title: Chromatin accessibility in MC38/gp100 cells after type I PRMT inhibitor treatment

city: Houston

first: Weiyi

last: Peng

state: Texas

address: 3517 Cullen Blvd, Room 3025

institute: University of Houston

summary: Immunotherapies have produced dramatic responses in reducing tumor growth and prolonging overall survival to unprecedented rates in melanoma, lung cancer, renal cancer and mismatch repair deficient colon cancer patients. Despite approvals for immune checkpoint inhibitors in a wide range of cancers, the majority of patients’ relapse following initial response to immunotherapy or fail to respond altogether. These failures can be attributed to an insufficient immune response against tumors and/or mechanisms co-opted by tumor cells to produce a suppressive tumor microenvironment. Therefore, identification of combination strategies to enhance the response rates of immunotherapies to a broader patient population are the current subject of intensive basic and clinical research. Type I PRMTs have been described as regulators of immune response pathways in several cell types by direct arginine methylation on specific substrates, as well as through indirect mechanisms. Recent work has suggested that arginine methylation may have a role in tumor immunity, yet these roles remain poorly understood. Using the skin cutaneous melanoma (SKCM) TCGA dataset, we show that increased expression of Type I PRMTs is associated with poor clinical response and decreased immune infiltration in melanoma patients. Through a series of preclinical tumor models, we demonstrate that inhibition of Type I PRMTs can increase hallmarks of an inflamed tumor microenvironment and sensitivity to inhibition of the PD-(L)1 signaling axis. Accordingly, Type I PRMT inhibition synergizes with immune checkpoint blockade to induce durable and effective antitumor responses in an array of immunocompetent tumor models. These data provide a rationale to combine Type I PRMT inhibitors with checkpoint blockade to maximize clinical benefit in cancer patients.

overall_design: Chromatin accessibility profile of MC38/gp100 cells treated with DMSO or 1uM GSK3368712 for 5 days

first: Peng

last: Weiyi

first: Shi

last: Leilei

first: Wang

last: Yunfei


title: Rhizobia Contribute to Salinity Tolerance in Common Beans ( Phaseolus vulgaris L.)

status: Public on Oct 31 2022

city: Jena

first: Clabe

last: Wekesa

state: State

address: Hans-Knöll-Str. 8

country: Germany

institute: MPI for Chemical Ecology

type: Expression profiling by high throughput sequencing

summary: Rhizobia are soil bacteria that induce nodule formation on leguminous plants. In the nodules, they reduce dinitrogen to ammonium that can be utilized by plants. Besides nitrogen fixation, rhizobia have other symbiotic functions in plants including phosphorus and iron mobilization and protection of the plants against various abiotic stresses including salinity. Worldwide, about 20% of cultivable and 33% of irrigation land is saline, and it is estimated that around 50% of the arable land will be saline by 2050. Salinity inhibits plant growth and development, results in senescence, and ultimately plant death. The purpose of this study was to investigate how rhizobia, isolated from Kenyan soils, relieve common beans from salinity stress. The yield loss of common bean plants, which were either not inoculated or inoculated with the commercial R. tropici rhizobia CIAT899 was reduced by 73% when the plants were exposed to 300 mM NaCl, while only 60% yield loss was observed after inoculation with a novel indigenous isolate from Kenyan soil, named S3. Expression profiles showed that genes involved in the transport of mineral ions (such as K+, Ca2+, Fe3+, PO43-, and NO3-) to the host plant, and for the synthesis and transport of osmotolerance molecules (soluble carbohydrates, amino acids, and nucleotides) are highly expressed in S3 bacteroids during salt stress than in the controls. Furthermore, genes for the synthesis and transport of glutathione and γ-aminobutyric acid were upregulated in salt-stressed and S3-inocculated common bean plants. We conclude that microbial osmolytes, mineral ions, and antioxidant molecules from rhizobia enhance salt tolerance in common beans.

overall_design: We performed meta-RNA-Seq to determine rhizobia transcriptome response when when the infected plants are exposed to 300 mM NaCl

first: Alexandra

last: Furch

first: Ralf

last: Oelmeuller


title: MC38/gp100 cells after type I PRMT inhibitor treatment

status: Public on Nov 01 2022

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Antigen-expanded CD8+ gd T cells with NK-like phenotype and function respond in persistent infection [scRNA-seq]

city: Chicago

first: Roshni

last: Roy Chowdhury

address: 924 E 57th Street

institute: University of Chicago

summary: Gamma Delta (gd) T cells play unique protective roles in different settings of acute and chronic infections. However, what they respond to and how they function in the acute versus chronic phases of the same infection remains unclear. It is well documented that cytolytic gd T cells that express Vg9Vd2 TCRs and respond to phosphoantigens (pAgs) expand in acute Mycobacterium tuberculosis (Mtb) infection in humans. However, most infections with Mtb manifest as a chronic, clinically asymptomatic state. While past work indicates that gd T cells contribute to Mtb infection control, their response during this phase of Mtb infection is not well understood. Here, we analyze peripheral blood gd T cells from a South African adolescent cohort and show that a unique CD8+ gd T cell subset with features of “memory inflation” expand in chronic Mtb infection. Using targeted scRNA-seq coupled with surface protein expression and multiparametric single cell pseudotime trajectory analysis, we identify the differentiation paths that these CD8+ gd T cells follow to develop into effectors in this infection state.

overall_design: We performed targeted scRNA-seq and concomitant surface protein and TCR sequencing on FACS sorted gd T cells from peripheral blood samples of six donors with persistent Mtb infection.

middle: R

last: Chowdhury

first: John

last: Valainis

first: Meng

last: Sun

first: Thomas

middle: J

last: Scriba

first: Mark

middle: M

last: Davis

first: Sean

middle: C

last: Bendall

first: Yueh-hsiu

last: Chien


title: Antigen-expanded CD8+ gd T cells with NK-like phenotype and function respond in persistent infection


title: Differential expression genes analysis in MC38/gp100 cell line with DMSO or type I PRMT inhibitor treatment

overall_design: mRNA profiles of MC38/gp100 cells treated with DMSO or 1uM GSK3368712 for 5 days


title: Gene expression profile of macrophages in aneurysm lesions at the growth phase.

city: Suita City

first: Akihiro

last: Okada

state: Osaka

address: 6-1 Kishibe-Shinmachi

department: Department of Molecular Pharmacology

country: Japan

institute: National Cerebral and Cardiovascular Center

summary: Recent experimental studies have defined intracranial aneurysms as a macrophage-mediated chronic inflammatory disease affecting intracranial arteries. We used single cell RNA sequencing (scRNA-seq) to analyze the population of macrophages in aneurysm lesions at the growth phase.

overall_design: The previously-established aneurysm model of rats was used. Macrophages were labeled with the fluorescent protein and isolated by a laser-microdissection method and analyzed using scRNAseq.

first: Aoki

last: Tomohiro


title: The role of miR-199a-3p in epithelial to mesenchymal transition of keratinocytes

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

summary: We found that miR-199a-3p expression is decreased in cSCC biopsies and cell lines compared to normal skin biopsies or normal keratinocytes cell.  To understand the role lost expression of miR-199a-3p might have in tumorigenesis of keratinocytes, we aimed to fine possible biochemical pathways and possible targets of miR-199a-3p in cSCC. In order do so, we overexpressed miR-199a-3p in cSCC and used microarrays to find global gene expression affected by miR-199a-3p.

overall_design: Two cSCC cell lines Met-I and SCL-II were generated, each either over-expressing miR-199a-3p or control plasmid. From these cells, RNA extraction and hybridization on Affymetrix microarrays.

first: Adi

last: Mizrahi

first: Moamen

last: Masalha

first: Tal

last: Meningher

first: Aviv

last: Barzilai

first: Devorah

last: Gur-Wahnon

first: Iddo

middle: Z

last: Ben-Dov

first: Joshua

last: Kapenhas

first: Jasmine

last: Jacob-Hirsch

first: Raya

last: Leibowitz-Amit

first: Yechezkel

last: Sidi

first: Dror

last: Avni


title: De novo emergence, existence, and demise of a protein-coding gene in murids [mouse]

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

summary: Genes, principal units of genetic information, vary in complexity and evolutionary history. Less-complex genes (e.g. long non-coding RNA (lncRNA) expressing genes), readily emerge de novo from non-genic sequences and have high evolutionary turnover. Genesis of a gene is facilitated by adoption of functional genic sequences from retrotransposon insertions. However, protein-coding sequences in extant genomes rarely lack any connection to an ancestral protein-coding sequence. Here, we describe remarkable evolution of the murine gene D6Ertd527e and its orthologs in the rodent Muroidea superfamily. The D6Ertd527e emerged in a common ancestor of mice and hamsters as an lncRNA-expressing gene. A major contributing factor was a long terminal repeat (LTR) retrotransposon insertion carrying an oocyte-specific promoter and one of the first exons of the gene. The gene survived as an oocyte-specific lncRNA in several extant rodents while in some others the gene or its expression was lost. In the ancestral lineage of Mus musculus, the gene acquired protein-coding capacity where the bulk of the coding sequence formed through CAG (AGC) trinucleotide repeat expansion and duplications. These events gave rise to a cytoplasmic serine-rich maternal protein, which has no discernable role. Knock-out of D6Ertd527e in mice affects neither fertility nor the maternal transcriptome. While this evolving gene is not showing a notable function in laboratory mice, its documented evolutionary history in Muroidea during the last ~40 million years provides a textbook example of how a several common mutation events can support de novo gene formation, evolution of protein-coding capacity, as well as gene’s demise.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of GV stage oocytes from mouse:  - 3x wild-type as control  - 3x D6Ertd527e knock-out

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Jan

last: Petrzilek


title: De novo emergence, existence, and demise of a protein-coding gene in murids [chinese hamster]

overall_design: Comparative gene expression profiling analysis of RNA-seq data of GV stage oocytes from chinese hamster (Cricetulus griseus):  - 2x wild-type


title: Overexpression of Transcription Factor GATA6 in Human Coronary Artery Smooth Muscle Cells in vitro

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

country: Sweden

institute: Lund University

summary:
Vascular smooth muscle cell plasticity plays a pivotal role in the pathophysiology of vascular diseases. Despite compelling evidence demonstrating the importance of transcription factor GATA6 in vascular smooth muscle, the functional role of GATA6 remains poorly understood.
The aim of this study was to elucidate the role of GATA6 on cell migration and to gain insight into GATA6-sensitive genes in smooth muscle. Therefore, we performed Affymetrix microarray analysis on human coronary artery smooth muscle cells after overexpressing GATA6 by adenovirus transduction and compared it to control which are cell transduced with Ad-CMV-null.

overall_design: Overexpression of human GATA6 gene was achieved using adenoviral constructs. Cells were transduced 24 hours after seeding with 100 MOI of Ad-CMV-GATA6. Media was changed after 96 hours of virus transduction and kept for additional 48 hours. Ad-CMV-null was used as a control.

