title: Evidence for a unique RNA motif in orchestrating Orthomyxoviridae splicing

city: New York

first: Justin

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

summary: Our laboratory has generated evidence that Archaean L7Ae serves as a unique inhibitor of orthomyxovirus splicing, and as such, can inhibit replication of this class of viruses. Here, we utilize RNA-sequencing to analyze how Archaean L7Ae impacts the transcriptome of a human cell line. Results showed that L7Ae had minimal impact on host transcriptonal response despite retaining its properties to inhibit orthomyxovirus replication.

overall_design: Comparative differential expression data between 293T cells that were transfected with pCAGGS-eGFP (control) or pCAGGs-L7ae (experimental) and harvested 24 hours post transfection

first: Kohei

last: Oishi

first: Daniel

last: Blanco-Melo

first: Andrew

last: Kurland

first: Jeffrey

last: Johnson

last: tenOever


title: Gene expression of Acanthamoeba castellanii under long-term co-culture condition

status: Public on Mar 10 2023

city: Tainan City

first: Wei-Chen

last: Lin

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

type: Expression profiling by high throughput sequencing

summary: The gene expression of A. castellanii cultured with low-nutrient medium and heat-killed bacteria for 21 days. The RNA-seq analysis was performed by Illumina HiSeq platform. The treated A. castellanii was compared with amoeba cultured in growth medium.

overall_design: The A. castellanii as cultured with 20% PYG medium was diluted 1:4 by Page’s Amoeba Saline (PAS) and heat-killed E. coli. To produce the heat-killed E. coli DH5α, the bacteria with OD = 1.0 was collected by centrifugation and suspended in the corresponding medium (100% or 20% PYG medium). Then, the suspended E. coli DH5α were heated at 100℃ for 10 minutes. The heat-killed bacteria were finally diluted into 2.0×106 CFU/mL. Hundred units/ml of ampicillin were added to each medium.

first: Chih-Ming

last: Tsai


title: Comparative transcriptome data of multi tissues in response to different environmental light-dark cycles

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

country: China

institute: Yangzhou University

summary: It is well known that host-microbes and immunity interactions are influenced by dietary patterns, as well as daily environmental light-dark (LD) cycles that entrain circadian rhythms in the host. Emerging data has highlighted the importance of diet patterns and timing on the interaction among circadian rhythms, gut microbiome, and immunity, however, their impacts on LD cycles are less reported. Therefore, we aim to study how LD cycles regulate the homeostatic crosstalk between gut microbiome, hypothalamic and hepatic circadian clock oscillations and immunity. We hypothesized that different environmental LD cycles: (1) constant darkness, LD0/24; (2) short light, LD8/16; (3) normal LD cycle, LD12/12; (4) long light, LD16/8; and (5) constant light, LD24/0, may affect immunity and metabolism to varying degrees. Therefore, 240 mice were managed with chow diets (CD) and antibiotics treatments (ABX) under five different LD cycles for 42 days. The liver (LIV), hypothalamus (HYP), inguinal white adipose tissue (iWAT),  ileum epithelium (ILE), colon epithelium (COL), jejunum epithelium (JEJ), cecum epithelium (CEC),  spleen (SPL), mammary gland (MAG), and thymus gland (THY) tissues were obtained for studying their impacts immunity using RNA-Seq data.

overall_design: Firstly, two hundreds and forty 10-week-old C57BL/6N murine line were selected and supplied, all mice were initially maintained under the same standard laboratory conditions to harmonize the environment and diets. The initial body weight of each mouse was 19-20 g. After acclimatization for 7 days, the mice were then randomly divided into following two parts: chow diets parts (CD, n = 120), and antibiotics treatment parts (ABX, n = 120). Adequate sterilized drinking water and pelleted feed (irradiation by Co60) were provided for CD mice, and the diets were consisted of corn, soybean, wheat, chicken and fish meal, vegetable oil, and a variety of customized vitamins and trace elements. Mice from ABX parts received same sterilized feed but added a cocktail of broad-spectrum antibiotics in their drinking water.Then, all 240 mice from CD and ABX parts were randomly divided into 10 groups to receive following 5 light-dark cycles : (1) 0 h light/24 h dark fed with CD (CD_LD0/24, n = 24); (2) 8 h light/16 h dark fed with CD (CD_LD8/16, n = 24); (3) 12 h light/12 h dark fed with CD (CD_LD12/12, n = 24); (4) 16 h light/8 h dark fed with CD (CD_LD16/8, n = 24); (5) 24 h light/0 h dark fed with CD (CD_LD24/0, n = 24); (6) 0 h light/24 h dark fed with ABX (ABX_LD0/24, n = 24); (7) 8 h light/16 h dark fed with ABX (ABX_LD8/16, n = 24); (8) 12 h light/12 h dark fed with ABX (ABX_LD12/12, n = 24); (9) 16 h light/8 h dark fed with ABX (ABX_LD16/8, n = 24); and (10) 24 h light/0 h dark fed with ABX (ABX_LD24/0, n = 24). Each mouse was maintained in a single cage in an environmentally controlled warehouse that allowed for manipulating light-dark cycles according to regulations, and light-dark cycles were controlled with an LED light strip of 150 to 200 lx and a temperature of 4500 to 5000 K, with the lights being turned off for 24 h of LD0/24; the lights being turned on at CT6 (defined as ZT0) and turned off at ZT8 of LD8/16; the light being turned on at ZT0 and turned off at ZT12 of LD12/12; the light being turned on at ZT0 and turned off at ZT16 of LD16/8; and the lights being turned on for 24 h of LD24/0. The trough, drinking fountain, and litter were changed every day after the lights were turned on at ZT0. Temperature within the warehouse was 22-24 °C, relative humidity was 55-65%, and negative pressure ventilation was used. The experimental lasted for 42 days and was under strict environmental control conditions.


title: Hypertrophic chondrocytes and osteogenesis in P6 mouse tibia

status: Public on Mar 13 2023

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: It has been shown that hypertrophic chondrocyte (HC) can become osteoblast, contributing to the formation of trabecular bone and endosteum. However, it is unclear what genes regulate the process of differentiation from chondrocyte to osteoblast. Conditional knock-out of Irx 3 and Irx5 in HCs can reduce the trabecular bone amount and there is also some evidence that ablation of Irx3 and Irx5 in HCs can promote bone marrow adipogenesis. In order to investigate the gene regulatory network with different dosage of Irx3/5 in HC descendants (i.e. in Loss-of-Function mutant and heterozygous control), we collected HC descendant cells from proximal tibia of mice at postnatal day 6 and performed single cell RNA seq with 10X Genomics System to profile the gene expression pattern in HC descendants.

overall_design: We sequenced one sample. Cells were harvested from proximal and distal tibia. The sample (a pool of two tibia from the same male P6 mouse) is on Col10a1Cre;Rosa26-Tdtomato;Irx3 +/Δ;Irx5 +/- (Irx3/5 heterozygous control). Cells with or without Tdtomato fluoresence are digested out by sequential digestion, enriched by sequential centrifugation and resuspension and subject to standard 10X Genomics protocol.

first: Tan

last: Zhijia

first: Kong

last: Mingpeng

first: Kathryn

middle: S

last: Cheah


title: Expression data from mothers, placentas, and newborns in the Democratic Republic of Congo

city: Gainesville

first: Chu

last: Hsiao

state: FL

address: 2033 Mowry Rd

department: Anthropology

country: USA

institute: University of Florida

summary:
Maternal stress has long been associated with lower birthweight but mechanisms remain elusive. This study explored how maternal stress may impact changes in gene expression within a cohort of mother-placenta-newborn triads in the eastern Democratic Republic of Congo
We used microarrays to detail the global programme of gene expression underlying the impact of maternal stress on newborn birthweight and identified that global placental gene expression may partially mediate the negative impact of maternal war stress on newborn birthweight.

overall_design: Samples from Homo sapiens sapiens mother, newborn, and placenta triads were collected at the time of birth for RNA extraction and hybridization on the Human Clariom D microarray (Affymetrix GeneChip system).

middle: J

first: Conne

last: Mulligan


title: Colonic and cecal microbiome profiles in response to different environmental light-dark cycles

summary: It is well known that host-microbes and immunity interactions are influenced by dietary patterns, as well as daily environmental light-dark (LD) cycles that entrain circadian rhythms in the host. Emerging data has highlighted the importance of diet patterns and timing on the interaction among circadian rhythms, gut microbiome, and immunity, however, their impacts on LD cycles are less reported. Therefore, we aim to study how LD cycles regulate the homeostatic crosstalk between gut microbiome, hypothalamic and hepatic circadian clock oscillations and immunity. We hypothesized that different environmental LD cycles: (1) constant darkness, LD0/24; (2) short light, LD8/16; (3) normal LD cycle, LD12/12; (4) long light, LD16/8; and (5) constant light, LD24/0, may affect immunity and metabolism to varying degrees. Therefore, 240 mice were managed with chow diets (CD) and antibiotics treatments (ABX) under five different LD cycles for 42 days. The colonic (co) and cecum (ce) contents were obtained for studying their impacts on gut microbiome using 16S rRNA sequencing.

overall_design: Firstly, two hundreds and forty 10-week-old C57BL/6N murine line were selected and supplied, all mice were initially maintained under the same standard laboratory conditions to harmonize the environment and diets. The initial body weight of each mouse was 19-20 g. After acclimatization for 7 days, the mice were then randomly divided into following two parts: chow diets parts (CD, n = 120), and antibiotics treatment parts (ABX, n = 120). Adequate sterilized drinking water and pelleted feed (irradiation by Co60) were provided for CD mice, and the diets were consisted of corn, soybean, wheat, chicken and fish meal, vegetable oil, and a variety of customized vitamins and trace elements. Mice from ABX parts received same sterilized feed but added a cocktail of broad-spectrum antibiotics in their drinking water.Then, all 240 mice from CD and ABX parts were randomly divided into 10 groups to receive following 5 light-dark cycles : (1) 0 h light/24 h dark fed with CD (CD_LD0/24, n = 24); (2) 8 h light/16 h dark fed with CD (CD_LD8/16, n = 24); (3) 12 h light/12 h dark fed with CD (CD_LD12/12, n = 24); (4) 16 h light/8 h dark fed with CD (CD_LD16/8, n = 24); (5) 24 h light/0 h dark fed with CD (CD_LD24/0, n = 24); (6) 0 h light/24 h dark fed with ABX (ABX_LD0/24, n = 24); (7) 8 h light/16 h dark fed with ABX (ABX_LD8/16, A2, n = 24); (8) 12 h light/12 h dark fed with ABX (ABX_LD12/12, A3, n = 24); (9) 16 h light/8 h dark fed with ABX (ABX_LD16/8, A4, n = 24); and (10) 24 h light/0 h dark fed with ABX (ABX_LD24/0, A5, n = 24) (Fig. 1D). Each mouse was maintained in a single cage in an environmentally controlled warehouse that allowed for manipulating light-dark cycles according to regulations, and light-dark cycles were controlled with an LED light strip of 150 to 200 lx and a temperature of 4500 to 5000 K, with the lights being turned off for 24 h of LD0/24; the lights being turned on at CT6 (defined as ZT0) and turned off at ZT8 of LD8/16; the light being turned on at ZT0 and turned off at ZT12 of LD12/12; the light being turned on at ZT0 and turned off at ZT16 of LD16/8; and the lights being turned on for 24 h of LD24/0. The trough, drinking fountain, and litter were changed every day after the lights were turned on at ZT0. Temperature within the warehouse was 22-24 °C, relative humidity was 55-65%, and negative pressure ventilation was used. The experimental lasted for 42 days and was under strict environmental control conditions.


