title: Tra2b's Ultraconserved Poison Exon relays TCR stimulation to shape T cell fate [N4T4Seq]

summary: Analysis of transcript changes with enough depth for evaluation of splicing changes between CD8+ T cells from mice receiving high affinity SIINFEKL (N4) and moderate affinity SIITFEKL (T4) peptide + anti-OX40/anti-41BB costimulation

overall_design: OT-I CD8+ T cells from the spleens of mice 4 days after stimulation with N4 or T4 peptide (+anti-OX40/anti-41BB costimulation)


title: Cancer-associated SF3B1-K700E mutation controls immune responses by regulating Treg function via aberrant Anapc13 splicing

status: Public on Jun 01 2024

city: Duarte,

first: Yun

last: Shi

state: CA

address: 1500 E Duarte Rd

country: USA

institute: City of Hope

type: Expression profiling by high throughput sequencing

summary: Recurrent somatic mutations in spliceosome factor 3b subunit 1 (SF3B1) are identified in hematopoietic cell-derived malignancies, with SF3B1-K700E being the most common one. Here we show that Treg specific expression of SF3B1-K700E (Sf3b1K700Efl/+/Foxp3YFP-Cre) results in spontaneous autoimmune phenotypes including enlarged spleen and tissue infiltration with IFN-γ-producing CD4+ T cells. CD4+ T cells from Sf3b1K700Efl/+/Foxp3YFP-Cre mice display defective Treg differentiation and inhibitory function, which is demonstrated by failed prevention of adoptive transfer colitis by Sf3b1K700Efl/+/Foxp3YFP-Cre Tregs. Mechanically, SF3B1-K700E induces an aberrant splicing event that results in reduced expression of a cell proliferation regulator Anapc13 due to insertion a 231 bp DNA fragment to the 5’ untranslated region (UTR). Forced expression of Anapc13 gene restores the differentiation and ability of Sf3b1K700Efl/+/Foxp3YFP-Cre Tregs to prevent adoptive transfer colitis. Our results thus highlight the impact of a hematological malignancy-associated SF3B1 mutation on immune responses and indicate a potential relationship between splicing factor mutation-dysregulated immune responses and cancer development.

overall_design: To investigate the influnce of Cancer-associated SF3B1-K700E mutation in the Treg cell differentiation,we sort Naive CD4+ T cells  from Sf3b1K700E/fl or Sf3b1K700E/fl /Cd4Cre mice were differentiated into Tregs in 48-well plates in the presence of TGFβ (5 ng/ml), hamster anti-CD3 , hamster anti-CD28,anti–IL-4, and anti-IFNγ for 36 hours. CD4+ cells after 36 hours of Treg differentiation were collected and subjected to RNA extraction with the RNeasy Mini Kit (QIAGEN).  Comparative gene expression and splicing events profiling analysis using data obtian from RNA-Seq data.

first: Wencan

last: Zhang

first: Qiong

last: Ja

first: Xiancai

last: Zhong

first: Prajish

last: Lyer

first: Hongmin

last: Wu

first: Yate-Ching

last: Yuan

first: Yuqi

last: Zhao

first: Lili

last: Wang

first: Zhenyu

last: Jia

first: Zuoming

last: Sun


title: Complimentary vertebrate Wac models exhibit phenotypes relevant to DeSanto-Shinawi Syndrome

city: Davis

first: Karol

last: Cichewicz

address: 1544 Newton Ct

department: Center for Neuroscience

institute: UC Davis

summary: Monogenic syndromes are associated with neurodevelopmental changes that result in cognitive impairments, neurobehavioral phenotypes including autism and attention deficit hyperactivity disorder (ADHD), and seizures. Limited studies and resources are available to make meaningful headway into the underlying molecular mechanisms that result in these symptoms. One such example is DeSanto-Shinawi Syndrome (DESSH), a rare disorder caused primarily by pathogenic variants in the WAC gene. Individuals with DESSH syndrome exhibit a recognizable craniofacial gestalt, developmental delay/intellectual disability, neurobehavioral symptoms that include autism, ADHD, behavioral difficulties and seizures. However, no thorough studies from a mammalian model exist to understand how these changes occur. To overcome this, we developed both murine and zebrafish Wac deletion mutants and studied whether their phenotypes recapitulate those described in individuals with DESSH syndrome. We show that the two Wac models exhibit craniofacial and behavioral changes, reminiscent of abnormalities found in DESSH syndrome. In addition, each model revealed impacts to GABAergic neurons and further studies showed that the mouse mutants are susceptible to seizures. These studies begin to uncover some biological underpinnings of DESSH syndrome and elucidate the biology of Wac, with advantages in each model.

overall_design: 14 WT controls and 10 Wac HETs; 7 males and 7 females, and 5 males and 5 females, respectively.

first: Kang-Han

last: Lee

first: April

middle: M

last: Stafford

first: Maria

last: Pacheco-Vergara

first: Cesar

middle: P

last: Canales

first: Nicolas

last: Seban

first: Melissa

last: Corea

first: Darlene

last: Rahbarian

first: Kelly

last: Bonekamp

first: Dariangelly

last: Cruz

first: Alyssa

last: Gill

first: Hye-Eun

last: Hwang

first: Katie

middle: L

last: Uhl

first: Tara

middle: E

last: Jager

first: Marwan

last: Shinawi

first: Xiaopeng

last: Li

first: Andre

last: Obenaus

first: Shane

last: Crandall

first: Juhee

last: Jeong

first: Alex

middle: S

last: Nord

first: Cheol-Hee

last: Kim

first: Daniel

last: Vogt


title: RNA seq of pediartic patients in oneset of early T-cell precursor acute lymphoblastic leukemia

city: Moscow

first: Elena

last: Zerkalenkova

address: Samora Mashela str., 1

country: Russia

institute: Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology

summary: Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) develops from very early cells with the potential for both T-cell and myeloid differentiation. The ambiguous nature of leukemic blasts in ETP-ALL may lead to immunophenotypic alterations at relapse. Here, we address immunophenotypic alterations and related classification issues, as well as genetic features of relapsed pediatric ETP-ALL. RNAseq was performed with the primary goal of crypric gene fusions search within subcohorts of relapsed and non-relapsed patients with sufficient material available. Overall, 3 relapsed and 8 non-relapsed patients were tested. As a relsult, 1 relasped and 3 non-relapsed patients were found to carry leukemia-specific fusions, of those 3 were confurmed by FISH (2 cases of ETV6 rearrangements and one PICALM::MLLT10-positive case) while only one cryptic rearrangement was caught in a non-relapsed patient (BCL11B cryptic rearrangement negative by FISH). Other 7 patients were not found to carry any leukemia-specisic fusions.

overall_design: Whole bone marrow was taken from patients in the oneset of the disease with >80% bone marrow blasts. RNAseq was performed to search for cryptic leukemia-specific fusion transcripts.

first: Alexandra

last: Borkovskaya


title: Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (BS-seq)

city: Hohhot

first: jing

last: wang

state: Nei Mongol

address: Zhaojun Road

country: China

institute: Inner Mongolia University

type: Methylation profiling by high throughput sequencing

summary: While DNA methylation in other tissues can be approximated through model species, the dynamic distribution and regulatory significance of DNA methylation in the rumen, a unique organ in ruminant, remain largely unknown. Here, we employed whole-genome bisulfite sequencing (WGBS), transcriptomics, and histone modification data to compare fetal and adult stages of bovine rumen with other tissues, including pluripotent stem cells (PSCs) approximating pre-implantation embryos. We found extensive methylation differences, including CG methylation (mCG) and non-CG methylation (mCH; H represents A, C and T) between the rumen at fetal and adult stages and other tissues and PSCs. These differentially methylated regions (DMRs) are closely associated with other epigenetic regulatory components, such as transcription factors (TFs) and histone modifications. These DMRs can also combine to form large hypo CG-DMRs to regulate a cluster of functionally related genes. We elucidated the reasons for morphological and functional differences between fetal and adult rumen at the epigenetic level and the interactions between epigenetic modifications and gene expression. This study highlights the differences in methylation patterns between the rumen and other tissues during development and the role of DNA methylation in controlling gene expression and establishing tissue-specific functions.

overall_design: To assess the cytosine DNA methylation landscape during bovine development, we generated sequencing data for Holstein bovine fetal tissues (forebrain, hindbrain, testes, heart, liver, lung, kidney, muscle, rumen) and various bovine pluripotent stem cells (bESCs-F7, bESCs-F7-5, bESCs-F7-50, bEPSCs-AGS, bEPSCs-B18). Culture of bovine embryonic stem cell lines: The bovine embryonic stem cell line bESCs-F7 was established using the CTFR system. Two treatment methods were employed for bESCs-F7 using MM-102: one involved treating bESCs-F7 with a high concentration (50 μM) of MM-102 for 7 days, followed by normal culturing for 5 passages before characterization, labeled as bESCs-F7-102 (50). The other involved long-term treatment with a low concentration (5 μM) of MM-102, followed by characterization after 5 passages of culturing, labeled as bESCs-F7-102 (5). Bovine induced pluripotent stem cells and the bEPSCs-B18 cell line were established using the LCDM system. And bEPSCs-AGS was using a 500mL system, including 485mL of basic mTeSR1 medium, 5.0 mL of 100×Penicillin-Streptomycin Solution, 0.1 mM 2-mercaptoethanol, 1 μM GSK3β inhibitor CHIR99021, 0.3 μM Lck/Src inhibitor WH-4-023, 5 μM Tankyrase inhibitor XAV939, 5 μM classic WNT signaling pathway inhibitor IWR-1, 50 μg/mL Vitamin C, 10 ng/mL Leukemia Inhibitory Factor (LIF), and 20.0 ng/mL Activin A for culturing bovine Embryonic Pluripotent Stem Cells.

first: Jing

last: Wang

first: Wen

last: Yuan

first: Fang

last: Liu

first: Xueling


title: Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (RNA-seq)


title: Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (CUT&Tag-seq)


title: Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (ATAC-seq)


title: Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (ChIP-seq)


title: Construction of N6 Methyladenosine Atlas in Yak Epididymis Reveals the Process of Sperm Maturation Modification

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

summary: The epididymis is an important component of the male reproductive system and a crucial site for sperm maturation. During the process of sperm maturation through the epididymis, the effective payload of SncRNA significantly changes, which may be related to epigenetic modifications. Unfortunately, the N6 Methyladenosine (m6A) modification profile of the epididymis has not yet been established. In this study, the MeRIP seq combined with RNA seq method was used to analyze the m6A modification levels in the head, body, and tail of yak epididymis. It was found that the level of m6A in the epididymis significantly increased, and differentially methylated RNAs (DMRs) in the proximal end of the epididymis were significantly enriched in Gap junction, ErbB signaling pathway, and mTOR signaling pathway, participating in cell communication and sperm maturation processes. In the distal epididymis, DMRs are enriched in Apoptosis, FoxO signaling pathway, PI3K Akt signaling pathway, and TNF signaling pathway, which are involved in sperm autophagy, oxidative stress, and sperm maturation. In addition, we identified key genes with significant changes in m6A levels but no differences in RNA levels, including YY1 associated factor 2 (YAF2), Fork head box J2 (FOXJ2), and Fork head box O1 (FOXO1), suggesting that these genes are modified by m6A to affect translation processes and participate in sperm maturation. In summary, our study established an m6A map of the epididymis, which is beneficial for further understanding the maturation process of sperm and revealing more information related to male infertility.

