title: Thwarting Metabolic Dysfunction-Associated Fatty Liver Disease (MAFLD) with Common Bean: Dose- and Sex-Dependent Protection against Hepatic Steatosis

status: Public on Mar 12 2023

city: Fort Collins

first: Henry

last: Thompson

state: CO

address: 1173 Campus Delivery

institute: Colorado State University

summary: Consumption of beans protects from the development of obesity. We established that dietary bean exerts dose- and sex-dependent effects on the liver transcriptome in the context of lipid metabolism, which prevents the onset of metabolic-associated fatty liver disease.

overall_design: C57BL6/J female and male mice were fed isocaloric diets containing 0%, 35%, or 70% of total dietary protein derived from whole-cooked white kidney beans. Total RNA was isolated from their liver tissue samples and subjected to RNA-seq analysis to deduce molecular mechanism of bean effects.

first: Tymofiy

last: Lutsiv

first: John

middle: N

last: McGinley

first: Elizabeth

last: Neil

first: Michelle

last: Foster


title: Identifying endogenous superior and inferior neural progenitor cells

status: Public on Mar 10 2023

city: Beijing

first: Zhenhua

last: Chen

state: China

address: West Beichen Road, Olympic Village, Beijing

department: State Key Laboratory of Molecular Development Biology

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: Stem cell competition controls organ size, maintains tissue homeostasis and optimizes long-term tissue function through eliminating cells less fit than their neighbors, but whether competitive interaction occurs between neural stem cells in the developing brain and its mechanistic drivers remains enigmatic. We applied single-cell RNA sequencing of mouse E11.5 medial cortex and bulk RNA sequencing of AnnexinV positive, PI negative cells to identify the loser cell in the natural state.

overall_design: Single cell sequencing of mouse E11.5 medial cortex. Bulk RNA sequencing of AnnexinV positive, PI negative  and AnnexinV, PI double negative cells.

first: Xue-Lian

last: Sun

first: Qing-Feng

last: Wu


title: Epigenetic dysregulation from chromosomal transit in micronuclei [DLD-1 CUT&RUN]

status: Public on Mar 13 2023

city: New York

first: Albert

middle: S

last: Agustinus

state: New York

address: 408 East 69th Street, Room 419-G

country: USA

institute: Memorial Sloan Kettering Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromosomal instability (CIN) and epigenetic reprograming are characteristic of advanced and metastatic human cancers, yet whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei, and subsequent micronuclear envelope rupture significantly disrupt normal histone post-translational modifications, a phenomenon conserved across humans and mice as well as cancer and non-transformed cells. Mislocalization of missegregating chromosomes during anaphase promotes loss of Histone H2B ubiquitination enrichment of histone H3 trimethylation, whereas micronuclear rupture engenders loss of histone H3 acetylation and histone H2A ubiquitination. Using fluorescence lifetime imaging, ATAC-see, and ATAC-seq we show that micronuclei exhibit profound differences in chromatin accessibility. Additionally, chromosomes that are reincorporated into the primary nucleus after transient encapsulation in micronuclei exhibit durable epigenetic dysregulation. Thus, in addition to genomic copy number alterations, CIN can serve as a vehicle for stochastic epigenetic reprogramming and heterogeneity in cancer.

overall_design: CUT&RUN using H3K4me3, H3K27me3 and H3K27ac antibodies on single cell clones DLD-1 cells that mis-segregates only the Y-chromosomes and their parental control The colones obtained from CEN-SELECT strategy from Ly et al., Nat. Genet. 2019

first: Bhargavi

last: Dameracharla

first: Peter

last: Ly

first: Epi

last: Cypher


summary: We reveal that Axin2 mediates stem cell competition in developing brain.

overall_design: Single cell sequencing of mouse E11.5 Axin2 mutant cell and Axin2 positive cell using SmartSeq2 protocol.  Dosal diencephalon and ventral diencephalon at mouse E10.5 were dissociated for bulk RNA-seq.

first: Xize

last: Guo


title: Gene expression profile at single cell level of phagocytic myeloid cells in autochthonous lung cancer model

city: South San Francisco

first: Daniel

middle: R

last: Lu

state: CA

address: 750 Gateway Blvd, Suite 100

institute: Amgen

summary: Phagocytosis is a critical process undertaken by myeloid cells in the tumor microenvironment. We used single-cell RNA-seq (scRNAseq) to investigate molecular and cellular consequences of neoplastic cell engulfment using a tdTomato genetically engineered mouse model.

overall_design: CD45-positive and CD45-negative populations from the lung tissue of SPC-creER KRAS-G12D mice were isolated by Fluorescence-activated cell sorting (FACS) analyzed using scRNAseq with antibody-based cell hashing.

first: Michael

middle: A

last: Gonzalez

first: Vanessa

last: Arias

first: Chi-Ming

last: Li

first: Kristin

middle: V

last: Tarbell

first: Monte

last: Winslow


title: PAIP1 promote the progress of liver cancer via regulating expression of immune and inflammatory response associated genes

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Poly(A) binding protein interacting protein 1 (PAIP1) is a translation regulator and also regulate the decay of mRNA. PAIP1 has also been reported to be a marker of increased invasive potential of liver cancer. However, the underlying molecular mechanism of PAIP1 in liver cancer is still unclear. Here, the gene expression profile of HepG2 cells transfected with PAIP1 shRNA (shPAIP1) was compared with cells transfected with empty vector (shCtrl). The results showed that shPAIP1 extensively affects the transcriptional level of 893 genes in HepG2 cells. In particular, GO analysis showed that a large number of up-regulated genes were annotated with terms including cell cycle and WNT receptor signaling pathway. The down-regulated genes were enriched in some pathways including immune response and inflammatory response. qPCR confirmed that PAIP1 knockdown significantly negatively or positively affected the expression of selected DEGs including interleukin-10 signaling pathway genes in HepG2 cells. Expression analysis of TCGA revealed that PAIP1 had positive correlations with IL1R2 and PTAFR in liver tumor tissue, respectively. Our results demonstrated that PAIP1 was not only a translation regulator, but also a transcription regulator in liver cancer. Thus, our study provides important cues for further study on the regulatory mechanism of PAIP1 in liver cancer

overall_design: Transcrptional profile of  HepG2 cells with/without PAIP1 Knockdown were generated

first: Jianfeng

last: Zheng

first: Ming

last: Liang


title: Liver in NOG-TKm30 mice: Control vs ortho-toluidine treatment

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

country: Japan

institute: Osaka Metropolitan University Graduate School of Medicine

summary: The gene expression profling between Control and ortho-toluidine exposure for 4 weeks in liver of NOG-TKm30 female mice.

overall_design: Female 16-week-old NOG mice expressing HSVtk mutant clone 30 cDNA under the control of mouse transthyretin gene enhancer/promoter (NOG-TKm30 mice) were treated with 0 or 0.6% ortho-toluidine (OTD) for 1 week and 0 or 0.3% OTD for 3 weeks (totally 4 weeks treatment). After treatment, mice were sacrificed, and removed livers. Control and OTD treatment: 3 control female mice, 5 OTD-treated female mice, respectively. Mixed 3 or 5 samples from each group for each RNA-seq.


title: Tumor-derived extracellular vesicles and particles systemically promote Kupffer cell-induced fatty liver disease and drug-metabolizing dysregulation

status: Public on Mar 09 2023

first: Linda

last: Bojmar

state: NY

address: 413 E 69th St, Belfer Research Bldg

department: Department of Pediatrics

institute: Weill Cornell Medicine

summary: Cancer is a systemic disease that includes several noted features, such as pre-metastatic niche formation, cachexia, and immune dysregulation. However, the mechanisms underlying multi-organ failure remain to be further investigated. Here, we show that inflammation, fatty liver, and dysregulated metabolism are hallmarks of systemically affected livers in various animal tumor models and cancer patients in the absence of hepatic metastasis. We identify that tumor-derived extracellular vesicles and particles (EVPs) are crucial mediators of cancer-induced hepatic functional reprogramming. Tumor EVPs package multiple fatty acids, such as palmitic acid, and target Kupffer cells upregulating TNFα via Toll-like receptor 4, which in turn promotes a pro-inflammatory microenvironment leading to fatty liver disease and downregulates metabolic pathways, such as fatty acid metabolism and oxidative phosphorylation. Strikingly, ablation of Kupffer cells or TNFα blockade markedly abrogates the tumor-induced excess hepatic lipid droplet accumulation. We show that tumor implantation or pre-treatment with tumor EVPs decreases the expression of Cytochrome P450 genes and attenuates drug metabolism in mice. Notably, increased fatty livers and decreased Cytochrome P450 genes are observed in tumor-free livers in cancer patients. Thus, tumor-derived EVP uptake in the liver may lead to reduced tolerance of drug toxicity in cancer patients. Our results highlight the role of tumor EVPs in dysregulating hepatic functions and its potential to serve as therapeutic targets along with Kupffer cell-induced TNFα inhibition to prevent fatty liver disease and enhance anti-cancer chemotherapy.

overall_design: Comparative RNA-seq analysis of the liver of patients with localized pancreatic cancer (PC), who did not develop liver metastasis during subsequent follow-up, with the liver of patients with non-cancerous lesions of the pancreas (PanIN, retention cysts, duodenal adenoma), or normal liver adjacent to resected hepatocellular adenoma

first: Constantinos

last: Zambirinis

first: Gang

last: Wang

first: Jonathan

last: Hernandez

first: William

last: Jarnagin

first: David

last: Lyden


title: Aging alters mechanisms underlying voluntary movements in spinal motor neurons of mice, primates and humans.

city: Providence

first: Gregorio

last: Valdez

state: RI

address: 70 Ship St

institute: Brown University

summary: Spinal motor neurons have been implicated in the loss of motor function that occurs with advancing age. However, the cellular and molecular mechanisms that impair the function of these neurons during aging remain unknown. Here, we show that motor neurons do not die in old female and male mice, rhesus monkeys, and humans. Instead, these neurons selectively shed excitatory synaptic inputs throughout the soma and dendritic arbor during aging. By examining the translatome , we also show that aging alters the molecular composition of motor neurons in both male and female mice. Aging motor neurons present with changes in genes and molecular pathways with roles in glia-mediated synaptic pruning, and inflammation. They also exhibit changes in pathways with roles in axonal regeneration caused by axotomy and Amyotrophic Lateral Sclerosis (ALS). Thus, we have identified cellular and molecular mechanisms altered in aged motor neurons that could serve as therapeutic targets to preserve motor function during aging.

overall_design: RNA bound to Hemagglutinin-tagged ribosomal protein L22 (HA-RPL22) was co-immunoprecipated from the spinal cords of male 3, 12, 18 and 24 month-old and female 3, 12 and 18 month old Chat-Cre; Ribotag mice in which HA-RPL22 is conditionally expressed under the choline acetyl transferase (ChAT) promoter to enrich for motor neuron transcripts.

first: Ryan

middle: W

last: Castro

first: Mikayla

last: Lopes

first: Robert

middle: E

last: Settlage


title: An interferon gamma response signature links myocardial aging and immunosenescence