title: Vascular oxidative stress causes neutrophil arrest in brain capillaries, leading to decreased cerebral blood flow and contributing to memory impairment in a mouse model of Alzheimer’s disease

city: Ithaca

first: Nancy

last: Ruiz-Uribe

address: 526 Campus Rd B35 Weill Hall

department: Biomedical Engineering

institute: Cornell University

summary: To investigate differences in gene expression between 10-11 month old WT and APP/PS1 mice treated with NOX2 inhibitor or scrambled control (SC) after two weeks of 10 mg/kg treatment

overall_design: Comparative gene expression profiling analysis of RNA-seq data for brain microvessel samples of 10-11 month old WT and APP/PS1 mouse

middle: E

first: Oliver

last: Bracko

first: Sabyasachi

last: Dash

first: Hiroki

last: Uchida

first: Teresa

last: Sanchez

first: Chris

middle: B

last: Schaffer


title: Ectomesenchymal Six1 controls mandibular skeleton formation.

city: Shanghai

first: Songyuan

last: Luo

address: 639 Zhi-Zao-Ju Road

institute: Shanghai Ninth People’s Hospital

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

overall_design: Refer to individual Series


title: RNA-seq based transcriptome profiles of the human testis tissues across multiple conditions, with an intention to mainly study non-obstructive azoospermia

city: Bengaluru

first: Kshitish

middle: K

last: Acharya

state: Karnataka

address: Electronic City Ph 1

country: India

institute: Institute of Bioinformatics and Applied Biotechnology

summary: To study alternatively spliced isoforms expressed differently in the testis of donors with Non-Obstructive Azoospermia (NOA), testicular biopsies were collected from donors with NOA condition (as identified by cytological examination) and Obstructive Azoospermia (OA), and Varicocele (VA) conditions. The biopsy samples were stored in RNA-later solution (Ambion, cat # AM7024), according to the manufacturer's guidelines. RNA was extracted using the RiboPure kit (Ambion cat # AM1924). Two normal commercial testicular RNA (Clontech cat. no.: 636533, Asian: lot no: 1105041; Caucasian: lot. no.: LOT1105214A) samples were also used. The RNA quality was checked with formaldehyde agarose gel electrophoresis as well as a micro-volume spectrophotometer. For NGS, testicular RNA from 8 NOA, 2 OA and 2 Varicocele donors were used. Paired-end library preparation was carried out using Illumina TruSeq RNA Library Prep Kit v2, and sequencing was done using the Illumina HiSeq 2000. After quality checks, seqtk (https://github.com/lh3/seqtk) was used for trimming low-quality reads. Alignments, identification of transcripts and the chimeric/transplice molecules, and their quantification were performed by Kallisto software. Sample segregation according to the corresponding donor condition was confirmed via clustering RNA-seq data from the samples.

overall_design: Transcriptome profiles from eight NOA samples were compared with those from 15 control samples (six sequenced newly, and nine public datasets). The control samples included 4 from donors with disorders with complete testicular spermatogenesis (two each with OA and VA).

first: K

middle: A

last: Kshitish

first: Balagannavar

last: Govindkumar

first: Basavaraju

last: Kavyashree


title: Ectomesenchymal Six1 controls mandibular skeleton formation [CUT&Tag]

summary: Craniofacial development requires intricate cooperation of multiple transcription factors and signaling pathways. Six1 is a critical transcription factor regulating craniofacial development. However, the exact function of Six1 during craniofacial development remains elusive. In this study, we investigated the function of Six1 in mandible development using a Six1 knockout mouse model (Six1-/-) and a cranial neural crest-specific, Six1 conditional knockout mouse model (Six1f/f; Wnt1-Cre). The Six1-/- mice exhibited multiple craniofacial deformities, including severe microsomia, high-arched palate, and uvula deformity. Importantly, the Six1f/f; Wnt1-Cre mice recapitulate the microsomia phenotype of Six1-/- mice, thus demonstrating that the expression of Six1 in ectomesenchyme is critical for mandible development. We further showed that the knockout of Six1 led to abnormal expression of osteogenic genes within the mandible. Moreover, the knockdown of Six1 in C3H10 T1/2 cells reduced their osteogenic capacity in vitro. Using RNA-seq, we showed that both the loss of Six1 in the E18.5 mandible and the Six1 knockdown in C3H10 T1/2 led to the dysregulation of genes involved in embryonal skeletal development. In particular, we showed that Six1 binds to the promoter of Bmp4, Fat4, Fgf18, and Fgfr2, and promotes their transcription. Collectively, our results suggest that Six1 plays a critical role in the regulation of mandibular skeleton formation during mouse embryogenesis.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) for transcription factors Six1 in C3H10T1/2 cells.

first: Zhixu

last: Liu

first: Qian

last: Bian

first: Xudong

last: Wang


title: Ectomesenchymal Six1 controls mandibular skeleton formation [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and Six1kd of C3H10T1/2 cells and Six1+/+ vs Six1-/- of E18.5 mice mandible tissue.


title: Revisiting chromatin packaging in mouse sperm [CUT&RUN]

city: Boston

first: Qiangzong

last: Yin

state: MA

address: 3 Blackfan St, CLS building 440A

department: Medicine

institute: BIDMC/Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mammalian sperm exhibit an unusual and heavily-compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression in the early embryo. Scores of genome-wide surveys in sperm have reported patterns of chromatin accessibility, histone localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low levels of cell-free chromatin. In the absence of proper sperm lysis we readily recapitulate multiple prominent genome-wide surveys of sperm chromatin, suggesting that these profiles primarily reflect contaminating cell-free chromatin. Removal of cell-free DNA, along with appropriate lysis conditions, are required to reveal a sperm chromatin state distinct from any yet reported. Using ATAC-Seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with genes expressed during late spermiogenesis. Histone modification and chromosome folding studies also strongly support the hypothesis that prior studies suffer from contamination, but technical challenges associated with reliably preserving the architecture of the compacted sperm head prevent us from confidently assaying true localization patterns for these epigenetic marks. Together, our studies strongly argue that our knowledge of mammalian chromosome packaging remains largely incomplete, and motivate future efforts to more accurately characterize genome organization in mature sperm.

overall_design: Histone modification profiling in mouse sperm samples that are pre-treated with Dnase or DTT using CUTandRUN

first: Chih-Hsiang

last: Yang

first: Olga

last: Strelkova

first: Yu

last: Sun

first: Sneha

last: Gopalan

first: Liyan

first: Job

last: Dekker

first: Thomas

middle: G

last: Fazzio

first: Xin

middle: Z

last: Li

first: Johan

last: Gibcus

last: Rando


title: Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted anti-cancer therapy

first: José

middle: L

last: McFaline-Figueroa

email: jm5200@columbia.edu, joselmc@uw.edu

institute: Columbia University

overall_design: Single-cell RNA-seq libraries were generated using three-level single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) of untreated or small molecule inhibitor exposed A172, T98G, U87MG, GBM4, GBM8, GSC0131, and GSC0827 glioblastoma brain cancer cells. In a subset of experiments A172, T98G and U87MG engineered to express dCas9-KRAB or dCas9-SunTag for CRISPR/Cas9 mediated gene knockdown or overexpression, respectively, were genetically perturbed for HPRT1, components of the mismatch repair machinery, 522 protein kinases. Different cells and different treatments were hashed and pooled prior to sci-RNA-seq using a nuclear barcoding strategy. This nuclear barcoding strategy relies on the fixation of barcodes containing well-specific oligos that are specific to a given cell type, replicate, or treatment condition. For genetically perturbed experiments, targeted capture and enrichment of gRNA-containing transcripts were performed.

first: J

first: S

last: Srivatsan

first: A

last: Hill

first: M

last: Gasperini

first: D

last: Jackson

first: L

last: Saunders

last: Domcke

last: Regalado

first: P

last: Lazarchuck

last: Alvarez

first: R

last: Monnat

last: Shendure

first: C

last: Trapnell


title: Pituitary RNA-seq in Egr1cKO mice

status: Public on Mar 11 2023

city: Blacksburg

first: Hehuang

last: Xie

state: VA

address: 1015 Life Science Cir

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

summary: Sex difference in pituitary gene expression of Egr1cKO mice and controls

first: Cody

last: Swilley

first: Yuze

last: Zheng

first: Yu

last: Lin


title: Transcriptome analysis of wild-type (WT) and CDH1 knockout (KO) human Gastric Organoids (hGOs)

city: Fukuoka

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

country: Japan

institute: Kyushu University

summary: We conducted transcriptome analysis usin next generation sequencing of paired WT or CDH1 KO hGO cells established from three patients' fundic gands. Compared to WT hGOs, CDH1 KO hGO cells showed higher expression of matrix metalloproteinase (MMP) genes and genes that regulate inflammation and angiogenesis. We showed that the migration ability of CDH1 KO hGO cells was mediated by upregulation of MMPs and this effect was abolished by specific inhibitor of MMPs in vitro. MMP-3 protein was expressed in clinical samples of E-cadherin deficient signet ring cell carcinoma (SRCC) of the stomach.  Our study represents that  MMPs are promising candidates for novel therapeutic targets for E-cadherin-deficient SRCC.

overall_design: mRNA profiles of three paired WT and CDH1 KO hGO cells derived from three patients' stomach.

first: Kyoko

last: Yamaguchi

first: Jumpei

last: Nogami


title: Gene expression of monocytes from rheumatoid arthritis patients treated with bDMARDs and methotrexate.

status: Public on Mar 09 2023

city: Torino

first: Federico Alessandro

last: Ruffinatti

state: Torino

address: via Accademia Albertina 13

department: Department of Life Sciences and Systems Biology

country: Italy

institute: University of Turin

summary: It is well documented that patients affected by rheumatoid arthritis (RA) have distinct susceptibility to the different biologic Disease-Modifying AntiRheumatic Drugs (bDMARDs) available on the market, probably because of the many facets of the disease. Monocytes are deeply involved in the pathogenesis of RA and we therefore evaluated and compared the transcriptomic profile of monocytes isolated from patients on treatment with methotrexate alone or in combination with tocilizumab, anti-TNFalpha or abatacept, and from healthy donors. Differential expression analysis of whole-genome transcriptomics yielded a list of regulated genes suitable for functional annotation enrichment analysis. Specifically, abatacept, tocilizumab and anti-TNFalpha cohorts were separately compared with methotrexate using a rank-product-based statistical approach, leading to the identification of 78, 6, and 436 differentially expressed genes, respectively.

overall_design: Gene expression profiling was performed on primary monocyte cultures from a total of 31 samples, according to the following experimental design: 10 samples from healthy patients, 6 samples from MTX-, 5 samples from abatacept-, 5 samples from anti-TNFalpha-, and 5 samples from tocilizumab-treated patients.

