title: Embryo response to different progesterone concentrations during superovulation of Holstein heifers

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: Greater progesterone (P4) concentrations during the follicular growth have been associated with greater quality of embryos produced by superovulated cows and heifers. However, it is yet to be determined the mechanisms by which oocyte exposure to greater P4 concentrations improves early embryo quality. The objective of this study was to evaluate the impact of different P4 concentrations during superovulation on the transcriptome profile of early bovine embryos. A total of 63 post-puberty Holstein heifers were randomly assigned into two experimental groups: High P4 (n = 31) and Low P4 (n = 32). Heifers received a pre-synchronization protocol followed by a protocol of superovulation that included the allocated P4 treatment. Embryo collection was performed 7 days post artificial insemination and embryos were evaluated for stage of embryonic development and grades of quality. Embryos graded as good/excellent quality (High P4: n = 27; Low P4: n = 27) were randomly allocated in 3 biological replicates per treatment group, balanced for stage of embryonic development. Transcriptome analysis suggested that exposure to different concentrations of P4 during superovulation promote changes in gene expression of 7 days old embryos that may be related to their developmental competence. These modifications are associated with downregulation of beta-estradiol pathway, upregulation of trophoblast-related genes and downregulation of WNT signalling pathway. Our results suggest a potential sensitivity of future embryos to follicular P4 levels but do not allow to conclude if the effect is from the oocyte, the oviduct, or the uterus response to P4.

overall_design: Heifers underwent to a pre-synchronization protocol followed by a protocol of superovulation that included the allocated P4 treatment. Embryos were collected 7 d post-artificial insemination (AI) and were evaluated for fertilization, stage of embryonic development, and grades of quality. Embryos were randomly allocated in 3 biological replicates per treatment group on which we performed gene expression profiling using RNAseq. Finally, we identified differential expression of genes between treatment groups.

first: Jessica

middle: C

last: Marques

first: Joyce

middle: P

last: Maciel

first: Clément

last: Plessis

first: Ronaldo

last: Cerri


title: Whole geneome methylation sequencing for bull fertility DNA mehylation biomarker

status: Public on Jun 04 2024

city: quebec

first: ying

last: zhang

address: 735 Ave.Neree tremblay

country: Canada

institute: UNIVERSITY LAVAL

type: Methylation profiling by high throughput sequencing

summary: High fertility and low fertility bulls were screened from the a 6000 bull database and then identify the sperm-derived DMR and DMC that assoiated with bull ferrtility via whole genome methtlation sequencing

overall_design: Methylation characteristic of the bull sperm that associated with bull fertility

first: Ying

last: Zhang

first: Camila

last: Bruna de Lima

first: Remi

last: Labrecque


title: Sphingolipid metabolism controls mammalian heart regeneration

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

country: China

institute: Sun Yat-sen University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Utilization of lipids as energy substrates after birth causes cardiomyocyte (CM) cell-cycle arrest and loss of
regenerative capacity in mammalian hearts. Beyond energy provision, proper management of lipid composition is crucial for cellular and organismal health, but its role in heart regeneration remains unclear. Here, we
demonstrate widespread sphingolipid metabolism remodeling in neonatal hearts after injury and find that
SphK1 and SphK2, isoenzymes producing the same sphingolipid metabolite sphingosine-1-phosphate
(S1P), differently regulate cardiac regeneration. SphK2 is downregulated during heart development and determines CM proliferation via nuclear S1P-dependent modulation of histone acetylation. Reactivation of
SphK2 induces adult CM cell-cycle re-entry and cytokinesis, thereby enhancing regeneration. Conversely,
SphK1 is upregulated during development and promotes fibrosis through an S1P autocrine mechanism in
cardiac fibroblasts. By fine-tuning the activity of each SphK isoform, we develop a therapy that simultaneously promotes myocardial repair and restricts fibrotic scarring to regenerate the infarcted adult hearts.

overall_design: The epigenomic landscape of heart of 3 day old mice in response to injury.

first: Xiaoqian

last: Ji

first: Yun

last: Li

first: Zihao

last: Chen


title: Dynamically expressed genes provide candidate viability biomarkers in a model coccidian

city: Beltsville

first: Matt

last: Tucker

state: MD

address: 10300 Baltimore Ave, BARC-East Bldg 1040 Rm 104-5

department: Agricultural Research Service

country: USA

institute: USDA

type: Expression profiling by high throughput sequencing

summary:
Purpose: Parasites of the genus Eimeria, and the closely related human pathogen Cyclospora cayetanensis, cause enteric disease in livestock and people worldwide. These coccidian parasites must undergo maturation (sporulation) before becoming infectious. Understanding oocyst maturation would benefit attempts to reduce the harm they cause to veterinary and human health. No animal model exists to study C. cayetanensis and the parasite cannot be grown in culture.  We assessed transcription in maturing oocysts of Eimeria acervulina, a widespread chicken parasite, in order to identify markers of viability and those that may differentiate immature and mature oocysts. We also investigated predicted gene function and determined which of this parasite’s genes also occur in C. cayetanensis.
Methods: E. acervulina oocysts were collected from chickens (3 biological replicates) and allowed to sporulate for 24 hours. RNA was extracted from oocysts that were collected every four hours and subjected to RNA-Sequencing. Data were screened for constitutively expressed genes throughout the time course. We also identified differentially expressed genes between immature and mature oocysts.  We performed functional characterization of constitutively -expressed and significantly differentially-expressed genes and also biochemical pathway analysis.   RT–qPCR validation on selected constitutively and differentially-expressed genes was performed using SYBR Green assays.
Results: RNA-Seq yielded ~2 billion paired-end reads, 92% of which mapped to the E. acervulina genome. The ~6,900 annotated genes underwent temporally-coordinated patterns of gene expression. Fifty-three constitutively expressed genes each contributed >1,000 TPM throughout, including those encoding cation-transporting ATPases, an oocyst wall protein, a palmitoyltransferase, membrane proteins, and hypothetical proteins. These genes were enriched for 285 gene ontology (GO) terms and 13 genes were associated with a total of 17 KEGG pathways, defining housekeeping processes and functions important throughout sporulation. Expression of more than 40% of these genes (2,928) differed in sporulated vs. unsporulated oocysts; of these, nearly two-thirds (1,843) increased their expression over time. Eight genes expressed most in unsporulated oocysts, and encoding proteins promoting oocyst maturation and development, could be assigned to 37 GO terms and 5 KEGG pathways. Fifty-six genes underwent significant upregulation in sporulated oocysts, each contributing at least 1,000 TPM. Of these, 40 were annotated by 215 GO assignments and 9 were associated with 18 KEGG pathways, encoding products involved in respiration, carbon fixation, energy utilization, invasion, motility, and stress and detoxification responses. Several RT-qPCR assays confirmed RNA-Seq as a valid means to estimate gene expression.
Conclusions: Sporulation orchestrates coordinated changes in the expression of many coccidian genes, most especially those important to metabolic activity. These data elucidate the biology of coccidian development, provide means to evaluate the maturity of parasite cohorts, and may prove useful in predicting infectiousness. Moreover, because many of these genes have homologues in C. cayetanensis, they may prove useful as biomarkers for infectiousness.

overall_design: E. acervulina oocysts from chickens (3 biological replicates) were collected every four hours over a 24 hour sporulation time course for RNA-Seq

first: Matthew

middle: S

first: Celia

last: O'Brien

first: Mark

last: Jenkins

first: Ben

last: Rosenthal


title: Interactions between genistein and Wnt pathway in colon adenocarcinoma and early embryos

status: Public on Jun 03 2024

city: Waltham

first: Yerbol

last: Kurmangaliyev

state: MA

address: 415 South Street, MS 029

department: Biology

institute: Brandeis University

summary: The Wnt signaling pathway is one of the most ancient and pivotal signaling cascades, governing diverse processes in development and cancer regulation. Within the realm of cancer treatment, genistein emerges as a promising candidate due to its multifaceted modulation of various signaling pathways, including the Wnt pathway. Despite promising preclinical studies, the precise mechanisms underlying genistein's therapeutic effects via Wnt modulation remain elusive. In this study, we unveil novel insights into the therapeutic mechanisms of genistein by elucidating its inhibitory effects on Wnt signaling through macropinocytosis. Additionally, we demonstrate its capability to curtail cell growth, proliferation, and lysosomal activity in the SW480 colon adenocarcinoma cell model. Furthermore, our investigation extends to the embryonic context, where genistein influences gene regulatory networks governed by endogenous Wnt pathways. Our findings shed light on the intricate interplay between genistein, Wnt signaling, membrane trafficking, and gene regulation, paving the way for further exploration of genistein's therapeutic potential in cancer treatment strategies.

overall_design: To investigate how genistein treatment affects gene regulatory networks during development, we treated Xenopus embryos with genistein at the 4-cell stage and collected them at stage 9.5 for RNA sequencing. In addition to genistein, we used two established Wnt activators: BIO (6-bromoindirubin-3'-oxime) and Chiron (CHIR 99021). All four conditions were profiled in triplicates and used for differential gene expression analysis.

first: Nydia

last: Tejeda-Muñoz

middle: Z


title: Landscape of microenvironment in Randall's plaque by single-cell sequencing

first: Zezhen

last: Liu

state: Guangdong

address: #.1 Kangda Road, Haizhu District

institute: The First Affiliated Hospital of Guangzhou Medical University

summary: Randall's plaque is significantly associated with occurrence of nephrolithiasis. However, the microenvironment of Randall's plaque is poorly characterized. To investigate the microenvironment of Randall's plaque, we analyzed single-cell RNA data of 3 Randall's plaque and 3 normal renal papillae tissue and identified 11 different cell types. We screened differentially expressed genes among all cell types between Randall's plaque and normal renal papillae. The microenvironment showed two cell types with multiple stone formation-associated transcriptomic programs. Contrary to previous studies, we did not observe macrophages M1/M2 imbalance. Notably, we detected ossification-associated macrophage is enrich in Randall's plaque and validated GPNMB and ACP5 were potential biomarkers on osteoblasts-associated macrophage. We also identified an endothelial subset harboring active communication (COL15A1+ PCDH17+ endothelial, DPECs) with other cells. Together with Immunofluorescence, we validated ossification-associated macrophage and DPECs are enriched in Randall's plaque tissue. Finally, cell-to-cell communication revealed that Loop of Henle, DPECs and osteoblasts-associated macrophages were the main source of SPP1 signaling. Our work will further the understanding of the microenvironment among Randall's plaque tissues and provide deep insight into immune modulation.