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

summary: Aging entails profound immunological transformations that can negatively impact the myocardial biology and predispose to myocardial diseases. However, preclinical research in the immune-cardiology field is mostly conducted in young healthy animals, which potentially weakens its translational relevance. Herein, we sought to investigate how the aging T-cell compartment impacts myocardial cell biology in elderly. By investigating the paired-wised age-related shifts in the heart and its draining lymph nodes, our study provides evidence for an increased myocardial IFN-gamma signaling, which is associated with inflammatory and metabolic shifts typically seen in heart failure (HF).

overall_design: We phenotyped the antigen-experienced CD44high T cells purified from heart-draining lymph nodes of 2, 6, 12, and 18-months old C57BL/6 mice using single-cell RNA / T-cell receptor (TCR) sequencing (sc-seq). Simultaneously, we profiled all non-cardiomyocyte cell subsets purified from 2- and 18-months old hearts and integrated our data with publicly available cardiomyocyte sc-seq datasets. With aging, the heart-draining lymph node and myocardial T cells underwent spontaneous clonal expansion and exhibited an up-regulated pro-inflammatory transcription signature, marked by an increased interferon-g (IFN-g) production. In parallel, all major myocardial cell populations showed an increased IFN-g responsive signature with aging. In the aged cardiomyocytes, a stronger IFN-g response signature was paralleled by dampening of expression levels of transcripts related to most metabolic pathways, especially oxidative phosphorylation. Likewise, induced pluripotent stem cells-derived cardiomyocytes (iPSC-CM) exposed to chronic low grade IFN-g treatment showed a similar inhibition of metabolic activity.

first: Diyaaeldin

last: Ashour

first: Sabine

last: Rebs

first: Panagiota

last: Arampatzi

first: Jan

last: Dudek

first: Richard

last: Schulz

first: Ulrich

last: Hofmann

first: Stefan

last: Frantz

first: Clement

last: Cochain

first: Katrin

last: Streckfuß-Bömeke

first: Gustavo

middle: C

last: Ramos


title: A kinome-wide CRISPR screen identifies CK1α as a novel target to overcome enzalutamide resistance of prostate cancer

city: lexington

first: Jinghui

last: Liu

state: KY

address: Room 352, HEALTHY KENTUCKY RESEARCH BUILDING, 760 Press Avenue

institute: University of Kentucky

summary: Utilizing a kinome-wide CRISPR-Cas9 knockout screen, we identified casein kinase 1 alpha (CK1α) as a novel therapeutic target to overcome enzalutamide resistance. To dissect the underlying mechanisms of targeting CK1α to sensitize cancer cells to ENZA, we performed RNA sequencing of 22Rv1 cells upon CK1α knockout or overexpression. We found that CK1α regulated double-strand break (DSB)-response signaling.

overall_design: 1, CRISPR screen identifies novel targets to overcome enzalutamide resistance. 2, RNA sequening to address the mechanisms of targeiting the target to overcome enzalutamide resistance.

first: Yue

last: Zhao

first: Xiaoqi


title: The Preexisting T Cell Landscape Determines Response to T Cell-Engagers Therapy

city: Calgary

first: Nizar

last: Bahlis

state: Alberta

address: 3330 Hospital Dr NW HMRB328

department: Divisions of Hematology and Oncology

country: Canada

institute: University of Calgary

summary: Adaptive immunotherapy including bispecific T cell engagers (TCE) has shown promise in the treatment of various cancers, but clinical responses are heterogeneous and often not durable. As response to TCE is suggested to be independent of tumor recognition and T cell state, molecular determinants or mediators of primary and acquired resistance towards TCE remain poorly understood.   Here, we identify conserved behaviors of bone marrow residing CD4+ and CD8+ T cells in multiple myeloma patients undergoing TCE therapy. We show that the bone marrow immune landscape reacts to TCE therapy with cell state-dependent clonal T cell expansion and herewith infer coupling of tumor recognition via MHC-I, T cell exhaustion and clinical response. While we find the abundance of exhausted-like memory CD8+ T cell clones to be associated with clinical response failure, we describe loss of target epitope and MHC class I expression as tumor-intrinsic mechanisms of acquired resistance to TCE.

overall_design:
Bone marrow resident CD3 cells were isolated by magnetic bead separation and analyzed using 10x Genomics 5' scRNA/VDJ sequencing and 3' scRNA.
PT* samples: patients treated with anti-BCMA TCE
CART_* samples: patients treated with anti-BCMA CAR T
PT*_pre samples: prior initiation of therapy time point
PT*_late samples: post initiation of therapy time point (Some of the late samples are relapse samples as indicated in the sample titles)

middle: J

first: Paola

last: Neri

first: Mirco

last: Friedrich


title: Single-Cell Transcriptomic Heterogeneity Between Conduit and Resistance Rat Mesenteric Arteries

city: Albuquerque

first: Jay

last: Naik

state: NM

address: 915 Camino De Salud

department: Cell Biology and Physiology

institute: University of New Mexico SOM

summary: The vascular endothelium contains morphologically similar cells throughout, but individual cells along the length of a single vascular tree or in different regional circulations function quite dissimilarly. When observations made in large arteries are extrapolated to explain the function of endothelial cells (EC) in the resistance vasculature/microcirculation, only a fraction of these observations are consistent between artery sizes. To what extent endothelial (EC) and vascular smooth muscle (VSMC) cells from different arteriolar segments of the same tissue differ phenotypically at the single-cell level remains unknown. Therefore, single-cell RNA-seq (10x Genomics) was performed using a 10X Genomics Chromium system.

overall_design: Cells were enzymatically digested from large (>300 µm) and small (<150 µm) mesenteric arteries from 6 adult male Sprague-Dawley rats, pooled to create six samples (3 rats/sample, 3 samples/group). Therefore, single-cell RNA-seq (10x Genomics) was performed using a 10X Genomics Chromium system.

first: Emily

last: Morin

first: Sophia

last: Salbato

first: Laura

last: Gonzalez-Bosc

first: Nancy

last: Kanagy

first: Kathryn

last: Brayer

first: Jacob

last: Anderson


title: CRISPR screens identify gene targets at breast cancer risk loci [HiChIP]

city: Brisbane

first: Jonathan

last: Beesley

state: QLD

address: 300 Herston Rd Herston

country: Australia

institute: QIMR Berghofer

summary: Genome-wide association studies (GWAS) have identified >200 loci associated with breast cancer (BC) risk. The majority of candidate causal variants (CCVs) are in non-coding regions and likely modulate cancer risk by regulating gene expression. However, pinpointing the exact target of the association, and identifying the phenotype it mediates, is a major challenge in the interpretation and translation of GWAS.

overall_design: Transcriptome, open chromatin, and chromatin interaction profiling using RNA-seq, ATAC-seq and H3K27ac-mediated HiChIP of six immortalized mammary epithelial cell lines representing breast cells with either a luminal progenitor signature (K5+/K19+, K5+/K19-), a mesenchymal signature (B80-T17, mesHMLE) or a more epithelial like signature (B80-T5, HMLE)


title: Mesenchymal loss of p53 alters stem cell capacity and models human soft tissue sarcoma traits [bulk RNA-seq]

status: Public on Mar 08 2023

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

institute: National Center for Global Health and Medicine

summary: Soft tissue sarcomas (STSs) are a heterogeneous group of tumors that originate from mesenchymal cells. p53 is frequently mutated in human STS. In this study, we found that the loss of p53 in mesenchymal stem cells (MSCs) mainly causes adult undifferentiated soft tissue sarcoma (USTS). MSCs lacking p53 show changes in stem cell properties, including differentiation, cell cycle progression, and metabolism. The transcriptomic changes and genetic mutations in murine p53-deficient USTS mimic those seen in human STS. Furthermore, single-cell RNA sequencing revealed that MSCs undergo transcriptomic alterations with aging, which is a risk factor for certain types of UST, and that p53 signaling decreases simultaneously. Moreover, we found that human STS can be transcriptomically classified into six clusters with different prognoses, different from the current histopathological classification. This study paves the way for understanding MSC-mediated tumorigenesis and provides an efficient mouse model for sarcoma studies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow CD45-Ter119-CD31-LepR+CD140a+ mesenchymal stem cells either from p53 WT or p53 KO mice, and sarcoma derived from bone/bone marrow of p53 KO mice.

first: Yuriko

last: Sorimachi

first: Hiroshi

last: Kobayashi

first: Shuhei

last: Koide

first: Atsushi

last: Iwama


title: CRISPR screens identify gene targets at breast cancer risk loci [ATAC-seq]


title: hetIL-15 locoregional administration

city: Bethesda

first: Katherine

last: Goldfarbmuren

state: MD

address: 41 Center Dr

department: Advanced Biomedical Computational Science

institute: NCI, Frederick National Laboratory for Cancer Research

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

overall_design: Refer to individual Series


title: Human p11-mediated re-direction of phagosomes to the recycling endosome-expulsion pathway by a fungal pathogen

city: Jena

first: Leijie

last: Jia

address: Adolf-Reichwein-Straße 23

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: The decision whether endosomes in mammalian cells enter the degradative or non-degradative pathway is of fundamental importance for killing of ingested pathogens and an essential basic mechanism whose malfunctioning has pathological consequences. We discovered that the human p11 protein is a decisive factor for directing phagosomes either to the degradative or secretory pathway. The HscA protein present on the spore surface of the human-pathogenic fungus Aspergillus fumigatus anchors p11 on the phagosome and thereby inhibits phagosome maturation that would result in for expulsion of spores. The clinical relevance of our findings is supported by the identification of an SNP in the non-coding region of the human p11 gene that affects its mRNA level and is associated with protection against invasive pulmonary aspergillosis.

overall_design: The mRNA of human lung epithelial H441 cells without or with A. fumigatus infection were sequenced

first: Lei-Jie

first: Muhammad

last: Rafiq

first: Axel

last: Brakhage


title: Integrator complex subunit 15 controls mRNA splicing and is critical for eye development

city: Yokohama

first: Yuki

last: Yamaguchi

address: 4259 Nagatsuta

department: Life Science and Technology

institute: Institute of Science Tokyo

summary: The eye and brain are composed of elaborately organized tissues, development of which is supported by spatiotemporally precise expression of a number of transcription factors and developmental regulators. Here we report the molecular and genetic characterization of Integrator complex subunit 15 (INTS15). INTS15 was identified in search for the causative gene(s) for an autosomal-dominant eye disease with variable individual manifestation found in a large pedigree. While homozygous INTS15 knockout mice are embryonic lethal, mutant mice lacking a small C-terminal region of INTS15 show ocular malformations similar to the human patients. INTS15 is highly expressed in the eye and brain during embryogenesis and stably interacts with the Integrator complex to support snRNA 3′ end processing. Its knockdown resulted in missplicing of a large number of genes, probably as a secondary consequence, and substantially affected genes associated with eye and brain development. Moreover, studies using human iPS-derived neural progenitor cells showed that INTS15 is critical for axonal outgrowth in retinal ganglion cells. This study suggests a new link between general transcription machinery and a highly specific hereditary disease.