first: Ziqiang

last: Ding

first: Xingdong

first: Jie

last: Pei

first: Xian

last: Guo


title: Deciphering Mycobacterium tuberculosis glycan epitopes through clustering of human polyclonal and isolating novel monoclonal antibodies II

city: Bronx

first: Jacqueline

last: Achkar

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary:
The immunomodulatory mycobacterial surface antigen lipoarabinomannan (LAM) with its immunogenic glycan component arabinomannan (AM) facilitates Mycobacterium tuberculosis’ (Mtb) escape from the host’s immune response. Some but not all antibodies against AM can protect against TB. To better understand which of AM’s structures to target, we must first identify the spectrum of its epitopes.
Through isolating and characterizing a panel of novel human mAbs with binding to distinct AM OS motifs, we further defined the glycan epitope structures, identified a new epitope, and determined their differences among mycobacterial strains.

overall_design: Monoclonal antibodies at 5 ug/ml were tested for direct binding to 30 synthetic oligosaccharides

first: Tingting

last: Chen

first: Yanyan

first: Todd

last: Lowary


title: Kentucky assay: C5 ketone (2-pentanone)

city: Lexington

first: Tim

last: McClintock

state: KY

address: 780 Rose St.

department: Physiology

institute: University of Kentucky

summary:
Mice have 1,100 odorant receptors.  Nearly all are orphan receptors.  The pattern of receptor responses to odorants is the input that allows the brain to detect and discriminate odors
The Kentucky assay measures the function of each of the 1,100 odorant receptors and 14 TAARs  in vivo.

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or 2-pentanone were subjected to microarray analysis using Clariom S arrays

first: Timothy


title: Kentucky assay: C5 acid (pentanoic acid)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or pentanoic acid were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C8 alcohol (octanol)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or octanol were subjected to microarray analysis using Clariom S arrays


title: Deconstruction of cellular dynamics after treatment of volumetric muscle loss injury with extracellular matrix

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2800 Plymouth Rd.

department: Biomedical Engineering

institute: University of Michigan

summary: Volumetric muscle loss (VML) is an acute loss of a critical volume of skeletal muscle that results in inflammation, fibrotic scarring in muscle tissue, and permanent muscle defects. The cellular and molecular processes that underlie fibrosis induced from VML injury need to be evaluated in larger animal models. Therefore, we used a canine model of VML alongisde treatment with an extracellular matrix (ECM) hydrogel. Treatment with the ECM hydrogel improved muscle regenerative responses and decreased proportions and spatial signatures of fibrotic and inflammatory cell populations.

overall_design: For single-nuclear RNA sequencing, samples were collected from biopsy samples of untreated canine skeletal muscle tissues at  0, 7, and 14 days post volumetric muscle loss (VML) injury. Canine tissues from animals at 0, 7, and 14 days post VML were collected for spatial gene expression profiling. Samples wereflash-frozen, OCT embedded, muscle tissue. Canine tissues were collected in different wound locations (mid or edge) in treated samples. There were a total of 4 replicates for untreated samples, 3 untreated samples at 7 days post injury, 3 untreated samples at 14 days post injury, and 4 ECM-treated samples at 14 days post injury.

middle: A

first: Adrienne

last: Giannone

last: Larouche

first: Grace

last: Kenny

first: Paula

last: Fraczek


title: Kentucky assay: C5 alcohol (1-pentanol)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or pentanol were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C8 acid (octanoic acid)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or octanoic acid were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C6 ketone (2-hexanone)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or 2-hexanone were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C6 alcohol (hexanol)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or hexanol were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C8 ketone (2-octanone)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or 2-octanone were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C6 acid (hexanoic acid)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or hexanoic acid were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C7 alcohol (heptanol)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or heptanol were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: C7 acid (heptanoic acid)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or heptanoic acid were subjected to microarray analysis using Clariom S arrays


title: Nab-paclitaxel induces DNA damage and inhibits M2 polarization of macrophages to achieve radiosensitization of cholangiocarcinoma cells.

city: Wuhan

first: Ningyu

state: Hubei

address: JIEFANG ROAD1277#

department: Cancer Center, Union Hospital

institute: Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China

summary: Through transcriptome sequencing, it was determined that AMPK is a key pathway involved in the radiosensitization effect of nab-paclitaxel, and its sensitization effect may be attributed to ZMAT3 and NF- κB signaling pathway is closely related.

overall_design: In order to investigate the mechanism of nab-paclitaxel in enhancing radiotherapy sensitivity of cholangiocarcinoma, we used a cholangiocarcinoma cell line TFK1, and set up a blank control group, a radiotherapy group (6Gy), a chemotherapy group  (nab-paclitaxel 1.62ng/ml), and a combination treatment group (nab-paclitaxel 1.62ng/ml+RT 6Gy). After 24 hours of treatment, total RNA was extracted for transcriptome sequencing in different treatment groups.

first: Wang

last: Ningyu

first: Huang

last: Ai

first: Mei

last: Xiangping

first: Ma

last: Hong


title: Deciphering Mycobacterium tuberculosis glycan epitopes through clustering of human polyclonal and isolating novel monoclonal antibodies I

summary:
The immunomodulatory mycobacterial surface antigen lipoarabinomannan (LAM) with its immunogenic glycan component arabinomannan (AM) facilitates Mycobacterium tuberculosis’ (Mtb) escape from the host’s immune response. Some but not all antibodies against AM can protect against TB. To better understand which of AM’s structures to target, we must first identify the spectrum of its epitopes.
We here used synthetic AM oligosaccharide motifs to deplete sera from subjects along the spectrum of Mtb infection. Performing cluster analysis, we were able to predict AM’s immunogenic structures and delineate how antibody reactivity to them is influenced by Mtb infection states.

overall_design: Human plasma samples were tested for direct binding to 30 synthetic oligosaccharides

last: Liu


title: Kentucky assay: C7 ketone (2-heptanone)

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or 2-heptanone were subjected to microarray analysis using Clariom S arrays


title: Single Cell Landscape of Left Atria Reveals Amphiregulin and Insulin-like Growth Factor 1 as Surrogate Markers in Patients with Atrial Fibrillation.

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

country: Japan

institute: Kobe University Graduate School of Medicine

summary: Atrial fibrillation (AF) is strongly associated with strokes, heart failure, and increased mortality. Inflammation plays a role in the pathophysiology of AF; however, how inflammation in AF is sustained and induces fibrosis is unclear. Therefore, this study aimed to identify the characteristic monocyte–macrophage heterogeneity and the cell–cell interactions between immune and non-immune cells at a single cell level in the left atrial (LA) tissues of patients with AF who underwent LA appendectomies. Myeloid cells were divided into five macrophage clusters, TNF+, two IL1B+, TREM2+, LYVE1+ resident macrophages, three monocyte clusters, five dendritic cell clusters, neutrophils, and mast cells. The CellChat analysis revealed that IL1B+ macrophages send epidermal growth factor (EGF) signalling to fibroblasts and resident macrophages send IGF1 singalling to cardiomyocytes. When compared to openly published control samples, Amphiregulin (AREG) was the most upregulated gene in monocytes and monocyte-derived IL1B+ macrophages in the AF group. We also found that AREG levels in serum were higher in patients with AF than controls. EGF signalling from IL1B+ macrophages could be therapeutic targets for AF, and AREG could be a functional biomarker for AF.

overall_design: CD45 positive cells of human left atium samples were isolated by Fluorescence-activated cell sorting and analyzed using scRNAseq, moreover, all cells of human left atium samples were analyzed using snRNAseq

first: Yuya

last: Suzuki


title: Glucocorticoid promotes metastasis of colorectal cancer via co-regulation of glucocorticoid receptor and TET2 (ChIP-Seq)

city: Shenzhen

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

summary: Background  Glucocorticoids (GCs), commonly used for anti-inflammatory and cancer treatments, have been linked to the promotion of cancer metastasis. Yet, the molecular mechanisms behind this potential remain poorly understood. Clarifying these mechanisms is crucial for a nuanced understanding and potential refinement of GC therapies in the context of cancer treatment. Methods  In HEK293T cells, co-immunoprecipitation (Co-IP) and chromatin immunoprecipation sequencing (ChIP-seq) were used with antibodies of GR and TET family proteins (TET1, TET2, TET3). Drup repositioning was performed through the LINCS database, using common genes of GR and TET2 in HEK293 and HCT116 cell lines with CRC differentially expressed genes (DEGs). Cell migration and invasion were tested in colorectal cancer (CRC) cell lines with varying glucocorticoid receptor (GR) expression, i.e., HCT116 and HT29 cell lines.  Findings  Dexamethasone (Dex) treatment resulted in a significant difference in cell migration rates in two CRC cell lines with disparate GR expression levels. Co-IP and ChIP-seq analyses substantiated the interaction between GR and TET family proteins in HEK293T cells. Belinostat, the selected compound, was successfully validated for its potential to counteract the effects of GC-induced inversion in CRC cells in vitro. Transcriptomic analyses of Belinostat-treated HCT116 cells revealed down-regulation of target genes associated with cancer metastasis..  Interpretation This study provides valuable insights into the molecular mechanisms underlying GC-induced metastasis, introducing newly repositioned compounds that could serve as potential adjuvant therapy to GC treatment. Furthermore, it opens avenues for exploring novel drug candidates for CRC treatment.

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) for GR, TET1, TET2, TET3 in HCT116 and HT29 cells.

first: Yanwei

last: Song

first: Shuqiang

last: Ren

first: Shumei

last: Wu

first: Weidong

first: Chenghao

last: Hu

first: Siting

last: Feng

first: Xinyu

first: Du

last: Zhang

first: Rui

last: Tu

first: Fei


title: The transcriptomic landscape of multiple organs in CHIKV-infected Rhesus monkeys and mice

city: 昆明市

first: Lin

last: dongdong

state: 云南

address: 云南省昆明市五华区茭菱路

institute: Peking Union Medical College

type: Non-coding RNA profiling by high throughput sequencing

summary: Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has emerged as a significant public health concern due to its ability to cause severe arthralgia and occasionally fatal cases. The virus has been shown to infect a wide range of tissues, including the heart, liver, spleen, lungs, kidneys, and brain, leading to a spectrum of clinical manifestations.This study aims to investigate the impact of CHIKV infection on the transcriptome of various organs in rhesus monkeys and mice, providing insights into the molecular mechanisms underlying the pathogenesis of CHIKV in different host species.The transcriptome analysis revealed significant alterations in gene expression across the infected tissues in both species.