first: Guohua

last: Zeng


title: Loss of mitochondrial pyruvate transport initiates cardiac glycogen accumulation and heart failure

city: St. Louis

first: Michelle

last: Brennan

state: MO

address: 1100 South Grand Blvd

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

summary: Background: Heart failure involves metabolic alterations including increased glycolysis despite unchanged or decreased glucose oxidation. The mitochondrial pyruvate carrier (MPC) regulates pyruvate entry into the mitochondrial matrix, and cardiac deletion of the MPC in mice causes heart failure. How MPC deletion results in heart failure is unknown. Methods: We performed targeted metabolomics and isotope tracing in wildtype (fl/fl) and cardiac-specific Mpc2-/- (CS-Mpc2-/-) hearts after in vivo injection of 13C-glucose. Cardiac glycogen was measured biochemically and by transmission electron microscopy. Cardiac glucose uptake of 2-deoxyglucose was measured and western blotting performed to analyze insulin signaling and enzymatic regulators of glycogen synthesis and degradation. Isotope tracing and glycogen analysis was also performed in hearts from mice fed either low-fat diet or a ketogenic diet previously shown to reverse the heart failure in CS-Mpc2-/- mice. Cardiac glycogen was also assessed in mice infused with angiotensin-II that were fed either low-fat or ketogenic diet. Results: Failing CS-Mpc2-/- hearts contained normal levels of ATP and phosphocreatine, suggesting their heart failure is not caused by energetic stress. These hearts displayed increased enrichment from 13C-glucose and increased glycolytic metabolite pool sizes. 13C enrichment and pool size was also increased for the glycogen intermediate UDP-glucose, as well as increased enrichment of the glycogen pool. Glycogen levels were increased ~6-fold in the failing CS-Mpc2-/- hearts, and glycogen granules were easily detected by electron microscopy. This increased glycogen synthesis occurred despite enhanced inhibitory phosphorylation of glycogen synthase and reduced expression of the priming enzyme glycogenin-1. In young, non-failing CS-Mpc2-/- hearts, increased glycolytic 13C enrichment occurred, but glycogen levels remained low and unchanged compared to fl/fl hearts. Feeding a ketogenic diet to CS-Mpc2-/- mice reversed the heart failure and normalized the cardiac glycogen and glycolytic metabolite accumulation. Cardiac glycogen levels were also elevated in mice infused with angiotensin II, and both the cardiac hypertrophy and glycogen levels were improved by ketogenic diet. Conclusions: Our results indicate that loss of MPC in the heart increases glycolytic metabolism and ultimately glycogen accumulation and heart failure, while a ketogenic diet can reverse both the glycogen accumulation and heart failure. We conclude that maintaining mitochondrial pyruvate import and metabolism is critical for the heart, unless cardiac pyruvate metabolism is dramatically reduced by consumption of a ketogenic diet.

overall_design: We performed gene expression profiling analysis between the left ventricle of hearts from 6 fl/fl and 6 CS-Mpc2-/- 30 week old chow-fed mice. RNA samples in each group were pooled in groups of two, resulting in three samples per group.

first: McCommis

last: Kyle

first: Weiss

last: Rachel


title: Transcriptomic profile of the hippocampus after status epilepticus in wildtype and EZH2 neuronal knockout mice.

city: Madison

first: Olivia

middle: Rose

last: Hoffman

email: ohoffman@wisc.edu, asroopra@wisc.edu

state: WI

address: 1111 Highland Avenue

department: Department of Neuroscience

institute: University of Wisconsin-Madison

summary: EZH2 is a key epigenetic regulator that catalyzes histone methylation to effect transcriptional repression. Preliminary data suggested that EZH2 induction is a protective response mounted by the brain in response to seizures. To investigate the impact of EZH2 deletion in hippocampal neurons under pathological conditions, we generated whole transcriptome profiles using RNA sequencing in saline and kainate-treated wild-type (EZH2nWT) mice, as well as homozygous EZH2 neuronal knockout (EZH2nHom) mice. Our results reveal significant alterations in gene expression patterns in the hippocampus of EZH2nHom compared to EZH2nWT mice, particularly following kainate-induced seizures. Overall, our study provides valuable insights into the transcriptional changes induced by EZH2 deletion in hippocampal neurons, highlighting its importance in regulating gene expression in response to epileptogenic insults.

overall_design: To investigate the protective role of EZH2 induction after seizures, we used Synapsin1-Cre to generate EZH2 wildtype (EZH2nWT) and conditional neuronal knockout mice (EZH2nHom) on a C57BL6 background. We used a repeated low-dose kainate model to induce status epilepticus, injecting controls with saline to produce four experimental conditions: saline:WT, kainate:WT, saline:EZH2nHom, kainate:EZH2nHom. Whole hippocampi were harvested four days after induction of status epilepticus.

middle: R

first: Barry

middle: A

last: Schoenike

first: Avtar

last: Roopra


title: Association of CXCL14 in the Human Airway Epithelium with Chronic Obstructive Lung Disease and Lung Cancer

status: Public on Jun 05 2024

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: CXCL14, a recently described chemokine constitutively expressed in various epithelia, has multiple putative roles in inflammation and carcinogenesis. Based on the knowledge that cigarette smoking and the smoking-induced disorders, such as chronic obstructive pulmonary disease (COPD) and lung cancer, are associated with inflammation, we hypothesized that the airway epithelium, the primary site of smoking-induced pathologic changes in COPD and adenocarcinoma, responds to cigarette smoking with an altered CXCL14 gene expression as a part of disease-relevant molecular phenotype. Microarray analysis with subsequent TaqMan PCR validation revealed very low constitutive CXCL14 gene expression in the airway epithelium of healthy nonsmokers (n=53) which was strongly up-regulated in healthy smokers ( n=59; p<0.001) and further increased in COPD smokers (n=23; p<10-7 vs nonsmokers; p<0.005 vs healthy smokers). In smokers, CXCL14 expression inversely correlated with lung function parameters FEV1 and FEV1/FVC. Genome-wide analysis also showed that up-regulated correlation of CXCL14 expression with genes related to cell growth and proliferation, squamous differentiation and cancer. The analysis of 193 lung adenocarcinoma samples demonstrated a dramatic up-regulation of CXCL14 in a smoking-dependent manner. [need to include survival data once we get it]. Together, these data suggest that smoking-induced expression of CXCL14 in association with genome-wide reprogramming of processes related to tissue homeostasis, differentiation and tumorigenesis, represents a novel molecular link between cigarette smoking, COPD and lung cancer.

overall_design: Affymetrix arrays were used to assess the expression of CXCL14 gene expression data in small airway epithelium obtained by fiberoptic bronchoscopy of 53 healthy non-smokers and 59 healthy smokers and 23 smokers with COPD.

first: Rachel

last: Sackrowitz

first: Renat

last: Shaykhiev

first: Prince

last: Bonsu

first: Bradely

last: Witover

first: Barbara

last: Ferris

first: Camelia

last: Sime

first: Robert

middle: J

last: Downey

first: Ronald

middle: G

last: Crystal


title: Human AML1-ETO driven acute myeloid leukemia (AML) shows a dysfunctional immune microenvironment.

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

summary: AML is a genetically heterogeneous, aggressive hematological malignancy induced by distinct oncogenic driver mutations. Cancer immunosurveillance is a coordinated response from innate and adaptive immune cells against cancer cells. The effect of specific AML oncogenes on immune activation or suppression has not been investigated.

overall_design: Bone marrow from AML patients or  healhy controls were obtained and Ficoll gradient seperated to extract mononuclear cells. Cells were sorted for immune cell fraction (CD34-CD45+) and subject to 3' single cell RNA sequencing using 10x Genomics  platform.

first: Rebecca

last: Austin

first: Steven

middle: W

last: Lane


title: Vitamin A-Derived Retinoic Acid Contributes to Muscle Stem Cell and Mitochondrial Function [RNA-Seq]

city: Ann Arbor

first: Carlos

last: Aguilar

state: MI

address: 2800 Plymouth Rd

department: Biomedical Engineering

institute: University of Michigan

summary: Vitamin A is an exogenous micronutrient that is derived solely from diet and metabolized into retinoic acid, which acts as an antioxidant and transcriptional regulator. Here we show that obstruction of dietary Vitamin A drives mitochondrial and cell cycle dysfunction in MuSCs and myoblasts that mimics old age. The receptor for vitamin A derived retinol, Stra6, was found to be diminished with MuSC activation and in old age. The loss of Stra6 in myogenic progenitors resulted in accumulation of mitochondrial reactive oxygen species, as well as changes in mitochondrial morphology and respiration. Pharmacological targeting of Stra6 and retinoic acid signaling in myogenic progenitors and aged MuSCs reverted oxidative damage, enhanced mitochondrial function, and improved maintenance of quiescence. These results demonstrate that Vitamin A regulates mitochondria and metabolism in MuSCs to promote quiescence. These results highlight a unique mechanism connecting stem cell function with vitamin intake.

overall_design: Young Pax7-nTnG mice were fed either a Vitamin A-deficient diet or a control diet for 8 weeks, after which they were administed tamoxifen to activate GFP labeling of muscle stem cells (MuSCs). GFP+ MuSCs were isolated via FACS and sorted directly into Trizol RNA-lysis reagent. RNA was submitted for Illumina sequencing and differential gene expression profiling was conducted between Vitamin A-deficient samples and control samples.

first: Paula

middle: M

last: Fraczek


title: Vitamin A-Derived Retinoic Acid Contributes to Muscle Stem Cell and Mitochondrial Function [scRNA-Seq]

overall_design: Aged (24 months) female C57 Bl/6J mice were administered 3 intramuscular (in the tibialis anterior, gastrocnemius, and quadricep muscles) injections of ATRA, CD3254, and BMS961 or a DMSO vehicle control over the course of a week. After treatment, hindlimb muscles were dissected and digested, and single cell suspensions were submitted for 10x Genomics single cell RNA-sequencing. n=2 mice were pooled per condition for scRNA-Seq.


title: Acupuncture potentiates anti-PD-1 efficacy by promoting CD5+ dentritic cells and T cell-mediated tumor immunity in breast cancer

city: changchun

first: xu

last: xiaoru

address: No1035.Boshuo Street,Jingyue Economic Development District

institute: Changchun University of Chinese Medicine

summary: Acupuncture has been considered as an available complement therapy against various malignancy cancer by regulating immunity. However, it is not clear whether acupuncture influences the antitumor immune efficacy of PD-1 inhibitor. This study evaluates the efficacy of acupuncture combined with PD-1 inhibitor on the antitumor immune response against breast cancer and revealed the potential molecular mechanisms based on RNA-Seq transcriptome analysis. The results depicted that acupuncture combined with PD-1 inhibitor significantly hindered tumor development by inducing tumor cell apoptosis and inhibiting tumor growth, angiogenesis and metastasis. RNA-Seq analysis indicated that the different expression genes upon acupuncture intervention mainly enriched in immune response, T cell activation and cytokine interaction etc. items containing immune cell-related CD genes (CD5, CD4 and CD8 etc.). Acupuncture stimulation enhanced CD5 expression that had a positive correlation with overall survival of breast cancer patients. The improved immunity including the enhancement of CD5+ dendritic cell, CD4+ and CD8+ T cell content as well as various cytokine (IL-2, IL-6, TNF-α, IFN-γ) secretion in serum was found upon acupuncture combination with PD-1 inhibitor treatment. Taken together, present work reveals that acupuncture intervention promotes the antitumor immune response of PD-1 inhibitor, providing a prospective therapy for ICI therapy against breast cancer.

