title: Polyploidized Rice Improves Plant Height and Yield through Regulating Expression of Yield Related Genes.

status: Public on Jan 30 2024

city: Suzhou

first: Shiqin

address: No.1 Jianxiong Road, Taicang, Suzhou

institute: Suzhou Chien-Shiung Institute of Technology,

summary: Polyploidization is one of the effective ways to improve plant height and yield of rice (Oryza sativa L.). However, the molecular mechanism of regulation is not yet fully understood. Here, we investigated the agronomic traits of diploid (Balilla-2x) and tetraploid (Balilla-4x) of japonica rice variety Balilla. Compared with Balilla-2x, Balilla-4x exhibited significantly increased plant height, spike length and yield per plant. RNA-seq analysis of  the leaves of  Balilla-2x and Balilla-4x was performed and the results showed that the expression levels of yield related genes (e.g., STH1, OsYUC9, and OsDEP1) were significantly upregulated in Balilla-4x rice plants, these genes are related to plant height and panicle development. These results indicated that polyploidization changed the expression of genes related to agronomic traits such as plant height and spike length, thereby increasing rice yield. This study provides a further basis for understanding the yield of rice after polyploidization, and can serve as a new theoretical reference for breeding high-yielding rice varieties achieved.

overall_design: Balilla-2x (O. sativa ssp. japonica, 2n = 2x = 24) is a low seed setting rate rice variety from Italy, and the artificially synthesized tetraploid (‘Balilla-4x’, 2n = 4x = 48) is a doubling of ‘Balilla’ diploid (Balilla-2x).  The rice plants (Balilla-2x and Balilla-4x) used in this study, grew in the paddy field of experimental fields in Shanghai during the natural growing seasons, and the leaves were sampled for RNA-seq analysis.

first: Xu

last: He

first: Xiaomei

last: Mao

first: Ye

last: Zhang

first: Lingzhi

last: zhang

first: Yan

last: Ao

first: Wei

first: Xuhao

last: Zhao

first: Tao

last: Jiang


title: Single-Cell Sequencing of PBMC Reveals Monocyte-Mediated Inflammation Is Enhanced in Crizotinib-Induced Paroxysmal Atrial Fibrillation

city: ShenZhen

first: jiao

last: zhao

state: US and Canada only

address: 1088 Xueyuan Avenue, Shenzhen 518055, P.R. China

country: China

institute: Southern University of Science and Technology

type: Expression profiling by high throughput sequencing

summary: The cause of atrial fibrillation (AF) is unclear and is associated with organic heart disease, pre-excitation syndrome, and other underlying conditions. Medications may also cause AF, such as chemotherapeutic agents. Crizotinib is used as a multi-target protein kinase inhibitor in the treat-ment of non-small cell lung cancer. The most common adverse events with crizotinib are nausea, diarrhoea and vomiting. There are also side effects such as hepatotoxicity, interstitial pneumonitis, prolonged QT interval, and bradycardia. Here, we report a case of crizotinib-induced AF. For the first time, we used peripheral blood mononuclear cells before and after the onset of paroxysmal AF for single-cell sequencing analysis with the aim of determining the mechanism of AF. The single-cell sequencing results and retrospective study showed that monocytes were the most dynamic cell type in the peripheral blood at the onset of AF and increasing proportion of monocytes is an important feature of atrial fibrillation. Meanwhile, retrospective studies have also shown that a higher level of inflammation is a characteristic of patients with AF. Monocyte-mediated adipogenesis-related sig-naling pathway, GALECTIN signaling, and chemokine overexpression were characteristic of pe-ripheral blood mononuclear cells at the onset of AF. At the same time, we found an elevated level of inflammation and an elevated red cell distribution width (RDW) in this patient. These clinical findings corroborate each other with the results of the single-cell analysis, suggesting that inflam-mation is a very important feature in the development of AF.

overall_design: single-cell RNA-seq analysis of the PBMCs from patient in the stage of use (day8), and stage of withdrawal (day16) after crizotinib administration (day0), the patient discontinued crizotinib on day 11, and AF disappeared on day 12.


title: Glioma-Induced Alterations in Excitatory Neurons are reversed by mTOR Inhibition

city: New York

first: Athanassios

last: Dovas

state: NY

address: 1130St Nicholas Avenue

country: USA

institute: Columbia University

summary: Gliomas are highly aggressive brain tumors characterized by poor prognosis and composed of diffusely infiltrating tumor cells that intermingle with non-neoplastic cells in the tumor microenvironment, including neurons. Neurons are increasingly appreciated as important reactive components of the glioma microenvironment, due to their role in causing hallmark glioma symptoms, cognitive deficits, and seizures, as well as potentially driving glioma progression. Separately, mTOR signaling has been shown to have pleiotropic effects in the brain tumor microenvironment, including regulation of neuronal hyperexcitability. However, the local cellular level effects of mTOR inhibition on glioma-induced neuronal alterations are not well understood. Here we employed neuron-specific profiling of ribosome-bound mRNA via ‘Ribotag’, morphometric analysis, and intravital imaging, along with pharmacological mTOR inhibition to investigate the impact of glioma burden on excitatory neuronal pathophysiology as well as the impact of mTOR inhibition on these neuronal alterations. The Ribotag analysis of peritumoral excitatory neurons showed an upregulation in transcripts encoding for F-actin binding and other dendritic spine-enriched proteins. Light and electron microscopy analyses revealed marked decreases in dendritic spine density in peritumoral neurons. Intravital two-photon imaging in peritumoral excitatory neurons revealed progressive alterations in neuronal activity, both at the population and single neuron level, throughout tumor growth. Intravital two-photon imaging also revealed altered stimulus-evoked somatic calcium activity, both in rate and temporal alignment, which was most pronounced in neurons with high-tumor burden. A single acute dose of AZD8055, a mTORC1 and mTORC2 inhibitor reversed the translational effect of glioma on neurons, increased dendritic spine density, and functional neuronal alterations. These results point to mTOR-driven pathological plasticity in neurons at the infiltrative margin of glioma – manifested by alterations in ribosome-bound mRNA, dendritic spine morphology, and stimulus-evoked neuronal activity. Collectively, our work identifies the pathological changes that peritumoral neurons experience as both hyperlocal and reversible under the influence of mTOR inhibition, providing foundational knowledge for developing therapies targeting neuronal signaling in glioma.

overall_design:
In order to study the translational alterations in the neurons of glioma-bearing mice, we implanted glioma cells in the cortex of Camk2a-Cre-Rpl22HA mice.
We isolated total and immunoprecipitated (IP) polysomal RNA from three groups of mice: control (no tumor), tumor and tumor treated with the mTOR inhibitor AZD8055
We determined neuronally enriched genes in the tumor condition by perfoming DESeq2 between tumor input and IP fractions, then proceeded to compare the three conditions.

first: Daniela

last: Torres

first: Sohani

middle: D

last: Sharma

first: Peter

last: Canoll

middle: A

last: Sims


title: Schizophrenia risk gene ZNF804A controls ribosome localization and synaptogenesis in developing human neurons

city: London

first: Laura

last: Sichlinger

address: 5 Cutcombe Rd

country: United Kingdom

institute: King's College London

summary: ZNF804A was amongst the first genes robustly associated with schizophrenia based on findings from large-scale genomic studies. Previous research has implicated ZNF804A inthe regulation of gene expression and synaptic function, but the role this gene plays inneurodevelopment and in relation to schizophrenia pathogenesis remains unclear. To study the function of this gene during neurodevelopment, we generated isogenichuman induced pluripotent stem cells (hiPSCs) with reduced ZNF804A expression, differentiated them into developing cortical glutamatergic neurons and studied theirtranscriptomic, synaptic and protein signatures. Mutant neurons showed modest changes in gene expression. However, high-content confocal imaging revealed increased excitatory synapse density in mutant neurons. Cell-compartment specific proteomic analysis further revealed that mutant neurons had higher levels of ribosomal andtranslational proteins in their neurites, and high-content imaging confirming increased local protein synthesis efficiency. Overall, these results demonstrate that in human developing cortical glutamatergic neurons, ZNF804A regulates excitatory synapse formation potential via increased local protein translation.

overall_design: This study aimed to investigate the role of the schizophrenia susceptibility gene ZNF804A through transcriptomic analysis in a relevant cellular model. We conducted a comprehensive expression profile of ZNF804A during glutamatergic cell development, identifying immature post-mitotic forebrain neurons as a suitable model. CRISPR/Cas9 genome editing was employed to induce mutations in ZNF804A, and bulk RNAseq was performed to assess transcriptional changes.

first: Lucia

last: Dutan Polit

first: Rodrigo

middle: R

last: Duarte

first: Timothy

last: Powell

first: Deepak

middle: P

last: Srivastava


title: Estrogen-independent Epigenetic Mechanisms Regulate Gender Dimorphisms in Cardiac Reparative Functions of Bone Marrow Progenitor Cells

city: Philadelphia

first: Charan

middle: Thej

last: Gurrala

state: Pennsylvania

address: 3500 N Broad St, MERB 983

department: Aging + Cardiovascular Discovery Center

institute: Temple University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The complex role of Naked cuticle in Drosophila wing development

status: Public on Jan 31 2024

city: Nanjing

first: Rui

last: Wang

state: Jiangsu

address: 2 Sipailou Road

department: School of Life Science and Technology

institute: Southeast University

summary: It is of tremendous interests to understand how Wnt signaling is regulated in a precise manner both temporally and spatially. Naked cuticle (Nkd) acts as a negative-feedback inhibitor for Wingless (Wg, a fly Wnt) signaling in Drosophila embryonic development. In the present study, we show that nkd is essential for wing pattern formation, such that both gain and loss of nkd result in the disruption of Wg target expression in larvae stage and abnormal adult wing morphologies. Our results of high-throughput sequencing suggest that nkd have profound effects on Drosophila wing development with several critical signaling pathways involved, we conclude that Nkd inhibits the canonical Wg pathway during Drosophila wing development beyond embryonic stage and may play a mediated role in cross-talk between development-related pathways.

overall_design: mRNA profiles of third instar larval wing discs expressing GFP or Nkd recombinant proteins under the control of MS1096-Gal4.