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus

overall_design: Following experimental infection with CHIKV, tissues from the heart, liver, spleen, lungs, kidneys, and brain were harvested from both rhesus monkeys and mice. Transcriptome sequencing was performed to analyze the global gene expression changes in response to the viral infection.

first: Dongdong

last: Lin

first: Cong

last: Tang


title: HINT2 Protects Against Pressure Overload-induced Cardiac Remodeling Through Mitochondrial Pathways

first: Ziying

last: Zhou

address: Jiefang Road 238

institute: Renmin Hospital of Wuhan University

summary: Histidine triad nucleotide-binding protein 2 (HINT2) is an enzyme found in mitochondria that functions as nucleotide hydrolase and transferase. Prior studies have demonstrated that HINT2 plays a crucial role in ischemic heart disease but the significance of HINT2 in cardiac hypertrophy remains unknown. Therefore, the current study aims to determine the role of HINT2 in cardiac remodeling. HINT2 expression was found to be lower in failing hearts and hypertrophic cardiomyocytes. The mice that overexpressed HINT2 exhibited reduced myocytes hypertrophy and cardiac dysfunction in response to stress. Conversely, the deficiency of HINT2 in the heart of mice resulted in a worsened hypertrophic phenotype. Further analysis indicated that the upregulated genes were primarily associated with the oxidative phosphorylation and mitochondrial complex I pathway in the HINT2-overexpressed mice after aortic banding (AB) treatment. This suggests that HINT2 upregulated the expression of NDUFs genes. In cellular studies, the protective effect of overexpressing HINT2 was nullified. Lastly, we predicted that THRB might regulate HINT2 transcriptional activity. To conclusion, the current study showcased that HINT2 alleviates pressure overload-induced cardiac hypertrophy by depending on the activity and assembly of mitochondrial complex I. Thus, targeting HINT2 could be a novel therapeutic intervention for reducing cardiac remodeling.

overall_design: To understand the protective effects of HINT2, we performed RNA-seq assays on HINT2-TG mouse hearts and NTG hearts after AB treatment.

first: Haihan

last: Liao

first: Qizhu


title: The role of adipocyte lipolysis during dermal fibrosis

city: New Haven

first: Elizabeth

middle: Ann

last: Caves

state: Connecticut

address: 260 Whitney Ave

department: Molecular, Cellular and Developmental Biology

institute: Yale University

summary: Lipolysis is an early event during derma; fibrosis progression. We wanted to see how the loss of lipolysis impacted cell dynamics within the

overall_design: The mouse model, AdiCreER; mT/mG; Atglfl/fl, are able to conditionally knock out adipocyte lipolysis. Male mice between 6-8 weeks are shaved and receive 1 dose of topical tamoxifen on the back skin 2 days prior to injections. Mice were then injected subcutaneously for 5 days with either PBS or Bleomycin Sulfate. Back skin was collected and dissociated and submitted for scRNA-sequencing.

first: Valerie

last: Horsley


title: Characterization of extracellular vesicles in plasma and synovial fluid of horses with naturally occurring post-traumatic osteoarthritis: An exploratory study to identify transcriptomic profiles.

city: Raleigh

first: Shannon

last: Connard

state: NC

address: 1060 William Moore Drive

department: Clinical Sciences

institute: North Carolina State University

summary: Objective: The objective of this study was to characterize extracellular vesicles (EVs) in plasma and synovial fluid obtained from horses with and without naturally occurring post-traumatic osteoarthritis (PTOA). Animals (Samples): EVs were isolated from plasma and synovial fluid from horses with (n = 6) and without (n = 6) PTOA. Methods: Plasma and synovial fluid EVs were characterized with respect to quantity, size, and surface markers. Small RNA sequencing was performed and differentially expressed miRNAs underwent bioinformatic analysis to identify putative targets and to explore potential associations with specific biological processes. Results: Plasma and synovial fluid samples from horses with PTOA had a significantly higher proportion of exosomes and a lower proportion of microvesicles compared to horses without PTOA. Small RNA sequencing revealed several differentially expressed miRNAs including miR-144, miR-219-3p, and miR-199a-3p in plasma and miR-199a-3p, miR-214, and miR-9094 in synovial fluid EVs. Bioinformatics analysis of the differentially expressed miRNAs highlighted their potential role in fibrosis, differentiation of chondrocytes, apoptosis, and inflammation pathways in PTOA. Clinical Relevance: We have identified dynamic molecular changes in small non-coding signatures of plasma and synovial fluid EVs in horses with naturally occurring PTOA. These findings could serve to identify promising biomarkers in the pathogenesis of PTOA, to facilitate the development of targeted therapies, and to aid in establishing appropriate translational models of PTOA.

overall_design:
A single pooled sample containing EVs from 6 horses for each group including plasma control (n=1), plasma PTOA (n=1), synovial fluid control (n=1), synovial fluid PTOA (n=1)
**Submitter states that the intact R2 (raw data) mate file for the Synovial fluid  control sample ('SynFld-Control_R2_001.fastq.gz') is unavailable and thus only R1 file is provided**

first: Kyla

last: Ortved


title: Manipulating the transcriptome and chromatin accessibility in T cells through CRISPR-induced alternative splicing of IKZF1 (ATACseq)

city: Gainesville

first: Jeremy

middle: Robert Barker

last: Newman

state: FL

address: 2033 Mowry Road

department: Genetics Institute

institute: University of Florida

summary: Genome-wide association studies have identified statistically significant associations between genetic variants in or near the IKZF1 gene and several autoimmune disorders. IKZF1, encoding the transcription factor Ikaros, produces at least 10 distinct transcripts via alternative splicing.  To explore the role of alternative splicing of IKZF1 in mature T cells, we generated a panel of Jurkat T-cell clones with various truncating mutations in IKZF1 exon 4, exon 6 or both. Differences among clones in gene expression, chromatin accessibility, and protein abundance were assessed by RNA-seq, ATAC-seq and immunoblotting. Clones with single targeting events in either exon 4 or 6 clustered separately from double-targeted clones on multiple parameters, but overall, clone responses were highly heterogeneous. Perturbation of IKZF1 splicing resulted in significant differences in expression and chromatin accessibility of other autoimmunity-associated genes and elicited compensatory expression changes in other IKZF family members. Our results suggest that even modest perturbations of IKZF1 splicing can have significant effects on gene expression and function in mature T cells.

overall_design: Exons 4 and 6 of the human IKZF1 gene in Jurkat cell lines were edited using CRISPR/Cas9.  Chromatin accessibility profiling was performed using ATAC-seq of four WT clones, seven clones with edits in IKZF1 exon 4, five clones with edits in IKZF1 exon 6, and eight clones with edits in IKZF1 exons 4 and 6. Analysis of chromatin accessibility was performed comparing WT clones to CRISPR-edited clones based on exons edited and protein detection.

first: Lucia

last: Pastor

middle: R

first: Colin

last: Callahan

first: M

last: Atkinson

first: S

last: Onengut-Gumuscu

first: P

last: Concannon


title: HuR targetome analysis in THP-1 macrophages using HuR FLASH-Seq.

city: Hangzhou

first: Zhicheng

last: Pan

address: 79 Qingchun Road

department: Department of Cardiology

institute: The First Affiliated Hospital, Zhejiang University School of medicine

summary: FLASH, a novel method, was utilized to identify binding sites of RNA-binding proteins (RBPs) with single-nucleotide resolution (Nucleic Acids Res 2020;48:e15). In order to identify HuR target genes in THP-1 macrophages after circARCN1 regulation, we performed FLASH experiments using the anti-HuR antibody on THP-1 macrophages with circARCN1 knockdown or overexpression. The resulting FLASH products were then subjected to RNA sequencing.

overall_design: HuR FLASH experiments were conducted using the anti-HuR antibody on wild type THP-1 macrophages (two replicates, THP1-FLASH-1 and THP1-FLASH-2), and THP-1 macrophages with circARCN1 knockdown (THP1-SH-FLASH) or overexpression (THP1-OE-FLASH). The resulting FLASH products were then subjected to RNA sequencing.


title: Conditioning of porcine kidneys during dynamic preservation with exosomes derived from Urine Progenitor Cells

city: Poitiers

first: Sebastien

last: Giraud

address: CHU de Poitiers

country: France

institute: IRMETIST UMR INSERM U1313, Université de Poitiers, CHU de Poitiers service de Biochimie

summary: Backgroud: among strategies to limit ischemia/reperfusion (IR) injuries in transplantation, cell therapy using stem cells to condition/repair transplanted organ appears promising. We hypothesized that using a cell therapy based on exosomes derived from Urine Progenitor Cells (UPCs) during hypothermic and normothermic machine perfusion can prevent IR-related kidney damages.  Methods: we isolated and characterized porcine UPCs and their exosomes (Exo). Then these were used in an ex vivo preclinical porcine kidney preservation model. Kidneys were subjected to warm ischemia (32min) then preserved by Hypothermic Machine Perfusion (HMP) for 24h before 5h of Normothermic Machine Perfusion (NMP). Three groups were performed (n=5-6): Group 1 (G1): HMP/vehicle + NMP/vehicle, Group 2 (G2): HMP/Exo + NMP/vehicle, Group 3 (G3): HMP/Exo + NMP/Exo.  Results: porcine UPCs were successfully isolated from urine and fully characterized as well as their exosomes which were found of expected size/phenotype. RNA-seq performed on kidney biopsies showed different profiles between G1 and G3 with regulation of potential IR targets of Exo therapy. Conclusions: we showed the feasibility/efficacy of UPC-exosomes for hypothermic/normothermic kidney conditioning prior to transplantation, paving the way of combining machine perfusion with exosome-based cell therapy for organ conditioning.

overall_design: Porcine kidneys (5-6/group), from Dutch Landrace pigs (6 months to 1 year old)  were collected after 32 min of warm ischemia and submitted to 24h of Hypothermic Machine Perfusion (HMP) followed by 5h Normothermic Machine Perfusion (NMP). Porcine kidneys of Group 1 were injected with PBS-1X during both HMP and NMP; Porcine kidneys of Group 2 were injected with Exosomes during HMP only; Porcine kidneys of Group 3 were injected with Exosomes during both HMP and NMP. At the end of NMP, kidneys were immediately sampled and snap frozen in liquid nitrogen.

first: Perrine

last: Burdeyron

first: Maryne

last: Lepoittevin

first: Sonia

last: Brishoual

first: Maïté

last: Jacquard

first: Virginie

last: Ameteau

first: Nadègen

last: Boildieu

first: Estelle

last: Lemarie

first: Jonathan

last: Daniel

first: Frédéric

last: Martins

first: Nina

last: Jordan

first: Marine

last: Coué

first: Raphaël

last: Thuillier

first: Henri

last: Leuvenink

first: Luc

last: Pellerin

first: Thierry

last: Hauet

first: Clara

last: Steichen


title: Single-cell RNA sequencing in Kawasaki disease II

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary: We performed single-cell RNA sequencing (using Cell Ranger Single Cell Pipeline v.4.0.0 to process data de-multiplexing, barcode processing, and single cell 3' gene counting generated by the 10X Chromium platform) in KD patients (within 24 hours before IVIG treatment) and age-matched fever controls.