overall_design:
To evaluate the therapeutic effect of acupuncture combined with PD-1 inhibitor on anti-tumor immune response of breast cancer, we revealed its potential molecular mechanism based on RNA-Seq transcriptome analysis.
The results indicated that acupuncture combined with PD-1 inhibitors significantly hindered tumor development by inducing tumor cell apoptosis and inhibiting tumor growth, angiogenesis, and metastasis. RNA-Seq analysis revealed that the differentially expressed genes upon acupuncture intervention were mainly enriched in immune response, T cell activation, and cytokine interaction, involving immune cell-related CD genes (e.g., CD5, CD4, and CD8).

first: Xiaoru

last: Xu


title: A systems genomics and genetics approach to identify the genetic regulatory network for lignin content in Brassica napus seeds

city: Saskatoom

first: wentao

last: zhang

state: SK

address: 110 Gymnasium Pl

institute: NRC-Canada

summary: Seed quality traits of oilseed rape, Brassica napus (B. napus), exhibit quantitative inheritance determined by its genetic makeup and the environment via the mediation of a complex genetic architecture of hundreds to thousands of genes. Thus, instead of single gene analysis, network-based systems genomics and genetics approaches that combine genotype, phenotype, and molecular phenotypes offer a promising alternative to uncover this complex genetic architecture. In the current study, systems genetics approaches were used to explore the genetic regulation of lignin traits in B. napus seeds.  Four QTL (qLignin_A09_1, qLignin_A09_2, qLignin_A09_3, and qLignin_C08) distributed on two chromosomes were identified for lignin content. The qLignin_A09_2 and qLignin_C08 loci were homologous QTL from the A and C subgenomes, respectively. Genome-wide gene regulatory network analysis identified eighty-three subnetworks (or modules); and three modules with 910 genes in total, were associated with lignin content, which was confirmed by network QTL analysis. eQTL (expression quantitative trait loci) analysis revealed four cis-eQTL genes including lignin and flavonoid pathway genes, cinnamoyl-CoA-reductase (CCR1), and TRANSPARENT TESTA genes TT4, TT6, TT8, as causal genes. The findings validated the power of systems genetics to identify causal regulatory networks and genes underlying complex traits. Moreover, this information may enable the research community to explore new breeding strategies, such as network selection or gene engineering, to rewire networks to develop climate resilience crops with better seed quality.

overall_design: cRNAs were amplified from total RNA samples (2 µg) and labeled with either cy3 or cy5 using the Quick Amp labeling kit, Two Color (Agilent, Catalogue: 5190-0444) according to the manufacturer’s instructions, followed by purification with the Qiagen RNeasy Mini Kit (Qiagen, Catalogue 74104) and quantification with a NanoDrop ND-1000. Purified cRNAs (2 µg) were fragmented and hybridized to the Agilent 4x44K Brassica arrays (Parkin et al., 2010) for 17 h at 65°C with a rotation of 10 rpm according to the manufacturer’s protocol. Arrays were washed with the Agilent Gene Expression Washing buffers according to the manufacturer’s protocol and scanned with GenePix 4000B as described by Parkin et al. (2010). Four and two biological replications were performed for the parental lines and the SG lines, respectively, with dye-swaps applied to the biological replicates to minimize dye effects from the two colour systems (Lee et al., 2004).

first: Wentao

last: Zhang

first: Erin

last: Higgins

first: Steve

last: Robinson

first: Clarke

last: Wayne

first: Kerry

last: Boyle

first: Andrew

last: Sharpe

first: Pierre

last: Fobert

first: Isobel

last: Parkin


title: The progression of ovarian endometriosis is facilitated by ASPM through its regulation of the cell cycle and the Wnt/β-catenin pathway

city: Liuzhou

first: Fengque

last: Zheng

state: Guangxi

address: NO.156 Heping Road, Liunan District

department: Department of Gynecology

institute: The Fourth Affiliated Hospital of Guangxi Medical University

summary: Gene expression profiling of endometrial stromal cells (ESCs) after transfection with si-NC or si-ASPM.

overall_design: ESCs (1×106) were placed in six-well plates 1 day prior to transfection. ESCs were transfected with 30 pmol of the Control control or ASPM siRNA usingwas transfected into ESCs with Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA, USA) at a concentration of 30 pmol. The GV230-ASPM plasmid was constructed by GeneChem (Shanghai, China). The cells were transfected with 2.5 μg of control or GV230-ASPM plasmids using with Optimi Lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) mixed with 2.5 μg of control or GV230-ASPM plasmid suspensions. ESCs were collected 48 h after transfection.


title: Microbiota dictate T cell clonal selection to augment graft-vs-host disease after stem cell transplantation

city: Seattle

first: Albert

last: Yeh

state: WA

address: 1100 Fairview Ave N.

department: Translational Sciences and Therapeutics

institute: Fred Hutchinson Cancer Center

summary: Allogeneic T cell expansion is the primary determinant of graft-versus-host disease (GVHD), and current dogma dictates that this is driven by histocompatibility antigen disparities between donor and recipient. This paradigm represents a closed genetic system within which donor T cells interact with peptide-MHC complexes, though clonal interrogation remains challenging due to the sparseness of the T cell repertoire. We developed a Bayesian model using donor and recipient TCR frequencies in murine stem cell transplant systems to define limited common expansion of T cell clones across genetically identical donor-recipient pairs. A subset of donor CD4 T cell clonotypes differentially expanded in identical recipients and were microbiota dependent. Microbiota-specific T cells augmented GVHD lethality and could target microbial antigen presented by gastrointestinal epithelium during an alloreactive response. The microbiota thus serves as a source of cognate antigen that contributes to clonotypic T cell expansion and the induction of GVHD independent of donor-recipient genetics.

overall_design: Male B6.Ptprca (CD45.1, Taconic) were divided into 3 groups representing exposure to different donor grafts (group 1, N=3: 0.5x106 CD4+ Marilyn (Allo) Tg (CD45.2+/CD90.1+); group 2, N=4: 0.5x106 Allo T with 1x106 CD4+ CBir1 T (CD45.2+/CD90.2+); group 3, N=3: 1x106 CD4+ CBir1 T). All recipients received 5x106 B6 (CD45.1+) bone marrow. Hashed and sorted splenocytes were harvested at day 6 to isolate Allo T (CD45.2+/CD45.1neg/CD90.1+) and CBir1 T (CD45.2+/CD45.1neg/CD90.1neg/Vβ14+) T cells for single cell RNA sequencing.

first: Olivia

last: Waltner

first: Shruti

last: Bhise

first: Scott

middle: N

last: Furlan

first: Geoffrey

last: Hill


title: A novel function of STAT3β in suppressing interferon response improves outcome in acute myeloid leukemia

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: To elucidate the role of STAT3β in acute myeloid leukemia (AML), we established a mouse model of STAT3β-deficient, MLL-AF9-driven AML. STAT3β-deficiency significantly shortened survival of leukemic mice confirming its role as a tumor suppressor. Furthermore, RNA sequencing revealed enhanced STAT1 expression and interferon (IFN) signaling upon loss of STAT3β.

overall_design: To investigate the differences in gene expression in STAT3β expressing and deficient leukemia cells, MLL-AF9-transformed fetal liver cells were generated and transplanted into immunocompromised mice. Leukemic blasts were isolated from bone marrow (n=3 per group) and spleen (n=3 per group) of diseased animals by sorting Venus+ cells using a BD FACSymphonyTM S6 Cell Sorter (BD Bioscience) and subjected to RNA sequencing.

first: Sophie

last: Edtmayer

first: Agnieszka

last: Witalisz-Siepracka

first: Bernhard

last: Zdársky

first: Dagmar

last: Stoiber


title: Development Of Pre-Clinical Murine Models For Fibrolamellar Hepatocellular Carcinoma

first: Julia

last: Arand

address: Schwarzspanierstr. 16

institute: Medical University of Vienna

summary: Fibrolamellar hepatocellular carcinoma(FLC) is a rare form of cancer that affects primarily adolescentsand young adults. FLC tumors are typically associated with an intrachromosomal deletion resulting in expression of a fusion protein between the chaperone DNAJ1B and the protein kinase PKA. FLC ischallenging to study because of its rarity and limited pre-clinical models. Here, we developed a novel transgenic mouse model of FLC. In this model, DNAJ1B-PKA expression in the liver of mouse embryos results in perinatal lethalityassociated with liver developmental defects, while DNAJ1B-PKA expression in the liver of adult mice initiates tumors resembling FLC at low penetrance. Some of these tumors can be serially propagated in 3D cultures and in allografts, including in syngeneic hosts. One such model shows growth inhibition upon treatment with the CDK4/6 inhibitor palbociclib. New pre-clinical models of FLC will provide novel insights into the biology of this rare cancerand may help identify novel therapeutic strategies.

overall_design: We generated transgenic mice by inserting a DNAJB1-PRKACA-GFP cDNA into the Rosa26 locus. Upon Cre-mediated recombination and self-cleaving of the fusion protein, this construct allows expression of the DNAJB1-PKA fusion found in human FLC and the GFP reporter. We crossed Rosa26 LSL-DNAJB1-PKA-GFP mice to Alb-Cre mice where the Cre recombinase is expressed under the control of the Albumin promoter and is turned on at mid-gestation in the liver. We performed RNA sequencing (RNA-seq) from livers dissected from control and transgenic embryos at embryonic day 18.5 (E18.5) (n=5 for control and n=4 for overexpression). To generate new models of Fibrolamellar hepatocellular carcinoma (FLC), we performed allograft experiments of these models into mice and treated with the CDK4/6 inhibitor palbociclib or control injections. We then performed gene expression profiling analysis and RNA-seq of PBS and palbociclib tumor samples (n=5 from each treatment group).

first: Julien

last: Sage

first: Andy

last: He

first: Garry

last: Coles

first: Griffin

last: Hartmann


title: Genome-wide identification of target genes for the transcription factors Sox2 and Sox3 in differentiated primary mouse oligodendrocytes

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

summary: To identify target genes of the transcription factors Sox2 and Sox3 in oligodendroglia in a genome-wide and unbiased approach, we cultured primary mouse oligodendroglia of wild type mice and mice with floxed alleles for Sox2 and Sox3, treated the cells with Tat-Cre to induce recombination, then kept cells under differentiating conditions, and isolated total RNA for RNA-Seq studies. Among others we detected substantial changes in the expression of genes associated with  the onset of terminal differentiation of oligodendrocytes.

overall_design: To identify potential target genes of the transcription factors Sox2 and Sox3 during the onset of oligodendroglial terminal differentiation, we generated wild type (Sox2Sox3_ctrl) and Sox2;Sox3-kockout (Sox2Sox3_dko) primary mouse oligodendroglia, performed RNA-Seq with the isolated total RNA after four days of differentiation, and generated comparative gene expression profiles.

first: Franziska

last: Fröb


title: Oxygen tension-dependent variability in the cancer cell kinome and response to combination therapies

