title: Small-molecule Inhibition of METTL3 Suppresses Tumor Growth and Promotes Neuroblastoma Differentiation [RNA-Seq STM]

status: Public on Apr 10 2024

city: Chicago

first: Susan

last: Cohn

state: IL

address: 5721 S. Maryland Ave.

department: Pediatrics

institute: University of Chicago

summary: The N6-methyladenosine (m6A) RNA modification is an important regulator of gene expression. m6A is deposited by a methyltransferase complex that includes methyltransferase-like 3 (METTL3) and methyltransferase-like 14 (METTL14). High levels of METTL3 and METTL14 drive the growth of many types of adult cancer, and METTL3/METTL14 inhibitors are emerging as new anticancer agents. However, little is known about the m6A epitranscriptome or the role of the METTL3/METTL14 complex in neuroblastoma, a common pediatric cancer. Here, we show that METTL3 knockdown or pharmacologic inhibition with the small molecule STM2457 leads to reduced neuroblastoma cell proliferation and increased differentiation. These changes in neuroblastoma phenotype were associated with decreased m6A deposition on transcripts involved in nervous system development and neuronal differentiation and increased stability and expression of target mRNAs. In preclinical studies, STM2457 treatment suppressed the growth of neuroblastoma tumors in vivo. Together, these results support the potential of METTL3/METTL14 complex inhibition as therapeutic strategy against neuroblastoma.

overall_design: RNA-Seq was performed in NGP and SK-N-BE2 cell lines following treatment with STM2457 or DMSO for 6 days.

first: Monica

last: Pomaville

first: Mohansrinivas

last: Chennakesavalu

first: Pingluan

last: Wang

first: Zhiwei

last: Jiang

first: Hui-Lung

last: Sun

first: Peizhe

last: Ren

first: Ryan

last: Borchert

first: Varsha

last: Gupta

first: Chang

last: Ye

first: Ruiqi

last: Ge

first: Zhongyu

last: Zhu

first: Mallory

last: Brodnik

first: Yuhao

last: Zhong

first: Kelley

last: Moore

first: Helen

last: Salwen

first: Rani

last: George

first: Malgorzata

last: Krajewska

first: Alexandre

last: Chlenski

first: Mark

middle: A

last: Applebaum

first: Chuan

last: He


title: Single-cell transcriptomics reveals a role for pancreatic duct cells as potential mediators of inflammation in diabetes mellitus

city: Leiden

first: Françoise

last: Carlotti

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

type: Expression profiling by high throughput sequencing

summary: Inflammation of the pancreas contributes to the development of diabetes mellitus. Although it is well-accepted that local inflammation leads to a progressive loss of functional beta cell mass that eventually causes the onset of the disease, the development of islet inflammation remains unclear. Here, we used single-cell RNA sequencing to explore the cell type-specific molecular response of primary human pancreatic cells exposed to an inflammatory environment. We identified a duct subpopulation presenting a unique proinflammatory signature among all pancreatic cell types. Overall, the findings of this study point towards a role for duct cells in the propagation of islet inflammation, and in immune cell recruitment and activation, which are key steps in the pathophysiology of diabetes mellitus.

overall_design: Islets from 3 diabetic donors and 1 Wolfram syndrome donor were cultured in CMRL 1066 medium with 5.5 mmol/L of glucose, 10% fetal calf serum, 20mg/mL ciprofloxacin, 50 mg/mL gentamycin, 2mmol/L L-glutamine, 10mmol/L HEPES and 1.2 mg/mL nicotinamide. Islets and islet-depleted tissue were cultured at 37°C in a 5% CO2- humidified atmosphere. Medium was refreshed upon receipt and every 2 days thereafter. The islet-depleted tissue was kept in its supplemented CMRL 1066 medium, then washed and stored overnight at 4°C in advanced DMEM/F12 with trypsin inhibitor (100ug/ml) before processing immediately in the morning.

first: Amadeo

last: Muñoz Garcia

first: Nathalie

last: Groen

first: Eelco

last: de Koning


title: Genome-wide identification of the translation ability of the RNC-SRP complex [RNA-seq]

status: Public on Apr 12 2024

city: Seoul

first: Min-kyung

last: Shin

address: Anam-ro

country: South Korea

institute: Korea University

summary: Ribosome profiling (Ribo-seq) analysis to identify number of ribosome-protected reads from CBC-associated mRNAs or eIF4E-associated mRNAs encoding either a signal sequence or transmembrane domain (TMD)

overall_design: Ribo-seqs and mRNA-seqs experiments were performed in HEK293T cell either undepleted or depleted of endogenous SRα. In HEK293T cells, mRNAs bound to either CBP80 or eIF4E were immunoprecipitated (IPed) and then subjected to ribo-seq.

first: Jae-Sung

last: Woo

first: Yoon

middle: K

last: Kim


title: Machine learning analysis to identify endometrial transcriptomic biomarkers predictive of pregnancy success following artificial insemination in dairy cows

city: Gainesville

first: Peter

last: Hansen

state: Florida

address: 2250 Shealy Drive

department: Department of Animal Sciences

country: USA

institute: University of Florida

summary: The objective of this research was to identify a set of genes whose transcript abundance is predictive of a cow’s ability to become pregnant following artificial insemination (AI). Endometrial epithelial cells from the uterine body were collected for RNA sequencing using the cytobrush method from 193 first-service Holstein cows at estrus prior to AI (day 0). A group of 253 first-service cows not used for cytobrush collection were controls. There was no effect of cytobrush collection on pregnancy outcomes at day 30 or 70, or on pregnancy loss between day 30 and 70.  There were 2 upregulated and 214 downregulated genes (FDR < 0.05, absolute fold change > 2-fold) for cows pregnant at day 30 versus those that were not pregnant. Functional terms overrepresented in the downregulated genes included those related to immune and inflammatory responses. Machine learning for fertility biomarkers with the R package BORUTA resulted in identification of 57 biomarkers that predicted pregnancy outcome at day 30 with an average accuracy of 77%. Thus, machine learning can identify predictive biomarkers of pregnancy in endometrium with high accuracy. Moreover, sampling of endometrial epithelium using the cytobrush can help understand functional characteristics of the endometrium at AI without compromising cow fertility.

overall_design: 193 lactating dairy cows underwent cytobrush collection of the uterine body directly before artificial insemination. RNA was extracted from the endometrial cells and subsequently underwent machine learning to predict biomarkers of pregnancy success.

first: Quinn

last: Hoorn

first: Maria

middle: B

last: Rabaglino

first: Thiago

middle: F

last: Amaral

first: Tatiane

middle: S

last: Maia

first: Fahong

last: Yu

first: John

last: Cole

middle: J


title: Small-molecule Inhibition of METTL3 Suppresses Tumor Growth and Promotes Neuroblastoma Differentiation [RNA-seq siMETTL3]

first: Susan

middle: L

last: Cohn

overall_design: RNA-Seq was performed in the Kelly cell line following treatment with siControl or siMETTL3 for 72 hours.

first: Monica

middle: M

last: Pomaville

first: Mohansrinivas

last: Chennakesavalu

first: Pingluan

last: Wang

first: Zhiwei

last: Jiang

first: Hui-Lung

last: Sun

first: Peizhe

last: Ren

first: Ryan

last: Borchert

first: Varsha

last: Gupta

first: Chang

last: Ye

first: Ruiqi

last: Ge

first: Zhongyu

last: Zhu

first: Mallory

last: Brodnik

first: Yuhao

last: Zhong

first: Kelley

last: Moore

first: Helen

last: Salwen

first: Rani

middle: E

last: George

first: Malgorzata

last: Krajewska

first: Alexandre

last: Chlenski


title: Small-molecule Inhibition of METTL3 Suppresses Tumor Growth and Promotes Neuroblastoma Differentiation [RNA-Seq Decay]

first: Susan

last: Cohn

overall_design: RNA-Seq was performed in Kelly and NGP cell lines following treatment with STM2457 or DMSO for 3 or 6 days, and incubation with actinomycin D for either 0, 3, or 6 hours.

first: Monica

last: Pomaville

first: Mohansrinivas

last: Chennakesavalu

first: Mark

last: Applebaum

first: Chuan

last: He


title: RFX6 haploinsufficiency predisposes to diabetes through impaired beta cell function

status: Public on Apr 11 2024

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

summary: We performed bulk RNA-seq analysis for CRISPR-Cpf1 mutated H1 cells that were differentiated into pancreatic cells. Homozygous mutant was compared to control cells (RFX6-/- vs RFX6+/+)  at stage 3 (PF) and stage 5 (EP), and heterozygous mutant was compared to control cells (RFX6-/+ vs  RFX6+/+) at stage 7 (SC-islets).

overall_design: RNA-seq

first: Hazem

last: Ibrahim

first: Diego

last: Balboa

first: Jonna

last: Saarimäki-Vire

first: Hossam

last: Montaser

first: Oleg

last: Dyachok

first: Per-eric

last: Lund

first: Muhmmad

last: Omar-Hmeadi

first: Om

middle: P

last: Dwivedi

first: Väinö

last: Lithovius

first: Tom

last: Barsby

first: Vikash

last: Chandra

first: Solja

last: Eurola

first: Jarkko

last: Ustinov

first: Tiinamaija

last: Tuomi

first: Päivi

last: Miettinen

first: Sebastian

last: Barg

first: Anders

last: Tengholm

first: Timo

last: Otonkoski


title: Small-molecule Inhibition of METTL3 Suppresses Tumor Growth and Promotes Neuroblastoma Differentiation [meRIP-Seq]

first: Susan

last: Cohn

overall_design: meRIP-Seq and RNA-Seq were performed in Kelly and NGP cell lines at 1 day and 6 days following treatment with STM2457 or DMSO. meRIP-Seq and RNA-Seq were performed in a mouse neuroblastoma xenograft (Kelly cell) tumor model treated with STM2457 or DMSO once a day for 14 days.

first: Monica

last: Pomaville

first: Mohansrinivas

last: Chennakesavalu

first: Pingluan

last: Wang

first: Zhiwei

last: Jiang

first: Hui-Lung

last: Sun

first: Peizhe

last: Ren

first: Ryan

last: Borchert

first: Varsha

last: Gupta

first: Chang

last: Ye

first: Ruiqi

last: Ge

first: Zhongyu

last: Zhu

first: Mallory

last: Brodnik

first: Yuhao

last: Zhong

first: Kelley

last: Moore

first: Helen

last: Salwen

first: Rani

last: George

first: Malgorzata

last: Krajewska

first: Alexandre

last: Chlenski

first: Mark

last: Applebaum

first: Chuan

last: He


title: Small-molecule Inhibition of METTL3 Suppresses Tumor Growth and Promotes Neuroblastoma Differentiation

first: Susan

last: Cohn

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

overall_design: Refer to individual Series


title: Repetitive element transcript accumulation is related to inflammaging in humans

status: Public on Apr 09 2024

city: Fort Collins

first: Thomas

last: LaRocca

state: CO

address: 1582 Campus Delivery

institute: Colorado State University

type: Methylation profiling by high throughput sequencing

summary: Inflammation is an established feature of many age-related diseases, and growing evidence implicates transcripts from repetitive elements in inflammatory signaling with aging. We generated transcriptomic (RNA-seq) and whole-genome bisulfite sequencing (WGBS, for methylation) data on frozen/biobanked peripheral blood mononuclear cells from middle-aged and older adults, as well as younger and older adults before and after an exercise intervention, to evaluate correlations among repetitive elements and inflammation, along with methylation of repetitive elements.

