title: Effects of scratching and engineered nanomaterials on gene profiles and microbiota in SKH-1 mice

city: Helsinki

first: Kuunsade

last: Maenpaa

address: Haartmaninkatu 3

country: Finland

institute: University of Helsinki

summary: Scratching damages upper layers of the skin, breaks this first line of immune defence, and leads to inflammation response, which often also modifies the microbiota of the skin. Although the healing of incision wounds is well-described, there are fewer studies on superficial wounds. We used a simulated model of skin scratching to study changes in the host transcriptome, skin microbiota, and their relationship. Additionally, we examined the effect of nanosized ZnO, TiO2, and Ag on both intact and damaged skin. At 24 h after exposure, the number of neutrophils was increased, 396 genes were differentially expressed, and microbiota compositions changed between scratched and intact control skin. At 7 d, the skin was still colonised by gut-associated microbes, including Lachnospiraceae, present in the cage environment, while the transcriptomic responses decreased. To sum up, the nanomaterial exposures reduced the relative abundance of cutaneous microbes on healthy skin, but the effect of scratching was more significant for the transcriptome than the nanomaterial exposure both at 24 h and 7 d. We conclude that superficial skin scratching induces inflammatory cell accumulation and changes in gene expression especially at 24 h, while the changes in the microbiota last at least 7 days.

overall_design:
The hairless SKH-1 mice were assigned into groups of 8 mice/group according to the timepoint (24 h or 7 d) and treatment (naive, PBS, scratching and PBS, scratching only, nanomaterial treatment, scratching and nanomaterial).
Total RNA was extracted from upper back skin biopsies, and 6/8 mice per group were chosen for sequencing with the Drop-seq-like protocol, which includes sample pooling.
Differential gene expression analysis was performed with the obtained gene expression matrix.

first: Kuunsäde

last: Mäenpää

first: Marit

last: Ilves

first: Lan

first: Harri

last: Alenius

first: Hanna

last: Sinkko

first: Piia

last: Karisola


title: Mechanobiological stimulation in organ-on-a-chip systems reduces hepatic drug metabolic capacity in favor of regenerative specialization

status: Public on Jan 22 2024

city: Tokyo

first: Stéphane

last: Poulain

address: Fw-203, 4-6-1, Komaba, Meguro-ku

department: Institute of Industrial Science

country: Japan

institute: The University of Tokyo

type: Expression profiling by high throughput sequencing

summary:
To investigate the effect of culture microenvironment in microphysiological systems on hepatocellular tissue performance in vitro, we established hepatocyte culture systems with gradually increased complexity.
Gene expression profiles of culture hepatocytes were evaluated from 8 groups based on oxygen supplementation, oxygen tension, paracrine signaling from endothelial cells, and hemodynamic shear stress.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary human hepatocytes exposed to varying culture microenvironmental cues.

first: Benedikt

last: Scheidecker

first: Masahiro

last: Sugimoto

first: Hiroshi

last: Arakawa

first: Soo Hyeon

last: Kim

first: Takumi

last: Kawanishi

first: Yukio

last: Kato

first: Mathieu

last: Danoy

first: Masaki

last: Nishikawa

first: Yasuyuki

last: Sakai


title: Phytochrome C and Low Temperature Promote the Expression and Red Light Signaling of Phytochrome D

status: Public on Jan 19 2024

city: Szeged

first: Gabor

last: Grezal

state: Csongrád

address: Temesvári krt. 62.

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Light is an ever-changing environmental parameter affecting almost every aspects of plant growth and development. It is perceived by photoreceptors, among them phytochromes (PHY) are responsible for monitoring the red and far-red part of the spectrum. Arabidopsis thaliana possesses five phytochromes genes, named through phyA-phyE. Whereas the function of phyA and phyB – that mediate most of the phytochrome responses – is extensively studied, our knowledge on other phytochromes are still rudimentary. To analyze phyD function we expressed it at high levels in different phytochrome deficient genetic backgrounds. We found that overexpressed phyD governs effective light signaling at low temperatures but only in cooperation with functional phyC. Under these conditions, opposite to phyB, phyD accumulates to high levels and this pool is stable under light illumination. Furthermore, the detectable photoconvertible phyD amount is proportional with the available protein amount indicating that the phyD pool contains fully functional photoreceptors. The thermal reversion of phyD is very fast suggesting that the thermosensing of phyD is based on its protein amount and not on its Pfr conformer stability, which was described for phyB. We also found that phyD and phyB associate to identical genomic locations and mediate similar gene expression changes, however the efficiency of phyD is lower. Taken together our data suggest that under certain conditions synergistic interaction of phyD and phyC substitutes phyB function thus increases the ability of plants to respond more flexible to environmental changes.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) with anti-GFP antibody that recognise PHYD-YFP and PHYB-GFP transgenic protein.

first: Gábor

last: Grézal

first: Csaba

last: Péter

first: Anita

last: Hajdu

first: László

last: Kozma-Bognár

first: Dániel

last: Silhavy

first: Ferenc

last: Nagy

first: Éva

last: Ádám

first: András

last: Viczián


title: Engineered co-cultures of iPSC-derived atrial cardiomyocytes and atrial fibroblasts for modeling atrial fibrillation [II]

city: Chicago

first: Salman

middle: R

last: Khetani

email: gbrown25@uic.edu, skhetani@uic.edu

state: IL

address: 851 S Morgan St, SEO 218

department: Biomedial Engineering

country: USA

institute: University of Illinois at Chicago

summary: Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia treatable with antiarrhythmic drugs, but patient responses are highly variable. Human induced pluripotent stem cell-derived atrial cardiomyocytes (iPSC-aCMs) are useful for discovering precision therapeutics, but current platforms yield an immature cellular phenotype and are not easily scalable for high-throughput screening. Here, we report that primary adult atrial, but not ventricular, fibroblasts induced greater functional iPSC-aCM maturation, partly through connexin-40 and ephrin-B1 signaling. We developed a protein patterning process within industry-standard multiwell plates to engineer patterned co-culture (PC) of iPSC-aCMs and atrial fibroblasts that significantly enhanced iPSC-aCM structural, electrical, contractile, and metabolic maturation for 6+ weeks versus conventional mono-/co-cultures. PC displayed greater sensitivity for detecting drug efficacy than monocultures, and enabled the modeling and pharmacological or gene editing treatment of an AF-like electrophysiological phenotype due to a sodium channel mutation. In conclusion, PC is useful to elucidate heterotypic cell signaling in the atria, drug screening, and to model AF.

overall_design: Comparison of primary human atrial cardiac fibroblasts (two donors) to primary ventricular cardiac fibroblasts (two donors)

first: Grace

middle: E

last: Brown

first: Yong

middle: D

last: Han

first: Dawood

last: Darbar


title: Oncogenic KRAS induces arginine auxotrophy in non-small cell lung cancer and confers a therapeutic vulnerability to SLC7A1 inhibition

status: Public on Jan 20 2024

city: Shanghai

first: Min

last: Huang

address: 555 Zuchongzhi Road, Pudong

department: State Key Laboratory of Drug Research

country: China

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

summary: The urea cycle is frequently rewired in cancer cells to meet the metabolic demands of cancer, yet our understanding about the regulatory mechanisms for this pathway in different types of cancer is very limited. In this study, we discover that oncogenic activation of KRAS in non-small cell lung cancer (NSCLC) silences the expression of arginosuccinate synthase 1 (ASS1), a urea cycle enzyme catalyzing the production of arginine from aspartate and citrulline, and thereby diverts the utilization of aspartate to pyrimidine synthesis to meet the high demand for DNA replication in KRAS-mutant NSCLC. Specifically, KRAS signaling facilitates a hypo-acetylated state in the promoter region of ASS1 gene in a histone deacetylase 3 (HDAC3)-dependent manner, which in turn impedes the recruitment of the transcription factor c-MYC for ASS1 transcription. ASS1 suppression in KRAS-mutant NSCLC cancer cells impairs the biosynthesis of arginine and renders growth dependency on SLC7A1, an arginine transmembrane transport, to import extracellular arginine. Depletion of SLC7A1 in both patient-derived organoid and xenograft models obtains a substantial therapeutic benefit in inhibiting KRAS-driven NSCLC growth. Together, our findings uncover a new role of oncogenic KRAS in rewiring urea cycle metabolism and identify SLC7A1-mediated arginine uptake as a therapeutic vulnerability in treating KRAS-mutant NSCLC.

overall_design: To investigate how oncogenic KRAS rewires metabolic enzymes in the urea cycle, we introduced KRAS-G12D mutant into human bronchial epithelial BEAS-2B cells (BEAS-2B-KRAS-G12D). We then performed gene expression profiling analysis using data obtained from RNA-seq of BEAS-2B-EV and BEAS-2B-KRAS-G12D.


title: Engineered co-cultures of iPSC-derived atrial cardiomyocytes and atrial fibroblasts for modeling atrial fibrillation [I]

overall_design: Examination of one iPSC-derived atrial cardiomyocyte line with baseline maturation compared to patterned coculture maturation.


title: RNA-binding protein TRA2A promotes glioblastoma by mediating m6A RNA modification of IFITs to recycle p-EGFR

city: Shenyang

first: li

last: bingwu

address: shenhe

institute: Shenyang Pharmaceutical University

summary: The RNA-binding protein Transformer 2 alpha homolog (TRA2A), previously identified as an alternative splicing factor, was reported as a crucial oncogene in recent years. However, the underlying mechanisms are poorly understood. In this study, we found that TRA2A is highly up-regulated in glioblastoma and is significantly correlated with clinical diagnosis and prognosis. We verified that TRA2A promotes the proliferation and metastasis of glioblastoma. Epitranscriptomic profiling further revealed Interferon-induced protein with tetratricopeptide repeat 1/2/3 (IFIT1/2//3) as the key RNA targets mediated by TRA2A, which further over-activates the EGFR-AKT signaling pathway by enhancing the recycling of p-EGFR. This work reveals a novel oncogenic mechanism of TRA2A in glioblastoma.

overall_design: Methylated RNA immunoprecipitation sequencing (meRIP-seq) for TRA2A-knockdown and control U-251 MG cells.

first: Bingwu

last: Li

first: Wanxu


title: Engineered co-cultures of iPSC-derived atrial cardiomyocytes and atrial fibroblasts for modeling atrial fibrillation

