title: Live or heat-killed Lactobacillus rhamnosus aerosolization decreases adenomatous lung cancer development in a mouse carcinogen-induced tumor model

status: Public on Nov 29 2022

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: One of the responsible factors involved in the progression of pre-malignant lung lesions to lung cancer is the increased immunosuppressive microenvironment of the lung, that is deeply infleunced by the microbiota. In this article, we have investigated if the perturbation of lung microbiota by antibiotics or probiotic aerosol, interferes with lung cancer development in a mouse carcinogen-induced tumor model. Specifically, the effect is mostly observed with aerosol with Lactobacillus Rhamnosus GG that results to impair lung cancer growth by promoting local immunity. This study points out to new and non-invasive strategy to treat individuals at risk of lung cancer.

overall_design:
Urethane-injected mice were vancomycin/neomycin (V/N)- or live- or dead- L. Rhamnosus GG (L.RGG)- aerosolized and tumor development was evaluated. Transcriptional profiling of lungs and IHC were performed.  Mice were sacrificed, tumor nodules were collected, and RNA was extracted using the RNeasy Mini Kit (Qiagen) for the gene expression profile. In L.RGG-treated groups the gene encoding the joining chain (JChain) of immunoglobulins was significantly increased.
LRGG M = heat-killed LRGG
LRGG V = live LRGG


title: Loss of Dnmt3a impairs hematopoietic homeostasis and myeloid cell skewing via the PI3Kinase pathway

status: Public on Nov 30 2022

city: Indianapolis

first: Reuben

last: Kapur

state: IN

address: 1044 W Walnut St

country: USA

institute: Indiana University

type: Expression profiling by high throughput sequencing

summary: To investigate the role of PI3K in Dnmt3a loss driven leukemia, bone marrow cells from wildtype or Dnmt3a knockout mice were assayed for differential gene expression.The signaling pathways by which DNMT3A mutations contribute to myeloid transformation are poorly understood. We investigated that loss of Dnmt3a in HSC/Ps results in myeloproliferation, which is associated with hyperactivation of the PI3Kinase pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  bone marrow cells from wildtype and Dnmt3a knockout mice

first: Palam

middle: L

last: Reddy

first: Kapur

last: Reuben


title: Differentiation-related epigenomic changes define clinically distinct keratinocyte cancer subclasses [methylation]

status: Public on Nov 28 2022

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

type: Methylation profiling by high throughput sequencing

summary: Keratinocyte cancers (KC) are the most prevalent malignancies in fair-skinned populations, posing a significant medical and economic burden to health systems. KC originate in the epidermis and mainly comprise basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC). Here we combined single-cell multi-omics, transcriptomics and methylomics to investigate the epigenomic dynamics during epidermal differentiation. We identified ~4,000 differentially accessible regions between undifferentiated and differentiated keratinocytes, corresponding to regulatory regions associated with key transcription factors. DNA methylation at these regions defined AK/cSCC subtypes with epidermal stem cell- or keratinocyte-like features. Using cell type deconvolution tools and integration of bulk and single-cell methylomes, we demonstrate that these subclasses are consistent with distinct cells-of-origin. Further characterization of the phenotypic traits of the subclasses, and the study of additional unstratified KC entities uncovered distinct clinical features for the subclasses, linking invasive and metastatic KC cases with undifferentiated cells-of-origin. Our study provides a thorough characterization of the epigenomic dynamics underlying human keratinocyte differentiation and uncovers novel links between KC cells-of-origin and their prognosis.

overall_design: One healthy sun-protected epidermis from the inguinoiliac region from a 62y/o male donor was analysed.

first: Lyko

middle: M

last: Rodríguez-Paredes


title: DAZL regulates proliferation of human primordial germ cell by direct binding to precursor miRNAs and enhances DICER processing  activity

city: BEIJING

first: XIAOYU

last: FENG

state: BEIJING

address: QINGHUAYUAN street，HAIDIAN distribute

country: China

institute: Tsinghua University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Understanding the molecular and cellular mechanisms of human primordial germ cells (hPGCs) is essential in studying infertility and germ cell tumorigenesis. Many RNA  binding proteins (RBPs) and non-coding RNAs are specifically expressed and functional during hPGC developments. However, the roles and regulatory mechanisms of these RBPs and non-coding RNAs, such as microRNAs (miRNAs), in hPGCs remain elusive. In this study, we reported a new regulatory function of DAZL, a germ cellspecific RBP, in miRNA biogenesis and cell proliferation. First, DAZL colocalized with miRNA let-7a in human PGCs and upregulated the levels of over a hundred mature miRNAs, including eight out of nine let-7 family, miR10, and miR199. Purified DAZL directly bound to the loops of precursor miRNAs with sequence specificity of GUU. The binding of DAZL to the precursor miRNA increased the maturation of miRNA by enhancing the cleavage activity of DICER. Furthermore, cell proliferation assay and cell cycle analysis confirmed that DAZL inhibited the proliferation of in vitro PGCs by promoting the maturation of these miRNAs. Evidently, the mature miRNAs  upregulated by DAZL silenced cell proliferation regulators including TRIM71. Moreover, DAZL inhibited germline-tumor-cell proliferation and teratoma formation. These results demonstrate that DAZL regulates hPGC proliferation by enhancing miRNA processing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT PGCLCs and oeDAZL PGCLCs and  expression profiling analysis of miRNA-seq for WT PGCLCs and its derivatives (shDAZL_4,shDAZL_6).

first: Feng

last: Xiaoyu

first: Xu

last: Shuting


title: RNAseq of CD4 T cells from female Rheumatoid arthritis patients

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

summary: RNAseq of CD4 cells from 24 female RA patients activated with aCD3 for 48 hours. Patients were collected crossectionally from the Rheumatology clinic during 2018. Age md 47, range 24-67 years, Disease duration md 5.5, range 1-30 years.

overall_design: 24 women with  rheumatoid arthritis, CD4 cells  from human PBMC isolated by positive selection on Dynabeads (cat.11331D), stimulated with anti-CD3 (OKT3, Sigma-Aldrich)  for 48h

first: Karin

last: Andersson

first: Malin

middle: C

last: Erlandsson

first: Nina

last: Oparina


title: Spatial Profiling Identifies Prognostic Features of Response to Adjuvant Therapy in Triple Negative Breast Cancer (TNBC)

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

summary:
Nanostring DSP was performed on 25 TMA cores from TNBC patients with separate tumour and stroma compartment samples
De proteins were identified in tumour and stromal compartments

overall_design: DE was performed by chemotherapy outcome and Overall survival analysis was performed

first: James

last: Monkman

first: Mark

last: Adams

first: Ken

last: O'Byrne


title: Stress induced accelerated aging in mouse eye [RNA-seq]

city: Irvine

first: Dorota

last: Skowronska-Krawczyk

state: California

address: 837 Health Sciences Rd, Gillespie Neuroscience Research Facility, Room#2226, Bench#8

department: Physiology & Biophysics

institute: UC Irvine

summary: Aging, a universal process that affects all cells in an organism, is a major risk factor for a group of neuropathies called glaucoma, where elevated intraocular pressure is one of the known stresses affecting the tissue. Our understanding of molecular impact of aging on response to stress in retina is very limited, therefore we developed a new mouse model to approach this question experimentally. Here we show that susceptibility to response to stress increases with age and is primed on chromatin level. We demonstrate that program activated by stress caused by ocular hypertension is similar to natural aging and involves activation of inflammation and senescence. Finally, we show that multiple instances of pressure elevation cause accelerated aging of young retina as measured on transcriptional and epigenetic level and is accompanied by changes in chromatin modifications. Our data suggests that molecular mechanism of aging is regulated at the level of epigenetic activation and repression and, therefore, might be modifiable. Lastly, this work further emphasizes the importance of early diagnosis and prevention as well as age-specific management of age-related eye-diseases, including glaucoma.

overall_design: To investigate whether the molecular changes in the aging retina can explain the observed functional decline of the visual system we performed a whole retina mRNA sequencing on retinas isolated from both 3-month and 18-month-old mice. 3-month-old bulk retinas (N=2) was set as control group to 18-month-old bulk retinas (N=2) in the natural aging related differential expression analysis in wildtype mouse. To capture age-dependent transcriptional changes in the retinas upon unilateral IOP elevation, RNA-seq analysis was performed on bulk retinas collected 2 days after 1 hour of constant 30mmHg IOP treatment from 3-month-old and 18-month-old wildtype C57BL/6J mice when retina ganglion cell loss is not yet observed.  For mice at each age (3 month or 18 month), unilateral untreated retinas (N=2) were set as control group to unilateral IOP (constant 30mmHg IOP for 1 hour) treated retina (N=2) in the intraocular pressure elevation related differential expression analysis in wildtype mouse. To investigated whether repeated mild IOP elevation in young animal can affect the expression levels of genes involved in the response to IOP stress, 3-month-old mice were treated with unilateral constant 30mmHg IOP elevation for 1 hour biweekly, four times in total. The contralateral eye served as a control to the recurring stress treated eye (N=2). Two days after the final IOP insult, retinas were collected and bulk RNA-seq was performed.

first: Qianlan

last: Xu

first: Cezary

last: Rydz

first: Viet

middle: A

last: Nguyen Huu

first: Lorena

last: Rocha


title: RNAseq of CD4 T cells treated with survivivin inhibitor YM155 for 24h

summary: CD4 T cells from 4 healthy women were activated with aCD3 and treated with the survivin inhibitor YM155, 10 ng/ml or control during 24 hours. The last 2 hours with upplement of IFNg. The objective was to understand the action of survivin (coded by BIRC5 gene) in CD4 T cells.

overall_design: 4 healthy women, paired analysis possible. CD4 cells from human PBMC isolated by positive selection on Dynabeads (cat.11331D), stimulated with anti-CD3 (OKT3, Sigma-Aldrich) treated for 24h with YM155, 0 or 10nM, (Selleck Chemicals, Houston, TX) last 2 hours with addition of IFNg (50ng/ml, Peprotech, Cranbury, NJ, USA)


title: Sex-biased gene expression in the common copepod Eurytemora affinis

city: Baltimore

first: Joana

middle: C.

last: Silva

state: MD

address: 801 West Baltimore St

institute: Institute for Genome Sciences, University of Maryland School of Medicine

summary: Analysis of the genes differentially expressed by male and female copepods, i.e. "sex-biased" genes; with an interest in sex-determination, sex-development, sex-differentiation, and the differentially expressed pathways.

overall_design: Total RNA was extracted from pools of adult male and female culture-reared Eurytemora affinis.

middle: B

last: Munro

first: Marijan

last: Posavi

first: Arthur

last: Brady

first: Joshua

last: Orvis

first: Suvarna

last: Nadendla

first: Kemi

last: Abolude

first: Priti

last: Kumari

first: Amol

last: Shetty

first: Carol

middle: E

last: Lee


title: Loss of Dnmt3a impairs hematopoietic homeostasis and myeloid cell skewing via the PI3Kinase pathway II

first: Reuben

last: Kapur

summary: Inhibition of PI3K rescues Dnmt3a loss driven leukemia. The signaling pathways by which DNMT3A mutations contribute to myeloid transformation are poorly understood. We investigated that loss of Dnmt3a in HSC/Ps results in myeloproliferation, which is associated with hyperactivation of the PI3Kinase pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  vehicle and PI3Kab-inhibitor treated WBM transplants of Dnmt3a knocokout cells.

