title: NSD1 deposits Histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons [ChIP-seq in vivo]

first: Nicole

last: Hamagami

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for histone histone modifications H3K36me2 and DNA methyltransferase DNMT3A in  2- and 8-week wildtype mouse cerebral cortex

first: Dennis

last: Wu

first: Adam

last: Clemens

first: Sabin

last: Nettles

first: Aidan

last: Li

first: Harrison

last: Gabel


title: CRISPR-based screening of small RNA modulators of bile susceptibility in Bacteroides thetaiotaomicron

status: Public on Jun 27 2023

city: Wuerzburg

first: Alexander

middle: J

last: Westermann

address: Am Hubland

department: Department of Microbiology, Biocenter

country: Germany

institute: University of Wuerzburg

summary: Microbiota-centric interventions are limited by our incomplete understanding of the gene functions of many of its constituent species. This applies in particular to small RNAs (sRNAs), which are emerging as important regulators in microbiota species yet tend to be missed by traditional functional genomics approaches. Here, we establish CRISPR interference (CRISPRi) in the abundant microbiota member Bac-teroides thetaiotaomicron for genome-wide sRNA screens. By assessing the abundance of different pro-tospacer-adjacent motifs, we identify the Prevotella bryantii B14 Cas12a as a suitable nuclease for CRISPR screens in these bacteria and generate an inducible Cas12a expression system. Using a luciferase reporter strain, we infer guide design rules for and use this knowledge to assemble a computational pipeline for automated gRNA design. By subjecting the resulting guide library to a phenotypic screen, we uncover the previously uncharacterized sRNA BTnc167 to increase susceptibility to bile salts, likely through the regulation of genes involved in Bacteroides cell surface structure. Our work lays the groundwork for systematically uncovering hidden functions of bacterial sRNAs under a variety of con-ditions and, generally, to unlock the genetic potential of these major human gut mutualists.

overall_design: CRISPRi screen in B. thetaiotaomicron. These samples consist of sequenced PCR products of the genomic region containing the gRNA/arrays. The "library" samples are the steady-state CRISPRi library,  the "tyg" samples are derived from B. thetaiotaomicron grown in rich medium, the "bile" samples are derived from B. thetaiotaomicron grown in rich medium + bile salts.

first: Gianluca

last: Prezza

first: Chunyu

last: Liao

first: Sarah

last: Reichardt

first: Chase

middle: L

last: Beisel


title: ESR1+ luminal epithelial cells contribute to androgen-independent prostate survival in the absence of SRD5A2

status: Public on Jun 26 2023

city: Boston

first: Christina

last: Sharkey

state: MA

address: 99 Brookline Ave Rm 389

department: Urology

country: USA

institute: Beth Israel Deaconess Medical Center

type: Expression profiling by high throughput sequencing

summary: Steroid 5α reductase 2 (SRD5A2) is crucial for prostatic development, converting testosterone to dihydrotestosterone (DHT). While 5α reductase inhibitors (5ARI) effectively reduce prostate size in benign prostate hyperplasia (BPH), their limited efficacy against BPH-related lower urinary tract symptoms (LUTS) and mechanisms of 5ARI resistance remain unclear. Here, we developed a Srd5a2-/- mouse model and employed single-cell RNA sequencing (scRNA-seq) to explore the impact of SRD5A2 absence on prostate cellular heterogeneity. Significant alterations in luminal epithelial (LE) populations were observed, alongside increased proportion and proliferative phenotype of estrogen receptor 1 (ESR1)+ Luminal Epithelia 2 (LE2) cells, following an SRD5A2-independent ESR1 differentiation trajectory. LE2 cells exhibited enhanced estrogen response gene signatures, suggesting alternative pathways for prostate growth without SRD5A2. Human prostate biopsy analysis revealed an inverse correlation between SRD5A2 expression and LE2 markers (ESR1 and PKCα). These findings provide insights into prostate biology, 5ARI resistance mechanisms, and potential targeted therapies for BPH-related LUTS.

overall_design: Single-cell sequencing was performed on three fresh prostate tissues, including one from Srd5a2-/- mice and two from Srd5a2+/- mice.

first: Xingbo

last: Long

first: Ra'ad

last: Al-Faouri

first: Douglas

last: Strand

first: Aria

middle: F

last: Olumi

first: Wang

last: Zongwei


title: Chromatin remodeling events associated with gARID are essential for gametocyte development in Plasmodium

status: Public on Jun 30 2023

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA-seq for tumor associated macrophages in hepatocellular carcinoma

status: Public on Jul 10 2023

city: Beijing

first: Yunxi

state: Beijing

address: 38 Xueyuan Rd, Haidian District

country: China

institute: School of Basic Medical Sciences, Peking University

summary: To investigate the relationship between MIF and SPP1, we induced THP-1 cells with lentivirus carrying SPP1 shRNA and negative control virus into HCC-TAMs and 4IPP-treated HCC-TAMs (tumor associated macrophages in hepatocellular carcinoma).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCC-TAMs, its KD derivatives (shSPP1) and 4IPP-treated HCC-TAMs.

first: Dongyu

last: Zhao

first: Jinhua

last: Wen


title: Global gene expression of Ad-OSCAR and subsequently 5-ASA treated mice with Control mice

city: Seoul

first: Gina

last: Ryu

address: Seodaemun-gu

country: South Korea

institute: Ewha

summary:
To examine the effects of Oscar and its inhibitor 5-ASA on articular cartilage, we established OSCAR overexpressed chondrocytes with adenovirus and treated 5-ASA subsequently.
Gene expression profiling analysis was performed using articular cartilage transcriptomes, with biologic replicates, generated by RNA-seq.

overall_design: Articular cartilage mRNA profiles of Ad-OSCAR infected mice with 5-ASA treated subsequently and control.

first: Soo-Young

last: Lee

first: Jihee

last: Kim


title: Interplay between acetylation and ubiquitination of Isw1 confers multidrug resistance in Cryptococcus neoformans

status: Public on Jun 20 2023

city: shenyang

first: Yang

last: Meng

address: Wenhua street num 11

department: College of Life and Health Sciences

institute: Northeastern University

summary: Cryptococcus neoformans poses a great threat to human communities, given that it quickly becomes resistant to available antifungal drugs. Herein, a conserved chromatin remodeler, Isw1, is shown to function as a master transcriptional modulator of genes responsible for multidrug resistance. It reciprocally controls drug resistance, and cells with disrupted ISW1 demonstrate profound resistance to fluconazole, ketoconazole, 5-fluorocytosine and 5-fluorouracil. Mass spectrometry reveals that Isw1 is both acetylated and ubiquitinated. These two protein posttranslational modifications confer an interplay regulation mechanism that controls Isw1 protein degradation via a ubiquitin-mediated proteasome and, consequently, C. neoformans resistance to drugs. Functional mutagenesis analysis of acetylation and ubiquitination sites reveals that the acetylation status of the lysine 97 residue on Isw1 coordinates its ubiquitination processes at lysines 113 and 441 by modulating the protein interactions between Isw1 and Cdc4, an E3 ligase. Clinical C. neoformans isolates overexpressing the undegradable ISW1 mutant demonstrate impaired drug-resistant phenotypes. Collectively, our studies reveal a sophisticated acetylation-Isw1-ubiquintation regulation axis that controls multidrug resistance in fungal pathogens.

overall_design: performed paired-end RNA-seq of Cryptococcus neoformans H99s as Control group and isw1∆ strains as in 50ml YPD broth  at OD600=0.8, respectively in biological triplicates.

first: Chen

last: Ding


title: Combinatorial blood platelets-derived circRNA and mRNA signature for early-stage lung cancer

status: Public on Jun 23 2023

city: Amsterdam

first: Silvia

last: D'Ambrosi

address: De Boelelaan 1118

country: Netherlands

institute: Amsterdam UMC

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

summary: Despite the diversity of liquid biopsy transcriptomic repertoire, numerous studies often 30 exploit only a single RNA type signature for diagnostic biomarker potential. This frequently results 31 in insufficient sensitivity and specificity necessary to reach diagnostic utility. Combinatorial biomarker approaches may offer a more reliable diagnosis. Here we investigated the synergistic contributions of circRNA and mRNA signatures derived from blood platelets as biomarkers for lung cancer detection. We developed a comprehensive bioinformatics pipeline permitting analysis of  platelet-circRNA and mRNA derived from non-cancer individuals and lung cancer patients. An optimal selected signature is then used to generate the predictive classification model using machine learning algorithm. Using an individual signature of 21 circRNA and 28 mRNA, the predictive  models reached an Area Under the Curve (AUC) of 0.88 and 0.81, respectively. Importantly, combinatorial analysis including both types of RNAs resulted in an 8-target signature (6 mRNA and 2 40 circRNA) enhancing the differentiation of lung cancer from controls (AUC of 0.92). Additionally, we identified five biomarkers potentially specific for early-stage detection of lung cancer. Our proof-of-concept study presents the first multi-analyte-based approach for the analysis of platelets-derived biomarkers, providing a potential combinatorial diagnostic signature for lung cancer detection.

overall_design: Blood platelets samples from lung cancer patients (n=30), asymptomatic individuals (n=27) and people with benign lung nodules (n=3) were analyzed using two different nCounter panels. The Human Immunology V2 Panel (NanoString Technologies) targets 594 genes involved in the immune response and a custom-made panel targeting 78 circRNAs (78 circRNA Panel), 6 linear reference genes and 4 mRNAs

first: Stavros

last: Giannoukakos

first: Mafalda

last: Antunes-Ferreira

first: Carlos

last: Pedraz-Valdunciel

first: Jillian

middle: W

last: Bracht

first: Nicolas

last: Potie

first: Ana

last: Gimenez-Capitan

first: Michael

last: Hackenberg

first: Alberto

last: Fernandez Hilario

first: Miguel

middle: A

first: Rafael

last: Rosell

first: Thomas

last: Wurdinger

first: Danijela

last: Koppers-Lalic


title: Growth Signaling Autonomy in Circulating Tumor Cells  Aids Metastatic Seeding

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

state: CA

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

summary: Self-sufficiency (autonomy) in growth signaling, the earliest recognized hallmark of cancer, is fuelled by the tumor cell’s ability to ‘secrete-and-sense’ growth factors; this translates into cell survival and proliferation that is self-sustained by auto-/paracrine secretion. Using breast cancer cells that are either endowed or impaired in growth signaling autonomy, here we reveal how autonomy impacts cancer progression. Autonomy is associated with enhanced molecular programs for stemness, immune evasiveness, proliferation, and epithelial-mesenchymal plasticity (EMP). Autonomy is both necessary and sufficient for anchorage-independent growth factor-restricted proliferation and resistance to anti-cancer drugs and is required for metastatic progression. Transcriptomic and proteomic studies show that autonomy is associated with self-sustained EGFR/ErbB signaling. A gene expression signature is derived (a.k.a., autonomy signature) which revealed that autonomy is induced in circulating tumor cells (CTCs) and particularly CTC clusters, the latter of which carry higher metastatic potential. Autonomy in CTCs tracks therapeutic response and prognosticates outcome. Autonomy is preserved during reversible (but not stable) EMT. These data support a role for growth signaling autonomy in multiple processes essential for the blood-borne dissemination of human breast cancer.