first: Hao

last: Xie

first: Lin

last: Yang

first: Ping


title: Estrogen-independent Epigenetic Mechanisms Regulate Gender Dimorphisms in Cardiac Reparative Functions of Bone Marrow Progenitor Cells [Cut & Tag]

summary: Historically, lower incidence of CVD and related deaths in women compared to men of the same age has been attributed to female sex hormones, particularly estrogen and its receptors. Autologous Bone marrow stem cell (BMSC) clinical trials for cardiac cell therapy overwhelmingly included male patients; however, meta-analysis data on these trials suggest a better functional outcome in women compared to men. Direct comparison of gender-specific cardiac reparative activity and estrogen-independent mechanisms that regulate gender-specific dimorphisms of BMSC has not been studied. This study was designed to identify sex hormone-independent mechanisms that regulate superior reparative properties of female endothelial progenitor cells (EPCs) post-MI, particularly epigenetic mechanisms. Male (M), female (F), and ovariectomized female (OVX) mice-derived EPCs were subjected to a series of molecular and epigenetic analyses followed by in vivo functional assessments of cardiac repair. RNA sequencing and other quantitative assays showed a similar genetic profile between F-EPCs and OVX-EPCs, distinct from M-EPCs that displayed significant up-regulation of inflammation-related genes.  F-EPCs and OVX EPCs secrete higher levels of proangiogenic factors, lower levels of proinflammatory cytokines and show better cardiac reparative activity after intra-cardiac injections in a male mouse model of myocardial infarction (MI).  Epigenetic sequencing revealed a marked difference in the occupancy of the gene repressive H3K9me3 mark, particularly at transcription start sites of key angiogenic and proinflammatory genes in male EPCs compared to female and ovariectomized EPCs. Our study unveiled that functional gender dimorphism in EPCs is, in part, mediated by differential epigenetic regulation of the proinflammatory and anti-angiogenic gene CCL3, orchestrated by the control of H3K9me3 by histone methyltransferase, G9a/Ehmt2. Our research highlights the importance of considering gender of donor cells for progenitor based tissue repair.

overall_design: To investigate estrogen-independent epigenetic mechanisms which regulate cardiac reparative properties of genderr dimorphic properties of endothelial progenitor cells

last: Thej

first: Raj

last: Kishore


title: Analysis of hnRNP K interacting RNAs in myeloid KG-1a cells

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

summary: HNRNPK is part of the minimally deleted region (MDR) in AML del(9q). To understand the function of hnRNP K in pathogenesis of this AML subtype, we analyzed the function of hnRNP K as an RNA binding protein in myeloid cells. Co-immunoprecipitated RNAs from hnRNP K and non-related control immunoprecipitation as well as input RNA were subjected to next generation sequencing. This analysis revealed an interaction of hnRNP K with 1076 RNAs, among them many mRNAs encoding transcription factors involved in myeloid differentiation and AML pathogenesis.

overall_design: Cytoplasmic extracts from KG-1a cells were subjected to immunopreciptiation with a hnRNP K specific antibody or a non-related control reaction. Total RNA from cytoplasmic extract was isolated as input. Three independent biological replicates were analyzed.

first: Kerstin

last: Rahn

last: Gan

first: Roland

last: Sonntag

first: Gernot

last: Marx

first: Tim

middle: H

last: Brümmendorf

first: Bernd

last: Denecke

first: Dirk

last: Ostareck

first: Antje

last: Ostareck-Lederer

first: Martina

last: Crysandt

first: Isabel

middle: S

last: Naarmann-de Vries


title: Gene expression profiling in cancer stem-like melanoma A2058 cells under normoxia and hypoxia

city: New Taipei City

first: Shaochen

last: Lee

address: 510 Zhongzheng Rd., Xinzhuang Dist.

department: School of Medicine

country: Taiwan

institute: FuJen Catholic University

summary: Analysis of gene expression and compare the significant changed genes with associated phenotypes

overall_design: Total RNA extracted from parental or cancer stem-like melanoma A2058 cells

first: ShaoChen


title: Targeting Circulating Labile Heme as a Defense Strategy Against Malaria

city: Oeiras

first: Rui

last: Martins

address: Rua da Quinta Grande 6

department: Inflammation

country: Portugal

institute: Gulbenkian Institute for Molecular Medicine

summary: Severe presentations of malaria emerge as parasites from Plasmodium spp. proliferate and lyse red blood cells (RBC), producing extracellular hemoglobin (HB). The heme prosthetic groups are released upon HB oxidation generating circulating labile heme. Here we asked whether scavenging of extracellular HB and/or labile heme, by haptoglobin (HP) and/or hemopexin (HPX), respectively, is protective against severe presentations of malaria. We found that circulating labile heme is an independent risk factor for cerebral and non-cerebral severe presentations of P. falciparum malaria. Labile heme was negatively correlated with HP and HPX, which were however, not risk factors for severe P. falciparum malaria. Genetic HP and/or HPX deletion in mice led to accumulation of labile heme in plasma and kidneys in response to Plasmodium (chabaudi chabaudi) infection. This was associated with increased mortality and acute kidney injury (AKI) in ageing but not adult mice, corroborated in P. falciparum malaria by a an inverse correlation between HPX and heme with serological markers of AKI. In conclusion, HP and HPX exert an age-dependent protective effect against malaria that counters the pathogenesis of AKI in mice and presumably in humans.

overall_design: Goal: To assess transcriptional differences in the kidney imposed by the lack of heme- and hemoglobin scavenging proteins Hemopexin (Hpx) and Haptoglobin (Hp), respectively, during malaria, as well as transcriptional differences in the kidney that are associated with ageing, within the same context of malaria and Hp/Hpx double knock-out mice. Procedure: We performed Next Generation Sequencing of kidney samples harvested from control (Hp+/+Hpx+/+) and hemopexin/haptoglobin double knock-out (Hp-/-Hpx-/-) C57BL/6 mice infected or not with Plasmodium chabaudi chabaudi (Pcc) at 9 weeks and 7 months of age (Samples collected on day 7 post-infection). We performed comparative analysis of gene expression between Pcc-infected adult (9 weeks old) and ageing (7 months old) mice, as well as between infected and uninfected control and Hp-/-Hpx-/- double knock-out mice.

first: Susana

last: Ramos

first: Viktoria

last: Jeney

first: Ana

last: Figueiredo

first: Tiago

last: Paixão

first: Maria

last: Rosário Sambo

first: Vatúsia

last: Quinhentos

first: Zélia

last: Gouveia

last: Carlos

last: Ferreira

first: Teresa

last: Pais

first: Hugo

last: Lainé

first: Pedro

last: Faísca

first: Sofia

last: Rebelo

first: Sílvia

last: Cardoso

first: Emanuela

last: Tolosano

first: Carlos

last: Penha-Gonçalves

first: Miguel

last: Soares


title: Primary bone marrow stromal cells in plasma cell disorders

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: Multiple myeloma (MM) and its premalignant precursor MGUS (monoclonal gammopathy of undetermined significance) are clonal plasma cell diseases that develop in the bone marrow (BM) and are dependent on microenvironmental interactions. Primary bone marrow stromal cells (BMSCs) are key players in the BM microenvironment, however, their role in MGUS/MM pathophysiology is not known. We therefore investigated potential disease-specific alterations in prospectively isolated BMSCs from MM, MGUS and healthy controls. Clear disease-related BMSC surface marker and gene expression differences were recorded, and deep sequencing identified shared MGUS/MM as well as MM-specific molecular signatures. Moreover, we identified genes that were deregulated in a disease-stage manner, thus reflecting the progression from normal to MGUS and MM. Analysis of primary BMSCs revealed disease-stage related protein and gene expression patterns, which provides novel insight into the stromal transitions and their functional implications for plasma cell disease development and progression.

overall_design:
RNA sequencing data from primary prospectively-isolated and bulk-sorted bone marrow stromal cells (BMSCs) defined as lin-CD45-CD71-CD235a-CD31-CD271+ from multiple myeloma (MM, n=10) and MGUS (n=5) patients in comparison with older healthy donor (n=7) BMSCs
Submitter declares that the raw data will be submitted to EGA because of patient privacy concerns.

first: Dimitra

last: Zacharaki

first: Stefan

last: Scheding


title: Estrogen-independent Epigenetic Mechanisms Regulate Gender Dimorphisms in Cardiac Reparative Functions of Bone Marrow Progenitor Cells [RNA-Seq]

first: Charan

last: Gurrala

last: Thej

first: Raj

last: Kishore


title: Nuclear VANGL2 inhibits mammary differentiation

city: Santa cruz

first: Chad

middle: Steven

last: Cockrum

state: CA

address: 329 sinsheimer labs

institute: University of California at Santa Cruz


title: Nuclear VANGL2 inhibits mammary differentiation [CUT&RUN]

summary: Planar cell polarity PCP proteins coordinate tissue morphogenesis by governing cell patterning and polarity. Asymmetrically localized on the plasma membrane of cells, transmembrane PCP proteins aretrafficked by endocytosis, suggesting they may have intracellular functions that are dependent or independent of their extracellular role, but whether these functions extend to transcriptional control remains unknown. Here, we show the nuclear localization of transmembrane, PCP protein, VANGL2, in undifferentiated, but not differentiated, HC11 cells, which serve as a model for mammary lactogenic differentiation. Loss ofVangl2function results in upregulation of pathways related to STAT5 signaling.We identify DNA binding sites and a nuclear localization signal in VANGL2, and use CUT&RUN to demonstrate recruitment of VANGL2 to specific DNA binding motifs, including one in theStat5apromoter. Knockdown KD ofVangl2in HC11 cells and primary mammary organoids results in upregulation ofStat5a,Ccnd1andCsn2, larger acini and organoids, and precocious differentiation; phenotypes rescued by overexpression ofVangl2, but notVangl2ΔNLS. Together, these results advance a paradigm whereby PCP proteins coordinate tissue morphogenesis by keeping transcriptional programs governing differentiation in check.

overall_design: Cleavage Under Targets & Release Using Nuclease, CUT&RUN, for VANGL2 in HC11 cells at two different stages, undifferentiated and differentiated.

first: Stefany

last: Rubio

first: Rut

last: Molinuevo

first: Natalia

last: Sanz-Gomez

first: Talieh

last: Zomorrodinia

first: Elina

last: Luong

first: Lucias

last: Rivas

first: Kora

last: Cadle

first: Julien

last: Menendez

first: Lindsay

last: Hinck


title: Overexpression of Let-7a Mitigates Diploidization in Mouse Androgenetic Haploid Embryonic Stem Cells

city: stockholm

first: wenteng

last: He

state: **Non-US resident**

address: solnavagen

institute: karolinska institutet

type: Non-coding RNA profiling by high throughput sequencing

summary: Mouse androgenetic haploid embryonic stem cells (mAG-haESCs) can be utilized to uncover gene functions, especially those of genes with recessive effects, and to produce semicloned mice when injected into mature oocytes. However, mouse haploid cells undergo rapid diploidization during long-term culture in vitro and subsequently lose the advantages of haploidy and the factors that drive diploidization are not well understood. In this study, we compared the small RNAs (sRNAs) of mAG-haESCs, normal ESCs and mouse round spermatids by high-throughput sequencing and identified distinct sRNA profiles. Several let-7 family members and miR-290-295 cluster miRNAs were found significantly differentially transcribed. Knockdown and overexpression experiments showed that let-7a and let-7g suppress diploidization while miR-290a facilitates diploidization. Our study revealed the unique sRNA profile of mAG-haESCs and demonstrated that let-7a overexpression can mitigate diploidization in mAG-haESCs. These findings will help us to better understand mAG-haESCs and utilize them as a tool in the future.