overall_design: RNA-seq was performed on peripheral blood mononuclear cell (PBMC) samples from 90 healthy, middle age and older adults. RNA-seq and WGBS were also performed on PBMC samples from a separate study of 10 young, healthy sedentary adults, and 13 healthy sedentary older adults before (T1) and after (T2) a 16-week supervised aerobic training intervention.


title: Oct4 redox sensitivity potentiates reprogramming and differentiation

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: N Campus Dr, Salt Lake City, UT 84103

department: Pathology

institute: University of Utah

summary: The transcription factor Oct4/Pou5f1 is a key component of the regulatory circuitry governing pluripotency. Oct4 is also widely used to generate induced pluripotent stem cells (iPSCs) from somatic cells. These observations provide compelling rationale to understand Oct4’s functions. Here we used domain swapping and mutagenesis to compare Oct4’s reprogramming activity with the paralog Oct1/Pou2f1, identifying a redox-sensitive DNA binding domain cysteine residue (Cys48) as a key determinant of both reprogramming and differentiation. In combination with the Oct4 N-terminus, mutating Oct1’s serine at this position to cysteine is sufficient to confer strong reprogramming activity. Conversely, Oct4C48S strongly reduces reprogramming potential. Oct4C48S renders the protein insensitive to oxidative inhibition of DNA binding. The same mutation prevents oxidation-mediated protein ubiquitylation. An engineered Pou5f1C48S point mutation has little effect on undifferentiated cells embryonic stem cells (ESCs), but upon retinoic acid (RA)-mediated differentiation causes retention of Oct4 expression, decreased proliferation, and increased apoptosis. Transcriptional profiling reveals that the retention of pluripotency also manifests at the RNA level. Pou5f1C48S ESCs also contribute poorly to adult somatic tissues and form less differentiated teratomas. Collectively, the data support a model in which Oct4 redox sensing is a positive reprogramming determinant during one or more reprogramming steps, and mediates Oct4 degradation during differentiation.

overall_design: To investigate the gene expression difference and similarity in parent and Oct4 C48S mutant Bl/6J ESC in pluripotent state as well as RA differentiation state, we extracted RNA from each cell line of two states for sequencing

first: Zuolian

last: Shen

first: Yifan

last: Wu

first: Asit

last: Manna

first: Kimberly

first: Mahesh


title: A virally encoded high resolution screen of cytomegalovirus host dependencies

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: Genetic screens have transformed our ability to interrogate cellular factor requirements in infection, yet current approaches are limited in their sensitivity, biased towards early stages of infection and provide only simplistic phenotypic information which is often based on infected cell survival. Here, by engineering human cytomegalovirus to express sgRNA libraries directly from the viral genome, we developed a sensitive, versatile, viral centric approach that allows profiling of different stages along viral infection in a pooled format. Using this approach, which we termed VECOS (Virus Encoded CRISPR-based direct readOut Screening system), we identified hundreds of novel dependency and restriction factors and we quantified their direct effects on viral genome replication, viral particle secretion and infectiousness of secreted particles, providing a multi-dimensional perspective on viral-host interactions. These high resolution measurements reveal that perturbations that alter late stages in HCMV life cycle mostly regulate HCMV particle quality rather than quantity, defining correct virion assembly as a critical stage that is heavily reliant on viral-host interactions. Overall, VECOS facilitates systematic high resolution dissection of human proteins' role along the infection cycle, providing a roadmap for in-depth dissection of host–herpesvirus interactions.

overall_design:
CRISPR/Cas9 based screen perfomed by creating an sgRNA library encoded in Human Cytomegalovirus (HCMV), where each virus expresses one sgRNA targeting one of 2000 genes in the human genome. Cas9-expressing fibroblasts were infected with the library at a low MOI, and sgRNA abundance was determined via deep sequuencing of sgRNA amplicon sequences, amplified from the viral genome.
Samples were collected at 10 days post infection, and sgRNA abundance was determined in the infected cells, in the secreted virus, and in the infectious virus population (by sequencing virses that established infection in WT fibroblasts. Each condition was done in triplicates, and the selection in Cas9-cells was performed in 3 sequential rounds. The input library was sequenced in three biological replicates, and the plasmid and BAC cloning stages were also sequenced.
To verify the effectivity of knockout by sgRNA expressed from the viral genome, viruses targeting two human genes (RRM2 and TRIP10) were used to infect Cas9 fibroblasts and the cells were harvested at different times post infection (0, 10, 24, 48, 72 hours), and PCR amplicons of the targeted seuqences in the human genome were deep sequenced.

first: Yaara

last: Finkel

first: Aharon

last: Nachshon

first: Einav

last: Aharon

first: Tamar

last: Arazi

first: Elena

last: Simonovsky

first: Martina

last: Dobesova

first: Avi

last: Gluck

first: Tal

last: Fisher

first: Richard

last: Stanton

first: Michal

last: Schwartz


title: Gene expression profiling of human fresh and cryopreserved sperm

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

country: Italy

institute: IRCCS AOU San Martino-IST

summary:
Cryopreservation process deregulates the expression of pathways important for fertility in human spermatozoa Study design, size, duration (max. 75 words): Semen samples were obtained from 20 normospermic men from April to May 2022. Each sample was divided in two aliquots. From one aliquot total RNA was immediately extracted. The second aliquot was slowly cryopreserved and after a week of storage in liquid nitrogen total RNA was extracted. A total of 13 paired RNA samples passed quality control and were analyzed after randomization into 4 pools, each of 6 patients. Participants/materials, setting, methods (max. 75 words): The men who participated in this study had a median age of 35.0 years (range: 29.0-46.0). RNA was extracted by miRNeasy Micro Kit (Qiagen), analyzed by High Sensitivity RNA on 2200 Tape Station system (Agilent), amplified by Ovation Pico WTA SystemV2 (Nugen), labeled and hybridized on GE 4x44K v2 microarrays (Agilent). The paired Significance Analysis of Microarray (SAM) was performed using the limma, hgug4112a.db and samr packages in R/BioConductor. Main results and the role of chance (max. 200 words): The expression profiles of cryopreserved sperm significantly differed from those of fresh sperm in 219 down-regulated and 28 up-regulated unique transcripts. The gene ontology analysis disclosed that cryopreservation downregulates genes involved in sperm motility by the mitochondria function (CABS1, SPATA19) and the correct organization of the sperm midpiece and flagellum cytoskeleton (ACTL7A, AKAP4, C9ORF24, CAPZB, CCIN, IQCG, ODF2, SPATA6, SPATA6L, TBC1D21), in fertilization (ACTL7A, AKAP4, PLCZ1, PRSS37, TUBGCP3), early embryo development (AGT, CLMN, DCC, DHRS3, EGFLAM, FAM20A, FREM1, GPI, HEMGN, KRTDAP, IFT172, MICAL2, MLF1, NF2, PGRMC2, PHACTR1, POPDC3, RO60, ROBO1, RORA, SGCA, SPRR2D, TCF4, TNC, TNNI3), oxidant detoxification (TXNDC29) and DNA repair (BRIP1, ERCC6, TRIP12), calcium ion binding and homeostasis (AMY1C, ANO1, ANO2, ASGR1, CABS1, CPNE9, FREM1, KCNIP2, ITPR3, PKD2L1, PLCZ1, SELENOK, SYN3, TNNI3). Upregulated genes were enriched in pathways related to the negative regulation of DNA damage response (ALOX15B, CD74, RPL10, SNAI1, THBS1), cellular response to calcium ion (ALOX15B, FOSB, HLA-DQB1, S100A4, THBS1), regulation of transcription (CD74, FOSB, HLA-DRB1, MAMLD1, RASD1, RPL10, SNAI1, TCF15, TLE1), protein stabilization (CD74), protein ubiquitination (BAG1, DCAF6, ERCC6, HERPUD2, KLHL7, MARCHF8, NF2, PSMA6, RNF133, SERGEF, TRIP12, UBE2DNL, UBL3, UBQLN3, ZNRF3) and ubiquitin protein ligase binding (GPI, HSPA1L, PRKAR2A, STX8).
The storage time of cryopreserved human spermatozoa does not affect pathways involved in fertility. Study design, size, duration This study included 24 normospermic men after their written informed consent, of whom 13 had cryostored semen for a short-time (1 week) and 11 had cryostored semen for a long-time (median 9 years, range 7-10).  RNA was extracted from each frozen-thawed sperm sample and randomized into pools (4 pools for short-time samples and 3 pools for long-time samples), each of 5-6 patients. Wide-transcriptome comparison of short- and long-time pools were analyzed. Participants/materials, setting, methods The study population had a median age of 34.5 years (range: 22-46), without significant difference between the two groups (p-value = 0.147). RNA was extracted by miRNeasy Micro Kit (Qiagen), analyzed by High Sensitivity RNA on 2200 Tape Station system (Agilent), amplified by Ovation Pico WTA SystemV2 (Nugen), labeled and hybridized on GE 4x44K v2 microarrays (Agilent). The unpaired Significance Analysis of Microarray (SAM) was performed using the limma, hgug4112a.db and samr packages in R/BioConductor. Main results and the role of chance Comparison of gene expression profiles between thawed sperm after a short or long storage period in liquid nitrogen identified 5 unique transcripts significantly upregulated in the latter group (DCP1A, FAM217A, HUWE1, MSI2, PCSKIN). Functional annotation enrichment has shown that the dysregulated transcripts are involved in methylation and protein binding. In particular, HUWE1 encodes an E3 ubiquitin protein ligase required for protein ubiquitination. The protein encoded by DCP1A is a decapping enzyme, necessary for the degradation of mRNAs. The RNA binding protein MSI2 regulates the expression of target mRNAs at the translation level. Interestingly, HUWE1 serves as a central node in cellular stress responses, cell growth and death, signal transduction, etc. During early embryonic development, siRNA-mediated knockdown of HUWE1 induced apoptotic cell death and inhibited normal embryonic development. Consistent with this finding, decreased HUWE1 staining in human embryos was found to be associated with poor embryo quality, suggesting that HUWE1 plays important roles in promoting embryonic development. DCP1A is also essential for embryonic development. Overall, no critical pathways involved in fertility are dysregulated during storage of sperm in liquid nitrogen and upregulation of genes important for early embryonic development may compensate for sperm cryoinjury.

overall_design: we analized the effect of cryopreservation comparing gene expression profiles of cryopreserved and fresh semen samples from the same patients (paired analysis) and the effect of long time of cryostorage comparing gene expression profiles of short time cryopreserved samples and long time cryopreserved samples  (unpaired analysis)

first: Adriana

last: Amaro

first: Francesco

last: Reggiani

first: Paola

last: Scaruffi


title: An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The nucleus is composed of functionally distinct membraneless compartments that undergo phase separation (PS). However, whether different subnuclear compartments are connected remains elusive. We identified a type of nuclear body with PS features composed of BAZ2A that associates with active chromatin. BAZ2A bodies depend on RNA transcription and BAZ2A non-disordered RNA-binding TAM domain. Although BAZ2A and H3K27me3 occupancies anticorrelate in the linear genome, in the nuclear space, BAZ2A bodies contact H3K27me3 bodies. BAZ2A-body disruption promotes BAZ2A invasion into H3K27me3 domains, causing H3K27me3-body loss and gene upregulation. Weak BAZ2A-RNA interactions, such as with nascent transcripts, promote BAZ2A bodies, whereas the strong binder long non-coding RNA (lncRNA) Malat1 impairs them while mediating BAZ2A association to chromatin at nuclear speckles. In addition to unraveling a direct connection between nuclear active and repressive compartments through PS mechanisms, the results also showed that the strength of RNA-protein interactions regulates this process, contributing to nuclear organization and the regulation of chromatin and gene expression.