first: Palam

last: Lakshmi reddy

first: Kapur

last: Reuben


title: RNAseq of colorectal cancer organoids

city: Tianjin

first: Hao

last: Zheng

address: Nankai University

department: college of life science

institute: Nankai University

summary: We tested transcript profile of colorectal cancer (CRC) organoid from CRC patients. We compared the transcripts profile change between drug resistant organoid and drug sensitive organoid.

overall_design: We cultured CRC patients derived tumor organoid and divided the tumor organoids into two groups according to drug sensitivity.

first: jinming

last: Liu

first: Yanping

last: Zhao

first: Gang

last: Hu

first: Lei

last: Du

first: Quan

last: Chen


title: circRNA expression profile in hepatocellular carcinoma (HCC) with metastasis, HCC without metastasis, and non-tumor tissues

city: Shijiazhuang

first: Ping

last: Gao

state: Hebei

address: No. 361 Zhongshan East Road

department: School of Public Health

institute: Hebei medical university

summary: circRNA microArray analysis from Arraystar were used to examine the expression profile in HCC with metastasis, HCC without metastasis, and non-tumor tissues

overall_design: Liver tissues from HCC surgery were distributed into three experimental groups: non-tumor tissue group, tumor without metastasis group and tumor with metastasis group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar)

first: Dian-Wu


title: Targeting MUC1-C sensitizes colorectal cancer cells to BRAF inhibitor

city: Boston

first: Yoshihiro

last: Morimoto

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: BRAF mutant colorectal cancer has a poor prognosis and gets resistant to BRAF inhibitors quickly. This study aims to clarify the mechanism of resistance to BRAFi. We found MCU1-C is overexpressed in BRAF mutant colorectal cancer and targeting MUC1-C genetically and pharmacologically sensitized Colorectal cancer cells to BRAF inhibitor. This finding suggests that MUC1-C could be a new therapeutic target for BRAF mutant colorectal cancer.

overall_design: RNA-seq in colorectal cancer cell lines


title: Missense mutation of c.635T>C in CAPN3 impairs muscle in-jury repair in a Limb-Girdel Muscular Dystropy Model

city: Shanghai

first: Jiajun

last: Qiu

address: West BeiJing Road

institute: Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine

summary: Limb-girdle muscular dystrophies (LGMD) is a group of muscle diseases characterized by pro-gressive muscle weakness and muscular atrophy of proximal muscles. Limb-girdle muscular dystrophy recessive 1 (LGMDR1), previously known as LGMD2A, is a specific LGMD caused by a gene mutation encoding the calcium-dependent neutral cysteine protease calpain-3 (CAPN3). In our previous study, a novel compound heterozygous mutation, c.635T>C causing missense mu-tation of p.Leu212Pro, was identified in LGMDR1 patients. For the investigation of the molecular mechanism for muscular dystrophy, LGMDR1 CAPN3-point-mutation mouse model was pre-pared by injecting into fertilized eggs of C57 mice the following: in vitro transcribed Cas9 mRNA, sgRNA for mutation sites, and homologous fragments. The LGMDR1 models displayed a mild and slow malnutrition phenotype until 10 months old. Western blot and immunofluorescence assay also showed that the expression level of CAPN3 protein in muscle tissue of mutant mice was similar to that of wild-type mice. Pathological results revealed that a few inflammatory cells infiltrated the endomyocytes of some homozygous mice at 10 months of age. Compared with wild-type mice, motor function was not significantly impaired in CAPN3 mutant mice. Interest-ingly, we found that the arrangement and ultrastructural alterations of mitochondria in the muscular tissue of homozygous mice at the electron microscopy level. Then, muscle regeneration of LGMDR1 was simulated using Cardiotoxin (CTX) to induce muscle necrosis and regeneration to trigger the injury modification process. A large number of inflammatory cells and damaged myofibers were observed in both mutant mice and wild type mice 3 and 6 days after CTX treat-ment. Fifteen and twenty-one days after treatment, the repair of diseased mice was significantly worse than that of control mice. RNA-seq results demonstrated that the expression of mito-chondrial-related functional genes was significantly down-regulated in mutant mice. Taken to-gether, our results strongly suggest that LGMDR1 mouse model with a novel c.635T >C mutation in CAPN3 gene was significant disfunction in muscle injury repair through impairing the mito-chondrion.

overall_design: Pathological analysis showed that the muscle tissue of wild-type mice had returned to normal 21 days after CTX treatment, while LGMDR1 mice still had obvious muscle injury. Therefore, four groups of experiments were set up, namely disease group (CN), disease injury group (CN-CTX), control group (NC) and control injury group (NC-CTX), with 3 mouse muscle samples in each group. Total RNA and DNA were extracted from the left gastrocnemius muscle of LGMDR1 mice and wild-type mice 21 days after CTX treatment (CTX treatment), and total RNA and DNA were extracted from the right gastrocnemius muscle without CTX treatment as control. Sent to Beijing Novogene company for transcriptome sequencing.

first: Hou-Shi

last: Ma

first: Xiu-Li

last: Gong

first: Wen-Xiu

last: Li

first: Qin

last: Cai

first: Yan-Wen

first: Xin-Bing

last: Guo

first: Zhao-Rui

last: Ren

first: Fanyi

last: Zeng

first: Jing-Bin

last: Yan


title: Effect of clinically observed BTK mutations on gene expression during cell proliferation and differentiation in TMD8 cells

city: 北京市

first: Hongwei

last: Yuan

state: 北京市

address: 北京市, 昌平区, 北京生命科学研究所

institute: National Institute of Biological Sciences, Beijing

summary: To investagate the clinically observed BTK C481S, C481F, C481Y and C481R mutations in the regulation of B cell receptor signaling, we extablished TMD8 cells expressing BTK C481S, C481F, C481Y and C481R in which endogenous BTK was inactivated by ibrutinib. We then performed gene expression profiling analysis using data obtained from RNA-seq of 20 different cells after DMSO or 10 nM ibrutinib treatment from two indenpendent experiments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from parental TMD8 cells and TMD8 cells expressing BTK C481S, C481F, C481Y and C481R after DMSO or 10 nM ibrutinib treatment 24 hours.

first: Ting

last: Han


title: Hippo signaling pathway maintains sinoatrial node homeostasis

city: Houston

first: Jun

last: Wang

state: TX

address: 6431 Fannin Street

institute: The University of Texas Health Science Center at Houston

summary: The sinoatrial node (SAN) functions as pacemaker of the heart to initiate and drive rhythmic heartbeats. The Hippo signaling pathway is a fundamental pathway for heart development and regeneration. Although abnormalities of Hippo pathway are associated with cardiac arrhythmias in human patients, yet its role in the SAN is unknown. We found that Lats1/2 inactivation caused severe sinoatrial node dysfunction (SND; sick sinus syndrome). Compared to the controls, Lats1/2 CKO mutants exhibited dysregulated calcium handling and increased fibrosis in the sinoatrial node, indicating Lats1/2 function through both cell-autonomous and non-cell-autonomous mechanisms. Notably, the Lats1/2 CKO phenotype was rescued by genetic deletion of Yap and Taz in the CCS, and these rescued mice had normal sinus rhythm and reduced fibrosis of the sinoatrial node, indicating that Lats1/2 function through Yap and Taz. CUT&Tag sequencing data showed that Yap regulates genes critical for calcium homeostasis such as Ryr2 and genes encoding paracrine factors important in intercellular communication and fibrosis induction such as Tgf-β1 and Tgf-β3. Consistently, Lats1/2 CKO mutants had decreased Ryr2 expression and increased Tgf-β1 and Tgf-β3 expression compared with control mice. We reveal for the first time that the canonical Hippo-Yap pathway has a pivotal role in functional homeostasis of the sinoatrial node.

overall_design:
We investigated key regulators of the Hippo pathway in the sinoatrial node by conditionally inactivating the Hippo signaling kinases Lats1 and Lats2 using the tamoxifen-inducible, cardiac conduction system (CCS)-specific Cre driver Hcn4CreERT2 and Lats1 and Lats2 conditional knockout (CKO) alleles. In addition, the Hippo signaling effectors Yap and Taz were conditionally inactivated in the sinoatrial node. To determine the function of the Hippo signaling pathway in the sinoatrial node and other CCS components, we conducted a series of physiological and molecular experiments including telemetry ECG recording, echocardiography, Masson’s Trichrome staining, calcium imaging, immunostaining, Cleavage Under Targets and Tagmentation (CUT&Tag) sequencing using antibodies against Yap1 or H3K4me3, qRT-PCR, and Western blotting.

R56HL142704 and R01HL142704 to Jun Wang;
T32HL07676 to Rich Gang Li;
R01HL163277, R01HL136389, and R01HL147108 to Na Li;
American Heart Association SDG19840000 and TPA970606 to Jun Wang;
American Heart Association 902940 to Mingjie Zheng;
American Heart Association 903251 to Rich Gang Li;
American Heart Association EIA936111 to Na Li.

first: Zheng

last: Mingjie

first: Wang

last: Jun


title: Integrative mRNA-miRNA interaction analysis associated with the immune response in the head kidney of rainbow trout (Oncorhynchus mykiss) after infectious hematopoietic necrosis virus infection

city: Lanzhou

first: jinqiang

last: huang

address: Yintanlu Stress

institute: Gansu Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Rainbow trout (Oncorhynchus mykiss) is an important cold-water fish widely cultivated in China. The frequent occurrence of viral diseases caused by infectious hematopoietic necrosis virus (IHNV) seriously restricted the healthy development of the rainbow trout farming industry. However, the immune defense mechanism induced by IHNV in rainbow trout has not been fully elucidated. In the present study, we detected mRNA and miRNA expression profiles in rainbow trout head kidney after IHNV infection and the expression patterns of key immune-related genes at different post-infection periods (0-, 6-, 12-, 24-, 48-, 72-, 96-, 120- and 144 hours post-infection (hpi)) using RNA-seq and qRT-PCR. The results showed that a total of 7486 genes and 277 miRNAs were differentially expressed, and numerous differentially expressed genes (DEGs) enriched in the immune-related pathways such as Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway, NOD-like receptor signaling pathway, cytokine-cytokine receptor interaction and JAK-STAT signaling pathway were significantly up-regulated, including LGP2, MDA5, TRIM25, IRF3, IRF7, TLR3, TLR7, TLR8, MYD88, IFN1, MX1 and VIG-1. Integration analysis identified six miRNAs (miR-141-y, miR-200-y, miR-144-y, miR-2188-y, miR-725-y and miR-203-y) that target at least four key immune-related genes (TRIM25, LGP2, TLR3, TLR7, IRF3 and IRF7). Expression analysis showed that TRIM25, MDA5, LGP2, TLR3, TLR7, IRF3, IRF7, IFN1, MX1 and VIG-1 genes increased firstly and then decreased, and reached peak expression at 48 hpi. These findings improve our understanding of the immune mechanism of rainbow trout infected with IHNV, and provide a basic data for future breeding for disease resistance in rainbow trout.

