title: PRDM16 Deficiency in Vascular Smooth Muscle Cells Aggravates Abdominal Aortic Aneurysm

city: Ann Arbor

first: Zhenguo

state: MI

address: 2800 Plymouth Road, NCRC BLDG26, Rm214N

department: MM Int Med-Cardiology

institute: University of Michigan

summary: Abdominal aortic aneurysm (AAA) is usually asymptomatic until life-threatening complications occur, predominantly involving aortic rupture. Currently, no drug-based treatments are available, primarily due to limited understanding of AAA pathogenesis. The transcriptional regulator PR domain–containing protein 16 (PRDM16) is highly expressed in the aorta, but its functions in the aorta are largely unknown. By RNA-seq analysis, we found that vascular smooth muscle cell–specific (VSMC-specific) Prdm16-knockout (Prdm16SMKO) mice already showed extensive changes in the expression of genes associated with extracellular matrix (ECM) remodeling and inflammation in the abdominal aorta under normal housing conditions without any pathological stimuli. Human AAA lesions displayed lower PRDM16 expression. Periadventitial elastase application to the suprarenal region of the abdominal aorta aggravated AAA formation in Prdm16SMKO mice. During AAA development, VSMCs undergo apoptosis because of both intrinsic and environmental changes, including inflammation and ECM remodeling. Prdm16 deficiency promoted inflammation and apoptosis in VSMCs. A disintegrin and metalloproteinase 12 (ADAM12) is a gelatinase that can degrade various ECMs. We found that ADAM12 is a target of transcriptional repression by PRDM16. Adam12 knockdown reversed VSMC apoptosis induced by Prdm16 deficiency. Our study demonstrated that PRDM16 deficiency in VSMCs promoted ADAM12 expression and aggravates AAA formation, which may provide potential targets for AAA treatment.

overall_design: Prdm16flox/flox mice (stock number 024992) and Myh11-CreERT2 mice (stock number 019079) were from the Jackson Laboratory and were backcrossed to C57BL/6 background. Prdm16flox/flox mice were crossbred with Myh11-CreERT2 mice (carrying the CreER cassette on the Y chromosome) to generate VSMCs specific Prdm16 knockout (Prdm16SMKO) mice. Eight- to ten-week-old male mice were treated with tamoxifen (75 mg/kg/day) in corn oil for 5 consecutive days by gavage. Two weeks later, total RNA from abdominal aorta were isolated with the RNeasy® micro kit (Cat# 74004, Qiagen).

first: Xiangjie

last: Zhao

first: Guizhen

first: Yanhong

last: Guo

first: Haocheng

last: Lu

first: Wenjuan

last: Mu

first: Juan

last: Zhong

first: Minerva

last: Garcia-Barrio

first: Jifeng

first: Y

middle: E

last: Chen

last: Chang


title: HeLa, ZBTB2-myc overexpression, 0.1% O2

status: Public on Jun 08 2023

city: Kyoto

first: Christalle

middle: CT

last: Chow

state: Kyoto

address: Sakyo Ward, Yoshidakonoecho

department: Graduate School of Biostudies

country: Japan

institute: Kyoto University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In order to identify candidate genes regulated by ZBTB2 under hypoxia, we examined the genomic occupancy of myc-tagged ZBTB2 in HeLa cells incubated under 0.1% oxygen.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for myc-tagged proteins in HeLa cells cultured under 0.1% oxygen for 24 hours and transfected with overexpression vectors for EGFP-myc (negative control) or ZBTB2-myc. Three biological replicates were prepared per condition.

middle: C

first: Minoru

last: Kobayashi

first: Gouki

last: Kambe

first: Hiroshi

last: Harada


title: Net39 protects muscle nuclei from mechanical stress during the pathogenesis of Emery-Dreifuss muscular dystrophy.

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

country: USA

institute: UTsouthwestern

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptome analysis of BT549 cells overexpressing SNHG15

city: Shantou

first: Zhou

last: Yanchun

state: Guangdong

address: Xinling Road

department: Pathophysiology

country: China

institute: Shantou University Medical College

summary: LncRNA SNHG15 is an oncogenic lncRNA in a variety of cancers including breast cancer, lung cancer, and hepatocellular carcinoma. To screen genes regulated by SNHG15, we performed RNA-seq with stable SNHG15-overexpression BT549 cells, using BT549-pcIP2 as control.

overall_design: This experiment is designed to evaluate differential expression genes through comparing mRNA profiling of SNHG15 overexpressing BT549 cells with vector control.  The RNA-Seq experiments and data analysis were performed at the Shanghai Biotechnology Corporation in Shanghai, China

last: Zhou

first: S

first: W

last: Gu


title: TONSOKU is required for the maintenance of repressive epigenetic modifications in Arabidopsis [MNase-seq]

city: Beijing

first: Danhua

last: Jiang

address: No. 1 West Beichen Road, Chaoyang District

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

type: Methylation profiling by high throughput sequencing

summary: Epigenetic inheritance requires the faithful maintenance of epigenetic marks such as certain chromatin modifications through DNA replication. Plant TONSOKU (TSK) and its animal orthologue TONSOKU-like (TONSL) act as readers for newly synthesized histones and assist in DNA replication via facilitating DNA damage repair at post-replicative chromatin. However, whether TSK/TONSL regulates chromatin replication and the maintenance of chromatin modifications remain elusive. In this study, we demonstrate that TSK is dispensable for global histone and nucleosome accumulation but necessary for maintaining repressive chromatin modifications including H3K9me2, H2A.W, H3K27me3 and DNA methylation. TSK physically interacts with H3K9 methyltransferases SUVH5 and SUVH6, and the Polycomb protein RING1a/b. Moreover, TSK mutation strongly enhances defects in Polycomb pathway mutants. TSK is intended to only associate with nascent chromatin until it starts to mature. We propose that TSK ensures proper epigenetic inheritance by supporting the recruitment of epigenetic modifiers to post-replicative chromatin in a critical short window of time following DNA replication.

overall_design: Transcriptome, MNase, H3k27me3, H2A.W and H3K9me2 enrichment, and DNA methylation were examined in Col or tsk-4 mutant

first: Lin

last: Wang

first: Mande

last: Xue

first: Huairen

last: Zhang


title: Identification of Target LncRNAs of IMP1 in T47D Cells by RIP-Seq technique

summary: IMP1 is a RNA binding protein shown to regulate translation, localization, or stability of their target RNAs. However, whether IMP1 can widely bind to lncRNAs and regulate their expression in Breast cancer cells remains to be confirmed. In this study, we used RNA binding protein immunoprecipitation-high throughput sequencing (RIP-Seq) technique to identify LncRNAs which bind to IMP1 protein in breast cancer cell line T47D cells.

overall_design: Cell lysates were prepared from cultured T47D cells and then incubated with protein A beads coated with anti-IMP1 antibody or normal IgG control at 4°C for 4 h in the presence of RNasin (200 U/mL) and protease inhibitors. After incubation, the supernatant was removed by a short centrifugation and the beads were washed three times in ice-cold lysis buffer. Immunoprecipitates were first verified by western blotting using the anti-IMP1 antibody. Total RNAs was extracted from individual precipitates with TRIzol reagent. The binding LncRNAs were analyzed by LncRNA-seq. The RNA-Seq experiments and data analysis were performed at the Shanghai Biotechnology Corporation in Shanghai, China.

first: P

last: Peng


title: N6-methyladenosine modification of FZR1 mRNA promotes gemcitabine resistance in pancreatic cancer

city: Guangzhou

first: Rui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: Pancreatic ductal adenocarcinoma (PDAC) is the most lethal cancer with limited therapeutic options, and gemcitabine insensitivity remains a major challenge. N6-methyladenosine (m6A) is a prevalent nucleotide modification in mRNA that has been linked to various biological processes in human diseases, yet its role in drug sensitivity of cancer remains largely unknown. Herein, by detecting the global m6A profile in a panel of gemcitabine-sensitive and gemcitabine-insensitive PDAC cells, we identified the key role of hyper-m6A modification of the master G0/G1 regulator Fizzy and Cell Division Cycle 20 Related 1 (FZR1) in regulating gemcitabine sensitivity. Targeting m6A modification of FZR1 improves the gemcitabine treatment response of gemcitabine-insensitive PDAC cells in vitro and in vivo. Mechanistically, Gem Nuclear Organelle Associated Protein 5 (GEMIN5) was identified as a novel m6A mediator that specifically binds to m6A-modified FZR1 and recruits the eIF3 translation initiation complex to accelerate FZR1 translation. Upregulation of FZR1 maintains the G0/G1 quiescent state and impairs gemcitabine sensitivity of PDAC cells. Further clinical analysis showed that both high levels of FZR1 m6A modification and FZR1 protein indicated a poor response to gemcitabine. These findings unveil the critical function for m6A modification in regulating gemcitabine sensitivity in PDAC and identify the m6A-FZR1 axis as a potential target to enhance gemcitabine response.

overall_design:
For m6A-seq, immunoprecipitated and input groups were analyzed with three cell lines for each group for a total of 6 samples.
PAR-CLIP using GEMIN5 antibody in PANC-1 cells.


title: CircRNA sequencing analysis of PTMC with lateral lymph node metastases and related clinical value studies of circRNA.

city: Chefoo Yantai Shandong China

first: Zhang

last: Ke

address: No. 20 Yuhuangding East Road, Zhifu District

institute: Yantai Yuhuangding Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: High-throughput sequencing was used to detect the expression profile of circRNA in PTMC of lymph node metastasis in lateral cervical region, and RT-qPCR was used to detect the expression of circRNA in cancer tissues and normal tissues adjacent to cancer. The receiver operating characteristic (ROC) curve and the area under ROC curve (AUC) were used to evaluate whether CircRNAs could be used as a biomarker for the diagnosis of thyroid cancer. Bioinformatics was used to predict the PTMC-related ceRNA mechanism of lateral cervical lymph node metastasis.

overall_design: 4 pairs of cancer tissues and normal paracancer tissues PTMC patients with cervical lymph node metastasis treated in the Department of Thyroid Surgery of Yuhuangding Hospital of Yantai with complete data were collected. The patients' cancer tissues and normal paracancer tissues were collected and stored in the refrigerator at -80℃ for long-term storage for high-throughput sequencing.

first: Zheng

last: Haitao


title: Chromatin accessibility and mitochondrial genotype from single cells of the retina and choroid in human MELAS (m.3243A>G) and control samples [scATAC-seq]

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: The mitochondrial m.3243A>G variant is known to cause retinal dystrophy and vision loss. We used mitochondria single cell ATAC sequencing to measure nuclear chromatin accessibility and mitochondrial heteroplasmy in single cells of the retina and choroid.

overall_design: Human retinas were dissected into neural retina and RPE/choroid from two regions (macular and peripheral). Samples were then dissociated to single cells using papain or collagenase respectivley. Samples from a MELAS patient and age/sex-matched healthy control donor were prepared.

