title: Single cell, multiomic analysis of SIV specific CD8 T cells from multiple anatomical sites

first: Jennifer

last: Simpson

state: MD

address: 4 Center Drive

institute: NIAID

summary: CD8+ T cells contribute to the antiviral response in simian immunodeficiency virus (SIV) infection in nonhuman primates subsequent to recognition of viral epitopes via the T cell receptor (TCR). In previous studies, we examined the TCR repertoire of CD8+ T cells specific for a single SIV immunodominant epitope, Gag-CM9 (CTPYDINQM), throughout SIV infection. We identified tissue specific TCR sequences and TCRs shared by multiple anatomical sites. We now sought to evaluate if the tissue localization or TCR sequence of a CM9 specific CD8+ T cell corresponds with a transcriptional phenotype. CM9 specific CD8+ T cells were sorted from blood, lymph nodes, spleen, and liver from SIV infected rhesus macaques. The cells were processed through a single cell sequencing protocol, creating a TCR amplified library and an RNA gene expression library for each cell. Gene Set Enrichment Analysis (GSEA) revealed no distinct transcriptional profiles for CM9 specific CD8+ T cells between different anatomical sites and between cells with shared or tissue specific TCRs. Similarly, no clear transcriptional profiles were associated with public clonotypes. CM9 specific CD8+ T cells from posttreatment controllers did exhibit enrichment of select pathways compared to non-controllers. These data suggest that, while antigen specific CD8+ T cells from non-controllers exhibit largely similar transcriptional profiles, altered transcription in antigen specific CD8+ T cells from post-treatment controllers may associate with viral control.

overall_design: We sorted antigen specific CD8 T cells from blood and tissues from chronically infected rhesus macaques. We then completed scRNA and scTCR seq.

first: Jen

first: Paul

last: Schaughency

first: Jason

last: Brenchley


title: Gene expression data from 1 year old SAMP8 mouse brain cortex after 5 mg/kg daily oral administration of TCQA for 1 month

status: Public on Jun 24 2024

city: Tsukuba

first: Yu Jia

last: Chen

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary:
Gene expression profiling study of cognitive-enhancing effect of TCQA in the senescence-accelerated mouse prone 8 (SAMP8) model of aging and Alzheimer’s disease
We used microarrays to detail the global gene expression underlying the mechanism of TCQA in SAMP8 mice brains

overall_design: According to the manufacturer's guide, the RNA was extracted using Isogen kit (Nip-pon Gene Co. Ltd., Japan). Then, RNA quantity and quality were determined using the NanoDrop 2000 spectrophotometer (ThermoScientific, USA). DNA microarray analysis was conducted on control and TCQA-treated SAMP8 mouse brain cortex samples using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer's instructions. In brief, complementary DNA (cDNA) was synthesized from 100 ng of RNA solutions. cRNA was synthesized from in vitro transcription of cDNA and then purified and reverse transcribed. Finally, single-stranded cDNA (ss-cDNA) was synthesized, purified, fragmented, and labeled following the manufacturer's instructions. Cartridge Array Hybridization was performed using the Clariom S array (Mouse; ThermoFisher Scientific) on the GeneChip™ Fluidics Station (ThermoFisher Scientific). Scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data obtained after scanning were analyzed using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific). The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value < 0.05 (one-way between-subjects ANOVA) and fold change > 2 (in linear space) were considered as differentially expressed genes (DEGs).

first: Ashley


title: UBE2D3 is an Intracellular Checkpoint in Pancreatic Ductal Carcinoma that Restricts CD8+ T-Cell Antitumor Immunity II

status: Public on Jun 23 2024

city: Hangzhou

first: Shiqun

last: Wang

state: Zhejiang Province

address: No. 150, Fucheng Road, Hangzhou Economic and Technological Development Zone

country: China

institute: Institute of Cancer and Basic Medicine, Chinese Academy of Sciences (CAS)

type: Expression profiling by high throughput sequencing

summary: Ubiquitylation is pivotal in regulating cellular responses, with its aberration implicated in tumor immune evasion. However, the impact of ubiquitin-conjugating enzymes (E2s) on this evasion remains unclear. Here, we employ a systematic approach to demonstrate that in pancreatic ductal carcinoma (PDAC), the inflammatory microenvironment induces overexpression of the E2 enzyme UBE2D3, contributing to tumor progression through non-oncogene codependent disorders. Through gene expression analyses and functional investigations, we elucidate a mechanism wherein cancer cells evade T cell immune responses by UBE2D3 binding to the ubiquitin ligase KLHL13 to co-ubiquitinate TAP2. This K63-linkage ubiquitination at the lysine 245 site of TAP2 impedes antigenic peptide transport by the TAP1/TAP2 complex, hindering p-MHC assembly and presentation in cancer cells. We demonstrate that genetic inhibition of UBE2D3 enhances tumor-specific CD8+ T cell proliferation and extends effector-memory-like phenotypes. Building on this, we develop a small-molecule inhibitor, QX-6, targeting the active site of UBE2D3 to disrupt its function. Pharmacologic inhibition of UBE2D3 blocks the ubiquitylation of antigen presentation-related substrates, leading to increased p-MHC presentation by cancer cells and reduced T cell exhaustion. Using immunocompetent and humanized models, we elucidate the therapeutic efficacy of targeting UBE2D3. Furthermore, we evaluate the synergistic anti-tumor effects of QX-6 in combination with KRAS-targeted TCR-T cell immunotherapy. In summary, our study reveals a post-translational modification mechanism wherein the intracellular checkpoint UBE2D3 regulates the TAP2 switch to control cancer cell evasion of CTLs, presenting a potential immunotherapeutic strategy to improve PDAC treatment outcomes.

overall_design: For single cell sequencing, C57/BL6 mice bearing KPC-shScramble or KPC-shUBE2D3-1 tumors for 30 d were euthanized. Three tumors from the same group were pooled to prepare single-cell suspension for isolating enough tumor-infiltrating CD8+ T cells. These cells were isolated by FCM, selecting live, single cells expressing CD45, CD3, and CD8.

first: Wenyan

last: Yang

first: Jiangjiang

last: Qin


title: The tRNA Gm18 Methyltransferase TARBP1 Promotes Hepatocellular Carcinoma Progression via Metabolic Reprogramming of Glutamine [tRNA-seq]

city: Shenzhen

first: Hao

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology (SUSTech)

type: Non-coding RNA profiling by high throughput sequencing

summary: Cancer cells rely on metabolic reprogramming to sustain the prodigious energetic requirements for rapid growth and proliferation. Glutamine metabolism is frequently dysregulated in cancers and is being exploited as a potential therapeutic target. In current study, we identified TARBP1 (TAR (HIV-1) RNA Binding Protein 1) as a novel driver gene critical for glutamine metabolic reprogramming in tumor through the CRISPRi/Cas9 screening. Our in vivo and in vitro assays demonstrated that TARBP1 is the methyltransferase of Guanosine 2'-O-methylation targeting position 18 (G18) of tRNAGln (TTG/CTG) and tRNASer (TGA/GCT), and loss of Gm18 modification diminishes the stability of tRNAs. Therefore, TARBP1 is critical for maintaining efficient translation of mRNA, in particular the glutamine transportor-ASCT2 (also known as SCL1A5). Importantly, TARBP1 is frequently amplified and overexpressed in HCC, consequentially promotes the protein synthesis of ASCT2 and glutamine import to fuel the growth of cancer cell, which is associated with poor patient survival. Taken together, this study reveals the critical role of TARBP1 in HCC progression through glutamine metabolic reprogramming and provides a potential target for tumor therapy.

overall_design: To identify the tRNAs that are regulated by TARBP1, tRNA-seq were carried out in wild-type and TARBP1-KO cell lines.

first: Yuci

first: Xiaoyan

last: Shi


title: Immune landscape of Isocitrate Dehydrogenase (IDH) stratified human gliomas [scRNA-seq]

city: Houston

first: Jeffrey

middle: Andrew

last: How

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gyn Onc & Reproductive Med

country: USA

institute: The University of Texas MD Anderson Cancer Center

summary: The brain tumor immune microenvironment (TIME) continuously evolves during glioma progression, but only a limited view of a highly complex glioma associated immune contexture across isocitrate dehydrogenase mutation (IDH) classified gliomas is known. Herein, we present an unprecedentedly comprehensive view of myeloid and lymphoid cell type diversity with our single cell RNA sequencing interrogation.

overall_design:
The  glioma associated CD45+ leukocyte were subjected to Fluorescence-activated cell sorting (FACS) from cryopreserved single cells. The leukocyte enriched single cell suspensions were obtained from freshly resected tumors of IDH-mutant primary (IMP; n=4), IDH-mutant recurrent (IMR; n=6), IDH-wild type primary (IWP; n=4), or IDH-wild type recurrent (IWR; n=4) glioma patients and quasi-normal non-glioma brain (NGB; n=3) from two epilepsy patients and a dysembryoplastic neuroepithelial tumor
*** Raw data are not provided for this study.  Raw data are protected by MD Anderson internal review board (IRB)-approved protocol numbers LAB03-0687, LAB04-0001 and 2012-0441 and Baylor College of Medicine IRB-approved protocol number H-13798. ***

first: Pravesh

last: Gupta

first: Minghao

last: Dang

first: Linghua

first: Krishna

last: Bhat


title: The tRNA Gm18 Methyltransferase TARBP1 Promotes Hepatocellular Carcinoma Progression via Metabolic Reprogramming of Glutamine [Ribo-seq]

overall_design: To identify the mRNAs translationally regulated by TARBP1, Ribo-seq were carried out in wild-type and TARBP1-KO cell lines. Input mRNAs and RPFs were isolated, ribosomal RNAs were depleted and cDNA libraries were prepared and sequenced according to the TruSeq Ribo Profile pipeline (Illumina).


