation towards a M1-like polarization state and increased of pro-inflammatory cytokines systemically, yielding potential further cooperative antitumor effects. Our results suggest the possibility of combining HDAC inhibitors with immunotherapies for the management of advanced metastatic BC.

overall_design: Analysis of bladder cancer cell lines 253J, J82, RT112 and TCCSUP control versus treated with CM-1758 with the IC50 dose for 48 h. 2 replicates per group were included.

middle: P

first: Lucia

last: Morales

first: Carolina

last: Rubio

first: Ester

last: Munera-Maravilla

first: Iris

last: Lodewijk

first: Cristian

last: Suárez-Cabrera

first: Victor

middle: G

last: Martinez

first: Mercedes

last: Pérez-Escavy

first: Miriam

last: Pérez-Crespo

first: Miguel

middle: A

last: Sánchez

first: Esther

last: Montesinos

first: Edurne

last: San José-Enériz

first: Xabier

last: Agirre

first: Felipe

last: Prosper

first: Antonio

last: Pineda-Lucena

first: Rui

last: Henrique

first: Marta

last: Dueñas

first: Margareta

last: Correia

first: Carmen

last: Jerónimo

first: Jesús

middle: M

last: Paramio


title: 3' RACE-seq of reporter LINE-1 and control mRNAs' 3' non-templated ends in 293T 'wild-type', XRN1 KO, DCP2 KO, DCP2 plus XRN1 KO cells

city: Poznan

first: Zbigniew

last: Warkocki

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

summary:
Human LINE-1 retrotransposons can mobilize in the human genome by a copy-and-paste machanism involving RNA intermediates. LINE-1 mRNA 3' ends play a major role in initiation of reverse transcription (a step retrotransposition).
To assess the impact of RNA 3’ end dynamics of LINE-1 mRNA on its retrotransposition potential in human cells we analyzed 3' non-templated ends on LINE-1, and control GAPDH and PABPC4 mRNAs by 3' RACE-seq. RNA was retrieved from multiple clonal 293T cells wild-type or knock-out in eitehr XRN1, DCP2, or both (DCP2 plus XRN1).

Publication: D Janecki, R Sen, N Szóstak, A Kajdasz, M Kordys, K Plawgo, D Pandakov, A Philips, Z Warkocki (2024): LINE-1 mRNA 3’ end dynamics shape its biology and retrotransposition potential. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad1251

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: 3’ RACE-seq on reporter LINE-1, GAPDH, PABPC4, and ACTB mRNAs from a total of 7 clonal wild-type 293T cells, 7 clonal XRN1 KO cell lines in 293T, 1 clonal DCP2 KO cell line in 293T, 1 clonal DCP2 plus XRN1 KO cell line in 293T. Also sequencing of artificial spike-ins with a known number of 0, 8, 16, 32, 64, and 128 consecutive A residues. Note a set of 4 cellular conditions: wild-type, XRN1 KO, DCP2 KO, and DCP2 plus XRN1 KO (based on cells obtained from dr Sarah Slavoff, Luo et al., 2020, 10.1021/acs.biochem.0c00069) was performed only for reporter LINE-1 and GAPDH, and not the other 2 mRNAs in 3 technical replicates. Libraries generated as described in Warkocki et al., 2018 (https://doi.org/10.1016/j.cell.2018.07.022) but PCR was done using the TaKaRa GLX polymerase.

first: Dorota

last: Adamska

first: Natalia

last: Szóstak

first: Arkadiusz

last: Kajdasz


title: Single-cell mRNA-sequencing reveals a regulatory network in Myh6-MCM;Ino80fl/fl heart with heart failure.

city: Beijing

first: li

last: wang

country: China

institute: State Key Laboratory of Cardiovascular Disease, Fuwai Hospital

summary: Among the multitude of genes that INO80 regulated, we sought to identify ones that acted more readily in response to INO80 overexpression, and whether those would form a regulatory network to execute a greater diversity of biological processes.

overall_design: To address these questions, we performed single-cell RNA-seq (scRNA-seq) using CMs isolated from mouse hearts at days 0, 1, 2 and 3 of Ino80 induction.

first: Li

last: Wang

first: Zongna

last: Ren


title: Anterior Pituitary Transcriptomics Following a High Fat Diet:  Impact of oxidative stress on organelle pathology

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: Anterior pituitary cells are highly active with regards to protein synthesis and secretion, processes which depend heavily on mitochondrial ATP production and functional endoplasmic reticula.  It is well known that obesity adds an allostatic overload to tissues, requiring them to adapt to inflammation and oxidative stress.  Therefore, we hypothesized that the pituitary is highly vulnerable to the stress of high fat diet-induced weight gain. In this study, we utilized a 10-15 week high fat diet (HFD, 60%) plus a thermoneutral housing paradigm, testing both male and female FVB.129P mice. We quantified serum hormones and cytokines, characterized the metabolic phenotype, and defined changes in the pituitary transcriptome using single-cell RNA-seq. Weight gain was significant by 3 weeks in HFD mice, and by 10 weeks all HFD groups had gained 20 g.  HFD females (15 weeks) had increased energy expenditure and decreased activity. All HFD groups showed increases in serum leptin, Il-6, resistin, MCP-1, and TNFα. HFD males had increased insulin; both HFD males and females had increased TSH, and HFD females had decreased serum prolactin and growth hormone (GH) pulse amplitude.  Pituitary scRNA-seq revealed modest or no changes in pituitary cell gene expression in the different cell types from HFD males after 10 or 15 weeks or HFD females after 10 weeks.  However, females exposed to a HFD for 15 weeks showed significant numbers of differentially expressed genes in lactotropes and stem cells.  Pathway analyses identified a reduction in pathways that supported protein translation, ribosome biogenesis, and oxidative phosphorylation, indicating mitochondrial dysfunction.  Collectively, these studies reveal that pituitary cells from males are more resilient to the oxidative stress of obesity than females and identify the most vulnerable pituitary cell populations in females.

first: Tiffany

middle: K

last: Miles

first: Angela

last: Odle

first: Stephanie

middle: D

last: Byrum

first: Alex

last: Lagasse

first: Anessa

last: Haney

first: Victoria

last: Ortega

first: Cole

middle: R

last: Bolen

first: Jewel

last: Banik

first: Milla

last: Reddick

first: Ashley

last: Herdman

first: Melanie

last: MacNicol

first: Angus

first: Gwen

middle: V

last: Childs


title: INO80 and heart failure.

first: li

type: Genome binding/occupancy profiling by high throughput sequencing


title: The effect of INO80 on chromatin accessibility  in the development of heart failure.

summary: In order to detect the effect of INO80 on chromatin accessibility, we will utilize the Assay for Transposase Accessible Chromatin with highthroughput sequencing (ATAC-Seq).

overall_design: ATAC-Seq in CMs isolated from control and INO80-OE mice (D2), respectively.

first: Li


title: Effect of INO80 overexpression on gene expression  in adult cardiomyocytes (CMs).

summary: To capture the swift changes in gene expression upon INO80-OE, we performed time-coursed (D0, D2, D4, and D6) RNA sequencing (RNA-Seq) following INO80 induction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ctrl and Ino80 overexpressing (INO80-OE) at 2, 4, and 6 days after tamoxifen treatment.

first: Zongna


title: The distribution of INO80 in the development of heart failure.

summary: We performed chromatin immunoprecipitation (ChIP) against the core subunit INO80 to determine its direct regulation on downstream targets.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for INO80 in CMs isolated from control and INO80-OE mice (D2) and sham and TAC 4W mice, respectively.


title: Effect of YBX1 knockdown on gene expression of differentiated C3H10T1/2 brown adipocytes

city: Changsha

first: Xu

last: Feng

state: Hunan

address: 87# Xiangya Road

department: Department of Endocrinology, Endocrinology Research Center

institute: Xiangya Hospital of Central South University

summary: To investigate the function of YBX1 in the regulation of brown adipose aging, differentiated C3H10T1/2 brown adipocytes were transfected with specific siRNAs targeting YBX1 or control siRNA. Total RNA was extracted at 48h after transfection to performed gene expression profiling analysis by high throughput RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for differentiated C3H10T1/2 brown adipocytes transfected with specific siRNAs targeting YBX1 or control siRNA.

first: Ruo-Yu

last: Zhou

first: Hai-Yan


title: RNAseq of human Multiple Sclerosis cortex with hnRNP A1 dysfunction

city: SASKATOON

first: Michael

middle: C

last: Levin

state: Saskatchewan

address: 701 Queen St, CMSNRC (Cameco Multiple Sclerosis Neuroscience Research Centre)

country: Canada

institute: University of Saskatchewan

summary: We sought to identify alterations in RNA expression and splicing in human grey matter from the brains of people with Multiple Sclerosis (MS) where we observe mislocalization of the RNA binding protein hnRNP A1. Thus, RNA was extracted from fresh-frozen post-mortem brain samples of three people with MS and compared to RNA extracted from fresh-frozen post-mortem brain samples of three healthy controls by RNAseq. Regions of interest in human grey matter were defined by immunostaining for hnRNP A1 to confirm grey matter regions with hnRNP A1 mislocalization in MS tissue, and grey matter regions with normal hnRNP A1 localization in control tissue, and the same region from an adjacent tissue section was dissected with a razor blade and used for RNA extraction and sequencing.

overall_design: Fresh-frozen post-mortem brain samples were collected from n=3 healthy controls, and from n=3 MS patients.

first: Hannah

middle: E

last: Salapa

first: S

last: Hammond


title: Early parental deprivation during primate infancy has a lifelong impact on gene expression in the male marmoset brain

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

summary: Adverse early life experiences are well-established risk factors for neurological disorders later in life. However, the molecular mechanisms underlying the impact of adverse experiences on neurophysiological systems throughout life remain incompletely understood. Previous studies suggest that social attachment to parents in early development are indispensable for infants to grow into healthy adults. In situations where multiple offspring are born in a single birth in common marmosets, human hand-rearing is employed to ensure the survival of the offspring in captivity. However, hand-reared marmosets often exhibit behavioral abnormalities, including abnormal vocalizations, excessive attachment to the caretaker, and aggressive behavior. In this study, comprehensive transcriptome analyses were conducted on hippocampus tissues, a neuroanatomical region sensitive to social attachment, obtained from human hand-reared (N = 6) and parent-reared male marmosets (N = 5) at distinct developmental stages. Our analyses revealed consistent alterations in a subset of genes, including those related to neurodevelopmental diseases, across different developmental stages, indicating their continuous susceptibility to the effects of early parental deprivation. These findings highlight the dynamic nature of gene expression in response to early life experiences and suggest that the impact of early parental deprivation on gene expression may vary across different stages of development.

