title: Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms

first: Roman

last: Stocsits

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

overall_design: Refer to individual Series


title: Digestive exophagy of bacterial biofilms by parasitic intestinal amoeba and its impact on stress tolerance, antibiotic resistance and cytotoxicity

status: Public on Oct 25 2023

city: Haifa

first: Serge

last: Ankri

address: 1 Efron street

department: Microbiology

country: Israel

institute: Technion

type: Expression profiling by high throughput sequencing

summary: The human protozoan parasiteEntamoeba histolyticais responsible for amebiasis, a disease endemic to developing countries.E. histolyticatrophozoites colonize the large intestine, primarily feeding on bacteria. However, in the GI, as well as in aquatic and soil microenvironments, bacterial cells form aggregates or structured communities, called biofilm, too large for phagocytosis. However, trophozoites are still able to invade and degrade bacteria under biofilm form by a mechanism mimicking digestive exophagy.  E.histolytica cysteine proteinase degrade TasA, one of the main component of the biofilm matrix. Biofilm also play an important role protecting trophozoites against oxidative stress. The specific mechanism suggests that amoeba is adapted to biofilm predation and may serve as a new unexplored reservoir of novel therapeutic approaches to treat biofilms. Consistently, amoeba’s products restored antibiotic sensitivity to biofilm cells. Furthermore, our findings here show that probiotic biofilms may serve as a protective shield for mammalian cells, hindering the progression of the parasite towards them.

overall_design: Entamoeba histolytica trophzoites incubated with planktonic cell of B.subtilis, biofilm of B.subtilis or alone (control)

first: Eva

last: Zanditenas

first: Meirav

last: Trebicz-Geffen

first: Divya

last: Kolli

first: Laura

last: Domínguez-García

first: Einan

last: Farhi

first: Liat

last: Linde

first: Diego

last: Romero

first: Matthew

last: Chapman

first: Ilana

last: Kolodkin-Gal


title: Establishing murine trophoblast organoids as a platform for CRISPR-Cas9 screening

city: Shanghai

first: Qinying

last: Ye

address: Haike Road #230

country: China

institute: ShanghaiTech University


title: Establishing murine trophoblast organoids as a platform for CRISPR-Cas9 screening [sgRNA]

summary: Murine trophoblast organoids contain trophoblast cell types. We used CRISPR SCREENING to analyze the trophoblast organoids derived from TS (mTOs).

overall_design: Trophoblast organoids in the maintenance condition and the differentiation condition were digested into single cells by accutase and papain, respectively.  NGS analysis.

first: Qian

last: Mao

first: Yiwen

last: Xu

first: Haopeng

last: Wang

first: Chao-Po

last: Lin


title: Cohesin mediates DNA loop extrusion and sister chromatid cohesion by distinct mechanisms [ChIP-seq]

city: Vienna

middle: R

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cohesin connects CTCF binding sites and other genomic loci in cis to form chromatin loops, and replicated DNA molecules in trans to mediate sister chromatid cohesion. Whether cohesin uses distinct or related mechanisms to perform these functions is unknown. Here we describe a cohesin hinge mutant, which can extrude DNA into loops but is unable to mediate cohesion. Our results suggest that the latter defect arises during cohesion establishment. The observation that cohesin’s cohesion and loop extrusion activities can be separated indicates that cohesin uses distinct mechanisms to perform these two functions. Unexpectedly, the same hinge mutant can also not be stopped by CTCF boundaries as well as wildtype cohesin. This suggests that cohesion establishment and cohesin’s interaction with CTCF boundaries depend on related mechanisms and raises the possibility that both require transient hinge opening to entrap DNA inside the cohesin ring.

overall_design: caibrated chromatin immunoprecipitation for ectopically expressed flag tagged SMC1 using flag antibody

first: Kota

last: Nagasaka

first: Wen

last: Tang


title: MORC2 promotes renal  carcinogenesis via epigenetically downregulating DAPK1

city: Guangzhou

first: Ning

address: 600 Tianhe road

institute: Sun Yat-sen University

summary: epigenetic regulation plays a vital role in renal carcinogenesis. Here，we found epigenetic regulator MORC2  promoted carcinogenesis in kidney. Mechanistically, MORC2 functioned as oncogene via epigenetically silencing canonical tumor suppressor DAPK1 in kidney. Therefore, aMORC2—DAPK1 pro—oncogenic axis was identified in kindey.

overall_design: mRNA profiles of wild-type Caki-1 cells and MORC2 stably-expressed Caki-1 cells.

first: Tong

last: Zheng

first: Yuqing

last: Tan

first: Ruojiao


title: Analysis of splicing abnormalities in the white matter of myotonic dystrophy type 1 brain using RNA-sequence

city: Nishinomiya

first: Kazuki

last: Yoshizumi

state: Hyogo

department: neurology

country: Japan

institute: Hyogo medical university

summary: Myotonic dystrophy type 1 (DM1) is a neuromuscular disorder caused by the genomic expansions of CTG repeats, in which RNA-binding proteins, such as muscleblind-like protein, are sequestered in the nucleus, and abnormal splicing is observed in various genes. Although abnormal splicing reportedly occurs in the brains of patients with DM1, it is relation to the central nervous system symptoms is unknown. Several imaging studies have indicated substantial white matter (WM) defects in patients with DM1. Here, we performed RNA-sequencing and analysis of CTG repeat lengths in the frontal lobe of patients with DM1, separating the grey matter (GM) and WM, to investigate the splicing abnormalities in the DM1 brain, especially in the WM. The results demonstrated the number of repeats in the GM tended to be increase, with several genes showing similar levels of splicing abnormalities in the GM and WM, suggesting that the WM defects in DM1 are not only caused by aberrant splicing of GM RNA but also of WM RNA, which could be attributed to abnormal splicing of glial cell RNAs.

overall_design: Using RNA-seq data, we compared cortical and white matter splicing differences in the brains of myotonic dystrophy type 1 patients with ALS as disease control.

first: Masamitsu

last: Nishi

first: Masataka

last: Igeta

first: Masayuki

last: Nakamori

first: Tsuyoshi

last: Matsumura

first: Harutoshi

last: Fujimura

first: Kenji

last: Jinnai

first: Takashi

last: Kimura


title: Establishing murine trophoblast organoids as a platform for CRISPR-Cas9 screening [scRNA-seq]

first: Qinying

last: Ye

summary: Murine trophoblast organoids contain trophoblast cell types. We used single cell RNA sequencing (scRNA-seq) to analyze the cellular composition of trophoblast organoids derived from placentae (mPOs).

overall_design: Trophoblast organoids in the maintenance condition and the differentiation condition were digested into single cells by accutase and papain, respectively.  The libraries were constructed on the 10X Genomics. Library samples were subjected to Illumina Nova-seq 6000 sequencing system with a sequencing depth of at least 50,000 reads per cell and 150-bp (PE150) paired-end reads.

first: Qian

first: Yuwen


title: Isotype switching in human memory B cells sets intrinsic antigen-affinity thresholds that dictate antigen-driven fates

city: Indianapolis

first: Prasida

last: Holla

state: IN

address: 1044 W walnut St

department: Pediatric Infectious Diseases

country: USA

institute: Indiana University School of Medicine

summary: Memory B cells (MBCs) play a critical role in protection against homologous and variant pathogen challenge by either differentiating to plasma cells (PCs) or to germinal center (GCs) B cells. The human MBC compartment contains both switched IgG+ and unswitched IgM+ MBCs and at present the contribution of these MBC subpopulations to protection is incompletely understood. We discovered that intrinsic antigen-affinity thresholds for activation were at least 100-fold higher for IgG+ as compared to IgM+ MBCs and that IgG+ MBCs when challenged responded only to high affinity antigens and differentiated almost exclusively towards PC fates. In contrast, IgM+ MBCs were eliminated by apoptosis by high affinity antigens and responded to low affinity antigens by differentiating towards GC B cell fates. Thus, IgG+ and IgM+ MBCs may play distinct yet complementary roles in response to pathogen challenge to ensure the immediate production of high affinity antibodies to homologous and closely related challenges and the generation of variant-specific MBCs through GC reactions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from naïve B cells (CD19+CD21+CD27-), IgM+ Memory B cells (CD19+IgM+CD21+CD27+) and IgG+ memory B cells (IgG+CD19+CD21+CD27+) from 5 healthy subjects, either unstimulated or stimulated with low- or high affintiy antigen bound to planar lipid bilayers in the presence or absence of TH media (anti-CD40+IL21+IL-4)

first: Susan

middle: K

last: Pierce

first: Abhijit

last: Ambegaonkar

first: Haewon

last: Sohn


title: Cigarette smoke-induced ferritinophagy exacerbates BMSCs and skeletal development

city: Chongqing

first: Zheng

last: Jing

address: #426 North Songshi Road

department: department of orthodontics

institute: Stomatological Hospital of Chongqing Medical University

summary: To investigate the underlying mechanism of damage to bone and bone marrow mesenchymal stem cells stimulated by cigarette smoke extract (CSE)

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of the same time points from bone marrow mesenchymal stem cells (BMSCs) treated by cigarette smoke extract (CSE) or not.

first: Yuzhou

last: Li

first: Shen

last: Yang


title: PD-1 Protects Bystander-Activated T Cells from Activation-Induced Cell Death

city: Sacramento

first: William

last: Murphy

state: CA

address: 2921 Stockton Blvd.

department: Dermatology

institute: University of California, Davis

summary: PD-1 is a critical T-cell checkpoint that suppresses nonantigen-specific bystander memory T-cell activation and proliferation but also protects them from apoptotic activation-induced cell death.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of differential gene expression between PD-1+ vs PD-1- Tcells either un culutured or cultured with rhIL-2.

first: Catherine

middle: T

last: Le

first: Cordelia

last: Dunai

first: Kevin

last: Stoffel

first: Arta

middle: M

last: Monjazeb

middle: J


title: KMT2D suppresses Sonic Hedgehog-driven medulloblastoma progression and metastasis

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center


title: Expression data from adult left ventricular heart tissue of hypereosinophilic mice and controls

city: Baltimore

first: Daniela

last: Cihakova M.D. Ph.D. D(ABMLI)

state: MD

address: 720 Rutland Avenue

department: Pathology-Immunopathology

institute: The Johns Hopkins University School of Medicine

summary: Hypereosinophilic syndrome is a progressive disease with extensive eosinophilia that results in organ damage.  Patients suffer from frequent cardiac pathologies and a high mortality rate. A better understanding of the mechanisms of eosinophil-mediated tissue damage would benefit the development of new therapies.   Here, we describe the cardiac pathologies that develop in a mouse model of hypereosinophilic syndrome. These IL-5 transgenic mice exhibited decreased left ventricular function already at a young age. Cardiac function worsened with age and heart weight increased. Moreover, hypereosinophilic mice developed different pathologies of the cardiac conductive system, including 2nd degree atrioventricular block and atrioventricular reentry. Cardiomyocytes from IL-5 transgenic mice showed reduced contractility. Despite immune infiltrates in the lungs, doppler echocardiography revealed no signs of pulmonary hypertension in these mice. Mechanistically, we demonstrated eosinophil infiltration of the heart tissue that lead to an inflammatory environment. Eosinophils were 100-fold more abundant in the hearts of hypereosinophilic mice than controls. Gene expression signatures showed tissue damage as well as repair and remodeling processes. Our results suggest that hypereosinophilia leads to infiltration of the heart tissue by eosinophils and tissue damage. The ongoing remodeling and repair processes are insufficient or maladapted to maintain heart function resulting in progressive deterioration.