title: Oxysterol Sensing through GPR183 Triggers Endothelial Senescence and Cardio-renal Injuries via Altering Circadian Signaling in Hypertension

city: Jinan

first: Qingqing

last: Chu

state: Shandong

address: wenhuaxilu 44

department: School of basic medical science

institute: Shandong University

summary:
Background: Despite endothelial dysfunction being considered as the initial step of the development of hypertension and associated cardio-renal syndromes, effective therapeutic strategies to prevent endothelial injuries are still lacking. GPR183 is a recently identified GPCR for oxysterols and hydroxylated metabolites of cholesterol. Here, we explored a previously unappreciated role of GPR183 in hypertension and age-related cardio-renal injuries.
Methods and results: Mice were treated with DOCA/Salt or AngII to induce hypertension. we found that endothelial GPR183 was significantly induced in aged or hypertensive mice, which was further confirmed in renal biopsies from elderly people or subjects with hypertensive nephropathy. In addition, we found that endothelial-specific GPR183 deletion markedly ameliorated endothelial senescence and cardio-renal injuries in hypertensive mice. Mechanistically, we found that GPR183 disrupted circadian signaling by inhibiting PER1 expression, thereby facilitating endothelial senescence and dysfunction through the cAMP/PKA/CREB signaling pathway. Importantly, pharmacological inhibition of the oxysterol-GPR183 axis by NIBR189 or Clotrimazole ameliorated endothelial senescence and cardio-renal injuries in hypertensive mice.
Conclusions: GPR183 is an attractive therapeutic target for hypertension and age-related diseases. Targeting GPR183 could provide novel strategies for managing hypertension and its associated cardio-renal injuries.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The gene expression of 2 samples from the DOCA mice was compared to 2 sham samples by RNA sequencing. The gene expression of 3 samples from the 24M mice was compared to 3 3M samples by RNA sequencing.  The gene expression of 1 sample from the Aged person was compared to 1 Young samples by RNA sequencing. The gene expression of 3 sample from the KO GPR183 mice was compared to 3 WT samples by RNA sequencing.

first: Xiaojie


title: Modeling 16p13.11 deletions in patient stem cell derived neurons

city: Boston

first: Kellen

last: Winden

state: MA

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

summary: 16p13.11 copy number variants (CNVs) have been associated with autism, schizophrenia, psychosis, intellectual disability, and epilepsy. The majority of 16p13.11 deletions or duplications occur within three well-defined intervals, and despite growing knowledge of the functions of individual genes within these intervals, the molecular mechanisms that underlie commonly observed clinical phenotypes remain largely unknown. Patient-derived, induced pluripotent stem cells (iPSCs) provide a platform for investigating the morphological, electrophysiological, and gene-expression changes that result from 16p13.11 CNVs in human-derived neurons. Patient derived iPSCs with varying sizes of 16p13.11 deletions and familial controls were differentiated into cortical neurons for phenotypic analysis. High-content imaging and morphological analysis of patient-derived neurons demonstrated an increase in neurite branching in patients compared with controls. Whole-transcriptome sequencing revealed expression level changes in neuron development and synaptic-related gene families, suggesting a defect in synapse formation. Subsequent quantification of synapse number demonstrated increased numbers of synapses on neurons derived from early-onset patients compared to controls. The identification of common phenotypes among neurons derived from patients with overlapping 16p13.11 deletions will further assist in ascertaining common pathways and targets that could be utilized for screening drug candidates. These studies can help to improve future treatment options and clinical outcomes for 16p13.11 deletion patients.

overall_design: A total of 15 samples were characterized. These 15 samples represent 3 patients (proband 1, proband 2, patient 3) and 2 controls (control 1 and control 2) collected across 3 differentiation replicates for triplicate samples from each patient or control

first: Elizabeth

middle: D

last: Buttermore

first: Nickesha

middle: C

last: Anderson

first: Pin-Fang

first: Syed

middle: M

last: Wafa

first: Sean

last: Dwyer

first: John

last: Micozzi

first: Nina

middle: R

last: Makhortova

first: Kristina

last: Kim

first: Bo

last: Zhang

first: Min-Joon

last: Han

first: Robin

middle: J

last: Kleiman

first: Catherine

middle: A

last: Brownstein

first: Mustafa

last: Sahin

first: Joseph

last: Gonzalez-Heydrich


title: Immune landscape of Isocitrate Dehydrogenase (IDH) stratified human gliomas [RNA-Seq]

first: Jeffrey

last: How

summary: The brain tumor immune microenvironment (TIME) continuously evolves during glioma progression, but only a limited view of a highly complex glioma associated immune contexture across isocitrate dehydrogenase mutation (IDH) classified gliomas is known. Herein, we present an unprecedentedly comprehensive view of myeloid and lymphoid cell type diversity with our m-RNA sequencing interrogation.

overall_design:
The glioma associated CD45+ (n=15) and CD45hi (n=3) and CD45lo (n=3)  leukocyte fractions were subjected to Fluorescence-activated cell sorting (FACS) from cryopreserved single cells. The leukocyte enriched single cell suspensions were obtained from freshly resected tumors of IDH-mutant primary (IMP; n=3), IDH-mutant recurrent (IMR; n=4), IDH-wild type primary (IWP; n=4), or IDH-wild type recurrent (IWR; n=4) glioma patients and quasi-normal non-glioma brain (NGB; n=1) from a dysembryoplastic neuroepithelial tumor.
*** Raw data are not provided for this study.  Raw data are protected by MD Anderson internal review board (IRB)-approved protocol numbers LAB03-0687, LAB04-0001 and 2012-0441 and Baylor College of Medicine IRB-approved protocol number H-13798. ***

first: Pravesh

last: Gupta

first: Minghao

last: Dang

first: Linghua

last: Wang

first: Krishna


title: A type 2 diabetes DNA methylation signature in monocytes exhibits ethnic specificity preferentially for Native Hawaiians

status: Public on Jun 22 2024

city: Honolulu

first: Christian

middle: Ka'ikekuponoaloha

last: Dye

state: HI

address: 641 Ilalo St. BSB 222K

department: Native Hawaiian Health

institute: University of Hawaii at Manoa

summary: Type 2 diabetes (T2D) is among the leading causes of death in the U.S. Ethnic differences in T2D prevalence are evident, including especially for Native Hawaiians (NHs) who remain disproportionately affected by it. This difference in T2D susceptibility involves an interplay between genetic and environmental factors, of which epigenetic mechanisms, including DNA methylation (DNAm) provide a novel approach to investigating gene-environment interactions of health and disease. Monocytes, an innate immune cell intrinsic to the inflammatory response, are a fundamental immune cell component that likely underlies T2D pathogenesis, given their involvement in inflammation and inflammation-associated insulin resistance and metabolic dysfunction. From participants enrolled into the Multiethnic Cohort Study (MEC), who self-identified as NH (n=152), Japanese American (JA; n=119), or White (n=121), we investigated monocyte-specific DNAm patterns in participants at a baseline visit, when free of T2D, using the HumanMethylation850K (850K) to determine whether monocytes harbor an ethnic-specific epigenetic signature of T2D risk that precedes T2D diagnosis. Using an epigenome-wide association study (EWAS), we found 904 significantly (q < 0.01) differentially methylated loci (DML) at a 5% difference in DNAm between participants who remained T2D free at a 15-year follow-up (i.e., controls) and those that would be diagnosed with T2D by follow-up (i.e., incident T2D) after adjusted for age, sex, and education level. These methylation differences were enriched at regulatory regions of the genome, including intergenic and intragenic regions. Notably, these DML were able to distinctly stratify NHs by T2D risk groups, however, this signature was inapparent in Whites and JAs. Likewise, NHs in the incident T2D group displayed a higher degree of DNAm variability. Sensitivity analysis with traditional risk factors (fasting glucose and body mass index [BMI]) and neighborhood socioeconomic status (nSES) found these risk factors had minimal effect on T2D risk-associated DML. Next, using a similar approach we found ethnic-specific DML in monocytes that was able to uniquely stratify NHs, JAs, and Whites, however, in NHs this epigenetic landscape displayed a higher degree of DNAm variability. Similarly, these DML were enriched at regulatory regions of the genome. In both cases, we found genes associated with biological functions and pathways relevant to monocyte functionality, including immune activation and cellular metabolism. Due to the higher degree of epigenetic variability in NHs, including especially NHs with T2D risk, we investigated differentially variable CpGs associated with T2D risk and ethnic-differences. We found differentially variable CpGs between T2D risk groups were able to stratify NHs with and without T2D risk, whereas it was unresolvable in JAs and Whites. Ethnic-specific DNAm variability clustered each ethnic population distinctly, and NH controls were further partitioned from NHs with T2D risk. Our findings suggest monocytes harbor a unique DNAm signature associated with T2D risk, which may be related to ethnic differences that underlie DNAm variability in monocytes. The increased epigenetic variability in monocytes from NHs may underlie epigenetic plasticity that could allow these cells to readily respond to adverse environmental conditions throughout the life course that may underlie long-term disease risk, whereas in other less susceptible populations with similar environmental exposure, this epigenetic plasticity may not be apparent in monocytes.

overall_design: We aimed to profile DNA methylation (DNAm) patterns from bead-enriched total monocytes (CD14+ CD16+/- monocytes) from Native Hawaiians, Japanese Americans, and Whites with variable risk for type 2 diabetes (T2D) using an epigenome-wide association study (EWAS) to determine whether there exists ethnic differences in DNAm that may underlie differential susceptibility to T2D. DNA collected from enriched monocytes (enrichment >65% monocytes) from 391 participants enrolled into the Multiethnic Cohort Study were analyzed using the Infinium HumanMethylation850 (850K), including 152 Native Hawaiians, 119 Japanese Americans, and 121 Whites, of which 171 participants would be diagnosed with T2D by the follow-up visit 15 years later (incident T2D) and 214 would remain T2D-free (controls).

first: Alika

last: Maunakea


title: Transcriptome sequencing of synovial tissues of knee osteoarthritis rats.

city: shanghai

first: ling

last: yang

address: Kong-Jiang Road 1665 in Shanghai

institute: Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Using transcriptome sequencing to screen the differntent expression genes in MIA-induced knee osteoarthritis (KOA) model rats compared with normal rats.

overall_design: SD rats were divided into two groups: KOA group and NC group, which in KOA group, we used an intra-articular injection of MIA in KOA group and none treatments in NC group. Four weeks after injection, we collected rat synovium tissues to preform transcriptome sequencing analysis of mRNA.

first: Ling

last: Yang


title: Transcriptomic evidence of lung repair in paediatric ARDS survival

city: Tianjin

first: Kuan

last: Li

state: Tianjin

address: Jingu road 890

institute: Tianjin Key Laboratory of Pulmonary Regenerative Medicine

summary: Pediatric patients survive from acute respiratory distress syndrome (ARDS) better than adults. However, immunological characteristics of lung tissue and peripheral circulation in pediatric ARDS has been scared.  A 10-year-old girl suffered from ARDS was treated with anti-infection, anti-inflammatory regimen and with ECMO support. Air leak was fixed by surgery. Surgically dissected lung biopsies and peripheral blood cells (PBCs) were obtained from this patient and other control subjects for single cell RNA sequencing analysis. Pathological examination was also conducted on the lung biopsy. Out data revealed transcriptional characteristics of PBCs and lung microenvironment during ARDS recovery phase, and pointed out that efficient oxygen supply, appropriate immune regulation, and adequate anti-infection treatment favor for the recovery of children from ARDS.