overall_design: Comaprison between parent-reared marmoset and human hand-reared marmoset at two developmental stage (young and aged).

first: Haruka

last: Shinohara

first: Makiko

last: Meguro-Horike

first: Takashi

last: Inoue

first: Miyuki

last: Shimazu

first: Machiko

last: Hattori

first: Hitoshi

last: Hibino

first: Kazumasa

last: Fukasawa

first: Erika

last: Sasaki


title: CLIPseq of hnRNP A1 from the spinal cords of mice with experimental autoimmune encephalomyelitis

summary: Experimental autoimmune encephalomyelitis (EAE) is a mouse model for multiple sclerosis (MS) a chronic autoimmune disease of the central nervous system. We have observed dysfunction of the RNA binding protein hnRNP A1 in neurons from the brains of patients with MS, and the spinal cords of mice with EAE. Here, we sought to characterize the consequences of EAE-induced dysfunction of hnRNP A1 on the RNAs it binds by using CLIPseq to establish both the normal central nervous system RNA binding profile of hnRNP A1 in the spinal cords of naive mice, and any alterations to the binding profile of hnRNP A1 in the spinal cords of mice with EAE.

overall_design: n=7 female C57Bl/6 mice were treated with MOG(35-55) at 8 weeks of age to induce experimental autoimmune encephalomeylitis (EAE). At 15 days post-clinical disease onset, mice were scored for disease severity and euthanized, along with n=3 age-matched naïve (healthy) control mice. Spinal cords from each animal were subjected to UV crosslinking, then lysed for immunoprecipitation in the presence of RNaseI with either an anti-hnRNP A1 antibody (each animal) or a control non-binding IgG2a (pooled Naive lysates [n=1] and pooled EAE lysates [n=1]). Input samples were also collected for each animal prior to immunoprecipitation. All samples were subjected to RNAseq, with input samples and pooled IgG2a immunoprecipitation samples providing "background" signal to subtract from the anti-hnRNP A1 immunoprecipitated samples.

first: Patricia

last: Thibault

first: Cole

last: Libner


title: REPLACED by GSE232887

city: Jerusalem

first: Guy

last: Kelman

address: Ein Kerem campus

country: Israel

institute: The Hebrew University of Jerusalem

summary: This dataset has been replaced by SuperSeries GSE232887.

first: Samuel

last: Abassah-Oppong

first: Brandon

middle: J

last: Mannion

first: Virginie

last: Tissières

first: Eddie

last: Rodríguez-Carballo

first: Anja

last: Ljubojevic

first: Fabrice

last: Darbellay

first: Tabitha

last: Festa

first: Carly

middle: S

last: Sullivan

first: Riana

last: Hunter

first: Catherine

last: Novak

first: Ingrid

last: Plajzer-Frick

first: Stella

last: Tran

first: Jennifer

last: Akiyama

first: Iros

last: Barozzi

first: Guillaume

last: Andrey

first: Javier

last: Lopez-Rios

first: Diane

last: Dickel

first: Axel

last: Visel

first: Len

last: Pennacchio

first: John

last: Cobb

first: Marco

last: Osterwalder


title: Innate immunity controls hair regeneration and growth via BMP signaling

city: Cleveland

first: Luyang

last: Xiong

state: OH

address: 9500 Euclid Ave

department: Lerner Research Institute

institute: Cleveland Clinic Foundation

summary: Tight immune defense against environment and a unique ability of self-repair are the hallmarks of epithelia. Here we show that innate immunity Toll like receptor 2 (TLR2) coordinates these key functions thereby promoting hair growth and tissue regeneration.   TLR2 is enriched in hair follicle stem cells (HFSCs) and its levels change in hair cycle and skin disorders. The lack of TLR2 in HFSCs diminishes activation and proliferation of HFSCs markedly prolonging the resting phase of hair cycle. Transcriptome profiling of HFSCs revealed that TLR2 regulates main hair regeneration pathways. TLR2 deletion upregulates inhibitory BMP7 signaling, while the blockade by Noggin restores deficient HFSCs proliferation in the absence of TLR2. In injury model TLR2 is required for both, tissue and hair regeneration. While endothelial TLR2 drives wound revascularization and closure, HFSC TLR2 controls hair regrowth. Endogenous TLR2 ligand produced in hair follicles promotes hair regeneration and growth via HFSC TLR2. Together, HFSC TLR2 drives stem cell proliferation, hair cycle and regeneration.

overall_design: Examination of transcriptome changes after TLR2 deletion from murine hair follicle stem cells.

first: Tatiana

last: Byzova


title: Comparison of Proteomic Expression Profiles after Radiation Exposure across Four Different Species

status: Public on Jan 03 2024

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

summary: There is a need to identify biomarkers of radiation exposure for use in development of circulating biodosimeters for radiation exposure and for clinical use as markers of radiation injury. Most research approaches for biomarker discovery rely on a single animal model. The current study sought to take advantage of a novel aptamer-based proteomic assay which has been validated for use in many species to characterize changes to the blood proteome after total-body irradiation (TBI) across four different mammalian species including humans. Plasma was collected from C57BL6 mice, Sinclair minipigs, and Rhesus non-human primates (NHPs) receiving a single dose of TBI at a range of 3.3 Gy to 4.22 Gy at 24 h postirradiation. NHP and minipig models were irradiated using a 60Co source at a dose rate of 0.6 Gy/min, the C57BL6 mouse model using an X-ray source at a dose rate of 2.28 Gy/min and clinical samples from a photon source at 10 cGy/min. Plasma was collected from human patients receiving a single dose of 2 Gy TBI collected 6 h postirradiation. Plasma was screened using the aptamer-based SomaLogic SomaScan® proteomic assay technology to evaluate changes in the expression of 1,310 protein analytes. Confirmatory analysis of protein expression of biomarker HIST1H1C, was completed using plasma from C57BL6 mice receiving a 2, 3.5 or 8 Gy TBI collected at days 1, 3, and 7 postirradiation by singleplex ELISA. Summary of key pathways with altered expression after radiation exposure across all four mammalian species was determined using Ingenuity Pathway Analysis (IPA). Detectable values were obtained for all 1,310 proteins in all samples included in the SomaScan assay. A subset panel of protein biomarkers which demonstrated significant (p < 0.05) changes in expression of at least 1.3-fold after radiation exposure were characterized for each species. IPA of significantly altered proteins yielded a variety of top disease and biofunction pathways across species with the organismal injury and abnormalities pathway held in common for all four species. The HIST1H1C protein was shown to be radiation responsive within the human, NHP and murine species within the SomaScan dataset and was shown to demonstrate dose dependent upregulation at 2, 3.5 and 8 Gy at 24 h postirradiation in a separate murine cohort by ELISA. The SomaScan proteomics platform is a useful screening tool to evaluate changes in biomarker expression across multiple mammalian species. In our study, we were able to identify a novel biomarker of radiation exposure, HIST1H1C, and characterize panels of radiation responsive proteins and functional proteomic pathways altered by radiation exposure across murine, minipig, NHP and human species. Our study demonstrates the efficacy of using a multispecies approach for biomarker discovery.

sample_organism:
Macaca mulatta
Homo sapiens
Sus scrofa
Mus musculus

overall_design: For this study Rhesus monkeys (Macaca mulatta) between 5–8 years of age received a single dose of TBI between 3.85 and 4.22 Gy. Plasma samples were collected at 24 h postirradiation using venipuncture collection. Pre- and postirradiation samples were matched for each individual animal. Animal care was conducted according to the Standard Operating Procedures of CiToxLAB North America under Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) standards.

first: Mary

last: Sproull


title: Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

summary: The recognition of 5’ splice site (5’ ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5’ ss recognition, we selectively humanized components of the yeast U1 snRNP to reveal the function of these components in 5’ ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yeast U1 (yU1) snRNA and the 5’ ss RNA duplex. We replaced the Zinc-Finger (ZnF) domain of yU1C with its human counterpart, which resulted in cold-sensitive growth phenotype and moderate splicing defects. Next, we added an auxin-inducible degron to yLuc7 protein and found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of PRP40 and Snu71 (two other essential yeast U1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yeast U1 snRNP, and splicing plays a major role in the regulation of mitochondria function in yeast.

overall_design: poly-A selected RNAseq of yeast (S. cerevisiae) with and without humanized U1C protein and with and without the splicing factor Luc7. RNAseq for the WT and h-yU1C were first performed with samples at OD600 ~5 for WT and ~8 for h-yU1C. To ensure the splicing differences observed were not complicated by the high OD (post-log phase), we repeated the RNAseq experiments at low OD600 ~0.4 for both the WT and h-yU1C. The latter data was used for the paper.

first: Rui

last: Zhao


title: Maternal Undernutrition Results in Transcript Changes in Male Offspring that May Promote Resistance to High Fat Diet Induced Weight Gain

first: Allen

last: Gies

summary: Maternal nutrition during embryonic development and lactation influences multiple aspects of offspring health. Using mice, this study investigates the effects of maternal caloric restriction (CR) during mid-gestation and lactation on offspring neonatal development and on adult metabolic function when challenged by a high fat diet (HFD). The CR maternal model produced male and female offspring that were significantly smaller, in terms of weight and length, and females had delayed puberty. Adult offspring born to CR dams had a sexually dimorphic response to the high fat diet.  Compared to offspring of maternal control dams, adult female, but not male, CR offspring gained more weight in response to high fat diet at 10 weeks. In adipose tissue of male HFD offspring, maternal undernutrition resulted in blunted expression of genes associated with weight gain and increased expression of genes that protect against weight gain.  Regardless of maternal nutrition status, HFD male offspring showed increased expression of genes associated with nonalcoholic liver disease (NAFLD). Furthermore, we observed significant, sexually dimorphic differences in serum TSH. These data reveal tissue- and sex-specific changes in gene and hormone regulation following mild maternal undernutrition, which may offer protection against diet induced weight gain in adult male offspring.

overall_design: Male FVB.129P2 mice were singly housed for at least 24 hours prior to mating. Female FVB.129P2 mice were introduced to males in the evening of proestrus (embryonic day -1), which was determined by vaginal cytology. Vaginal plugs were visualized the next morning to confirm that mating occurred. Embryonic day 0 (E0) was established as the day after mating, when the vaginal plug was visualized. On E0, mated females were singly housed and weighed. At E10, females were again weighed to verify pregnancy with an expected 3 g increase in weight from E0. Pregnant females, or dams, received ~25 g of food daily starting at E12 to visually acclimate to receiving less food. Dams were paired into two feeding groups: ad libitum (FED) and 20% calorie restricted (CR20). At E15, the caloric restriction began, with CR20 dams receiving 80% of the food the paired FED dam consumed from the previous day. Food intake was measured daily around 0930. The undernutrition continued until the offspring were euthanized or weaned. There was one exception to this protocol: The day before parturition, the FED dams consumed less than 3 g of food. To prevent CR20 dams from consuming young at any point in the study, 3 g of food was the minimum made available to CR20 dams. Therefore, if the FED dams consumed less than 3 g of food before parturition, available food to undernourished dams was not reduced below 3 g.  Pups were born around E19, with the average litter size being 8±1 pups.