overall_design: To investigate small RNA profile of mouse androgenetci embryonic stem cells, we constructed small RNA libraries of R1, mouse spermatids, and three mouse androgenetic embryonic stem cell lines for analyses and comparison

first: Wenteng

first: Hongming

last: Tang

first: Yuanyuan

last: Li

first: Mingzhu

last: Wang

first: Jiayu

last: Chen

first: Shaorong

last: Gao

first: Zhiming

last: Han


title: Nuclear VANGL2 inhibits mammary differentiation [RNA-seq]

first: Chad

last: Cockrum

overall_design: RNA-seq to compare gene expression in wild type versus Vangl2 knock-out cells

first: Stefany


title: Molecular characteristics of microglia in APOE-/-mice treated with APOE130-149 or control peptides after NMOSD induction

city: Beijing

first: Wei-Na

last: Jin

state: Beijing

address: NO.119, Southwest of the Fourth Ring Road, Fengtai District

department: China National Clinical Research Center for Neurological Diseases

institute: Beijing Tiantan Hospital, Capital Medical University

summary: NMOSD is an autoimmune astrocytopathy of the central nervous system, mediated by antibodies against aquaporin-4 water channel protein (AQP4-Abs), resulting in damage of astrocytes with subsequent demyelination and axonal damage. The extracellular communication through astrocyte-derived extracellular vesicles (ADEVs) has received a growing interest in association with astrocytopathies, however, to which extent ADEVs contribute to NMOSD pathogenesis remains unclear. Here, we demonstrate a significant increase in apolipoprotein E (APOE)-rich ADEVs in AQP4-Abs-positive NMOSD patients as well as in a murine model of NMOSD.To capture further insight regarding the effects of APOE on microglial functional status, scRNA-seq was performed to identify molecular characteristics of microglia of APOE-/- mice subjected to sham or NMOSD induction and treated with APOE130-149 or control peptides. We demonstrated  that APOE130-149 treatment has a substantial effect on microglial transcriptomes and biological features, suppressing molecules associated with microglia activation and pro-inflammatory functions.

overall_design: To capture insight regarding the effects of APOE on microglial functional status, scRNA-seq was performed to identify molecular characteristics of microglial cells of APOE-/- mice subjected to sham or NMOSD induction and treated with APOE130-149 or control peptides. CD45intCD11b+ cells were sorted from the mouse brain by flow cytometry on day 4 after NMOSD induction, and were subjected to single cell RNA sequencing. Data were pooled from 4 mice each group.

first: Shihe

last: Jiang

first: Xindi

first: Fu-Dong

last: Shi


title: Transcriptomic analysis GM12878 Lymphoblastoid cell line (LCL) upon CRISPR knockout of the individual NF-κB transcription factor.

city: Boston

first: Bidisha

last: Mitra

state: MA

address: 181 Longwood Avenue, 8th floor

department: Medicine

institute: Brigham and Women's Hospital

summary: RNA-seq was used to characterize the NF-κB transcription factor -mediated regulation of B-cell genome wide target genes in Latency III GM12878 Lymphoblastoid cell upon stable CRISPR knockout of the individual NF-κB transcription factors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data  GM12878 Lymphoblastoid cell line (LCL) cells upon stable CRISPR knock out each of the five NF-κB transcription factor (p50,p52, RelB, cRel or RelA). GM12878 cells bearing a non-targeting control is used as the control

first: Yijie

last: Ma

first: Michael

last: Walsh

first: Ziqi

last: Zhou

first: Nina

last: Beri

first: Rui

last: Guo

first: Laura

last: Murray-Nerger

first: Benjamin

middle: E

last: Gewurz


title: Transcriptomic analysis of EBV-negative Akata Burkitt Lymphoma Cell target genes upon  CRISPR knockout of the individual NF-κB transcription factor as well as induction of wildtype LMP1 expression

summary: RNA-seq was used to characterize the NF-κB transcription factor -mediated regulation of B-cell genome wide target genes upon inducible LMP1 expression . We created an inducible stable  EBV-negative Akata Burkitt Lymphoma cell line expressing LMP1 wildtype followed by stable CRISPR knockout of the individual NF-κB transciption factors (p52, RelB, p50, cRel or RelA) and 24 hours 250ng/ml doxycycline-induced LMP1 expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data  EBV-negative Akata Burkitt Lymphoma Cells upon stable CRISPR knock out each of the five NF-κB transcription factor (p50,p52, RelB, cRel or RelA) and inducible expression of the wildtype LMP1. Stable cell line with wildtype LMP1 induced expression and bearing a non-targeting control is used as the control


title: Circular RNA Cdr1as inhibits proliferation and delays injury-induced regeneration of the intestinal epithelium

city: Baltimore

first: Lan

last: Xiao

state: Maryland

address: HSF II S-211, 20 Penn Street

department: Surgery

institute: University of Maryland School of Medicine

summary: The data analysis includes five parts for the small RNA biotypes: miRNA, tsRNA (i.e. tRF & tiRNA), pre-miRNA, tRNA and snoRNA.

overall_design: to test the differential miR expression in cdr1as gene KO mice

first: Hee

middle: K

last: Chung

first: Naomi

first: Jason

first: Vivian

last: Yao

first: Cassandra

last: Cairns

first: Jaladanki

middle: N

last: Rao

first: Douglas

middle: J

last: Turner

first: Rosemary

last: Kozar

first: Myriam

last: Gorospe

first: Jian-Ying


title: KaedeGreen and Red CD8 T cells from vaccinia-GP33 infected skin

first: Vanessa

last: Cristaldi

address: 522 First Avenue

department: Dermatology

institute: NYU Langone Health

summary: In order to determine transcriptional differences between cells in the draining lymph node and those recently emigrating from the skin, we performed single cell RNA sequencing on KaedeGreen and KaedeRed CD8 T cells 12 days post infection with vaccinia-GP33. CD8+ cells were MACS enriched. Cells were stained with two tetramers (H2-Kb-B8R20-27 and H2-Db-GP33-41) conjugated to APC. Cells were then incubated with TotalSeq anti-APC (Biolegend, 408009)

overall_design: Kaede male and female mice were infected with 5x10^6 PFU of VV-GP33 on both ears via scarification. 11 days later ears were photoconverted with 405nm light. 24 hours after photoconversion, CD8 T cells were isolated from draining lymph nodes. Cells were sorted on CD8a+, CD44+, CD45+, Intravascular CD45-, Live (DAPI-).

first: Heim

last: Taylor

first: Lund

last: Amanda


title: Transcriptional profiling specifies the pathogen-specific human host response to infectious keratitis

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

summary:
PURPOSE
Corneal infections are a leading cause of visual impairment and blindness worldwide. Here we applied high-resolution transcriptomic profiling to assess the general and pathogen-specific molecular and cellular mechanisms during human corneal infection.
METHODS
Clinical diagnoses of herpes simplex virus (HSV) (n=5) and bacterial/fungal (n=5) keratitis were confirmed by histology. Healthy corneas (n=7) and keratoconus (n=4) samples served as controls. Formalin-fixed, paraffin-embedded (FFPE) human corneal specimens were analyzed using the 3' RNA sequencing method Massive Analysis of cDNA Ends (MACE RNA-seq). The cellular host response was investigated using comprehensive bioinformatic deconvolution (xCell) analyses and by integration with single cell RNA-seq data.
RESULTS
Our analysis identified 216 and 561 genes, that were specifically overexpressed in viral or bacterial/fungal keratitis, respectively, and allowed to distinguish the two etiologies. The virus-specific host response was driven by adaptive immunity and associated molecular signaling pathways, whereas the bacterial/fungal-specific host response mainly involved innate immunity signaling pathways and cell types. We identified several molecular mechanisms involved in the host response to infectious keratitis, including CXCL9, CXCR3, and MMP9 for viral, and S100A8/A9, MMP9, and the IL17 pathway for bacterial/fungal keratitis.
CONCLUSIONS
High-resolution molecular profiling provides new insights into the human corneal host response to viral and bacterial/fungal infection. Pathogen-specific molecular profiles may provide the foundation for novel diagnostic biomarker and therapeutic approaches that target inflammation-induced damage to corneal host cells with the goal to improve the outcome of infectious keratitis.

overall_design: Corneal tissue from humans with bacterial/fungal keratitis (n=5), viral keratitis (n=5), keratoconus (n=4), and normal controls (n=7).

first: Thabo

last: Lapp

first: Paola

last: Betancor

first: Günther

last: Schlunk

first: Claudia

last: Auw-Hädrich

first: Philip

last: Maier

first: Thomas

last: Reinhard

first: Julian

last: Wolf


title: Transcriptional profiling of TP53-proficient and deficient PCNAWT/WT;FancG+/+ (WT) and PCNAK164R/K164R;FancG-/- (DM) MEFs

city: Amsterdam

first: Heinz

last: jacobs

address: Plesmanlaan 121

country: Netherlands

institute: NKI

summary: We studied the role of TP53 in WT and DM MEFs. Here, we generated RNA-seq data from primary and p53kd mefs from two independent clones each for WT and DM mefs.

overall_design: Transcriptional changes in Primary WT and DM were compared. A similar comparison was made from TP53kd MEFs. Three technical replicates from two independent clones for each condition were analysed  for differential gene expression.

first: Ronak

last: Shah

first: Muhammad

last: Aslam

last: Jacobs


title: Functional immunophenotyping of blood neutrophils identifies novel endotypes of viral response in preschool children with recurrent wheezing

status: Public on Jan 29 2024

city: Atlanta

first: Min

last: Huang

address: WMB, 101 Woodruff Circle

institute: Emory University

summary: Preschool children with recurrent wheezing are heterogeneous, with differing responses to respiratory viral infections. Although neutrophils are crucial for host defense, their function has not been studied in this population. We performed functional immunophenotyping on isolated blood neutrophils from 52 preschool children with recurrent wheezing (aeroallergen sensitization, n=16; no sensitization, n=36). Blood neutrophils were purified and cultured overnight with polyinosinic:polycytidylic acid (poly(I:C)) as a viral analog stimulus. Neutrophils underwent next-generation sequencing with Reactome pathway analysis and were analyzed for cytokine secretion, apoptosis, myeloperoxidase and extracellular DNA release. CD14+ monocytes were also exposed to neutrophil culture supernatant and analyzed for markers of M1 and M2 activation. 495 genes, related largely to the innate immune system and neutrophil degranulation, were differently expressed in children with versus without aeroallergen sensitization. Functional experiments identified more neutrophil degranulation and extracellular trap formation (i.e., more myeloperoxidase and extracellular DNA) and less neutrophil pro-inflammatory cytokine secretion in children with aeroallergen sensitization. Neutrophils also shifted CD14+ monocytes to a more anti-inflammatory (i.e., M2) phenotype in sensitized children and a more pro-inflammatory (i.e., M1) phenotype in non-sensitized children. Although both groups experienced viral exacerbations, annualized exacerbation rates prompting unscheduled healthcare were also higher in children without aeroallergen sensitization after enrollment. Systemic neutrophil responses to viral infection differ by allergic phenotype and may be less effective in preschool children without allergic inflammation. Further studies of neutrophil function are needed in this population, which often has less favorable therapeutic responses to inhaled corticosteroids and other therapies directed at T2-high inflammation.