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

overall_design: Refer to individual Series


title: The circadian clock time tunes axonal regeneration

city: London

first: Franziska

last: Müller

address: Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

summary: Peripheral nervous system injuries lead to long-term neurological disability due to limited axonal regenerative ability. Injury-dependent and more recently injury-independent physiological mechanisms have provided important molecular insight into regenerative mechanisms. However, whether common molecular denominators underpinning both injury-dependent and independent biological processes exist remains unclear. We initially performed a comparative analysis of recently generated transcriptomic datasets associated with the regenerative ability of sciatic dorsal root ganglia (DRG). Surprisingly, circadian rhythms were identified as a the most significantly enriched biological process associated with regenerative capability. We demonstrate that DRG neurons possess an endogenous circadian clock with a 24h oscillations of circadian genes and that their regenerative ability displays a diurnal oscillation in a mouse model of sciatic nerve injury. Consistently, transcriptomic analysis of DRG neurons showed a significant time-of-day dependent enrichment for processes associated with neuronal development and axonal growth, for regeneration and circadian associated genes, including the core clock genes Bmal1 and Clock. Indeed, DRG-specific ablation of the non-redundant clock gene Bmal1showed that it is required for regenerative gene expression, neuronal intrinsic circadian axonal regeneration and target reinnervation. Lastly, Lithium, a chrono-active compound, enhanced nerve regeneration, in wildtype but not in clock genes Bmal1 and Cry1/2-deficient mice. Together, these data demonstrate that daily rhythms and the circadian clock fine-tune the regenerative response of DRG neurons, and they advocate for the use of chrono-active strategies in time-day dependent modulation of nerve repair.

overall_design: L4-6 dorsal root ganglia were extracted 72hr after a sciatic nerve injury at either Zeitgeber (ZT)8 or ZT20 followed by neuronal cell enrichment  that was processed for RNA-seq

first: Francesco

last: De Virgiliis

first: Matt

last: Danzi

first: Ilaria

last: Palmisano

first: Siimone

last: Di Giovanni


title: DMF-scMT-seq Linking Methylome and Transcriptome within Single Cells with Digital Microfluidics

city: Xiamen

first: Xing

last: Xu

address: 422, Siming South Road

institute: Xiamen University

type: Methylation profiling by high throughput sequencing

summary: Single-cell joint analysis of methylome and transcriptome reveals how the methylation regulates the transcriptional activity. However, traditional bench-top protocols for single-cell DNA methylation and RNA transcription co-detection are labor-intensive, cost-ineffective and contaminant-prone. Herein we establish DMF-scMT-seq, a highly-efficient and cost-effective method to simultaneously analyze single-cell DNA methylation and transcriptional activity based on digital microfluidics. DMF-scMT-seq automates the workflow of single-cell isolation, cellular hypotonic lysis, nucleic acid separation and methylome/transcriptome library construction in a contactless and addressable way. The system ensures high accuracy (R>0.85), high gene detection ability (14697 genes per cell at 4 million sequencing depth), and high CpG coverage (677198 CpG sites per cell at 1 million sequencing depth). By using DMF-scMT-seq, the relationship of DNA methylation and RNA transcription under different genomic contexts is resolved. We further apply DMF-scMT-seq to study the dynamics of transcription regulation with methylation-inhibiting anti-tumor Decitabine, and identify the methylated promoter/gene body driven genes in response to Decitabine treatment for the first time. It is anticipated that DMF-scMT-seq provides the potential to characterize the epigenetic regulatory network in other biological single-cell systems.

overall_design: Methylome and transcriptome profiles of different cancer cell lines

first: Xi

last: Zeng

first: Xin

last: Lin

first: Shiyan

first: Rui

last: Su

first: Jia

last: Song

first: Chaoyong

last: Yang


title: The functional role of CST1 and CCL26 in asthma development

city: Solna

first: Angela

last: Hoyer

address: Visionsgatan 4

country: Sweden

institute: Karolinska Institutet

summary:
Background:
Asthma is the most common chronic disease in children with an increasing prevalence in recent years. Its development depends on genetic and environmental factors and allergic sensitization is a known trigger. Dog allergens affect up to 30% of all children and dog dander-sensitized children show increased expression of cystatin-1 (CST1) and eotaxin-3 (CCL26). The aim of our study was to investigate the functional mechanism of CST1 and CCL26 in the alveolar basal epithelial cell line A549.
Methods:
A549 cells were transfected with individual overexpression vectors for CST1 and CCL26 and RNA sequencing was performed to examine the transcriptomics. DESeq2 was used to identify differentially expressed genes (= DEG) and ShinyGO v0.77 and Enrichr for pathway enrichment analysis.
Results:
The overexpression of CST1 resulted in a total of 23 DEG (3 upregulated and 20 downregulated) and the overexpression of CCL26 in a total of 113 DEG (3 upregulated and 110 downregulated). The gene ontology enrichment analysis showed a significant downregulation of type I and III interferon signaling pathway genes as well as interferon-stimulated genes.
Conclusion:
Our results indicate that an overexpression of CST1 and especially CCL26 cause a downregulation of interferon related genes. It might cause a higher disease susceptibility, mainly for allergic asthma, as CCL26 is an agonist for CCR-3-carrying cells, such as eosinophils and Th2 lymphocytes, mostly active in allergic asthma.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from A549 cells transfected with plasmids containing the human CST1 and CCL26 as well as the empty vector pCMV6-entry as control

first: Sandip

last: Chakraborty

first: Ingrid

last: Lilienthal

first: Jon

last: Konradsen

first: Cilla

last: Söderhäll

first: Shintaro

last: Katayama


title: Effect of BRM on BR-regulated gene expression during growth and development in Arabidopsis

city: Guangzhou

first: Tao

last: Zhu

address: 135 Xingang West Road, Guangzhou City

institute: Arabidopsis

summary: To clarify the genome-wide role of the BZR1-BAS complexes in BR-regulated transcriptional activation or repression processes, we conducted RNA-sequencing (RNA-seq) assay using Col, bzr1-1D, brm-1, and bzr1-1D brm-1 seedlings grown on the medium containing 2 ?M PPZ in the dark for five days.

overall_design: We conducted RNA-sequencing (RNA-seq) assay using Col, bzr1-1D, brm-1, and bzr1-1D brm-1 seedlings grown on the medium containing 2 microM PPZ in the dark for five days.

first: Chenlong

last: Li


title: Mrgpra1 controls neutrophil hyperactivation by balancing N1/N2 switch

city: Baltimore

first: Naina

last: Gour

state: MD

address: 745 N Wolfe st.

department: Neuroscience

institute: Johns Hokins University

summary: We want to understand the role of Mrgpra1 regulating neutrophil function. Mrgpra1-sufficient and Mrgpra1-deficient mice were infected with Streptococcus pneumoniae and lung neutrophils were flow-sorted 24h later for RNA-seq

overall_design: RNA from flow-sorted lung neutrophils (DAPIneg CD11b+Ly6G+)


title: Opioid receptor signaling suppresses leukemia by inducing TET-dependent DNA demethylation [ChIP-seq]

city: Hangzhou

first: Jun

last: Lu

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Acute myeloid leukemia (AML) is a type of heterogeneous and fatal hematopoietic malignancy. The ten-eleven translocation (TET) mediated DNA demethylation is known to be critically associated with AML pathogenesis. Through chemical compound screening, we found that the opioid receptor agonist, loperamide hydrochloride (OPA1), significantly suppresses AML cell viability. The potential therapeutic effects of opioid receptor agonists, especially OPA1, were then verified in AML cells in vitro, and t(11q23) and t(8;21) AML mouse models in vivo. OPA1-induced activation of OPRM1 enhanced the transcription of TET2, increased DNA 5-hydroxymethylcytosine (5hmC) modification, and in turn, activated NFκB signaling. Notably, AML with TET2 mutations or chemotherapy resistance were highly sensitive to OPA1. Our results reveal a previously unknown OPRM1-TET2-5hmC-TRAF2 regulatory axis in AML, and suggest that opioid agonists, particularly OPA1, an FDA-approved antidiarrheal drug, have therapeutic potential in AML, especially in TET2 mutated and chemotherapy-resistant AML, which have a poor prognosis.

overall_design: Examination of 2 different transcriptfactor in AML cells

first: Huanhuan

last: Zhao

last: Jiang


title: Opioid receptor signaling suppresses leukemia by inducing TET-dependent DNA demethylation

type: Methylation profiling by genome tiling array

overall_design: Bisulphite converted DNA from the 2 samples were hybridised to the Illumina Infinium 850k Human MethylationEPIC BeadChip.

first: Xi

last: jiang


title: Activating transcription factors Atf3/Atf4 drive early molecular events preceding neural stem cell differentiation and control neuron formation [Short]

status: Public on Jan 18 2024

city: Berlin

first: Rupert

middle: W

last: Overall

state: Berlin

address: Philippstraße 13

country: Germany

institute: Humboldt University of Berlin

summary: The generation of new neurons from neural stem cells is tightly controlled by transcriptional programs. To induce cell fate switches that establish neuronal identities, differentiating neural precursor cells (NPCs) must undergo rapid and dynamic gene expression changes. However, the neuronal fate-determining molecular events that precede NPC differentiation are incompletely understood. Using high temporal resolution transcriptional profiling of adult hippocampal NPC differentiation, we here identified the activating transcription factors Atf3 and Atf4 as early switch regulators that drive NPC fate and control neuron formation. We found that Atf3/4 are rapidly upregulated in NPCs upon induction of differentiation and drive dynamic gene expression changes associated with neurogenesis. Pharmacological and genetic perturbation of Atf4 demonstrated its importance for neuron formation. Sustained overexpression of Atf3 hampered neurogenesis by repressing long non-coding RNA Miat. Our results demonstrate the critical role of an Atf3/Atf4-controlled transcriptional network in driving early molecular events during neurogenesis.

overall_design: 17 samples from different timepoints after onset of differentiation

first: Jan-Hendrik

last: Claasen

first: Giannino

last: Patone

first: Norbert

last: Hübner

first: Gerd

last: Kempermann


title: Identify miRNAs involved in ER stress in wheat using miRNA sequencing

city: zhengzhou

first: Xing

last: Yu

state: Henan

address: 95 Wenhua Road

institute: Henan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: We used dithiothreitol (DTT) and tauroursodeoxycholic acid (TUDCA) to induce or suppress ER stress in wheat cells, respectively, with the aim to reveal the molecular background of ER stress responses using miRNA sequencing. After sequencing, we revealed a total of 1,939 miRNAs involved in the process of ER stress response, including 1,740 known miRNAs and 199 novel miRNAs.

overall_design: Experiments were established with three treatments: control (C), DTT (D), and DTT+TUDCA (T). Three independent biological replicates were performed, and a total of nine leaf samples were performed by miRNA sequencing.  Small RNA libraries were constructed from 6 mixed RNA pools comprising RNA from three chemical treatment groups. For each treatment group, two mixed RNA pools were assembled from three independent biological replicates.

first: Zeyu

last: Xin


title: Epigenetic regulation of NK cell-mediated immune response in multiple myeloma [CRISPR screening 2]

status: Public on Jan 23 2024

city: Boston

first: Jiye

last: Liu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Anti-CD38 monoclonal antibodies like Daratumumab (Dara) are effective in multiple myeloma (MM); however, drug resistance ultimately occurs and the mechanisms behind this are poorly understood. Here, we performed two in vitro genome-wide CRISPR screens to systematically discover the regulators of sensitivity to Dara-mediated antibody-dependent cellular cytotoxicity (ADCC) and identified KDM6A. The loss of KDM6A led to a marked downregulation in CD38 expression by increasing H3K27me3 on the CD38 promoter, resulting in resistance to Dara-mediated ADCC. Yet, adding back CD38 did not completely rescue this phenotype. In fact, KDM6A loss also downregulated CD48, which promoted Dara resistance by inhibiting natural killer cell activity. Lowering the H3K27me3 with an EZH2 inhibitor restored sensitivity to Dara through CD38 and CD48 upregulation. These findings suggest KDM6A loss as a mechanism of Dara resistance and explore the strategy of using an EZH2 inhibitor, one of which is already FDA-approved, to improve the response to Dara in MM.

