title: AoRab7A interacts with AoVps35 and AoVps41 to regulate vacuole assembly, trap formation, conidiation, and functions of proteasomes and ribosomes in Arthrobotrys oligospora

city: Kunming

first: xuewei

last: yang

address: Chenggong Campus,Yunnan University,Dongwaihuan South Road

institute: Yunnan University

summary: Rab GTPases regulate vesicle trafficking in organisms and play crucial roles in growth and development. Arthrobotrys oligospora is a representative species of nematode-trapping (NT) fungi, it can produce trapping devices for nematode predation. Our previous study found that deletion of Aorab7A abolished the trap formation and sporulation. Here, we investigated the regulatory mechanism of AoRab7A using transcriptomic, biochemical, and phenotypic comparisons. Transcriptome analysis, yeast library screening, and Y2H assays identified two vacuolar protein sorting (Vps) proteins, AoVps41 and AoVps35, as putative targets of AoRab7A. The deletion of Aovps41 and Aovps35 caused considerable defects in multiple phenotypic traits. We further found a close connection between AoRab7A, homotypic fusion, vacuolar protein sorting, and the retromer involved in vesicle-vacuole fusion, which triggered vacuolar fragmentation. Further transcriptome analysis showed that AoRab7A and AoVps35 play essential roles in many cellular processes and components including proteasomes, autophagy, fatty acid degradation, and ribosomes in A. oligospora. Furthermore, we verified that AoRab7A, AoVps41, and AoVps35 are involved in ribosome and proteasome functions. The absence of these proteins inhibited the biosynthesis of nascent proteins and enhanced ubiquitination. Our findings suggest that AoRab7A can interact with AoVps41 and AoVps35 to mediate vacuolar fusion and influence lipid droplet accumulation, autophagy, stress response, and secondary metabolism. These proteins are especially required for the conidiation and trap development of A. oligospora

overall_design: RNA-seq analysis between six wild-type samples and six mutant samples, with three biological replicates per sample, and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Yingmei

last: Zhu

first: Xuewei

last: Bai

first: Qianqian

last: Liu

first: Jinkui


title: Bulk RNA sequencing of total lung cells from 14 dpi of high-dose mtb on Atg14f/f and Atg14f/f-LysM-cre mice.

status: Public on Oct 13 2023

city: Beijing

first: Siwei

last: Feng

address: No.30,Shuangqing street

country: China

institute: Siwei Feng

type: Expression profiling by high throughput sequencing

summary: We found that several autophagy genes in myeloid cells are required to protect against high-dose Mtb (~1000cfu) infection. To understand the immune cell population in these mice after high-dose Mtb infection and what may contribute to the susceptibility, we did bulk RNAseq on mice infected with high-dose of Mtb strain Erdman.

overall_design: Lung cells from 14 dpi of high-dose mtb on Atg14f/f and Atg14f/f-LysM-cre mice. Cells pooled from 4 mice each, age 8-10 wks


title: Functional interrogation of twenty Type 2 Diabetes-associated genes using isogenic hESC-derived β-like cells [RNA-Seq]

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

country: USA

institute: Weill Cornell Medical College

summary: Genetic studies have identified numerous loci associated with type 2 diabetes (T2D), but the functional role of many loci has remained unexplored. In this study, we engineered isogenic knockout human embryonic stem cell (hESC) lines for 20 genes associated with T2D risk. We systematically examined β-cell differentiation, insulin production and secretion, and survival. We performed RNA-seq and ATAC-seq on hESC-β cells from each knockout line. Analyses of T2D GWAS signals overlapping with HNF4A-dependent ATAC peaks identified a specific SNP as a likely causal variant. In addition, we performed integrative association analyses and identified four genes (CP, RNASE1, PCSK1N and GSTA2) associated with insulin production, and two genes (TAGLN3 and DHRS2) associated with sensitivity to lipotoxicity. Finally, we leveraged deep ATAC-seq read coverage to assess allele-specific imbalance at variants heterozygous in the parental hESC line, to identify a single likely functional variant at each of 23 T2D GWAS signals.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for beta-like cells derived from WT hESC and its KO derivatives with knockout of 20 T2D associated genes

first: Dongxiang

last: Xue

first: Narisu

last: Narisu

first: D

middle: L

last: Taylor

first: Meili

last: Zhang

first: Caleb

last: Grenko

first: Michael

middle: R

last: Erdos

first: Lori

last: Bonnycastle

first: Tingfen

last: Yan

first: Neelam

last: Sinha

first: Francis

middle: S

last: Collins


title: Functional interrogation of twenty Type 2 Diabetes-associated genes using isogenic hESC-derived β-like cells [WGS]

first: Amy

middle: J

last: Swift


title: Functional interrogation of twenty Type 2 Diabetes-associated genes using isogenic hESC-derived β-like cells [ATAC-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing


title: The molecular mechanism of microtubule-binding protein CEP20 in regulating invasion and metastasis of non-small cell lung cancer

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: No. 3, Qingchun East Rd

department: Sir Run Run Shaw Hospital

institute: Zhejiang University

summary: Lung cancer is the leading cause of cancer-related death and poses a direct health threat in our country. Non-small cell lung cancer (NSCLC) represents the majority of lung cancer. Difficulty in early diagnosis and metastasis are the major cause of death of NSCLC patients. However, the molecular mechanism of NSCLC cell invasion and metastasis still remain unclear. So looking for new diagnosis methods and explore the key genes of metastasis are still priority in the field of NSCLC research. The microtubule and microtubule associated proteins have closely relationship with the development of cancer. According to the bioinformatics by using the public database and clinical NSCLC tumor samples, our accumulated evidences indicate that the expression of CEP20 is higher in NSCLC tissues. Patients with high CEP20 expression level associate with cancer invasion, metastasis and show low five-year survival rate. Based on these new findings, this project aims to study the regulation of CEP20 in microtubule dynamics in cell migration, and discover the molecular mechanism of FOR20 in regulating NSCLC cell invasion and metastasis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A549 cells and its KD derivatives (siCEP20, siCTR).

first: Sijie


title: Mapping cardiac remodeling in chronic Heart disease

city: Aachen

first: Mingbo

last: Cheng

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: Uniklinik RWTH Aachen

summary: we performed single nuclear RNA-sequencing of left ventricular nuclei from two murine models of cardio-renal disease using SV129 mice. We validated data using inducible genetic fate tracing combined with single cell RNA-sequencing as well as immunostaining and cell-culture models

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Male 129S2/SV mice (n=7) were obtained from Envigo and used 6-8 weeks old. Mice were group-housed and provided with ad lib access to water and standard chow, as well as environmental enrichment. A 12-hour light-dark cycle was maintained. During the study, mice were weighed weekly and had their condition recorded. ARRIVE guidelines were adhered to.  Animals were randomised to receive sham or subtotal nephrectomy surgery (STNx) using a random number generator website (random.org)  For sham surgery, animals had bilateral flank incisions and both kidneys isolated and manipulated. At 10 weeks animals had a timed overnight urine collection then were culled by an approved schedule 1 method and terminal blood sample obtained  (Figure 1a). For all animals tibia length was recorded. Urine and serum were analysed by in-house biochemical analysis service (surf.ed.ac.uk/facilities/specialist-assay-service/).      Six 129S2/SvPasOrlRJ wildtype male mice underwent ischemia reperfusion injury (IRI) plus uninephrectomy at the age of 11-12 weeks and were housed for 21 more weeks。 Mice were anesthetized with ketamine/xylazine (120/16 mg/kg body weight) and after disinfection, flanks were incised, the right kidney was clamped for 26min and the contralateral kidney was fully removed. Mice received buprenorphine for three more days (0.1mg/kg) to achieve analgesia. For genetic fate tracing of Gli1+ cells, we bred bigenic Gli1CreER;tdTomato using Gli1tm3(re/ERT2)Alj/J, JAX Stock #007913 and Rosa26tdTomato (i.e., B6-Cg-Gt(ROSA)26Sorttm(CAG-tdTomato)Hze/J    JAX Stock # 007909) mice. 6-7 week old male mice (n=7) received 3x 2 mg tamoxifen in corn oil with 3% ethanol via intraperitoneal injection to induce recombination, and underwent the unilateral IRI plus contralateral nephrectomy surgery at 21 days after the last tamoxifen dose. Mice were killed 21 weeks after surgery and the left ventricle was snap frozen in liquid nitrogen and transferred to -80°C. Serum urea was measured by clinically laboratory routine (Vitros 250, Ortho Clinical Diagnostics, Institut für Versuschtierkunde, Aachen). Heart weights were recorded (Sartorius 2007 MP, Germany) and normalized to tibia length, measured by a caliper (Forum, Germany).  Animal experiment protocols were approved by the LANUV-NRW, Germany and by the UK Home Office Regulations. All animal experiments were carried out in accordance with their guidelines.

first: Nadine

last: Kaesler

first: James

last: Nagai

first: Ivan

last: Costa

first: Rafael

last: Kramann


title: Genome wide CRISPR screen for BET inhibitor resisatnce in OCI-AML2 cells using Y. Kosuke library

city: Portland

first: Jeffrey

last: Tyner

state: OR

address: KR-HEM, 3181 SW Sam Jackson Park Road

institute: Oregon Health & Science University

summary: OCI-AML2 BETi-naive or JQ1 resistant cells were infected with CRISPR/Cas9 library, selected for puromycin resistance for integration events and exposed to JQ1/CPI-0610  or vehicle, DMSO, at 200nanoMolar for JQ1 and 500nanoMolar CPI-0610 concentrations.  Cells were collected at time 0 (post puromycin selection), day 14 JQ1 and 21 CPI-0610 , DNA was extracted and sgRNA barcodes were amplified. PCR library was deep sequenced using highthroughput Illumina platform Hiseq using 6 samples per lane.

overall_design: Performed comparisons of sgRNA read counts between DMSO and BETi (JQ1 or CPI-0610)  treated cells at corresponding time points.

first: Tamilla

last: Nechiporuk

first: Daniel

last: Bottomly

first: Kyle

last: Romine

first: Shannon

last: McWeeney


title: DNA methylation alternations in the offspring pancreatic tissue from hyperglycemic dams

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

type: Methylation profiling by genome tiling array

summary: Maternal hyperglycemia may disturb susceptibility in offspring. Pancreatic tissue from maternal hyperglycemia has CpG sites that exhibit differential DNA methylationregulated compared to control.

overall_design: We performed DNA methylation array analyses of offspring pancreatic tissue from hyperglycemic dams and control dams (n=3 per group).