overall_design: We examine expression data from three biological replicates each of left ventricular heart tissue of naïve wildtype controls, IL-5 transgenic (NJ.1638), and IL-5 transgenic ddblGATA1 mice, a total of nine mice. IL-5 transgenic mice develop hypereosinophilia and often die prematurely. We looked at cardiac gene expression to explore mechansims of cardiac pathology. Il-5 transgenic ddblGATA1 mice are included as a control with high IL-5 levels but no eosinophils.

last: Cihakova

first: Nicola

last: Diny


title: Comparative analysis of differential cellular genome and proteome regulation by HIV-1 and HIV-2 pseudovirions in the early phase of infection

status: Public on Oct 24 2023

city: Nyíregyháza

first: Judit

last: Dobránszki

state: Szabolcs-Szatmár-Bereg

address: Westsik Vilmos út 4-6.

department: Centre for Agricultural Genomics and Biotechnology

country: Hungary

institute: University of Debrecen

summary: In spite of the similar structure and genomic organization of human immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2), striking differences exist between them in terms of replication dynamics and clinical manifestation of infection. Although the pathomechanism of HIV-1 infection is well characterized, relatively few data are available regarding HIV-2 viral replication, and its interaction with host-cell proteins during the early phase of infection. We utilized proteo-transcriptomic analyses to determine differential genome expression and proteomic changes induced by transduction with HIV-1 / 2 pseudovirions during 8, 12, and 26 hour time-points in HEK-293T cells. We show that alteration in the cellular milieu was indeed different between the two pseudovirions. The significantly higher number of genes altered by HIV-2 in the first two time-points, suggest a more diverse, yet subtle effect on the host cell, preparing the infected cell for integration and latency. On the other hand, GO analysis showed that, while HIV-1 induced cellular oxidative stress and had a greater effect on the cellular metabolism, HIV-2 mostly affected genes involved in cell adhesion, extracellular matrix organization or cellular differentiation. Proteomics analysis revealed that HIV-2 significantly downregulated the expression of certain proteins that perhaps benefited its life-cycle and latency. Meanwhile HIV-1 influenced the cellular level of oxidative stress and cell death involved proteins.  Our study provides an insight into the understudied replication cycle of HIV-2 and enrich our knowledge about the use of HIV-based lentiviral vectors in general.

overall_design: To investigate the gene regulatation in the early phase of infection,we  performed RNA sequencing on HEK293T cells transduced with HIV-1, HIV-2, and mock pseudovirions at three time points following transduction (8, 12, 26 hours).

first: Tamás

last: Linkner

first: Viktor

last: Ambrus

first: Balázs

last: Kunkli

first: Zsófia

middle: I

last: Szojka

first: Gergő

last: Kalló

first: Éva

last: Csősz

first: Ajneesh

last: Kumar

first: Miklós

last: Emri

first: József

last: Tőzsér

first: Mohamed

last: Mahdi


title: Multimodal spatiotemporal transcriptomic resolution of embryonic palate osteogenesis [multiome RNAseq+ATACseq]

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: The terminal differentiation of osteoblasts and subsequent formation of bone marks an important phase in palate development that leads to the separation of the oral and nasal cavities. While the morphogenetic events preceding palatal osteogenesis are well explored, major gaps remain in our understanding of the molecular mechanisms driving the formation of this bony union of the fusing palate. Through bulk, single-nucleus, and spatially resolved RNA-sequencing analyses of the developing secondary palate, we identify a shift in transcriptional programming between embryonic days 14.5 and 15.5 pinpointing the onset of osteogenesis. We define spatially restricted expression patterns of key osteogenic marker genes that are differentially expressed between these developmental timepoints. Finally, we identify genes in the palate highly expressed by palate nasal epithelial cells, also enriched within palatal osteogenic mesenchymal cells. This investigation provides a relevant framework to advance palate-specific diagnostic and therapeutic biomarker discovery.

overall_design: Microdissected secondary palate tissue pooled from biological triplicate samples of same age / genotype

first: Jeremie

middle: O

last: Piña

first: Resmi

last: Raju

last: Roth

first: Emma

middle: W

last: Winchester

first: Parna

last: Chattaraj

first: Fahad

last: Kidwai

first: Fabio

last: Faucz

first: James

last: Iben

first: Apratim

last: Mitra

first: Kiersten

last: Campbell

first: Gus

last: Fridell

first: Caroline

last: Esnault

first: Justin

middle: L

last: Cotney

first: Rena

middle: N

last: D'Souza


title: KMT2D suppresses Sonic Hedgehog-driven medulloblastoma progression and metastasis [ATAC-seq]

first: Richard

last: Koche

summary: The major cause for treatment failure, morbidity and mortality amongst medulloblastoma patients is metastasis intracranially or along the spinal cord. The molecular mechanisms driving tumor metastasis in SHH-driven medulloblastoma (SHH-MB) patients remain largely unknown. In this study we used mouse models of SHH-MB to define a tumor suppressive role of KMT2D (MLL4), a gene frequently mutated in the most metastatic β-subtype. Strikingly, heterozygous loss of Kmt2d in conjunction with aberrant activation of the SHH pathway causes highly penetrant disease with decreased survival, hindbrain invasion and spinal cord metastasis. Loss of Kmt2d shifts the transcriptional and chromatin landscape of primary and metastatic tumor cells to preferentially upregulate pathways and genes associated with advanced stage cancer and metastasis including TGFβ, Notch, Atoh1, Sox2/9 and Myc. Our study provides strong evidence that secondary mutations in KMT2D will have prognostic value for identifying SHH-MB patients that are likely to develop metastasis.

overall_design: ATAC-seq of a mouse model of Sonic Hedgehog-driven medulloblastoma.

first: Reeti

last: Sanghrajka

middle: P

first: Alexandra

last: Joyner


title: Small RNA Microarray Analysis of MCT-Induced Right Ventricular Failure Reveals Novel tRNA-derived Small RNAs with Biomarker Potential for Pulmonary Arterial Hypertension

city: Changsha

first: Yusi

last: Chen

state: Hunan

address: 139 Renmin Road

institute: The Second Xiangya Hospital of Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary: Transfer RNA-derived small RNAs (tsRNAs) are important regulators of a variety of biological functions, however, it is yet unclear how tsRNAs work to cause pulmonary arterial hypertension (PAH). The goal of the current study was to gain a better understanding of how tsRNAs contribute to PAH pathogenesis.

overall_design: A rat model of PAH induced by monocrotaline (MCT) was established, and right ventricular tissues were obtained. Small RNA microarray was used to get the tsRNA expression profiles of the PAH group and the control group. Quantitative reverse transcription-PCR (real-time PCR) was used to confirm the results. Subsequently, the target genes of the 10 selected tsRNAs and their biological functions were then predicted using bioinformatics techniques.

first: Yi

last: Tang

first: Tengteng

last: Zhu

first: Jiang

last: Li


title: KMT2D suppresses Sonic Hedgehog-driven medulloblastoma progression and metastasis [RNA-seq]

overall_design: RNA-seq of a mouse model of Sonic Hedgehog-driven medulloblastoma.


title: Influence of evernic acid alone and in combination with temozolomide on gene expression of U-87 glioblastoma cell line

city: Bonn

first: Anastasiia

last: Shcherbakova

state: NRW

address: Sigmund-Freud-Straße, 25

country: Germany

institute: University Clinic Centre Bonn, Medical Clinic III

summary: to investigate the sensitization mechanism of temozolomide-resistant U-87 cells by evernic acid, we established gene expression of U-87 cells treated with evernic acid, temozolomide and their combinations compared to the gene expression of untreated cells. The NGS-core facility of the University Hospital Bonn of Bonn University performed the RNA-sequencing.

overall_design: cells were treated with evernic acid at 30 µM and 45 µM, with temozolomide at 600 µM, and with combinations of evernic acid and temozolomide at 35 µM + 320 µM, 20 µM + 380 µM and 20 µM + 580 µM

first: Gudrun

last: Ulrich-Merzenich


title: RNA-Binding Protein Trx regulates alternative splicing and promotes metastasis of HCC via interacting with LINC00152

city: 成都

first: xiangnan

last: teng

address: 四川大学华西医院

institute: 四川大学华西医院

summary:
RNA-binding proteins (RBPs) were reported to be the key regulator of epithelial-mesenchymal transition (EMT)-related post-transcriptional in tumor diseases.To explore the role of RBPs in metastasis of hepatocellular
To explore the role of RBPs in metastasis of hepatocellular carcinoma (HCC), whole transcription sequencing was conducted to identify differential RBPs between HCC with metastasis or without metastasis. The influence of RBPs on metastasis of HCC was verified by in vitro and in vivo experiments. Interaction of RBPs with non-coding RNAs was evaluated by RNA immune-precipitation and pull-down assay. RNA-seq whole genome sequencing and alternative splicing analysis were further performed to clarify post-transcription regulation mechanisms.

overall_design: 3 HCC tissues with metastasis and 3 HCC tissues without metastasis were selected for whole transcript sequencing. Total RNA was extracted and purified with magnetic beads. After fragmentation of 2nd-cycle single-stranded cDNA (ss-cDNA), sample was labeled and hybridized to the Affymetrix Human Gene 1.0ST Array. The data were analyzed with Robust Multichip Analysis (RMA) algorithm using default analysis settings and global scaling as normalization method by Partek® Genomics Suite 6.6. Values presented are log2 RMA signal intensity. Normalized data were further analyzed using one-way ANOVA to screen out the differential expression gene.

first: Jin

last: Shang

first: Lingyao

last: Du

first: XiangNan

last: Teng

first: Wei

last: Huang

first: Yonghong

last: Wang

first: Miao

last: Liu

first: Yuanji

last: Ma

first: Ming

first: Hong

first: Lang

last: Bai


title: A novel role of CDK2 inhibition in restraining microglial overactivation

city: Beijing

first: Xiaodan

last: Hu

address: Medical Building 304

institute: Tsinghua University

summary: Neuroinflammation driven by microglial overactivation is a significant contributor across a diverse range of neurological disorders. While MEF2C mutations have been associated with a syndromic form of autism spectrum disorder (ASD) and various other neurological disorders in humans, the role of MEF2C as a key immune checkpoint to restrain microglial overactivation remains elusive. In this study, we established MEF2C-knockout (KO) induced microglia-like cells (iMGLs) via differentiation of corresponding human pluripotent stem cells, and subsequently treated with LPS, as a disease model of overactivated microglia. Through high-throughput screening, we identified BMS265246, a CDK2 inhibitor, which effectively normalized overactivated phenotypes in LPS-stimulated MEF2C-KO iMGLs, nearing levels seen in WT counterparts. Mechanistically, absence of MEF2C instigated a sequential cascade encompassing p21 downregulation, CDK2 activation, RB phosphorylation and degradation, and NF-κB p65 subunit nuclear translocation, thereby intensifying inflammatory responses. Remarkably, BMS265246 treatment significantly rectified microglial overactivation and ASD behavioral defects in both global and microglia-specific Mef2C heterozygous mice. Overall, our findings elucidate a novel protective mechanism governed by MEF2C, and unveil CDK2 as a promising therapeutic target for treating various diseases influenced by overactivated microglia with aberrant MEF2C expression and/or CDK2 activation.