overall_design: Genome-wide CRISPR/cas9 screening in H929 cells for Dara resistance

first: Su

last: Wang

first: Kenneth

last: Anderson


title: Identify targets of miRNAs involved in ER stress in wheat using degradome sequencing

summary: We used dithiothreitol (DTT) and tauroursodeoxycholic acid (TUDCA) to induce or suppress ER stress in wheat cells, respectively, with the aim to reveal the molecular background of ER stress responses using degradome sequencing. After combined analysis of high-throughput sequencing, a total of 12,453 miRNA-target pairs were verified by degradome sequencing, and among them, 7,484 genes were targeted by 1,233 miRNAs.

overall_design: Experiments were established with three treatments: control (C), DTT (D), and DTT+TUDCA (T). Three independent biological replicates were performed, and a total of nine leaf samples were performed by degradome sequencing.


title: Activating transcription factors Atf3/4 drive early molecular events during neural stem cell differentiation and control neuron formation [RNA-seq]

overall_design: The transcription factors Atf3 and Atf4 were overexpressed during differentiation of neural precursor cells (NPCs) derived from the hippocampus of adult mice. Atf3/4-induced transcriptional changes in differentiating NPCs were detected using RNA sequencing.

first: Sara

last: Zocher

first: Klaus

last: Schughart


title: Genome-wide profiling of BRAHMA (BRM), BZR1, H3K4me3, H3K27me3, and H4K5ac with indicated growth conditions

first: Tao

last: Zhu

summary:
To investigate the effect of BR deficiency  on BRM occupancy in the genome.
Effect of BR on chromatin accessibility during growth and development in Arabidopsis
Examination the  occupancy of BRM, BZR1, H3K4me3, H3K27me3, and H4K5ac with indicated growth conditions

sample_organism:
Arabidopsis
Arabidopsis thaliana

platform_organism:
Arabidopsis
Arabidopsis thaliana

overall_design:
To clarify the genome-wide role of the BR in regulating chromatin accessiblity we conducted ATAC-seq assay using indicated samples.

Exploration of genome-wide profiling of BRAHMA (BRM), BZR1, H3K4me3, H3K27me3, and H4K5ac with indicated growth conditions

first: Chenlong

last: Li


title: Transcription factor Pbx4 regulates limb development and hematopoiesis in mice [RNA-seq]

city: Beijing

first: Chunsheng

last: Han

address: No.5, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We carried out RNA-seq analysis to identify genes that are potentially regulated by PBX4 in hindlimb bud cells of the E11.5 mice by comparing gene expression in KO vs WT mice.

overall_design: Hindlimb buds were extracted from E11.5 embryos using forceps under a stereoscope. Total RNAs were isolated using TRIzol (15596-026; Invitrogen). High-throughput sequencing libraries were constructed using the NEB-Next Ultra RNA Library Prep Kit for Illumina.

first: Yan

last: Ning

first: Xiwen

last: Lin


title: CTCF regulates hepatitis B virus cccDNA chromatin topology [ATAC-seq]

city: Birmingham

first: Csilla

last: Varnai

address: Haworth Building

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

summary: Hepatitis B Virus (HBV) is a small DNA virus that replicates via an episomal covalently closed circular DNA (cccDNA) that serves as the transcriptional template for viral mRNAs. The host protein, CCCTC-binding factor (CTCF), is a key regulator of cellular transcription by maintaining epigenetic boundaries, nucleosome phasing, stabilisation of long-range chromatin loops and directing alternative exon splicing. We previously reported that CTCF binds two conserved motifs within Enhancer I of the HBV genome and represses viral transcripts, however, the underlying mechanisms were not identified. We show that CTCF depletion in cells harbouring cccDNA-like HBV molecules and in de novo infected cells resulted in an increase in spliced transcripts, which was most notable in the abundant SP1 spliced transcript. In contrast, depletion of CTCF in cell lines with integrated HBV DNA had no effect on the abundance of viral transcripts and in line with this observation there was limited evidence for CTCF binding to viral integrants, suggesting that CTCF-regulation of HBV transcription is specific to episomal cccDNA. Analysis of HBV chromatin topology by Assay for Transposase Accessibility/sequencing (ATAC-Seq) revealed an accessible region spanning Enhancers I and II and the basal core promoter (BCP). Mutating the CTCF binding sites within Enhancer I resulted in a dramatic rearrangement of chromatin accessibility where the open chromatin region was no longer detected, indicating loss of the phased nucleosome up- and down- stream of the HBV enhancer/BCP. These data demonstrate that CTCF functions to regulate HBV chromatin conformation and nucleosomal positioning in episomal maintained cccDNA, which has important consequences for HBV transcription regulation.

overall_design:
To analyze chromatin accessibility of HBV cccDNA in HepG2-hNTCP cells by de novo infection with either wild type or CTCF BS1/2m (CTCF binding site 1 and 2 mutant) HBV genome and also to assess the effect of CTCF knockdown on the chromatin accessibility of integrated HBV genome in PLC/PRF5 cells.
ATAC-seq assay was performed on these cells and the chromatin accessibility of HBV genome in various conditions were compared and analyzed

first: Mihaela

middle: O

last: Dobrica

first: Christy

middle: S

last: Varghese

first: James

middle: M

last: Harris

first: Jack

last: Ferguson

first: Andrea

last: Magri

first: Roland

last: Arnold

last: Várnai

first: Joanna

middle: L

last: Parish

first: Jane

last: McKeating


title: Single cell RNA sequencing of rat lung tissues to characterize blast exposure-induced cell heterogeneity

city: Jinan

first: Lin

last: Zhang

state: Shandong

address: No.9-7 Jiangshuiquan Road

department: Clinical Medical Research Center for Women and Children Diseases

institute: Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University

summary: Coal mining carries inherent risks of catastrophic gas explosions capable of inflicting severe lung injury. Using a rat model, we explored mechanisms underlying alveolar epithelial damage and repair following a gas explosion. By performing scRNA-sequencing, we revealed that alveolar epithelial cells exhibited the most profound transcriptomic changes after gas explosion compared to other pulmonary cell types.

overall_design: To investigate the variation of lung cells, we exposed rats to blast explosion and matched them with control. The lung tissues of both groups were subjected to scRNA-sequencing.

first: Linqiang

last: Tian

first: Hong

first: Chunjie

last: Ding

first: Sanqiao

last: Yao

first: Wenjie

last: Ren


title: TRANSCRIPTOMIC ANALYSIS ON ENDOSCOPIC ULTRASOUND FINE NEEDLE ASPIRATION MATERIALS FROM PRIMARY PANCREATIC ADENOCARCINOMA

city: CLICHY

first: Camille

last: PIGNOLET

address: 100 Bd du Général Leclerc

department: CRI U1149

country: France

institute: INSERM

summary: The study aimed to compare the molecular profiles of metastatic, locally advanced, and resected primary pancreatic adenocarcinoma at the genomic and transcriptomic levels.    DNA and mRNA were extracted from endoscopic ultrasound-guided fine needle aspiration-biopsy material of primary tumors from 397 patients, and they were subsequently analyzed by targeted deep sequencing and RNAseq.

overall_design: populational analysis

first: R

last: Nicolle

first: C

last: Canivet

first: M

last: Ayadi

last: Pignolet

first: L

last: Buscail

first: B

last: Bournet


title: Single-cell RNA sequencing reveals preserved pancreatic endocrine cell identity and function by administration of a metabolite-based diet in autoimmune diabetes

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

summary: Objective: An altered gut bacterial composition is associated with the pathogenesis of type 1 diabetes and short-chain fatty acids are known to play a pivotal role in maintaining gut homeostasis. The effects of short-chain fatty acids on pancreatic islet cell function, insulin production and local immune-infiltration, however, remain elusive.Methods: Five-week-old female NOD mice were fed with an acetylated and butyrylated high-amylose maize-resistant starch (HAMSAB) or control diet for five consecutive weeks. The pancreata were harvested, islets isolated using collagenase, and dispersed into single cells by trypsin. Single-cell RNA sequencing was performed with 10x Chromium. The raw counts were analysed using RStudio with the Seurat package. Human embryonic stem cell-differentiated beta-like cells, mouse islets and INS-1E beta cell line were treated with acetate, butyrate and/or combination. Pro-inflammatory cytokines (IFN- + IL-1) were used for stress response and viability assays. Results: single-cell RNA sequencing analysis mapped the gene expression profiles of 4,301 and 4,113 individual islet cells from HAMSAB or HAMS fed mice, respectively. Cells were annotated into 11 clusters: 5 immune, 4 endocrine, acinar and endothelial cell types. The scRNA seq dataset indicated that T cells, B cells, macrophages, and dendritic cell subsets infiltrated the islets of Langerhans from both HAMSAB and HAMS-fed mice. Interestingly, HAMSAB induced an immune tolerogenic profile and lower cytotoxic Gzma+ CD8+ T cells. Moreover, HAMSAB maintained the expression of beta cell functional genes (i.e., Ins1, Ins2, G6pc2, Prlr and Iapp) and decreased the expression of genes associated with cellular stress (i.e., Fos, Impact, Stat1, Dusp1 and Hsp40/Dnajb1). Short-chain fatty acid treatment decreased pro-inflammatory cytokine-induced stress in mouse islets and INS-1E beta cells. In addition, HAMSAB preserved the identity of endocrine cells, evaluated by a decrease in dedifferentiated poly-hormonal cells expressing endocrine progenitor genes (MafA, Nfix). Importantly, short-chain fatty acids increased insulin levels in human embryonic stem cell-differentiated beta-like cells and improve transplantation outcome in NOD/SCID mice. Conclusions: Short-chain fatty acids prevent diabetes development in NOD mice, at least in part, by enhancing beta cell function and preserving the cell identity of endocrine cells under inflammatory-mediated autoimmune stress.

overall_design: Single-cell RNA-Seq of mouse pancreata fed with HAMS or HAMSAB diet

first: Sema

last: Eski

first: Manoja

last: Brahma

first: Ao

last: Li

first: Javier

last: Negueruela

first: Ylke

last: Bruggeman

first: Stéphane

last: Demine

first: Peng

last: Xiao

first: Alessandra

last: Cardozo

first: Nicolas

last: Baeyens

first: Luciano

last: Martelotto

first: Sumeet

middle: P

last: Singh

first: Eliana

last: Mariño

first: Conny

last: Gysemans

first: Esteban

last: Gurzov


title: Histone methylation mediated by NSD1 is required for the establishment and maintenance of neuronal identities

city: wuhan

first: zhao

last: chen

state: Hubei

address: shuiguohu

department: BIOLOGY

institute: wuhan university

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

overall_design: Refer to individual Series


title: OceanobacilluspicturaeAlleviatesCdstressandpromotesgrowthinsoybeanseedlings

city: Harbin

first: Yang

last: Shangjun

address: Mucai Street

institute: Northeast Agricultural University

summary: ThisresearchonOceanobacilluspicturaeprovidesnewinsightsintomitigatingCdstressinsoybeanplants,reducingsoilCdcontent,andpromotingsoybeanseedlingrootgrowth.Italsoidentifiesnovelgenesandmicrobialspeciesrelevanttothemicrobialreductionofsoilheavymetalpollutionandtheresponsemechanismsofsoybeanplantstoheavymetals.

