title: Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

status: Public on May 22 2024

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

type:
Other
Third-party reanalysis

summary: Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides, and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) which died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding twenty-eight chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive-X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth’s death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

relation:
Reanalysis of: GSM1551550
Reanalysis of: GSM1551551
Reanalysis of: GSM1551552
Reanalysis of: GSM1551553
Reanalysis of: GSM1551554
Reanalysis of: GSM1551555
Reanalysis of: GSM1551556
Reanalysis of: GSM1551557
Reanalysis of: GSM1551558
Reanalysis of: GSM1551559
Reanalysis of: GSM1551560
Reanalysis of: GSM1551561
Reanalysis of: GSM1551562
Reanalysis of: GSM1551563
Reanalysis of: GSM1551564
Reanalysis of: GSM1551565
Reanalysis of: GSM1551566
Reanalysis of: GSM1551567
Reanalysis of: GSM1551568
Reanalysis of: GSM1551569
Reanalysis of: GSM1551570
Reanalysis of: GSM1551571
Reanalysis of: GSM1551572
Reanalysis of: GSM1551573
Reanalysis of: GSM1551574
Reanalysis of: GSM1551575
Reanalysis of: GSM1551576
Reanalysis of: GSM1551577
Reanalysis of: GSM1551578

sample_organism:
Homo sapiens
Equus asinus
Bos taurus
Mammuthus primigenius
Elephas maximus indicus

overall_design: We use PaleoHi-C on a skin sample from a 52,000 woolly mammoth to assemble its genome using a reference assited 3D genome assembly method. We show how the method works by assembling a donkey genome, both de novo and using reference-assisted 3D genome assembly. We also assemble genomes of Asian and African elephants. We analyze and compare contact data for the woolly mammoth and the Asian and African elephants. We generate data for multiple Asian elephant tissues and show that the mammoth PaleoHi-C data contains cell-specific information. We map loops. We compare compartmentalization patterns to reveal genes whose transcription was potentially altered in mammoths vs. elephants. We use PaleoHi-C to infer 3D structures of woolly mammoth chromosomes. We perform a series of proof-of-principle experiments using beef to show that dehydration is beneficial for preservation of 3D genome architecture, even at elevated temperatures. The processed files also include reanalysis of GSM1551550-GSM1551578 (Rao, Huntley et al, 2014; Harris, Gu et al., 2023) and ENCFF531FEY (https://www.encodeproject.org/files/ENCFF531FEY).

first: Marcela

last: Sandoval-Velasco

first: Juan

last: Rodríguez

first: Cynthia

last: Pérez Estrada

first: Marc

last: Marti-Renom

first: M

last: Gilbert

first: Erez

last: Aiden


title: Direct transposition of native DNA for sensitive multimodal single-molecule sequencing II

status: Public on May 01 2024

city: San Francisco

first: Arjun

middle: S

last: Nanda

state: California

address: 1700 Owens St

department: Gladstone Institute for Data Science & Biotechnology

country: USA

institute: Gladstone Institutes / UCSF

summary: Concurrent readout of sequence and base modifications from long unamplified DNA templates by PacBio single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90–99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SMRT-Tag of 40 ng or more human DNA (approximately 7,000 cell equivalents) yielded data comparable to gold standard whole-genome and bisulfite sequencing. SAMOSA-Tag of 30,000–50,000 nuclei resolved single-fiber chromatin structure, CTCF binding and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization. Tagmentation thus promises to enable sensitive, scalable and multimodal single-molecule genomics for diverse basic and clinical applications.

overall_design: Chromatin profiling with m6dA methyltransferase footprinting of mESCs, followed by transposase-mediated PCR-free library construction in situ (SAMOSA-Tag) and single molecule sequencing.

first: Ke

last: Wu

first: Sivakanthan

last: Kasinathan

first: Megan

last: Ostrowski

first: Ansuman

middle: T

last: Satpathy

first: E

middle: A

last: Sweet-Cordero

first: Hani

last: Goodarzi

first: Vijay

last: Ramani


title: Direct transposition of native DNA for sensitive multimodal single-molecule sequencing III

overall_design: Chromatin profiling with m6dA methyltransferase footprinting of the OS152 osteosarcoma cell line, followed by transposase-mediated PCR-free library construction in situ (SAMOSA-Tag) and single molecule sequencing.


title: Single cell RNA-seq analysis of human dermal fibroblasts and human pluripotent stem cells

first: Akira

last: Kunitomi

state: CA

address: 1650 Owens Street

institute: The J. David Gladstone Institutes

type: Expression profiling by high throughput sequencing

summary: Human pluripotent stem cells have two major pluripotent states, primed and naive, and the heterogeneity among cell lines in each pluripotent state remains a major unresolved problem. We showed that the overexpression of H1FOO-DD, which has a short expression period by fusing the destabilized domain to the maternal-specific linker histone H1FOO, together with OCT4, SOX2, KLF4 and LMYC in human somatic cells improves the quality of reprogramming to primed and naive pluripotency.

overall_design: Cultured human dermal fibroblasts and primed pluripotent stem cell lines were sampled at specific time points, and analyzed by single cell RNA-seq

first: Tomoaki

middle: M

last: Kato

first: Masaki

last: Nomura


title: H1FOO-DD promotes efficiency and uniformity in reprogramming to naive pluripotency

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Single cell ATAC-seq analysis of human dermal fibroblasts and human pluripotent stem cells

overall_design: Cultured human dermal fibroblasts and primed human pluripotent stem cell lines were sampled at specific time points, and analyzed by single cell ATAC-seq

first: Mayumi

last: Oda


title: Gene expression profiles of human dermal fibroblasts and human pluripotent stem cells analyzed by bulk RNA-seq

overall_design: Cultured human dermal fibroblasts, primed and naive human pluripotent stem cell lines were sampled at specific time points, and analyzed by bulk RNA-seq

first: Takuya

last: Yamamoto


title: DNA methylation analysis of human primed and naive pluripotent stem cells

type: Methylation profiling by genome tiling array

overall_design: Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium Human Methylation 450K or EPIC BeadChip Kit


title: Plasticity and lineage commitment of individual Th1 cells are determined by stable T-bet expression quantities

status: Public on Apr 30 2024

city: Berlin

first: Ahmed

middle: Nabil

last: Hegazy

address: Hindenburgdamm 30

department: Department of Gastroenterology, Infectious Diseases and Rheumatology

country: Germany

institute: Charité - University Medicine Berlin

summary: T helper 1 (Th1) cell identity is defined by the expression of the lineage-specifying transcription factor T-bet. Here, we examine the influence of T-bet expression heterogeneity on subset plasticity by leveraging cell sorting of distinct in vivo-differentiated Th1 cells based on their quantitative expression of T bet and interferon . Heterogeneous T bet expression states were regulated by virus induced type I interferons and were stably maintained even after secondary viral infection. Exposed to alternative differentiation signals, the sorted subpopulations exhibited graded levels of plasticity, particularly toward the Th2 lineage: T bet quantities were inversely correlated with the ability to express the Th2 lineage-specifying transcription factor GATA 3 and Th2 cytokines. Reprogramed Th1 cells acquired graded, but stable mixed Th1+2 phenotypes with a hybrid epigenetic landscape. Continuous presence of T-bet in differentiated Th1 cells was essential to ensure Th1 cell stability. Thus, innate cytokine signals regulate Th1 cell plasticity via an individual cell-intrinsic rheostat to enable T cell subset adaptation to subsequent challenges.

overall_design: Adoptively transferred WT, Tbx21+/-, Tbx21-/- LCMV‑TCRtg CD4+ Thy1.1+ cells from LCMV-challenged mice were isolated and MACS-sorted on day 10 of infection. Cells were cultured for two rounds under neutral (5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-4 (11B11), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)) or Th2 conditions (30 ng/ml IL-4 (Sigma-Aldrich), 5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)). On day 4 of the second round of stimulations, the cells were harvested and processed for RNA-seq.  Two biological replicates per condition were sequenced using Illumina HiSeq 2000 paired-end 100 bp sequence type.

middle: N

first: Christoph

last: Kommer

first: Thomas

last: Höfer

first: Max

last: Löhning


title: Plasticity and lineage commitment of individual Th1 cells are determined by stable T-bet expression quantities (ChIP-Seq)

overall_design: Adoptively transferred WT, Tbx21+/-, Tbx21-/- LCMV‑TCRtg CD4+ Thy1.1+ cells from LCMV-challenged mice were isolated and MACS-sorted on day 10 of infection. Cells were cultured for two rounds under neutral (5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-4 (11B11), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)) or Th2 conditions (30 ng/ml IL-4 (Sigma-Aldrich), 5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)). On day 4 of the second round of stimulations the cells were harvested and processed for Chip-seq. Cells were incubated for 10min at room temperature with 1% formaldehyde. Cross-linking was terminated by addition of glycine to a final concentration of 125mM. ChIP was performed using iDeal ChIP-seq Kit (Diagenode) according to the manufacturer’s instructions. Antibodies against H3K4me3 (ab8580, Abcam), H3K4me1 (ab8895, Abcam), H3K27ac (ab4729, Abcam), H3K27me3 (ab6002, Abcam) and H3K9me3 (ab8898, Abcam) were used. Library preparation for ChIP-seq was performed using NEBNext ChIP-Seq library Prep Master Mix set kit. Two biological replicates per condition were sequenced using Illumina HiSeq 2000 (50bp single-end) sequencing technology. 12 indexes were used per sequencing lane.


title: Altered nucleocytoplasmic export of adenosine (A)-rich circRNAs by PABPC1 contributes to neuronal function [FB_KD_circRTN4_RNAseq]

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

summary: Circular RNAs (circRNAs) are upregulated during neurogenesis. Where and how circRNAs are localized, and what roles they play during this process have remained elusive. By comparing the nuclear and cytoplasmic circRNAs between H9 cells and H9-derived forebrain neurons (FB), we found a subset of adenosine (A)-rich circRNAs are restricted in H9 nuclei but exported to cytosols upon forebrain neuron differentiation. This differentiation-coupled circRNA subcellular relocation is modulated by the poly(A)-binding protein PABPC1. In the nucleus, newly produced (A)-rich circRNAs are bound by PABPC1 and the nuclear basket protein TPR to prevent their nucleocytoplasmic export. Modulation of (A)-rich motifs in circRNAs remarkably alters their subcellular localization. Enforced (A)-rich circRNAs in cytosols result in mRNA translation suppression. Furthermore, decreased nuclear PABPC1 upon neuronal differentiation enables the export of (A)-rich circRNAs including circRTN4(2,3), which is required for neurite outgrowth. These findings uncover subcellular localization features of circRNAs, linking their processing and function during neurogenesis.

overall_design: Ribo– RNA-seq of FB circRTN4(2,3) KD cells are used for circRTN4(2,3) function analysis.

first: Ling-Ling

last: Chen

first: Shi-Meng

last: Cao

first: Hao

first: Guo-Hua

last: Yuan


title: Altered nucleocytoplasmic export of adenosine (A)-rich circRNAs by PABPC1 contributes to neuronal function

overall_design: Total RNAs, cytoplasmic RNAs and nuclear RNAs of H9-derived forebrain neurons (FB) are extracted and sequenced for downstream RNA subcellular localization analysis.