first: Luigi

last: Lerra

last: Panatta

first: Dominik

last: Bär

first: Isabella

last: Zanini

first: Jennifer

middle: Y

last: Tan

first: Agnese

last: Pisano

first: Chiara

last: Mungo

first: Vikram

middle: G

last: Panse

first: Ana

middle: C

last: Marques


title: Loss of dihydroceramide desaturase drives neurodegeneration by disrupting endoplasmic reticulum and lipid droplet homeostasis in glial cells

status: Public on Apr 08 2024

city: St. Louis

first: James

last: Skeath

state: Missouri

address: 4515 Couch building, 4523 Clayton Ave

department: Genetics

institute: Washington University School of Medicine

summary: We performed high-throughput RNA sequencing to determine the transcriptional changes of infertile crescent (ifc) mutants as compared to wild-type controls in the dissected CNS in Drosophila melanogaster.

overall_design: We dissected and extracted RNA from 20-30 CNS of third instar larve for wild type or ifc mutant per sample, with five total samples per experimental group.

first: Yuqing

last: Zhu

first: Yi

first: Haluk

last: Lacin

first: Beth

last: Wilson


title: Coxsackievirus A10 impairs nail regeneration and induces onychomadesis by mimicking DKK1 to attenuate Wnt signaling

city: Beijing

first: jiabao

last: cao

address: Beichen west road

country: China

institute: Institute of microbiology, Chinese academy of science

summary: Coxsackievirus A10 (CV-A10) infection, a prominent cause of childhood hand-foot-and-mouth disease (HFMD), frequently manifests with the intriguing phenomenon of onychomadesis, characterized by nail shedding. However, the underlying mechanism is elusive. Here, we found that CV-A10 infection in mice could suppress Wnt/β-catenin signaling by restraining LDL-receptor-related protein 6 (LRP6) phosphorylation and β-catenin accumulation and led to onychomadesis.  Mechanistically, CV-A10 mimics Dickkopf-related protein 1 (DKK1) to interact with Kringle-containing transmembrane protein 1 (KRM1), the CV-A10 cellular receptor. We further found that Wnt agonist (GSK3β inhibitor) CHIR99021 can restore nail stem cell differentiation. These findings provide novel insights into the pathogenesis of CV-A10 and related viruses in onychomadesis and guide prognosis assessment and clinical treatment of the disease.

overall_design: Examination the gene expression profiles from PBS+Vaseline and Coxsackievirus A10-Vaseline and Coxsackievirus A10-CHIR  treated mice digits.

first: George

last: Gao

first: Ye-Guang

last: Chen

first: Jun

last: Wang

first: Yingzi

last: Cui

first: Jiabao

last: Cao

first: Xiaodan

first: Yuxuan

last: Zheng

first: Jianyu

last: Tong

first: Zhou


city: Hangzhou

first: Xiaochun

last: Yu

state: Zhejiang

address: 18 Shilongshan Street

institute: Westlake University

summary: We report the Ku80/Ku70 complex associated RNA in HEK293T cells using RNA-seq following PAR-Clip.

overall_design: Examination of Ku80/Ku70 complex associated RNA in HEK293T cells

first: Peng

last: Li

first: Xiaochen

last: Gai

first: Qilin

first: Qianqian

last: Yang


title: Macrophage MCT4 inhibition activates reparative genes and protects from atherosclerosis by histone H3 lysine 18 lactylation

city: Nanjing

first: Hong

last: Jiang

address: Longmian Road No.101

institute: Nanjing Medical University

summary: Macrophage activation is a hallmark of atherosclerosis, accompanied by a switch in core metabolism from oxidative phosphorylation to glycolysis. The crosstalk between metabolic rewiring and epigenetic modifications in macrophages is worthy of further investigation. Here, we found that lactate efflux-associated monocarboxylate transporter 4 (MCT4)-mediated histone lactylation is closely related to atherosclerosis. Histone H3 lysine 18 lactylation dependent on MCT4 deficiency activated the transcription of anti-inflammatory genes and tricarboxylic acid cycle genes, resulting in the initiation of local repair and homeostasis. Strikingly, histone lactylation is characteristically involved in the stage-specific local repair process during M1 to M2 transformation, whereas histone methylation and acetylation are not. Gene manipulation and protein hydrolysis-targeted chimerism (PROTAC) technology were used to confirm that MCT4 deficiency favors ameliorating atherosclerosis. Therefore, our study shows that macrophage MCT4 deficiency, which links metabolic rewiring and epigenetic remodeling, plays a key role in training macrophages to become repair and homeostasis phenotypes.

overall_design: ox-LDL-induced THP-1-derived macrophages with or without MCT4 deficiency, three samples for each group.


title: Gene expression changes in mouse kidney between 4 and 24-26 months of age

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Expression of many genes change as a function of age, but the specific genes and extent of expression changes differs between different conditions.  In this work we perform whole genome sequencing on RNA extracted from the kindeys of male and female wildtype mice at 4 and 24-26 months of age to assess changes in gene expression and alterations in pathways related to aging.

overall_design: To assess the effect of age on gene expression in the kidney mice were euthanized at 4 or 24-26 months of age under fed conditions and kidney tissue was snap frozen in liquid nitrogen.  We then performed gene expression profiling using RNAseq data obtained from these tissues.

first: Miguel

last: Calvo-Rubio

first: Rafael

last: de Cabo


title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation [bulk RNA-seq]

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: Tauopathies are age-associated neurodegenerative diseases whose mechanistic underpinnings remain elusive, partially due to lack of appropriate human models. Here, we engineered new human induced pluripotent stem cell (hiPSC)-derived neuronal lines to express 4R Tau and 4R Tau carrying the P301S MAPT mutation when differentiated into neurons. 4R-P301S neurons display progressive Tau inclusions upon seeding with Tau fibrils and recapitulate features of tauopathy phenotypes including shared transcriptomic signatures, autophagic body accumulation, and reduced neuronal activity. A CRISPRi screen of genes associated with Tau pathobiology identified over 500 genetic modifiers of seeding-induced Tau propagation, including retromer VPS29 and genes in the UFMylation cascade. In progressive supranuclear palsy (PSP) and Alzheimer’s Disease (AD) brains, the UFMylation cascade is altered in neurofibrillary-tangle-bearing neurons. Inhibiting the UFMylation cascade in vitro and in vivo suppressed seeding-induced Tau propagation. This model provides a robust platform to identify novel therapeutic strategies for 4R tauopathy.

overall_design: Bulk RNA sequencing of human iPSC-derived neurons expressing homozygous 4R Tau isoform with and without the P301S mutation, with and without K18-Tau fibril treatment (n=4-5per group).

first: Celeste

last: Parra Bravo

first: Alice

last: Giani

first: Jesus

last: Maero Perez

first: Zeping

last: Zhao

first: Yuansong

last: Wan

first: Avi

last: Samelson

first: Man

last: Wong

first: Alessandro

last: Evangelisti

first: Ethan

last: Cordes

last: Fan

first: Pearly

last: Ye

first: Daphne

last: Zhu

first: Tatyana

last: Pozner

first: Maria

last: Mercedes

first: Tark

last: Patel

first: Allan

last: Yarahmady

first: Gillian

last: Carling

first: Frederik

middle: H

last: Sterky

first: Virginia

last: Lee

first: Edward

first: Michael

last: DeTure

first: Dennis

middle: W

last: Dickson

first: Manu

last: Sharma

first: Sue-Ann

last: Mok

first: Wenjie

last: Luo

first: Mingrui

first: Martin

last: Kampmann

first: Shiaoching

last: Gong


title: Human iPSC 4R tauopathy model uncovers modifiers of tau propagation [scRNA-seq]

first: Li

last: Gan

overall_design: Single cell RNA sequencing of human iPSC-derived neurons expressing homozgyous 4R Tau isoform with the P301S mutation with and without K18-Tau fibril treatment (n=1 per group).

first: Celeste

last: Parra Bravo

first: Alice

last: Giani

first: Jesus

last: Maero Perez

first: Zeping

last: Zhao

first: Yuansong

last: Wan

first: Avi

last: Samelson

first: Man

last: Wong

first: Alessandro

last: Evangelisti

first: Ethan

last: Cordes

last: Fan

first: Pearly

first: Daphne


title: Spatially preserved multi-region transcriptomic subtyping and biomarkers of outcome with chemoimmunotherapy in extensive-stage small cell lung cancer [IMfirst_DSP cohort]

city: Madrid

first: Jon

last: Zugazagoitia

address: Avenida de Cordoba s/n

department: Medical Oncology

country: Spain

institute: Hospital Universitario 12 de Octubre

summary: Transcriptomic subtyping holds promise for personalized therapy in extensive stage small cell lung cancer (ES-SCLC). In this study, we aimed to assess intratumoral transcriptomic subtype diversity and to identify biomarkers associated with long-term chemoimmunotherapy benefit in human ES-SCLC. Our work highlights that high intratumoral heterogeneity, lack of consistent association with outcome, and unclear subtype-specific target expression are major challenges for SCLC subtype-based precision oncology. Pre-existing IFNϒ-driven immunity and mitochondrial metabolism seem key correlates of long-term efficacy for chemoimmunotherapy in ES-SCLC.

overall_design:
We used tumor samples from 32 ES-SCLC patients enrolled in the IMfirst clinical trial (EudraCT Number: 2019-002784-10) with adequate tumor material for spatially preserved transcriptomic analysis. The IMfirst study was a phase IIIb single arm multicenter trial evaluating the safety and effectiveness of PD-L1 blockade (atezolizumab) in combination with platinum-etoposide as first-line treatment in patients with ES-SCLC.
We retrieved pre-treatment, formalin-fixed and paraffin-embedded (FFPE), tumor specimens, which were centrally reviewed by an expert pathologist at the 12 de Octubre research facilities (Madrid, Spain).
Spatial mRNA profiling was done using the GeoMx Digital Spatial Profiling (DSP) system (NanoString). For this study, we used an mRNA assay that contained oligo-nucleotide-labeled, photocleavable, RNA-binding probes targeting the expression of ~1800 genes related to cancer pathways and anti-tumor immunity (Cancer Transcriptome Atlas, CTA, NanoString) plus additional custom-designed probes targeting the expression of three SCLC subtype-defining transcription factors not included in the CTA panel (NEUROD1, POU2F3, and YAP1).


title: Genetic activation of canonical RNA interference in mice [skeletal muscle]

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

type: Non-coding RNA profiling by high throughput sequencing

summary: Canonical RNA interference (RNAi) is sequence-specific mRNA degradation guided by small interfering RNAs (siRNAs) made from long double-stranded RNA (dsRNA) by RNase III Dicer. RNAi has different functions in eukaryotes including gene regulation, antiviral innate immunity or defense against transposable elements. In mammals, RNAi is constrained by inefficient cleavage of dsRNA by Dicer because it is adapted to produce microRNAs, a different class of small RNAs. An exception of the rule is highly active RNAi in mouse oocytes, which employs a truncated Dicer isoform (ΔHEL1). A homozygous mutation of murine Dicer to express only the truncated variant causes major dysregulation of microRNAs and perinatal lethality. Here, we report the phenotype and RNAi activity in DicerΔHEL1/wt mice, which are viable, fertile, slightly smaller, and show minimal miRNome changes. At the same time, endogenous siRNA levels are increased by an order of magnitude in DicerΔHEL1/wt mice. We show that siRNA abundance is limited by available dsRNA but not by the Protein Kinase R, an innate immunity factor shown to limit siRNA biogenesis in cultured cells. Using dsRNA expressed from a transgene, functional RNAi in vivo was successfully induced in the heart. DicerΔHEL1/wt mice thus represent a new model for researching mammalian canonical RNAi in vivo and offer an unprecedented platform for addressing earlier claims about its biological roles.