overall_design:
In this study, we established MEF2C-knockout (KO) induced microglia-like cells (iMGLs) via differentiation of corresponding human pluripotent stem cells, and subsequently treated with LPS, as a disease model of overactivated microglia. Our comprehensive analysis identified BMS265246 could rectify LPS-treated overactivated MEF2C KO iMGLs.
We then performed gene expression profiling analysis using data obtained from RNAseq of WT and MEF2C KO iMGLs treated with vehicle (n=3) and LPS (n=2), and MEF2C KO iMGLs treated with BMS265246 (BMS) in the presence of LPS (n=2).


title: Transcriptomic profiling of lymphocytic colitis highlights distinct diarrhoeal pathomechanisms

city: kiel

first: Archana

last: Bhardwaj

address: Rosalind-Franklin-Straße 12

institute: Institute of Clinical Molecular Biology (IKMB)

summary:
Background and Aims: The pathobiology of the non-destructive inflammatory bowel disease (IBD) lymphocytic colitis (LC) is poorly understood. Our aim was to define a LC-specific transcriptome to gain insight into LC pathology, identify genetic signatures uniquely linked to LC, and uncover potentially druggable disease pathways.
Methods: We performed whole mucosa bulk RNA-sequencing of LC and CC samples from patients with active disease, and healthy controls (n=4-10 per cohort). Differential gene expression was analyzed by gene-set enrichment and deconvolution analyses to identify pathologically relevant pathways and cells, respectively, altered in LC. Key findings were validated using reverse transcription quantitative PCR and/or immunohistochemistry. Finally, we compared our sequencing data to a previous cohort of ulcerative colitis and Crohn’s disease patients (n=4 per group) to distinguish non-destructive from classic IBD.
Results: The LC-specific transcriptome was defined by a limited mucosal immune response against microbiota compared to CC and classic IBD samples. In contrast, we noted a distinct induction of regulatory non-coding RNA species in LC samples. Moreover, compared to CC, we observed decreased water channel and cell adhesion molecule gene expression, which was associated with reduced intestinal epithelial cell proliferation.
Conclusions: We conclude that LC is a pathomechanistically distinct disease that is characterized by a dampened immune response despite massive mucosal immune cell infiltration. Our results point to regulatory micro-RNAs as a potential disease-specific feature that may be amenable to therapeutic intervention.

overall_design: Whole colonic mucosa mRNA profiles of lymphocytic colitis (LC), collagenous colitis (CC), and healthy controls (Hc).

first: Celia

last: Escudero-Hernández


title: Ewing sarcoma single-cell transcriptome analysis reveals functionally impaired antigen-presenting cells

city: Utrecht

first: Lindy

middle: L.

last: Visser

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Paediatric Oncology

summary: Novel therapeutic strategies are urgently needed for high-risk Ewing sarcoma (EwS) patients and for the reduction of severe side-effects for all patients. Immunotherapy may fill this need, but its successful application has been hampered by a lack of knowledge on the composition and function of the EwS immune microenvironment. Here, we explore the immune microenvironment of EwS, by single-cell RNA sequencing of 18 EwS primary tissue samples.

overall_design:
Eighteen Ewing sarcoma primary tissue samples from 11 patients were single-cell RNA sequenced using the CEL-seq2 method
------------------------
Authors state "Raw data are unavailable due to patient privacy concerns."

first: Margit

last: Bleijs

first: Thanasis

last: Margaritis

first: Marc

last: van de Wetering

first: Frank

last: Holstege

first: Hans

last: Clevers


title: Effects of MSC-derived exosomes on each M1 and M2 macrophages

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

summary: Here we report the change in gene expression in M1 and M2 macrophages followed indirect culture with bone marrow-derived MSCs

overall_design: RNA sequencing on M1 and M2 macrophages before and after indirect coculture with bone marrow-derived MSCs across a 0.4 uM filter

first: Yannick

last: Kenfack

first: Lauren

middle: S

last: Sherman

first: Yahaira

last: Naaldijk


title: Single-cell RNA sequencing analysis of porcine ovarian somatic cells in antral follicles

city: Shenzhen

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

summary: The antral follicle stage plays a crucial role in mammalian oocyte maturation, signifying the final stages of oocyte development and ovulation. This complex process relies on synchronized interactions between oocyte maturation and the proliferation of neighboring granulosa cells. Previous studies have identified two subtypes of granulosa cells in antral follicles: cumulus granulosa cells, located in the inner region, which surround and support the oocyte, and mural granulosa cells, present in the outer layers, which provide mechanical support to the follicular wall and possess steroidogenic functions. Despite the wealth of molecular data generated by these studies, many fundamental questions regarding key developmental events, granulosa cell heterogeneity, functional annotation, and the intricate relationship between somatic cells and oocytes still lack detailed, single-cell resolution-level investigations. In this study, we isolated follicular cells from porcine antral follicles and conducted scRNA-seq to analyze the single-cell transcriptomes of these cells. By identifying and sub-clustering ovarian cells, such as mural granulosa cells and cumulus granulosa cells, we elucidated the heterogeneity of granulosa cells in pigs.

overall_design: In this study, we isolated follicular cells from two healthy porcine antral follicles and conducted scRNA-seq using 10X genomics platform to analyze the single-cell transcriptomes of these cells.

last: Chen

first: Xiaolong

last: Yuan

first: Yuhan

last: Tian

first: Adnan

last: Khan

first: Fei


title: Chronic Active Epstein-Barr Virus Disease Originates from Infected Hematopoietic Stem Cells

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: Chronic active Epstein-Barr Virus (EBV) disease (CAEBV) is lethal syndrome due to persistent EBV infection. When diagnosed as CAEBV, EBV infection was observed in multiple hematopoietic lineages, but the etiology of CAEBV is still elusive. Bone marrow and peripheral cells derived from five CAEBV patients, one EBV-associated hemophagocytic lymphohistiocytosis (EBV-HLH) patient, and two healthy controls were analyzed. Multiple assays were applied to identify and characterize EBV-infected cells, including quantitative PCR (qPCR), PrimeFlow and single-cell RNA-sequencing (scRNA-seq). Based on scRNA-seq data, alterations in gene expression of particular cell types were analyzed between CAEBV patients and controls, and between infected and uninfected cells. One CAEBV patient was treated with allogeneic hematopoietic stem cell transplantation (HSCT), and the samples derived from this patient were analyzed again six month after HSCT. EBV infected the full spectrum of the hematopoietic system including both lymphoid and myeloid lineages, so as hematopoietic stem cells (HSCs) in the CAEBV patients. EBV-infected HSCs exhibited a higher differentiation rate towards downstream lineages, and the EBV infection had an impact on both the innate and adaptive immunity, resulting in inflammatory symptoms. EBV infected cells were thoroughly removed from the hematopoietic system after HSCT. Taken together, multiple lines of evidence presented in this study suggest that CAEBV disease originates from the infected hematopoietic stem cells.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design:
We analyzed bone marrow and peripheral cells derived from CAEBV patients and control donors with multiple single-cell RNA-sequencing (scRNA-seq) for both human transcriptomes and EBV-encoded RNA.
NOTE FROM SUBMITTER: We have sensitive patient data here and we want to submit only processed scRNA-seq output files. We are at the moment submitting the raw data to some other databank.

first: Jingshi

first: Min

last: Su

first: Zhao


title: Genome-wide identification of transcriptional targets for GR in Caki-1 cells

city: Zhengzhou

first: Kenan

last: Zhang

address: Jianshe Street

institute: The First Affiliated Hospital of Zhengzhou University

summary: To investigate the genome-wide transcription targets of GR in renal cell carcinoma, cleavage under targets and tagmentation (CUT&Tag) was performed in Caki-1 cells using antibodies againstGR. Following CUT&Tag,  DNAs were amplified using non-biased conditions, labeled, and sequenced with Illumina NovaSeq 150PE.

overall_design: Examination of transcriptional targets for GR in Caki-1 cells

first: Lin

last: He


title: Impact of the physical cellular microenvironment on the structure and function of a hepatocytes for drug toxicity applications

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

summary: It is widely recognised that cells respond to their microenvironment, which has particular implications for in vitro cell culture practices. Namely, growth cues provided by traditional 2D cell culture substrates are far removed from the native 3D structure of in vivo tissues. Culture geometry is one of many factors that differs between in vitro culture and in vivo cellular environments. This results in in vitro studies being so far removed from their native counterpart, that they lose some of their predictive capability and reliability. In this study we examine the cellular processes that occur when a cell is cultured on 2D or 3D surfaces for a short period of 8 days prior to use in functional assays, which we term: priming. We follow the process of mechanotransduction from cytoskeletal alterations, to changes to nuclear structure leading to alterations in gene expression. These changes in gene expression ultimately resulting in enhanced expression of functional proteins and improved functional capabilities. In this study, we use hepatocytes (HepG2 cells) as a model cell line, due to their commonplace use and robustness for drug toxicity screening. We demonstrate enhanced functionality and improved drug toxicity profiles that better reflect the clinical response in vivo. However, we expect these findings more broadly reflect in vitro cell culture practises across all areas of cell biology, demonstrating the fundamental impact of mechanotransduction in bioengineering, cell biology and in vitro assays.

overall_design: HepG2 (hepatocellular carcinoma) cells were grown for 8 days either on conventional 2D cell culture ware, or on a 3D topography using a porous, biologically inert polystyrene membrane. There are four replicates in each treatment.

first: Ben

last: Allcock

first: Wenbine

first: Kirsty

last: Goncalves

first: Henry

last: Hoyle

first: Alisha

last: Roberts

first: Rebecca

last: Quelch

first: Adam

last: Hayward

first: Jim

last: Cooper

first: Stefan

last: Przyborski


title: Next Generation Sequencing of scWAT from WT and Yapfl/fl/Tazfl/fl;AdipoqCre mice

first: Xun

last: Huang

address: Zhongguancun Street

institute: Peking University

summary: YAP, TAZ are transcriptional co-regulators involved in many important biological processes. But the functional roles in adipocytes are not well understood. So we sequenced the mRNA of scWAT deleted of Yap/Taz simulataneously to explore the roles of YAP/TAZ in adipocytes.

overall_design: Comparative profiling analysis of  gene expression  based on RNA-seq data of scWAT from 8 weeks old male WT and Yapfl/fl/Tazfl/fl;AdipoqCre mice.