last: Wu


title: Increased vascular smooth muscle cell senescence in aneurysmal Fibulin-4 mutant mice

city: Rotterdam

first: Sanne

last: Stefens

address: Dr. Molewaterplein 40

department: Molecular Genetics

country: Netherlands

institute: Erasmus MC

summary: Aortic aneurysms are dilations of the aorta that can rupture when left untreated. We used aneurysmal Fibulin-4R/R to further unravel the underlying mechanisms of aneurysm formation. RNA sequencing of 3-month-old Fibulin-4R/R aortas revealed significant upregulation of senescence-associated secretory phenotype (SASP) factors and key senescence factors, indicating involvement of senescence. Analysis of aorta histology and of vascular smooth muscle cells (VSMCs) in vitro confirmed the senescent phenotype of Fibulin-4R/R VSMCs by revealing increased SA-β-gal, p21 and p16 staining, increased IL-6 secretion, increased presence of DNA damage foci and increased nuclei size. Additionally, we found that p21 luminescence was increased in the dilated aorta of Fibulin-4R/R|p21-Luciferase mice. Our studies identify a cellular aging cascade in Fibulin-4 aneurysmal disease, by revealing that Fibulin-4R/R aortic VSMCs have a pronounced SASP and a senescent phenotype that may underlie aortic wall degeneration. Additionally, we demonstrated the therapeutic effect of JAK/STAT and TGF-β pathway inhibition as well as senolytic treatment on Fibulin-4R/R VSMCs in vitro. These findings can contribute to improved therapeutic options for aneurysmal disease aimed at reducing senescent cells.

overall_design: To investigate the underlying molecular mechanism of aneurysm formation, we performed RNA sequencing on the aortic arch of Fibulin-4 R/R mice and wildtype littermates at 3 months of age. Next, differential expression analysis was performed to compare the RNA expression in Fibulin-4 R/R aorta's to the RNA expression in wildtype aorta's.

middle: J

first: Arne

last: Ijpma

first: Yunlei

last: Li

first: Joyce

last: Burger

first: Paula

last: van Heijningen

first: Jeroen

last: Essers

first: Ingrid

last: van der Pluijm


title: ATACseq in muscle from mice treated with AAV-GFP or AAV-CAAHR

city: Gainesville

first: Terence

last: Ryan

address: 1864 Stadium Rd

institute: University of Florida

summary: This is an ATAC sequencing experiment to explore chromatin accessibility change in mouse skeletal muscle treated with either AAV-GFP or AAV-CAAHR (a constitutively active mutant aryl hydrocarbon receptor). Mice received intramuscular injection of the AAV 5 months before the harvest of muscle.

overall_design: Gastrocnemius muscle was used to isolate nuclei from mice treated with either AAV-GFP or AAV-CAAHR (constitutively active AHR).

middle: E


title: Calcineurin inhibition rescues alloantigen-specific central memory T cell subsets and promotes chronic GVHD

city: Seattle

first: Scott

last: Furlan

address: 1100 Fairview Ave N

institute: CRD

summary: Calcineurin inhibitors (CNIs) constitute the backbone of modern acute graft-versus-host disease (aGVHD) prophylaxis regimens but have limited efficacy in the prevention and treatment of chronic GVHD (cGVHD). We investigated the effect of CNIs on immune tolerance after stem cell transplantation with discovery-based single cell gene expression and T-cell receptor (TCR) assays of clonal immunity in tandem with traditional protein-based approaches and preclinical modeling. While CNIs suppress the clonal expansion in CD8+ T-cells, alloreactive CD4+ T-cell clusters preferentially expanded during GVHD. Moreover, CNIs mediated reversible dose-dependent suppression of T cell activation and all stages of donor T-cell exhaustion but favored the differentiation to central memory T-cells. Critically, CNIs promoted the expansion of both polyclonal and TCR-specific alloreactive central memory CD4+ T-cells with high self-renewal capacity that mediated cGVHD following drug withdrawal. In contrast to post-transplant cyclophosphamide (PT-Cy), CSA was ineffective in eliminating IL-17A-secreting alloreactive T cell clones that mediate cGVHD. Collectively, we show that although CNIs attenuate aGVHD, they paradoxically rescue alloantigen-specific central memory T-cells, especially within the CD4+ compartment in lymphoid and GVHD target tissues, thus predisposing to cGVHD. These data provide further evidence to caution against CNI-based immune suppression without concurrent approaches that eliminate alloreactive T-cell clones.

overall_design:
B6D2F1 recipients were transplanted with B6 BM (5x10^6) + B6 T cells (2x10^6) + TEa TCR transgenic T cells (1x10^3) and treated daily with saline or CSA (5 or 50 mg/kg/kg). Spleens were taken on day 7, pooled from every 2 mice (n = 6 mice per group) and barcoded with hashtag Total Seq C. Donor CD4+ and CD8+ T cells were sort purified and combined per group for single cell RNA sequencing.
Please note that we sequenced for mRNA and TCR; There are 3 samples and each sample contains CD4 T and CD8 T from 3 "animals (pooled from every two)". CD4 and CD8 T cells have different metadata column names so were not merged.

first: Ping

last: Zhang

first: Olivia

middle: G

last: Waltner

first: Shruti

last: Bhise

first: Simone

last: Minnie

first: Geoffrey

middle: R

last: Hill


title: Double stranded RNA formation leads to preferential nuclear export and gene expression

city: Göttingen

first: Heike

last: Krebber

address: Grisebachstraße 8

institute: Georg-August Universität Göttingen

summary: mRNAs are transcribed and processed in the nucleus before they are exported into the cytoplasm for translation. Export is mediated by the export receptor heterodimer Mex67-Mtr2 in yeast (TAP-p15 in humans). Interestingly, also many lncRNAs leave the nucleus but it is currently unclear why they travel into the cytoplasm. Here we show that antisense (as)RNAs accelerate mRNA export by annealing with their sense counterparts through the helicase Dbp2. These double-stranded (ds)RNAs dominate export compared to single-stranded (ss)RNA, as they have a higher capacity and affinity for the export receptor Mex67. In this way, asRNAs boost gene expression, which is beneficial for cells. This is particularly important upon expression program changes. Consequently, the degradation or prevention of the formation of dsRNA is toxic for cells. This mechanism illuminates the general cellular occurrence of asRNAs and explains their nuclear export.

overall_design: Total RNA was isolated from yeast with Trizol. From the total RNA, 90µg RNA was then incubated with 3µg J2 antibody and G-sepharose beads for 120 min at 4°C. The resulting supernatant was clarified a second time with the J2 antibody. The supernatant from the second round was sequenced as the unbound fraction. The J2 eluate from the first precipitation was, after repeated washing, purified with Trizol and sequenced as the J2-Eluate. 3 replicates are included.

first: Ivo

last: Coban


title: Single-nucleus Transcriptomics Reveals Cardiac Cell Type-specific Diversification in Metabolic Disease Transgenic Pigs

city: Beijing

first: Jiakun

last: Miao

address: No. 2 Yuanmingyuan West Road

department: Institute of Animal Science

institute: Chinese Academy of Agricultural Sciences

summary: Cardiac injury triggered by early metabolic disease is poorly investigated due to the complexity of pathophysiology. We comprehensively reveal the cellular landscape of healthy and metabolically disturbed heart through single-nucleus RNA sequencing, using the metabolic disease-susceptible transgenic pig model as material.

overall_design: We performed single-nucleus RNA sequencing on left ventricular myocardium from both  triple-transgenic pig(PNPLA3I148M-GIPRdn-hIAPP) (TG) and wild-type pig (WT).

first: Kaiyi

first: Yu

last: Yang

first: Shulin


title: Sarm1 knockout prevents type 1 diabetic bone disease in females independent of neuropathy

city: Saint Louis

first: Erica

middle: L

last: Scheller

state: MO

address: 660 S Euclid Ave

institute: Washington University

summary: Diabetic patients have a high risk of developing skeletal diseases accompanied by diabetic peripheral neuropathy (DPN). In this study, we isolated the role of DPN in skeletal disease with global and conditional knockout models of sterile-α and TIR-motif-containing protein-1 (Sarm1). SARM1, an NADase highly expressed in the nervous system, regulates axon degeneration upon a range of insults, including DPN. Global knockout of Sarm1 prevented DPN, but not skeletal disease, in male mice with type 1 diabetes (T1D). Female wild type mice also developed diabetic bone disease, but without DPN. Unexpectedly, global Sarm1 knockout completely protected female mice from T1D-associated bone suppression and skeletal fragility despite comparable muscle atrophy and hyperglycemia. Global Sarm1 knockout rescued bone health through sustained osteoblast function with abrogation of local oxidative stress responses. This was independent of the neural actions of SARM1, as beneficial effects on bone were lost with neural conditional Sarm1 knockout. This study demonstrates that the onset of skeletal disease occurs rapidly in both male and female mice with T1D completely independent of DPN. In addition, this reveals that clinical SARM1 inhibitors, currently being developed for treatment of neuropathy, may also have benefits for diabetic bone through actions outside of the nervous system.

overall_design:
RNAseq was performed using RNA extracted from marrow-depleted femur and tibia bones harvested from wild type (WT) and global Sarm1 knockout (Sarm1-KO) female mice at 11-weeks of age. Mice were further categorized by the presence or absence of streptozotocin induced type 1 diabetes, induced 3-weeks prior at the age of 8-weeks (four groups total: WT non-diabetic, Sarm1-KO non-diabetic, WT T1D, Sarm1-KO T1D). The 3-week time point was selected to capture gene changes early in the course of disease, around the time that changes in bone by microCT were beginning to emerge.