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

summary: Solid tumors are characterized by significantly lower oxygen (O2) levels. Despite this fact, routine preclinical cancer studies are performed under ambient O2 conditions. We have developed an experimental approach that allows us to collect, process and evaluate cancer and non-cancer cells under physioxia (3-5% O2), in such a way that there is very minimal exposure to air. In addition to evaluating mouse mammary tumor cell lines with respect to kinome changes due to ambient and physioxic O2 tensions, we applied single cell-RNA sequencing to determine transcriptomic changes that occur in primary human breast epithelial cells that were collected, processed and cultured in ambient air and physioxia. We demonstrate that ambient and physioxic O2 tensions induce unique transcriptomic changes in primary human breast epithelial cells that are concurrent with our observations in the tumor cells.

overall_design: Breast tissue samples were collected from two female healthy donors under physioxia. The harvested tissues were then minced into tiny pieces at 3% O2 and separated into two portions. Each tissue portion was then processed into single cells via enzymatic digestion in ambient air and physioxia respectively. The derived single cells were then expanded in culture in the respective O2 tensions. Cultured cells were harvested via trypsinization, followed by determination of viability by trypan blue exclusion. We generated cDNA libraries from ambient air and physioxia-derived cells from the two donors and subjected them to sequencing a read depth of ~50,000 reads per cell.

first: Adedeji

middle: K

last: Adebayo

first: Poornima

last: Bhat-Nakshatri

first: Brijesh

last: Kumar

first: Christopher

last: Davis

first: Steven

last: Angus

first: Hongyu

last: Gao

first: Nick

last: Green

first: Constance

last: Temm

first: Maggie

last: Granatir

first: George

last: Sandusky

first: Yunlong

last: Liu


title: Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells (chip-seq gradient)

city: Gif-sur-yvette

first: Matthieu

last: Gerard

address: Route Nationale

country: France

institute: CEA

summary: We report an in-depth analysis of nucleosomal and subnucleosomal organization at cis-regulatory elements (CREs) in mouse embryonic stem (ES) cells. We used chromatin fragmented by a moderate dose of micrococcal nuclease (MNase) as input for ChIP-seq with antibodies against histones and transcription factors, and high-coverage deep-sequencing. Centrifugation of chromatin through sucrose gradients, followed by ChIP-seq, allowed the characterization of different subclasses of subnucleosomal particles having distribution patterns specific to enhancers, gene promoters and CTCF binding sites. We also provide datasets showing that this particular chromatin organization of CREs is conserved in the human melanoma 501Mel cell line.

overall_design: Examination of histone and transcription factor enrichment by MNase ChIP-seq at canonical nucleosomes and subnucleosomal particles in mouse embryonic stem cells.

first: Marina

last: Nocente

first: Anida

last: Mesihovic Karamitsos

first: Emilie

last: Drouineau

first: Sophie

last: Chantalat

last: Gérard


title: Symmetry breaking and germ layer emergence through optogenetic Wnt activation in gastruloids

city: San Francisco

first: Chang

last: Kim

address: 505 Parnassus Ave

institute: UCSF

summary: Human gastrulation is a dynamic, complex, and poorly understood process. Starting from a seemingly homogenous population, cell and tissue organization during this process establishes the 3D organismal body plan. However, due to technical and ethical limitations, mechanisms of human gastrulation are largely unexplored. For example, it is generally unclear whether a spatially ordered, external cue is necessary for patterning, or whether the epiblast harbors the innate ability to differentiate and self-organize in the absence of asymmetric cues. Human pluripotent stem cells (hPSCs) fortunately offer the potential to model gastrulation, most notably through generation of 3D “gastruloids”. Here we use optogenetic control of Wnt signaling to establish a 3D hPSC gastruloid model and demonstrate the spatially-ordered emergence of the three germ layer lineages in the absence of exogenous asymmetrical cues.

overall_design: scRNA-seq was performed on the 10X Genomics Chromium platform using the V3.1 3' chemistry, sequencing was done on a Novaseq 6000 paired end reads with depth aimed for 50k reads per cell.


title: NSABP B-41: A Study of AC Followed by a Combination of Paclitaxel Plus Trastuzumab or Lapatinib or Both Given Before Surgery to Patients With Operable HER2 Positive Invasive Breast Cancer

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: We studied the effect on tumour response to neoadjuvant therapy of the substitution of lapatinib for trastuzumab in combination with weekly paclitaxel after doxorubicin plus cyclophosphamide treatment, and of the addition of lapatinib and trastuzumab combined after doxorubicin plus cyclophosphamide treatment in patients with HER2-positive operable breast cancer to determine whether there would be a benefit of dual HER2 blockade in these patients.

overall_design:
For this open-label, randomised phase 3 trial we recruited women aged 18 years or older with an ECOG performance status of 0 or 1 with operable HER2-positive breast cancer. Each received four cycles of standard doxorubicin 60 mg/m(2) and cyclophosphamide 600 mg/m(2) intravenously on day 1 every 3 weeks followed by four cycles of weekly paclitaxel (80 mg/m(2)) intravenously on days 1, 8, and 15, every 4 weeks. Concurrently with weekly paclitaxel, patients received either trastuzumab (4 mg/kg load, then 2 mg/kg intravenously) weekly until surgery, lapatinib (1250 mg orally) daily until surgery, or weekly trastuzumab plus lapatinib (750 mg orally) daily until surgery. After surgery, all patients received trastuzumab to complete 52 weeks of HER2-targeted therapy. Randomisation (ratio 1:1:1) was done centrally with stratification by clinical tumour size, clinical nodal status, hormone-receptor status, and age. The primary endpoint was the pathological complete response in the breast, and analysis was performed on an intention-to-treat population.  RNA sequencing processed gene expression data from 245 baseline tumor samples is available here.
The submitters declare that the raw, fastq data is to be made available through dbGaP (controlled access) and that the clinical data will be in the dbGAP submission complement to this GEO part.

first: Sandra

last: Swain

first: Gong

last: Tang


title: Circadian-affected tissue specificity is linked to aging and longevity

city: Shanghai

first: Renrui

last: Chen

address: No. 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences

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

overall_design: Refer to individual Series


title: Chromatin accessibility profiling in wild-type naïve, 1h, or 24h in vitro stimulated P14 CD8+ T cells

city: San Diego

first: Bryan

last: McDonald

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary:
To investigate the kinetics of chromatin accessibility dynamics in activated CD8+ T cells, we stimulated naïve P14 CD8+ T cells in vitro for 0h, 1h, or 24h
We then performed chromatin accessibility profiling analysis by ATAC-seq

overall_design: Chromatin accessibility profiling analysis by ATAC-seq for WT P14 CD8+ T cells at 0h (naïve), 1h, or 24h-post stimulation with anti-CD3, anti-CD28, and recombinant IL-2 in vitro

first: Brent

last: Chick


title: Predicting age in single cells and low coverage DNA methylation data [scRNA]

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: Ageing is the accumulation of changes and overall decline of the function of cells, organs and organisms over time. At the molecular and cellular level, the concept of biological age has been established and novel biomarkers of biological age have been identified, notably epigenetic DNA-methylation based clocks. With the emergence of single-cell DNA methylation profiling methods, the possibility to study biological age of individual cells has been proposed, and a first proof-of-concept study, based on limited single cell datasets mostly from early developmental origin, indicated the feasibility and relevance of this approach to better understand organismal changes and cellular ageing heterogeneity.   Here, we generated a large single-cell DNA methylation and matched transcriptome dataset from mouse peripheral blood samples, spanning a broad range of ages (10-101 weeks of age), and developed a robust single-cell DNA methylation age prediction model (scEpiAge-blood and also scEpiAge-liver). We find that our new scEpiAge can accurately predict age in a broad range of publicly available datasets, including very sparse data and it also predicts age in single cells. Interestingly, the epigenetic age distribution is wider than technically expected in 19% of single cells, suggesting that epigenetic age heterogeneity is present in vivo and may relate to functional differences between cells. In addition, we observe differences in epigenetic ageing between the major blood cell types. Our work provides a foundation for better single-cell and sparse data epigenetic age predictors and highlights the significance of cellular heterogeneity during ageing.

overall_design: Whole blood taken from wild type black 6 mice spanning a range of ages is processed using scM&T-seq to produce paired single-cell transcriptomes and single-cell methylomes.

first: Marc

last: Bonder

first: Stephen

last: Clark

first: Felix

last: Krueger

first: Siyuan

last: Luo

first: João

last: Agostinho de Sousa

first: Aida

last: Hashtroud

first: Thomas

last: Stubbs

first: Steffen

last: Rulands

first: Oliver

last: Stegle

first: Wolf

last: Reik

first: Ferdinand

last: von Meyenn


title: Predicting age in single cells and low coverage DNA methylation data


title: Predicting age in single cells and low coverage DNA methylation data [RRBS]

overall_design: DNA was extracted from various tissue of mice spanning a range of ages and DNA methylation analysed using RRBS.


title: Recurrent triple-negative breast cancer from cysteine deprivation loses tumorigenicity via downregulation of the CST4 signaling

city: HOUGHTON

first: TAHIYAT

last: ALOTHAIM

address: DOW 514,1400 Townsend Dr

department: Department of Biological Sciences

institute: Michigan Technological University

summary: Triple-negative breast cancer (TNBC) is an aggressive type of breast cancer with a high risk of recurrence following treatment. Inhibition of cysteine uptake by erastin effectively induces mesenchymal TNBC undergoing prompt ferroptosis. However, a small residual population of cancer cells keeps resistant and survived during the erastin treatments, which might mimic tumor relapse in patients after therapy. We enriched and established the erastin-resistant/recurrent TNBC cell models by multi-cycle challenges of erastin. Identified epigenetic compounds could abolish such resistance in recurrent cells. Intriguingly, recurrent TNBC failed to grow in anchorage-independent conditions, implying a loss of tumorigenicity. By analyzing transcriptomic profiling, recurrent TNBC displayed highly transcriptomic alterations and attenuated signaling processes, including K-Ras signaling. Knockout of CST4, a member of the cystatin gene family strongly suppressed in recurrent cells, significantly reduced the tumorigenic potential and K-Ras signaling. Our findings suggested that targeted cysteine therapy could be a valid treatment for TNBC with a low possibility of tumorigenicity formation.

overall_design: The MDA-MB-231 erastin-resistant/recurrent cells were established from their parental erastin-sensitive cells by multiple cycles of erastin treatment in vitro. RNA was extracted by RNAeasy kits (Qiagen) from the erastin-sensitive and erastin-resistant cells in triplicate. Transcriptomic profiling was analyzed by Affymetrix Clariom S Assay.

first: Tahiyat

last: Alothaim

first: Xiaohu


title: Small RNA profile of 2 biofluids from healthy individuals

first: Kai

last: Wang

address: 401 Terry Ave N

institute: Institute for Systems Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: Endogenous and exogenous extracellular RNAs will be characterized in two body fluids (plasma and CSF) collected at the same time from 180 healthy subjects ranging in age from 31 to 101 years old.  Small RNAs contained in these samples will be profiled by small RNA-seq using unfractionated biofluids and purified extracellular vesicles.