overall_design: WT and GIV-KO MDA-MB231 cells grown in 0% and 10% serum concentration in p10 dishes (Corning) for 16 h prior to harvest, and cell pellets were subsequently processed for RNA extraction using a kit (R2052, Zymo Research) as per manufacturer’s protocol. Isolated RNA has been processed for RNA sequencing in the Illumina NovaSeq 6000 platform.

first: Gary

middle: D

last: Luker


title: Comprehensive transcriptomic profiling of liver cancer identifies histone and PTEN are major regulators of scutellarein-induced anti-tumor activity

status: Public on Jun 15 2023

city: Jinju

first: Sang Eun

last: Ha

address: 501 Jinju-daero

department: Life Science and College of Veterinary Medicine

institute: Gyeongsang National University

summary:
The current study aimed to establish the candidate pharmacological targets of scutellarein and to identify its biological network.
We show that the use of RNA-seq data, with bioinformatics tools, can provide a valuable resource to identify the pharmacological targets that could have important biological roles in liver cancer.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data between scutellarein-treated and scutellarein-untreated HepG2 cells.
Raw data are available in NCBI BioProject PRJNA971341

first: Anjugam

last: Paramanantham

first: Hun Hwan

last: Kim

first: Pritam Bhagwan

last: Bhosale

first: Min Yeong

last: Park

first: Abuyaseer

last: Abusaliya

first: Jeong Doo

last: Heo

first: Won Sup

last: Lee

first: Gon Sup


title: Targeting HIF-2α in skeletal progenitors and their descendants for the radioprotection of bone

status: Public on Jun 24 2023

city: Durham

first: Colleen

last: Wu

state: NC

address: 450 Research Drive

department: Orthopaedics

institute: Duke University

summary: Radiotherapy continues to be a common treatment modality for cancer despite skeletal complications. Currently, there are no effective treatments for radiation-induced bone loss. Radiation induces substantial changes to the bone microenvironment; however, the effects of these changes on skeletal progenitors and their descendants remain elusive. Following radiation, LeprCre skeletal progenitors and their descendants, localize to hypoxic regions and exhibit HIF-2α stabilization, thus implicating a role for HIF-2α in radiation-induced bone loss. To test whether HIF-2α deficiency rescues radiation-induced bone loss, we conditionally ablated HIF-2α in LeprCre-expressing cells and their descendants. Compared to irradiated controls, irradiated LeprCre;Hif-2αfl/fl knock out mice demonstrate increased bone mass with values comparable to non-irradiated animals. Mechanistically, HIF-2α negatively regulates osteoblastogenesis, mineralization, and number of skeletal progenitors. To test whether HIF-2α can be targeted therapeutically, we administered PT2399, a potent and selective HIF-2α inhibitor whose structural analog belzutifan, has recently received FDA approval. Administration of PT2399 was sufficient to prevent radiation-induced bone loss in a single-limb irradiation model. As ~90% of patients on HIF-2α inhibitor treatment develop anemia, we constructed a PT2399-loaded bone-targeting nanocarrier (Aln-PT-NC) to increase on-target efficacy and reduce off-target kidney toxicity. Delivery of Aln-PT-NC completely prevented radiation-induced bone loss while reducing drug accumulation in the kidney. In this study, we identify HIF-2α as a negative regulator of bone formation in LeprCre skeletal progenitors and their descendants following radiotherapy and developed a bone-targeting HIF-2α therapeutic. Together, these studies highlight the clinical potential of Aln-PT-NC to be translated into a treatment regimen for bone radioprotection.

overall_design: To detemine the impact of loss of HIF-2 in LeprCre expressing cells after radiation exposure. Control mice (LepRCre;tdTomato+) and KO mice (LepRCre;tdTomato;HIF-2fl/fl) mice were exposed to 0 Gy or 4 Gy total body irradiation. 3 or 14 days post IR, long bones were collected and bone marrow was aspirated. Bone marrow cells were then sorted by FACS and we collected TdTomato+ cells for  RNA extraction. We then perfomed gene profiling anaysis on collected samples


title: DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and their microenvironment

status: Public on Jul 11 2023

city: Warsaw

first: Szymon

middle: Piotr

last: Baluszek

state: mazowieckie

address: Wilhelma Konrada Roentgena 5

department: Department of Molecular and Translational Oncology

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology

type: Methylation profiling by genome tiling array

summary: Chordomas are rare tumors of notochord remnants, occurring mainly in the sacrum and skull base. Despite of their unusually slow growth, chordomas are highly invasive and the involvement of adjacent critical structures causes treatment challenges. Due to the low incidence, the molecular pathogenesis of this entity remains largely unknown. This study aimed to investigate DNA methylation abnormalities and their impact on gene expression profiles in skull base chordomas. 32 tumor and 4 normal nucleus pulposus samples were subjected to DNA methylation and gene expression profiling with methylation microarrays and RNA sequencing. Genome-wide DNA methylation analysis revealed two distinct clusters for chordoma (termed subtypes C and I) with different patterns of aberrant DNA methylation. C Chordomas were characterized by general hypomethylation with hypermethylation of CpG islands, while I chordomas were generally hypermethylated. These differences were reflected by distinct distribution of differentially methylated probes (DMPs). Differentially methylated regions (DMRs) were identified, indicating aberrant methylation in known tumor-related genes in booth chordoma subtypes and regions encoding small RNAs in subtype C chordomas. Correlation between methylation and expression was observed in a minority of genes. Upregulation of TBXT in chordomas appeared to be related to lower methylation of tumor-specific DMR in gene promoter. Gene expression-based clusters of tumor samples did not overlap with DNA methylation-based subtypes. Nevertheless, they differ in transcriptomic profile that shows immune infiltration in I chordomas and up-regulation of cell cycle in C chordomas. Immune enrichment in chordomas I was confirmed with 3 independent deconvolution methods and immunohistochemistry. Copy number analysis showed higher chromosomal instability in C chordomas. Nine out of eight had deletion of CDKN2A/B loci and downregulation of genes encoded in related chromosomal band. No significant difference in patients’ survival was observed between tumor subtypes, however, shorter survival was observed in patients with higher number of copy number alterations.

overall_design:
Comparative gene expression and DNA methylation between chordoma (32) and nucleus pulposus (4) samples

Kallisto expression quantification is available on GitHub:
https://github.com/SBaluszek/chordoma_RNA_met/blob/main/count_table.csv

middle: P

first: Mateusz

last: Bujko


title: Brain and blood single-cell transcriptomic analysis in acute and subacute phases after experimental stroke

status: Public on Jun 14 2023

city: New York

first: Josef

last: Anrather

state: NY

address: 407 East 61st Street

department: BMRI

institute: Weill Cornell Medical College

summary: The secondary immune response to ischemic stroke progresses for days to weeks and involves glial and brain endothelium activation, recruitment of peripheral immune cells, and release of cytokines and chemokines. Whereas there is evidence that the acute inflammatory response contributes to the progression of ischemic brain injury, on the other hand, recent research points at a more multifaceted role of immune cells in brain ischemia, where immune cells participate in repair processes during the sub-acute and chronic stages. Here we used single-cell sequencing to gain deeper insights into the impact of ischemic stroke on signature and the heterogeneity of brain immune cells, endothelial cells and circulating leukocytes in mice.

overall_design: Single-cell RNA profiling of CD45intermediate and CD45high immune cells and CD45negative/Ly6chigh endothelial cells isolated from mice 2 and 14 days after transient middle cerebral artery occlusion or sham surgery. Single-cell RNA profiling of peripheral blood leukocytes from mice 2 and 14 days after transient middle cerebral artery occlusion or sham surgery.

first: Lidia

last: Garcia-Bonilla

first: Gianfranco

last: Racchumi


title: IBD CosMx NanoString data from colonic mucosa

status: Public on Jun 13 2023

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

summary: Inflammatory bowel diseases (IBDs) including ulcerative colitis (UC) and Crohn’s disease (CD) are chronic inflammatory diseases with increasing worldwide prevalence that show a perplexing heterogeneity in manifestations and response to treatment. We applied spatial transcriptomics at single-cell resolution (CosMx Spatial Molecular Imaging) to human inflamed and uninflamed intestine.

overall_design: CosMxTM technology [CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex) + 20 custom genes; Nanostring, USA] was applied to 9 FFPE samples: 3 non-IBD healthy controls, 3 CD and 3 UC with a mean of 19 fields of view (FoVs) per sample. The mean area explored was 11,53 mm2 per sample. The following cell surface markers were used for morphology visualization: B2M/CD298, PanCK, CD45, CD3 antibodies and DAPI.

first: Alba

last: Garrido-Trigo

first: Holger

last: Heyn


title: Timecourse of poly(I:C) treated in vivo fibrosarcoma tumors

status: Public on Jun 04 2023

city: Nedlands

first: Rachael

middle: M

last: Zemek

state: WA

address: 15 hospital Ave

department: Cancer Centre

country: Australia

institute: Telethon Kids Institute

summary: WEHI-164 tumors treated with intratumoral injections of poly(I:C), daily for 6 days

overall_design: 3 per timepoint; Day 0 (untreated), day 1, day 3, day 5, day 7


title: Transcriptome analysis of mutant p53 (p53-V272M, p53-R282W) rescued by arsenic trioxide (ATO)

status: Public on Jun 03 2023

city: Shanghai

first: Yigang

last: Tang

address: No 197 RUIJIN ER RD

institute: Shanghai Jiaotong University

summary: The goals of this study are to compare transcriptome of mutant p53 rescued by arsenic trioxide

overall_design: Treat isogenic HCT116 (p53-/-) cells (infected with p53-V272M, p53-R282W) with ATO

first: Min

last: Lu


title: Effect of depletion of NatD on gene expression of MDA-MB-231 breast cancer cells

city: Nanjing

first: Mengying

last: Xing

address: 163 Xianlin Avenue

department: The State Key Laboratory of Pharmaceutical Biotechnology

institute: Nanjing University

summary: To investigate the function NatD in the regulation of breast cancer progression, we established MDA-MB-231 cell lines in which each target gene has been knocked down by CRISPR.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDA-MB-231 cells and its K0 derivatives (NatD-KO).

first: Bing

last: Yao

first: Quan

last: Zhao


title: EZH2 inhibtion and IFNy treatment of patient derived organoids [scRNA-Seq]

status: Public on Jun 01 2023

city: Lexington

first: Jinpeng

last: Liu

state: Kentucky

address: 800 Rose St

institute: Markey Cancer Center

summary: We report the transcriptomics of primary murine lung squamous cell carcinomas in mice treated with EZH2 inhibition and anti-PD1

overall_design: To understand the cellular heterogeneity and responses to EZH2 inhibition and anti-PD1 therapies in lung squamous cell carcinoma

first: Christine

last: Brainson

first: Tanner

last: DuCote

first: Xufeng

last: Qu


title: EZH2 inhibtion and IFNy treatment of patient derived organoids [RNA-seq]

summary: We report the transcriptomics of squamous lung cancer patient derived tumoroids treated with EZH2 inhibitor and IFNy