first: Shangjun

last: Yang

first: Xue

last: Han

first: Jun


title: Activating transcription factors Atf3/Atf4 drive early molecular events preceding neural stem cell differentiation and control neuron formation

first: Rupert

last: Overall


title: Transcriptome and biochemical parameters analysis in rainbow trout (Oncorhynchus mykiss) reveals physiological changes and molecular mechanisms in response to chronic and acute hypoxia stress

city: Lanzhou

first: QI

last: Wang

state: Gansu

address: Yintan Road Street

department: College of Animal Science and Technology

institute: Gansu Agricultural University

summary: Dissolved oxygen (DO) has an important impact on fish survival and reproduction, and is also one of the keys limiting conditions for healthy fish life. Rainbow trout (Oncorhynchus mykiss), an economically significant cold-water fish globally, are highly susceptible to hypoxia stress. However, the physiological changes and molecular mechanisms of rainbow trout under different hypoxic conditions are still unknown. In the present study, we used RNA-seq analysis and measurement of biochemical parameters at different time points (0-, 4-, 8-, 12-, 24 h) under acute (3.0 ± 0.1 mg/L), chronic (4.5 ± 0.1 mg/L) hypoxic stress and reoxygenation (R12-, R24 h) to reveals the physiological changes and molecular mechanism of the hypoxic stress response in rainbow trout. The transcriptome results showed that a total of 424 differentially expressed genes (DEGs) were identified in the CM-vs-Tm12M, CM-vs-Ts12M and Tm12M-vs-Ts12M groups and the genes for FOXO signaling pathway, p53 signaling pathway, Adipocytokine signaling pathway, Autophagy, Glycine, serine and threonine metabolism, etc. were significantly enriched under hypoxic stress, as shown by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes enrichment analyses (KEGG) and Gene Set Enrichment Analysis (GSEA). Based on DEGS expression trend analysis, the most significant 2 clusters were selected to construct protein-protein interaction (PPI) networks, which resulted in the prediction of ddit4, txnip, slc3a2 and p4ha1 as the hypoxia-induced hub genes in cluster 7. fgg, f7, serpina1 and serpinf2 are the hypoxia-induced hub genes of cluster 3. This study preliminarily elucidated the adaptive mechanism of rainbow trout in response to hypoxic stress and provide a basis for the study of the molecular mechanism of fish adaptation to different hypoxic stresses.

overall_design: In order to systematically identify genes related to the effect of hypoxic stress on the muscle metabolism of rainbow trout, the transcriptomic profiling of rainbow trout under acute and chronic hypoxic stress was studied.

first: Jinqiang

last: Huang

first: Qi


title: CTCF regulates hepatitis B virus cccDNA chromatin topology

first: Csilla

last: Varnai


title: Circulating tumor cell analysis from stage III lung cancer patients

city: Ann Arbor

first: Sunitha

last: Nagrath

state: Michigan

address: 2800 Plymouth Road

institute: University of Michigan

summary:
Imaging technologies only detect progression after it has occurred, which may be well after tumor growth or disease progression has begun. In this work, we determined whether circulating tumor cell (CTC) quantification, PD-L1 expression on CTCs, or CTC gene expression can be used as a blood-based biomarker to predict patient outcomes in stage III NSCLC. The primary endpoint was disease progression, either locoregional, distant, or death.
We used immunoaffinity graphene oxide (GO) chip to isolated CTCs from stage III NSCLC patients, and extracted bulk RNA materials from isolated CTC samples and conducted microarray gene expression profiling.

overall_design: At three timepoints (Pre-TX, W4, W10) through treatment, blood samples from 27 stage III NSCLC patients were processed for CTC isolation and RNA analysis using the immunoaffinity graphene oxide (GO) microfluidic chip. A total of 76 samples were included in the analysis. Only one device were used for RNA analysis per patient sample.

first: Emma

middle: A

last: Purcell

first: Zeqi

last: Niu


title: Activating transcription factors Atf3/Atf4 drive early molecular events preceding neural stem cell differentiation and control neuron formation [Long]

overall_design: 35 samples from different timepoints after onset of differentiation

first: Gerardo

middle: B

last: Ramírez-Rodríguez

first: Lu

last: Lu

first: Robert

last: Williams

first: Gerd

last: Kempermann


title: Single cell transcriptomic analysis of human tissue (Retina and RPE/Choroid)

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

summary: Human retina and RPE/choroid from healthy and age-related macular degeneration donors

overall_design: Expression profiling by high throughput sequencing


title: MOTS-c peptide binding protein

city: Xi'an

first: Yue

last: Zhai

address: #169, Changle West Road

institute: Fourth Military Medical University

summary: To elucidate the molecular mechanism of MOTS-c against NASH progression, we screened for potential MOTS-c binding proteins using biotin-labeled MOTS-c and HuProt human proteome microarray.

overall_design: Biotin-MOTS-c was incubated with human proteome microarray to screen the positive signals

first: Huanyu


title: The noncanonical cGAS-STING-PERK pathway enables a selective translation program and underlies organ fibrosis

first: Li

last: Shen

state: Zhejiang Province

institute: Life Sciences Institute, Zhejiang University

summary: Innate DNA sensing via the cGAS-STING pathway surveys both microbial invasion and cellular damage, constituting a ubiquitous mechanism for host defense and tissue homeostasis. However, very little is known about the signaling mechanism(s) and physiological impacts downstream of cGAS-STING signaling and independent of the classical TBK1-IRF3-IFN cascade. Here, we identified an unrecognized STING-PERK-eIF2α signaling axis that was specific and controlled cap-dependent translation, a fundamental cellular process. STING, upon activation by 2'3'-cyclic GMP-AMP (cGAMP), robustly bound and directly activated the endoplasmic reticulum (ER)-located kinase PERK, and this process was upstream of IRF3 activation and independent of the unfolded protein response (UPR) and TBK1/IKKε. Innate DNA sensing suppressed global translation programs but selectively ensured the activation of some pathways by PERK-mediated eIF2α phosphorylation and the rapid regulation of protein synthesis, enabling translational modulation of immune responses. Notably, the STING-PERK-eIF2α axis is an evolutionarily primitive component of STING-TBKI-IRF3-IFN signaling and is physiologically critical in pulmonary and renal fibrosis as well as in the regulation of cellular senescence. Therefore, these findings establish the first noncanonical pathway of the cGAS-STING mechanism and demonstrate the physiological importance of this STING-triggered selective translation, which we propose as a promising therapeutic target for fibrotic diseases.

overall_design: HEK293 cells transfected with Vector/STING/MAVS for two replicates are performed Polysome sequencing.

first: Dan

last: Zhang

first: Yezhang

last: Zhu

first: Pinglong

last: Xu


title: CTCF regulates hepatitis B virus cccDNA chromatin topology [RNA-seq]

overall_design:
We previously reported that siRNA-mediated depletion of CTCF resulted in an increased abundance of HBV transcripts with no effect on cccDNA levels.
To further investigate the role of CTCF in regulating spliced and non-spliced HBV transcripts, CTCF was silenced in HepG2 cells containing episomal maintained replicating HBV cccDNA-like molecules (called HepG2-HBV-Epi cells) and
viral transcripts in scrambled siRNA control (siScr) or CTCF siRNA (siCTCF) samples analysed by RNA sequencing.

first: Mihaela

last: Dobrica

first: Christy

last: Varghese

first: James

last: Harris

first: Jack

last: Ferguson

first: Andrea

last: Magri

first: Roland

last: Arnold

last: Várnai

first: Joanna

last: Parish

first: Jane

last: McKeating


title: ATR inhibition using gartisertib enhances cell death and synergises with temozolomide and radiation in patient-derived glioblastoma cell lines

city: Callaghan

first: Paul

last: Tooney

state: AUSTRALIA

address: University Drive

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: University of Newcastle, Australia

summary: Glioblastoma is an aggressive and highly invasive disease that often resists treatment. Tumour cells can restrict the DNA-damaging effects of temozolomide (TMZ) and radiation therapy (RT) using the DNA damage response (DDR) mechanism which activates cell cycle arrest and DNA repair pathways. Ataxia-telangiectasia and Rad3-Related protein (ATR) plays a pivotal role in the recognition of DNA damage induced by chemotherapy and radiation and downstream activation of DDR pathways. Furthermore, a growing body of evidence indicates DNA damage and inhibition of ATR can stimulate a proinflammatory response that activates innate immunity against tumour cells. Here, we investigated the change of gene expression of treated glioblastoma cell lines from TMZ+RT and ATR inhibition (using gartisertib (M4344)) combined with TMZ+RT.

overall_design: We treated glioblastoma cell lines (n=12) with DMSO control, TMZ+RT and M4344+TMZ+RT (2x biological replicates) and cells were grown for 4 days before RNA was extracted for downstream gene expression analysis.

first: Mathew

last: Lozinski

first: Nikola

last: Bowden

first: Moira

middle: C

last: Graves

first: Michael

last: Fay

first: Bryan

last: Day

first: Brett

last: Stringer


title: Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver

city: Toronto

first: Diana

last: Nakib

state: ON

address: 101 College Street

country: Canada

institute: University of Toronto

summary: Primary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts. Due to a limited understanding of the underlying pathogenesis of disease, there remains a paucity of treatment options. As such, we sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that outside PSC scar regions, hepatocytes are transitioning to bile duct cells, whereas within the scars, there is an accumulation of immune cells. Of these cells, macrophages that typically contribute to tissue repair were enriched in immunoregulatory genes and were less responsive to stimulation. These cells are likely involved in maintaining hepatic inflammation and could be targeted in novel therapeutic development.

overall_design: scRNA-seq

first: Tallulah

last: Andrews

first: Gary

last: Bader

first: Ian

last: McGilvray

first: Sonya

last: MacParland


title: FE1 lung epithelial cells: Control vs nanoparticle, microparticle, metal chloride exposed

city: Ottawa

first: Sabina

last: Halappanavar

address: 251 Sir Frederick Banting Driveway

institute: Health Canada

overall_design: Purified and extracted RNA from pelleted immortalized mouse lung epithelial cells (FE1) exposed to 0 - 118 ug/mL zinc oxide (ZnO), aluminum oxide (Al2O3), nickel oxide (NiO), and titanium dioxide (TiO2) nanoparticles (NPs) and microparticles (MPs), as well as zinc chloride (ZnCl2), aluminum chloride (AlCl3), and nickel chloride (NiCl2) for 2, 24, and 48 Hrs.