overall_design: smRNA-seq of plasma and CSF samples from 180 healthy individuals, no replicates

first: David

last: Galas

first: Elaine

last: Peskind

first: Saroja

last: Somasundaram

first: Alton

last: Etheridge

first: Nikita

last: Sakhanenko


title: An RNA-seq study in Friedreich ataxia patients identified miR148a-3p as a putative prognostic biomarker of the disease.

city: Barcelona

first: Jaïr

middle: Dilmé

last: Capó

state: Barcelona

address: C/ Sardenya 416

country: Spain

institute: Sequentia Biotech

summary: Friedreich’s Ataxia (FRDA) is a life-threatening hereditary ataxia with an incidence of 1:50,000 individuals in the Caucasian population and only one therapeutic drug approved solely in the United States. FRDA is a multi-systemic neurodegenerative disease; cardiac abnormalities are one of the major complications and the predominant cause of premature death. The onset of FRDA typically occurs between the ages of 5 and 15. Given the complexity and heterogeneity of the clinical features and the variability of their onset, the identification of biomarkers able to evaluate disease progression and to monitor the efficacy of treatments is essential to facilitate decision making in clinical practice. We performed an RNA-seq study evaluating the expression level of circulating small non-coding RNAs (sncRNA) on PBMCs of FRDA patients and of healthy donors (CTRL). A hierarchical clustering algorithm (HCA) detected a sncRNAs signature able to distin-guish CTRL from the majority of FRDA patients. Among the differentially expressed sncRNA, microRNAs are the most relevant group. Hsa-miR-148a-3p resulted significantly upregulated in FRDA plasma samples (p<0.05). Noteworthy, hsa-miR-148a-3p increase was significant also when LOFA (late onset FRDA patients) group was compared with control group (p<0.05). Analysis of ROC curve combining the expression values of hsa-miR-148a-3p and hsa-miR-223-3p, previously identified by our group and confirmed in this study, revealed an AUC of 0.86 with 95% confidence interval 0.77 to 0.95 (p-value <0.001). An in silico prediction analysis of target genes of both miRNA, indicated IL6ST gene, an interesting marker of neuroinflammation in FRDA, as a common target gene.

overall_design:
The identification of a miRNA profile occurring during the natural history of FRDA disease could be of relevance as miRNA levels change with disease progression and/or pharmacological interventions, and the identification of new miRNAs could contribute to the design of novel therapeutic strategies and improve clinical decisions.
The aim of this study was to find a miRNA signature associated with the progression of the disease. Thus, we performed an RNA-seq study by NGS on peripheral blood mononuclear cells (PBMCs) of FRDA patients (grouped on the basis of the onset of clinical signs and severity; n=12) and one group of matched age and sex healthy donors (CTRL; n=4). Our study evaluated the expression level of circulating small non-coding RNAs (sncRNA), i.e not only miRNAs, but also snoRNAs, snRNAs and piRNAs. The 12 FRDA patients were chosen among those with an early onset of neurological symptoms (<14 years) and a worse course of the disease (named early-onset group, EOG, n= 4); those with an intermediate onset of neurological symptoms (14-25 years) and a slight disease course (intermediate-onset group, IOG, n= 4) and those with a late onset of neurological symptoms (>25 years) and a slow disease course (late-onset group, LOG, n= 4) .

first: Francesca

last: Amati

first: Florence

last: Malisan

first: Chiara

last: Vancheri

first: Elena

last: Morini

first: Andrea

last: Quatrana


title: Circadian-affected tissue specificity is linked to aging and longevity [sleep deprivation experiment]

first: Renrui

last: Chen

summary: Tissue specificity is a fundamental property of an organ that affects numerous biological processes, including aging and longevity, and is regulated by the circadian clock. However, the distinction between circadian-affected tissue specificity and other tissue specificities remains poorly understood. Here, using multi-omics data on circadian rhythms in mice, we discovered that approximately 35% of tissue-specific genes are directly affected by circadian regulation. These circadian-affected tissue-specific genes have higher expression levels and are associated with metabolism and hepatocyte cells. They also exhibit specific features in long-reads sequencing data. Notably, these genes are associated with aging and longevity at both the gene level and at the network module level. The expression of these genes oscillates in response to caloric and time-restricted feeding regimens, which have been demonstrated to promote longevity. In addition, aging and longevity genes are disrupted in various circadian disorders. Our study indicates that the modulation of circadian-affected tissue specificity is essential for understanding the circadian mechanisms that regulate aging and longevity at the genomic level.

overall_design: The sleep deprivation experiment followed previously reported protocols (Lu et al. 2021). Mice were randomly assigned to either the experimental or control group. The experimental group was subjected to a sleep deprivation instrument, which involved forced locomotion through a slowly rotating drum (40 cm in diameter, 0.4 m per min) while having access to food and water. All mice in experimental group were placed in the sleep deprivation device for 10 h (6:00 AM–4:00 PM) during their normal resting phase while the control animals were undisturbed. Then we collected two replicates of 4 peripheral circadian tissues (forebrain, cerebellum, liver, kidney) were obtained at next six circadian time (CT) points with an interval of 4 h (CT4, CT8, CT12, CT16, CT20, and CT24)

first: Ziang

last: Zhang

first: Junjie

last: Ma

first: Bing

last: Liu

first: Zhengyun

last: Huang

first: Ganlu

last: Hu

first: Ju

first: Ying

last: Xu

first: Guang-Zhong


title: STING is essential for TLR8 induced IFN

city: Ithaca

first: Karla

middle: Yvonne

last: García-Martínez

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

summary: The innate immune system is equipped with multiple receptors to detect microbial nucleic acids and induce type I interferon (IFN) to restrict viral replication. When dysregulated these receptor pathways induce inflammation in response to host nucleic acids and promote development and persistence of autoimmune diseases like Systemic Lupus Erythematosus (SLE). IFN production is regulated by the Interferon Regulatory Factor (IRF) transcription factor family of proteins that function downstream of several innate immune receptors such as Toll-like receptors (TLRs) and Stimulator of Interferon Genes (STING). Although both TLRs and STING activate the same downstream molecules, the pathway by which TLRs and STING activate IFN response are thought to be independent. Here we show that STING plays a previously undescribed role in human TLR8 signaling. Stimulation with the TLR8 ligands induced IFN secretion in primary human monocytes, and inhibition of STING reduced IFN secretion from primary monocytes from 8 healthy donors. We demonstrate that TLR8-induced IRF activity was reduced by STING inhibitors. Moreover, TLR8-induced IRF activity was blocked by inhibition or loss of IKKε, but not TBK1. Bulk RNA transcriptomic analysis supported a model where TLR8 induces transcriptional responses associated with SLE that can be downregulated by inhibition of STING. These data demonstrate that STING is required for full TLR8-to-IRF signaling and provide evidence for a new framework of crosstalk between cytosolic and endosomal innate immune receptors, which could be leveraged to treat IFN driven autoimmune diseases.

overall_design: 2x10^6 THP-1 WT or STING cells were treated with DMSO or 500ng/mL H151 for 1 hour, then stimulated with media or 10ug/mL TL8 for 8 hours. After 8 hours RNA was collected using trizol.

first: Jingyi

first: Joshua

last: Jones

first: Alexandra

last: Woo

first: Erika

last: Aucapina

first: Ilana

last: Brito

first: Cynthia

last: Leifer


title: Small Nucleolar RNAs in the Dlk1-Gtl2 Imprinting Locus Maintains LT-HSC Self-renewal by Regulation of rRNA Modification and Translation [scRNA-Seq]

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

institute: Zhejiang University

summary: Small nucleolar RNA (snoRNA) are non-coding RNAs, which participate in the cleavage and chemical modification of ribosomal RNAs (rRNAs) and small nuclear RNAs. However, the roles of snoRNA in homeostasis of hematopoietic stem cells(HSCs) have not been studied. We isolated four hematopoietic stem and progenitor cells (HSPCs) (LT-HSCs, IT-HSCs, ST-HSCs, and MPPs) from the bone marrow (BM) of C57BL/6 mice and performed small RNA-seq. We found SnoRNAs belonging to SNORD113-114 cluster were specifically enriched in LT-HSCs, and their expression decreased dramatically with HSC differentiation. To explore function of snoRNAs in SNORD113-114 cluster in HSCs, we established maternally KO mice by CRISPR-Cas9 technology. Here, we used scRNA-seq to examine HSC RNA profiles influenced by SNORD113-114 cluster KO.

overall_design: Single cell RNA profiles of HSC from WT/Mat KO mice.

first: Hui

last: Wang

first: Zhaoru

first: Yingli

last: Han

first: Penglei

last: Jiang

first: Pengxu

last: Qian


title: Small Nucleolar RNAs in the Dlk1-Gtl2 Imprinting Locus Maintains LT-HSC Self-renewal by Regulation of rRNA Modification and Translation [RiboMeth-seq]

summary: Small nucleolar RNA (snoRNA) are non-coding RNAs, which participate in the cleavage and chemical modification of ribosomal RNAs (rRNAs) and small nuclear RNAs. However, the roles of snoRNA in homeostasis of hematopoietic stem cells(HSCs) have not been studied. We isolated four hematopoietic stem and progenitor cells (HSPCs) (LT-HSCs, IT-HSCs, ST-HSCs, and MPPs) from the bone marrow (BM) of C57BL/6 mice and performed small RNA-seq. We found SnoRNAs belonging to SNORD113-114 cluster were specifically enriched in LT-HSCs, and their expression decreased dramatically with HSC differentiation. To explore function of snoRNAs in SNORD113-114 cluster in HSCs, we established maternally KO mice by CRISPR-Cas9 technology. Here, we used RiboMeth-seq to examine rRNA 2’-O-me modification changes influenced by SNORD113-114 cluster KO.

overall_design: Examination of rRNA 2’-O-me modification in Lin- cells from WT/Mat KO mice.

last: Zhang


title: Small Nucleolar RNAs in the Dlk1-Gtl2 Imprinting Locus Maintains LT-HSC Self-renewal by Regulation of rRNA Modification and Translation [ncRNA-seq]

summary: Small nucleolar RNA (snoRNA) are non-coding RNAs, which participate in the chemical modification of ribosomal RNAs (rRNAs) and small nuclear RNAs. However, the roles of snoRNA in homeostasis of hematopoietic stem cells(HSCs) have not been studied. We isolated four hematopoietic stem and progenitor cells (HSPCs) (LT-HSCs, IT-HSCs, ST-HSCs, and MPPs) from the bone marrow (BM) of C57BL/6 mice and performed small RNA-seq. We found SnoRNAs belonging to SNORD113-114 cluster were specifically enriched in LT-HSCs, and their expression decreased dramatically with HSC differentiation. To explore function of snoRNAs in SNORD113-114 cluster in HSCs, we established maternally KO mice by CRISPR-Cas9 technology. Here, we used a modified small RNA-seq method to examine snoRNA profile in KO mice.

overall_design: Examination of snoRNA profiles Lin- cells from WT/Mat KO mice.