overall_design: Lung tissues and peripheral blood samples were collected for single-cell transcriptomic analyses.

first: Licheng

last: Song

first: Xiaoyang

last: Hong

first: Kun

last: Xiao

first: Guoxin

last: Mo

first: Mengli

last: Zheng

first: Fei

last: Xie

first: Yuhong

last: Liu

first: Pengfei

first: Tianyu

last: Sun

first: Qiushuang

last: Feng

first: Aiguo

last: Zhou

first: Chen

last: Yao

first: Jing

first: Huaiyong

last: Chen

first: Lixin


title: Effect of a dendritic cells derived extracellular vesicle as therapeutic vaccine platform to induce neuroprotective immunity for spinal cord injury

city: Harbin

first: Sikai

last: Wang

address: Baojian Road

institute: Second Affiliated Hospital of Harbin Medical University

summary: we designed a nano-vaccine platform using dendritic cell-derived small extracellular vesicles (DsEVs) as carriers for MBP87-99A91(A91-DsEVs) to induce a neuroprotective immunity for spinal cord injury.

overall_design: We performed gene expression profilling analysis using data obtained from RNA-seq of A91-DsEVs treatment group and control group (PBS group) at 3 time points, there were 4 samples in A91-DsEVs treatment group in each time point, and 3 samples in PBS group at each time point

first: guanglei

first: Fawang

last: Zhang

first: Yufu


title: GrB-Fc-KS49, a human immuno-oncology therapeutic agent to EMP2 using a human fusion protein containing granzyme b, reshapes the tumor microenvironment by altering immune cell recruitment in breast cancer

city: Los Angeles

first: Madhuri

last: Wadehra

state: CA

address: 675 Charles Young Dr. South

institute: UCLA

summary:
Background: Granzyme B (GrB) is a key effector molecule, delivered by cytotoxic T lymphocytes and natural killer cells during immune surveillance to induce cell death. Fusion proteins and immunoconjugates represent an innovative therapeutic approach to specifically deliver a deadly payload to target cells. Epithelial membrane protein-2 (EMP2) is highly expressed in invasive breast cancer, including triple negative breast cancer, and represents an attractive therapeutic target.
Methods: We designed a novel fusion protein (GrB-Fc-KS49) composed of an active GrB fused to an anti-EMP2 single chain antibody tethered through the IgG heavy chain (Fc) domain. The protein was expressed by HEK-293E cells. We assessed the construct’s GrB enzymatic activity, anti-EMP2 binding affinity, cytotoxicity against a panel of breast cancer cells, pharmacokinetics, toxicity profile, and in vivo efficacy.
Results: GrB-Fc-KS49 exhibited comparable GrB enzymatic activity to commercial GrB, as well as high affinity to an EMP2 peptide, with the dissociation constant in the picomolar range. The fusion protein rapidly internalized into EMP2+ breast cancer cells and showed in vitro cytotoxicity to cell lines expressing surface EMP2, with IC50 values below 100 nM for most positive lines.  Ex vivo stability at an elevated temperature (37°C) indicated a half-life exceeding 96h while in vivo pharmacokinetics indicated a bi-exponential plasma clearance, with a moderate initial clearance (t1/2α = 18.4 h) and a much slower terminal clearance rate (t1/2β = 73.1 h). No significant differences between the vehicle control and the GrB-Fc-KS49 was detectable in a Chem16 toxicity panel. In vivo efficacy against a TNBC syngeneic mouse model
EMT6 mouse model resulted in a reduction in cell proliferation compared to controls (p=0.02).  Treatment using a second syngeneic model (4T1/FLuc) confirmed these results and resulted in a dramatic reduction in cell proliferation (p = 0.001) and increase in cell death by TUNEL (p=0.02) compared to controls. In addition to a significant impact on cell proliferation (p=0.005), GrB-Fc-KS49 treatment also resulted in a dramatic increase of tumor infiltrating CD45+ cells (p=0.002), and redistribution of tumor-associated macrophages (TAMs) which was confirmed by transcriptomic analysis of tumors post treatment.
Conclusions: GrB-Fc-KS49 showed high specificity to EMP2 and cytotoxicity towards EMP2 positive cells. In vivo, GrB-Fc-KS49 reduced tumor burden by direct targeting as well as increasing recruitment of immune cells into the tumor microenvironment, suggesting that GrB-Fc-KS49 is a promising therapeutic for further development against breast cancer.

overall_design: Balb/c syngeneic mice bearing EMT-6 breast cancer tumors were treated with GrB-Fc-KS49 vs. control three times over 10 days.

first: Wadehra

last: Madhuri

first: Mohamedali

last: Khalid

first: Casero

last: David


title: The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling [CHiC]

status: Public on Jun 21 2024

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

summary: Macrophages play a critical role in bridging the innate and adaptive immune systems, which requires timely and precise transcription control when responding to danger signals. Gene expression networks in macrophages have been profiled extensively in recent decades with the advancement of high-throughput sequencing technologies. However, unveiling critical mechanistic insights into control of diverse transcriptional networks has proven to be challenging. Recent evidence has suggested that the accessibility of chromatin structure can provide an integral means of transcription regulation. We have used the relatively recent Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq) method to assess chromatin accessibility with optimal resolution in mouse bone marrow derived macrophages during the course of lipid- A stimulation. This advanced method enabled us to characterize the chromatin state of genome-wide regulatory regions. By applying a quantitative systematic approach, we obtained mechanistic insights into the highly selective role of the major transcription factors, NF-κB and IRF3, in nucleosome remodeling and transcription regulation.

overall_design: Long distant interactions to promoters were captured for DNA sequencing in WT clone.   Data generated from bone marrow-derived macrophages stimulated with lipid-A for 0 and 120 minutes.

first: An-Chieh

first: Brandon

last: Thomas

middle: T


title: The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling [4C]

overall_design: Long distant interactions to target bait (peak68866) were captured for DNA sequencing in bone marrow-derived macrophages stimulated with lipid-A for 0 and 2 hours.


title: UBE2D3 is an Intracellular Checkpoint in Pancreatic Ductal Carcinoma that Restricts CD8+ T-Cell Antitumor Immunity

first: Shiqun

overall_design: For bulk RNA-seq, 1 x 106 KPC-shScramble and KPC-shUBE2D3-1 cells were inoculated in 6-well plates. After 24 h, cells were harvested. Total RNA was isolated and purified using TRIzol (ThermoFisher, 15596018) following the manufacturer’s protocol. Comparative gene expression profiling analysis of RNA-seq data for KPC-shScramble and KPC-shUBE2D3 cell line in vitro

first: Wenyan

last: Yang

first: Jiangjiang

last: Qin


title: The Molecular Mechanisms of m6A Methylation Modification in Regulating Bolting and Flowering in Radish

city: Guiyang

first: wu

middle: lin

last: jun

state: Guizhou

address: Xibei Street

institute: guizhou university

summary: N6-methyladenosine (m6A) is a crucial epigenetic modification in mRNA and the most abundant methylation in eukaryotes. However, research on m6A modification in radish (Raphanus sativus) is not as extensive as in model plants. In this study, we analyzed m6A modification during the vegetative and reproductive growth stages of radish using m6A-seq and RNA-seq to explore its potential role in bolting and flowering. The results showed that m6A peaks significantly increased during the reproductive growth stage compared to the vegetative stage, with more m6A modification sites in the stop codon, 3' UTR, and promoter regions. Overexpression of the RsALKBH10B gene led to a global reduction in m6A modification and resulted in an early bolting and flowering phenotype, with transcription levels of key flowering factors RsSOC1 and RsFT increasing by 10-40 fold. Correlation analysis between differential m6A modification and differentially expressed genes indicated that genes such as RsSUF4, RsAGL13, and RsCDF5 might regulate bolting and flowering. Overexpression of RsSUF4 delayed bolting and flowering and decreased overall m6A modification levels; in positive transgenic plants, higher m6A levels of RsSUF4 were associated with lower transcription levels. These findings suggest that m6A methylation may regulate gene expression related to bolting and flowering in radish by affecting mRNA stability, ultimately leading to bolting and flowering.

overall_design: In this study, we collected radish leaf material XHT at 30 days after sowing (nutrient growth stage, VG) and 120 days after sowing (reproductive growth stage, F) for m6A methylome sequencing, mining of differential genes, and functional validation of genes.

first: Linjun

last: Wu

first: Xiaobo

last: Luo


title: A HigB-like toxin induces non-replicating Salmonella inside macrophages by inhibiting RNase III-dependent rRNA maturation [sehB_RNA-Seq]

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Many bacteria are often resistant to antibiotic treatment and drugs because, even if these drugs are effective, bacteria can slow down their growth rate and thus attenuate the effectiveness of the drug. A similar growth-rate control is detected in pathogenic bacteria that infect and persist inside their hosts. The bacterial growth rate within host cells can be regulated by multiple signaling pathways, most of which are still unknown. A toxin-antitoxin (TA) system is one of the candidates for controlling bacterial growth because the TA system could slow down growth by expressing a toxin component. The toxin protein can be neutralized by the antitoxin component, serving as a non-heritable phenotypic switch for growth rate. In this study, we investigated a type II toxin-antitoxin system from the intracellular bacterial pathogen Salmonella enterica serovar Typhimurium. We characterized residues required for toxin’s activity and a potential mechanism of the toxin by searching for its target via bacterial two-hybrid screening. Understanding the underlying mechanism of toxin-mediated persister formation and growth rate control within host cells will provide a new alternative to treat antibiotic resistant bacteria or intracellular bacteria surviving within host cells.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: We performed an RNA-Seq between the sehB mutant and wild type to analyze how the mRNA profile changed under the influence of overexpressed sehA as a result of sehB deletion.

first: Soomin

last: Choi

first: Seungwoo

last: Baek

first: Eunna

first: YoonKi

last: Kim

first: Eun-Jin

last: Lee


title: Tryptophan 2, 3-dioxygenase positive matrix fibroblasts fuel breast cancer lung metastasis via kynurenine-mediated ferroptosis resistance of metastatic cells and T cell dysfunction II

city: Chongqing

first: yong

middle: can

last: liu

address: No.1, Yi-Xue-Yuan Road, Yu-zhong District, Chongqing 400016, China.

