title: Spatial transcriptomics of glioblastoma second surgery samples to compare progression and pseudoprogression

city: Columbus

first: Jose

middle: Javier

last: Otero

state: Ohio

address: 333 W 10th Ave, 4170 Graves Hall

institute: The Ohio State University

summary: We performed spatial transcriptomics on a case series of different clinical subtypes of glioblastoma second surgery samples due to novel enhancement following chemoradiation that were confirmed based on clinico-pathologic outcome as disease progression (PD) or pseudoprogression (psPD). All samples showed mixed histologic presentation (Control, Inflammatory, or Hypercellular)  which complicated disease interpretation by pathology. Our goals were to (1) determine if spatial transcriptomics could better distinguish between PD and psPD than bulk RNA approaches in mixed samples, (2) determine which differentially expressed genes (DEGs) and estimated immune cell populations distinguish PD and psPD in similar histologic sites, and (3) identify varying molcular processes through gene ontology that separate PD and psPD in similar presenting areas.

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: NanoString Digital Spatial Profiling (DSP) with human Whole Transcriptome Atlas (WTA) was performed on glioblastoma samples with 4 showing progression (PD) and 4 showing pseudoprogression (psPD) taken from brain resection at second surgery.

first: Wesley

last: Wang


title: Higher Incidence of Embryonic Defects in Mouse Offspring Conceived with Assisted Reproduction from Fathers with Sperm Epimutations

status: Public on Dec 05 2023

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

type: Methylation profiling by high throughput sequencing

summary: Assisted reproductive technologies (ART) account for 1-6% of live births in developed countries. While most children conceived using ART are healthy, increases in birth and genomic imprinting defects have been reported; such abnormal outcomes have been attributed to underlying parental infertility and/or the ART used. Here, we assessed whether paternal genetic and lifestyle factors, that are associated with male infertility and affect the sperm epigenome, can influence ART outcomes. We examined how paternal factors, Dnmt3L haploinsufficiency and/or diet-induced obesity, in combination with ART (superovulation, in vitro fertilization, embryo culture and embryo transfer), could adversely influence embryo development and DNA methylation patterning in mice. While male mice fed high-fat diets (HFD) gained weight and showed perturbed metabolic health, their sperm DNA methylation was minimally affected by the diet. In contrast, Dnmt3L haploinsufficiency induced a marked loss of DNA methylation in sperm; notably, regions affected were associated with neurodevelopmental pathways and enriched in young retrotransposons, sequences that can have functional consequences in the next generation. Following ART, placental imprinted gene methylation and growth parameters were impacted by one or both paternal factors. For the embryos conceived by natural conception, the abnormality rates were similar for WT and Dnmt3L+/- fathers. In contrast, paternal Dnmt3L+/- genotype, as compared to WT fathers, resulted in a 3-fold increase in the incidence of morphological abnormalities in embryos generated by ART. Together, the results indicate that embryonic morphological and epigenetic defects associated with ART may be exacerbated in offspring conceived by fathers with sperm epimutations.

overall_design: We examined the effect of Dnmt3L haploinsufficiency (Dnmt3L Het) and/or high fat diets (HFD) on the sperm epigenome (DNA methylation), as well as whether these two factors could influence embryo development after the use of assisted reproductive technologies (ART). Both wildtype (WT) and Dnmt3L Het male mice, starting at 8 weeks of age, were fed either a HFD with 60% kcal from fat or a matched-control-diet (MCD) with 10% kcal from fat; both diets contained 2 mg/kg folate. Males were fed the diets for 11-13 weeks, before breeding, ART or sperm collections. For natural matings, 2 CF1 females were placed into cages with one WT or Dnmt3L Het male; the day on which we observed a vaginal plug was denoted as E0.5. Midgestation embryos and placentas were collected 10 days later. For ART, eight week old CF1 females were superovulated by IP injection of 5 IU of PMSG followed by 5 IU HCG. IVF was performed in human tubal fluid using sperm from WT or Dnmt3L Het males on diets (MCD or HFD) and superovulated CF1 female oocytes. Fertilized oocytes were transferred to KSOM with 1⁄2 amino acids under mineral oil and cultured at 37°C, humidified and reduced oxygen conditions (5% O2, 5% CO2 and 90% N2) for 4 days. Blastocysts acquired from the embryo culture were transferred to 2.5 dpc pseudopregnant recipient CF1 female mice. Ten blastocysts were transferred to each female using a non-surgical embryo transfer device. Embryo transfer day is determined as embryonic day 3.5 (E3.5) and midgestation embryos and placentas were collected 8 days later.  Once breeding/ART was completed with the male mice, mature sperm from the cauda epididymides were collected with the swim-out method and kept at -80°C until DNA isolation was performed