overall_design: Peripheral blood samples were collected from five KD patients (include three KD patients with following development of coronary artery lesions) within 24 hours before IVIG treatment, two febrile controls and two healthy subjects in EDTA collection tubes (vender) and centrifuged at 400 × g for 5 min at 4 °C. The cell viability of purified white blood cells (WBC) exceeded 90%.

first: Ho-Chang

last: Kuo

first: Ying-Hsien

last: Huang

first: Kuang-Jer


title: Glucocorticoid promotes metastasis of colorectal cancer via co-regulation of glucocorticoid receptor and TET2 (RNA-Seq)

first: Epigenomics

last: Gao

overall_design: RNA-seq was performed to investigate cell migration situation with GC. We established two colorectal cancer (CRC) cell lines with varying glucocorticoid receptor (GR) expression (HCT116 and HT29). We then investigate cell invasion with two drugs (Dex and belinostat) treated in CRC cells (HCT116 and HT29).

first: Yanwei

last: Song

first: Shuqiang

last: Ren

first: Shumei

last: Wu

first: Weidong

last: Liu

first: Chenghao

last: Hu

first: Siting

last: Feng

first: Xinyu

first: Du

last: Zhang

first: Rui

last: Tu

first: Fei


title: Genome-wide map of TRIM33, CDK9 and S2 Pol II binding sites in common dendritic cell progenitors

city: Beijing

first: Xiangyi

last: Shen

address: D303 Zhengyutong Medical Building, Tsinghua University

department: The Institute for Immunology, School of Medicine

institute: Tsinghua University

summary: Transcriptional control of dendritic cell (DC) development has not been fully understood. TRIM33, a transcription co-factor was found to be crucial for transcription regulation during the development of DCs. Genome wide binding site analysis with CUT&Tag  revealed co-localization of TRIM33 with CDK9 and Serine 2 phosphorylated RNA polymerase (S2 Pol II) in the common dendritic cell progenitors (CDPs).

overall_design: CD11c–CD127–CD117intFLT3+ CDPs were sorted by flow cytometry from the bone marrow of wild-type C57BL/6 mice. 1x10^5 cells per sample were subjected to CUT&Tag assay and library construction with the Hyperactive In-Situ ChIP Library Prep Kit purchased from Vazyme under manufactorer's instructions. TRIM33, CDK9, S2 Pol II antibodies , and control IgG were used. Quality-checked libraries were sequenced on an Illumina HiSeq X Ten platform to generate PE150 reads.

first: Tingting

last: Guo

first: Li


title: Investigating the cross-talk between circRNAs and PKR and its implication in the immune response in MS

city: San Sebastián

first: David

last: Otaegui

state: Guipuzcoa

address: Paseo Dr begiristain s/n

department: Neurosciences

country: Spain

institute: Biodonostia Research institute

summary: Circular RNAs (circRNAs) have emerged as a new type of endogenous non-coding RNA characterized by their covalently closed circular structure and a backspliced junction (BSJ) resulting from a back-splicing process. In the last years, several studies have shown that circRNAs are important modulators in the immune system, activation of inflammation, antibacterial and antiviral responses as well as autoimmune diseases, such as multiple sclerosis. In the last years, it has been proposed that a subset of circRNA form imperfect double-stranded structures that allow them to interact with PKR (double stranded RNA-activated protein kinase), an intracellular protein responsible for recognizing long double stranded RNAs, usually viral RNAs, in the cytoplasm and trigger an anti-viral response of the cell. Taking into account the implication of the innate immune response in multiple sclerosis pathophysiology and the discovery of circRNA deregulation in multiple sclerosis patients, we wanted to investigate the circRNA-PKR crosstalk and its implication in the pathology of multiple sclerosis. Using an in vitro model of the anti-viral response and RNA-seq to characterize circRNA expression, we observed that poly (I:C) (a double-stranded RNA) stimulation produces a global downregulation of circRNA, PKR phosphorylation and immune-related gene activation and that these effects are reversed when treatment is stopped. Additionally, we found that the overexpression of double stranded RNA-containing circRNAs is able to reduce the PKR phosphorylation and the activation of immune-related pathways induced by poly(I:C). Finally, we measured the PKR phosphorylation in PBMCs isolated from multiple sclerosis patients in relapse and remission phases, but we did not obtain conclusive results since there is a very big variability between samples. In conclusion, this work reinforces the evidence on the mechanism describing the interaction between PKR and circRNA containing double-stranded structures and their role in the immune response.  Besides, our experiments highlight the importance of the structure in circRNA function.  Lastly, it also sheds some light into the possible implication of the circRNA-PKR axis in multiple sclerosis although further research is needed to make a better characterization of this mechanism in order to understand its potential role in the regulation of the immune response of the disease.

overall_design: HeLa cells overexpressing 3 different circRNAs stimulated with poly(I:C) or unstimulated. Additionally, a control condition with cells without circRNA overexpression is included (empty vector) both in stimulated and unstimulated conditions. In total 8 conditions (3 circRNA overexpression + control both stimulated and unstimulated). Two replicates per conditions were sequenced.

first: Leire

last: Iparraguirre

first: Andoni

last: Gonzalez-Maestro

first: Saioa

last: García-Serrano

first: Lucía

last: Sepúlveda

first: Maider

last: Muñoz-Culla


title: Morphogenesis and regeneration share a conserved core transition cell state program that control lung epithelial cell fate

city: New York

last: Ke

state: New York

address: 650 West 168th Street

institute: Columbia University

summary: We isolated and identified a population of Icam1/Nkx2-1 epithelial progenitors harboring a transitional state program remarkably conserved in humans and mice during lung morphogenesis and regeneration

overall_design: Epcam+ or Epcam+Icam1+ cells from E14.5 mouse embroynic lungs are isolated and proceeded to single cell sequencing

first: Benjamin

last: van Soldt


title: Transcriptome analysis of circulating circRNA expression profiles from patients with coronary artery disease and healthy controls

first: Zhicheng

last: Pan

summary: Transcriptome analysis of Peripheral Blood Mononuclear Cells (PBMC) samples from nine participants, including three in the Ctrl group, three in the (stable angina) SA group, and three in the acute coronary syndrome (ACS) group, was performed.

overall_design: We included 9 participants into our study: 3 healthy controls without coronary artery stenosis confirmed by coronary angiography, 3 patients diagnosed with stable angina, 3 patients diagnosed with acute coronary syndrome. PBMCs were isolated from whole blood samples of these patients. Total RNA was extracted from the PBMC samples. The integrity of the extracted RNA was assessed. For library construction, 1 μg of the total RNA was utilized. To remove rRNA, the RiboZero Magnetic Gold Kit was employed. Subsequently, the KAPA Stranded RNA-Seq Library Prep Kit was used to construct the RNA-sequencing library. Sequencing was performed on an Illumina HiSeq 4000 system using the HiSeq 3000/4000 SBS kit (Illumina).


title: A G-quadruplex-binding platinum complex induces cancer mitochondrial dysfunction through dual-targeting mitochondrial and nuclear G4 enriched genome

city: Chengdu

first: Kuang

middle: ke

last: li

state: Sichuan

address: No.17, Block 3, Southern Renmin Road

department: West China School of Pharmacy

institute: sichuang university

summary: G-quadruplex DNA (G4) is a non-canonical structure forming in guanine-rich regions, which play a vital role in cancer biology and are now being acknowledged in both nuclear and mitochondrial (mt) genome. However, the impact of G4-based targeted therapy on both nuclear and mt genome, affecting mt function and its underlying mechanisms remain largely unexplored. Here, we demonstrated that the G4-binding platinum(II) complex, Pt-ttpy, shows a highest accumulation in the mitochondria of A2780 cancer cells as compared with two other platinum(II) complexes with no/weak G4-binding properties, Pt-tpy and cisplatin. Pt-ttpy induces mtDNA deletion, copy reduction and transcription inhibition, hindering mt protein translation. Functional analysis reveals potent mt dysfunction without reactive oxygen species (ROS) induction. Mechanistic study by RNA-seq, Chip- seq and CUT-RUN shows Pt-ttpy impairs most nuclear-encoded mt ribosome genes’ transcription initiation through dampening the recruiting of TAF1 and NELFB to their promoter with G4-enriched sequences. In vivo studies show Pt-ttpy's efficient anti-tumor effects, disrupting mt genome function with fewer side effects than cisplatin. This study underscores Pt-ttpy as a G4-binding platinum(II) complex, effectively targeting cancer mitochondria through dual action on mt and nuclear G4-enriched genomes without inducing ROS, offering promise for safer and effective platinum-based G4-targeted cancer therapy.

overall_design: Observe the changes in gene transcription levels of A2780 after treatment with different drugs, and use differential gene analysis to identify the genes targeted by Pt-ttpy.

first: Keli

last: Kuang

first: Chunyan

last: Li

first: Fatlinda

last: Maksut

first: Tao

last: Jia


title: Manipulating the transcriptome and chromatin accessibility in T cells through CRISPR-induced alternative splicing of IKZF1 (RNAseq)

first: Jeremy

last: Newman

overall_design: Exons 4 and 6 of the human IKZF1 gene in Jurkat cell lines were edited using CRISPR/Cas9. Gene expression profiling was performed using RNA-seq of four WT clones, seven clones with edits in IKZF1 exon 4, five clones with edits in IKZF1 exon 6, and eight clones with edits in IKZF1 exons 4 and 6. Analysis of gene expression was performed comparing WT clones to CRISPR-edited clones based on exons edited and protein detection.

first: Lucia

last: Pastor

first: Colin

last: Callahan

first: M

last: Atkinson

first: S

last: Onengut-Gumuscu

first: P

last: Concannon


title: Effect of ferrostatin-1 and liproxstatin-1 during TNF-induced HT-29 cells apoptosis

city: Jinan

first: Yanqing

state: Shandong province

address: No. 44 Wenhua West Road，Lixia district,

department: Gastroenterology

institute: Shandong University

summary: Ulcerative colitis (UC) is an inflammatory disease characterized by an uncontrolled inflammatory response. Previous study showed that the immunological impairment elicted the alteration of inflammatory mediators, and ferroptosis was implicated with the lethal accumulation of reactive oxygen species (ROS).We have already found that lipid ROS level was elevated in both murine DSS colitis model and TNF-a-induced cell apoptosis model in vitro.Then we here use two ferroptosis inhibitors ferrostatin-1 and liproxstatin-1 trying to eliminate lipid ROS in order to relive the symptoms of colitis.But we strikingly notice that liproxstatin-1 could increase TNF-induced cell apoptosis instead of protecting cells from death as we expected before while the other inhibitor ferrostatin-1 could protect cells from death indeed.To evaluate the underlying mechanism, we performed the experiment using high-throughput sequencing and get data to explain the reason why liproxstatin-1 could increase TNF-induced cell apoptosis .