first: Tiffany

last: Miles

first: Melody

middle: L

last: Allensworth-James

first: Angela

last: Odle

first: Ana

last: Silva Moreira

first: Anessa

last: Haney

first: Alexandra

middle: N

last: Lagasse

first: Stephanie

last: Byrum

first: Angelica

last: Riojas

first: Melanie

last: MacNicol

first: Angus

first: Gwen

last: Childs


title: Cellular landscapes of osteogenically differentiated valvular interstitial cells stimulated with XCT790-loaded nanoparticles

city: Hangzhou

first: Jinyong

last: Chen

state: Zhejiang

address: Jiefang Road 88

department: Department of Cardiology

institute: Second Afliated Hospital, Zhejiang University School of Medicine

summary: The pathogenesis of calcific aortic valve disease (CAVD) is unknown. XCT790 is a specific inhibitor of estrogen-associated receptor alpha (ERR-alpha) that inhibits valve calcification in mouse models. Here, we designed a nanocarrier targeting osteoblast-differentiated valve interstitial cells (VICs) for targeted delivery of XCT790 to the calcified area. We stimulated osteogenic differentiated VICs with this targeting nanoparticle, and performed RNA-seq to assess transcriptional alterations of VICs and explore specific mechanisms.

overall_design: Human aortic valve interstitial cells (AVICs) were cultured with growth medium, osteogenic differentiation medium, or osteogenic differentiation medium supplemented with XCT790-loaded nanoparticles for 6 days.

first: Tanchen

last: Ren

first: Lan

last: Xie

first: Jianan

last: Wang

first: Xianbao

last: Liu


title: RNA-seq analysis of Ogt regulated genes in smooth muscle cells (VSMCs)

city: Xin Xiang

first: xiwen

last: xiong

address: 602 Jinsui Road

department: School of Forensic Medicine

institute: Xinxiang Medical University

summary: To investigate the roles of Ogt in smooth muscle cells (SMCs), we crossed Ogt floxed mice and SM22-CreER mice to generate inducible SMC Ogt specific knockout mice. Aorta tissues from these mice were isolated and RNA were extracted and performed RNAseq analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for aorta tissues from Ogt floxed control and Ogt SMC specific knockout mice.

first: Xiwen

last: Xiong


title: Exploring molecular profiles of osteogenically differentiated aortic valvular interstitial cells

summary: Aortic valve calcifications are often associated with calcium deposition and tissue mineralization, resulting in stiffness and dysfunction. To better understand the diversity of molecular and cellular processes for calcification in valve structures, we isolated human aortic valve interstitial cells (AVICs) and exposed them to calcification stimulation. RNA-seq revealed that in response to calcified stimuli, AVIC activates a robust ossification program, although the signaling pathways, cellular processes, and osteogenesis-related markers involved are diverse. In conclusion, this study provides a wealth of information suggesting that the pathogenesis of aortic valve calcification may be much more than previously understood.

overall_design: Human aortic valve interstitial cells (AVICs) were cultured with growth medium or osteogenic differentiation medium for 6 days.


title: The totipotent 2C-like state safeguards genomic stability of mouse embryonic stem cells

city: Kunming

first: Li

middle: Qiao

last: hua

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

summary: Mouse embryonic stem cells (ESCs) sporadically transition to a transient totipotent state that resembles blastomeres of the 2-cell embryo stage, which has been proposed to contribute to exceptional genomic stability, one of the key features of mouse ESCs. However, the biological significance of the rare population of 2C-like cells (2CLCs) in ESC cultures remains to be tested. Here, we generated an inducible reporter cell system for specific elimination of 2CLCs from the ESC cultures to disrupt the equilibrium between ESCs and 2CLCs. We show that removing 2CLCs from the ESC cultures leads to dramatic accumulation of DNA damage, genomic mutations and rearrangements, indicating impaired genomic instability. Furthermore, 2CLCs removal results in increased apoptosis and reduced proliferation of mouse ESCs. Together, our data reveal that transition to the privileged 2C-like state is a major component of the intrinsic mechanisms that maintain exceptional genomic stability of mouse ESCs for long-term self-renewal.

overall_design: To investigate the effects of removal of 2C-like cells (2CLCs) on the long-term self  renewal of mouse embryonic stem cells (ESCs), we generated an inducible reporter cell system (2C::HSVTK reporter cell line) to eliminate 2CLCs specifically by adding Ganciclovir to ESC culture medium. After removal of 2CLCs, we collected Ganciclovir and DMSO treated 2C::HSVTK reporter cells (each two repeats) for whole genome sequencing (WGS) to dissect the genomic mutations and rearrangements after removel of 2CLCs.

first: Jiameng

last: Dan

first: Zeling

last: Du

first: Meiqi

last: Lin

first: Qiaohua

last: Li


title: eCV: Enhanced coefficient of variation and IDR extensions for reproducibility assessment of NGS experiments with multiple replicates.

city: San Diego

first: Stephanie

last: Bruns

state: California

address: 5770 Oberlin Dr

institute: Eclipsebio

summary: Reproducibility assessment is essential in extracting reliable scientific insights from high-throughput experiments. Inconsistency between technical replicates poses a challenge, particularly evident in NGS technologies based on immunoprecipitations, where the need for reproducibility in peak identification is a well-acknowledged limitation. While the Irreproducibility Discovery Rate (IDR) method has been instrumental in assessing reproducibility, its standard implementation is constrained to handling only two replicates. In the current era of steadly growing sample sizes, facilitated by multiplexing and reduced sequencing costs, highly performing methods that handle any number of replicates are desirable.

overall_design: RBP-eCLIP  experiment targeting RBFOX2 in samples from HEK293T cells. Information submitted for the following samples: RBFOX2_eCLIP_IP_1, RBFOX2_eCLIP_IP_2, RBFOX2_eCLIP_IP_3, RBFOX2_eCLIP_IP_4, RBFOX2_eCLIP_Input_1, RBFOX2_eCLIP_Input_2, RBFOX2_eCLIP_Input_3 and RBFOX2_eCLIP_Input_4.

first: Agustin

last: Gonzalez-Reymundez

first: Kylie

last: Shen

first: Diana

last: Cox


title: Modulating the Response to Benzo[a]pyrene when CYP1A1 and CYP1B1 are Knocked Down

city: Jung-gu

first: Min

last: Kim

state: Seoul

address: 30, Pildong-ro 1-gil

country: South Korea

institute: Dongguk university

summary: Benzo[a]pyrene is a Group 1 carcinogen. It undergoes metabolism in the liver through CYP1A1 and CYP1B1 enzymes. This study was conducted to investigate the response to benzo[a]pyrene in the liver when these enzymes are knocked down.

overall_design: To investigate the role of CYP1B1 and CYP1A1 on B[a]P-induced response, CYP1A1 and CYP1B1 were knocked down by siRNA.

first: Kyung-Bin

last: Bu

first: Seung-cheol

last: Lee


title: Sequencing of the hippocampal transcriptome of vestibular spatial disorientation mice

city: Xi'an

first: Tong

last: Chang

state: Shaanxi Province

address: No.169, Changle West Road

department: School of Aerospace Medicine

institute: Air Force Medical university

summary: In summary, this study developed a mouse model for SD by combining rotational stimulation and visual occlusion. Evaluation of the model showed physiological changes, impaired motor and cognitive function, and neuronal activation in the hippocampus. Transcriptomic analysis revealed a possible underlying mechanism of SD. These findings lay a foundation for further investigation into the molecular mechanisms underlying SD.

overall_design: Vestibular spatial disorientation was stimulated by multi-axis rotation coupling in mice, and the hippocampus was immediately obtained for transcriptome sequencing


title: Smooth muscle-derived adventitial progenitor cells direct atherosclerotic plaque composition complexity in a Klf4-dependent manner

first: Mary

last: Weiser-Evans

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

summary: We previously established that vascular smooth muscle-derived adventitial progenitor cells (AdvSca1-SM) preferentially differentiate into myofibroblasts and contribute to fibrosis in response to acute vascular injury. However, the role of these progenitor cells in chronic atherosclerosis has not been defined. Using an AdvSca1-SM cell lineage tracing model, scRNA-Seq, flow cytometry, and histological approaches, we confirmed that AdvSca1-SM-derived cells localized throughout the vessel wall and atherosclerotic plaques, where they primarily differentiated into fibroblasts, smooth muscle cells (SMCs), or remained in a stem-like state. Krüppel-like factor 4 (Klf4) knockout specifically in AdvSca1-SM cells induced transition to a more collagen-enriched fibroblast phenotype compared to WT mice. Additionally, Klf4 deletion drastically modified the phenotypes of non-AdvSca1-SM-derived cells, resulting in more contractile SMCs and atheroprotective macrophages. Functionally, overall plaque burden was not altered with Klf4 deletion, but multiple indices of plaque composition complexity, including necrotic core area, macrophage accumulation, and fibrous cap thickness, were reduced. Collectively, these data support that modulation of AdvSca1-SM cells through KLF4 depletion confers increased protection from the development of potential unstable atherosclerotic plaques.

overall_design: AdvSca1-SM lineage tracing mice (Klf4 WT or KO) were treated with tamoxifen to knock in YFP reporter and flox out Klf4 (in the case of KO mice). Athero mice were given PCSK9 AAV injections at 0 and 2 weeks, then put on high fat/high cholesterol diet to induce atherosclerosis; control mice did not receive PCSK9 and were left on standard chow. 3 mice per condition were pooled, and aortic sinus, aortic arch, BCA, and carotid arteries were processed into a single cell digest. Samples were FACS sorted for YFP expression, then each sample was sequenced separately.