overall_design: Preschool children 12-59 months of age with recurrent wheezing and at least one wheezing episode treated with systemic corticosteroids in the previous 12 months were included in the study. Recurrent wheezing was defined as a lifetime history of two or more episodes of wheezing, each lasting at least 24 hours and requiring reated treatment with albuterol sulfate. Children with aeroallergen sensitization were compared to children without aeroallergen sensitization. Aeroallergen sensitization was defined as one or more positive aeroallergen specific IgE tests.

first: Anne

middle: M

last: Fitzpatrick

first: Rishikesan

last: Kamaleswaran

first: Jocelyn

last: Grunwell


title: PTEN-induced kinase 1 (PINK1) ameliorates autoimmune disease via negative regulation of the STAT3-Th17 axis

city: Seoul

first: Mi-La

last: Cho

address: 222,Banpo-daero, Seocho-gu

country: South Korea

institute: The Catholic University of Korea

summary: Th17-related genes increased in T cells from PINK1-deficient mice. Th17 and Treg cells were increased and decreased in PINK1-deficient cells, respectively, and phosphorylation of signal transducer and activator of transcription 3 (STAT3) was increased in PINK1-deficient cells.

overall_design:
toal 2sampls   Samples of B6 T cell condition: 1  Samples of PINK1 KO T cell condition: 1
total 2 samples:
Samples of B6 T cell condition: 1
Samples of PINK1 KO T cell condition: 1

first: Jin-Seok

last: Woo


title: IL-1β promotes MPN disease initiation by favoring early clonal expansion of JAK2-mutant hematopoietic stem cells

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: JAK2-V617F is the most frequent somatic mutation causing myeloproliferative neoplasm (MPN). JAK2-V617F can be found in healthy individuals with clonal hematopoiesis of indeterminate potential (CHIP) with a frequency much higher than the prevalence of MPN. The factors controlling the conversion of JAK2-V617F CHIP to MPN are largely unknown. We hypothesized that IL-1β mediated inflammation can favor this progression. We established an experimental system using bone marrow (BM) transplantations from JAK2-V617F and GFP transgenic (VF;GFP) mice, that were further crossed with IL-1β-/- or IL-1R1-/- mice. To study the role of IL-1β and its receptor on monoclonal evolution of MPN, we performed competitive BM transplantations at high dilutions with only 1-3 hematopoietic stem cells (HSCs) per recipient. Loss of IL-1β in JAK2-mutant HSCs reduced engraftment, restricted clonal expansion, lowered the total numbers of functional HSCs, and decreased the rate of conversion to MPN. Loss of IL-1R1 in the recipients also lowered the conversion to MPN, but did not reduce the frequency of engraftment of JAK2-mutant HSCs. WT recipients transplanted with VF;GFP BM that developed MPN had elevated IL-1β levels and reduced frequencies of mesenchymal stromal cells (MSCs). Interestingly, frequencies of MSCs were also reduced in recipients that did not develop MPN, had only marginally elevated IL-1β levels and displayed low GFP-chimerism resembling CHIP. Anti-IL-1β antibody preserved high frequencies of MSCs in VF;GFP recipients and reduced the rate of engraftment and the conversion to MPN. Our results identify IL-1β as a potential therapeutic target for preventing the transition from JAK2-V617F CHIP to MPN.

overall_design: 25 samples, originating from mice engrafted with bone-marrow cells from donor mice of 4 different genotypes: WT, VF, VF;IL-1b-/-, and VF;IL-1R1-/-. Tamoxifen induction of the JAK2 mutant construct was performed after 16 weeks. Mice were sacrificed 2 weeks or 4 weeks after beginning of tamoxifen induction, and hemapoeitic stem cells were sorted for bulk RNA-sequencing (low-input protocol).

first: Shivam

last: Rai

first: Radek

last: Skoda

first: Julien

last: Roux


title: Protein UFMylation regulates ribosomal DNA double-stranded break repair

city: Montreal

first: Marlene

last: Oeffinger

state: Quebec

address: 110 Ave Pins Ouest

department: Center for Genetic and Neurological Diseases,

country: Canada

institute: IRCM

summary: Ribosomal DNA (rDNA) arrays are highly repetitive regions of the genome which encode essential genes required to produce ribosomes. DNA double-stranded breaks (DSBs) generated within rDNA genes elicit a unique cellular response involving robust transcriptional silencing and nucleolar reorganization into ‘cap’ structures at the nucleolar periphery. This process is coordinated by the nucleolar scaffolding protein TCOF1, which functions to recruit the DNA repair proteins NBS1 and TOPBP1 that activate the ATM and ATR kinases, resulting in ribosomal RNA (rRNA) transcriptional silencing and nucleolar segregation. However, the DNA damage and repair response at rDNA arrays remains incompletely understood.  Here, we investigate the cellular response to rDNA DSBs using proteomics and genetic CRISPR-Cas9 screening. We show that the protein UFMylation pathway and the HUSH complex are important for cell viability and survival in response to rDNA DSBs, and that the E3 UFM1-ligase UFL1 and its heterodimer DDRGK1 are associated with TCOF1 at nucleolar caps. Loss of UFL1 leads to impaired ATM activation, reduced rRNA transcriptional silencing, and an overall reduction in nucleolar segregation. We identified ATM, UNC45A and SMC6 as UFMylated proteins, in which UFMylation may facilitate ATM activation and segregation of damaged rDNA to the nucleolar periphery. Altogether, our findings provide the first evidence for a role for UFMylation in rDNA DSB repair.

overall_design:
To determine the genes essential for rDNA DSB repair, we conducted a genome-wide CRISPR-Cas9 screen in hTERT-RPE1 p53-/- cells expressing DD-HA-ER-I-PpoI. These cells were transdcued with the TKOv3 sgRNA library and split into techincal replicates after transduction and selection ("A" and "B").
Cells were treated with negaive control DMSO or Shield-1 + 4-OHT to induce rDNA DSBs 1 day after passaging over the course of 20 days. Sequencing timepoints correspond to T0, T16,  and T24 (T=0 is 3 days after intial viral infection used to represent the intial transduced library).

first: Pudchalaluck

last: Panichnantakul

first: Lisbeth

last: Aguilar

first: Evan

last: Daynard

first: Mackenzie

last: Guest

first: Colten

last: Peters

first: Jackie

last: Vogel


title: Blood transcriptome profiling reveals distinct gene networks induced by mRNA vaccination against COVID-19

city: Hamburg

first: Marylyn

middle: M.

last: Addo

address: Martinistraße 52

institute: University Medical Center Hamburg-Eppendorf

summary: Messenger RNA (mRNA) vaccines represent a new class of vaccines that has been shown to be highly effective during the COVID-19 pandemic and that holds great potential for other preventative and therapeutic applications. Understanding the underlying mechanisms of the immune responses induced by this novel vaccine type and their relation to vaccine responses might help to further refine and optimize future vaccine design. In this study, we conducted an in-depth analysis of the blood transcriptome before and 24h after second and third vaccination with licensed mRNA vaccines against COVID-19 in humans, following a prime vaccination with either mRNA or ChAdOx vaccines. Utilizing an unsupervised weighted gene correlation network analysis, we identified distinct gene networks of co-varying genes characterized by either an expressional up- or down-regulation in response to vaccination. Down-regulated networks were associated with cell metabolic processes and regulation of transcription factors, while up-regulated networks were associated with myeloid differentiation, antigen presentation, and antiviral, interferon-driven pathways. Within this interferon-associated network, we identified highly connected hub genes such as STAT2 and RIGI, potentially playing important regulatory roles in the vaccine-induced immune response. The expression profile of this network significantly correlated with S1-specific IgG levels at the follow-up visit in vaccinated individuals. Those findings could be corroborated in an independent cohort of mRNA vaccine recipients. Collectively, insights from this study might contribute to current research endeavors aimed at further enhancing/ or optimizing vaccine-induced immunity.

overall_design: We collected whole blood for RNA-seq from 15 and 10 vaccine recipients both before (Pre) and 24 hours (24h) after the second (V2) and third (V3) COVID-19 vaccinations, respectively. All included participants received two mRNA booster vaccinations, following primary vaccination with either ChAdOx or an mRNA vaccine (see metadata). Seven participants were sampled both at V2 and V3. We compared the transciptional profile 24h after vaccination with the pre-vaccination profile at both vaccinations to analyze vaccine-induced changes in the transcriptome.

first: Riemann

last: Lennart

first: Weskamm

last: Leonie M.

first: Mayer

last: Leonie

first: Odak

last: Ivan

first: Hammerschmidt

last: Swantje

first: Sandrock

last: Inga

first: Friedrichsen

last: Michaela

first: Ravens

first: Hansen

last: Gesine

first: Addo

last: Marylyn M.

first: Förster

last: Reinhold


title: Smad4 Loss in the Mouse Intestinal EpitheliumAlleviates the Pathological Fibrotic Response to Injury in the Colon

city: Hoboken

first: Thompson

last: Hui

state: New Jersey

address: McLean 327

department: Chemistry and Chemical Biology

institute: Stevens Institute of Technology

summary: Mucosal healing is associated with better clinical outcomes in patients with inflammatory bowel diseases (IBDs). Unresolved injury and inflammation, on the other hand, increases pathological fibrosis and the predisposition to cancer. Loss of Smad4, a tumor suppressor, is known to increase colitis-associated cancer in mouse models of chronic IBD. Since common biological processes are involved in both injury repair and tumor growth, we sought to investigate the effect of Smad4 loss on the response to epithelial injury.  To study the injury response, an IBD mouse model of acute inflammation using dextran sulphate sodium (DSS) was used. Smad4 was knocked out only in the mouse intestinal epithelium, treated with DSS, and the early molecular and morphological response compared to its wildtype counterpart.   We find that Smad4 loss alleviates pathological fibrosis and enhances mucosal repair. Transcriptomic changes specific to the epithelium indicate molecular changes that affect peri-crypt epithelial extracellular matrix (ECM), that might contribute to the enhanced mucosal repair, and in preventing the fibrotic response.  We find that biological processes that promote tumor progression might facilitate the wound healing response and reduce the pathological fibrotic response to DSS. Therefore, these repair processes could be exploited, if uncoupled from the tumorigenic effect, to develop therapies that promote non-pathological wound healing and to prevent fibrosis.

overall_design: Gene expression prolifiling was performed on wildtype and Smad4 knockout colon epithelium of mice of C57/BL6 enriched background, with or without three days of DSS in drinking water consumed ad libitum.

first: Zahra

last: Hashemi

first: Steven

last: Zukowski

first: Ansu

last: Perekatt


title: Systems biology analysis reveals distinct molecular signatures promoting immune responsiveness to the BNT162b COVID-19 vaccine

city: Hannover

first: Reinhold

last: Förster

address: Carl-Neuberg-Str. 1

department: Institute of Immunology

institute: Hannover Medical School

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

overall_design: Refer to individual Series


title: Systems biology analysis reveals distinct molecular signatures promoting immune responsiveness to the BNT162b COVID-19 vaccine [scRNA-seq]

summary: Human immune responses to COVID-19 vaccines display a large heterogeneity of induced immunity and the underlying immune mechanisms for this remain largely unknown. Using a systems biology approach, we longitudinally profiled a unique cohort of female high and low responders to the BNT162b vaccine, who were known from previous COVID-19 vaccinations to develop maximum and minimum immune responses to the vaccine. We utilized high dimensional flow cytometry, bulk and single cell mRNA sequencing and 48-plex serum cytokine analyses. We revealed early, transient immunological and molecular signatures that distinguished high from low responders and correlated with B and T cell responses measured 14 days later. High responders featured a distinct transcriptional activity of interferon-driven genes and genes connected to enhanced antigen presentation. This was accompanied by a robust cytokine response related to Th1 differentiation. Both transcriptome and serum cytokine signatures were confirmed in two independent confirmatory cohorts. Collectively, our data contribute to a better understanding of the immunogenicity of mRNA-based COVID-19 vaccines, which might lead to the optimization of vaccine designs for individuals with poor vaccine responses.