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To determine that EZH2 inhibition and IFNy upregulate genes involved in antigen presentation machinery and immunogenicity


title: Genome-wide CRISPR screen reveals tumor-intrinsic responses to radiotherapy

status: Public on Jul 06 2023

city: Houston

first: Citu

state: Texas

address: 7000 Fannin Street

department: McWilliams School of Biomedical Informatics

institute: University of Texas Health Science Centre

summary: Radiation therapy (RT) is one of the most commonly used anti-cancer therapies. However, the landscape of cellular response to irradiation, especially to a single high-dose irradiation, remains largely unknown. In this study, we performed a whole-genome CRISPR loss-of-function screen and revealed temporal inherent and acquired responses to RT. Specifically, we found that loss of the IL1R1 pathway led to cellular resistance to RT. This is in part due to the involvement of radiation-induced IL1R1-dependent transcriptional regulation, which relies on the NF-κB pathway. Moreover, the mitochondrial anti-apoptotic pathway, particularly the BCL2L1 gene, is crucially important for cell survival following radiation. BCL2L1 inhibition combined with RT dramatically impeded tumor growth in several breast cancer cell lines and syngeneic models. Taken together, our results suggest that the combination of an apoptosis inhibitor such as a BCL2L1 inhibitor with RT may represent a promising anti-cancer strategy for solid cancers including breast cancer.

overall_design: MCF10A wild-type, IL1R1-KO, IL1RAP-KO cells (each with two biological replicates) with or without RT were collected. Total RNA was extracted (Qiagen), and an Illumina TruSeq Stranded Total RNA Library Prep Kit was used to prepare the library after rRNA depletion. mRNA sequencing was conducted at NextSeq 550 (Illumina) to generate 75-bp paired ends.

first: Ling

last: Yin

first: Xiaoding

last: Hu

first: Guangsheng

last: Peng

first: Mengfan

first: You

last: Zhou

first: Huimin

last: Zhang

last: Huang

first: Siting

last: Li

first: Jie

first: Zhongming

first: Xu

last: Feng

first: Junjie

last: Chen


title: Cancer-specific alternative polyadenylation shapes tumor phenotypes in vivo

city: Seattle

first: Austin

middle: Max

last: Gabel

address: 1100 Fairview Ave. N., B3-111

department: Computational Biology

institute: Fred Hutchinson Cancer Center

summary: Alternative polyadenylation (APA) is strikingly dysregulated in many cancers. Although APA dysregulation is frequently associated with poor prognosis, the biological importance of most APA events remains unclear simply because few have been functionally studied. Here, we performed a CRISPR/Cas9-based screen to assess individual APA events’ contributions to tumor growth in vivo. Forcing use of specific polyadenylation sites altered mRNA and protein levels to modify mouse melanoma growth in an immunocompetent host. Our screen highlighted APA events of potential clinical relevance. For example, forced Atg7 3′ UTR lengthening in mouse melanoma reduced ATG7 protein levels and tumor immune infiltration; similarly, in human melanoma, a long ATG7 3′ UTR and low mRNA levels were significantly associated with reduced anti-tumor T cell activity and failure of immune checkpoint blockade. Our data demonstrate that cancer-associated APA plays a causative role in tumorigenesis and motivate future studies of the therapeutic potential of modulating APA.

overall_design: Comparative Poly(A) sequencing for B16-F10 melanoma and Melan-A cells (melanocyte cell line) completed 6x replicates. RNA-seq of 3x cells and 5x tumors of B16-F10 Cas9-expressing cells treated with a paired-guide RNA that force 3' UTR lengthening in the gene Atg7, relative to a control unexpressed gene (Crabp1).

first: Robert

middle: K

last: Bradley


title: The PD-1/PD-L1 pathway maintains an immunosuppressive environment essential for neonatal heart regeneration [scRNA-seq]

city: Dallas

first: Miao

last: Cui

address: UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.

institute: UTSW

summary: The adult heart responds to injury by scarring with consequent loss of contractile function, whereas the neonatal heart possesses the ability to regenerate. We compared the immune response to injury in neonatal and adult mouse hearts and discovered that the PD1/PD-L1 immune checkpoint pathway is highly activated in regenerative hearts but is silenced in later life. Deletion of the PD1 receptor or inactivation of its PD-L1 ligand prevented regeneration of neonatal hearts after injury. Our findings reveal a previously unrecognized role of the PD1/PD-L1 pathway in the control of heart regeneration through modulating T cell activity and inflammation following injury and provide new inroads into the control of adult tissue regeneration.

overall_design: We analyzed the transcriptome of CD45+ immune cells from PD1 homozygous and heterozygous deletion mice at 7 days after either myocardial infarction or sham surgery performed at P2.

first: Eric

last: Olson


title: The PD-1/PD-L1 pathway maintains an immunosuppressive environment essential for neonatal heart regeneration

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

overall_design: Refer to individual Series


title: An integrated analysis of gut microbiota and the brain transcriptome reveals host-gut microbiota interactions following traumatic brain injury

city: Hangzhou

first: Wangxiao

last: Bao

address: Qingchun Road 79#

institute: Zhejiang University School of Medicine

summary: Objectives: The aim of this study was to reveal the transcriptomic profile of the cerebral cortex in traumatic brain injury (TBI) mice. Methods: A controlled cortical impact (CCI) device was used to establish a TBI model. The gene expression in the cerebral cortex was detected by whole-transcriptome sequencing (RNA-Seq).

overall_design: Brain tissues of five mice with traumatic brain injury (TBI) and five naïve mice were collected.


title: The PD-1/PD-L1 pathway maintains an immunosuppressive environment essential for neonatal heart regeneration [Spatial]

overall_design: We analyzed spatial transcriptome transverse sections collected from  PD1 homozygous and heterozygous heart at 7 days after myocardial infarction performed at P2.


title: RBM33 Acts as an m6A Reader Essential for ALKBH5-mediated m6A Demethylation and Head and Neck Squamous Carcinoma Tumorigenesis

city: Chicago

first: Allen

last: Zhu

state: Illinois

address: 929 E 57th St, Room E331

institute: University of Chicago

first: Fang

last: Yu

middle: C

first: Shun

last: Liu

first: Chuan

last: He

first: Zhijian

last: Qian


title: EZH2 inhibtion and IFNy treatment of patient derived organoids

status: Public on May 31 2023

first: Jinpeng


title: EZH2 inhibtion and IFNy treatment of patient derived organoids [ChIP-seq]

summary: We report the chromatin landscape of squamous lung cancer patient derived tumoroids treated with EZH2 inhibitor and IFNy

overall_design: To determine chromatin peaks changed by EZH2 inhibition and IFNy upregulate at genes involved in antigen presentation machinery and immunogenicity

first: Christine

last: Brainson

first: Tanner

last: DuCote


title: Reanalysis of transcriptomic profiling of isolated CTC from 31 patients

first: Pradipta

last: Ghosh

summary: The CTC-iChip microfluidic device [PMID: 23552373 ] enables isolation of rare viable circulating tumor cells (CTCs) directly from whole blood specimens of patients with cancer. Reanalysis of freshly isolated CTC from 31 women with hormone receptor positive metastatic breast cancer.

relation:
Reanalysis of: GSM4289350
Reanalysis of: GSM4289425
Reanalysis of: GSM4289447
Reanalysis of: GSM4289452
Reanalysis of: GSM4289336
Reanalysis of: GSM4289370
Reanalysis of: GSM4289381
Reanalysis of: GSM4289400
Reanalysis of: GSM4289386
Reanalysis of: GSM4289396
Reanalysis of: GSM4289388
Reanalysis of: GSM4289390
Reanalysis of: GSM4289403
Reanalysis of: GSM4289404
Reanalysis of: GSM4289406
Reanalysis of: GSM4289412
Reanalysis of: GSM4289382
Reanalysis of: GSM4289324
Reanalysis of: GSM4289434
Reanalysis of: GSM4289429
Reanalysis of: GSM4289323
Reanalysis of: GSM4289340
Reanalysis of: GSM4289335
Reanalysis of: GSM4289363
Reanalysis of: GSM4289353
Reanalysis of: GSM4289358
Reanalysis of: GSM4289367
Reanalysis of: GSM4289369
Reanalysis of: GSM4289365
Reanalysis of: GSM4289380
Reanalysis of: GSM4289371

overall_design: Reanalysis of transcriptomic profiling of freshly isolated CTC from 31 women with hormone receptor positive metastatic breast cancer.

first: Gary

last: Luker


title: DNA-guided transcription factor cooperativity shapes face and limb mesenchyme [RNA-seq]

status: Public on May 30 2023

city: Stanford

first: Seungsoo

last: Kim

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

summary: Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how ‘Coordinator’, a long DNA motif comprised of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, while HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in shared regulation of genes involved in cell-type and positional identities, and ultimately shapes facial morphology and evolution.

overall_design: PolyA RNA sequencing (RNA-seq) and Thiol (SH)-Linked Alkylation for the Metabolic sequencing of RNA (SLAM-seq) of human cranial neural crest cells with dTAG-mediated targeted depletion of TWIST1, ALX1, MSX1, or PRRX1, or knockout of ALX4.

first: Sahin

last: Naqvi

first: Maram

last: Bader

first: Mervenaz

last: Koska

first: Christy

last: Luong

first: Angela

last: Pogson

first: Joanna

last: Wysocka


title: Single cell immune landscape of human atherosclerosis reveals the transcriptional signature of PLIN2hi/TREM1hi inflammatory lipid-associated macrophages and its association with cerebrovascular complications.

status: Public on May 22 2023

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

summary: Atherosclerosis is a lipid-driven inflammatory disease.However, evidence emerging so far from single cell atlases suggests a dichotomy between lipid associated and inflammatory macrophage states. Here, we present the most inclusive reference atlas of human intraplaque immune cell communities to date.

overall_design:
Carotid plaques were collected from patients undergoing carotid endarterectomy. Tissues were enzymatically digested, and single cells were sorted for CD45+ cells.
CD45+ single cell suspensions were processed using   the 10x Genomics platform with the aim to captue 5,000 cells/sample

first: Lea

last: Dib

first: Lada

last: Koneva

middle: N

first: Claudia

last: Monaco


title: DNA-guided transcription factor cooperativity shapes face and limb mesenchyme


title: DNA-guided transcription factor cooperativity shapes face and limb mesenchyme [ATAC-seq]

overall_design: ATAC-seq of human cranial neural crest cells with dTAG-mediated targeted depletion of TWIST1, ALX1, MSX1, or PRRX1, or knockout of ALX4.


title: DNA-guided transcription factor cooperativity shapes face and limb mesenchyme [CUT&RUN]

overall_design: CUT&RUN for the TFs TWIST1, ALX4, TCF3, AP2a, CTCF, V5(TWIST1), or IgG control, in human cranial neural crest cells with endogenous degron and epitope tagging of TWIST1 upon dTAG-mediated targeted TF depletion.


title: Transcriptomic profiling of Triticum aestivum L. cv Thatcher at 0, 7 and 14 days post infection with Puccinia triticina TBDG (11-180-1)

status: Public on May 20 2023

city: Ottawa

first: Michele

last: Loewen

state: Ontario

address: 100 Sussex Drive

country: Canada

institute: National Research Council of Canada (NRC)

summary: Differential gene expression analysis of RNASeq data from flag leaves from Triticum aestivm L. cv Thatcher at different time points and infection statuses upon infection with the leaf rust pathogen Pucinia triticina TBDG (11-180-1).

overall_design: Triticum aestivum L. cv Thatcher'' flag leaves were harvest at 0, 7 and 14 days post infection with the leaf rust pathogen Pucinia triticina TBDG (11-180-1) to evalute the impact of infection on gene expression profiles.