overall_design: INTS15/C7orf26 siRNA- or control siRNA-transduced HeLa cells analyzed 48 or 72 h after transfection

first: Tadashi

last: Yokoi

first: Taku

last: Tanaka

first: Noriyuki

last: Azuma


title: Single-cell RNA sequencing reveals unique alterations in the immune landscape and Treg subpopulations in mice after Echinococcus granulosus infection [TCR BCR]

city: Yinchuan

first: Jianwen

last: Wu

address: victory street

institute: Ningxia Medical University

summary: Cystic echinococcosis (CE) is a common zoonotic parasitic disease that seriously impacts public health. However, the full spectrum of immune cell changes in Echinococcus granulosus (E. granulosus) infection, especially the negative immune regulation of subpopulations of regulatory T cells (Treg), are not yet well understood. In this study, we aimed to identify the panoramic landscape of changes in immune cells and molecules and the distinct alterations in Treg subpopulations in mice infected with E. granulosus. We used single-cell RNA sequencing and single-cell T/B cell receptor sequencing to analyze 53,298 cells from the spleen and peripheral blood mononuclear cells (PBMCs) of healthy and E. granulosus-infected mice. We used immunofluorescence combined with RNA fluorescence in situ hybridization and quantitative real-time polymerase chain reaction to verify the sequencing results. Our results showed organ-specific immune system alterations in mice infected with E. granulosus. E. granulosus-infected mice induced a subpopulation of CD4+ cells with type I interferon production potential. Furthermore, there were seven different Treg cell subpopulations in vivo at three stages of differentiation, and Treg subpopulations of different classes and different stages of differentiation showed tissue specificity. After infection, the Lag3hi Treg and Gpr83+Igfbp4+ naïve Treg subpopulations were specifically induced in PBMCs and spleen, respectively. Furthermore, T follicular helper 2(Tfh2) cells with high expression of Cxxc5 and Spock2 were found in E. granulosus-infected mice. Additionally, combined single-cell immunome repertoire sequencing analysis revealed that gene fragment expression of multiple VJ-paired combinations of T cell receptor β chains were downregulated after infection. Our data uncovered changes in the full spectrum of immune cells in mice following E. granulosus infection, including subpopulations of cells that have not been emphasized in previous studies. These results further enrich the study of the bidirectional immunomodulatory mechanism and offer a different perspective for subsequent studies of E. granulosus infection.

overall_design: Examination of mice spleen and PBMCs cells by single cell sequencing

first: Jing

last: Xiao

first: Min

last: Bai

first: Chunli

last: Shi

first: Yunzhuo

last: Xin

first: Wei

last: Zhao

first: Xiaoping

last: Gao

first: Mei

last: Yin

first: Jiaqing


title: Single-cell RNA sequencing reveals unique alterations in the immune landscape and Treg subpopulations in mice after Echinococcus granulosus infection


title: Mapping the immune cell microenvironment by digital spatial profiling in muscle tissue injected with the venom of Daboia russelii

status: Public on Mar 07 2023

city: Charlottesville

first: Ana Karina

last: de Olliiveirra

state: VA

address: 1340 Jefferson Park Avenue

department: Department of Pathology

institute: UVA

summary: Pathological and inflammatory events in muscle after injection of snake venoms vary in different regions of the affected tissue and at different time intervals. In order to study such heterogeneity in the immune cell microenvironment, a murine model of muscle necrosis based on the injection of the venom of Daboia russelii was used.

overall_design: Histological and immunohistochemical methods were utilized to identify areas in muscle tissue with a different extent of muscle cell damage, based on the presence of hypercontracted muscle cells, a landmark of necrosis, and on the immunostaining for desmin. GeoMx Digital Spatial Profiler (NanoString) was used for assessing the presence of markers of various im-mune cells by comparing high-desmin (non-damaged) and low-desmin (damaged) regions.

first: Ana

middle: K

last: de Oliveira

first: Patcharin

last: Pramoonjago

first: Alexandra

last: Rucavado

first: Christopher

last: Moskaluk

first: Dilza

middle: T

last: Silva

first: Teresa

last: Escalante

first: José

middle: M

last: Gutiérrez

first: Jay

last: Fox


title: CRISPR screens identify gene targets at breast cancer risk loci [RNA-seq]

first: Jonathan

last: Beesley


title: Elucidation of the liver pathophysiology of COVID-19 patients using liver-on-a-chips

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

summary: SARS-CoV-2 induces severe organ damage not only in the lung but also in the liver, heart, kidney, and intestine. It is known that COVID-19 severity correlates with liver dysfunction, but few studies have investigated the liver pathophysiology in COVID-19 patients. Here, we elucidated liver pathophysiology in COVID-19 patients using organs-on-a-chip technology and clinical analyses. First, we developed liver-on-a-chip (LoC) which recapitulating hepatic functions around the intrahepatic bile duct and blood vessel. We found that hepatic dysfunctions, but not hepatobiliary diseases, were strongly induced by SARS-CoV-2 infection. Next, we evaluated the therapeutic effects of COVID-19 drugs to inhibit viral replication and recover hepatic dysfunctions, and found that the combination of anti-viral and immunosuppressive drugs (Remdesivir and Baricitinib) is effective to treat hepatic dysfunctions caused by SARS-CoV-2 infection. Finally, we analyzed the sera obtained from COVID-19 patients, and revealed that COVID-19 patients, who were positive for serum viral RNA, are likely to become severe and develop hepatic dysfunctions, as compared with COVID-19 patients who were negative for serum viral RNA. We succeeded in modeling the liver pathophysiology of COVID-19 patients using LoC technology and clinical samples.

overall_design: Total RNA was isolated from hepatocytes of uninfected or infected ibd- or bv-LoCs, and then RNA-seq was performed. At day 4 after the infection, total RNA was collected and RNA-seq was performed.


title: Genome-wide CRISPR Screening of Chondrocyte Maturation Newly Implicates Multiple Genes in Longitudinal Skeletal Growth and Height-GWAS Associated Loci [GPLC_sorted_RNAseq]

status: Public on Mar 06 2023

city: Boston

first: Nora

last: Renthal

state: MA

address: 3 Blackfan Circle

department: Endocrinology

institute: Boston Children's Hospital

summary:
The current study pairs human height GWAS data with CRISPR-based genome-wide knock out (KO) screens using an in vitro assay of chondrocyte proliferation and maturation to identify genes and gene pathways of biological relevance to human growth plate maturation.
Our CRISPR screen detects relevant candidates for regulating human growth plate maturation, illustrating the value of functional studies in tissues of biological relevance as orthogonal data sets to refine likely causal genes from large-scale human genetic studies.

overall_design: WT GPLCs were grown for 4 days or 15 days in culture, and FACS sorted for the cell surface marker of chondrocyte maturation, CD200. RNAseq was performed to compare these timepoints and groups

first: John

last: Baronas

first: Joel

last: Hirschhorn


title: Genome-wide CRISPR Screening of Chondrocyte Maturation Newly Implicates Multiple Genes in Longitudinal Skeletal Growth and Height-GWAS Associated Loci


title: Effect of a point mutation at Keap1 C151 on hepatic  gene expression in mice treated with Bardoxolone Methyl (CDDO-Me)

city: Seattle

first: Yoko

last: Yagishita

state: WA

address: 1100 Fairview Ave N

department: Public Health Sciences

institute: Fred Hutchinson Cancer Center

summary: To investigate the role of Keap1 C151 for induction of gene expression in mouse liver, comprehensive gene expression profiles were compared in the livers of wild-type, Nrf2 knockout, and mice harboring a point mutation at Keap1 C151 (C151S) treated with either CDDO-Me or vehicle

overall_design: Gene expression profiling analysis of RNA-seq data in the livers of three genotypes of mice (wild-type, Nrf2-knockout, Keap1 C151S knock-in) treated with one dose (30 umol/kg BW) of CDDO-Me or vehicle after 24 hours

first: Tonibelle

last: Gatbonton-Schwager

first: Tanvi

last: Joshi

first: Nobunao

last: Wakabayashi

first: Harini

last: Srinivasan

first: Takafumi

last: Suzuki

first: Masayuki

last: Yamamoto

first: Thomas

last: Kensler


title: Genome-wide CRISPR Screening of Chondrocyte Maturation Newly Implicates Multiple Genes in Longitudinal Skeletal Growth and Height-GWAS Associated Loci [GPLC_CRISPR_seq]

overall_design:
GPLCs transduced with Cas9 and a genome-wide CRISPRko library were grown for 4 days or 15 days in culture, and FACS sorted for the cell surface marker of chondrocyte maturation, CD200. gDNA-based gene barcode counts from sequencing were used to perform differential analysis between KOs in the top 10% of CD200 expressing cells and the bottom 10% of CD200 expressing cells.
A smaller secondary screening CRISPRko library was designed based on performance in the primary screen, and used for validation of top targets


title: Comparison of weanling obfactory bulb (OB) and cortical (CT) brain capillary endothelial cells (BCECs) with or without La Crosse Virus infection

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

summary: To investigate the brain region specific (OB versus CT) deferences exterted by BCECs in a model of La Crosse Virus infection

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq using BCECs  isolated from OB and CT isolated from mock or La Crosse virus (intraperitoneal) inoculated weanling mice (3 samples each)

first: Basu

last: Rahul

first: Ganesan

last: Sundar

first: Winkler

last: Clayton

first: Anzick

last: Sarah

first: Martens

last: Craig

first: Peterson

last: Karin

first: Fraser

last: Iain


title: Identification of age-specific gene regulators of La Crosse virus neuroinvasion and Pathogenesis.


title: Metabolic reprogramming by Acly inhibition using SB-204990 alters glucoregulation and modulates molecular mechanisms associated with aging

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

country: Spain

institute: CABIMER

summary: ATP-citrate lyase is a central integrator of cellular metabolism in the interface of protein, carbohydrate, and lipid metabolism. The physiological consequences as well as the molecular mechanisms orchestrating the response to long-term pharmacologically induced Acly inhibition are unknown. We report here that the Acly inhibitor SB-204990 improves metabolic health and physical strength in wild-type mice when fed with a high-fat diet, while in mice fed with healthy diet results in metabolic imbalance and moderated insulin resistance. By applying a multiomic approach using untargeted metabolomics, transcriptomics, and proteomics, we determined that, in vivo, SB-204990 plays a role in the regulation of molecular mechanisms associated with aging, such as energy metabolism, mitochondrial function, mTOR signaling, and folate cycle, while global alterations on histone acetylation are absent. Our findings indicate a mechanism for regulating molecular pathways of aging that prevents the development of metabolic abnormalities associated with unhealthy dieting. This strategy might be explored for devising therapeutic approaches to prevent metabolic diseases.

overall_design: RNA from murine liver was extracted and hybridized on Affymetrix microarrays. We sought to obtain the  transcriptional profile of liver tissue of mice fed a standard diet or a high fat diet treated or not with SB-204990

last: Sola-García

first: María

last: Cáliz-Molina

first: Isabel

last: Villanueva

first: Michael

last: Petr

first: Concepción

last: Panadero-Morón

first: Daniel

last: González-Morán

last: Martín-Vázquez

first: Álvaro

last: Narbona-Pérez

first: Livia

last: López-Noriega

first: Guillermo

last: Martínez-Corrales

first: Raúl

last: López-Fernández-Sobrino

first: Lina

last: Carmona-Marin

first: Enrique

last: Martínez-Force

first: Oscar

last: Yanes

last: Vinaixa

last: López-López

first: José

last: Reyes

first: Joaquín

last: Dopazo

first: Franz

last: Martín

first: Benoit

last: Gauthier

first: Morten

last: Scheibye-Knudsen

first: Vivian

last: Capilla-González

last: Martín-Montalvo


title: Translatome profiling of warm temperature (35°C -> 38.5°C) treated mouse embryonic fibroblast cells in the presense or absence of PI3K inhibitor, 17β-hydroxy wortmannin

first: Masao

last: Doi

department: Department of Systems Biology

institute: Kyoto University, Graduate School of Pharmaceutical Sciences

summary: To see a possible effect of PI3K inhibition on a physiological warm temperature shift (WTS, 35°C to 38.5°C)-induced ribosomal accumulation on the Per2 minimal uORF, we performed Ribo-seq using dexamethasone-synchronized WTS-treated mouse embryonic fibroblast cells with or without 17β-hydroxy wortmannin (wortm) treatment at a circadain rising phase of Per2.