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Tong

last: Wang

first: Xiaojing


title: Lamin A upregulation reorganizes the genome during rod photoreceptor degeneration

status: Public on Oct 12 2023

city: Ottawa

first: Pierre

last: Mattar

state: ON

address: CCW6109, Box 511, 501 Smyth Rd.

country: Canada

institute: OHRI

summary: Two proteins have previously been shown to be necessary and sufficient to tether heterochromatin at the nuclear envelope. The lamin B receptor (Lbr) is expressed during development, but downregulates upon rod differentiation. A second tether is the intermediate filament lamin A (LA), which is not normally expressed in murine rods.To determine how heterochromatin tethering affects the genome, we used in vivo electroporation to misexpress LA or Lbr in mature rods in the absence of degeneration, resulting in the restoration of conventional nuclear architecture. Using scRNA-seq, we show that reorganizing the nucleus via LA/Lbr misexpression has only minor effects on rod gene expression. Next, using ATAC-seq, we show that LA and Lbr similarly increase genome accessibility. Novel ATAC-seq peaks tended to distal to genes, but some peaks were associated with stress-responsive genes. Together, our data reveal that heterochromatin tethers have a global effect on genome accessibility, and suggest that LA –dependent genome reconfiguration might contribute to the stress response of rod photoreceptors.

overall_design: Control, lamin A, or Lbr expression plasmids were transfected into retinal progenitor cells in vivo at P0.  After ~8 weeks, retinas were harvested and dissociated using Accutase. Cells were sorted via flow cytometry using reporter gene expression and Dapi exclusion to gate viable, transfected cells. For ATAC-seq experiments, we utilized a rod-specific reporter plasmid (pRho2.2-DsRed) to mark rods specifically. ATAC-seq data were generated from FACs sorted rods following Buenrostro et al. (PMID: 25559105). Briefly, 50 000 flow sorted cells were lysed in cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Lysed nuclei were tagmented using 6.5 µl of TDE1 transposase from the Nextera DNA Flex Library kit (Illumina). Samples were purified using Zymo-Spin IC columns (Zymo), and libraries constructed according to the Nextera workflow. Libraries were cleaned up using the AMPure XP kit (Beckman Coulter). PE 150 sequencing was performed using the NextSeq 500 platform to a read-depth of 25-35 million reads per sample.  Data were processed using the Galaxy platform. Fastq files were processed with Fastq Groomer, Trimmomatic, and mapped to the mm10 genome using Bowtie2. We used Macs2 to call narrowpeaks.

first: Ivana

last: Herrera

first: José

middle: A

last: Fernandes


title: Transcriptome sequencing identifies tuberous root development related genes in sweet potato

city: Xuzhou

first: Jiahao

last: Zhu

address: Shanghai Road 101

institute: Jiangsu Normal University

summary: To screen genes related to the development of sweet potato tuberous roots, the high throughput sequencing of different stages of sweet potato tuberous roots was performed. The fibrous roots (FR; roots at 20 dap), developing tuberous roots (DR; roots at 60 dap) and mature tuberous roots (MR; roots at 120 dap) of Ipomoea batatas (L.) Taizhong 6 and MBP3 overexpressed lines were used for transcriptome analysis. Totally, we identified 5488 differentially expressed genes between different stage tuberous roots of Taizhong6 and 14312 differentially expressed genes between the tuberous roots of Taizhong6 and MBP3 overexpressed lines, by calculating the gene FPKM in each sample and conducting differential gene analysis. This study provides a foundation for the mechanism analysis of sweet potato tuberous root development.

overall_design:
The Ipomoea batatas (L.) Taizhong 6 and MBP3 overexpressed plants were planted in a greenhouse at Jiangsu Normal University. The fibrous roots (FR; roots at 20 dap), developing tuberous roots (DR; roots at 60 dap) and mature tuberous roots (MR; roots at 120 dap) of Taizhong 6 were collected and used for RNA extraction and transcriptome analysis.
To screen tuberous root formation- and development-related  genes, transcriptome sequencing of sweet potato roots in different periods (FR, DR and MR) was performed.


title: Chemoproteomic capture of RNA binding activity in living cells

city: Charlottesville

first: Dina

last: Bai

state: VA

address: McCormick Rd.

department: Chemistry

institute: University of Virginia

summary: Proteomic methods for RNA interactome capture (RIC) rely principally on crosslinking native or labeled cellular RNA to enrich and investigate RNA-binding protein (RBP) composition and function in cells. The ability to measure RBP activity at individual binding sites by RIC, however, has been more challenging due to the heterogenous nature of peptide adducts derived from the RNA-protein crosslinked site. Here, we present an orthogonal strategy that utilizes clickable electrophilic purines to directly quantify protein-RNA interactions on proteins through photoaffinity competition with 4-thiouridine (4SU)-labeled RNA in cells. Our photo-activatable-competition and chemoproteomic enrichment (PACCE) method facilitated detection of >5,500 cysteine sites across ~3,000 proteins displaying RNA-sensitive alterations in probe binding. Importantly, PACCE enabled functional profiling of canonical RNA-binding domains as well as discovery of moonlighting RNA binding activity in the human proteome. Collectively, we present a chemoproteomic platform for global quantification of protein-RNA binding activity in living cells.

overall_design:
Transcriptome of HEK293T was monitored for changes as the result of 4-thiouridine treatment (4SU, 16 hr, 37 C, 100uM), clickable electrophilic purine  (CEP, 1 hr, 37 C, 25 uM) treatment and a combination of both treatments.
We then performed gene expression profiling of three indepdent replicates in a single cell line.

first: Andrew

last: Heindel

first: Jeffrey

middle: W

last: Brulet

first: Xiantao

first: Michael

last: Founds

first: Adam

middle: H

last: Libby

middle: C

last: Lemke

first: David

middle: M

last: Leace

first: Thurl

middle: E

last: Harris

first: Markus

last: Hafner

first: Ku-Lung

last: Hsu


title: Single-cell RNA sequencing reveals a hierarchical transcriptional regulatory network of terpenoid biosynthesis in cotton secretory glandular cells

city: Shanghai

first: Longxian

last: Chen

address: 300 Fenglin Road

institute: CAS Center for Excellence in Molecular Plant Sciences

summary: Plants can synthesize a wide range of terpenoids in response to various environmental cues. However, the specific regulatory mechanisms governing terpenoid biosynthesis at the cellular level remain largely elusive. Herein, we employed single-cell RNA sequencing (scRNA-seq) to comprehensively characterize the transcriptome profile of cotton leaves and established a hierarchical transcriptional network regulating cell-specific terpenoid production.

overall_design: Gene expression profiling of scRNA-seq data from cotton leaves

first: J

middle: Q

last: Huang


title: Single-cell RNAseq of control and COMT-KO glioma tumors in mice.

city: Durham

first: Meng

last: Jiao

address: 905 S lasalle St

institute: Duke University

summary: Next-generation sequencing (NGS)-derived transcriptomic profiling was carried out to compare the transcriptomic changes mediated by COMT knockout CT2A glioblastoma tumors using an orthotopic mouse model.

overall_design: Here, we collected 7 control glioma tumor samples on Day 12 and 3 COMT-KO samples on Day 12 and 3 samples on Day 25 from mouse brains. CD45 positive immune cells were sorted and subjected for single-cell RNAseq. Individual samples were labeled with single-cell mutiplexing anitbodies and pooled for sequencing.

first: Chen

last: Yu

first: Sejiro

last: Littleton

first: Chuan-yuan

last: Li


title: To investigate the effects of NRF2 inhibitors (pyrimethamine and mitoxantrone) on mRNA expression in a human esophageal squamous cell carcinoma cell line (KYSE70 cells)

city: Camden

first: Xiaoxin

middle: Luke

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

summary: To study the effects of NRF2 inhibitors (pyrimethamine or mitoxantrone) on human esophageal squamous cell carcinoma cells.

overall_design: 10 µM pyrimethamine or 20 nM mitoxantrone vs. control for 72 h.

first: Chorlada

last: Paiboonrungruang

first: Zhaohui

last: Xiong


title: To investigate the effects of NRF2 inhibitors (pyrimethamine) on mRNA expression in mouse esophageal epithelium.

summary: To study the effects of NRF2 inhibitors (pyrimethamine) on mRNA expression in mouse esophageal epithelium.

overall_design: PYR was administered after tamoxifen induction, then esophageal epithelium were harvested when the mice were sacrificed at Week 3.


title: HMGB2 is important for liver regeneration through transient accumulation of lipid droplets in hepatocytes

status: Public on Oct 14 2023

city: Miyazaki

first: Narantsog

last: Choijookhuu

state: Miyazaki

address: Kiyotake

department: Anatomy

country: Japan

institute: University of Miyazaki

summary: Liver regeneration is an well orchestrated compensatory process that regulated by multiple factors. We recently reported the importance of chromatin protein, a high-mobility group box 2 (HMGB2) in mouse liver regeneration, however, it’s molecular mechanism is not yet understood. In this study, we aimed to study how HMGB2 regulates hepatocyte proliferation during liver regeneration.   Wild-type (WT) and HMGB2-knockout (KO) mice were 70% partial hepatectomized (PHx), and liver tissues were analyzed by microarray, immunohistochemistry, qPCR and western blotting. In vivo experimental findings were confirmed by in vitro experiments using HMGB2 gene knockdown in combination with de novo lipogenesis model. In WT mouse, HMGB2-positive hepatocytes were co-localized with cell proliferation markers, whereas, hepatocyte proliferation was significantly decreased in HMGB2-KO mice. Oil red-O staining detected the transient accumulation of lipid droplets at 12-24 h in WT mouse livers, however, decreased amount of lipid droplets were found in HMGB2-KO mouse livers, and it was prolonged until 36 h. Microarray, immunohistochemistry and qPCR results were demonstrated that lipid metabolism related genes were significantly decreased in HMGB2-KO mouse livers. In vitro experiments demonstrated that decreased lipid droplets in HMGB2-knockdown cells correlated with decreased cell proliferation activity. HMGB2 is involved in the regulation of liver regeneration through transient accumulation of lipid droplets in hepatocytes.

overall_design: Microarray analysis was used to screen for genes that are related to HMGB2 expression. RNA was isolated from WT and HMGB2-KO mouse livers (n = 3 each), and cRNA was prepared. cRNA from each sample was hybridized to a pre-equilibrated Clariom S mouse microarray chip, which was then washed, stained, and scanned in an HP ChipScanner (Affymetrix Inc., Santa Clara, USA).


title: Expression data changes induced by one round migration through 3 μm pores in T-ALL cells

city: Madrid

first: Javier

last: Redondo-Muñoz

address: C/ Ramiro de Maeztu 9

country: Spain

institute: Centro de Investigaciones Biológicas Margarita Salas - CSIC

summary: One round migration through 3 μm pores promotes changes in transcription of T-ALL cells

overall_design: Jurkat cells were maintained in culture in RPMI 1640 medium with L-glutamine and 125 mM HEPES (Sigma Aldrich, St. Louis, MO, USA) and 10% fetal bovine serum, FBS (Sigma-Aldrich) and maintained in 5% CO2 and 37ºC. Jurkat cells were allowed to migrate across 3 μm transwell inserts for 24h. Control (non-migrated cells) and one-round migration (ORM) cells were collected from the bottom chamber of Transwell inserts (Corning Costar, 6.5 mm diameter, 3 μm pore size) after 24h. Cells were lysed and mRNA was isolated and hybridized on Affymetrix microarrays to compare expression profiles. We used 2 replicates of each sample.