first: Luigia

last: Fresu

first: Federico

first: Maria

last: Talmon


title: NFE2L2 mutations enhance radioresistance in head and neck cancer by modulating intratumoral myeloid cells

city: Stanford

first: Li

last: Guan

state: California

address: 269 Campus dr, CCSR, Room 1230

institute: Stanford University, Radiation Oncology

summary: To identify the mechanism by which Nrf2E79Q mediates RT resistance and CB-839 overcomes RT resistance in Nrf2E79Q, we performed RNA sequencing of SAS cells stably expressing either Nrf2WT or Nrf2E79Q treated with RT±CB-839 and analyze the differentially expressed genes in Nrf2E79Q vs. Nrf2WT cells.

overall_design: Nrf2WT or Nrf2E79Q SAS cells were pretreated with 0.1μM CB-839 or vehicle for 24 hours, then irradiated (4 Gy). RT was performed as previously described(14) using a 225kVp cabinet x-ray irradiator filtered with 0.5 mm Cu (IC-250, Kimtron Inc.). Thus 4 groups were created, including Nrf2WT+RT, Nrf2E79Q+RT, Nrf2WT+RT+CB-839, Nrf2E79Q+RT+CB-839. All the experiments were performed in triplicate, generating a total of 12 samples. Next, RNA was isolated using Trizol (Catalog# 15596026, Invitrogen) 24 hours after RT. Library preparation and RNA sequencing were performed by Novogene via Illumina platforms based on mechanism of SBS (Sequencing by synthesis).


title: SMARCA4 knockdown upregulates expression of myogenic genes in medulloblastoma

city: Navi Mumbai

first: Neelam

middle: V

last: Shirsat

state: Maharashtra

address: Kharghar, Sector 21

department: Shirsat Lab

institute: Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre

summary: SMARCA4 gene is mutated in a subset of Group 3 medulloblastomas. ShRNA mediated downregulation of SMARCA4 expression in three Group 3 medulloblastoma cell lines upregulated the expression of myogenic/muscle differentiation related genes as studied by the transcriptome analysis.

overall_design: The expression of SMARCA4 was downregulated in a doxycycline-inducible manner in Group 3 medulloblastoma cell lines using the lentiviral vector tet-pLKO-puro. Total RNA was prepared from doxycycline-treated cells expressing the SMARCA4 shRNA and those expressing the vector alone  and the parental cells . Libraries were prepared from the polyA-enriched RNA fraction using the Illumina Truseq RNA library preparation kit and sequenced on the Illumina Hiseq 2500 platform

last: Vishwanath  Shirsat


title: B cell receptor signaling in germinal centers prolongs survival and primes B cells for selection [single cell RNA-Seq]

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Germinal centers (GCs) are sites of B cell clonal expansion, diversification, and antibody affinity selection. This process is limited and directed by T follicular helper cells that provide helper signals to B cells that endocytose, process, and present cognate antigens in proportion to their B cell receptor (BCR) affinity. Under this model, the BCR functions as an endocytic receptor for antigen capture. How signaling through the BCR contributes to selection is not well understood. To investigate the role of BCR signaling in GC selection, we developed a tracker for antigen binding and presentation and a Bruton’s tyrosine kinase drug-resistant-mutant mouse model. We showed that BCR signaling per se is necessary for the survival and priming of light zone B cells to receive T cell help. Our findings provide insight into how high-affinity antibodies are selected within GCs and are fundamental to our understanding of adaptive immunity and vaccine development.

overall_design: LZ B1-8 BTKC481S and LZ B18 BTKWT cells were sorted from acalabrutinib or vehicle treated hosts.

first: Spencer

middle: T

last: Chen

first: Anna

last: Gazumyan

first: Melissa

last: Cipolla

first: Michel

middle: C

last: Nussenzweig


title: lncRNA MAGI2-AS3 suppresses castration-resistant prostate cancer proliferation and migration via the miR-106a-5p/RAB31 axis

city: Chongqing

first: Guo

last: Yang

address: 1 Youyi Road, Yuzhong District

department: Department of Urology

institute: The First Affiliated Hospital of Chongqing Medical University

summary: To explore the downstream mechanisms that may be regulated by the MAGI2-AS3/miR-106a-5p axis to inhibit PCa progression

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the overexpression of MAGI2-AS3 or miR-106a-5p in 22RV1 cells.

first: Ting

last: Li

first: Zhen

last: Quan

first: Jiayu

last: Liu


title: Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis

first: Andrea

last: Califano

address: 1130 St. Nicholas Avenue

department: Department of Systems Biology

institute: Califano Laboratory of Systems Biology

summary: Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. By leveraging progress in proteomic technologies and network-based methodologies over the past decade we developed VESPA—an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations—and used it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogation of tumor-specific enzyme/substrate interactions accurately inferred kinase and phosphatase activity, based on their inferred substrate phosphorylation state, effectively accounting for signal cross-talk and sparse phosphoproteome coverage. The analysis elucidated time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring that was experimentally confirmed by CRISPRko assays, suggesting broad applicability to cancer and other diseases.

overall_design: This experiment represents a large-scale, pooled CRISPR knockout (CRISPRko) screen validtion experiment, targeting all annotated human kinases, phosphatases and E3 ligases (Methods) of two human colorectal cancer cell lines HCT-15 and NCI-H508, perturbed with two drug compounds (linsitib, trametinib). Data was measured with four different guides per target.

first: George

last: Rosenberger

first: Mikko

last: Turunen

first: Aaron

last: Griffin


title: Droplet-based genome-wide forward genetic screening of astrocyte-microglia communication mechanisms

first: Michael

last: Wheeler

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

summary: SPEACC-seq is a novel high-throughput method which enables forward genetic screens to identify cell-cell interaction mechanisms that uncovered an astrocyte-microglia regulatory circuit mediated by amphiregulin and IL33-ST2. signaling. Cell-cell interactions in the central nervous system (CNS) play central roles in neurologic diseases. However, little is known about the specific molecular pathways involved, and methods for their systematic identification are limited. For example, several factors mediate microglia-astrocyte interactions that promote CNS pathology, but less is known about regulatory interactions that limit tissue pathology. Here we report the development of SPEACC-seq (Stimulation, Perturbation, and Encapsulation of interACting Cells followed by Sequencing), a forward genetic screening platform which combines genome-wide CRISPR/Cas9 perturbations, cell co-culture in picoliter droplets, and microfluidic-based fluorescence activated droplet sorting to identify mechanisms of cell-cell communication. Using SPEACC-seq in combination with an in vivo perturb-seq screen, we identified microglia-produced amphiregulin as a suppressor of disease promoting astrocyte responses in experimental autoimmune encephalomyelitis (EAE), a pre-clinical model of multiple sclerosis (MS). The production of microglial amphiregulin was induced via ST2 signaling by IL-33 released from astrocytes during EAE. Indeed, the genetic inactivation of ST2 or amphiregulin in microglia, or IL-33 or amphiregulin signaling in astrocytes resulted in the worsening of EAE, suggesting that IL-33-induced microglial amphiregulin limits disease-promoting astrocyte responses associated with CNS pathology. This regulatory loop was also detected in human astrocytes and microglia both in vitro and in MS patient CNS samples. In summary, we developed SPEACC-seq, a high-throughput, droplet-based forward genetic screening platform for the identification of cell-cell interaction mechanisms, which identified a novel microglia-astrocyte negative feedback loop that limits CNS pathology.

overall_design: For samples with 4OTR Prefix the experiment is designed to study the effect of IL33 knockout and ST2 knockout in Astrocytes and Microglia (3 samples for each condition in each cell type); for samples with 4M67 prefix the experiment contain samples with Areg knockout and Egfr knockout in Astrocytes and Microglia (3 samples for each condition). In the end two single cell experiment is conducted on the CNS tissue in Naive Mouse and EAE induced Mouse.

first: Hong-Gyun

last: Lee

first: Zhaorong

first: Iain

last: Clark

first: Francisco

last: Quintana


title: MACE-sequencing of carotid neointimal tissue isolated by laser capture microdissection following carotid wire injury in mice

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe Universität Frankfurt am Main

summary: To identify gene expression signatures in the neointima throughout the stages of vascular injury including inflammation, resolution and remodeling.

overall_design: Gene expression profiling of time points following carotid wire injury compared to basal state (pre-injury).

first: Giulia

last: Buchmann

first: Ralf

last: Brandes


title: Carotid injury in mice


title: CDK13 phosphorylates the translational machinery and promotes tumorigenic protein synthesis

city: Wuhan

first: xie

last: ting

address: Donghu road

institute: Wuhan University

summary: Cyclin-dependent kinases 13 (CDK13) has been suggested to phosphorylate RNA polymerase II and is involved in transcriptional activation. However, whether CDK13 catalyzes other protein substrates and how CDK13 contributes to tumorigenesis remain largely unclear. Herein, we identify key translation machinery components 4E-BP1 and eIF4B as novel CDK13 substrates. CDK13 directly phosphorylates 4E-BP1 at Thr46 and eIF4B at Ser422 such that genetic or pharmacological inhibition of CDK13 perturbs RNA translation. Polysome profiling analysis shows that MYC oncoprotein synthesis depends on the CDK13-regulated translation in colorectal cancer (CRC), and CDK13 is required for CRC cell proliferation. As mTORC1 has been shown to phosphorylate the 4E-BP1 and eIF4B, knockdown or inhibition of CDK13 in combination with mTORC1 inhibitor rapamycin further dephosphorylates 4E-BP1 and eIF4B and blocks protein synthesis. As a result, dual inhibition of CDK13 and mTORC1 accelerated CRC cell death and again MYC were significantly downregulated upon combination treatment. These findings demonstrate a pro-tumorigenic role of CDK13 in CRC and shed light on the role of CDK13 in protein synthesis by direct phosphorylation of translation initiation factors. Therefore, therapeutic targeting of CDK13 alone or in combination with rapamycin may pave a new way for CRC treatment.

overall_design: We used colon cancer cell lines as a model system, and performed  RNA-seq to study the transcriptional mechanism of CDK13.

first: Hudan

first: Chao

last: Wu

last: Xie


title: mRNA sequencing of epithelial cells from the esophagus and tongue

city: Anderlecht

first: Alizee

last: Vercauteren Drubbel

address: 808 route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary: In this study, we used RNA sequencing to characterize a new population of taste buds found in the esophagus and compared them to their lingual counterpart. We concluded that esophageal taste buds share many markers with lingual taste buds althoug they seem to express less taste receptors in average.

overall_design: Oesophageal and lingual mRNA profiles of Krt8-YFP mice by deep sequencing using Illumina

first: Benjamin

last: Beck

first: Alizée


title: Single cell mRNA sequencing on esophageal and lingual cells

summary: In this study, we uncovered through single cell RNA sequencing (scRNA-seq) of mouse esophagus epithelium a population of taste buds clustered in the cervical segment of the esophagus.  We compared this taste bud population to their lingual counterpart. We concluded that these taste buds have the same cellular composition than the ones from the tongue. State-of-the-art transcriptional regulatory network analysis allowed the identification of specific transcription factors associated to the differentiation of immature progenitors into the three different taste bud cell types in the tongue and the esophagus.