first: Jinqiang

last: Huang

first: Tongzhen

last: Sun


title: A gut microbial metabolite of dietary polyphenols reverses obesity-driven hepatic steatosis

city: Cleveland

first: Lucas

last: Osborn

state: Ohio

address: 9500 Euclid Ave

institute: Cleveland Clinic Foundation

summary: The molecular mechanisms by which dietary fruits and vegetables confer cardiometabolic benefits remain poorly understood. Historically, these beneficial properties have been attributed to the antioxidant activity of flavonoids. Here, we reveal that the host metabolic benefits associated with flavonoid consumption actually hinge on gut microbial metabolism. However, flavonoids are consumed in a largely glycosylated form, rendering them poorly available for small intestinal absorption and subjecting them to microbial metabolism in the colon. We show that a single gut microbial flavonoid catabolite is sufficient to reduce diet-induced cardiometabolic disease burden in mice. Dietary supplementation with elderberry extract attenuated obesity and continuous delivery of the catabolite 4-hydroxphenylacetic acid was sufficient to reverse hepatic steatosis. Analysis of human gut metagenomes revealed that under one percent contains a flavonol catabolic pathway, underscoring the rarity of this process. Our study will impact the design of dietary and probiotic interventions to complement traditional cardiometabolic treatment strategies.

overall_design: Comparison of liver mRNA transcription profiles after 6 weeks of treatment with either control or 4-hydroxyphenylacetic acid (4-HPAA) suncutaneous pellets. N=6 per group.

middle: J


overall_design: In the present study, we detected mRNA and miRNA expression profiles in rainbow trout head kidney after IHNV infection and the expression patterns of key immune-related genes at different post-infection periods (0-, 6-, 12-, 24-, 48-, 72-, 96-, 120- and 144 hours post-infection (hpi)) using RNA-seq and qRT-PCR.


title: CD4 T cells

first: Maria

last: Bokarewa

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

overall_design: Refer to individual Series


title: Survivin ChIPseq

summary: ChIPseq analysis of survivin chromatin binding in activated CD4+ T cells

overall_design: 12 women, CD4 cells from PBMC isolated by positive selection on Dynabeads (cat.11331D),  ConA+LPS for 72h, pooled into 4 samples. ChIPseq using anti-Survivin antibodies (2 microg/ml, 10811, SantaCruz Biotechnology). DNA purified by the EpiTect ChIP OneDay kit (Qiagen).

first: Karin

last: Andersson

first: Malin

last: Erlandsson

first: Nina

last: Oparina


title: Therapy resistant primitive stem cells in chronic myelogenous leukemia are characterized by low c-Kit expression and altered SCF response

city: Birmingham

first: Ravi

last: Bhatia

state: Alabama

address: 1824 6th Avenue South

department: Hematology/Oncology

institute: University of Alabama at Birmingham

summary: Leukemia stem cells (LSC) in chronic myelogenous leukemia (CML) resist elimination with tyrosine kinase inhibitors (TKI) and persist as a source of disease recurrence. LSC populations are heterogeneous, but the most primitive, drug-resistant subsets are not well characterized. Previous studies indicate that variable cell-surface expression of the c-Kit receptor identifies heterogeneous hematopoietic stem cells (HSC) populations. We found that c-Kit expression is reduced on CML LSC compared to normal HSC. Long-term engraftment and leukemia generation capacity was restricted to low c-Kit expressing (c-KitLow) LSC, which showed increased quiescence and inflammatory gene signatures expression. The c-Kit ligand, stem cell factor (SCF), expanded normal HSC but drove maturation of CML LSC. The proportion of c-Kitlow LT-HSC was increased with TKI treatment. Supplementary SCF treatment enhanced elimination of committed but not primitive CML LT-HSC in TKI-treated mice. Low c-Kit expression identifies primitive, treatment-resistant LSC subpopulations with distinct regulatory characteristics, that are critical therapeutic targets.

overall_design: Comparing  CML c-KitHigh and c-KitLow Leukemic stem cells against Normal c-KitHigh and c-KitLow Hematopeitic stem cell in murine bone marrow

first: Mansi

last: Shah

first: Shaowei

last: Qiu

first: Hui

last: Li

first: Mason

last: Harris

first: Jainbo

last: He

first: Ajay

last: Abraham

first: David

last: Crossman

first: Andrew

last: Paterson

first: Robert

middle: S

last: Welner


title: The gene expression change of MDA-MB-231 treated with HDAC/G4 dual-targeting compound

city: guangzhou

first: XinChen

last: Jiang

state: guangdong

address: 中国广州大学城外环东路132号

institute: school of pharmaceutical sciences, SUN YAT-SEN UNIVERSITY

summary: The HDAC/G4 dual compound a6 was developed to improve G4 targeting efficiency and anticancer activity in triple-negative breast cancer cells. In order to explore the relationship between G4 functions and a6 treatment, we performed RNA-seq to analyze the proportion of G4-related differentially expressed genes and KEGG pathway enrichment.

overall_design: The RNA-Seq data of MDA-MB-231 cells treated without (Ctrl) or with single-targeting compound (SAHA or 1) or dual-targeting compound (a6)

first: Xinchen


title: circular RNA (circRNA) expression profile in intestinal stem cells

city: Beijing

first: Zhimin

address: Yuanmingyuang west road 2

institute: Chinese Agricultural University

summary: To explore the role of circRNAs in  intestinal stem cells, we isolated small intestinal crypts from C57BL/6 mice and performed high throughput circRNA-seq.

overall_design:
Then RNA-sequencing analysis were performed and highly expressed circRNAs were identified.
Total RNAs were extracted from small intestinal crypts and subjected to RNA-sequencing analysis  through MGISEQ2000 platform

last: Guo

first: Zusen

last: Fan


title: RNAseq of CD4 T cells treated with survivivin inhibitor YM155 for 72h

first: Maria

last: Bokarewa

summary: CD4 T cells from 4 healthy women were activated with aCD3 and treated with the survivin inhibitor YM155, 10 ng/ml or control during 72 hours. The last 2 hours with upplement of IFNg. The objective was to understand the action of survivin (coded by BIRC5 gene) in CD4 T cells.

overall_design: 4 healthy women, paired analysis possible. CD4 cells from human PBMC isolated by positive selection on Dynabeads (cat11331D), stimulated with anti-CD3 (OKT3, Sigma-Aldrich) treated for 72h with YM155, 0 or 10nM, (Selleck Chemicals, Houston, TX) last 2 hours with addition of IFNg (50ng/ml, Peprotech, Cranbury, NJ, USA)

first: Karin


title: RNA sequencing analysis of the amygdala in mouse model of alcohol drinking

city: Belmont

first: Joy

last: Otten

state: Massachusetts

address: 115 Mill Street

institute: McLean Hospital

summary:
Repeated excessive alcohol consumption is a risk factor for alcohol use disorder (AUD).  Although AUD has been more common in men than women, women develop more severe behavioral and physical impairments.  However, relatively few new therapeutics targeting development of AUD have been validated.  Here, to gain a better understanding of molecular mechanisms underlying alcohol intake, we conducted a genome-wide RNA-sequencing analysis in female mice exposed to different modes (acute vs chronic) of ethanol drinking.  We focused on transcriptional profiles in amygdala including the central and basolateral subnuclei, brain areas previously implicated in alcohol drinking and seeking.  We found distinct gene expression patterns and canonical pathways induced by both acute and chronic intake.  Surprisingly, both drinking modes triggered similar transcriptional changes, including up-regulation of ribosome-related/translational pathways and myelination pathways, and down-regulation of chromatin binding and histone modification.  Notably, multiple genes that were significantly altered with alcohol drinking, including Atp2b1, Hspa4, Slc4a7, Sbno1, Ubxn2b, Nfkb1, Nts, and Hdac2, had previously been associated with human AUD via GWAS or other genomic studies.  In addition, subsequent analyses of hub genes and upstream regulatory pathways predicted that voluntary ethanol consumption affects epigenetic changes via histone deacetylation pathways, oligodendrocyte and myelin function, and the oligodendrocyte-related transcription factor, Sox17.
Overall, our results suggest that the expression of oligodendrocyte-related genes in the central and basolateral subnuclei of the amygdala is sensitive to voluntary alcohol drinking.  These findings suggest potential molecular targets for future therapeutic approaches to prevent the development of AUD, particularly in women, due to repeated excessive alcohol consumption

overall_design: Comparative gene expression profiling analysis from RNA-seq data collected from the amygdala of mice subjected to acute and chronic alcohol drinking paradigm

first: Junghyup

last: Suh

first: Sharvari

last: Narendra

first: Torsten

last: Klengel


title: Effect of treatment with A11 (20 M) on human iPS derived microglia under inflammatory conditions

city: Cambridge

first: William

last: Ralvenius

address: 43 Vassar St

institute: MIT

summary:
Investigation of the anti-inflammatory effects of A11
Performed after a two day treatment of A11, with and without co-treatment with IFNγ, TNFɑ, TGFβ and LPS

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iPS microglia cells and after treatment with A11 and IFNγ, TNFɑ, TGFβ and LPS

first: Celia

last: Fernandez

first: Fan

last: Gao

first: Li-Huei

last: Tsai


title: A pleiotropic hypoxia-sensitive EPAS1 enhancer is disrupted by adaptive alleles in Tibetans [RNA-seq TeloHAEC]

city: Chicago

first: Anna

last: Di Rienzo

state: IL

department: Human Genetics

institute: University of Chicago

summary: Background & Aims:  A major focus of human genetics research has been to identify locally adapted alleles in global populations. In Tibetans, noncoding alleles in EPAS1 – who’s protein product HIF-2 is a key driver of the response to hypoxia – carry some of the strongest signatures of positive selection found in humans, yet their functional mechanism has never been systematically examined. Here we report the discovery of three enhancers within EPAS1, whose activity is significantly disrupted by Tibetan alleles in one or more key organs (endothelium, kidney, and heart). We further characterize one of these enhancers (ENH5) whose activity was found to be not only allele-specific, but also hypoxia-dependent in all three cell types. Deletion of this enhancer results in downregulation of EPAS1 and HIF-2 targets in acute hypoxia as well as a blunting of the transcriptional response to sustained hypoxia. In vivo deletion of the orthologous ENH5 in mice results in dysregulation of gene expression across multiple tissues. We propose that pleiotropic adaptive effects of the Tibetan alleles in EPAS1 underlie the strong selective signal at this gene.

overall_design: Sustain Hypoxia RNA-seq (teloHAECs): For sustained hypoxia experiments, three independent clonal isolates of ENH-5 KO and WT control teloHAECs were plated at very low confluence in two sets of 6-well plates and allowed to adhere overnight. The following day, one set of plates were placed in a humidified incubator contained within the box, and the entire box was maintained at 37C, 5% CO2, 1%O2. The cells were fed every two days for 14 days and then harvested. RNA-seq library prep and sequencing were performed at the University of Chicago Genomics core and run together on the Illumina NovaSEQ (PE 100bp).