first: Paula

last: Ashe


title: Rat cytomegalovirus efficiently replicates within dendritic cells and affects both surface marker and gene expression

status: Public on May 15 2023

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary: Dendritic cells (DC) play a crucial role in generating and maintaining antiviral immunity. While DC are implicated in the antiviral defense by inducing T cell responses, they can also become infected by Cytomegalovirus (CMV). CMV is not only highly species-specific but also specialized in evading immune protection, and this specialization is in part due to characteristic genes encoded by a given virus. Here, we investigated whether RCMV can infect XCR1+ DC and if infection of DC alters the expression of cell surface markers and migration behavior. We demonstrate that wild-type RCMV and a _vxcl1 mutant virus infect splenic rat DC ex vivo and identify viral assembly compartments. Replication-competent RCMV reduced XCR1 and MHCII surface expression. Further, gene expression of infected DC was analyzed by single cell RNA-sequencing. RCMV infection reverted a state of DC activation that was induced by DC cultivation. On the functional level, we observed impaired chemotactic activity of infected XCR1+ DC compared to mock treated cells. We therefore speculate that as a result of RCMV infection, DC exhibit diminished XCR1 expression and are thereby inhibited from the lymphocyte crosstalk.

sample_organism:
Rattus norvegicus
Murid betaherpesvirus 8

overall_design: Dendritic cells were isolated from rat spleens, and RNA extracted immediately (input samples) or after 24 hours of treatment as indicated.

first: Julia

last: Madela-Mönchinger

first: Silver

last: Wolf

first: Agnieszka

last: Bauer

first: Lars

last: Möller

first: Vanda

last: Juranić Lisnić

first: Markus

last: Landthaler

first: Anna

last: Malyshkina

first: Sebastian

last: Voigt


title: Interleukin-3 coordinates glial-peripheral immune crosstalk to incite multiple sclerosis

status: Public on May 16 2023

first: Donghoon

last: Lee

address: 1399 Park Ave

department: Psychiatry, Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Multiple sclerosis (MS) is a neuroinflammatory disease of the central nervous system (CNS). While CNS-resident glial cells and infiltrating immune cells contribute to MS pathogenesis, the networks that govern peripheral-central immune crosstalk and coordinate functionality among these ontologically distinct populations remain unclear. Here we show, in mice and humans, that astrocyte- and CD44hiCD4+ T cell-sourced interleukin-3 (IL-3) programs microglia and infiltrating myeloid cells to exacerbate neuroinflammation by inciting a cellular recruitment program that drives the accrual of immune cells in the CNS thereby worsening MS and its preclinical model experimental autoimmune encephalomyelitis (EAE). We find that CNS-resident astrocytes and peripherally-derived CD44hiCD4+ T cells generate IL-3 while resident microglia and infiltrating monocytes, macrophages, and dendritic cells respond to the cytokine by expressing IL-3Rɑ, IL-3's specific receptor. Astrocytic and T cell IL-3 elicit an immune migratory, recruitment, and chemotactic program by IL-3Rɑ+ myeloid cells that enhances immune cell infiltration into the CNS leading to exacerbated neuroinflammation, demyelination, and clinical disease. Multiregional single-nuclei RNA sequencing (snRNAseq) of human CNS tissue from unaffected controls and MS patients reveals the appearance of a subset of IL3RA-expressing myeloid cells in MS plaques with unique recruitment, migratory, and chemotactic programing and function. In humans with MS, IL3RA expression by plaque myeloid cells and IL-3 levels in the cerebrospinal fluid (CSF) predict myeloid and T cell abundance and recruitment into the CNS. Together, our findings establish IL-3:IL-3RA signaling as a bidirectional glial-peripheral immune crosstalk network that promotes neuroinflammation, prompts immune cell recruitment to the CNS, and worsens MS.

overall_design: Description of samples and human subjects: Twelve fresh frozen brain tissue specimens, consisting of 6 MS cases (4 males and 2 females, age: 64±6) and 6 unaffected controls (4 males and 2 females, age: 63±3.3), were obtained through the NIH NeuroBiobank from the Human Brain and Spinal Fluid Resource Center, UCLA. All neuropsychological, diagnostic, and autopsy protocols were approved by the respective Institutional Review Boards. For the cases, each specimen contained a visible plaque and adjacent normal-appearing white matter (NAWM) and normal-appearing gray matter (NAGM). The unaffected control specimens consisted of NAWM and NAGM.

first: John

last: Fullard

first: Panos

last: Roussos


title: Multi-omics analysis of mutagenized S. rimosus reveals synergistic changes that drive oxytetracycline production towards industrial efficiency and opens a new route to heterologous polyketides

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

institute: Bielefeld University

summary: The present work provides a multi-omics systems-wide view on S. rimosus. Using genomics, transcriptomics, proteomics, and metabolomics, we compared the wild type with an OTC-overproducing derivative, previously obtained by classical mutagenesis. The integration of the data provided a deep insight into the underlying metabolic and regulatory networks that mediate high-level OTC formation. Strikingly, the overproducer revealed a synergistically activated supply of acetyl-CoA and malonyl CoA and increased abundance of various CoA thioesters.

overall_design: Comparison of the transcriptomes of two mutant strains, a hyperproducer derived from the wildtype by chemical mutagenesis and a null mutant derived from the hyperproducer by tergeted deletion of the OTC production cluster, against the wildtype strain. All cells were grown for 24h in liquid medium, all experiments were performed in triplicate

first: Selma

last: Beganovic

last: Rückert-Reed

first: Hilda

last: Sucipto

first: Wei

last: Shu

last: Gläser

first: Andriy

last: Luzhetskyy

first: Jörn

last: Kalinowski

first: Christoph

last: Wittmann


title: Initiation Phase Cellular Reprogramming Rejuvenates DNA Damage Repair Defect In The Ercc1 Accelerated Aging Mouse Model

status: Public on May 11 2023

city: Rochester

first: Francesco

last: Morandini

address: 402 Hutchison Hall

institute: University of Rochester

summary: Unlike aging somatic cells, which exhibit a decline in molecular fidelity and eventually reach a state of replicative senescence, pluripotent stem cells can indefinitely replenish themselves while retaining full homeostatic capacity. The conferment of beneficial -pluripotency related traits via in vivo partial cellular reprogramming (IVPR) significantly extends lifespan and restores aging phenotypes in mouse models. Although the phases of cellular reprogramming are well characterized, details of the rejuvenation processes are poorly defined. Here we created the first reprogrammable accelerated aging mouse model with a DNA damage repair defect to better understand the effects of reprogramming on a key driver of aging. Using enhanced partial reprogramming by combining small molecules with the Yamanaka factors, we observed potent reversion of DNA damage, significant upregulation of multiple DNA damage repair processes, and restoration of the epigenetic clock is observed. In addition, we present evidence that TGFb inhibition of the ALK5 or ALK2 receptor is able to phenocopy some benefits including epigenetic clock restoration suggesting a role in the mechanism of rejuvenation during partial reprogramming.

overall_design: Fibroblasts from WT, ERCC1 d/-, OSKM, Oct4-GFP mice and crosses were isolated from the tail tip or skin and cultured. For reprogramming experiments, doxycycline was added to the medium for 2 or 4 days. For TGFB inhibition experiments, small molecule TGBF inhibitors were added to the medium.

first: Patrick

last: Paine

first: Cheyenne

last: Rechsteiner

first: Gabriela

last: Desdin Mico

first: Calida

last: Mrabti

first: Andrei

last: Seluanov

first: Vera

last: Gorbunova

first: Alejandro

last: Ocampo


title: A female mosquito salivary protein-driven influx of myeloid cells facilitates flavivirus transmission

status: Public on May 18 2023

city: Beijing

first: Zhaoyang

last: Wang

address: Shuangqing Road 30

institute: Tsinghua University

summary: Mosquitoes transmit many flaviviruses of global public health significance. Efficient viral transmission to mammalian hosts requires mosquito salivary factors that modulate local host responses, such as recruitment of virus-permissive myeloid cells to the bite sites. However, the specific salivary components facilitating viral transmission and their mechanisms of action remain largely unknown. Here, we showed that a female mosquito salivary gland-specific protein, named Aedes aegypti Neutrophil Recruitment Protein (AaNRP), acts as a key salivary component to facilitate the transmission of Zika (ZIKV) and dengue (DENV) viruses. AaNRP promotes a rapid influx of neutrophils followed by virus-susceptible myeloid cells toward mosquito bite sites, which facilitate establishment of local infection and systemic dissemination. Mechanistically, AaNRP engages TLR1 and TLR4 of skin resident macrophages and activates MyD88-dependent NF-κB signaling to induce the expression of neutrophil chemoattractants. Inhibition of MyD88-NF-κB with dietary resveratrol, a phytochemical, neutralizes the AaNRP effects, thus reducing flavivirus transmission by mosquitoes. This study offers mechanistic insight into saliva-aided viral transmission and provides a potential prophylactic target.

overall_design: We investigated the underlying mechanism of the mosquito bite-mediated promotion of neutrophil infiltration by a single-cell RNA sequencing (scRNA-Seq). The skin of mouse footpads at 4 hpb or without mosquito bites was isolated for enzymatic digestion. The total skin CD45+ immunocytes were flow-sorted and subjected to 10x genomics scRNA-Seq.

first: Kaixiao

last: Nie

first: Yan

last: Liang

first: Jichen

last: Niu

first: Xi

last: Yu

first: Yibin

last: Zhu


title: DNA-guided transcription factor cooperativity shapes face and limb mesenchyme [ChIP-seq]

first: Seungsoo

last: Kim

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27ac, TWIST1, and/or V5-tagged homeodomain TFs (ALX1, MSX1, PRRX1), in dissected mouse embryos, human RS4;11 cells, HEK293 cells transfected with bHLH and HD TFs, and human cranial neural crest cells with dTAG-mediated targeted depletion of TWIST1, ALX1, MSX1, or PRRX1, or knockout of ALX4.

first: Sahin

last: Naqvi

first: Maram

last: Bader

first: Mervenaz

last: Koska

first: Christy

last: Luong

first: Angela

last: Pogson

first: Joanna

last: Wysocka


title: Chloroplast nucleoid is organized by membrane association of transcribed genes [SOLINA]

status: Public on May 10 2023

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

summary: Chloroplasts are organelles responsible for photosynthesis. They originated form a procaryotic ancestor in the process of endosymbiosis and contain their own genomes. The chloroplast genome is packaged into a chromatin-like structure known as the nucleoid. The internal arrangement of the nucleoid, molecular mechanisms of DNA packaging and connection of the nucleoid structure to gene expression remain poorly understood. We show that Arabidopsis thaliana chloroplast nucleoids have a unique organization driven by DNA binding to the thylakoid membranes. Membrane association of specific DNA regions is correlated with high levels of transcription, high protein occupancy and reduced DNA accessibility. Genes with low levels of transcription are further away from the membranes, have lower protein occupancy and higher DNA accessibility. Gene-specific disruption of transcription in sigma factor mutants causes a corresponding reduction in membrane association, indicating that RNA polymerase activity causes DNA tethering to the membranes. We propose that transcription organizes the chloroplast nucleoid into a transcriptionally active membrane-associated core and a less active Periphery.