overall_design: Oesophageal and lingual single cell mRNA profiles of wild type or Krt8-YFP mice by deep sequencing using 10x genomic and Illumina


title: mRNA and scRNA-seq on on esophageal and lingual cells

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

overall_design: Refer to individual Series


title: Single-cell transcriptome of the basal murine carotid artery

summary: Acute vascular injury is an unwelcome consequence of invasive treatments designed to alleviate symptoms of vascular stenosis. Resulting fibrotic scarring and neointima formation may result in loss of lumen diameter and diminished vascular function. Understanding of the key phases of acute inflammation, resolution and remodeling has the potential to minimise unwanted effects on the vasculature and therefore improve patient outcomes. The cellular landscape of blood vessels is highly hetergeneous in nature, and therefore data at single-cell resolution is of high relevance to this problem. Herein, the cellularity of murine carotid artery tissue is described in a cell- and time-resolved manner. Single-cell RNA-sequencing of carotid tissue isolated at time-points ranging from uninjured vessel to 14 days post-injury enabled the recapitulation of all stages of vascular injury. In these data, a sub-population of smooth muscle cells which also arises in atherosclerosis and myocardial infarction was identified. So-called stem cells/endothelial cells/monocytes (SEM) cells are candidates for repopulating injured vessels, and were amongst the most proliferative cell clusters following wire-injury of the carotid artery. Transcriptional signatures reflecting SEM gene expression patterns could also be detected in bulk RNA-sequencing of neointimal tissue isolated by laser capture microdissection. These data indicate that phenotypic plasticity of smooth muscle cells is highly important to the progression of lumen loss following acute vascular insult.

overall_design: Uninjured, homeostatic murine carotid arteries were isolated and subjected to single-cell RNA-sequencing.


title: B cell receptor signaling in germinal centers prolongs survival and primes B cells for selection [bulk RNA-seq]

first: Thiago

last: Oliveira

overall_design:
GC B1-8 c-Myc-GFP cells were sorted based on Myc-GFP and NP-Ea fluorescence.
mNnN: Myc Negative NP Negative
mNnP: Myc Negative NP Positive
mPnN: Myc Positive NP Negative
mPnP: Myc Positive NP Positive

first: Spencer

last: Chen

first: Anna

last: Gazumyan

first: Melissa

last: Cipolla

first: Michel

last: Nussenzweig


title: Nuclear localization of fly Pcif1 is required for gene regulation and fertility

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

summary: Here we show that Pcif1 mutant flies display a reduced fertility which is particularly marked in females. Deep sequencing analysis of Pcif1 mutant ovaries revealed transcriptome changes with a notable increase in expression of genes belonging to the mitochondrial ATP synthetase complex.

overall_design: The RNA-seq was used to analyze the gene expression changes in ovaries of Pcif1M6stop and Pcif1F9ΔNLS fly lines when compared to control  Pcif1BG02557 fly line. Three biological replicas were analyzed for each line.

last: Franco

first: Emmanuel

last: Taillebourg

first: Elena

last: Delfino

first: David

last: Homolka

first: Nathalie

last: Gueguen

first: Emilie

last: Brasset

first: Radha

middle: R

last: Pandey

first: Marie-Odile

last: Fauvarque


title: A deep mutational scan of the MHC class I-specific chaperone TAPBPR for sites important for peptide editing

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois at Urbana Champaign

summary: TAP-binding protein-related (TAPBPR) is an endoplasmic reticulum-resident chaperone that facilitates class I MHC (MHC-I) processing and peptide loading.  TAPBPR has (1) chaperone function to stabilize misfolded or partially folded nascent MHC-I substrates, and (2) editing function, in which it catalyzes the exchange of low affinity for high affinity antigenic peptides in the MHC-I peptide-binding groove.  TAPBPR-TM is a chimera of the TAPBPR ectodomain and a canonical TM domain, which escapes the endoplasmic reticulum to reach the cell surface.  We reasoned that at the cell surface, TAPBPR-TM is more likely to interact with folded MHC-I and thus surface interactions will be more representative of editing function.  When tapasin, a homolog of TAPBPR and the main MHC-I-specific chaperone, is knocked out, surface trafficking of HLA-A2 (a human MHC-I allele) is severely diminished, but surface HLA-A2 levels are rescued by over-expression of TAPBPR-TM.  Using this assay as the foundation for a fluorescence-based selection, we deep mutationally scanned 104 positions on TAPBPR-TM to identify sites critical for engaging folded MHC-I.

overall_design: A chimeric fusion was constructed between the extracellular domains of human TAPBPR and the transmembrane helix of HLA-G.  The chimera, called TAPBPR-TM, has higher activity for functional replacement of tapasin than wild type TAPBPR.  A library was constructed in TAPBPR-TM in which 104 positions where diversified with degenerate NNK codons.  The library was transfected in to tapasin-knock out Expi293F cells after 1500-fold dilution with a carrier plasmid; this ensures most cells express no more than a single sequence variant and there is a tight connection between genotype and phenotype.  Cells expressing the TAPBPR-TM library were stained for surface HLA-A2 with R-phycoerythrin-conjugated anti-HLA-A2 clone BB7.2, and the 0.5% of cells with the highest fluorescence were collected by FACS.  Following Illumina sequencing, the frequencies of mutations from transcripts in the sorted cells were compared to their respective frequencies in the naive plasmid library.  The calculated enrichment ratios are a proxy for relative activity of the TAPBPR-TM sequence variants.

first: Christine

last: Devlin


title: Genome-wide analyses of organ-specific DNA methylation and transcription in Arabidopsis thaliana

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 1001 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

type: Methylation profiling by genome tiling array

type: Expression profiling by genome tiling array

summary:
DNA methylation at cytosine residues is an essential event for the normal development of multicellular eukaryotes. In mammals, de novo DNA methylation is restored to normal levels by the time of implantation, while epigenetic states of plant genes are often inherited over generations.
Keywords: Organ comparison in methylome and transcriptome

overall_design: All plants used in this study were of the Arabidopsis thaliana ecotype Columbia accession. The met1 and drm1 drm2 cmt3 triple mutant were published previously.

first: Junshi

last: Yazaki

first: Hiroshi

last: Shiba

first: Yoshiaki

last: Tarutani

first: Kōichi

last: Nishida

first: Seiji

last: Takayama

first: Huaming

first: Qian

last: Peng

first: Akira

last: Isogai


title: Single-cell transcriptome of the murine carotid artery following acute injury

first: Timothy

last: Warwick

overall_design: Murine carotid arteries were isolated at different time points post-injury, digested, and submitted for single-cell RNA-sequencing.

first: Giulia

last: Buchmann

first: Ralf

last: Brandes


title: Increased retinoic acid signalling decreases lung metastasis in salivary adenoid cystic carcinoma by inhibiting the noncanonical Notch1 pathway [scRNA-seq]

city: peking

first: kong

last: lu

address: capital medical university

institute: ccmu

summary: MYB-NFIB fusion and NOTCH1 mutation are hallmark genetic events familiar in SACC that promote lung metastasis. However, abnormal expression of MYB and NOTCH1 was also observed in without MYB-NFIB fusion and NOTCH1 mutation. Here, through single-cell RNA sequencing (scRNA-seq) and exome target capture sequencing in two SACC patients without MYB-NFIB fusion and NOTCH1 mutation, we explore in-depth the molecular mechanisms of lung metastasis. Twenty-five types of cells in primary and metastatic tissues were identified via Seurat clustering and categorized into four main stages ranging from near normal to cancer state based on the normal tissue occupancy for each cell cluster. In this context, we identified the Notch signalling pathway enrichment in almost all cancer cells; trajectory and sub-clustering analyses investigated deeply cancer progenitor-like cell clusters in primary tumour-associated lung metastases, in which signature genes enriched in the ‘MYC_TARGETS_V2’ gene set. In vitro, we detected the complexes of the NICD1-MYB-MYC by Co-immunoprecipitation (Co-IP) and incidentally identified retinoic acid (RA) signalling as endogenous antagonists of the ‘MYC_TARGETS_V2’ gene set. Following this, we validate that all-trans retinoic acid (ATRA) reduces the lung metastasis in SACC via correcting erroneous cell differentiation mainly caused by aberrant NOTCH1 or MYB expression. Bioinformatic and immunohistochemical (IHC) analyses of four primary tissues and eleven metastatic lung tissues from patients with SACC suggested that RA system insufficiency partially promotes lung metastasis. These findings imply the value of diagnosis and treatment of the RA system.

overall_design: Cells from fresh tumour tissues were isolated for the preparation of single-cell suspensions via the ChromiumTM Single Cell 3’ Solution technique and analysed by BioMiao Biological Technology (Beijing) Co., Ltd. The 6 sample sequenced were primary salivary gland ACC (A), adjacent normal tissue (AP), lung metastses (A1, B1, C1) and adjacent normal lung tissue (F).

first: Meng-jiao

last: Zhou

first: Jia-jie

last: Yang


title: Increased retinoic acid signalling decreases lung metastasis in salivary adenoid cystic carcinoma by inhibiting the noncanonical Notch1 pathway [ChIP-seq]

summary:
MYB-NFIB fusion and NOTCH1 mutation are hallmark genetic events familiar in SACC that promote lung metastasis. However, abnormal expression of MYB and NOTCH1 was also observed in without MYB-NFIB fusion and NOTCH1 mutation. Here, through single-cell RNA sequencing (scRNA-seq) and exome target capture sequencing in two SACC patients without MYB-NFIB fusion and NOTCH1 mutation, we explore in-depth the molecular mechanisms of lung metastasis. Twenty-five types of cells in primary and metastatic tissues were identified via Seurat clustering and categorized into four main stages ranging from near normal to cancer state based on the normal tissue occupancy for each cell cluster. In this context, we identified the Notch signalling pathway enrichment in almost all cancer cells; trajectory and sub-clustering analyses investigated deeply cancer progenitor-like cell clusters in primary tumour-associated lung metastases, in which signature genes enriched in the ‘MYC_TARGETS_V2’ gene set. In vitro, we detected the complexes of the NICD1-MYB-MYC by Co-immunoprecipitation (Co-IP) and incidentally identified retinoic acid (RA) signalling as endogenous antagonists of the ‘MYC_TARGETS_V2’ gene set. Following this, we validate that all-trans retinoic acid (ATRA) reduces the lung metastasis in SACC via correcting erroneous cell differentiation mainly caused by aberrant NOTCH1 or MYB expression. Bioinformatic and immunohistochemical (IHC) analyses of four primary tissues and eleven metastatic lung tissues from patients with SACC suggested that RA system insufficiency partially promotes lung metastasis. These findings imply the value of diagnosis and treatment of the RA system.
Cells from fresh tumour tissues were isolated for the preparation of single-cell suspensions via the ChromiumTM Single Cell 3’ Solution technique and analysed by BioMiao Biological Technology (Beijing) Co., Ltd.