overall_design: Bulk small RNA-seq of 9 mouse skeletal muscle samples in three different genotypes: - 3x wt - 3x DicerSOM/wt Pkr–/– Tg(MosIR) - 3x DicerΔHEL1/wt Pkr–/– Tg(MosIR)

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Valeria

last: Buccheri


title: Bulk RNA-Seq of actinic keratoses

city: Stanford

first: Carolyn

last: Lee

state: CA

address: 269 Campus Drive

institute: Stanford University School of Medicine

summary: RNA-Seq was performed on 8 actinic keratoses (AK) to identify differentially expressed genes in AK vs normal skin and cutaneous squamous cell carcinoma

overall_design: Total RNA was then isolated from actinic keratoses using QIAshredder (Qiagen) and Trizol (ThermoFisher) followed by DNA removal with the TURBO DNA-free ki t (Ambion) according to the manufacturer’s instructions. RNA integrity was verified using an Agilent 2100 Bioanalyzer. RNA-Seq libraries were prepared with the mRNA Seq Sample Prep K it (Illumina, Inc.) as recommended by the manufacturer. 101 bp paired-end sequencing reads were obtained using the Illumina HiSeq platform.

first: Kenneth

last: Tsai

first: Tomas

last: Bencomo

first: Kimal

last: Rajapakshe

first: Cristian

last: Coarfa


title: Mitochondrial regulation of bone homeostasis via mitochondria transfer [II]

city: Shanghai

first: Peng

last: Ding

address: No.600, Yishan Road

department: Orthopaedics

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

summary: To reveal an unappreciated mechanism of mitochondrial regulation of skeletal metabolic homeostasis via mitochondria transfer and provide new insights of the mechanism of glucocorticoid-induced osteoporosis progression.

overall_design: MtD2pos and mtD2neg CD11b+ myeloid cells were separated from Prx1creMitodendra+/+ mouse bone marrow and performed unbiased RNA-sequencing to test whether mitochondria transfer from osteolineage to osteoclastic lineage cells is associated with alterations in activities of osteoclastic lineage cells.

first: Junjie

last: Gao

first: Chuan

first: Jialun

last: Mei

first: Jian

last: Zhou


title: Transcriptional profiling of myeloid cells (CD11b) and astrocytes (ACSA2) from the striatum and the midbrain of control and parkinsonian animals in the MPTP mouse model

city: Pamplona

first: Maria S.

last: Aymerich

state: Navarra

address: Calle Irunlarrea, 1

department: Biochemistry and Genetics

institute: Universidad de Navarra

summary: Neuroinflammation is a common hallmark of neurodegenerative diseases such as Parkinson’s disease (PD). Here, we questioned about the activation state of glial cells along the degeneration process of dopaminergic terminals in the striatum and loss of neuronal cell bodies in the midbrain. We hypothesized that MPTP administration pattern would produce different inflammatory responses that could modify the course of nigrostriatal degeneration.  To reproduce the dopaminergic impairment in a PD experimental mouse model, we used two different MPTP-administration patterns: subacute (sMPTP) and chronic (cMPTP). Bulk RNA sequencing of purified midbrain microglia/myeloid cells of sMPTP mice showed an anti-inflammatory phenotype, while midbrain microglia/myeloid cells of cMPTP mice showed a pro-inflammatory and phagocytic phenotype. Midbrain astrocytes presented a phagocytic phenotype in sMPTP mice. In the striatum, microglia presented a continuous pro-inflammatory state in sMPTP and cMPTP conditions. In this region, astrocytes presented a remarkable activated and phagocytic state in sMPTP mice which was attenuated with the chronicity of MPTP administration.

overall_design: Different patterns of MPTP intoxication were used. In the subacute MPTP (sMPTP) regimen, 30 mg/kg of MPTP dissolved in saline were administered intraperitoneal (i.p.) for 5 consecutive days. Control mice were injected with serum. In the chronic MPTP (cMPTP) regimen, mice received 10 i.p. injections of MPTP (20 mg/kg in saline) together with probenecid (250 mg/kg in saline) to retard the renal clearance of toxic metabolites of MPTP. Both compounds were injected twice a week along 5 weeks in two consecutive injections separated 30-60 minutes. Control mice received 10 i.p. injection of probenecid at the same concentration as parkinsonian animals. Upon sacrifice, the striatum and the ventral midbrain were dissected out to prepare a cell suspension from each region. CD11b+ myeloid cells and ACSA2+ astrocytes were subsequently separated for bulk mRNA sequencing (N = 3 animals/group).

first: M


title: Arginine methylation-mediated FXR1-G4 RNA binding in cancer cells

city: Albuquerque

first: Viswanathan

last: Palanisamy

state: NM

address: 2325 Camino de Salud NE,

department: Internal Medicine

institute: University of New Mexico

summary: The RBP, FXR1, is overexpressed in many epithelial tumors containing a canonical RGG box domain. FXR1 controls post-transcriptional gene regulation through changes in mRNA turnover and translation of target genes. Here we show that arginine methyltransferase PRMT5- mediated specific arginine methylation of FXR1 increases its stability in cancer cells. FXR1-dependent gene signatures show decreased expression and instability of G4-rich sequences containing mRNAs such as CDKN1A, PLK2, TCN2, and TRAF4. Furthermore, structural features of FXR1 and G4-RNA interactions provide novel insights into the critical arginine amino acids of FXR1 essential for G4-RNA-binding and turnover activity. In addition, analysis of the eCLIP data provides various RNA targets and the G-rich sequence motifs of FXR1 in head and neck cancer cell line. Thus, our results indicate that PRMT5-mediated methylation of FXR1 binding with G4-RNAs favors mRNA stability and turnover, contributing to cancer cell growth and proliferation.

overall_design: To Investigate the post-transcriptional regulation of FXR1, we used 74B head and neck cancer cell lines and UV irradited them to identify the FXR1 interacting RNA sequences.

first: Anitha

last: Vijaakumar

first: Palanisamy

last: Viswanathan


title: Clocking out and letting go to unleash green biotech applications in a photosynthetic host

city: Nashville

first: Carl

middle: Hirschie

last: Johnson

state: Tennessee

address: 465 21st Avenue South, U-8215 BSB/MRBIII

department: Biological Sciences

institute: Vanderbilt University

summary: Cyanobacteria are attractive hosts for producing pharmaceuticals, renewable fuels, and chemicals due to their ability to use sunlight as their energy source. Despite the application of traditional genetic tools such as the identification of strong promoters to enhance the expression of heterologous genes, however, cyanobacteria have lagged behind other microorganisms such as E.coli and yeast as economically efficient bioreactors. The previous approaches have ignored large-scale constraints within cyanobacterial metabolic networks on transcription, predominantly the pervasive control of gene expression by the circadian (daily) clock. Here we adopt a novel strategy and show that reprogramming gene expression within cyanobacteria by inactivation of the circadian oscillator coupled with release of circadian repressor elements in the transcriptional regulatory pathways enables a dramatic enhancement of expression in cyanobacteria of heterologous genes encoding both catalytically active enzymes and polypeptides of biomedical significance.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: To investigate the potential of the genes labA and kaiA in enhancing production of bioproducts, we created strains of the cyanobacterial model Synechococus elongatus PCC 7942 in which i) labA had been knocked-out, ii) kaiA had been overexpressed through a Zinc-induced promoter or iii) both modifications were done, and perfomed RNAseq on cultures that were given a 12h dark pulse and were collected after 12h in LL.

first: Yao

last: Xu

first: Maria Luísa

last: Jabbur

first: Tetsuya

last: Mori

first: Jamey

middle: D

last: Young


title: Genetic activation of canonical RNA interference in mice [thymus]

first: Filip

last: Horvat

overall_design:
Bulk small RNA-seq of 12 mouse thymus samples in four different genotypes:
- 3x wt
- 3x DicerSOM/wt Pkr-/– Tg(MosIR)
- 3x DicerΔHEL1/wt Pkr+/– Tg(MosIR)
- 3x DicerΔHEL1/wt Pkr–/– Tg(MosIR)

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Valeria

last: Buccheri


title: Genetic activation of canonical RNA interference in mice [liver]

overall_design:
Bulk small RNA-seq of 15 mouse liver samples in five different genotypes:
- 3x wt
- 3x DicerSOM/wt Pkr+/– Tg(MosIR)
- 3x DicerSOM/wt Pkr–/– Tg(MosIR)
- 3x DicerΔHEL1/wt Pkr+/– Tg(MosIR)
- 3x DicerΔHEL1/wt Pkr–/– Tg(MosIR)


title: Genetic activation of canonical RNA interference in mice [heart]

overall_design:
Bulk small RNA-seq of 15 mouse heart samples in five different genotypes:
- 3x wt
- 3x DicerSOM/wt Pkr+/– Tg(MosIR)
- 3x DicerSOM/wt Pkr–/– Tg(MosIR)
- 3x DicerΔHEL1/wt Pkr+/– Tg(MosIR)
- 3x DicerΔHEL1/wt Pkr–/– Tg(MosIR)


title: Genetic activation of canonical RNA interference in mice

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

overall_design: Refer to individual Series


title: Mouse ovarian P2 dataset for the protein atlas of ovarian aging

city: Goettingen

first: Sarah Mae

last: Penir

address: Am Fassberg 11

department: Department of Meiosis

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

summary: We used the scRNAseq data to map the specificity of the transcripts of the long-lived proteins to ovarian cell types.

overall_design: Postnatal ovaries were isolated from P2 mice and were subjected to single-cell RNA sequencing.

first: Sarah

first: Melina

last: Schuh


title: Altered gene expression in multiple key pathways in MSCs from people with osteoporosis compared to people who do not have osteoporosis

city: Maynooth

first: Fearon

last: Cassidy

address: Kathleen Lonsdale Institute of Human Health

country: Ireland

institute: Maynooth University

summary: Osteoporosis is caused by imbalanced bone remodelling homeostasis and is highly prevalent in post-menopausal women. The impact of osteoporosis on mesenchymal stromal cells (MSCs) is a key area of research as they are the progenitors of osteoblasts and are therefore critical to bone homeostasis. TBioinformatic analysis of transcriptional profiling data revealed specific misregulation of genes involved in the processing and trafficking of cellular components, as well as downregulation of Neo1 which has an important role in controlling cell fate choice. These data indicate that the therapeutic targeting of bone marrow MSCs to increase their numbers, to support the appropriate processing of cellular contents, or to redirect cell fate choice may provide new methods for the treatment of osteoporosis, thereby reducing fracture-associated morbidity and improving quality of life for the 200 million people living with osteoporosis globally.

overall_design:
mRNA profiles of human bone marrow-derived mesenchymal stromal cells from people with osteoporosis compared to people who do not have osteoporosis.
--------------------------------------------------------------
Authors state the following regarding the raw data: Cannot provide due to patient confidentiality.