title: Predicting age in single cells and low coverage DNA methylation data [scBS]

first: Laura

last: Biggins

first: Marc

last: Bonder

first: Stephen

last: Clark

first: Felix

last: Krueger

first: Siyuan

last: Luo

first: João

last: Agostinho de Sousa

first: Aida

last: Hashtroud

first: Thomas

last: Stubbs

first: Steffen

last: Rulands

first: Oliver

last: Stegle

first: Wolf

last: Reik

first: Ferdinand

last: von Meyenn


title: ASH1L guards cis-regulatory elements against cyclobutane pyrimidine dimer induction [ChIP-seq]

status: Public on Jun 02 2024

city: Zurich

first: Michelle

last: Yancoskie

address: Winterthurerstr. 260

department: Vetsuisse Faculty

country: Switzerland

institute: Institute of Veterinary Pharmacology and Toxicology, University of Zurich

summary: The histone methyltransferase ASH1L, first discovered for its role in transcription, has been shown to accelerate the removal of ultraviolet (UV) light-induced cyclobutane pyrimidine dimers (CPDs) by nucleotide excision repair. Previous reports demonstrated that CPD excision is most efficient at transcriptional regulatory elements, including enhancers, relative to other genomic sites. Therefore, we analyzed DNA damage maps in ASH1L-proficient and ASH1L-deficient cells to understand how ASH1L controls enhancer stability. This comparison showed that ASH1L protects enhancer sequences against the induction of CPDs besides stimulating repair activity. ASH1L reduces CPD formation at C-containing but not at TT dinucleotides, and no protection occurs against pyrimidine-(6,4)-pyrimidone photoproducts or cisplatin crosslinks. The diminished CPD induction extends to gene promoters but excludes retrotransposons. This guardian role against CPDs in regulatory elements is associated with the presence of H3K4me3 and H3K27ac histone marks, which are known to interact with the PHD and BRD motifs of ASH1L, respectively. Molecular dynamics simulations identified a DNA-binding AT hook of ASH1L that alters the distance and dihedral angle between neighboring C nucleotides to disfavor dimerization. The loss of this protection results in a higher frequency of C–>T transitions at enhancers of skin cancers carrying ASH1L mutations compared to ASH1L-intact counterparts.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K4me1 and H3K27ac in ASH1L-proficient and ASH1L-deficient U2OS cells not exposed to UV or 3 hours after UV-C exposure (20 J/m2). ChIP-seq samples and input controls were performed in biological triplicates.
Please note that each processed data file was generated from both ChIP and Input samples, and is linked to the corresponding ChIP sample records.

first: Reihaneh

last: Khaleghi

first: Anirvinya

last: Gururajan

first: Aadarsh

last: Raghunathan

first: Aryan

last: Gupta

first: Sarah

last: Diethelm

first: Corina

last: Maritz

first: Shana

last: Sturla

first: Marimuthu

last: Krishnan

first: Hanspeter

last: Naegeli


title: Effect of epithelial depletion of Kdf1 on gene expression alteration during tooth crown development

city: Beijing

first: Jiayu

last: Wang

address: Haidian District,Beijing,China

institute: Peking university

summary: In our study, we observed that mice lacking epithelial Kdf1 exhibited rounded and blunt molar cusps, accompanied by abnormal folding of dental epithelium, suggesting that  epithelial Kdf1 played a regulatory role in molar crown morphogenesis. Nevertheless, the mechanism within dental epithelium regulating tooth crown morphogenesis remains unclear.

overall_design: To explore the downstream molecular alterations of Kdf1 deletion, we conducted RNA-Seq of inner enamel epithelium tissue from the mandibular first molar.

first: Miao

last: Yu


title: Spongy moth gene expression during female pupal development

city: Quebec City

first: Christopher

middle: Ian

last: Keeling

state: QC

address: 1055 rue du PEPS

department: Canadian Forest Service

institute: Natural Resources Canada

summary: Female adult spongy moths vary in their flight capacity depending upon their origin and subspecies. Asian spongy moth (Lymantria dispar asiatica) females (such as the RM strain here) can fly whereas European spongy moth (Lymantria dispar dispar) females cannot (such as the CT strain here). We hypothesized that the genetic origins of these differences in flight capacity would be reflected in differences in gene expression during metamorphosis (the pupal stage). To test this, we compared the gene expression at days 1, 3, 5, 8, and 11 of pupal development of female pupae from CT and RM strains.

sample_organism:
Lymantria dispar dispar
Lymantria dispar asiatica

overall_design: Overall there are 30 female pupa samples, two strains (RM and CT), sampled at days 1, 3, 5, 8, and 11. Each sample type has 3 biological replicates (individual pupae).

middle: I

first: Catherine

last: Béliveau

first: Melody

last: Keena

first: Michel

last: Cusson


title: Circadian-affected tissue specificity is linked to aging and longevity [Differential expression analysis of liver and kidney]

first: Renrui

last: Chen

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver and kidney in mice (wild type and sleep deprivation). Each tissue sampled every 4 hours for 1 days with 4 replicates.

first: Ziang

last: Zhang

first: Junjie

last: Ma

first: Bing

last: Liu

first: Zhengyun

last: Huang

first: Ganlu

last: Hu

first: Ju

first: Ying

last: Xu

first: Guang-Zhong


title: Small Nucleolar RNAs in the Dlk1-Gtl2 Imprinting Locus Maintains LT-HSC Self-renewal by Regulation of rRNA Modification and Translation [Polysome RNA RNA-seq]

first: Jiang

last: Penglei

summary: Small nucleolar RNA (snoRNA) are non-coding RNAs, which participate in the cleavage and chemical modification of ribosomal RNAs (rRNAs) and small nuclear RNAs. However, the roles of snoRNA in homeostasis of hematopoietic stem cells(HSCs) have not been studied. We isolated four hematopoietic stem and progenitor cells (HSPCs) (LT-HSCs, IT-HSCs, ST-HSCs, and MPPs) from the bone marrow (BM) of C57BL/6 mice and performed small RNA-seq. We found SnoRNAs belonging to SNORD113-114 cluster were specifically enriched in LT-HSCs, and their expression decreased dramatically with HSC differentiation. To explore function of snoRNAs in SNORD113-114 cluster in HSCs, we established maternally KO mice by CRISPR-Cas9 technology. Here, we used RNA-seq to examine polysome RNA profiles in KO mice.

overall_design: Polysome RNA profiles of bone marrow cells from WT/Mat KO mice.

first: Hui

first: Zhaoru

first: Yingli

last: Han

first: Penglei

last: Jiang

first: Pengxu

last: Qian


title: Whole-transcriptome analysis illustrates evolving transcriptional human response to injury in acute wounds and scars

city: Seattle

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: The goal of this study was to use RNA sequencing to identify novel genes involved in wound healing and scar formation in human burn wounds and scars. RNA was isolated from 108 human samples comprising of uninjured skin (n=26), acute burn wounds (n=54), and hypertrophic scars (HTS) (n=30). Genes with at least 1.5-fold change and a p-value less than 0.05 with a false discovery rate of 0.05 were considered differentially expressed. Samples were sequenced using Illumina Hi-Seq sequencers, and pathway/Gene Ontology (GO) Enrichment analysis was conducted using iPathwayGuide. Comparing wounds to uninjured skin, we found 9,311 differentially expressed genes, accounting for 1,017 GO terms. Comparing HTS to uninjured skin, we found 7,299 differentially expressed genes, accounting for 1,022 GO terms.  By analyzing the whole transcriptome, we characterized dominant genes expressed temporally in wounds and scars. This study reveals the complexity of these processes and helps to bring novel genes to light.

overall_design: For this study, RNA was isolated from 108 human samples comprising of uninjured skin (n=26), acute burn wounds (n=54), and hypertrophic scars (HTS) (n=30). Samples were collected from patients admitted to the UW Medicine Regional Burn Center and undergoing an operation for burn injury from 2002 to 2018. Samples consisted of discarded burn wounds, scars, and donor skin that were stored as part of an IRB exempt human tissue repository. All samples were de-identified upon collection. Specific to the wound samples, when able, samples were collected at periphery of the burn wound to include the epithelial edge where the transition from wound to normal tissue exists as previously described.[8] Tissue samples were minced and placed in cryogenic vials for either snap freezing in liquid nitrogen within 20 minutes of collection or placement in RNALater (Invitrogen, Carlsbad, CA) and stored in 4°C overnight to allow the solution to penetrate the tissue. All samples were transferred to -80°C for long term storage.

first: Jamie

last: Oh

first: Stephen

last: Sibbett

first: Laura

last: Muffley

first: Shari

last: Honari

first: Theo

last: Bammler

first: Saman

last: Arbabi

first: Nicole

last: Gibran


title: ASH1L guards cis-regulatory elements against cyclobutane pyrimidine dimer induction

first: Michelle

last: Yancoskie

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K4me1 and H3K27ac in ASH1L-proficient and ASH1L-deficient U2OS cells not exposed to UV or 3 hours after UV-C exposure (20 J/m2). ChIP-seq samples and input controls were performed in biological triplicates.

first: Reihaneh

last: Khaleghi

first: Anirvinya

last: Gururajan

first: Aadarsh

last: Raghunathan

first: Aryan

last: Gupta

first: Sarah

last: Diethelm

first: Corina

last: Maritz

first: Shana

last: Sturla

first: Marimuthu

last: Krishnan

first: Hanspeter

last: Naegeli


title: A enzymatic program that assembles amyloids [ePAT]

city: Miami

last: Lee

state: FL

department: Biochemistry & Molecular Biology

institute: University of Miami

summary: We uncover an enzymatic program that controls intracellular amyloidogenesis. ePAT confirmation of starRNA using long-read sequencing.

overall_design: Long read seq. of ePAT reaction from 28S-3'end of Amyloid-bodies obtained from 60min heat shocked MCF-7 cells.

first: Michael

last: Bokros


title: Partial hepatectomy accelerates colorectal metastasis by priming a prometastatic niche in the liver

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

institute: University Medical Center Freiburg

summary: Despite being the standard of care for patients with Stage IV colorectal cancer (CRC), the effects of a resection of liver metastasis on the metastatic disease are poorly understood. To elucidate the influence of surgical metastasectomies on metastasized CRC, we investigated the cellular and molecular effects of partial hepatectomy in a mouse model of orthograde CRC liver metastasis.

overall_design: We performed bulk RNA sequencing with RNA isolated from macroscopically healthy livers from mice that were subjected to partial hepatectomy in a model of orthograde colorectal liverr metastasis. We compared 4 preoperative samples to 4 liver samples after partial hepatectomy.

first: Jost

last: Lünstedt


title: Clostridioides difficile-mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation.