institute: Chongqing medical university

summary: Background: Tumor metastasis is a major threat to cancer patient survival. The organ-specific niche plays a pivotal role in tumor organotropic metastasis. Fibroblasts serve as a vital component of the metastatic microenvironment, but how heterogeneous metastasis-associated fibroblasts (MAFs) promote organotropic metastasis is poorly characterized. Here, we aimed to decipher the heterogeneity of MAFs and elucidate the distinct roles of these fibroblasts in pulmonary metastasis formation in breast cancer. Methods: Mouse models of breast cancer pulmonary metastasis were established using an in vivo selection method of repeated injections of metastatic cells purified from the mouse lung. Single-cell RNA sequencing (scRNA-seq) was employed to investigate the heterogeneity of MAFs. Transgenic mice were used to examine the contribution of tryptophan 2, 3-dioxygenase positive matrix fibroblasts (TDO2+ MFs) in lung metastasis.. Results:  We uncovered three subtypes of MAFs in the lung metastatic microenvironment and their transcriptome profiles changed dynamically as lung metastasis evolves. As the predominant subtype, matrix fibroblasts (MFs) were exclusively marked by platelet-derived growth factor receptor alpha (PDGFRA) and mainly located on the edge of the metastasis, and T cells were enriched around MFs. Notably, high MFs signatures were significantly associated with poor survival in breast cancer patients. Lung metastases were markedly diminished and the suppression of T cells was dramatically attenuated in MF-depleted experimental metastatic mouse models. We found that TDO2+ MFs control pulmonary metastasis by producing kynurenine (KYN), which upregulated FTH1 level in disseminated tumor cells (DTCs), enabling DTCs to resist ferroptosis. Moreover, TDO2+ MFs-secreted the chemokines CCL8 and CCL11 recruited T cells. TDO2+ MF-derived KYN induced T cell dysfunction. Conditional knockout of Tdo2 in MFs diminished lung metastasis and enhanced immune activation. Conclusions: Our study reveals crucial roles of TDO2+ MFs in promoting lung metastasis and DTCs' immune evasion in the metastatic niche. It suggests that targeting the metabolism of lung-specific stromal cells may be an effective treatment strategy for breast cancer patients with lung metastasis.

overall_design: To address how fibroblasts subgroups contribute to disseminated tumor cells growth and metastasis formation in the lung, bulk RNA-seq of purified fibroblasts subgroups (normal MFs, N-MFs; normal MyoFs, N-MyoFs; metastasis MFs, M-MFs; metastasis MyoFs, M-MyoFs) was carried out.Gene expression profiling  was compared between N-MFs and M-MFs (N-MyoFs and M-MyoFs)  using the bulk RNA-seq data.

first: Yongcan

last: Liu

first: Shanchun

last: Chen

first: Manran


title: A chemical screen identifies PRMT5 as a therapeutic vulnerability for paclitaxel-resistant triple-negative breast cancer

first: Sheyu

last: Zhang

address: Dongfang Road 150

institute: Hangzhou Institute of Medicine Chinese Academy of Sciences

summary: Paclitaxel -resistant   triple negative breast cancer (TNBC) remains one of the most challenging breast cancers to treat. Using an epigenetic chemical probe screen, we uncover an acquired vulnerability of paclitaxel-resistant TNBC cells to protein arginine methyltransferases (PRMTs) inhibition. Analysis of cell lines and in-house clinical samples demonstrates that resistant cells evade paclitaxel killing through stabilizing mitotic chromatin assembly. Genetic or pharmacologic inhibition of PRMT5 alters RNA splicing, particularly intron retention of Aurora kinases B (AURKB), leading to a decrease in protein expression, and finally results in selective mitosis catastrophe in paclitaxel-resistant cells. These findings are fully recapitulated in a patient derived xenograft (PDX) model generated from a paclitaxel-resistant TNBC patient, providing the rationale for targeting PRMTs in paclitaxel-resistant TNBC.

overall_design: To explore the role of PRMT5 in paclitaxel-resistant triple-negative breast cancer (TNBC), we established paclitaxel-resistant cell lines derived from TNBC cell lines (MDA-MB-436, Hs578T). We then performed RNA-seq sequencing on the paclitaxel-resistant cells treated with a PRMT5 inhibitor (LLY283 or GSK591, 1μM). Additionally, to validate the clinical significance of PRMT5 in overcoming paclitaxel resistance, we conducted RNA-seq sequencing on patient-derived xenograft (PDX) models generated from paclitaxel-resistant TNBC patients treated with a PRMT5 inhibitor (LLY283, 40mg/kg).


title: The clock gene BHLHE40 and atypical CCNG2 control androgen-induced cellular senescence as a novel tumor suppressive pathway in prostate cancer

city: Jena

first: Mehdi

last: Heidari Horestani

state: Thüringen

address: Am klinikum1

country: Germany

institute: Jena University Hospital

summary: The androgen receptor (AR) is a therapeutic target of prostate cancer (PCa). Targeted AR therapy commonly uses androgen deprivation therapy (ADT) and AR antagonists to reduce androgen levels and inhibit tumor growth. Surprisingly, treatment with supraphysiological androgen level (SAL) can also inhibit the growth of PCa. SAL (R1881) was shown to induce cellular senescence in PCa. Knockdown of BHLHE40 in C4-2 and LNCaP cell lines indicates that BHLHE40 mediates SAL-induced cellular senescence as a possible tumor suppressive pathway. The RNA-seq from BHLHE40 knocked down C4-2 cells confirmed that BHLHE40 regulates cellular senescence and associated pathways. Interestingly, a large overlap of differentially expressed gene sets was identified between BHLHE40 regulated transcriptome and the SAL-changed transcriptome leading to four classes of up-and downregulated BHLHE40 transcriptome landscapes overlapping with that of AR. Further RNA-seq analyses revealed that the tumor suppressive cyclin G2 (CCNG2) emerged as a novel downstream target of BHLHE40. Knockdown of CCNG2 suggests that it mediates SAL-induced cellular senescence providing evidence of a novel pathway by the AR-BHLHE40-CCNG2 axis to mediate androgen-induced cellular senescence as a novel tumor suppressive pathway in PCa cells.

overall_design: Expression profiling of BHLHE40 KD C4-2 cells treated with DMSO or SAL (R1881) by high throughput sequencing

first: Aria

last: Baniahmad


title: Adiponectin regulated by IAA in Paneth cells controls renewal and differentiation of gut stem cells to maintain homeostasis of epithelial cells (small intestinal epithelium)

first: Yun Huan

last: Gao

address: 94 Weijin Road, Nankai District, Tianjin

institute: Nankai University

summary: Crypt cells (mainly stem and transit amplifying (TA) cells) in Adipfl/flpVilli-CreT (gut epithelial cell adiponectin conditioned knockout) mice exhibited stronger ability of renewal and differentiation. ScRNA-seq found that there had much more enrichment intestinal stem and TA cells in Adipfl/flpVilli-CreT mice. The renewal and development of gut epithelial cells in irradiated or DSS (dextran sulfate sodium) treated Adipfl/flpVilli-CreT mice was faster than control Adipfl/flp mice. In vitro culture gut organoid of Adipfl/flpVilli-CreT mice exhibited faster growth than those from Adipfl/flp mice.

overall_design: To further determine the effects of adiponectin from Paneth cells on the gut stem and TA cells, we performed scRNAseq on crypt-enriched whole small intestinal epithelium from control Adipfl/fl mice and Adipfl/flpVilli-CreT mice.

first: Xiaomin

last: Su

first: Juanjuan

last: Wang

first: Hang

first: Rongcun


title: An isogenic E. coli population gives rise to multiple persister phenotypes

city: Brookings

first: Nicholas C

last: Butzin

state: SD

address: 1224 Medary Ave.

department: Biology and Microbiology

institute: South Dakota State University

summary: Antibiotic treatment typically eliminates a significant portion of a bacterial population, leaving behind a smaller subset of tolerant cells that can survive the treatment. These tolerant cells hinder the effectiveness of the antibiotic, potentially leading to the development of antibiotic resistance within the population. Antibiotic tolerance differs from resistance: tolerant cells are unable to grow or reproduce in the presence of the antibiotic, but they can proliferate once the antibiotic is removed. However, in cases of resistance, the antibiotic loses its efficacy entirely, posing a significant threat to public health. Our study challenges the long-held consensus that persisters are completely dormant and are of one single population. Our results clearly show that persisters are not as dormant as once thought, and multiple populations of persisters form during lethal antibiotic treatment despite the cells being genetically identical. We compared the transcriptome profiles at different time points to investigate the dynamic changes and/or existence of multiple persister subpopulations in response to lethal antibiotic ampicillin (Amp) and ciprofloxacin (Cip) treatment in E. coli.

overall_design: Stationary phase cells were diluted 1:100 times in pre-warmed MMB+ media and treated with Amp (0.1 mg/mL) for 24 h, and samples were isolated for RNA sequencing before antibiotic treatment (0 h) and after antibiotic treatment at 3 h, 6 h, and 24 h.

first: Tahmina

last: Hossain

first: K M

last: Rahman

first: Ruqayyah

last: Amaratunga

first: Nicholas

first: Abhyudai

last: Singh


title: Senescence defines a distinct subset of myofibroblasts that orchestrates immunosuppression in pancreatic cancer

city: St. Louis

first: David

last: DeNardo

state: MO

address: 425 S Euclid Ave

department: Department of Medicine

institute: Washington University in St. Louis

summary: Therapeutic resistance in PDAC is largely attributed to a unique tumor microenvironment embedded with an abundance of cancer associated fibroblasts (CAFs). Distinct CAF populations were recently identified, but the phenotypic drivers and specific impact of CAF heterogeneity remain unclear. In this study, we identify a subpopulation of senescent myofibroblastic CAFs (SenCAFs) in mouse and human PDAC. These SenCAFs are a subset of myofibroblastic CAFs that localize near tumors ducts, have distinct phenotypes and accumulate with PDAC progression. To assess the impact of endogenous SenCAFs in PDAC, we employed a LSL-KRASG12D;p53flox;p48-CRE;INK-ATTAC (KPPC-IA) mouse model of spontaneous PDAC with inducible senescent cell depletion. Senescence depletion with the KPPC-IA model or with the senolytic drug ABT263/Navitoclax, delayed tumor progression, reduced fibrosis, and relieved immune suppression in macrophages and T lymphocytes. Collectively, our findings demonstrate that SenCAFs promote PDAC progression and immune cell dysfunction.

overall_design: Examination of the tumor microenvironment with depletion of senescent fibroblasts in PDAC

first: Jad

last: Belle

first: John

last: Baer

first: Devashish

last: Sen


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_SW1783_batchF

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

institute: Korean Institute of Oriental Medicine

summary: This study aimed to identify transcript expression induced by tonifying herbal medicines (THM) and modes of action (MOA) of THM in A549 cell line. For the production of THM-induced transcripts, tonifying herbal medicines water extract (THW) and tonifying herbal medicines ethanol extract (THE) were used.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin, LY294002, and thioridazine 10uM, respectively), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively.