first: Gurbet

last: Karahan

first: Josee

last: Martel

first: Sophia

last: Rahimi

first: Mena

last: Farag

first: Fernando

last: Matias

first: Amanda

middle: J

last: MacFarlane

first: Donovan

last: Chan


title: Cancer-immune expressional variation in glioblastoma second surgery samples to compare progression and pseudoprogression

status: Public on Dec 04 2023

department: Pathology

country: USA

summary: We performed cancer-immune gene expression analysis on a case series of glioblastoma second surgery samples due to novel enhancement following chemoradiation that were confirmed based on clinico-pathologic outcome as disease progression (PD) or pseudoprogression (psPD). This was accomplished using an nCounter Pancancer 360 IO panel. Our goals were to (1) determine if psPD events could be distinguished from PD events using differences in immune cell activation versus cancer cell proliferation and (2) examine whether samples stratified based on their molecular profile in the same way as documented clinico-pathologic diagnosis.

overall_design: NanoString nCounter pancancer 360 IO panel testing was performed on 48 glioblastoma samples with 27 showing progression (PD) and 21 showing pseudoprogression (psPD) taken from brain resection at second surgery. Sample designation was based upon clinico-pathologic correlation from the electronic health record.


title: Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

country: Spain

institute: CSIC-Instituto de Neurociencias de Alicante

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Although Kdm1a is the most expressed histone demethylase in neurons, its molecular function in the adult brain remains unknown. Here, we found that inducible and forebrain-restricted knockout (ifKO) mice, in which Kdm1a is specifically eliminated in forebrain excitatory neurons during adulthood, display a prominent transcriptional and epigenomic dysregulation signature characterized by the neuronal expression of nonneuronal genes. The combination of super-resolution microscopy images and multi-omic analysis integrating transcriptome, epigenome and chromatin conformation data showed that these genes are target of the polycomb repressor complex 2 (PRC2) and locate in H3K27me3-microdomains encapsulated within the euchromatin compartment. Furthermore, functional assays revealed that both the catalytic activity and the N-terminus intrinsically disordered region of Kdm1a, which provides phase separation properties, are needed to maintain the boundaries between these silent micro-domains and the active chromatin environment. As a result, Kdm1a loss led to the spreading of active histone modifications into the PRC2-repressed genes causing their de-repression. Intriguingly, the investigation of aged mice suggested that these boundaries may also weaken during natural aging. Overall, these results underscore the role of Kdm1a safeguarding chromatin compartmentalization, nuclear phase separation and gene silencing in the adult and aging brain.

overall_design: Expression profiling, Genome binding/occupancy profiling, and chromosome conformation capture by high throughput sequencing for WT and ifKO-Kdm1a mice. Chromatin interaction analysis with paired-end tag sequencing for CTCF in WT.

first: Beatriz

last: del Blanco

first: Angel

last: Barco


title: Transcriptomic analysis of Col,arf2-7,stop1 responding to NAA.

city: qingdao

first: jia

middle: jia

last: liu

address: qingdaojimoaoshanwei

country: China

institute: shandong university

summary: Our objective is to study root stem cell niche. We isolated total RNA from the roots tips of 5-day-old Col-0,arf2-7 and stop1 seedlings. New genes after responding to NAA treatment, during the root development, are discovered.

overall_design: We isolated total RNA from the roots tip of seedlings with or without NAA treatment.

first: Jiajia

last: Liu

first: ZhaoJun

last: Ding


title: SERS analysis of cancer cell-secreted purines reveals a unique paracrine crosstalk in MTAP-deficient tumors