first: Fatima

last: Daoud


title: Transcriptome analysis of in vitro hematopoietic stem cells (HSC) and stage 3 (ST3) NK cell progenitors cells

city: Ghent

first: Georges

last: Leclercq

address: C. Heymanslaan

country: Belgium

institute: Ghent University


title: Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV16 E7

city: Philadelphia

first: Elizabeth

middle: A

last: White

state: PA

address: 3610 Hamilton Walk, 203C Johnson Pavilion, Mail Code 6114

department: Otorhinolaryngology

institute: University of Pennsylvania

summary: This RNA-seq study in primary human forekin keratinocytes was to define genes that are differetially expressed in the presence or absence of HPV16 E7 or the HPV16 E7 E80A/D81A variant.

overall_design: mRNA profiles in primary HFK were generated for the following samples (# of replicates): GFP (3), HPV16 E7 (2), HPV16 E7 E80A/D81A (3)


title: Low input RNA-seq of TMRM-High and TMRM-Low HSCs.

city: Guangzhou

first: Meng

last: Zhao

state: Guangdong

address: Zhongshan 2nd Road

country: China

institute: Sun Yat-sen University

summary: TMRM-High HSCs significantly enriched proteotoxic genes than TMRM-Low HSCs, in parallel to the differentially expressed carbon metabolism genes, cell cycle activation genes, and self-renewal genes.

overall_design: Low input RNA-seq on HSCs

first: Changzheng

last: Li


title: RNA sequencing of decidua reveals differentially expressed genes in recurrent pregnancy loss

city: Wuhan

first: Yuehan

address: Jiefang Ave.

department: Tongji Medical School

institute: Huahzong University of Science and Technology

summary: Differentially expressed genes (DEGs) in decidua from recurrent pregnancy loss (RPL) patients by utilizing RNA sequencing (RNA-seq) technology have not been well characterized before.In the current study, four RPL patients and three control women were recruited to conduct RNA-seq, and 153 genes comprising 69 were upregulated and 84 downregulated showed different expression levels between the health control and RPL groups.

overall_design: Decidual tissues were collected during the procedure of dilation and curettage (D&C) after the ultrasonic diagnosis of fetal stopping developing in the uterus from four recurrent pregnancy loss patients. And decidua tissue from three control women was also collected during the procedure of D&C.

first: Shujie

last: Liao

first: Lei

last: Jin


title: Modulation of RNA splicing enhances response to BCL2 inhibition in leukemia

city: South San Francisco

first: Simon

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie


title: Cell type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening

city: New York

first: Jimin

last: Tan

state: NY

address: 435 E 30th St

institute: NYU Langone

summary: Experimental methods for measuring 3D chromatin organization, such as Hi-C, are costly and have technical limitations, restricting their broad application particularly in high-throughput genetic perturbations. We present C.Origami, a deep neural network model that performs de novoprediction of cell type–specific chromatin organization using as inputs the DNA sequence and two cell type–specific genomic features — chromatin accessibility and CTCF binding. C.Origami predicts chromatin organization within a 2 mega-base window and enables in silico experiments to examine the impact of genetic perturbations on chromatin interactions in pathologies such as cancer. We assess how individual DNA elements contribute to the organization of 3D chromatin organization and identify a compendium of cell type–specific trans-regulators across multiple cell types. We demonstrate that cell type–specific in silico genetic perturbation and screening, enabled by C.Origami, can be used to systematically discover chromatin regulatory mechanisms in both normal and disease-related biological systems.

overall_design: ATAC-seq is performed on CUTLL1 cell line to evaluate chromatin accessibility

first: Francesco

last: Boccalatte


title: Effect of hormonal therapy on the otoconial changes caused by estrogen deficiency

city: Toon

first: Takahiro

last: Nakata

address: Shitsukawa

department: Otolaryngology, Head and Neck Surgery

institute: Ehime University Graduate School

summary:
To examine the effect of hormonal therapy on otoconial changes caused by estrogen deficiency, we dissected the utricle and extracted its total RNA.
We performed gene expression analysis using data obtained from RNA-seq of four groups.

overall_design: Comparative gene expression analysis of RNA-seq data for sham operation with vehicle, ovariectomy with vehicle, ovariectomy with estradiol, and ovariectomy with raloxifene.

first: Naohito

last: Tokunaga


title: Insulin and IGF-1 elicit robust transcriptional regulation to modulate autophagy in astrocytes

city: Old Westbury

first: Ying-Tao

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

summary: Insulin is a principal metabolic hormone. It regulates a plethora of metabolic pathways in peripheral tissues. Recent studies have shown that insulin signaling plays fundamental roles in the brain. Loss of insulin action in astrocytes leads to impaired brain glucose sensing and behavioral abnormalities in mice. How insulin signaling modulates astrocyte function and neural circuits is not completely known.

overall_design: Using next-generation RNA sequencing, we show that insulin significantly regulates the expression of over 1,200 genes involved in multiple functional processes in primary astrocytes. The closely related insulin-like growth factor 1 (IGF-1) triggers similar robust transcriptional reprogramming in astrocytes. Thus, over 50% of the significantly regulated genes are regulated by both ligands. As expected, these commonly regulated genes are highly enriched in pathways involved in lipid and cholesterol biosynthesis. Additionally, insulin and IGF-1 induce the expression of genes involved in ribosomal biogenesis, while suppressing the expression of genes involved in autophagy, indicating a common role of insulin and IGF-1 on protein homeostasis in astrocytes. By comparing insulin responsiveness in astrocytes without endogenous IR, IGF1R or both, we show that only IR/IGF1R double knockout astrocytes display blunted insulin-dependent suppression of autophagy genes, including p62, Ulk1/2, and several Atg genes, indicating both IR and IGF1R can elicit insulin-dependent transcriptional regulation on autophagy. In summary, insulin/IGF-1 potently suppresses autophagy in astrocytes through transcriptional regulation, indicating a potential important role of astrocytic insulin/IGF-1 signaling on proteostasis. Impairment of this regulation in insulin resistance and diabetes may contribute to neurological complications related to diabetes.

first: Shawn

last: Geffken

first: Sohyun

last: Moon

first: Weikang

last: Cai


title: Modulation of RNA splicing enhances response to BCL2 inhibition in leukemia [eCLIP]

summary: Therapy resistance is a major challenge in the treatment of cancer. Here, we performed CRISPR/Cas9 screens across a broad range of therapies used in acute myeloid leukemia (AML) to identify genomic determinants of drug response. Our screens uncovered a selective dependency on RNA splicing factors whose loss preferentially synergized with the BCL2 inhibitor venetoclax. Loss of the splicing factor RBM10 augmented response to venetoclax in leukemia yet was completely dispensable for normal hematopoiesis. Combined RBM10 and BCL2 inhibition led to mis-splicing and inactivation of the inhibitor of apoptosis XIAP and downregulation of BCL2A1, an anti-apoptotic protein implicated in venetoclax resistance. A novel inhibitor of splicing kinase families CLKs and DYRKs led to intron retention of key splicing factors identified from our screens, synergized with venetoclax, and overcame resistance to BCL2 inhibition. Our findings underscore the central importance of splicing in modulating apoptosis and provide a strategy to improve venetoclax-based treatments.

overall_design: To determine RNA binding profile of RBM10, Enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP) was performed in MOLM13 cells in quadruplicate using  an RBM10 antibody or a negative control.

first: Eric

last: Wang

first: Abdel-Wahab

last: Omar


title: Modulation of RNA splicing enhances response to BCL2 inhibition in leukemia [RNA-seq]

overall_design: Parental or Cas9+sgRNA expressing MOLM13 cells were cultured in vitro in triplicate and treated with Venetoclax, alone and in combination with SM09419, or DMSO vehicle control for 48 hours prior to RNA-sequencing.


title: Next Generation Sequencing Facilitates Quantitative Analysis of DSS-induced colitis receiving Sulfasalazine and Berberine colonrectum Transcriptomes

city: shanghai

first: li

last: zihao

address: dongchuan road 800

institute: shanghai jiao tong university

summary: We had one goal to perform this study: DSS-induced colitis receiving Sulfasalazine and Berberine colonrectum Transcriptomes

overall_design: Comparison of transcriptome of colonrectum samples of DSS-induced colitis receiving Sulfasalazine and Berberine

first: Zihao

first: Zecheng

last: Luo


title: Systematic analysis of IL-1 cytokine signaling by high-risk HPV oncoproteins

first: Elizabeth

last: White

summary: Human papillomavirus (HPV) E6 and E7 oncoproteins are expressed at all stages of HPV-mediated carcinogenesis and are essential drivers of cancers caused by high-risk HPV. Some of the activities of HPV E6 and E7, such as their interactions with host cellular tumor suppressors, have been characterized extensively. There is less information about how high-risk HPV E6 and E7 alter cellular responses to cytokines that are present in HPV-infected tissues and are an important component of the tumor microenvironment. We used several models of HPV oncoprotein activity to assess how E6 and E7 alter the cellular response to the pro-inflammatory cytokine IL-1beta. Models of early-stage HPV infection (human keratinocytes expressing HPV16 E6 and E7) and models of established HPV-positive head and neck cancers (patient-derived xenografts, head and neck cancer cell lines) exhibited similar dysregulation of IL-1 pathway genes and suppressed responses to IL-1beta treatment. Such overlap in cell responses supports that changes induced by HPV E6 and E7 early in infection could persist and contribute to a dysregulated immune environment throughout carcinogenesis. HPV E6 and E7 also drove the upregulation of several suppressors of IL-1 cytokine signaling, including SIGIRR, both in primary keratinocytes and in cancer cells. SIGIRR knockout was insufficient to increase IL-1beta-dependent gene expression in the presence of HPV16 E6 and E7, suggesting that multiple suppressors of IL-1 signaling contribute to dampened IL-1 responses in HPV16-positive cells.

overall_design:
This RNA-seq study in primary human forekin keratinocytes was to define genes that are differentially expressed in the presence or absence of HPV16 E6 and E7 oncoproteins, with and without treatment with the pro-inflammatory cytokine IL-1beta.
mRNA profiles in primary HFK were generated for the following samples (# of replicates): untreated GFP/GFP (3), GFP/GFP treated with 0.5 ng/ml IL-1B for 3h (3), untreated HPV16 E6/E7 (3), HPV16 E6/E7 treated with 0.5 ng/ml IL-1B for 3h (3).


title: Oxoeicosanoid signaling promotes early antimicrobial defense in zebrafish (Danio rerio)

first: Yanan

last: Ma

state: New York

address: 430 east 67st street

department: Cell Biology

institute: Memorial Sloan Kettering Cancer Center

summary: RNAseq was performed on hcar1-4+/+ and hcar1-4-/- zebrafish larvae with (2 h and 4 h) or without (0 h) Pseudomonas aeruginosa (PA) ear infection. The transcriptome profile generated here reveals PA14 infection-induced differential gene expression patterns between hcar1-4-/- and hcar1-4+/+ siblings.

overall_design: Pseudomonas aeruginosa resuspended in standard E3 was injected into the otic vesicle of hcar1-4+/+ and hcar1-4-/- zebrafish larvae. Uninjected zebrafish larvae served as control. Total RNA was extracted before or after 2 hours and 4 hours of infection, and processed to following sequencing.