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_SW1783_batchD


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_SW1783_batchE


title: A HigB-like toxin induces non-replicating Salmonella inside macrophages by inhibiting RNase III-dependent rRNA maturation [sehA_RNA-Seq]

first: Yong-Joon

last: Cho

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: We used RNA-seq to determine if the profile of mono-phosphated-OH and mono-phosphated mRNA differed between the sehA mutant and a strain that overexpressed sehA by arabinose induction.

first: Soomin

last: Choi

first: Seungwoo

last: Baek

first: Eunna

first: YoonKi

last: Kim

first: Eun-Jin

last: Lee


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_HepG2_batchE

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin 10uM), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively.
Please note that the RCM_tonifying_HepG2.txt contains processed data for all batch samples and the corresponding data column header is indicated in the sample description field.


title: Integrative multi-omics analyses identify molecular subtypes of head and neck squamous cell carcinoma with distinct therapeutic vulnerabilities

city: Nanjing

first: Yanling

state: Jiangsu

address: NO.136 Hanzhong Road

institute: Nanjing Medical University

summary: Substantial heterogeneity in molecular features, patient prognoses, and therapeutic responses in head and neck squamous cell carcinomas (HNSCC) highlights the urgent need to develop molecular classifications that reliably and accurately reflect tumor behavior and inform personalized therapy. Here, we leveraged the similarity network fusion bioinformatics approach to jointly analyze multi-omics datasets spanning copy number variations, somatic mutations, DNA methylation, and transcriptomic profiling and derived a prognostic classification system for HNSCC. The integrative model consistently identified three subgroups (IMC1-3) with specific genomic features, biological characteristics, and clinical outcomes across multiple independent cohorts. The IMC1 subgroup included proliferative, immune-activated tumors and exhibited a more favorable prognosis. The IMC2 subtype harbored activated EGFR signaling and an inflamed tumor microenvironment with cancer-associated fibroblast/vascular infiltrations. Alternatively, the IMC3 group featured highly aberrant metabolic activities and impaired immune infiltration and recruiting. Pharmacogenomics analyses from in silico predictions and from patient-derived xenograft model data unveiled subtype-specific therapeutic vulnerabilities including sensitivity to cisplatin and immunotherapy in IMC1 and EGFR inhibitors (EGFRi) in IMC2, which was experimentally validated in patient-derived organoid models. Two signatures for prognosis and EGFRi sensitivity were developed via machine learning. Together, this integrative multi-omics clustering for HNSCC improves current understanding of tumor heterogeneity and facilitates patient stratification and therapeutic development tailored to molecular vulnerabilities.

overall_design: Gene expression profiling analysis of RNA-seq data for organoids from 13 patients with head neck squamous cell carcinoma (HNSCC).

first: Pengfei

last: Diao

first: Yibin

last: Dai

first: An

first: Xiaoxuan

last: Bu

first: Ziyu

first: Jin

last: Li

first: Yaping

last: Wu

first: Hongbing

last: Jiang

first: Jie

last: Cheng


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_SW1783_batchC

first: Musun


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_SW1783_batchB


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_HepG2_batchA

summary: This study aimed to identify transcript expression induced by tonifying herbal medicines (THM) and modes of action (MOA) of THM in HepG2 cell line. For the production of THM-induced transcripts, tonifying herbal medicines water extract (THW) and tonifying herbal medicines ethanol extract (THE) were used.


title: Comparing preprocessing strategies for 3D-Gene microarray data of extracellular vesicle-derived miRNAs

city: Nagoya

first: Masahiro

last: Nakatochi

state: Aichi

address: 1-1-20 Daiko-Minami, Higashi-ku

institute: Nagoya University

summary: miRNAs derived from serum EVs of ALS patients obtained in two batches

overall_design: Venous blood samples were collected from 28 and 47 patients from the first and second cohorts, respectively, to isolate EVs and perform miRNA microarray analyses. The first and second cohorts had 10 common patients, for whom we evaluated data consistency and batch effects in a preprocessing pipeline comparison. If S001-S010 in batches 1 and 2 have the same number, they refer to samples obtained from the same patient.

first: Yuto

last: Takemoto

first: Daisuke

last: Ito

first: Shota

last: Komori

first: Yoshiyuki

last: Kishimoto

first: Shinichiro

last: Yamada

first: Atsushi

last: Hashizume

first: Masahisa

last: Katsuno


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_HT29_batchB

last: Park

summary: This study aimed to identify transcript expression induced by tonifying herbal medicines (THM) and modes of action (MOA) of THM in HT29 cell line. For the production of THM-induced transcripts, tonifying herbal medicines water extract (THW) and tonifying herbal medicines ethanol extract (THE) were used.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin and LY294002 10uM, respectively), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively.
Please note that the RCM_tonifying_HT29.txt contains processed data for all batch samples and the corresponding data column header is indicated in the sample description field.


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_HT29_batchC


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_HT29_batchA


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_SW1783_batchA


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_HepG2_batchC


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_A549_batchD

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin 10uM), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively.


title: The tRNA Gm18 Methyltransferase TARBP1 Promotes Hepatocellular Carcinoma Progression via Metabolic Reprogramming of Glutamine

city: Shenzhen

first: Hao

last: Chen

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology (SUSTech)

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

overall_design: Refer to individual Series


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_HepG2_batchD


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_A549_batchC


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_A549_batchB


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_HepG2_batchB


title: Network Analysis Reveals Age- and Virus-Specific Circuits in Nasal Epithelial Cells of Extremely Premature Infants

city: Vienna

first: Lukas

last: Wisgrill

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

summary: Analysis of influenza A and respiratory synctial virus infections in cultured nasal epithelial cells at the air-liquid interface (ALI) of adult, term, and preterm infants.

overall_design: Comparative gene expression analysis of unstimulated, influenza A (H3N2), and respiratory syncytial virus stimulated nasal epithelial cells of adult, term and preterm infants (n=5 per group).

first: Harri

last: Alenius


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_HT29_batchD


title: Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer [strand specific RNA-seq]

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Thymine DNA Glycosylase (TDG) is a versatile protein involved in DNA mismatch repair, DNA demethylation, and transcriptional regulation. Here, we identify TDG as a synthetic essential effector in p53-deficient tumours. We found that deletion of TDG inhibits cell proliferation specifically in p53-deficient cancer cells. Using a genetically engineered mouse model of lung adenocarcinoma (LUAD), we demonstrate that depletion of TDG suppresses tumour growth in the p53-deficient context. Notably, A novel and selective inhibitor developed to disrupt the DNA binding activity of TDG exhibits therapeutic efficacy against p53-deficient tumours in both cellular and xenograft models. Mechanistically, TDG coordinates with p53 to orchestrate the transcription of RNA helicase DHX9, which functions to eliminate dsRNA. Depletion of TDG in p53-deficient cells results in the downregulation of DHX9 and aberrant cytoplasmic double-strand (dsRNA) accumulation derived from Alu elements, subsequently activating the RIG-I/MDA5-MAVS mediated antiviral response. Moreover, single-cell RNA-sequencing analysis revealed the depletion of TDG in p53-deficient tumours facilitates the recruitment of tumour-infiltrating lymphocytes. We observed that TDG inhibition combined with immune checkpoint blockade (ICB) achieved a strong synergistic anti-tumour effect in p53-deficient tumours. This study highlights the function of TDG in maintaining p53-deficient tumour growth and provides an alternative therapeutic target for p53-deficient cancers.

overall_design: Transposable elements expression analysis of strand-specific RNA-seq data for listed cells.

first: Jiaxin

last: Zhou


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_A549_batchE


title: Hypoxia-ischemia-induced Ntoco promotes ferroptosis via the Hnrnpab-mediated NF κB/Lcn2 axis following traumatic brain injury in mice

city: Chengdu

first: Linbo

last: Gao

state: Sichuan

address: No. 17, Section 3, Renmin South Road, Wuhou District

institute: Sichuan University

summary: Evidence supports the contribution of long non-coding RNAs (lncRNAs) and ferroptosis to traumatic brain injury (TBI) pathogenesis. However, lncRNA regulation in TBI-induced ferroptosis remains poorly understood. Herein, we identified an lncRNA, named noncoding transcript of chemokine (C-C motif) ligand 4 (Ccl4) overlapping (Ntoco), which was upregulated in TBI mice. The upregulation was initiated by hypoxia ischemia induced lower enrichment of H3K27me3 on the Ntoco promoter. Ntoco knockdown inhibited neuron ferroptosis, ameliorated spatial memory and lesion volume following TBI. Ntoco overexpression promoted neuron ferroptosis and recruited microglia to provoke an inflammatory response via Ccl4. Mechanistically, Ntoco facilitated K48-linked ubiquitination and protein degradation by binding to Hnrnpab, which suppressed NF-κB/Lcn2 signal axis activation, including decreased phosphorylation of IkBα, increased phosphorylation of IKKα/β, nuclear translocation of the NF-κB p65 subunit, and elevated Lcn2 expression. These data indicated that targeting Ntoco to mitigate ferroptosis might be a potential therapeutic strategy for TBI.

overall_design: To further reveal the signaling pathways associated with Ntoco, we performed high-throughput transcriptome sequencing and KEGG pathway enrichment analysis of HT22 cells that knocked down and overexpressed Ntoco.

first: Qiang

last: Wang


title: Search for PTH-induced genes in MC3T3-E1 cells

city: Chiba

first: Chisato

last: Sampei

address: Yamazaki 2641

institute: Tokyo university of science

summary: To identify the changes of mRNA expressions by PTH-treatment for 1 hr in mouse osteoblastic cell line MC3T3-E1, we performed RNA-sequencing (RNA-seq).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of cells treated with PTH.