overall_design: The data consists of 3 replicates of SOLiNA during light and darkness in Col0 wt plants; and during illumination in the sigma factor mutants sig2 and sig6.

first: V

first: Andrzej

middle: T

last: Wierzbicki


title: Chloroplast nucleoid is organized by membrane association of transcribed genes [IPOD]

overall_design: The data consists of 4 replicates of chloroplast IPOD including input controls in Col0 wt plants.  IPOD represents protein footprints (for all DNA-bound proteins).


title: Single-cell 5’ RNA-seq profiles of E16.5 forebrains in WT and Zfp661 knockout mice

status: Public on May 09 2023

city: Bethesda

first: Jinpu

last: Jin

address: Building 6B, Room 2B-211, 6 Center Drive

institute: NICHD

summary: In this assay, we aimed to investigate the impact of ZFP661 on the expression diversity of clustered protocadherin genes (Pcdhs). To accomplish this, we conducted single-cell 5’ RNA-seq analysis on developing mouse forebrains at embryonic day 16.5 (E16.5). Our findings reveal that ZFP661 enhances the expression diversity of Pcdhs by balancing the usage of Pcdh isoforms.

overall_design: We compared the usage of Pcdh isoforms and the expression diversity of Pcdhs between wild-type (WT) and Zfp661 knockout (KO) developing forebrains at E16.5. Two pairs of littermates, consisting of WT and Zfp661 KO mice, were utilized for the experiment.

first: Todd

last: Macfarlan


title: Specific processing of meiosis related transcript is linked to final maturation in human oocytes

status: Public on May 27 2023

city: Barcelona

first: Sara

last: Pietroforte

address: Balmes 236

institute: Eugin Group

summary: Human meiosis in oocytes entails a fine regulation of the transcriptome to support late oocyte growth and early embryo development, both key to reproductive success. Currently, little is known about the co- and post-transcriptional mRNA processing mechanisms regulating the last meiotic passages, which contribute to transcriptome complexity and influence translation rates.   We analyzed gene expression changes, splicing and pre-mRNA processing in an RNA sequencing set of 40 oocytes at different meiotic maturation stages, both in vivo ovulated and matured in vitro. We found abundant UTR processing, mostly at the 3’-, of meiosis-related genes between the stages of GV and MII, supported by the differential expression of spliceosome and pre-mRNA processing related genes. Importantly, we found very little differences among GV oocytes across several lengths of in vitro maturation, as long as they did not reach MII, suggesting a specific association of RNA processing and successful meiosis transit. Changes in protein isoforms are minor, though specific and consistent for genes involved in chromosome organization and spindle assembly. In conclusion, we reveal a dynamic transcript remodeling during human female meiosis, and show how pre-mRNA processing, specifically 3’-UTR shortening, drives a selective translational regulation of transcripts necessary to reach the final meiotic maturation.

overall_design:
For single-cell RNA sequencing analysis, 40 oocytes at different maturation stages were collected: 10 oocytes were included in the study as GV immediately after ovum pick-up, 10 as MII after in vitro maturation (IVM, IVM-MII), 10 as GV that failed to mature after IVM (FTM-GV) and 10 MII were collected in vivo (IVO-MII) and included in the study after vitrification/warming.

**Raw data and processed data are not provided due to the EU's General Data Protection Regulation (GDPR)**

first: Montserrat

last: Barragan

first: Anna

last: Ferrer-Vaquer

first: Manuel

last: Irimia

first: Elena

last: Ibañez

first: Mina

last: Popovic

first: Rita

last: Vassena

first: Filippo

last: Zambelli


title: Transcriptome-wide gene expression analysis of Formalin-Fixed Paraffin-Embedded (FFPE) biopsies of prostate cancer (PCa)

status: Public on Sep 08 2023

city: Leipzig

first: Michael

last: Rade

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary:
Clinical manifestation of PCa is highly variable. Aggressive tumors require radical treatment, while clinically non-significant ones may be suitable for active surveillance. We have previously developed the prognostic ProstaTrend signature mainly on prostatectomy specimens by application of transcriptome‐wide microarray and RNA-sequencing (RNA-Seq) analyses. We used a cohort of 185 tumor specimens obtained from FFPE biopsies for RNA-Seq to facilitate the application of ProstaTrend at the beginning of routine PCa diagnostic.
All patients of the FFPE biopsy cohort were treated by radical prostatectomy (RPx) and median follow-up for biochemical recurrence (BCR) was 9 years. Based on the transcriptome data of the FFPE biopsies, we filtered ProstaTrend for genes susceptible to FFPE-associated degradation via regression analysis. ProstaTrend was additionally restricted to genes with concordant prognostic effects in the RNA-Seq TCGA prostate adenocarcinoma (PRAD) cohort to ensure robust and broad applicability. The prognostic relevance of the refined Transcriptomic Risk Score (TRS) was analyzed by Kaplan-Meier curves, Cox-regression models in our FFPE-biopsy cohort and 9 other public datasets from PCa patients with BCR as primary endpoint.
The TRS based on the revised ProstaTrend signature, which included 204 genes, was significantly associated with BCR in the FFPE biopsy cohort (Cox-regression p-value <0.001). The TRS retained prognostic relevance when adjusted for Gleason Score (GS). We confirmed a significant association with BCR in 9 independent cohorts with a total of 1109 PCa patients. Comparison of the prognostic performance of the TRS with 17 other prognostically relevant PCa panels revealed that the revised ProstaTrend was among the best-ranked panels.

overall_design:
Total RNA of FFPE biopsy specimens of 185 PCa patients were assessed for gene expression profiling by strand-specific total RNASeq. 179 samples passed the quality filter, 3 samples were excluded because time to BCR was not recorded. In total, we analyzed transcriptome data from 176 patients, 75 of whom had a BCR during follow-up.
The submitter declares "Raw data cannot be submitted to GEO due to patient privacy issues"

first: Markus

last: Kreuz

first: Angelika

last: Borkowetz

first: Ulrich

last: Sommer

first: Conny

last: Blumert

first: Susanne

last: Füssel

first: Catharina

last: Bertram

first: Dennis

last: Löffler

first: Dominik

last: Otto

first: Livia

last: Wöller

first: Carolin

last: Schimmelpfennig

first: Ann-Cathrin

last: Gottschling

first: Pia

last: Hönscheid

first: Gustavo

last: Baretton

first: Manfred

last: Wirth

first: Christian

last: Thomas

first: Friedemann

last: Horn

first: Kristin

last: Reiche


title: scRNA-seq analysis of in vitro cultured monkey embryos

city: kunming

first: Ci

middle: bai

last: quan

address: bodalu

institute: lpbr

summary: Primates embryo implants into the maternal uterus, forms three germ layers and begin early organogenesis, such as neurulation, heart formation, during the first 4 weeks of development. Although, this stage represents a milestone in early embryonic development of primate, our understanding remains limited. Here, we optimized our previously established in vitro culture system, which enable the ex-utero culture of cynomolgus monkey up to 25 days. Morphology histological, and single-cell RNA sequencing analyses confirm that the in vitro cultured embryos recapitulate key events of in vivo development. Using this platform, we delineate monkey early-stage lineage trajectory and genetic programs accompanying the neural, mesoderm and endoderm speciﬁcation, as well as primordial germ cell–like cell (PGCLC). Thus, this culture system represents a valuable and easily accessible platform to study and manipulate early primate embryogenesis, which cannot easily accomplish in vivo.

overall_design: single cell RNA sequencing  of in  vitro cultured monkey embryos were performed using 10x Genomics Chromium

first: Tao

last: Tan


title: High-resolution Hi-C maps in EV and ZFP661-3HA OE mESCs

first: Jinpu

last: Jin

summary: In this assay, we aimed to investigate the impacts of ZFP661 on the permeability of CTCF barriers to chromatin interactions. To achieve this, we generated high-resolution Hi-C maps using empty vector (EV) control and ZFP661-3HA overexpressing (OE) mESCs. Our findings demonstrate that ZFP661 suppresses the trapping of cohesin at the CTCF barriers and modulates their permeability.

overall_design: We compared the alteration of insulation scores at CTCF barriers that are co-occupied with ZFP661 and those that are not, and also evaluated the transition between the two types of competitive interactions (being trapped at the CTCF barriers and those passing over them) after overexpressing ZFP661. Each genotype was represented by two biological replicates.

first: Todd

last: Macfarlan


title: Capture Hi-C in (EV and ZFP661-3HA OE) mESCs and E16.5 mouse forebrains

summary: This assay aimed to investigate the regulatory role of ZFP661 in modulating the permeability of CTCF barriers. To achieve this, we generated Capture Hi-C maps on several regions bound by ZFP661 using E16.5 forebrains from wild-type (WT) and Zfp661 knockout (KO) mice, as well as empty vector (EV) control and ZFP661-3HA overexpressing (OE) mESCs. Our findings reveal that ZFP661 modulates the permeability of CTCF barriers, thereby balancing between the interactions that are trapped at the barriers and those passing over them.

overall_design: We compared the interactions being trapped at the barriers and those passing over them in WT and Zfp661 KO E16.5 forebrains, as well as EV control and ZFP661-3HA OE mESCs. For the E16.5 forebrain samples, three pairs of littermates were used, while two biological replicates were used for each genotype in mESCs.


title: Alternation of gene expression when expressing FASN-CTF in ced-3(-) null animalsn under ER stress

first: Benjamin

last: Weaver

address: 6001 Forest Park Rd

department: Pharmacology

institute: University of Texas Southwestern Medical Center

summary: To investigate how  FASN-CTF affect gene expression under ER stress, we expressed auxin-induced-degron (AID) controlled  FASN-CTF transgene in ced-3(-) animals which had elevated stress response.

overall_design: We compared gene expression profile of ced-3(-) ( K-NAA treatment, CtrL) and ced-3(-) with FASN-CTF expression (no auxin treatment, CtOE).

first: Wei

last: Hai

first: Weaver

last: Yi

last: Benjamin


title: Effect of ATRX deficiency on gene expression of RCAS-nTva derived murine gliomas

status: Public on May 08 2023

city: Houston

last: Whitfield

state: TX

address: 5918 Belrose Dr

institute: MD Anderson/UT Health GSBS

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

overall_design: Refer to individual Series


title: Effect of ATRX deficiency on gene expression of RCAS-nTva derived murine gliomas [RNA-seq: ATRX_Immuno_Tumor]

summary: To investigate the impact of ATRX loss on tumor microenvironment we generated ATRX-intact and -deficient tumors in immune competent mice with the RCA-nTva system. Mice were injected with a tumorigenic RCAS construct (PDGFa and shTP53) and an RCAS bearing CRE recombinase. This was performed in mice that were ATRX wt and ATRX floxed.

overall_design: We performed expression profiling using bulk RNA-sequencing of 3 tumors in each group.

first: Ben

last: Whtifield

first: Prit

last: Malgulwar

first: David

last: Irvin

first: Jason

last: Huse


title: Effect of ATRX deficiency on gene expression of RCAS-nTva derived murine gliomas [RNA-seq: ATRX_Immuno_cell_line]

summary: To investigate the impact of ATRX loss on tumor microenvironment we generated ATRX-intact and -deficient tumors in immune competent mice with the RCA-nTva system. Mice were injected with a tumorigenic RCAS construct (PDGFa and shTP53) and an RCAS bearing CRE recombinase. This was performed in mice that were ATRX wt and ATRX floxed. Tumors were then harvested, processed, and cell lines were generated and cultured for downstream analysis.