first: Allison

last: Dubner

first: Sizhao

last: Lu


title: Assessment of miRNA expression levels in an HCM mouse model containing mutation in Myh6 gene

city: London

first: Seda

last: Eminaga

address: Westminster Bridge Road, St Thomas's Hospital

department: Cardiovascular Division

country: United Kingdom

institute: King's College London

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Single-cell immune profiling reveals markers of emergency myelopoiesis that distinguish severe from mild respiratory syncytial virus (RSV) disease in infants

city: Leuven

first: Deniz

last: Oner

address: Gaston Geenslaan

country: Belgium

institute: KU Leuven

summary: While the majority of infants infected with respiratory syncytial virus (RSV) exhibit mild or no symptoms, approximately 3 million children under the age of five are hospitalized every year due to complications from RSV. This research sought to explore the biological processes and related biomarkers responsible for the varied manifestations of RSV disease in young infants. The goal is to pave the way for a more precise categorization of RSV-infected infants based on their medical requirements. Whole blood samples are collected from infant case-control cohort study, the RESCEU case-control cohort is a multinational, multicenter, observational study (clinical trial registration number: NCT03756766). Infants < 12 months old with RSV disease were recruited from the University Medical Center Utrecht (UMCU) in The Netherlands, Hospital Clínico Universitario de Santiago (SERGAS) in Spain, Imperial College (IMPERIAL) National Health Service Trust (NHS) and Oxford University Hospital NHS Trust (OXFORD) in the United Kingdom during the RSV seasons 2017-2018, 2018-2019, and 2019-2020. Healthy controls without underlying comorbidities were recruited outside of the RSV season.  Eligibility criteria included hospitalization for less than 48 hours at enrolment or within 96 hours of disease onset, no previous receipt of medications to treat RSV infection, no prior exposure to an investigational RSV vaccine or medication, no previous receipt of immunoglobulins or monoclonal antibodies, and had not used montelukast or oral steroids within seven days before enrolment. Infants with co-morbidities were not evaluated in the manuscript.  RSV was detected using RSV point-of-care test (POCT) by either a rapid antigen detection test (Alere I) (Alere Inc, Waltham, Massachusetts) or rapid RSV polymerase chain reaction (PCR) test at the hospital setting, or a RSV PCR test at the laboratory. Convalescence samples were collected 7 ±1 weeks after a positive RSV diagnostic test result. We used microarray to assist us to identify biomarkers for severe RSV disease.

overall_design:
Healthy infants and infants with mild (RSV-infected, non-hospitalized), moderate (RSV-infected, hospitalized without mechanical ventilation), and severe (RSV-infected, hospitalized with mechanical ventilation) RSV disease were recruited during the acute RSV infection and at convalescence. Whole blood samples were analysed using Clariom GOScreen human assay in 384 well plate format. Infants with comorbidities excluded from the downstream comparative analyses.
The clinical data necessary for batch correction (site of sample collection) is accessible by request only from the submitting party.

first: Nevena

last: Zivanovic

last: Öner

first: Yann

last: Abraham

first: Joseph

last: McGinley

first: Simon

middle: B

last: Drysdale

first: Joanne

last: Wildenbeest

first: Marjolein

last: Crabbe

first: Greet

last: Vanhoof

first: Kim

last: Thys

first: Ryan

last: Thwaites

first: Hannah

last: Robinson

first: Louis

last: Bont

first: Peter

last: Openshaw

first: Federico

last: Martinón-Torres

first: Andrew

last: Pollard

first: Jeroen

last: Aerssens


title: Assessment of miRNA expression levels in an HCM mouse model containing R403Q mutation in Myh6 gene

first: Seda

last: Eminaga

summary: We compared the expression levels of miRNAs in heart tissue from HCM vs WT mice, using gene expression profiling data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for aged WT (n=3) and HCM mutant mice (n=3).

first: Danos

last: Christodolou


title: Transcriptional Comparison of Human and Murine Retinal Neovascularization

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

summary: Background: Retinal neovascularization (RNV) as a result of retinal ischemia, such as in proliferative diabetic retinopathy (PDR) and retinopathy of prematurity (ROP), can lead to vitreous hemorrhage, tractional retinal detachment, and irreversible loss of vision if left untreated. Although panretinal laser photocoagulation and anti-vascular endothelial growth factor (VEGF) injections are efficient treatment modalities, a significant number of patients do not respond to either treatment. This clinical finding suggests that other, previously unrecognized mediators and signaling pathways may contribute to RNV development and could represent valuable targets for future treatments.  Methods: In search of phylogenetically conserved angiogenic mediators, we examined the transcriptional profile of murine RNV from C57BL/6J mice (n=14) in the oxygen-induced retinopathy (OIR) model as well as human RNV membranes from PDR patients (n=7), who had undergone vitrectomy and compared them with corresponding control tissues (n=13, 10 respectively). Genes that were differentially expressed (DEGs) between RNV and control samples were identified for human and murine samples and their associated gene ontology (GO) clusters analyzed. Lastly, human and murine DEGs were compared to identify phylogenetically conserved factors.  Findings: Transcriptional profiles of murine RNV showed that DEGs linked to the activation of the innate immune system (Msn, Cd34), extracellular matrix organisation (Col4a1, Gfap), and regulation of angiogenesis (Col4a2, Fgf2) were significantly upregulated both at the ischemic, preproliferative stage of the disease (OIR p14) as well as at the proliferative stage (OIR p17). While similar GO terms were upregulated in human RNV, only a small overlap in DEGs between both species was detected. Phylogenetically conserved mediators upregulated in both murine and human RNV included ANGPT2, S100A8, MCAM, EDNRA, MRC1, and CCR7.  Interpretation: This study identifies phylogenetically conserved inflammatory and pro-angiogenic mediators that are significantly upregulated in both murine and human RNV. Among them, MCAM, ENDRA and MRC1 emerged as the most upregulated, phylogenetically conserved DEGs not yet implicated in human RNV, thus representing potential new treatment targets for ischemic retinal diseases.

overall_design: Retinal tissue from the OIR mouse model from the following groups: nonOIR p14 (n=7), nonOIR p17 (n=6), OIR p14 (n=6), and OIR p17 (n=8).

first: Laurenz

last: Pauleikhoff

first: Stefaniya

last: Boneva

first: Myriam

last: Böck

first: Anja

last: Schlecht

first: Günther

last: Schlunk

first: Hansjürgen

last: Agostini

first: Julian

last: Wolf


title: Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_WT]

first: Fang

last: Ye

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: Chromatin accessibility and transcriptome profiling are the most critical tools in single-cell technologies. Here, we present Microwell-seq3, a high-throughput and easy-to-handle platform for high-sensitive single-nucleus chromatin accessibility or full-length gene expression profiling. The method combined pre-indexing and a dual-pass “chip-in-tube” strategy for nuclei loading and DNA amplification. Therefore, Microwell-seq3 does not require specialized equipment and is suitable for any molecular biology lab with simple consumables and thermal cycler. We applied Microwell-seq3 to profile the chromatin accessibility in more than 200,000 single nuclei and the full-length transcriptome in about 50,000 nuclei from multiple adult mouse tissues. Joint analysis of cell-type specific regulatory elements and total RNA uncovered cell type heterogeneity and differentially expressed genes in brain compared with previous polyadenylated transcripts capturing methods. Gene regulatory networks based on full-length transcriptome and chromatin accessibility provided improved cell-cell communications in neurons and glia. Finally, we applied Microwell-seq3 to comprehensively characterize malignant cells in spontaneous tumors from aging mouse.

overall_design: Single nuclei RNA-sequencing  and ATAC-sequencing for multiple tissues from normal C57BL/6 mouse (8 weeks).

first: Shuang

last: Zhang

first: Yuting

last: Fu


title: Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_Tumor]

overall_design: Single nuclei RNA-sequencing  and ATAC-sequencing for four tumor tissues from normal aging C57BL/6 mouse (18 months).


title: pH dependence of a GPR4 selective antagonist hampers its therapeutic potential

first: Jun

last: Yin

address: 4245 Sorrento Valley Blvd. I

department: Computational Biology and Data Science

institute: Ferring Research Institute

summary: Inflammatory bowel disease (IBD) is characterized by chronic mucosal inflammation of the gastrointestinal tract and is associated with extracellular acidification of mucosal tissue. Several extracellular pH-sensing receptors, including G protein-coupled receptor 4 (GPR4), play an important role in the regulation of inflammatory and immune responses and GPR4 deficiency has been shown to be protective in IBD animal models. To confirm the therapeutic potential of GPR4 antagonism in IBD, we tested Compound 13, a selective GPR4 antagonist, in the IL10-/- mouse model of colitis. Despite reasonable bioavailability, Compound 13 treatment did not improve colitis in this model and there were no signs of target engagement. Interestingly, Compound 13 behaved as an “orthosteric” antagonist, i.e., its potency was pH-dependent and mostly inactive at pH levels lower than 6.8 with preferential binding to the inactive conformation of GPR4. Mutagenesis studies confirmed Compound 13 likely binds to the conserved orthosteric binding site in G protein-coupled receptors, where a histidine sits in GPR4 likely preventing Compound 13 binding when protonated in acidic conditions. While the exact mucosal pH in the human disease and relevant IBD mice models is unknown, it is well established that the degree of acidosis is positively correlated with the degree of inflammation, suggesting Compound 13 is not an ideal tool to study the role of GPR4 in moderate-to-severe inflammatory conditions.

overall_design: Gene expression profiling analysis of RNAseq from distal colons of wildtype and IL10 knockout mice treated with Compound 13 and anti-p40

first: Jacek

last: Stalewski

first: Amy

middle: Y

last: Shih

first: Romeo

last: Papazyan

first: Jocelyn

last: Ramirez

first: Gerardo

last: Ibanez

first: Peng

last: Hsiao

first: Yong

last: Yue

first: Calen

last: Badger

first: Shije

last: Wu

first: Akemi

last: Ueki

first: Bryan

last: Fuchs

first: Marie-Laure

last: Rives


title: A gene expression atlas for oat grain – from initiation to germination

city: Bundoora

first: Mathew

middle: G

last: Lewsey

state: VIC

address: AgriBio, 5 Ring Rd

department: Animal, Plant and Soil Sciences

country: Australia

institute: La Trobe University

summary: To invistage the transcsriptome re-programming from oat grain development to germination

overall_design: Comparative gene expression profiling analysis of time-series RNA-seq data for oat grain development and germination.

first: Changyu

last: Yi

first: Marta

last: Peirats-Llobet

first: Amanda

last: Waters

first: Monika

last: Doblin

first: Tony

last: Bacic

first: James

last: Whelan


title: Transcriptome analysis of FAK inhibitor in liver cancer cell lines

city: Chong Qing

first: Xianfeng

last: Li

address: Da ping

department: Department of Gastroenterology, Daping Hospital

institute: Army Medical University (Third Military Medical University)

summary: MEF2D was involved in metastasis of liver cancer through regulation of ECM signal including FAK.

overall_design: SMMC-7721 HCC cells was treated with FAK inhibitor.

first: Junyu

last: Xiang

first: Ni

last: Zhang

first: Bin

last: Wang


title: Gene expression of immune cells in a lung cancer mouse model

city: Los Angeles

first: Tian-hao

state: CA

address: 650 Charles E Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

summary: We used in situ vaccination with autologous dendritic cell secreting CCL21, in combination with immune checkpoint inhibitor, anti-PD-1, to treat oncogene-driven non-small cell lung cancer in a murine model. The single cell transcriptome of the treated cancer tissues were measured.