first: Huang

last: Xun

first: Qiu

last: Yifu


title: 12-month-old ATM-null mouse cerebellar transcriptome

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

summary:
In cerebellar atrophy of 12-month-old ATM-null mice, transcriptome  upregulations concern most neurotransmission and neuropeptide pathways,   while downregulations affect prominently Itpr1, Usp2 and non-coding RNA  In cerebellar atrophy of 12-month-old ATM-null mice, transcriptome  upregulations concern most neurotransmission and neuropeptide pathways,   while downregulations affect prominently Itpr1, Usp2 and non-coding RNA
The autosomal recessive disorder Ataxia-Telangiectasia is caused by dysfunction of stress response protein ATM. In the nucleus of proliferating cells, ATM senses DNA double-strand breaks and coordinates their repair. This role explains T-cell dysfunction and tumor risk. However, it remains unclear whether this function is relevant for postmitotic neurons and underlies the cerebellar atrophy, since ATM is cytoplasmic in postmitotic neurons. Here, we used ATM-null mice that survived early immune deficits by bone-marrow transplantation, and reached initial neurodegeneration stages at 12 months of age. Global cerebellar transcriptomics demonstrated ATM depletion to trigger upregulations in most neurotransmission and neuropeptide systems. Downregulated transcripts were found for the ATM interactome component Usp2, many non-coding RNAs, ataxia genes Itpr1, Grid2, immediate early genes and immunity factors. Allelic splice changes affected prominently neuropeptide machinery, e.g. Oprm1. Validation experiments with stressors were performed in human neuroblastoma cells, where ATM localized only to cytoplasm, similar to brain. Effect confirmation in SH-SY5Y cells occurred better after ATM depletion and osmotic stress better than nutrient / oxidative stress, rather than ATM kinase inhibition or DNA stressor bleomycin. Overall, we provide pioneer observations from a faithful A-T mouse model, which suggest general changes in synaptic and dense-core vesicle stress adaptation.

overall_design: Clariom D microarray profile 4 WT versus 4 ATM-null cerebellar tissues

first: Georg

last: Auburger

first: Júlia

last: Canet-Pons


title: Transcriptomics and Metabolomics analysis of Kcnj16 knockout rats

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

summary: We hypothesized that deletion of Kcnj16 decreased the blood pressure and kidney damage by altering the inflammatory and metabolic pathways of Dahl Salt Sensitive Rats

overall_design: All rats used were male. At the age of 11-12 weeks old, rats were placed in metabolic cages for 24-hour urine collection. Prior to euthanasia, rats were anesthetized with isoflurane for arterial blood collection as well as kidney flushing with PBS. The left kidneys were removed and snapped frozen for RNA-sequencing analysis. All RNA were extracted from the cortex of the left kidneys.

last: Staruchenko


title: The b-carboline harmine is an immunomodulator in cutaneous leishmaniasis favoring the balance towards a protective immune response

city: Epalinges

first: Sanam

last: Peyvandi

address: Ch. Boveresses 155

country: Switzerland

institute: University of Lausanne

summary: Here, we investigated the impact of synthetic b-carboline harmine (ACB1801),  on the immune response and pathology resulting from infection with a drug-resistant Leishmania major strain causing non-healing cutaneous lesion.  Exposure to ACB1801 impacted only slightly parasite viability and parasite burden in host macrophages in vitro. However, it significantly increased MHC-II and co stimulatory molecules expression on infected DCs, suggesting enhanced immune response. Accordingly, ACB1801 monotherapy significantly decreased lesion development and parasite burden in Leishmania infected C57BL/6 mice, with similar efficacy than the widely used Amphotericin B therapy. ACB1801 impact on the immune response was validated by transcriptomics analysis showing enrichment of TNF-a, IFN-g and MHC-II Ag presentation signatures in the draining lymph nodes of treated mice. Increased frequency of protective CD4+IFN-g+TNF-α+ T cells and reduced suppressive IL-10+FoxP3- T cells was observed by flow cytometry. ACB1801 was further shown to act via the downregulation of Aryl hydroxyl receptor (AhR) signaling, decreasing immunosuppressive cytokines. Thus, these results suggest a potential use for ACB1801 alone or in combination therapy.

overall_design: C57BL/6 mice were injected with 2x105 LmSd metacyclic promastigotes into the ear dermis (i.d.). The treatments with ACB1801 or vehicle were started at day 12 post infection for 10 consecutive days. Draining lymph nodes were recovered in RLT plus buffer, homogenized using tissue lyzer. mRNA was extracted using Qiagen RNAeasy mini kit. Contralateral LNs were used as non-infected controls.

first: Peyvandi

last: Sanam

first: Fabienne

last: Cottier

first: Annette

last: Ives


title: The fungal pathogen Cryptococcus neoformans adapts to the host environment through TOR-mediated remodeling of phospholipid asymmetry

city: Iowa City

first: Damian

last: Krysan

state: IA

address: 25 South Grand, 2040 ML

department: Division of Pediatrics & Infectious Disease

institute: University of Iowa Hospitals and Clinics

summary: Cryptococcus spp. are environmental fungi that first must adapt to the host environment before they can cause life-threatening meningitis in immunocompromised patients. Host CO2 concentrations are 100-fold higher than the external environment and strains unable to grow at host CO2 concentrations are not pathogenic. Using a genetic screening and transcriptional profiling approach, we found that the TOR pathway is critical for C. neoformans adaptation to host CO2 partly through Ypk1-dependent remodeling of phosphatidylserine asymmetry at the plasma membrane. We also identified a C. neoformans ABC/PDR transporter (PDR9) that is highly expressed in CO2-sensitive environmental strains, suppresses CO2-induced phosphatidylserine remodeling, and increases susceptibility to host concentrations of CO2. Interestingly, regulation of plasma membrane lipid asymmetry by the TOR-Ypk1 axis is distinct in C. neoformans compared to S. cerevisiae. Finally, host CO2 concentrations suppress the C. neoformans pathways that respond to host temperature (Mpk1) and pH (Rim101), indicating that host adaptation requires a stringent balance among distinct stress responses.

overall_design: To investigate the effects of host levels of CO2 compared to enviornmental levels of CO2 on Cryptococcus neoformans H99 gene expression over time or in a transcription factor mutant strain background, RIM101, comapred to H99 at 24 hours.

first: Laura

middle: C

last: Ristow

first: Andrew

last: Jezewski

first: Benjamin

last: Chadwick

first: Mark

middle: A

last: Stamnes

first: Xiaorong

last: Lin


title: A cell transcriptomic profile reveals the molecular mechanisms of adipocytes in mammary gland across development

city: Yaan

first: Yongliang

last: Fan

address: 36 Xinkang Road

institute: Sichuan Agricultural University

summary: Studying composition and developmental mechanisms in mammary gland is crucial for healthy growth of the newborn. Here, we constructed the largest transcriptomic dataset of mammary gland cells thus far. The dataset captured 126,829 high-quality nuclei from adipocytes, endothelial cells, epithelial cells, fibroblasts cells, immune cells, myoepithelial cells and precursor cells at five timepoint of mammary development. Remarkably, adipocytes were annotated in the mammary gland for the first time at both snRNA-seq and spatial transcriptome levels. Histological observation and cell type annotations indicated that the living space of adipocytes was compressed to a great extent during lactation. The cell-cell interaction pathway indicated that to maintain their own survival, adipocytes in lactation eliminated chemokines and avoided the phagocytosis of immune cells through the chemokine receptor-ligand pairs, such as CCL21-ACKR4. In the period of natural involution, we speculated that adipocytes inhibited apoptosis based on the activation of ADI-POQ-ADIPOR2 pairs, which was further confirmed in the spatial transcriptome level. Meanwhile, we found that the dedifferentiation of epithelial cells was initiation, that is, they were converted into mesenchymal stem cells. Another vital feature of remodeling mammary gland was that other cells seem to be actively cleared by immune cells via the IL34-CSF1R pathway. Our cell transcriptomic profile constitutes an essential reference for future studies in the development and remodeling of the mammary gland.

overall_design: we used ten swine mammary glands from five developmental stage to generate the largest swine cell transcriptomic dataset thus far, in which adipocytes in mammary gland were identified for the first time.


title: Gene expression in mouse splenic CD4+CD25+ (Treg) cells from Ikzf2-/-, Ikzf4-/- and double Ikzf2-/-Ikzf4-/- (dKO) mice

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

country: France

institute: IGBMC

summary:
CD4+CD25+ cells were sorted from the spleen of 6-7 week old mice
WT, Ikzf4-/- and dKO mice (group 1) were processed separately from a a second group (group2) containing Ikzf2-/- and their WT controls. Group 1 originates from an ultra clean sterile bioBubble, while group 2 originates from a specific pathogne free facility. In each group 3 samples were analyzed for each genotype.

first: Philippe

last: Kastner


title: Helios KO Tregs

summary: Transcriptome of splenic Treg cells (CD4+CD25+) from 7-week old WT and Ikzf2-/- mice (RNA-seq)


title: Pharmacological target dysfunction cell  cycle pathways induce vulnerabilities of chemotherapy in colorectal cancer

city: Gunagzhou

first: Zhaoliang

last: Yu

address: No. 26, Yuancun Erheng Road

institute: The sixth Affiliated Hospital of Sun Yat-sen University

summary: Dysfunction of cell cycle genes can lead to mitosis disruption and chromosomal instability (CIN), which is blamed for poor prognosis in colorectal cancer (CRC) patients, no matter with chemotherapy or not. Discovery therapeutic targets to abnormal cell cycle pathways in CRC may help to improve current therapy. By genome-widely profiling of differential expressed genes in 54 pairs of human colorectal tumor with matched normal mucosa, we found a functional enrichment in PLK1 signaling. Tumors with enriched PLK1 signaling are accompanied with dysfunction pathways related to cell cycle. Total PLK1 and phosphorylated PLK1 protein expression are associated with tumor recurrence and poor overall survival in a cohort of CRC patients. Combining PLK1 inhibitor with oxaliplatin shows a synergize effect to suppress the growth of CRC cell lines, xenograft tumors, preclinical patient-derived organoid and patient-derived xenograft tumors. RNA-seq data reveals that the cell cycle pathways were activated in oxaliplatin group but inhibited after PLK1 inhibitor treatment.  CDC7 may be a key downstream effector of PLK1 induced oxaliplatin resistance and can be druggable. Further investigation showed that PLK1 inhibitor suppress the CDC7 expression via c-MYC transcriptional control. A strong positive correlation between PLK1 and CDC7 has been further confirmed in patients. Strikingly, functional studies confirm that combining CDC7 inhibitor with oxaliplatin can recapitulate the synergize effect in various CRC models, highlighting pharmacological target PLK1-MYC-CDC7 signaling as a potential therapeutic strategy for oxaliplatin based chemotherapy.

overall_design: RNA-seq for DLD1 cells upon treatment of oxaliplatin and volasertib.

first: Peng

last: Deng

first: Jing

last: Tan


title: Upregulated Vav2 signaling induces a transcriptomic rewiring in epidermal stem cells