first: Olivia

last: Gray

first: Jennifer

last: Yoo

first: Débora

middle: R

last: Sobreira

first: Jordan

last: Jousma

first: David

last: Witonsky

first: Noboru

last: Sakabe

first: Nanduri

last: Prabhakar

first: Ying-Jie

last: Peng

first: Yun

last: Fang

first: Marcelo

last: Nobréga


title: A pleiotropic hypoxia-sensitive EPAS1 enhancer is disrupted by adaptive alleles in Tibetans [mouse RNA-seq]

overall_design: Mouse RNA-seq: At age 9 weeks the mice were placed in pairs, one KO and one WT, into a custom hypobaric hypoxia chamber as described in ref [17] . The pressure was set to 280-290 mmHg which is equivalent to ~8% O2 and the mice were left overnight (~16.5 hours). The following morning, both mice were removed together and euthanized one at a time in a randomly selected order via urethane injection as described in [18]. Mice were rapidly dissected and left kidney, right adrenal gland, left lung, left and right atria, and left and right ventricle were all independently flash frozen in either RLT Plus buffer (kidney, adrenal gland, lung) or Trizol (all heart tissues) and stored at -80C degrees. Once all tissues had been collected from all three pairs of mice, tissues were removed from -80C and homogenized. RNA was extracted one tissue at a time using RNeasy Plus Mini kit (Qiagen, 74134) in a Qiagen Qiacube for all samples stored in RLT buffer and by hand using RNeasy plus mini kit with Qiagen Dnase treatment (RNase-Free DNase Set, cat#79254). RNA was extracted and quality was assessed on an Agilent BioAnalyzer. The RIN was recorded for each sample. RNA-seq library preparation was performed using the TruSeq RNA Library Preparation Kit v2, Set B (Illumina, RS-122-2002). RNA-seq libraries were submitted to the University of Chicago Genomics Core where they were sequenced across 7 lanes of the Illumina HiSeq4000 (one organ per lane, balanced by genotype) with an average of 69.6M 50bp single end reads per sample.


title: A pleiotropic hypoxia-sensitive EPAS1 enhancer is disrupted by adaptive alleles in Tibetans [CapHiC]

overall_design: Capture Hi-C: five million HAECs were grown in normoxia for 24 hours, then harvested and counted, then corsslinked with 1% formaldehyde treatment. Cross-linked chromatin was digested with MboI endonuclease (New England Biolabs, R0147). Subsequently, the restriction fragment overhangs were filled in and the DNA ends were marked with biotin-14-dATP (Life Technologies, 19524-016). The biotin-labeled DNA was sheared and pulled down using Dynabeads MyOne Stretavidin T1 beads (Life Technologies, 65602). The in situ Hi-C library was amplified directly off of the T1 beads with six cycles of PCR, using Illumina primers and protocol (Illumina, 2007). Promoter capture was performed as described[8].The in situ Hi-C library was hybridized to 81,735 biotinylated 120-bp custom RNA oligomers (CustomArray, Inc. www.customarrayinc.com)) targeting promoter regions (four probes/ RefSeq transcription start sites). After hybridization, post-capture PCR (eight amplification cycles) was performed on the DNA bound to the beads via biotinylated RNA. Each library was sequenced on a full lane of an Illumina HiSeq 4000 machine. Standard promoter capture Hi-C analyses were performed using HOMER.


title: A pleiotropic hypoxia-sensitive EPAS1 enhancer is disrupted by adaptive alleles in Tibetans [Paired ATAC-seq & RNA-seq]

overall_design: ATAC-sec/RNA-sec in HAECs: Paired ATAC-seq and RNA-seq were performed on primary human aortic endothelial cells (HAECs). Triplicate samples of cells cultured for 24 hours in either normoxia (21% O2) or hypoxia (1% O2), were harvested in parallel and processed into ATAC-seq libraries using the Nextera DNA library prep kit (FC-121-1030) or RNA-seq libraries using TruSeq RNA Library Preparation Kit v2, Set B (Illumina, RS-122-2002)


title: A pleiotropic hypoxia-sensitive EPAS1 enhancer is disrupted by adaptive alleles in Tibetans

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transgenic mice with an R342X mutation in Phf6 have reduced protein levels and behavior deficits yet few prominent features of Börjeson-Forssman-Lehmann Syndrome (BFLS).

city: Ottawa

first: Dave

last: Picketts

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine

country: Canada

institute: OHRI

summary: The PHF6 mutation, R342X, is a recurrent cause of Börjeson-Forssman-Lehmann Syndrome (BFLS), a neurodevelopmental disorder (MIM#301900). We generated transgenic mice with the identical substitution using CRISPR technology. We show that the R342X mutation causes a reduction in PHF6 protein levels, in both mice and humans, from nonsense mediated decay and nonsense-associated alternative splicing. MRI studies indicated that R342X mice had a reduced brain volume on a mixed genetic background but developed hydrocephaly and a high incidence of postnatal death on a C57BL/6 background. Cortical development proceeded normally while hippocampus and hypothalamus relative brain volumes were reduced. Behavior testing demonstrated deficits in associative learning, spatial memory and an anxiolytic phenotype, although other BFLS clinical features were not observed in the R342X mice. We performed RNA-seq analysis on the cerebral cortices of neonatal R342X mice with the purpose of finding a relationship between gene expression profiles, the behavioral phenotype and the cortical morphology.

overall_design: Assess the change in gene expression profiles in mouse cortex due to the R342X mutation in Phf6

first: Raies

last: Ahmed


title: DYRK1A regulates B cell class switch recombination through phosphorylation of MSH6

status: Public on Nov 27 2022

city: Rehovot

first: Ziv

last: Shulman

address: Herzl St 234

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Effective protection from viral infections depends on the antibody-specific isotype. Here, we found that the protein kinase, DYRK1A, is essential for B cell-mediated protection from viral infection and vaccination through regulation of class switch recombination (CSR). Dyrk1a-deficient B cells were impaired in CSR activity in vivo and in vitro. Phospho-proteomic screens and kinase-activity assays identified MSH6, a DNA mismatch repair protein, as a direct substrate for DYRK1A, and deletion of a single phosphorylation site attenuated CSR. After CSR and germinal center seeding, DYRK1A was required for proper clonal expansion of antigen-specific B cells through attenuation of proliferation. These findings reveal DYRK1A-mediated biological mechanisms of antibody-mediated immune responses that may be used for manipulation in antibody-mediated autoimmunity

overall_design: RNAseq of WT and Dyrk1a cKO DZ or LZ GC B cells, seven days after immunization

first: Liat

last: Stoler-Barak

first: Hadas

last: Hezroni


title: RNA-seq-mediated transcriptome analysis of mouse primary cortical neurons

city: beijing

first: chao

last: wei

address: No. 10, Xitiao, Youanmenwai, Fengtai District, Beijing

institute: capital medical university

summary: Purpose: RNA-seq analysis of the Transcript-Level change during the ferroptosis process. The goals of this study are to analyze the transcriptome profiling (RNA-seq)  of the mouse cortical neurons after Hemin (50 μM) and/or 4-OI (10 μM) treatment.

overall_design: Differential expression analysis of mouse cortical neurons treatment with DMSO, 4-OI (10 μM), Hemin (50 μM) and Hemin (50 μM) +4-OI (10 μM) for 24 h.

first: Qian

last: Li


title: Genome-wide analysis of genes regulated by miR-126-3p in primary human lung microvascular endothelial cells (HLMVEC)

city: Denver

first: William

last: Janssen

state: CO

address: 1400 Jackson St

institute: National Jewish Health

summary: The goal of this study is to investigate the cell type-specific targets of miR-126-3p in human lung microvascular endothelial cells (HLMVEC). Following the transfections of HLMVEC with non-targeting negative controls, miR-126 mimics, or miR-126 antisense inhibitors, we calculated the copy number concentration of miR-126 in each sample and performed genome-wide RNA sequencing. Plotting the gene expression data for each transfection condition (Scramble, 126-OE and 126-KD) against their respective miR-126 concentrations, we performed a linear regression analysis to discover genes that were the most sensitive to changes in miR-126 levels. We identified 1258 genes that were upregulated and 1436 genes that were downregulated by miR-126-3p. Further comparison between the downregulated genes in HLMVEC and targets predicted by online databases including TargetScan and miRDB revealed 6 genes as potential direct targets of miR-126-3p. Our study is the first to report targets of miR-126-3p in HLMVEC and demonstrate the effect of miR-126 level alteration on the HLMVEC global transcriptome. These results add to the diverse functions of miR-126-3p in different endothelial cell types and provide basis for the development of cell type-specific treatment for lung diseases.

overall_design: Whole-genome expression profile were assessed on HLMVEC transfected with scramble control, miR-126-3p mimics, and miR-126-3p antisense hairpin inhibitors. Experiments were repeated in HLMVEC from 3 distinct donors as biological replicates.

first: Danting

last: Cao

first: Irina

last: Petrache

first: Kelsey

last: Anderson


title: The long noncoding RNA AC018926.2 plays a crucial role in palmitic acid exposure-compromised osteogenic potential of periodontal ligament stem cells

status: Public on Nov 26 2022

city: Xi’an

first: Honglei

last: Qu

address: 145, Changlexi Road

department: Department of Periodontology

institute: School of Stomatology, Fourth Military Medical University

summary: This study investigated the cellular response of human periodontal ligament stem cells (PDLSCs) to elevated levels of a specific fatty acid (FA), namely, palmitic acid (PA) and the role of long noncoding RNAs (lncRNAs) in regulating PA exposure-compromised osteogenic potential of PDLSCs. It was found that exposure of PDLSCs to abundant PA led to decreased osteogenic differentiation of cells. Through microarray analysis and gain/loss-of-function studies, AC018926.2 was identified and validated as the lncRNA that was most sensitive to PA and a regulator in the process of PDLSC osteogenic differentiation under a PA condition. Then, RNA sequencing and KEGG analysis demonstrated that AC018926.2 upregulated integrin α2 (ITGA2) expression at the transcriptional level and therefore activated ITGA2/FAK/AKT signaling. Further functional studies revealed that inactivation of ITGA2/FAK/AKT signaling by silencing ITGA2 counteracted the enhancement of the PDLSC osteogenic potential induced by AC018926.2 overexpression. Moreover, the results of bioinformatics analysis and the RNA immunoprecipitation (RIP) assay suggested that AC018926.2 might transcriptionally regulate ITGA2 expression by binding to poly (ADP-ribose) polymerase 1 (PARP1). Our data suggest that AC018926.2 plays a crucial role in PA exposure-compromised osteogenic potential of PDLSCs.

overall_design: PDLSCs were incubated in osteogenic medium with the presence of palmitic acid (PA) or osteogenic medium with the presence of fatty acid-free bovine serum albumin (BSA) for 14 days. All experiments were performed with 3 biological replicates.

first: Hong-Lei

first: Li-Juan

last: Sun

first: Rui-Xin

last: Wu

first: Fa-Ming

last: Chen


title: Targeting Epsins by nanotherapy regulates lipid metabolism and promotes ABCG1-mediated cholesterol efflux to fortify atheroma regression.

city: Boston

first: Xinlei

last: Gao

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

overall_design: Refer to individual Series


title: Function of RNF31  in the Triple Negative Breast Cancer

city: xinxing

first: huijie

last: yang

address: Hongqi District, Xinxiang City

institute: Xinxiang Medical University

summary: To investigate the  function of RNF31  in the Triple Negative Breast Cancer.

overall_design: MDAMB231 cell mRNA samples were summarized in six samples, divided into two groups, siControl and siRNF31. Comparative gene expression profiling analysis of RNA-seq data for MDAMB231 cells treated with siControl and siRNF31.