first: Ana

last: de Lope-Planelles

first: Raquel

last: González-Novo

first: Elena

last: Madrazo

first: Gracia

last: Peralta

first: María

middle: P

last: Cruz

first: Héctor

last: Zamora

first: Verónica

last: Torrano

first: Horacio

last: López

first: Pedro

last: Roda

first: Francisco

last: Monroy


title: CDK4/6i enhances the antitumor effect of PD1 antibody by promoting TLS formation in ovarian cancer

city: Xian

first: Wangyou

last: Feng

address: 169 Changle Western Road

institute: Air Force Medical University

summary: Ovarian cancer is insensitive to immunotherapy and has a high mortality rate. CDK4/6 inhibitors (CDK4/6i) regulate the tumor microenvironment and play an antitumor role. Our previous research demonstrated that lymphocyte aggregation (tertiary lymphoid structures, TLS) was observed after CDK4/6i treatment. This may explain the synergistic action of CDK4/6i with the anti-PD1 antibody. However, the key mechanism by which CDK4/6i promotes TLS formation has not been elucidated. We examine the link between TLS and prognosis. Animal models and high-throughput sequencing were used to explore the potential mechanism by which CDK4/6i promotes TLS formation. Our results showed the presence of TLSs was associated with a favorable prognosis for ovarian cancer. CDK4/6i promoted TLS formation and enhanced the immunotherapeutic effect of the anti-PD1 antibody. The potential mechanism of CDK4/6i affecting the formation of TLS may be through modulating SCD1 and its regulatory molecules ATF3 and CCL4. Our findings provide a theoretical basis for the application of CDK4/6i in ovarian cancer.

overall_design: After the mouse ovarian cancer model was established and treated with PBS, CDK4/6i, PD-1 antibody and combination therapy, the tumor tissue was taken for sequencing afterwards

first: Dongbo

last: Jiang

first: Hong

last: Yang

first: Jia


title: ATAC-seq of murine splenic B cell populations

first: Ashley

middle: Stephen

last: Doane

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: ATAC-seq in murine naive B cells, germinal center B cells, and total B cells stimulated with LPS ex vivo and transduced with empty vector or Ocab (Pou2af1) expression vector.

overall_design: Naïve and germinal center B cell populations were isolated by FACS from mouse splenocytes.  Splenic total B cells were stimualted by LPS and transduced with empty vector or Ocab expression vector.


title: Enhancing glioblastoma radiotherapy by COMT inhibition

first: Meng

last: Jiao

summary: Next-generation sequencing (NGS)-derived transcriptomic profiling was carried out to compare the transcriptomic changes mediated by COMT knockout in U87 cells. We found significant enrichment of gene signatures involving IFNa/b signaling in COMT-KO U87 cells compared to control cells. Our analysis also demonstrated that COMT deficiency interferes with mitochondrial functions and induces the expression of genes associated with the anti-viral RNA sensing pathway.

overall_design: mRNA expression profiles of control and COMT-KO U87 cells.

first: Xuhui

last: Bao

first: Chuan-Yuan

last: Li


title: RNA sequencing of peripheral blood in amyotrophic lateral sclerosis reveals distinct molecular subtypes: considerations for biomarker discovery

city: Sydney

first: Kelly

last: Williams

state: NSW

address: 75 Talavera Road

department: Motor Neuron Disease Centre

country: Australia

institute: Macquarie University

summary: Aim: Amyotrophic lateral sclerosis (ALS) is a heterogeneous neurodegenerative disease with limited therapeutic options. A key factor limiting the development of effective therapeutics is the lack of disease biomarkers. We sought to assess whether biomarkers for diagnosis, prognosis or cohort stratification could be identified by RNA sequencing (RNA-seq) of ALS patient peripheral blood. Methods: Whole blood RNA-seq data were generated for 96 Australian sporadic ALS (sALS) cases and 48 healthy controls (NCBI GEO accession GSE234297). Differences in sALS-control gene expression, transcript usage and predicted leukocyte proportions were assessed, with pathway analysis used to predict the activity state of biological processes. Weighted Gene Co-expression Network Analysis (WGCNA) and machine learning algorithms were applied to search for diagnostic and prognostic gene expression patterns. Unsupervised clustering analysis was employed to determine whether sALS patient subgroups could be detected. Results: 245 differentially expressed genes were identified in sALS patients relative to controls, with enrichment of immune, metabolic and stress related pathways. sALS patients also demonstrated switches in transcript usage across a small set of genes. We established a classification model that distinguished sALS from controls with an accuracy of 78% (sensitivity: 79%, specificity: 75%) using the expression of 20 genes. Clustering analysis identified four patient subgroups with gene expression signatures and immune cell proportions reflective of distinct peripheral effects. Conclusions: Our findings suggest that peripheral blood RNA-seq can identify diagnostic biomarkers and distinguish molecular subtypes of sALS patients however, its prognostic value requires further investigation.

overall_design: RNA sequencing of peripheral blood from 96 sporadic amyotrophic lateral sclerosis patients and 48 matched healthy controls.

first: Natalie

last: Grima

first: Sidong

last: Liu

first: Dean

last: Southwood

first: Lyndal

last: Henden

first: Andrew

last: Smith

first: Albert

last: Lee

first: Dominic

middle: B

last: Rowe

first: Susan

last: D'Silva

first: Ian

last: Blair


title: Single-cell transcriptome analysis of the germ cells and somatic cells during mitotic quiescence stage in goats

last: Wang

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: As goats are important domestic animals, the regulation of germline and gonadal somatic cells in goats during the mitotic quiescence phase has not been investigated previously. In this study, we employed single-cell RNA sequencing to identify transcriptional signatures of major prospermatogonia and somatic cell types of the testes in goats from E85, E105 and E125.

overall_design: we obtained goat testis tissues from 3 embryonic stages (E85, E105 and E125) with ethical approval and performed scRNA-seq in this study

first: Min

last: Chen

first: Hang


title: Effect of MIT-001 on gene expression in aged mouse ovaries

city: Seoul

first: Min-Hee

last: Kang

state: Seoul

address: 120 Neungdong-ro

department: Stem Cell and Regenerative Biotechnology

country: South Korea

institute: Konkuk University

summary: This study aimed to assess the potential of the anti-inflammatory agent MIT-001 to mitigate ovarian dysfunction resulting from aging

overall_design: We then performed gene expression profiling analysis using data obtained from mRNA-seq of ovarian tissue from young(8wks), old(65wks) and MIT-001-treated old(65wks) mice.

first: Jae


title: Arraystar m6A-mRNA Epitranscriptomic Microarray Analysis of Atopic Dermatitis and healthy controls

city: Changsha

first: Zeng

last: Jinrong

address: No.138 Tongzipo Rd, Yuelu District, Changsha, Hunan, China, 410013

institute: the Third Xiangya Hospital, Central South University

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: To investigate the potential mechanism of m6A modification in the development of AD

overall_design:
In the study presented here, m6A ArrayStar apparent transcriptome profiling was performed in  skin tissues from normal human and lesional skin tissue from patients with AD
Note: These are dual channel arrays that have been analyzed as a single-channel array experiment. Therefore there is a sample (GSM) for each channel.

first: Jinrong

last: Zeng


title: Inhibition of METTL3 results in a cell-intrinsic interferon response that enhances anti-tumour immunity [RNA-seq]

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

institute: Peter MacCallum Cancer Centre

summary: Therapies that enhance anti-tumour immunity have dramatically changed the natural history of a range of cancers. Consequently, leveraging non-overlapping mechanisms to further increase the immunogenicity of cancer cells remains a major priority. Here, using a novel inhibitor of the RNA methyltransferase, METTL3, we demonstrate that enzymatic inhibition and a global decrease in N6-methyladenosine (m6A) results in double stranded RNA formation and a profound cell-intrinsic interferon response. By monitoring nascent mRNA, we show that the downstream induction of interferon stimulated genes (ISG) is coupled to a global increase in mRNA stability due to decreased m6A. One of the primary sequelae of this process is an increased expression and stability of genes associated with antigen presentation via MHC-I3. With unbiased global CRISPR screens we demonstrate that components of dsRNA sensing and interferon signalling are the primary mediators that potentiate T-cell killing of cancer cells following METTL3 inhibition. As PDL1, a key immune checkpoint, is also induced by interferon3, we show in a range of immunocompetent mouse models that whilst METTL3 inhibition alone is equally efficacious to anti-PD1 therapy, the combination has far greater pre-clinical activity. Importantly, using SPLINTR barcoding4, we demonstrate at single clone resolution that anti-PD1 and METTL3 inhibition target distinct malignant clones and the combination of these therapies augment anti-tumour immunity to overcome clones insensitive to the single agents. Together these data provide the molecular and pre-clinical rationale for employing METTL3 inhibitors to promote anti-tumour immunity in the clinical setting.

overall_design: AT3 cells were treated with DMSO, 20µM STM2457 or 2µM STM3006 in triplicate for 24 and 48h

last: Guirguis


title: Promoter R-loops Recruit U2AF1 to Modulate Its Phase Separation and RNA Splicing

city: Riverside

first: Yinsheng

state: California

address: 501 Big Springs Road

institute: UC-Riverside

summary: R-loops and guanine quadruplexes (G4s) are secondary structures of nucleic acids that are ubiquitously present in cells, and are enriched in promoter regions of genes. By employing a bioinformatic approach based on overlap analysis of transcription factor ChIP-seq datasets, we found that many splicing factors, including U2AF1 whose recognition of 3¢ splicing site is crucial for pre-mRNA splicing, exhibit pronounced enrichment at endogenous R-loop- and DNA G4-structure loci in promoter regions of human genes. We revealed that U2AF1 can bind directly to R-loops and DNA G4 structures at low nM binding affinity. Additionally, we showed the ability of U2AF1 to undergo phase separation, which could be stimulated by binding with R-loops, but not duplex DNA, RNA/DNA hybrid, DNA G4, or single-stranded RNA. We also demonstrated that U2AF1 binds to promoter R-loops in human cells, and this binding competes with U2AF1’s interaction with 3¢-splicing site, thereby modulating pre-mRNA splicing. Together, we uncovered a group of candidate proteins that can bind to both R-loops and DNA G4s, revealed the direct and strong interaction of U2AF1 with these nucleic acid structures, and unveiled new functions of this interaction, i.e., promotion of phase separation of U2AF1 and modulation of mRNA splicing. Our work also established, for the first time, a biochemical basis for U2AF1’s occupancy in gene promoters.

overall_design: Genome-wide profiling analysis of POLR2A in wildtype HEK293T cells and U2AF1 knockdown or DHX9 knockdown HEK293T cells

first: Xiaomei

last: He


title: Alcohol dehydrogenase 1B emerged prominent in the carcinogenesis of oro- and hypopharyngeal cancers in Genome-Wide Study in areca-quid endemic area

city: TauYau

first: Yun-Shien

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary: Head and neck squamous cell carcinomas (HNSqCC) are related with cigarette, alcohol and areca quid (AQ). In the era of precision preventive medicine, susceptible genetic markers for HNSqCCs were investigated by genome-wide association manner.