first: Kathleen

middle: Louise

last: Furtado

email: klfurtado@ucdavis.edu, kfurtado@unc.edu

address: 125 Mason Farm Road

summary: In a healthy colon, the stratified mucus layer serves as a crucial innate immune barrier to protect the epithelium from microbes. Mucins are complex glycoproteins that serve as a nutrient source for resident microflora but can be exploited by pathogens. We aimed to understand how the intestinal pathogen, Clostridioides diffiicile, independently uses or manipulates mucus to its benefit. Using a 2-D primary human intestinal epithelial cell model to generate physiologic mucus, we assessed C. difficile-mucus interactions through growth assays, RNA-Seq, biophysical characterization of mucus, and contextualization of an established genome-scale metabolic network reconstruction (GENRE). We found that host-derived mucus promotes C. difficile growth both in vitro and in an infection model. RNA-Seq revealed significant upregulation of genes related to metabolism in response to mucus, including genes involved in sugar uptake, the Wood-Ljungdahl pathway, and the glycine cleavage system. In addition, we identified differential expression of genes related to sensing and transcriptional control. Analysis of mutants with deletions in highly upregulated genes reflected the complexity of C. difficile-mucus interactions, with potential interplay between sensing and growth. Mucus also stimulated biofilm formation in vitro, which may in turn alter viscoelastic properties of mucus. Context-specific metabolic modeling confirmed differential metabolism and predicted importance of enzymes related to serine and glycine catabolism with mucus. Subsequent growth experiments supported these findings, indicating mucus is an important source of serine. Our results better define responses of C. difficile to human gastrointestinal mucus and highlight a flexibility in metabolism that may influence pathogenesis.

overall_design:
To assess the trasncriptional response of C. difficile to gastrointestinal mucus, we supplemented a C. difficile minimal medium (CDMM; from Cartman and Minton, Applied Environmental Microbiology, 2010) with 50 µg/mL mucus. C. difficile cultures were grown to exponential phase (OD600 ~0.5) before collection, RNA isolation, and RNA-sequencing.
Mucus was derived from primary human epithelial cells or porcine gastric mucus. Mucus was purified using 3K NMWL filters (Amicon), resuspended in PBS, and its total protein concentration quantified using Pierce BCA Assay to enable standardization. Only mucus from primary human epithelial cells was considered in the study above, as this mucus came from a more clinically relevant source, but reads from samples supplemented with commercial porcine gastric mucus (Type III, Sigma) are included here for public record.

middle: L


title: A enzymatic program that assembles amyloids [FLAM-seq]

first: Stephen

summary: We uncover an enzymatic program that controls intracellular amyloidogenesis. FLAM-seq. analysis of purified Amyloid bodies identifies starRNA.

overall_design: FLAM-seq. of polyadenylated RNA purified nucleoli and Amyloid-bodies obtained from untreated or 60min heat shocked MCF-7 cells, respectively.


title: ZmNF-YA1 contributes to maize thermotolerance by regulating heat shock response

city: qingdao

first: yaling

last: yang

address: Shandong University, Qingdao 266237, China;

institute: Shandong University

summary: Maize is a staple food, feed, and industrial crop. Heat stress (HS) is one of the major stresses affecting maize production and is usually accompanied by other stresses, such as drought. Our previous study identified a heterotrimer complex, ZmNF-YA1-YB16-YC17, in maize. ZmNF-YA1 and ZmNF-YB16 were positive regulators of the drought stress response and were involved in maize root development. In this study, we investigated whether ZmNF-YA1 confers HS tolerance in maize. The ZmNF-YA1 mutant and overexpression lines were used to test the role of ZmNF-YA1 in maize thermotolerance. The ZmNF-YA1 mutant was more temperature-sensitive than the WT, while the ZmNF-YA1 overexpression lines showed a thermotolerant phenotype. Higher malondialdehyde content and reactive oxygen species accumulation were observed in the mutant, followed by WT and overexpression lines after HS treatment, while an opposite trend was observed for chlorophyll content. RNA-seq was used to analyze transcriptome changes in W22 and nf-ya1 plants in response to HS at great depths. Based on their expression profiles, the HS response-related differentially expressed genes in nf-ya1 and W22 were grouped into seven clusters via k-means clustering. Gene Ontology (GO) enrichment analysis of Clade 1, in which ZmNF-YA1 and HS induced, GO terms for protein refolding and protein stabilization, and terms for various stress responses were considerably enriched. Thus, the contribution of ZmNF-YA1 to protein stabilization, refolding, and regulation of ABA, ROS, and heat/temperature signaling may be the major reason why ZmNF-YA1 overexpression enhanced heat tolerance, and the mutant showed a heat-sensitive phenotype.

overall_design: RNA-seq was used to analyze transcriptome changes in W22 and nf-ya1 plants in response to HS.

first: Yaling

last: Yang

first: Zhaoxia

last: Li

first: Juren

last: Zhang


title: Integrative multi-omics analysis reveals conserved cell-projection deficits in human Down syndrome brains

city: Genova

first: Laura

last: Cancedda

state: Genova

address: Via Morego, 30

department: Brain Development and Disease

country: Italy

institute: Italian Institute of Technology

summary: Down syndrome (DS) is the most common genetic cause of cognitive disability. However, it is largely unclear how triplication of a small gene subset may impinge on diverse aspects of DS brain physiopathology. Here, we took a multi-omic approach and simultaneously analyzed by RNA-seq and proteomics the expression signatures of two diverse regions of human postmortem DS brains. We found that the overexpression of triplicated genes triggered global expression dysregulation, differentially affecting transcripts, miRNAs, and proteins involved in both known and novel biological candidate pathways. Among the latter, we observed an alteration in RNA splicing, specifically modulating the expression of genes involved in cytoskeleton and axonal dynamics in DS brains. Accordingly, we found an alteration in axonal polarization in neurons from DS human iPSCs and mice. Thus, our study provides an integrated multilayer expression database capable of identifying new potential targets to aid in designing future clinical interventions for DS.

overall_design: Refer to individual Series

first: Mohit

last: Rastogi

first: Andrea

last: Contestabile


title: Integrative multi-omics analysis reveals conserved cell-projection deficits in human Down syndrome brains [TotalRNAseq]

summary: Down syndrome (DS) is the most common genetic cause of cognitive disability. However, it is largely unclear how the triplication of a small gene subset may impinge on diverse aspects of DS brain physio-pathology. Here, we took a multi-omics approach and simultaneously analyze by RNA-seq and proteomics the expression signature of two diverse regions of human postmortem DS brains. We found that the overexpression of triplicated genes triggered global expression dysregulations differentially affecting transcripts, miRNA and proteins involved in both known and novel candidate pathways. Among the latter, we observed alteration of RNA splicing in DS brains specifically altering the expression of genes involved in cytoskeleton and axonal dynamics. Accordingly, we found alteration in axonal polarization in neurons from both DS human induced-pluripotent-stem cells and mice. Thus, our study provides an integrated multi-layer expression database capable of identifying new potential targets to possibly aid design future clinical interventions in DS.

overall_design: Comparative gene and transcript expression profiling analysis for RNAseq data from postmortem hippocampal and cortical samples from DS and control individuals


title: Integrative multi-omics analysis reveals conserved cell-projection deficits in human Down syndrome brains [smallRNAseq]

overall_design: Comparative gene expression profiling analysis for RNAseq data from postmortem hippocampal and cortical samples from DS and control individuals


title: CDK4/6 inhibits the STING signaling axis through RB1-dependent and RB1-independent pathways in prostate cancer

status: Public on Jun 01 2024

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

summary: The efficacy of immunotherapy in prostate cancer is not satisfactory due to the “cold” tumor microenvironment and the paucity of neoantigens. The STING-TBK1-IRF3 signaling axis as core molecules of the innate immune system is increasingly recognized as a candidate target for cancer immunotherapy. Previou studies reported that CDK4/6 inhibitors induced DNA damage to activate the cGAS-STING pathway. However, the underlying mechanisms of how CDK4/6 inactivated the cGAS-STING pathway are still elusive. Here we revealed that treatment with CDK4/6 inhibitors enhance the anti-tumor effect of STING agonists in prostate cancer cells. Mechanically, CDK4/6 phosphorylated TBK1 at S527 to inactive the STING signaling pathway independent of RB1 in prostate cancer cell. Then, we also found that CDK4/6 phosphorylated RB1 at S249/T252 to induce the interaction of RB1 with TBK1 and diminish the phosphorylation of TBK1 at S172, which also suppresses the activation of the STING pathway. Collectively, we found that CDK4/6 inhibits the STING/TBK1/IRF3 axis through RB1-dependent and RB1-independent pathways in prostate cancer cells. These insights provide the novel evidence for CDK4/6 suppressing the innate immune response of prostate cancer.

overall_design: Comparative gene expression profiling of RNA-seq data from  cells treated with the indicated constructs

first: Xin

last: Jin

last: zeng


title: Small Nucleolar RNAs in the Dlk1-Gtl2 Imprinting Locus Maintains LT-HSC Self-renewal by Regulation of rRNA Modification and Translation

first: Jiang

last: Penglei

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


title: Integrative genomic analysis of Korean high-grade serous ovarian cancer

city: Seongnam-si

first: Dong Min

last: Shin

address: 700, Daewangpangyo-ro, Bundang-gu

country: South Korea

institute: Theragen Bio

summary: Ovarian cancer is one of the most common gynecologic malignancies globally, which is a significant cause of morbidity and mortality, accounting for 207,252 new deaths each year. The 5-year survival rate of this cancer is reported to be 26-42% and is often diagnosed in an advanced stage. Epithelial ovarian cancer (EOC) is a heterogeneous disease that comprises various histological subtypes. Of them, high-grade serous ovarian cancer (HGSOC) is the most common cancer subtype (70-80%), which is highly aggressive and grows rapidly. Despite the initial success observed with cytoreductive surgery and platinum-based chemotherapy, over 75% of HGSOC patients experience relapse following completion of first-line therapy. The challenge of tailoring therapeutic interventions to control progressive disease is compounded by the inherent cellular heterogeneity and genomic instability characteristic of HGSOC. While platinum chemotherapy remains the cornerstone of contemporary treatment, the grim reality persists that a majority of EOC patients develop chemotherapy resistance, resulting in a five-year survival rate of less than 50%. Numerous ovarian cancer studies have underscored the prognostic significance of factors such as age at diagnosis, disease stage, grade, histology, residual disease post-surgery, and disease recurrence. The genetic predisposition towards EOC indicates that high-grade HGSC exhibits significant chromosomal instability and carries mutations in the tumor protein 53 (TP53) gene, as well as mutations in the breast cancer genes BRCA1/2. Molecular markers like BRCA1/2 mutations and homologous repair deficiency in HGSOC have been validated as predictive of response to platinum therapy and poly-ADP polymerase (PARP) inhibitors. Furthermore, recent research has shed light on the prognostic potential of immune cell populations infiltrating ovarian tumor tissue. The Cancer Genome Atlas (TCGA) and other genomic studies of HGSOC have conducted extensive genomic and transcriptomic analyses of HGSOC to delineate its genomic landscape and facilitate the development of targeted therapies for this highly lethal malignancy. Key findings from previous studies include the prevalent mutation of TP53 genes, frequent and widespread DNA copy number alterations, identification of transcriptional signatures associated with clinical outcome and molecular subtype, and diverse mechanisms of BRCA1/2 inactivation. However, most studies have focused on HGSOC of white populations, and there is limited comprehensive molecular characterization of East Asian HGSOC, including those from Korea. In this study, we aimed to discern clinical and molecular factors distinguishing 123 HGSOC patients from the Korean population through an integrated analysis of clinical features, germline variants, somatic genomic alterations, and the tumor immune microenvironment.