first: Féaron

first: Cynthia

last: Coleman

first: Ana

last: Soriano Arroquia

first: Katarzyna

last: Goljanek-Whysall


title: Genetic activation of canonical RNA interference in mice [spleen]

overall_design:
Bulk small RNA-seq of 24 mouse spleen samples in six different genotypes:
- 4x wt
- 2x Dicerwt/wt Pkr–/– Tg(MosIR)
- 3x DicerSOM/wt Pkr+/– Tg(MosIR)
- 6x DicerSOM/wt Pkr–/– Tg(MosIR)
- 3x DicerΔHEL1/wt Pkr+/– Tg(MosIR)
- 6x DicerΔHEL1/wt Pkr–/– Tg(MosIR)


title: VSMC gene in normal kdney and chronic kidney mice

city: Aurora

first: Makoto

last: Miyazaki

address: 12700 E 22nd PL Denver CO

institute: University of Colorado

summary: Analysis of RNAs from VSMCs to find altered pathways in VSMC by CKD

overall_design: total RNA obtained from isolated VSMC of DBA  mice.


title: Tonic type 2 immunity controls autoimmunity in the skin

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

institute: Pusan National University

summary: The existence of immunoregulatory mechanisms that control autoimmunity in non-lymphoid tissues remains unclear. Through transcriptomic and lipidomic analyses, we found that psoriasis is tightly associated with a significant downregulation of fatty acid metabolism and biosynthesis pathways as well as Th2 signature genes. Among lipids-activated transcription factors, LXR and PPAR were required for fatty acid homeostasis and resistance to psoriasis in mice. STAT6 played a role in the homeostatic expression of LXR and PPARγ in the skin. Additionally, innate lymphoid cells established tonic type 2 immunity in normal skin by producing IL-13 continually. Mice lacking tonic type 2 immunity were more susceptible to psoriatic inflammation in vivo. In human skin, inhibiting tonic type 2 immunity worsened psoriasis-like inflammation and IL-17 production, while activating LXR or PPAR inhibited them. Therefore, tonic type 2 immunity is an essential tissue checkpoint that represses autoimmunity and maintains lipid homeostasis in the skin.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ear skins with chemical treatments (GW3965 or Troglitazone).

first: Yeonseok

last: Chung


title: Genome-wide CRISPR screening using cell lines that harbor the mutant hTERT-CRISPR allele.

city: Chuo-ku

first: Mitsuhiro

last: Machitani

state: Tokyo

address: 5-1-1 Tsukiji

country: Japan

institute: National Cancer Center Research Institute

summary: To assess the biological significances of p-hTERT in ALT cells, we used the CRISPR-Cas9 system targeting the hTERT gene and performed genome-wide CRISPR screening, which identified genes in the Fanconi anemia/BRCA pathway as synthetic lethal partners of hTERT.

overall_design: We established two U2OS cell clones with heterozygous mutations in the hTERT gene locus by CRISPR-Cas9 system. Genome-scale CRISPR loss of function screen were performed using these cells. Two replicates for each cell were included.

first: Akira

last: Nomura

first: Kenkichi

last: Masutomi


title: U2OS cells and hTERT CRISPR clones


title: Mitochondrial regulation of bone homeostasis via mitochondria transfer [RNA-seq]

first: Peng

last: Ding

summary: Recent studies have demonstrated that mitochondria can be transferred between different cell types to control metabolic homeostasis. However, whether the mitochondria transfer network occurred in the skeletal system or regulate skeletal metabolic homeostasis in vivo is not fully elucidated. Herein, we found that osteolineage cells transfer mitochondria to CD11b+ myeloid, B220+ lymphoid and hematopoietic stem and progenitor cells (HSPCs), of which monocytes/macrophages received the most transferred mitochondria. This process was inhibited by GC treatment contributing to the progression of glucocorticoid-induced osteoporosis (GIOP). Further analysis demonstrated that osteolineage cells transfer mitochondria to osteoclastic lineage cells via Miro1 mediated direct contact, and altered the glutathione metabolism, leading to the ferroptosis of osteoclastic lineage cells, thus inhibiting osteoclast activities. These findings revealed an unappreciated mechanism of mitochondrial regulation of skeletal metabolic homeostasis via mitochondria transfer and provide new insights of the mechanism of GIOP progression.

overall_design: Comparative gene expression profile analysis of RNA-seq data in BMM, mOCs and OCPs with or without mitochondrial transplant

first: Junjie

last: Gao

first: Jian

last: Zhou

first: Chu‘an

first: Jialun

last: Mei


title: Mitochondrial regulation of bone homeostasis via mitochondria transfer

overall_design: Purified mT/mG mtD2pos and mtD2neg osteoclast progenitors (OCPs) after coculture and OCPs without co-culture (Ctrl) were sorted and performed unbiased RNA-sequencing to test whether mitochondria transfer from osteolineage to osteoclastic lineage cells is associated with alterations in activities of osteoclastic lineage cells.

first: Chuan


title: Transcriptome data from U2OS cells and hTERT CRISPR clones

summary: To assess the biological significances of p-hTERT in ALT cells, we used the CRISPR-Cas9 system targeting the hTERT gene and performed RNA-seq to analyze the profile of gene expression in hTERT-CRISPR clones (clone#1 and #2). The subsequent gene ontology (GO) analysis showed enrichment of genes involved in cell cycle process and DNA replication within genes down-regulated in hTERT-CRISPR clones.

overall_design: We established two U2OS cell clones with heterozygous mutations in the hTERT gene locus by CRISPR-Cas9 system. Transcriptome data of wild-type U2OS cells and the hTERT CRISPR clones (clone#1 and #2) were obtained by the RNA-seq analysis. Two replicates for each cell.


title: Transcriptional analysis of T cells derived from individuals with neurodevelopmental disorder carrying de novo heterozygous PSMD11 variants

status: Public on Apr 07 2024

city: Nantes

first: Frédéric

last: Ebstein

address: IRS-UN - 8 quai Moncousu - BP 70721

department: L'unité de recherche de l'institut du thorax, Inserm UMR 1087

country: France

institute: French Institute of Health and Medical Research (Inserm)

summary: Gene expression profiling on T cells to investigate the effects of PSMD11 loss-of-function variants on the immune system using the Nanostring nCounter® Human AutoImmune Profiling Panel.

overall_design: Peripheral blood mononuclear cells (PBMC) isolated from blood draws from patients and healthy dnonors were subjected to polyclonal stimulation with phytohemagglutinin (PHA) and interleukin-2 (IL-2) to expand naive T cells. After 3 weeks of culture, total RNA was isolated from resting T cells for gene expression analysis.

first: Maja

last: Studencka-Turski


title: Transcriptome profiling of Pseudomonas syringae pv. syringae  9644 in rich media and hrp-inducing minimum media

city: Birmingham

first: Andrea

last: Vadillo Dieguez

address: Edgbaston

country: United Kingdom

institute: University of Birmingham

summary: Pseudomonas syringae pv. syringae 9644 (Pss9644) is a  causal agent of bacterial cherry canker causing necrotic symptoms on leaves, fruits, gummosis and canker in woody tissues of sweet cherry (Prunus avium). To understand which virulent factor genes were expressed in vitro, Pss9644 was grown in rich media (King's B Broth) and minimum media (hrp-inducing minimum media). The latter mimics the in planta environment.

overall_design: Pss9644 was grown in King's B broth overnight. Later, it was diluted (OD= 0.1) until grown to log phase (OD=0.6).  Cells were washed and shaking incubated in King's B broth and hrp-inducing minimum media  Cells were harvested after 5 hours post incubation. Total RNA was extracted. RNA samples underwent ribosomal depletion before sequencing.

last: Vadillo-Dieguez

first: Michelle

middle: T

last: Hulin

first: John

last: Connell


title: The CD8+ T cell tolerance checkpoint triggers a transcriptionally and epigenetically distinct differentiation state defined by protein translation defects

city: Melbourne

first: Ian

last: Parish

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: In this study, we examined the differentiation trajectory of CD8+ T cells undergoing peripheral tolerance by scRNAseq and ATACseq and compared their differentiation to that of CD8+ T cells under going effector/memory differentiation or exhaustion. We found that tolerant CD8+ T cells adopt a unique differentiation trajectory distinct from all other states examined. We additionally used bulk RNAseq to identify key gene modules controlled by antigen and/or bystander information. We found that tolerance was only breached by the combined actions of antigen load and inflammation, which synergistically induced gene modules linked to increased protein translation.

overall_design:
Cells were index sorted and scRNAseq was performed by MARS-seq.

The open chromatin regions of Naïve, Tolerance and Effector CD8+ T cells was assessed and compared by ATACseq.

Using bulk RNAseq, we examined the contribution of antigen load and bystander inflammation to the transcriptional profile of CD8+ T cells undergoing peripheral tolerance.

first: Willem

last: Van Der Byl

first: Tim

last: Peters

first: Antonio

last: Ahn


title: miRNA expression data from HPC-EVs

city: Wu Han

first: YUE

last: YUAN

institute: tongji medical college

summary:
EVs derived from HPCs could affect the progression of S. japonicum-induced fibrosis. Considering the EVs’ cargo, small RNAs account for a large proportion of cargoes in EVs, and act as one of the critical post-transcriptional regulators in cell-to-cell communication. Among them, miRNAs are the most studied and their regulatory roles in host–pathogen interactions are increasingly clear. HPCs are a kind of stem cells with potentially bidirectional differentiation ability and interact with hepatic stellate cells during liver injury. The activation of HPCs play an important role during S. japonicum-induced liver fibrosis.
We used microarrays to detail the gene expression of SEA-EVs and CON-EVs derived from HPC cell line, LE/6.

overall_design: LE/6 was selected and cultured with soluble egg antigen (SEA) from S. japonicum or PBS for 24hours. Then cell culture medium from LE/6 was harvested and stored at -80℃ until isolation of EVs. Isolated EVs were collected to detect the miRNA expression.

first: Yue

last: Yuan

first: Qian

last: Chen


title: Effect of depletion of CPSF6 on gene expression of Hep3B hepatocellular carcinoma cells

city: Seoul

first: Deok Yong

last: Sim

address: 26 Kyungheedae-ro

institute: Kyunghee university

summary: To investigate the associated pathway of CSPF6, we established a hep3B cell line in which the target gene was broken down by siRNA.

overall_design:
High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 500 (Illumina, Inc., USA).
Comparative gene expression profiling analysis of RNA-seq data for si-control and si-CPSF6 in hep3B cells

first: Deok

first: Sung-Hoon

last: kim


title: Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation [Hoxb8-FL Brie sgRNA-Seq]

city: New York

first: Ioanna

last: Tiniakou

address: 435 E 30th St

institute: NYU Langone

summary: The development of all dendritic cells (DCs) including antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs) is controlled by the growth factor Flt3 ligand (Flt3L) and its receptor Flt3. We genetically dissected this common Flt3L-driven pathway of DCs differentiation using CRISPR/Cas9-based dropout screening in a Flt3L-dependent progenitor cell line. Genome-wide screening identified multiple regulators of DC differentiation including the glycosylphosphatidylinositol transamidase complex and arginine methyltransferase Carm1, whose role was confirmed in vivo. It also showed that negative regulators of mTOR signaling, including the subunits of TSC and GATOR1 complexes, restricted progenitor growth but enabled DC differentiation, demonstrating that a TSC- and GATOR1-mediated shutdown of mTOR is required for the process. An orthogonal screen focused on transcriptional regulators showed that Trim33 (TIF-1g) is required for DC differentiation. Conditional targeting in vivo revealed an essential role of Trim33 in the development of all DCs, but not of monocytes or granulocytes. In particular, inducible deletion of Trim33 caused a rapid loss of all DC progenitors, pDCs and the cross-presenting cDC1 subset. The loss of Trim33 from DC progenitors caused spontaneous interferon and inflammatory response, aberrant induction of macrophage-specific genes, and failure to induce DC differentiation program. Collectively, these data elucidate common mechanisms that control Flt3L-driven differentiation of the entire DC lineage, and identify Trim33 as its essential regulator.