>>>Submitter states that raw data are not available due to file loss<<<

first: Jennifer

last: Brazill

first: Ivana

last: Shen

first: Clarissa

last: Craft

first: Kristann

last: Magee

first: Jay

last: Park

first: Madelyn

last: Lorenz

first: Amy

last: Strickland

first: Natalie

middle: K

last: Wee

first: X

first: Alec

last: Beeve

first: Gretchen

last: Meyer

first: Jeffrey

last: Milbrandt

first: Aaron

last: DiAntonio


title: Primary oocytes with cellular senescence features are involved in ovarian aging in mice

city: Columbia

first: Lei

last: Lei

address: 920 East Campus Dr

department: of Obstetrics, Gynecology and Women's Health

institute: University of Missouri School of Medicine

summary: In mammalian females, quiescent primordial follicles serve as the ovarian reserve and sustain normal ovarian function and egg production via folliculogenesis. The loss of primordial follicles causes ovarian aging. Cellular senescence, characterized by cell cycle arrest and production of the senescence-associated secretory phenotype (SASP), is associated with tissue aging. In the present study, we report that some quiescent primary oocytes in primordial follicles become senescent in adult mouse ovaries. The senescent primary oocytes share senescence markers characterized in senescent somatic cells. The senescent primary oocytes were observed in young adult mouse ovaries, remained at approximately 15% of the total primary oocytes during ovarian aging from 6 months to 12 months, and accumulated in aged ovaries. Administration of a senolytic drug ABT263 to 3-month-old mice reduced the percentage of senescent primary oocytes and the transcription of the SASP cytokines in the ovary. In addition, led to increased numbers of primordial and total follicles and a higher rate of oocyte maturation and female fertility. Our study provides experimental evidence that primary oocytes, a germline cell type that is arrested in meiosis, become senescent in adult mouse ovaries and that senescent cell clearance reduced primordial follicle loss and mitigated ovarian aging phenotypes.

overall_design: We compared the transcriptomes of mouse ovaries during natral aging (3 months, 6 months, 9 months, 12 months, 18 months, and 25 months). We also compared the transcriptomes between ABT263 treated ovaries and control ovaries of 6 months and 9 months old mice

first: Yan

last: Hao

first: Xiaobin

last: Zheng


title: TLR7-dependent eosinophil degranulation links psoriatic skin inflammation to small-intestinal inflammatory changes

city: Inchon

first: YunJae

last: Jung

address: 155 Gaetbeol-ro, Yeonsu-gu

department: Microbiology

country: South Korea

institute: College of Medicine, Gachon University

summary: Increased intestinal permeability can exacerbate psoriasis, a systemic inflammatory disease with complex pathogenesis.  Using a mouse model of psoriasis elicited by the TLR7 ligand imiquimod, we found that psoriatic dermatitis was accompanied by small-intestinal inflammatory changes associated with eosinophil degranulation which led to impaired intestinal barrier integrity.  Inflammatory responses in the skin and small intestine were accelerated in mice that are prone to eosinophil degranulation.  Caco-2 human intestinal epithelial cells treated with media containing eosinophil granule proteins exhibited signs of inflammation and damage.  Imiquimod-induced skin and intestinal inflammatory changes were attenuated in eosinophil-deficient mice, and this attenuation was counteracted by eosinophil transfer.  Imiquimod levels and eosinophil distribution were positively correlated in the intestine.  TLR7-deficient mice did not show intestinal eosinophil degranulation and exhibited attenuated skin and small-intestinal inflammation following imiquimod application.  These results suggest a TLR7-dependent bidirectional skin-to-gut communication in psoriatic inflammation, and that intestinal inflammatory changes can accelerate psoriasis.

overall_design: At 8-10 weeks of age, the mice received a daily topical dose of 62.5 mg IMQ cream (5%) (Aldara™) or vehicle cream (Vaseline) on the shaved back and the right ear for 5-8 sequential days.

first: Hee

last: Kiim

first: Jinsun

last: Jang


title: Disruption of nucleotide biosynthesis reprograms mitochondrial metabolism to inhibit adipogenesis

status: Public on Apr 29 2024

city: Nashville

first: Elma

last: Zaganjor

state: TN

address: 2222 Pierce Ave

institute: Vanderbilt University

summary: A key organismal response to overnutrition involves the development of new adipocytes through the process of adipogenesis. Preadipocytes sense changes in the systemic nutrient status and metabolites can directly modulate adipogenesis. We previously identified a role of de novo nucleotide biosynthesis in adipogenesis induction, whereby inhibition of nucleotide biosynthesis suppresses the expression of the transcriptional regulators PPARg and C/EBPa. Here, we set out to identify the global transcriptomic changes associated with the inhibition of nucleotide biosynthesis. Through RNA sequencing (RNAseq), we discovered that mitochondria were the most altered transcriptional signature in response to inhibition of nucleotide biosynthesis. Blocking nucleotide biosynthesis induced rounded mitochondrial morphology, and altered mitochondrial function, and metabolism, reducing levels of tricarboxylic acid cycle intermediates, and increasing fatty acid oxidation (FAO). The loss of mitochondrial function induced by suppression of nucleotide biosynthesis was rescued by exogenous expression of PPARg. Moreover, inhibition of FAO restored PPARg expression, mitochondrial protein expression, and adipogenesis in the presence of nucleotide biosynthesis inhibition, suggesting a regulatory role of nutrient oxidation in differentiation. Collectively, our studies shed light on the link between substrate oxidation and transcription in cell fate determination.

overall_design: Comparative gene expression analysis of primary SVF cells that were undifferentiated, differentiated for 6 days with vehicle control or mizorbine (MIZ). 3 biological replicates were used per group.

first: Julia

last: Pinette

first: Jacob

middle: W

last: Myers

first: Woo

middle: Y

first: Heather

last: Bryant

first: Genesis

last: Wilson

first: Zer

last: Vue

first: Elizabeth

last: Nunn

first: Matthew

last: Cottam

first: Antentor

middle: O

last: Hinton

first: Jessica

middle: B

last: Spinelli

first: Jean-Philippe

last: Cartailer


title: Double-stranded RNA formation leads to preferential nuclear export and gene expression

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: mRNAs are transcribed and processed in the nucleus before they are exported into the cytoplasm for translation. Export is mediated by the export receptor heterodimer Mex67-Mtr2 in yeast (TAP-p10 in humans). Interestingly, also long non-coding RNAs (lncRNAs) leave the nucleus and so-called XUTs (Xrn1 sensitive unstable transcripts) accumulate in the cytoplasm of the degradation defective xrn1∆ mutant. Curiously, it is currently unclear why so many lncRNAs travel into the cytoplasm. Here we show that such ncRNAs accelerate mRNA export by annealing with their sense counterparts through the helicase Dbp2. These double stranded (ds) RNAs dominate export, because Mex67 has a higher affinity to dsRNAs and more molecules bind. Cells benefit from this mechanism as it quickly regulates gene expression, which is particularly important upon expression program changes. Consequently, prevention of the dsRNA formation or destroying dsRNAs is lethal to cells. This mechanism could explain the general cellular occurrence of antisense RNAs.

overall_design: Cytoplasmic fractionation and RNA extraction.

first: Ivo

middle: C

last: Coban

first: Heike

last: Krebber

first: Orr

last: Shomroni


title: Altered lipid homeostasis underlies selective neurodegeneration in SNX14 deficiency [1 month]

city: Philadelphia

first: Thomas

last: Roule

state: Pennsylvania

address: 3501 Civic Center Boulevard  5th Floor CTRB-5400

institute: CHOP

summary: Spinocerebellar Ataxia Autosomal Recessive 20 (SCAR20) is a rare disorder caused by mutation in the SNX14 gene. The symptoms of the disorder including coarse face, poor or lack of speech, delayed or absent of motor function, and most markedly, cerebella atrophy with Purkinje cell degeneration. SNX14 has been localized to ER and shown to play a vital role in facilitating the formation of lipid droplet and maintaining the lipid saturation balance in cell membrane. Meanwhile, it has also been localized to other subcellular organelles, including lysosome and endo-lysosome, and has been suggested to participate in the autophagy responses. However, the previous researches were performed in vitro or ex vivo, and how disrupted SNX14 led to Purkinje cell degeneration in the SCAR20 cerebella in vivo remained unexplored. Here, we report the first animal model that manifested the SCAR20 symptoms, by introducing a 1bp deletion in Snx14 in mice via CRISPR-Cas9. We performed RNAseq to analyse the pathway changes caused by Snx14 KO.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of cerebella and cortices from 2-3 mice of SNX14 KO mice and their control littermates.

first: Yijing

last: Zhou

first: Naiara

last: Aquizu-Lopez


title: Genome-wide identification of oncogenic fusions in lung cancer by functional translocation sequencing

city: Boston

first: Roberto

last: Chiarle

state: Massachusetts

address: 300 Longwood Avenue

institute: Children’s Hospital Boston and Harvard Medical School

summary: Fusions involving tyrosine kinases are oncogenic drivers in lung cancer and other solid tumors but also mediate resistance to targeted therapy. Despite gene rearrangements involving tyrosine kinases tending to show recurrent patterns in solid tumors, little is known about their mechanisms of formation and their selection process. To elucidate these mechanisms, we developed a functional high-throughput, genome-wide translocation sequencing (F-HTGTS) approach. We applied F-HTGTS to lung cancer cells under the selective pressure of EGFR inhibition to map genome-wide translocations when a DNA double-strand break occurs in the ALK, RET, ROS1 or NTRK1 tyrosine kinase. We found that translocations form spontaneously with several partners in the genome, generate functional fusion proteins and induce resistance to EGFR inhibitors. Several of these proteins reproduce precisely the fusions found in NSCLC patients either as original driver events or secondary to development of resistance to targeted therapy. Therefore, F-HTGTS is an approach that allows rapid and comprehensive mapping of tyrosine kinase fusions in the genome from common oncogenic kinases and provide insights on their mechanisms of formation.

overall_design: We applied a genome-wide translocation technique we previously developed (High-Throughput Genomic Translocation Sequencing approach, HTGTS) to identify translocation partners from DNA double strand breaks (DSBs) introduced into the ALK intron 19 locus in PC-9 cell before and after treatment with EGFR inhibitors, osimertinib.

first: Taek-Chin

last: Cheong

first: Qi

last: Wang


title: Altered lipid homeostasis underlies selective neurodegeneration in SNX14 deficiency.

overall_design: Refer to individual Series


title: Targeting Dependency on a Paralog Pair of CBP/p300 against De-repression of KREMEN2 in SMARCB1-Deficient Cancers

city: Chuo-ku

first: Hideaki

last: Ogiwara

state: Tokyo

address: 5-1-1, Tsukiji

department: Division of Cancer Therapeutics

country: Japan

institute: National Cancer Center Research Institute

summary: SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex, is the causative gene of rhabdoid tumors and epithelioid sarcomas. Here, we identify a paralog pair of CBP and p300 as a synthetic lethal target in SMARCB1-deficient cancers by using a dual siRNA screening method based on the “simultaneous inhibition of a paralog pair” concept. Treatment with CBP/p300 dual inhibitors suppresses growth of cell lines and tumor xenografts derived from SMARCB1-deficient cells but not from SMARCB1-proficient cells. SMARCB1-containing SWI/SNF complexes localize with H3K27me3 and its methyltransferase EZH2 at the promotor region of the KREMEN2 locus, resulting in transcriptional downregulation of KREMEN2. By contrast, SMARCB1 deficiency leads to localization of H3K27ac, and recruitment of its acetyltransferases CBP and p300, at the KREMEN2 locus, resulting in transcriptional upregulation of KREMEN2, which cooperates with the SMARCA1 chromatin remodeling complex. Simultaneous inhibition of CBP/p300 leads to transcriptional downregulation of KREMEN2, followed by apoptosis induction via monomerization of KREMEN1 due to a failure to interact with KREMEN2, which suppresses anti-apoptotic signaling pathways. Taken together, our findings indicate that simultaneous inhibitors of CBP/p300 could be promising therapeutic agents for SMARCB1-deficient cancers.

overall_design: NT indicates that non-treated and non-transfected cells were harvested.  A485 indicates that cells treated with 2 μM A-485 for 24 h were harvested. CP-C27 indicates that cells treated with 0.2 μM CP-C27 for 24 h were harvested. siRNA (siNT, siCBPsip300, siKREMEN2) indicates that cells transfeted with siRNA for 48 h or 96 h were harvested.