overall_design: Meng-jiao Zhou


title: Increased retinoic acid signalling decreases lung metastasis in salivary adenoid cystic carcinoma by inhibiting the noncanonical Notch1 pathway [RNA-seq_KD]

overall_design: We performed RNA-seq analysis of cells exposed to different treatments or conditions, including ATRA, NOTCH1 and/or MYB knockdown (MYB_KD and NICDKD and Double_KD), and MYB overexpression (MYBCDNA); these data are available in the Dr.Tom system (Beijing Genomics Institute, BGI).


title: Increased retinoic acid signalling decreases lung metastasis in salivary adenoid cystic carcinoma by inhibiting the noncanonical Notch1 pathway [RNA-seq_treated]

overall_design: We performed RNA-seq analysis of cells exposed to different treatments or conditions, including ATRA (AT), cisplatin(DDP) and their combination (ATD); NOTCH1 and/or MYB knockdown, and MYB overexpression; these data are available in the Dr.Tom system (Beijing Genomics Institute, BGI).


title: Increased retinoic acid signalling decreases lung metastasis in salivary adenoid cystic carcinoma by inhibiting the noncanonical Notch1 pathway

city: Beijing

first: Gexuan

last: Feng

address: FengtaiNo.10, Youanmen Waixi 1st Alley

institute: Capital Medical University

overall_design: We performed RNA-seq analysis of cells exposed to different treatments or conditions, including ATRA, NOTCH1 and/or MYB knockdown, and MYB overexpression; these data are available in the Dr.Tom system (Beijing Genomics Institute, BGI).


title: Mechanisms of muscle degeneration in Drosophila third instar larval musculature upon Tropomodulin (Tmod) knockdown.

city: New York

first: Mary

last: Baylies

institute: Memorial Sloan Kettering Cancer Center

summary: The knockdown of Tmod, an actin-capping protein, decreases the expression of proteasomal degradation genes and increase expression of oxidative metabolism genes. It is also critical for the correct expression of larval actin isoforms.

overall_design: Performed gene expression profiling analysis using data obtained from RNA-seq of 2 experimental groups (tmodRNAi vs mCherryRNAi), with 3 samples each. Each sample contains the transcriptome of 7-10 Drosophila larva muscle enriched lysates.

first: Carolina

last: Zapater i Morales


title: PTEN phosphatase inhibits metastasis

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: PTEN encodes a tumor suppressor with lipid and protein phosphatase activities whose dysfunction has been implicated in melanomagenesis; less is known about how its phosphatases regulate melanoma metastasis. We show that PTEN expression negatively correlates with metastatic progression in human melanoma samples and a PTEN-deficient mouse melanoma model. Wildtype PTEN expression inhibited melanoma cell invasiveness and metastasis in a dose-dependent manner, behaviors that specifically required PTEN protein phosphatase activity. PTEN phosphatase activity regulated metastasis through Entpd5. Entpd5 knockdown reduced metastasis and IGF1R levels while promoting ER stress. In contrast, Entpd5 overexpression promoted metastasis and enhanced IGF1R levels, while reducing ER stress. Moreover, Entpd5 expression was regulated by the ER stress sensor ATF6. Altogether, our data show that PTEN phosphatase activity inhibits metastasis by negatively regulating the Entpd5/IGF1R pathway through ATF6, thereby identifying novel candidate therapeutic targets for the treatmtreatingwith PTEN mutant melanoma.

overall_design: The genes expressed in three groups were compared with the control group (16C) in three replications.

first: Yanlin

last: Yu

first: Meng

last: Dai

first: Liping

last: Huang

first: Weiping

first: Ellen

first: Arnulfo

last: Mendoza

first: Helen

last: Michael

first: Chand

last: Khanna

first: Marcus

last: Bosenberg

first: Martin

last: McMahon

first: Glenn

last: Merlino


title: Single-nucleus sequencing data from developing and adult mouse olivocochlear neurons

city: Boston

first: Lisa

last: Goodrich

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

summary: Transcriptional diversity of mouse olivocochlear neurons (OCNs) was examined using single-nucleus sequencing of brainstem cholinergic neurons at P1, P5, and P26-P28. This dataset includes multiple brainstem cell types, including OCNs and several other populations of cranial motor neurons.

overall_design: Cholinergic nuclei were labeled using ChAT-Cre to drive expression of the nuclear localized Rosa26-Sun1-GFP reporter. GFP+ cells from the ventral brainstem were selected via fluorescence-activated cell sorting (FACS) and nuclei were captured using the 10x genomics single-cell 3' platform.

first: Michelle

middle: M

last: Frank


title: Effect of CTTN on SKBR3 breast cancer cells (RNA-seq)

city: Seoul

first: Gu

last: Kong

address: 222, Wangsimni-ro, Seongdong-gu

department: College of Medicine

country: South Korea

institute: Hanyang University

summary: RNA-sequencing analysis of control and CTTN-overexpressed SKBR3 cell lines. CTTN (also known as EMS1), an actin-binding protein, is highly amplified in several human cancers, including breast carcinomas. Results provide insight into the transcriptional regulation of CTTN in breast cancer.

overall_design: SKBR3 cells were stably infected with lentiviruses encoding either control(pLVX vector) or CTTN cDNA (pLVX-CTTN) and selected using puromycin. Total RNA was isolated from control- and CTTN-overexpressed SKBR3 stable cells using Trizol reagent. For each of the 2 conditions, 3 biological replicates were included

first: Sojeong

last: Moon

first: Hyung

last: Choi

first: Hyungyong

last: Kim


title: Yap governs a lineage-specific neuregulin1 pathway-driven adaptive resistance to RAF kinase inhibitors

first: Mahesh

last: Saqcena

address: 1275 York Ave, Box 296

department: Human Oncology and Pathogenesis Program

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: RNA-seq of tumor cells sorted from YAPS127A and BrafV600E/YAPS127A mouse thyroid tumors

summary: We performed high-throughput RNA sequencing of tumor cells sorted from YAPS127A and BrafV600E/YAPS127A to investigate YAP dependency and driver cooperativity in thyroid tumor progression.

overall_design: mRNA profiles of thyroid cancer cells from YAPS127A and BrafV600E/YAPS127A mice.

first: Maria

last: RGarcia-Rendueles

first: James

last: Fagin

first: Jeffrey

last: Knauf


title: RNAseq analysis of Pseudozyma hubeiensis BOT-O on glucose or xylose before and after nitrogen-starvation

city: LUND

first: Daniel

middle: P

last: Brink

address: Naturvetarvagen 14

department: Applied Microbiology

country: Sweden

institute: Lund University

summary: Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source.

overall_design: The transcriptome response of the basidiomycete yeast P. hubeiensis BOT-O were assessed during exponential growth and during nitrogen-starvation. The yeast was grown in nitrogen-limited YNB on either glucose or xylose, with an initial carbon-to-nitrogen ratio of 80 g/g. RNAseq samples were taken from four growth conditions in three biological replicates each, for a total of 12 samples. The conditions were: exponential growth on glucose or xylose (Ogt1 and Oxt1), and nitrogen-starvation on glucose or xylose (Ogt2 and Oxt2). Biological replicates are denoted in the filenames by an A, B or C.

first: Friederike

last: Mierke

first: Joakim

last: Norbeck

first: Verena

last: Siewers

first: Thomas

last: Andlid


title: The Proteome and Transcriptome of Stress Granules and P-Bodies during Human T Lymphocytes Activation

city: Toulouse

first: Don-Marc

last: Franchini

address: 2 Av. Hubert Curien

country: France

institute: CRCT

summary: Stress granules (SGs) and processing bodies (PBs) are membraneless cytoplasmic assemblies regulating mRNAs under environmental stress such as viral infections, neurological disorders, or cancer. Upon antigen stimulation, T lymphocytes mediate their immune functions under regulatory mechanisms involving SGs and PBs. However, the impact of T cell activation on such complexes, in term of formation, constitution and relationship remains unknown. Here, by combining proteomic, transcriptomic and immunofluorescence approaches, we simultaneously characterized the SGs and PBs from primary human T lymphocytes pre- and post-stimulation. The proteomes and transcriptomes of SGs and PBs were identified, unveiling an unanticipated molecular and functional complementarity. Notwithstanding, these granules keep distinct spatial organizations and abilities to interact with mRNAs. This comprehensive characterization of the RNP granule proteomic and transcriptomic landscapes provides a unique resource for future investigations on SGs and PBs in T lymphocytes.

overall_design: To identified the RNAs in SGs and PBs of primary human T lymphocytes, we first isolated CD3+ T lymphocytes from PBMCs of 5 human healthy donors. SGs and PBs were isolated from T Lymphocytes following 72 h stimulation with CD3/CD28 activating beads. In addition, total cytosolic (CYT) RNAs were extracted.

first: Nicolas

last: Curdy

first: Juan

last: Cerapio Arroyo

first: Jean-Jacques

last: Fournié


title: RNA-seq profiling of thymocytes from wildtype and Lmo2-transgenic mice

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Deregulated expression of oncogenic transcription factors is a common cause of T-cell acute lymphoblastic leukemia (T-ALL). However, the molecular and cellular effects of these transcription factors on developing T-cell progenitors are poorly understood. Here we show that the initial effect of the oncogenic transcription factor Lmo2 is to cause an almost complete block in differentiation at the DN2 stage of T-cell development.

overall_design: DN2 and DN3 thymocytes were obtained from neonatal (2-3 weeks old) Lmo2-transgenic mice and from their wild-type counterparts. DN3 thymocytes were also obtained from 6-10 week-old transgenic and wildtype mice. Three biological replicates were obtained for cell type / age / genotype combination.

first: Hesham

last: Abdulla

first: Matthew

last: McCormack

first: Gordon

last: Smyth


first: kong

last: lu

overall_design: Refer to individual Series


title: Glomerular and Tubular Transcriptome in the Cprobe Cohort

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan


title: RNA-seq of human thyroid cancer cell lines expressing sh-mirE-YAP or YAPS127A

first: Mahesh

last: Saqcena

summary: We performed high-throughput RNA sequencing of stable lines with dox-inducible expression of sh-mirE-YAP or of the constitutively nuclear YAPS127A mutant  to investigate YAP dependency and its role in tumorogenesis.

overall_design: mRNA profiles of human thyroid cancer cell lines treated with/without doxycyclin to express sh-mirE-YAP or of the constitutively nuclear YAPS127A mutant

first: Maria

last: Garcia-Rendueles

first: James

last: Fagin


title: Tubular Transcriptome in the Cprobe Cohort

summary: We used microarrays to analyze the transcriptome of microdissected renal biopsies from patients with kidney disease and living donors. We derived pathway specific scores for Angiopoietin-Tie signaling pathway activation at mRNA level (or transcriptome level) for individual patients and studied the association of pathway activation with disease outcomes.

overall_design:
Tubular gene expression data from micro dissected human kidney biopsy samples  from patients with chronic kidney disease(Lupus, DN, IgA,HT, TN) and healthy living donors.
Profiling was performed on Affymetrix ST2.1 microarray platform.

first: Felix

last: Eichinger

first: Bradley

last: Godfrey

first: Jiahao

last: Liu

first: Matthias

last: Kretzler

first: Wenjun

last: Ju


title: Glomerular Transcriptome in the Cprobe Cohort

overall_design: Glomerular gene expression data from micro-dissected human kidney biopsy samples  from patients with chronic kidney disease(Lupus, DN, IgA,HT, TN) and healthy living donors. Profiling was performed on Affymetrix ST2.1 microarray platform.