overall_design: Single-cell transcriptome (scRNA-seq) of CD3-CD19- cells of COVID-19 vaccine high-responders (HR) and low-responders (LR) before the third (booster) COVID-19 vaccination with BNT162b (pre), as well as 24 hours (24h) and 48 hours (48h) after the vaccination were analyzed.

first: Ivan

last: Odak

first: Lennart

last: Riemann

first: Inga

last: Sandrock

first: Anne

last: Cossmann

first: Gema

last: Morillas Ramos

first: Swantje

last: Hammerschmidt

first: Christiane

last: Ritter

first: Michaela

last: Friedrichsen

first: Ahmed

last: Hassan

first: Alexandra

last: Dopfer-Jablonka

first: Metodi

last: Stankov

first: Leonie

last: Weskamm

first: Marylyn

last: Ravens

first: Stefanie

last: Willenzon

first: Anja

last: Schimrock

first: Jasmin

last: Ristenpart

first: Annika

last: Janssen

first: Joana

last: Barros-Martins

first: Gesine

last: Hansen

first: Christine

last: Falk

first: Georg

last: Behrens


title: Characterization of resistance to tumor-localized interleukin-2 and interleukin-12 therapy in pet dogs with advanced malignant melanoma

city: Cambridge

first: K

middle: Dane

last: Wittrup

state: Massachusetts

department: Koch Institute for Integrative Cancer Research

institute: Massachusetts Institute of Technology

summary: Pet dogs with oral melanoma were treated in a dose-escalation trial with collagen-anchored interleukin-2 and interleukin-12 following a single 9Gy dose of radiation therapy. Dogs that progressed during, or after, treatment and were ultimately euthanized had tissue collected from primary and metastatic tumors to analyze gene expression and assess mechanisms of resistance to this therapy.

overall_design: Fifteen client-owned dogs with malignant melanoma (n=14 oral melanoma, n=1 periocular melanoma) were recruited to receive intratumoral doses of interleukin-2 and interleukin-12 collagen-binding fusion proteins at different dose levels. The first cohort (1x, n=3) received IL-2 (17.4 ug/kg) and IL-12 (2.08 ug/kg); the second cohort (2x, n=6) received 2x the initial dose (i.e. 34.8 ug/kg IL-2, 4.16 ug/kg IL-12) and was the expansion cohort after encountering toxicity at higher doses; the third cohort (3.3x, n=4) received 3.3x the initial dose (i.e. 57.4 ug/kg IL-2; 6.86 ug/kg IL-12), and the final cohort (5x, n=2) received 5x the initial dose (i.e. 87 ug/kg IL-2; 10.4 ug/kg IL-12). Up to 6 doses of cytokine were provided at 2-week intervals and were dosed after a single 9Gy focal radiation dose to the primary tumor. Dogs were periodically examined following treatment to monitor responses, and dogs that were ultimately euthanized due to cancer progression (n=8, 53.3%) had their primary and metastatic tumors collected for analysis. Tumor tissue was formalin-fixed and paraffin-embedded prior to RNA extraction (Qiagen FFPE RNEasy) and QC on Bioanalyzer (Agilent). Gene expression was analyzed through hybridization to the Nanostring Canine IO nCounter panel set probes, with quantification by Nanostring Digital Analyzer. Expression data was analyzed using Nanostring nSolver software to examine modes of tumor resistance to the RT + IL-2 and IL-12 therapy.

first: Jordan

last: Stinson

first: Matheus

last: Passos Barbosa

first: Timothy

last: Fan


title: Malignant peripheral nerve sheath tumor (MPNST) and MPNST-like entities defined by DNA methylation profile in pediatric and juvenile population

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

type: Methylation profiling by genome tiling array

summary: The diagnosis of Malignant peripheral nerve sheath tumors (MPNSTs) can be challenging, but is aided by their characteristic DNA methylation profile (DMP). An MPNST-like group, characterized by retained H3K27me3 expression, was recently recognized. To evaluate the diagnostic usefulness of DMP in pediatric/juvenile MPNSTs, we selected pediatric/juvenile malignancies from the Bambino Gesù Children's Hospital DMP database. DMP revealed unexpected molecular heterogeneity in histologically homogenous MPNSTs/Atypical neurofibromas, while samples with MPNST-like DMP manifested histological diversity. In conclusion, DMP is useful in diagnosing MPNST, discriminating morphologic mimics classified as MPNST in premolecular era, and investigating the MPNST-like ‘hybrid’ group in pediatrics.

overall_design: Bisulphite converted DNA from the 42 samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip v1


title: Expression analysis of SHOT-RNA KD in LNCaP

city: Philadelphia

first: Megumi

last: Shigematsu

state: PA

address: 1020 Locust St

institute: Thomas Jefferson University

summary: Analysis of expression changes upon knockdown of specific SHOT-RNAs in LNCaP cells

overall_design: siRNA-mediated knockdown of SHOT-RNAs was performed in LNCaP cells, and the levels of mRNAs were compared to control siRNA knockdown.

first: Yohei

last: Kirino


title: Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space [4C-seq]

city: RAMAT GAN

first: Garima

last: Chaturvedi

state: TEL AVIV

address: mAX VEANNA WEB, STREET 1

department: The Mina and Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

summary: Radiation therapy is commonly used to treat glioblastoma multiforme (GBM) brain tumor. Ionizing radiation (IR) induces dose- specific variations in transcriptional programs, implicating they are tightly regulated and critical components in the tumor response and survival.  Yet, our understanding of the downstream molecular events triggered by lethal vs sublethal IR doses is limited. Herein, we report that variations in the genetic programs are positively and functionally correlated with the exposure to lethal or sublethal IR doses. Genome architecture analysis revealed that gene regulation is spatially and temporally coordinated with DNA repair kinetics. Radiation-activated genes were pre-positioned in active sub-nuclear compartments and were up-regulated following DNA damage response, while the DNA repair activity shifted to the inactive heterochromatic spatial compartments. The IR dose affected the levels of DNA damage repair and transcription modulation, but not the order of events, which was linked to their spatial nuclear positioning. Thus, distinct coordinated temporal dynamics of DNA damage repair and transcription reprogramming in the active and inactive sub-nuclear compartments highlight the importance of high-order genome organization in synchronizing the molecular events following IR.

overall_design:
To explore the genome architecture in response to irradiation, we conducted 4C-seq. U251 cells were subjected to irradiation at doses of 1Gy and 6Gy, followed by cell collection at three time points: 0 hours, 6 hours, and 12 hours post-irradiation.
To capture the spatial environment of IR-responsive genes and nonresponsive genes, 4C-seq was performed using the following baits - BTG2, TRIM29, PRSS35, PPIB, HCRTR2.

first: Olga

last: Loiza

first: Orly

last: Yoron

first: Avital

last: Sarusi-Portuguez


title: Il-17 Signaling in Primary Sclerosing Cholangitis Patient-Derived Organoids

city: Rochester

first: Alexander

middle: Quinn

last: Wixom

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: The pathogenesis of primary sclerosing cholangitis (PSC) is unclear, although studies implicate IL-17A as an inflammatory mediator in this disease. However, a direct assessment of IL-17 signaling in PSC cholangiocytes is lacking. Cholangiocytes obtained from PSC and non-PSC patients by endoscopic retrograde cholangiography (ERC) were cultured as extrahepatic cholangiocyte organoids (ECO). The ECO were treated with vehicle or IL-17A and assessed by NanoString analysis, single cell RNA sequencing (scRNA-seq), and whole genome sequencing (WGS). The secretome was assessed by Olink analysis. Unsupervised clustering of all integrated scRNA-seq data identified 8 cholangiocyte clusters which did not differ between non-PSC and PSC ECO. However, PSC ECO cells demonstrated a much more robust response to IL-17 treatment, noted by an increased number of differentially expressed genes (DEG) after the treatment with IL-17A, compared to non-PSC ECO.  After rigorous filtering, WGS identified the presence of somatic mutations that were shared between PSC ECO. However, no somatic mutations dysregulating genes in the IL-17 pathway were identified. The secretome of PSC ECO contained more abundant chemokines and cytokines under basal conditions and following IL-17A stimulation when compared to non-PSC ECO. In conclusion, PSC and non-PSC patient derived ECO respond differently to IL-17 stimulation regardless of mutational status, suggesting a change in epigenetic regulation and the implication of this pathway in the pathogenesis of PSC.

overall_design: Extrahepatic cholangiocyte organoids (ECO) from PSC (n=4) and non-PSC patients (n=4), all at passage 3, were treated with vehicle or human recombinant IL-17A (100 ng/mL) for 24 hours. The organoids underwent trypsin digestion followed by mechanical dissociation to obtain single cell suspensions in PBS + 0.1% BSA and were submitted to the Gene Analysis Core of the Medical Genome Facility (Mayo Clinic, Rochester, MN) for scRNA-seq analysis.

first: Ana

last: Garcia Moreno

first: Gregory

last: Gores


title: Systems biology analysis reveals distinct molecular signatures promoting immune responsiveness to the BNT162b COVID-19 vaccine [bulk RNA-seq]

first: Reinhold

last: Förster

overall_design: With the submitted dataset, we compared the transcriptonal profile of vaccine COVID-19 vaccine high-responders (HR) and low-responders (LR) before the third (booster) COVID-19 vaccination with BNT162b (pre), and 24 hours (24h), 48 hours (48h), and 14 days afterwards (14d).

first: Ivan

last: Odak

first: Lennart

last: Riemann

first: Inga

last: Sandrock

first: Anne

last: Cossmann

first: Gema

last: Ramos

first: Swantje

last: Hammerschmidt

first: Christiane

last: Ritter

first: Michaela

last: Friedrichsen

first: Ahmed

last: Hassan

first: Alexandra

last: Dopfer-Jablonka

first: Metodi

last: Stankov

first: Leonie

last: Weskamm

first: Marylyn

last: Addo

last: Ravens

first: Stefanie

last: Willenzon

first: Anja

last: Schimrock

first: Jasmin

last: Ristenpart

first: Annika

last: Janssen

first: Joana

last: Barros-Martins

first: Gesine

last: Hansen


title: Organ-Chips Enhance the Maturation of Human iPSC-Derived Dopamine Neurons

city: Los Angeles

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: While cells in the human body function in an environment where the blood supply constantly de-livers nutrients and removes waste, cells in conventional tissue culture well platforms are grown with a static pool of media above them and often lack maturity, limiting their utility to study cell biology in health and disease. In contrast, organ-chip microfluidic systems allow the growth of cells under constant flow, more akin to the in vivo situation. Here, we differentiated human induced pluripotent stem cells into dopamine neurons and assessed cellular properties in conventional multi-well cultures and organ-chips. We show that organ-chip cultures, compared to multi-well cultures, provide an overall greater proportion and homogeneity of dopaminergic neurons as well as increased levels of maturation markers. These organ-chips are an ideal platform to study mature dopamine neurons to better understand their biology in health and ultimately in neurological disorders.