first: Ting

last: Zhuang

first: Jian

last: Zhu

first: Huijie

last: Yang

first: Min

last: Xue


title: Fibroblasts orchestrate the pathogenesis of fibrotic and glial scar in spinal cord injury

city: Shanghai

first: Runzhi

last: Huang

state: Shanghai

address: No 289 Xincun Road

institute: Department of Orthopaedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China

summary: Spinal cord injury (SCI) is a severe neurological dysfunction, and its pathogenesis remains inadequately understood. Here, to spatiotemporally decode the cellular and molecular pathogenesis of SCI, we performed spatial transcriptomics analysis of 12,930 single cells from 21 samples of SCI contusion model mice. We identified the specific cellular subtypes, differentially expressed genes (DEGs), cell signaling networks, site-specific genes (SSGs), and transcription factors involved in SCI. Our analysis indicated that fibroblasts served as the hub of intracellular communication in the SCI site, sent continuous immune signals to neurocytes, and induced the other cell types to express high levels of the fibroblast marker gene Col1a2. Pseudotime analysis visualized trajectories that emerged from fibroblasts, passed through microglia and ended at neurons after SCI. When the proportion of fibroblasts and their cellular communications were attenuated by solu-medrol treatment, the BMS and MEP performance of SCI mice increased significantly; moreover, the ratio of Col1a2+ cells decreased markedly, and a new subtype of fibroblasts expressing Arg1 appeared. Our results highlight the vital pathological position of fibroblasts and indicate it as a significant therapeutic target for SCI.

overall_design: Eight-week-old C57 mice were subjected to contusion SCI (10 mice) or sham operation (2 mice) and then used for specimen extraction. The sections collected included 14 cross sections (Cro) (6 sections taken at 7 days post SCI (dpi), 6 sections taken at 14 dpi, and 2 sections taken from the sham control) and 7 coronal sections (Cor) (2 sections taken at 7 dpi, 2 sections taken at 14 dpi, one section taken at 7 dpi after solu-medrol therapy at 6 dpi, one section taken at 14 dpi after solu-medrol therapy at 6 dpi, and one section taken from the sham control).


title: Noncanonical Il-1β maturation in microglia impairs cognition in chronic kidney disease via neuronal IL1R signaling

city: leipzig

first: silke

last: zimmermann

state: Sachsen

institute: Universitätsklinikum Leipzig

summary: While cognitive impairment is common in peripheral diseases such as chronic kidney disease (CKD), mechanistic insights and effective therapies are lacking. Here, we show that microglial potassium (K+) dyshomeostasis induces noncanonical IL-1β maturation and neuronal dysfunction via IL-1R signaling in CKD. Despite inflammasome activation in the brain, microglial caspase-1 deficiency does not improve inflammation and cognition in CKD mice. Noncanonical IL-1β maturation in microglia is mediated by the cathepsin C–caspase-8 pathway. Restoring K+ homeostasis in microglia or genetically inhibiting neuronal IL-1R1 signaling abolishes CKD-induced cognitive impairment. Microglial K+ dyshomeostasis and noncanonical microglial IL-1β maturation may therefore be druggable targets in some forms of cognitive impairment. These insights identify a new intercellular microglia–neuron crosstalk and identify potential therapeutic targets to combat inflammasome-induced neuronal dysfunction.

overall_design: We performed single nuclei RNAseq in order to investigate gene expression profiling in brain cells of the cortex in chronic kidney disease versus control/sham mice.

first: Zimmermann

last: Silke

first: Isermann

last: Berend

first: Bondareva

last: Olga

first: Sheikh

last: Bilal N.


title: miRNA sequencing

first: Li

last: Lin

address: shanghaihuangpu

institute: Shanghai Jiaotong university

summary: We established a BCG-infected THP-1 cell model in vitro, obtained the total RNA of cell culture supernatant exosomes and total RNA of the infected group and the uninfected group, and performed miRNA sequencing analysis to find exosomes related to tuberculosis infection The body-derived miRNA is verified by cell lines and primary cells, and the diagnostic value of small sample clinical samples and preliminary functional research and exploration are explored for candidate molecules.

overall_design: 4 samples (BCG-infected THP-1 exosome and cell group/BCG-uninfected THP-1 exosome and cell)


title: Targeting Epsins by nanotherapy regulates lipid metabolism and promotes ABCG1-mediated cholesterol efflux to fortify atheroma regression [scRNA-seq]

summary: Excess cholesterol accumulation in lesional macrophages elicits complex responses in atherosclerosis. Epsins, a family of endocytic adaptors, fuel the progression of atherosclerosis; however, the underlying mechanism and therapeutic potential of targeting Epsins remains unknown. In this study, we determined the role of Epsins in macrophage-mediated metabolic regulation. We then developed an innovative method to therapeutically-target macrophage Epsins with specially-designed S2P-conjugated lipid nanoparticles (NPs), which encapsulate small interfering RNAs to suppress Epsins.Our findings suggest that targeting Epsins in lesional macrophages may offer therapeutic benefits for advanced atherosclerosis by reducing CD36-mediated lipid uptake and increasing ABCG1-mediated cholesterol efflux.

overall_design: The aortas were isolated from WT and DKO mice on normal or western diet. The aorta cells were used to perform single-cell RNA-seq.

first: Kui

last: Cui

first: Beibei

last: Wang

first: Kaifu

first: Hong


title: SOX2-positive retinal stem cells are identified in adult human pars plicata by single-cell transcriptomic analyses

city: Chongqing

first: Zongren

last: Xu

state: Chongqing

address: 1 Youyi Road, Yuzhong District, Chongqing, China

department: ophthalmology department

institute: The First Affiliated Hospital of Chongqing Medical University

summary: Stem cell therapy is a promising strategy to rescue visual impairment caused by retinal degeneration. Previous studies have proposed controversial theories about whether in situ retinal stem cells (RSCs) are present in adult human eye tissue. Single-cell RNA sequencing (scRNA-seq) has emerged as one of the most powerful tools to reveal the heterogeneity of tissue cells. By using scRNA-seq, we explored the cell heterogeneity of different subregions of adult human eyes, including pars plicata, pars plana, retinal pigment epithelium (RPE), iris and neural retina (NR). We identified one subpopulation expressing SOX2 as RSCs, which were present in the pars plicata of the adult human eye. Further analysis showed the identified subpopulation of RSCs expressed specific markers AQP1 and TSPAN12. We therefore isolated this subpopulation using these two markers by flow sorting and found that the isolated RSCs could proliferate and differentiate into some retinal cell types, including photoreceptors, neurons, RPE cells, microglia, astrocytes, horizontal cells, bipolar cells and ganglion cells; whereas, AQP1- TSPAN12- cells did not have this differentiation potential. In conclusion, our results showed that SOX2-positive RSCs are present in the pars plicata and may be valuable for treating human retinal diseases due to their proliferation and differentiation potential.

overall_design: pars plicata, pars plana, RPE, iris and NR cells were isolated from the eyes of 6 donors and profiled with single-cell RNA sequencing(10× Genomics).cDNA libraries were generated using the Chromium Single cell 3’ V3 kit.

first: Xiaotang

first: Wei

last: Fan

first: Shengping

last: Hou


title: Promoting in vivo Adult Liver Organ Growth with Bacteria without Fibrosis and Tumorigenesis

status: Public on Nov 25 2022

city: Rockville

first: Yanggu

last: Shi

address: 9430 Key West AVe #128

institute: Arraystar

summary: Strategies that promote functional organ growth with minimal adverse effects are the ultimate goal of regenerative medicine but no single approach is currently available for organ level repair. Here, using an evolutionary adapted in vivo infection model - Mycobacterium leprae, with host cell reprogramming ability and its natural animal host, the nine-banded armadillo (Dasypus novemcinctus) that harbor bacteria in the highly regenerative liver - we present an in vivo model for promoting adult liver growth at organ level without adverse effects. Experimentally infected armadillos harboring bacteria in the liver, but not infection-resistant or drug-treated animals, showed a significantly increased total liver: body weight ratio, indicative of bacterial-driven liver organ growth in living animals. The machine-learning approach revealed an increase in healthy liver lobule number with a proportionate expansion of the hepatocyte mass with integrating vasculature and biliary networks responsible for functional liver growth. Intriguingly, infected enlarged livers show intact microarchitecture but without evidence of hepatocellular damage, fibrosis/scarring or tumorigenesis. Reactivation of armadillo liver progenitor and developmental genes/proteins, as well as upregulation of growth-, metabolism- and differentiation-associated markers with minimal change in oncogenes or tumor suppressor genes, suggests that bacteria have adapted dynamic regenerative, homeostasis and reprogramming mechanisms to promote de novo organogenesis while maintaining tissue integrity and tumor preventive strategies for host-dependent bacterial propagation. Thus, our model may facilitate the unravelling of in vivo endogenous regenerative pathways that effectively re-engage liver organ growth, with broad implications.

overall_design: Triplicate RNA samples isolated from 24-month ML-infected, 30-month ML-infected and two control Armadillo livers were collected and used for paired-end sequencing. This was used for differential gene expression analysis between infected and control samples.

first: Samuel

last: Hess

first: Timothy

last: Kendall

first: Maria

last: Pena

first: Keitaro

last: Yamane

first: Daniel

last: Soong

first: Linda

last: Adams

first: Richard

last: Truman

first: Anura

last: Rambukkana


title: Zygotic genome activation by the totipotency pioneer factor Nr5a2 IV

city: Munich

first: Pavel

middle: Andreevich

last: Kravchenko

state: Planegg

address: Am Klopferspitz 18

department: Totipotency

institute: Max-Planck-Institute of Biochemistry

summary: Life begins with a switch in genetic control from the maternal to the embryonic genome during zygotic genome activation (ZGA). Despite its importance, the essential regulators of ZGA remain largely unknown in mammals. Based on de novo motif searches, we identified the orphan nuclear receptor Nr5a2 as a key activator of major ZGA in mouse 2-cell embryos. Nr5a2 is required for progression beyond the 2-cell stage. It binds to its motif within SINE B1/Alu retrotransposable elements found in cis-regulatory regions of ZGA genes. Chemical inhibition suggests that 72% of ZGA genes are regulated by Nr5a2 and potentially other orphan nuclear receptors. Nr5a2 promotes chromatin accessibility during ZGA and binds nucleosomal DNA in vitro. We conclude that Nr5a2 is an essential pioneer factor that regulates ZGA.

overall_design: Single embryo RNA seq of SR1848 treated (41), SR1848 + Nr5a2 OE (67) and DMSO control (29) 2C embryos.

first: Johanna

last: Gassler

first: Wataru

last: Kobayashi

first: Imre

last: Gáspár

first: Siwat

last: Ruangroengkulrith

first: Adarsh

last: Mohanan

first: Laura

middle: G

last: Hernandez

first: Maximilian

last: Kümmecke

first: Aleksandar

last: Lalic

first: Robert

last: Ashburn

first: Nikita

last: Rifel

first: Maciej

last: Zaczek

first: Antoine

last: Vallot

last: Rico

first: Sabrina

last: Ladstätter

first: Kikuë

last: Tachibana


title: Heterogeneous activation of Wnt/β-catenin signaling in prostate cancer

city: New York

first: Naitao

last: Wang

state: NY

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

summary: To study the heterogeneous activation of Wnt/β-catenin signaling in prostate cancer, we established a Wnt/β-catenin signaling reporting system 7xTCF-EGFP. We then sorted out GFP+ cells and GFP- cells and compared their properties on both molecular and cellular levels.