first: King

middle: L

last: Hui

first: Gelashvili

last: Zaza

first: Philipp

last: Niethammer


title: Transcriptomic analysis of the chorioallantois in equine premature placental separation.

city: Urakawa

first: Harutaka

last: Murase

state: Hokkaido

address: 535-13, Nishicha

institute: Japan Racing Association

summary: The transcripts from equine chorioallantois of thirty-three premature placental separation and four control were compared.

overall_design: Placental tissues were collected either at the farm (n=13) or from placentas submitted to the University of Kentucky Veterinary Diagnostic Laboratory (UKVDL) (n=24). The villous CA tissues were collected immediately adjacent to the cervical star at a site with grossly apparent chorionic villi. Samples from this site were preserved in RNAlater® for RNA sequencing. Total RNA was isolated from tissue samples using RNeasy Mini Kit (#74104: Qiagen). RNA concentrations and quantities were confirmed using the Nanodrop 2000 spectrophotometer (ThermoFisher Scientific, MA, USA). Then, RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). All samples had a 260/280 ratio >2.0 and RNA integrity number (RIN) >7.0.

first: Hossam

last: El-Sheikh Ali

first: Kirsten

middle: E

last: Scoggin

first: Rebecca

last: Ruby

first: Barry

last: Ball


title: Liver gene expression profile in human NAFLD (men and women)

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

summary: Liver gene expression was analyzed in liver samples collected from patients with NAFLD.

overall_design: Liver samples were selected from a biopsy-proven NAFLD participant cohort established in the hepatology department of the Centre Hospitalier Universitaire de Toulouse. The 80 biopsies were from 48 men and 32 women. This cohort was approved by ANSM (National Agency for the Safety of Medicines and Health Products) and local ethics committee in 2015 (ClinicalTrial.gov: NCT02390232) and by Minister of Higher Education, Research and Innovation in 2017 (DC-2017-2984).

first: Arnaud

last: Polizzi

first: Alexia

last: Laroyenne

first: Sarra

last: Smati

first: Claire

last: Naylies

first: Anthony

last: Emile

first: Yannick

last: Lippi

first: Alexandra

last: Montagner

first: Pierre

last: Gourdy

first: Christophe

last: Bureau

first: Maeva

last: Guillaume


title: macroH2A2 overexpression in head and neck squamous cell carcinoma cell line T-HEp3.

city: New york

first: DAN

last: SUN

address: 1468 Madison Avenue,

institute: Ichan School of Medicine at Mount Sinai

summary: We report the RNA expression profile in the restoration of macroH2A2 in tumorigenic (T-HEp3) HNSCC cell line. T-HEp3 is a human epidermoid carcinoma, which grows on chorioallantoic membreane and metastasizes with high efficency into the organs of chick embryo. Upon serial paasage for more than 50 times in vitro , T-HEp3 loses tumorigenic and metastatic potential and termed as dormant D-HEp3. This is an ideal cell line model system to study cancer dormancy.

overall_design: RNA sequencing was performed in T-HEp3 cell line with control (H2B-GFP expression) or with macroH2A2 overexpression.

first: Dan

last: Sun

first: Julio

last: Aguirre-Ghiso


title: Single Cell RNA Sequencing of Fresh and Frozen Human Atheroma Tissue

city: Palo Alto

first: Siddhartha

last: Jaiswal

state: CA

address: 240 Pasteur Dr

department: Pathology

institute: Stanford University School of Medicine

summary: We conducted a comparison of scRNA-seq on four paired fresh and cryopreserved atheroma samples, two from coronary arteries and two from carotid arteries, to determine whether it is possible to obtain comparable data from frozen samples.  After enzymatic digestion into single cell suspensions, we sorted CD45+ cells from half of each sample and immediately processed these using the 10X Genomics scRNA-seq workflow after collection, while the other half was frozen in liquid nitrogen. After cryopreservation for an average of 7 days, the other half of each sample was thawed and sorted identically to the fresh samples.

overall_design: scRNA-seq of four paired fresh and cryopreserved atheroma samples

first: Herra

last: Ahmad

first: Daniel

last: Nachun


title: Requirement of hepatic pyruvate carboxylase during fasting, high fat and ketogenic diet

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

summary: Pyruvate has two major fates upon entry into mitochondria, the oxidative decarboxylation to acetyl-CoA or the biotin-dependent carboxylation to oxaloacetate via pyruvate carboxylase (Pcx).  Here we have generated mice with a liver specific knockout of Pcx to understand its role in hepatic mitochondrial metabolism under disparate physiological states including a 24 hour fast, as well as ketogenic and high fat diets. These data ultimately show the requirement of Pcx-mediated anapleorsis in the liver under disparate metabolic conditions.

overall_design: RNA-seq on liver tissue from 9wk old male wild-type and Pcx liver-specific knockout mice fasted for 24 hours.


status: Public on Oct 29 2022

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

institute: Fourth Military Medical University

summary: Aging-associated transcriptome changes in liver sinusoidal endothelial cells. RNA was prepared from liver sinusoidal endothelial cells of the male 8 weeks and 24 months old C57BL/6J mice.RNA samples were then subjected to RNA-sequencing and gene expression profiling analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver sinusoidal endothelial cells isolated from 24 months or 8 weeks mice

first: Juanli

last: Duan

first: Jingjing

last: Liu

first: Lin

last: Wang


title: Neurons and glial cells acquire a senescent signature after repeated mild traumatic brain injury in a sex-dependent manner

city: Toronto

first: Gary

last: Bader

state: Ontario

address: 160 College St

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: This study compared gene expression signatures between mice with repeated mild traumatic brain injury (rmtbi) and sham controls.

overall_design: Mice received three repeated mild closed skull head injuries or sham surgeries. The ipsilateral hemisphere, excluding brainstem and cerebellum, were used for scRNAseq to compare expression between rmTBI mice and sham controls.

first: Nicole

last: Schwab

first: Daria

last: Taskina

first: Emily

last: Leung

first: Brendan

last: Innes

first: Lili-Naz

last: Hazrati


title: In Vivo efficacy assessment of the CDK4/6 inhibitor palbociclib and the PLK1 inhibitor volasertib in Human Chordoma Xenografts

city: PARIS

first: Sophie

last: VACHER

address: 26 rue d'Ulm

institute: Institut Curie

type: Genome variation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain

city: Seattle

first: Xiaonan

last: Fu

state: WA

address: 1705 NE Pacific St

department: Biochemistry

institute: University of Washington

summary: Despite wide applications in tissue mapping and vastly improved imaging and omics technologies, spatial, genome-wide assays of gene expression are yet to reliably achieve the resolution and sensitivity approaching dissociative single-cell RNA sequencing. Here, we introduce Pixel-seq, a spatial barcoding method using “continuous” polony gels of ≤ 1 µm feature resolution for capturing tissue RNAs and precise aggregation of mapped transcripts into individual cells. The single-cell assay was demonstrated on mapping the most common brain structures, neuron layers and clusters, creating a three-dimensional atlas of the mouse parabrachial nucleus, and discovering neuropathic pain-associated gene regulation, glial transcriptomic dynamics, and cell-cell communication in the homeostatic adult brain. Our results highlight the necessity of the non-dissociative single-cell sequencing for mapping structural and functional heterogeneity in tissues.

overall_design: 1. Method demonstration (1 mouse olfactory bulb section); 2. PBN structure and activity mapping (7 mouse PBN sections)

first: Li

last: Sun

first: Runze

last: Dong

first: Jane

middle: Y

last: Chen

first: Runglawan

last: Silakit

first: Yiing

last: Lin

first: Shin

first: Richard

middle: D

last: Palmiter

first: Liangcai

last: Gu


title: Prevalence of multi-resistant plasmids in hospital inhalable particulate matter  (PM) and its impact on horizontal gene transfer

city: Hangzhou

first: Zhen-Chao

last: Zhou

address: Yuhangtang Road

institute: Zhejiang University

summary: Antibiotic resistance is exacerbated by the exchange of antibiotic resistance genes (ARGs) between microbes from diverse habitats. Plasmids are important ARGs mobile elements and are spread by horizontal gene transfer (HGT). In this study, we demonstrated the presence of multi-resistant plasmids from inhalable particulate matter (PM) and its effect on gene horizontal transfer. Three transferable multi-resistant plasmids were identified from PM in a hospital, using conjugative mating assays and nanopore sequencing. pTAir-3 contained 26 horizontal transfer elements and 10 ARGs. Importantly pTAir-5 harbored carbapenem resistance gene (blaOXA) which shows homology to plasmids from human and pig commensal bacteria, thus indicating that PM is a media for antibiotic resistant plasmid spread. In addition, 125 μg/mL PM2.5 and PM10 significantly increased the conjugative transfer rate by 110% and 30%, respectively, and augmented reactive oxygen species (ROS) levels. Underlying mechanisms were revealed by identifying the upregulated expressional levels of genes related to ROS, SOS, cell membranes, pilus generation, and transposition via genome-wide RNA sequencing. The study highlights the airborne spread of multi-resistant plasmids and the impact of inhalable PM on the horizontal transfer of antibiotic resistance.

overall_design: Bacterial conjugation experiments after PM2.5 exposure.

first: Hong


title: Effect of six different diets on liver gene expression

first: Hervé

last: Guillou

summary: Male and female mice (Bl6/J) were fed a chow diet (control 1 and control 2) or a High fat diet (HFD) or a Choline deficient High fat diet (CD HFD) or a Western Diet (WD) or a Western Diet supplemented with glucose and fructose in drinking water (WD glucose fructose) for 15 weeks.

overall_design: Eleven-week old C57BL/6J male and female mice were purchased from Charles River, kept for two weeks of acclimatization, then randomly allocated to the different experimental groups. Body weight and food intake were measured weekly. Mice were killed at ZT16.

first: Sarra

last: Smati

first: Arnaud

last: Polizzi

first: Claire

last: Naylies

first: Yannick

last: Lippi

first: Pierre

last: Gourdy


title: Effect of hepatocyte-restricted deletion of PPARalpha on liver gene expression in response to fasting in mice from both sexes

summary: Wild-type (LWT) and mice with hepatocyte restricted deletion of PPARalpha (LKO) mice were fasted fro 24 hours.

overall_design: Gene expression was analyzed in the liver of Wild-type (LWT) mice and in the liver of mice lacking PPARalpha (LKO) in hepatocyte. Analysis were performed both in male and in female mice. Mice were either fed ad libitum or fasted for 24 hours. Mice were fourteen-week old.