overall_design: We performed expression profiling using bulk RNA-sequencing on cell lines derived from the above described tumor model. This was done on 3 technical replicates from the same 2 cell lines.


title: Remodelling of the endothelial cell transcriptional program via paracrine and DNA-binding activities of MPO [polyA-enriched total RNA-Seq]

status: Public on May 03 2023

city: Mainz

first: Yulia

last: Kargapolova

state: Rheinland-Pfalz

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: Myeloperoxidase (MPO) is an enzyme, which functions in host defence by catalysing the formation of reactive oxygen intermediates. Synthesized majorly by myeloid progenitor cell types and neutrophils MPO is released into vascular lumen during inflammation, where it may adhere and internalize the endothelial cells coating vascular walls. Here we describe the moonlighting properties of MPO and its regulation of gene transcription in endothelial cells upon nuclear internalization. We show that MPO independently of its enzymatic activity possess chromatin binding properties in vitro and in cyto.  Upon nuclear translocation, MPO changes chromatin condensation. Locally at sites of binding, MPO drives de-condensation of chromatin and at the regions flanking MPO binding sites drives an increased chromatin condensation. MPO-guided changes in chromatin condensation lead to activation of endothelial-to-mesenchymal transition in ECs and enhanced migratory potential. Moreover, MPO directly binds to the double-stranded RNA binding protein and transcription factor ILF3 and facilitates translocation of its isoform NF90 into the nucleus. This results in positive regulation of expression of VEGFA, as well lowered stability of CXCL1 and CXCL8 transcripts due to loss of cytoplasmic ILF3.

overall_design: polyA-enriched mRNA profiles of MPO treated and mock treated HUVECs

first: Ruiyuan

last: Zheng

first: Argyris

last: Papantonis

first: Stephan

last: Baldus


title: Remodelling of the endothelial cell transcriptional program via paracrine and DNA-binding activities of MPO [3-end-Seq]

overall_design: 3'-end RNA-Seq of HUVECs: ctr_siRNActr, MPO2h_siRNActr, ctr_siRNAILF3, MPO2h_siRNAILF3


title: Remodelling of the endothelial cell transcriptional program via paracrine and DNA-binding activities of MPO


title: Gene expression profile at single cell level of syngeneic ovarian tumors from mice treated with inhibitory Activin-A antibody or control IgG

status: Public on May 01 2023

city: los angeles

first: Sandra

last: Orsulic

state: california

address: 10833 Le conte ave

department: OBGYN

institute: UCLA

summary: Effective targeting of cancer-associated fibroblasts (CAFs) is hindered by the lack of specific biomarkers and a poor understanding of the mechanisms by which different populations of CAFs contribute to cancer progression. While the role of TGFβ in CAFs is well-studied, less attention has been focused on a structurally and functionally similar protein, Activin A (encoded by INHBA), which is typically associated with poor survival and advanced stage in ovarian cancer. Here, we identified INHBA(+) CAFs as key players in tumor promotion and immune evasion. In syngeneic ovarian cancer mouse models, intraperitoneal injection of the Activin A neutralizing antibody attenuated tumor progression and infiltration with the host INHBA(+) CAFs and M2 macrophages. Collectively, our study identified an INHBA(+) subset of pro-tumoral CAFs as a potential therapeutic target in ovarian cancer.

overall_design: To facilitate uniform recruitment of host fibroblasts to the tumor, we used the peritoneal abrasion-facilitated C57BL/6 p53/myc/Hras model in which peritoneal wound healing facilitates the recruitment of fibroblasts into the tumor. C57BL/6 mice with peritoneal abrasion were injected i.p. with syngeneic p53/myc/Hras ovarian cancer cells (genotype: p53-/-, myc, Hras). One day after cancer cell injection, the mice received daily i.p. injections of the Activin A neutralizing antibody (n=8) or control IgG (n=7).  After 10 days of treatment, mice were euthanized to assess the intraperitoneal tumor burden. Mice treated with the Activin A neutralizing antibody had smaller tumor lesions at the site of peritoneal abrasion.

first: Maria

middle: S

last: Recouvreux


title: Remodelling of the endothelial cell transcriptional program via paracrine and DNA-binding activities of MPO [ATAC-seq]

overall_design: ATAC-Seq, MPO treated and untreated HUVECs

first: Theodoros

last: Georgomanolis


title: Local antigen is required for CD8+ tissue resident memory T cell (Trm) generation in large intestine

status: Public on Apr 30 2023

city: Geneva

first: Liqing

last: Cheng

address: 1 rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary:
The specifying signals provided by the tissue microenvironment to promote acquisition of Trm features vary across anatomical niches, and those delivered in the large intestine (LI) remain largely uncharacterized. Here we show that following migration of activated T cells from the priming lymph nodes, antigen recognition in the tissue microenvironment is crucial to establish LI CD8 Trm. In the absence of tissue-confined antigen, T cells fail to generate memory precursors and to accumulate in the tissue. Local antigen presentation boosts Trm generation in a dose-dependent manner, and prompts transient acquisition of a distinctive transcriptional program including key signatures of gut Trm. The definitive transcriptional landscape of LI Trm cells comprises both features that are shared with Trm at other locations, as well as unique elements.
Our findings identify antigen presentation in the gut microenvironment as a key step in the generation of large LI CD8 Trm, providing key insight for the optimization of mucosal immunization strategies.

overall_design: Based on our previous study, to have a more comprehensive understanding of large intestine lamina propria (LILP) Trm cells, we established Listeria-OVA (Lm-OVA) oral infection model combining with OTI cell transfer. At day30, spleen memory OTI cells were sorted, followed by bulk RNA-seq. Thus, we can have a direct comparison between spleen memory T and LILP Trm cells.

first: Simone

last: Becattini


title: A quantitative model for the transcriptional landscape of the bacterial cell cycle

status: Public on May 02 2023

city: New York City

first: Itai

last: Yanai

address: 435 East 30th Street

institute: NYU Langone Health

summary: Regulation of gene activity during the cell cycle is fundamental to bacterial replication but is challenging to study in unperturbed, asynchronous bacterial populations. Using single cell RNA-sequencing of heterogeneous Staphylococcus aureus populations, we uncovered a global gene expression pattern dominated by chromosomal position. We show that this pattern results from the effect of DNA replication on gene expression, and in Escherichia coli, changes under different growth rates and modes of replication. By constructing a quantitative model in each species that links replication to cell cycle gene expression, we identified divergent genes that may be instead subject to distinct regulation, and applied this cell cycle framework to characterize heterogeneity in responses to antibiotic stress. Our approach reveals a highly dynamic cell cycle transcriptional landscape and may be broadly applicable across species.

sample_organism:
Escherichia coli
Staphylococcus aureus
Bacillus subtilis

overall_design:
scRNA-seq by the PETRI-seq method was performed on bacteria of species Escherichia coli and Staphylococcus aureus.
scRNA-seq by the PETRI-seq method was performed on bacteria of species Escherichia coli and Bacillus subtilis.

first: Andrew

last: Pountain


title: Deconstructing replicative senescence heterogeneity of human mesenchymal stem cells at single cell resolution reveals therapeutically targetable senescent cell sub-populations

city: Brisbane

first: Atefeh

last: Taherian Fard

address: St Lucia

institute: The University of Queensland

summary: Cellular senescence is characterised by a state of permanent cell cycle arrest. While cellular senescence is a recognised driver of organismal ageing, the extent of heterogeneity within and between different senescent cell populations remains largely unclear. Here we combined cell biological and single cell RNA-sequencing approaches to investigate heterogeneity of replicative senescence in human ESC-derived mesenchymal stem cells (esMSCs) as MSCs are the cell type of choice for the majority of current stem cell herapies and senescence of MSC is a recognized driver of organismal ageing. We identified three senescing esMSC subpopulations and their associated maker genes, allowing us to identify potential drug targets that may delay the emergence of senescent MSCs in vitro and perhaps in vivo in the future.

overall_design: Mesenchymal stem cells undergoing replicative senescence. Three timepoints and three biological replicates in each timepoint. Over all 9 samples.

first: Jessica

last: Mar

first: Ernst

last: Wolvetang


title: Organization, genomic targeting and assembly of three distinct SWI/SNF chromatin remodeling complexes in Arabidopsis [ChIP-seq]

status: Public on Apr 24 2023

city: Guangzhou

first: yaoguang

last: yu

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

summary: Switch defective/sucrose non-fermentable (SWI/SNF) complexes are evolutionarily conserved multi-subunit machines that play vital roles in chromatin architecture regulation for modulating gene expression via sliding or ejection of nucleosomes in eukaryotes. In plants, perturbations of SWI/SNF subunits often result in severe developmental disorders. However, the subunit composition, pathways of assembly, and genomic targeting of the plant SWI/SNF complexes remain undefined. Here, we reveal that Arabidopsis SWI/SNF complexes exist in three distinct final form assemblies: BRM-associated SWI/SNF complexes (BAS), SYD-associated SWI/SNF complexes (SAS) and MINU-associated SWI/SNF complexes (MAS). We show that BAS complexes are equivalent to human ncBAF, whereas SAS and MAS complexes evolve in multiple subunits unique to plants, suggesting a plant-specific functional evolution of SWI/SNF complexes. We further demonstrate overlapping and specific genomic targeting of the three plant SWI/SNF complexes on chromatin and reveal that SAS complexes are necessary for the correct genomic localization of the BAS complexes. Finally, by focusing on the SAS and BAS complexes, we establish a requirement for both the core module subunit and the ATPase in the assembly of the plant SWI/SNF complexes. Together, our work highlights the divergence of SWI/SNF chromatin remodelers during the eukaryote evolution and provides a comprehensive landscape for understanding the plant SWI/SNF complexes organization, assembly, genomic targeting, and function.

overall_design: NOT PROVIDED; REQUESTED

first: Chenlong

last: Li

first: Wei

last: Fu

first: Yaoguang

last: Yu


title: Dissolution of RNA condensates by the embryonic stem cell protein L1TD1 [RNA-seq]

status: Public on Apr 26 2023

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

institute: Sejong University

summary: L1TD1 is a cytoplasmic RNA-binding protein that is specifically expressed in pluripotent stem cells and, unlike its mouse paralogue, is essential for the maintenance of stemness in human cells. Although L1TD1 is the only known domesticated gene from a LINE-1 (L1) retroelement, the functional legacy from its ancestral protein, ORF1p of L1, and the novelty are so far unknown. Here, we determined RNAs associated with L1TD1 and found that, like ORF1p, L1TD1 binds L1 RNAs, localizes to high-density ribonucleoprotein (RNP) condensates, and increases L1 retrotransposition. Unexpectedly, L1TD1 enhanced the translation of a subset of mRNAs enriched in the condensates. In HeLa cells, ectopically expressed L1TD1 facilitated the dissolution of stress granules and granules formed by pathological mutations of TDP-43 and FUS. The glutamate-rich domain and the ORF1-homology domain facilitated dispersal of the RNPs and induced autophagy, respectively. These results provide insights into how L1TD1 regulates gene expression in pluripotent stem cells. We propose that the ability of L1TD1 to dissolve stress granules may provide novel opportunities for treatments of neurodegenerative diseases caused by disturbed stress granule dynamics.