overall_design: Cells were stained with Zombie-NIR LIVE/DEAD stain and CD45 antibody for 20 min a 4oC. Viable leukocytes were sorted using BD Biosceinces Aria II cell sorter with 100-mm nozzle. The 10X Genomics platform (10X Genomics, Pleasanton, CA) was utilized for assessing single-cell transcriptomic. In brief, sorted immune cells were loaded into 10X Genomics Chromium microfluidic chips with 3’ v3 chemistry to generate single-cell gelbead emulsions (GEMs).

first: Ramin

last: Salehi-rad

first: Yushen

last: Du


title: RNAseq analysis of  Human endothelial TeloHAEC in response to Estradiol, 4-hydroxytamoxifen and the cotreatment

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

country: France

institute: CNRS UMR 6290

summary: Aim: To compare the transcriptional responses to 17β-estradiol (E2), 4-hydroxytamoxifen (4-OHT)  and the cotreatment in Human endothelial TeloHAEC cells transduced with hERα-WT (hERα-WT)

overall_design: Human endothelial TeloHAEC ERα-WT (hERα-WT) mRNA profiles  treated for 6 hours with DMSO, E2, 4-OHT or the co-treatment were generated by deep sequencing using Illumina NovaSeq sequencer

first: Chanaëlle

last: Fébrissy

first: Marine

last: Adlanmerini

first: Christel

last: Péqueux

first: Coralie

last: Fontaine

first: Julie

last: Guillermet-Guibert

first: Jean-François

last: Arnal

first: Françoise

last: Lenfant


title: Enhancing aortic valve drug delivery with PAR2-targeting magnetic nano-cargoes for calcification alleviation

first: Jinyong

last: Chen


title: Photoresponsive transcriptomes changes in cry1cry2 and m6A methyltransferase mutants

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

summary: Cryptochromes are blue light receptors in plants and animals.  m6A methyltransferase FIO1 and MTA interact with CRYs, here we show the RNA-seq data of cry1cry2, fio1 and mta mutants in dark and blue light.

overall_design: RNA-seq of cry1cry2, fio1, mta

first: Bochen

last: Jiang

first: Xu

first: Chentao

last: Lin


title: Microenvironmental CXCL12 Deletion Enhances Flt3-ITD Acute Myeloid Leukemia Stem Cell Response to Therapy by Reducing p38 MAPK Signaling

city: Birmingham

first: Nicholas

last: Anderson

state: AL

address: 1824 S 6th Ave

institute: University of Alabama at Birmingham

summary: Fms-like tyrosine kinase 3 (Flt3) tyrosine kinase inhibitors (Flt3-TKI) have improved outcomes for patients with Flt3-mutated acute myeloid leukemia (AML) but are limited by resistance and relapse, suggesting persistence of leukemia stem cells (LSC). Here we utilized a Flt3-internal tandem duplication (Flt3-ITD) and Tet2-deleted AML genetic mouse model to characterize Flt3-ITD AML LSC and their resistance to Flt3-TKI. We show that LSC were enriched within the primitive ST-HSC population. CXCl12-expressing osteoprogenitors were increased in the Flt3-ITD AML marrow and FLT3-ITD LSC showed increased expression of the CXCL12 receptor CXCR4. CXCL12 deletion from the microenvironment enhanced AML targeting by combined Flt3-TKI and chemotherapy treatment with enhanced LSC targeting. We found that both treatment and CXCL12 deletion partially reduced p38 mitogen-activated protein kinase (p38) signaling with increased, but not complete, reduction seen with combined treatment and CXCL12 deletion. Our studies suggest that p38 contributes to CXCL12-mediated maintenance of AML LSC following Flt3-TKI and chemotherapy treatment, but that p38 inhibition enhances AML LSC response to treatment to a greater extent than CXCL12 deletion alone. This study supports a role for p38 signaling in CXCL12-mediated protection of AML LSC from treatment and provide a rationale for targeting p38 signaling to enhance Flt3-ITD AML targeting.

overall_design: FACS-sorted ST-HSC were isolated from CXCL12 WT or CXCL12 KO mice transplanted with Flt3-ITD TET2 KO AML bone marrow then treated with either vehicle controls or combination cytarabine, doxorubicin, and quizartinib

first: Hui

last: Li

first: Mason

middle: W

last: Harris

first: Shaowei

last: Qiu

first: David

last: Crossman

first: Harish

last: Kumar

first: Vipul

last: Sheth

first: Puneet

last: Agarwal

first: Takashi

last: Nagasawa

first: Andrew

last: Paterson

first: Robert

last: Welner

first: Ravi

last: Bhatia


title: Comparative Analysis of Methods to Reduce Activation Signature Gene Expression in PBMCs

city: Montreal

first: Martine

last: Tetreault

state: QC

address: 900 Rue Saint-Denis

institute: CRCHUM

summary: Preserving the in vivo cell transcriptome is essential for accurate profiling, yet factors during cell isolation including time ex vivo and temperature induce artifactual gene expression, particularly in stress-responsive immune cells. In this study, we investigated two methods to mitigate ex vivo activation signature gene (ASG) expression in peripheral blood mononuclear cells (PBMCs): transcription and translation inhibitors (TTis) and cold temperatures during isolation. Comparative analysis of PBMCs isolated with and without TTis revealed reduced ASG expression. However, TTi treatment impaired responsiveness to LPS stimulation in subsequent in vitro experiments. In contrast, cold isolation maintained experimental flexibility while similarly down-regulating ASG expression compared to TTis. Notably, addition of TTis during cold isolation offered minimal additional advantages. Thus, while both TTis and cold isolation effectively reduced ASG expression, we found cold isolation to be a more practical approach.

overall_design:
To study activation signature gene mitigating protocols for blood mononucleated cells (PBMCs), we isolated and treated PBMCs in different experimental conditions.
Gene expression profiling was performed from patient-derived peripheral blood mononucleated cells (PBMCs) to compare two activation signature gene-mitigating cell isolation protocols; addition of transcription and translation inhibitors or cold temperature.
Transcriptomic signatures were also compared from time-point thaw samples from PBMCs isolation using a standard protocol at room temperature and incubated in vitro for 0, 2, or 24 hours.

first: Lovatiana

last: Andriamboavonjy

first: Adam

last: MacDonald

first: Laura

last: Hamilton

first: Marjorie

last: Labrecque

first: Jason

last: Karamchandani

first: Jo

middle: A

last: Stratton


title: Establishing mRNA and miRNA interactions driving disease heterogeneity in ALS patient survival (microarray)

city: SHEFFIELD

first: Rachel

last: Waller

state: South Yorkshire

address: SITraN, 385A Glossop Road

department: Neuroscience

institute: The University of Sheffield

summary:
Transcriptomic analysis of lymphoblastoid cell lines from ALS patients with varying disease duration
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease, associated with the degeneration of both upper and lower motor neurons of the motor cortex, brainstem and spinal cord. Death in most patients results from respiratory failure within 3-4 years from symptom onset. However, due to disease heterogeneity some individuals survive only months from symptom onset while others live for several years. Identifying specific biomarkers that aid in establishing disease prognosis, particularly in terms of predicting disease progression, will help our understanding of ALS pathophysiology and could be used to monitor a patient’s response to drugs and therapeutic agents.  Transcriptomic profiling technologies are continually evolving, enabling us to identify key gene changes in biological processes associated with disease. MicroRNAs (miRNAs) are small non-coding RNAs typically associated with regulating gene expression, by degrading mRNA or reducing levels of gene expression. Being able to associate gene expression changes with corresponding miRNA changes would help to distinguish a more complex biomarker signature enabling us to address key challenges associated with complex diseases such as ALS.

overall_design: The present study aimed to investigate the transcriptomic profile (mRNA and miRNA) of lymphoblastoid cell lines (LCLs) from ALS patients to identify key signatures that are distinguishable in those patients who suffered a short disease duration (< 12 months) compared to those that had a longer disease duration (>6 years). Affymetrix Human Exon 1.0ST GeneChip microarrays were used to assess mRNA/gene changes, while small RNA sequencing of miRNA extracted from peripheral LCL’s from ALS patients with short and long disease was performed using the Illumina TruSeq Small RNA library preparation kit and Illumina HiScanSQ.

first: Joanna

last: Bury

first: Charlie

last: Appleby-Mallinder

first: Matthew

last: Wyles

first: George

last: Loxley

first: Aditi

last: Babel

first: Saleh

last: Shekari

first: Mbombe

last: Kazoka

first: Helen

last: Wolff

first: Paul

last: Heath

first: Pamela

last: Shaw

first: Janine

last: Kirby


title: Establishing mRNA and miRNA interactions driving disease heterogeneity in ALS patient survival (miRNA-Seq)

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease, associated with the degeneration of both upper and lower motor neurons of the motor cortex, brainstem and spinal cord. Death in most patients results from respiratory failure within 3-4 years from symptom onset. However, due to disease heterogeneity some individuals survive only months from symptom onset while others live for several years. Identifying specific biomarkers that aid in establishing disease prognosis, particularly in terms of predicting disease progression, will help our understanding of ALS pathophysiology and could be used to monitor a patient’s response to drugs and therapeutic agents.  Transcriptomic profiling technologies are continually evolving, enabling us to identify key gene changes in biological processes associated with disease. MicroRNAs (miRNAs) are small non-coding RNAs typically associated with regulating gene expression, by degrading mRNA or reducing levels of gene expression. Being able to associate gene expression changes with corresponding miRNA changes would help to distinguish a more complex biomarker signature enabling us to address key challenges associated with complex diseases such as ALS.  The present study aimed to investigate the transcriptomic profile (mRNA and miRNA) of lymphoblastoid cell lines (LCLs) from ALS patients to identify key signatures that are distinguishable in those patients who suffered a short disease duration (< 12 months) compared to those that had a longer disease duration (>6 years). Transcriptional profiling of miRNA-mRNA interactions from LCL’s in ALS patients revealed dysregulation of genes involved in cell cycle, DNA damage and RNA processing in patients with longer survival from disease onset compared to those with short survival.   Understanding these particular miRNA-mRNA interactions and the pathways in which they are involved may help to distinguish potential therapeutic targets that could exert neuroprotective effects to prolong the life expectancy of ALS patients.