middle: K

first: Budd

middle: A

last: Tucker

first: Robert

middle: F

last: Mullins


status: Public on Jun 09 2023

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: RNA-seq and ChIP-seq for H3K79me3 and H3K79me2 in mESCs and preimplantation embryos

first: Aushaq

middle: B

last: Malla

first: Haoming

last: Yu

first: Zachary

last: Smith


title: Non-random distribution of mitochondrial m.3243A>G heteroplasmy in human retina and its impact on cellular phenotype


title: Mapping Bcl11b binding in in vitro differentiated resident memory T cells [ChIP-seq]

city: Tampa

first: Dorina

last: Avram

state: Fl

address: 12902 Magnolia Drive, MRC4

department: Department of Immunology

institute: Moffitt Cancer Center

summary: The transcription factor (TF) networks that regulate the differentiation of resident versus circulating memory CD8+ T cells are incompletely understood. Here we show that the TF Bcl11b restricts gut resident memory (Trm) cell differentiation, while promoting splenic T central memory (Tcm) and effector memory (Tem) cell differentiation. The reduction of Bcl11b-deficient splenic Tcm and Tem cells was not due to major alterations in their programs, but rather due to the increased homing of their precursors to the small intestine. However, Bcl11b-deficient resident memory precursor cells upregulated residency program, including the TFs Ahr and Prdm1 (encoding Blimp1), and downregulated Tcf7, which restricts the residency program and promotes tissue egress. Bcl11b directly bound at Ahr and Prdm1, as well as at Tcf7 genes. Abrogating Ahr and Prdm1, or restoration of Tcf7 expression in Bcl11b-deficient cells led to partial correction of the excessive resident memory cell differentiation. Functionally, Bcl11b-deficient memory CD8+ T cells had an impaired recall response, but anti-tumor immunity was increased in adoptive cell therapy. Bcl11b also repressed the residency program in human CD8+ T cells and human Bcl11b low tumor-infiltrating lymphocytes showed increased residency gene expression. Thus, Bcl11b plays a critical role in balancing the circulating and tissue residency programs and reveals a potential novel target for cancer immunotherapies.

overall_design: Examination of Bcl11b binding in iTrm cells

first: Eric

last: Helm

first: Tomas

last: Zelenka


title: The Class VIII myosin ATM1 is integral for root apical meristem function

city: Ames

first: Natalie

middle: M

last: Clark

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

summary: Myosins are evolutionarily conserved motor proteins that interact with actin filaments to  regulate organelle transport, cytoplasmic streaming and cell growth. Plant specific Class XI  myosin proteins direct cell division and root organogenesis. However, the roles of Class VIII  myosin proteins in plant growth and development are less understood. Here, we investigated  the function of an auxin-regulated Class VIII myosin, Arabidopsis thaliana Myosin 1 (ATM1),  using genetics and live cell microscopy. ATM1 is a plasmodesmata-localized protein that is  enriched in actively dividing cells in the root apical meristem (RAM). Loss of ATM1 function  results in impaired primary root growth due to decreased RAM size and reduced cell  proliferation in a sugar dependent manner. Examination of stem cell marker line expression in  atm1-1 indicated impaired division of the lateral root cap and columella cells and a diminished  auxin response. Transcriptome analysis of atm1-1 linked these growth defects to dysregulation  of cell cycle and auxin pathway genes. Complementation of ATM1 loss-of- function mutant  restored root growth and cell cycle progression in the root meristem. Collectively, these results  provide novel evidence that ATM1 functions to influence cell proliferation and differentiation in  primary roots in response to auxin and sugar cues.

overall_design: Col-0 (control) and atm1-1 (mutant) seedlings were grown on media supplemented with or without (mock) 15mM glucose or sucrose for 5 days (5DO). Three biological replicates were collected for each condition.

first: Damilola

last: Olatunji

first: Dior

middle: R

last: Kelley


title: Regulation of CD8+ T cell differentiation by the transcription factor Bcl11b


title: Transcriptional Profile of ZIKV Infection in HTR8 cells and U251 cells

status: Public on Jun 07 2023

city: Shenzhen

first: Qiqi

last: Chen

state: Guangdong Province

address: Guangming District, Shenzhen City, Guangdong Province

department: School of Public Health (Shenzhen)

institute: Sun Yat-sen University

summary: To identify the various host factors involved in ZIKV infection, we compared the transcriptional profile for ZIKV-infected human first-trimester placenta trophoblast cell (HTR8) and glioblastoma astrocytoma (U251-MG). Our results demonstrated that the common IFN, inflammatory cytokine, and chemokine production were activated upon ZIKV infection of these two cell types while serval DEGs were enriched in distinct biological processes related to the characteristics of cell types. Our findings identified multiple host factors associated with ZIKV pathogenesis and potential treatment of congenital zika syndrome (CZS)

overall_design: We identified the differentially expressed genes through transcriptome analyses between mock-infected and ZIKV-infected HTR8 cells and U251 cells, the ZIKV-infected group and the mock-infected group had three samples.

first: Nina

first: Shike

last: Zeng


title: Role of PG1626 in Porphyromonas gingivalis ATCC33277

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

summary: Wild type Porphyromonas gingivalis strain ATCC33277 (V3176) and PG1626 - deficient mutant (V3177) were grown in iron replete conditions was used to compare to  Porphyromonas gingivalis strains grown in iron chelated conditions.

overall_design: Samples of wildtype P. gingivalis  ATCC33277 V3176 and V3177 PG1626 mutant were grown in an overnight culture of BHI media. The overnight cultures served to inoculate cultures of BHI media starting at an OD660 of approximately 0.05. Cultures were grown with and without dipyridyl to mid-log phase, centrifuged, and stored at -20 °C.

first: Qin

last: Gui


title: Homo- and heterodimerization of bHLH transcription factors balance stemness and bipotential differentiation in the Drosophila adult intestine

city: Colchester

first: Joaquin

last: de Navascues Melero

state: Essex

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

summary: Multipotent adult stem cells must balance self-renewal with differentiation into various mature cell types. How this activity is molecularly regulated is poorly understood. By using genetic and molecular analyses in vivo, we show that a small network of basic Helix-Loop-Helix (bHLH) transcription factors controls both stemness and bi-potential differentiation in the Drosophila adult intestine. We find that homodimers of Daughterless (Da, homolog to mammalian E proteins) maintain the self-renewal of intestinal stem cells and antagonise the activity of heterodimers of Da and Scute (Sc, homolog to ASCL and known to promote intestinal secretory differentiation). Using RNAseq, we also find that Da and Sc induce complex transcriptional profiles in undifferentiated cells, which must be balanced by intestinal stem cells to perform their function. We find a novel role for the HLH factor Extramacrochaetae (Emc, homolog to Id proteins), titrating Da and Sc to promote absorptive differentiation. We further show that Emc prevents committed absorptive progenitors from de differentiating, underscoring the plasticity of these cells. Switching physical interaction partners in this way enables the active maintenance of stemness, but primes stem cells for differentiation along two alternative fates. Such regulatory logic could be recapitulated in other bipotent stem cell systems.

overall_design: The samples consist of adult intestinal midguts of the genotype esg-Gal4, tub-gal80[ts], UAS-GFP crossed to either a control strain or to strains with UAS- responder lines for either 'monomeric' daughterless, daughterless-specific RNAi, scute or the forced homodimer construct da:da. After activation of the transgene expression, the GFP+ cells were FAC-sorted, and their total RNA extracted, and sent for library preparation and sequencing to a commercial vendor. This was done in two batches, the first one comprising UAS-daughterless and UAS-daughterless-RNAi, the second with UAS-scute and UAS-da:da. Each batch had their control samples. Three replicates were prepared for each genotype (except for UAS-daughterless, which only had 2). Each replicate required pooling intestines from ~100 flies.

first: Jerome

last: Korzelius

first: Joaquín

last: de Navascués


title: Genome wide mapping of chromatin accessibility in resident memory precursor cells [ATAC-seq]

overall_design: Examination of changes to chromatin accessibility in resident memory precursor cells caused by the removal of Bcl11b.


title: Gene expressions of human gastric cancer cell lines

city: Kashiwa

first: Shogo

last: Kumagai

state: Chiba

address: 6-5-1 Kashiwanoha

institute: National Cancer Center

summary: We compared gene expressions between two gastric cancer cell lines overexpressing RHOA wild-type or Y42C

overall_design: MKN1, a human gastric cancer cell line, overexpressed RHOA wild-type or Y42C was made using pBABE-puro vector. Total RNA was extracted from the two cell lines and subjected to microarray analysis.

first: Hiroyoshi

last: Nishikawa


title: Methylation mediated LINC00261 suppresses pancreatic cancer progression

city: Chongqing

first: Songsong

last: Liu

state: Chongqing

address: No. 30 Gaotanyan Street, Shapingba District

institute: Army Medical University

summary: To the best of our knowledge, this is the first study presenting detailed evidences for the underlying role of LINC00261 in pancreatic cancer both in vitro and in vivo. Also, we thoroughly explored the clinical value of LINC00261 in multicenter cohorts and developed an individualized predictive model of survival. To investigate the potential downstream pathway of LINC00261, we performed RNA-seq using two PANC-1 cell groups: LINC00261 knockdown and control.

overall_design: PANC-1 cells were transfected with LINC00261 siRNA and control . Total RNA was extracted from the samples using the TRIzol method. The total RNA extracted from the samples was tested by a NanoDrop 2000 and denaturing gel electrophoresis. RNA Sequencing Analysis were performed after the sample quality control.

first: Huaizhi

last: Wang


title: Single Cell Transcriptomics of Bone Marrow Derived Macrophages reveal Ccl5 as a marker of Direct IFNAR-independent Responses to DNA Sensing

city: La Jolla

first: Kevin

middle: Robert

last: King

email: krking@health.ucsd.edu, krking@ucsd.edu

state: CA

address: 9500 Gilman Dr

department: Bioengineering; Medicine

institute: University of California San Diego

summary: Bone marrow derived macrophages (BMDMs) are a common model for macrophage type 1 interferon responses. We used single cell RNA-seq (scRNA-seq) to identify direct responders for dsDNA sensing.

overall_design: Bone marrow cells were isolated from C57BL/6J wild-type and IFNAR -/- mice. The cells were treated with macrophage colony-stimulating factor (M-CSF) and then stimulated with control vehicle, dsDNA, or dsDNA and IFNAR antibody for analysis with scRNA-seq.

first: Emily

last: McCarty

first: Justin

last: Yu

first: Van

last: Ninh

first: David

last: Calcagno

first: Jodi

last: Lee


title: Prenatal exposure to benzo[a]pyrene depletes ovarian reserve and masculinizes embryonic ovarian germ cell transcriptome transgenerationally [Bisulfite-Seq]