sample_organism:
Mus musculus
unidentified plasmid

platform_organism:
Mus musculus
unidentified plasmid

overall_design: sgRNA-Seq of Hoxb8-FL cells transduced with genome-wide mouse CRISPR Brie library

first: Boris

last: Reizis


title: Arginase inhibitor reduces fungal dissemination in murine pulmonary cryptococcosis by promoting anti-cryptococcal immunity

status: Public on Apr 06 2024

city: Klong-luang

first: Pornpimon

last: Angkasekwinai

state: Patumthani

country: Thailand

institute: Thammasat University

summary: Elevation of arginase enzyme activity in the lung contributes to the pathogenesis of various chronic inflammatory diseases and infections. Inhibition of arginase expression and activity is able to alleviate those effects. Here, we investigated the immunomodulatory effect of arginase inhibitor in C. neoformans infection. In the pulmonary cryptococcosis model that was shown to recapitulate human infection, we found arginase expression was excessively induced in the lung during the late stage of infection. To inhibit the activity of arginase, we administered a specific arginase inhibitor, nor-NOHA, during C. neoformans infection. Inhibition of arginase reduced eosinophil infiltration and level of IL-13 secretion in the lungs. Whole lung transcriptome RNA-sequencing analysis revealed that treatment with nor-NOHA resulted in shifting the Th2-type gene expression patterns induced by C. neoformans infection to the Th1-type immune profile, with higher expression of cytokines Ifng, Il6, Tnfa, Csf3, chemokines Cxcl9 and Cxcl10 and transcription factor Stat1.  More importantly, mice treated with arginase inhibitor had more infiltrating brain leukocytes and enhanced gene expression of Th1-associated cytokines and chemokines that are known to be essential for protection against C. neoformans infection. Inhibition of arginase dramatically attenuated spleen and brain infection, with improved survival. Taken together, these studies demonstrated that inhibiting arginase activity induced by C. neoformans infection can modulate host immune response by enhancing protective type-1 immune response during C. neoformans infection.  The inhibition of arginase activity could be an immunomodulatory target to enhance protective anti-cryptococcal immune responses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from the lung of PBS-treated or C. neoformans-infected BALB/c mice treated with PBS or nor-NOHA (at 14 days postinfection) with three biological replicates.

first: Adithap

last: Hansakon


title: Characterizing the transcriptional role of L-DOPA and antimycin A on mitichondrial regulation in Cryptococcus neoformans using a cir1 knockout strain

city: Vancouver

first: James

last: Kronstad

state: BC

address: 2185 E Mall

department: Mircobiology and Immunology

country: Canada

institute: University of British Columbia

summary: Proper mitochondrial function is critical for the ability of the fungal pathogen Cryptococcus neoformans to cause disease. Mitochondrial dysfunction of WT cells treated with antimycin A or L-DOPA, or on cells lacking Cir1 is evident from this dataset. These experiments revealed influences on transcript levels of genes encoding Fe-S cluster assembly components and the response to oxidative stress in Cryptococcus neoformans.

overall_design: Wildtype strains were treated with and without L-DOPA or antimycin A for 6 hours after a 16 hour initial growth period in rich and minimal media respectively prior to RNA isolation. The cir1 knockout strain was also grown in rich media for 16 hours prior to RNA isolation. 3 biological replicates were used for each treatment.

first: Christopher

last: Lee

first: Anna

last: Brisland

first: Peng

last: Xue


title: Genetic activation of canonical RNA interference in mice [brain]

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

institute: Institute of Molecular Genetics of the ASCR

summary: Canonical RNA interference (RNAi) is sequence-specific mRNA degradation guided by small interfering RNAs (siRNAs) made from long double-stranded RNA (dsRNA) by RNase III Dicer. RNAi has different functions in eukaryotes including gene regulation, antiviral innate immunity or defense against transposable elements. In mammals, RNAi is constrained by inefficient cleavage of dsRNA by Dicer because it is adapted to produce microRNAs, a different class of small RNAs. An exception of the rule is highly active RNAi in mouse oocytes, which employs a truncated Dicer isoform (ΔHEL1). A homozygous mutation of murine Dicer to express only the truncated variant causes major dysregulation of microRNAs and perinatal lethality. Here, we report the phenotype and RNAi activity in DicerΔHEL1/wt mice, which are viable, fertile, slightly smaller, and show minimal miRNome changes. At the same time, endogenous siRNA levels are increased by an order of magnitude in DicerΔHEL1/wt mice. We show that siRNA abundance is limited by available dsRNA but not by the Protein Kinase R, an innate immunity factor shown to limit siRNA biogenesis in cultured cells. Using dsRNA expressed from a transgene, functional RNAi in vivo was successfully induced in the heart. DicerΔHEL1/wt mice thus represent a new model for researching mammalian canonical RNAi in vivo and offer an unprecedented platform for addressing earlier claims about its biological roles.

overall_design:
Bulk small RNA-seq of 12 mouse brain samples in four different genotypes:
- 3x wt
- 3x DicerSOM/wt Pkr–/– Tg(MosIR)
- 3x DicerΔHEL1/wt Pkr+/– Tg(MosIR)
- 3x DicerΔHEL1/wt Pkr–/– Tg(MosIR)

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Valeria

last: Buccheri


title: Pulmonary gene expression after ischemia reperfusion in young and old mice

city: Sendai

first: Hozumi

last: Motohashi

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

department: Medical Biochemistry

institute: Tohoku University

summary: To examine the age-related vulnerability to lung ischemia reperfusion injury, pulmonary gene expression profiles after lung ischemia reperfusion were compared between young and old mice.

overall_design: 8-12 week-old and 22-24 month-old male C57BL/6J mice were used. The left pulmonary artery, vein, and bronchus were clamped all at once, and the ischemia was maintained in the left lung for 60 min. 1 hour and 1 day after the reperfusion, mice were sacrificed, and their lung tissues were processed for RNA purification.

first: Kazuki

last: Hayasaka

first: Yoshinori

last: Okada


title: Lysosome activity-dependent changes of gene expression in BMDM after LPS treatment

summary: We report changes of gene expression in lysosome-inhibited BMDM after LPS treatment.

overall_design: RNA-seq analysis in BMDM treated with lysosome inhibitors after LPS treatment.

first: Hiroki

last: Sekine

first: Hayato

last: Anzawa

first: Kengo

last: Kinoshita


title: Oxygen-dependent changes of gene expression in BMDM after LPS treatment

summary: We report oxygen-dependent changes of gene expression in BMDM after LPS treatment.

overall_design: RNA-seq analysis in BMDM differentiated under different oxygen concentrations after LPS treatment.

first: Fumiki

last: Katsuoka


title: Oxygen-dependent changes and lysosome activity-dependent changes of gene expression in BMDM after LPS treatment

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

overall_design: Refer to individual Series


title: Comprehensive analysis of circular RNA profiling in AZD9291-resistant non-small cell lung cancer cell lines

status: Public on Apr 05 2024

city: Shanghai

first: Tianxiang

last: Chen

address: Shanghai Chest hospital

institute: Shanghai Chest Hospital

summary: Considering the important role of circular RNAs (circRNAs) in cancers, we established AZD9291-resistant NSCLC cell lines (H1975/AZDR and HCC827/AZDR) and used microarray analysis to determine the circRNA expression profiles of the cells. The H1975/AZDR and HCC827/AZDR cell lines were induced by gradually increasing the drug concentration. CircRNA microarray expression profiles were obtained from H1975, HCC827, H1975/AZDR, and HCC827/AZDR cells and validated by quantitative reverse transcription PCR. Expression data were analyzed bioinformatically.

overall_design: We first established AZD9291-resistant H1975 and HCC827 cell lines (H1975/AZDR and HCC827/AZDR) by gradually increasing concentrations of AZD9291 for 72 hours with a recovery period between treatments.The newly established H1975/AZDR and HCC827/AZDR cell lines were maintained in a medium containing 10μM AZD9291, while the parental H1975 and HCC827 cell lines were cultured in drug-free medium.

first: Yunhai

last: Yang

first: Qingquan

last: Luo

first: Jizhuang

first: Yu

last: Gu

first: Jia

last: Huang


first: Mitsuhiro

last: Machitani

summary: To investigate the function of p-hTERT in nuclear speckles, we isolated hTERT complex by immunoprecipitation with an anti-hTERT mAb from nuclear speckles purified biochemically and conducted RIP-seq analysis for RNAs associated with hTERT in nuclear speckles.

overall_design: RNA Immunoprecipitation sequencing (RIP-seq) for hTERT in nuclear speckles biochemically purified  from HeLa cells. Two replicates were included.

first: Akira

last: Nomura

first: Kenkichi

last: Masutomi


title: Neuronal DAMPs exacerbate neurodegeneration via astrocytic RIPK3 signaling

city: Piscataway

first: Brian

last: Daniels

state: NJ

address: 604 Allison Road

department: Cell Biology and Neuroscience

institute: Rutgers, The State University of New Jersey

summary: Astrocyte activation is a common feature of neurodegenerative diseases. However, the ways in which dying neurons influence the activity of astrocytes is poorly understood. RIPK3 signaling has recently been described as a key regulator of neuroinflammation, but whether this kinase mediates astrocytic responsiveness to neuronal death has not yet been studied. Here, we used the MPTP model of Parkinson’s disease to show that activation of astrocytic RIPK3 drives dopaminergic cell death and axon damage. Transcriptomic profiling revealed that astrocytic RIPK3 promoted gene expression associated with neuroinflammation and movement disorders, and this coincided with significant engagement of DAMP signaling. Using human cell culture systems, we show that factors released from dying neurons signal through RAGE to induce RIPK3-dependent astrocyte activation. These findings highlight a mechanism of neuron-glia crosstalk in which neuronal death perpetuates further neurodegeneration by engaging inflammatory astrocyte activation via RIPK3.

overall_design: We performed bulk RNAsequencing of isolated midbrain tissue homogenates. Samples were derived from mice harboring a specific deletion of Ripk3 in astrocytes (R3AC+) or littermate controls (R3AC-) 3 days following treatment with MPTP or Saline. Each sample represents a distinct animal.

first: Nydia

last: Chang

first: Evan

last: DaPrano

first: Wesley

middle: R

last: Evans

first: Marialaina

last: Nissenbaum

first: Micheal

last: McCourt

first: Diego

last: Piscoya

first: Marissa

last: Lindman

first: Tsui-Wen

last: Chou

first: Colm

last: Atkins

first: Alexander

last: Kusnecov

first: Rafiq

last: Huda


title: ZNF397 Deficiency Triggers TET2-driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer [5hmC-seq]

city: Dallas

first: Ping

last: Mu

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Cente

summary: Cancer cells exhibit phenotypical plasticity and epigenetic reprogramming, which allows them to evade lineage-dependent targeted treatments by adopting lineage plasticity. The underlying mechanisms by which cancer cells exploit the epigenetic regulatory machinery to acquire lineage plasticity and therapy resistance remain poorly understood. We identified Zinc Finger Protein 397 (ZNF397) as a bona fide coactivator of the androgen receptor (AR), essential for the transcriptional program governing AR-driven luminal lineage. ZNF397 deficiency facilitates the transition of cancer cell from an AR-driven luminal lineage to a Ten-Eleven Translocation 2 (TET2)-driven lineage plastic state, ultimately promoting resistance to therapies inhibiting AR signaling. Intriguingly, our findings indicate that a TET2 inhibitor can eliminate the AR targeted therapies resistance in ZNF397-deficient tumors. These insights uncover a novel mechanism through which prostate cancer acquires lineage plasticity via epigenetic rewiring and offers promising implications for clinical interventions designed to overcome therapy resistance dictated by lineage plasticity.