overall_design:
A case-control design and 659 male HNSqCC patients between Mar 1996 and Dec 2016 were recruited with 2400 normal controls. Single nucleotide polymorphisms (SNPs) array (Affymetrix Axion Genome-Wide TWB 2.0 Array Plate) was utilized to investigate patients’ susceptible genetic loci to develop HNSqCCs.
Analyzing the allele frequencies of the 664,994 autosomal SNPs from 659 HNSqCCs cases, seven SNPs scattered loci in chr. 5, 7, 9, 11, and 19 reached the threshold of genome-wide significance (Pc < 1.0669 × 10-7). When narrowing into oropharyngeal cancer (n=331), two clustered regions in chr 4 and chr 6 were significantly different from normal population. Imputation successfully identified the missense alteration of SNP region as in ADH1B (https://genome.ucsc.edu, hg38). The top correlated locus is rs1229984 (p = 1x10-11). Further adjusting the exposures of smoking, alcohol drinking and AQ chewing, a region in chr. 12 was identified as independent region for the susceptibility of oropharyngeal cancer and was related with alcohol metabolism. ADH1B rs1229984 AA genotype had better OS compared with AG and GG genotypes (p = 0.042) in oropharyngeal cancer. GG genotype in rs1229984 significantly was occurred younger than other genotypes (p = 0.001 and p < 0.001) in oropharyngeal cancer who drank alcohol.

first: Shiang-Fu

last: Huang


title: Attenuation of PTBP2 facilitates fibroblast to neuron conversion by promoting alternative splicing of neuronal genes

city: Buffalo

first: Jian

last: Feng

state: NEW YORK

address: 955 Main St, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

summary: The direct conversion of human skin fibroblasts to neurons has a low efficiency and unclear mechanism. Here, we show that the knockdown of PTBP2 (nPTB) significantly enhanced the transdifferentiation induced by ASCL1, MiR124-9/9* and p53 shRNA to generate mostly GABAergic neurons. Longitudinal RNAseq analyses identified the continuous induction of many RNA Splicing Regulators (RSRs). Among these, the knockdown of RBFOX3, which encodes the mature neuronal marker NeuN, significantly abrogated the transdifferentiation. Overexpression of RBFOX3 significantly enhanced the conversion induced by AMp; the enhancement was occluded by PTBP2 knockdown. We found that PTBP2 attenuation significantly favored neuron-specific alternative splicing (AS) of many genes involved in synaptic transmission, signal transduction, and axon formation. RBFOX3 knockdown significantly reversed the effect, while RBFOX3 overexpression enhanced it. The study reveals the critical role of neuron-specific AS in the direct conversion of human skin fibroblasts to neurons by showing that PTBP2 attenuation enhances this mechanism in concert with RBFOX3.

overall_design: Transcriptomic profiling of induced neurons mediated by ASCL1, miR124-9/9*, p53 shRNA and PTBP2 shRNA at day 3, 7, and 14 using human skin fibroblasts.

first: Binglin

last: Zhu

first: Li

last: Li

first: Emily

last: Fisher

first: Ping

last: Zhong

first: Zhen

last: Yan


title: Transcriptome analysis of the response to pine wilt nematode in fungi Graphilbum sp.

city: Hangzhou

first: Zhou

last: Duanxu

state: zhejiang

address: wushu street NO.666

institute: Zhejiang Agriculture and Forest University

summary: Transcriptomic profile between the control and treatment showed that differentially expressed genes were enriched on  regulation of response to stimulus,regulation of cell cycle process, peptidyl-amino acid modification, regulation of cell communication, fatty acid elongation, arachidonic acid metabolism, ribosome and oxidative phosphorylation

overall_design: RNA-seq analysis between three wild-type samples and three pine wilt nematode treatment samples, with three biological replicates per sample.

first: Duanxu

last: Zhou

first: Xiu

last: Su


title: Transcriptomics provides novel insights into the regulatory mechanism of lncRNA HIF1A-AS1 on VSMCs

city: Wuhan

first: Wenying

address: Shizi Street No.1

institute: Huazhong Agricultural University

summary: In current study, using a lentivirus-based expression system, we observed that overexpressing HIF1A-AS1 successfully promoted apoptosis, significantly altered cell cycle distribution and greatly facilitated migration in VSMCs, further highlighting the robust promoting effects of HIF1A-AS1 to TAA. Moreover, transcriptomics was implemented to uncover its underlying mechanism. A total of 175 differentially expressed genes (DEGs) were identified, with some of them enriched in apoptosis, migration and cell cycle related pathways. Intriguingly, some DEGs were annotated in vascular development or coagulation function pathways. In view of this, we suggested HIF1A-AS1 mediated the progression of TAA by not only regulating the function of VSMC cells, but also altering vascular development or coagulation function. Lastly, RT-qPCR confirmed the veracity and reliability of RNA-sequencing results.

overall_design: Examination the overexpression of HIF1A-AS1 in VSMCs.

first: Zhiqiang

last: Gong


title: Multi-omic profiling of the developing human cerebral cortex at the single cell level

city: New York City

first: Jaroslav

last: Bendl

state: New York

address: One Gustave L. Levy Place, Department of Genetics and Genomics Sciences, Box 1210

department: Genetics and Genomics Sciences

institute: Icahn School of Medicine at Mount Sinai

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

overall_design: Refer to individual Series


title: Inhibition of Mertk Receptor Signaling Enhances Bone Regeneration After Tooth Extraction

city: Ann Arbor

first: Joseph

last: Decker

state: Michigan

address: 1011 N University Avenue

department: Cariology, Restorative Sciences, and Endodontics

institute: University of Michigan

summary: Regeneration of alveolar bone is an essential step in restoring healthy function following tooth extraction.  Growth of new bone in the healing extraction socket can be variable and often unpredictable when systemic comorbidities are present, leading to the need for additional therapeutic targets to accelerate the regenerative process. This study examined the effect of signaling through the TAM (Tyro3, Axl, Mertk) family of receptors on alveolar bone regeneration. We performed RNA sequencing on human alveolar bone stem cells treated with a pan-TAM inhibitor in vitro.  We also performed RNA sequencing on tissue isolated from the extraction socket of WT and Mertk-\- mice.

overall_design: Comparison of inhibition of TAM signaling (Tyro3, Axl, Mertk) on bone differentiation and healing.  One data set examines human stem cells in culture with TAM inhibitor, and the other compares WT and Mertk knockout mice during healing following tooth extraction.

first: Ann


title: SWI/SNF chromatin remodelers target enhancers via interaction with Eya1 and Six2 to specify metanephric fate and maintain nephron progenitor pool

city: New York

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

summary: Eya1 is a critical regulator for establishing nephron fate and acts upstream of Six2. However, how Eya1-centered network operates remains elusive. Here we identified Eya1's interacting factors via mass-spectrometry and show that Eya1 and Six2 interact with Brg1-based SWI/SNF chromatin-remodeling complex in the kidney. Brg1 specifies the nephron fate and regulates Eya1 expression through binding to multiple cis-regulatory-elements. In the nephron-progenitors, Brg1/Six2 co-occupy cis-regulatory-elements at key loci and Brg1-recruitment to many of these regions is disrupted in the absence of Six2. We demonstrate Six2-dependent Brg1-occupancy to Mycn promoter and two distal enhancers of Pbx1, all of which direct nephron-progenitor-specific expression in response to binding to Six2. RNA-seq analysis reveals that depletion of Brg1 leads to upregulation of genes for podocyte-lineages and aberrant activation of cell-death inducing factors. Together, this study highlights an essential function of the Brg1-BAFs in cooperation with Eya1/Six2 in enhancer-mediated regulation of gene expression in the nephron-progenitors.

overall_design: We sequenced RNA isolated from kidney FACS-purified from control and Brg1-cKO conditions.

first: Jun

first: Jinshu

last: Xu

first: Huihui

last: Jiang

last: Shen

first: Pin-Xian


title: CALR-mutated cells are vulnerable to combined inhibition of the proteasome and the endoplasmic reticulum stress response

first: María José

last: Jiménez

state: Madrid

address: C. de Melchor Fernández Almagro, 3

department: Structural Biology

institute: Spanish National Cancer Research Centre

summary: Cancer is driven by somatic mutations that provide a fitness advantage. While targeted therapies often focus on the mutated gene or its direct downstream effectors, imbalances brought on by cell-state alterations may also confer unique vulnerabilities. In myeloproliferative neoplasms (MPN), somatic mutations in the calreticulin (CALR) gene are disease-initiating through aberrant binding of mutant CALR to the thrombopoietin receptor MPL and ligand-independent activation of JAK-STAT signaling. Despite these mechanistic insights into the pathogenesis of CALR-mutant MPN, there are currently no mutant CALR-selective therapies available. Here, we identified differential upregulation of unfolded and ubiquitinylated proteins, the proteasome and the ER stress response in CALR-mutant hematopoietic stem cells and megakaryocyte progenitors. We further found that combined pharmacological inhibition of the proteasome and IRE1-XBP1 axis of the ER stress response preferentially targets Calr-mutated stem and progenitors over wild-type cells in vivo, resulting in an amelioration in the MPN phenotype. Together, these findings leverage loss of proteostasis in Calr-mutant MPN to identify combinatorial dependencies that may be targeted for therapeutic benefit.

overall_design: Long-term hematopoietic stem cells of MxCre or Calr 52/del52 MxCre mice were FACS-sorted 14 days after induction of Cre expression following pI:pC injections. Cells were sorted by the following surface markers: lineage negative, CD117 (kit) positive sca-1 positive, CD48 negative CD150 positive cells.

first: Jonas

last: Jutzi

first: Anna

last: Marneth

last: Mullally


title: Expression data changes induced by several rounds of migration through small pores in T-ALL cells

first: Javier

middle: Redondo

last: Muñoz

address: C. Ramiro de Maeztu, 9

department: Molecular Biomedicine

institute: Centro de Investigaciones Biológicas Margarita Salas (CSIC)

summary: Persistent migration through narrow spaces confers permanent phenotypical and functional consequences to T-ALL cells, influencing the genetic instability and inducing nuclear heterogeneity.

overall_design: Jurkat cells (T-ALL cell line) were used for RNA extraction and hybridization on Affymetrix microarrays. Migratory-altered (MA) cells (a.k.a. Pseudolines or PL) were generated by inducing three rounds of migration through 3um transwell inserts. The MA cells resulted from this method as well as the Jurkat control cells were kept in culture conditions. Then, cells were lysed and mRNA was extracted to compare expressions profiles. We used two replicates of each condition.