first: Andrey

last: Boyadzhiev

first: Andrew

last: Williams


overall_design: Single cell and single nucleus RNA profiling by high throughput sequencing


title: Gene expression profile at single cell level of skin cells isolated from db/db mice

status: Public on Jan 17 2024

city: Tianjin

first: Chunqiu

last: Zhang

address: NO 94 Weijin Road

institute: Nankai University

summary: The Janus liposozyme robustly eradicates infections and rapidly promotes wound closure and re-epithelialization on diabetic skin wound infected with methicillin-resistant S. aureus (MRSA). We used single cell RNA sequencing(scRNA-seq) to deep analyse local immune homeostasis manipulated by Janus on skin cells obtained from db/db mice .

overall_design: db/db mice were infected with methicillin-resistant S. aureus (MRSA) and then were randomly divided into two groups: (i) PBS as control; (ii) TSeL with light irradiation (TSeL+L). Subsequently, skin tissues were harvested on day15 and further dissociated  into single cells without separating dermis and epidermis. And skin cells were analyzed using scRNA-seq.

first: Tingting

last: Wei

first: Tiezheng

last: Pan

first: Xiuping

last: Peng

first: Song


title: Histone methylation mediated by NSD1 is required for the establishment and maintenance of neuronal identities [WGBS]

first: zhao

last: chen

summary: The formation of the mammalian neocortex during development requires coordinated establishment of functional regions at proper anterior-posterior and medial-lateral positions – area patterning, as well as neocortical layers. Although key transcription factors (TFs) were known to specify and maintain cell fates, mechanisms underlying how TFs are precise expressed and repressed are largely elusive. Here we showed that NSD1, the methyltransferase for histone H3 lysine 36 dimethylation (H3K36me2), controls both areal and layer identities of the neocortex. Nsd1-ablated neocortex showed prominent areal shift of all four primary functional regions and aberrant wiring of major cortico-thalamic-cortical projections. Nsd1 conditional knockout mice displayed defects in spatial memory, motor learning and coordination, reminiscent of patients with the Sotos syndrome carrying NSD1 mutations. Although projection neurons (PN) of neocortical layers were mostly properly produced and positioned upon Nsd1 deletion, post-mitotic PNs could not establish their layer-specific identities. More strikingly, in adult Nsd1 conditional knockout neocortices, superficial-layer PNs progressively mis-expressed markers for deep-layer PNs. Moreover, neocortical PNs ablated with Nsd1 remained immature morphologically and electrophysiologically. Loss of NSD1 in post-mitotic PNs causes genome-wide loss of H3K36me2 and re-distribution of DNA methylation, which accounts for diminished expression of neocortical layer specifiers but ectopic expression of non-neural genes. Our findings revealed that H3K36me2 mediated by NSD1 is required for establishment and maintenance of region- and layer-specific neocortical identities.

overall_design: Whole-genome bisulfite sequencing in somatosensory cortices of 2.5 month old mice.

first: Yue

last: Zheng

first: Chen

last: Zhao

first: Qiulin

last: Song

first: Lichao

last: Xu

first: Bo

first: Xiangfei

last: Kong

first: Shaowen

last: Li

first: Xiang

first: Ying

last: Shen

first: Lenan

last: Zhuang

first: Min

last: Wu

last: Liu

first: Yan

last: Zhou


title: Repurposing amiodarone as a targeted SIRT3 activator that induces autophagic/mitophagic cell death in acute myelocytic leukemia

city: Chengdu

first: Wei

state: 四川省

address: 林荫街8号

institute: Sichuan University

summary: We made a RNAseq in HL-60 cells to measure the changes in global transcript levels in HL-60 cells after amiodarone treatment.

overall_design: HL-60 cells were analyzed by RNAseq in the presence or absence of 10 μM amiodarone for 24 h.

first: Jin

first: Wenke

last: Jin


title: Maresin 1 Repletion Improves Muscle Regeneration After Volumetric Muscle Loss

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

summary: The acute traumatic or surgical loss of skeletal muscle, known as volumetric muscle loss (VML), is a devastating type of injury that results in exacerbated and persistent inflammation followed by fibrosis. The mechanisms that mediate the magnitude and duration of the inflammatory response and ensuing fibrosis after VML remain understudied, and as such, the development of regenerative therapies has been limited. To address this need, we profiled how lipid mediators, which are potent regulators of the immune response after injury, varied with VML injuries that heal or result in fibrosis. We observed that non-healing VML injuries displayed increased pro-inflammatory eicosanoids and a lack of pro-resolving lipid mediators. Treatment of VML with a pro-resolving lipid mediator synthesized from docosahexaenoic acid, called Maresin 1, ameliorated fibrosis through reduction of neutrophils and macrophages and enhanced recovery of muscle strength. These results expand our knowledge of the dysregulated immune response that develops after VML and identify a novel immuno-regenerative therapeutic modality in Maresin 1.

overall_design:
Bilateral 2mm biopsy punch defects were administered to the tibialis anterior muscles of young mice, then treated with maresin 1 or vehicle on days 1, 3, and 5 post injury. At 7 days post injury, mice were humanely euthanized, TAs extracted, pooled according to treatment, digested into single cell suspensions, labeled with 10x genomics cell multiplexing oligos (one per treatment), pooled, FACSed to remove debris and dead cells (7-AAD positive), then analyzed by single cell RNA sequencing.

TA muscles from mice were given a VML injury and treated with either Maresin 1 or Vehicle at 1,3,5 dpi. Muscles were collected at 7 dpi and digested into single cell suspensions and processed for single cell sequencing.

first: Jesus

last: Castor-Macias

first: Jacqueline

last: Larouche

first: Emily

last: Wallace

first: Bonnie

last: Spence

first: Alec

last: Eames

first: Benjamin

last: Yang

first: Carol

last: Davis

first: Susan

middle: V

last: Brooks

first: Krishna

last: Maddipati

first: James

middle: F

last: Markworth


title: A conserved paint box underlies color pattern diversity in Estrildid finches.

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Many animals exhibit typical color patterns that have been linked to key adaptive functions, yet the developmental mechanisms establishing these crucial designs remain unclear. Here, we surveyed color distribution in the plumage across a large number of passerine finches. Despite extreme apparent pattern diversity, we identified a small set of conserved color regions whose combinatory association can explain all observed patterns. We found these domains are instructed by signals from embryonic somites and lateral plate mesoderm, and through profiling and comparative analyses, produced a molecular map marking putative color domains in the developing skin. This revealed cryptic pre-patterning common to differently colored species, uncovering a simple molecular landscape underlying extensive color pattern variation.

overall_design: identification of molecules spatially restricted to presumptive color domains, three dorsal and four ventral regions of the embryonic skin at hh28, in triplicate

first: Magdalena

last: Hidalgo

first: Camille

last: Curantz

first: Nicole

last: Quenech'Du

first: Thanh-Lan

last: Gluckman

first: Julia

last: Neguer

first: Samantha

last: Beck

first: Ammara

last: Mohammad

first: Marie

last: Manceau


title: Histone methylation mediated by NSD1 is required for the establishment and maintenance of neuronal identities [RNA-seq]

first: zhao

last: chen

overall_design: Comparative gene expression profiling analysis of RNA-seq data for somatosensory cortices of 2.5 month old control and Nsd1Nex-cKO mice.

first: Yue

last: Zheng

first: Chen

last: Zhao

first: Qiulin

last: Song

first: Lichao

last: Xu

first: Bo

last: Zhang

first: Xiangfei

last: Kong

first: Shaowen

last: Li

first: Xiang

first: Ying

last: Shen

first: Lenan

last: Zhuang

first: Min

last: Wu

last: Liu

first: Yan

last: Zhou


title: Histone methylation mediated by NSD1 is required for the establishment and maintenance of neuronal identities [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K36me2 in somatosensory cortices of 2.5 month old mice.


title: CRISPR-engineered MLL-AF4 BCP-ALL

city: Stanford

first: Feng

last: Pan

state: CA

address: 265 Campus Drive

department: Pathology

institute: Stanford University School of Medicine

overall_design: Refer to individual Series


title: Quantitative Analysis of iPSC-macrophage differentiated by different system

city: La Jolla

first: Dan

last: Kaufman

state: California

address: 9500 Gilman Dr.

institute: University of California San Diego

summary: We compared transcriptome of iPSC-macrophages differentiated by adherence and spinner systems to determine if there is discrapency between the systems

overall_design: mRNA profiles of 2 different iPSC-macrophages types differentiated by adherence and spinner systems

first: Meng-Wei

last: Ko

first: Yuelin

first: Manuel

last: Fierro


title: Interrogating the potency of primordial germ cells by injection into early mouse embryos

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: Primordial germ cells (PGCs) are the earliest precursors of the gametes. During normal development PGCs only give rise to oocytes or spermatozoa. However, PGCs can acquire pluripotency in vitro by forming embryonic germ (EG) cells and in vivo during teratocarcinogenesis. Classic embryological experiments directly assessed the   potency of PGCs by injection into the pre-implantation embryo. As no contribution to embryos or adult mice was observed, PGCs have been described as unipotent. Here we demonstrate that PGCs injected into 8-cell embryos can initially survive, divide and contribute to the developing inner cell mass. Apoptosis-deficient PGCs exhibit improved survival in isolated epiblasts, and can form naïve pluripotent embryonic stem cell lines. However, contribution to the post-implantation embryo is limited, with no functional incorporation observed.  In contrast, PGC-like cells show extensive contribution to mid-gestation chimaeras. We thus propose that PGC formation in vivo establishes a latent form of pluripotency that prevents chimaera contribution.

overall_design: Five primordial germ cells- embryonic stem cells (PGC-ESC) Bax knockout (KO) cell lines and three PGC-ESC Puma/Noxa double knockout (DKO) cell lines. As controls we included two previously derived BaxKO ESC lines, one Bax heterozygous ESC line and four matched wildtype ESC lines derived simultaneously from the host embryos. In addition, for comparison we included epiblast-like cells (EpiLCs) derived in vitro from 2 host ESC lines and 3 PGC-ESC DKO lines.

first: Lessly

last: Sepulveda-Rincon

first: Yi-Fang

last: Wang

first: Chad

last: Whilding

first: Obah

last: Ojarikre

first: Nabuhiko

last: Hamazaki

first: Katsuhiko

last: Hayashi

first: James

last: Turner

first: Harry

middle: G

last: Leitch


title: Multiregional sampling of primary glioblastoma specimens

city: Calgary

first: Marco

last: Gallo

state: AB

address: 2500 University Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

summary: Glioblastoma (GBM), the most common malignant tumor originating in the brain remains incurable with few treatment advances despite decades of investigation. Treatment failure is often attributed to intratumoral heterogeneity, which fosters tumor evolution and selection of resistant clones. However, intratumoral heterogeneity and tumor evolution remain poorly understood in GBM as studies are typically based on single tissue biopsies and lack spatial context. Here, we have utilized pre-operative MRI scans and intra-operative 3-D surgical neuronavigation for 10 primary IDH-WT GBM patients to acquire 103 tissue samples that represent maximal tumor diversity and are mapped by 3-D spatial coordinates. We combine insights from deconvolution of GBM transcriptomes and chromatin landscapes with single-cell analysis to assess intratumoral heterogeneity of each program at the cellular level and to distinguish neuronal, glial, and immune programs aberrantly active in tumor cells from their counterparts in normal cells. Collectively, these data provide unprecedented insight into GBM intratumoral heterogeneity and evolution from single-cell to whole-tumor 3D spatial resolution, redefining current understanding and providing a rich resource of targets for therapeutic investigation.