overall_design: We used Dex-synchronized WTS-treated MEF cells treated with or without wortm. WTS and wortm was applied 24 h after Dex synchronization (i.e., circadian rising phase of Per2). Two independent experiments were performed.

first: Doi

last: Masao

first: Iwasaki

last: Shintaro

first: Miyake

last: Takahito


title: Postnatal administration of S-adenosylmethionine restores developmental AHR activation-induced deficits in CD8+ T cell function during influenza A virus infection

city: Rochester

first: Christina

middle: Marie

last: Post

address: 601 Elmwood Ave, Box EHSC

department: Environmental Medicine

institute: University of Rochester School of Medicine & Dentristry

summary: Developmental exposures can influence life-long health; yet, approaches to counteract negative consequences of developmental toxicity are limited due to poor understanding of cellular mechanisms. The aryl hydrocarbon receptor (AHR) binds many small molecules, including numerous pollutants. Developmental exposure to the signature environmental AHR ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) significantly dampens the adaptive immune response to influenza A virus (IAV) in adult offspring. CD8+ cytotoxic T lymphocytes (CTL) are crucial for successful resolution. Their effectiveness depends not only on the number generated, but also on the complexity of their functionality; that is, polyfunctional CD8+ T cells are more effective. Prior studies showed that developmental AHR activation significantly reduced the number of virus-specific CD8+ T cells during infection, but the impact on CD8+ T cell functions is less clear. Other studies showed that developmental exposure was associated with differences in DNA methylation in CD8+ T cells. Yet, empirical evidence that differences in DNA methylation are causally related to altered CD8+ T cell function is lacking. Accordingly, there were two main objectives: to ascertain whether developmental AHR activation affects CTL function, and to determine whether differences in DNA methylation contribute to the reduced CD8+ T cell response to infection. Flow cytometry and Simplified Presentation of Incredibly Complex Evaluations (SPICE) were used to measure CD8+ T functions, including CTL polyfunctionality. Triggering AHR during development significantly reduced CTL polyfunctionality. Developmentally exposed mice were treated with S-adenosylmethionine (SAM), to increase DNA methylation, or Zebularine, to diminish DNA methylation. SAM restored CTL polyfunctionality and boosted the number of virus-specific CD8+ T cells. Zebularine did not attenuate the impact of maternal TCDD treatment on the CTL response. These results indicate that DNA hypomethylation, initiated by developmental exposure to an AHR-binding chemical, contributes to durable changes in antiviral CD8+ CTL responsive capacity later in life. Thus, deleterious consequence of development exposure to environmental chemicals are not permanently fixed, opening the door for interventional strategies to improve health.

overall_design: Comparison of gene expression in CD44hiCD8+ and CD44loCD8+ T cells from IAV-infected female offpsring developmentally exposed to either VEH or TCDD.

first: Jason

last: Myers

first: Bethany

last: Winans

first: B

middle: P

last: Lawrence


title: Extracellular vesicles and particles derived from tumors with extrahepatic metastatic tropism induce liver dysregulation

city: New York

first: David

last: Lyden

address: 413 East 69th Street, Room BB1228

department: Cell and Developmental Biology

institute: Weill Cornell Medicine

summary: Cancer is a systemic disease that includes several noted features, such as pre-metastatic niche formation, cachexia, and immune dysregulation. However, the mechanisms underlying multi-organ failure remain to be further investigated. Here, we show that inflammation, fatty liver, and dysregulated metabolism are hallmarks of systemically affected livers in various animal tumor models and cancer patients in the absence of hepatic metastasis. We identify that tumor-derived extracellular vesicles and particles (EVPs) are crucial mediators of cancer-induced hepatic functional reprogramming. Tumor EVPs package multiple fatty acids, such as palmitic acid, and target Kupffer cells upregulating tumor necrosis factor alpha (TNFα) via Toll-like receptor 4 (Tlr4), which in turn promotes a pro-inflammatory microenvironment leading to fatty liver formation and downregulates metabolic pathways, such as fatty acid metabolism and oxidative phosphorylation. Strikingly, ablation of Kupffer cells or TNFα blockade markedly abrogates the tumor-induced excess hepatic lipid droplet accumulation. We show that tumor implantation or pre-treatment with tumor EVPs decreases the expression of Cytochrome P450 genes and attenuates drug metabolism in mice. Notably, increased fatty livers and decreased Cytochrome P450 genes are observed in tumor-free livers in cancer patients. Thus, tumor-derived EVP uptake in the liver may lead to reduced tolerance of drug toxicity in cancer patients. Our results highlight the role of tumor EVPs in dysregulating hepatic functions and its potential to serve as therapeutic targets along with Kupffer cell-induced TNFα inhibition to prevent fatty liver formation and enhance anti-cancer chemotherapy.

overall_design:
Transcriptomic analysis (RNA sequencing) of the livers isolated from tumor (B16F10, or K7M2, or 67NR, or B16F1, or 4T1) -bearing mice, or EVP (B16F10-TE-EVPs, or K7M2-TE-EVPs, or B16F10-CL-EVPs, or K7M2-CL-EVPs, or B16F10_exomeres, or B16F10-Exo-S, or B16F10-Exo-L) -educated mice, and their respective controls.
Transcriptomic analysis (RNA sequencing) of the murine primary hepatocytes after treatment with TNFalpha or PBS control.

first: Gang

last: Wang

first: Haiying

last: Zhang


title: Multi-omics profiling of the impact of an Angiotensin (1-7)-expressing probiotic combined with exercise training in aged male rats

city: Birmingham

first: Thomas

last: Buford

state: Alabama

address: 1313 13th Street South

institute: University of Alabama at Birmingham

summary: Angiotensin (1-7) [Ang (1-7)] is an active heptapeptide of the non-canonical arm of the renin-angiotensin system that modulates molecular signaling pathways associated with vascular and cellular inflammation, vasoconstriction, hyperplasia and fibrosis. Pre-clinical evidence suggests that Ang (1-7) is a promising therapeutic target that may ameliorate physical and cognitive decline in prevalent age-related diseases, but its short half-life and low oral bioavailability reduce its applicability in clinical care. This study evaluated a genetically modified probiotic (GMP) that expresses Ang (1-7) as a potential approach to overcome these barriers. We gave this GMP with and without moderate exercise training and evaluated cross-tissue (prefrontal cortex, hippocampus, colon, liver and skeletal muscle) multi-omics responses in aged male rats

overall_design: This study was a 3x2 prospective randomized trial with a total length of 12-weeks. Male F344BN rats (n= 8-13/group) were randomized to one of three treatments: (i) buffer (Con: n= 25); (ii) a probiotic-Lactobacillus paracasei (LP= 22); or to, (iii) a GMP-Lactobacillus paracasei engineered to express Ang (1-7) (LPA: n= 17). Additionally, these groups were further randomized to a moderate exercise intervention (CONEx : n= 13: LPEx: n=11: LPAEx: n= 8) or to a control group without exercise training (CONSed: n= 12: LPSed: n=11: LPASed: n= 9). The treatment groups were orally gavaged with 2x1011 CFU/kg body weight of probiotics or an equal volume of buffer 3 times per week. Groups randomized to the exercise intervention (CONEx: n= 13: LPEx: n=11: LPAEx: n= 8) performed a treadmill intervention, 5 days per week for 12 weeks.

first: Liliana

last: Baptista

first: Emily

middle: L

last: Zumbro

first: Zachary

last: Graham

first: Abigail

last: Hernandez

first: Taylor

last: Buchanan

first: Yi

last: Sun

first: YouFeng

last: Yang

first: Anisha

last: Banerjee

first: Amrisha

last: Verma

first: Qiuhong

last: Li

first: Christy

last: Carter


title: RNA-seq of cochlea in mice with a frameshift mutation in the reading frame of thyroid hormone receptor α1

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

summary: Thyroid hormone is known to be required for inner ear development. The influence of the thyroid hormone receptor α1 is however unclear, as most previous studies point to a predominant function of the TRβ1/2 isotypes. We report a RNA-seq analysis which completes a full histological and functional analysis showing that mice carrying a mutation of the TRα1 receptor have mild alteration of inner ear.

overall_design: Whole inner ear RNA was extracted from heterozygous mutant mice carrying a frameshift mutation which alters the function of TRα1. These RNA were compared to RNA extracted from wild-type littermates.

first: Romain

last: Guyot

first: Corentin

last: Affortit

first: Fabian

last: Blanc

first: Suzy

last: Markossian

first: Jean-Charles

last: Ceccato

first: Jean-Luc

last: Puel

first: Jing


title: CRISPR screens identify gene targets at breast cancer risk loci

first: Jonathan

last: Beesley

institute: QIMR Berghofer


title: Longitudinal gene expression profiling identifies a poor risk subset of patients with ABC-type Diffuse Large B Cell Lymphoma

city: London

first: Findlay

last: Bewicke-Copley

address: John Vane Science Centre, Barts Cancer Institute

country: United Kingdom

institute: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London

summary: Despite the effectiveness of immuno-chemotherapy, 40% of patients with diffuse large B-cell lymphoma (DLBCL) experience relapse or refractory disease. Longitudinal studies have previously focused on the mutational landscape of relapse but falling short of providing a consistent relapse-specific genetic signature. In our study, we have focussed attention on the changes in gene expression profile accompanying DLBCL relapse using archival paired diagnostic/relapse specimens from 38 de novo DLBCL patients. Cell of origin remained stable from diagnosis to relapse in 80% of patients, with only a single patient showing COO switching from ABC to GCB. Analysis of the transcriptomic changes that occur following relapse suggest ABC and GCB relapses are mediated via different mechanisms. We developed a 30-gene discriminator for ABC-DLBCLs derived from relapse-associated genes, that defined clinically distinct high and low risk subgroups in ABC-DLBCLs at diagnosis in datasets comprising both population-based and clinical trial cohorts. This signature also identified a population of <60-year-old patients with superior PFS and OS treated with Ibrutinib-R-CHOP as part of the PHOENIX trial. Altogether this new signature adds to the existing toolkit of putative genetic predictors now available in DLBCL that can be readily assessed as part of prospective clinical trials.

overall_design: Gene expression profiels for 76 paired diagnosis and relapse DLBCL biopsies from 38 patients were generated using the Ion AmpliSeq™ Human Gene Expression assay.