first: Ana

last: de Lope-Planelles

first: Raquel

last: Gonzalez-Novo

first: Elena

last: Madrazo

first: Héctor

last: Zamora-Carreras

first: Verónica

last: Torrano

first: Horacio

last: López-Menéndez

first: Pedro

last: Roda-Navarro

first: Francisco

last: Monroy

last: Redondo-Muñoz


title: All-in-one Engineering Multifunctional Nanoplatforms for Sensitizing Tumor Low-Temperature Photothermal Therapy in vivo

status: Public on Oct 11 2023

city: chongqing

first: ke

last: li

address: shazheng street 174

institute: chongqing university

summary: To determine the effects of photothermal therapy on regulatory genes and molecular pathways of mouse triple negative breast cancer cells (4T1 cells), we studied the RNA sequences of 4T1 cells treated with medium (control), MoS2 NPs and MoS2 NPs + NIR (808 nm).

overall_design: mRNA profiles of 4T1 cells treated by medium, MoS2 NPs and MoS2 NPs+NIR were generated by deeping sequencing, using Illumina HiSeq2000.

first: Kaiyong

last: Cai

first: Ke

last: Li


title: Transcriptomes of maize leaf sheath tissues in wild-type and lncRNA GARR2 knockout lines

city: Yangzhou

first: Yijun

last: Wang

state: Jiangsu

address: Wenhui

institute: Yangzhou University

summary:
Purpose: We aim to reveal maize transcriptomic changes in wild-type and lncRNA GARR2 knockout lines.
Methods: RNA-seq was used to reveal transcriptome of maize biological replicates of wild-type and lncRNA GARR2 knockout lines.
Results: Differnentically expressed transcritps were identified by the comparison of biological replicates of wild-type and lncRNA GARR2 knockout lines.
Conclusions: We identified differentially expressed genes in lncRNA GARR2 knockout lines.

overall_design: RNA-seq of biological replicates of leaf sheaths from wild-type and lncRNA GARR2 knockout lines using HiSeq 2500 System with a 150 bp paired-end module.


title: High throughput analysis of B cell dynamics and neutralizing antibody development during immunization with a novel clade C HIV-1 envelope

city: Atlanta

first: rohini

last: mopuri

state: GA

address: 954 Gatewood Rd NE

institute: Emory National Primate Research Center

summary: A protective HIV-1 vaccine has been hampered by a limited understanding of how B cells acquire neutralizing activity. Our previous vaccines expressing two different HIV-1 envelopes elicited robust antigen specific serum IgG titers in 20 rhesus macaques; yet serum from only two animals neutralized the autologous virus. Here, we used high throughput immunoglobulin receptor and single cell RNA sequencing to characterize the overall expansion, recall, and maturation of antigen specific B cells longitudinally over 90 weeks. Diversification and expansion of many B cell clonotypes occurred broadly in the absence of serum neutralization. However, in one animal that developed neutralization, two neutralizing B cell clonotypes arose from the same immunoglobulin germline and were tracked longitudinally. Early antibody variants with high identity to germline neutralized the autologous virus while later variants acquired somatic hypermutation and increased neutralization potency. The early engagement of precursors capable of neutralization with little to no SHM followed by prolonged affinity maturation allowed the two neutralizing lineages to successfully persist despite many other antigen specific B cells. The findings provide new insight into B cells responding to HIV-1 envelope during heterologous prime and boost immunization in rhesus macaques and the development of selected autologous neutralizing antibody lineages

overall_design: 20 Indian origin rhesus macaques (Macaca mulatta), including 17 male and 3 female, were immunized intramuscularly as follows: week 0 and week 8 with pGA1-SHIV-1-R66M/Z1800M DNA; week 16 and week 24 with recombinant Modified Vaccinia Ankara(MVA)-SHIV-1-R66M/Z1800M; weeks 53 and 61 with either gp120 or trimer gp140 protein HIV-1 envelope protein. The animals were split into 2 groups of 10 animals each and one group received reagents derived from the HIV-1 T/F Env Z1800M E4.02 sequence while the other received reagents derived from the HIV-1 T/F Env R66M O20.03 sequence. For the protein immunizations, the groups of 10 were further subdivided with 5 animals receiving gp120 protein and the other 5 animals receiving the stabilized gp140 trimer.

first: Rohini

last: Mopuri

first: Sarah

last: Welbourn

first: Tysheena

last: Charles

first: Pooja

last: Ralli-Jain

first: David

last: Rosales

first: Samantha

last: Burton

first: Areeb

last: Aftab

first: Kathryn

last: Pellegrini

first: Amit

last: Upadhyay

first: Steven

last: Bosinger

first: Cynthia

last: Derdeyn


title: Parathyroid hormone exacerbates pulmonary hypertension through hypoxia-induced parathyroid hormone receptor upregulation.

city: Tokyo

first: Yusuke

last: Joki

address: 2-1-1 Hongo

department: Cardiovascular Biology and Medicine

institute: Juntendo University, Graduate School of Medicine

summary: Pulmonary hypertension (PH) is an incurable right heart failure disease. Parathyroid hormone (PTH) is secreted from the parathyroid gland and plays a crucial role in calcium homeostasis. PTH also acts on the cardiovascular system and affects cardiovascular prognosis. We assessed whether the regulation of PTH affected PH in a hypoxia (Hx)-induced PH mouse model. PTH treatment exacerbated right ventricular hypertrophy and right ventricular systolic pressure in Hx mice. Our data showed how is PTH effected for PH model murine lung.

overall_design: To investigate the regulation of PTH affected PH.Hypoxia (Hx)-induced PH mice were administered PTH daily for 3 weeks.

first: Tohru

last: Minamino

first: Hakuoh

last: Konishi


title: Systems biological assessment of the temporal dynamics of immunity to a viral infection in the first weeks and months of life

city: Palo Alto

first: Dmitri

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary: The dynamics of innate and adaptive immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to SARS-CoV-2 infection in infants and young children in the first weeks and months of life by analyzing blood samples collected before, during, and after infection with Omicron and Non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, were stably maintained for >300 days. Antigen-specific memory B cell (MCB) responses were durable for 150 days but waned thereafter. Somatic hypermutation of V-genes in MCB accumulated progressively over 9 months. The innate response was characterized by upregulation of activation markers on blood innate cells, and a plasma cytokine profile distinct from that seen in adults, with no inflammatory cytokines, but an early and transient accumulation of chemokines (CXCL10, IL8, IL-18R1, CSF-1, CX3CL1), and type I IFN. The latter was strongly correlated with viral load, and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single- cell transcriptomics. Consistent with this, single-cell ATAC-seq revealed enhanced accessibility of chromatic loci targeted by interferon regulatory factors (IRFs) and reduced accessibility of AP-1 targeted loci, as well as traces of epigenetic imprinting in monocytes, during convalescence. Together, these data provide the first snapshot of immunity to infection during the initial weeks and months of life.

overall_design: Blood from COVID-19 infected infants and young children (Omciron and pre-omicron, n=37) and healthy controls (n=53) was collected in Tempus tubes and analyzed using RNA-seq. Pre-omicron acute samples were collected longitudinally with paired healthy control.

first: Florian

last: Wimmers


title: Multi-omic profiling of the developing human cerebral cortex at the single cell level [snRNA-seq]

first: Jaroslav

last: Bendl

summary: Human brain development starts during embryogenesis and extends postnatally to adulthood. During this time, the cellular complexity of the brain is established via dynamic changes in gene expression, mediated, in part, by the spatiotemporal activity of cis-regulatory elements. To better understand these processes, we performed simultaneous profiling of gene expression and chromatin accessibility in 45,549 individual nuclei, isolated from the human cortex across 6 broad developmental time-points from fetus to adult. We identified cell-type specific domains in which chromatin accessibility is highly correlated with gene expression. Differentiation pseudotime trajectories of gene expression in neuronal subpopulations indicate that chromatin accessibility at cis-regulatory elements precedes transcription and that dynamic changes in chromatin structure play a critical role in neuronal lineage commitment. In addition, using lineage-specific genes and peaks, we mapped cell-type specific genetic loci implicated in neuropsychiatric traits, including schizophrenia, major depressive disorder and bipolar disorder. Together, our results describe the complex regulation of cell composition at critical stages in lineage determination, serve as a developmental blueprint of the human brain and shed light on the impact of spatiotemporal alterations in gene expression on neuropsychiatric disease.

overall_design: snRNA-seq

first: Panos

last: Roussos

first: John

middle: F

last: Fullard

first: Kaiyi

last: Zhu


title: Recurrent Chimeric RNA, CTNNBIP1-CLSTN1 Regulates Cell Proliferation through SERPINE2 in Non-neoplastic Human Cells

city: Charlottesville

first: Fujun

last: Qin

address: 345 Crispell Dr.

department: Pathology

institute: University of Virginia

summary: Conventional wisdom that chimeric RNAs and proteins being peculiarity of carcinoma is being challenged, as more evidence are accumulated supporting that chimeric RNAs are widely spread in noncancerous tissues and cells. One particular chimeric RNA, CTNNBIP1-CLSTN1 produced by cis-splicing between two neighboring genes, has been detected in a variety of normal tissues. However, the details of its functionality are not clear. Here, we report that this fusion transcript is expressed in almost all tissues, and a wide range of cell types including fibroblasts, epithelial, stem, vascular endothelial cells, and hepatocytes. The expression level in non-cancerous cell lines is also not evidently different from that in the cancer cell lines. Furthermore, silencing CTNNBIP1-CLSTN1 significantly reduces cell proliferation rate, by inducing G2/M arrest in cell cycle progress and apoptosis in at least three cell types. Importantly, rescue experiments confirmed that the cell cycle arrest can be regained by exogenous expression of the chimera, but not the wild type parental gene. Further evidence is provided that CTNNBIP1-CLSTN1 regulates cell proliferation through SERPINE2. In conclusion, CTNNBIP1-CLSTN1 chimeric transcript widely exists in normal physiology, and undertakes essential cellular maintenance roles. It represents an example of a new class of fusion RNA, dubbed “housekeeping chimeric RNAs”.