title: Oxidative Stress-initiated One-carbon Metabolism drives Interleukin-10-producing B Cells to Resolute Pneumonia (ATAC-Seq)

city: shanghai

first: Ying

last: Fu

address: Dongan road

institute: Fudan university

summary: Metabolic reprogramming for regulatory B cell generation in infectious diseases remains unknown. With a Pseudomonas aeruginosa-induced pneumonia model, we report IL-10-producing B cells (IL-10+B cells) are indispensable for spontaneous remission of the infection. The accumulation of cytosolic reactive oxygen species (ROS) is responsible for the IL-10 producing within B cells. Of note, ROS scavenging downregulated the one-carbon metabolism and the depletion of one-carbon metabolic methyl transfer enzyme serine hydroxymethyl transferase 1 (Shmt1) led to decreased IL-10+ B cells production both in vitro and in vivo. Mechanistically, one-carbon flux enhanced the availability of methyl groups, which altered histone H3 lysine 4 methylation at Il10 loci and led to massive IL-10 production in B cells. Therefore, the metabolic-associated drug ethacrynic acid (EA) was screened out and potentially restored infectious pneumonia accompanied by increased IL-10+ B cells. The results provide a new insight that ROS serve as modulators to resolute inflammation by reprogramming one-carbon metabolism in lung B cells.

overall_design: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed to show the accessibility in the Il10 loci iunder the ROS scavenging condition. Splenic B cells were isolated and cultured under correspondent stimulations after 24h (αIgM, αIgM+LPS, αIgM+LPS+NAC, the cells from multiple mice were pooled together). 1 × 107 experimental and control groups cells were individually collected, normalized to ATAC-seq assay. ATAC-seq was performed as previously described (Buenrostro et al., 2013) at Shanghai Jiayin Biotechnology Co., Ltd. (Shanghai, China).

first: Baichao

last: Yu

first: Qi

last: Wang

first: Zhou

last: Lu

first: Hushan

last: Zhang

first: Dan

first: Feifei

last: Luo

first: Ronghua

last: Liu

first: Luman

first: Yiwei

last: Chu


title: Differential microRNA editing may drive target pathway switching in human temporal lobe epilepsy

city: Dublin 2

first: Kelvin

middle: E How

last: Lau

state: Dublin

address: York House, 31A, York Street, Dublin 2

department: Medical Physics & Physiology

country: Ireland

institute: Royal College of Surgeons in Ireland (RCSI)

summary: Transcriptional profiling of human-iPSC derived neurons treated with antimir-edited-miR-376a-3p at site +6 (Anta-E), antimir-native-miR-376a-3p (Anta-N) and scramble (Scr)

overall_design: Three-condition experiment, Scramble (control) vs. Antamir-E-miR-376a-3p, Scramble (control) vs.  Antimir-N-miR-376a-3p, and Antimir-E-miR-376a-3p vs. Antimir-N-miR-376a-3p. Biological replicates: 8 scramble (controls), 8 antagmir-E-miR-376a-3p, and 8 antimir-N-miR-376a-3p . Each biological replicate is human-iPSC derived neurons that have been differentiated for 30 days. Neurons were transfected with 300 nM of scramble,  anta-E or anta-N for 48 hours, and later subjected to RNA extraction for transcriptome analysis.

first: David

last: Henshall

first: Elena

last: Langa


title: Skeletal muscle and plasma microRNA profiling among patients with gastrointestinal cancer

city: Torino

first: Giovanni

last: Birolo

state: TO

address: Via Santena 19

department: Medical Sciences

country: Italy

institute: University of Turin

summary: We profiled microRNAs and other small non-coding RNAs in skeletal muscle and plasma samples obtained from gastrointestinal cancer patients and controls and evaluated the association of differentially expressed small non-coding RNAs with the level of muscularity.

overall_design: Small non-coding RNA profiling using a next-generation sequencing approach.

first: Alessio

last: Molfino

first: Marc

last: Beltrà

first: Maria

middle: I

last: Amabile

first: Roberta

last: Belli

last: Belloni

first: Serena

last: De Lucia

first: Lorena

last: Garcia-Castillo

last: Imbimbo

first: Giuseppe

last: Nigri

first: Barbara

last: Pardini

first: Paola

last: Costelli

first: Maurizio

last: Muscaritoli


title: RNA sequence analysis of mouse retina samples obtained from ApoE-/- mice infused with Ang II or saline

city: Beijing

first: Lihui

last: Meng

address: Dongcheng Strict

institute: Peking Union Medical College Hospital

summary: To investigate the molecular mechanisms of the role of Ang II in retina artery changes, we conducted the transcriptomic analysis of RNA-seq of retnas isolated from ApoE-/- mice infused with Ang II or saline to identify differentially expressed genes.

overall_design: Comparison of mouse retina samples obtained from ApoE-/- infused with Ang II and saline.

first: Shiyu

last: Cheng

first: Xinyu

last: Zhao

first: Youxin

last: Chen


title: Single-Cell Transcriptome Analysis Identifies Key Components of Tumor Microenvironment for Extranodal Natural Killer/T-cell lymphoma

city: Guangzhou

first: Jinxin

last: Bei

state: Guangdong

address: No. 651, Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

summary: Extranodal natural killer/T-cell lymphoma (NKTCL) is an aggressive Epstein-Barr virus (EBV)-associated lymphoma with heterogeneous tumor behaviors and clinical outcomes. Here, we profiled tumor microenvironment (TME) of NKTCL through single-cell transcriptome analysis of 137,304 cells from 10 tumor-blood pairs. We identified six malignant subtypes with diverse transcriptional signatures, among which LMP1+ NK_C9_CXCL13 was characterized with oncogenic and immunosuppressive potentials as well as an axial role in malignant transformation. Moreover, ligand-receptor analyses and multiplex immunofluorescent staining assays revealed intensive interactions among malignant NK, tumoral myeloid, and T cells, fostering immunosuppressive TME in NKTCL. Furthermore, co-culture assays revealed that malignant cells induced the development of immunosuppressive and pro-tumorigenic tumor-associated macrophages (TAMs) through high expression of CSF1 and hampered the recruitment of normal NK cells through broad secretion of a dipeptidylpeptidase DPP4 in NKTCL. Lastly, we revealed the inter-patient heterogeneity of NKTCL with distinct EBV transcription and TAM infiltration in multiple patient cohorts, of which high and low were favorable prognostic indicators for NKTCL patients, respectively. Collectively, for the first time to our knowledge, our study dissects the heterogeneous composition of NKTCL TME at single-cell resolution, which provides insights into understanding the pathogenic mechanisms of NKTCL and developing novel therapeutic strategies against NKTCL.

overall_design:
We performed single-cell RNA sequencing on patients with NKTCL and obtained 137,304 cells from 10 tumor-blood pairs. Raw data will be uploaded to China Genomic Sequence Archive (GSA), according to the Regulations on the Management of Human Genetic Resources in China, and we will provide the accession number once the paper is accepted.
Note from submitter: Considering the law due to human patient privacy concerns from the human genetics resources department of China, raw data will be uploaded to GSA-human database.

first: Yiqi

last: Li

first: Chunling

last: Luo

first: Shuai

last: He

first: Yang

last: Liu

first: Jiaxin

last: Jiang

first: Roujun

last: Peng


title: A dual role for CDK-Mediator in controlling Polycomb-dependent topology and priming genes for induction [Hi-C]

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Precise control of gene expression is essential for normal development. This is thought to rely on mechanisms that enable communication between gene promoters and other regulatory elements. In embryonic stem cells (ESCs) the CDK-Mediator (CDK-MED) complex has been reported to topologically link gene regulatory elements to enable gene expression and also prime genes for induction during differentiation. Here we discover that CDK-MED contributes little to overall genome organisation in ESCs, but interestingly has a specific and essential role in controlling interactions between inactive gene regulatory elements bound by the Polycomb repressive complexes (PRCs). These interactions are facilitated by CDK-MED but rely on canonical PRC1. However, through separation of function experiments, we reveal that the collaboration between CDK-MED and cPRC1 in creating long-range interactions does not function to prime genes for induction during differentiation. Instead, we discover that priming relies on a topology-independent mechanism whereby the CDK module supports core Mediator engagement with gene promoters to support gene activation.

overall_design: Pofile of genomic distribution of Polycomb (canonical PRC1 and H3K27me3), CDK-Mediator (CDK8) and core Mediator (MED14) was profiled in Med13/13l fl/fl ESCs, in which the CDK-Mediator can be conditionally depleted. Pofile of genomic distribution of CDK-Mediator (CDK8) was profiled in Pcgf4-/-Pcgf2 fl/fl ESCs, in which the canonical PRC1 can be conditionally depleted.

first: Robin

middle: H

first: Robert

last: Klose


title: Transcriptomic characterization of colon smooth muscle in young murine.

city: Shanghai

first: Fan

last: Yang

address: No. 1954, Huashan Road

department: Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders

institute: Bio-X Institutes, Shanghai Jiao Tong University

summary: The enteric nervous system (ENS) and SIP (Smooth muscle cells-Interstitial cells of Cajal-PDGFRα+ cells) syncytium play an important role in controlling gastrointestinal motility. This study aimed to investigate the dynamic regulatory mechanisms of the ENS-SIP system on colon motility during postnatal development. Colonic samples of postnatal 1 week (PW1), PW3, and PW5 old murine were characterized by RNA sequencing, qRT-PCR, and immunoblotting. The current study showed that ENS and glial cells including ICCs and PDGFRα+ cells become increasingly mature in both the postnatal proximal and distal colon. The transcriptional expression of Pdgfrα, c-Kit, P2ry1, Nos1, and Slc18a3, and the protein expression of nNOS, c-Kit, and ANO1 significantly increased with age. In conclusion, during postnatal development, molecular data demonstrated the gradual maturation of ICC and PDGFRα+ cells, including nitrergic and cholinergic nerves and purinergic receptors. Our findings are important in understanding the role of ENS and interstitial cells with specific receptors for the generation of mature colonic migrating motor complexes in young murine colons.

overall_design: There are three groups included in this study, PW1, PW3 and PW5. Three biological replicates (i.e. 3 animals) were used in each group. And, PW1 samples were used as controls.

first: FAN

first: Qian-qian

last: Wang

first: Zhi-hao

last: Wu

first: Peng

first: Jian-feng

first: Jun

first: Shi-jiao

last: Lu

first: Xiao-fang

last: Sun

first: Brian

last: Perrino

first: Jie


title: Genome-wide transcriptome analysis of GOS2:NF-YA5-GR transgenic rice after DEX treatment

city: Pyeongchang

first: Jun Sung

last: Seo

state: Gangwon

address: Pyeongchangdaero 1447

department: Company-affiliated research institute

institute: LaSemilla Co. Ltd.