title: Effect of SigA depletion and SigB knockout on the global transcription of Mtb

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

institute: Center for Cellular and Molecular Biology

summary: Analyzing differences in transcriptome profile of RvΔsigA (SigA conditional knockdown strain) in presence of anhydrotetracycline and transcriptome profile of RvΔsigB (SigB knockout strain) compared to control.

overall_design: RvΔsigA was inoculated at 0.05 OD, in presence or absence of 1mM/ml anhydrotetracycline. Post 3 days total RNA was islolated and RNA seq was performed. RvΔsigB was inoculated at 0.05 OD and grown to 0.8 OD, after which RNA was isolated and RNA sequencing was carried out.

first: Biplab

last: Singha

middle: k

last: singh

first: Divya

last: Sowpati

first: Vinay

last: Nandicoori


city: Nanjing

first: Yu

last: Zhang

state: Jiangsu

address: No.215,Guangzhou Road

department: Respiratory Medcine

institute: Nanjing Chest Hospital

summary: Circular RNAs (circRNAs) play important roles in tumorigenesis, including lung cancer. However, the expression profile and clinical value of circRNAs in lung adenocarcinoma remains unclear. This study aimed to establish the circular RNA expression profile of lung adenocarcinoma tissue and determine its potential diagnostic and prognostic value.

overall_design: The global expression profile of circRNAs in lung adenocarcinoma tissue was determined from five paired lung adenocarcinoma and adjacent normal tissue specimens.


title: Genome-wide distribution of H1t in mouse spermatogenic cells.

city: Imabari-shi

first: Koji

last: Hayakawa

state: Ehime

address: 1-3 Ikoino-oka

department: Department of Toxicology, Faculty of Veterinary Medicine

institute: Okayama University of Science

summary: We report genome-wide distribution of Linker histone variant H1t in mouse spermatogenic cells. We found that H1t was mainly located at around transcriptional start site of genic area, positively correlated with the gene expression. This study using ChIP-seq analysis provides genomic distribution of H1t in mouse spermatogenic cells.

overall_design: ChIP-seq of Linker histone variant H1t in mouse spermatogenic cells.

first: Ruiko

last: Tani


title: A heterodimer of α and β hemoglobin chains functions as an innate anticancer agent

status: Public on Mar 08 2023

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: Metastatic (as well as tumor) microenvironments contain both cancer-promoting as well as cancer restraining factors. The balance between these opposing forces determines the fate of cancer cells that disseminate to secondary organ sites. In search for microenvironmental drivers or inhibitors of metastasis, we identified, in a previous study, the beta subunit of hemoglobin (HBB) as a lung-derived antimetastatic factor. In the present study, exploring mechanisms leading to melanoma brain metastasis, we discovered that brain-derived factors restrain proliferation and induce apoptosis and necrosis of brain-metastasizing melanoma cells. Employing various purification procedures, we identified a heterodimer composed of hemoglobin alpha and beta chains that performs these anti-metastatic functions. Neither the alpha nor the beta subunit alone were inhibitory. An alpha/beta chain dimer chemically purified from human hemoglobin inhibited the cell viability of primary melanomas, melanoma brain metastasis (MBM), and breast cancer cell lines. The dimer-induced DNA damage, cell cycle arrest at the SubG1 phase, apoptosis, and significant necrosis in four MBM cell lines. Proteomic analysis of dimer-treated MBM cells revealed that the dimer downregulates the expression of BRD4, GAB2, and IRS2 proteins playing crucial roles in cancer cell sustainability and progression.

overall_design: 24 samples ; 4 cell lines, treatment and control for each in triplicates

first: Maharrish

last: Chelladurai

first: Dan

last: Xu

first: Sivan

last: Izraely

first: Roman

last: Bengaiev

first: Orit

last: Sagi-Assif

first: Weirong

last: Yuan

last: Pasmanik Chor

first: Dave

middle: S

last: Hoon

first: Wuyuan

last: Lu

first: Isaac

last: Witz


title: RNA-seq of human primary endothelial cells

city: Cardiff

first: Frank

last: Wessely

address: Maindy Road

department: UK DRI

country: United Kingdom

institute: Cardiff University

summary: Endothelial cells represent the key cellular components of the blood-brain barrier, whose selective permeability presents a challenge for drug delivery. A better understanding of molecular proteins specific for brain endothelial cells compared to endothelial barries in different tissues can highlight novel blood-brain barrier transport targets.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human primary endothelial cells obtained from 3 tissues (brain - HBMEC, lung - HPMEC, liver - HHSEC). Cells were purchased from vendors ScienCell Research Laboratories and Innoprot.

first: Martin

last: Lenter

first: Axel

middle: H

last: Meyer

first: German

last: Leparc

first: Caleb

last: Webber


title: SLC7A1 is a novel candidate for the transport of therapeutics across the blood-brain barrier

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


title: B cell receptor signaling in germinal centers prolongs survival and primes B cells for selection

city: NEW YORK

first: Thiago

last: Oliveira

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University


title: ncRNA Sequencing facilitates quantitative analysis of differently expressed genes in the peripheral blood mononuclear cells from healthy controls and patients with systemic lupus erythematosus

city: guangzhou

first: cuicui

last: wang

state: guangdong

address: 1 Pan Fu Road

department: rheumatology

institute: Guangzhou First People’s Hospital, The Second Affiliated Hospital of South China University of Technology

summary: To further explore the role of long non-coding RNAs in the systemic lupus erythematosus (SLE), we assessed the transcriptome of PBMCs from healthy controls and SLE patients using ncRNA sequencing analysis. The data were analyzed for differential expression with a nominal P<0.05. Our study aimed to discover novel biomarkers for SLE diagnosis and prognosis.

overall_design:
To detect differently expressed LncRNAs (P<0.05) by ncRNA sequencing in PBMCs from three healthy controls and five SLE patients
Definitions:
DUIZHAOZU stands for healthy control(HC) or CK
BINGRENZU stands for systemic lupus erythematosus(SLE)

first: Cuicui

last: Wang

first: Shiwen

first: Yanting

last: Zeng

first: Fangfei

last: Li


title: snRNA-seq of nuclei isolated with microvessel-enrichment procedure applied to frozen post-mortem brain tissue

summary: Vascular cell types are under-represented in standard single-nucleus RNA-Seq studies of human frozen post-mortem brain tissue. The dataset represents the pilot data obtained with the first version of a microvessel- enrichment protocol to obtain a higher percentage of endothelial cells as the key cellular component of the blood-brain barrier.

overall_design: Two brain samples from one healthy control and one Alzheimer's disease patient (BRAAK stage 6 with amyloid angiopathy), were processed as described in the extract protocol and snRNA-Seq using the 10x Genomics platform was carried out.

first: Ese

last: Ifie

first: Olaf

last: Ansorge

first: Zameel

last: Cader


title: Study on the mechanism of glycyrrhizic acid attenuating gefitinib-induced hepatotoxicity in mice

city: Zhengzhou

first: Shuaifei

state: Henan

address: Jinshui East Road 156

institute: Henan University of Chinese Medicine

summary: To study the hepatotoxic effects of gefitinib in mice and to explore the mechanism of action of glycyrrhetinic acid in attenuating gefitinib hepatotoxicity.

overall_design: Comparative gene expression profiling of RNA-seq data from mouse liver administered with gefitinib and glycyrrhizic acid.

first: Xiaoting

last: Yin

first: Yucheng


title: miRNAs expression data from the exosomes of normal and oxygen glucose deprivation(OGD)-treated brain microvascular endothelial cell

city: Changsha

first: Mengqi

last: Zhang

address: 87 Xiangya Road

institute: Xiangya Hospital

summary:
Brain microvascular endothelial cell (BMEC) injury can affect neuronal survival by modulating immune responses through the microenvironment.
We used microarrays to detail the miRNAs expression in the exosomes from normal and oxygen glucose deprivation (OGD)-cultured BMECs.

overall_design: The BMECs were exposed to OGD and a normal culture medium for 4 h. Exosomes from the culture supernatants were collected using a Cell Supernatant Exosome Extraction Kit. MiRNAs extracted from EVs secreted from were BMECs with OGD exposure, compared with those extracted from EVs secreted from normal culture conditions.


title: TIM-1 inhibits cancer cell proliferation by regulating IFIT2 and is correlated with prognosis in bladder cancer

city: nanchang

first: chao

last: zhu

address: Yongwai Main Street

institute: The First Affiliated Hospital of Nanchang University, Donghu District, Nanchang City, Jiangxi Province

summary: Bladder cancer (BC) is one of the most common cancers in the world. T-cell immunoglobulin and mucin domain 1 (TIM-1) are involved in the progression of multiple tumors. However the role of TIM-1 in BC progression is poorly understood. In this study, we searched the Gene Expression Profiling Interactive Analysis (GEPIA) database and performed immunohistochemistry (IHC) to assess TIM-1 protein expression in bladder cancer (BC) patients. The results demonstrated that BC with high TIM-1 expression was associated with longer overall survival (OS) and disease-specific survival (DSS) than BC with low TIM-1 expression. Overexpression of TIM-1 inhibits BC cell proliferation in both cell culture and animal experiments. RNA sequencing data indicated that interferon-induced protein with tetratricopeptide repeats (IFIT) genes induced by interferon-α (IFN-α) were significantly enriched among the genes upregulated by TIM-1 overexpression. Mechanistically, our data revealed that TIM-1 promotes IFN-α release and activates the IFIT2/p-STAT1 pathway, which is known to be related to tumor cell proliferation. Moreover, knockdown of IFIT2 in TIM-1-overexpressing BC cells hinders the tumor suppressive effect of TIM-1. Our results revealed that TIM-1 is a potential molecular marker for BC prognosis and indicate that high TIM-1 expression suppresses BC cell proliferation in an IFIT2/p-STAT1-dependent manner.

overall_design: RNA-Seq was performed using GeneChem (China). Correlation analysis of TIM-1 and the transcriptome included the following three steps: (1) expression analysis (2) differential expression analysis and (3) functional enrichment analysis of differentially expressed genes.Gene Ontology (GO) enrichment analysis was conducted using the TopGO software.

first: Aiping

last: Le


title: m6A Demethylase ALKBH5 attenuates doxorubicin-induced cardiotoxicity via posttranscriptional stabilization of Rasal3

city: Hangzhou

first: Rifeng

last: Gao

state: Zhejiang

address: No. 88 Jiefang Road

institute: Zhejiang University

summary: The clinical application of anthracyclines such as doxorubicin (DOX) is limited due to their cardiotoxicity. N6-methyladenosine (m6A) plays an essential role in numerous biological processes. However, the roles of m6A and m6A demethylase ALKBH5 in DOX-induced cardiotoxicity (DIC) remain unclear. In this research, DIC models were constructed using Alkbh5-knockout (KO), Alkbh5-knockin (KI), and Alkbh5-myocardial-specific knockout (ALKBH5flox/flox, αMyHC-Cre) mice. Cardiac function and DOX-mediated signal transduction were investigated. As a result, both Alkbh5 whole-body KO and myocardial-specific KO mice had increased mortality, decreased cardiac function, and aggravated DIC injury with severe myocardial mitochondrial damage. Conversely, ALKBH5 overexpression alleviated DOX-mediated mitochondrial injury, increased survival, and improved myocardial function. Mechanistically, ALKBH5 regulated the expression of Rasal3 in an m6A-dependent manner through posttranscriptional mRNA regulation and reduced Rasal3 mRNA stability, thus activating RAS3, inhibiting apoptosis through the RAS/RAF/ERK signaling pathway, and alleviating DIC injury. These findings indicate the potential therapeutic effect of ALKBH5 on DIC.