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary: People are exposed to polycyclic aromatic hydrocarbons, like benzo[a]pyrene (BaP), via inhalation of particulate matter air pollution and ingestion of grilled and smoked foods. Prenatal exposure to BaP destroys germ cells in ovaries, causing earlier onset of ovarian senescence post-natally. Developing testes are affected at higher doses than ovaries. However, it is not known if adverse effects are transmitted to subsequent generations. We orally dosed pregnant female mice (F0) with 0.033, 0.2, or 2 mg/kg-day BaP or vehicle from embryonic day (E) 6.5-11.5 (F1 offspring) or E6.5-15.5 (F2 and F3). Ovarian germ cell and follicle numbers were significantly decreased in F3 females at all doses of BaP; testicular germ cells were not affected. E13.5 germ cell RNA-sequencing revealed significantly increased expression of male-specific genes in female germ cells across generations and BaP doses. Our study demonstrated that F0 BaP exposure partially disrupted sexual identity of female germ cells transgenerationally.

overall_design: Whole genome bisulfite sequencing of FACS-enriched mouse primordial germ cells with or without gestational exposure to banzo[a]pyrene: Repeated Experiment (F3 primordial germ cells)

first: Jinhwan

last: Lim

first: Ulrike

last: Luderer


title: Efficacy of antiviral therapy and host-virus interactions visualized using serial liver sampling with fine-needle aspirates

city: Toronto

first: Adam

last: Gehring

state: ON

address: 101 College St

country: Canada

institute: UHN

summary: Infection-dependent transcriptional changes and the impact of antiviral therapy on viral replication can be measured in longitudinal human liver biopsies using single-cell RNA sequencing data

overall_design:
Investigator-initiated, phase 4 study in which recruited patients received TAF 25mg once daily for 48 weeks. The total duration of the study to End of Follow-up was 48 weeks. After Week 48, participants were offered 2 years of TAF therapy. Sample collection 0, 12, 24 w was chosen to analyze immune responses based on ALT normalization rates. This mono-center study was conducted at Toronto Centre for Liver Disease, Canada.
>>>Raw data for human samples not available due to patient privacy concerns<<<

first: Samuel

last: Kim

first: Jeffrey

last: Wallin

first: Yanal

last: Ghosheh

first: Muhammad

last: Zahoor

first: Juan

middle: D

last: Sanchez Vasquez

first: Shirin

last: Nkongolo

first: Scott

last: Fung

first: Patricia

last: Mendez

first: Jordan

last: Feld

first: Harry

middle: L

last: Janssen


title: Retinal transcriptome of neonatal mice after optic nerve injury

first: Ling-Ping

last: Cen

address: North Dongxia Road

institute: JSIEC

summary: We performed RNA-seq analysis on the normal and 6-hour post-ONC retinas from the embryonic day (E) 20, postnatal day (P) 1 and P3 mice to determine the retinal transcriptome profiles. The identified differentially expressed genes (DEGs) could be associated with the degeneration of axonal growth capacity after birth, and axonal regeneration. Subsequent K‐means, GO, KEGG, PPI, and GSEA analysis revealed the biological processes and regulatory pathways involved in the DEGs.

overall_design: Gene expression profiling analysis was performed using data obtained from RNA-seq of whole retinal cells.

first: Shi-Qi

last: Yao

first: Meng

last: Wang

first: Jia-Jian

last: Liang

first: Tsz

last: Ng


title: Protecting RNA Integrity for Spatial Transcriptomics While Improving Immunofluorescent Staining Quality

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

summary: In comparison to bulk sequencing or single cell sequencing, spatial transcriptomics preserves the spatial information in tissue slices and can even be mapped to immunofluorescent stainings. This enables to unravel complex interactions of neighboring cells or to link cell morphology to transcriptome data. The 10x genomics visium spatial assay offers to combine spatial transcriptomics with immunofluorescent staining of cryo-sectioned tissue slices. We applied this technique to 10 µm fresh frozen mouse brain slices and developed a protocol that still protects RNA integrity while improving buffers for immunofluorescent staining. We investigated the influence of various parameters on RNA integrity and on antibody binding of blocking, staining as well as wash buffers. Finally, we propose a protocol that does not alter RNA integrity in comparison the 10x genomics demonstrated protocol but allows the usage of several antibodies that have not been compatible with the protocol before. In addition, we discuss the influence of the tested parameters which offers further development of application specific staining protocols.

overall_design:
Transcriptome data of a newly established immunostaining protocol improving spatial transcriptomic applications
Treatment PCI stands for Peritoneal contamination and infection.

first: Nina

last: Hahn

first: Martin

last: Bens

first: Christin

last: Reißig

first: Marin

last: Kempfer

first: Lars

last: Schmidl

first: Christian

last: Geis


title: Genetically diverse mouse models of SARS-CoV-2 infection reproduce clinical variation in type I interferon and cytokine responses in COVID-19.

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

summary: Inflammation in response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection drives severity of coronavirus disease 2019 (COVID-19), with effective versus dysregulated responses influenced by host genetics. To understand mechanisms of inflammation, animal models that reflect genetic diversity and clinical outcomes observed in humans are needed. We report a mouse panel comprising the diverse genetic backgrounds of the Collaborative Cross founder strains crossed to K18-hACE2 mice that confers high susceptibility to SARS-CoV-2. Infection of CC x K18-hACE2 F1 progeny resulted in a spectrum of weight loss, survival, viral replication kinetics, histopathology, and cytokine profiles, some of which were sex-specific. Importantly, early kinetics of type I interferon (IFN) responses, and a regulated proinflammatory response were  required for control of SARS-CoV-2 replication in PWK x K18-hACE2 mice that were highly resistant to severe disease. Thus, dynamics of inflammatory responses observed in COVID-19 can be modeled in diverse mouse strains that provide a genetically tractable platform for understanding antiviral immunity.

overall_design: Spatial transcriptomics comparison of mouse lung FFPE samples infected with SARS-CoV-2

first: Shelly

last: Robertson

first: Olivia

last: Bedard

first: Kristin

last: McNally

first: Carl

last: Shaia

first: Chad

last: Clancy

first: Matthew

last: Lewis

first: Rebecca

last: Broeckel

first: Abhilash

middle: I

last: Chiramel

first: Gail

last: Sturdevant

last: Rosenke

first: Sarah

last: Anzick

first: Elvira

last: Forte

first: Christoph

last: Preuss

first: Candice

middle: N

last: Baker

first: Jeffrey

last: Harder

middle: G

last: Shannon

first: Catherine

last: Brunton

first: Steven

last: Munger

first: Daniel

last: Bruno

first: Justin

last: Lack

first: Jacqueline

last: Leung

first: Amirhossein

last: Shamsaddini

first: Paul

last: Gardina

first: Jian

last: Sun

last: Holland

first: Nadia

last: Rosenthal

first: Sonja

last: Best


title: VIRMA-mediated m6A modification profilling in human nasopharyngeal carcinoma

first: Zi-Qi

last: Zheng

address: No. 651 Dongfeng east road, Yuexiu district, Guangzhou

institute: Sun Yat-sen University Cancer Center

summary:
Several studies revealed an underlying disordered m6A regulatory network in human nasopharyngeal carcinoma (NPC). However, the roles of m6A regulators and sequential m6A dysregulation in NPC remain largely unknown. In the present study, we investigated the role of VIRMA and its underlying mechanisms in NPC.
We performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) to identify the potential downstream targets of VIRMA that might be essential in NPC using  HONE-1 cells with or without VIRMA silenced (two biological replicates).

overall_design: Total RNA recovered from HONE-1 cells were used to acquire different modification profiles of mRNAs and lncRNAs using MeRIP-seq. In this way, this study reveal the critical role of VIRMA to control the transcription program of NPC, and provide a potential biomarker and therapeutic target for NPC.

first: Zhuo-Hui

last: Huang

first: Ye-Lin

last: Liang

first: Ying


title: A Novel Single Vector Intersectional AAV Strategy for Interrogating Cellular Diversity and Brain Function

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: As the discovery of cellular diversity in the brain accelerates, so does the need for functional tools that target cells based on multiple features, such as gene expression and projection target. By selectively driving recombinase expression in a feature-specific manner, one can utilize intersectional strategies to conditionally promote payload expression only where multiple features overlap. We developed Conditional Viral Expression by Ribozyme Guided Degradation (ConVERGD), a single-construct intersectional targeting strategy that combines a self-cleaving ribozyme with traditional FLEx switches. ConVERGD offers benefits over existing platforms, such as expanded intersectionality, the ability to accommodate larger and more complex payloads, and a vector design that is easily modified to better facilitate rapid toolkit expansion. To demonstrate its utility for interrogating neural circuitry, we employed ConVERGD to target an unexplored subpopulation of norepinephrine (NE)-producing neurons within the rodent locus coeruleus (LC) identified via single-cell transcriptomic profiling to co-express the stress-related endogenous opioid gene prodynorphin (Pdyn). These studies showcase ConVERGD as a versatile tool for targeting diverse cell types and reveal Pdyn-expressing NE+ LC neurons as a small neuronal subpopulation capable of driving anxiogenic behavioral responses in rodents.

overall_design: Smart-seq were used to profile DBH positive rodent locus coeruleus (LC) neurons

first: Alex

last: Hughes

first: Brittany

last: Pollard

first: Jesse

last: Gammons

first: Phillip

last: Chapman

first: Jay

last: Bikoff

first: Lindsay

last: Schwarz


title: Integrated transcriptome and metabolome analysis of mechanism on intranasal spray insulin against vascular dementia

city: Changsha

first: Liang

last: Tang

address: No 1501, Leifeng road

institute: Changsha Medical University

summary:
to investigate the effects and mechanism of insulin on 2-VO induced vascular dementia (VD) rat models.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hippocampus in CK, VD and INS+VD groups.


title: Gene expression of Dcir-/- osteoclasts induced by M-CSF and RANKL

city: Sendai

first: Tomonori

last: Kaifu

state: Miyagi

address: 1-15-1 Fukumuro Miyagino ku

department: Faculty of Medicine

institute: Tohoku Medicine and Pharmaceutical University

summary:
Purpose: DCIR is an inhibitory type of C-type  lectin receptor that regulates osteoclast (OC) formation and functions. This study aimed to find the genes of OCs that could be regulated through DCIR.
Method: Bone marrow cells from WT and Dcir-/- mice were cultured in M-CSF for 2 days and the the cells were further cultured in M-CSF and RANKL. RNA profiles were generated by deep sequencing, in triplicate, using Illumina NovaSeq.
Results: We detected xxx gense that were higher expression in Dcir-/- OCs, compared with WT OCs,  with a fold change ≥1.5 and p value <0.05.
Conclusion: Our data showed that Dcir deficiency in OCs changed the gene expression pattern, compared to WT OCs, which are induced by M-CSF and RANKL.

overall_design: mRNA profiles of WT and Dcir-/- osteoclasts for 2 days culture aftre RANKL stimulation

first: Kenji

last: Shimizu


title: Effect of androgen; gonad- and androgen receptor on gene expression in mouse kidney and liver

city: Los Angeles

first: Jing

last: Liu

state: California

address: 1425 San Pablo St.