summary:
Purpose: The goals of this study are screening the putative target genes regulated by OsNF-YA5 using DEX(dexamethason) inducible system.
Methods: 10-day-old GOS2::OsNF-YA5-GR plants grown on MS solid media were treated with 50 μM dexamethasone (DEX) solution containing 0.02% (w/v) Silwet L-77. For mock treatments, 0.02% Silwet L-77 was sprayed into rice plants. To minimize the effect by the treatment, plants were pre-treated with 0.02% Silwet L-77 3 hours before DEX treatment). Total RNAs were extracted using the RNeasy plant mini kit (Qiagen, USA) according to the manufacturer’s instruction. cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (v2) (Macrogen, Korea). Single-end sequences were obtained using IRGSP (v 1.0) and raw sequence reads were trimmed to remove adaptor sequence, and those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software (Bolger et al., 2014). To map the reads to reference genome, all reads were assembled with annotated genes from the Rap-DB database [http://rapdb.dna.affrc.go.jp; IRGSP (v 1.0)] using TopHat software (https://ccb.jhu.edu/software/tophat/index.shtml). After mapping reads to a reference genome, differentially expressed genes (DEGs) were selected using a cut-off change of at least 2-fold change (DEX/mock) and Student’s t-test (P < 0.1). The selected DEGs were grouped by hierarchical clustering analysis (Complete Linkage).
Results: RNA sequencing analysis revealed that 81 (3 hr DEX treatment) and 88 (9 hr DEX treatment) genes were up-regulated. In comparison, 61 (3 hr DEX treatment) and 45 (9 hr DEX treatment) genes were down-regulated in GOS2:OsNF-YA5-GR transgenic plants by DEX treatment compared to mock treatment. Among 161 up-regulated genes, 71 genes (44%) were also up-regulated in N starvation conditions. GO term analysis of up-regulated genes revealed that 59-76% of genes were involved in the metabolic process, and 10%-12% were transporter (Extended Data Fig. 4c). These results suggested that OsNF-YA5 regulated the genes involved in the metabolic process.
Conclusions: OsNF-YA5 positively regulated the genes involved in the nitrogen metabolic process including amino acid and nitrate/peptide transporters.

overall_design: mRNA profiles of 10-day-old GOS2::OsNF-YA5-GR plants grown on MS solid media after 50 μM DEX or mock treatment.

first: Ju-Kon

last: Kim


title: Establishing mRNA and microRNA interactions driving disease heterogeneity in Amyotrophic lateral sclerosis

first: Rachel

last: Waller

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

overall_design: Refer to individual Series


title: Identification of Key Genes Associated with Macrophage Autophagy in ApoE-/- Mice Atherosclerosis by Aortic Gene Expression Profile

city: JiNan

first: Meirong

last: Zhu

address: NO. 105  Jiefang Road

institute: Jinan Central Hospital

summary: This study aimed to investigate genes associated with the development of atherosclerosis in the aorta of ApoE-/- mice

overall_design: Eight-week-old ApoE-/- mice were fed either a normal purified laboratory or Western Diet for 6 or 22 weeks. High-throughput sequencing technology was used to analyze the transcriptome of four groups of aorta under each experimental condition.

first: Tongyu

last: Jin

first: Aihua

first: Shanchao

last: Zhang


title: RPL8 extensively regulates the expression and alternative splicing of cancer-related genes

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: Objective: In our study, we aimed to explore the molecular mechanism of RPL8 in tumors by analyzing over-expression of RPL8  in  HeLa  cells.   Method: Two experimental  groups and control groups were setup. The experimental groups adopted Hela cells transfected by RPL8 plasmid ,  and  the  control  group  used  the  Hela  cells  transfected by blank  plasmid. The  total  mRNA  of  the  cells  were extracted  after  transfection for 48  hours and the expression  level  of  mRNA was detected by using high-throughput  sequencing  technology.  Then R Bioconductor  software  package  edgeR  was  used  to  screen  differentially  expressed genes and TopHat2 was used to analyze the splice site of each sample. Finally, GO and KEGG  analysis  of  differentially  expressed  genes  and  differential  alternative splicing events were performed, and the top ten functional pathways were selected for  display.    Results: Overexpression  of  RPL8  produced  a  large  number  of differentially expressed genes and differential alternative splicing. Many of these differentially  expressed  genes  and  differential  alternative  splicing  genes were enriched in tumor-related pathways, including inflammation, positive regulation of cell proliferation , Angiogenesis, etc. In addition, many of these differentially expressed  genes  have  been  shown  to  be  closely  related  to  the  occurrence  and development  of  tumors.    Conclusion: RPL8  can  widely  regulate  the  expression  and alternative splicing of tumor-related genes.

overall_design: Detecting the expression level of differential genes and alternative splicing after RPL8 overexpression in HeLa cells,

first: Yang

last: Gui

first: Tian

last: Zheng


title: Transcriptome analysis revealed key genes and pathways of nitrate in the prevention of hypoxia-induced small intestinal epithelial injury

status: Public on Jan 02 2024

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Our study helps to understand the transcriptome level changes in small intestines exposed to hypoxia after nitrate supplementation, to find out which genes or signaling pathways nitrate plays a role in by activating or inhibiting them.

overall_design: In this study, we isolated small intestine from wild mice exposed to hypoxia (7%O2) for 7 days(Hypoxia) and gave them 4mM nitrate supplementation(Hypoxia+Nitrate). The Hypoxia group and the Hypoxia+Nitrate group (4 samples each) were subjected to RNA sequencing.

first: Yifan

last: Xu

first: Jian

last: Zhou

first: Songlin


title: Integrated multi-omics analysis for non-smoking female lung adenocarcinoma in Xuanwei, China

city: kunming

first: guanjian

last: Li

address: 519 Kunzhou Road

institute: Yunnan Cancer Hospital

summary: Xuanwei lung cancer (XWLC) is well-known for its high incidence and mortality, especially among non-smoking female patients. However, the molecular mechanism is still unclear. Here, we performed a comprehensive transcriptomic, proteomic, and phosphoproteomic characterization of tumors and matched normal adjacent tissues from three non-smoking female XWLC patients with lung adenocarcinoma (LUAD). Integrated transcriptome and proteome analysis revealed dysregulated molecules and pathways in tumors and identified enhanced metabolic-disease coupling. Non-coding RNAs were widely involved in post-transcriptional regulatory mechanisms to coordinate the progress of LUAD, and also partially explained the molecular differences between RNA and protein expression patterns. Phosphoproteome provided evidence support for new phosphate sites, reporting the potential roles of core kinase family members and key kinase pathways involved in metabolism, immunity, as well as homeostasis. In addition, by comparing with the previous large-scale LUAD researches, we emphasized the higher degree of oxidative phosphorylation (OXPHOS) in Xuanwei LUAD, and pointed that VIPR1 deficiency aggravated immune dysfunction. Overall, our integrated multi-omics analysis provided a powerful resource for a systematic understanding of the molecular structure of XWLC and proposed therapeutic opportunities based on redox metabolism and immune cell infiltration.

overall_design: To reveal the mechanism of XWLC, we performed transcriptome, proteome, and phosphoproteome of the tumors and adjacent tissues of three non-smoking female lung adenocarcinoma patients in Xuanwei City.

first: Guangjian

first: Chunlin

last: Gao

first: Ying

last: Chen


title: Gene expression profiles in the inner ears of Fscn2 knockout mice compared with the control mice

city: Yantai

first: Wenjing

last: Shang

state: Shandong

address: NO.346 Guanhai Road

institute: Binzhou Medical University

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

summary: Fscn2-/- mouse is a typical model of age-related hearing loss which exhibits progressive hearing impairment and outer hair cell loss from 3 weeks of age. To investigate the molecular mechanism of hearing loss in Fscn2 knockout mice, gene expression profiling was performed on the inner ears for Fscn2+/+ and Fscn2-/- mice at 8 weeks of age using microarray analysis. Hearing screening tests at 8 weeks of age showed that the auditory brainstem response thresholds of Fscn2-/- mice were increased to 70-75 dB SPL at stimuli of click, while those of Fscn2+/+ mice were within the normal range(< 55 dB SPL). Microarray analysis identified a total of 244 differentially expressed mRNAs, including 72 upregulated and 172 downregulated genes, and a total of 688 differentially expressed lncRNAs, including 300 upregulated and 388 downregulated genes in Fscn2-/- mice, compared to Fscn2+/+ mice.

overall_design: Gene expression profiling was performed on the inner ears for 3 Fscn2+/+ mice and 3 Fscn2-/- mice at 8 weeks of age using Agilent Mouse lncRNA Microrray V3. Hearing screening tests at 8 weeks of age showed that the auditory brainstem response thresholds of Fscn2-/- mice were increased to 70-75 dB SPL at stimuli of click, while those of Fscn2+/+ mice were within the normal range(< 55 dB SPL).

first: Fengchan

last: Han

last: Ma

first: Ting


title: Endocannabinoid biosynthetic enzymes regulate pain response via LKB1-AMPK signaling

city: Charlottesville

first: Dina

last: Bai

state: VA

address: McCormick Rd.

department: Chemistry

institute: University of Virginia

summary: Diacylglycerol lipase-beta (DAGLB) serves as a principal 2-arachidonoylglycerol (2-AG) biosynthetic enzyme regulating endocannabinoid and eicosanoid metabolism in immune cells including macrophages and dendritic cells. Genetic or pharmacological inactivation of DAGLb ameliorates inflammation and hyper-nociception in preclinical models of pathogenic pain. These beneficial effects have been assigned principally to reductions in downstream pro-inflammatory lipid signaling, leaving alternative mechanisms of regulation largely underexplored. Here, we apply quantitative chemical- and phospho-proteomics to discover that disruption of DAGLb in primary macrophages leads to LKB1-AMPK signaling activation, resulting in reprogramming of the phosphoproteome and bioenergetics. Notably, AMPK inhibition reversed the antinociceptive effects of DAGLb blockade, thereby directly supporting DAGLβ-AMPK crosstalk in vivo. Our findings uncover signaling between endocannabinoid biosynthetic enzymes and ancient energy sensing kinases to mediate cell biological and pain responses.

overall_design: Test the mRNA levels in DAGLB KO and WT cells. Both cells were further stimulated with LPS (PBS as vehicle). Cell resources are bone marrow derived macrophages from DAGLB WT and KO mice.