overall_design: We performed MeRIP-seq and MeRIP-seq-Qpcr analysis on the myocardial tissues of ALKBH5flox/flox (n = 3, ALKBH5flox/flox-DOX group) and ALKBH5flox/flox, αMyHC-Cre (n = 3, ALKBH5flox/flox, αMyHC-Cre-DOX group) treated with doxorubicin.

first: Yiqing

last: Yang


title: Distinct differences in immunological properties of equine orthobiologics revealed by functional and transcriptomic analysis using an activated macrophage readout system

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: Multiple biological therapies for orthopedic injuries are marketed to veterinarians, despite a lack of rigorous comparative biological activity data to guide informed decisions in selecting a most effective compound. Therefore, the goal of this study was to use relevant bioassay systems to directly compare the anti-inflammatory and immunomodulatory activity of three commonly used orthobiological therapies (OTs): mesenchymal stromal cells (MSC), autologous conditioned serum (ACS), and platelet rich plasma (PRP). Equine monocyte-derived macrophages were used as the readout system to compare therapies, including cytokine production and transcriptomic responses.

overall_design: Macrophages were stimulated with IL-1ß and treated 24 hours with orthobiologicss, washed and cultured an additional 24 hours to generate supernatants. Secreted cytokines were measured by multiplex immunoassay and ELISA. To assess global transcriptomic responses to treatments, RNA was extracted from macrophages and subjected to full RNA sequencing

first: Lyndah

last: Chow

first: Lynn

last: Pezzanite

first: Laurie

last: Goodrich


title: Transcriptomic analysis the mechanism of detoxification metabolism induced by different insecticide in Spodoptera frugiperda

city: jinan

first: Yuanxue

state: Shandong

address: No.202 Gongyebei Road

institute: Shandong Academy of Agricultural Sciences

summary: In order to clarify the molecular mechanism of metabolic detoxification in Spodoptera frugiperda, the enzyme activity assay and transcriptome sequencing analysis were used to screen and identify the relevant genes related to metabolic detoxification after induced by insecticides at LC50 dose.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for different insecticide treatment

first: Jianhua

first: Aiyu

first: Ming

last: Zhao


title: Self-assembled Matrigel-free iPSC-derived liver organoids demonstrate wide-ranging highly-differentiated liver functions

city: San francisco

first: Tammy

last: Chang

address: 513 parnassus Ave.

institute: UCSF

summary: Investigate the functional capabilities of human iPSC-derived liver organoids generated on Matrigel or self-assembed in rotating wall vessel (RWV) via bulk RNA-seq, RT-qPCR and immunostaining, to provide a simple and high-throughput way to generate Matrigel-free liver organoids for research and clinical applications

overall_design: Comparative gene expression profiling analysis of RNA-seq data for monolayer different differentiated stage iPSCs and  organoids growing with matrigel or RWV.

first: Yun

last: Weng

first: Simon

last: Han

first: Maria

last: Sekyi

first: Tao

last: Su

first: Aras

middle: N

last: Mattis


title: A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea [Synchronization RNA-seq]

city: Qingdao

first: yunfeng

address: 72 Binhaidadao, Aoshanwei, Jimo

institute: Shandong University

summary: Cell cycle regulation is of paramount importance for all forms of life. Here we report that a conserved and essential cell cycle-specific transcription factor (designated as aCcr1) and its viral homologs control cell division in Sulfolobales. We show that the transcription level of accr1 reaches peak during active cell division (D-phase) subsequent to the expression of CdvA, an archaea-specific cell division protein. Cells over-expressing the 58-aa-long RHH (ribbon-helix-helix) family cellular transcription factor as well as the homologs encoded by large spindle-shaped viruses Acidianus two-tailed virus (ATV) and Sulfolobus monocaudavirus 3 (SMV3) display significant growth retardation and cell division failure, manifested as enlarged cells with multiple chromosomes. aCcr1 over-expression results in downregulation of 17 genes (>4-folds) including cdvA. A conserved motif, aCcr1-box, located between the TATA-binding box and the translation initiation site in the promoters of 13 out of the 17 highly repressed genes, is critical for aCcr1 binding. The aCcr1-box is present in the promoters of cdvA genes across Sulfolobales, suggesting that aCcr1-mediated cdvA repression is an evolutionarily conserved mechanism by which archaeal cells dictate cytokinesis progression, whereas their viruses take advantage of this mechanism to manipulate the host cell cycle.

overall_design: S. islandicus REY15A cells were synchronized as previously described with slight modifications. Briefly, cells were first grown aerobically at 75°C with shaking (145 rpm) in 30 ml of STV medium. When the OD600 reached 0.6-0.8, the cells were transferred into 300 ml STV medium with an initial estimated OD600 of 0.05. When the OD600 reached 0.15-0.2, acetic acid was added at a final concentration of 6 mM and the cells were blocked at G2 phase of the cell cycle after 6h treatment.6 mM acetic acid can synchronize S. islandicus REY15A in the G2 phase. Then, the cells were collected by centrifugation at 3,000 g for 10 min at room temperature to remove the acetic acid and washed twice with 0.7% (w/v) sucrose. Finally, the cells were resuspended into 300 ml of pre-warmed STV medium and cultivated as above for RNA-seq analysis.

first: Yunfeng

first: Junfeng

last: Liu

first: Mart

last: Krupovic

first: Yulong

last: Shen


title: Gene expression patterns of pediocin-producing Corynebacterium glutamicum strains

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

institute: Saarland University

summary:
Strains: non-producing refernece strain pXMJ19 (CR099 pXMJ19; Goldbeck et al., 2021) and Pediocin-producer pxMJ19 ped (CR099 pXMJ19 Ptac pedACDCg, Goldbeck et al., 2021)
Pediocin-producing and non-producing strains of Corynebacterium glutamicum were compared in a whole genome microarray analysis setup in order to identify potential strain optimization targets

overall_design: 3 biological replicates of the pediocin-producing strain pXMJ19 ped were compaired to 3 biological replicates of the non-producing strain pXMJ19 during the main production phase that was identified during previous experiments

first: Jens

last: Christmann

first: Christoph

last: Wittmann


title: Study on the pathogenesis of MiR-6324 regulating diarrheal irritable bowel syndrome and bioinformatics analysis

city: Chengdu

first: Jin

last: XIAO

address: No.37, Twelve Bridges Road, Jinniu District, Chengdu, Sichuan Province

institute: Chengdu University of TCM

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate whether miRNAs in the colon tissue of rats in the IBS-D group differ from those in the blank group, we performed high-throughput sequencing of miRNAs

overall_design: High-throughput sequencing of miRNAs in colon tissue of two groups of rats

first: Min

last: CHEN

first: Yanlin

last: YANG

first: Yanni

last: ZHOU


title: Gene expression profile of Human synovial sarcoma cell lines treated with a PI3K inhibitor

city: Tokyo

first: Sho

last: Isoyama

state: Tokyo

address: 3-8-31 Ariake, Koto-ku

department: Cancer Chemotherapy Center

institute: Japanese foundation for cancer research

summary: Translocation-related sarcomas (TRSs) harbor an oncogenic fusion gene generated by chromosome translocation and account for approximately one-third of all sarcomas; however, effective targeted therapies have not yet been established. We previously reported that a pan-PI3K inhibitor, ZSTK474, was suggested to be effective for sarcomas in a phase I clinical trial, and demonstrated its efficacy in preclinical model, particularly in cell lines from synovial sarcomas (SS), Ewing’s sarcomas (ES) and alveolar rhabdomyosarcomas (ARMS), all of which harbor chromosomal translocation. Actually, ZSTK474 selectively induced apoptosis in these types of sarcoma cell lines, but the precise mechanism of apoptosis induction remained unclear. Here, we performed transcriptional analyses in SS cell lines including Aska-SS, SYO-1, Yamato-SS and Fuji treated with or without ZSTK474. Gene set enrichment analyses (GSEA) and Gene ontology (GO) analysis revealed that SS cell lines treated with ZSTK474 significantly reduced signatures of PI3K signaling. In addition, upon treatment with ZSTK474, the expression of apoptosis and cell cycle related genes was significantly changed. Importantly, PI3K inhibitors triggered induction of PUMA and BIM, resulting in loss of mitochondrial membrane potential, and the expression knockdown of these genes by RNA interference efficiently suppressed the apoptosis, suggesting their functional involvement in the apoptosis progression. In contrast, TRS-derived cell lines/patient-derived cells from alveolar soft part sarcoma (ASPS), CIC-DUX4 sarcoma and dermatofibrosarcoma protuberans failed to undergo apoptosis nor induce PUMA and BIM expression, as well as cell lines derived from non-TRSs and carcinomas. These results indicate that PI3K inhibitors selectively induce apoptosis in selective TRSs such as ES and SS via the induction of PUMA and BIM and subsequent loss of mitochondrial membrane potential, which would be a proof of concept for PI3K-targeted therapy especially for such TRS patients.

overall_design: Human synovial sarcoma cell lines (Aska-SS, SYO-1, Yamato-SS and Fuji) were treated with the PI3K inhibitor, ZSTK474, at 0, 0.3 or 3 μM for 24 hours.

first: Naomi

last: Tamaki

first: Shingo

last: Dan


title: Diagnosis potential of subarachnoid haemorrhage using miRNA signatures isolated plasma-derived extracellular vesicles

city: Nanjing

first: Bin

last: Sheng

address: Zhongshan road 321

department: Department of Neurosurgery

institute: Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School

summary: differencent miRNAs as prognostic biomarkers for aSAH patients

overall_design: 6 patients blood


title: Supplementation with α-ketoglutarate improved the efficacy of anti-PD1 melanoma treatment through epigenetic modulation of PD-L1

first: Nian

state: Hunan

address: Xiangya road 87#

department: Department of Dermatology

institute: Xiangya Hospital, Central South University

summary: Patients with advanced melanoma have shown an improved outlook after receiving anti-PD1 therapy, but the low response rate restricts clinical benefit; therefore, enhancing anti-PD1 therapy efficacy remains a major challenge. Here, our findings show significantly higher abundance of α-KG in healthy controls, anti-PD1-sensitive melanoma-bearing mice, and anti-PD1-sensitive melanoma patients; moreover, supplementation with α-KG enhanced the efficacy of anti-PD1 immunotherapy and increased PD-L1 expression in melanomas via STAT1/3. We also found that supplementation with α-KG significantly increased methylcytosine dioxygenase TET2/3, which led to an increased 5-hydroxymethylcytosine (5-hmC) level in the PD-L1 promoter. As a consequence, STAT1/3 had been recognized and stabilized in PD-L1 promoter to upregulate PD-L1 expression. Importantly, single-cell sequencing of preclinical samples and analysis of clinical data revealed that the TET2/3-STAT1/3-CD274 signaling was associated with sensitivity to anti-PD1 treatment in melanoma. Taken together, we provide a novel insight into α-KG's function in melanoma anti-PD1 treatment and supplement of α-KG is a novel promising strategy to improve the efficacy of anti-PD1 therapy.