first: Mariko

last: Sasaki


title: Gene expression analysis at single cell level from the CNS of mice that harbored Melanoma and recieved Anti-PD1 antibody or Isotype control antibody treatment

status: Public on Apr 27 2024

city: Freiburg

first: Chintan

last: Chhatbar

address: Breisacher strasse 64

department: Department of Neuropathology

institute: Uniklinikum Freiburg

summary: Immue checkpoint blockade (ICB) has significantly improved the overall survival of melanoma patients. Despite high success rates, patients often experience side effects that are collectively termed as immune related adverse events that potentially target any organ including the CNS. However, the role of microglia in ICB-induced neurotoxicity was unclear. We studied the impact of microglial activation in response to ICB. ScRNA sequencing was employed to decipher diverse microglia populations and other cell types from the cortex.

overall_design: Melanoma cells were intravenously injected. Anti PD1 or Isotype control antibodies was given intra peritoninally at a concentration of 250µg/ dose on the following days - Day1,4,8,16,22. The mice were scarificed on day 23 and brains were isolated. Cell populations from the cortex of the mice were isolated and enriched for microglia by flourescent activated nuclear sorting (FACS) and analyzed using sn RNA sequencing

first: Robert

last: Zeiser

first: Janaki

last: Vinnakota

first: Gianni

last: Monaco


title: TAZ is involved in breast cancer cell migration via regulating actin dynamics

city: Daegu

first: HongSeok

last: Choi

address: 680, Gukchaebosang-ro, Jung-gu

department: School of medicine

institute: Kyungpook national university

summary:
Background: Cancer metastasis is dependent on cell migration. Several mechanisms, including epithelial-to-mesenchymal transition (EMT) and actin fiber formation, could be involved in cancer cell migration. As a downstream effector of the Hippo signaling pathway, transcriptional coactivator with PDZbinding motif (TAZ) is recognized as a key mediator of the metastatic ability of breast cancer cells. We aimed to examine whether TAZ affects the migration of breast cancer cells through the regulation of EMT or actin cytoskeleton.
Methods: MCF-7 and MDA-MB-231 cells were treated with siRNA to attenuate TAZ abundance. Transwell migration assay and scratch wound healing assay were performed to study the effects of TAZ knockdown on cancer cell migration. Fluorescence microscopy was conducted to examine the vinculin and phalloidin. Semiquantitative immunoblotting and quantitative real-time PCR were performed to study the expression of small GTPases and kinases. Changes in the expression of genes associated with cell migration were examined through next-generation sequencing.
Results: TAZ-siRNA treatment reduced TAZ abundance in MCF-7 and MDA-MB- 231 breast cancer cells, which was associated with a significant decrease in cell migration. TAZ knockdown increased the expression of fibronectin, but it did not exhibit the typical pattern of EMT progression. TGF-b treatment in MDA-MB-231 cells resulted in a reduction in TAZ and an increase in fibronectin levels. However, it paradoxically promoted cell migration, suggesting that EMT is unlikely to be involved in the decreased migration of breast cancer cells in response to TAZ suppression. RhoA, a small Rho GTPase protein, was significantly reduced in response to TAZ knockdown. This caused a decrease in the expression of the Rho-dependent downstream pathway, i.e., LIM kinase 1 (LIMK1), phosphorylated LIMK1/2, and phosphorylated cofilin, leading to actin depolymerization. Furthermore, myosin light chain kinase (MLCK) and phosphorylated MLC2 were significantly decreased in MDA-MB-231 cells with TAZ knockdown, inhibiting the assembly of stress fibers and focal adhesions.
Conclusion: TAZ knockdown inhibits the migration of breast cancer cells by regulating the intracellular actin cytoskeletal organization. This is achieved, in part, by reducing the abundance of RhoA and Rho-dependent downstream kinase proteins, which results in actin depolymerization and the disassembly of stress fibers and focal adhesions.

overall_design: To investigate the impact of TAZ on the metastasis of cancer cells, TAZ knockdown was induced in MDA-MB-231 cells, a metastatic breast cancer cell line, by treating them with TAZ-siRNA, followed by observation of changes. Subsequently, we conducted RNA-sequencing using three samples from each group treated with control-siRNA and TAZ-siRNA, respectively, to analyze transcriptomics. Changes in genes involved in cancer cell metastasis and cell motility were analyzed based on NGS data.

first: Hongseok

first: Hyoju

last: Jang

first: Tae-hwan

last: Kwon


title: The involvement of RIPK4 in TNF-α-stimulated IL-6 and IL-8 production by melanoma cells

city: Krakow

first: Ewelina

last: Madej

address: Gronostajowa 7

department: Department of Biophysics and Cancer Biology

country: Poland

institute: Jagiellonian University

summary: The receptor-interacting protein kinase 4 (RIPK4) plays an oncogenic role in melanoma by regulating NFκB and Wnt/β-catenin pathways. As its role in melanoma remains not fully understood, we examined the effects of its downregulation on melanoma transcriptomics. Using RNA-seq, we observed broad transcriptome changes in WM266.4 cells upon RIPK4 downregulation, indicating a complex role for RIPK4 in regulating adhesion, migration, proliferation, and inflammatory processes in melanoma cells. Furthermore, our study highlights the potential functional partners of RIPK4, such as BIRC3, TNF-α receptors, and MAP2K6.

overall_design: To investigate the effects of RIPK4 silencing on melanoma cell fate, we silenced RIPK4 in WM266.4 human melanoma cells. Subsequently, we performed bulk RNA-seq to examine the transcriptional changes using gene expression profiling analysis. The experiment comprised three replicates.

first: Agnieszka

last: Wolnicka-Glubisz


title: Gene expression profile at single cell level of pair human mucinous colorectal adenocarcinoma(MCA) tissues and adjacent normal colon tissues

status: Public on Apr 28 2024

city: Shanghai

first: guangyong

last: zheng

address: cailun road 1200

institute: shutcm

summary: We provided a comprehensive landscape of tumor tissues and normal counterparts for MCA in a single-cell resolution level

overall_design: Six pair tumor and normal samples  were collected from changzheng hospital, naval medical university of China, with written informed consent of patients

first: Haiyang

first: Guangyong

last: Zheng

first: Xin

last: Luan

first: Weidong

last: Zhang


title: Spatial transcriptomics reveals functional compartmentalization of mucinous colorectal adenocarcinoma

summary: We performed spatial transcriptomics to profile compositional and spatial distribution of hetergeneous cell populations in mucinous colorectal adenocarinoma

overall_design: Tumor and adjacent normal tissues of one patient were collected for spatial transcriptomics

last: Zhou


title: Mucinous colorectal adenocarcinoma

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


title: Discovery of Varicella zoster virus circular RNA with nanopore long-read sequencing

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Varicella-zoster virus (VZV), an alphaherpesvirus, causes chickenpox (varicella) in young children with an annual minimum of 140 million new cases and herpes zoster in senior, a painful and debilitating disease with 3-5‰ incidence. A complex structural transcriptome of VZV, which numerous novel transcripts, transcript isoforms, and unknown splice events are found during cell infection. Circular RNA (circRNA), a newly important component of the transcriptome, is increasing discoveries of circRNA function in mammalian cells. However, VZV encoded circRNA remains unexplored. The code used in this study and extended data are available from the GitHub repository (https://github.com/ShaominYang/VZV_circRNA)

overall_design: Using deep RNA-seq following RNase R treatment, we identified and charactered 35, 076 and 54 human and VZV pOka strain circRNAs respectively from VZV infected neuroblastoma cell (SH-SY5Y). We collected VZV infected human neuroblastoma cell (SH-SY5Y). A deep nanopore long-read sequencing, which combines rolling circular reverse transcription and nanopore sequencing following RNase R treatment was performed.

first: Shaomin

last: Yang


title: Altered lipid homeostasis underlies selective neurodegeneration in SNX14 deficiency [1 yr]

first: Thomas

last: Roule

first: Yijing

first: Naiara

last: Aquizu-Lopez


title: Comparison the transcriptional changes in the mutation of VZV circVLTs

summary: Sequence analyses shown that most exons of VZV circVLTs were overlapped with ORFs, except for exon5, which was an ideal mutation position. Using a galK positive/counter selection VZV bacteria artificial chromosome (BAC) system, we replaced upstream (104,765-104,785 Mutation2, pOKA-M2) or downstream (104,785-104,805, Mutation1, pOKA-M1) of circVLTs BSJ exon5 with 20 bp random sequences in VZV genomic DNA level. The code used in this study and extended data are available from the GitHub repository (https://github.com/ShaominYang/VZV_circRNA)

overall_design: ARPE-19 cells were infected with VZV pOKA-WT, pOKA-M1 and pOKA-M2. RNA-seq was used to quantify the expression of cellular and viral genes


title: A UL26-PIAS1 complex antagonizes anti-viral gene expression during Human Cytomegalovirus infection

city: Rochester

first: Jessica

last: Ciesla

state: New York

address: 601 Elmwood ave

department: Biochemistry

institute: University of Rochester

summary: Viral disruption of innate immune signaling is a critical determinant of productive infection. The Human Cytomegalovirus (HCMV) UL26 protein prevents anti-viral gene expression during infection, yet the mechanisms involved are unclear. We used TurboID-driven proximity proteomics to identify putative UL26 interacting proteins during infection to address this issue. We find that UL26 forms a complex with several immuno-regulatory proteins, including several STAT family members and various PIAS proteins, a family of E3 SUMO ligases. Our results indicate that UL26 prevents STAT phosphorylation during infection and antagonizes transcriptional activation induced by either interferon α (IFNA) or tumor necrosis factor α (TNFα). Additionally, we find that the inactivation of PIAS1 sensitizes cells to inflammatory stimulation, resulting in an anti-viral transcriptional environment similar to ΔUL26 infection. Further, PIAS1 is important for HCMV cell-to-cell spread, which depends on the presence of UL26, suggesting that the UL26-PIAS1 interaction is vital for modulating intrinsic anti-viral defense.

overall_design: Comparative gene expression profiling analysis of RNA-seq data fot MRC5 fibroblasts transduced with CRISPR RNPs completex to non-targeting guide (ntg) or PIAS1-targeted sgRNAs (PIAS1KO). Cells treated with vehicle or TNFα (3 ng/mL) for 24 hr.

first: Kai-Lieh

last: Huang

first: Eric

last: Wagner

first: Joshua

last: Munger


title: Discovery of Varicella zoster virus circular RNA with short read sequencing

summary:
Varicella-zoster virus (VZV), an alphaherpesvirus, causes chickenpox (varicella) in young children with an annual minimum of 140 million new cases and herpes zoster in senior, a painful and debilitating disease with 3-5‰ incidence. A complex structural transcriptome of VZV, which numerous novel transcripts, transcript isoforms, and unknown splice events are found during cell infection. Circular RNA (circRNA), a newly important component of the transcriptome, is increasing discoveries of circRNA function in mammalian cells. However, VZV encoded circRNA remains unexplored. In this study we demonstration that VZV derived circRNAs are biologically functional and contributed to viral pathogenesis.
Using deep RNA-seq following RNase R treatment, we identified and charactered 35, 076 and 54 human and VZV pOka strain circRNAs respectively from VZV infected neuroblastoma cell (SH-SY5Y).