title: Tmprss2 maintains epithelial barrier integrity and transepithelial sodium transport

city: Lausanne

first: Muriel

last: Auberson

address: Bugnon 27

department: Department of Biomedical Sciences

country: Switzerland

institute: Université de Lausanne

summary: Membrane-bound serine proteases are well known regulators of ENaC. More recently, they have also been identified as regulators of tight junction complexes. Here, we demonstrate that within the kidney, the serine protease Tmprss2 is co-expressed with the alpha subunit of ENaC, whereas Furin is primarily expressed in ENaC-negative cortex cells. In mCCDcl1 kidney cells, aldosterone-induced ENaC and Scnn1a-specific overexpression is accompanied by increased Tmprss2 gene expression, whereas Scnn1a silencing does not alter Tmprss2 transcription, suggesting that ENaC depends on Tmprss2 expression. This was confirmed by CRISPR-Cas9 Tmprss2 knockout which significantly downregulates Scnn1a gene and protein expression, and thus ENaC-mediated transepithelial sodium transport. Additionally, RNA sequencing analyses unveiled a drastic downregulation in EpCAM and claudin-3 and -7 gene expression, resulting in reduced protein expression also confirmed by immunocytochemistry. In summary, our data clearly demonstrates that the serine protease Tmprss2 is important in maintaining the epithelial tight junction barrier, in addition to regulating ENaC function via Scnn1a expression.

overall_design: mRNA was harvested from three sequential passages, in triplicate, from two single control mCCDcl1 cell clones and two Tmprss2 knockout clones generated by CRISPR-Cas9.

first: Olivia

last: Rickman

first: Emma

last: Guignard

first: Thomas

last: Chabanon

first: Giovanni

last: Bertoldi

first: Edith

last: Hummler


title: RNA sequencing of low grade neuroepithelial tumors associated with epilepsy

city: Tokyo

first: Satoshi

last: Miyashita

address: 4-1-1, Ogawahigashimachi, Kodaira

department: Institute of Neuroscience

institute: National Center of Neurology and Psychiatry

summary: Low grade neuroepithelial tumor is the major cause of epilepsy Low-grade neuroepithelial tumors are major causes of drug-resistant focal epilepsy. The BRAF V600E mutation is frequently observed in low grade neuroepithelial tumor and linked to poor seizure outcomes. However, its molecular role in epileptogenicity remains elusive. To understand the molecular mechanism underlying the epileptogenicity in LEAT with the BRAF V600E genetic mutation (BRAF V600E-LEAT), we conducted RNA sequencing (RNA-seq) analysis using surgical specimens of BRAF V600E-LEAT obtained and stored at a single institute. bioinformatics analysis using this dataset identified 2,134 differentially expressed genes between BRAF V600E-LEAT and control. Additionally, gene set enrichment analysis provided novel insights into the association between estrogen response-related pathways and the epileptogenicity of BRAF V600E-LEAT patients.

overall_design: We performed bulk RNAseq analysis using surgical specimens of 21 BRAF V600E-LEAT and 4 controls. All specimens were taken and stored in a single institute.

first: Keiya

last: Iijima

first: Shinichiro

last: Taya

first: Masaki

last: Iwasaki

first: Mikio

last: Hoshino


title: Semaglutide reduces tumor burden in the GAN diet-induced obese and biopsy-confirmed mouse model of NASH-HCC with advanced fibrosis

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

summary: We applied RNA sequencing (RNA-seq) to study the gene expression profile in the liver of GAN DIO-NASH-HCC mice (non-tumorous tissue samples, n=9; tumor samples, n=9) and chow-fed controls (healthy liver samples, n=5)). Comparing tumour tissue of GAN DIO-NASH-HCC mice to healthy chow-fed controls, we find that tumors of GAN DIO-NASH-HCC mice show widespread regulations of genes associated with human HCC. Human HCC can be classified into three categories (S1-S3). Using the human S1-S3 gene classification described by Hoshida Y. et al. (2009), we find that GAN DIO-NASH-HCC tumors resemble the human S1 class of proliferating HCC tumors with poor prognosis.

overall_design: RNA-seq of poly A-enriched RNA isolated from GAN DIO-NASH-HCC mice (non-tumorous tissue samples, n=9; tumour samples, n=9) and chow-fed controls (healthy liver samples, n=5)).

first: Martin

middle: R

last: Madsen

first: Maja

last: Andersen


title: USP13 Drives Lung Squamous Cell Carcinoma via Switching Lung Club Cell Lineage Plasticity

city: Washington

first: Juntae

last: Kwon

state: Dristrict of Colombia

address: 3970 Reservoir Rd NW

country: USA

institute: Georgetown University

summary: Lung squamous cell carcinoma (LUSC) is associated with high mortality and limited targeted therapies. USP13 is one of the most amplified genes in LUSC, and yet its role in lung cancer is largely unknown. Here, we establish a novel mouse model of LUSC by overexpressing USP13 in KrasG12D/+; Trp53flox/flox background (KPU). KPU model faithfully recapitulates the key pathohistological, molecular features, and cellular pathways of human LUSC. We found that USP13 altered lineage-determining factors such as NKX2-1 and SOX2 in club cells (CC10+) of the airway and reinforced the fate of club cells to squamous carcinoma development. We also showed a strong molecular association between USP13 and MYC, leading to the upregulation of squamous programs in murine and human lung cancer cells. Collectively, our data demonstrate USP13 as a molecular driver of lineage plasticity in club cells and provide mechanistic insight that may have potential implications for the treatment of NSCLC.

overall_design: To analyze the function of USP13 in lung cancer development, we established  lung cancers from KP and KPU mice by intratracheal injection of Ad5-CMV-Cre virus

first: Cecil

last: Han


title: Collagen I and fibromodulin induce tenogenic differentiation of hASCs

first: Tian

last: Tu

address: 639 Zhi Zao Ju Road

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: Collagen I and fibromodulin, which was immobilized on PLCL nanoyarn,  induced tenogenic differentiation of hASCs

overall_design: control versus COL1+Fmod

first: Tu

last: Tian

first: Wang

last: Wenbo

first: Wu

last: Jinglei

first: Liu

last: Wei


title: Transcriptome reprogramming through alternative splicing triggered by apigenin drives cell death in triple negative breast cancer

city: East Lansing

first: Andrea

last: Doseff

state: Michigan

address: 4153 BPS, 567 Wilson Rd

department: BPS

institute: Michigan State University

summary: Apigenin reprogrammes the transcriptome of TNBC through alternative splicing thereby exerting anti-proliferative and pro-apoptotic activities. Our findings underscore the potential impact of nutraceuticals for improved TNBC prevention and treatment.

overall_design: Comparative alternative splciing analyses of RNA-seq data for triple negative breast cancer MDA-MB-231 cells treated with vehicle or apigenin (DMSO, Api). Twp biological replicates analyzed for both conditions.

first: Daniel

last: Arango


title: GPNMB+Gal-3+ Hepatic Parenchymal Cells Promote Immunosuppressive Microenvironment Formation and Hepatocellular Carcinogenesis.

first: qiudong

last: zhao

address: 225 Changhai Road

department: Tumor Immunology and Gene Therapy Center

institute: Shanghai Eastern Hepatobiliary Surgery Hospital

summary: Hepatocellular carcinoma (HCC) involves a multistep pathological process in which heterogenous cells are evolved to shape an immunosuppressive microenvironment. Yet it remains largely unknown regarding the specific cell populations and their evolving routes essential for HCC development. Here, we created a rat model mimicking human HCC and generated a single-cell resolution atlas to HCC development. Specifically, we identified three populations of hepatic parenchymal cells during HCC progression, i.e., metabolic hepatocyte (HC Meta ), hepatic progenitor cell-like population with differentiation potential (HPC-like Diff ) and immunosuppressive malignant transformation subset (H-M Immu ). These three distinct subpopulations formed an oncogenic trajectory depicting a dynamic landscape of hepatocyte carcinogenesis, with signature genes reflecting the transition from HPC-like Diff to H-M Immu . Cross-species comparative analysis further revealed the H-M Immu subset to be highly conserved. Importantly, the H-M Immu (GPNMB + Gal-3 + ) cells exhibit both malignant and immunosuppressive properties. Moreover, SOX18 was found to be required for the generation of GPNMB + Gal-3 + H-M Immu cells and for their ability to form tumors. Enrichment of GPNMB + Gal-3 + H-M Immu subset was found to be associated with poor prognosis and higher rate of recurrence for HCC patients. Collectively, we unraveled the single-cell evolving mechanism of HCC and uncovered GPNMB + Gal-3 + H-M Immu cells as a major subset contributing to the immunosuppressive microenvironment and HCC malignance

overall_design: Rats treated with DEN up to 16 weeks

first: Yan

last: Meng

first: Qiudong

last: Zhao

last: Sang

first: Jianping

last: Liao


title: Functional and molecular impact of triamcinolone acetonide on primary human bone marrow mesenchymal stem cells

city: Huddinge

first: HONG

last: QIAN

state: Stockholms Lan

address: Neo, HERM, Floor 7, Hälsovägen 7,

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

summary: Joint pain, either traumatic or degenerative, is a common cause of morbidity. Triamcinolone acetonide (TA), a common glucocorticoid, has been used as symptomatic treatment for joint pain for decades. However, besides its relatively short-lived therapeutic effects, TA may have potentially devastating effects by altering the normal healing process to restore and maintain the cellular entities that contribute to tissue regeneration of the synovial joint. Mesenchymal stem cells (MSCs) have been shown to hold great potential in tissue regeneration due to their multipotency in regenerating osteoblasts, chondrocytes and adipocytes and their immunomodulatory properties. So far, it remains largely unclear how TA treatment affects MSC activities.

overall_design: Bone  Marrow mesenchymal stem cells (MSCs) were plated and subjected to either triamcinolone acetonide 10nM in complete DMEM or in complete DMEM only as control for 24 h. The cells were then collected and lysed in RLT buffer (Qiagen, Germantown, MD, USA) and kept at -80°C

first: Maritha

last: Kumlin

first: Johanna

last: Ungerstedt

first: Huan

last: Cai

first: Li

last: Felländer-Tsai

first: Hong

last: Qian


title: Transcriptome study of MX1 overexpression on down syndrome derived aminocytes(DSACs)

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

country: China

institute: Henan Provincial People's Hospital

summary: MX1 mediated AP-1 involved transcriptional regulation play an important role in the pathogenesis of DS through integration analysis of ATAC-seq and RNA-seq. To confirm the function of MX1 in DS, we applied RNA-seq to explore the difference between MX1-OE and Blank group

overall_design: Human MX1 coding sequence (CDS, Gene ID:4599) was cloned into the lentivirus backbone pcSLenti-EF1-EGFP-F2A-Puro-CMV-MCS-WPRE to construct MX1-OE plasmid (OBIO Biosciences, Shanghai, China). MX1-OE lentivirus was produced through MX1-OE plasmid transfection into HEK-293 T cells together with the packaging plasmids. Then the Normal aminocytes were infected with MX1-OE lentivirus and backbone lentivirus infected aminocytes were used as Blank group.

first: Zhenglong

last: Guo

first: Bingtao

last: Hao

first: Shixiu