overall_design: Single nucleus RNA sequencing of normal control iPS-derived dopamine neuron cultures co-cultured with primary midbrain astrocytes grown in either 1) 2D (plate) format or 2) 3D organ-on-chip (chip) format

first: Maria

middle: G

last: Otero

first: Alexander

last: Laperle

first: George

last: Lawless

first: Zachary

last: Myers

first: Marian

last: Castro

first: Jaquelyn

last: Villalba

first: Clive

last: Svendsen


title: Dectin-1 ligands produce distinct training phenotypes in human monocytes through differential activation of signaling networks

first: Quen

last: Cheng

address: 10833 LeConte Ave

institute: UCLA

summary: Cells of the innate immune system retain memory of prior exposures through a process known as innate immune training. b-glucan, a Dectin-1 ligand purified from the Candida albicans cell wall, has been one of the most widely utilized and well-characterized ligands for inducing innate immune memory. However, many Dectin-1 agonists exist, and it is not known whether all Dectin-1 ligands produce the same phenotype. Using a well-established in vitro model of trained immunity, we compared two commercially available Dectin-1 agonists with the gold standard b-glucan represented in the literature. We found that depleted zymosan, a b-glucan purified from the Saccharomyces cerevisiae cell wall through alkali treatment, produced near identical training effects as C. albicans b-glucan. However, untreated zymosan produced a distinct training effect from b-glucans at both the transcript and cytokine level. Training with zymosan diminished, rather than potentiated, induction of key cytokines such as TNF, IL-12, and IL-6. Zymosan activated NFkB and AP-1 transcription factors more strongly than b-glucans. The addition of the toll-like receptor (TLR) ligand Pam3CSK4 was sufficient to convert the training effect of b-glucans to a phenotype resembling training with zymosan. We conclude that differential activation of TLR signaling pathways determines the phenotype of innate immune training induced by Dectin-1. These findings bring clarity to the specific question of which Dectin-1 agonists produce prototypical training effects and provides broader insight into how signaling networks regulate innate immune training at large.

overall_design: Bulk RNA sequencing data from human monocyte-derived macrophages trained with zymosan, depleted zymosan, or beta-glucan and stimulated with LPS

first: Kylie

last: Farrell

first: Jeffrey

last: Fenn

first: Sara

last: Makanani

first: Jonathan

last: Siemsen


title: Comparison of syngeneic tumor models reveals different tumor microenvironments with distinct subsets of cancer-associated fibroblasts polarized by infiltrating T cells

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Murine syngeneic tumor models have been extensively used for cancer research for several decades. These tumor models are very simplistic cancer models, but recent reports have, however, indicated that the different inoculated cancer cells can lead to the formation of very different tumor microenvironments (TMEs). Importantly, these types of tumor models have been instrumental in driving the discovery and development of cancer immunotherapies. In order to gain more knowledge from studies based on syngeneic tumor models it is essential to know in more details the cellular and molecular composition of the TME in the different models. It is also important to know about other parameters such as the mechanical tumor stiffness of the different models. This type of knowledge can be used for the rational selection of tumor models for specific studies and for studying the correlation between different tumor-promoting parameters. Here, we compare the tumor microenvironment (TME) of tumors derived from six different commonly used syngeneic tumor models. Using flow cytometry and transcriptomic analyses we show that strikingly different TMEs are formed by the different cancer cell lines. The differences are reflected as changes in abundance and phenotype of myeloid, lymphoid and stromal cells in the tumors. The gene expression profile of tumors from the different models supported the different cellular composition of the TMEs and indicate that different mechanisms of immune suppression are employed in the different tumor models. Cancer-associated fibroblasts also acquire very different phenotypes in the different tumor models. These differences include differential expression of genes encoding ECM proteins, MMPs, and immunosuppressive factors. In consistence with these observations, the mechanical stiffness of the tumors from different models do not simply correlate to the number of infiltrating CAFs even though collagen produced by stromal cells is an important reason for the increased stiffness of tumors. The gene expression profiles suggest that CAFs can contribute to the formation of an immunosuppressive TME and flow cytometry analyses show CAFs express high levels of PD-L1 in the immunogenic tumor models MC38 and CT26. Comparison with CAF subsets identified in other studies show that CAFs from the different models are skewed towards specific subsets. CAFs from CT26 tumors show similarities to iCAFs and myCAFs, and in athymic mice without infiltrating cytotoxic T cells, CAFs express lower levels of PD-L1 and lower levels of fibroblast activation markers.

overall_design: Tumors derived from six commonly used syngeneic tumor models were excised and RNA was isolated from a tumor fragment. RNA was isolated using the Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

first: Marie-Louise

last: Thorseth

first: Marco

last: Carretta

first: Daniel

last: Madsen


title: Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space [RNA-seq]

first: Garima

last: Chaturvedi

overall_design: To assess transcriptional changes in response to irradiation, RNA-seq was performed. In these experiments, U251 cells were subjected to irradiation at doses of 1Gy and 6Gy, followed by cell collection at three time points: 0 hours, 6 hours, and 24 hours post-irradiation.

first: Olga

last: Loiza

first: Orly

last: Yoron

first: Avital

last: Sarusi-Portuguez


title: Tenascin-C expressing touch dome keratinocytes exhibit characteristics of all epidermal lineages [ATAC-seq]

city: Bronx

first: Deyou

last: Zheng

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: TD keratinocytes in the adult skin possess molecular characteristics of other epidermal lineages, thereby giving it the unique tri-potential capacity

overall_design: Touchdome, IFE and HF keratinocyte was purified from P60 TNC-CREER; tdTomato by FACS sorting. DNA from the sorted cells was analyzed by ATAC-seq.

first: Minh

middle: B

last: Nguyen

first: Pooja

last: Flora

first: Meagan

middle: C

last: Branch

first: Xian

middle: Y

first: Maria

last: Kasper

first: Elena

last: Ezhkova


title: Decoding the Universal Human Chromatin Landscape through Teratoma-Based Profiling

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University


title: Tenascin-C expressing touch dome keratinocytes exhibit characteristics of all epidermal lineages [RNA-seq]

overall_design: Touchdome, IFE and HF keratinocyte was purified from P60 TNC-CREER; tdTomato by FACS sorting. RNA from the sorted cells was analyzed by RNA-seq.


title: Ribosomal protein L24 mediates mammalian microRNA processing in an evolutionarily conserved manner

city: Jerusalem

first: Yonat

last: Tzur

address: Givat Ram Campus

institute: Hebrew University of Jerusalem

summary:
To pursue miR-608’s functional impact and elucidate mechanisms regulating its expression, we created transgenic mice expressing miR-608.
We further found that its levels are regulated by RPL24 and performed RPL24 knockdown experiments in HEK293T cells.

overall_design: Small RNA sequencing from HEK293T cells after RPL24 knockdown using siPOOLs.

first: Hermona

last: Soreq


title: Tenascin-C expressing touch dome keratinocytes exhibit characteristics of all epidermal lineages.


title: Total RNAseq of K562 cells with a doxycycline-inducible U2AF1S34F or U2AF1WT

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

institute: Omiics ApS

summary: Mutations in the splicing factor gene U2AF1 are relatively common in myelodysplastic neoplasms (MDS) and are associated with an inferior prognosis, but the molecular mechanisms underlying this are not fully elucidated. Circular RNAs (circRNAs) have been implicated in cancer, but it is unknown how mutations in splicing factors may impact on circRNA biogenesis. Here, we used RNA-sequencing to investigate the effects of U2AF1 mutations on circRNA expression in K562 cells with doxycycline-inducible U2AF1S34F or U2AF1WT.

overall_design: K562 cells with doxycycline-inducible expression of U2AF1WT or U2AF1S34F (generated previously, PMID 31011167) were subjected to total RNA sequencing (not PolyA selected), and circRNA reads were detected using the pipeline CIRI2.

first: M

last: Walter

first: Srivatsan

last: Nonavinkere

first: T

last: Ahmed

first: L

last: Kristensen

first: E

last: Wedge


title: Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space

first: Garima

last: Chaturvedi


title: Effect of HPV E5 on tumor on immune response and tumor development

city: La Jolla

first: Sayuri

last: Miyauchi

address: 3855 Health Sciences Drive

institute: University of California, San Diego

summary: To investigate the functions of HPV16 E5, we established empty vector or HPV16 E5-transduced CAL-27 and DC2.4 cell lines. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells lines.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative gene expression profiling analysis of RNA-seq data for empty vector or HPV16 E5-expressing CAL-27 and DC2.4

first: Andrew

last: Sharabi


title: Comparative transcriptome analysis of periodontitis and peri-implantitis in the same subject

city: Yangsan-si

first: Yeongjoo

last: Kim

institute: Pusan National University

summary: This study included 20 participants (10 healthy subjects and 10 patients with periodontitis and peri-implantitis). Gingival tissue samples (10 healthy, 10 periodontitis, and 10 peri-implantitis tissues) were collected, RNAs were extracted, and RNA sequencing and analysis were performed.

overall_design: RNA-Seq in gingival tissue samples from healthy control and paired perodontal/peri-implantal case-overlapped patients

first: Jung-Min

last: Oh

first: Hyojae

last: Son

first: Yun

middle: H

first: Hyun-Joo


title: Association of SNPs in the PAI1 Gene with Disease Recurrence and Clinical Outcome in Bladder Cancer

first: Hideki

last: Furuya

address: 110 N. George Burns Road, Davis 2025

institute: Cedars Sinai Medical Center

summary: Bladder cancer is one of the most common cancer types worldwide and is characterized by a high rate of recurrence. Previous studies have demonstrated that plasminogen activator inhibi-tor-1 (PAI1) plays an important role in bladder cancer development. The aim of our retrospective study was to assess the effects of PAI1 mutational status in bladder tumors. In this study, we evaluated the mutational status of PAI1 in a series of independent cohorts, comprised of a total of 660 subjects. We identified two clinically relevant 3’ untranslated region (UTR) single nucleotide polymorphisms (SNPs) in PAI1. Caucasian patients with at least one of the SNPs had high risk of recurrence and shorter survival. Additional studies using cell lines demonstrated that one SNP increased the anti-apoptotic effect of PAI1, and another lose the control of cancer cellular growth. This study underscores the relevance and influence of these SNPs in bladder cancer.