overall_design: Assay for transcriptome profiling of Wnt/β-catenin signaling active and inactive cells.

first: Wei

middle: Q

last: Gao


title: Single cell RNA seq of colonic tissue from intestinal epithelial-specific Sprouty2-deleted mice and controls

first: Cambrian

middle: Yangshao

last: Liu

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

summary: In this study we asked how loss of Sprouty2 remodels colonic tissue and function. We show that loss of Sprouty2 promotes IL-13 signaling to regulate colonic secretory cells and furthermore identify deep crypt secretory cells as a reservoir for the host defense peptide RELMbeta.

overall_design: To compare the transcriptomic profiles of isolated colonic single cells from VillinCre/Sprouty2-floxxed mice versus Sprouty2-floxxed control mice

middle: Y

first: Michael

last: Schumacher

first: Mark

last: Frey


title: RNA sequencing of sorted colonic NMUR1+ ILC2s and CD4 T cells

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

overall_design:
Nmur1-eGFP+ ILC2s, Nmur1-eGFP+ CD4 T cells and Nmur1-eGFP– CD4 T cells were sort-purified from the colons of Nmur1iCre-eGFP mice that had been exposed to DSS for 5 days and then allowed to recover on water for 3 days. Throughout this time, they were administered PBS or NMU by intraperitoneal injection every other day.
3 mice were in each treatment group, and samples from each mouse were analyzed as independent samples.

first: Amy

last: Tsou

first: Hiroshi

last: Yano

first: David

last: Artis


title: Targeting Epsins by nanotherapy regulates lipid metabolism and promotes ABCG1-mediated cholesterol efflux to fortify atheroma regression [RNA-seq]

first: Xinlei

overall_design: We performed RNA-seq analysis of WT, ABCG1-KO and Epsin-DKO macrophages.

first: Kui

last: Cui

first: Beibei

first: Kaifu

last: Chen

first: Hong


title: CD47-SIRPα axis blockade in NASH promotes necroptotic hepatocyte clearance by liver macrophages and decreases hepatic fibrosis

first: Fang

last: Li

department: Medicine

institute: Columbia University Irving Medical Center

summary: Necroptosis contributes to hepatocyte death (HC) in non-alcoholic steatohepatitis (NASH), but the fate and roles of necroptotic hepatocytes (necHCs) in NASH remain unknown. We show here that the accumulation of necHCs is associated with worsening NASH in humans and in mice with diet-induced NASH and that NASH liver showed evidence of impaired necHC clearance by liver macrophages. Further, the "don't-eat-me" ligand CD47 on HCs and its receptor, SIRPα, on liver macrophages, were markedly upregulated in human and mouse NASH. In vitro, anti-CD47 or anti-SIRPα promoted necHC engulfment by primary liver macrophages. In a proof-of-concept mouse model of inducible HC necroptosis, anti-CD47 increased necHC uptake by liver macrophages and inhibited hepatic stellate cell (HSC) activation, which is responsible for liver fibrogenesis. Most importantly, treatment of two mouse models of diet-induced NASH with anti-CD47 or anti-SIRPα increased the uptake of necHC by liver macrophages and decreased HSC activation and liver fibrosis. These findings provide evidence that impaired clearance of necHCs by liver macrophages due to CD47-SIRPα upregulation contributes to fibrotic NASH and suggest therapeutic blockade of the CD47-SIRPα axis as a strategy to decrease the accumulation of necHCs in NASH liver and dampen the progression of hepatic fibrosis.

overall_design: Male C57BL/6J mice were fed the Fructose-Palmitate-Cholesterol diet (FPC, Envigo, #TD. 160785 PWD)  for 16 weeks to provoke NASH.  Between weeks 8 and 16, mice received IgG or anti-CD47 (Bio-X-Cell, #BE0283, 200 µg/mouse) through intraperitoneal injection (n = 7-8 mice/group). Liver tissue were used for RNA-sequencing.

first: Hongxue

last: Shi

first: Xiaobo

first: Brennan

last: Gerlach

first: Arif

last: Yurdagul

first: Mary

last: Moore

first: Sharon

last: Zeldin

first: Hanrui

last: Zhang

first: Bishuang

last: Cai

first: Ze

last: Zheng

first: Luca

last: Valenti

first: Ira

last: Tabas


title: Single-cell RNA-seq analysis of the lymphoproliferative disorders triggered by defective LAT signalosome. Modulation of the pathology in the context of two additional mutations, Stat6KO or Grap2KO

city: Marseille

first: Rudy

last: AUSSEL

address: Parc Scientifique et Technologique de Luminy

country: France

institute: CIML

summary: LatY136F mice in which tyrosine 136 of the LAT adaptor is mutate accumulate CD4+ T cells that trigger a fast-onset autoimmune and inflammatory condition called LAT signaling pathology (LSP). Its histopathological manifestations resemble those of human IgG4-related disease (IgG4-RD), an inflammatory condition unifying a constellation of clinical entities leading to multi-organ damage. LatY136F mice deprived of STAT6 transcription factor develop a lymphoproliferative disorder with a kinetics and magnitude identical to that of LatY136F mice. Consistent with a role of STAT6 in Th2 differentiation, the LatY136F x Stat6KO lymphoproliferative disorder is characterize by a lymphoproliferation of both CD4 and CD8 Tc producing high levels of IFN-g. This Tc proliferation is associated with massive B cell proliferation and hyperglobulinemia G2a and G2b. Using single-cell RNA sequencing, we analyzed 48287 CD4 and CD8 T cells isolated from the spleen of LatY136F and LatY136F x Stat6KO mice over the period that leads to LSP installation.  In this study, LatY136F lymphoproliferative disorder is also analyze in Grab2KO mice. Unexpectedly, LatY136F x Grap2KO mice present a lymphoproliferative disorder similar to the one observed in LatY136F mice but this time TCRgd Tc.

overall_design: Lymphoid cells were isolated from spleen of LatY136F, LatY136F x Stat6KO and LatY136F x Grap2KO mice. T cell are first enriched and then purified by cell sorting. Library are processed using Chromium Single Cell 3’ kit from 10X Genomics (California, USA). Sequencing was realized on a NovaSeq6000 system (Illumina). FASTQ raw files were processed using Cell Ranger software (v2.1.1, default parameters), which performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting. Reads were aligned to the mouse mm10 genome.

first: Anais

last: Joachim

last: Aussel

first: Léna

last: Gélard

first: Marie

last: Malissen

first: Bernard


title: IgG profiling using AIT’s 16k protein microarray’ for elucidating the IgG profile of a memory-B cells and a “Novel” cell population

city: Leuven

first: Xavier

last: Bossuyt

address: Herestraat 49

country: Belgium

institute: UZ Leuven

summary:
Plasma cells are not restricted to the CD27+  phenotype: characterization of CD27-CD43+ antibody secreting cells.
Circulating antibody secreting cells are present in peripheral blood of healthy individuals reflecting continued activity of the humoral immune system.  Antibody secreting cells typically express CD27.  We describe and characterize a small population of antibody secreting class switched CD19+CD43+ B cells that lack expression of CD27 in peripheral blood of healthy subjects. Class switched CD27-CD43+ B cells possess characteristics of conventional plasmablasts as they spontaneously secrete antibodies, are morphological similar to antibody secreting cells, show downregulation of B cell differentiation markers, and have a gene expression profile related to conventional plasmablasts. Despite these similarities, we observed differences in IgA and IgG subclass distribution, expression of homing markers, replication history, frequency of somatic hypermutation and antibody response to vaccination. Their frequency is altered in immune-mediated disorders. In order to study the antibody signature we evaluated immune reactivity to 7390 human proteins by protein microarray.

overall_design: CD27-CD43+ and CD27+CD43+ as well as CD27-CD43- and CD27+CD43- B cells from 3 different healthy donors were stimulated in vitro with CpG and the supernatants were concentrated and used for protein microarray-based profiling.  As an insufficient number of  CD43+CD27+ and CD43-C27- cells was available, the antibody signature of these cells could not be studied. Thus the antibody repertoire of CD43+CD27- cells was compared to the antibody repertoire of CD43-CD27+ B cells by protein microarray.

first: Doreen

last: Dillaerts

first: Andreas

last: Weinhaeusel


title: Metabolism of Eriocitrin in the Gut and its Regulation on Gut Microbiota in Mice

city: Hangzhou

first: zuorui

last: xie

address: Zhejiang Gongshang University

institute: ZFM

summary: Eriocitrin, found in lemon fruit, has shown a wide range of biological properties. Herein, to evaluate the intestinal metabolic profile of eriocitrin in colon, the flavonoids in mice colon contents were identified by ultra performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS), and a total of 136 flavonoids were found, including eriocitrin and its six metabolites (eriodictyol, homoeriodictyol, hesperetin, eriodictyol-3'-O-glucoside, hesperetin-7-O-glucoside and eriodictyol-7-O-(6''-O-galloyl) glucoside). Mice colon contents were used for 16S rDNA gene sequencing and gas chromatography-mass (GC-MS). Resultu showed that eriocitrin significantly alters the beta diversity of the gut microbiota, the probiotics such as Lachnospiraceae_UCG_006 were significantly enriched, and the production of butyrate, valerate and hexanoate in the colon pool of short-chain fatty acids (SCFAs) were significant increased. The spearman's association analysis performed some intestinal bacteria may be involved in the metabolism of eriocitrin. Collectively, our results preliminarily suggesting the metabolism of eriocitrin in the gut, demonstrate alterations of eriocitrin on gut microbiota, which warrants further investigation to determine its potential use in food and biomedical applications.

overall_design: Six-week-old male Institute of Cancer Research (ICR) mice (n=12) were randomly divided into eriocitrin treatment and control group (6 males per group). After 2-weeks of feeding, mice were abrosiaed with CO2 asphyxiation after 12h fasting, and colon faeces of mice were collected and stored at -80℃ until later microbial analysis.