first: Tadayoshi

last: Hayata


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_HT29_batchE

first: Musun


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_A549_batchA

first: Seongwon

last: Cha

first: Jin-Mu

last: Yi


title: Acquisition of CCDC88A/GIV through Tumor-Stroma Tunnels Promotes Aggressive Phenotypes of Estrogen Receptor-Positive Breast Cancer [dataset1]

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

summary: Estrogen receptor-positive (ER+) breast cancer commonly disseminates to bone marrow, where interactions with mesenchymal stromal cells (MSCs) shape disease trajectory. We modeled these interactions using tumor-MSC co-cultures and using an integrated transcriptome-proteome-network-analyses workflow identified a comprehensive catalog of contact-induced changes. Induced genes/proteins—some borrowed and others tumor-intrinsic response—were not recapitulated merely by conditioned media. Protein-protein interaction networks reveal the rich connectome between the ‘borrowed’ and ‘intrinsic’ components. Bioinformatic analyses helped prioritize one of the ‘borrowed’ components, CCDC88A/GIV, a bona-fide multi-modular metastasis-related protein. MSCs upregulated GIV in ER+ breast cancer cells through connexin (Cx)43-facilitated intercellular long-distance transport. Stable expression of GIV recapitulated ~20% of both the ‘borrowed’ and the ‘intrinsic’ gene induction patters observed during contact cocultures, conferred resistance to clinical anti-estrogen drugs, and enhanced tumor dissemination. These data provide a multiomic insight into the role of MSC→tumor cell intercellular transport and validate as proof-of-concept how transport of one such candidate, GIV, from the haves (MSCs) to have-nots (ER+ breast cancer) orchestrates aggressive disease states.

overall_design: To investigate to what extent GIV alone reproduces key effects of MSCs on ER+ breast cancer cells, we stably expressed full-length GIV in MCF7 cells. Western blotting confirmed expression of full-length GIV in MCF7-GIV cells as compared with minimal amounts of spliced GIV in control MCF7 cells. Even with stable overexpression, MCF7-GIV cells had lower amounts of GIV than expressed physiologically by HS5 cells. We performed RNA sequencing on MCF7-GIV cells after overnight growth in no serum, no estrogen, 25 mM glucose.

first: Gary

last: Luker


title: Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer [scRNA-seq]

city: shanghai

overall_design: We used single cell RNA sequencing (scRNA-seq) to analyze the tumour-infiltrating lymphocytes in subcutaneous KP tumours

first: Yanhao

last: Yu


title: Acquisition of CCDC88A/GIV through Tumor-Stroma Tunnels Promotes Aggressive Phenotypes of Estrogen Receptor-Positive Breast Cancer [dataset3]

overall_design: Co-culture model of bone marrow mesenchymal stem cells (MSCs)(HS5 and HS27a) and breast cancer cells (T47D). Co-cultured cancer and stromal cells were separated before performing RNA sequencing. Data sets also include monoculture samples of cancer and stromal cells as well as cancer cells with conditioned medium from stromal cells.


title: Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin accessibility analysis of ATAC-seq data for listed cells.


title: Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer [CUT&Tag]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for TDG and p53  as well as CUT&Tag for P300 and the histone modifications H3K9me3, H3K4me3 in B16 cells.


title: FBXW7 coordinates postprandial muscle glucose metabolism and maintenance of skeletal muscle mass

city: Shanghai

first: Xuelian

last: Xiong

address: NO. 180, Fenglin Road

department: Zhongshan Hospital, Fudan University

institute: Department of Endocrinology and Metabolism

summary: In this study, we show that muscle-specific inactivation of FBXW7 elicits striking defects in postprandial glucose metabolism and failure to maintain skeletal muscle mass in adult mice. Further, mice lacking FBXW7 exhibited impaired endurance capacity and exacerbated HFD-induced insulin resistance and postprandial hyperglycemia. At the mechanistic level, RNAseq and quantitative proteomic analysis revealed global effects of FBXW7 deficiency on skeletal muscle transcriptome and proteome. This work illustrates a prominent role of FBXW7 in integrating postprandial nutritional signals to coordinate glucose metabolism and muscle mass maintenance.

overall_design: We performed RNAseq analysis on RNA isolated from  quadriceps muscles of Fbxw7 muscle specific KO mice and control mice

first: E


title: Acquisition of CCDC88A/GIV through Tumor-Stroma Tunnels Promotes Aggressive Phenotypes of Estrogen Receptor-Positive Breast Cancer [dataset2]

overall_design: Co-culture model of bone marrow mesenchymal stem cells (MSCs)(HS5 and HS27a) and ER+ breast cancer cells (MCF7). Co-cultured cancer and stromal cells were separated before performing RNA sequencing. Data sets also include monoculture (MC) samples of cancer and stromal cells as well as cancer cells with conditioned medium (CM) from stromal cells.


title: SP1 undergoes phase separation and activates RGS20 expression through super-enhancers to promote lung adenocarcinoma progression (CUT＆RUN)

status: Public on Jun 20 2024

city: Harbin

first: Fang

last: Liu

address: Harbin health care road

institute: Harbin Medical University

summary: Lung adenocarcinoma (LUAD) is the leading cause of cancer-related death worldwide, but the underlying molecular mechanisms remain largely unclear. The transcription factor SP1 plays a crucial role in the development of various cancers, including LUAD. Recent studies have indicated that master transcription factors may form phase-separated macromolecular condensates to promote super-enhancer assembly and oncogene expression. In this study, we demonstrated that SP1 undergoes phase separation and that its zinc finger 3 in the DNA binding domain is essential for this process. Through CUT&RUN using antibodies against SP1 and H3K27ac, we discovered a significant correlation between SP1 enrichment and super-enhancer elements, identified the regulator of G protein signaling 20 (RGS20) gene as the most likely target regulated by SP1 through super-enhancer mechanisms, and verified this finding using different approaches. The oncogenic activity of SP1 relies on its phase separation ability and RGS20 gene activation, which can be abolished by GSK-J4, a demethylase inhibitor. Together, our findings provide the first evidence that SP1 regulates its target oncogene expression through phase separation and super-enhancer mechanisms, thereby promoting LUAD cell progression. This study also revealed a novel target for LUAD therapies through intervening in SP1-mediated super-enhancer formation.

overall_design: We investigate the H3K27ac histone modification or SP1 profiles of  H1299 cell lines.

first: Liying

last: Shan

first: Wenmeng


title: Plastid signaling triggers HDA6-mediated epigenetic programs during environmental sensing in plants [Bisulfite-seq]

city: University Park

first: Ha Eun

last: Jeh

state: PA

address: 362 Frear N Bldg

institute: Penn State University

type: Methylation profiling by high throughput sequencing

summary: Plants adapt to environmental changes by adjusting growth and defense, and the role of epigenetic modifications in this process is unclear. Sensing and adjusting to environmental changes are more important in certain tissues such as epidermis, vasculature, meristem, and reproductive tissues. These tissues possess sensory plastids that are specialized in environmental sensing. We show perturbation of four sensory plastid proteins MSH1, PPD3, CUE1, and SAL1 induce gene expression and DNA methylation changes targeted to networks associated to environmental sensing, with significant overlap with hda6-induced CHG hypermethylated genes at 12-hr daylength. At 16-hr daylength, hda6 loses CHG hypermethylation in gene body, and sensory plastid mutants have weaker phenotypes and DNA methylation- and gene expression- associated gene networks. We show daylength-responsive epistatic interaction between sensory plastid mutants with hda6. We also show that hda6 mutation confers daylength memory and, with msh1, enhanced tolerance to heat stress and biotic stress. These results suggest that HDA6 mediates programmed adjustments in plant phenotype triggered by sensory plastid-to-nucleus retrograde signaling in response to daylength and environmental cues.

overall_design: Aboveground tissues were collected at bolting or flowering stage. Three full-sib biological replicates were collected for each conditions. Five half-sib biological replicates were collected for hda6 Gen3, msh1/hda6 Gen2, and wild type samples.

first: Ha

middle: E

first: Devidutta

last: Samantaray

first: Sally

last: Mackenzie


title: Effects of Potassium Perchlorate on Developing Medaka Primordial Germ Cells

city: Greensboro

first: Ramji

middle: Kumar

last: Bhandari

state: NC

address: 321 McIver St

department: Biology

institute: University of North Carolina Greensboro

summary: The present study examined the effects of 0, 10, 100, and 1000 μg/L potassium perchlorate exposure on PGCs of medaka embryos and the expression pattern of genes that maintain PGCs integrity and epigenetic processes.

overall_design: To investigate the effect of potassium perchlorate on medaka development , fertilized eggs were exposed to 0, 10, 100, and 1000 μg/L of potassium perchlorate for 15 days and developmental defects were examined. Three biological replicates for each treatment

middle: K


title: Acquisition of CCDC88A/GIV through Tumor-Stroma Tunnels Promotes Aggressive Phenotypes of Estrogen Receptor-Positive Breast Cancer.


title: EZH2 protects mucosal melanoma from ferroptosis via the KLF14-SLC7A11 signaling pathway (ChIP-Seq)

city: Beijing

first: Haizhen

last: Du

state: Beijing

address: No.52 Fucheng Road, Haidian District

institute: Peking University Cancer Hospital and Institute

summary: Background: Mucosal melanoma (MM) is epidemiologically, biologically, and molecularly distinct from cutaneous melanoma. Current treatment strategies have failed to significantly improve the prognosis for MM patients. This study aims to identify therapeutic targets and develop combination strategies by investigating the mechanisms underlying the tumorigenesis and progression of MM. Methods: We analyzed the copy number amplification of EZH2 in 547 melanoma patients and investigated its correlation with clinical prognosis. Utilizing cell lines, organoids, and patient-derived xenograft models, we assessed the impact of EZH2 on cell proliferation and sensitivity to ferroptosis. Further, we explored the mechanisms of ferroptosis resistance associated with EZH2 by conducting RNA sequencing and chromatin immunoprecipitation sequencing. Results: EZH2 copy number amplification was closely associated with malignant phenotype and poor prognosis in MM patients. EZH2 was essential for MM cell proliferation in vitro and in vivo. Moreover, genetic perturbation of EZH2 rendered MM cells sensitized to ferroptosis. Combination treatment of EZH2 inhibitor with ferroptosis inducer significantly inhibited the growth of MM. Mechanistically, EZH2 inhibited the expression of KLF14, which binds to the promoter of SLC7A11 to repress its transcription. Loss of EZH2 therefore reduced the expression of SLC7A11, leading to reduced intracellular SLC7A11-dependent glutathione synthesis to promote ferroptosis. Conclusion: Our findings not only establish EZH2 as a biomarker for MM prognosis, but also highlight the EZH2-KLF14-SLC7A11 axis as a potential target for MM treatment.