last: Smatti


title: Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci (RNA-Seq 2)

status: Public on Oct 28 2022

city: Boston

first: Chad

middle: Brandon

last: Stein

state: MA

address: 240 Longwood Ave

institute: Harvard Medical School

summary: Pausing of RNA polymerase II (RNAPII) in early elongation is critical for gene regulation. Paused RNAPII can be released into productive elongation by the kinase P-TEFb or targeted for premature termination by the Integrator complex. Integrator comprises endonuclease and phosphatase activities, driving termination through cleavage of nascent RNA and removal of stimulatory phosphorylation. To probe the direct consequences of Integrator activity, we generated a degron system to rapidly deplete the Integrator endonuclease INTS11. Degradation of INTS11 elicits a nearly universal increase in RNAPII escape from promoter regions. However, these RNAPII complexes fail to achieve optimal elongation rates and reveal continued Integrator phosphatase activity. Short transcripts are thus selectively upregulated by INTS11 loss, including many non-coding RNAs, transcription factors and signaling regulators. Together, our data indicate a common function for INTS11 at all RNAPII loci, with differential effects on particular genes, pathways or RNA biotypes reflecting transcript lengths rather than Integrator specificity.

overall_design: Examination of 6 samples by RNA-seq (3 biological replicate sets of INTS11Halo cells treated with DMSO or PROTAC for 16 hours)

first: Karen

last: Adelman

first: Eric

last: Wagner

middle: B

first: Andrew

last: Field

first: Claudia

last: Mimoso

first: ChenCheng

last: Zhao

first: Kai-Lieh

last: Huang


title: Effect of pemafibrate on liver gene expression in wild-type mice and in mice with hepatocyte-restricted deletion of PPARalpha

summary: We analyzed the effect of chronic (14 days) treatment with a selective PPARalpha agonist on liver gene expression in vivo in mice (B6/J). The experiment was done in mice from both sexes. The experiment was done in both wild-type (LWT) and in mice with hepatocyte-restricted deletion of PPARalpha.

overall_design: Ten-week-old Male and female PPARahep+/+ (LWT) and PPARahep-/-  (LKO) received the PPARα agonist pemafibrate (0,1 mg/kg/day) or vehicle (Carboxymethyl cellulose 0,5%) by gavage for 14 days (n=6 animals/genotype/treatment/sex).

first: Anthony

last: Emile

first: Alexandra

last: Montagner


title: Transcriptomic changes in the pituitary when pituitary enhancer of the Nr5a1 gene is deleted

city: Kurume

first: Yuichi

last: Shima

state: Fukuoka

address: Asahimachi 67

department: Department of Anatomy

institute: Kurume University School of Medicine

summary: NR5A1 is expressed in the pituitary gonadotropes and regulates their functional differentiation. We have previously identified a pituitary-specific enhancer region located in the 6th intron of the Nr5a1 gene. In this study, deletion of the pituitary enhancer by genome editing abolished the expression of NR5A1 in the pituitary gland, confirming the functional importance of the enhancer. Transcriptomic changes in the enhancer-deleted mouse pituitary were revealed in both males and females.

overall_design: We collected pituitaries from control mice (n=4 for male and female) and the mice in which pituitary enhancer of the Nr5a1 gene is deleted (n=4 for male and n=3 for female).

first: Kanako

last: Miyabayashi


title: Co-targeting of HDAC, PI3K, and Bcl-2 Results in Metabolic and Transcriptional Reprograming and Decreased Oxidative Phosphorylation in Acute Myeloid Leukemia

city: Lake Orion

first: Katie

middle: Hege

last: Hurrish

state: MI

address: 2902 Regency Dr.

institute: Wayne State University School of Medicine

summary: To investigate the potential gene expression changes as a result of CUDC-907 and venetoclax treatment, MV4-11 cells were pre-treated with CUDC-907 for 8 hours followed by venetoclax for 1 hour or left untreated  for controls. We then performed a comparative gene expression profiling analysis of RNA-seq data for C3H10T1/2 cells and its KD derivatives (shKDM4D, shNFIB, and shMLL1).

overall_design: Control, VEN, CUDC-907, VEN + CUDC-907

first: Hurrish

last: Katie H.

first: Qiao

last: Xinan

first: Li

last: Xinyu

first: Ge

last: Y.


title: The mutational landscape of cancer’s vulnerability to ionizing radiation

status: Public on Oct 30 2022

city: Chicago

first: Mohamed

last: Abazeed

state: IL

address: 303 E Superior St Lurie

department: Radiation Oncology

institute: Northwestern University

summary: Individual variant or wild type gene expression after constitutive transduction in immortalized lung ephithelial cells (BEAS-2B). The hypothesis is that variant gene expression is associated with radiation resistance or sensitivity. The results provide transcriptomic information on genes variants that conferred radiation resistance or sensitivity.

overall_design: Total mRNA obtained from BEAS2B cells transduced with the indicated gene variants and their corresponding wild type alleles.

first: Abazeed

last: Mohamed

first: Gopal

last: Priyanka


title: De novo emergence, existence, and demise of a protein-coding gene in murids

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

institute: Institute of Molecular Genetics of the ASCR

sample_organism:
Cricetulus griseus
Mus musculus

platform_organism:
Cricetulus griseus
Mus musculus


title: Single-cell RNA-seq of airspace cellular subsets after inflammation and membrane damage

city: London

first: Claudio

last: Bussi

state: London

address: 1 Midland Road, Host-Pathogen Lab NE422

country: United Kingdom

institute: The Francis Crick Institute

summary: scRNA-seq data from an in vivo model of endomembrane damage. Data show that agents inducing endomembrane damage, such as silica particles, regulate the mitochondrial function and metabolism of macrophages.

overall_design: Mice were exposed to silica crystals or red-fluorescent silica beads by intratracheal intubation, and bronchoalveolar lavage cells were analyzed by single-cell RNA-seq.

first: Nourdine

last: Bah

first: Maximiliano

last: Gutierrez


title: Single-molecule identification of the target RNAs of different RNA binding proteins simultaneously in cells

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

institute: Duke University School of Medicine

summary: N6-methyladenosine (m6A) plays critical roles in gene expression control by recruiting the cytoplasmic reader proteins YTHDF1,2 and 3. Recently, the function of YTHDF proteins and whether they bind to shared or distinct sets of methylated mRNAs in cells has been the subject of debate. Here, we developed TRIBE-STAMP, an approach for single-molecule detection of the target RNAs of two RNA binding proteins simultaneously in cells. Applying TRIBE-STAMP to the YTHDF proteins revealed that most target mRNAs are shared among the three YTHDF proteins. Surprisingly, we also found that individual mRNA molecules can be bound by more than one YTHDF protein throughout their lifetime. Furthermore, we show that YTHDF proteins bind sequentially to target methylated mRNAs, with YTHDF1 binding before YTHDF2 or YTHDF3. Our data reveal shared molecular interactions among the YTHDF proteins and support a model in which YTHDF1 and YTHDF3 are unlikely to promote rapid mRNA decay.

overall_design: YTHDF1, YTHDF2 and YTHDF3 RIP-TRIBE in HEK293T cells expressing YTHDF-ADAR proteins and YTHDF-3xFLAG proteins.

first: Mathieu

middle: N

last: Flamand

first: Ke

last: Ke


title: Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci (TT-seq)

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

overall_design: Examination of 6 samples by TT-seq (3 biological replicate sets of INTS11Halo cells: DMSO- and PROTAC-treated)

first: Eric

last: Wagner

first: Chad

last: Stein

first: Andrew

last: Field

first: Claudia

last: Mimoso

first: ChenCheng

last: Zhao

first: Kai-Lieh

last: Huang


title: In Vivo efficacy assessment of the CDK4/6 inhibitor palbociclib and the PLK1 inhibitor volasertib in Human Chordoma Xenografts [RNA-seq]

first: Sophie

last: VACHER

summary: We evaluated the tumor efficacy of the CDK4/6 inhibitor palbociclib in two chordoma Patient’s Derived Xenograft (PDX) models to validate and identify novel therapeutic approaches.

overall_design: Gene expression analysis of RNA-seq data for two chordoma PDX models (CD3 and CD7), without treatment and after palbociclib treatment.

first: Thibault

last: Passeri

first: Ahmed

last: Dahmani

first: Julien

last: Masliah-Planchon

first: Rania

last: El Botty

last: Vacher

first: Elisabetta

last: Marangoni

first: Fariba

last: Némati

first: Sergio

last: Roman-Roman

first: Homa

last: Adle-Biassette

first: Hamid

last: Mammar

first: Sébastien

last: Froelich

first: Ivan

last: Bièche

first: Didier

last: Decaudin


title: Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci (PRO-Seq)

first: Karen

last: Adelman

overall_design: Examination of 4 samples by PRO-seq (2 biological replicate sets of INTS11Halo cells: DMSO- and PROTAC-treated)

first: Eric

last: Wagner

first: Chad

last: Stein

first: Andrew

last: Field

last: Mimoso


title: An automated feeding system for the African killifish reveals effects of dietary restriction on lifespan and allows scalable assessment of associative learning

city: Stanford

first: Jingxun

last: Chen

address: 290 Jane Stanford Way, Room E365

institute: Stanford University - Stanford, CA

summary: To study the effect of dietary restriction on killifish, we generated transcriptomes (RNA-seq) for the livers and brains of male and female killifish that had been subjected to different dietary treatements.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the livers and brains of male and female killish that had been subjected the dietary treatment (ad libitum vs. dietary restriction) for 5 weeks.

first: Emma

middle: K

last: Costa

first: Param

middle: P

last: Singh


title: HIRA loss transforms FH deficient cells [ChIP-Seq]

city: Cologne

first: Lorea

last: Valcarcel

address: FREZZA Lab, CECAD Research Center Faculty of Medicine University Hospital Cologne Joseph-Stelzmann-Str. 26

institute: CECAD

summary: Fumarate Hydratase (FH) is a mitochondrial enzyme that catalyses the reversible hydration of fumarate to malate in the TCA cycle. Germline mutations of FH lead to HLRCC, a cancer syndrome characterised by a highly aggressive form of renal cancer(1). Although HLRCC tumours metastasise rapidly, FH-deficient mice develop premalignant cysts in the kidneys, rather than carcinomas(2). How Fh1-deficient cells overcome these tumour suppressive events during transformation is unknown. Here, we perform a genome-wide CRISPR/Cas9 screen to identify genes that, when ablated, enhance the proliferation of Fh1-deficient cells. We found that the depletion of the HIRA enhances proliferation and invasion of Fh1-deficient cells in vitro and in vivo. Mechanistically, Hira loss enables the activation of MYC and its target genes, increasing nucleotide metabolism specifically in Fh1-deficient cells, independent of its histone chaperone activity. These results are instrumental for understanding mechanisms of tumorigenesis in HLRCC and the development of targeted treatments for patients.

overall_design: Control (Fh1 flfl), Fh1 deficient (Fh1-/-) alone or with Hira loss (g1Hira) were used to perform a H3.3 chip analysis.

last: Valcarcel-Jimenez

first: Christian

last: Frezza


title: HIRA loss transforms FH deficient cells

overall_design: Refer to individual Series


title: HIRA loss transforms FH deficient cells [RNA-Seq]

summary:
Purpose: Identifying transcriptional changes led by Hira loss in FH deficient cells
Methods: RNA was extracted from the cell lines using QIAGEN kit folloging the manufacturer instructions. RNA concentrator kit was used to guarantee RNA quality.
Results/Conclusion: We identified MYC/E2F1 signatures as the top upregulated ones controlling the oncogenic events occuring in Fh1 and Hira deficient cells.