first: F

first: K

last: Korfi

first: S

last: Araf

first: B

last: Hodkinson

first: E

last: Kumar

first: T

last: Cummin

first: M

last: Ashton-Key

last: Barrans

last: Van Hoppe

first: C

last: Burton

last: Elshiekh

last: Rule

first: N

last: Crosbie

first: A

last: Clear

last: Calaminici

first: H

last: Runge

first: R

last: Hills

first: D

last: Scott

first: L

last: Rimsza

first: G

last: Menon

last: Sha

first: J

last: Davies

last: Nagano

last: Painter

last: Smith

last: Gribben

last: Naresh

last: Westhead

last: Okosun

last: Steele

last: Hodson

last: Balasubramanian

first: P

last: Johnson

last: Wang

last: Fitzgibbon


title: Prerequisite endocardial-mesenchymal transition for cardiac trabecular angiogenesis

city: Bronx

first: Pengfei

last: Lu

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: We used single cell RNA sequencing (scRNAseq) to show that ventricular endocardial cells generate trabecular vessels through an angioEMT mechanism.

overall_design: We did E12.5, E13.5, E14.5 and E15.5 whole heart scRNAseq and intergated these 4 stage data together. We analyzed endothelial cell clusters and compared different subclusters in a stage-dependent diffence within subclusters, to find the potential mechanism of how ventricular endocardial cells generate trabecular vessels.

first: Bingruo

last: Wu

first: Yidong

first: Megan

last: Russell

first: Yang

last: Liu

first: Deyou

last: Zheng

first: Bin

last: Zhou


title: Comparison of weanling and adult brain capillary endothelial cells (BCECs) with vehicle or Poly I:C treatment

first: Craig

last: Martens

summary: To investigate the immunologic and age-related deferences exterted by BCECs with or without immunostimulation

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq using ex vivo isolated BCECs  isolated from vehicle and Poly I:C stimulated weanling and adult mice (3 samples each)

first: Rahul

last: Basu

first: Sundar

last: Ganesan

first: Clayton

last: Winkler

first: Sarah

last: Anzick

first: Karin

last: Peterson

first: Iain

last: Fraser


title: Transcriptomic analysis of murine lung tumor cells upon genetic KrasG12V ablation

status: Public on Mar 05 2023

city: Madrid

first: Ruth

last: Álvarez-Díaz

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

institute: Spanish National Cancer Research Center (CNIO)

summary: To identify the mechanisms driving resistance upon KrasG12V ablation, we established lung cancer cell lines that carried loxP sequences flanking the exon 1 of Kras containing the G12V mutation (Kras +/loxG12Vlox), and lacked Trp53 alleles (Trp53 -/-). Tumor cells were infected with Adeno-Cre particles to excise the floxed sequences and individual cells that survived were expanded for further analysis.

overall_design: Gene expression profiling analysis of parental lung tumor cells Kras (+/loxG12Vlox);Trp53(-/-) and resistant lung tumor cells Kras (+/-);Trp53(-/-)

first: Mariano

last: Barbacid

first: Matthias

last: Drosten

first: Marina

last: Salmon


title: Effects of DAB2IP depletion on gene expression in HCT116 cells

first: Abigail

last: Miller

address: 77 Avenue Louis Pasteur NRB 466

institute: Mass General Brigham

summary: To study DAB2IP function on colon cancer, we depleted DAB2IP in HCT116 cells using shDAB2IP or shCNT(scramble) as a control.

overall_design: Cells were transduced with  shCNT or shDAB2IP lentivirus.  After selection and recovery, cells were seed at 5x10^5 and collected 2 days later (70% confluency). RNA was harvested and sequenced using NGS.

first: Karen

last: Cichowski


title: MYC regulates chromatin interactions in prostate cancer [ChIP-seq]

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

summary: We used RNA-Seq, ChIP-Seq and HiChIP to assess the role of MYC in the chromatin interactions of prostate cancer

overall_design: RNA-Seq, ChIP-Seq and HiChIP in 22Rv1 cells with or without MYC overexpression

first: Zhao

last: Wei

first: Housheng

middle: H

last: He


title: MS2-affinity purification coupled with RNA sequencing (MAPS) revealed MicF sRNA targetome.

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

department: Biochemistry

institute: University of Sherbrooke

summary: In this study, we performed MAPS (MS2-affinity purification coupled with RNA sequencing) to draw the interacting map of MicF small regulatory RNA in vivo.

overall_design: Identification of RNAs co-purified with MS2-MicF in a rne131 ΔmicF strain. MicF (without MS2) was used as control.

first: David

last: Lalaouna


title: Effects of DAB2IP expression on gene expression in DLD1  cells

summary: To assess the function of DAB2IP in colon cancer, we expressed DAB2IP or control LACZ in DLD1 cells which lack DAB2IP.

overall_design: Cells were transduced with FB LACZ or FB DAB2IP.  After selection and recovery, cells were seed at 5x10^5 and collected 2 days later (70% confluency). RNA was harvested and sequenced using NGS.


title: MYC regulates chromatin interactions in prostate cancer [RNA]


title: Transcriptome and translatome profiling of warm temperature (35°C -> 38.5°C) treated mouse embryonic fibroblast cells

first: Masao

last: Doi

summary: To see a possible effect of a physiological warm temperature shift (WTS, 35°C to 38.5°C) on Per2 transcription and translation in mammalian cells, we performed RNA-seq and Ribo-seq using dexamethasone-synchronized mouse embryonic fibroblast cells with or without WTS treatment at a circadain rising phase of Per2.

overall_design: We used Dex-synchronized MEF cells treated with or without 2-h WTS. WTS was applied 24 h after Dex synchronization (i.e., circadian rising phase of Per2). Three independent experiments were performed.

first: Doi

last: Masao

first: Iwasaki

last: Shintaro

first: Miyake

last: Takahito


title: Transcriptional profiling of fetal forebrain using single cell/nuclei RNAseq, bulk RNAseq and CUT&RUN

status: Public on Mar 03 2023

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

summary: This study aims to profile transposable element expression in human fetal forebrain

overall_design: We performed 10x single cell/nuclei RNAseq of fetal forebrain to characterize transcriptional changes of gene and transposable elements in different cell types of the fetal human forebrain. We complimented our analysis using bulk RNAseq and H3K4me3 CUT&RUN.

first: Raquel

last: Garza


title: SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance.

city: Strasbourg

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

institute: IGBMC

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Tissue transglutaminase exacerbates renal fibrosis via alternative activation of monocyte-derived macrophages

city: Nagoya

first: Hideki

last: Tatsukawa

state: AICHI

address: Furo-cho, Chikusa

institute: Nagoya University

summary: To elucidate the reason why the tissue transglutaminase (TG2) knockdown and inactivation suppressed M2 macrophage polarization, we explored genes whose expression was regulated by TG2 activity and investigated the molecular mechanism underlying this.

overall_design: Comparative gene expression analysis of differentiated human macrophages treated with IL-4 or TG2 inhibitors by RNA-seq data.

first: Kiyotaka

last: Hitomi


title: METTL3-mediated m6A modification controls splicing factor abundance and contributes to CLL progression [MeRIP-seq]

city: Monrovia

first: Lili

last: Wang

state: CALIFORNIA

address: 1218 South Fifth Ave.

department: Systems biology

institute: City of Hope

type: Methylation profiling by high throughput sequencing

summary: RNA splicing dysregulation is a hallmark of cancers, promoting the onset and progression of disease. In chronic lymphocytic leukemia (CLL), spliceosome mutations leading to aberrant splicing occur in ~20% of patients. However, the underlying mechanism for splicing defects in spliceosome unmutated CLL cases remains elusive. Through an integrative transcriptomic and proteomic analysis, we discover proteins involved in RNA splicing are post-transcriptionally upregulated in CLL cells, resulting in splicing dysregulation. The abundance of splicing (factors) complexes is an independent risk factor and associated with poor prognosis in CLL. Moreover, increased splicing factor expression is highly correlated with METTL3, an RNA methyltransferase that modifies N6-methyladenosine (m6A) on mRNA. METTL3 is essential for cell growth in vitro and in vivo, and controls splicing factor protein expression in a methyltransferase-dependent manner through m6A modification mediated ribosome recycling and decoding process.  Our results uncover a novel regulatory axis of METTL3 for splicing dysregulation in CLL and highlight m6A modification as a major contributor to spliceosome mutation-independent splicing defects that lead to CLL progression.

overall_design: MeRIP seq of METTL3 Knock out vs control

first: Yiming

last: Wu

first: Meiling

last: Jin


title: METTL3-mediated m6A modification controls splicing factor abundance and contributes to CLL progression [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data


title: METTL3-mediated m6A modification controls splicing factor abundance and contributes to CLL progression [Ribo-seq]

overall_design: Comparative riboseq data of METTL3 knock out vs Control in HG3 cell line


title: Simultaneous activation of Tor and suppression of ribosome biogenesis by TRIM-NHL proteins promotes terminal differentiation

city: Cambridge

first: Tamsin

middle: Joy

last: Samuels

address: Downing Street

department: Department of Genetics

institute: University of Cambridge

summary: Tissue development and homeostasis depend on the balance between growth and terminal differentiation, but the mechanisms coordinating these processes remain elusive. Accumulating evidence indicates that ribosome biogenesis (RiBi) and protein synthesis, two cellular processes sustaining growth, are tightly regulated and yet can be uncoupled during stem cell differentiation. Using the Drosophila adult female germline stem cell (GSC) and larval neuroblast (NB) systems, we show that Mei-P26 and Brat, two Drosophila TRIM-NHL paralogs, are responsible for uncoupling RiBi and protein synthesis during differentiation. In differentiating cells, Mei-P26 and Brat activate the Target of rapamycin (Tor) kinase to promote translation, while concomitantly repressing RiBi. Depletion of Mei-P26 or Brat results in defective terminal differentiation, which can be rescued by ectopic activation of Tor together with suppression of RiBi. Our results indicate that uncoupling RiBi and translation activities by TRIM-NHL activity creates the conditions required for terminal differentiation.

overall_design: The effect of Mei-P26 overexpression or depletion on Drosophila female germline stem cells was studied using RNAseq

first: Jinghua

last: Gui

first: Katarina

middle: Z

last: Grobicki

first: Felipe

last: Teixeira


title: SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance.. [scRNAseq]

summary: Renal medullary carcinoma (RMC) is an aggressive tumour driven by bi-allelic loss of SMARCB1 and tightly associated with sickle cell trait. However, the cell-of-origin and oncogenic mechanism remain poorly understood. Using single-cell sequencing of human RMC, we defined transformation of thick ascending limb (TAL) cells into an epithelial-mesenchymal gradient of RMC cells associated with loss of renal epithelial transcription factors TFCP2L1, HOXB9 and MITF and gain of MYC and NFE2L2-associated oncogenic and ferroptosis resistance programs. We describe the molecular basis for this transcriptional switch that is reversed by SMARCB1 re-expression repressing the oncogenic and ferroptosis resistance programs leading to ferroptotic cell death. Ferroptosis resistance links TAL cell survival with the high extracellular medullar iron concentrations associated with sickle cell trait, an environment propitious to the mutagenic events associated with RMC development. This unique environment may explain why RMC is the only SMARCB1-deficient tumour arising from epithelial cells, differentiating RMC from rhabdoid tumours arising from neural crest cells.

overall_design: ScRNA-seq of naive RMC  tumor, treated RMC tumor with its native adjacent tissue, and patient-derived xenograft RMC tumor.