overall_design: RNA-seq results for ovarian cancer patients with different clinical information

first: Youngwook

last: Kim

first: Jeongseon


title: Glucose derived carbon nanosphere (CSP) conjugated TTK21, an activator of the histone acetyltransferases CBP/p300, ameliorates amyloid-beta 1-42 induced deficits in plasticity and associativity in hippocampal CA1 pyramidal neurons

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: The master epigenetic regulator lysine acetyltransferase (KAT) p300/CBP plays a pivotal role in neuroplasticity and cognitive functions. Recent evidence has shown that in several neurodegenerative diseases, including Alzheimer’s disease (AD), the expression level and function of p300/CBP are severely compromised, leading to altered gene expression causing pathological conditions. Here, we show that p300/CBP activation by a small molecule TTK21, conjugated to carbon nanosphere (CSP) ameliorates Aβ-impaired long-term potentiation (LTP) induced by high frequency stimulation, theta burst stimulation and synaptic tagging/capture (STC). This functional rescue was correlated with CSP-TTK21induced changes in transcription and translation. Mechanistically, we observed that the expression of a large number of synaptic plasticity- and memory-related genes was rescued, presumably by the restoration of p300/CBP mediated acetylation. Collectively, these results suggest that small molecule activators of p300/CBP could be a potential therapeutic molecule for neurodegenerative diseases like AD

overall_design: TTK21, an activator of the acetyltransferase function of CBP/p300 when conjugated with glucose-based carbon nanospheres (CSP), hence termed as CSP-TTK21  (Chatterjee et al., 2013), restored acetylation of histone H2B in the hippocampus of THY-Tau22 mice, a mouse model with AD-related Tau pathology (Chatterjee et al., 2018). Moreover, CSP-TTK21 also upregulated the expression of plasticity-related genes and improved spatial memory in these mice.   In this study, we found that CSP-TTK21 could also rescue synaptic plasticity deficits caused by acute Aβ exposure in the CA1 area of rat hippocampal slices. We showed that CSP-TTK21 could restore long-term potentiation and late-associative plasticity induced by high-frequency tetanization and theta burst stimulation. Furthermore, we demonstrated that this rescue of functional synaptic plasticity was concomitant with the CSP-TTK21-mediated restoration of plasticity-related gene expression.

first: Sreedharan

last: Sajikumar

first: Tapas

last: Kundu

first: Akash

last: Singh

first: Madavan

last: Vasudevan


title: Evidence that inflammation-associated fibroblasts (IAFs) originate from Edil3 stromal "mesitocytes" in the colon following radiation injury

city: Fontenay-Aux-Roses

first: Fabien

last: Milliat

address: 31 avenue de la division Leclerc

institute: IRSN

summary: Stromal cells present in the colon crypt provide proliferation and differentiation signals to the epithelial cells, thereby maintaining their integrity and stimulating the regeneration process. Cancer patients treated for tumors located in the abdominopelvic region may develop radiation proctitis, a condition characterized by a strong mucosal inflammation. In this work, single-cell RNA sequencing approaches were combined with spatial transcriptomics to characterize colonic stromal cells in depth, both in control conditions and in the context of radiation-induced ulceration. The present study identifies a novel stromal marker, Edil3 (EGF-like repeats and discoidin domains 3), which defines the major stromal population of the colon. This population is spatially and functionally distinct from telocytes and trophocytes and is expressed along the crypt with a functional proliferation-differentiation axis . This population, which we propose to name "mesitocytes," cooperates with vascular cells to control inflammation and epithelial proliferation. We demonstrate that radiation-induced ulcerated areas are characterized by the presence of inflammation-associated fibroblasts (IAFs) deriving from mesitocytes.

overall_design: scRNA-seq datas of Stroma cells from Colon from Male C57BL/6JRj control mice (CTR9, n=9)  or from colon 2 weeks from irradaiation from  mice were exposed to irradiation at 26 GY focus on the colorectal area (IR_W2, n=7).  A total of 16 samples is included in this study.

first: Martin

last: Jestin


title: A genome-wide screen for peroxisome regulators connects peroxisomes with Wnt signaling through RNF146 and tankyrase

city: Santa Barbara

first: Chris

last: Richardson

address: UCSB

department: Molecular, Cellular, and Developmental Biology

institute: UCSB

summary: Peroxisomes are membrane-bound organelles that help cells specialize their metabolism. In humans, peroxisomes are required for normal development, yet the genes regulating peroxisome function remain unclear. Thus, we performed a genome-wide CRISPRi screen to identify novel factors involved in peroxisomal homeostasis. We found that transcriptional inhibition of RNF146, an E3 ligase activated by poly(ADP-ribose), dramatically reduced the import of proteins into peroxisomes. The observed RNF146-mediated loss of peroxisome import depended on the stabilization and activity of the poly(ADP-ribose) polymerase tankyrase, which binds the peroxisomal membrane protein PEX14. We propose a model in which RNF146 and tankyrase regulate peroxisome import efficiency by tuning PARsylation of proteins at the peroxisome membrane. Interestingly, we found that perturbations to peroxisomes altered tankyrase’s selection of substrates, including the beta-catenin destruction complex component AXIN1. The loss of peroxisomes caused tankyrase and RNF146-dependent degradation of AXIN1 and a concomitant increase of beta-catenin transcription. Together, these observations not only suggest previously undescribed roles for RNF146 in peroxisomal regulation, but also a novel role in bridging peroxisome function with Wnt/beta-catenin signaling during development.

overall_design: To investigate transcriptional changes in aperoxisomal cells, we established Hct116 cell lines in which peroxisomal genes were stably inhibited by CRISPRi


title: Pure Estrogen Receptor Antagonists Potentiate Capecitabine Activity in ESR1-mutant Breast Cancer

city: Boston

first: Rinath

last: Jeselsohn

state: MA

address: 450 Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: The ESR1 ligand binding domain activating mutations are the most prevalent genetic mechanism of acquired endocrine resistance in metastatic hormone receptor-positive breast cancer. These mutations confer endocrine resistance that remains estrogen receptor (ER) dependent. We hypothesized that in the presence of the ER mutations, continued ER blockade with endocrine therapies that target mutant ER is essential for tumor suppression even with chemotherapy treatment. Here, we conducted comprehensive pre-clinical in vitro and in vivo experiments testing the efficacy of adding fulvestrant to fluorouracil (5FU) and the 5FU pro-drug, capecitabine, in models of wild-type (WT) and mutant ER. Our findings revealed that while this combination had an additive effect in the presence of WT-ER, in the presence of the Y537S ER mutation there was synergy. Notably, these effects were not seen with the combination of 5FU and selective estrogen receptor modulators, such as tamoxifen, or in the absence of intact P53. Likewise, in a patient derived xenograft (PDX) harboring a Y537S ER mutation the addition of fulvestrant to capecitabine potentiated tumor suppression. Moreover, multiplex immunofluorescence revealed that this effect was due to decreased cell proliferation in all cells expressing ER and was not dependent on the degree of ER expression. Taken together, these results support the clinical investigation of the combination of ER antagonists with capecitabine in patients with metastatic hormone receptor-positive breast cancer who have experienced progression on endocrine therapy and targeted therapies, particularly in the presence of an ESR1 activating mutation.

overall_design: MCF7 cells without (WT ER) or with DOX induced expression of the Y537S ER mutation were treated with vehicle (DMSO), 5FU (1000 nM), fulvestrant (10 nM), or combination treatment of 5FU plus fulvestrant for 12 hours. Then, cells were harvested (as duplicates) for downstream RNA analysis. Comparative RNAseq analysis of ER-mutant PDX1526 samples under four treatment conditions (Vehicle, Fulvestrant, Capecitabine, and Fulvestrant+Capecitabine) and two timepoints (10 days and 28 days).

first: Albert

last: Grinshpun


title: Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [mTorSeq]

city: Farmington

first: Anthony

last: Vella

state: Connecticut

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

summary: Analysis of transcript changes with enough depth for evaluation of splicing changes between CD8+ T cells from mice receiving no stimulation, N4 stimulation, or N4 stimulation after treatment with Torin inhibitor

overall_design: OT-I CD8+ T cells from mice 12 hours without treatment, with treatment with DMSO and stimulation with N4 , or with treatment with Torin and stimulation with N4

first: Timofey

last: Karginov

first: Antoine

last: Menoret


title: Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [Tra2bKO]

summary: Analysis of transcript changes with enough depth for evaluation of splicing changes between naïve, scrambled control CD8+ T  or Tra2bKO CD8+ T cells from mice

overall_design: OT-I naïve (day 0), scrambled Control or Tra2bKO CD8+ T cells from the spleens and lymph nodes of mice 4 days after stimulation with SIINFEKL + anti-OX40/anti-41BB (costimulation)


title: Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [ASO_RNASeq]

summary: Analysis of transcript changes with enough depth for evaluation of splicing changes between CD8+ T cells from human donor PBMCs receiving no stimulation,CD3/CD28 stimulation plus scrambled ASO, or CD3/CD28 plus Tra2b-PE ASO

overall_design: CD8+ T cells from human donors 48 hours after receiving no stimulation,CD3/CD28 stimulation plus scrambled ASO, or CD3/CD28 plus Tra2b-PE ASO


title: Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [PEKOSeq]

summary: Analysis of transcript changes with enough depth for evaluation of splicing changes between scrambled control CD8+ T  or Tra2b-PE KO CD8+ T cells from mice

overall_design: OT-I scrambled Control or Tra2b-PEKO CD8+ T cells from the lungs of of mice 16 days after OVA-influenza infection


title: Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [CLIP-seq]

summary: Analysis of Tra2b binding sites in Naïve and Effector CD8+ T cells from spleens and lymph nodes of OT-I mice unstimulated or stimulated with SIINFEKL peptide + anti-OX40/41BB for 4 days

overall_design: Naïve and Effector (SIINFEKL+antiOX40/41BB 4 days) OT-I CD8+ T cells from spleens and lymph nodes of mice


title: Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A genome-wide screen for peroxisome regulators connects peroxisomes with Wnt signaling through RNF146 and tankyrase [Amplicon-sequencing]

overall_design: We performed a genome-wide CRISPRi screen for genes that regulate peroxisome formation and maintenance. The starting point is a Pex-ZeoR cell line, in which the efficiency of peroxisome import is linked to cell viability by fusing the fluorescent marker mVenus and a peroxisomal targeting signal (PTS1) to the gene encoding resistance to Zeocin. Cells with functional peroxisomes sequester the Zeocin resistance protein (ZeoR), thereby preventing them from neutralizing Zeocin. By contrast, cells with reduced peroxisome import should accumulate mVenus-ZeoR-PTS1 in the cytoplasm where it can neutralize Zeocin, conferring a selective advantage in the presence of Zeocin. Knockdown of genes that promote peroxisomes should increase viability when challenged with Zeocin. Knockdown of genes that inhibit peroxisome formation should decrease viability when challenged with Zeocin.