overall_design: Transcriptional study of Fh1 proficient cells (Fh1 fl/fl), Fh1 deficient cells (Fh1-/-) and Hira loss through the use of a gRNA (Fh1 fl/fl g1Hira and Fh1-/- g1Hira)


title: Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci (ChIP-Seq 2)

overall_design: ChIP-seq examination of 4 samples (2 biological replicate sets each of INTS11Halo cells: DMSO- and PROTAC-treated for RNAPII Ser5P)

middle: R

first: Claudia

first: ChenCheng

last: Zhao

first: Kai-Lieh

last: Huang


title: Genomewide m6A mapping uncovers dynamic changes in the m6A epitranscriptome of cisplatin-treated apoptotic HeLa cells

city: Izmir

first: Bünyamin

last: Akgül

state: Urla

address: Gulbahce Campus

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

summary: We have performed a epitranscriptomics study in which we first tretaed DMSO as a negative control and cisplatin in HeLa cells. Total RNA was isolated from control as well as CP treated cells and apoptotic rate was determined by flow cytometry. Total RNAs were subjected to miCLIP to identify differentially m6A methylated RNAs. We then transcriptionally analyzed apoptotic genes which have differential m6A methylation in CP tretament by qPCR. Afterthat, candidate genes were examined at the level of translation by polysome fractioantion assay.

overall_design: Total RNA was isolated from negative control (DMSO) and cisplatin treated HeLa cells in triplicate to perform miCLIP assay.

first: Azime

last: Akcaoz

first: Ayse

last: Gelmez

first: Buket

last: Saglam

first: Ozge

last: Tuncel

first: Ipek

last: Erdogan

first: Bunyamin

last: Akgul


title: G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects

city: Worcester

first: Athma

last: Pai

address: 368 Plantation Street, AS5-2057

department: RNA Therapeutics Institute

institute: UMASS Medical School

summary: Evaluation of the effect of 3 ASOs targeting FXN on mRNA levels

overall_design: PolyA RNA seq for ASOs targeting the Frataxin gene. Single-end 75 cycles, 3 replicates per treatment.

first: Feng

last: Wang

first: Ezequiel

last: Calvo-Roitberg

first: Jonathan

last: Watts


title: Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci (RNA-Seq)

first: Karen

last: Adelman

overall_design: Examination of 6 samples by RNA-seq (3 biological replicate sets of F121-9 cells: control knockdown; INTS11 knockdown); also 2 biological replicate sets of untreated F121-9 cells

first: Eric

middle: J

last: Wagner

first: Chad

last: Stein

first: Andrew

last: Field

last: Mimoso


title: Mitochondrial cristae architecture protects against mtDNA release and inflammation

city: Beijing

first: Baiyu

last: He

address: No. 7, Science Park Road, Zhongguancun Life Science Park

institute: National Institute of Biological Sciences

summary: Mitochondrial damage causes mtDNA release to activate type I interferon (IFN-I) response via the cGAS-STING pathway. mtDNA-induced inflammation promotes autoimmune and aging-related degenerative disorders. However, the global picture of inflammation-inducing mitochondrial damages remains obscure. Here we performed a mitochondria-targeted CRISPR-knockout screen for regulators of the IFN-I response. Strikingly, our screen revealed dozens of hits enriched with key regulators of cristae architecture, including phospholipid cardiolipin and protein complexes such as OPA1, MICOS, SAM, MIB, PHB, and the F1Fo-ATP synthase. Disrupting these cristae organizers consistently induced mtDNA release and STING-dependent IFN-I response. Furthermore, robust STING-dependent IFN-I response was induced in vivo by knocking out MTX2, a subunit of the SAM complex whose null-mutations cause progeria in human. Taken together, beyond revealing the central role of cristae architecture to prevent mtDNA release and inflammation, our results mechanistically link mitochondrial cristae disorganization and inflammation, two emerging hallmarks of aging and aging-related degenerative diseases.

overall_design: We performed RNA-seq in MEF cell lines to find out how prominent is the IFN-I response among all the cellular transcriptional changes in mutant cells with cristae disorganization. The cell lines we used for RNA-seq in this study include 3 Knockout cell lines (CHCHD3 KO, MTX2 KO, DNAJC11 KO) and 1 WT cell for control, 2 DOX-induced KD cell lines (OPA1-DOX, Mic60-DOX) with their un-induced samples (OPA1, Mic60) for control, 1 un-induced non-targeting-control-shRNA cell line(NC) and Dox-induced NC-shRNA (NC-DOX) cell lines for negative control. Each cell line has 3 biological replicates for RNA-seq. We also performed RNA-seq in mouse tissue to determine if cristae disorganization activates the IFN-I response in vivo. We generated  MTX2 liver-specific KO (MTX2-LKO) mice and non-targeting control (NTC) mice as control.  For RNA-seq, we used RNA from liver of 5 mice (12-week old) of each group for biological replicates.

first: Huatong

last: Yu

first: Shanshan

last: Liu

first: Huayun

last: Wan

first: Song

last: Fu

first: Siqi

first: Jun

last: Yang

first: Zihan

last: Zhang

first: Huanwei

last: Huang

first: Qi

last: Li

first: Zhaodi

last: Jiang

first: Fengchao

first: Qinghua

first: Hui


title: Transcriptome of the NR5A1 expressing pituitary gonadotropes

first: Yuichi

last: Shima

summary: NR5A1 is expressed in the pituitary gonadotropes and regulates their functional differentiation. In this study, transcriptomes of the pituitary gonadotropes which are sorted from Ad4BP-BAC-EGFP mice were revealed in males and females.

overall_design: Pituitary gonadotropes were collected from Ad4BP-BAC-EGFP mouse pituitary, and RNA profiles in EGFP-expressing cells were analyzed (n=4 for male and female).

first: Kanako

last: Miyabayashi


title: Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci

first: Karen

last: Adelman

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


title: Alteration of global transcription by the artificial sweetener acesulfame K in Acinetobacter baumannii AB5075

status: Public on Oct 27 2022

city: Uxbridge

first: Rubén

last: de Dios

state: Middlesex

address: Kingston Lane

department: Life Sciences

institute: Brunel University London

summary:
We perform RNA-seq comparing a treatment with 1.33% acesulfame K to a mock treatment in A. baumannii AB5075 in order to describe the alterations in global transcription produced by this artificial sweetener.
A. baumannii AB5075 cultures were grown in LB medium in the presence of 1.33% acesulfame K or a water control (3 biological replicates per condition) until reaching mid-exponential phase. At this point, cells were harvested, treated with RNAlate for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample.
As a result, 212 genes appeared upregulated in the presence of acesulfame K, whereas 252 were downregulated. In highlights, the gene functional groups showing the strongest transcriptional alterations were those related to twtching motility and natural transformation (downregulation of genes involves in biogenesis and control of Type IV pili and com genes), as well as genes involved in iron acquisition and siderophore biosynthesis and an uncharacterised gene cluster that might be involved in detoxification of sulfonamide compounds.

overall_design: Three independent replicates of A. baumannii AB5075 were grown to mid-exponential phase in LB medium supplemented with 1.33% acesulfame K and compared to three independent replicates grown in the same conditions but receiving a mock treatment (equivalent volume of water).

first: Chris

last: Proctor

first: Evgenia

last: Maslova

first: Sindija

last: Dzalbe

first: Ronan

last: McCarthy


title: Stress-induced transcriptional readthrough into neighboring genes is linked to intron retention

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

institute: Technion

summary: Exposure to certain stresses leads to readthrough transcription downstream of gene ends. Here we found that this phenomenon impacts the expression of genes located downstream to readthrough genes, whereby readthrough transcription proceeds into downstream genes, termed read-in genes. Using polyA-selected RNA-seq data from mouse fibroblasts, we identified widespread read-in in heat shock, oxidative and osmotic stress conditions. Read-in genes share distinctive genomic characteristics; they are extremely short, mainly due to less, shorter, introns, and they are highly GC rich. Furthermore, using ribosome footprint profiling we found that the translation of genes with high degrees of read-in is significantly reduced. Strikingly, read-in genes show extremely high levels of intron retention during stress, mostly in their first intron. While read-in genes share features that are generally associated with increased likelihood of intron retention, such as short introns and high GC content, intron retention in read-in genes during stress exceeds greatly beyond what is expected given their genomic properties. Finally, we found that first introns in read-in genes have weaker 5’ and 3’ splice sites. Our data portray a relationship between read-in and intron retention, suggesting it may have co-evolved to facilitate reduced translation of read-in genes during stress.

overall_design: Induction of various types of stress in NIH3T3 cells, followed by transcriptome and translatome analysis.

first: Shani

last: Hadar

first: Anatoly

last: Meller


title: Regulatory functions of 5′ terminal sequences in  mRNA synthesis, translation and decay

city: New Haven

first: Carson

last: Thoreen

state: CT

address: 333 Cedar St. SHM B 145

department: Cellular and Molecular Physiology

institute: Yale School of Medicine

summary:
Purpose: The 5’ end of a mRNA is a target for key factors in mRNA translation and mRNA destabilization, whereas its sequence is determined by the exact site where transcription initiates. The goal of this study is to see how different 5’ end sequences affect mRNA levels, mRNA translation and mRNA stability.
Methods: We expressed a reporter Renilla luciferase gene of which the first nucleotides at its 5’ end were random 7-mer sequences in HeLa cells. After treatment with RNA polymerase inhibitor Actinomycin D, mTOR inhibitor Torin 1, or vehicle (DMSO) cells were lysed and the reporters 5’ ends were sequenced, either directly or after separating strongly translated and poorly translated mRNA molecules on a sucrose gradient.
Results: We found that the first 7 nucleotides of a mRNA have a strong impact on mRNA translation and its regulation and on mRNA stability.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Systematic study of the effect of the 5' end sequence of a mRNA on its expression, translation and stability.

first: Antonia

middle: M

last: van den Elzen


title: In Vivo efficacy assessment of the CDK4/6 inhibitor palbociclib and the PLK1 inhibitor volasertib in Human Chordoma Xenografts [Target-seq]

city: PARIS

first: Sophie

last: VACHER

address: 26 rue d'Ulm

institute: Institut Curie

summary: Analysis of gene mutations and copy number variation status by an in-house next-generation sequencing (NGS) panel. The panel includes 571 genes of interest in oncology for diagnosis, prognosis, and theranostics including chordomas genes of interest.

overall_design: Three chordoma Patient’s Derived Xenograft (PDX) models (CD3, CD7 and CD39) and corresponding germline samples were analyzed.