overall_design: 5hmC-Seq samples were analyzed, triplicate data, sgNTsamples are control samples.


title: ZNF397 Deficiency Triggers TET2-driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer [ATAC-seq]

overall_design: ATAC-seq samples were analyzed, triplicate data, sgNT samples and sgZNF397 samples were control samples.


title: iPSCs-derived NK cells with site-specific integration of CAR19 and IL24 at the multi-copy rDNA locus enhanced antitumor activity and proliferation

city: Changsha

first: Yuxuan

last: Zhang

state: Hunan

address: 110 Xiangya Road

department: School of Life Sciences

institute: Central South University

summary: The generation of CAR-NK cells using induced pluripotent stem cells (iPSCs) has emerged as one of the paradigms for manufacturing off-the-shelf universal immunotherapy.iPSCs here were site-specifically integrated at the ribosomal DNA (rDNA) locus with interleukin 24 (IL24) and CD19-specific chimeric antigen receptor (CAR19), and successfully differentiated into iPSCs-derived NK (iNK) cells followed by expansion using magnetic beads in vitro. To explore the anti-tumor phenotype of CAR-loaded iNK cells and the likely role of IL24, RNA from four iNK cells was isolated, sequenced, and gene expression of the cell populations were compared.

overall_design:
To explore the molecular mechanism underlying the anti-tumor phenotype of CAR-loaded iNK cells and the potential impact of IL24 on CAR-loaded iNK cells, iPSCs were site-specifically integrated at the ribosomal DNA (rDNA) locus with interleukin 24 (IL24) and CD19-specific chimeric antigen receptor (CAR19), and successfully differentiated into iPSCs-derived NK (iNK) cells followed by expansion using magnetic beads in vitro.
We then performed gene expression profile analysis using data obtained from RNA-seq of four iNK cells populations.
Comparative gene expression profile analysis using data obtained from RNA-seq of the four iNK cells (CAR19-IL24-iNK, CAR19-iNK cells, LV-CAR19-iNK cells and iNK cells).

first: Qingxin

last: Shi

first: Peiyun

last: Wang

first: Chujun

last: Huang

first: Shuqing

last: Tang

first: Miaojin

last: Zhou

first: Qian

last: Hu

first: Lingqian

last: Wu

first: Desheng

last: Liang


title: ZNF397 Deficiency Triggers TET2-driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer [RNA-seq]

overall_design: Examination of transcriptomic changes in LNCaP/AR prostate cancer cell lines with modifications of ZNF397 gene. There is total 4 different conditions with 3 biological replicates each.


title: ZNF397 Deficiency Triggers TET2-driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer [ChIP-seq]

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Androgen Receptor (AR) in prostate cancer cells with modification of ZNF397 gene.
ChIP-Seq analysis, replicates included, sgNT groups as control group.


title: ZNF397 Deficiency Triggers TET2-Driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer


title: Antibacterial activities of the algal bromophenol methylrhodomelol against Pseudomonas aeruginosa

city: Münster

first: Verena

last: Spiegler

address: Corrensstraße 48

institute: University of Münster

summary: Methylrhodomelol (1) is a bromophenol from the red alga Vertebrata lanosa (L.) T.A.Christensen that has been associated with antimicrobial properties. Aim of the current study was therefore, to assess the antimicrobial potential of this compound in more detail against the gram-negative pathogen Pseudomonas aeruginosa. 1 exerted weak bacteriostatic activity against different strains when grown in minimal medium, whereas other phenolics were inactive. In addition, 1 (35 and 10 µg/mL) markedly enhanced the susceptibility of multidrug resistant P. aeruginosa towards the aminoglycoside gentamicin, while it did not affect the viability of Vero kidney cells up to 100 µM. Finally, pyoverdine release was reduced in bacteria treated at sub-inhibitory concentration, but no effect on other virulence factors was observed. Transcriptome analysis of treated versus untreated P. aeruginosa indicated an interference of 1 with bacterial carbon and energy metabolism, which was corroborated by RT-qPCR and decreased ATP-levels in treated bacteria.

overall_design: Comparative gene expression analysis of untreated versus treated (methylrhodomelol 75 µM) bacteria at one timepoint.

first: Joshua

last: Jacobtorweihen

first: Anja

last: Hartmann

first: Stefanie

last: Hofer


title: Liver Cullin 3 knockout transcriptomics

city: Oklahoma City

first: Tiangang

last: Li

state: OK

address: 975 NE 10th St

institute: University of Oklahoma Health Sciences Center

summary: To investigate the liver transcriptomics of WT and liver Cullin 3 KO mice on chow diect (CD) and Westrn diet (WD)

overall_design: C57BL/6 Cul3 flox mice were on CD or WD for 13 weeks, then AAV-TBG-Null or AAV-TBG-Cre were injected to these mice to generate WT and liver Cul3 KO mice, respectively. Mice were maintained on the same diet (eitehr CD or WD) for additional 5 weeks and tissues were collected for analysis.

first: Lijie

last: Gu

first: Rachael

last: Sharp


title: Chromatin Landscape Instructs Precise Transcription Factor Regulome during Embryonic Lineage Specification [RNA-seq]

first: Liping

address: 1239 Siping Road

institute: Tongji University

summary: Embryos originate from fertilized eggs and are shaped through continuous cell division and differentiation, accompanied by dramatic changes in transcription, translation, and metabolism. Epigenetic information and transcription factors (TFs) play indispensable roles in regulating these processes. Recently, the trophoblast regulator TFAP2C was found to be essential in initiating the earliest cell fate decisions. However, Tfap2c transcripts are still detectable in both the inner cell mass (ICM) and trophectoderm (TE) of blastocysts, raising questions regarding how TFAP2C functions once these two lineages are established. In this study, we delineated the dynamics of TFAP2C during the mouse peri-implantation stage and elucidated its collaboration with the key lineage regulators CDX2 and NANOG. Importantly, we proposed that de novo formation of H3K9me3 in the extraembryonic ectoderm during implantation antagonizes TFAP2C binding to crucial developmental genes, thereby maintaining its lineage identity. Together, this research highlights the plasticity of the epigenetic environment in designating the genomic binding of highly adaptable lineage-specific TFs and regulating embryonic cell fates.

overall_design: Using CRISPR/Cas9 technology, we knocked out both Suv39h2 and Prdm2 genes. Mouse extraembryonic ectoderm was collected at E6.5 and E7.5 stages for total RNA-seq sequencing, and three replicates of sequencing data were obtained before and after the gene knockout.

first: Shanru

last: Yi

first: Guang

last: Yang

first: Rui

last: Gao


title: BAP-seq proximity labeling of subcellular compartments

city: Chicago

first: Bryan

last: Dickinson

state: IL

address: 929 E 57th St

department: Chemistry

institute: UChicago

summary: HEK293T cells expressing BS2 in different compartments (cytosol, mitochondria, nucleus, nucleolus) were labeled with AC-2. Subsequent enrichment of labeled RNAs, PolyA capture and RNA-seq reveals RNA populations in those compartments.

overall_design: Differentially Expressed Gene (DEG) analysis of transcripts enriched in different compartments

first: Shubhashree

last: Pani

first: Tian

last: Qiu


title: Arginine methylation-mediated FXR1 binding with RNAs in cancer cells

city: ALBUQUERQUE

first: Viswanathan

last: Palanisamy

state: New Mexico

address: MSC01 1230 1 Univ of NM

department: Division of Molecular Medicine

institute: University of New Mexico Health Sciences Center

summary: FXR1 is an RNA binding protein and it is post traslationally modified by a methyltrasferase to facilitate its RNA binding activity FXR1 is methylated by PRMT5, an arginine methyltransferase, to promote its stability and facilitate its association with mRNAs. Both genetic and small molecule PRMT5 inhibition failed to methylate recombinant as well as the endogenous FXR1, resulting in protein instability and downregulation of FXR1 target mRNA levels in HNSCC cells. To study the differentially regulated gene under the loss of PRMT5, we knocked- down the PRMT5 using shRNA and confirmed the transcript and protein levels using qRT PCR and immunoblot respectively.

overall_design: PRMT5 shRNA and control shRNA plasmids were used to transfect UMSCC74B cells. Cells were incubated at the appropriate condition for 72 h and mRNA levels and the protein expression were analyzed by qRT-PCR and immunoblot respectively.

first: Anitha

last: Vijayakumar


title: GigaMUGA SNP data of wild mice from Barcelona Robertsonian System (BRbS)

status: Public on Apr 04 2024

city: Bellaterra

first: Cristina

last: Marín García

state: Barcelona

address: Plaça Cívica

institute: Universitat Autònoma de Barcelona

summary: The Barcelona Robertsonian system (BRbS) presents mice with standard karyotype (diploid number 40) but also carrying Robertsonian fusions (ehich lead to variable diploid numbers ranging from 28 to 39). To study the heterogeneity of their genetic background and possible genome divergence between them, samples from three populations were genotyped.

overall_design: To investigate the degree of the genetic different between mice within and between populations, we genotyped 24 mice from three different populations included in the BRbS.  Sample types included two standard populations (CFB and CTR) and one Robertsonian population (VDC).

last: Marin-Garcia

first: Aurora

last: Ruiz-Herrera


title: Extraembryonic gut endoderm cells undergo programmed cell death during development (WGBS)

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

summary: Despite a distinct developmental origin, extraembryonic cells in mice contribute to gut endoderm and converge to transcriptionally resemble their embryonic counterparts. Notably, extraembryonic progenitors share a non-canonical epigenome, raising several pertinent questions, including whether this landscape is reset to match the embryonic regulation and if these cells persist into later development. Here, we developed a two-color lineage tracing strategy to track and isolate extraembryonic cells over time. We find that extraembryonic gut cells display substantial memory of their developmental origin including retention of their original DNA methylation landscape and resulting transcriptional signatures. Furthermore, we show that extraembryonic gut cells undergo programmed cell death and neighboring embryonic cells clear their remnants via non-professional phagocytosis. By midgestation, we no longer detect extraembryonic cells in the wild type gut while they persist and differentiate further in p53 mutant embryos. Our study provides key insights into the molecular and developmental fate of extraembryonic cells inside the embryo.

overall_design: DNA methylation profiling of sorted gut endoderm cells with embryonic and extraembryonic origin.