overall_design: To investigate the reason for different effects of the two ferroptosis inhibitors ferrostatin-1 and liproxstatin-1 during TNF-induced HT-29 cells apoptosis，we firstly use human Recombinate TNF-a to induce HT-29 cell apoptosis.At the same time, we treat the TNF-a induced cell line using 20um ferrostatin-1 or 20um liproxstatin-1 for 72h.Then we collect cells to extract RNA and perform sequencing for next step.Notably,we also add 20um ferrostatin-1 or 20um liproxstatin-1 to the normal cell line which is not treated by TNF-a for 72h to exclude the effects of ferrostatin-1 and liproxstatin-1 on steady state cell.We then perform gene expression profiling analysis using data obtained from RNA-seq of 3 control groups and 3 treated groups:control,control+ferrostatin-1,control+liproxstatin-1,TNF-a，TNF-a+ferrostatin-1，TNF-a+liproxstatin-1.Each group has 3 technical replicates.

first: Xiuli

last: Zuo

first: Ruijia


title: Effect of 4-HDHA during TNF-induced HT-29 cells apoptosis

summary: Ulcerative colitis (UC) is an inflammatory disease characterized by an uncontrolled inflammatory response. Previous study showed that the immunological impairment elicted the alteration of inflammatory mediators, and ferroptosis was implicated with the lethal accumulation of reactive oxygen species (ROS).We performed lipidomics sequencing of TNF-a treated cell line mimicking the colitis in vivo.Surprisingly, we found that 4-HDHA,an autoxidation product of docosahexaenoic acid (DHA),had anti-apoptosis effect on colon epithelial cell line.To evaluate the underlying mechanism of the specific lipid perioxidin’s anti-apoptosis effect, we performed the experiment using high-throughput sequencing and get data to explain the reason why 4-HDHA could decrease TNF-induced cell apoptosis.

overall_design: To investigate the reason why 4-HDHA could rescue TNF-a induced cell death, we use human recombinate TNF-a to induce HT-29 cell apoptosis.At the same time, we treat the TNF-a induced cell line with 4-HDHA (the concentration is 600nm)for 72h.To exclude the effect of 4-HDHA on normal steady state cell, we treat the normal cell line with 4-HDHA(the same concentration as TNF-a treated group)Then we collect cells to extract RNA and perform sequencing for next step.We perform gene expression profiling analysis using data obtained from RNA-seq of 2 control groups and 2 treated groups:control,control+4-HDHA,TNF-a,TNF-a +4-HDHA.Each group has 3 technical replicates.


title: The gene expression of regulatory T cells in the brain and spinal cord

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

summary: Among T cells, regulatory T cells (Tregs) are the centers of immune tolerance and, like normal T cells, are generally born in the thymus gland, activated in secondary lymphoid tissues such as lymph nodes, and accumulate at sites of infection. On the other hand, it has been reported that there are Tregs that are resident in non-lymphoid tissues or that accumulate in damaged tissues. In this study, we focused on Tregs in the central nervous system and analyzed Tregs in mouse models of experimental autoimmune encephalomyelitis (EAE), cerebral infarction, and Alzheimer's disease.

overall_design: To examine the tissue or disease specific gene expression of regulatory T cells (Tregs) in the brain and spinal cord with CNS diseases, such as ischemic stroke, EAE, or Alzheimer’s disease, we performed bulk RNAseq of Tregs from several mouse models of these diseases.

first: Mashiro

last: Watanabe

first: Ako

last: Matsui


title: Bacteria can anticipate and adaptively respond to the seasons

city: Nashville

first: Carl

middle: Hirschie

last: Johnson

state: Tennessee

address: 465 21st Avenue South, U-8215 BSB/MRBIII

department: Biological Sciences

institute: Vanderbilt University

summary: Photoperiodic Time Measurement (PPTM) is the ability of plants and animals to measure differences in day/night-length (photoperiod, PP) and use that information to anticipate seasonal changes in key environmental factors such as annual changes in average temperature. This timekeeping phenomenon, which is well documented for higher organisms, enables processes such as gonadal growth/regression, flowering, hibernation, and diapause to optimally adapt to annual transformations of the environment. We discovered PPTM capability in cyanobacteria, which is unexpected since cyanobacteria are unicellular prokaryotes with generation times as short as 5-6 hours. Therefore PPTM is not confined to eukaryotes with long generation times. Here we show that cyanobacteria can distinguish between short and long daylengths (photoperiods) and respond to short winter-like days by developing an enhanced resistance to cold. This capability develops over several cycles of photoperiod, and therefore they harbor a “photoperiodic counter” that is a common characteristic of PPTM in higher organisms. These photoperiodic responses are dependent on the presence of the kaiABC genes that encode the central circadian clockwork in cyanobacteria. Short days that herald winter stimulated desaturation of membrane lipids, which is a seasonally adaptive response to lower temperatures. Long vs. short days evoke differential programs of gene transcription, including differential expression of stress response genes, suggesting that PPTM originally evolved from stresses that recur seasonally. Therefore, PPTM is a property of much simpler organisms than previously appreciated, with important implications for the evolution of biological timekeeping mechanisms.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: In our recent work, we describe that cyanobacteria are capable of anticipating seasonal changes and exhibit photoperiodic responses. To investigate what genes and pathways could be involved in the establishment of this response, we performed RNAseq in 1) wild-type and 2) circadian clock knock-outs (∆kaiABC) strains of the cyanobacterial model Synechococcus elongatus PCC 7942. We used two different photoperiods, 1) short-day (LD8:16, 8h of dark, 16h of darkness), which we demonstrate to be inducible of a photoperiodic resistance to cold, and 2) long-day (LD16:8), which does not induce increased cold resistance. As we observed that the photoperiodic response takes multiple cycles of LD to develop, we performed the RNAseq in samples collected after 1) 1 LD cycle, which is not sufficient to induce the response, 2) 4 LD cycles, which is sufficient to induce a complete response, and 3) 8 LD cycles, which is the condition most used throughout our manuscript. All samples were collected at their respective middays, and had been exposed to ~60h of light of 40µE m-2 s-1 intensity prior to collection.

first: Maria

last: Jabbur

middle: H


title: The gene expression of the brain and spinal cord

overall_design: To examine the tissue specific gene expression of the brain and spinal cord with EAE, we performed bulk RNAseq of brain and spinal cord from EAE mouse model.


title: Effects of 4-HDHA on gene expression in colonic tissue of colitis mice

summary: To investigate the roles of 4-HDHA in the regulation of cell function and gene expression of colonic tissue, we treated colitis mice with 4-HDHA intravenously. Then, we performed gene expression profiling analysis using data obtained from RNA-seq of colonic tissue of colitis mice treated with or without 4-HDHA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for colons from adult C57BL/6 mice that were treated with 3% DSS continuously for 7 days. The mice were divided into two groups:one group was treated with PBS( 200ul/20g/day ) intravenously and the other group was treated with 5um 4-HDHA (diluted in PBS,200ul/20g/day) intravenously .The injection was along with 3% DSS for 7 days.


title: Improving Human Cardiac Organoid Design Using Transcriptomics

city: Charleston

first: Nathaniel

last: Hyams

state: SC

address: 68 President St

department: Bioengineering

institute: Clemson University

summary: Cardiovascular disease (CVD) is the leading cause of death worldwide. To this end, human cardiac organoids (hCOs) have been developed for improved organotypic CVD modeling over conventional in vivo animal models. Utilizing human cells, hCOs hold great promise to bridge key gaps in CVD research pertaining to human-specific conditions. hCOs are multicellular 3D models which resemble heart structure and function. Varying hCOs fabrication techniques leads to functional and phenotypic differences. To investigate heterogeneity across hCO platforms, we performed a transcriptomic analysis utilizing bulk RNA-sequencing from four previously published unique hCO studies. We further compared selected hCOs to 2D and 3D hiPSC-derived cardiomyocytes (hiPSC-CMs), as well as fetal and adult human myocardium bulk RNA-sequencing samples. Upon investigation utilizing Principal Component Analysis (PCA), K-means clustering analysis of key genes, and further downstream analyses such as Gene Set Enrichment (GSEA), Gene Set Variation (GSVA), and GO term enrichment, we found that hCO fabrication method influences maturity and cellular heterogeneity across models. Thus, we propose that adjustment of fabrication method will result in an hCO with a defined maturity and transcriptomic profile to facilitate its specified applications, in turn maximizing its modeling potential.

relation:
Reanalysis of: GSM2422325
Reanalysis of: GSM2422326
Reanalysis of: GSM2422327
Reanalysis of: GSM5501720
Reanalysis of: GSM5501721
Reanalysis of: GSM5501722
Reanalysis of: GSM4635310
Reanalysis of: GSM4635311
Reanalysis of: GSM4635312
Reanalysis of: GSM3122186
Reanalysis of: GSM3122187
Reanalysis of: GSM3122188
Reanalysis of: GSM6412469
Reanalysis of: GSM6412470
Reanalysis of: GSM6412471
Reanalysis of: GSM6412466
Reanalysis of: GSM6412467
Reanalysis of: GSM6412468
Reanalysis of: GSM2463759
Reanalysis of: GSM2463760
Reanalysis of: GSM2463761
Reanalysis of: GSM2463762
Reanalysis of: GSM1536184
Reanalysis of: GSM1536185
Reanalysis of: GSM1536186
Reanalysis of: GSM1536187
Reanalysis of: GSM1536192
Reanalysis of: GSM1536193
Reanalysis of: GSM2463767

overall_design: Total study utilizes 35 raw FASTQ files from across 7 studies. GSE91383 (n = 3), GSE181397 (n = 3), GSE153185 (n = 9),   GSE209997 (n = 6), GSE93841 (n = 4), GSE113871 (n = 3), GSE62913  (n = 7) were reanalyzed for the purposes of this study. Raw FASTQ files were selected from studies of interest, adaptors were trimmed using Trimmomatic, QC'ed, and mapped to hg38 using RNASTAR. FeatureCounts was used to generate counts files, which were normalized and analyzed using the R package "DESeq2".

first: Charles

last: Kerr

first: Dimitrios

middle: C

last: Arhontoulis

first: Jean

last: Ruddy

first: Ying

last: Mei


title: Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening (RNA-Seq for Nynrin cko HSC)

city: Chongqing

first: CHENGFANG

last: ZHOU

address: No. 30, Gaotanyan Street.