first: Ping

last: Li

first: Xia

last: Meng

first: Hongchen

last: Wu

first: Jiayi

last: Xiong

first: Yongquan

first: Lin

last: Chen

first: Qing

last: Gu


title: Isoformic PD-1 is tumorigenic in hepatocellular carcinoma through seemingly exhausted αβ T cells

city: Hong Kong

first: Zhiwu

last: Tan

address: 21 Sassoon Road, Pokfulam

country: Hong Kong

institute: University of Hong Kong

summary:
Purpose: To investigate functional differences between Δ42PD-1+ and PD-1+ T cells in HCC patients
Methods: Δ42PD-1+, PD-1+ T and Δ42PD-1-PD-1- T cells were isolated by cell sorting from HCC patient’s PBMCs and performed the BD Rhapsody single-cell RNA sequencing with focus on 259 T cell-relevant transcripts
Results: Data were obtained from 3 separate T cell subsets, including 3,758 PD-1+, 3,242 Δ42PD-1+ and 4,626 Δ42PD-1-PD-1- T cells, respectively.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Comparison of T cell-relevant transcripts between Δ42PD-1+, PD-1+ T and Δ42PD-1-PD-1- T cell subsets

first: Zhiwei

first: Kwan

last: Man


title: DNA/RNA helicase DHX36 is required for late stages of spermatogenesis

status: Public on Nov 24 2022

first: Zhang

middle: ke

last: jia

address: Xuhui district yueyang road 320

institute: CAS

summary: Spermatogenesis is a highly complex developmental process that typically consists of mitosis, meiosis, and spermiogenesis. DNA/RNA helicase DHX36, a unique guanine-quadruplex (G4) resolvase, play crucial roles in a variety of biological processes. We previously showed that DHX36 is highly expressed in male germ cells with the highest level in zygotene spermatocytes. Here, we delete Dhx36 in advanced germ cells with Stra8-GFPCre, and found that a Dhx36 deficiency in the differentiated spermatogonia leads to meiotic defects and abnormal spermiogenesis. These defects in late stages of spermatogenesis arise from dysregulated transcription of G4-harboring genes, which are required for meiosis. Thus, this study reveals that Dhx36 play crucial roles in the late stages of spermatogenesis.

overall_design: We performed comparative gene expression profiling analysis using data obtained from RNA-seq of zygotene spermatocytes isolated from wild-type and Dhx36 mutant spermatogenesis synchronous mice.

first: Kejia

last: Zhang


title: Zygotic genome activation by the totipotency pioneer factor Nr5a2 II

first: Pavel

last: Kravchenko

overall_design: Single embryo RNA seq of Nr5a2 (55) and control (57) knockdown 2C embryos.

first: Johanna

last: Gassler

first: Wataru

last: Kobayashi

first: Imre

last: Gaspar

first: Siwat

last: Ruangroengkulrith

first: Adarsh

last: Mohanan

first: Laura

last: Hernandez

first: Maximilian

last: Kümmecke

first: Aleksandar

last: Lalic

first: Robert

last: Ashburn

first: Nikita

last: Rifel

first: Maciej

last: Zaczek

first: Antoine

last: Vallot

last: Rico

first: Sabrina

last: Ladstätter

first: Kikuë

last: Tachibana


title: RNA-seq analysis identifies the impact of fine particles (PM2.5) on nasal mucosa-derived fibroblasts.

first: Hai

last: Lin

address: No. 600, Yishan Road, Xuhui District

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: In this study, we performed high-throughput sequencing to evaluate the gene expression profile of nasal mucosa-derived fibroblasts treated with PM2.5.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for nasal mucosa-derived fibroblasts treated with PM2.5 (n=3) or not (n=3).

first: Weitian

last: Zhang


title: Cortical wiring by synapse type-specific control of local protein synthesis

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Neurons use local protein synthesis to support their morphological complexity, which requires independent control across multiple subcellular compartments up to the level of individual synapses. Here we identify a signaling pathway that regulates the local synthesis of proteins required to form excitatory synapses on parvalbumin-expressing (PV+) interneurons in the mouse cerebral cortex. This process involves regulation of the TSC subunit 2 (Tsc2) by the Erb-B2 receptor tyrosine kinase 4 (ErbB4), which enables local control of mRNA translation in a cell type-specific and synapse type-specific manner. Ribosome-associated mRNA profiling reveals a molecular program of synaptic proteins downstream of ErbB4 signaling required to form excitatory inputs on PV+ interneurons. Thus, specific connections use local protein synthesis to control synapse formation in the nervous system.

overall_design: RNAseq of ribosome-associated RNAs from P15 synaptosomes of MGE-derived interneurons in 4 samples from ErbB4 conditional knockout mice and 4 samples from control mice

first: Clémence

last: Bernard

first: Oscar

last: Marín

first: Beatriz


title: Arraystar m6A-mRNA&lncRNA Epitranscriptomic Microarray Service for 6 Mouse samples

city: 南京市栖霞区迈皋桥街道合班村122号职防所

first: xinwei

last: shi

address: 迈皋桥街道

institute: 江苏省疾病预防控制中心职防所

summary: Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed by Bioanalyzer 2100 or Mops electrophoresis. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, the total RNAs were immunoprecipitated with anti-N6-methyladenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar RNA Labeling protocol. The cRNAs were combined together and hybridized onto Arraystar Mouse mRNA&lncRNA Epitranscriptomic Microarray (8x60K, Arraystar). After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in a certain proportion were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed to show the distinguishable m6A-methylation pattern among samples.

overall_design: In this study, mouse pulmonary artery smooth muscle cells were divided into three normoxic treatment groups (control group) and three hypoxic treatment groups (experimental group). Total RNA was extracted and quantified to detect genome-wide m6A modified mRNA levels and screen possible m6A downstream genes.

first: Shi

last: XinWei

first: Xu

last: Ming

first: Sun

last: Kai


title: Zygotic genome activation by the totipotency pioneer factor Nr5a2 III

first: Pavel

last: Kravchenko

overall_design: Single embryo RNA seq of SR1848 treated (80) and DMSO control (56) 2C embryos.

first: Johanna

last: Gassler

first: Wataru

last: Kobayashi

first: Imre

last: Gaspar

first: Siwat

last: Ruangroengkulrith

first: Adarsh

last: Mohanan

first: Laura

last: Hernandez

first: Maximilian

last: Kümmecke

first: Aleksandar

last: Lalic


title: Targeting cancer glycosylation repolarizes tumor-associated macrophages allowing effective immune checkpoint blockade

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Immune checkpoint blockade (ICB) has significantly improved the prognosis of cancer patients, but the majority experience limited benefit, evidencing the need for new therapeutic approaches. Upregulation of sialic acid-containing glycans, termed hypersialylation, is a common feature of cancer-associated glycosylation, driving disease progression and immune escape via the engagement of Siglec-receptors on tumor-infiltrating immune cells. Here, we show that tumor sialylation correlates with distinct immune states and reduced survival in human cancers. The targeted removal of Siglec-ligands in the tumor microenvironment, using an antibody-sialidase conjugate, enhances anti-tumor immunity and halts tumor progression in several mouse tumor models. Using single-cell RNA sequencing, we reveal desialylation mechanistically to repolarize tumor-associated macrophages (TAMs) and identify Siglec-E on TAMs as the main receptor for hypersialylation. Finally, we show genetic and therapeutic desialylation, as well as loss of Siglec-E, to synergize with ICB. Thus, therapeutic desialylation represents a novel immunotherapeutic approach, shaping macrophage phenotypes and augmenting the adaptive anti-tumor immune response.

overall_design: C57BL/6 mice carrying established B16D5-HER2 tumors were treated with the tumor-targeted sialidase E-301 or its catalytically inactive control variant E-301 LOF, with or without PD-1/CTLA-4 blockade. CD45+ tumor-infiltrating immune cells were sorted from 5 pooled mice 7 days after the initial treatment.

first: Michal

last: Stanczak

first: David

last: Sanin

first: Erika

middle: L

last: Pearce

first: Heinz

last: Läubli


title: Zygotic genome activation by the totipotency pioneer factor Nr5a2

overall_design: RNA seq on small batches of MII eggs and early preimplantation mouse embryos in triplicates in WT C57BL/6i strain and in B6CAST F1 hybrids.


title: Ischemia–reperfusion injury in the murine lung

city: Toon

first: Tomohisa

last: Sakaue

address: Shitsukawa

department: Cardiovascular and Thoracic Surgery

country: Japan

institute: Ehime University

summary: Lung ischemia–reperfusion (IR) injury increases the mortality and morbidity of patients undergoing lung transplantation. The objective of this study was to determine the key initiator of lung IR injury and to evaluate pharmacological therapeutic approaches using a functional inhibitor against the identified molecule. In a mouse hilar clamp model, the combination of RNA sequencing revealed that neutrophils-derived S100A8/A9 plays a central role in inflammatory reactions in lung IR injury.

overall_design: To elucidate the molecular mechanism underlying ischemia-reperfusion injury, RNA sequencing using Illumina Miseq was performed on samples obtained from pulmonary tissues.

first: Kentaro

last: Nakata

first: Mikio

last: Okazaki

first: Rie

last: Kinoshita

first: Yuhei

last: Komoda

first: Dai

last: Shimizu

first: Haruchika

last: Yamamoto

first: Shin

last: Tanaka

first: Ken

last: Suzawa

first: Kazuhiko

last: Shien

first: Kentaroh

last: Miyoshi

first: Hiromasa

first: Toshiaki

last: Ohara

first: Seiichiro

last: Sugimoto

first: Masaomi

last: Yamane

first: Akihiro

last: Matsukawa

first: Masakiyo

last: Sakaguchi

first: Shinichi

last: Toyooka


title: Myeloid, B, and T lineage regeneration from pluripotent stem cells by defined transcription factors

city: Guangzhou

first: Jinyong

last: Wang

state: GuangDong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

summary: We identified that synergistic and inducible expression of specific transcription factors  in pluripotent stem cells gave rise to engraftable iHPC capable of developing into multiple lineages including myeloid cells, T cells, and B cells in the C57BL/6 recipients. The regenerative myeloid, T, and B cells were detected in multiple tissues including peripheral blood, bone marrow and spleen. We performed single cell RNA-seq on the sorted GFP+CD45.2+ cells from the peripheral blood of recipients at 16 weeks after iHPC transplantation. Single-cell transcriptome illustrated the existence of regenerative myeloid cells, T cells, and B cells. The cell hierarchy of regenerative myeloid cells, T cells, and B cells in vivo resembles those of natural counterparts.

overall_design: At 16 weeks after iHPC transplantation, we sorted the GFP+CD45.2+ cells from the peripheral blood of recipients for Droplet-based scRNA-seq.  Droplet-based scRNA-seq datasets were produced using a Chromium system (10x Genomics) following manufacture’s instruction.

first: Qitong

last: Weng

first: Yunqing

last: Lin


title: Zygotic genome activation by the totipotency pioneer factor Nr5a2 I

first: Pavel

last: Kravchenko

first: Johanna

last: Gassler

first: Wataru

last: Kobayashi

first: Imre

last: Gaspar

first: Siwat

last: Ruangroengkulrith

first: Adarsh

last: Mohanan

first: Laura

last: Hernandez

first: Maximilian

last: Kümmecke

first: Aleksandar

last: Lalic

first: Robert

last: Ashburn

first: Nikita

last: Rifel

first: Maciej

last: Zaczek

first: Antoine

last: Vallot

last: Rico

first: Sabrina

last: Ladstätter

first: Kikuë

last: Tachibana


title: RNA-Seq profiling of circular RNAs and the oncogenic role of circPVT1 in cutaneous squamous cell carcinoma

city: SHenyang

first: Shuang

last: Chen

address: 77 Puhe road, Shenbei new district, Shenyang city, Liaoning province

institute: China Medical University

summary: Circular RNAs(circRNAs),which are a type of non-coding RNA with a special structure, have attracted the attention of researchers in recent years.As a high throughput gene screening method, RNA-seq has been widely used in tumor research.In present study,we assessed the expression pattern of circRNAs in CSCC via RNA-seq on CSCC and matched paracancerous samples. We further identified  circPVT1 as being overexpressed in CSCC tissues and cells.Subsequently, we identified the characteristics of circPVT1 in A431 and SCL1 cells.Finally, we designed an siRNA for the junction of circPVT1 and confirmed that the knockdown of circPVT1 could inhibit the proliferation, migration, and invasion of CSCC cells.In summary, using RNA-seq we established the expression profile of circRNAs in CSCC, and the allowed us to examine of the role of circPVT1as an oncogene in this context, highlighting this circRNA as a potentialtarget for CSCC therapy.