overall_design: The submission includes samples from chromatin immunoprecipitation sequencing (ChIP-seq) experiments conducted on HMVII cells, a mucosal melanoma cell line. The primary objective of these experiments is to investigate the binding sites and genomic regions associated with EZH2, a key regulator in melanoma progression.

first: Lijie

last: Hou

first: Huan


title: Distinct actions of the cold water on host metabolism, gut barrier and microbiome-metabolites gut-brain modules in mice

city: Xi'an

first: Li juan

last: Sun

address: 229 Taibai North Road, Xi'an

institute: Northwest University

summary: The increased consumption of various beverages has been paralleled by an epidemic of several intestinal diseases around the world, such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS) and colorectal cancer. Mounting evidence have shown that excessive consumption of beverages increases the risk of IBD and IBS. In addition, sugar-sweeter, food additives and food ingredients were identified to play important roles in these conditions. Consuming cold beverage is common among some people, especially in the youngsters. However, whether the cold stress contribute directly to host metabolism, gut barrier and gut-brain axis is unclear. In an intestinal function disorder model induced by cold water in mice, we investigated changes in gut transit, anxiety and depression like behavior. To evaluate the effect of cold water on gut barrier, we investigate the tight junctions in the colon. In addition, we employed RNA sequencing transcriptomic analysis to identify genes potentially driving the gut injury, and in parallel, examine the gut microbiota and metabolites in the feces.In an intestinal function disorder model induced by cold water in mice, we investigated changes in gut transit, anxiety and depression like behavior. To evaluate the effect of cold water on gut barrier, we investigate the tight junctions in the colon. In addition, we employed RNA sequencing transcriptomic analysis to identify genes potentially driving the gut injury, and in parallel, examine the gut microbiota and metabolites in the feces.

overall_design: Expression profile of colon tissue from control mice and cold water treated mice

first: Lijuan

first: Yue

last: Chen

first: Jianxia

last: Song

first: Qiangqiang

last: Yuan


title: Single Nucleus DNA Sequencing of Flow Sorted Archived Frozen and Formalin Fixed Paraffin Embedded Solid Tumors

city: Scottsdale

first: Xianfeng

state: AZ

address: 13400 E Shea Blvd

institute: Mayo Clinic

summary: Archived tissues are a vast resource of annotated clinical samples. To expand their use for translational studies, we optimized flow sorting and sequencing of single nuclei from archived frozen and FFPE tumor tissues. Our methods, which include isolation and preparation of intact nuclei suitable for library preparations, quality control (QC) metrics for each step, and a single cell sequencing bioinformatic processing and analysis pipeline, were validated with flow sorted nuclei from matching frozen and FFPE ovarian cancer surgical samples and a sequencing panel of 553 amplicons targeting single nucleotide and copy number variants in genes of interest.

overall_design: frozen and FFPE matching paired ovarian cancer tissue

first: Jocelyn

last: Chapman

first: Michael

last: Barrett

first: Yumei

last: Zhou


title: Plastid signaling triggers HDA6-mediated epigenetic programs during environmental sensing in plants [RNA-seq]

first: Ha Eun


title: bHLH transcription factors cooperate with chromatin remodelers to regulate cell fate decisions during Arabidopsis stomatal development

city: Stanford

first: Dominique

middle: C.

last: Bergmann

address: 371 Jane Stanford Way

institute: Stanford University

summary: The development of multi-cellular organisms requires coordinated changes in gene expression that are often mediated by the interaction between transcription factors (TFs) and their corresponding cis-regulatory elements (CREs). During development and differentiation, the accessibility of CREs is dynamically modulated by the epigenome. How the epigenome, CREs and TFs together exert control over cell fate commitment remains to be fully understood. In the Arabidopsis leaf epidermis, meristemoids undergo a series of stereotyped cell divisions, then switch fate to commit to stomatal differentiation. Newly created or reanalyzed scRNA-seq and ChIP-seq data confirm that stomatal development involves distinctive phases of transcriptional regulation and that differentially regulated genes are bound by the stomatal basic-helix-loop-helix (bHLH) TFs. Targets of the bHLHs often reside in repressive chromatin before activation. MNase-seq evidence further suggests that the repressive state can be overcome and remodeled upon activation by specific stomatal bHLHs. We propose that chromatin remodeling is mediated through the recruitment of a set of physical interactors that we identified through proximity labeling – the ATPase-dependent chromatin remodeling SWI/SNF complex and the histone acetyltransferase HAC1. The bHLHs and chromatin remodelers localize to overlapping genomic regions in a hierarchical order. Furthermore, plants with stage-specific knock-down of the SWI/SNF components or HAC1 fail to activate specific bHLH targets and display stomatal development defects. Together these data converge on a model for how stomatal TFs and epigenetic machinery cooperatively regulate transcription and chromatin remodeling during progressive fate specification.

overall_design: Chromatin Immunoprecipitation DNA sequencing (ChIP-seq) for FAMA with anti-MYC antibody using a MYC tagged FAMA line, and control WT line that does not contain the transgene. Micrococcal Nuclease digestion with deep sequencing (MNase-seq) in seedlings with MUTE induced with estradiol or mock control. Replicates were pooled.

first: Ao

first: Juliana

middle: L

last: Matos


title: EZH2 protects mucosal melanoma from ferroptosis via the KLF14-SLC7A11 signaling pathway (RNA-Seq)

overall_design: To elucidate EZH2's role in mucosal melanoma progression, we performed RNA-seq  analysis on HMV-II cells with EZH2 knockdown by shRNA. The primary objective of this study is to investigate the gene expression profiles associated with EZH2 activity and identify key molecular pathways and gene networks influenced by EZH2.

last: Yu


title: Stress granule-mediated sequestration of EGR1 mRNAs correlates with lomustine-induced cell death prevention

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary:
Some chemotherapy drugs influence the formation of stress granules (SGs), cytoplasmic RNA foci involved in stress response pathways. The exact role of SGs in promoting cell survival or apoptosis needs further clarification. The chemotherapy drug lomustine induces SG formation by activating the eIF2α kinase HRI (EIF2AK1). We performed a DNA microarray transcriptome analysis to identify genes affected by lomustine-induced stress and to explore the role of SGs.
Our findings show that lomustine specifically regulates the expression of the pro-apoptotic EGR1 gene. The presence of EGR1 mRNA in SGs correlates with reduced translation of EGR1 mRNA. Lomustine likely sequesters EGR1 mRNA into SGs, preventing its ribosomal translation and thereby limiting apoptosis. This supports a model where SGs selectively sequester specific mRNAs in response to stress, modulate their translation, and thus determine the fate of stressed cells.

overall_design: The  human-derived HAP1 (parental, S51A, ΔHRI, ΔGCN2, ΔPKR, ΔPERK,  ΔEGR1 and ΔATF4) cell lines were purchased from Horizon Discovery,  UK. The mutations in ΔHRI, ΔGCN2, ΔPKR and ΔPERK cell lines were confirmed by sequencing. Furthermore, parental,  S51A, ΔHRI, ΔGCN2, ΔPKR and ΔPERK cell lines had already been used in another study, and their susceptibility for SG analysis was already  confirmed (Aulas et al., 2018). HAP cell lines were cultured in Iscove’s modified Dulbecco’s medium (IMDM, Gibco #12440-053) supplemented with 10% FBS (Thermo Fisher Scientific #10270106) and 1% penicillin-streptomycin. All cell lines were maintained at 37°C with 5% CO2. All cells were frequently tested for mycoplasma contamination using a MycoAlert Mycoplasma Detection Kit (Lonza, LT07-418).

first: Marta

last: Leśniczak-Staszak

first: Paulina

last: Pietras

first: Ryan

last: Johnston

first: Mateusz

last: Sowiński

first: Małgorzata

last: Andrzejewska

first: Michał

last: Nowicki

first: Ewelina

last: Gowin

first: Shawn

last: Lyons

first: Pavel

last: Ivanov

first: Witold

last: Szaflarski


title: The role of inflammatory macrophages in pathophysiology of experimental autoimmune myocarditis

city: Cracow

first: Karolina

last: Tkacz

address: ul. Wielicka 256

institute: Jagiellonian University Medical College

summary: Myocarditis is an inflammatory disease of the cardiac muscle characterized by an influx of inflammatory cells, predominantly of myeloid lineage. The progression of myocarditis to a dilated cardiomyopathy phenotype and heart failure is markedly influenced by TGF-β signalling. The aim of this study was to investigate the role of TGF-β signalling in inflammatory cardiac macrophages in the development of myocarditis and post-inflammatory fibrosis. Experimental autoimmune myocarditis (EAM) was induced in the LysM-Cre x R26-stop-EYFP x Tgfbr2-fl/fl transgenic mice showing impaired TGF-β signalling in the myeloid lineage and the LysM-Cre x R26-stop-EYFP control mice. Inflammatory macrophages were sorted from the inflamed hearts and analyzed for differential gene expression using whole genome transcriptomics.

overall_design: To investigate the role of TGF-β signalling in inflammatory cardiac macrophages in the development of myocarditis and post-inflammatory fibrosis we used LysM-Cre x R26-stop-EYFP x Tgfbr2-fl/fl transgenic mice showing impaired TGF-β signalling in the myeloid lineage and the LysM-Cre x R26-stop-EYFP control mice. We induced myocarditis and collected inflamed heart. Sorted inflammatory cardiac macrophages were used for whole genome transcriptomics.

first: Przemysław

last: Błyszczuk


title: RNA-seq of DRG-derived cell culture

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

institute: University Hospital Würzburg

summary: We performed mRNA-seq to characterize cultured dorsal root ganglia (DRG) cells from adult mice. Our data is based on ~25 million reads per sample in six independent RNA preparations. The transcript per millions (TPM) gene count distribution was homogenous between individual cultures. We analyzed the transcriptome for marker genes of different cell types present in the DRG. Expression profiles pointed to a sensory progenitor-like cell type originating from peripheral glial cells of the adult DRG. Such progenitor cells are interesting for reprogramming.

overall_design: Profiling of cells in 7 day old cell culture of dorsal root ganglia of adult mouse based on 6 biological replicates.