first: Thibault

last: Passeri

first: Ahmed

last: Dahmani

first: Julien

last: Masliah-Planchon

first: Rania

last: El Botty

last: Vacher

first: Elisabetta

last: Marangoni

first: Fariba

last: Némati

first: Sergio

last: Roman-Roman

first: Homa

last: Adle-Biassette

first: Hamid

last: Mammar

first: Sébastien

last: Froelich

first: Ivan

last: Bièche

first: Didier

last: Decaudin


title: Single nuclei RNAseq analysis of HD mouse model and human brain reveals impaired 1 oligodendrocyte maturation and potential causal regulators

city: New York

first: Osama

last: Al-Dalahmah

state: NY

address: 630 West, 168th Street

department: Pathology and Cell Biology

institute: Columbia University

summary: A challenge in treating Huntington’s disease (HD) is the complexity of affected brain regions and cell types. We carried out a systematic analysis of cell type-specific changes in cortex and striatum from R6/2 mice at 8 and 12w, and in three regions of human HD post-mortem tissue using single nucleus RNA sequencing. We discovered major expression changes in oligodendrocytes (OLs) and oligodendrocyte precursors (OPCs), suggesting that many OLs were arrested in an immature state. Causal gene network analysis implicates PRKCE and SWI/SNF in abnormal OL maturation. PRKCE protein was dramatically decreased in mouse and human HD, and its regulator, diacylglycerol lipids, were decreased in human HD at very early stages. ATACseq of mouse glia showed increased accessibility of sites regulated by SWI/SNF subunit Smarca4 in HD, further implicating Prkce-SWI/SNF. We identified differences between 8w and 12w mice in the induction of OPC 37 maturation, with 12w mice most similar to human. Disrupted cell-to-cell signaling between medium spiny neurons and OL, that may contribute to neuronal dysfunction, was identified in both human HD and R6/2 mice using ligand-receptor analysis. These findings reveal novel insights into OL pathology that spans multiple brain regions in humans and mice and suggest therapeutic strategies.

overall_design: Examination of snRNAseq profiles of human glial and neuronal cells from three different postmortem brain regions (cingulate cortex, caudate nucleus, and nucleus accumbens) from seven Huntington disease and six control donors


title: The role of hepatic endothelial c-Kit in regulating the homeostasis and pathogenesis of the liver

city: Xi'an

first: Bai

last: Ruan

address: No.169, Changle Road

institute: Fourth Military Medical University

summary: To investigate the role of hepatic EC-specific endothelial marker—c-Kit in the regulation of vascular homeostasis and liver pathogenesis. We firtly generated endothelial cell-specific conditional c-Kit knock out and their control mice. LSECs isolated from control and EC-specific c-Kit KO mice were subjected to RNA-seq. Second, c-Kit+ LSECs were purified using anti-CD117 magenetic beads and the eluted fraction was further incubated with anti-CD146 magnetic beads to obtain c-Kit- LSECs. c-Kit- LSECs and c-Kit+ LSECs were thereafter compared through transcriptome analysis as well. To further elucidate the function of c-Kit+ LSECs in modulating NASH pathogenesis of the liver challenged by MCD-diet, bulk CD146+ LSECs were purified from MCD mice (4w) subjected with c-Kit+ or c-Kit- LSECs infusion respectively at the last week, and compared by RNA-sequencing.

overall_design: Liver sinusoidal endothelial cells were isolated from indicated mice as described in the summary and were subjected to RNA sequencing, in triplicate or quadruplicate, using Illumina HiSeq 3000.

first: Wang

last: Lin

first: Ruan

last: Bai

first: Duan

last: Juanli


title: Metabolic pathways enriched according to ERG status are associated with biochemical recurrence in Hispanic/Latino patients with prostate cancer

city: Bogotá

first: Natalia

middle: Lizeth

last: Acosta Vega

state: Bogotá, D.C.

country: Colombia

institute: Instituto Nacional de Cancerología - Colombia

summary: Background  The role of ERG-status molecular subtyping in prognosis of prostate cancer (PCa) is still under debate. In this study, we identified differentially expressed genes (DEGs) according to ERG-status to explore their enriched pathways and implications in prognosis in Hispanic/Latino PCa patients.   Methods  RNA from 78 Hispanic PCa tissues from radical prostatectomies (RP) were used for RNA-sequencing. ERGhigh/ERGlow tumor groups were determined based on the 1.5-fold change median expression in non-tumor samples. DEGs with a False Discovery Rate (FDR) < 0.01 and a fold change > 2 were identified between ERGhigh and ERGlow tumors and submitted to enrichment analysis in MetaCore. Survival and association analyses were performed to evaluate biochemical recurrence (BCR)-free survival.   Results  The identification of 150 DEGs between ERGhigh and ERGlow tumors revealed clustering of most of the non-BCR cases (60%) into de ERGhigh group and most of the BCR cases (60.8%) in ERGlow group. Kaplan-Meier survival curves showed a worst BCR-free survival for ERGlow patients, and a significant reduced risk of BCR was observed for ERGhigh cases (OR = 0.29 (95%CI, 0.10-0.8). Enrichment pathway analysis identified metabolic-related pathways, such as the renin-angiotensin system and angiotensin maturation system, the linoleic acid metabolism, and polyamines metabolism in these ERG groups.  Conclusions  ERGlow tumor cases were associated with poor BCR-free survival in our Hispanic/Latino patients, with metabolism-related pathways altered in the BCR progression.  Impact  Our findings suggest the need to dissect the role of diet, metabolism and lifestyle as risk factors for more aggressive PCa subtypes.

overall_design: Differentially expressed genes (DEGs) between ERGhigh and ERGlow tumor groups from RNA-seq samples from FFPE tissues.

last: Acosta-Vega

first: Rodolfo

last: Varela

first: Jorge

last: Mesa

first: Jone

last: Garai

first: Melody

middle: C

last: Baddoo

first: Alberto

last: Gómez-Gutiérrez

first: Silvia

last: Serrano-Gómez

first: Marcela

last: Nuñez Lemus

first: Martha

last: Serrano

first: Jovanny

last: Zabaleta

first: Alba

last: Combita

first: María

last: C Sanabria-Salas


title: Targeting APLN/APJ restores blood-testis barrier and improves spermatogenesis in murine and human diabetic models

city: Guangzhou

first: Xinyan

last: Yang

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

department: Developmental Biology

institute: Southern Medical University

summary: Type 2 diabetes mellitus is one of the most prevalent metabolic diseases affecting multiple organs, including reproductive disorders in male diabetic patients. However, the molecular mechanisms that contribute to spermatogenesis dysfunction in diabetic patients have not yet been fully elucidated. Here, we performed Smart-seq2 to examine the transcriptome of diabetic patients' testis cells at single cell resolution including all major cell types of the testis. Intriguingly, whereas spermatogenesis appears largely preserved, the gene expression profiles of Sertoli cells and the blood-testis barrier (BTB) structure were dramatically impaired. Among the deregulated pathways, the Apelin (APLN) peptide /Apelin-receptor (APJ) axis was hyper-activated in diabetic patients. Mechanistically, APLN is produced locally by Sertoli cells upon high glucose treatment, which subsequently suppressed the production of carnitine and repressed the expression of cell adhesion genes in Sertoli cells. Together, these effects culminated in BTB structural dysfunction. Finally, using the small molecule APLN receptor antagonist, ML221, we show that blocking APLN/APJ significantly ameliorated the BTB damage and, importantly, improved functional spermatogenesis in diabetic db/db mice. We also translated and validated these findings in cultured human testis. Our findings identify the APLN/APJ axis as a promising therapeutic target to improve reproduction capacity in male diabetic patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Here we performed scRNA sequencing for 900 individual human testicular cells including spermatogonia, spermatocytes, spermatids, and testicular somatic cells (soma) from donors with diabetes mellitus.

The normal samples used in this study are from GSE106487 (GSM2838842-GSM2838908). To better integrate the normal samples and the diabetes samples, the raw data of the normal samples were re-analyzed using an analysis process consistent with that of the diabetes samples.

**Note from submitter: Due to the Regulations of the People's Republic of China on the Management of Human Genetic Resources, raw data related to humans needs to be uploaded to the National Genomics Data Center, China National Center for Bioinformation (CNCB-NGDC), so we cannot upload raw data to NCBI.**

The raw data is stored at https://ngdc.cncb.ac.cn/gsa-human/ , and the accession number is HRA000976.

first: Xiaoyang

last: Zhao

first: Zhaoting

last: Liu

first: Shuan

last: Rao

first: Ke

last: Song

first: Jiexiang


title: Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci (ChIP-Seq)

city: Boston

first: Karen

last: Adelman

institute: Harvard Medical School

summary: Pausing of RNA polymerase II (RNAPII) in early elongation is critical for gene regulation. Paused RNAPII can be released into productive elongation by the kinase P-TEFb or targeted for premature termination by the Integrator complex. Integrator comprises endonuclease and phosphatase activities, driving termination through cleavage of nascent RNA and removal of stimulatory phosphorylation. To probe the direct consequences of Integrator activity, we generated a degron system to rapidly deplete the Integrator endonuclease INTS11. Degradation of INTS11 elicits a nearly universal increase in RNAPII escape from promoter regions. However, these RNAPII complexes fail to achieve optimal elongation rates and reveal continued Integrator phosphatase activity. Short transcripts are thus selectively upregulated by INTS11 loss, including many non-coding RNAs, transcription factors and signaling regulators. Together, our data indicate a common function for INTS11 at all RNAPII loci, with differential effects on particular genes, pathways or RNA biotypes reflecting transcript lengths rather than Integrator specificity.

overall_design: ChIP-seq examination of 8 samples (2 biological replicate sets each of INTS11Halo cells: DMSO- and PROTAC-treated for INTS3 and INTS11); also 2 biological replicates of INTS11 ChIP-seq in F121-9 cells

first: Eric

last: Wagner

first: Chad

last: Stein

first: Andrew

last: Field

first: Claudia

middle: A

last: Mimoso

first: ChenCheng

first: Kai-Lieh

last: Huang


title: scRNA-seq/CITE-seq analysis of aortic CD45+ cells from mice expressing Jak2V617F mutation in myeloid cells

status: Public on Oct 26 2022

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: JAK2V617F mutation is associated with an increased risk for athero-thrombotic cardiovascular disease, but its role in aortic disease development and complications remains unknown. In a cohort of patients with myeloproliferative neoplasm, JAK2V617F mutation was identified as an independent risk factor for dilation of both the ascending and descending thoracic aorta. Using single-cell RNA-seq, complementary genetically-modified mouse models, as well as pharmacological approaches, we found that JAK2V617F mutation was associated with a pathogenic pro-inflammatory phenotype of perivascular tissue-resident macrophages, which promoted deleterious aortic wall remodeling at early stages, and dissecting aneurysm through the recruitment of circulating monocytes at later stages. Finally, genetic manipulation of tissue-resident macrophages, or treatment with a Jak2 inhibitor, ruxolitinib, mitigated aortic wall inflammation and reduced aortic dilation and rupture. Overall, JAK2V617F mutation drives vascular resident macrophages toward a pathogenic phenotype and promotes dissecting aortic aneurysm.

overall_design: Aortic CD45+ cells were sorted from control mice (Jak2-WT; n=5) and mice with a myeloid specific expression of mutated JAK2 variant Jak2V617F (Jak2-V617F-MyC; n=5) and processed for scRNA-seq with CITE-seq

first: Clement

last: Cochain

first: Panagiota

last: Arampatzi

first: Hafid

last: Ait-Oufella


title: Musashi-1 is a master regulator of aberrant translation in Group 3 medulloblastoma