department: Department of Regenerative Medicine  & Stem Cell Biology

institute: University of Southern California

summary:
To investigate mechanisms underlying renal sex differences, we performed whole kidney RNA-seq on wild type C57BL/6J mice (Jackson Laboratory) at postnatal 0, 2, 4, 8 and 79 weeks old. We also profiled wild type adult C57BL/6NCrl (Charles River Laboratory) and adult castrated, ovariectomized mice when the surgeries for gonadal removal were performed at the age of around 3 weeks old. Tissue specific Ar (androgen receptor), Tbx10 and Neurog2 knockout mice were maintained at F1 cross Arc/c floxed allele to Six2TGC/+ CRE strain.
To examine the acute response of testosterone, we injected testosterone to adult castrated and ovariectomized mice and collected kidneys 24 hours later for bulk RNA-seq. To compare the mechanisms of Ar in regulating sex differences systemetically or locally in kidney and liver, we obtained bulk RNA-seq for kidneys and livers from ubiquitous, nephron-specific and hepatocyte-specific knockout of Ar by Sox2CRE/+, Six2TGC/+ and Albumin-CRE mouse strain respectively.

overall_design: Total RNA were collected for RNA-seq from minced 1) kidneys of C57BL/6J (Jackson Laboratory) at postnatal age 0, 2, 4, 8 and 79 weeks old; 2) kidneys of wild type C57BL/6NCrl mice (Charles River Laboratory), and those underwent castration or ovariectomy at around 3 weeks old that were injected with testosterone or oil control at 8~11 weeks old; 3) kidneys of adult conditional knockout by nephron-specific CRE strain Six2TGC/+ for Ar, Tbx10 and Neurog2 ; 4) kidneys and livers from ubiquitous removal of Ar by Sox2-CRE strain; 5) livers of hepatocyte-specific removal of Ar by Albumin CRE for both sexes.

first: Andrew

last: McMahon


title: Effects of 3-HAA on HCC by regulating the heterogeneous macrophages—A single-cell RNA-seq analysis

city: Hangzhou

first: Xue

last: Chen

state: Zhejiang

address: No.79, Qingchun Road, Shangcheng Distric

department: The First Affiliated Hospital

institute: Zhejiang University

summary: CyTOF data showed that 3-HAA significantly increased the percentage of F4/80hiCX3CR1loKi67loMHCIIhi macrophage and decreased the percentage of F4/80loCD64+PD-L1lo macrophages. scRNA-seq analyses demonstrated that 3-HAA administration was proved to regulate the function of M1 macrophages, M2 macrophages, and proliferating macrophages.

overall_design: We developed an orthotopic HCC model and administration with 3-HAA by intraperitoneal injection. Furthermore, cytometry by time-of-flight (CyTOF) and single-cell RNA sequencing (scRNA-seq) analyses were carried out to define the immune landscape of HCC.

first: Chen

last: Xue

first: Xinyu

last: Gu

first: Qiuxian


title: Effect of SX-682 treatment on gene expressions of three murine cell lines.

city: Nashviile

first: Ann

last: Richmond

state: TN

address: 2220 Pierce Avenue

department: Department of Pharmacology and Dermatology

institute: Vanderbilt University School of Medicine

summary: To identify tumor-specific transcriptional changes following SX-682 treatment, we performed RNA sequencing on each of the MelanA, B16F0, and B16F10 cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for each of the MelanA, B16F0, and B16F10 cell lines treated with SX-682 versus non-treatment controls.

first: Jinming

last: Yang

first: Kensey

last: Bergdorf

first: Qi

first: Xiao


title: mRNA expression analysis in primary renal tubular cells.

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

institute: RWTH Aachen University Medical School

summary: Activation of hypoxia-inducible transcription factors (HIF) leading to expression of hundred of target genes is a fundamental mechanism in acute and chronic kidney disease mediating protective but also possibly harmful effects. Furthermore, dysregulation of the HIF pathway in chronic kidney disease causes renal anemia through insufficient induction of erythropoietin (EPO) in interstitial cells. Hence, pharmacological compounds to treat renal anemia by stabilizing HIF have recently been introduced to the clinical practice. RNA-seq analysis was performed in primary renal tubular cells to analyse the effect of HIF stabilization on the expression of pathogenic Mucin1 (MUC1) variants. This study links the regulation of the kidney-disease gene MUC1 with the HIF-pathway in renal tubular cells.

overall_design:
This study consists of RNA-seq samples from five individuals.
>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Johannes

last: Schödel

first: Stephanie

last: Naas


title: Effect of CXCR2 knockout on gene expression of BRAFV600E/PTEN-/- mice

summary: To elucidate the mechanism by which CXCR2 perturbation in melanocytes could alter initiation and growth of BrafV600E/Pten-/- melanoma, we examined the transcriptome of tumors arising in BrafV600E/Pten-/-/Cxcr2WT (n=7) and BRAFV600E/PTEN-/-/CXCR2-/- (n=8) mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data between BRAFV600E/PTEN-/-/CXCR2-/- and BrafV600E/Pten-/-/Cxcr2WT mice.


title: Effect of SX-682 on gene expression for BrafV600E/PTEN-/- mice.

summary: To evaluate the effect of the dual CXCR1/CXCR2 inhibitor SX-682 on tumor growth, BrafV600E/PTEN-/- mice were fed with either SX-682 chow (0.756 g/kg of SX-682, Syntrix Pharmaceuticals, Inc) or control chow for RNA-seq analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BrafV600E/PTEN-/- mice treated with SX-682 versus control.


title: Effect

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: Effect of CXCL1 and CXCL1 with SX-682 on gene expression for human epidermal melanocytes (NHEM) cells.

summary: To gain insight into how CXCL1 activation of CXCR2 regulates the expression of stemness and differentiation markers, RNAseq analysis was performed on normal human epidermal melanocyte (NHEM) cultures treated with CXCL1 or with CXCL1 and SX-682.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NHEM cells treated with CXCL1 or CXCL1 plus SX-682 to NHEM cells containing vehicle.


title: Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics

city: St. Louis

first: Dennis

last: Zhu

state: MO

address: 660 South Euclid Avenue

institute: Washington University

summary: To examine the role of the essential transcription factor CarD in regulating gene expression in Mycobacterium smegmatis, we performed

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Mycobacterium smegmatis cells expressing mutant alleles of the CarD protein (R25E, K125E, I27W) versus a strain expressing WT CarD.

middle: X

first: Christina

last: Stallings


title: ChIPseq analysis of changes in binding of TFCP2L1 antibody in B16F0 cells in response to SX-682 treatment.

summary: To define the activity of TFCP2L1 following CXCR2 perturbation, we performed chromatin immunoprecipitation and sequencing analysis (CHIPseq) on B16F0 tumorigenic melanoma cells following treatment with vehicle or SX-682.

overall_design: ChIPseq data for mouse melanoma B16F0 cells treated with SX-682 or DMSO control, and DNA is pulled down with TFCP2L1 antibody or IgG isotope control.

first: Weifeng

last: Luo

first: Mariso

last: Ramirez


title: Characterization of a robust mouse model for heart failure with preserved ejection fraction

city: St Louis

first: Tiandao

last: Li

address: 4444 Forest Park Ave

summary:
Heart failure with preserved ejection fraction (HFpEF) is a clinical syndrome with multisystem organ dysfunction in which patients develop symptoms of HF as the result of high left ventricular (LV) diastolic pressure
Continuous infusion of angiotensin II and phenylephrine (AngII/PE) demonstrates a strong HFpEF phenotype
RNAseq data demonstrate activation of pathways leading to myocardial metabolic changes, activation of ECM deposition, microvascular rarefaction, and pressure and volume related myocardial stress

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the whole LV myocardium in WT C57Bl6J/129X1 hybrid mice infused with NaCl or AngII/PE for 3 days

first: David

last: Ornitz

first: Dzmitry

last: Matsiukevich


title: Alterations of ribosomal RNA pseudouridylation in human breast cancer

city: Trento

first: Erik

last: Dassi

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

summary: RNA modifications are key regulatory factors for several biological and pathological processes. They are abundantly represented on ribosomal RNA (rRNA), where they contribute to regulate ribosomal function in mRNA translation. Altered RNA modification pathways have been linked to tumorigenesis as well as to other human diseases. In this study we quantitatively evaluated the site-specific pseudouridylation pattern in rRNA in breast cancer samples exploiting the RBS-Seq technique involving RNA bisulfite treatment coupled with a new NGS approach. We found a wide variability among patients at different sites. The most dysregulated positions in tumors turned out to be hypermodified with respect to a reference RNA. As for 2’O-methylation level of rRNA modification, we detected variable and stable pseudouridine sites, with the most stable sites being the most evolutionary conserved. We also observed that pseudouridylation levels at specific sites are related to some clinical and bio-pathological tumor features and are able to distinguish different patient clusters. This study is the first example of the contribution that newly available high-throughput approaches for site specific pseudouridine detection can provide to the understanding of the intrinsic ribosomal changes occurring in human tumors.

overall_design: RBS-seq of 77 bisulfite-treated and untreated breast cancer samples and 5 reference samples

first: Lorenzo

last: Montanaro

first: Chiara

last: Barozzi


title: Effect of Peripheral Cellular Senescence on Brain Aging and Cognitive Decline

city: Gainesville

first: Thomas

middle: C

last: Foster

state: FL

address: 1149 S Newell Dr.

department: Neuroscience

institute: University of Florida

summary: We test the idea that peripheral cellular senescence is a major driver of age-related cognitive impairment, such that treatment with the brain impermeable senolytic, ABT-263, can preserve cognition and markers of brain aging thought to underlie cognitive decline. Male F344 rats were treated from 12-18 months of age with quercetin + dasatinib or ABT-263 or vehicle and were compared to young (6 month). Senolytic treatments had similar effects in decreasing peripheral markers of senescence and the senescence-associated secretory phenotype (SASP), including plasma levels of several cytokines, rescued memory and hippocampal synaptic transmission, and decreased expression of immune response genes in the dentate gyrus (DG). Across senolytic treatment groups, differential DG gene expression was observed for cellular senescence and pathways linked to senescence, including negative regulation of cell death, ribosomes, and microglial activation consistent with differential access of dasatinib and ABT-263 to the brain. Finally, both senolytic treatments preserved the blood-brain barrier suggesting that leakage of clinically significant amounts of ABT-263 into the brain is unlikely. The results indicate that preserved cognition was due to removal of peripheral senescent cells, decreasing systemic inflammation that normally drives neuroinflammation, BBB breakdown, and impaired synaptic function.

overall_design: Transcriptional profiles were analyzed in the DG sub-region of hippocampus from rats belonging to various groups: young (YNG, n = 10), aged vehicle (AV, n = 12), Aged + DQ (ADQ, n = 11), Aged + ABT-263 (AA, n = 11) treated rats.

first: Vivekananda

last: Budamagunta

first: Ashok

last: Kumar

first: Asha

last: Rani

first: Linda

last: Bean

first: Sahana

last: Sindhu

first: Yang

first: Daohong

last: Zhou


title: Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts [RNA-seq]