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

summary:
Signals emanating from Rho GTPases play pivotal roles in epidermal stem cell homeostasis. However, the agents regulating Rho GTPase output within the epidermal stem cell niche are poorly known.
Here, we report that the Rho exchange factor Vav2 regulates the epidermal stem cell transcriptome in an age-dependent manner.

overall_design: Epidermal stem cells (CD34+;Itga6+) from dorsal skin of 0.6-, 1-, 2.5-, 4-, 6- and 12-month-old WT and Vav2Onc mice (n = 3 per time point and genotype). Data from WT mice can also be found at GSE137176.

first: L

middle: F

first: Mauricio

last: Menacho-Márquez

first: Sonia

last: Rodríguez-Fdez

first: Antonio

last: Abad

first: Salvador

last: Benitah

first: Xosé

last: Bustelo


title: Transcriptional changes caused by ablation of neuropeptide FF receptor-1 (NPFFR1)

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: University of Ulm

summary: We compared inguinal fat depots of wild-type (WT) and NPFFR1 deficient (NPFFR1-KO) mice at postnatal day 6. In this project, we sequence 6 samples used DNBseq platform, averagely generating about 32.03 M reads per sample. The average mapping ratio with reference genome is 95.49%, the average mapping ratio with gene is 73.18%; A total of 19,886 genes were detected.

overall_design: 3 WT samples compared to 3 NPFFR1-KO samples.


title: Defective IRE1α Pathway Caused by Abnormal PAX6 Expression Led to Specific Human Diabetes

status: Public on Oct 23 2023

city: Beijing

first: Jianchen

last: Wu

address: Medical Building, c304

institute: Tsinghua University

summary: PAX6 is an important β cell transcription factor. We used single cell RNA sequencing (scRNA-seq) to analyze the impact of PAX6 deficiency on β cell transcriptomes.

overall_design: human pluripoten stem cells-derived WT, PAX6+/- and PAX6-/- β cells were analyzed using scRNA-seq


title: Characterization of the genes that were regulated by feeding with Lactococcus kimchii

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

summary: In the present study, we investigated the effect of Lactococcus kimchii on healthspan using Caenorhabditis elegans as a model animal. The healthspan of the adult C. elegans fed the mixture of E. coli OP50 and Lactococcus kimchii was significantly longer than that of animals fed sole OP50 (control). Transcriptional profiling comparing Lactococcus kimchii- and control-fed animals suggested that genes related to insulin-like signaling pathway were upregulated by Lactococcus kimchii.

overall_design: Transcriptional profiling of three-day-old worms that were fed OP50 or the mixture of OP50 and Lactococcus kimchii for five days, by deep sequencing, using Illumina HiSeq.


title: The expression profiles of miRNAs in exosomes derived from H2O2-treated and untreated HaCaT cells

city: Xi'an

first: Jingjing

last: Ma

address: No. 127 Changlexi Road

institute: Fourth Military Medical University

summary: Vitiligo is a skin disease characterized by the destruction of epidermal melanocytes due to oxidative stress and autoimmune response. As the main responder to oxidative stress, keratinocytes facilitate melanocyte loss under oxidative stress by inducing melanocyte death and recruiting antigen-specific CD8+ T cell to skin to destroy melanocytes. It has been proved that keratinocytes secrete abundant functional exosomes, but the role of exosomes secreted from keratinocytes under oxidative stress in vitiligo pathogenesis is unknown. We found that oxidative stress enhanced the secretion of exosomes from keratinocytes. These exosomes (OS-Exos) administration aggravated melanocyte loss and CD8+ T cell infiltration in the epidermis of tail in the vitiligo mouse model, thereby driving vitiligo progression. OS-Exos suppressed the survival of melanocytes while promoting the proliferation and activation of CD8+  T cells in vitro. As miRNAs contained in OS-Exos might be responsible for the functions of OS-Exos on melanocytes and CD8+ T cells, we employed small RNAs-seq analysis to screen miRNAs enriched in OS-Exos as compared to those in Exos (from untreated HaCaT cells). The hierarchical clustering analysis and the volcano plot showed the distinct signatures of known miRNAs as well as novel miRNAs between OS-Exos and Exos. In total, 276 differentially expressed miRNAs were discovered, with 134 and 142 miRNAs displaying significant up- or down-regulation, respectively, in OS-Exos compared with Exos (P<0.05; fold change≥2. The above data suggest that miRNAs enriched in OS-Exos might contribute to the facilitatory role of OS-Exos in vitiligo progression.

overall_design: Human keratinocyte cell line HaCaT was treated with 0.4mM H2O2 for 24h and exosomes in the culture media were extracted using ultracentrifugation. Exosomes derived from H2O2-treated or untreated HaCaT were indicated as OS-Exos or Exos, respectively. The control group is Exos and the experimental group is  OS-Exos. Each group has 3 replicates.

first: Zhe

last: Jian


title: RNA-seq and sRNA-seq analysis of rice lines of wild type and its mutant II

city: Hangzhou

first: Xiaoli

last: Jin

state: Zhejiang

address: Yuhangtang road 866

institute: Zhejiang University

summary: The study was conducted to characterize the  mutant; identify the candidate gene for the mutant trait with the map-based cloning approach; investigate the segregation of target gene with the mutant characteristics, and examine the metabolic pathways of differentially expressed genes between WT and its mutant with comparative transcriptome analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for he WT (Zhenong 34) and sg34 mutant.


title: RAPID RESISTANCE TO BET INHIBITORS IS MEDIATED BY FGFR1 IN GLIOBLASTOMA

city: Washington

first: Nagi

last: Ayad

state: DC

address: 3800 Reservoir Rd NW

institute: Georgetown University

summary: Bromodomain and extra-terminal domain (BET) proteins are therapeutic targets in several cancers including the most common malignant adult brain tumor glioblastoma (GBM). Multiple small molecule inhibitors of BET proteins have been utilized in preclinical and clinical studies. Unfortunately, BET inhibitors have not shown efficacy in clinical trials enrolling GBM patients. One possible reason for this may stem from resistance mechanisms that arise after prolonged treatment within a clinical setting. However, the mechanisms and timeframe of resistance to BET inhibitors in GBM is not known. To identify the temporal order of resistance mechanisms in GBM we performed quantitative proteomics using multiplex-inhibitor bead mass spectrometry and demonstrated that intrinsic resistance to BET inhibitors in GBM treatment occurs rapidly within hours and involves the fibroblast growth factor receptor 1 (FGFR1) protein. Additionally, small molecule inhibition of BET proteins and FGFR1 simultaneously induces synergy in reducing GBM tumor growth in vitro and in vivo. Further, FGFR1 knockdown synergizes with BET inhibitor mediated reduction of GBM cell proliferation. Collectively, our studies suggest that co-targeting BET and FGFR1 may dampen resistance mechanisms to yield a clinical response in GBM.

overall_design:
To study the effect of BET inhibition and/or FGFR inhibition on aquired resistance for glioblastoma in vivo we implanted PDX GBM39 cells into Nu/nu mice and treated with birabresib, futibatinib, birabresib+futibatinib, or DMSO as a control. We collected tumors for RNA sequencing when mice began a physical decline
We then perfomed RNA-sequencing on 2 tumors per treatment group (birabresib, futibatinib, birabresib+futibatinib) and 3 tumors for DMSO control
We compared gene expression across replicates to assess differences in gene ontology between the treatment groups and the control group.

first: Anna

last: Jermakowicz

first: Alison

last: Kurimchak

first: Katherine

last: Johnson

first: Florence

last: Guglielmetti

first: Simon

last: Kaeppeli

first: Maurizio

last: Affer

first: Hari

last: Pradhyumnan

first: Robert

last: Suter

first: Winston

last: Walters

first: Maria

last: Cepero

first: James

last: Duncan

middle: G


title: Slow Cycling and Durable Flt3+ Progenitors Contribute to Blood Production under Native Conditions

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: The dynamics of the hematopoietic flux responsible for blood cell production in native conditions remains a matter of debate. Using CITE-seq analyses, we uncovered a distinct progenitor population that displays a cell cycle gene signature similar to the one found in quiescent hematopoietic stem cells. We further determined that the CD62L marker can be used to phenotypically enrich this population in the Flt3+ multipotent progenitor (MPP4) compartment. Functional in vitro and in vivo analyses validated the heterogeneity of the MPP4 compartment and established the quiescent/slow-cycling properties of the CD62L– MPP4 cells. Furthermore, studies under native conditions revealed a novel hierarchical organization of the MPP compartments in which quiescent/slow-cycling MPP4 cells sustain a prolonged hematopoietic activity at steady state while giving rise to other lineage-biased MPP populations. Altogether, our data characterize a durable and productive quiescent/slow-cycling hematopoietic intermediary within the MPP4 compartment and highlight early paths of progenitor differentiation during unperturbed hematopoiesis.

overall_design: Single-cell CITE-Seq of mouse LSK cells sorted from a pool of four 2-months-old C57Bl/6J mice

first: Michael

last: Solomon

first: Baobao

last: Song

first: Vinothini

last: Govindarajah

first: Samantha

last: Good

first: Ashok

last: Arasu

first: E.

middle: B

last: Hinton

first: Kairavee

last: Thakkar

last: Bartram

first: Marie-Dominique

last: Filippi

first: Jose

last: Cancelas

first: H.

last: Grimes

first: Damien

last: Reynaud


title: Gene expression profiling of neuroendocrine (NE) and non-neuroendocrine (non-NE) cells derived from ex vivo cultures of small cell lung cancer (SCLC) circulating tumour cell-derived explant (CDX) model

city: Manchester

first: Caroline

last: Dive

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road

institute: Cancer Research UK Manchester Institute

summary: To determine molecular processes in vasculogenic mimicry (VM) competent human SCLC CDX, we profiled gene expression by RNA sequencing in separated NE (VM deficient) and non-NE (VM competent) cells from four CDX cultured on plastic or on Matrigel.

overall_design: Ex vivo cultures of SCLC CDX contain mixtures of suspension (NE) and adherent (non-NE) cells. Separated adherent and suspension cultures were established from four CDX and grown on plastic or Matrigel. Formation of branching networks by cells on Matrigel is an established in vitro surrogate assay for VM competence. When NE and non-NE cell subpopulations were cultured on Matrigel only the non-NE adherent cells formed branching VM networks. To test the hypothesis that a VM-specific signature would be observed only in non-NE cells forming VM networks on Matrigel, RNA sequencing of NE and non-NE CDX cells cultured on plastic or Matrigel for 24 hours was performed.

first: Kathryn

last: Simpson

first: Sarah

last: Pearsall


title: Regulation of gene expression by miR-124 or VAMP3 in SK-N-SH cells

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

summary: To study how miR-124 and VAMP3 may regulate human neuroblastoma, thee human neuroblastoma cell line SK-N-SH were transiently transfected to overexpress miR-124 or VAMP3, and total RNA was isolated 48 hours after transfection and subject to RNA-seq.

overall_design: Total RNA was isolated from control, miR-124, or VAMP3 overexpressing SK-N-SH cells 48h after transfection and RNA-seq analysis was performed.