overall_design: RNA-seq of mRNAs associated ribosome in L1TD1-depleted cells, RNA-seq of mRNAs in RNA condensates in human embryonic stem cells.


title: ZmNRT1.1B (ZmNPF6.6) determines nitrogen use efficiency via regulation of nitrate transport and assimilation in maize

status: Public on Apr 25 2023

city: BeiJing

first: huairong

last: cao

state: Haidian

address: West Yuanmingyuan Road

institute: China Agricultural University

summary: Nitrate (NO3-) is crucial for optimal plant growth and development and often limits crop productivity at the low availability. In comparison with model plant Arabidopsis, the molecular mechanisms underlying NO3- acquisition and utilization remain largely unclear in maize. In particular, only a few genes have been exploited to improve nitrogen use efficiency (NUE). Here, we demonstrated that NO3--inducible ZmNRT1.1B (ZmNPF6.6) positively regulated NO3--dependent growth and NUE in maize. We showed that the tandem duplicated proteoform ZmNRT1.1C is irrelevant to maize seedling growth under nitrate supply, however, loss-of-function of ZmNRT1.1B significantly weakened plant growth under adequate NO3- supply in both hydroponic and field conditions. 15N-labeled NO3- absorption assay indicated that ZmNRT1.1B mediated high-affinity NO3--transport and root-to-shoot NO3- translocation. Furthermore, upon NO3- supply, ZmNRT1.1B promotes cytoplasmic-to-nuclear shuttling of ZmNLP3.1 (ZmNLP8), which co-regulates the expression of genes involved in NO3- response, cytokinin biosynthesis and carbon metabolism. Remarkably, overexpression of ZmNRT1.1B in modern maize hybrids improved grain yield under nitrogen (N) limiting fields. Taken together, our study revealed a crucial role of ZmNRT1.1B in high-affinity NO3- transport and signaling and offers valuable genetic resource for breeding nitrogen use efficient high-yield cultivars.

overall_design: 18 samples with 3 biological replicats. Wild type vs mutant comparison,KNO3 vs KCl comparison

first: H

last: Cao

first: Z

last: Jia

first: L

last: Yuan


title: Cellular and transcriptional impacts of ruxolitinib versus IFN-gamma neutralization in mouse models of HLH

city: Memphis

first: Kim

last: Nichols

state: TN

address: 262 Danny Thomas Pl

department: Oncology

institute: St. Jude Children's Research Hospital

summary: Hemophagocytic lymphohistiocytosis is a cytokine storm syndrome characterized by the excessive activation of myeloid and T cells. In primary HLH (pHLH), disease pathophysiology is driven by CD8 T cells proliferation and IFNg production. Therefore, targeting IFNg has been a viable option for the treatment of HLH. Since many cytokines that signaling throught the JAK/STAT pathway, including IFNg, largely drive cytokine storm in HLH, we and others have demonstrated that targeting JAK1/2 with ruxolitinib is effective in ameliorating disease manifestations in pre-clinical models of HLH. Both IFNg and ruxolitinib treatments have also shown great efficacy in dampening inflammation in patients with HLH, albeit not completely. Since ruxolitinib treatment does not fully inhibit IFNg production, we sought to determine the effect of combining ruxolitinib treatment with IFNg neutralization as a treatment option in a LCMV-infected Prf1 mice. We aimed to elucidate the effects of these treatments on the main hematologic and cellular parameters of disease. Moreover, we determined the main changes in the transcriptional landscape on CD8 T cells isolated from mice infected with LCMV either untreated or treated with aIFNg, ruxolitinib, or combination treatments. We demonstrate that combination treatment was very effective in reversing anemia and thrombocytopenia, but failed to reduce splenomegaly, hypercytokinemia, and myeloid and T cell numbers compared to ruxolitinib treatment. Transcriptional analysis revealed distinct pathways targeted by aIFNg and ruxolitinib; while aIFNg was more effective in downregulating the expression of interferon gamma response genes, allograft rejection, and complement genes, ruxolitinib treated CD8 T cells displayed a reduction in expression of genes involved in reactive oxygen species, glycolysis, E2F targets, and protein secretion pathways. Therefore, this study provide novel insights on the effects of combining ruxolitinib treatment with IFNg neutralization in the treatment of primary HLH.

overall_design: RNA sequencing analysis of CD8 T cells sorted on day 9 p.i.  from Prf1-/- naïve mice, LCMV-infected untreated, or treated in vivo with aIFNg, ruxolitinib, or combination treatment (day 4-8 p.i.)

first: Sabrin

last: Albeituni

first: Ninad

last: Oak

middle: E


title: Transposon Insertion Sequencing to study the genetic interactions between V. cholerae WT cells and two mutant strains in absence or presence of subinhibitory doses of tobramycin

city: Paris

first: André

last: Carvalho

address: 28 Rue du Dr Roux

country: France

institute: Institut Pasteur

summary: This study was conducted to study which genes or functions become important or expendable in two V. cholerae mutants compared to the WT. This was assessed directly by conjugating a Mariner Transposon with WT or mutant cells and obtaining a bank of hundreds of thousands of mutants which we consider as the T=0. We then subjected these banks to 16 generations in rich media with or without 50% MIC of tobramycin (which we call T=16gen). At both T0 and T16gen we extracted the genomic DNA of these banks and sequenced it to identify the regions where the transposon is inserted in each strain at the different conditions.

sample_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: For each strain, three biological replicates were used. J085 strain corresponds to V. cholerae WT strain, H505 corresponds to the vchM (vca0198) mutant and M092 corresponds to the double mutant (vca0762-vca0763).

first: Sebastian

last: Aguilar Pierlé


title: RNA expression profiles of drug-resistant TNBC cell lines after chemotherapy

status: Public on Apr 22 2023

first: MINWOO

last: KIM

state: Seoul

address: 50-1 Yonsei-ro, Seodaemum-gu

institute: Yonsei University College of Medicine

summary: The impact of three different chemodrugs (Adriamycin, Taxotere, Cytoxan) on the breast cancer cell line (MDA-MB-468) was analyzed compared to the parental cell by RNA-sequencing.

first: Min Woo

last: Kim

first: Jee Ye

first: Seung Il


title: Arsenic trioxide inhibits lung metastasis of breast cancer by suppression of TP53, TGFβ and TNFα signaling pathways

status: Public on Apr 16 2023

city: FuZhou

first: Haiwei

last: Wang

state: FuJian

address: Daoshan road 180

institute: Fujian Maternity and Child Health Hospital

summary: Metastasis is the main cause of mortality of breast cancer. To explore the mechanisms of arsenic trioxide (ATO) in inhibition of breast cancer metastasis, ATO regulated genes in breast cancer MDA-MB-231 and LM2-4175 cells were studied. After data analysis, ATO regulated genes were involved in TP53, TGFβ and TNFα signaling pathways. Furthermore, TGFβ and TNFα activated genes in breast cancer MDA-MB-231 cells were studied.

overall_design: MDA-MB-231 and LM2-4175 cells were treated with ATO 5μM for 0, 6, 12, 24 and 36 hours. MDA-MB-231 cells were treated with TGFβ or TNFα for 2 hours. Total RNA was collected and profiled to Affymetrix microarray.


title: RhoA GEF Mcf2lb regulates rosette integrity during collective cell migration

status: Public on Apr 19 2023

city: Portland

first: Alex

last: Nechiporuk

state: OR

address: 3181 SW Sam Jackson Park Road

institute: Oregon Health and Science Univ

summary: During development, multicellular rosettes serve as important cellular intermediates in the formation of diverse organ systems. Multicellular rosettes are transient epithelial structures that are defined by the apical constriction of cells towards the rosette center. Due to the important role these structures play during development, understanding the molecular mechanisms by which rosettes are formed and maintained is of high interest. Utilizing the zebrafish posterior lateral line primordium (pLLP) as a model system, we identify the RhoA GEF Mcf2lb as a regulator of rosette integrity. The pLLP is a group of ~150 cells that migrates along the zebrafish trunk and is organized into epithelial rosettes; these are deposited along the trunk and will differentiate into sensory organs called neuromasts (NMs). Using single-cell RNA sequencing and whole-mount in situ hybridization, we showed that mcf2lb is expressed in the pLLP during migration. Given the known role of RhoA in rosette formation, we asked whether Mcf2lb plays a role in regulating apical constriction of cells within rosettes. Live imaging and subsequent 3D analysis of mcf2lb mutant pLLP cells showed disrupted apical constriction and subsequent rosette organization. This in turn resulted in a unique posterior Lateral Line phenotype: an excess number of deposited NMs along the trunk of the zebrafish. Cell polarity markers ZO-1 and Par-3 were apically localized, indicating that pLLP cells are normally polarized. In contrast, signaling components that mediate apical constriction downstream of RhoA, Rock-2a and non-muscle Myosin II were diminished apically. Altogether our results suggest a model whereby Mcf2lb activates RhoA, which in turn activates downstream signaling machinery to induce and maintain apical constriction in cells incorporated into rosettes.

overall_design: Cells from Tg(-8.0claudinB: lynGFP)zf106; TgBAC(cxcr4b:F-tractin-mCherry) transgenic line were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of GFP and mCherry signal and analyzed using scRNAseq.

first: Hannah

last: Olson

first: Amanda

last: Maxfield

first: Nicholas

last: Calistri

first: Laura

last: Heiser

middle: V


title: Optimized alternative ordering of dapagliflozin and sacubitril-valsartan in post-myocardial infarction heart failure

status: Public on Apr 13 2023

city: Tianjin

first: Wenqi

last: Tao

address: 190 Jieyuan Road, Hongqiao District, Tianjin?

institute: Tianjin Union Medical Center

summary: We tested it in an animal model of myocardial infarction to ensure whether early initiation of dapagliflozin (DAPA), or different orders of combination with sacubitril-valsartan would result in a greater improvement of heart function than sacubitril-valsartan alone in post-myocardial infarction heart failure.

overall_design: Total RNA extractions of the left ventricles from cardiac tissues of sham group, MI group and DAPA group (3 biological replicates per group) were performed

first: W

last: Yang

first: Qing

last: Zhang

first: Shuli

last: Bi

first: Z

last: Yao


title: p120 RasGAP and ZO-2 promote the tumor suppressor function of p190A RhoGAP

status: Public on Apr 15 2023

city: Boston

first: Steen

last: Hansen

state: MA

address: Enders Building, Room 1016

department: GI Division

institute: Boston Children's Hospital

summary: ARHGAP35 encoding p190A RhoGAP (p190A) was identified by GWAS as a major human cancer gene. Our published studies have determined that p190A is a tumor suppressor that activates the canonical Hippo pathway. To elucidate how p190A signals in this context, we performed mass spectrometry to identify p190A binding proteins. Two interactors were identified significantly more frequently than others: p120 RasGAP (p120) and ZO-1. Originally p190A was cloned via its direct binding to p120, hence validating our approach. In addition, we found that p190A also binds to ZO-2. The interaction of p190A with ZO-2 is dependent on p120, thus suggesting formation of a ternary complex. Next, we determine that both p120 and ZO-2, but not ZO-1, are necessary for p190A to activate LATS kinases and suppress tumorigenesis in a xenograft mouse model. Moreover, the interactions with p120 and ZO-2 are essential for transcriptional modulation by p190A, including the CDH1 gene encoding E-cadherin, which we previously have demonstrated is essential for p190A signaling. Collectively, this work identifies a novel tumor suppressor interactome of p190A, which includes ZO-2, an established constituent of the Hippo pathway, and p120, which in spite of its strong association with Ras signaling, is essential for p190A to activate LATS kinases.