overall_design: We collected VZV infected human neuroblastoma cell (SH-SY5Y), containing 3 replicates. A deep RNA-seq following RNase R treatment was performed. The code used in this study and extended data are available from the GitHub repository (https://github.com/ShaominYang/VZV_circRNA)


title: Transcriptome analysis to compare control and Ahed-deficient hematopoietic stem and progenitor cells (HSPC) and erythroblasts [RNA-Seq]

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Mutations in genes intimately involved in the occurrence of haemotological cancers remains largely unknown. Here, we report a novel functional gene in hematopoiesis, which was discovered by screening mutant embryonic stem cells (ESCs). The gene, named “attenuated haematopoietic development” (Ahed), encoded an uncharacterised protein located in the nucleus. Ahed conditional knockout (cKO) mice were generated by mating with Vav1-cre transgenic mice. We found that Ahed cKO foetuses became anaemic after E14.5 and died before birth. Flow cytometric analysis showed that erythroid cells significantly decreased in E14.5 Ahed cKO livers. By contrast, the fetal liver contained a substantial number of lineage-Sca-1+c-KitHi (LSK) cells, whose phenotype corresponded to hematopoietic stem/progenitor cells. Transplantation experiments revealed that Ahed-deficient LSK cells were unable to reconstitute haematopoiesis in vivo. We confirmed the downregulation of expression levels of HSC-related genes, such as Gata2, Lmo2, and Runx1 in E14.5 FL LSK cells in Ahed cKO mice. In addition, upstream regulator analyses revealed that the GATA2 pathway was most significantly hampered in both FL and adult BM. Collectively, these data determined that Ahed is indispensable for functional haematopoietic stem/progenitor cells.

overall_design: Lin- Sca1+ c-Kit+ (LSK) CD48- HSC-enriched fractions and Lin- CD71Hi Ter119-/Lo pro-erythroblasts were sorted from fetal liver (FL) and adult bone marrow (BM) of control or Ahed-deficient mice; Ahedfl/+; Vav1-cre (control) and Ahedfl-/-; Vav1-cre (cKO) in E14.5 FL and Rosa26-CreERT2 (R26CE) Ahedfl/+ (control) mice and R26CE Ahedfl/fl (cKO) in BM. We conducted RNA-seq analyses to compare the gene expression features of haematopoietic cells derived from the FL and adult BM of control or Ahed-deficient mice.

first: R

last: Nakai

first: T

last: Sudo

first: D

last: Okuzaki

last: Yokota


title: Reducing cholesteol in macrophages alters epigemone

status: Public on Apr 26 2024

city: Madison

first: Jeffrey

last: Dilworth

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin

summary: Cholesterol reduction in macrophages by methyl-beta-cyclodextran (MCD) alters gene expression and genomic configuration in a cholesterol specific fashion.

overall_design: ATAC-seq was performed on RAW macrophages, treated with MCD (5 mM, 1 hour) or without. Two replicates were performed for untreated control (ctl); two replicastes for MCD treated cells MCD).

first: Zeina

last: Salloum

first: Kiran

last: Nakka

first: Xiaohui

last: Zha


title: A scalable derivative-free optimizer trained through learning to optimize approach to interpret drug response mechanism network

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

institute: KAIST

summary: With the emergence of various drug-based treatment strategies, many drug response prediction models have been developed to understand their effects. However, in order to gain comprehensive understanding of a drug response, a prediction model should reflect the underlying biological mechanisms, but the current models suffer from interpretability and scalability problems. Machine learning-based prediction models base their predictions on inferred features, which usually are not well correlated with biological mechanisms, posing a challenge on interpretability of its response predictions. In this regard, using Boolean modeling schemes may allow interpretations on mechanisms that contribute to a particular response, but optimizing Boolean models is difficult because of their high dimensional search space and discontinuous loss function. Here, we developed a scalable derivative-free optimizer for weighted sum Boolean network through meta-reinforcement learning. By using graph network and coordinate-wise policy, our learned optimizer can optimize high dimensional Boolean networks containing over 100 parameters of arbitrary structure, showing higher sample efficiency compared with other meta-heuristic algorithms. The optimized Boolean networks successfully predict the drug responses congruent with public databases and in-house experimental data. Moreover, mechanistic analysis of optimized networks shows reliable interpretability of the predictions by meaningful suggestions of known basket trial drug response prediction markers.

overall_design: RNA-seq of SW48, SW620 colorectal cancer cell lines in the presence or absence of Trametinib

first: Yunseong

last: Kim

first: Younghyun

last: Han

first: Jonghoon

last: Lee

first: Ja-Il

last: Joo

first: Chun-Kyung

first: Seong-Hoon

last: Jang

first: Junsoo

last: Kang

first: Taeyoung

first: Kwang-Hyun

last: Cho


title: Cholesterol in macrophage regulate gene expersion with or without LPS [statin and LPS RNA-seq]

summary: cholesterol reduction in macrophages by methyl-b-cyclodextran (MCD) or statin alters gene expression.  When activated by inflammatory stimilus LPS, macrophages responded in a cholesterol specific fashion.

overall_design: RNA-seq was performed on rest RAW macrophages, treated with MCD or statin.  Similar RNA-seq also performed on macropahges stimulated with LPS. Two replicates were performed for untreated control (ctl),; two replicates for MCD and statin treated cells (MCD and Statin), respectively.  Control cells were stimulated with LPS (ctl-LPS), two replicates, and also statin treated cells were stimulated LPS identically (statin-LPS).

first: Kristin

last: Dauner


title: Transcriptome analysis to compare alternative splicing between control and Ahed-deficient hematopoietic stem and progenitor cells (HSPCs) [RNA-Seq]

first: Daisuke

last: Motooka

summary: We discovered a novel functional gene "Ahed" by screening mutant embryonic stem cells (ESCs). We confirmed that Ahed deletion was disruptive to multiple hematopoietic lineages, and Ahed-deficient HSPCs were unable to reconstitute hematopoiesis in vivo. A search through the biophysical interactions of ORFeome-based complexes 3.0 (BioPlex 3.0) network database indicated a close correlation of Ahed protein in the RNA splicing process. Therefore, we conducted  RNA-Seq analysis on triplicate differentiated populations comparing control and Ahed cKO FL LSK cells to verify the reproducibility of our findings. Skewed splicing patterns were observed in diverse transcripts for numerous genes, including PU.1, Ythdf2, Sel1l, and Zfp60, which are known to play important roles in hematopoiesis.

overall_design: We performed RNA-Seq analysis on triplicate differentiated populations comparing control or Ahed cKO Lin- Sca1+ c-Kit+ (LSK) cells in E14.5 fetal liver.

first: R

last: Nakai

first: Y

last: Yasumizu

first: T


title: PvSDP1 and its role in Extracellular Vesicles-Mediated Intrasplenic Infections in Plasmodium vivax

status: Public on Apr 25 2024

city: Badalona

first: Alberto

last: Ayllon-Hermida

state: Barcelona

address: Cami de les Escoles/Carretera de Can ruti s/n

department: PVREX

country: Spain

institute: ISGlobal

summary: Recent studies indicate that the human spleen contains over 95% of the total parasite biomass during chronic asymptomatic infections caused by Plasmodium vivax. Previous studies have demonstrated that extracellular vesicles (EVs) secreted from infected reticulocytes facilitate binding to human spleen fibroblasts (hSFs) and identified parasite genes whose expression was dependent on an intact spleen. Here, we characterize the P. vivax spleen-dependent hypothetical gene (PVX_114580). Using CRISPR/Cas9, PVX_114580 was integrated into P. falciparum 3D7 genome and expressed during asexual stages. Immunofluorescence analysis demonstrated that the protein, which we named P. vivax Spleen-Dependent Protein 1 (PvSDP1), was located at the surface of infected red blood cells in the transgenic line and this localization was later confirmed in natural infections. Plasma-derived EVs from P. vivax-infected individuals (PvEVs) significantly increased cytoadherence of 3D7_PvSDP1 transgenic line to hSFs and this binding was inhibited by anti-PvSDP1 antibodies. Single-cell RNAseq of PvEVs-treated hSFs revealed increased expression of adhesion-related genes. These findings demonstrate the importance of parasite spleen-dependent genes and EVs from natural infections in the formation of intrasplenic niches in P. vivax, a major challenge for malaria elimination.

overall_design: Human spleen fibroblast (hSFs) that have been stimulated with Extracellular vesicles derived from plasma of P. vivax-infected individuals. After 48h stimulation, stimulated-hSFs and control non-stimulated hSFs were submitted for scRNA-seq in 10X genomics platform. Also, in the same sequencing process, non-related hematopoietic Bel-A cells were sequenced.

first: Iris

last: Aparici-Herraiz

first: Ane

last: Larrinaga

first: Hernando

last: Del Portillo

first: Carmen

last: Fernandez-Becerra


title: Generation of allogenic and xenogeneic functional muscle stem cells for intramuscular transplantation [scRNA-seq]

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: Satellite cells, the stem cells of skeletal muscle tissue, hold a remarkable regeneration capacity and therapeutic potential in regenerative medicine. However, low satellite cell yield from autologous or donor-derived muscles hinders the adoption of satellite cell transplantation for the treatment of muscle diseases, including Duchenne muscular dystrophy (DMD). To address this limitation, here we investigated whether satellite cells can be derived in allogeneic or xenogeneic animal hosts. First, injection of CRISPR/Cas9-corrected mouse DMD-induced pluripotent stem cells (iPSCs) into mouse blastocysts carrying an ablation system of host satellite cells gave rise to intraspecies chimeras exclusively carrying iPSC-derived satellite cells. Furthermore, injection of genetically corrected DMD-iPSCs into rat blastocysts resulted in the formation of interspecies rat-mouse chimeras harboring mouse satellite cells. Remarkably, iPSC-derived satellite cells or derivative myoblasts produced in intraspecies or interspecies chimeras restored dystrophin expression in DMD mice following intramuscular transplantation, and contributed to the satellite cell pool. Collectively, this study demonstrates the feasibility of producing therapeutically competent stem cells across divergent animal species, raising the possibility of generating human muscle stem cells in large animals for regenerative medicine purposes.

overall_design: Contribution of mouse induced pluripotent stem cells-derived cell types to the skeletal muscle tissue of rat-mouse chimera was assessed and compared to the composition of the SD rat-derived skeletal muscle tissue using scRNA-seq.

first: Ajda

last: Lenardič

first: Seraiana

last: Domenig

first: Joel

last: Zvick

first: Monika

last: Tarnowska-Sengül

first: Nicola

last: Bundschuh

first: Regula

last: Furrer

first: Falko

last: Noé

first: Christine

last: Trautmann

first: Giada

last: Bacchin

first: Pjeter

last: Gjonlleshaj

first: Xhem

last: Qabrati

first: Evi

last: Masschelein

first: Katrien

last: De Bock

first: Christoph

last: Handschin

first: Ori

last: Bar-Nur


title: Generation of allogenic and xenogeneic functional muscle stem cells for intramuscular transplantation [RNA-seq]

overall_design: Transcriptional analysis of PAX7-purifed myoblasts derived from intraspecies mouse chimeras.