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: The airway epithelial cell line, 16HBE14o-, is an important cell model for studying airway disease. 16HBE14o- cells were originally generated from primary human bronchial epithelial cells by SV40-mediated immortalization, a process that is associated with genomic instability through long-term culture. Here we explore the heterogeneity of these cells, with respect to expression of the cystic fibrosis transmembrane conductance regulator (CFTR) transcript and protein. We isolate clones of 16HBE14o- with stably higher and lower levels of CFTR in comparison to bulk 16HBE14o-, designated CFTRhigh and CFTRlow. Detailed characterization of the CFTR locus in these clones by ATAC-seq and 4C-seq showed open chromatin profiles and higher order chromatin structure that correlate with CFTR expression levels. . Transcriptomic profiling of CFTRhigh and CFTRlow cells showed that the CFTRhigh cells had an elevated inflammatory/ innate immune response phenotype. These results encourage caution in interpreting functional data from clonal lines of 16HBE14o- cells, generated after genomic or other manipulations.

overall_design: Comparative gene expression profiling of 12 RNA-seq datasets (3 replicates each of 2 16HBE14o- CFTR-high clones or 2 16HBE14o- CFTR-low clones)

first: Jenny

last: Kerschner

first: Alekh

last: Paranjapye


title: Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts [4C-seq]

overall_design: Analysis of the 3D chromatin architecture with 4C-seq at the CFTR locus to determine interaction frequencies between elements in 16HBE14o- CFTR-high vs 16HBE14o- CFTR-low cells


title: Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts.


title: Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts [ATAC-seq]

overall_design: ATAC-seq to examine open chromatin in single cell clones isolated from bulk 16HBE14o- cells


title: Digital Spatial Profiling of immuno-oncology proteins in mouse hepatocellular carcinoma xenograft treated with THIO-based combination immune therapie

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: THIO (6-thio-dG) is a nucleoside analog that induces telomeric DNA damage and triggers activation of anti-tumor immunity in several cancer types such as lung and colorectal cancers. To evaluate its effect in hepatocellular carcinoma (HCC), THIO in combination with the current standard care first-line therapy for advanced HCC, anti-PD-L1 and anti-analyze, was tested in immunocompetent mice subcutaneously implanted with syngeneic HCC cell line (Hep55.1c). Formalin-fixed paraffin-embedded (FFPE) tumor tissues were collected after the treatment, and therapeutic modulations of the tumor immune landscape were assessed with Digital Spatial Profiling of 38 immuno-oncology-related proteins in region of interest (ROI) and intra-ROI segments enriched for T cells, other leukocytes, and HCC/stromal cells.

overall_design: Immunocompetent black 4 mice were subcutaneously implanted with a syngeneic mouse HCC cell line (Hep55.1c). After tumor nodules were formed, mice were treated with vehicle control, THIO, anti-PD-L1 + anti-VEGF, or anti-PD-L1 + anti-VEGF + THIO (n=1 per group). Mice were sacrificed at the end of the treatment, and FFPE tumor tissue blocks were generated. One representative animal was selected for each treatment group, and subjected to Digital Spatial Profiling of 38 immuno-oncology-related proteins. Immunofluorescent (IF) staining of morphology markers (CD3, CD45, pan-cytokeratin [Pan-CK]) was first performed, and based on the IF and H&E staining, region of interest (ROI) was defined in each tissue section. Within each ROI, segments were subsequently selected based on the IF staining enriched for T cells (CD3+), other leukocytes (CD3-/CD45+), and HCC/stromal cells (CD3-/CD45-/Pan-CK+/-), and abundance of the 38 immuno-oncology-related proteins was determined by using the GeoMx Digital Spatial Profiler (NanoString).

first: Naoto

last: Kubota

first: Ilgen

last: Ogunrinde

first: Jerry

last: Shay


title: Decoding the Genomic regions that R-loop distributed associated with A3B expression

city: Shanghai

first: Nestor

last: Zhang

address: Dongchuan Road

institute: Shanghai Jiao Tong University

summary: R-loop CUT&Tag in OMM2.3 cells with A3B knocked down

overall_design: R-loop CUT&Tag was implemented in A3B knockdown and control OMM2.3 cells transfected with V5 tagged RNASEH1_D210N plasmid.

first: Chunyan

last: Zong

first: Zhe

first: Li

last: Gao

first: Jianfeng

last: Shen


title: Cyproconazole induces altered expression of adipogenic and osteoblast genes in zebrafish

city: Bloomington

first: Maria

last: Bondesson

state: IN

address: 2401 N Milo Sampson Ln

department: Department of Intelligent Systems Engineering

institute: Indiana University

summary: To investigate gene expression changes induced by the fungicide cyproconazole that affect skeletal development in zebrafish, zebrafish embryos were treated with cyproconazole followed by mRNA sequencing.

overall_design: Comparative gene expression profiling between untreated control and cyproconazole treated zebrafish embryos.

first: Savini

last: Thrikawala

first: Fahmi

last: Mesmar

first: Cecilia

last: Williams


title: RNA-seq of T cell with/without lycorine treatment in vitro and RNA-seq of T cell in spleen and allograft

city: NEW BRUNSWICK

first: Xiaosheng

last: Tan

state: NJ

address: 89 French St

institute: RUTGERS

summary: To examine the transcriptomic changes of T cells in response to lycorine, and to compare the transcriptomic changes in spleen T cell and allograft-infiltrating T cell.

overall_design: In vitro experiment, we stimulated mice or human T cells with anti-CD3/anti-CD28 in the presence/absence of lycorine. In vivo experiment, we purified  CD4+ and CD8+ T cell from spleen and allograft.

first: Gang

last: Chen


title: Streptozotocin induces renal proximal tubular injury through p53 signaling activation

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

summary: Streptozotocin (STZ) is an anti-cancer drug that is primarily used to treat neuroendocrine tumors (NETs) in clinical settings and develop type 1 diabetes rodent models in experimental fields. STZ is incorporated into cells through the glucose transporter, GLUT2, which is primarily expressed in pancreatic β-cells or proximal tubular epithelial cells in the kidney. However, its cytotoxic effects on kidney cells have been underestimated and the underlying mechanisms remain unclear. We herein demonstrated that DNA damage and subsequent p53 signaling were responsible for the development of STZ-induced tubular epithelial injury. We detected tubular epithelial DNA damage in NET patients treated with STZ. Unbiased transcriptomics of tubular epithelial cells in vitro showed the activation of the p53 signaling pathway by STZ. STZ induced DNA damage and activated p53 signaling in vivo in a dose-dependent manner, resulting in reduced membrane transport. The localization of STZ-induced kidney injury was limited to within the kidney cortex, which was independent of blood glucose. The pharmacological inhibition of p53 and sodium-glucose transporter 2 (SGLT2) mitigated STZ-induced epithelial injury. However, the cytotoxic effects of STZ on pancreatic β-cells were preserved in SGLT2 inhibitor-treated mice. The present results demonstrate the strong proximal tubular-specific cytotoxicity of STZ and the underlying mechanisms in vivo, which may be ameliorated by a SGLT2 inhibitor pretreatment. Since the cytotoxic effects of STZ against β-cells were not impaired by dapagliflozin, a pretreatment with a SGLT2 inhibitor has potential as a preventative remedy for kidney injury in NET patients treated with STZ.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control NRK-52E cells and STZ-treated NRK-52E cells.


title: Bulk RNA-seq of eyes isolated from wildtype and Stra6 knockout mice maintained on either a vitamin A sufficient or deficient diet

first: Johannes

last: von Lintig

address: 2109 Adelbert Road

department: Pharmacology

summary: Vitamin A deficiency is detrimental to the visual system throughout the lifecycle. Abundant expression of the retinoid transporter STRA6 in the retinal pigment epithelium (RPE) and homeostatic blood levels of retinol binding protein ensure the eyes are adequately supplied with the nutrient. STRA6 deficiency interrupts the supply pathway, but vitamin A in chylomicrons compensates for its failure. However, dependency on the chylomicron delivery pathway makes the eyes of STRA6-deficient mice vulnerable to dietary vitamin A deprivation. How the eyes adapt to vitamin A status has not been studied in molecular detail, and therefore we used RNA-seq to focus on diet-induced changes. We observed that mild ocular vitamin A deficiency was linked to an increase in transcript abundance levels of genes coding for proteins of stress pathways and a decrease in levels of transcripts coding for proteins of pathways of visual sensitivity and perception. These changes correlate with a loss of visual sensitivity and accumulation of fluorescent debris in the retina. Additionally, severe vitamin A deficiency decreased the transcript levels of genes involved in cell adhesion, cell differentiation, and transport of small molecules pathways. This response correlated with alterations in epithelial cell morphology and a “leaky” RPE barrier. Together, our analyses of STRA6-deficient mice define adaptive responses associated with ocular vitamin A status and reveal a previously unknown role of STRA6 in the maintenance and functioning of the outer blood-retina barrier.

overall_design: Bulk RNA-Seq experiments were carried out using the RPE-choroid tissue isolated from wildtype and Stra6 knockout mice fed a vitamin A sufficient or deficient diet for 12 weeks. Five biological replicates were analyzed for each of four conditions (two genotypes; two diets per genotype). The wildtype, vitamin A sufficient samples were used as the control group.

first: J

last: Moon

first: G

last: Zhao

first: E

last: Jankowsky


title: Decoding the Genes that A3B regulated

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for A3B in OMM2.3 and 92.1 cells.

overall_design: A3B ChIP-seq was implemented in OMM2.3 and 92.1 cells with negative control IgG.


title: Gastric cancer cells treated with exosomes derived from Fusobacterium nucleatum infected MKN-28 cells [RNA-seq]

city: Jinan

first: Xin

state: Shandong

address: 107 Wenhua Xi Road

institute: Qilu Hospital, Shandong University

summary: To investigate the role of Fusobacterium nucleatum (Fn) in the development of gastric cancer, we extracted exosomes from the culture supernatant of MKN-28 cells treated with Fn or PBS, co-cultured them with AGS cells, and analyzed their RNA-seq data for gene expression profiling.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AGS cells treated with Fn49256-GCEx or GCEx.

first: Yiwei

last: Xin

first: Xinru

last: Gui

first: Yi


title: Prenatal exposure to benzo[a]pyrene depletes ovarian reserve and masculinizes embryonic ovarian germ cell transcriptome transgenerationally I

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

institute: MGH Cancer Center

summary: People are exposed to polycyclic aromatic hydrocarbons, like benzo[a]pyrene (BaP), via inhalation of particulate matter air pollution and ingestion of grilled and smoked foods. Prenatal exposure to BaP destroys germ cells in ovaries, causing earlier onset of ovarian senescence post-natally. Developing testes are affected at higher doses than ovaries. However, it is not known if adverse effects are transmitted to subsequent generations. We orally dosed pregnant female mice (F0) with 0.033, 0.2, or 2 mg/kg-day BaP or vehicle from embryonic day (E) 6.5-11.5 (F1 offspring) or E6.5-15.5 (F2 and F3). Ovarian germ cell and follicle numbers were significantly decreased in F3 females at all doses of BaP; testicular germ cells were not affected. E13.5 germ cell RNA-sequencing revealed significantly increased expression of male-specific genes in female germ cells across generations and BaP doses. Our study demonstrated that F0 BaP exposure partially disrupted sexual identity of female germ cells transgenerationally.