title: Microglial Rac1 is essential for experience-dependent brain plasticity and cognitive performance

city: Porto

first: Tiago

last: Almeida

address: Rua Alfredo Allen

country: Portugal

institute: i3s - Instituto de Investigação e Inovação em Saúde da Universidade do Porto

summary: Microglia, the largest population of brain immune cells, continuously interact with synapses to maintain brain homeostasis. We aimed at understanding the role of Rac1 on microglia functions. Here, we used conditional cell-specific gene targeting in mice with multi-omics approaches, and demonstrated that the RhoGTPase Rac1 was an essential requirement for the microglia to sense and interpret the brain microenvironment, and for crucial microglia-synapse crosstalk driving experience-dependent plasticity, a fundamental brain property impaired in several neuropsychiatric disorders.

overall_design: Microglia were isolated by MACS (CD11b+ cells) from 3 Rac1fl/fl (CT) and 3 Cx3cr1CreER+/:Rac1fl/fl (Rac1 cKO) and total RNA was extracted. Sequencing was performed on an Ion Torrent S5XL sequencerTM (Thermo Scientific)

first: Renato

last: Socodato

first: Camila

last: Portugal

first: Evelyn

last: Santos

first: Joana

last: Tedim-Moreira

first: João

last: Galvão-Ferreira

first: Teresa

last: Canedo

first: Filipa

last: Baptista

first: Ana

last: Magalhães

first: António

last: Ambrósio

first: Cord

last: Brakebusch

first: Boris

last: Rubinstein

first: Irina

last: Moreira

last: Summavielle

first: Inês

last: Mendes Pinto

last: Relvas


title: Effect of 15-PGDH inhibition on skeletal muscle after sciatic nerve transection by single nuclei analysis

city: Stanford

first: Yu Xin

last: Wang

state: California

address: 269 Campus Dr

institute: Stanford University School of Medicine

summary: There are currently no approved treatments for the weakness and paralysis that result from loss of peripheral nerve function with aging, trauma, or neuromuscular disease. Here we use single nuclei sequencing to show that denervation due to transection of the sciatic nerve triggers a striking increase in the prostaglandin degrading enzyme 15-hydroxyprostaglandin dehydrogenase (15-PGDH) in skeletal muscle.

overall_design: Sciatic nerve on one leg of a C57BL6 mouse was surgically ressected, then mice were either treated with IP injection of a 15-PGDH inhibitor daily or vehicle. Single nuclei analysis was performed on skeletal muscle of contralateral (innervated) or the SNT (denervated) legs.

first: Yu

first: Mohsen

last: Afshar

first: Helen

last: Blau


title: 3D gene regulation network in glioma ferroptosis

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

summary: Erastin is a small molecular compound which inhibits the system Xc- and prevents the import of cystine, reducing glutathione (GSH) biosynthesis and glutathione peroxidase 4 (GPX4) activity, and finally inducing cell death via ferroptosis. To establish a model of Erastin induced ferroptosis in glioma cells, U87 cells were treated of Erastin (10 μM, 72 h). Combination analysis of HiChIP, ChIP-seq and RNA-seq data suggests that change of chromatin loops mediated by 3D chromatin structure regulate gene expressions in glioma ferroptosis. Genes that regulated by 3D chromatin structure include genes that were reported function in ferroptosis like MDM2 and TXRND1. We propose a new regulatory mechanism governing glioma cell ferroptosis by 3D chromatin structure.

overall_design: 2 biological replicates were analyzed for Erastin-treated glioma U87 cells (10 μM, 72 h) and control U87 cells by RNA-seq, 2 biological replicates of H3K27ac ChIP-seq for U87, 2 biological replicates of H3K27ac ChIP-seq for Erastin (10 μM, 72 h)-treated U87 cells, 2 biological replicates of H3K4me1 ChIP-seq for U87, 2 biological replicates of H3K4me1 ChIP-seq for Erastin (10 μM, 72 h)-treated U87 cells,  2 biological replicates of H3K27ac HiChIP for U87, 2 biological replicates of H3K27ac HiChIP for Erastin (10 μM, 72 h)-treated U87 cells.

first: Lu

last: wange

first: Liu

last: Man

first: Zhang

last: lei

first: Wang

last: Wenbin

last: han


title: b1 integrin signaling governs necroptosis via the chromatin remodeling factor CHD4

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

summary: Fibrosis, characterized by sustained activation of myofibroblasts and excessive extracellular matrix (ECM) deposition, is known to be associated with chronic inflammation. RIPK3, a key kinase mediating TNF-driven necroptosis signaling, is upregulated in fibrosis and contributes to the TNF-mediated inflammation. In biliary duct ligation-induced liver fibrosis, we found that myofibroblasts are the major cell type expressing RIPK3. Genetic ablation of b1 integrins, the major profibrotic ECM receptors in fibroblasts, not only abolished ECM fibrillogenesis but also blunted RIPK3 expression via an epigenetic mechanism mediated by the chromatin remodeling factor CHD4. While the function of CHD4 has been conventionally linked to NuRD and ChAHP complexes, we found that CHD4 potently repressed a set of genes, including Ripk3, with high locus specificity but independent of either the NuRD or ChAHP complex. Thus, our data uncover that b1 integrin intrinsically links fibrotic signaling to RIPK3-driven inflammation via a novel mode of action of CHD4.

overall_design: Chromatin accessibility analysis by ATAC-seq of Control, Chd4KO and Gatad2a/b DKO

first: Zhiqi

last: Sun

first: Filippo

first: Gunnar

last: Schotta

first: Veit

last: Hornung


title: O-GlcNAc transferase promotes glioblastoma through genes responsible for cell survival, invasion and inflammation

city: Al Ain

first: Suraiya

last: Ansari

address: Tawam

country: United Arab Emirates

institute: United Arab Emirates University

summary: Metabolic reprogramming has emerged as one of the key hallmarks of cancer cells. Various metabolic pathways are dysregulated in cancers including hexosamine biosynthesis pathway (HBP). Protein O-GlcNAcylation catalyzed by O-GlcNAc transferase (OGT), the effector of HBP is found to be upregulated in most cancers. Post-translational O-GlcNAcylation of various signaling and transcriptional regulators could promote cancer cell maintenance and progression through protein stability and gene expression regulation. Indeed, among majority of O-GlcNAcylated proteins are gene specific transcription factors and chromatin regulators. Therefore, investigating the role of OGT in particular types of cancers is crucial. Here, we have investigated the role of OGT in glioblastoma. OGT knockdown and chemical inhibition led to reduced glioblastoma cell proliferation and downregulation of many genes known to play key roles in glioblastoma cell proliferation, migration and invasion.We knocked down OGT and OGA enzyme expression by shRNAs followed by RNA sequencing was carried.

overall_design: Total RNA was isolated using MasterPure RNA isolation Kit. Ribosomal RNA was depleted. Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit


title: RNA-seq data of 5D4- or Calcein AM-treated MDA-MB-468

city: Houston

first: Weei-Chin

last: Lin

state: TX

address: R410, One Baylor Plaza

department: Medicine and Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Investigate the transcriptomic profiles of 5D4 treatment, Calcein AM treatment, and TopBP1 depletion.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDA-MB-468 cells after 5D4 or Calcein AM treatment or after TopBP1 knockdown. Each condition has four biological replicates.

first: Fang-Tsyr


title: Metabolic adaptation of skeletal muscle to acute, short-term environmental oxygen restriction in mice

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

summary: Skeletal muscle is the largest tissue in the body and mainly relies on mitochondrial oxidative metabolism for sustainable ATP production. Reduced oxygen availability, also known as hypoxia, can be caused by high altitude or pathology and impacts mitochondria. Whereas long-term hypoxia results in increased reliance on glycolysis, reduced fatty acid oxidation and a decreased skeletal muscle mass, the in vivo mechanisms of adaptation of skeletal muscle to acute hypoxia remain elusive. Therefore, we aimed to provide an integrated description of the response of the M. gastrocnemius to acute hypoxia. Fasted male C57BL/6JOlaHsd mice were exposed to 12% oxygen representing normobaric hypoxia versus 21% oxygen (normoxia) for six hours (n=12 mice per group). Whole-body energy metabolism and the transcriptome response of the M. gastrocnemius mice was analyzed and confirmed by acylcarnitine determination and RT-qPCR. On whole-body level, six hours of hypoxia reduced energy expenditure, increased blood glucose and tended to further decrease the respiratory exchange ratio (RER). Whole genome transcriptome analysis revealed upregulation of the FOXO signalling pathway including an increased expression of Trib3, which was positively correlated with blood glucose. Apart from upregulation of Cpt1a, which negatively correlated with the RER, and SLC25a25 (Cact), fatty acid β-oxidation was not regulated. Together with significantly increased muscle C14 and C16-acylcarnitines this supports no increased fatty acid catabolism in muscle. In addition, the hypoxia-induced FOXO activation could also be connected to altered gene profiles related to fiber type switching, extracellular matrix remodelling, muscle differentiation and the denervation of neuromuscular junctions (NMJ). Conclusively, our results suggest that an acute, six hours exposure of mice to hypoxia impacts M. gastrocnemius via FOXO1, initiating alterations in skeletal muscle that may ultimately contribute to tissue remodelling. This supports an early role of hypoxia in tissue alterations in hypoxia-associated conditions such as aging and obesity. The observed impact of hypoxia on denervated NMJ is novel and warrants further investigation.

overall_design: Two-condition experiment, normoxia (20.9% oxygen) vs. hypoxia (12% oxygen) treated mice. Biological replicates: 12 control (normoxia) replicates, 12 hypoxia replicates.

first: L

last: Duivenvoorde

first: EM

first: I

last: van der Stelt

first: J

last: Keijer


title: Molecular mechanisms of task allocation in workers of the red imported fire ant, Solenopsis invicta

city: College Station

first: Jesse

last: Starkey

state: Texas

address: Minnie Bell Heep Center, Suite 412 2475 TAMU

department: Entomology

institute: Texas A&M University

summary: The red imported fire ant Solenopsis invicta is an invasive pest in the USA, eastern Asia and Australia that causes billions worth of damage where it has been introduced. In the insect colony, workers perform tasks based on their age as well as the subcaste, where the younger workers as well as the members of the smaller subcastes of workers tend to remain in the nest and tend to the brood while the older ants as well as the members of the larger subcastes of workers leave the nest to perform activities such as foraging. In eusocial insects, juvenile hormone has been identified to be a catalyst for behavioral changes among the worker caste, but the involvement of this hormone in S. invicta task allocation has not been investigated. Here, we conducted RNAseq analysis to identify genes associated with worker division of labor by comparing the expression profiles of foragers and nurses from the medium subcaste. Additionally, we evaluated the changes in the transcriptome of nurses in response to the application of the juvenile hormone analog, S-hydroprene. We found 816 differentially expressed genes between foragers and nurses and 100 differentially expressed genes between nurses treated with acetone and nurses treated with S-hydroprene. Here, we focused on the differentially expressed genes between foragers and nurses that were associated with different molecular pathways such as energy metabolism, glycolysis, juvenile hormone synthesis and metabolism, and immunity. Our results showed that the juvenile hormone analog induced changes in worker gene expression, some of which were as expected if the juvenile hormone is involved in regulating the shift from nursing to foraging in S. invicta workers. This analysis and data from this experiment can provide a slew of potential target genes to be used for control of this invasive pest.