first: Seraina


title: Generation of allogenic and xenogeneic functional muscle stem cells for intramuscular transplantation

first: Adhideb

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Gene expression profiling of mouse embryonic stem cells with single-cell RNA sequencing

status: Public on Apr 24 2024

city: Nijmegen

first: Oscar

last: Garcia-Blay

state: Gelderland

address: Heyendaalseweg 135

department: Biophysical Chemistry

institute: Institute for Molecules and Materials (Radboud University)

summary: Differences in gene-expression profiles between individual cells can give rise to distinct cell fate decisions. Yet how localisation on a micropattern impacts initial changes in mRNA, protein, and phosphoprotein abundance remains unclear. To identify the effect of cellular position on gene expression, we developed a scalable antibody and mRNA targeting sequential fluorescence in situ hybridization (ARTseq-FISH) method capable of simultaneously profiling mRNAs, proteins, and phosphoproteins in single cells. We studied 67 (phospho-)protein and mRNA targets in individual mouse embryonic stem cells (mESCs) cultured on circular micropatterns. To validate the detection of the mRNA targets quantified with ARTseq-FISH, we utilized single-cell RNA sequencing to profile a comparable population of mouse embryonic stem cells.

overall_design: Mouse embryonic stem cells (mESCs) were seeded and growth in serum/LIF conditions. 30 hours post-seeding, cells were detached from the culture surface and frozen in preparation for single-cell RNA sequencing. Single-cell RNA sequencing was performed from a freshly thawed sample, through single-cell barcoding (10x Genomics Chromium) and sequencing  (NextSeq 2000; Single Cell 3'v3 chemistry).

first: Óscar

last: García-Blay

first: Maike

last: Hansen


title: Loss of the proteasome deubiquitinase USP14 induces growth defects and a senescence phenotype in colorectal cancer cells.

city: Linköping

first: Johannes

middle: Artiaga

last: Gubat

address: Ing. 68 Campus US. Linköpings Universitet

department: Biomedical and Clinical Sciences

country: Sweden

institute: Linköping university

summary: The proteasome-associated deubiquitinase USP14 has attracted significant attention in recent years due to its potential as a drug target. Here, we employ an inducible USP14 knockout system to dissect early phenotypic and gene expression alterations following USP14 loss. Transcriptomic analysis revealed widespread changes in the expression of actin cytoskeleton components associated with shifts in cellular actin distribution and morphology, as well as changes in the deubiquitinase expression profile. We observed an increase in ubiquitin turnover that appeared to be offset by the upregulation of polyubiquitin genes UBB and UBC.

overall_design: HCT116 cells bearing floxed USP14 exon 5 was lentivirally transduced with either Cre recombinase + GFP or GFP alone. Cre transduction results in the complete knockout of USP14. Cre + GFP - and GFP-transduced cells were enriched through flow cytometry and expanded. At D14 post transduction, the cells were harvested for bulk RNA sequencing

first: Padraig

last: D'arcy


title: MiR-146a alleviates inflammatory bowel disease in mice through systematical regulation of multiple genetic networks

city: Yangpu

first: Changgeng

last: Peng

state: Shanghai

address: Siping Road 1239

department: School of Medicine

institute: Tongji University

summary:
Inflammatory bowel disease (IBD) is a multiple-genes-involved chronic disease and current available targeted drugs for IBD only deliver moderate efficacy. Whether there is a single gene that systematically regulates IBD is not yet known. Here we showed that the expression of miR-146a in colon was elevated in Dextran Sulfate Sodium Salt (DSS)-induced IBD mice and patients with IBD. DSS induced dramatic body weight loss and much more rectal bleeding, shorter colon length and colitis in miR-146a knock-out mice than wild type (WT) mice. The miR-146a mimics alleviated DSS-induced symptoms in both DSS-induced miR-146a-/- and WT mice. Further RNA sequencing illustrated that deficiency of miR-146a de-repressed majority of DSS-induced IBD-related genes which cover multiple genetic regulatory networks in IBD, and supplement of miR-146a mimics inhibited expression of many IBD-related genes.
DOI 10.3389/fimmu.2024.1366319

overall_design: Experiment1: Bulk RNA of colon profiling data from 3 untreated wild type,3 DSS-treated wild type and 3 DSS-treated miR-146a knock-out mice.  Experiment2: Bulk RNA of colon profiling data from 6 (3 females+3 males) DSS+saline treated and 5  (3 females+2males) DSS+miR-146a_mimics treated miR-146a knock-out mice.

first: Fengting

last: Zhu

first: Taotan

last: Yang


title: Cholesterol in macrophage regulate gene expersion with or without LPS [MCD and LPS RNA-seq]

first: Jeffrey

last: Dilworth

first: Kristin

last: Dauner

first: Xiaohui

last: Zha


title: TCAF1 Promotes TRPV2-mediated Ca2+ Release in Response to Cytosolic DNA to Protect Stressed Replication Forks

first: Abigael

last: Cheruiyot

address: 1 Joslin Place

institute: Joslin Diabetes Center

summary: The protection of the replication fork structure under stress conditions is essential for genome maintenance and cancer prevention. A key signaling pathway for fork protection involves TRPV2-mediated Ca2+ release from the ER, which is triggered after the generation of cytosolic DNA and the activation of cGAS/STING. The resulting CaMKK2/AMPK activation and subsequent Exo1 phosphorylation prevent aberrant fork processing, thereby ensuring genome stability. However, it remains poorly understood how the TRPV2 channel is activated by the presence of cytosolic DNA. Here we show that the TRPM8 channel-associated factor 1 (TCAF1) plays a key role in promoting TRPV2-mediated Ca2+ release under replication stress or other conditions that activate cGAS/STING. Mechanistically, TCAF1 promotes Ca2+ release by facilitating the dissociation of STING from TRPV2, thereby relieving TRPV2 repression. Consistent with this function, TCAF1 is required for fork protection, chromosomal stability and cell survival after replication stress.

overall_design: To investigate how STING-TRPV2 dissociation occurs under replication stress, we carried out a genome-wide CRISPR/Cas9 screen in an effort to identify additional factors that regulate TRPV2 in the Ca2+-dependent pathway required for fork protection and cell survival in the presence of replication stress.

first: Lingzhen

last: Kong

first: Shan

last: Li

first: Chen

last: Cheng

first: Jiayi

last: Yuan

first: Yichan

first: Sydney

last: Hwang

first: Daniel

last: Foust

first: Ning

last: Tsao

first: Emily

last: Wilkerson

first: Nima

last: Mosammaparast

first: M

last: Major

first: David

last: Piston

first: Zhongsheng

last: You


title: Ribosome profiling reveals the role of yeast RNA-binding proteins Cth1 and Cth2 in translational regulation

first: Vyacheslav

last: Labunskyy

state: MA

address: 609 Albany St

department: Department of Dermatology

institute: Boston University School of Medicine

summary: Iron serves as a cofactor for enzymes involved in several steps of protein translation, but the control of translation during iron limitation is not understood at the molecular level. Here, we report a genome-wide analysis of protein translation in response to iron deficiency in yeast using ribosome profiling. We show that iron depletion affects global protein synthesis and leads to translational repression of multiple genes involved in iron-related processes. Furthermore, we demonstrate that the RNA-binding proteins Cth1 and Cth2 play a central role in this translational regulation by repressing the activity of the iron-dependent Rli1 ribosome recycling factor and inhibiting mitochondrial translation and heme biosynthesis. Additionally, we found that iron deficiency represses MRS3 mRNA translation through increased expression of antisense long non-coding RNA. Together, our results reveal complex gene expression and protein synthesis remodeling in response to low iron, demonstrating how this important metal affects protein translation at multiple levels.

overall_design: RNA-Seq and Ribo-Seq analyses of wild-type (W303a) and cth1Δcth2Δ knockout strains cultured in Fe-sufficient conditions (0H), and after a short- (3H) or long-term (6H) exposure to Fe deficiency, achieved by the addition of the Fe2+-specific chelator bathophenanthroline disulfonate (BPS).

first: Hanna

last: Barlit


title: Transcriptome of ovarian cancer cells overexpressing SYNCRIP or SNU13

first: Ksenia

middle: S

last: Anufrieva

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

summary: We showed that in response to chemotherapy, dying cancer cells can secrete spliceosomal components into the extracellular space. These therapy-induced secretomes enriched with spliceosomal components promote the chemoresistance of recipient tumor cells. We demonstrated that spliceosomal proteins SNU13 and SYNCRIP can relocalize from dying tumor cells to recipient tumor cells via extracellular vesicles. To investigate whether the increased abundance of splicing factors could be the reason for the acquisition of a more aggressive phenotype by tumor cells, we got SKOV3 cell lines stably overexpressing SYNCRIP or SNU13. These cell lines were more resistant to cisplatin compared to control cell line expressing empty vector. Next, to investigate how the therapy response is formed in tumor cells with and without overexpression of spliceosomal proteins SNU13 or SYNCRIP, we performed RNAseq analysis of these cells before and 24 hours after cisplatin treatment. Enrichement analyses showed that in response to cisplatin, genes associated with DNA repair and cell cycle regulation were upregulated in cancer cell lines overexpressing SYNCRIP or SNU13 compared with control cells. This study revealed previously unknown signaling molecules in the microenvironment of ovarian cancer that have potential clinical significance.

overall_design: SKOV3 cell lines stably overexpressing SYNCRIP or SNU13 and control SKOV3 cell line expressing empty vector pCDH were treated or untreated with cisplatin (40 uM) for 24 hours. Then, transcriptomic profiling was performed.

first: Victoria

last: Shender


title: Transcriptomic profiles of ovarian cancer cells isolated from paired cancer ascites before and after chemotherapy

summary: Chemotherapy in complex with surgical removal remain the most common approaches in cancer treatment, but their effectiveness is limited by the emergence of chemoresistance. In order to reveal changes in transcriptomic profiles of cancer cells remaining after platinum-based chemotherapy, we created primary cultures of cancer cells isolated from paired ascites of ovarian cancer patients taken at the time of diagnosis and after neoadjuvant chemotherapy. Enrichment analysis revealed significant activation of genes associated with DNA repair and cell cycle regulation in tumor cells after chemotherapy.

overall_design: We established primary cultures of ovarian cancer cells isolated from paired ascitic fluids from 7 patients before and after chemotherapy. Total RNA was isolated from early passages of cancer cells. Transcriptome profiles for the obtained samples were generated using HiSeq 2500.


title: Effect of therapy-induced secretomes on the transcriptome of ovarian cancer cells

summary: Exogenous signals from drug-stressed cancer cells promote acquisition of a more aggressive phenotype of neighboring tumor cells. Recently, we examined how cancer cell secretome changes in response to chemotherapy. We showed that tumor therapy-induced secretomes significantly increased resistance of cancer cells to subsequent cisplatin treatment but we did not observed the same phenomenon on normal fibroblasts. To elucidate how therapy-induced secretomes affect the transcriptomic profiles of recipient tumor cells, we incubated SKOV3 cells for 3 days with secretomes from control or dying cancer cells. The same conditions were used for normal fibroblasts. Enrichment analysis of differentially expressed genes in SKOV3 cells incubated with therapy-induced secretomes identified prominent up-regulation of genes involved in coordination of mitotic processes, G2/M transition checkpoints and DNA repair. These findings demonstrate that under stress condition cancer but not normal cells can secrete signaling molecules into the exracellular space and contribute to the emergence of tumor chemoresistance during short time period.