overall_design: We transfected mock, PAI1 WT, or  PAI1 mutant plasmids in 2 human urothelial cell lines, and then performed microarray

first: Charles

last: Rosser


title: Multi-omics characterization of MEK inhibitor resistant pancreatic cancer based on a genetically engineered mouse model-derived in vitro system

city: Essen

first: Laura

last: Godfrey

address: Hufelandstraße 55

institute: DKTK Partner Site Essen/Düsseldorf

summary: Tumor heterogeneity and therapy resistance are hallmarks of pancreatic ductal adenocarcinoma (PDAC). Emerging evidence supports treatment-induced resistance to be a multifactorial process mediated by cellular plasticity involving epigenetic regulation. Here, we used a multi-omics approach to analyze in detail molecular mechanisms underlying MEK inhibitor (MEKi) resistance. Therefore, we characterized different cell stages (parental, MEKi resistant, reverted after different passages of drug withdrawal) in primary cell lines derived from a genetic PDAC mouse model, thereby minimizing inter-individual heterogeneity that could distort genome-wide analyses.

overall_design: RNA-sequencing of six primary murine pancreatic ductal adenocarcinoma cell lines. Three to four differrent cell stages (MEKi treatment naive, MEKi resistant, MEKi resistant and drug withdrawal for 5 or 12 passages) were analyzed

first: Jan

last: Forster

first: Sven-Thorsten

last: Liffers

first: Sven

last: Rahmann

first: Jens

last: Siveke


title: Human Adult Glial Progenitors Are Transcriptionally Distinct from Their Fetal Counterparts [scRNA-seq]

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

summary: Glial progenitor cells (GPCs), the primary source of oligodendrocytes and astrocytes in the human CNS, emerge during the 2nd trimester of human development and subsequently colonize the brain, where a pool remains throughout adulthood.  While fetal GPCs are highly migratory and proliferative, there is evidence that their capacities diminish throughout aging or as a result of demyelination-induced exhaustion, thus compromising their ability to mobilize, remyelinate, and self-renew.  To investigate this mechanism, we first utilized bulk and scRNA-Sequencing to characterize the human fetal GPC pool and leveraged these data to elucidate transcriptional discrepancies in adult human GPCs.  This revealed age-induced transcriptional shifts towards loss of proliferative competency and the potential onset of senescence. Further, we inferred adult networks of direct repressive transcription factor activity that may drive functional decline during GPC aging.  Finally, we coupled these data with miRNA profiling of both populations to establish both upstream and parallel arms of repression that may stifle the functional aptitude of aged GPCs.  These identified upstream regulators may be ideal therapeutic targets toward rejuvenating GPCs crippled by mitotic exhaustion or aging.

overall_design: Human brain samples were obtained under approved Institutional Review Board protocols from consenting patients at Strong Memorial Hospital at the University of Rochester.  Brain tissue was obtained from normal GW 18-24 cortical and/or VZ/SVZ dissections or adult white matter/cortex epileptic resections (18,19, and 27 years old for mRNA, 8, 20, 43, and 54 years old for miRNA).  Fetal GPC acquisition, dissociation and immunomagnetic sorting of A2B5+/PSA-NCAM- cells were as described (Windrem et al., 2004). GPCs were isolated from dissociated tissue using a dual immunomagnetic sorting strategy: depleting mouse anti-PSA-NCAM+ (Millipore, DSHB) cells, using microbead tagged rat anti-mouse IgM (Miltenyi Biotech), then selecting A2B5+ (clone 105; ATCC, Manassas, VA) cells from the PSA-NCAM- pool, as described (Windrem et al., 2004; Windrem et al., 2008). After sorting, cells were maintained for 1-14 days in DMEM-F12/N1 with 10 ng/ml bFGF and 20 ng/ml PDGF-AA. Alternatively  CD140a/PDGFRA-defined GPCs were isolated and sorted using MACS as described (Sim et al., 2011b), yielding an enriched population of CD140+ glial progenitor cells.

first: John

last: Mariani

first: Erin

middle: R

last: Kesel

first: Nguyen

middle: P

last: Huynh

first: Devin

last: Chandler-Militello

middle: A


title: Noninvasive neuromodulation protects against doxorubicin-induced cardiotoxicity and inhibits tumor growth

status: Public on Jan 28 2024

city: Wuhan

first: Mengjie

last: Xie

state: Hubei province

address: 99 Ziyang Road, Wuhan City, Hubei Province

institute: Wuhan University Renmin Hospital

summary: Doxorubicin (Dox) poses a considerable threat to patients owing to its cardiotoxicity, thus limiting its clinical utility. Optimal cardioprotective intervention strategies are needed to suppress tumor growth but also minimize cardiac side effects. Here, we showed that tVNS improved the imbalanced autonomic tone, ameliorated impaired cardiac function and fibrosis, attenuated myocyte apoptosis, and mitochondrial dysfunction compared to those in the Dox group. The beneficial effects were attenuated by methyllycaconitine citrate (MLA). The transcript profile revealed that there were 248 differentially expressed genes and the protection of tVNS and retardation of MLA were related to inflammatory response and NADPH oxidase activity. In addition, tVNS synergizing with Dox inhibited tumor growth and lung metastasis and promoted apoptosis of tumor cells in an anti-tumor immunity manner. These results indicated that non-invasive neuromodulation can play a dual role in preventing Dox-induced cardiotoxicity and suppressing tumor growth through inflammation and oxidative stress.

overall_design:
Dox group: treated with Dox
Dox+tVNS group: treat with Dox and tragus vagus nerve stimulation (tVNS)
MLA group: treat with Dox, tVNS and methyllycaconitine citrate(MLA)


title: A2B5 and CD140 sorted cells from human adult or fetal brain samples

summary: Cells were isolated from adult or fetal samples, using either A2B5 or CD140 as selection marker.

overall_design: Human mRNA was isolated from glial progenitor cells sorted on either A2B5 (adult WM from epileptic resection) or CD140a (fetal cortex, 19-20.1 week), with four biological replicates per group. cDNA was generated with the SMARTer Ultra Low RNA kit (Clontech), and libraries were created for sequencing with the NexteraXT DNA kit (Illumina). Sequencing was performed on an Illumina HiSeq 2500v4, with all samples in one batch. An average of about 30 million 100bp reads per sample were obtained after trimming and filtering reads with Trimmomatic. Reads were aligned to the human genome with STAR, read counts for genes were generated by Feature Counts, and differential expression analysis was performed with DESeq2.

first: Adam

last: Cornwell

first: Mikhail

last: Osipovitch

first: Fraser

last: Sim

first: Kuypers

last: Nicholas

first: Christopher

last: Wu

first: Line

last: Nilsson

first: Isabel

last: Pena

first: Sarah-Jehanne

last: Benraiss

first: Romane

last: Auvergne


title: Microarray analysis of gene expression in Pinus thunbergii to the pine wood nematode infection.

city: Hitachi

first: Tomonori

last: Hirao

state: Ibaraki

address: 3109-1 Ishi, Juo

department: Forest Bio-research Center

country: Japan

institute: Forest Tree Breeding Center, Forestry and Forest Products Research Institute

summary: Investigation of transcriptional changes, associated with infection-induced physiological changes in resistant or susceptible trees.

overall_design: Stem tissue of control samples and inoculated samples was collected 2 cm below the inoculated stem apex at 0, 1, 3, and 7 days post-inoculation (dpi) from biological repeats in resistant and susceptible trees (total 16 samples)

first: T

first: A

last: Watanabe


title: RNA-sequencing reveals signaling pathway associated with cell adhesion in Fam83h-mutated cells

first: Xueqing

last: Zheng

address: Luoyu Road

institute: Wuhan University

summary: Truncation mutations in family with sequence similarity, member H (FAM83H) gene cause autosomal dominant hypocalcified amelogenesis imperfecta (ADHCAI). The aim of this study was to explore the effects of truncated FAM83H on enamel development. High throughput RNA-sequencing was used to detect the dysregulated signaling pathways in Fam83h-mutated LS8 cells. According to mRNA-sequencing, pathway related to cell adhesion was the most notably clustered in Fam83h-mutated cells. Immunofluorescence analysis further revealed decreased protein expression of desmoglein 3, a component of desmosomes, in Fam83h-mutated cells.

overall_design: RNA-seq in the LS8 cell line before and after mutation of Fam83h (c.1186C > T, p.Q396*)

first: Yaling

last: Song


title: Injectable anti-inflammatory supramolecular nanofiber hydrogel to promote ranibizumab therapy in age-related macular degeneration treatment

city: Shanghai

first: huiqin

last: Gao

address: 639 Zhizao’ju Road

institute: Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai,

summary: The exact pathogenesis of age-related macular degeneration (AMD) leading to visual impairment and severe vision loss is still unclear, and the currently available treatments are often unsatisfactory. Previous studies have demonstrated both oxidative stress-induced damage to the retinal pigment epithelium (RPE) and inflammation are involved in AMD. Although anti-vascular endothelial growth factor (VEGF) therapy can impair the growth of new blood vessels, serious side effects were found with repeated monthly intravitreal injections. Here, an injectable hydrogel based on an anti-inflammatory betamethasone phosphate (BetP) drug (BetP-Gel) was designed to enable long-term efficient release of ranibizumab (RZB) to attenuate choroidal neovascularization (CNV), reduce vascular leakage and inhibit vascular proliferation in the retina, which significantly increased the effective treatment time of ranibizumab compared with that in clinical practice. In particular, experimental data with in vitro and in vivo models revealed that BetP-Gel itself had a strong ability to scavenge intracellular reactive oxygen species (ROS) and reduce tumour necrosis factor-α (TNF-α) as well as interleukin (IL-1β, IL-6, IL-8, and IL-18) inflammatory cytokines, inhibiting ROS- and inflammation-induced retinal damage. Altogether, the carrier-free system (RZB@BetP-Gel) could serve as a novel antioxidant, anti-inflammatory and anti-neovascularization agent for the treatment of AMD.

overall_design: BetP-Gel promote ranibizumab therapy in age-related macular degeneration treatment

first: Huiqin

first: Muchao

last: Chen

first: Zhuang

last: Liu

first: Ping

last: Gu


title: BMI1 is required for melanocyte stem cell maintenance and hair pigmentation

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: The epigenetic repressor BMI1 plays an integral role in promoting the self-renewal and proliferation of many adult stem cell populations, and also tumor types, primarily through silencing the Cdkn2a locus, which encodes the tumor suppressors p16Ink4a and p19Arf. However, in cutaneous melanoma, BMI1 drives epithelial-mesenchymal transition programs, and thus metastasis, while having little impact on proliferation or primary tumor growth. This raised questions about the requirement and role for BMI1 in melanocyte stem cell (MeSC) biology. Here, we demonstrate that murine melanocyte-specific Bmi1 deletion causes premature hair greying, which results from gradual MeSC loss. We establish that MeSC loss begins in the second hair cycle and is accompanied by melanocyte depletion. RNA-seq of MeSCs revealed that Bmi1 deletion induces transcriptional upregulation of p16Ink4a and p19Arf, mirroring the central role of BMI1 in other stem cell contexts. Additionally, the glutathione S-transferase enzymes Gsta1 and Gsta2 are downregulated by BMI1 loss, raising the possibility that MeSCs could be susceptible to oxidative stress. Accordingly, treatment with the antioxidant N-acetyl cysteine (NAC) partially rescued melanocyte expansion. Together, our data establish a critical role for BMI1 in MeSC maintenance that reflect a partial role for suppression of oxidative stress, and likely transcriptional repression of Cdkn2a.