first: Alexandra

last: Helleux

first: Bujamin

last: Vokshi

first: Rachida

last: Bouarich

first: Valeria

last: Manriquez

first: Mamy

last: Jean De Dieu Andrianteranagna

first: Irwin

first: Gabriel

last: Malouf

first: Franck

last: Bourdeaut


title: Effect of ITGB6 induction on transcriptome of breast myoepithelial cells

first: Richard

last: Grose

address: Charterhouse Sq

institute: Queen Mary University of London

summary: To investigate the effects of ITGB6 induction of breast myoepithelial cells (1089 and primary myoepithelial cells), we induced expression of ITGB6 utilising the TET-On system for 48 hr.

overall_design: Cells (1089 or primary myoepithelial cells) were seeded in 2D and treated with doxycyline to induce overexpression of ITGB6 for 48 hr. 1089 cells were also treated with 10 uM of TGFBRi (SB431542) for 48 hr.  Experiments were performed with two biological replicates per sample. Each sample has multiple raw fastq files, corresponding to different sequencing lanes (e.g., L001, L002, L003, L004) and different reads (e.g., R1, R2).

first: Shayin

last: Gibson

first: Edward

last: Carter


title: SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance. [RNAseq]

first: Guillaume

last: Davidson

overall_design: Wild type RMC-2C and RMC219 were cultured in adequate media and modified to express a doxycycline-inducible transgene coding for SMARCB1. Cells were treated with either DMSO or with 2uM of doxycycline for 12 or 48 hours.

first: Marc

last: Rippinger


title: Transcriptomic analysis of sotorasib-resistant patient-derived xenograft (PDX) lung tumor cells

first: Ruth

last: Álvarez-Díaz

summary: To characterize sotorasib resistance in lung adenocarcinomas (LUAD), we implanted pieces derived from a patient-derived KRAS-G12C positive xenograft (PDX) lung tumor model in immunocompromised mice

overall_design: Gene expression profiling analysis of sotorasib-resistant lung tumors using patient-derived xenograft (PDX)

first: Mariano

last: Barbacid

first: Matthias

last: Drosten

first: Marina

last: Salmon


title: Malonylation of Acetyl-CoA Carboxylase 1 Promotes Hepatic Steatosis and Is Attenuated by Ketogenic Diet in NAFLD

city: Guangzhou

first: Hancheng

last: Qin

state: Guangdong

address: No.600 Tianhe Road

department: Department of Endocrinology and Metabolism

institute: the Third Affiliated Hospital of Sun Yat-sen University

summary: Protein post-translational modifications (PTMs) participate in important bioactive regulatory processes and therefore can help elucidate the pathogenesis of non-alcoholic fatty liver disease (NAFLD). Here, we investigate the involvement of PTMs in ketogenic diet (KD)-improved fatty liver by multi-omics and reveal a core target of lysine malonylation, acetyl-CoA carboxylase 1 (ACC1). ACC1 protein levels and Lys1523 malonylation are significantly decreased by KD. It is discovered that a malonylation-mimic mutant in ACC1 increases its enzyme activity and stability to promote hepatic steatosis, whereas the malonylation-null mutant upregulates the ubiquitination degradation of ACC1. A customized Lys1523ACC1 malonylation antibody confirms the increased malonylation of ACC1 in the NAFLD samples. Overall, the lysine malonylation of ACC1 is attenuated by KD in NAFLD and plays an important role in promoting hepatic steatosis. Malonylation is critical for ACC1 activity and stability, highlighting the anti-malonylation effect of ACC1 as a potential strategy for treating NAFLD.

overall_design:
Mouse models and dietary intervention
Seven-week-old male C57BL/6 mice were purchased from GemPharmatech (Nanjing, China). After an acclimation period of one week, the mice were randomly divided into CD, HFD, iCD, and iKD groups (n = 6/group). Mice were fed a CD (11 % fat [kcal%]; Guangdong Medical Laboratory Animal Center, Guangzhou, China) in the CD group or a HFD (58 % fat [kcal%]; D12331; Research Diets, New Brunswick, NJ, USA) in the HFD group for 16 weeks. Mice in the iCD group were fed a HFD or CD sequentially at 2-week intervals for 16 weeks. Mice in the iKD group were fed a HFD or KD (90.5 % fat [kcal%], TD.160153, Envigo, USA) at 2-week intervals for 16 weeks. Blood and liver samples were collected after an overnight fast.
Animal experiments complied with the ARRIVE guidelines and the National Institutes of Health Guide for the Care and Use of Laboratory Animals. All protocols were approved by the Institutional Animal Care and Use Committee of the Sun Yat-sen University (approval number: 2020000276).
RNA sequencing
Total RNA was isolated using a RNeasy Plus Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. The integrity and concentration of the total RNA were assessed using an Agilent 2100 Bioanalyzer System (Agilent Technologies, Palo Alto, CA, USA) and an Agilent RNA 6000 Nano Kit (Agilent Technologies). Samples with an RNA integrity number >8 were selected for use. RNA sequencing (RNA-Seq) and data analysis were performed by Pan-Guarantee Biotechnology Co. Ltd. (Guangzhou, China). Libraries were constructed using 1 μg of total RNA and prepared using the NEBNext ultra RNA Library Prep Kit (New England Biolabs, Beijing, China). Sequencing was performed using an Illumina HiSeq4000 to generate 150 bp paired-end reads. Quality trimmed reads were mapped onto the mouse genome (mm10) by HISAT233, and gene expression in terms of fragments per kilobase of transcript per million (FPKM) mapped reads of genes overlapping with gene annotations in Ensembl release 96 was calculated using RSEM (v1.1.17) 34. RNAs differential expression analysis was performed using edgeR (v 3.14.0)35 software between two different groups (n= 4). Genes with a false discovery rate < 0.05 and absolute fold change≥ 2 were considered differentially expressed genes.

first: Fen

last: Xu

first: Huanyi

last: Cao


title: SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance. [ChIPseq and Cut&Tag]

overall_design: RMC2C cells were modified to integrate a doxycyline-inducible copy of either SMARCB1 or mCHERRY control. 48Hrs after doxycyline treatment, roughly 10¹⁰ cells were either crosslinked using 0,4% PFA for fixed ChIP-seq (MYC and H3K27ac) or simply harvested for native ChIP-seq (BRG1). 100Ug of extracted chromatin was used for IP before DNA extraction and sequencing.  For Cut&Tag (BRG1 and SMARCB1), 24hrs after doxycycline treatment, roughly 500,000 cells were harvested in native conditions and handled using the Active Motif Cut&Tag kit.

first: Bujamin

last: Vokshi


title: MYC regulates chromatin interactions in prostate cancer [HiChIP]

first: Haiyang

last: Guo

overall_design: RNA-Seq, ChIP-Seq and HiChIP in 22Rv1 cells with or without MYC overexpression

first: Zhao

last: Wei

first: Housheng

last: He


title: Transcriptomic characterization of sotorasib-resistant tumors in Kras-G12C/Trp53-driven LUAD in genetically engineered mice

summary: To characterize sotorasib resistance in lung adenocarcinomas (LUAD), we generated genetically engineered mice (Kras-G12C, Trp53-KO) and compared the transcriptional profiles of untreated and sotorasib-resistant tumors

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sotorasib-resistant lung tumors in mice


title: Gene expression in HeLa cells expressing GFP-IRF3 (non-targeting control and clonal knockouts of DDX58, MAVS, ATP13A1, CAPN15, TADA2B, MED16, and MED24) following Sendai virus (SeV) infection or hpRNA transfection

first: Paul

last: Blainey

address: 415 Main Street

institute: Broad Institute

summary: IRF3 translocates from the cytoplasm to the nucleus upon recognition of a cytoplasmic RNA stimulus by RIG-I or MDA5. Using an optical pooled CRISPR knockout screen in HeLa-Cas9 cells, we identified ATP13A1, CAPN15, TADA2B, MED16, and MED24 as novel genes affecting the translocation of IRF3 upon Sendai virus infection. We generated isogenic clonal knockout HeLa-Cas9 lines and confirmed that loss of these five novel genes results in either decreased (ATP13A1 and CAPN15) or increased (TADA2B, MED16, and MED24) translocation of IRF3 upon Sendai virus or synthetic hpRNA stimulation.

overall_design: Biological replicates were defined as replicate stimulations (n = 3 or 4 biological replicates, 1-2 sgRNAs per knockout).

first: Rebecca

last: Carlson

first: Nir

last: Hacohen


title: Regulation of chromatin accessibility in hypoxia condition

city: Warsaw

first: Monika

last: Dzwigonska

address: 3 Pasteur Street

country: Poland

institute: Nencki Institute of Experimental Biology, PAS

summary: Hypoxia leads to significant changes at the histone modification marks, including increasing methylation of H3K4, H3K9 and H3K27. However, the overall effect on chromatin accessibility is not fully understood. Here, we employed an ATACseq method on PFA-fixed mouse glioma cell line GL261to test the genomewide chromatin accessibility changes in response to two hypoxic conditions: moderate hypoxia (1% O2) and severe hypoxia (<0.1% O2).

overall_design: Examinnation of chromatin accessibility with ATACseq in mouse glioma cells line (GL261) in response to severe (<0.1% O2) or mild hypoxia (1% O2) compare to normoxia conditions on PFA fixed cells.

first: Jakub

last: Mieczkowski

first: Katarzyna

middle: B

last: Leszczynska


title: YBX1 integration of oncogenic PI3K/mTOR signalling regulates the fitness of malignant epithelial cells.

city: Melbourne

first: Charbel

last: Darido

state: VIC

address: 305 Grattan street

department: Cancer Research

institute: Peter MacCallum Cancer Center


title: YBX1 integration of oncogenic PI3K/mTOR signalling regulates the fitness of malignant epithelial cells [RNA-seq]

summary: In heterogeneous head and neck cancer (HNC), subtype-specific treatment regimens are currently missing. An integrated analysis of patient HNC subtypes using single-cell sequencing and proteome profiles revealed an epithelial-mesenchymal transition (EMT) signature within the epithelial cancer-cell population. The EMT signature coincided with PI3K/mTOR inactivation in the mesenchymal subtype. Conversely, the signature was suppressed in epithelial cells of the basal subtype which exhibits hyperactive PI3K/mTOR signalling. We further identified YBX1 phosphorylation, downstream of the PI3K/mTOR pathway, restrains basal-like cancer cell proliferation. In contrast, YBX1 acts as a safeguard against the proliferation-to-invasion switch in mesenchymal-like epithelial cancer cells, and its loss accentuates partial-EMT and in vivo invasion. Interestingly, phospho-YBX1 that is mutually exclusive to partial-EMT, emerged as a prognostic marker for overall patient outcomes.      Expression profiling by high throughputsequencing were performed to explore the underlying molecular mechanisms.

overall_design: The RNA sequencing analysis of head and neck cancer (HNC) cell lines SCC15 and SCC25 upon YBX1 knockout.   The RNA sequencing analysis of normal oral cells (OKF6) and HNC cells (SCC15 and SCC25).