department: Department of Hematology, Southwest Hospital

institute: Army Medical University

summary: Mitochondria have recently been identified as a critical regulator for the homeostasis of hematopoietic stem cells (HSCs). However, the mechanism underlying HSC regulation still needs to be clarified. Here, we identify transcription factor Nynrin as a novel regulator of HSC maintenance through modulation of mitochondrial function. We demonstrate that Nynrin is highly expressed in HSC under steady and stress state. Nynrin knockout leads to significantly decreased long-term HSC frequency, markedly reduced HSC dormancy, and self-renewal capacity in steady-state and stress hematopoiesis. We observed abnormal mitochondrial metabolism and mitochondrial permeability transition pore (mPTP) opening in Nynrin-deficient HSCs. Notably, Nynrin-deficient HSCs are more compromised in tolerance of irradiation- and 5-fluorouracil-induced stresses and exhibit typical phenotypes of necrosis. In contrast, overexpression of Nynrin in HSC is resistant to the radiation. Mechanistically, Nynrin deletion induces transactivation of Ppif. Overexpression of cyclophilin D (CypD), the protein encoded by the Ppif gene, causes mPTP opening, mitochondrial swelling, ROS overinduction, and cell necrosis. Both blocking the function of CypD by using cyclosporin A (CsA) or reducing the expression of Ppif could inhibit Nynrin deficiency-induced mitochondrial metabolism enhancement and ROS overproduction, thereby evidently rescuing the impairment of HSCs in Nynrin mutant mice. Collectively, our data, for the first time, characterize Nynrin as a critical regulator of HSC function acting through the Ppif/mPTP mitochondria axis and highlight the importance of Nynrin in HSC maintenance. These data provide new insights into the mechanisms for controlling HSC fate.

overall_design: The construct of the whole cDNA library for low number HSCs (500 cells)from Nynrin cko mice was performed as previously described (Chen et al., 2017). In brief, about 3000 HSCs of BMs from Nynrinfl/flTie2-Cre or Nynrinfl/fl mice were sorted by FACS. cDNA was synthesized according to Jun Chen et al. (2017). The mRNA library was constructed using TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme) and TruePrepTM Index Kit V2/V3 for Illumina® (Vazyme) for sequencing. Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter). Each library was quantified using a Qubit fluorometer (Thermo Fisher Scientific), and the size distribution was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA). The Illumina HiSeq 2000 platform sequenced libraries as 350-bp pair-ended reads.

first: Chengfang

last: Zhou

first: Mei

last: Kuang

first: Yu

last: Hou


title: Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening (ChIP_Seq)

overall_design: Chromatin immunoprecipitation DNA-sequencing for promoter binding sites of 3×Flag-Nynrin-Tg mice Lin--cells


title: Rescue of lysosomal acid lipase deficiency in mice by AAV liver gene transfer

city: EVRY

first: Corre

last: Guillaume

address: 1 rue de l'internationale

institute: GENETHON

summary: Lysosomal acid lipase deficiency (LAL-D) is an autosomal recessive disorder caused by mutation in LIPA gene, which results in fat accumulation in liver and spleen leading to multi-organ failure. The severe form of LAL-D (infantile-onset; ≤5% residual LAL activity), if left untreated, results in premature death within the first year of life due to failure to thrive and hepatic insufficiency. Enzyme replacement therapy is the only available supportive treatment consisting in weekly systemic injection of recombinant LAL. Here, we characterize a novel LAL-D mouse model and develop a curative gene therapy treatment based on the in vivo administration of recombinant AAV8 (rAAV8) vector encoding for human LIPA transgene under the control of hepatocyte-specific promoter. We define the minimal AAV dose required to rescue disease lethality and to produce and secrete sufficient LAL to correct cholesterol and triglycerides accumulation in liver, spleen, blood cells and plasma. Finally, using liver transcriptomic and biochemical analysis, we also show the impairment of mitochondria associated with LAL-D and its recovery by gene therapy. Overall, our in vivo gene therapy strategy achieves stable long-term LAL expression to correct disease phenotype in LAL-D mouse model and opens a new therapeutic option for LAL-D patients.

overall_design: To further investigate the dysregulation of gene expression associated with LAL deficiency or its correction upon gene therapy, we performed transcriptomic analysis on liver of  WT, Lipa-/- (KO)  and treated Lipa-/- (KOT)  mice at 12- and 34-week post-injection.

first: Marine

last: Laurent

first: Rim

last: Harb

first: Christine

last: Jenny

first: Julie

last: Oustelandt

first: Francesca

last: Landini

first: Guillaume

last: Corre

first: Anais

last: Brassier

first: Laetitia

last: Van Wittenberghe

first: Dagmar

last: Kratky

first: Giuseppe

last: Ronzitti

first: Consiglia

last: Pacelli

first: Mario

last: Amendola

first: Simon

last: Jimenez

first: Jérémie

last: Cosette

first: Aristide

last: Ferrante

first: Nemanja

last: Vujic

first: Claudia

last: Piccoli


title: Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening （human_HSC_RNA_Seq)

first: CHENGFANG

last: ZHOU

overall_design:
CD34+ cells were enriched from total bone marrow cells  accroding to EasySep™ Human Progenitor Cell Enrichment Kit II. TheCD34+  cells werewere irradiated with 2Gy γ-rays.
We then performed gene expression profiling analysis using data obtained from RNA-seq of human CD34+
Comparative gene expression profiling analysis of RNA-seq data for nonirradiated CD34+ and  irradiated CD34+

first: Chengfang

last: Zhou

first: Mei

last: Kuang

first: Yu

last: Hou


title: The juxtaposition of Taurine in Bronchopulmonary Dysplasia

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
Background: Metabolic dysregulation has been implicated in bronchopulmonary dysplasia development. Taurine is an essential amino acid for neonates and is critically involved in glucose and fatty acid metabolism. Neonatal tissue obtains taurine mainly through the taurine transporter. The biological role of taurine in neonatal lung development has never been explored. As glucose metabolism mechanistically modulates angiogenesis and angiogenesis is the central player for neonatal lung development, we hypothesize that taurine depletion contributes to bronchopulmonary dysplasia development.   Results: Although most genes and proteins for oxidative phosphorylation were enriched in hyperoxia pup lungs, the complex-1 activity decreased. The decrease in taurine-dependent complex-1 core subunits, ND5 and ND6, in hyperoxia lungs reasonably explained the discrepancy. Metabolomics analysis demonstrated decreased lung taurine with increased blood taurine of hyperoxia pups, compatible with the decreased taurine transporter expression. Decreased glycosylation and increased degradation explained the decreased taurine transporter expression. The results of the complementary study using tunicamycin and tauroursodeoxycholic acid studies supported that endoplasmic reticulum stress contributes to decreased taurine transporter expression in hyperoxia lungs. The effect of taurine treatment on reducing endoplasmic reticulum stress, increasing ND5 and ND6 expression, angiogenesis, and, most importantly, the alveolar formation is beneficial to hyperoxia rat pups.
Conclusion: Hyperoxia exposure causes endoplasmic reticulum stress, increases taurine transporter degradation, and leads to taurine depletion in the neonatal lungs with subsequent metabolic dysregulation, resulting in poor alveolar formation of the neonatal lungs. We provide evidence of the never-being-reported protective role of taurine in neonatal lung development. The fact that taurine attenuates the severity of bronchopulmonary dysplasia by reducing hyperoxia-induced endoplasmic reticulum stress and mitochondrial dysfunction indicates its therapeutic potential for treating bronchopulmonary dysplasia.

overall_design: Sprague-Dawley rat pups exposed to >90% oxygen (hyperoxia) were used as the bronchopulmonary dysplasia phenotype between postnatal days one and ten. Some rat pups received tunicamycin or tauroursodeoxycholic acid to study the effect of endoplasmic reticulum stress. Taurine was used as rescue therapy. Plasma and lungs were obtained at postnatal day ten for multiomics analyses.  The dam and pups were cared for in either >90% oxygen chamber (HOX) or room air (NOX) from postnatal day 1 to day 10 (P1-P10). An oxygen sensor continuously monitored oxygen concentrations (Reming Bioinstruments Co., Redfield, NY). Pups were then recovered in room air between P11-P21. Pups were caged with nursing dams while the dams were alternated between oxygen environments to diminish oxygen toxicity. Lungs obtained at P21 from both NOX and HOX groups were used for transcriptomic studies using Affymetrix chips, histology, and immunoblots.

first: Xigang

last: Jing

first: Yekai

last: Wang

first: Mark

last: Roethle

first: Shuang

last: Jia

first: Michelle

last: Teng

first: Ganesh

last: Konduri

middle: J

first: Kirkwood

last: Pritchard Jr.

first: Billy

middle: W

last: Day

first: Yan

last: Jin

first: Stephen

last: Naylor

first: Haiwaei

last: Gu

first: Jainhai

last: Du

first: Ru-Jeng


title: Host transcriptomic response to a bacterial toxin at single-nuclei resolution

city: Columbia

first: Wesley

last: Warren

state: MO

address: 1201 Rollins St.

department: Animal Sciences

institute: University of Missouri

summary: We are studying the host immune response to a bacterial toxin in the chicken spleen and bursa. We performed snRNAseq to analyze the various immune cell types that play a role in combating the infection and the cell-type transcriptional response.

overall_design: In this study, we used Avian Disease and Oncology Laboratory (ADOL) White Leghorn line 6 birds at 5 weeks of age and performed snRNAseq to determine the splenic cell-type transcriptomic changes occurring in LPS-infected and non-infected states. Birds at five weeks of age were injected intravenously with LPS-derived from E. coli (55: B5 Millipore Sigma) and timed body temperature responses to LPS systemic treatment were recorded at 1, 4, 10, and 24 hours post inoculation to ensure the biphasic body temperature elevation was observed. Control birds were given 150 microliters of phosphate buffered saline, (PBS).  Spleen and bursae were asepectically removed, homeogenized, and single nuclei were used to generate a snRNAseq library used for downstream analyses including cell type identification, cell-to-cell communication, pathway enrichment analysis, and protein network analysis.