overall_design:
Single-nucleus ATAC-sequencing of multiregionally profiled glioblastoma specimens
Raw data not available due to patient privacy concerns, and has been submitted to EGA instead.

first: Katrina

last: Ellestad

first: Ana

last: Nikolic

first: Radhika

last: Mathur

first: Joseph

last: Costello


title: Nucleos(t)ide analogs for hepatitis B virus infection differentially regulate the growth factor signaling in hepatocytes

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

summary: Recent clinical studies have suggested that the risk of developing hepatocellular carcinoma might be lower in chronic hepatitis B (CHB) patients receiving tenofovir disoproxil fumarate (TDF) than in patients receiving entecavir (ETV), although there is no difference in biochemical and virological remission between two drugs.  The effects of nucleoside analogs (NsAs; lamivudine and ETV) or nucleotide analogs (NtAs; adefovir disoproxil [ADV], TDF, and tenofovir alafenamide [TAF]) on cell growth and the expression of growth signaling molecules were investigated. The tumor inhibitory effects of NsAs or NtAs were evaluated using a mouse xenograft model, and protein phosphorylation profiles were investigated.

overall_design: 1,373 signal transduction proteins with a glutathione S-transferase-tag were synthesized and loaded onto a glutathione-coated glass slide. Every protein was spotted (approximately 500 nL per spot) six times (n = 6) per slide, while ensuring they did not denature or dry. During spotting, humidity was maintained at 40%–60%, and the wetness of each drop was confirmed by microscopic observation of the liquid droplets. Cell lysates of 100 μg total protein were applied to the array with additional ATP at 30°C for 3 h. After termination of the kinase reaction, the array was washed with Tris-buffered saline containing 0.05% Tween 20 and stained with a 4G10 phosphorylated protein-specific antibody (Merck, #05-1050) and a secondary fluorescein-conjugated antibody (Thermo, #A21235) to detect the phosphorylated tyrosine residues. Signal data were averaged (n=6), filtered and normalized by BRB-ArrayTools (https://brb.nci.nih.gov/BRB-ArrayTools).

first: Ryogo

last: Shimizu

first: Kazuhisa

last: Murai

first: Harumi

last: Kagiwada

first: Katsuhisa

last: Horimoto


title: RNA pol II assembly affects ncRNA expression

city: Jaen

first: Ana I.

last: Garrido-Godino

address: Paraje Las Lagunillas s/n

country: Spain

institute: University of Jaen

summary: Pervasive transcription of RNA pol II has been addressed in several organisms. In S. cerevisiae, ncRNAs derived from pervasive transcription of RNA pol II have been further classified based on their sensitivity to different decay pathways, transcription termination pathways, or specific conditions for their expression. In this study, we demonstrate that altering RNA pol II assembly by using an rpb1 mutant, leads to a general drop in ncRNA transcription. We provide evidences that defects in RNA pol II assembly lead to a reduction in cryptic transcription, mainly of CUTs, a feature which is not influenced by the levels of its bidirectional open reading frame (ORF).  This feature is not dependent on a defect of exosome function. We propose that a defect in transcription termination could account for the reduction in ncRNAs in the rpb1 mutant.

overall_design: Two independent biological replicates of each Saccharomyces cerevisiae strain were cultured in YPD liquid medium at 30ºC  until OD600 of about 0.8. After RNA extraction, sequencing cDNA libraries were performed using the QuantSeq 3' mRNA-Seq Library Prep Kit form Illumina following the manufacturer instructions.

middle: I

first: Ishaan

last: Gupta

first: Vicent

last: Pelechano

first: Francisco

last: Navarro


title: Age-related noncanonical TRMT6–TRMT61A signaling impairs hematopoietic stem cells

city: Hangzhou

first: Xiaoyu

last: Li

state: Zhejiang

address: 866 Yuhangtang Road

department: SCHOOL OF BASIC MEDICAL SCIENCES

institute: Zhejiang University

summary: We reported the tRNA-m1A sequencing results performed in young and aged hematopoietic stem and progenitor cells. Our results defined aging-associated alterations of tRF in hematopoietic stem and progenitor cells and identifed a subset of tRF as hallmark of HSC aging.RNA-seq data analysis of WT v.s. Trmt6/61a-TG hematopoietic stem cell (lineage-, c-kit+ Sca-1+ CD135-, CD34-), the two population of hematopoietic stem cell (HSC) were purified from the bone marrow of WT and Trmt6/61a-TG mice, revealed that differnent expression of WT v.s. Trmt6/61a-TG hematopoietic stem cell.Results provide insight into the role of TRMT6/61A complex in HSC.

overall_design: Total 8 m1A-seq samples were analyzed.There are two treatment (AlkB treatment and control) and two age states (Old and Young), and each state are two replications.The AlkB-treated sequencing samples were also utilized for the analysis of tRFs. Total 4 RNA-seq samples were analyzed.There are two genotypes(WT and Trmt6/61a-TG),and each state are two replications.

first: Jianwei

last: Wang

first: Chengqi

last: Yi

first: Hanqing

last: He

first: Xiaoting

last: Zhang


title: Lefamulin targets ILF3 to overcome targeted therapy resistance in hepatocellular carcinoma

city: nanjing

first: ying

last: zheng

address: 639 Longmian Avenue, Jiangning District

institute: China pharmaceutical university

summary: Acquired resistance represents a critical clinical challenge to molecular targeted therapies such as tyrosine kinase inhibitors (TKIs) treatment in hepatocellular carcinoma (HCC). Therefore, it is urgent to explore new mechanisms and therapeutics that can overcome or delay resistance. Here, we identified a U.S. Food and Drug Administration (FDA)-approved pleuromutilin antibiotic that overcomes sorafenib resistance in HCC cell lines, cell line-derived xenograft (CDX) and hydrodynamic injection mouse models. We demonstrated that lefamulin targets and binds Interleukin Enhancer-binding Factor 3 (ILF3) to inhibit sorafenib-induced mitochondrial ribosomal protein L12 (MRPL12) upregulation. Mechanistically, lefamulin directly binds to Ala-99 of ILF3 and interferes with acetyltransferase general control non-depressible 5 (GCN5) and CREB binding protein (CBP) mediated acetylation of Lys-100, which disrupting the ILF3-mediated transcription of MRPL12 and subsequent mitochondrial biogenesis. Clinical data further confirmed that high ILF3 or MRPL12 expression was associated with poor survival and targeted therapy efficacy in HCC. Conclusively, our findings suggest that ILF3 is a potential therapeutic target for overcoming resistance to TKIs, and lefamulin may be a novel combination therapy strategy for HCC treatment with sorafenib and regorafenib.

overall_design: To investigate how lefamulin overcomes sorafenib resistance in HCC, we conducted RNA sequencing (RNA-seq) on the HepG2 cells treated with DMSO or lefamulin

first: Ying

last: Zheng

first: Shengtao

last: Ye

first: Shiyu

last: Huang

first: Yang

last: Cheng

first: Yanqiu

first: Yingrong

last: Leng

first: Mengmeng

first: Enyi

last: Wu

first: Junxin

last: Chen

first: Lingyi

last: Kong

first: Hao


title: ABCA7 deficiency causes neuronal dysregulation by altering mitochondrial lipid metabolism

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: ABCA7 loss-of-function variants are associated with increased risk of Alzheimer’s disease (AD).  Using ABCA7 knockout human iPSC models generated with CRISPR/Cas9, we investigated the impacts of ABCA7 deficiency on neuronal metabolism and function. Lipidomics revealed that mitochondria-related phospholipids, such as phosphatidylglycerol and cardiolipin were reduced in the ABCA7-deficient iPSC-derived cortical organoids. Consistently, ABCA7 deficiency induced alterations of mitochondrial morphology accompanied by reduced ATP synthase activity and exacerbated oxidative damage in the organoids.

overall_design: In order to investigate the ABCA7 loss of function in human cells, we generated isogenic ABCA7  knockout iPSC lines by using CRISPR/Cas9. The iPSCs were differentiated into cortical organoids and analyzed 60 days after the differentiation.

first: Keiji

last: Kawatani

first: Takahisa

last: Kanekiyo


title: Analysis of Lsm protein-mediated regulation in the haloarchaeon Haloferax mediterranei

city: Sant Vicent del Raspeig

first: María José

middle: Antonio

last: Bonete

state: Alicante

address: Carretera San Vicente del Raspeig s/n

department: Agroquímica y Bioquímica

institute: Universidad de Alicante

summary: The transcriptional analysis of the HM26-ΔSm1 deletion mutant versus the parental strain HM26 was performed under nitrogen and carbon starvation for 120 h. These contrasts allow us to analyze the effect that the deletion of the Sm1 motif has under these conditions and, therefore, allow us to know which genes are regulated by the Lsm protein under the conditions analyzed.

overall_design: Four-condition experiments with four biological replicates, combined in a loop design.

first: G

last: Payá

first: V

last: Bautista

first: S

last: Pastor-Soler

first: M

last: Camacho

first: J

last: Esclapez

middle: J


title: Differences in gene expression in CRPC cell line C4-2 before and after Cyclin-Dependent Kinase 12 (CDK12) knockdown using CRISPR-Cas9

city: Shenzhen

first: Haozhe

last: Zhang

state: Guangdong

address: No.1088 Xueyuan Avenue

department: Department of biochemistry

institute: Southern University of Science and Technology

summary: CDK12 is a transcription-related CDK that is commonly mutated in different types of cancers. In prostate cancer, defective CDK12 has been identified as a new subtype with a worse prognosis and widespread drug resistance. CRPC is a malignant stage of recurrent prostate cancer following treatment, with a higher frequency of CDK12 mutations compared to early-stage prostate cancer. To investigate the impact of CDK12 defects on the overall gene expression in CRPC cells, we used CRISPR-Cas9 technology to generate CDK12 knockout and control C4-2 cell lines, followed by high-throughput transcriptome sequencing (RNA-seq). Our results demonstrate that CDK12 defects affect the expression of numerous genes in CRPC cells, providing insights into the regulatory role of CDK12 in prostate cancer development.

overall_design: To investigate the effects of CDK12 deficiency on CRPC cells. We constructed CDK12 knockout and control cell lines using CRISPR-Cas9 technology. Next, we extracted total RNA from the cells and performed high-throughput transcriptome sequencing. We then performed gene expression profiling analysis using data obtained from RNA-seq and comparative gene expression profiling analysis of RNA-seg data for C4-2 VEC cell and its KO derivatives (VEC, CDK12KO)—three replicates per sample.