overall_design: analyzing differential gene expression in control and CTNNBIP1-CLSTN1 knocking down cells

first: Chen

last: Chen

first: Yue

last: Tang

first: Hui

last: Li


title: A Replicative Recombinant HPV16 E7 Expression virus upregulates CD36 in C33A cells

city: Dalian

first: Yunting

last: Shao

address: No.2 Linggong Road, Ganjingzi District

institute: School of Biomedical Engineering, Dalian University of Technology

summary: Objective: In past decades, the role of high-risk HPV (HR-HPV) infection in cancer pathogenesis has been extensively studied. The viral E7 protein expressed in pre-malignant cells has been identified as an ideal target for immunological intervention. However, the cultivation of HPV in vitro remains a significant challenge, as well as the lack of methods for expressing the HPV E7 protein and generating replication-competent recombinant viral particles, which posed a major obstacle to further exploration of the function and carcinogenic mechanisms of the E7 oncoprotein. Therefore, it is imperative to investigate novel methodologies to construct replication-competent recombinant viral particles that express the HPV E7 protein to facilitate the study of its function.  Methods: We initiated the construction of recombinant viral particles by utilizing the ccdB-Kan forward/reverse screening system in conjunction with the Red/ExoCET recombinant system. We followed the infection of C33A cells with the obtained recombinant virus to enable the continuous expression of HPV16 E7. Afterwards, the total RNA was extracted and performed transcriptome sequencing using RNA-Seq technology to identify differentially expressed genes associated with HPV-induced oncogenicity.  Results: We successfully established replicative recombinant viral particles expressing HPV16 E7 stably and continuously. The C33A cells were infected with recombinant viral particles to achieve overexpression of the E7 protein. Subsequently, RNA-Seq analysis was conducted to assess the changes in host cell gene expression. The results revealed an upregulation of the CD36 gene, which is associated with the HPV-induced oncogenic pathways, including PI3K-Akt and p53 signaling pathway. qRT-PCR analysis futher identified that the upregulation of the CD36 gene due to the expression of HPV16 E7.  Conclusion: The successful expression of HPV16 E7 in cells demonstrates that the replicated recombinant virus retains the replication and infection abilities of Ad4, while also upregulating the CD36 gene involved in the PI3K-Akt signaling and p53 pathways, thereby promoting cell proliferation. The outcome of this study provides a novel perspective and serves as a solid foundation for further exploration of HPV-related carcinogenesis and the development of replicative HPV recombinant vaccines capable of inducing protective immunity against HPV.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C33A cells, C33A cells infected with Ad4  and  recombinant virus Ad4-HPV16E7.

first: Yunji

last: Zheng

first: Hongtu

last: Cui

first: Zhangrong

last: Lou

first: Peng

last: Wang

first: Chengjun

last: Wu


title: Key patient demographics shape innate immune topography in non-critical hypoxic COVID-19 pneumonia

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

summary: Risk of severe disease and death due to coronavirus 2019 (COVID-19) is increased in certain patient demographic groups, including those who are of advanced age, male sex, and obese body mass index. Investigations of the biological variations that contribute to this risk have been hampered by heterogeneous severity, with immunologic features of critical disease potentially obscuring differences between risk groups. To examine immune heterogeneity related to demographic risk factors, we enrolled 38 patients hospitalized with clinically homogeneous COVID-19 pneumonia – defined as oxygen saturation <94% on room air without respiratory failure, septic shock, or multiple organ dysfunction – and performed single-cell RNA-sequencing of leukocytes collected at admission. Examination of individual risk factors identified strong shifts within neutrophil and monocyte/dendritic cell compartments, revealing altered immune cell type-specific responses in higher-risk COVID-19 patient subgroups. Specifically, we found transcriptional evidence of altered neutrophil maturation in aged versus young patients and enhanced cytokine responses in monocytes/dendritic cells of male versus female patients. Such innate immune cell alterations may contribute to outcome differences linked to these risk factors. They also highlight the importance of diverse patient cohorts in studies of therapies targeting the immune response in COVID-19.

overall_design: Study involved enrollment of 38 patients presenting to the hospital with COVID-19 and 3 healthy controls. See paper Methods for inclusion/exclusion criteria. Whole blood was collected within 1 day of hospitalization and buffy coats isolated for generation of scRNA-seq libraries. No replicates are included.

first: Allison

last: Billi

first: Jason

last: Knight

first: Yogen

last: Kanthi


title: Linear epitope mapping in the E and NS1 proteins of dengue and Zika viruses: prospection of peptides for vaccines and diagnostics GA_DZ_V2

city: San Lorenzo

first: Victor

middle: Hugo

last: Aquino

state: Central

address: Dr. Cecilio Báez c / Dr. Gaspar Villamayor

department: Research Institute for Health Sciences

country: Paraguay

institute: National University of Asuncion

summary: Dengue and Zika are two mosquito-borne diseases of great concern, affecting mainly the tropical and subtropical regions worldwide. The arrival of Zika virus (ZIKV) in dengue virus (DENV) endemic areas imposed challenges for differential diagnosis and the development of candidate vaccines. The use of peptides has shown great potential to achieve these goals. We aimed to identify the linear epitope profile recognized by the serum samples of dengue and Zika patients in the E and NS1 proteins of DENV and ZIKV to select peptides with the potential for the development of diagnostic tests and vaccines. Analysis of a peptide microarray platform with serum samples of dengue and Zika patients demonstrated that the epitopes were evenly distributed across the entire viral proteins, showing no preference for particular regions. However, several epitopes were within epitope hot spots constituted by clusters of peptides recognized in more than 30% of the sub-arrays analyzed with individual or pools of serum samples. The serum samples of dengue and Zika patients showed a high level of cross-reaction for epitopes in the DENV and ZIKV proteins. Analysis of an additional peptide microarray platform containing selected peptides based on the results of the first screening showed that three peptides (DENV: TQGEPSLNEEQDKRF and TQTVGPWHLGKLEID; ZIKV: LELDPPFGDSYIVIG), highly specific for their cognate viruses (p<0.05), were within the epitope hot spots; however, these peptides showed low detection rates (32.5, 35.0, and 28.6%, respectively). We also found two peptides (DENV: WEVEDYGFGVFTTNI and LELDFDLCEGTTVVV) in the epitope hot spots detected by both dengue and Zika patients with similarly high rates (arbitrary detection rate cut-off threshold of ≥40%). The epitope hot spots harbor several immunodominant epitopes recognized by a higher number of individuals when compared to the 15 aa sequence peptides. Therefore, the entire epitope hot spots, spanning up to ~30 aa, would have more potential than peptides of only 15 aa to serve as antigens in diagnostic tests and vaccine developments.

platform_organism:
Dengue virus
Zika virus

overall_design: Based on the results obtained from the GA_DZ_V1 platform, several 15-amino acid peptides (n=248) were chosen for the design of this peptide microarray slide. The peptide microarray slide comprised five identical sub-arrays, each containing duplicated spots of viral peptides (PEPperPRINT, Heidelberg, Germany). Additionally, the sub-arrays incorporated 38 spots of the influenza virus YPYDVPDYAG peptide and 36 spots of the poliovirus KEVPALTAVETGAT peptide. These peptides served as negative and positive controls, respectively, in the immunoassays. This microarray platform was evaluated with serum samples obtained from dengue (n=40) and Zika (n=21) patients, as well as uninfected controls (n=3). An individual serum sample was included in each sub-array during the immunodetection assay.

last: Hugo Aquino

first: Marcilio

last: Fumagalli

first: Angélica

last: Silva

first: Bento

last: Vidal de Moura Negrini

first: Alejandra

last: Rojas

first: Yvalena

last: Guillen

first: Cynthia

last: Bernal

first: Luiz

last: Tadeu Moraes Figueiredo


title: Linear epitope mapping in the E and NS1 proteins of dengue and Zika viruses: prospection of peptides for vaccines and diagnostics GA_DZ_V1

overall_design: The array contained 15aa linear peptides with overlapping sequences 13 aa covering the entire E (393 aa without the transmembrane region) and NS1 proteins of DENV-1 (GenBank AKQ00011), DENV-2 (GenBank AGX15379), DENV-3 (GenBank AFK83760), DENV-4 (GenBank AEW50183), and ZIKV (GenBank AMA12085) isolates. The linear epitopes were mapped with serum samples of dengue (n=19) and Zika (n=28) patients in 16 and 11 arrays, respectively. The serum samples from healthy individuals (n=4) with negative serological tests for dengue and Zika but vaccinated against yellow fever were analyzed in 3 arrays and served as controls.


title: Linear epitope mapping in the E and NS1 proteins of dengue and Zika viruses: prospection of peptides for vaccines and diagnostics


title: Transcriptome expression of WT and mir163 mutant

city: Taichung City

first: Jeng-Shane

last: Lin

state: Taiwan (R.O.C.)

address: Room 516, Life Science Building,145 Xingda Rd., South Dist.

institute: National Chung Hsing University

summary: To understand regulation mechanism of miR163, transcriptomes of WT and mir163 mutant plants were dissected.  Total RNAs from 7-day-old seedlings were isolated for library construction and analyzed by RNA-seq via Illumina HiSeq platform. Raw sequences were obtained from the Illumina Pipeline software Illumina bcl2fastq v2.17.1.14 and expected to generate 6 G per sample.

overall_design: Examination of transcriptome expression in WT and  mir163 mtuamt


title: Epigenome analysis of schwannomas arising as part of segmental schwannomatosis due to somatic mosaic SOX10 indel mutations

city: Stanford

first: David

middle: A.

last: Solomon

address: 300 Pasteur Dr, Lane L216

institute: Stanford University School of Medicine

summary: Genome-wide DNA methylation profiling of 6 schwannomas arising as part of segmental schwannomatosis due to somatic mosaic SOX10 indel mutations. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of 6 schwannomas.

overall_design: Bisulfite converted genomic DNA extracted from the 6 schwannoma tumor samples was hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips.  Patient #1 is UCSF segmental schwannomatosis #1 and has four tumor samples labeled a, b, c, and d.  Patient #2 is UCSF segmental schwannomatosis #2 and has two tumor samples labeled a and b.


title: Expression of retinoblatoma

city: Changsha

first: Sha

last: Wang

address: 87 Xiangya Road

institute: Xiangya Hospital

summary: Retinoblastoma is the most frequent intraocular malignancy in children. Little is known on the molecular basis underlying the biological and clinical behavior of this cancer. Here, using gene expression profiles, we demonstrate the existence of two major retinoblastoma subtypes that can be divided into six subgroups.

overall_design: Gene expression of 114 samples retinoblastomas tumor using the Hg-U133 Plus 2.0 Affymetrix array


title: Difamilast treatment inhibits the expression of inflammatory mediators in bone marrow-derived basophils (BMBAs) stimulated by IL-3 + IL-33

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

institute: Institute of Science Tokyo

summary: In this study, we explored gene expression profiles of IL-3+IL-33-stimulated BMBAs treated with difamilast, a highly selective PDE4B inhibitor. We identified that difamilast-treated basophils showed downregulated expression of inflammaory mediators including Il4, Il6 and Il13.

overall_design: Bone marrow-derived basophils were stimulated with IL-3+IL-33 or control PBS for 4hrs in the presence of difamilast or vehicle DMSO, and were subjected to bulk RNA-seq analysis.

first: Kazufusa

last: Takahashi

first: Junya

last: Ito

first: Hajime

last: Karasuyama

first: Kenichi

last: Ohashi


title: Exosomal microRNA signature from plasma-derived extracellular vesicles in gastric cancer

city: Bogotá

first: Andrés

last: Rincón-Riveros

address: Calle 1a #9-85

department: Grupo de investigación en biología del cáncer

country: Colombia

institute: Instituto Nacional de Cancerología

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular vesicles are structures surrounded by a lipid bilayer that facilitate intercellular communication by transporting biomolecules. These vesicles are now commonly referred to as part of liquid biopsy. In this study, we examine the characterization of miRNAs found in extracellular vesicles from patients with both benign gastric diseases and gastric cancer. By studying these miRNAs, we aim to identify potential biomarkers for gastric cancer.