first: Elaina

last: Sculley

first: Edward

last: Rice

first: Jacqeline

last: Smith

first: Jim

last: Kaufman

first: Yvonne

last: Dreschler

first: Hans

last: Cheng

first: Cari

last: Hearn

first: Melissa

last: Monson


title: Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening (scRNA-Seq)

first: CHENGFANG

last: ZHOU

summary:
Mitochondria have recently been identified as a critical regulator for the homeostasis of hematopoietic stem cells (HSCs). However, the mechanism underlying HSC regulation still needs to be clarified. Here, we identify transcription factor Nynrin as a novel regulator of HSC maintenance through modulation of mitochondrial function. We demonstrate that Nynrin is highly expressed in HSC under steady and stress state. Nynrin knockout leads to significantly decreased long-term HSC frequency, markedly reduced HSC dormancy, and self-renewal capacity in steady-state and stress hematopoiesis. We observed abnormal mitochondrial metabolism and mitochondrial permeability transition pore (mPTP) opening in Nynrin-deficient HSCs. Notably, Nynrin-deficient HSCs are more compromised in tolerance of irradiation- and 5-fluorouracil-induced stresses and exhibit typical phenotypes of necrosis. In contrast, overexpression of Nynrin in HSC is resistant to the radiation. Mechanistically, Nynrin deletion induces transactivation of Ppif. Overexpression of cyclophilin D (CypD), the protein encoded by the Ppif gene, causes mPTP opening, mitochondrial swelling, ROS overinduction, and cell necrosis. Both blocking the function of CypD by using cyclosporin A (CsA) or reducing the expression of Ppif could inhibit Nynrin deficiency-induced mitochondrial metabolism enhancement and ROS overproduction, thereby evidently rescuing the impairment of HSCs in Nynrin mutant mice. Collectively, our data, for the first time, characterize Nynrin as a critical regulator of HSC function acting through the Ppif/mPTP mitochondria axis and highlight the importance of Nynrin in HSC maintenance. These data provide new insights into the mechanisms for controlling HSC fate.
Nynrin gene may play an important role in hematopoietic reconstitution.We used single cell RNA sequencing (scRNA-seq) to analyze the expression of nynrin in hemopoietic progenitor cell.

overall_design: Lin- cells were enriched from C57/B6 mice according to the EasySep™ Mouse Hematopoietic Progenitor Cell Isolation Kit.Lin- cells were analyed using scRNA-seq.

first: Chengfang

last: Zhou

first: Mei

last: Kuang

first: Yu

last: Hou


title: Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping [RNA-seq]

city: ShenZhen

first: Rui

last: Chen

state: GuangDong

address: Southern University of Science and Technology

summary: Synthetic transcriptional activators based on CRISPR/Cas technology can be enhanced by intrinsically disordered regions (IDRs). However, the potential of all IDRs in this regard remains uncertain, and the mechanisms underlying their influence are a subject of debate. Here, we examined 12 well-known IDRs by fusing them to the dCas9-VP64 activator. Our findings reveal that seven IDRs could augment activation, albeit independently of their phase separation properties. Moreover, modular domains (MDs), which facilitate multivalent interactions but are ineffective in enhancing dCas9-VP64 activity on their own, showed substantial enhancement in transcriptional activation when combined with dCas9-VP64-IDR. By varying the number of gRNA binding sites and combining dCas9-VP64 with the IDRs and MDs of different multivalent capabilities, we uncovered that optimal, rather than maximal, cis-trans cooperativity enables the most robust activation. Finally, targeting promoter-enhancer pairs with our IDR-enhanced activation system yielded synergistic effects, potentially further amplifiable by induced functional chromatin looping.

overall_design: To investigate which dCas9-VP64-FUS CRISPRa induce off-target effect when activate gene transcription, we performed mRNA sequencing to assess the transcriptome of HEK-293R cells expressing dCas9-VP64-FUS with either gTetO or a scrambled gRNA

first: Wei

first: Huanhuan

last: Cui


title: ERK5 sustains autocrine mitogenic balance for cell fate specification in human pluripotent stem cells [4 cell line RNA-seq]

city: macau

first: Chengcheng

last: SONG

address: universtiy of macau

department: fhs

country: Macau

institute: university of macau

summary: To investigate the function ERK5 in the regulation of mitogen expression in multiple cell lines, we processed RNA-seq analysis of H1/H9 ESCs and NL1/NL4 hiPSCs lines.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of H1/H9 ESCs and NL1/NL4 hiPSCs lines.

last: Song

first: Guokai


title: RNA-seq analysis of the WT and bcas2-KO zebrafish embryos at 3 dpf

city: Wuhan

first: Fei

last: Liu

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: The splicing factor Bcas2 is involved in several biological processes including tumorigenesis, gametogenesis, and hematopoiesis. The alternative splicing events and downstream genes regulated by Bcas2 have not yet been investigated at the transcriptome level in zebrafish. In this study, we conducted RNA-sequencing analysis on the WT and bcas2 knockout zebrafish embryos (3 dpf) to identify the global differentially expressed genes (DEGs) and differential splicing events (DSEs). 868 DEGs (293 up and 575 down) were identified and genes related to spliceosome, mRNA splicing, and mRNA processing were significantly upregulated, suggesting a negative feedback of the splicing pathway. Besides, 664 DSEs related to 593 genes were identified and sequence signature analysis of these DSEs revealed that the alternatively spliced exons affected by bcas2 knockout have relatively shorter length, longer upstream and downstream introns, and weaker 5’ or 3’ splicing sites, when compared with the control exons. Furthermore, we demonstrated that the exon 5 of ikzf1 gene, a transcription factor related to lymphocyte differentiation, was preferably skipped in the bcas2 knockout embryos, resulting in the deletion of 11 aa between the two conserved zinc finger domains of Ikzf1. Accordingly, several downstream genes, such as rasgrp2 and rgs2, were significantly downregulated and the lymphocyte generation was impaired in the bcas2 knockout embryos. Taken together, our work depicts the global changes of gene expression and alternative splicing caused by bcas2 knockout in zebrafish embryos and reveals an important role of Bcas2-regulated alternative splicing of ikzf1 in lymphoid hematopoiesis.

overall_design: WT and bcas2-KO zebrafish embryos at 3 dpf were seletecd through FLRP-mediated genetyping. Embryos of the same genotype were pooled for total RNA extraction. The genotype of each pooled sample was further comfirmed by RT-PCR and Sanger sequencing. Qualified RNA samples were sent for RNA sequencing to identify differentially expressed genes (DEGs) and differential splicing events (DSEs).

first: Yunali

last: Zhao

first: Shanshan

last: Yu

first: Daji

last: Luo


title: Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan

city: Baltimore

first: Dwight

last: Bergles

state: MD

address: 725 North Wolfe St., WBSB 1001

department: Neuroscience

institute: Johns Hopkins University

summary: Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1α and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts.

overall_design: Matn4-mEGFP OPCs from 1) 6x P30 cortex, 2) 4x P180 cortex, 3) 5x P360 cortex, 4) 5x P720 cortex to study the effect of aging on the transcriptome of OPCs in the mouse cortex

first: Dongeun

last: Heo

first: Loyal

last: Goff


title: Protective effect and mechanism of lipid perioxide in TNF-a induced apoptosis of intestinal epithelial cells in IBD.

first: Yanqing

last: Li

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: ATAC-seq datasets for chromatin accessibility quantification during decidualization in mice

city: beiijing

first: wei

last: zhao

address: Haidian Distric

institute: China Agricultural University

summary: We performed ATAC-seq to screen out key transcriptional factors that regulated decidualization.

overall_design: uterine stromal cells were isolated and cultured for decidualization induction. Cells were treated with or without oxamate. Cells were collected for ATAC-seq


title: Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping.

institute: Southern University of Science and Technology


title: Transcriptome analysis revealed the characteristics and functions of long non-coding RNAs in the hypothalamus during sexual maturation in goats

city: Tai'an

first: Qing

address: Tai’an, Shandong Province, P.R. China

institute: College of Animal Science and Veterinary Medicine

summary: To reveal the transcriptomic changes of hypothalamic tissue in goats from birth to sexual maturity, we performed transcriptome sequencing of Jining Grey Goat hypothalamic tissues at four developmental stages after birth. A total of 20 libraries from four different development stages (5 goats per stage) were successfully constructed, and the corresponding mRNA and lncRNA expression profile were obtained.

overall_design: To investigate the dynamics of hypothalamic transcriptome expression profiles at four developmental stages after birth, we performed RNAseq sequencing using hypothalamic tissues from goats at four developmental stages, with five biological replicates per developmental stage. All goats had free access to food and water under the same rearing environment and management conditions.

first: Tianle

last: Chao

first: Jianmin

last: Wang


title: Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening.

first: CHENGFANG

last: ZHOU


title: CRISPRi-targeted raw RNA-seq data in iPSC-derived neurons. In this study, we performed RNA-sequencing to test transcriptomic changes of CRISPRi-targetd MIR family TE (chr11: 47608036-47608220) in iPSC-derived neurons.

city: Cleveland

first: Feixiong

last: Cheng

state: Ohio

address: 9500 Euclid Ave

department: Genomic Medicine

institute: Cleveland Clinic

summary: Despite its broad role in human disease, transposable element (TE) dysregulation of quantitative trait loci (QTL) has not been well-characterized in brain aging or Alzheimer’s disease (AD). Here, we leveraged large-scale human RNA-sequencing (RNA-seq), whole-genome sequencing (WGS), and QTL data (xQTL) from three brain biobanks to comprehensively characterize dysregulation of TE expression dysregulation across diverse pathobiology of AD, including tau, amyloid-β, APOE genotypes, and sex. Joint-analysis of WGS and RNA-seq data identified 26,188 genome-wide significant TE expression QTLs (teQTLs) that were associated with expression of 1,453 locus-TEs in human aging brains. Subsequent colocalization analysis of teQTLs with GWAS loci from 278,950 AD cases and 1,780,303 controls further identified likely causal genes for AD (FDFT1 and C1QTNF4) that were regulated by brain teQTLs. In addition, an elevated intergenic TE from the MIR family (chr11: 47608036-47608220) was found to suppress expression of the anti-inflammation related gene C1QTNF4 (its nearest gene) via long-range enhancer-promoter chromatin interaction in neurons. Lastly, CRISPR interference (CRISPRi) assays identified a neuron-specific suppressive role of the activated MIR family TE on expression of anti-inflammatory genes in human induced pluripotent stem cells (iPSC)-derived neurons, including C1QTNF4. In conclusion, we demonstrate that TEs play crucial functional roles in gene regulation in the aging human brain and that analysis of teQTLs identifies AD risk genes and advances our understanding of brain aging and AD. This approach could aid investigation of other complex brain disorders as well.

overall_design:
To investigate the regulatory roles of MIR family (chr11: 47605296-47605575), we peformed CRISPRi assays in iPSC-derived neurons. And then peformed RNA-sequencing of CRISPRi-targeted and empty vectors using iPSC-derived neurons.
Comparative gene expression profiling analysis of bulk RNA-seq data for CRISPRi-targeted iPSC-derived neurons and its empty controls

first: Yayan

last: Feng

first: Xiaoyu

last: Yang

first: Yin

last: Shen


title: Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping [ChIA-PET]

first: Rui

last: Chen

overall_design: To verify that the increased transcriptional activation resulted from enhanced long-range chromatin interactions, we examined HS2-associated looping before and after ABA treatment using ChIA-PET

first: Wei

first: Huanhuan

last: Cui

first: Zhongyuan

last: Tian

first: Meizhen

last: Zheng


title: Genome-wide identification of transcriptional targets for H4K12la  during uterine stromal cells decidualization in mice

summary: To explore the potential mechanism responsible for the role of H4K12la during decidualization, we performed Cleavage Under Targets & Tagmentation (CUT&Tag) analysis using in vitro decidualization model to identify candidate genes regulated by H4K12la.