first: Julia

last: Batki

first: Dennis

last: Schifferl

first: Adriano

last: Bolondi

first: Maria

last: Walther

first: Lars

last: Wittler

last: Grosswendt

first: Bernhard

last: Herrmann

first: Alexander

last: Meissner


title: Extraembryonic gut endoderm cells undergo programmed cell death during development (RRBS)

first: Stefanie


title: The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

institute: University of South Florida

summary:
Purpose: In malaria parasites, the regulation of mRNA translation, storage and degradation is a critical aspect of gene expression, especially during the life stage transition. Since the DEAD-box helicases are involved in RNA metabolism, we wanted to determine whether pfdozi disruption led to altered mRNA abundance in P. falciparum.
Methods: In this study, we functionally characterized the DEAD-box RNA helicase PfDOZI in the human malaria parasite Plasmodium falciparum and discovered its functions on mRNA metabolism during development. We generate a pfdozi gene knockout (KO) parasite line. 1). The transcriptomic analysis via RNAseq to the asexual parasites at four stages (ring, early trophozoite, late trophozoite, and schizont)(10h, 20h, 30h, and 40h post-invasion) and the sexual stage (gametocytes) between KO and wildtype (WT) 3D7 parasite line were performed in triplicate. Total RNA was isolated from the purified parasites using the Quick-RNA MiniPrep kit (Zymo Research). RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained. Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2. Differentially expressed genes are determined by DESeq2 with Padj < 0.01 and absolute log2 fold change higher than 1. 2). To investigate the function of pfdozi in stress response, both KO and WT parasites at the schizont stage were cultured under stress conditions. RNAs were harvested for the transcriptomic analysis via RNAseq. 3). To identify the mRNA targets of PfDOZI in schizonts and gametocytes, we performed RNA-immunoprecipitation (RIP) coupled with next-generation sequencing from the PfDOZI::GFP parasites. A gaussian mixture model with a set of stringent criteria, including a read-depth coverage greater than 10, a fold enrichment ratio greater than 2, and posterior probabilities higher than 0.95 in both replicates.
Results: 1). RNA-seq analysis identified up-regulation of 18, 4, 7 and 130 genes and  down-regulation of 104, 44, 28 and 15 genes in the Δpfdozi parasite compared to WT 3D7 (fold change ≥ 2 and adjusted P (Padj) < 0.01) at ring (10h), early trophozoite (20h), late trophozoite (30h) and schizont (40h) stage, respectively. Our results showed that pfdozi disruption led to the upregulation of invasion-related genes in schizonts;  2). RNA-seq analysis revealed that the effect of pfdozi disruption on gametocytes was substantially more profound than in asexual stages, with 842 downregulated and 752 upregulated transcripts (fold change ≥2, Padj < 0.01) in the Δpfdozi gametocyte. About 80% of these markedly reduced transcripts are gametocyte/ookinete-specific transcripts. Genes related to microtubule/cytoskeleton, cellular respiration, and crystalloid were significantly enriched among the downregulated genes, which agrees with the defective morphogenesis of the Δpfdozi gametocytes. 3). RNAseq analysis showed that under the stress conditions, the WT parasites showed three-fold more upregulated transcripts (591) than downregulated (149), suggesting that significantly more transcripts were protected from degradation under stress conditions. In contrast, the Δpfdozi parasites had a much higher proportion (57%, 463) of downregulated than that of upregulated transcripts (43%, 346) under such stress conditions. 4). The RIP-seq analysis collectively identified the potential target mRNAs of the PfDOZI complex(es) in P. falciparum schizonts and gametocytes, identified 823 and 1377 transcripts as potential target mRNAs of the PfDOZI complexes in schizonts and gametocytes, respectively. Our data also showed significant overlaps with genes whose expression was disturbed upon pfdozi disruption.
Conclusions: Collectively, we have demonstrated that PfDOZI, likes its metazoan orthologs, is a versatile regulator of mRNA metabolism, and these functions are dynamically regulated during development with stage-specific characteristics.

overall_design: Expression profiling of Δpfdozi parasites at different stages or stress conditions, and mRNA targets of pfdozi

first: Hui

last: Min

first: Jun

last: Miao

first: Liwang

last: Cui


title: Australian Chronic Allograft Dysfunction I

city: Westmead

first: Harry

last: Robertson

state: NSW

address: 176 Hawkesbury Rd

department: Centre for Transplant and Renal Research

institute: Westmead Institute for Medical Research

summary: The Australian Chronic Allograft Dysfunction (AUSCAD) study is an ongoing single centre cohort study at Westmead hospital in Australia. In this section of the study, we aimed to identify biomarkers for rejection phenotypes in kidney transplant recipients, 3-months after their transplant. Our study recruited 70 patients, each having whole blood taken at the time of their 3-month protocol biopsy.

overall_design:
70 patients had paired renal allograft biopsies and blood draws collected 3-months post-transplant at Westmead hospital. Biopsies collected from patients were scored by a single pathologist using the Banff19 scoring schema. A composite definition of rejection (rej) was used for this study. Specially, patients with T-cell mediated rejection (TCMR), antibody mediated rejection (ABMR) and mixed rejection phenotypes were classified as a rejection blood sample.
Peripheral blood was collected into PAXgene Blood RNA tubes (Qiagen, Germany), left at room temperature for 5 hours, and stored at -80°C until RNA extraction. RNA was extracted by using PAXgene Blood miRNA kit (Qiagen, Germany). RNA samples were frozen and stored at -80°C.Frozen RNA samples were then sent to Australian Genome Research Facility (AGRF), Melbourne, Australia. Sample QC and library preparation were performed in-house by AGRF, and the resultant libraries sequenced using the NovaSeq 6000 platform (Illumina).

first: Jennifer

last: Li

first: Elivira

last: Jiminez-Vera

first: Natasha

last: Rogers

first: Ellis

last: Patrick

first: Philip

last: O'Connell


title: Extraembryonic gut endoderm cells undergo programmed cell death during development (RNA-seq)

first: Sara

last: Hetzel

overall_design: Transcriptome profiling of sorted gut endoderm cells with embryonic and extraembryonic origin.

first: Julia

last: Batki

first: Dennis

last: Schifferl


title: Life-long persistence of nuclear RNAs in the mouse brain

city: Dresden

first: Tomohisa

last: Toda

address: Tatzberg 41

institute: DZNE

overall_design: Refer to individual Series


title: Extraembryonic gut endoderm cells undergo programmed cell death during development (scRNA-seq)

overall_design: Single-cell RNA-seq profiling of sorted gut endoderm cells with embryonic and extraembryonic origin.

first: Adriano

last: Bolondi

first: Maria

last: Walther

first: Lars

last: Wittler

last: Grosswendt

first: Bernhard


title: Arabidopsis mRNA export factor MOS11: molecular interactions and role in abiotic stress responses

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

institute: University of Regensburg

summary: TREX (transcription and export) is a multi-subunit complex that links synthesis, processing and export of mRNAs. It interacts with the RNA helicase UAP56 and export factors such as MOS11 and ALYs to facilitate nucleocytosolic transport of mRNAs. Plant MOS11 is a conserved, but sparsely researched RNA-binding export factor, related to yeast Tho1 and metazoan CIP29/SARNP. Using biochemical approaches, the domains of MOS11 required for interaction with UAP56 and RNA-binding were identified. Further analyses revealed marked genetic interactions between MOS11 and ALY genes. Cell fractionation in combination with transcript profiling demonstrated that MOS11 is required for export of a subset of mRNAs that are shorter and more GC-rich than MOS11-independent transcripts. The central α-helical domain of MOS11 proved essential for physical interaction with UAP56 and for RNA-binding. MOS11 is involved in the nucleocytosolic transport of mRNAs that are upregulated under stress conditions and accordingly mos11 mutant plants turned out to be sensitive to elevated NaCl concentrations and heat stress. Collectively, these results establish that mRNA export is critically involved in the plant response to stress conditions and that MOS11 plays a prominent role.

overall_design: To investigate export defects in mos11 mutants, RNA was isolated in nuclear and cytoplasmic fractions from wild type Arabidopsis Thaliana (Col-0) and mos11 mutants

first: Amelie

last: Rödel

first: Christoph

last: Moehle

first: Klaus

last: Grasser


title: Extraembryonic gut endoderm cells undergo programmed cell death during development


title: Epigenetic differences in long non-coding RNA expression in Finnish and Russian Karelia teenagers with contrasting risk of allergy and asthma

city: Helsinki

first: Piia

last: Karisola

state: Southern Finland

address: Haartmaninkatu 3

department: Medical Faculty, Human Microbes Research Program Unit

institute: University of Helsinki

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

summary: The objective of the study was to investigate long non-coding RNA (lncRNA) expression profiles of blood mononuclear cells (PBMC), to identify lncRNAs that act at the interphase of microbiome-mediated immune homeostasis in allergy/asthma.

overall_design: Venous blood samples were collected from healthy  and asthmatic individuals from Finland (n=69) and Russia (n=75) yielding altogether 144 study subjects. PBMCs were separated and totRNA extracted for microarray analyses.

first: Joseph

last: Ndika

first: Vilma

last: Lahti

first: Nanna

last: Fyhrquist

first: Tiina

last: Laatikainen

first: Tari

last: Haahtela

first: Harri

last: Alenius


title: The Myc-Associated Zinc Finger Protein (MAZ) controls STAT1-mediated antiviral response by reshaping epigenome [MeDIP-Seq]

city: Bethesda

first: Gary

last: Felsenfeld

address: 9000 Rockville Pike

institute: NIH

summary:
The objectives of this study are to understand the regulatory roles of MAZ in biological processes using the NGS-deriveed ChIP-seq, DNA-MEDIP-seq and RNA-seq data in HAP1 control cells and MAZ knockout cells.  Our comparative analysis of these data generated from the HAP1 control and MAZ KO cells shows that MAZ is required for recruiting STAT1 to its target sites by reshaping epigenetic landscape in the human genome, thereby mediating antiviral response cells.
MEDIP-seq was performed using the MagMeDIP-seq Package from Diagenode in HAP1 control and HAP1 MAZ knockout  cells following manufacturer's instructions.

overall_design: MeDIP-seq data of HAP1 control cells and MAZ kockout cells were generated by deep sequencing in duplicate using Illumina GAIIx. The MEDIP-seq sequence reads were aligned with Bowtie2 followed by calling peaks with MACS2 software. Distribution  of  DNA methylation was analyzed using Deeptools and other software.

first: Tiaojiang

last: Xiao

first: Xin

last: Li


title: Foxp striatal compensation (ATAC-Seq)

first: Genevieve

last: Konopka

department: Neuroscience

institute: University of Texas Southwestern Medical Center

summary: Spiny projection neurons (SPNs) of the striatum are critical in integrating neurochemical information to coordinate motor and reward-based behavior. Mutations in the regulatory transcription factors expressed in SPNs can result in neurodevelopmental disorders (NDDs). Paralogous transcription factorsFoxp1andFoxp2, which are both expressed in the dopamine receptor 1 (D1) expressing SPNs, are known to have variants implicated in NDDs. Utilizing mice with a D1-SPN specific loss ofFoxp1,Foxp2, or both and a combination of behavior, electrophysiology, and single-nuclei RNA (snRNA-seq) and single-nuclei Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq), we find that loss of both genes results in impaired motor and social behavior as well as increased firing of the D1-SPNs. Differential gene expression analysis of snRNA-seq data implicates genes involved in autism risk, altered electrophysiological properties, and neuronal development and function. These data indicate complementary roles betweenFoxp1andFoxp2in the D1-SPNs.

overall_design: The transcription factors Foxp1 and Foxp2 are both expressed in the D1-SPNs of the striatum. We used single nuclei assay for transposase-accessible chromatin sequencing (snATAC-Seq) in both juvenile (P9) mouse striatum to investigate how loss of one or both of these genes from the D1-SPNs alters chromatin accessibility.

first: Newaz

last: Ahmed

first: Nitin

last: Khandelwal

first: Ashley

last: Anderson

first: Ashwinikumar

last: Kulkarni

first: Karthigayini

last: Sivaprakasam

first: Jay

last: Gibson