overall_design: Performed transcriptomic analyses of fire ant worker samples taken from Illumina NovaSeq

first: Cecilia

last: Tamborindeguy


title: Bulk RNA-seq of wild type, HNF4A-knockout (KO), HNF4G-KO, and HNF4A/4G-double KO (DKO) kidney organoids

city: St. Louis

first: Yasuhiro

last: Yoshimura

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

summary: We performed bulk RNA-seq and compared complehensive gene expression profiles of kidney organoids induced from wild type, HNF4A-KO, HNF4G-KO, and HNF4A/4G-DKO iPS cell lines.

overall_design: Expression profiling by high throughput sequencing

first: Benjamin

middle: D

last: Humphreys


title: HNF4A

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

overall_design: Refer to individual Series


title: Kif2a operates as a gatekeeper of nociception in sensory neurons

city: Rehovot

first: Avraham

last: Yaron

address: Herzl st. 234

institute: Weizmann Institute of Science


title: Kif2a operates as a gatekeeper of nociception in sensory neurons [RNA-seq - 6 months]

summary: Comparison of the Dorsal root ganglia (DRG) transcriptome of WT and Kif2a conditional knockout animals at six months of age

overall_design: RNA from DRGs from Kif2a floxed and Kif2a floxed with Advillin cre animals has been extracted and subjected to mRNA sequencing

first: Swagata

last: Dey

first: Ester

last: Feldmesser

first: Noa

last: Wigoda


title: Cleavage under targets and release using nuclease (CUT&RUN) sequencing for HNF4A in human adult kidney and kidney organoid-derived proximal tubular cells

summary: We performed CUT&RUN sequencing to characterize HNF4A binding sites in human adult kidney and kidney organoid-derived proximal tubular cells.

overall_design: CUT&RUN sequencing for HNF4A in human adult kidney and kidney organoid-drived proximal tubular cells.

first: Yoshiharu

last: Muto


title: Kif2a operates as a gatekeeper of nociception in sensory neurons [RNA-seq - 1 month]

summary: Comparison of the Dorsal root ganglia (DRG) transcriptome of WT and Kif2a conditional knockout animals at one months of age


title: Kif2a operates as a gatekeeper of nociception in sensory neurons [RNA-seq - 3 months]

summary: Comparison of the Dorsal root ganglia(DRG) transcriptome of WT and Kif2a conditional knockout animals at three months of age


title: Combined transcriptome and T cell receptor alpha/beta (TRA/TRB) single cell RNA sequencing of donor-reactive T cells in stable kidney transplant recipients before and 3-5 years post-transplant.

city: Rotterdam

first: Amy

middle: Catharina Johanna

last: van der List

address: Wytemaweg 80

department: Internal Medicine

institute: Erasmus MC

summary: A combined single cell RNA sequencing approach determined both transcriptomic profiles and complete V(D)J variable regions of TR transcripts from individual alloreactive T cells of stable kidney transplant recipients (N=7) prior to and 3-5 years after transplantation

overall_design: Peripheral blood mononuclear cells (PBMCs) were stimulated with CD3-negative PBMCs of their donor or a third party control. Following stimulation, alloreactive T cells were isolated from PBMCs by Fluorescence-activated cell sorting (FACS) according to the presence CD137 signal and analyzed using scRNAseq.

first: Nicolle

middle: H

last: Litjens

first: Rutger

last: Brouwer

first: Mariska

last: Klepper

first: Xander

last: Den Dekker

first: Wilfred

last: van Ijcken

first: Michiel

last: Betjes


title: Effect of RREB1 knockdown using siRNA in A673 Ewing sarcoma cells (RNA-seq)

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

institute: Institut Curie

summary: Ewing sarcoma (EwS) is a rare bone and soft tissue malignancy driven by chromosomal translocations encoding chimeric transcription factors, such as EWSR1-FLI1, that bind GGAA motifs forming novel enhancers that alter nearby expression. We propose germline microsatellite variation at the 6p25.1 EwS susceptibility locus could impact downstream gene expression and EwS biology. We performed targeted long-read sequencing of EwS blood DNA to characterize variation and genomic features important for EWSR1-FLI1 binding. We identified 50 microsatellite alleles at 6p25.1 and observed EwS cases had longer alleles (>135 bp) with more GGAA repeats. The 6p25.1 GGAA microsatellite showed chromatin features of an EWSR1-FLI1 enhancer, and regulated expression of RREB1, a transcription factor associated with RAS/MAPK signaling. RREB1 knockdown reduced proliferation and clonogenic potential, and reduced expression of cell cycle and DNA replication genes. Our integrative analysis at 6p25.1 details increased binding of longer GGAA microsatellite alleles with acquired EWSR-FLI1 to promote Ewing sarcomagenesis by RREB1-mediated proliferation.

overall_design: A673 cells were transfected with siRNA to RREB1 and control siRNA. 72h after transfection, cells were collected, RNA was extracted and used for RNA-Seq.

first: Sandrine

last: Grossetête

first: Calvin

last: Rodrigues

first: Mitchell

last: Machiela


title: Transcriptomic analysis of 4NQO-induced oral squamous cell carcinoma with agonistic anti-CD40 treatment

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: To investigate the anti-tumor effect of agonistic anti-CD40, 4NQO-indued OSCC mice with agonistic anti-CD40.

overall_design: Gene expression profile

first: Y

middle: M

last: Lee

last: Chen

first: C

middle: T

last: Tan


title: In vivo growth of subclones derived from Lewis lung carcinoma is determined by the tumor microenvironment not intrinsic proliferative ability

city: Zhengzhou

first: gangyu

state: He Nan

address: No 127  Dongming Road

institute: The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital

summary: Heterogeneity is a fundamental feature of human tumors and plays a major role in drug resistance and disease progression. In the present study, we selected single-cell-derived cell lines (SCDCLs) derived from Lewis lung carcinoma (LLC1) cells to investigate tumorigenesis and heterogeneity. SCDCLs were generated using limiting dilution. Five SCDCLs were subcutaneously injected into wild-type C57BL/6N mice; however, they displayed significant differences in tumor growth. Subclone SCC1 grew the fastest in vivo, whereas it grew slower in vitro. The growth pattern of SCC2 was the opposite to that of SCC1. Genetic differences in these two subclones showed marked differences in cell adhesion and proliferation. Pathway enrichment results indicate that signal transduction and immune system responses were the most significantly altered functional categories in SCC2 cells compared to SCC1 cells in vitro. The number and activation of CD3+ and CD8+ T cells and NK cells in the tumor tissue of tumor-bearing mice inoculated with SCC2 were significantly higher, whereas those of myeloid cells were significantly lower, than those in the SCC1 and LLC1 groups. Our results suggest that the in vivo growth of two subclones derived from LLC1 was determined by the tumor microenvironment rather than their intrinsic proliferative cell characteristics.

overall_design: Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion), following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples with an RNA integrity number ≥ 7 were subjected to subsequent analysis. Libraries were constructed using the TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. These libraries were then sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.Transcriptome sequencing and analysis were conducted by OE Biotech (Shanghai, China). Raw data were processed using Trimmomatic software. Reads containing poly-N and low-quality reads were removed to obtain clean reads. The clean reads were then mapped to the reference genome using hisat2. The FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by HTSeq-count. Differentially expressed genes (DEGs) were identified using the DESeq (2012) R package to estimate the size factors. A p-value < 0.05 and a fold-change > 2 or < 0.5 were set as the thresholds for significant differential expression. Hierarchical cluster analysis of DEGs was performed to explore gene expression patterns. GO enrichment and KEGG pathway enrichment analyses of DEGs were performed using the software R based on a hypergeometric distributions.

first: Benling

last: Xu

first: Long

last: Yuan

first: Zibing

last: Wang

first: Quanli

last: Gao


title: kallikrein-related peptidase 8 inhibition protects the pulmonary endothelium during endotoxemic lung injury

city: Shanghai

first: xiaoyan

last: Zhu

address: NO.800 Xiangyin Road

institute: The Second Military Medical University

summary: To gain insights into the mechanisms responsible for KLK8-induced endothelial injury, dysregulated genes were analyzed by RNA-Seq,  in the Ad-KLK8 treated MLVECs, as compared with Ad-Control treated MLVECs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pulmonary endothelium

first: Xiaoyan


title: In vivo PIWI slicing in mouse testes deviates from rules established in vitro

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: Purified endogenous mouse MIWI fails to cleave mismatched targets in vitro. Surprisingly, here we find using knock-in mouse models that piRNA target sites with cleavage-site mismatches are precisely sliced in vivo. This is identical to the slicing outcome in knock-in mice where targets are identified by perfect complementarity base-pairing with the piRNA. Additionally, we find that such pachytene piRNA-guided MIWI/MILI slicing in vivo failed to initiate phased piRNA production from the specific target mRNA we studied. Instead, the two slicer cleavage fragments were retained in PIWI proteins as a pre-piRNA and 17-19 nt by-product fragments. Our results indicate that PIWI slicing rules established in vitro are not respected in vivo, and that all targets of PIWI slicing are not substrates for piRNA biogenesis.

overall_design: We designed four knock-in mouse lines: two lines with one or ten sites perfectly complementary to the pachytene piRNA piR-A (1xPerf, 10xPerf) and two lines with one or  ten sites having mismatches at positions 10-11 (1xBulge,10xBulge). The piRNA targeted sites were inserted into 3′UTR of Ythdc2. We  immunoprecipitated and sequenced the MILI and MIWI associated small RNAs to search for piRNAs generated by piR-A cleavage and used RNA-seq to analyze the gene expression changes. Two biological replicas were analyzed.

first: Mark

last: Dowling

first: Nicole

last: Raad

first: David

last: Homolka

first: Pascal

last: Gos

first: Radha

last: Raman Pandey


title: Rational identification of novel drug targets and vaccine candidates against the cattle tick, Rhipicephalus microplus

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

summary: Control of complex parasites via vaccination remains challenging, with the current combination of vaccines and small drugs remaining the choice of control strategy. The development of new vaccines against complex endo- and ectoparasites remains challenging and more studies are providing evidence that multicomponent vaccines will be needed for the development of protective vaccines against parasites. The development of multicomponent vaccines, require an in-depth understanding of parasite biology which remains insufficient for ticks. With the rapid development and spread of acaricide resistance in ticks, new targets for acaricide development also remains to be identified, along with novel targets that can be exploited for the design of lead compounds. In this study, we analysed the differential gene expression of Rhipicephalus microplus ticks that were fed on cattle vaccinated with a multi-component vaccine (Bm86 and 3 putative Bm86-binding proteins). The data was scrutinised for the identification of vaccine targets, small drug targets and novel pathways that can be evaluated in future studies. Limitations associated with targeting novel proteins for vaccine and/or drug design is also discussed and placed into the context of challenges arising when targeting large protein families and intracellular localised proteins. Lastly, this study provide insight into how Bm86-based vaccines may reduce successful uptake and digestion of the bloodmeal and overall tick fecundity.