overall_design: Examination of transcriptional targets for H4K12la during uterine stromal cells decidualization in mice. During decidualization induction, cells were treated with  oxamate, the selective inhibitor of LDHA.


title: Mesenchymal stromal cell reprogramming and aberrant inflammatory signalling in myelofibrosis: insights from single-cell RNA sequencing

city: Manchester

first: Naseer

middle: Jr

last: Basma

address: Cancer Research UK Manchester Institute, Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary: Myelofibrosis (MF) is a myeloproliferative neoplasm driven by mutations that impact the JAK/STAT signaling in blood cells, eventually causing fibrosis, splenomegaly, and reduced lifespan. To better understand MF, we performed scRNAseq profiling of collagenase-digested bone marrow biopsy samples to identify disrupted cellular pathways for potential treatment. Comparative analysis of 9 MF samples vs. 7 normal controls vs. 4 MF patients after allogeneic transplant showed striking differences in cell type composition and transcriptional profiles. Of note, Compositional comparisons identified the non-hematopoietic stromal cell fraction as harboring the biggest differences with, surprisingly, a proportional relative depletion of mesenchymal stromal cells (MSCs) and enrichment of endothelial cells (ECs) in MF vs. normal controls. Concomitant transcriptional differences were observed between MSCs recovered from MF vs. normal control sample, characterised by reduced expression of hematopoietic support factor genes (eg, KITLG, CXCL12, ANGPTL2, NCAM2, CSF1) and increased expression of extracellular matrix (ECM) genes (eg, FN1, COL1A2, COL3A1, DCN, SPARC), features which suggest an explanation for the increased frequency of graft failure following allograft in MF versus other hematologic malignancies.  Single-Cell rEgulatory Network Inference and Clustering (SCENIC) indicated transcription factors with either increased (eg, NR2F2, RUNX2, FOXP2) or decreased (eg, CEBPA, FOXC1, and PPARG) transcriptional activity as candidate master transcriptional regulators of the observed MSC reprogramming in MF.  Within the hematopoietic fraction, and agnostic of JAK inhibitor treatment status, comparison of MF vs. control cells unexpectedly revealed significant upregulation of interferon response genes, especially in CD14+ monocytes, but also in neutrophils and their progenitors, centred on expression of interferon-stimulated gene factor 3 (ISGF3) genes IRF9 and STAT1/2. Comparison of MF samples according to ruxolitinib treatment status indicated that ruxolitinib induced downregulation of an NFκB-centered inflammatory program, particularly in neutrophils.  Finally, ligand-receptor analysis using NicheNet identified TGFB1, IL1B, and TNF as top predicted ligands for induction of the MF signature in MSCs. While myeloid cells were top producers of these factors, their expression did not vary between MF vs. controls, suggesting other mechanisms, such as prolonged retention of ligand in the ECM, are important.  In summary, our comparative scRNA analysis of BM cells from MF patients and controls – the largest reported to date – reveals (i) transcriptional reprogramming of MSCs leading to reduced expression of hematopoietic support factor and increased expression of ECM genes; and (ii) increased expression of interferon and NFkB inflammatory pathways in myeloid cells.

overall_design: Bone marrow cells from digested human trephine biopsy tissue were subjected to Fluorescence-activated cell sorting (FACS) to isolate the haematpoeitic and microenvironmental fraction of cells, then analyzed using scRNAseq. Comparative analysis was then done to compare cells from myelofibrosis patients and healthy controls.

first: Alexia

last: Strickson

first: Kristian

last: Gurashi

first: Maria

last: Kleppe

first: John

last: Weightman

first: Hugh

middle: Y

last: Rienhoff Jr

first: Joanna

last: Storer

first: Tim

last: Somervaille


title: RNA-seq of rice roots treated with or without Fo10 under Cd

city: Shanghai

first: Ziai

last: Qi

address: Fenglin 300 Road

institute: CAS Center for Excellence in Molecular Plant Sciences

summary: Using RNA-seq to study the DEGs of the root treated with or without Fo10 under Cd

overall_design: Examination of DEGs using RNA-Seq

first: Tianyu

last: Gu

first: Yating

last: Wang

first: Siying

first: Jing

last: Yan

first: Huapeng

last: Qiu

first: Yanxuan

last: Yu

first: Zijun

last: Fang

first: Junmin

first: Jiming

last: Gong


title: Impact of shear stretch and oxygen toxicity on pulmonary MSC of the preterm infant.

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: Bronchopulmonary dysplasia (BPD) represents one of the most important sequelae of preterm birth affecting more than 20% of infants born below 32 weeks. Mechanical ventilation exerting shear stress (cyclic mechanical stress, CMS) and oxygen toxicity (hyperoxia, Hox) mainly contribute to the pathogenesis of BPD. The study proposal aims to separate the impact of CMS and Hox on pulmonary mesenchymal stem cells (MSC) isolated from preterm infants participating in the DZL PROTECT-AIRR cohort study in a world-wide unique in vitro setting. The impact of rhythmic 2D and 3D stretch to MSC cell cultures alone and in combination with different fractions of oxygen is evaluated with respect to MSC phenotype, transcriptional regulation, protein alterations and paracrine secretion.

overall_design: 6 groups with 8-16 biological replicates

first: Judith

last: Behnke

first: Harald

last: Erhardt


title: NF-κB-induced expression of T-bet suppresses proliferation of malignant B cells and is associated with good prognosis in chronic lymphocytic leukemia

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

institute: DKFZ


title: NF-κB-induced expression of T-bet suppresses proliferation of malignant B cells and is associated with good prognosis in chronic lymphocytic leukemia [scRNA-seq]

summary: The T-box transcription factor T-bet is encoded by Tbx21 and was identified to play a role in aging and tissue localization of B cells. T-bet expression was detected in malignant B cells but its potential role in B-cell malignancies remains largely unexplored. We used single cell RNA sequencing (scRNA-seq) and the assay for transposase accessible chromatin using sequencing (scATAC-seq) to analyze the regulatory role of T-bet in TCL1 leukemia.

overall_design: Tbx21-KO (-/-) and Tbx21-WT (+/+) TCL1 cells were expanded in immunodeficient NSG animals and analyzed using scRNA-seq and scATAC-seq.

first: Karsten

last: Rippe

first: Philipp

last: Roessner

first: Martina

last: Seiffert


title: NF-κB-induced expression of T-bet suppresses proliferation of malignant B cells and is associated with good prognosis in chronic lymphocytic leukemia [scATAC-seq]


title: Electro-metabolic coupling in multi-chambered vascularized human cardiac organoids

city: Jerusalem

first: Avner

last: Ehrlich

address: Silberman 3-512, Edmond J. Safra Campus (Givat Ram)

country: Israel

institute: The Hebrew University of Jerusalem

summary: The study of cardiac physiology and disease is hindered by physiological differences between humans and small-animal models. Here, we report the generation of multi-chambered vascularized human cardiac organoids under anisotropic stress, and their applicability to study electro-metabolic coupling in cardiac tissue. The organoids are derived from human induced pluripotent stem cells, and integrate sensors for the simultaneous measurement of oxygen uptake, extracellular field potentials and cardiac contraction at resolutions higher than 10 Hz. The microphysiological system allowed us to find that 1-Hz cardiac respiratory cycles are coupled with electrical activity rather than with mechanical activity, that calcium oscillations drive a mitochondrial respiration cycle, that the pharmaceutical or genetic inhibition of electro-mitochondrial coupling results in arrhythmogenic behaviour, and that the induction of arrythmia by the chemotherapeutic mitoxantrone can be partially reversed by the co-administration of metformin. Microphysiological cardiac systems may further facilitate the study of the mitochondrial dynamics of cardiac rhythms and advance the understanding of cardiac physiology.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Recent work demonstrated that geometric confinement induces a central cavity to form in cardiac organoids . Other developmental studies showed that complex partitioning only occurs following the development of the cardiac vasculature. To mimic this developmental step, we seeded a mixture of hiPSC-derived cardiomyocytes (hiPSC-CMs) and rat primary cardiac microvascular endothelial cells (CECs) in geometrically-confining microwells. The tissue contracted into a single mass in 4 days and started beating after 10 days. Cardiac organoids were cultured over the next weeks, acquiring smooth exterior and synchronized behaviour following 25 days of culture. GFP-expressing endothelial cells reveal that vascular networks begin forming on day 10, developing into complex circumferentially-aligned networks by day 25. To validate these structural findings we carried out RNA sequencing of the cardiac organoids, comparing their expression to multiple human cardiac tissues, and hiPSC-CMs from two-dimensional cultures. Cardiac organoids showed expression signatures associated with pacemaker (sinoatrial and atrioventricular nodes), endocardium, and epicardium cells, as well as cardiac fibroblasts.

first: Ehrlich

last: Avner

first: Ghosheh

last: Mohammad

first: Nahmias

last: Yaakov


title: NLRP14 deficiency contributes to female infertility and early embryo arrest

city: Jinan

first: Rongrong

last: Zhang

address: 44 Wenhuaxi Road

institute: Shandong University

summary: Oocyte maturation is vital to attain full competence required fertilization and embryogenesis. As a maternal effect factor, NLRP14 is preferentially expressed in mammalian oocytes and early embryos. Yet the role and molecular mechanism of NLRP14 in oocyte maturation and early embryogenesis is largely unknown. Whether NLRP14 deficiency accounts for human infertility with oocyte and embryo defects remains to be elucidated. Here, NLRP14 is identified essential for establishment of competent oocytes that can sustain early embryo development. Maternal deficiency of Nlrp14 results in sterility characterized by oocyte maturation defects and early embryo arrest. Nlrp14 ablation leads to compromised oocyte quality and developmental competence due to impaired oocyte cytoplasmic and nuclear maturation. Mechanistically, NLRP14 interacts with UHRF1 in oocyte cytoplasm to protect it from proteasome-dependent degradation, and perturbs maternal mRNA zygotic-decay and zygotic genome activation during maternal-zygotic transition. Furthermore, compound heterozygous pathogenic variants in NLRP14 gene are identified in infertile women with early embryonic arrest, which interrupt the NLRP14-UHRF1 interaction or UHRF1 protein expression. Our data uncover a vital role of NLRP14 as a new cytoplasmic-specific modulator of UHRF1 in oocyte meiotic maturation and early embryogenesis, which should provide new insights into risk prediction and genetic diagnosis for female infertility.

overall_design: We performed RNA-seq of oocytes and embryos of wild type and Nlrp14 knockout mice at four stages to obtain and analyze the gene expression profiles.

first: Wenzhe

first: Ling

last: Wu

first: Chendi

last: Zhu

first: Chuanxin

first: Chengpeng

last: Xu

first: Shidou

last: Zhao

first: Xinchen

last: Liu

first: Ting

last: Guo

first: Yueshuang

last: Lu

first: Lei

last: Li

first: ZiJiang

last: Chen

first: Yingying

last: Qin

first: Xue

last: Jiao