overall_design: We collected secretomes from donor SKOV3 cells and normal fibroblasts treated or untreated with cisplatin. Recipient SKOV3 cells were incubated for 3 days with secretomes from donor SKOV3 cells before and after therapy. Recipient fibroblasts were incubated for 3 days with secretomes from donor fibroblasts before and after therapy. Total RNA was isolated from recipient SKOV3 cells and fibroblasts. Transcriptome profiles for the obtained samples were generated using HiSeq 2500 System (Illumina).


title: Therapy-induced Secretion of Spliceosomal Components Mediates Pro-Survival Crosstalk Between Ovarian Cancer Cells

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


title: Defective transfer of parental histone decreases frequency of homologous recombination in budding yeast

first: haiyun

last: gan

address: xueyuan lu 1068

institute: Shenzhen Institute of Advanced Technology

summary: Recycling of parental histones is an important step in epigenetic inheritance. During DNA replication, DNA polymerase epsilon subunit DPB3/DPB4 and DNA replication helicase subunit MCM2 are involved in the transfer of parental histones to the leading and lagging DNA strands, respectively. Single Dpb3 deletion (dpb3[DELTA]) or Mcm2 mutation (mcm2-3A), which each disrupt one parental histone transfer pathway, leads to the other[prime]s predominance. However, the impact of the two histone transfer pathways on chromatin structure and DNA repair remains elusive. In this study, we used budding yeast Saccharomyces cerevisiae to determine the genetic and epigenetic outcomes from disruption of parental histone H3-H4 tetramer transfer. We found that a dpb3[DELTA]/mcm2-3A double mutant did not exhibit the single dpb3[DELTA] and mcm2-3A mutants[prime] asymmetric parental histone patterns, suggesting that the processes by which parental histones are transferred to the leading and lagging strands are independent. Surprisingly, the frequency of homologous recombination was significantly lower in dpb3[DELTA], mcm2-3A, and dpb3[DELTA]/mcm2-3A mutants relative to the wild-type strain, likely due to the elevated levels of free histones detected in the mutant cells. Together, these findings indicate that proper transfer of parental histones to the leading and lagging strands during DNA replication is essential for maintaining chromatin structure and that high levels of free histones due to parental histone transfer defects are detrimental to cells.

overall_design: We synchronized yeast cells (Wile type and other mutant cells) at G1 and released into early S phase in the presence of BrdU, and hydroxyurea (HU). We then performed BrdU immunoprecipitation using anti-BrdU antibodies following single-strand DNA library preparation and sequencing (ssSeq). we also performed protein ChIP followed by single-strand DNA sequencing (ChIP-ssSeq) for H3K56ac, H3K4me3. The sequencing tag was mapped to both Watson (red) and Crick (blue) strands of the reference genome.

first: Chuanhe

last: Yu

first: Haiyun

last: Gan

first: Srinivasu

last: Karri

first: Yi

last: Yang

first: Jiaqi

last: Zhou


title: Microglia from a SLE models

city: Chicago

first: Carla

middle: Marie

last: Cuda

state: IL

address: 240 E Huron St. M300

department: Medicine-Rheumatology

institute: Northwestern University

summary: We isolated CD45+CD11b+ microglia from mouse models of SLE and their respective controls.

overall_design: Brain CD45+CD11b+ immune cells were isolated from brains of  mice by FACS and 3' scRNA-seq was performed.

middle: M

first: Deborah

last: Winter


title: RNA-seq profiling of human hematopoietic cell populations across development.

city: Los Angeles

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

institute: UCLA

summary: We profiled the transcriptome of human hematopoietic stem and progenitor cell populations from embryonic emergence to adulthood.

overall_design: RNAseq of sorted human hematopoietic populations (CD34+CD38-CD90+)

last: Mikkola


title: Transcriptomic profiles of ovarian cancer cells incubated with autologous ascitic fluids from patients before and after chemotherapy

city: Boston

summary: Ovarian cancer is characterized by transcoelomic metastasis into the peritoneal cavity. The peritoneal malignant ascites is enriched with ovarian cancer cells and a small amount of tumor-associated immune cells which create a unique microenvironment actively contributing to progression of the disease. However, it is remain unclear how chemonaive and post-chemotherapy ovarian cancer ascitic fluids influence on cancer cells. To address this issue, we performed RNAseq analysis of primary cultures of ovarian cancer cells incubated for 3 days in the presence of ascites from the same patients before and after chemotherapy. We found that ascites after therapy causes a significant changes in transcriptomic profiles of cancer cells, and these changes are similar in samples obtained from all patients (n=4). Enrichment analysis of differentially expressed genes in tumor cells incubated with ascites after chemotherapy identified prominent up-regulation of genes associated with DNA repair, mitotic cell cycle regulation, and cell cycle checkpoints. These findings demonstrate how ascitic fluids persisted after chemotherapy can contribute to the emergence of tumor chemoresistance during short time period.

overall_design: We established primary cultures of ovarian cancer cells isolated from ascitic fluids of 4 ovarian cancer patients before chemotherapy. Early passages of these cancer cells were incubated for 3 days in the presence of autologous ascitic fluids (25% v/v) from patients before and after chemotherapy. Total RNA was isolated from early passages of cancer cells. Transcriptome profiles for the obtained samples were generated using HiSeq 2500 and NextSeq 500 System (Illumina).


title: Physiochemical interaction between osmotic stress and a bacterial exometabolite promotes plant disease

status: Public on Apr 23 2024

city: Cologne

first: Fantin

last: Mesny

address: Carl-von-Linné-Weg 10

department: Plant-Microbes interaction

institute: Max Planck Institute for Plant Breeding Research

summary: Various microbes isolated from healthy plants are detrimental under laboratory conditions, indicating the existence of molecular mechanisms preventing disease in nature. Here, we demonstrated that application of sodium chloride (NaCl) in natural and gnotobiotic soil systems is needed to induce plant disease caused by an otherwise non-pathogenic root-derived Pseudomonas brassicacearum isolate (R401). Disease caused by combinatorial treatment of NaCl and R401 triggered extensive, root-specific transcriptional reprogramming that did not involve down-regulation of host innate immune genes, nor dampening of ROS-mediated immunity. Instead, we identified and structurally characterized the R401 lipopeptide brassicapeptin A as necessary and sufficient to promote disease on salt-treated plants. Brassicapeptin A production transitions R401 from being beneficial to being detrimental on salt-treated plants by disturbing host ion homeostasis, thereby bolstering bacterial infection and susceptibility to osmolytes. We conclude that the interaction between a global change stressor and a bacterial exometabolite drives disease emergence in the plant microbiome.

overall_design: Root and shoot samples of Arabidopsis thaliana inoculated with heat-killed/alive Pseudomonas Root401 bacteria at NaCl concentration of 0mM/100mM

first: Felix

last: Getzke

first: Lei

last: Wang

first: Nienke

last: Denissen

first: Ka-Wai

last: Ma

first: Hidde

last: Wesseler

first: Paul

last: Schulze-Lefert

first: Till

middle: F

last: Schäberle

first: Stéphane

last: Hacquard


title: Triclosan administration to humanized UDP-glucuronosyltransferase 1 neonatal mice induces UGT1A1 through a dependence on PPARα and ATF4

city: San Diego

first: Andre

middle: Alberto

last: Weber

state: CA

address: 9500 Gilman Dr. La Jolla

institute: UCSD

summary: Triclosan (TCS) is an antimicrobial toxicant found in a myriad of consumer products and has been detected in human tissues, including breastmilk. We have evaluated the impact of lactational TCS on UDP-glucuronosyltransferase 1A1 (UGT1A1) expression and bilirubin metabolism in humanized UGT1 (hUGT1) neonatal mice. In hUGT1 mice, expression of the hepatic UGT1A1 gene is developmentally delayed resulting in elevated total serum bilirubin (TSB) levels. We found that newborn hUGT1 mice breastfed or orally treated with TCS presented lower TSB levels along with induction of hepatic UGT1A1. Lactational and oral treatment by gavage with TCS leads to the activation of hepatic nuclear receptors CAR, PPARα, and stress sensor, ATF4. When CAR-deficient hUGT1 mice (hUGT1/Car-/-) were treated with TCS, TSB levels were reduced with a robust induction of hepatic UGT1A1, leaving us to conclude that CAR is not tied to UGT1A1 induction. Alternatively, when PPAR-deficient hUGT1 mice (hUGT1/Ppar-/-) were treated with TCS, hepatic UGT1A1 was not induced. Additionally, we had previously demonstrated that TCS is a potent inducer of ATF4, a transcriptional factor linked to the integrated stress response. When ATF4 was deleted in liver of hUGT1 mice (hUGT1/Atf4∆Hep), and these mice treated with TCS, we observed superinduction of hepatic UGT1A1. Oxidative stress genes in livers of hUGT1/Atf4∆Hep treated with TCS were increased, suggesting that ATF4 protects liver from excessive oxidative stress. The increase oxidative stress may be associated with superinduction of UGT1A1. The expression of ATF4 in neonatal hUGT1 hepatic tissue may play a role in the developmental repression of UGT1A1.

overall_design: To investigate the pathways affected by TCS administration and deletion of ATF4 in the liver of neonates, we performed an RNA-sequencing.

first: Max

last: Chang

first: Christopher

last: Benner

first: Robert

last: Tukey


title: Translatomics reveals the role of dietary calcium addition in regulating muscle fat deposition in pigs

status: Public on Apr 22 2024

city: Nanning

first: Jingsu

last: Yu

state: Guangxi

address: Daxuedong Road, Xixiangtang District

department: College of Animal Science and Technology

institute: Guangxi University

summary: Intramuscular fat (IMF) in pork holds significant importance for economic performance within the pig industry and dietary calcium supplementation enhances the accumulation of intramuscular fat. Additionally, calcium ions inhibit translation and reduce protein synthesis. However, the mechanism by which calcium regulates IMF deposition in muscle through translation remains largely unknown. In this study, we compared the ribosome profiles of the longissimus dorsi muscles of trigram pigs from the normal calcium (NC) group or calcium supplement (HC) group by Ribo-seq, and RNA-seq. By integrating multiple-omics analysis, we further discovered 437 genes that were transcriptionally unchanged but translationally altered and these genes


title: Neratinib, a pan ERBB/HER inhibitor, restores sensitivity of PTEN-null, BRAFV600E melanoma to BRAF/MEK inhibition

city: Indianapolis

first: Steven

middle: P

last: Angus

state: IN

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University School of Medicine

summary: Approximately 50% of melanomas harbor an activating BRAFV600E mutation. Standard of care involves a combination of inhibitors targeting mutant BRAF and MEK1/2, the substrate for BRAF in the MAPK pathway. PTEN loss of function mutations occur in 40% of BRAFV600E melanomas, resulting in increased PI3K/AKT activity that enhances resistance to BRAF/MEK combination inhibitor therapy. To compare the response of PTEN null to PTEN wild type cells in an isogenic background, CRISPR was used to knock out PTEN a melanoma cell line that harbors a BRAFV600E mutation. RNA sequencing and functional kinome analysis revealed the loss of PTEN led to an induction of FOXD3 and an increase in expression of the FOXD3 target gene, ERBB3/HER3. Inhibition of BRAF and MEK1/2 in PTEN null, BRAFV600Ecells dramatically induced expression of ERBB3/HER3 relative to wild type cells. A synergy screen of epigenetic modifiers and kinase inhibitors in combination with BRAFi/MEKi identified the pan ERBB/HER inhibitor, neratinib, as reversing the resistance observed in PTEN null, BRAFV600Ecells. The findings indicate that PTEN null BRAFV600E melanoma exhibits increased reliance on ERBB/HER signaling when treated with clinically approved BRAFi/MEKi combinations. Future studies are warranted to test neratinib reversal of resistance in patient melanomas expressing ERBB3/HER3 in combination with its dimerization partner ERBB2/HER2.