overall_design: Three pairs of cutaneous squamous cell carcinoma tissues and their corresponding adjacent non-cancerous tissues were detected by circRNA-sequencing.

first: Chundi

last: He


title: m6A sequencing analysis of chicken hepatic mRNA under normal and LPS stimulated conditions

city: Xinxiang

first: Yanhong

last: Zhang

state: Henan

address: 90, Huanlan road

institute: Henan institute of science and technology

summary: Here, the m6A modification patterns in chicken liver at the acute stage of LPS-stimulated inflammation and at the normal state were explored via m6A and RNA sequencing and bioinformatics analysis. A total of 7815 m6A peaks distributed in 5066 genes were identified in the normal chicken liver, and were mostly located in the CDS, 3’UTR region and around the stop codon. At 2 h after the LPS intraperitoneal injection, the m6A modification pattern changed, and showed 1200 different m6A peaks. The hyper- and hypo-m6A peaks were differentially located, with the former mostly located in the CDS region and the later in the 3’UTR and in the region near the stop codon. The hyper- or hypo methylated genes were enriched in different GO ontrology and pathways. Co-analysis revealed a significantly positive relationship between the fold change of m6A methylation level and the relative fold change of mRNA expression. Moreover, protein and protein interaction analysis showed that genes with altered m6A methylation and mRNA expression levels were clustered in processes involved in lipid metabolism, immune response, DNA replication and protein ubiquitination. CD18 and SREBP-1 were the two hub genes clustered in the immune process and lipid metabolism, respectively. Hub gene AGPAT2 was suggested to link the immune response and lipid metabolism clusters in the PPI network. This study presented the first m6A map of broiler chicken liver at the acute stage of LPS induced inflammation. The findings may shed lights on the possible mechanisms of m6A-mediated lipid metabolism disorder in inflammation.

overall_design: Examination of the m6A modification in hepatic mRNA of boilers under normal and LPS stimulated conditions

first: Feng

last: Guo

first: Jinyou

last: Ma


title: The Role of Non-Conserved Long Noncoding RNA, RP11-184M15.1, in Human Macrophage Function

status: Public on Nov 23 2022

first: Chenyi

last: Xue

institute: Columbia University

summary: Through deep RNA-seq of human monocyte-derived macrophages, we identified RP11-184M15.1, a human macrophage-specific lincRNA, to be highly induced in the cytoplasm of IL-4-stimulated macrophage. Preliminary data showed that treatment of IL-4-stimulated THP1 human macrophages with RP11-184M15.1 small interfering RNA (siRNA) repressed apoptosis of resolving macrophages, as shown by decreased Annexin V+ macrophages, and reduced protein expression of cleaved PARP. Biotinylated RP11-184M15.1 pulldown coupled with mass spectrometry indicated an interaction between RP11-184M15.1 and zinc finger RNA-binding protein (ZFR). RIP corroborated the proposed interaction between RP11-184M15.1 and ZFR. RNAInter revealed mRNAs predicted to interact with ZFR, and some of those genes (e.g., ALYREF, CCNYL1) were also differentially expressed in RNA-seq data of control versus RP11-184M15.1 knockdown in IL-4-stimulated THP1 macrophages. qPCR validated that ALYREF and CCNYL1 expression are reduced with RP11-184M15.1 knockdown. In contrast, with ZFR siRNA, ALYREF and CCNYL1 mRNA expressions were elevated. Thus, a hypothesis to be further tested is that RP11-184M15.1 interacts with ZFR to regulate mRNA stability in IL-4-stimulated macrophages.  Nuclear RNA export factor 1 (NXF1) was also validated by RIP to interact with RP11-184M15.1. NXF1 is a known interacting partner of ALYREF in the transcription-export (TREX) complex. With RP11-184M15.1 knockdown, the protein level of ALYREF decreased, and Ingenuity Pathway Analysis (IPA) of RNA-seq data of control versus RP11-184M15.1 knockdown revealed that THO complex subunit 5 homolog (THOC5), another component of the TREX complex, may be an upstream regulator. In addition, past studies have revealed that ALYREF and NXF1 are involved in nuclear export of inflammatory mRNAs and proinflammatory macrophage phenotype, respectively. With RP11-184M15.1 knockdown, there was decreased expression of inflammatory macrophage-associated genes. It may be possible that RP11-184M15.1 functions in mRNA export, along with NXF1 and ALYREF.

overall_design: THP1 (ATCC TIB-202) were differentiated to macrophages using 100ng/mL phorbal-12-myristate-13-acetate (PMA; Sigma-Aldrich, P8139) for 24 hours in RPMI 1640+10%FBS, followed by 24-hour incubation with IL-4. Knockdown of RP11-184M15.1 was achieved by transfecting THP1 macrophages with small interfering RNA (siRNA) (Qiagen) using Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher Scientific; 13778150) before differentiation with IL-4. Upon KD, the samples were subjected to RNA-sequencing and downstream analysis of the data were performed to understand potential function of RP11-184M15.1, and qPCR was performed for validation of gene targets. In vitro RNA pulldown and mass spectrometry was also performed to identify potential RNA-binding protein to RP11-18M15.1 RNA immunoprecipitation assay was performed to validate the mass spectrometry data. RNAscope was used to visualize RP11-184M15.1.

first: Esther

last: Cynn


title: Identifying new pronostic markers of IBD

first: Franck

last: Galland

address: 163 avenue de Luminy

institute: centre d'immunologie de Marseille Luminy

summary: Studying the variations in VNN1 expression at different stages of the disease and under therapy,

overall_design: A IBD biobank was generated starting with biopsy samples collected from patients suffering from CD or UC and diagnosed as clinically quiescent (Q) or in active phase of the disease (A). Patients were even not-treated at the period of diagnosis (NT) or responders or not to various therapies such as 5-ASA, anti-TNFalpha biologics (aTNF), corticoids (Cort) or immunosuppressors (IS). Controls were taken from non-inflammatory healthy portions of colon (CTRL).   Transcriptome profiling was performed with RNA-Seq.

first: Philippe

last: Naquet


title: H3K4me3 modification in zebrafish kidney after acute kidney injury

city: chongqing

first: Zhongwei

address: xinqiao

institute: Xinqiao Hospital

summary: Total DNA of uninjured, 3 dpi, and 5 dpi zebrafish kidneys were used were used for total DNA extraction and ChIP assays

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K4me3 in zebrafish kidney.

first: Chi

last: Liu

first: Xiaoliang

first: Jiangping

first: Wenmin

last: Yang


title: RNA-sequencing analysis of Intestinal stem cells from wild-type and circBtnl1-deficient mice

city: Beijing

first: Hui

address: Datun road 15

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: To explore the role of circular RNA circBtnl1 on self-renewal of intestinal stem cells（ISCs）, we isolated Lgr5-GFP+ ISCs from wild-type or circBtnl1-deficient mice.

overall_design:
Then RNA-sequencing analysis were performed and differentially expressed transcriptional factors were identified.
Total RNAs were extracted from Intestinal stem cells and subjected to RNA-sequencing analysis  through BGISEQ-500 platform

first: Zusen

last: Fan


title: Transcriptomic anlaysis of the early response of the colonic epithelium to colitis induction by dextran sodium sulfate (DSS)

summary: We compared the transcriptional signatures of the colonic mucosa from control mice (WT) versus mice deficient for the epithelial pantetheinase Vnn1 (Vnn1KO) or overexpressing Vnn1 specifically in intestinal epithelial cells (VIVA transgenic mice), during the development of DSS-induced colitis.

overall_design: We performed a microarray analysis from total RNAs prepared from laser microdissected samples of colon epithelial layer, under basal conditions (CT) or at day 4 of the DSS-colitis protocol (J4), i.e before any clinical sign of overt inflammation.


title: CITE-seq & scRNAseq profiling of myeloid cells in naïve & LLC-bearing mice

city: TARRYTOWN

first: Jing

state: NEW YORK

address: 777 OLD SAW MILL RIVER ROAD

institute: Regeneron Pharmaceuticals

summary: Monocyte heterogeneity is poorly understood in tumors.  Here we utilize scRNAseq to profile monocyte and myeloid cell diversity in tumor and non-tumor-bearing mice.

overall_design: Blood, spleen, and tumor CD11b+ myeloid cells were enriched by magnetic separation prior to staining with oligo-tagged antibodies for CITEseq and scRNAseq

first: He

last: Jing

first: Kwart

last: Dylan

first: Wang

last: Bei

first: Skokos

last: Dimitris


title: Genetic architecture of natural variation of cardiac performance: from flies to Humans

city: La Jolla

first: Georg

last: Vogler

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Deciphering the genetic architecture of human cardiac disorders is of fundamental importance but their underlying complexity is a major hurdle. We investigated the natural variation of cardiac performance in the sequenced inbred lines of the Drosophila Genetic Reference Panel (DGRP). Genome Wide Associations Studies (GWAS) identified genetic networks associated with natural variation of cardiac traits which were used to gain insights as to the molecular and cellular processes affected. Non-coding variants that we identified were used to map potential regulatory non-coding regions, which in turn were employed to predict Transcription Factors (TFs) binding sites. Cognate TFs, many of which themselves bear polymorphisms associated with variations of cardiac performance, were also validated by heart specific knockdown. Additionally, we showed that the natural variations associated with variability in cardiac performance affect a set of genes overlapping those associated with average traits but through different variants in the same genes. Furthermore, we showed that phenotypic variability was also associated with natural variation of gene regulatory networks. More importantly, we documented correlations between genes associated with cardiac phenotypes in both flies and humans, which supports a conserved genetic architecture regulating adult cardiac function from arthropods to mammals. Specifically, roles for PAX9 and EGR2 in the regulation of the cardiac rhythm were established in both models, illustrating that the characteristics of natural variations in cardiac function identified in Drosophila can accelerate discovery in humans.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from human induced pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) and its KD derivatives (siEGR2, siPAX9).

first: Perrin

last: Laurent

first: Vogler

last: Georg

first: Colas

last: Alexandre R


title: A genetic disorder reveals a hematopoietic stem cell regulatory network co-opted in leukemia [RNA-Seq]

city: Cambridge

first: Liming

last: Tao

address: 415 Main Street

institute: Broad Institute of Harvard and MIT

summary: we uncover a key transcriptional network involving hundreds of genes that is required for HSC self-renewal.

overall_design: MECOM impact on the hematopoietic stem cells

first: Richard

last: Void

first: Fulong

last: Yu

first: Vijay

last: Sankaran

first: Regev

last: Aviv


title: RNAseq analysis of in vivo and in vitro isolated tumor monocyte subsets and macrophages

last: He

summary: Mouse tumor monocytes ("Tu.Mons") can be separated by surface CD88 and Sca1 expression levels

overall_design: Tu.Mon subsets and tumor macrophages were purified by FACS using a Sony MA900 cell sorter.