overall_design: Whole genome bisulfite sequencing of FACS-enriched mouse primordial germ cells with or without gestational exposure to banzo[a]pyrene.

first: Jinhwan

last: Lim

first: Ulrike

last: Luderer


title: Gastric cancer cells treated with exosomes derived from Fusobacterium nucleatum infected MKN-28 cells [miRNA-seq]

last: Zhang

summary: To investigate the role of Fusobacterium nucleatum (Fn) in the development of gastric cancer, we extracted exosomes from the culture supernatant of MKN-28 cells treated with Fn or PBS, co-cultured them with AGS cells, and analyzed their miRNA-seq data for gene expression profiling.

overall_design: Comparative gene expression profiling analysis of miRNA-seq data for AGS cells treated with Fn49256-GCEx or GCEx.


title: Prenatal exposure to benzo[a]pyrene depletes ovarian reserve and masculinizes embryonic ovarian germ cell transcriptome transgenerationally

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

overall_design: Refer to individual Series


title: Prenatal exposure to benzo[a]pyrene depletes ovarian reserve and masculinizes embryonic ovarian germ cell transcriptome transgenerationally II

overall_design: Whole genome bisulfite sequencing of FACS-enriched mouse primordial germ cells with or without gestational exposure to banzo[a]pyrene: Repeated Experiment


title: Comparative RNA sequencing of the jejuna of two lines of chickens divergently selected for antibody response to sheep red blood cells, with and without antigen exposure

city: Raleigh

first: Shelly

middle: Jones

last: Nolin

state: NC

address: 2711 Founders Dr

department: Prestage Dept of Poultry Science

institute: NC State University

summary: Two lines of White Leghorn chickens have been continuously divergently selected for high (HAS) or low (LAS) 5 day post injection antibody titer to injection with sheep red blood cells (SRBC) for over 40 generations.  Much remains to be understood about their antibody response phenotypes, therfore we chose to sequence the transcriptomes of the jejunum from individuals of the two lines which had (HASI/LASI) and had not (HASN/LASN) been injected with SRBC to examine differences in gene expression related to divergent selection and antibody response.

overall_design: Investigate differential jejunum gene expression from 24 chickens total: 6 each HASN, LASN, HASI, and LASI, to compare differences between lines with regard to genetic selection (HAS vs LAS) and within lines in response to antigen exposure (I vs N)

first: Christopher

last: Ashwell

first: Frank

last: Edens

first: Paul

last: Siegel


title: Transcriptomic analyzes of bone biopsies from patients with renal osteodystrophy (ROD)

city: Chicago

first: Valentin

last: David

state: Illinois

address: 320 E Superior Street

department: Medicine

institute: Northwestern University

summary: RNAseq of bone biopsies of healthy patients and patients with renal osteodystrophy.

overall_design: Total RNA was isolated from transiliac bone biopsies of patients with renal osteodystrophy and healthy patients and submitted for RNAsequencing.

first: Aline

last: Martin

first: Rosa

last: Moyses

first: Marta

last: Calle


title: Sex-based comparison of CD4+ T cell DNA methylation patterns in SLE reveals pro-inflammatory epigenetic changes in men

city: Pittsburgh

first: Amr

middle: H

last: Sawalha

state: PA

address: 4401 Penn Avenue

institute: University of Pittsburgh

type: Methylation profiling by genome tiling array

summary: Male patients with systemic lupus erythematosus (SLE) experience severe disease compared to female patients, despite the disease being more prevalent in females.  For the time, we compared genome-wide differential methylation in CD4+ T cells between male (n=12) and female (n=10) SLE patients.

overall_design: Illumina Infinium MethylationEPIC array of genomic DNA from CD4+ T cells extracted from peripheral blood mononuclear cells of 12 male SLE patients and 10 female SLE patients.

first: Mustafa

last: Ali

first: Patrick

last: Coit


title: Role of HNF4a in osteoblasts [RNA-seq]

summary: Murine osteoblast-like cell line MC3T3-E1 subclone 4 (ATCC CRL-2593) (ATTCC, Manassas, USA) were stably transfected using 4D-Nucleofector System (Lonza, Basel, Switzerland) to generate cells that overexpress Hnf4α1, Hnf4α2 or an empty vector (Ctr). RNAseq and differential expression analyzes were used to highlight the importance of HNF4a1 and HNF4a2 in osteoblastogenesis

overall_design: mRNA profiles of differentiated MC3T3 osteoblasts overexpressing HNF4a1 or HNF4a2

last: Martinez Calle


title: The role of ELF3 in GIS-NEC and SCLC

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

summary: Genome-wide profiling of open chromatin, histone modifications and ELF3 binding site by ATAC-seq and CUT&Tag assay in ECC4, A99 and DMS53.

overall_design: ATAC-seq and CUT&Tag were perfomed for GIS-NEC and SCLC cell lines.

first: Hidenori

last: Tanaka


title: Role of HNF4a in bone

summary: RNAseq of osteocyte and osteoblasts enriched  bone fraction  from the tibiae of 6 week-old male mice with a conditional  deletion of Hnf4a in osteoblasts and and WT littermates.

overall_design: Hnf4αflox/+ (B6.129X1(FVB)-Hnf4αtm1.1Gonz/J) and osteocalcin-Cre (B6.FVB-Tg(BGLAP-cre)1Clem/J) mice were crossed to generate Hnf4αflox/flox (WT) and Hnf4αflox/flox-Cre (Hnf4αcKO). At 6 weeks, mice were sacrificed, and tibiae were excised, epiphyses  removed and bone marrow flushed. Total RNA was isolated and submitted for RNAsequencing.


title: Mettl3 mediated m6A methylation in human bronchial epithelial cells exposed to cigarette smoke extract

city: Quanzhou City

first: Yaping

state: Fujian Province

address: No. 34, Zhongshan North Road

institute: The Second Affiliated Hospital of Fujian Medical University

summary: To investigate the mRNA m6A modification profiling in 16-HBE cells with or without siRNA-mediated Mettl3 knockdown exposed to cigarette smoke extract, we performed m6A MeRIP-seq with the total RNA extracted from two samples.

overall_design: m6A MeRIP-seq of 16-HBE cells with or without siRNA-mediated Mettl3 knockdown exposed to cigarette smoke extract, two samples, each sample includes three replicates.

first: Lixing

last: Wang

first: Xiangdong

first: Yiming

last: Zeng


title: Role of HNF4a in osteoblasts [ChIP-seq]

summary: Murine osteoblast-like cell line MC3T3-E1 subclone 4 (ATCC CRL-2593) (ATTCC, Manassas, USA) were stably transfected using 4D-Nucleofector System (Lonza, Basel, Switzerland) to generate cells that overexpress Hnf4α1, Hnf4α2 or an empty vector (Ctr). ChIPseq analyzes were used to highlight the importance of HNF4a1 and HNF4a2 in osteoblastogenesis.

overall_design: We  immunoprecipitated HNF4α in samples isolated from cells overexpressing Hnf4α1, Hnf4α2 or Ctr MC3T3 cultures using two different polyclonal antiHNF4α antibodies purchased from 1) Aviva or 2) Abcam. In parallel, we generated two stable cell lines overexpressing Hnf4α2 coupled with a carboxy (Hnf4α2C-Halo-Tg) or amino (Hnf4α2N-Halo-Tg) terminal Halo tag and used an anti-Halo antibody to IP these cells. Cells were cultured into osteoblastic medium for 21 days. Cell cultures  were subjected to ChIP assay following the protocol provided by manufacturer (SimpleChIP Plus Enzymatic Chromatin IP Kit with magnetic beads, Cell Signaling Technology, Danvers MA, USA). Briefly, protein-chromatin crosslinking was carried out in cell medium containing 1% formaldehyde (Sigma-Aldrich, St. Louis, MO, USA) at room temperature for 10 minutes. After stopping the crosslinking reaction using 10X glycine for 5 min, cells were washed 3 times in PBS and scraped into cold PBS containing protease inhibitor cocktail. Collected cells were centrifuged at 2000xg for 5 min at 4C. After nuclei extraction, chromatin was digested with micrococcal nuclease, and nuclear membranes were disrupted by sonication. Lysates were clarified by centrifugation at 9400xg for 10 min at 4C. Per IP reaction, 10 µg of digested, cross-linked chromatin were incubated with anti-HNF4α antibodies for immunoprecipitation: 5 µg of OASG03561 (Aviva Systems Biology, San Diego, CA, USA), 10 µg of ab41898 (Abcam, Cambridge, UK), or 10 µg of anti-Halotag antibody (G9281, Promega, Madison, WI, USA) for 4h at 4C. Then, 30 μl of Dynabeads Protein G Magnetic Beads was added to the IP chromatin solution and incubated for 2h at 4C. After several washing steps using buffers with ascending NaCl concentrations, chromatin was eluted, and the supernatant was incubated with proteinase K overnight at 65C to reverse crosslinking. Finally, DNA fragments were purified using silica columns. For each condition, we used three separate biological replicates and one input control. The total DNA library for each individual sample was prepared using the TruSeq ChIP-Seq Library Prep Kit (Illumina, San Diego, CA), and the bar-coded cDNA libraries were sequenced for 100 bp single reads using  the Illumina Hiseq 4000. The ENCODE pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) v 1.7.1 was used to identify naive overlapping peaks in each experiment. Enriched regions were consolidated based on their representation in two or more experiments as follow: HNF4α1/2 peaks if detected in samples expressing Hnf4α1 and Hnf4α2; HNF4α1 peaks if detected in two or more samples overexpressing Hnf4α1 or Ctr cells; HNF4α2 peaks if detected in two or more samples overexpressing Hnf4α2 or Ctr cells.


title: Effect of SRMS deficiency on gene expression upon cisplatin treatment in human ovarian cancer cells

city: San Antonio

first: Yunhan

last: Jiang

address: 7703 Floyd Curl Dr

institute: University of Texas Health Science Center at San Antonio

summary: This study was designed to evaluate the transcriptomic alterations upon SRMS deficiency after cisplatin exposure in a human ovarian cancer cell line.

overall_design: Ovarian cancer ES-2 cells expressing control vector or SRMS shRNA were treated with 15μM cisplatin for 8 hours. The cancer cells were then applied for RNA isolation and RNA sequencing. Each sample have three replicates.

first: Yizhu

last: Lin

first: Lingtao

last: Jin


title: Gastric cancer cells treated with exosomes derived from Fusobacterium nucleatum infected MKN-28 cells

first: Xin

last: Zhang


title: RNA-seq for miR-205 inducible hair follicle stem cells and ScRNAseq for miR-205 inducible back skin samples

first: Rui

last: Yi

address: 765 N FAIRBANKS CT

department: Pathology, Feinberg School of Medicine


title: Functional analysis QSER1

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

summary: In this study, we found that QSER1 is a generic anti-apoptosis factor suppressing the p53 target apoptotic genes irrespective of p53 status.