overall_design: Two condition experiment. Controls: Adult ticks fed on control non-vaccinated cattle. Biological replicates: Adult ticks fed on vaccinated cattle.

first: Christine

last: Maritz-Olivier

first: Killian

last: Mariette

first: Olivier

last: Abraham

first: Jan

middle: E

last: Crafford

first: Christian

last: Stutzer


title: Co-culture of human prostate cancer cells and mouse osteoblasts as a model for tumor dormancy in bone metastasis

city: Toledo

first: Shang

last: Su

state: Ohio

address: 3000 Transverse Dr

department: Cell and Cancer Biology

institute: The University of Toledo

summary: Prostate cancer (PCa) cells, when disseminated to the bone, may stay quiescent or dormant for years before proliferation into overt metastases. Previous studies suggest that osteoblasts, the bone forming cells, may be responsible for induction of dormancy of bone-disseminated prostate cancer cells.

overall_design: We have established an in vitro co-culture system between human prostate cancer C4-2B cells and mouse osteoblast MC3T3-E1 cells in a ration of 1:30 to consistently and robustly induce the dormant phenotypes and representative dormant markers.  To further characterize the dormancy signature of PCa cells in bone, we applied high-throughput RNA-Seq to profile the transcriptomes of co-cultured C4-2B cells and MC3T3-E1 cells, as well as both cells cultured alone as control.

first: Ruihua

last: Liu

first: Ke

first: Bin

last: Chen

first: Xiaohong

last: Li


title: Notch Signaling in the Thyroid is Essential for Adult Homeostasis.

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.


title: Notch Signaling in the Thyroid is Essential for Adult Homeostasis (scRNAseq thyroid)

summary: Notch signaling between neighboring cells vitally contributes to specifying their identity and function, during development and in the adult. Here, we demonstrate that selective blockade of the Notch ligands JAG1 and JAG2 disrupts thermoregulation in adults by decreasing circulating thyroid hormones and thyroid function. By exploiting single-cell methods to carefully evaluate the thyroid, an understudied apex endocrine organ, we discovered unexpected thyrocyte heterogeneity, marked by three distinct thyrocyte subtypes with different Notch activation patterns.

overall_design: Male mice of 10-12 weeks were treated with a single intraperitoneal injection of the Notch blocking antibodies (aJ1aJ2: 20mg/kg each; aN1aN2: 5, 10 mg/kg respectively; and anti-Ragweed isotype control: 40 mg/kg). 6 thyroids per sample were extracted at the time of necropsy, cut with a razor blade and digested in pool with 0.05mg/ml Liberase TM for 30min at 42C to isolate single cells.

first: Lluc

last: Mosteiro

last: Siebel


title: Notch Signaling in the Thyroid is Essential for Adult Homeostasis (RNAseq BAT)

summary: Notch signaling between neighboring cells vitally contributes to specifying their identity and function, during development and in the adult. Here, we demonstrate that selective blockade of the Notch ligands JAG1 and JAG2 disrupts thermoregulation in adults by decreasing circulating thyroid hormones and thyroid function. Sequencing data in BAT demonstrates that Notch inhibition increases thermoregulation genes and this depends on thyroid hormones.

overall_design: Male mice of 10-12 weeks were treated with a single intraperitoneal injection of the Notch blocking antibodies (aJ1aJ2: 20mg/kg each; aN1aN2: 5, 10 mg/kg respectively; aN1aN2aN3: 5,10, 20 mg/kg respectively and anti-Ragweed isotype control: 40 mg/kg). Exogenous administration of thyroxine (T4) and 3-Iodotrionine (T3) was performed by intraperitoneal injection of 1ug/g BW of T4 and 0.05?g/g BW T3 diluted in PBS, daily starting at day 2 of the antibody treatment. Tissues were collected and snap frozen at the time of necropsy.


title: Notch Signaling in the Thyroid is Essential for Adult Homeostasis (RNAseq thyroid)

summary: Notch signaling between neighboring cells vitally contributes to specifying their identity and function, during development and in the adult. Here, we demonstrate that selective blockade of the Notch ligands JAG1 and JAG2 disrupts thermoregulation in adults by decreasing circulating thyroid hormones and thyroid function. Sequencing data demonstrates that Notch inhibition decreases thyrocyte markers and mitochondrial genes.


title: Understanding the molecular basis of pheneotypic heteroegenity in mouse model of triple negative breast cancer (TNBC) using RNA sequencing

city: Trivandrum

first: Radhika

last: Nair

state: Kerala

address: Poojappura

department: Cancer Research Program

country: India

institute: Rajiv Gandhi Centre for Biotechnology

summary: We injected GFP tagged mouse metastatic breast cancer cell line, 4T1 (4T1GFP)  into the mammary fat-pad of BALB/c mice. From 4T1GFP primary tumor, we obtained two distinct tumor cell subpopulations that differed in terms of their in vitro and in vivo phenotypes with one subpopulation being more aggresive compared to the other. We performed transcriptomic analysis using RNA sequencing to identify the molecular mediators of this intratumoral phenotypic heterogeneity.

overall_design: Transcriptomic analysis was performed on three independent replicates of aggressive 4T1A and non-aggressive  4T1NA 4T1GFP subpopulations to identify the molecular regulators of intratumoral phenotypic heterogeneity

first: Archana P

last: Thankamony

first: Reshma

last: Murali

first: Priyanka

last: Chakraborty

first: Nitheesh

last: Karthikeyan

first: Binitha Anu

last: Vargheese

first: Vishnu Sunil

last: Jaikumar

first: Mohit Kumar

last: Jolly


title: Transcriptome analysis of ATG-silenced pollen

city: Wuhan

first: Xuemei

last: Zhou

address: 182 Minyuan Road, Hongshan district

institute: South-Central University for Nationalities

summary: The goal of present study aimed to investigate the impact of downregulation of ATG2 and ATG5 on pollen transcriptome.

overall_design: Pollen from wild type, ATG2-silenced and ATG5-silenced plants were collected for RNA-seq. Three independent replicates were performed for ecah genotype.


title: RNA sequencing  Facilitates Quantitative Analysis of ANGPTL8 on Lipid metabolism in liver of chow mice

status: Public on Oct 22 2023

city: Nanjing，Zhenjiang

first: Zhicong

last: Zhao

state: Jiangsu province

address: 163 Xianlin Avenue，438 Jiefang Road

institute: School of life sciences, Nanjing university, Affiliated Hospital of Jiangsu University

summary: We report the use of transcriptome sequencing in the intervention of ANGPTL8 in the regulation of triglyceride level. We constructed the adenovirus-mediated overexpression and knockdown of ANGPTL8 in wild-type mice and obtained the differential genes of ANGPTL8 regulating serum triglyceride level by transcriptomic sequencing. We identified 234 differentially expressed ANGPTL8 response genes, 113 genes are up-regulated in ANGPTL8 overexpression，and down-regulated in ANGPTL8 knock-down. 121 genes are up-regulated in ANGPTL8 down-knock, and down-regulated in ANGPTL8 overexpression. This study provides a framework for the network regulation mechanism of ANGPTL8 controlling triglyceride level.

overall_design: Exploring the Signal Network of ANGPTL8 Regulating Lipid Metabolism Through RNA sequencing

first: Lian

first: Zhongming

last: Yang

first: Guoyue

last: Yuan


title: MHC II regulation of CD8+ T cell tolerance and  implications in autoimmunity and cancer immunotherapy

city: Xiamen

first: Guo

last: Fu

address: No. 422, Siming South Road, Xiamen, Fujian, China.

institute: Xiamen University

summary: Previous studies suggested the presence of MHC class II-reactive CD8+ T cells in humans and animals, but little is known about their identity, development and function. In this study, we discovered a group of CD8+ T cells bearing T cell receptors (TCRs) reactive to both MHC I and II molecules in MHC II-deficient mice. We cloned their TCRs and analyzed their development and function. In wild type animals, thymocytes bearing those TCRs were purged by negative selection. In the absence of MHC II, they developed into CD8+ T cells and entered the peripheral T cell pool. When encountering MHC II in the periphery, they underwent robust activation and proliferation, attacked self-tissues, and caused lethal autoimmune diseases. In adoptive T cell therapy, CD8+ T cells bearing those TCRs were able to efficiently control MHC II-expressing tumors. This study opens the door to investigate dual-reactive CD8+ T cells, their development and selection in the thymus, and the peril and promise when their normal development and selection are compromised.

overall_design: Naïve CD8 T cells were isolated from WT or MHC II-/- mice, labeled with CTV, adoptively transferred into 15 irradiated B6 mice respectively, with one million CD8 T cells per mouse. Splenocytes were isolated and CTV- fast-proliferating cells were sorted. All 0.02 million CTV- WT CD8 T cells sorted and 0.15 million out of 1.2 million CTV- MHC II-/- CD8 T cells sorted were subjected to 10x genomics TCR sequencing.

first: Xiaojuan

first: Zhe

last: Huang


title: Genome-wide methylation profiles of post-mortem tissue samples (human) 3

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

type: Methylation profiling by genome tiling array

summary: In this study, 60 post-mortem tissue samples comprising four tissue types (dermis, epidermis, and muscle) were collected from autopsies of 20 Koreans aged 18 to 78. 250 ng of genomic DNA (gDNA) was employed to generate DNA methylation profiles utilizing the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA) at Macrogen Inc. (Macrogen, Seoul, Korea).

overall_design: DNA methylation profiling of sixty post-mortem tissue samples was conducted using the Infinium MethylationEPIC Beadchip array.

first: Jeong Min


title: Genome-wide methylation profiles of post-mortem tissue samples (human) 2

summary: In this study, 60 post-mortem tissue samples comprising four tissue types (kidney, liver, and lung) were collected from autopsies of 20 Koreans aged 18 to 78. 250 ng of genomic DNA (gDNA) was employed to generate DNA methylation profiles utilizing the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA) at Macrogen Inc. (Macrogen, Seoul, Korea).


title: RNA sequencing to identify UNC-49-regulated genes in C. elegans defense against pathogen infection

city: Changsha

first: Zhongfan

last: Zheng

address: No. 27 Tianma Road

country: China

institute: Hunan university

summary: To gain molecular insights on how UNC-49 regulates C. elegans innate immunity, we used RNA sequencing to profile gene expression in unc-49(e407) animals relative to wild-type animals with or without P. aeruginosa(PA14) infection. We found that UNC-49 suppresses the expression of insulin pathway genes, and lack of UNC-49-mediated suppression in unc-49(e407) animals contributes to their improved survival against P. aeruginosa infection.

overall_design: Three replicates of four groups of RNA samples (unc-49(e407) and wild-type L4-stage animals with or without exposure to P. aeruginosa for 24 hrs) were sequenced. Gene expression was compared between groups to identify UNC-49-regulated genes under uninfection or infection conditions.

first: Haijun

last: Tu