overall_design: H661 cells, which harbor defined ARHGAP35 loss-of-function alterations, were restored with wild-type p190A expression to generate H661-p190A cells. H661 cells were also restored with p190A mutant (Y1087F+Y1105F), we abbreviate this mutant p190A(Y2F). To generate H661-p190A cells with knockout of TJP1 and TJP2, H661-p190A cells were transduced with lentivirus encoding Cas9 and TJP1 or TJP2 sgRNA. Global transcriptomes were profiled by bulk RNA-Seq for H661-control cells, H661-p190A cells, H661-p190A(Y2F) cells, H661-p190A+TJP1-ko cells, H661-p190A+TJP2-ko cells. To investigate the H661 cell line specific Hippo pathway gene sets, we generated H661+p190A+LATS1/2-kd cells as well as H661+p190A as control, for which we have tested their function in our previous Oncogene 2020 paper (doi.org/10.1038/s41388-020-1385-2).

first: Hanyue

last: Ouyang


title: Dissolution of RNA condensates by the embryonic stem cell protein L1TD1

first: Young-Soo

last: Kwon

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

overall_design: Refer to individual Series


title: Characterizing adjuvants’ effects at the murine immunoglobulin repertoire level

status: Public on Apr 07 2023

first: Feng

last: Feng

state: United States

address: 650 Albany Street X248

institute: Boston University

summary: We developed an improved library prep protocol and standardized the data analysis pipeline for accurate repertoire profiling. In addition, two metrics were implemented to assess repertoire clone properties. We then studied systemically the effects of two adjuvants, CpG and Alum, on the Ig heavy chain repertoire using the ovalbumin (OVA) challenged mouse model. Ig repertoires of different tissues (spleen and bone marrow) and isotypes (IgG and IgM) were examined and compared in terms of sequence mutation frequency, IGHV gene usage, CDR3 length, rescaled Hill numbers for clonal diversity, and clone selection strength. As a result, Ig repertoires of different tissues or isotypes exhibited distinguishable profiles at the non-immunized steady state. Adjuvanted immunizations further resulted in statistically significant alterations in Ig repertoire compared with PBS or OVA alone immunized groups. Lastly, we applied unsupervised machine learning techniques – multiple factor analysis and clustering – to identify Ig repertoire signatures in different compartments and under varying immunizations.

overall_design: Age-matched C57BL/6J mice were immunized with ovalbumin with or without adjuvants (PBS control, Ova alone, Ova+CpG and Ova+Alum). There were three mice in each group. A week after the fourth immunization, BMs and spleens were harvested, total RNA were isolated, and IgSeq library was prepared. Sequencing was done on the Illumina HiSeq 2500 platform with pair-end 2x250 chemistry.  Each sample received on average 1M paired reads. The data were demultiplexed and preprocessed with an newly-developed pipeline.  Then we studied Ig repertoire profiles in different tissues (BM vs spleen) and under different adjuvant effects (CpG vs Alum) by comparing IGHV gene segment usage, mutation frequency, CDR3 length, clonal diversity, and clone selection strength.

first: Yumei

first: Rachel

last: Yuen

first: Thomas

last: Kepler


title: Characterization of long-term ex vivo expansion of tree shrew spermatogonial stem cells

status: Public on Apr 06 2023

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

summary: Purpose: The goals of this study are to clarify influence of long-term expansion on the spermatogenesis potential of tree shrew spermatogonial stem cells （SSCs）

overall_design: Transcriptome comparation of tree shrew SSCs at the passage of 17, 26, 41 and 53. Assessment the role of nicotinamide ribose  in treated or untreated tree shrew SSCs

first: Cong

last: Li


title: Identification of genes induced or suppressed by TSH

city: Research Triangle Park

first: Hong Soon

last: Kang

state: NC

address: 111 T.W. Alexander Dr.

department: IIDL

institute: NIH/NIEHS

summary: Gene expression profiles were compared in thyroid gland from mice fed normal diet (ND) and Low iodine diet (LID).

overall_design: RNA was extrtacted from WT and Pax8Cre driven Glis3 conditional KO (cKO)  mice fed ND and LID and exmained the gene expression by RNA-Seq analysis.

first: Anton

last: Jetten

first: Hong

first: Sara

last: Grimm


title: Characteristics and anatomic location of PD-1+TCF1+ stem-like CD8 T cells in chronic viral infection and cancer

status: Public on Apr 02 2023

city: Suwon-si

first: Se Jin

last: Im

state: Gyeonggi-do

address: 2066, Seobu-ro, Jangan-gu

department: Department of Immunology

institute: Sungkyunkwan University School of Medicine

summary: CD8 T cells play an essential role in anti-tumor immunity and chronic viral infections. Recent findings have delineated the differentiation pathway of CD8 T cells in accordance with the progenitor-progeny relationship of TCF1+ stem-like and Tim-3+TCF1- more differentiated T cells. Here we investigated the characteristics of stem-like and differentiated CD8 T cells isolated from several murine tumor models and human lung cancer samples in terms of phenotypic and transcriptional features as well as their location compared to virus-specific CD8 T cells in the chronically LCMV-infected mice. We found that CD8 tumor-infiltrating lymphocytes (TILs) in both murine and human tumors exhibited overall similar phenotypic and transcriptional characteristics compared to corresponding subsets in the spleen of chronically infected mice.

overall_design: Primary and metastatic tumors in lung tissues were obtained from 19 patients with stage I-IV. Stem-like (Tim-3-CD28+ PD-1+) and exhausted (Tim-3+ PD-1+) human CD8 T cells were sorted from frozen TIL samples isolated from NSCLC patients.  And naive (CCR7+CD45RA+CD58-CD95-) CD8 T cells from a healthy subject.

first: Se

middle: J

first: Rafi

last: Ahmed


title: Transcriptomic changes in the medial prefrontal cortex of juvenile rat offspring after induced birth with oxytocin

status: Public on Apr 05 2023

city: St. Louis

first: Arvind

last: Palanisamy

state: MO

address: 660 S Euclid Ave

department: Anesthesiology

institute: Washington University School of Medicine

summary: We report changes in the medial prefrontal cortical transcriptome of male and female rat offspring after induced birth with oxytocin using RNA-seq analysis.

overall_design: We performed RNA-seq analysis to examine differential gene expression in the mPFC of P45 male and female rat offspring after elective birth induction with oxytocin or saline (n=6 animals/sex/treatment). With an FDR adjusted p ≤ 0.05 and linear FC ≥ 2, we identified a small number of mostly non-overlapping genes that were significantly differently expressed in male and female oxytocin-exposed offspring.


title: Fission Yeast TORC1 Promotes Cell Proliferation through Sfp1, a Transcription Factor Involved in Ribosome Biogenesis

status: Public on Apr 01 2023

city: HERSHEY

first: Yen Teng

last: Tai

state: PA

address: 700 HMC Cres Rd

department: Biochemistry and Molecular Biology

institute: Penn State College of Medicine

summary: To study the TORC1-mediated transcriptional regulation of the genes involved in ribosome biosynthesis in fission yeast

overall_design: Comparative gene expression profiling analysis of RNA-seq data for fission yeasts (wild type and knockout mutants of sfp1, ifh1 and fhl1 genes)

first: Tomoyuki

last: Fukuda

first: Yuichi

last: Morozumi

first: Hayato

last: Hirai

first: Arisa H.

last: Oda

first: Yoshiaki

last: Kamada

first: Yutaka

last: Akikusa

first: Tomotake

last: Kanki

first: Kunihiro

last: Ohta

first: Kazuhiro

last: Shiozaki


title: Nasopharyngeal lymphatic plexus serves as a central hub for drainage of cerebrospinal fluid [Aged]

city: Daejeon

first: Myung Jin

last: Yang

institute: Institute for Basic Science

summary: To investigate the heterogeneity of murine nasopharyngeal LECs, CD31+ PDPN+ LECs from the aged mouse nasopharynx were FACS sorted and single-cell RNA seq was performed

overall_design: NasoPharyngeal LECs (CD31+ PDPN+) were FACS sorted and single-cell libraries were made

first: Gou

middle: Y

last: Koh

first: Myung


title: C. elegans ADARs promote organismal survival to pathogen infection

city: Bloomington

first: Heather

middle: Ann

last: Hundley

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

summary: Here, we reveal that the Caenorhabditis elegans ADAR proteins promote survival of animals exposed to several opportunistic human pathogens. Our data indicate that ADARs help maintain proper levels of cuticular collagen genes, which in turn affects defense of the nematode to these bacteria.

overall_design: High throughput sequencing of L4 whole animals RNA-seq libraries exposed to either Pseudomonas aeruginosa strain PA14 or OP50

first: Alfa

last: Dhakal

first: Chinnu

last: Salim


title: Integrated multi-omics and bioinformatic methods to reveal the mechanisms of sinomenine against diabetic nephropathy

city: xiamen

first: Yan

last: Li

state: Fujian

address: Zhenhai road

institute: Xiamen University

summary: To investigate the function and the molecular mechanism of sinomenine in treating diabetic nephropathy via transcriptomics study.

overall_design: In-vivo study, DN rats were randomized to be treated with vehicle or SIN (20mg/kg or 40 mg/kg) daily by gavage for 8 weeks. Then, the pharmacological effect of SIN on DN and the potential mechanisms were also evaluated in vivo by biochemical evaluation, histopathological examination, transcriptomics, and metabolomics.

first: Huakui

last: Zhan


title: Transcriptional analysis of ATRX deficiency in a M059J model

status: Public on Mar 31 2023

city: Durham

first: David

last: Ashley

address: 203 Research Dr, MSRB1

department: Neurosurgery

institute: Duke University

summary: Stimulating the innate immune system has been explored as a therapeutic option for the treatment of gliomas. Inactivating mutations in ATRX, a defining molecular alteration in IDH-mutant astrocytomas, have been implicated in dysfunctional immune signaling. However, little is known about the interplay between ATRX loss and IDH mutation on innate immunity. To explore this biology, we generated ATRX knockout glioma models in the presence and absence of the IDH1R132H mutation. ATRX-deficient glioma cells were sensitive to dsRNA-based innate immune agonism and exhibited impaired lethality and increased T-cell infiltration in vivo. However, the presence of IDH1R132H dampened baseline expression of key innate immune genes and cytokines in a manner restored by genetic and pharmacological IDH1R132H inhibition. IDH1R132H co-expression did not interfere with the ATRX KO-mediated sensitivity to dsRNA. Thus, ATRX loss primes cells for recognition of dsRNA, while IDH1R132H reversibly masks this priming. This work reveals innate immunity as a therapeutic vulnerability of astrocytoma.

overall_design: RNAseq analysis of ATRX-intact or ATRX-deficient M059J cells.

first: Seethalakshmi

last: Hariharan

first: Michelle

middle: L

last: Bowie

first: Kevin

last: Stevenson


title: Transcriptional analysis of ATRX deficiency in a CT2A glioma model

overall_design: RNAseq analysis of ATRX-intact or ATRX-deficient CT2A cells.