first: Yuchen

last: Bai


title: YBX1 integration of oncogenic PI3K/mTOR signalling regulates the fitness of malignant epithelial cells [RPPA]

summary: In heterogeneous head and neck cancer (HNC), subtype-specific treatment regimens are currently missing. An integrated analysis of patient HNC subtypes using single-cell sequencing and proteome profiles revealed an epithelial-mesenchymal transition (EMT) signature within the epithelial cancer-cell population. The EMT signature coincided with PI3K/mTOR inactivation in the mesenchymal subtype. Conversely, the signature was suppressed in epithelial cells of the basal subtype which exhibits hyperactive PI3K/mTOR signalling. We further identified YBX1 phosphorylation, downstream of the PI3K/mTOR pathway, restrains basal-like cancer cell proliferation. In contrast, YBX1 acts as a safeguard against the proliferation-to-invasion switch in mesenchymal-like epithelial cancer cells, and its loss accentuates partial-EMT and in vivo invasion. Interestingly, phospho-YBX1 that is mutually exclusive to partial-EMT, emerged as a prognostic marker for overall patient outcomes.      Expression profiling by reverse-phase protein array were performed to explore the underlying molecular mechanisms.

overall_design: The reverse-phase protein array analysis of head and neck cancer (HNC) cell lines SCC15 and SCC25 upon YBX1 knockout.   The reverse-phase protein array analysis of normal oral cells (OKF6) and HNC cells (SCC15 and SCC25).   The reverse-phase protein array analysis of mouse tissues (wildtype, Grhl3cKO, Pik3ca, Pik3caGrhl3cKO tumours and adjacent tissues)


title: Transcriptional response to SARS-CoV-2 infection in human autopsy lung samples

city: Boston

first: Megan

last: Sperry

address: 3 Blackfan Circle

institute: Wyss Institute at Harvard University

summary: RNA-sequencing of human lung samples derived from COVID-19 patient autopsy.

overall_design: Lung samples derived from COVID-19 patient autopsy. Experiments using samples from human subjects were conducted in accordance with local regulations and with the approval of the institutional review board at the Icahn School of Medicine at Mount Sinai under protocol HS#12-00145.

first: Benjamin

middle: R

last: tenOever


title: Transcriptomic analysis of hepatocyte-like cells generated by doxycycline inducible expression of HNF4A, HNF1A and FOXA3

city: Valencia

first: Roque

last: Bort

address: Campanar 21

department: Unidad Hepatologia Experimental

institute: IIS La Fe

summary: We have generated an immortal fibroblast-derived cell line without malignant traits capable of being efficiently and easily reprogrammable into hepatocyte-like cells under standard culture conditions by combining hTERT expression and a polycistronic vector inducible with doxycycline.

overall_design:
Human fibroblasts were immortalized with hTERT and infected with a lentiviral vector containing a polycistronic 2A cassette expressing HNF4A, HNF1A and FOXA3 under the control of Tetracycline Response Elements (iHDF-T).
After single cell cloning, we selected a specific clone named P3G4. This clone was expanded for more than 80 population doublings (PD). We reprogrammed by doxycycline addition, low and high PD iHDF-T into hepatocyte-like cells (diHLC-T).
RNA from PD low and high iHDF-T as well as diHLC-T were analyzed by RNAseq in triplicates. RNA isolated from 24hr-cultured primary hepatocytes from three different donors were used as controls.

first: Guillem

last: Garcia-Llorens

first: Eugenia

last: Pareja


title: Murine platelet miRNA pattern and its regulation by a MK/platelet-specific genetic ablation of Dicer.

city: Tübingen

first: Oliver

last: Borst

address: Otfried-Müller-Street 10

department: Internal Medicine III- Cardiology

institute: University Clinic Tübingen

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To assess the platelet miRNA pattern which is regulated in a Dicer-dependent manner, we conducted a global screen of platelet miRNA expression of murine platelets from Dicerlox/lox and DicerPf4∆/Pf4∆ mice using Next-generation deep sequencing analysis.
Methods: Platelets were isolated from 10- to 12-week-old Dicerlox/lox and DicerPf4Δ/Pf4Δ mice of male sex. Total RNA including miRNA was isolated from murine platelets using the QIAsymphony RNA Kit. The sequencing library was prepared using the QIAseq miRNA Library Kit with 10 to 20 ng input. The libraries were pooled in an equimolar fashion and sequenced on a NovaSeq6000 as paired-end reads with a sequencing depth of >12 Mio clusters (i.e. read-pairs) per sample.
Results: we were able to detect a total of 427 miRNAs in these platelets, of which 81 were significantly regulated (> |0.5| logFC threshold) in a Dicer-dependent manner. The majority of miRNAs were significantly downregulated, but a smaller proportion of miRNAs was slightly, but significantly upregulated in platelets lacking Dicer.
Conclusions: this study discloses differential expression patterns of further platelet miRNAs that potentially link multiple intercellular processes and pathways implicated in several stages of the pathogenesis of myocardial I/R injury

overall_design: Platelets miRNA profiling of 10- to 12-week-old Dicerlox/lox and DicerPf4Δ/Pf4Δ mice of male sex

first: Jan

last: Schütte

first: Nicolas

last: Casadei


title: Gene expression data from Brazilian pediatric ependymoma samples.

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

summary: Ependymoma (EPN) is the third most common central nervous system (CNS) tumor in childhood and, recently, has been classified in nine robust molecular subgroups (Pajtler et al., 2015). However, molecular and clinical features of pediatric EPNs from Brazilian cohorts remain unexplored. Herein, we aimed to analyze the gene expression profile among three different molecular subgroups: ST-EPN-RELA, ST-EPN-YAP1 and PF-EPN-A.

overall_design: Gene expression profiles from pediatric ependymoma samples (n=10) using high throughput sequencing.

first: L

middle: G

last: Tone

first: C

middle: A

first: E

last: Valera

last: Carlotti

first: R

last: Queiroz


title: Retinal organoids provide a suitable tool for toxicological drug screening – a comprehensive study validating well-known drug effects on retinal organoids

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

institute: Newcastle University

summary: Drug toxicity screening on retina is essential for the development of safe therapies for a large number of diseases, whilst preserving visual acuity and function. To this end, retinal organoids derived from human pluripotent stem cells (hPSCs) provide a suitable screening platform due to their similarity to human retina and the ease of generation in large-scale formats, offering almost unlimited excess of tissue. Two hPSC cell lines were differrentiated to retinal organoids which comprised all key retinal cell types in multiple nuclear and synaptic layers, enabling the maintenance of retinal ganglion and bipolar cells and moreover allowed the development of subtypes as revealed by the single cell RNA-Seq analysis. Ketorolac, Digoxin, Thioridazine, Sildenafil, Ethanol and Methanol were used to screen drug effects on retinal organoids. Exposure of the hPSC-derived retinal organoids to Diogxin, Thioridazine and Sildenafil exposure resulted in photoreceptor cell death, while Digoxin and Thioridazine additionally affected all other cell types, including Müller glia cells. Ethanol and Methanol caused an upregulation in retinal ganglion cell related geneexpression. All drug treatments activated astrocytes, indicated by dendrites sprouting into neuroepithelium and upregulation of astrocyte related genes. The ability to resond to light was presereved in organoids although the number of active retinal ganglion cells decreased after drug expsoure. These data indicate comparable drug effects in organoids to those reported in in vitro models and/or in humans, thus providing first robust experimental evidence of their suitability for toxicological studies.

overall_design: Retinaol organoids were cultured till day 200 of differerntiation, followed by drug exposure for 24 h, except for Sildenafil. Incubation was 7 days for Sildenafil treatment. Drugs tested were: Digoxin (40nM), Thioridazine (135uM), Sildenafil (225uM), Ethanol (500mM), Methanol (0.4%) and Ketorolac (2.5mM). The vehicle control was treated with PBS.

first: M

first: B

last: Dorgau

first: J

last: Collin

last: Queen


title: METTL3-mediated m6A modification controls splicing factor abundance and contributes to CLL progression

first: Lili

last: Wang

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

overall_design: Refer to individual Series


title: Global mapping of the SARS-CoV-2 microRNA interactome

city: Copenhagen

last: Fossat

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

summary: Using the CLEAR-CLIP methodology (PMID: 26602609) combined with high throughput sequencing, all the binding sites of the Argonaute (AGO) proteins on SARS-CoV-2 RNAs were identified as well as the miRNAs contributing to each binding site. Consequently, SARS-CoV-2 mutants were engineered to investigate the functional relevance of the main binding sites. The effect of the infection on the cellular miRNAs was also investigated using the same CLEAR-CLIP data and RNA-Seq analysis.

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus

overall_design: The work was done with the SARS-COV-2 virus strain DK-AHH1 (PMID: 33903110). Monkey kidney VeroE6 cells and human lung A549hACE2 cells were used as model systems for infection. All experiments were performed with a multiplicity of infection (MOI) of 0.001 and the cells collected for experiments 48 hours after the initiation of infection. The experimental setup for CLEAR-CLIP was as follow for each cell line: 1.5-2 million cells (VeroE6) or 2.5 million cells (A549hACE2) were seeded in each of 8 x 10 cm dishes. The day after, the cells in 5 x dishes were infected. Two days later, the cells of all 8 x dishes were collected and processed for CLEAR-CLIP independently for each dish but in parallel. Among the 5 x infected samples, one was processed without cross-linking, another was processed using a non-specific antibody instead of the pan-AGO antibody. This resulted in 3 x infected replicates (NFO147_A-C for VeroE6; NFO175_A-C for A549hACE2), 3 x non-infected replicates (NFO147_F-H for VeroE6; NFO175_F-H for A549hACE2), 1 x non-cross-linked infected control (NFO147_D for VeroE6; NFO175_D for A549hACE2) and 1 x non-specific-immunoprecipitation infected control (NFO147_E for VeroE6; NFO175_E for A549hACE2). Loss-of-binding (1L: C10039G + A10042U; 2L: U11377A + U11380A; 3L: C17462G + U17466C; 4L: U19869A + G19872C; 5L: U25434A + G25437A; 6L: U26732A + C26735U) ang Gain-of-binding (3G: A17465U; 5G: U25435G) SARS-CoV-2 mutants were engineered for six mains miRNA binding sites identified and CLEAR-CLIP performed for each of them in both cell lines (NFO181 samples). Furthermore, an RNA-Seq experiment was performed for 3 x replicates infected with wild-type SARS-CoV-2 and 3 x non-infected replicates for each cell lines (NFO190). For this last experiment, samples were also collected 72 hours after the initiation of infection for the A549hACE2 cells.

first: Emma

last: Lundsgaard

first: Rui

last: Costa

first: Lizandro

last: Rivera-Rangel

first: Louise

last: Nielsen

first: Lotte

middle: S

last: Mikkelsen

first: Santseharay

last: Ramirez

first: Jens

last: Bukh

first: Troels

last: Scheel


title: Analysis of cell type heterogeneity in breast tissue II

status: Public on Mar 02 2023

city: Berkeley

first: Iain

middle: Christopher

last: Clark

state: CA

address: 374 Stanley Hall

institute: University of California, Berkeley

summary: We used 10X Chromium single cell RNA-sequencing to study single cells from dissociated breast tissue

overall_design: 10X scRNAseq of dissociated breast tissue

first: Kiet

last: Phong

first: Zev

last: Gartner

first: Aaron

last: Zhang

first: Adam

last: Abate


title: Comparative analysis of transcriptomic changes induced by zearalenone and bisphenol A in human ovarian cancer cells [mRNA_seq]

city: Debrecen

first: Melinda

last: Szilágyi-Bónizs

address: Egyetem tér 1

department: Human Genetics

country: Hungary

institute: University of Debrecen

summary: In this study we compared the global transcriptomic response of human ovarian cells to zeralenone (ZEA; mycotoxin) and bisphenol A (BPA; plastic additive) with the effect of physiological estradiol (E2). For this purpose we applied the PEO1 human ovarian cell line that was treated with 10 nM ZEA, 100 nM BPA and 10 nM E2. Transcriptomic profile was compared by mRNA sequencing (Illumina NextSeq 500).