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Transcripts bound to Musashi-1 (MSI1) are explored in Group 3 medulloblastoma (G3 MB) and neural stem cells harvested from the cerebellar portion of a embryonal brain

overall_design: SU_MB002, a treatment refractory G3 MB cell line, and NSC201cb as described above is UV cross-linked with 600mJ and immunoprecipitated with MSI1 antibody. The enhanced cross-linking and immunoprecipitation protocol was followed as previously described (Van Nostrand et al, 2016). Each cell sample contains two biological replicate IPs (AIP, BIP) each normalized over a single size-matched input (AI).

first: Michelle

last: Masayo Kameda

first: EnChing

last: Luo

first: Brian

last: Yee

first: Kevin

last: Brown

first: Sheila

last: Singh


title: Therapeutic activity of GARP:TGF-b1 blockade in murine primary myelofibrosis

city: Brussels

first: Christophe

last: Vanderaa

address: Avenue Hippocrate 74

institute: UCLouvain

summary: Primary myelofibrosis (PMF) is a myeloproliferative neoplasm characterized by clonal expansion of myeloid cells, notably megakaryocytes (MKs), and aberrant cytokine production leading to bone marrow (BM) fibrosis and insufficiency. Current treatment options are limited. TGF-b1, a profibrotic and immunosuppressive cytokine, is involved in PMF pathogenesis. While all cell types secrete inactive, latent TGF-b1, only a few activate the cytokine via cell type-specific mechanisms. The cellular source of the active TGF-b1 implicated in PMF is not known. Transmembrane protein GARP binds and activates latent TGF-b1 on the surface of regulatory T lymphocytes (Tregs) and MKs or platelets. Here, we found increased expression of GARP in BM and spleen of mice undergoing PMF and tested the therapeutic potential of a monoclonal antibody that blocks TGF-b1 activation by GARP-expressing cells. GARP:TGF-b1 blockade reduced not only fibrosis, but also clonal expansion of transformed cells. Using mice carrying a genetic deletion of Garp in either Tregs or MKs, we found that the therapeutic effects of GARP:TGF-b1 blockade in PMF imply targeting GARP on Tregs. These therapeutic effects, accompanied by increased IFN-g signals in the spleen, were lost upon CD8 T cell depletion. Our results suggest that selective blockade of TGF-b1 activation by GARP-expressing Tregs increase a CD8 T cell-mediated immune reaction that limits transformed cell expansion, providing a novel approach that could be tested to treat patients with myeloproliferative neoplasms.

overall_design: RNAseq of spleens collected from non-treated MPLW508A mice on days 13 and 20 were compared to establish signatures of PMF progression. RNAseq of spleens collected on day 34 from MPLW508A mice responding to 58A2 were compared to non-treated controls to analyze effects of treatment with 58A2.

first: Sara

last: Lecomte

first: Julien

last: Devreux

first: Grégoire

last: de Streel

first: Nicolas

last: van Baren

first: Violaine

last: Havelange

first: David

last: Schröder

first: Noora

last: Vaherto

last: Vanhaver

first: Noémie

last: Dupuis

first: Christian

last: Pecquet

first: Pierre

last: Coulie

first: Stefan

last: Constantinescu

first: Sophie

last: Lucas


title: Sex differences in RBM20 cardiomyopathy

city: Heidelberg

first: Maarten

last: van den Hoogenhof

state: (select)

address: In Neuenheimer Feld 669

institute: Institute of Experimental Cardiology

summary: In this study, we investigated potential sex differences in a Rbm20 knockout mouse model. We used RNA sequencing of bulk RNA from the left ventricle of male and female wildtype and Rbm20 knockout mice.

overall_design: 10-week old male and female wildtype and Rbm20 knockout mice were sacrificed, their hearts were harvested, and RNA from the LV was isolated and used for RNA sequencing.

first: Mark

last: Pepin


title: Effect of alisertib and navitoclax on gene expression in B16 melanoma tumors

city: Columbus

first: Anna

last: Vilgelm

state: OH

address: 460 W 12th Ave

institute: The Ohio State University

summary: To investigate how tumor cells respond to alisertib and navitoclax single agents and combonation therapy in vivo, mice with melanoma were treated with these agents or vehicle-contol. RNAseq was used to investigate gene expression in tumors

overall_design: C57Bl/6 mice were injected with B16 melanoma cells and treated with alisertib and navitoclax for 11 days

first: Vijaya

last: Bharti


title: Biosynthesis of membrane-spanning lipids in Thermoanaerobacter ethanolicus and Thermotoga maritima

city: 't Horntje (Texel)

first: Diana

middle: X.

last: Sahonero-Canavesi

address: Landsdiep 4

country: Netherlands

institute: NIOZ

sample_organism:
Thermoanaerobacter ethanolicus
Thermotoga maritima

overall_design: Refer to individual Series


title: Single cell RNA-sequencing identifies a paracrine interaction that may drive oncogenic Notch signaling in human adenoid cystic carcinoma

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

institute: The Hebrew University of Jerusalem

summary: Salivary adenoid cystic carcinoma (ACC) is a rare but biologically unique biphasic tumor, consisting of malignant myoepithelial and luminal epithelial cells. MYB and Notch signaling have been implicated in the pathophysiology of these tumors, but in vivo descriptions of these two programs in human tumors and investigation into their active coordination remain incomplete. We utilized single cell RNA-sequencing to profile human head and neck ACC, including the first comparison of primary ACC with a matched local recurrence. We define expression heterogeneity in these rare tumors, uncovering previously unappreciated diversity in myoepithelial and luminal cell expression. We discover differential expression of Notch ligands DLL1, JAG1, and JAG2 in myoepithelial cells, suggesting a paracrine interaction that may support oncogenic Notch signaling. We further validated this selective expression in three published cohorts of ACC patients. Our data provide a potential explanation for the biphasic nature of low and intermediate grade ACC and may help direct new therapeutic strategies against these tumors.

overall_design:
Fresh biopsies of head and neck salivary ACC were collected at the time of surgical resection. Post-operatively, H&E stained sections were reviewed by a dedicated head and neck pathologist and assessed for growth pattern and immunohistochemical staining profile to confirm the pathologic diagnosis of ACC, based upon histomorphologic criteria outlined in the WHO Classification of Head and Neck Tumours. Only cases unequivocally classified as ACC were included in the final dataset.
NOTE: RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns.

first: Anuraag

middle: S

last: Parikh

first: Sidharth

middle: V

last: Puram


title: Epigenome analysis of neuroblastoma cell  treated by NEN under normoxia and hypoxia

city: palo alto

first: Jiangbin

last: ye

state: California

address: 269 Campus Drive CCSR-South 1245

institute: Stanford university

summary: Genome wide DNA methylation profiling of neuroblastoma cell SK-N-BE(2) treated by 1µM NEN under normoxia and hypoxia for 24hrs. The IInfinium Human MethylationEPIC BeadChip v1.0 B5 was used to obtain DNA methylation profiles across approximately 850,000 methylation sites in the genome of neuroblastoma. Samples included 4 group with 3 biological replicates: (1) normoxia_CTRL (2) normoxia_NEN (3) hypoxia_CTRL (4) hypoxia_NEN

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium epic Human Methylation Beadchip v1.0 B5

last: Ye

first: Haowen

last: Jiang


title: Biosynthesis of membrane-spanning lipids in Thermoanaerobacter ethanolicus

summary: This study was conducted to identify the genes involved in the synthesis of membrane-spanning  lipids in Thermoanaerobacter ethanolicus JW 200.

overall_design: Thermoanaerobacter ethanolicus was cultivated under anaerobic conditions in 80 ml batch cultures in 250 ml serum bottles. Cultures were incubated either at 60°C or 45°C growth temperatures. Samples were derived from three replicates at each condition. The cells were harvested at mid exponential, late exponential, and stationary phases.

middle: X

first: Melvin

last: Siliakus

first: Laura

last: Villanueva

first: Alejandro

last: Abdala


title: Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)

city: Tokyo

first: Kotaro

last: Chihara

address: 1-23-1 Toyama

department: Research Center for Drug and Vaccine Development

institute: National institute of infectious diseases

summary: New methods for the global identification of RNA-protein interactions have led to greater recognition of the abundance and importance of RNA-binding proteins (RBPs) in bacteria. Here, we expand this tool kit by developing SEC-seq, a method based on a similar concept as the established Grad-seq approach. In Grad-seq, cellular RNA and protein complexes of a bacterium of interest are separated in a glycerol gradient, followed by high-throughput RNA-sequencing and mass spectrometry analyses of individual gradient fractions. New RNA-protein complexes are predicted based on the similarity of their elution profiles. In SEC-seq, we have replaced the glycerol gradient with separation by size exclusion chromatography, which shortens operation times and offers greater potential for automation. Applying SEC-seq to Escherichia coli, we find that the method provides a higher resolution than Grad-seq in the lower molecular weight range up to ~500 kDa. This is illustrated by the ability of SEC-seq to resolve two distinct, but similarly sized complexes of the global translational repressor CsrA with either of its antagonistic small RNAs, CsrB and CsrC. We also characterized changes in the SEC-seq profiles of the small RNA MicA upon deletion of its RNA chaperones Hfq and ProQ and investigated the redistribution of these two proteins upon RNase treatment. Overall, we demonstrate that SEC-seq is a tractable and reproducible method for the global profiling of bacterial RNA-protein complexes that offers the potential to discover yet-unrecognized associations between bacterial RNAs and proteins.

overall_design: Applying SEC-seq to Escherichia coli

first: Milan

last: Gerovac

first: Jens

last: Hör

first: Jörg

last: Vogel


title: Biosynthesis of membrane-spanning ether lipids in Thermotoga maritima

summary: This study was conducted to identify the genes involved in the synthesis of membrane-spanning ether lipids in Thermotoga maritima MSB8.

overall_design: Thermotoga maritima was cultivated in basal media under anaerobic conditions. Cultures were incubated either at optimal (80°C) or lower (55°C) growth temperatures. Samples were derived from five replicates at each condition. The cells were harvested at early exponential, exponential, and stationary phases.

last: Abdala Asbun


title: Single-cell RNA-seq of mouse kidneys undergoing ferroptosis

city: Kyoto

first: Yoshihiko

last: Kobayashi

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Institute for Life and Medical Sciences

institute: Kyoto University

summary: We performed single-cell transcriptomics analyses (10x Chromium 3' v3.1) using dissociated total kidney cells to identify the difference in gene expression patterns and signaling pathways between male and female mouse kidneys after selective induction of ferroptotic stress in renal tubular epithelial cells.

overall_design: Single-cell RNA-seq (10x Chromium 3' v3.1) in male and female mouse kidneys of Pax8rtTA; tetOCre; Gpx4 knockout mouse lines and their littermates.