first: Hailiang

last: Hu

first: Yu

last: Yin


title: Targeting pyroptosis with nanoparticles to alleviate neuroinflammatory for preventing secondary damage following traumatic brain injury

first: Hongmei

last: Liu

address: No. 1088, Xueyuan Avenue

department: Department of Biomedical Engineering

summary: Post-traumatic neuroinflammation is a key driver of secondary injury after traumatic brain injury (TBI). Pyroptosis, a proinflammatory form of programmed cell death, considerably activates strong neuroinflammation and amplifies the inflammatory response by releasing inflammatory contents. Therefore, treatments targeting pyroptosis may beneficially effects for the treatment of secondary brain damage after TBI. Herein, a cysteine-alanine-glutamine-lysine (CAQK) peptide-modified β-lactoglobulin (β-LG) nanoparticle was constructed to deliver disulfiram (DSF), C-β-LG/DSF, to inhibit pyroptosis and decrease neuroinflammation, thereby preventing TBI-induced secondary injury. In the post-TBI mice model, C-β-LG/DSF selectively targets the injured brain, increases DSF accumulation, and extends the time of the systemic circulation of DSF. C-β-LG/DSF can alleviate brain edema and inflammatory response, inhibit secondary brain injury, promote learning, and improve memory recovery in mice after trauma. Therefore, this study likely provided a new approach for reducing the secondary spread of TBI.

overall_design: The brain tissues were collected from the brain injury (or the same anatomical site) in the Sham group (only the skull was drilled open, the dura was opened, and no brain tissue was damaged), the TBI group (the brain injury model of heavy fall), and the C-β-LG/DSF group (the tail vein injection of C-β-LG/DSF after TBI), and the brain tissues were collected for high-throughput RNA-seq. The expression of pyroptosis and inflammation-related genes in each group was analyzed.

first: Xuefeng

first: Xuyang

last: Huang

first: Diancheng

last: Hang

first: Jiaqi

last: Jin

first: Shanshan

last: Li

first: Yufu

last: Zhu


title: CCDC88B interacts with RASAL3 and ARHGEF2 to regulate dendritic cell function in neuroinflammation and colitis

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

institute: McGill University

summary: CCDC88B is a risk factor for several chronic inflammatory diseases in humans and its inactivation causes a migratory defect in DCs in mice. CCDC88B belongs to a family of cytoskeleton-associate scaffold proteins that feature protein:protein interaction domains. Here, we identified the Rho/Rac Guanine Nucleotide Exchange Factor 2 (ARHGEF2) and the RAS Protein Activator Like 3 (RASAL3) as CCDC88B physical and functional interactors. Mice defective in Arhgef2 or Rasal3 show dampene  neuroinflammation, and display altered cellular response and susceptibility to colitis; ARHGEF2 maps t a human Chromosome 1 locus associated with susceptibility to IBD. Arhgef2 and Rasal3 mutant DCs show altered migration and motility in vitro, causing either reduced (Arhgef2) or enhanced (Rasal3) migratory properties. The CCDC88B/RASAL3/ARHGEF2 complex appears to regulate DCs migration by modulating activation of RHOA, with ARHGEF2 and RASAL3 acting in opposite regulatory fashions, providing a molecular mechanism for the involvement of these proteins in DCs immune functions.

overall_design: Single cell RNA sequencing of immune cells (CD45+) cell sorted from dissociated C57BL/6 mouse colons.

first: Philippe

last: Gros

first: Nassima

last: Fodil

first: Thiviya

last: Jeyakumar


title: Integrative analysis of the lipidome and transcriptome in Chinese Kazakh patients with esophageal squamous cell carcinoma

city: Urumqi

first: Qingchao

last: Sun

state: Xinshi District

address: 137 Liyushan South Road

institute: The First Affiliated Hospital of Xinjiang Medical University

summary: Esophageal squamous cell carcinoma (ESCC) is characterized as a metabolic disorder characterized by lipid metabolic reprogramming. To investigate the regional characteristics of ESCC patients in Xinjiang Province, China, and lipid metabolism, in this study, we described the characteristics of the serum lipid composition in Kazakh ESCC patients by performing an integrated analysis of the transcriptome and lipidomic data. Serum samples from 30 Kazakh ESCC patients and 30 healthy individuals were subjected to targeted lipid metabolomics analysis via UPLC‒MS/MS, while 3 tumor samples and matched adjacent normal tissues from 30 ESCC patients were subjected to transcriptome analysis. Compared with those in the healthy group, we observed obvious changes in the serum lipid subclass content, chain length and unsaturation in the ESCC patients. Integrated lipidomic and transcriptomic analyses revealed that unsaturated fatty acid biosynthesis, fatty acid metabolism, lipid degradation, cholesterol metabolism and the AMPK signaling pathway were enriched in tumor tissues. In addition, RT–qPCR results demonstrated that genes closely related to these pathways were differentially expressed between the ESCC group and the healthy control group. Considering the key role of AMPK in lipid metabolism, we conducted a targeted lipid metabolomics analysis on AMPK-knockdown esophageal cancer cells by UPLC‒MS/MS. These findings suggested that AMPK might be correlated with lipid metabolism in Kazakh ESCC patients, identifying potential therapeutic targets of AMPK and other lipid metabolism-related markers against the progression of ESCC.

overall_design: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

first: Ruixue

first: Liwei

first: Haiping


title: The transcriptional and translational landscape of HCoV-OC43 infection

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

summary: The coronavirus HCoV-OC43 circulates continuously in the human population and is a frequent cause of the common cold. Here, we generated a high-resolution atlas of the transcriptional and translational landscape of OC43 at various timepoints following infection of human lung fibroblasts. Using ribosome profiling, we quantified the relative expression of the canonical open reading frames (ORFs) and identified several unannotated ORFs, including short upstream ORFs and a putative ORF nested inside the M gene. In parallel, we analyzed the cellular response to infection. Endoplasmic reticulum (ER) stress response genes are transcriptionally and translationally induced, but conventional antiviral genes remain mostly suppressed. At the same time, we observed widespread aberrant translation across cellular transcripts, including over 3′UTRs and of noncoding transcripts normally targeted by the nonsense mediated decay pathway. Taken together, our work provides a genomic resource for further study of OC43 and the cellular response to infection.

overall_design: Human lung fibroblast (MRC5) cells were infected with the coronavirus OC43, and samples were collected for transcriptomic (RNAseq) and translatomic (Riboseq) analysis at various timepoints following infection.


title: Analyses of potential miR-410 target genes

city: Augusta

first: Sang Ho

last: Kwon

state: Georgia

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta Univeristy

summary: We used microarray analyses of miR-CON vs miR-410 overepxressing PC3 and C42B cells to identify potential miR-410 targtes in these prostate cancer cell lines

overall_design: Stable cell lines expressing miR-410/miR-Con were grown to logarithmic phase, RNA was extracted followed by hybridization on Affymterix microarrays

first: Sharanjot

last: Saini


title: Hsa_circ_0081065 exacerbates OSAHS-induced EndMT via regulating miR-665/HIF-1α signal axis and HIF-1α nuclear translocation

city: Jinan

first: guanghao

last: zhang

address: NO.247 Beiyuan street

institute: The second hospital of Shandong University

summary: CircRNA is widely involved in various physiological and pathological biological processes. However, the function of circRNAs in obstructive sleep apnea hypopnea syndrome (OSAHS) has not been fully elucidated. Therefore, this study aims to investigate the key circRNA in OSAHS and clarify the molecular mechanism of it in OSAHS

overall_design: The differentially expressed circRNAs was identified by transcriptome sequencing analysis in intermittent hypoxia(IH) model. GO and KEGG enrichment analysis was performed to the differentially expressed circRNAs. Circular characteristics of hsa_circ_0081065 in HUVECs was detected by RT-qPCR. Sublocalization of hsa_circ_0081065 was examined by FISH. Function of hsa_circ_0081065 on endothelial to mesenchymal transition (EndMT) was estimated by detecting the expression of EndMT related markers. RNA-pull down, RIP, EMSA,dual-luciferase reporter assay and immunofluorescence staining was used to detect the relationship between hsa_circ_0081065, miR-665 and HIF-1α

first: Guanghao

last: Zhang


title: Integrated comparative transcriptome and physiological analysis reveals the mechanisms underlying genotype variations in ammonium tolerance

city: Changsha

first: Haifei

last: Chen

address: nongda road

institute: Hunan Agricultural University

summary: Several mechanisms have been proposed to explain NH4+ toxicity. However, the core information about the biochemical regulation of plants in response to ammonium toxicity is still lacking. In this study, the tissue content of NH4+was found the main cause for NH4+ toxicity, and the cellular threshold was 50 μg/g. Furthermore, ammonium led to the reprogramming of the transcriptional profile, as genes related to trehalose-6-phosphate and zeatin biosynthesis were downregulated, whereas genes related to nitrogen metabolism, camalexin, stilbenoid and phenylpropanoid biosynthesis were upregulated. Further analysis revealed that a large number of genes, which enriched in phenylpropanoid and stilbenoid biosynthesis, were uniquely upregulated in the NH4+- tolerant ecotype Or-1. These results suggested that the NH4+-tolerant ecotype showed a more intense response to ammonium by activating defense processes and pathways. Importantly, the tolerant ecotype had a higher 15NH4+ uptake and NPE, but lower NH4+, indicating the tolerant ecotype maintained a low NH4+ level, mainly by promoting ammonium assimilation rather than inhibiting NH4+ uptake. The carbon and nitrogen metabolism analysis revealed that the tolerant ecotype had a stronger carbon skeleton (2-OG) production capacity with higher levels of hexokinase (HK), pyruvate kinase (PK), and GDH activity to assimilate free NH4+. Taken together, the results revealed the threshold for ammonium toxicity and the core mechanisms utilized by plants in response to ammonium, which are consequently of ecological and agricultural importance

overall_design:
The seedlings were grown in a nitrate nutrient solution for 5 d, then transferred to 1 mM Ca(NO3)2 or 1 mM (NH4)2SO4 for 1 d. The total RNA was then extracted from the roots of the NH4+-tolerant and -sensitive ecotypes.