overall_design: BRAFV600E A375 melanoma cells, wild type ("WT"), two PTEN KO clones ("KO5", "KO11"), PI3K-overexpressing ("PI3K"), or PI3K-H1047R-overexpressing ("H1047R", were treated with vehicle for 1 day or with 100nM dabrafenib and 10nM trametinib ("DT") for 1 day (acute, "A") or 7 days (chronic "C").


title: METTL3 deficiency aggravates hepatic ischemia/reperfusion injury in mice by activating the MAPK signaling pathway

city: Wu Han

first: jun

last: gong

state: Hu Bei

address: 1095 Jiefang Ave

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

summary: Inflammatory responses, apoptosis, and oxidative stress, are key factors that contribute to hepatic ischemia/reperfusion (I/R) injury, which may lead to the failure of liver surgeries, such as hepatectomy and liver transplantation. The N6-methyladenosine (m6A) modification has been implicated in multiple biological processes, and its specific role and mechanism in hepatic I/R injury require further investigation. We found that METTL3 may be involved in regulating this process.  Therefore, we constructed an ischemia-reperfusion model with Hepatocyte-specific METTL3 knockdown (HKD) mice, and performed RNA- sequencing analysis with wild-type mice as controls.

overall_design: Hepatocyte-specific METTL3 knockdown (METTL3-HKD) mice and METTL3-Flox mice were subjected to 1 h of ischemia and subsequent reperfusion for 6 h. Their livers were collected for RNA sequencing.

first: Yang

last: Gao

first: Chunle

last: Zhao

first: Jun

last: Gong


title: ZDHHC20-Mediated S-Palmitoylation of YTHDF3 Stabilizes MYC mRNA to Promote Pancreatic Cancer Progression

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

summary: Post-translational modifications of malignant transformation and tumor maintenance in pancreatic ductal adenocarcinoma (PDAC) in the context of KRAS signaling remains largely unexplored. Here, we used the KPC mouse model to examine the effect of palmitoylation on pancreatic cancer progression. ZDHHC20, upregulated by KRAS, is abnormally overexpressed and associated with poor prognosis in patients with pancreatic cancer. Dysregulation of ZDHHC20 promotes pancreatic cancer progression in a palmitoylation-dependent manner. ZDHHC20 inhibits lysosomal localization and degradation of YTHDF3 through S-palmitoylation of Cys474, which can result in abnormal accumulation of the oncogenic product MYC and thereby promote the malignant phenotypes of cancer cells. Further, we designed a biologically active YTHDF3-derived peptide to competitively inhibit YTHDF3 palmitoylation mediated by ZDHHC20, which in turn downregulated MYC expression and inhibited the progression of KRAS mutant pancreatic cancer. Thus, these findings highlight the therapeutic potential of targeting the ZDHHC20-YTHDF3-MYC signaling axis in pancreatic cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the PANC-1 cells after kncokdown of ZDHHC20.

first: Xin

last: Jin

first: Huan

last: Zhang


title: METTL3-mediated chromatin contacts promote phase separation during senescence.

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

overall_design: Refer to individual Series


title: METTL3-mediated chromatin contacts promote phase separation during senescence [fastGro-seq]

summary: Cellular senescence is a stable state of growth arrest that emerges as a response to stress. The methyltransferase complex (MTC) has been shown to facilitate the expression of the senescence-associated secretion phenotype (SASP) factors via genome-wide redistribution. However, whether and how MTC impacts on the three-dimensional (3D) chromatin organization and its functional implications during senescence remain largely unknown. Here we show that the MTC complex coordinates its enzymatic activity-dependent and -independent functions to enforce cellular senescence. Specifically, METTL3-mediated chromatin loops induce Hexokinase 2 (HK2) expression during senescence. The elevated HK2 expression subsequently promotes liquid-liquid phase separation (LLPS), manifesting as stress granules. These phase-separated stress granules act as reservoirs to sequester cell-cycle related mRNAs harboring polymethylated m6A sites, impeding their efficient translation. Overall, we uncover a mechanism by which senescent cells utilize phase-separated stress granules, facilitated by MTC-mediated HK2 activation, to sequester cell-cycle related mRNAs in governing senescence-associated stable growth arrest.

overall_design: fastGro-seq to monitor nascent gene transcription in control and senescent IMR90 cells with vector, METTL3, or METTL4 knockdown.

first: Chen

last: Wang

first: Connor

last: Hill

first: Rugang

last: Zhong


title: FOXA2/AP-1 drives prostate cancer lineage plasticity [PDX ChIP-seq]

first: Zifeng

state: Massachusetts

address: 100 Morrissey Blvd, ISC/4610

department: CPCT

institute: UMASS Boston

summary: FOXA (Forkhead Box Protein A) family proteins function as pioneer transcription factors by loosening the compact chromatin structure and facilitating access for other transcription factors. The role of FOXA1 has been intensively studied in normal prostate epithelial cells and the adenocarcinoma subtype of prostate cancer (PCa) where it acts as a critical pioneer factor for the chromatin binding of androgen receptor (AR). Recent studies have indicated the emergence of FOXA2 as an adaptive response to AR signaling inhibition, particularly in prostate tumors that have undergone lineage reprogramming to a neuroendocrine PCa subtype. However, the molecular basis for this transition from FOXA1 to FOXA2 and its role in regulating the development of PCa lineage plasticity remains unclear. In this study, we show that FOXA2 binds to distinct chromatin regions in multiple AR-null PCa models with different molecular subtypes and that its binding is dependent on an epigenetic factor, LSD1. More importantly, we demonstrate that FOXA2 can function as a major pioneer factor of JUN and govern the chromatin binding of AP-1 complex in PCa exhibiting lineage plasticity. Mechanistically, differential reprogramming of JUN activates lineage-specific super-enhancers that may promote PCa progression by enhancing cell state transitions to multiple lineages. Overall, our study reveals a pivotal function of the LSD1-FOXA2 axis in rewiring AP-1 to induce differential transcriptional reprogramming required for PCa lineage plasticity.

overall_design:
ChIP-seq analysis of FOXA1, FOXA2, AR, H3K27Ac in PDX201.1 and PDX201.2 cells.

>>>Submitter states that raw data are not available due to patient privacy concerns.<<<

first: Luke

middle: A

last: Selth

first: Scott

last: Townley

first: Changmeng

last: Cai


title: FOXA2/AP-1 drives prostate cancer lineage plasticity [RNA-seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative gene expression profiling analysis was performed on RNA-seq data from PC3 cells under hormone-depleted conditions, which were transfected with siFOXA2, siJUN, and siNTC and treated with vehicle, LSD1 inhibitor ORY-1001 (10μM), and C12 (0.5μM) for 24 hours. We also conducted a similar analysis on RNA-seq data from NCI-H660 cells transfected with siFOXA2, siJUN, and siNTC. Furthermore, we carried out a comparative gene expression profiling analysis in LNCaP cells with stable FOXA2 overexpression (LN-FOXA2-OE) and negative control cells under hormone-depleted conditions.


title: Effect of extracellular spliceosomal snRNAs on the transcriptome of ovarian cancer cells

first: Ksenia

last: Anufrieva

summary: Exogenous signals from drug-stressed cancer cells accelerate the proliferation of neighboring tumor cells and promote to acquire a more aggressive phenotype. We have recently found an exciting phenomenon: drug-stressed cancer cells secrete various components of the spliceosome: proteins and a number of snRNAs. We have observed this phenomenon both in vitro (culture media from cancer cell lines [Pavluykov M. et al., 2018]) and in vivo (ovarian cancer ascites after chemotherapy [Shender V. et al., 2014]). The aim of this study was to elucidate the role of secreted spliceosomal snRNAs in intercellular communication. We constructed synthetic U12 and U6atac snRNAs close to the natural structure, including some non-canonical nucleotides imitating post-transcriptional RNA modifications. RNAseq analysis of SKOV3 cells transfected with U6atac or U12 snRNA analogs has shown that both exogenous snRNAs lead to an increase of abundance of proteins related to cell cycle regulation and M phase. It has been recently shown that a number of spliceosomal proteins affect regulation of the cell cycle, in particular the M phase [Maslon et al., 2014]. Here we demonstrated that not only spliceosomal proteins but also spliceosomal snRNAs (U12 and U6atac) affect cell cycle gene expression. This study revealed previously unknown signaling molecules in the microenvironment of ovarian cancer that have potential clinical significance.

overall_design: SKOV3 cells were transfected with in vitro synthesized snRNAs: U12, U6atac snRNAs, or a control GFP mRNA fragment (89 nucleotides). SKOV3 cells treated with empty transfectant were taken as a contol. Transcriptomic profiling was performed 48 h after transfection.

first: Victoria

last: Shender


title: IL-6 blockade prevents costimulation blockade-resistant allograft rejection by promoting intragraft regulation in T cell-depleted recipients [GIL]

status: Public on Apr 21 2024

city: Vienna

first: Moritz

last: Muckenhuber

state: Vienna

address: Währinger Gürtel 18-20

department: General Surgery

country: Austria

institute: Medical university of vienna

summary: The efficacy of costimulation blockade (CTLA4Ig/belatacept) in transplantation is reduced by an increased incidence of T cell-mediated rejection, which also persists after induction therapy with anti-thymocyte globulin (ATG). Herein, we investigate why ATG fails to prevent costimulation blockade-resistant rejection and how this barrier can be overcome. ATG did not prevent graft rejection in a murine heart transplant model of CTLA4Ig therapy and induced a pro-inflammatory cytokine environment. While ATG improved the balance between Tregs and effector T cells in the peripheral compartment, it had no such effect within cardiac allografts, which showed signs of inflammation. Neutralizing IL-6 alleviated inflammation, increased intragraft Treg frequencies long-term, and enhanced intragraft IL-10 and Th2 cytokine expression. IL-6 blockade together with ATG led to long-term, rejection-free heart graft survival under CTLA4Ig therapy. Combining ATG with IL-6 blockade prevents costimulation blockade-resistant rejection, thereby eliminating a major impediment to clinical use of costimulation blockers in transplantation.

overall_design: to investigate the effects of IL-6 blockade on intragraft leukocyte signaling patterns, we performed gene expression profiling of data obtained via RNAseq of flow sorted graft infiltrating leukocytes isolated from fully mismatched murine cardiac allografts explanted from recipients treated with or without IL-6 blockade explanted 14 days after transplantation.

first: Thomas

last: Wekerle

first: Sophia

last: Derdak


title: FOXA2/AP-1 drives prostate cancer lineage plasticity