overall_design: We have extracted extracellular vesicles from patients with gastric cancer and benign gastric diseases. Then, we extracted the small RNAs with Qiagen's miRNeasy kit. The characterization of small RNAs in the vesicles was performed with BGI's Small RNA Sequencing services, which applies DNBSEQ™ sequencing technology platforms.

first: Liliana

last: López-Kleine

first: Josefa

last: Rodríguez

first: Victoria

last: Villegas


title: ESX1 gene as a potential candidate responsible for male infertility in nonobstructive azoospermia

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary: Infertility is a problem that affects around 15% of couples. In 40-50% of these couples male infertility is involved. The cause of male infertility is still poorly diagnosed and treated. One of the entities of male infertility is disturbed spermatogenesis, which can lead to nonobstructive azoospermia (NOA), with no sperm cells in the ejaculate. The whole genome sequencing (WGS) allow us to identify novel rare variants in potentially NOA-associated genes. One of them was ESX1 gene. The aim of the study was to activate the ESX1 gene using CRISPRa technology in testicular seminoma cells - TCam2. In this study we achieved the successful activation of ESX1 gene in genetically modified TCam-2 cells using CRISPRa system, in which the expression level of ESX1 gene was significantly higher compared to WT cells and negative control with non-targeted sgRNA (p<0.01). These results were successfully confirmed at protein level by using Western blotting and immunofluorescence. Using RNA-seq analysis we determined the genes that were potentially regulated by ESX1 gene. Such genes associated with proliferation and apoptosis process: CCND1, KDR, WNT11, LGALS3, LINC00662, PDE1C, RPS6KA5, FGF4, NANOG, L1TD1, which were differently expressed in cells with ESX1 gene activation in comparison to the controls (p<0.05).

overall_design: The comparative analysis of gene expression profiles by RNA-Seq between modified TCam-2 cells with activated ESX1 gene using CRISPRa system (n=3) compared to WT cells (n=3) and negative control with non-targeted sgRNA (n=3)

first: Malcher

last: Agnieszka


title: ERRα fosters running endurance by driving myofiber aerobic transformation and fuel efficiency

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

institute: McGill University

summary:
Objective: Estrogen related receptor α (ERRα) occupies a central node in the transcriptional control of energy metabolism, including in skeletal muscle, but whether modulation of its activity can directly contribute to extend endurance to exercise remains to be investigated. The goal of this study was to characterize the benefit of mice engineered to express a physiologically relevant activated form of ERRα on skeletal muscle exercise metabolism and performance.
Methods: We recently shown that mutational inactivation of three regulated phosphosites in the amino terminal domain of the nuclear receptor ERRα impedes its degradation, leading to an accumulation of ERRα proteins and perturbation of metabolic homeostasis in ERRα3SA mutant mice. Herein, we used a multi-omics approach in combination with physical endurance tests to ascertain the consequences of expressing the constitutively active phospho-deficient ERRα3SA form on muscle exercise performance and energy metabolism.
Results: Genetic heightening of ERRα activity enhanced exercise capacity, fatigue-resistance, and endurance. This phenotype resulted from extensive reprogramming of ERRα global DNA occupancy and transcriptome in muscle leading to an increase in oxidative fibers, mitochondrial biogenesis, fatty acid oxidation, and lactate homeostasis.
Conclusion: Our findings support the potential to enhance physical performance and exercise-induced health benefits by targeting molecular pathways regulating ERRα transcriptional activity.

overall_design: ChIP-seq analysis of liver or skeletal muscle isolated from WT and ERRα 3SA phospho-mutant mice on a C57BL/6N genetic background.

first: Charlotte

last: Scholtes

first: Hui

last: Xia

first: Catherine

middle: R

last: Dufour

last: Giguere


title: Canonical and nuclear mTOR specify distinct transcriptional programs in androgen-dependent prostate cancer cells [ChIP-Seq]

summary: mTOR is a serine/threonine kinase that controls prostate cancer (PCa) cell growth in part by regulating gene programs associated with metabolic and cell proliferation pathways. mTOR- mediated control of gene expression can be achieved via phosphorylation of transcription factors, leading to changes in their cellular localization and activities. mTOR also directly associates with chromatin in complex with transcriptional regulators, including the androgen receptor (AR). Nuclear mTOR (nmTOR) has been previously shown to act as a transcriptional integrator of the androgen signaling pathway in association with the chromatin remodeling machinery, AR, and FOXA1. However, the contribution of cytoplasmic mTOR (cmTOR) and nmTOR and the role played by FOXA1 in this process remains to be explored. Herein, we engineered cells expressing mTOR tagged with nuclear localization and export signals dictating mTOR localization. Transcriptome profiling in AR-positive PCa cells revealed that nmTOR generally downregulates a subset of the androgen response pathway independently of its kinase activity, while cmTOR upregulates a cell cycle-related gene signature in a kinase-dependent manner. Biochemical and genome-wide transcriptomic analyses demonstrate that nmTOR functionally interacts with AR and FOXA1. Ablation of FOXA1 reprograms the nmTOR cistrome and transcriptome of androgen responsive PCa cells. This works highlights a transcriptional regulatory pathway in which direct interactions between nmTOR, AR and FOXA1 dictate a combinatorial role for these factors in the control of specific gene programs in PCa cells.

overall_design: mTOR ChIP-seq experiments in LNCaP cells with shRNA-mediated knockdown of FoxA1 or shEV (empty vector) control treated with 10nM R1881 or vehicle (EtOH) control for 24h.

first: Yonghong

last: Chen


title: RUNX1-ETO translocations must proceed CSF3R mutations to promote acute myeloid leukemia development

city: Portland

first: Julia

last: Maxson

state: OR

address: 2720 S Moody Ave

institute: Oregon Health and Science University

summary: Acute myeloid leukemia (AML) is a deadly blood cancer character by an overproduction of immature myeloid cells. AML has a high degree of genetic diversity, and the presence or absence of particular genetic alterations can greatly impact prognosis. In AML, patients with CSF3R mutations exhibit high relapse rates and poor overall survival. A recent study found that 90.5% of patients with CSF3R mutations had cooccurring RUNX1-ETO (8;21), CBFB-MYH11, or CEBPA mutations7. The RUNX1-ETO and CBFB-MYH11 translocations disrupt the core binding factor complex, an important transcriptional regulator in myeloid development. In this study, we evaluated how RUNX1-ETO modifies CSF3RT618I-driven transcriptional changes to promote the production of myeloblasts in AML. We find that RUNX1-ETO accelerates CSF3R-driven oncogenesis both in vitro and in vivo. Furthermore, RUNX1-ETO impairs the ability of CSF3R to drive myeloid differentiation associated transcriptional programs resulting in the production of immature myeloblasts which characterize this disease.

overall_design: RNA-Seq of HoxB cells expressing RUNX1-ETO and CSF3R-T618I in an order-dependent manner.

first: Sarah

last: Carratt

first: Garth

last: Kong

first: Theodore

last: Braun


title: Xenograft mouse model to investigate tropism to the CNS and retina in primary central nervous system lymphoma (second batch)

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Primary diffuse large B-cell lymphoma (DLBCL) of the central nervous system (PCNSL) is a rare, extranodal lymphoma. Primary vitreo-retinal lymphoma (PVRL) occurs in 15-25% of PCNSL. CNS involvement also occurs in systemic diffuse large B-cell lymphoma, termed secondary central nervous system lymphoma (SCNSL). Despite intensive treatment, patient outcomes are poor when compared to DLBCL without CNS involvement. How and why lymphoma cells home to the CNS and vitreo-retinal compartment remains unknown. In vivo models to study lymphoma cell tropism are urgently needed. We therefore established and characterized 2 primary and 2 secondary patient-derived CNS lymphoma xenograft mouse models using immunohistochemistry, flow cytometry and nucleic acid sequencing technology. In spleen reimplantation experiments, we characterized the dissemination pattern of orthotopic and heterotopic xenografts and performed RNA sequencing to detect differences on the transcriptome level. Moreover, we found that lymphoma cells in PCNSL xenografts home to the eye after intrasplenal implantation in around 60% of cases, similar to PVRL. This in vivo tumor model preserves key features of this rare lymphoma entity and can be used to explore pathways that are critical for CNS and retinal tropism with the goal to find potential new targets for novel therapeutic approaches .

overall_design: In total 4 human-derived xenograft (PDX) samples were analysed. Flow cytometry cell sorting with human CD19 antibody was used to isolate lymphoma cells from spleen or CNS PDX.

first: Melanie

last: Boerries

first: Lisa

middle: K

last: Isbell

first: Nikolas

last: von Bubnoff


title: Membrane-proximal motifs are the primary determinants of signaling strength differences between type I and III interferon receptors

city: Princeton

first: Aaron

last: Lin

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

summary: Interferons (IFNs) play crucial roles in antiviral defenses. Despite utilizing the same JAK-STAT signaling cascade, type I and III IFN receptors produce different magnitudes and dynamics in the phosphorylation of signal transducers and activators of transcription (STATs), gene transcription and antiviral responses. Prior studies have tested the role of ligand binding affinity and receptor expression level on IFN receptor signaling strength; however, the ability of intracellular domains to differentiate type I and III IFN signaling has not been previously examined. Therefore, we engineered synthetic, heterodimeric type I and III IFN receptors that can be stably expressed at similar levels in human cells and respond to the same ligand. Even when controlling for ligand binding and receptor expression, we find that our synthetic type I receptors produce a greater magnitude of STAT phosphorylation and gene expression than the corresponding type III receptors. Furthermore, our results show that short <55 amino acid “box motifs” known to bind JAK1 are sufficient to encode differences between type I and III receptors. Altogether, our work indicates that specific regions within the intracellular domains of IFNAR2 and IFNLR1 encode different downstream signaling strengths that allow type I and III receptors to produce distinct signaling outcomes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U2OS cells expressing chimeric EPOR-interferon receptors, treated with EPO or IFNs, at multiple time points.