Submitter states that missing raw files are due to file loss.


title: Single-cell RNA-sequencing of umbilical cord blood reveals impaired fetal immune homeostasis by gestational diabetes mellitus

first: Yan

address: Ren Min Zhog street

institute: The Second Xiangya Hospital of Central South University

summary: Gestational diabetes mellitus (GDM), the most prevalent metabolic disorder during pregnancy, has long-term risks of metabolic diseases that might persist in adulthood. However, the underlying mechanisms remain unclear. Here, we profiled 78,767 cord blood mononuclear cells (CBMCs) from GDM and healthy mothers’ fetuses by single-cell RNA sequencing (scRNA-seq).

overall_design: Single-cell suspensions from cord blood mononuclear cell of 4 GDM mothers and 3 healthy mothers were prepared and single cell RNA-seq libraries were generated using 3' V2 chemistry kit on Chromium Single cell controller (10x Genomics).

first: Xia

first: Min

last: Yin

first: Xinyu


title: Transcriptome analysis of adenomyosis eutopic endometrium reveals molecular mechanisms involved in adenomyosis-related implantation failure and pregnancy disorders

city: Valencia

first: Hortensia

last: Ferrero

state: Valencia

address: Avenida Fernando Abril Martorell 106, Torre A

department: Reproductive Medicine

institute: Instituto de Investigación Sanitaria La Fe / Fundación IVI

summary: Women with adenomyosis are characterized by having defective decidualization, impaired endometrial receptivity and/or embryo-maternal communication, and implantation failure. However, the molecular mechanisms underlying adenomyosis-related infertility remain unknown, mainly because of the restricted accessibility and the difficult preservation of endometrial tissue in vitro. We have recently shown that adenomyosis patient-derived endometrial organoids, maintain disease-specific features while differentiated into mid-secretory and gestational endometrial phase, overcoming these research barriers and providing a robust platform to study adenomyosis pathogenesis and the associated molecular dysregulation related to implantation and pregnancy disorders. For this reason, we aim to characterize the dysregulated mechanisms in the mid-secretory and gestational endometrium of patients with adenomyosis by RNA-sequencing. Endometrial organoids were derived from endometrial biopsies collected in the proliferative phase of women with adenomyosis (ADENO) or healthy oocyte donors (CONTROL) (n=15/group) and differentiated into mid-secretory (-SECorg) and gestational (-GESTorg) phases in vitro. Following RNA-sequencing, the significantly differentially expressed genes (DEGs) (FDR<0.05) were identified, and the top 20 were selected for subsequent functional enrichment analysis and QIAGEN Ingenuity Pathway Analysis (IPA). Statistical differences in gene expression were evaluated with the Student’s t-test or Wilcoxon test. We identified 1,430 DEGs in ADENO-SECorg and 1,999 DEGs in ADENO-GESTorg. In ADENO-SECorg, upregulated genes included OLFM1, FXYD5, and RUNX2, which are involved in impaired endometrial receptivity and implantation failure, while downregulated genes included RRM2, SOSTDC1, and CHAC2 implicated in recurrent implantation failure. In ADENO-GESTorg, upregulated CXCL14 and CYP24A1 and downregulated PGR were related to pregnancy loss. IPA predicted a significant inhibition of ID1 signaling, histamine degradation, and activation of HMGB1 and Senescence pathways, which are related to implantation failure. Alternatively, IPA predicted an inhibition of D-myo-inositol biosynthesis and VEGF signaling, and upregulation of Rho pathway, which are related to pregnancy loss and preeclampsia. In conclusion, Identifying dysregulated molecular mechanisms in mid-secretory and gestational endometrium of adenomyosis women contributes to the understanding of adenomyosis-related implantation failure and/or pregnancy disorders revealing potential therapeutic targets. Following experimental validation of our transcriptomic and in silico findings, our differentiated adenomyosis patient-derived organoids have the potential to provide a reliable platform for drug discovery, development, and personalized drug screening for affected patients.

overall_design: To investigate implantation and early pregnancy complications related with adenomyosis, this study uses next-generation sequencing and compares the differential gene expression profiles of control endometrial organoids and adenomyosis endometrial organoids, differentiated into mid-secretory and gestational endometrial phase.

first: Elena

last: Juárez-Barber

first: Ana

last: Corachán

first: Maria

last: Carbajo-García

first: Amparo

last: Faus

first: Carmen

last: Vidal

first: Juan

last: Giles

first: Antonio

last: Pellicer

first: Irene

last: Cervelló


title: Lefamulin targets ILF3 to overcome targeted therapy resistance in hepatocellular carcinoma []

first: ying

last: zheng

overall_design: To investigate how lefamulin overcomes sorafenib resistance in HCC, we conducted RNA sequencing (RNA-seq) on the HepG2-derived xenografts of vehicle control, sorafenib, lefamulin, and the combination treated Balb/c nude mice

first: Ying

last: Zheng

first: Shengtao

last: Ye

first: Shiyu

last: Huang

first: Yang

last: Cheng

first: Yanqiu

first: Yingrong

last: Leng

first: Mengmeng

last: He

first: Enyi

last: Wu

first: Junxin

first: Lingyi

last: Kong

first: Hao


title: Gene expression in occlusive vein grafts following CABG of human

city: Tianjin

first: Xiankun

last: Liu

address: South  Taierzhuang road num 261

institute: Tianjin Chest Hospital

summary: To further understand the mechanism approach to occlusive vein grafts, we have employed RNA-seq to identify key genes in occlusive venin grafts following CABG in human. The occluded vein graft and intraoperative spare great saphenous vein of patients undergoing clinical re-coronary artery bypass grafting were obtained for RNA-seq.  The sequencing results were cleaned and bioinformatics annlysis was conducted by using WGCNA and a variety of online databases and software. The key genes or proteins affecting the occurrence of vein graft restenosis were screened out(ITGB2), and the expression level of the target genes or proteins was verified by real-time PCR and Western blot. And to further learn the effect of ITGB2 in human primary venous smooth muscle cells, ITGB2 gene was silenced by SiRNA. The effect of ITGB2 silencing on proliferation, migration and invasion of venous smooth muscle cells after PDGF-BB-stimulation were detected by Edu assay, scrathch experiment and transwell experiment. And Edu assay showed that ITGB2 silencing could inhibit the proliferation of PDGF-BB sitmulated smooth muscle cells. Scratch assay showed that ITGB2 silencing inhibited the migration of PDGF-BB stimulated smooth muscle cells. Transwell assay showed that ITGB2 silencing significantly inhibited the invasion of PDGF-BB stimulated smooth muscle cells. It is indicated that ITGB2 was the key gene in vein graft restenosis,and may be the potential treatment target in restenosis patients.

overall_design: The occluded vein graft(O) and intraoperative spare great saphenous vein(C) of three patients undergoing clinical re-coronary artery bypass grafting were obtained. The expression of mRNA was obtained in tissues.

first: Yunpeng

last: Bai

first: Zhigang

last: Guo

first: Lianqun

last: Wang


title: Reconstructing the gene regulatory network that shaped the evolution of larval sensory structure with a long ciliary tuft in Cnidaria.

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

institute: Marine Biological Association of the UK

summary: Cnidarians are the only non-bilaterian group to evolve ciliated larvae with an apical sensory organ integrated with neurons, possibly homologous to the bilaterians. Within cnidarians, an apical organ with a ciliary tuft is identified only in sea anemones. Whether this apical tuft has evolved independently in anthozoans or alternatively originated in the eumetazoans and was lost independently in specific groups of cnidarians and bilaterians is uncertain.

sample_organism:
Aurelia aurita
Acropora millepora
Nematostella vectensis
Acropora tenuis

overall_design: Here, we generated transcriptomes of the apical domain during the planula stage of four species representing three key groups of cnidarians: Aurelia aurita (medusozoan Scyphozoa), Nematostella vectensis (Actiniaria), and Acropora millepora & Acropora tenuis (Scleractinia). Using an ortholog-analysis approach, we revealed the active and dynamic anteroposterior gene regulatory network in all three cnidarian groups.

first: Vengamanaidu

last: Modepalli

first: Eleanor

last: Gilbert


title: Interconnected lineage trajectories link conventional and NK-like exhausted CD8+ T cells beneficial in T1D

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

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

overall_design: Refer to individual Series


title: Epigenomic features and potential functions of PEG and PDS favorable DNA G-quadruplexes in rice

city: Nanjing

first: huang

middle: ran

last: ran

address: weigang 1

institute: Nanjing Agricultural College

summary: We provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology

first: Wenli

last: Zhang

first: Ranran

first: Yilong

last: Feng


title: Early Involvement of Peripherally Derived Monocytes in Inflammation in an NMO-Like Mouse Model

city: Seouol

first: Moonhang

last: Kim

state: Seoul

address: 71, Daehak-ro, Jongno-gu, Seoul, Korea

country: South Korea

institute: Biomedical Research Institute


title: Single cell multi-omics analysis of chronic myeloid leukemia links cellular heterogeneity to therapy response

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

institute: BMC

summary: The advent of tyrosine kinase inhibitors (TKIs) as treatment of Chronic Myeloid Leukemia (CML) is a paradigm in molecularly targeted cancer therapy. Nonetheless, TKI insensitive leukemia stem cells (LSCs) persist in most patients, even after years of treatment. Here, we used cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to generate high-resolution single cell multiomics maps from CML patients stratified according to molecular response (BCR-ABL IS %) following 12 months of TKI therapy. Simultaneous measurement of global gene expression profiles together with >40 surface markers from the same cells revealed that each patient harbored a unique composition of stem and progenitor cells at diagnosis demonstrating that cellular heterogeneity is a hallmark of CML. The patients with treatment failure at 12 months of therapy had markedly higher abundance of molecularly defined primitive cells at diagnosis compared to the optimal responders. The multi-modal feature landscape enabled visualization of the primitive fraction as a mix of Lin-CD34+38-/low BCR-ABL1+ LSCs and BCR-ABL1- HSCs in variable ratio across patients and guided their prospective isolation by a combination of CD26 and CD35 cell surface markers.

overall_design:
We performed CITE-seq on two FACS sorted cell populations (Lin-CD34+, Lin-CD34+CD38-) from nine CML bone marrow samples from patients with chronic phase CML at diagnosis.
NOTE FROM SUBMITTER: The data comes from living human subjects which is why we cannot provide the raw sequences. This is to be complaint with the GDPR that operates in the EU from which this data comes.

first: Rebecca

last: Warfvinge

first: Göran

last: Karlsson


title: Early Involvement of Peripherally Derived Monocytes in Inflammation in an NMO-Like Mouse Model [Monocytes]

summary: Neuromyelitis optica (NMO) is an autoimmune inflammatory disease that primarily affects the spinal cord and optic nerves in the central nervous system (CNS). It is characterized by the presence of immunoglobulin G (IgG) antibodies against aquaporin 4, a protein found in astrocytes (known as NMO-IgG). Monocytes/macrophages and microglia accumulate at the active injury sites and contribute to the disease process. However, it is unclear whether these active cells originate from circulating monocytes/macrophages or resident microglia. Recent studies have investigated the role of microglia/macrophages in multiple sclerosis (MS) using specific microglial markers, such as P2ry12 and Tmem119, and have shown that active cells are derived from microglia. In contrast, the function of monocyte/macrophages and microglia in NMO has not been extensively studied. Therefore, this study aims to analyze the functions of monocytes/macrophages and microglia using microglial markers (P2ry12 and Tmem119) in an NMO-like mouse model and evaluate their role in the pathophysiology of NMO.

overall_design: Cells were labeled with CD45, CD11b, P2ry12, Ly6C and Ly6G, and sorted CD45+CD11b+P2ry12-Ly6C+Ly6G- cells for monocytes

first: SungMin