first: Shintaro

last: Ide

first: Tomokazu

last: Souma


title: Long-read transcriptomic sequencing of Plasmodium falciparum malaria parasite reveals isoforms with alternative 5′ ends

city: Khlong Nung

first: Pavita

last: Kaewprommal

state: Pathum Thani

department: NBT

country: Thailand

institute: NSTDA

summary: The Plasmodium falciparum human malaria parasite genome is incompletely annotated and does not accurately represent the transcriptomic diversity of this species. To address this need, we performed long-read transcriptomic sequencing. To increase representation of mRNA isoforms expressed during intraerythrocytic stages, RNA was extracted from samples taken at time-points from synchronized cultures. 5 capped mRNA was enriched and converted to cDNA library. The cDNA libraries were sequenced on Nanopore and PacBio long-read platforms. Candidate non-redundant isoforms were annotated from each library dataset for creating a new transcript annotation catalog. Isoforms with alternative 5 ends represented the largest class of novel isoforms, although the majority of these do not seem to represent the products of alternative transcription initiation events. We suggest that most isoforms do not encode protein isoforms and instead represent RNA decay products.

overall_design: Isoform profiles in ring, trophozoite and schizont stages of P. falciparum intraerythrocytic development obtained from total RNA and nuclear RNA samples

first: Philip

last: Shaw

first: Chayaphat

last: Wongsombat

first: Sissades

last: Tongsima

first: Sumalee

last: Kamchonwongpaisan

first: Jittima

last: Piriyapongsa


title: In vitro infection of murine osteoclast by the parasite Leishmania infantum

city: Erlangen

first: Didier

last: Soulat

address: Wasserturm strasse 3/5

department: Institute of Clinical Microbiology, Immunology and Hygiene

institute: University Hospital of Erlangen and Friedrich-Alexander-University (FAU) Erlangen-Nürnberg

summary:
To investigate the effect of infection of osteoclast by Leishmania infantum, we infected diffentiating bone marrow derived osteoclast with the parasite at day 2 of differentiation
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cultures of cells infected for 24 hours compared to 4 control cultures.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine osteoclast infected by Leishmania infantum

first: Chaobo

last: Lai

first: Jennifer

last: Heinemann

first: Ulrike

last: Schleicher

first: Georg

last: Schett

first: Christian

last: Bogdan

first: Aline

last: Bozec


title: cytoDRIP-seq in HeLa cells

city: Stanford

first: Karlene

middle: Anne

last: Cimprich

address: 318 Campus Drive

institute: Stanford University

summary: R-loops are three-stranded nucleic acid structures that have important regulatory roles in cells. Deregulation of R-loop dynamics, however, can lead to DNA damage and genome instability, which results from the action of endonucleases such as XPG on R-loops. The mechanism by which this R-loop processing occurs and the impact on the cell remain unclear. Here, we show that cells with R-loops induced by deregulation of the RNA-DNA helicase Senataxin (SETX), the breast cancer gene BRCA1, or RNA splicing, accumulate cytoplasmic RNA-DNA hybrids in an XPG-dependent manner. Sequencing of cytoplasmic hybrids upon loss of SETX shows that they are derived from a subset of nuclear RNA-DNA hybrids that have longer lifetimes, signal on both sense and antisense strands and contain regions with switches in nucleotide skew. We further show that induced cytoplasmic hybrids bind the pattern recognition receptors cGAS and TLR3, activating IRF3 and inducing apoptosis. Ataxia oculomotor apraxia type 2 (AOA2) patient cells which harbor a mutated SETX also exhibit XPG-dependent activation of the innate immune response.  These findings identify RNA-DNA hybrids as novel, immunogenic nucleic acid species which aberrantly accumulate in the cytoplasm of cells upon R-loop processing, and can ultimately induce cell apoptosis. We anticipate that aberrant R-loop processing and subsequent innate immune activation may be a pathological process that contributes to many disease states, such as neurodegeneration and cancer.

overall_design: IgG and S9.6 IP cytoplasmic extracts following control and SETX knockdown in HeLa cells

first: Magdalena

last: Crossley

first: Chenlin

last: Song

first: Michael

last: Bocek


title: Defining the spatial-molecular map of fibrotic tendon healing and the drivers of Scleraxis-lineage cell fate and function

status: Public on Oct 25 2022

city: Rochester

first: Jessica

last: Ackerman

address: 605 Elmwood Ave

institute: University of Rochester

summary: Spatial transcriptomic analysis of murine FDL tendons following acute injury and repair to evaluate spatiotemporal programming of tendon healing

overall_design: Hindpaws from Scx-Ai9 mice (Scx-lin+ cells labeled with tdTomato fluorescence prior to surgery) were collected at D0, 14, 21, and 28 post-injury (in duplicate) for ST analysis of healing tendons using the 10X Visium platform

first: Katherine

last: Best

first: Samantha

last: Muscat

first: Anne

last: Nichols

first: Elizabeth

last: Pritchett

first: Chia-Lung

last: Wu

first: Alayna

last: Loiselle


title: Self-cleaving guide RNAs enable pharmacological selection of precise gene editing events in vivo

city: Portland

first: Amita

last: Tiyaboonchai

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Pediatrics

institute: Oregon Health & Science University

summary: In this study we compared the gene expression of mice that had received the rAAV-GR-Cypor scgRNA and rAAV-spCas9 with and without APAP selection.  APAP selected mice were also compared to mice which had received the  rAAV-GR-Hpd miRNA.

overall_design: Livers from terminally harvested mice were isolated and RNA was extracted using RNAzol. Gene expressions profiles and expression of integrated rAAV constructs were compared between the different groups.

last: Vonada

first: Jeffrey

last: Posey

first: Leslie

last: Wakefield

first: Carl

last: Pelz

first: Markus

last: Grompe


title: Synthetical lethality of Werner helicase and mismatch repair   deficiency is mediated by p53 and PUMA in colon cancer

city: Pittsburgh

first: Lin

last: Zhang

state: Pennsylvania

address: 5117 Centre Ave, Hillman Cancer Ctr Rm2.42a, 5117 Centre Ave

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: Synthetic lethality is a powerful approach for targeting oncogenic drivers in cancer. Recent studies revealed that cancer cells with microsatellite instability (MSI) require Werner (WRN) helicase for survival; however, the underlying mechanism remains unclear. In this study, we found that WRN depletion strongly induced p53 and its downstream apoptotic target PUMA in MSI colorectal cancer (CRC) cells. p53 or PUMA deletion abolished apoptosis induced by WRN depletion in MSI CRC cells. Importantly, correction of MSI abrogated the activation of p53/PUMA and cell killing, while induction of MSI led to sensitivity in isogenic CRC cells. Rare p53-mutant MSI CRC cells are resistant to WRN depletion due to lack of PUMA induction, which could be restored by wildtype p53 knock-in or reconstitution. WRN depletion or treatment with the RecQ helicase inhibitor ML216 suppressed in vitro and in vivo growth of MSI CRCs in a p53/PUMA_x0002_dependent manner. ML216 treatment was efficacious in MSI CRC patient-derived xenografts (PDX). Interestingly, p53 gene remains wildtype in the majority of MSI CRCs. These results indicate a critical role of p53/PUMA-mediated apoptosis in the vulnerability of MSI CRCs to WRN loss, and support WRN as a promising therapeutic target in p53-wildtype MSI CRCs.

overall_design: mRNA profiles of microsatellite instable (MSI) parental HCT116 cells and microsatellite stable (MSS) HCT116 cells with transfer of chrosomes 3 and 5 (HCT116 CH3+5) transfected with control scrambled siRNA or siRNA against Werner helicase for 36 hours

first: Suisui

last: Hao

first: Jingshan

last: Tong

first: Anupma

last: Jha

first: Denise

last: Risnik

first: Darleny

last: Lizardo

first: Xinyan

last: Lu

first: Ajay

last: Goel

first: Patricia

middle: L

last: Opresko

first: Jian

last: Yu


title: Heterogeneity of neutrophils and inflammatory responses in patients with COVID-19 and healthy controls

city: Ann Arbor

first: Jintao

last: Xu

state: MI

address: 2215 Fuller Rd

institute: University of Michigan Hospital

summary: We undertook an unbiased, detailed analysis of neutrophil responses in adult patients with COVID-19 and healthy controls, to determine whether distinct neutrophil phenotypes could be identified during infections compared to the healthy state. Single-cell RNA sequencing analysis of peripheral blood neutrophils from hospitalized patients with mild or severe COVID-19 disease and healthy controls revealed distinct mature neutrophil subpopulations, with relative proportions linked to disease severity. Disruption of predicted cell-cell interactions, activated oxidative phosphorylation genes, and downregulated antiviral and host defense pathway genes were observed in neutrophils obtained during severe compared to mild infections. Our findings suggest that during severe infections, there is a loss of normal regulatory neutrophil phenotypes seen in healthy subjects, coupled with the dropout of appropriate cellular interactions.

overall_design: we recruited adult subjects hospitalized with mild or severe SARS-CoV-2 infections, in order to examine how neutrophil phenotypes changed based upon the severity of infection over time, compared to healthy adults. we employed single-cell RNA sequencing (scRNA-seq) analysis of the peripheralneutrophil immune response to SARS-CoV-2. Fresh neutrophils from human subjects is needed in order to determine whether mature neutrophils have the ability to adopt distinct phenotypes, and how these phenotypes change during clinically significant respiratory infections such as SARS-CoV-2.

first: Bing

last: He

first: Kyle

last: Carver

first: Debora

last: Vanheyningen

first: Brian

last: Parkin

first: Lana

last: Garmire

first: Michal

last: Olszewski

first: Jane

last: Deng


title: Osteopontin Exacerbates High-Fat Diet-induced Metabolic Disorders in a microbiome-dependent Manner

city: Hangzhou

first: Jianing

last: Chen

address: Qingchun Road 79#

institute: Zhejiang university

summary: Gut microbiota is involved in metabolic disorders. However, microbiome-based therapeutic interventions are not always effective, which might be due to interference of the host factors. Here, we first identified a strong positive correlation between OPN levels and BMI in humans. Next, we confirmed that OPN could aggravate high-fat diet induced metabolic disorders in mice. Importantly, we found that fecal microbiota transplantation from OPN-deficient mice significantly alleviated metabolic disorders in WT mice. OPN directly induces remodeling of the gut microbiota both in vitro and in vivo. These findings indicate that OPN could contribute to metabolic disorders by inducing an alteration of gut microbiota. OPN regulated the relative abundance of Lactobacillus by decreasing the adhesion of Lactobacillus to intestinal epithelial cells through Notch signaling pathway. These data identify OPN may serve as a potential pharmaceutical target for weight control and metabolic disorders treatment.

sample_organism:
Bacteria
Mus musculus
feces metagenome

platform_organism:
Bacteria
Mus musculus
feces metagenome

overall_design: Specific pathogen-free female mice and OPN-deficient mice (B6.129S6(Cg)-Spp1tm1Blh/J) of same background (C57BL/6J) were both originally from Jackson Laboratory (Bar Harbor, Maine, USA). Four-week-old female wild-type (WT) mice and OPN-deficient (KO) mice were sacrificed after a 24-week continuing high-fat diet (HFD, 60 kcal percent fat, cat#D12492; from Research Diets, Inc) or a normal diet (ND) containing approximately 4% kcal fat.

first: Ping

last: Zeng

first: Lan

last: Gong

first: Hongyan

last: Diao