overall_design: NOT PROVIDED; REQUESTED

first: Chengqi

first: Xiru

last: Zhao


title: Transcriptome analysis in hair follicle stem cells after miR-205 induction in mouse

summary: Through phenotypical study, we found that miR-205 can promote hair growth. The goals of this study is to identify direct targets of miR-205 in hair follicle stem cells and determine whether and how miR-205 promotes hair growth by activating hair follicle stem cell.

overall_design: Examination of transcriptome in hair follicle stem cells extracted from mouse adult back skin after 2-day miR-205 induction.

first: Jingjing


title: Fmo5(-/-) mouse: liver transcriptomics

city: London

first: Elizabeth

last: Shephard

address: Gower Street

institute: University College London

summary: We report the consequences of the disruption of the Fmo5 gene on transcription of genes in liver.

overall_design: Comparison of liver gene expression in wild-type and Fmo5(-/-) mice

first: Ian

last: Phillips

first: Sunil

last: Veeravalli


title: Effect of depletion of A3B on gene expression of 92.1 cells and overexpression of A3B on gene expression of MEL290 cells

first: Nestor

summary:
To investigate the function of A3B, we established 92.1 cell lines with A3B knocked down and MEL290 cell lines with A3B overexpression.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cell lines with two replicates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 92.1 cell lines (shCTRL and shA3B) and MEL290 cell lines (NC and A3B OE).

first: Chunyan

last: Zong

first: Zhe

first: Jianfeng

last: Shen


title: Prenatal exposure to benzo[a]pyrene depletes ovarian reserve and masculinizes embryonic ovarian germ cell transcriptome transgenerationally [RNA-seq]

first: Toshihiro

last: Shioda

state: MA

department: Center for Cancer Research

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS-enriched mouse primordial germ cells with or without gestational exposure to banzo[a]pyrene.

first: Jinhwan

last: Lim

first: Ulrike

last: Luderer


title: The effect of diet and breed on global gene expression profiles of animals divergent for RFI

city: Meath

first: Clare

last: Mckenna

address: Dunsaney

department: Animal Bioscience

country: Ireland

institute: Teagasc

summary: The selection of cattle with high feed efficiency is of paramount importance with regard to reducing feed costs in the beef industry. Developing predictive biological markers specifically for improved feed efficiency is an attractive alternative to direct measurement on large numbers of animals.Evidence is provided that, effects of RFI on gene expression in muscle of beef cattle are not consistent across breed type or dietary phase. These novel observations challenge the practicality of selecting and breeding for low RFI animals across different diets and stages of development. Perhaps, future research should be directed at utilising different diets to harness the full genetic potential of animal based on breed or stage of maturity. Further to this, evidence is provided from our own work and that of others that less efficient HF steers consuming zero grazed grass are under increased stress as demonstrated by an upregulation of immune function in these animals.

overall_design: Residual feed intake was calculated in in Charolais (CH) and Holstein Freisan (HF) under ad libitum feeding conditions aross varying diets, which were subsequently ranked, within breed and diet, as high (n=12) or low (n=12) residual feed intake. RNA sequencing was performed on liver and skeletall muscle biopsies from high and low residual feed intake animals in order to identify differentially expressed genes that may be associated with this trait.

first: David

middle: A

last: Kenny

first: Richard

middle: K

last: Porter

first: Sinead

last: Waters

first: Gordon

last: Blackshields


title: Mitochondrial transfer disrupts mTORC1/Akt signaling modulating biogenesis and respiration

city: Madrid

first: Aurora

middle: Gomez

last: Duran

state: Madrid

address: Maria maeztu

department: Molecular Biomedicine

country: Spain

institute: Centro de Investigaciones Biologicas

summary: Mitochondrial DNA (mtDNA) mutations are a major cause of maternally-inherited disease and have no treatment. Prevention strategies are critically important, but current clinical approaches are far from satisfactory. Legislation has changed in the UK to permit the development of mitochondrial transfer in human embryos, but major concerns have been raised about the mis-match of nuclear and mtDNA from ‘three parents’, with late sequelae being passed through the germ-line to subsequent generations. Matching donor and recipient mtDNA haplogroups is the proposed solution, but the effects of ‘haplogroup matching’ have not been tested experimentally. Here we show major changes in the cellular transcriptome both between and within the major mtDNA haplogroups when mitochondria are transferred between cells on a fixed nuclear genetic background. Larger differences were seen between phylogenetically related sub-haplogroups J1 and J2 which differ by only six nucleotides, than between the major haplogroups and known pathogenic mtDNA mutations. mtDNA transfer altered key cell signaling pathways, most notably the mTOR/Akt and the inflammatory cascade. This affected mitochondrial biogenesis, oxygen consumption, and ATP synthesis, and was blocked by rapamycin. These findings identify a key mediator in retrograde nuclear-mitochondrial signaling which is sensitive to subtle changes in mtDNA sequence. Given the established role of mTOR in cancer, neurodegeneration, and metabolic disease, this provides a mechanism for the association between inherited mtDNA variants and common late onset diseases, and demonstrates unexpected and dramatic effects of mitochondrial transfer not corrected by close haplogroup matching.

overall_design: 2 cell lines per haplogroup were included plus the recipient cell (Rho0, 143B, osteosarcoma)

last: Gomez-Duran

first: Gavin

last: Hudson

first: Yaobo

last: Xu

first: Mauro

last: Santibanez-Koref

first: Eduado

last: Ruiz-Pesini

first: Patrick

middle: F

last: Chinnery


title: Germ cell-specific eIF4E1b regulates maternal mRNA translation to ensure zygotic genome activation

city: Bethesda

first: Guanghui

last: Yang

state: Maryland

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

summary:
Translation of maternal mRNAs is detected before transcription of zygotic genes and is essential for mammalian embryo development. How certain maternal mRNAs are selected for translation instead of degradation and how this burst of translation affects zygotic genome activation remain unknown. Using gene-edited mice, we document that the oocyte-specific eukaryotic translation initiation factor 4E family member 1b (eIF4E1b) is the regulator of maternal mRNA expression that ensures subsequent reprogramming of the zygotic genome. In oocytes, eIF4E1b binds to transcripts encoding translation machinery proteins, chromatin remodelers, and reprogramming factors to promote their translation in zygotes and protect them from degradation. The protein products are thought to establish an open chromatin landscape in one-cell zygotes to enable transcription of genes required for cleavage stage development. Our results define a program for rapid resetting of the zygotic epigenome that is regulated by maternal mRNA expression and provide new insights into the mammalian maternal-to-zygotic transition.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcript responses of lipid accumulation in Auxenochlorella pyrenoidosa to varying nitrogen deprivation

status: Public on Jun 06 2023

city: Shanghai

first: Liufu

last: Wang

address: No. 999, Huchenghuan Rd

institute: Shanghai Ocean University

summary: Varying levels of nitrogen deprivation can improve lipid accumulation differently in microalgae, whose underlying regulations are unknown. To investigate the related mechanisms, Auxenochlorella pyrenoidosa was exposed to 1.5, 1, 0.5 and 0 g/L sodium nitrate (NaNO3) for 5 days and RNA-seq were detected.

overall_design: The experimental design includes 1.5, 1, 0.5 and 0 g/L NaNO3 groups, which have three biological repetition. The 1.5 g/L NaNO3 group is the control group.

first: Xuxiong

last: Huang


title: Transcriptome Analysis of Diffuse Large B Cell Lymphoma Cells Inducibly Expressing MyD88 L265P Mutation Identifies Upregulated CD44, LGALS3, NFKBIZ, and BATF as Downstream Targets of Oncogenic NF-κB Signaling

city: Ostrava

first: Matous

last: Hrdinka

address: Syllabova 19

country: Czech Republic

institute: University of Ostrava

summary: In this study, we used a doxycycline (DOX) inducible gene expression system to introduce MyD88, a gene associated with lymphoma, into the U2932 lymphoma cell line. We performed a transcriptomic analysis (RNA-seq) to identify differentially expressed genes due to the MyD88 L265P oncogenic mutation. This study aimed to investigate the impact of MyD88 L265P oncogenic signaling on lymphoma cells by analyzing the transcriptomic response of model cell lines.

overall_design: To introduce MyD88 wt or L265P into the cells, we transduced the U2932 cell line with lentiviral particles containing the pLVX_TetOne inducible system. After 24 hours of induction with DOX hyclate, we harvested the cells and extracted the total RNA. At least 2 μg of total RNA was sent to Macrogen Europe for TruSeq stranded mRNA library generation and RNA-seq analysis on a NovaSeq 6000 Illumina platform. We used a total of 12 samples, with 3 samples for each condition (MyD88 wt -/+ DOX and MyD88 L265P -/+ DOX).

first: Marcello

last: Turi

first: Anjana

last: Anilkumar Sithara

first: Lucie

last: Hofmanová

last: Žihala

first: Dhwani

last: Radhakrishnan

first: Alexander

last: Vdovin

first: Sofija

last: Knápková

first: Tereza

last: Ševčíková

first: Zuzana

last: Chyra

first: Tomáš

last: Jelínek

first: Michal

last: Šimíček

first: Annamaria

last: Gullà

first: Kenneth

last: Anderson

first: Roman

last: Hájek

first: Matouš


title: Effect of combinatorial transcription factor overexpression on iPSC-derived endothelial cells

city: Cambridge

first: Raleigh

middle: Miller

last: Linville

address: 43 Vassar St

institute: Massachusetts Institute of Technology

summary: We aimed to investigate how transcription factors alter brain-specific and zonation-identity of endothelial cells. We used a dox-inducible lentivirus to increase expression of specific combinations of transcription factors expressed by human brain endothelial cells in iPSC-derived endothelial cell (iEC) monolayers. Using SMART-seq we compared gene expression profiles and benchmarked gene expression to iPSC-derived brain microvascular endothelial-like cells (iBMECs).

overall_design: iPSC-derived endothelial cells (iECs) were differentiated from WTC-ZO1 iPSC line and then transduced with an 'all-in-one' dox on lentivirus system.  Non-transduced iPSC-dervied endothelial cells and iPSC-derived brain microvascular endothelial-like cells (iBMECs) were used as a control.  Combinations of arterial (HEY1, PRDM16), capillary (LEF1, KLF2, TSC22D1, FOXP1), or venous (PPARD, FLI1, TSHZ2) transcription factors were utilized.

first: Linville

last: Raleigh

first: Heiman

last: Myriam


title: Transcriptome sequencing analysis of GADD45B and HOPX gene overexpression in human cutaneous melanoma

city: Changchun

first: Song

last: He

address: No.1977 Xinzhu Road, Lvyuan District, Changchun City, Jilin Province

institute: Jilin University

summary: We first overexpressed two genes, GADD45B and HOPX, in human malignant melanoma cells A375 cells, and then performed transcriptome sequencing. The related differential gene expression and the alteration of related signaling pathways were obtained by comparing with the control group. This study provides a reference and basis for the treatment of human melanoma.