first: Emily

middle: V

last: Mesev

first: Emma

last: Guare

first: Brigitte

middle: L

last: Heller

first: Florian

last: Douam

first: Britt

last: Adamson

first: Jared

last: Toettcher

first: Alexander

last: Ploss


title: Loss of KDM6B confers resistance to lipotoxicity through epigenetic downregulation of G0S2 expression in NASH-related HCC

first: Shu

last: Shimada

address: 1-5-45 Yushima

department: Department of Molecular Oncology

institute: Tokyo Medical and Dental University

summary:
Background& Aims: The incidence of nonhepatitis B and nonhepatitis C viral (NBNC)- HCC has been rising in recent years due to the increase in NAFLD and NASH　worldwide with fibrosis. However, the molecular mechanisms underlying the progression of these HCC are not fully understood. Here we observed that KDM6B, an H3K27 demethylase, was commonly downregulated in human NBNC-HCC and mouse NASH-related HCC by microarray analysis. The study aims to elucidate the molecular mechanism of KDM6B downregulation in NBNC-HCC including NASH-related HCC.
Approach & Results: By immunohistochemistry, KDM6B expression was decreased in 28.7% of human HCC tissues, most of which were NBNC-HCC type. The low KDM6B expression group was accompanied by NASH in the adjacent liver. The KDM6B knockout (KO) HCC cells altered pathways of lipid metabolism by microarray and GSEA analysis. The KDM6B-KO cells significantly decreased lipid accumulation and cell reduction rates. Expression of two lipid-metabolism-related genes, G0S2 and ACSL1, were suppressed in the KDM6B-KO cells and the histone H3K27 trimethylation levels at the promoter regions were decreased when compared to the wild-type cells. Knockdown of G0S2 but not ACSL1 expression showed resistance to lipotoxicity in HCC cells. Moreover, inhibition of ATGL, a downstream target of G0S2, caused a decrease in lipid accumulation and cell proliferation.
Conclusions: KDM6B regulates G0S2 expression via histone demethylation of its promoter region. Decreased KDM6B-dependent G0S2 expression through the histone modification pathway causes resistance to lipotoxicity, which may be involved in the carcinogenic mechanism of NASH-related HCC among NBNC-HCC.

overall_design: KDM6B-konckout hepatocellular carcinoma cells wete established by using the CRISPR/Cas9 system.

first: Megumi

last: Hatano

first: Yoshimitsu

last: Akiyama

first: Kohei

last: Yagi

first: Keiichi

last: Akahoshi

first: Michiko

last: Ito

first: Minoru

last: Tanabe

first: Yoshihiro

last: Ogawa

first: Shinji

last: Tanaka


title: UBE2A/B is the trans-acting factor mediating mechanotransduction and contact inhibition

city: Tianjin

first: Mingwei

last: Feng

state: Tianjin

address: Weijin road No.92

department: SPST

institute: Tianjin University

summary: Mechanotransduction converts mechanical stimuli into biochemical signals to regulate cell growth, differentiation, and survival. However, how mechanotransduction is linked to gene expression remains poorly understood. Here, we report the identification of UBE2A as an mechano-sensitive trans-acting factor, which translocates from the cytosol to the nucleus upon mechanical stimuli. UBE2A is an E2 enzyme that catalyzes ubiquitination of histone, which eventually results in transcription activation of downstream genes. Using ChIP-seq and RNAseq analysis, we identify downstream genes of UBE2A, including YAP1, a well-known mechanotransducer. Knock-down of UBE2A/B significantly downregulates YAP1 protein expression. Our findings identify the new mechanotransduction pathway that regulates gene expression through histone ubiquitination by UBE2A/B.

overall_design: Genome wide examination of UBE2A binding region in human skeleton muscle cell

first: Fumihiko

last: Nakamura


title: Dot1L regulates the rate of lung alveolar regeneration through control of oxidative phosphorylatio

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Alveolar type 1 and type 2 cells comprise the epithelial component of the lung alveolus where gas exchange occurs. AT2 cells harbor progenitor activity and can self-renew and differentiate into AT1 cells during homeostasis and after injury. To identify epigenetic pathways that control the AT2-AT1 regenerative response in the lung, we performed an organoid screen using a library of pharmacological epigenetic inhibitors. This screen identified Dot1L as a potential regulator of AT2 growth and differentiation. To explore the role of Dot1L in vivo, we genetically inactivated Dot1L during lung development, showing that this leads to precocious activation of both AT1 and AT2 gene expression. Loss of Dot1L in adult AT2 cells leads to accelerated AT1 differentiation after acute lung injury. Single cell transcriptome analysis of lineage traced AT2 cells reveals the presence of a new AT2 cell state upon loss of Dot1L, and reveals that Dot1L regulates a complex gene expression network that includes critical transcription factors such as Id1 and Id2 and oxidative phosphorylation genes. Taken together, these data demonstrate that Dot1L regulates an epigenetic pathway in the lung essential for alveolar epithelial development and regeneration after acute injury.

overall_design: To identify epigenetic pathways that control the AT2-AT1 regenerative response in the lung, we performed an organoid screen using a library of pharmacological epigenetic inhibitors, and identified Dot1L as a potential regulator of AT2 growth and differentiation. To explore the role of Dot1L in vivo, we genetically inactivated Dot1L during lung development, and in adult AT2 cells followed by lung acute injury treatments including flu and hyperoxia.  To further define the underlying mechanisms,  we performed  scRNA-seq and ChIP-seq analyses.

first: Shanru

last: Li

first: Edward

last: Morrisey


title: Characterizing the Impact of Simvastatin on TCDD-Induced Liver Injury Utilizing Single-Nuclei RNA Sequencing

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

summary: Objective: 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is associated with metabolic syndrome (MetS) in humans and hepatic effects similar to non-alcoholic fatty liver disease through activation of the aryl hydrocarbon receptor (AHR) pathway. Dysregulation of cholesterol homeostasis, an aspect of MetS, is linked to NAFLD pathogenesis, and TCDD exposure is also linked to the suppression of genes that encode key cholesterol biosynthesis steps and changes in serum cholesterol levels. In a previous experiment, treating mice with TCDD in the presence of simvastatin, a 3-Hydroxy-3-Methylglutaryl-CoA Reductase (HMGCR) competitive inhibitor, increased toxicity in male mice, compared to TCDD alone. The aim of this study was to deduce a possible mechanism(s) for this increased liver injury.   Methods: Male C57Bl/6 mice were treated with vehicle control or TCDD via oral gavage and were fed either standard or simvastatin-laced chow. Single nuclei RNA sequencing (snRNASeq) was performed in mouse liver to investigate the impact of treatment on distinct liver cell (sub)types that may explain differences in pathology between treatments.   Results: We demonstrated that co-treated mice experienced exacerbated wasting and increased AHR activation compared to TCDD alone. Furthermore, relative proportions of cell (sub)types were different between TCDD alone and co-treated mice including important mediators of NAFLD progression such as hepatocytes and Kupffer cells. Co-treated mice promoted upregulation of lipid metabolism in hepatocytes, which is consistent with decreased fat accumulation seen in previous studies. Interestingly, the proportion of plasmacytoid dendritic cells (pDCs) increased in only co-treated mice, which may play an important role in the differences in immune cell infiltration between treatment groups.  Conclusions: Our results suggest simvastatin co-treatment promotes a worse prognosis of TCDD-induced injury in mice and alterations in immune infiltration between treatments may influence liver injury severity.

overall_design: Nuclei were isolated from frozen livers of male C57BL/6 mice either gavaged with sesame oil vehicle or 30 ug/kg TCDD every 4 days for 28 days and fed with normal chow or chow laced with 500 mg/kg simvastatin beginning 3 days prior to first TCDD treatment

first: Amanda

last: Jurgelewicz

first: Jack

last: Harkema

first: Tim

last: Zacharewski

first: John

middle: J

last: LaPres


title: Pancreatic β cell SERCA2 deficiency leads to impaired proinsulin processing and reduced ER to Golgi protein trafficking

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

summary: Impaired proinsulin processing is observed in both type 1 and type 2 diabetes.  We have previously shown that reductions in endoplasmic reticulum (ER) calcium (Ca2+) in the pancreatic β cell arising from impaired activity of the Sarcoendoplasmic Reticulum Ca2+ ATPase (SERCA) pump are associated with increased proinsulin secretion. However, the mechanisms responsible for reduced proinsulin processing in the context of SERCA2 deficiency remain incompletely understood. To test this, we developed mice with β cell specific SERCA2 deletion (βS2KO mice) and S2KO INS1 cells. βS2KO mice exhibited age-dependent glucose intolerance and reduced glucose-stimulated insulin secretion without evidence of impaired insulin sensitivity. ER Ca2+ levels in islets from βS2KO mice were significantly reduced, while serum proinsulin/insulin (PI/I) ratios and whole pancreas PI/I content were elevated. Immunoblot analysis of βS2KO islets and S2KO INS-1 cells revealed reduced active forms of the proinsulin processing enzymes, PC1/3, PC2 and CPE. Restoration of SERCA2b via adenoviral transduction in S2KO INS1 cells was sufficient to restore PC1/3 and PC2 maturation and enzyme activity. Brefeldin A treatment in INS1 cells recapitulated the impairments in PC1/3 and PC2 maturation observed in S2KO cells, suggesting a disturbance in protein trafficking between the ER and Golgi. Consistent with this, trafficking assays were performed using a vesicular stomatitis virus G (VSVG) protein construct and revealed a significantly slower rate of VSVG movement from the ER to the Golgi in S2KO INS1 cells. Moreover, pancreas sections from βS2KO mice showed increased co-localization of proinsulin and ProPC2 in the early compartments of the secretory pathway. Taken together, these data suggest that loss of SERCA2 activity and ER Ca2+ loss in the pancreatic β cell leads to impaired proinsulin processing via reduced maturation and trafficking of proinsulin processing enzymes.

overall_design: Using the RNASeq data, identify differentially expressed genes between SERCA2 knock out model and wild type

first: Hitoshi

last: Iida

first: Tatsuyoshi

last: Kono

first: Staci

last: Weaver

first: Preethi

last: Krishnan

first: Chih-Chun

last: Lee


title: ATAC-seq and RNA-seq for Breast Cancer Cells

city: New York

first: Ekta

last: Khurana

address: 1305 York Ave

institute: Weill Cornell Medicine


title: Xenograft mouse model to investigate tropism to the CNS and retina in primary central nervous system lymphoma (first batch)

first: Geoffroy

last: Andrieux

summary: Primary diffuse large B-cell lymphoma (DLBCL) of the central nervous system (PCNSL) is a rare, extranodal lymphoma. Primary vitreo-retinal lymphoma (PVRL) occurs in 15-25% of PCNSL. CNS involvement also occurs in systemic diffuse large B-cell lymphoma, termed secondary central nervous system lymphoma (SCNSL). Despite intensive treatment, patient outcomes are poor when compared to DLBCL without CNS involvement. How and why lymphoma cells home to the CNS and vitreo-retinal compartment remains unknown. In vivo models to study lymphoma cell tropism are urgently needed. We therefore established and characterized 3 primary and 4 secondary patient-derived CNS lymphoma xenograft mouse models using immunohistochemistry, flow cytometry and nucleic acid sequencing technology. In spleen reimplantation experiments, we characterized the dissemination pattern of orthotopic and heterotopic xenografts and performed RNA sequencing to detect differences on the transcriptome level. Moreover, we found that lymphoma cells in PCNSL xenografts home to the eye after intrasplenal implantation in around 60% of cases, similar to PVRL. This in vivo tumor model preserves key features of this rare lymphoma entity and can be used to explore pathways that are critical for CNS and retinal tropism with the goal to find potential new targets for novel therapeutic approaches .

overall_design: In total 8 human-derived xenograft (PDX) samples and 3 human samples were analysed. Flow cytometry cell sorting with human CD19 antibody was used to isolate lymphoma cells from spleen, liver or CNS PDX.

first: Melanie

last: Boerries

first: Lisa

last: Isbell

first: Nikolas

last: von Bubnoff