overall_design: Four replicates of melanocyte stem cells with targeted disruption of Bmi1 compared with four replicates of wild-type melanocyte stem cells .

first: Molly

last: Wilson

first: Paul

last: Danielian

first: Roberta

last: Ferretti

first: Jacqueline

last: Lees


title: Effect of phox2a knockout on the molecular profiles of hindbrain vestibular neurons in the larval zebrafish (bulk RNA-Seq)

status: Public on Jan 27 2024

city: New York

first: David

last: Schoppik

address: 435 E 30th St

department: Neuroscience Institute

institute: New York University Grossman School of Medicine

summary: Sensorimotor reflex circuits engage distinct neuronal subtypes, defined by precise connectivity, to transform sensation into compensatory behavior. Whether and how motor partner populations shape the subtype fate and connectivity of their pre-motor counterparts remains controversial. Here, we discovered that motor partners are dispensable for proper connectivity across an entire vestibular reflex circuit that stabilizes gaze. We first measured activity following vestibular sensation in pre-motor projection neurons after constitutive loss of their extraocular motor neuron partners.We observed normal responses and topography consistent with unchanged functional connectivity between sensory neurons and projection neurons. Next, we show that projection neurons remain anatomically and molecularly poised to connect appropriately with their motor partners. Lastly, we show that the transcriptional signatures of projection neuron subtypes develop independently of motor partners. Our findings comprehensively overturn a long-standing model: that connectivity in the circuit for gaze stabilization is retrogradely determined by motor partner-derived signals. By defining the contribution of motor neurons to canonical sensorimotor circuit assembly, our work speaks to comparable processes in spinal circuits and advances our understanding of general principles of neural development.

overall_design: Hindbrain vestibular neurons, labeled by Tg(-6.7Tru.Hcrtr2:GAL4-VP16);Tg(UAS:E1b-Kaede), harvested from zebrafish embryos between 72-74 hpf. Embyros were from two conditions: larvae from a stable line of phox2a-/- mutants, and sibling controls (phox2a+/+ or +/-). Fluorescent neurons were isolated by fluorescence activated cell sorting (FACS) according to Kaede fluorescence. Four experimental repeats were performed, each generating two samples (phox2a-/- and sibling control). Bulk RNA sequencing was performed.

first: Dena

last: Goldblatt

first: Basak

last: Rosti

first: Kyla

last: Hamling

first: Paige

last: Leary

first: Harsh

last: Panchal

first: Marlyn

last: Li

first: Hannah

last: Gelnaw

first: Stephanie

last: Huang

first: Cheryl

last: Quainoo


title: Molecular characterization of hindbrain vestibular neurons in the larval zebrafish (scRNA-Seq)

summary: The molecular logic that specifies and assembles closely-related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate, topography, and circuit assembly. We used single-cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely-related subtypes into functional circuits.

overall_design: Hindbrain vestibular neurons, labeled by Tg(-6.7Tru.Hcrtr2:GAL4-VP16);Tg(UAS:E1b-Kaede), harvested from zebrafish embryos between 72-74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting (FACS) according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or after a previously identified "midpoint" in hindbrain vestibular neuron development (36 hpf), labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.


title: RNA sequencing of cortical neurons from Kat6b deficient mouse foetuses

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary:
The RNA sequencing data are part of a study reporting and investigating a mouse model of the Say-Barber-Biesecker-Young-Simpson (SBBYS) syndrome (OMIM:603736) and demonstrating proof-of-principle efficacy of postnatal treatment with sodium valproate (VPA) or acetyl-carnitine (ALCAR). The KAT6B gene encodes a histone lysine acetyltransferase. The RNA sequencing experiments identified genes that are differentially  expressed between Vehicle treated Kat6b+/– and Kat6b+/+ cortical neurons and the subset genes that are restored to normal expression after treatment with ALCAR or VPA.
Cortical neurons were isolated from four Kat6b+/– and four Kat6b+/+ E16.5 mouse cerebral cortex. Cells from each cortical neuron isolate were cultured with 1 mM ALCAR, 1 mM VPA or untreated medium (Vehicle) for 4 days.

overall_design: There were n=4 mice of each genotype, Kat6b+/–  (Dec/+) or Kat6b+/+ (wild type - WT). Neurons from each mice were subject to three treatments (ALCAR, VPA or vehicle). Each RNA library sample was sequenced twice (as identified by the date, 300823 or 080923 on the data files) to increase sequencing depth. These are pure technical replicates and were combined in the analysis. Differential analyses were performed indepently for the ALCAR/Vehicle and VPA/Vehicle sample groups, identifying differentially expressed genes between the various treatment/genotype group combinations.

first: Gordon

middle: K

last: Smyth

first: Anne

last: Voss

first: Maria

middle: I

last: Bergamasco

first: Tim

last: Thomas


title: The Tec family kinase Itk is not required for Th17 responses during Hypersensitivity pneumonitis

city: Ithaca

first: Avery

last: August

address: 930 Campus Road

institute: Cornell University

summary: IL-2 inducible tyrosine kinase (Itk) is a Tec family non-receptor tyrosine kinase that is known to regulate T-helper cell differentiation and function. It has been established that Itk postively regulates T helper 17 cells.  However, in a model of hypersensitivity pneumonitis we found T helper 17 cells develop independently of Itk.  Therefore, we compared the transcriptomes of WT and Itk-/- T helper 17 cells following exposure with Saccharopolyspora rectivirgula by RNA sequencing.

overall_design: Th17 cells were isolated from the lungs of 4-6 week old male and female WT and Itk-/-  IL17-GFP/Foxp3-RFP mice using flow sorting.

first: Jessica

last: Elmore

first: Weishan


title: Revealing the Grammar of Small RNA Secretion Using Interpretable Machine Learning II

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

summary: Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes. However, the mechanisms that govern their sorting and secretion are still not well understood. In this study, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequence. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis, and confirmed that primary RNA sequence is a major determinant in small RNA secretion. Additionally, we used ExoGRU to reveal cis and trans factors that underlie small RNA secretion, including known and novel RNA-binding proteins, e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. We used exoCLIP to reveal the RNA interactome of HNRNPA2B1 and RBM24 in extracellular vesicles. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into complex processes such as small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications.

overall_design: Using a machine learning model to dissect the primary sequences and structural features of small RNAs in the extracellular and intracellular compartments.

first: Bahar

last: Zirak

first: Mohsen

last: Naghipourfar

first: Ali

last: Saberi

first: Delaram

last: Pouyabahar

first: Amirhossein

last: Zarezadeh

first: Lixi

last: Luo

first: Lisa

last: Fish

first: Doowon

last: Huh

last: Sharifi-Zarchi


title: CD38-directed, single-chain T cell-engager targets leukemia stem cells through IFNγ-induced CD38 expression [bulkRNAseq]

city: Duarte

first: Mariam

last: Murtadha

address: 1500 E. Duarte Rd

institute: City of Hope

summary: Treatment resistance of leukemia stem cells (LSCs) and suppression of the autologous immune system represent major challenges to achieve a cure in acute myeloid leukemia (AML). Although AML blasts generally retain high levels of surface CD38 (CD38pos), LSCs are frequently enriched in the CD34posCD38neg blast fraction. Here, we report that IFNγ reduces LSCs clonogenic activity and induces CD38 upregulation in both CD38pos and CD38neg LSC-enriched blasts. IFNγ-induced CD38 upregulation depends on IRF-1 transcriptional activation of the CD38 promoter. To leverage this observation, we created a novel compact, single-chain CD38-CD3 T cell engager (BN-CD38) designed to promote an effective immunological synapse between both CD8 and CD4 T cells and CD38pos AML cells. We demonstrate that BN-CD38 engages autologous CD4pos and CD8pos T cells and CD38pos AML blasts leading to T cell activation and expansion and to the elimination of leukemia cells in an autologous setting. Importantly, BN-CD38 engagement induces the release of high levels of IFNγ, driving the expression of CD38 on CD34posCD38neg LSC-enriched blasts and their subsequent elimination. Critically, while BN-CD38 showed significant in vivo efficacy across multiple disseminated AML cell lines and patient derived xenograft models, it did not affect normal hematopoietic stem cell clonogenicity and the development of multi-lineage human immune cells in CD34pos humanized mice. Taken together, this study provides important insights to target and eliminate AML LSCs.

overall_design: CD34pos cells were isolated from BM-MNCs from 3 AML relapsed patients using CD34 MicroBead Kit and were either treated with vehicle or IFNγ at a concentration of 10 ng/ml overnight.  RNA was extracted and subjected to bulk RNA seq.

first: Flavia

last: Pichiorri

first: John

last: Williams

first: Guido

last: Marcucci

first: Alex

last: Pozhitkov


title: CD38-directed, single-chain T cell-engager targets leukemia stem cells through IFNγ-induced CD38 expression [scRNAseq]

overall_design: AML BM-MNCs were thawed and suspended in 20% FBS IMDM medium. One million MNCs were plated per well in 24-well plates and either treated with IFNγ at 10 ng/ml for 5 hours or vehicle as a control. At 5 hours, cells were collected and processed using the 10x Genomics Chromium Controller and the Chromium Single Cell 3′ Library & Gel Bead Kit (PN-120237) following the standard manufacturer’s protocol.


title: Effects of gene-by-environment interaction on the mRNA profile in the light of differential susceptibility

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary:
Purpose: Investigation of effects of early adversity in mice deficient for serotonin transporter on mRNA expression in the context of differential susceptibility
Methods: Following prenatal stress and behavioural screening in adulthood, month old females, either wildtype or carrying a heterozygous knockout of the serotonin transporter gene, were sacrificed, brains extracted, the hippocampi of both hemispheres dissected, blended and separated in two protions. From one of these portions RNA was extracted. Extracted RNA was further processed by an external company, i.e. IGA Technologies (Udine, Italy). Following library preparation, samples were sequenced on the illumina HiSeq2000 platform (single end, 50 bp, 30 million reads/sample). Reads were mapped to the Mus musculus GRCm38.p5 genome using STAR (Dobin et al. 2013). Following mapping, the reads per position were determined using HTSeq (Anders et al. 2015). These counts were then used for the analysis of differentially expressed genes (DEGs) using the R package DeSeq2 (Love et al. 2014).
Results: dependent on the serotonin transporter genotype and behaviourally determined susceptibility to early life adversity, animals displayed distinct gene expression. As expected, the effect sizes and significances were rather subtle.
Conclusion: the modulation of differential susceptibility seems to be modulated by distinct mRNA expression profiles, dependent on the serotonin transporter genotype

overall_design:
RNA expression affected in serotonin transporter deficient or wildtype offspring of prenatal stress that do or do  not succumb to the adverse effects of prenatal stress, i.e. vulnerable or resilient offspring
[contributor] IGA Technologies (Undine, Italy)

first: K

last: Lesch

first: D

last: van den Hove

first: M

last: Weidner

middle: U

first: L

last: Eijjsen