overall_design: Examination of downstream gene expression and intrinsic mechanisms following overexpression of two genes in human malignant melanoma.

first: Bao

last: Yuan

first: Zhonghao

last: Ji

first: Yu

last: Ding


title: Neuroprotective protein ADNP-dependent histone remodeling complex promotes Th2 immune cell differentiation (scRNA-Seq)

first: Ana

last: Ferreira

address: Francis Crick Avenue, Cambridge Biomedical Campus

institute: MRC - Laboratory of Molecular Biology

summary: Type-2 immune responses are critical in tissue homeostasis, anti-helminth immunity and allergy. Th2 cells produce interleukin (IL)-4, IL-5 and IL-13 from the type-2 gene cluster under regulation by transcription factors (TFs) including GATA3. To better understand this system we performed CRISPR-Cas9 screens targeting 1131 TFs during Th2 cell differentiation. We discovered that ADNP is indispensable for immune reactions to allergen. Mechanistically, ADNP performs a previously unappreciated role in gene activation forming a critical bridge in the transition from pioneer TFs to chromatin remodelling by recruiting CHD4 and BRG1. Although GATA3 and AP-1 bound the type-2 cytokine locus in the absence of ADNP, they were unable to initiate histone acetylation or DNA accessibility, resulting in highly impaired type-2 cytokine expression. Similar ADNP-dependent regulation was observed for the Maf and Il4ra genes which are known regulators of Th2 differentiation. Our results demonstrate an important role for ADNP in promoting immune cell specialization.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cd4Cre versus Cd4CreAdnpfl/fl naïve T cells and  CD4+ST2+ T helper cells.

first: Aydan

last: Szeto

first: Paula

last: Clark

first: Alastair

last: Crisp

first: Patrycja

last: Kozik

first: Helen

middle: E

last: Jolin

first: Andrew

middle: J

last: McKenzie


title: Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.Cut&Tag]

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Using a combination of single-cell multi-omics, lineage tracing and functional assays, we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells (HECs) during zebrafish embryogenesis.

overall_design: Hematopoietic stem and progenitor cells (HSPCs) are considered as a heterogeneous population, but where and how HSPC heterogeneity occurs remain unclear. Here, we performed scRNA-seq and scATAC-seq with zebrafish 36 hpf VDA-derived kdrl+runx1-, kdrl+runx1+, and kdrl-runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish, we performed STRT-seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry- hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency, we performed scRNA-seq with the sorted ECs (kdrl+runx1-), HECs (kdrl+runx1+) and hematopoietic cells (kdrl-runx1+) from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC, we examined genome-wide spi2 binding by cut-tag assay in fli1a-flag-spi2-EGFP+ cells sorted from trunk region of Tg (fli1a-flag-spi2-GFP) embryos at 36 hpf.

first: Jun

last: Xia


title: Neuroprotective protein ADNP-dependent histone remodeling complex promotes Th2 immune cell differentiation (ChIP-Seq)

overall_design: ChIP-seq data comparing Cd4Cre with Cd4CreAdnpflox Th2 cells


title: Neuroprotective protein ADNP-dependent histone remodeling complex promotes Th2 immune cell differentiation (RNA-Seq)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Adnp sgRNA-targeted versus non-targeted Th2 cells.


title: Histone post translation modification differences during the Plasmodium schizont-to-ring transition [ChIP-seq]

first: Evelien

middle: M

last: Bunnik

address: 7703 Floyd Curl Dr.

department: Microbiology, Immunology, and Molecular Genetics

summary: Gene expression in malaria parasites is subject to various layers of regulation, including histone post-translational modifications (PTMs). Gene regulatory mechanisms have been extensively studied during the main developmental stages of Plasmodium parasites inside erythrocytes, from the ring stage following invasion to the schizont stage leading up to egress. However, gene regulation in merozoites that mediate the transition from one host cell to the next is an understudied area of parasite biology. Here, we sought to characterize gene expression and the corresponding histone PTM landscape during this stage of the parasite lifecycle through RNA-seq and ChIP-seq on P. falciparum blood stage schizonts, merozoites, and rings, as well as P. berghei liver stage merozoites. In both hepatic and erythrocytic merozoites, we identified a subset of genes with a unique histone PTM profile characterized by depletion of H3K4me3 in their promoter regions. These genes were upregulated in merozoites and rings, had roles in protein export, translation, and host cell remodeling, and shared a DNA motif. These results indicate that similar regulatory mechanisms may underlie merozoite formation in the liver and blood stages. We also observed that H3K4me2 was deposited in gene bodies of gene families encoding variant surface antigens in erythrocytic merozoites, which may facilitate switching of gene expression between different members of these families. Finally, H3K18me and H2K27me were uncoupled from gene expression and were enriched around the centromeres in erythrocytic merozoites, suggesting roles in the maintenance of chromosomal organization during schizogony. Together, our results demonstrate that extensive changes in gene expression and histone landscape occur during the schizont-to-ring transition to facilitate productive erythrocyte infection. The dynamic remodeling of the transcriptional program in hepatic and erythrocytic merozoites makes this stage attractive as a target for novel anti-malarial approaches that may have activity against both the liver and blood stages.

sample_organism:
Plasmodium berghei
Plasmodium falciparum

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone PTMs in Plasmodium falciparum schizonts, merozoites, and rings, and Plasmodium berghei hepatic merozoites.

first: Ashley

middle: B

last: Reers


title: Transcriptional differences during the Plasmodium schizont-to-ring transition [RNA-seq]

overall_design: RNA-sequencing (RNA-seq) for Plasmodium falciparum schizonts and merozoites. Three replicates are included for each timepoint.


title: Single cell RNA-seq analysis of mouse miR-205 inducible adult back skin

first: Rui

last: Yi

summary: Through phenotypical study, we found that miR-205 can promote hair growth. The goal of this study is to determine how miR-205 effects epithelial cellular states and how miR-205 promotes hair growth at single cell level.

overall_design: Examination of transcriptome at single cell level in epithelial  and dermal cells extracted from mouse adult back skin at P53.

first: Jingjing

last: Wang


title: Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.STRT-seq]


title: Histone post translation modification and Transcriptional differences during the Plasmodium schizont-to-ring transition

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

platform_organism:
Plasmodium berghei
Plasmodium falciparum


title: Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scATAC-seq]


title: Human podocyte cell line mRNA-seq

city: Wuhan

first: Feng

last: Liu

state: Hubei

address: Air Road 13

institute: Tongji Medical College, Huazhong University of Science and Technology

summary: To investigate the downstream targets of the enhanced circHIPK3 expression accounting for high glucose-induced podocyte injury by RNA-seq

overall_design: In order to screen downstream genes regulated by circHIPK3 (hsa_circ_0000284), transcriptome analysis was performed in human podocyte cells transfected with circHIPK3-overexpression lentivirus and an empty lentivirus.

first: Liu

last: Feng

first: Chun

last: Zhang

first: Hua

last: Su


title: Administration of AGNHW enhances neurogenesis and angiogenesis in a mouse model of experimental cerebral ischemia injury

status: Public on Jun 05 2023

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: To explore the internal mechanism of AGNHW therapeutic effects on stroke mice, we performed RNA sequencing (RNA-seq) analysis in MCAO mice. The results showed that AGNHW changed the gene expression profile in the brain of stroke mice after administration

overall_design: TRIzol reagent was used to extract RNA from the brains of mice in sham, vehicle and AGNHW group. RNA quality was determined by Agilent 2100 Bioanalyzer. Illumina HiSeq 2500 platform was used for high-throughput sequencing by Anuolu Company in Beijing.

first: Jinyue

last: Zhao


title: Inflammatory and interferon gene expression signatures in patients with mitochondrial disease

first: Peter

last: McGuire

state: MD

address: 10 Center Dr, Building 10, Room 7N260A

department: NHGRI

institute: NIH

summary: People with mitochondrial disease are susceptible to metabolic decompensation and neurological symptom progression in response to an infection. Increasing evidence suggests that mitochondrial dysfunction may cause chronic inflammation, which may promote hyperresponsiveness to pathogens and neurodegeneration. We collected whole blood and isolated peripheral blood mononuclear cells from mitochondrial disease patients and healthy controls and examined transcriptional changes to identify common gene signatures of immune dysfunction in mitochondrial disease. We performed GSEA analyses and identified a positive enrichment of inflammatory and type I interferon gene sets in mitochondrial disease patients, coincident with a negative enrichment of T cell and B cell gene sets.

overall_design:
Gene expression profiling analysis of RNAseq data comparing PBMCs isolated from mitochondrial disease patients and healthy controls.
NOTE FROM SUBMITTER: This submission only includes processed data files for reasons of patient privacy. We will be uploading raw data to dbGaP under controlled access at accession number phs003299.

first: Emily

last: Warren

first: Eliza

last: Gordon-Lipkin

first: Foo

last: Cheung

first: Jinguo

last: Chen

first: Amrita

last: Mukherjee

first: Richard

last: Apps

first: John

middle: S

last: Tsang

first: Jillian

last: Jetmore

first: Melissa

middle: L

last: Schlein

first: Shannon

last: Kruk

first: Yuanjiu

last: Lei

first: A

middle: P

last: West


title: RNA expression profiles of HER2-positive advanced gastric or gastroesophageal junction cancer and healthy gastric mucosa control FFPE samples

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: A subgroup of patients with HER2-positive metastatic gastric and gastroesophageal junction cancers shows long-term response under trastuzumab maintenance monotherapy. Obviously, HER2 status alone is not able to identify these patients. We performed this study to identify potential new prognostic biomarkers for this long-term responding patient group. Tumor samples of 18 patients with HER2-positive metastatic gastric and gastroesophageal junction cancer who underwent trastuzumab treatment were retrospectively collected from multiple centers. Patients were divided into long-term responding (n=6) or fast-progression group (n=12) according to progression-free survival (PFS≥12 months vs PFS<12 months).We performed microarray-based gene expression analysis to investigate differences in immune cell populations between the patient groups.

overall_design: We retrospectively collected 18 FFPE tumor samples of HER2-positve metastatic or locally advanced gastric or gastroesophageal junction adenocarcinomas (GC/GEJC) prior to trastuzumab treatment and 5 healthy gastric mucosa FFPE samples as control. The patients were divided into long-term responding (PFS>=12, group 1) or fast progressing group (PFS<12, group 2) according to progression-free survival.

first: Isabel

last: Porth

last: De La Torre

first: Timo

last: Gaiser


title: Neuroprotective protein ADNP-dependent histone remodeling complex promotes Th2 immune cell differentiation (ATAC-Seq)

first: Ana

last: Ferreira

overall_design: ATACseq data comparing Cd4Cre with Cd4CreAdnpflox Th2 cells

first: Aydan

last: Szeto

first: Paula

last: Clark

first: Alastair

last: Crisp

first: Patrycja

last: Kozik

first: Helen

last: Jolin

first: Andrew

last: McKenzie


title: Neuroprotective protein ADNP-dependent histone remodeling complex promotes T helper 2 immune cell differentiation

overall_design: Refer to individual Series