overall_design: For the tumor immunotherapy model, B16F10 (100 µl RPMI 1640 containing 5 × 10^5 cells)  were collected and injected into the right abdomen of female C57BL/6 mice (7-8-week-old) (SLAC Laboratory Animal Co., Ltd., Shanghai, China). When the tumor volume reached approximately 50 cubic millimeters, the tumors were randomly grouped (six in each group) and injected intraperitoneally with corn oil (vehicle) (Aladdin, China), 100 mg/kg α-KG (Sigma-Aldrich, USA), IgG2a (BioXCell, BE0089, USA) or PD1 mAb (BioXCell, BE0146, USA) for 9-11 days.Tumor tissues were collected from the vehicle, α-KG, anti-PD1 mAb and α-KG+anti-PD1 groups of mice, with four independent tumor tissue samples collected from each group.

first: JiangLin

last: Zhang

first: Xiang

last: Chen

first: Cong

last: Peng


title: A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea [RNA-seq]

first: yunfeng

last: Yang

overall_design: Strains of Sis/pSeSD and Sis/pSeSD-aCcr1 were cultured in ATV medium under the conditions as described above. For transcriptomic analysis, culture was inoculated with an initial OD600 of 0.05. The cells were pelleted at 6,000 g for 10 min after 12 h of cultivation when the OD600 reached approximately 0.2. The pellet was resuspended in 1 ml PBS buffer. The cells were pelleted again and stored at -80°C. Total RNA was extracted using the Trizol reagent (Ambion, Austin, TX, USA). Total amounts and the integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Transcriptomic analysis was performed by Novogene (Beijing, China). About 3 μg of high-quality RNA per sample was used for the construction of RNA-Seq libraries. The libraries are sequenced by the Illumina NovaSeq 6000. Clean reads were aligned to the reference genome sequence of S. islandicus REY15A (31). The resulting data were then analysed by Fragments Per Kilobase of transcript sequence per Million base pairs sequenced (FPKM) analysis to reveal expression levels of all genes in the S. islandicus genome. Differential genome expression analysis (over-expression of aCcr1 versus empty vector) was performed using the DEGSeq R package. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate padj<0.05 and |log2(foldchange)| > 0 were set as the threshold for significantly differential expression.

first: Yunfeng

first: Junfeng

last: Liu

first: Mart


title: A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea

overall_design: Refer to individual Series


title: The effect of TRPM7 kinase inactivation on expression levels of the genes involved in insulin production and cell cycle regulation in pancreatic islets

city: Muenchen

first: Noushafarin

last: Khajavi

state: Bavaria

address: Goethestr. 33

department: Walther-Straub-Institut für Pharmakologie und Toxikologie

institute: LMU

summary:
To investigate the function of TRPM7 kinase in the regulation of insulin production and beta cell proliferation, we used a mouse model harboring a single point mutation at the active site of the enzyme Trpm7tm1.1Mkma (K1646R, Trpm7R/R)
We then performed gene expression profiling analysis using data obtained from RNA-seq of isolated islets of Trpm7R/R mice and their control littermates after 16 weeks exposure to the obesogenic diet

overall_design: Comparative gene expression profiling analysis of RNA-seq data for isolated islets of Trpm7R/R mice and their control littermates (3 mice per genotype)

first: Khajavi

last: Noushafarin

first: Beyerle

last: Philipp

first: Thomas

last: Gudermann


title: Discovery of drugs and the underlying mechanisms for the treatment of Ac-KLF5-mediated prostate cancer bone metastasis

city: Shenzhen

first: Jin-Tang

middle: and

last: Dong

state: Guangdong

address: 1088 Xueyuan Blvd., Research Building 2B

institute: Southern University of Science and Technology

summary: Prostate cancer is a common male malignancy, with high frequency of bone metastases that are associated with life-threatening mortality. Recently, given that acetylated-KLF5 plays a critical role in promoting prostate cancer bone metastasis (PCBM), actylated-KLF5 may be a potential therapeutic strategy. In this study, we identified nitazoxanide, an FDA-approved anthelmintic agent with remarkable inhibitory activity against acetylated-KLF5 induced bone metastasis. RNA sequencing was performed on PC3-KQ and PC3-KR cells in the presence or absence of NTZ (5 μM). We identified 268 differentially expressed genes, which are upregulated (127) or downregulated (114) in KQ cells compared to KR cells and can be reversed by NTZMechanistically, nitazoxanide downregulated MYBL2 and TIMM8A and upregulated CALB1, COL4A4, COL4A3, SPOCK2, and TMPRSS2, which was associated with a better overall survival.

overall_design: Prostate cancer mRNA profiles of DMSO-treated and NItazoxanide-treated cells

first: Qingqing

last: Huang

first: Mingcheng

first: Bingbiao

last: Lin

first: Xin

last: Fu


title: Biallelic TET2 mutation sensitizes to 5’-azacitidine in acute myeloid leukemia. Stolzel et al. JCI Insight. [Illumina Infinium]

city: Newcaslte upon Tyne

first: James

middle: Mark

last: Allan

address: Herschel Building

institute: Newcastle University

summary: To investigate the impact of TET2 loss on global genomic methylation in HEL acute myeloid leukaemia (AML) cells. HEL AML cells, which have a monoallelic TET2 mutation, were targeted by CRISPR to inactivate the remaining TET2 allele, generating isogenic cell clones with either monoallelic or biallelic TET2 mutation.

overall_design: The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs in 3 indepenent HEL AML cell clones with monoallelic TET2 mutation and 3 independent cell clones with biallelic TET2 mutation.

first: Wei-Yu

first: Devi

last: Nandana


title: Biallelic TET2 mutation sensitizes to 5’-azacitidine in acute myeloid leukemia. Stolzel et al. JCI Insight. [RNA-Seq]

summary: To investigate the impact of TET2 loss on global transcription in HEL acute myeloid leukaemia (AML) cells. HEL AML cells, which have a monoallelic TET2 mutation, were targeted by CRISPR to inactivate the remaining TET2 allele, generating isogenic cell clones with either monoallelic or biallelic TET2 mutation.

overall_design: We then performed comparative gene expression profiling analysis using data obtained from RNA-seq of 3 indepenent cell clones with monoallelic TET2 mutation and 3 independent cell clones with biallelic TET2 mutation.


title: A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea [ChIP-seq]

overall_design: Chromatin immunoprecipitation (ChIP-Seq) was performed according to Takemata et al.(39) with slight modifications. Briefly, the cells were collected 3 hours after synchronization, cross-linked by adding 1% formaldehyde for 15 minutes, and quenched with a final concentration of 125 mM glycine. The cells were pelleted by centrifugation at 5,000 g for 10 minutes and washed with PBS. The cells were then resuspended in TBS-TT buffer (20 mM Tris, 150 mM NaCl, 0.1% Tween-20, 0.1% Triton X-100, pH 7.5) and fragmented by sonication until the DNA fragments were of 200-500 bp. After centrifugation (10,000 g for 15 minutes), a 100 µl aliquot of the DNA-containing supernatant was kept apart to be uses as an input control and the remaining sample was divided into two aliquots. One aliquot was incubated with anti-aCcr1 antibody-coated protein A beads (Cytiva) and the other was incubated with pre-immune serum-coated protein A beads, which served as a nonspecific binding control (Mock control). After incubation at 60 °C for 10 hrs, the samples were collected and the captured DNA was purified by using the DNA Cycle-Pure Kit (Omega) according to the manufacturer's instruction. The input samples were treated as above without the addition of antiserum and beads. The purified DNA was used for ChIP-Seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system

last: Krupovic

first: Yulong

last: Shen


title: Biallelic TET2 mutation sensitizes to 5’-azacitidine in acute myeloid leukemia. Stolzel et al. JCI Insight.

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


title: Gene expression profile at single cell level of MDAMB468 and CAL51 cell lines

city: Naples

first: Gennaro

last: Gambardella

address: Via Campi Flegrei 34,

institute: Telethon Institute of Genetics and Medicine (TIGEM)

summary: MDAMB468 and CAL51 are two triple negative breast cancer cell lines. They were sequenced to test the cell mapper algorithm we developed.

overall_design: Single cell capture was performed with DROP-seq platform implemented in our lab.

first: Gambardella

last: Gennaro

first: Simona

last: Pellecchia

first: Gaetano

last: Viscido


title: Delta (B1.617.2) variant of SARS-CoV-2 induces severe neurotropic patterns in K18-hACE2 mice

city: Iksan

first: Gun-Hee

last: Lee

address: 820-120 Hana-ro, Iksan, Jeonbuk

institute: Korea zoonosis research institute, Jeonbuk National University

summary: To investigated neurotropic patterns between the B1.617.2 (Delta) and Hu-1 variants (Wuhan early strain) in K18-hACE2 mice.

overall_design: Comparative gene expression profiles of RNA-seq data for mice brain infected with SARS-CoV-2.

first: Hu-Hee

last: Yang

first: Myeon-Sik

first: Dae-Min

last: Kim

first: Bumseok

first: Dongseob

last: Tark

first: Sangmin

last: Kang


title: Integrative analysis of green ash phloem transcripts and proteins during an emerald ash borer infestation

city: Québec

first: Christine

last: Chiu

state: QC

country: Canada

institute: Laurentian Forestry Centre

summary:
We performed RNA-seq and proteomics on naturally infested green ash (F. pennsylvanica) trees at low, medium and high levels of increasing emerald ash borer (A. planipennis) infestation.
Our integrative analysis of the RNA-Seq and proteomics data identified 14 proteins and 4 transcripts that contribute most to the difference between highly infested and low infested trees.

overall_design: Comparative transcript profiling analysis of RNA-seq data of F. pennsylvanica with high, medium and low levels infestation of Agrilus planipennis

first: Gervais

last: Pelletier

first: Florence

last: Roux-Dalvai

first: Julien

last: Prunier

first: Arnaud

last: Droit

first: Armand

last: Séguin


title: Tobacco Smoke Exacerbates Filifactor alocis Pathogenicity

city: Louisville

first: David

middle: Albert

last: Scott

state: KY

address: 501 S Preston St

department: OIID

institute: University of Louisville

summary: RNA sequencing was used to identify genes up- and down-regulated when Fa was grown in cigarette smoke media

overall_design: F alocis grown in BHI in anaerobic conditions was passaged into BHI  or CSE (BHI with smoke extract to a concentration of 1000ng/ml nicotine) at mid log stage.    RNA from original culture and from each second passage condition was prepared using MP Fast Prep and RNeasy kit.  RNA seq was performed on each passage and up and down-regulated genes unique in passage from BHI to CSE were analysed.

first: Mina

last: Iskander

first: Gwyneth

middle: J

last: Lamont

first: Jinlian

last: Tan

first: Silvia

last: Uriarte

middle: A