first: Annemarie

last: Sodmann

first: Thorsten

last: Bischler


title: Dual inhibition of P38 MAPK and JNK pathways preserves stemness markers and alleviates premature activation of Muscle Stem Cells during isolation

city: Créteil

first: Teoman

last: Ozturk

address: 8 rue du Général Sarrail

country: France

institute: INSERM IMRB U955

summary: Adult skeletal muscle contains resident Muscle Stem Cells (MuSC) with high myogenic and engraftment potentials, making them suitable for cell therapy and regenerative medicine approaches. However, purification process of MuSC remains a major hurdle to their use in the clinic. Indeed, muscle tissue enzymatic dissociation triggers a massive activation of stress signaling pathways, among which P38 and JNK MAPK, associated with a premature loss of MuSC quiescence. While the role of these pathways in the myogenic progression of MuSC is well established, the extent to which their dissociation-induced activation affects the functionality of these cells remains unexplored. We assessed the effect of P38 and JNK MAPK induction on stemness marker expression and MuSC activation state during isolation by pharmacological approaches. MuSC functionality was evaluated by in vitro assays and in vivo transplantation experiments. We performed a comparative analysis of the transcriptome of human MuSC purified with pharmacological inhibitors of P38 and JNK MAPK (SB202190 and SP600125, respectively) versus available RNAseq resources. We monitored PAX7 protein levels in murine MuSC during muscle dissociation and demonstrated a two-step decline partly dependent on P38 and JNK MAPK activities. We showed that simultaneous inhibition of these pathways throughout the MuSC isolation process preserves the expression of stemness markers and limits their premature activation, leading to improved survival and amplification in vitro as well as increased engraftment in vivo. Through a comparative RNAseq analysis of freshly isolated human MuSC, we provide evidence that our findings in murine MuSC could be relevant to human MuSC. Based on these findings, we implemented a purification strategy, significantly improving the recovery yields of human MuSC. Our study highlights the pharmacological limitation of P38 and JNK MAPK activities as a suitable strategy to qualitatively and quantitatively ameliorate human MuSC purification process, which could be of great interest for cell-based therapies.

overall_design: We compared the transcriptome of hMuSC purified following our protocol (referred to as hMuSC-40/PI) to that of hMuSC isolated after 120 min of dissociation without inhibitors previously published (hMuSC-120/no PI).

first: Nathalie

last: Didier


title: RIPK1 protects naïve and regulatory T cells from TNFR1-induced apoptosis

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

summary: The T cell population size is stringently controlled before, during, and after immune responses, as improper cell death regulation can result in autoimmunity and immunodeficiency. RIPK1 is an important regulator of peripheral T cell survival and homeostasis. However, whether different peripheral T cell subsets show a differential requirement for RIPK1 and which programmed cell death pathway they engage in vivo remains unclear. In this study, we used mesenteric lymph node (mLN) cells of Ripk1 KO mice, Ripk1/Casp8 double KO mice and their respective wild types to investigate this.

overall_design: Four mLN samples: Ripk1 KO mice, Ripk1/Casp8 double KO mice and their respective wild type littermates.

first: Jelle

last: Huysentruyt

first: Wolf

last: Steels

first: Mario

last: Ruiz Perez

first: Mike

last: Vadi

first: Tatyana

last: Divert

first: Kayleigh

last: Flies

first: Nozomi

last: Takahashi

first: Bart

middle: N

last: Lambrecht

first: Wim

last: Declercq

first: Tom

last: Vandenberghe

first: Jonathan

last: Maelfait

first: Peter

last: Vandenabeele

last: Tougaard


title: Comparison of RNA-Seq libraries for degraded RNA between SMART-Seq, xGen and RamDA-Seq

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

institute: Kanazawa Medical University Hospital

summary: Standard method of RNA-Seq captures mRNA by poly(A) capturing using Oligo dT beads, which is not suitable for degraded RNA. Here, we used three commercially available RNA-Seq library preparation kits (SMART-Seq, xGen Broad-range and RamDA-Seq) using random primer instead of Oligo dT beads. To evaluate the performance of these methods, we compared that the correla-tion, the number of detected expressing genes and the expression levels with Standard RNA-Seq method.SMART-Seq with rRNA depletion has relative advantages for RNA-Seq using low input and de-graded RNA.

overall_design: To evaluate the performance of these methods, we compared that the correlation, the number of detected expressing genes and the expression levels with Standard RNA-Seq method.

first: Yo

last: Niida


title: Excavation of biomarker candidates for the diagnosis of Talaromyces marneffei infection via genome-wide prediction and functional annotation of secreted proteins

city: nanning

first: jing

last: dan

state: Guangxi

address: Shuangyong Road, Qingxiu District,Nanning, 530021,China

institute: guangxi medicial university

summary: Talaromyces marneffei is the third most common infectious pathogen in AIDS patients and leads to the highest death rate in Guangxi, China. The lack of reliable biomarkers is one of the major obstacles in current clinical diagnosis, which largely contributes to this high mortality. Here, we present a study that aimed at identifying diagnostic biomarker candidates through genome-wide prediction and functional annotation of Talaromyces marneffei secreted proteins. A total of 584 secreted proteins then emerged, including 382 classical and 202 non-classical ones. Among them, 87 newly obtained functional annotations in this study. The annotated proteins were further evaluated by combining RNA profiling and homology comparison. Three proteins were ultimately highlighted as biomarker candidates with robust expression and remarkable specificity. The predicted phosphoinositide phospholipase C and the galactomannoprotein were suggested playing an interactive immune game though metabolism of arachidonic acid. And therefore, they hold promises in developing new tools for clinical diagnosis of Talaromyces marneffei, possibly also serve as molecular targets of future therapy.

overall_design: Standard strain of T. marneffei ATCC18224 was obtained from American Type Culture Collection (ATCC) and cultured under yeast condition. In brief, fungus was expanded in 37℃ for 14 days, with 200-220 rpm rotation in RPMI 1640 medium plus 10% FBS (Fetal Bovine Serum). Fungus was then precipitated with centrifuge of 14000 g for 10 minutes60. RNA samples were then extracted and sequenced in GeneChem (China). Three independent biological replicates were set in parallel from culture to profiling. Reads were calculated and normalized for each unique transcript.

first: Wudi

last: Wei


title: Prokaryotic N1-methyladenosine erasers maintain tRNA m1A modification levels in Streptomyces venezuelae.

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: tRNA modifications help maintain tRNA structure and facilitate stress responses. Found in all three kingdoms of life, m1A tRNA modification occurs in the T loop of many tRNAs and stabilizes tertiary tRNA structure and impacts translation. M1A in T loop is known to be reversible by three mammalian demethylase enzymes, which bypasses the need of turning over the tRNA molecule to adjust their m1A levels in cells. However, no prokaryotic tRNA demethylase enzyme has been identified. Using Streptomyces venezuelae as a model organism, we confirmed the presence and quantitative m1A tRNA signatures using mass spectrometry and high throughput tRNA sequencing. We identified two RNA demethylases that can remove m1A in tRNA and confirmed the activity of a previously annotated tRNA m1A writer. Using single gene knockouts of these erasers and the m1A writer, we subjected these strains to stress conditions and found dynamic changes to m1A levels in many tRNAs. Phenotypic characterization highlighted changes to their growth and altered antibiotic production. Our identification of the first prokaryotic tRNA demethylase enzyme paves the way for investigating new mechanisms in global translational regulation in bacteria.

overall_design: To investigate the changes to m1A modification levels across tRNA populations in Streptomyces venezuelae. Streptomyces venezuelae strains were grown in control and stress conditions, after which RNA was collected from each condition and underwent MSR-seq. Generated libraries were sequenced using Illumina technology. After initial processing of reads, libraries were aligned to a curated tRNA reference file. Associated tRNA properties (modification, charging and abundance) were calculated using a custom pipeline using Python and R scripts.

first: Marcus

last: Foo

first: Luke

last: Frietze

first: Behnam

last: Enghiad

first: Yujie

last: Yuan

first: Chris

last: Katanski

first: Huimin

last: Zhao


title: Impact of RUNX3 KO on H3K27ac abundance in human NK cells

city: St. Louis

first: Jacqueline

last: Payton

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: The surface receptor CD8a is present on 20-80% of human (but not mouse) NK cells, yet its function on NK cells remains poorly understood. CD8a expression on donor NK cells was associated with a lack of therapeutic responses for leukemia patients in prior studies, thus we hypothesized that CD8a may impact critical NK cell functions. Here, we discovered that CD8a- NK cells had improved control of leukemia in xenograft models, compared to CD8a+ NK cells, likely due to an enhanced capacity for proliferation. Unexpectedly, CD8a expression was induced on approximately 30% of previously CD8a- NK cells following IL-15 stimulation. These ‘induced’ CD8a+ (‘iCD8a+’) NK cells had the greatest proliferation, responses to IL-15 signaling, and metabolic activity, compared to those that sustained existing CD8a expression (‘sustained CD8a+) or those that remained CD8a- (‘persistent CD8a-‘). These iCD8a+ cells originated from an IL-15Rb high NK cell population, with CD8a expression dependent on the transcription factor RUNX3. Moreover, CD8A CRISPR/Cas9 deletion resulted in enhanced responses through the activating receptor NKp30, possibly by modulating KIR inhibitory function. Thus, CD8a status identifies human NK cell capacity for IL-15-induced proliferation and metabolism in a time-dependent fashion and exhibits a suppressive effect on NK cell activating receptors

overall_design: CUT&TAG was performed on control and RUNX3 KO human NK cells, and abundance of histone modifications H3K27ac was quantified. Briefly, freshly isolated NK cells were electroporated with RUNX3 or TRAC sgRNA and Cas9 mRNA, cultured in vitro in 5 ng/mL IL-15 for 9 days, and processed using the Active Motif CUT&TAG-IT assay kit

first: Celia

last: Cubitt

first: Todd

last: Fehniger


title: Comparing gene expression in ABT-199 (venetoclax) sensitive and resistant diffuse large B cell lymphoma cell (DLBCL) lines

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

summary: RNA-sequencing was performed to evaluate gene expression changes between ABT-199 (venetoclax) sensitive and resistant matched diffuse large B cell lymphoma cell lines

overall_design: RNA-sequencing gene expression profiles were generated in two different ABT-199 (venetoclax) sensitive and resistant matched diffuse large B cell lymphoma cell lines

first: Christine

last: Eischen