overall_design: The PEO1 human epithelial ovarian cell line was treated with 10 nM E2, 10 nM ZEA and 100 nM BPA. Total RNA was isolated 8 h-s after the treatment.

last: Szilágyi

first: Éva

last: Márton

first: Alexandra

last: Varga

first: András

last: Penyige

first: Zsuzsanna

last: Birkó

first: István

last: Balogh

first: Bálint

last: Nagy


title: A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [gRNA_SCREEN]

city: Chicago

last: Williams

state: Ilinois

address: 240 East Huron

department: Department of Medicine, Allergy and Immunology

institute: Northwestern University

summary: The genome is pervasively transcribed to produce a vast array of non-coding RNAs (ncRNAs). Long noncoding RNAs (lncRNAs) are transcripts of > 200 nucleotides and are best known for their ability to regulate gene expression. Enhancer RNAs (eRNAs) are subclass of lncRNAs that are synthesized from enhancer regions and have also been shown to coordinate gene expression. The biological function and significance of most lncRNAs and eRNAs remain to be determined. Epithelial to mesenchymal transition (EMT) is a ubiquitous cellular process that occurs during cellular migration, homeostasis, fibrosis, and cancer-cell metastasis. EMT-transcription factors, such as SNAI1 induce a complex transcriptional program that coordinates the morphological and molecular changes associated with EMT. Such complex transcriptional programs are often subject to coordination by networks of ncRNAs and thus can be leveraged to identify novel functional ncRNA loci. Here, using a genome-wide CRISPR activation (CRISPRa) screen targeting ~10,000 lncRNA loci we identified ncRNA loci that could either promote or attenuate EMT. We discovered a novel locus that we named SCREEM (SNAI1 cis-regulatory eRNAs expressed in monocytes). The SCREEM locus contained a cluster of eRNAs that when activated using CRISPRa induced expression of the neighboring gene SNAI1, driving concomitant EMT. However, the SCREEM eRNA transcripts themselves appeared dispensable for the induction of SNAI1 expression. Interestingly, the SCREEM eRNAs and SNAI1 were co-expressed in activated monocytes, where the SCREEM locus demarcated a monocyte-specific super-enhancer. These findings suggest an unexpected role for SNAI1 in monocytes. Exploration of the SCREEM-SNAI axis could reveal novel aspects of monocyte biology.

overall_design: HBEC3-KT--human bronchial immortalized epithelial cell line-- 330million cells were transduced (stably expressing dcas9-vp64 and P65) with pooled sgRNA contained lentiviral particles at a MOI of 0.3 (1000X representation of the library in surviving cells). Th transduced cells were selected with Zeocin (50ug/ml) for 14-days (maintaining a 500X per passage i.e. 50 million cells). The SAM expressing HBEC3-KT cells (Zeocin  [sgRNA-hsf1-lib; (50ug/ml)], Hygromycin  [p65(10ug/ml)], and blasticidin  [dcas9-vp64(10ug/ml)] were then treated with 10ng/ml of TGFβ1 (R&D) for 72hrs. Subsequently, the cells were harvested and processed for CD44+ sorting. Note, for cell sorting using BD FACSAria II sorter, 120-micron tip was used to let free flow of large mesenchymal-like cells. We sorted ~50X representation of the library from CD44-low (bottom 10% of the peak) and CD44-high (top 10% of the peak) cells. Genomic DNA were harvested from sorted populations using the Quick-DNA plus (Zymo Research) according to the manufacturer’s protocol. To determine distribution of the sgRNA, the spectrophotometer quantified gDNA product was sequenced using primers (listed in Supplementary file 1 of this paper) in Illumina MiSeq (80 cycles of read 1 (forward) and 8 cycles of index 1 with a 5% PhiX control to improve library diversity in order to cover >50 reads per sgRNA in the library).

first: Dinesh

last: Uthaya Kumar

first: Marina

last: Yurieva

first: Jessica

last: Grassmann

first: Lina

last: Kozhaya

first: Derya

last: Unutmaz


title: Connexin 43-mediated neurovascular interactions regulate neurogenesis in the adult brain subventricular zone.

city: Charlottesville

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

summary: To gain a deeper understanding of the Connexin (Cx)-43-dependent molecular regulation of neural stem behavior, we used scRNAseq approach on endothelial cells (ECs) and neural stem and progenitor cells (NSPCs) from knock out mice.

overall_design: Adult brain subventricular zone ECs and NSPCs were isolated by fluorescence-activated cell sorting (FACS) based on specific markers (ECs: CD31+Glast-CD45-) and NSPCs (CD31-Glast+CD45-) and analyzed using scRNAseq

first: Nafiisha

last: Genet

first: Gael

first: Nicholas

last: Chavkin

first: Umadevi

first: Karen

last: Hirschi


title: Chip seq of in vitro induced senescent myeloid cells treated with HDAC inhibitor

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

country: Switzerland

institute: Institute of oncology research

summary: To understand the epigenetic regulations in in vitro induced senescent myeloid cells, we used Romidepsin (regulator of hyston H3) and we analysed how the genes get regulated.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K9AC in in vitro induced senescent myeloid cells after treatment with Romidepsin

first: Troiani

last: Martina

first: Alimonti

last: Andrea


title: A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [SNA1_RNA-Seq]

first: Adam

overall_design: HBEC3-KT, human bronchial immortalized epithelial cell line was CRISPR-activated with either sgRNAs targeting SCREEM locus or non-targeting sgRNAs and treated with or without TGFB1.  RNA extracted from these cells were then sequenced.


title: A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [RIBO_RNA]


title: A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes


title: Dynamic Activity in cis-Regulatory Elements of Leukocytes Identifies Transcription Factor Activation and Stratifies COVID-19 Severity in ICU Patients [RNA-seq]

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: The transcription factors programs mediating the immune response to COVID-19 and disease outcomes are not fully understood. Capturing active transcription initiation from cis-regulatory elements such as enhancers and promoters by capped-small (cs)RNA-seq, in contrast to capturing the steady-state transcripts by conventional RNA-seq, allows unbiased identification of the underlying transcription factors activity and regulatory pathways. Here, we profile the acute changes in transcription initiation in peripheral leukocytes from critically ill COVID-19 patients, thereby identifying transcription factor (TF) motifs that track the severity of COVID19-associated lung injury, disease resolution, and outcome. Unbiased clustering reveals distinct subsets of cis-regulatory elements that delineate the regulation of specific pathways, cell types, and the combinatorial activity of transcription factors. We find evidence of critical roles for regulatory networks driven by signal-dependent and lineage determining transcription factors, showing that STAT/BCL6 and E2F/MYB regulatory programs from myeloid cell populations are activated in patients with poor disease outcomes and associated with single nucleotide genetic variants implicated in COVID-19 susceptibility. More broadly, we demonstrate how capturing acute, disease-mediated changes in transcription initiation can provide insight into the underlying molecular mechanisms and stratify patient disease severity.

overall_design: Comparison of transcriptional activity over time among COVID-19 patients with varying disease severity. Total RNA was obtained from whole blood samples.

first: Michael

last: Lam

first: Sascha

last: Duttke

first: Christopher

middle: W

last: Benner

first: Nicole

last: Coufal


title: Dynamic Activity in cis-Regulatory Elements of Leukocytes Identifies Transcription Factor Activation and Stratifies COVID-19 Severity in ICU Patients [csRNA-seq]

overall_design: Comparison of transcriptional activity over time among COVID-19 patients with varying disease severity. RNA from whole blood was processed to capture nascent transcription using csRNA-seq).


title: Single-nucleus sequencing deciphers lineage trajectories in rice pistils [snRNA-seq]

city: Singapore

first: Hao

last: Yu

address: 16 Science Drive 4

country: Singapore

institute: National University of Singapore

summary: Angiosperms possess a characteristic life cycle with an alternation of sporophyte and gametophyte generations, which happens in plant organs like pistils. Rice pistils contain ovules and receive pollen for successful fertilization to produce grains. The cellular expression profile in rice pistils is largely unknown. Here we show a cell atlas of rice pistils before fertilization by droplet-based single-nucleus RNA sequencing. The Ab initio marker identification validated by in situ hybridization assists the cell-type annotation, revealing cell heterogeneity between ovule and carpel lineages.

overall_design: Perform snRNA-seq for 1N (haploid; gametophyte) and 2N (diploid; sporophyte) nuclei and bulk RNA-seq for nuclei of pistils and whole cells of upper and lower part of pistils

first: Chengxing

last: Li

first: Songyao

last: Zhang


title: Single-nucleus sequencing deciphers lineage trajectories in rice pistils [bulk RNA-seq]


title: RNA sequencing of human gastric cancer drug treatment organoids

city: HongKong

first: Suetyi

last: Leung

address: Queen Mary Hospital, Pokfulam Road

department: Department of Pathology

institute: The University of Hong Kong

summary: Using RNA sequencing, we profile transcriptome dervied from human gastric cancer organoids after drug treatment.

overall_design:
Gastric cancer organoids were treated with 5-fluorouracil and cisplatin with IC10 and dose increased gradually until reaching IC50 or at dose which organoids remained alive but did not proliferate.
Submitters state that they will release raw fastq files on ENA with study ID PRJEB60472

first: Suet

middle: Y


title: RNA sequencing of in vivo sorted C12FDG+ MDSCs and C12FDG- MDSCs

overall_design: Examination of the differences between senescent and not senescent MDSCs


title: CF (1567) vs CFTR-corrected (1566) iPSC-airway at ALI

first: Feiya

last: Wang

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

summary: To interrogate the intrinsic effect of CFTR on airway epithelium; to interrogate the presence of FOXi1+ASLC3+ ionocyte population. Description of samples:1567 (F508del CF patient of rapid progressive phenotye) and 1566 (isogenic CFTR-repaired pair). iPSC-derived airway epithelium, s/p D15CD47hi/CD26lo sort, 210DCYI media x

overall_design: CF and syngeneic CFTR-corrected iPSC-derived airway epithelium, s/p D15CD47hi/CD26lo sort, 210DCYI media x

first: Ruby

first: Jonathan

last: Lindstrom-Vautrin

first: Darrell

last: Kotton


title: CF (1565) vs CFTR-corrected (1564) iPSC-airway at ALI

summary: Purpose of experiment :To 1) evaluate for the presence of pulmonary ionocytes, 2) investigate the role of the CFTR in airway epithelium. Description of samples: 1564 (CF-repaired), 1565 (CF DF508homozygous) iPSC-airway epithelium through basal cell intermediate. iPSC-D15CD47/CD26sort- NGFR sort x 2

overall_design: CF and syngeneic CFTR-corrected iPSC-airway epithelium through basal cell intermediate.  iPSC-D15CD47/CD26sort- NGFR sort x 2