status: Public on Dec 03 2023

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary: The tumor microenvironment (TME) is a dynamic pseudoorgan that shapes the development and progression of cancers. It is a complex ecosystem shaped by interactions between tumor and stromal cells. Although the traditional focus has been on the paracrine communication mediated by protein messengers, recent attention has turned to the metabolic secretome in tumors. Metabolic enzymes, together with exchanged substrates and products, have emerged as potential biomarkers and therapeutic targets. However, traditional techniques for profiling secreted metabolites in complex cellular contexts are limited. Surface-enhanced Raman scattering (SERS) has emerged as a promising alternative due to its nontargeted nature and simplicity of operation. Although SERS has demonstrated its potential for detecting metabolites in biological settings, its application in deciphering metabolic interactions within multicellular systems like the TME remains underexplored. In this study, we introduce a SERS-based strategy to investigate the secreted purine metabolites of tumor cells lacking methylthioadenosine phosphorylase (MTAP), a common genetic event associated with poor prognosis in various cancers. Our SERS analysis reveals that MTAP-deficient cancer cells selectively produce methylthioadenosine (MTA), which is taken up and metabolized by fibroblasts. Fibroblasts exposed to MTA exhibit: i) molecular reprogramming compatible with cancer aggressiveness, ii) a significant production of purine derivatives that could be readily recycled by cancer cells, and iii) the capacity to secrete purine derivatives that induce macrophage polarization. Our study supports the potential of SERS for cancer metabolism research and reveals an unprecedented paracrine crosstalk that explains TME reprogramming in MTAP-deleted cancers.

overall_design: HBF in control conditions vs HBF treated with MTA to resemble the phenotype in MTAP -/- Tumors.

first: Pablo

middle: S

last: Valera

first: Javier

last: Plou

first: Isabel

last: García

first: Ianire

last: Astobiza

first: Cristina

last: Viera

first: Ivan

middle: R

last: Sasselli

first: Arkaitz

last: Carracedo

first: Luis

middle: M

last: Liz-Marzán

first: José

middle: E

last: Martin


title: Identification of potential miRNA–mRNA regulatory network contributing to cytarabine resistance HL60 cells [array]

city: Kaohsiung

first: Yu-Hsin

last: Tseng

address: No.100, Tzyou 1st Rd., Sanmin Dist.

department: Department of Pediatrics

country: Taiwan

institute: Kaohsiung Medical University Hospital

summary: Cytarabine is the main drug for acute myeloid leukemia (AML) treatment; however, drug resistance hinders the treatment of AML. Although microRNA (miRNA) alteration is one of the well-recognized mechanisms underlying drug resistance in AML, few studies have investigated the role and function of miRNAs in the development of cytarabine resistance. In this study, total RNA was isolated from parental HL60 and cytarabine resistant HL60 (R-HL60) cells. Subsequently, miRNAs and mRNAs were detected using small RNA sequencing and gene expression array, respectively. The miRNAs and genes with ≥ 2-fold difference in expression between HL60 and R-HL60 cells were screened out. Negatively correlated miRNA–mRNA pairs were selected as candidate miRNA–mRNA target pairs by using the miRDB, Targetscan or miRTar databases. Functional enrichment analysis of differentially expressed genes (DEGs) included in the candidate miRNA–mRNA network was performed. The results revealed that CCL2, SOX9, SLC8A1, ICAM1, CXCL10, SIPR2, FGFR1, OVOL2, MITF, and CARD10 were simultaneously involved in seven GO pathways, namely the regulation of cell migration, regulation of locomotion, regulation of cellular component movement, cell migration, locomotion, cell motility, localization of cell. These genes were negatively correlated with the altered miRNAs (miR-1-3p, miR-155-5p, miR-1255b-5p, miR-200c-5p, miR-3609, miR-1285-3p, miR-124-3p, miR-146a-5p, miR-497a-5p, and miR-3150a-5p), suggesting that they are the potential targets of the miRNAs to regulate cell migration behavior or ability. Therefore, our results advance our understanding of the regulatory mechanism underlying cytarabine resistance development, specifically related to miRNAs.

overall_design: Total RNA was isolated from parental HL60 and cytarabine resistant HL60 (R-HL60) cells. Subsequently, mRNAs were detected using gene expression array.

first: Yu

middle: H


title: Role of mechanical signal in regulating neutrophil function

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: It is not understood, how mechanical signals influence the behavior and action of circulating cells in our body. Previous studies showed that the process of migration through narrow slits might enhance lifespan of polymorpho-nuclear cells (PMN / neutrophil). But it is unknown, how the mechanical signal is received, relayed, and translated into specific phenotype shift in PMN. Here we investigated whether compressional force affects defense system of circulating lymphocytes by increasing their killing ability during migration through narrow endothelial junctions. To decipher the receiving and transducing components of this mechanical signal relay process, we performed gene expression analysis between transmigrated and non-transmigrated neutrophils. Comparison of early gene-expression pattern of transmigrated and non-transmigrated neutrophils revealed a huge change in gene expression profile. Molecular and genetic analysis of the proteins revealed from gene-expression analysis led us to understand the mechanism of mechanical signal relay from the neutrophil membrane to bacterial-killing machinery. As neutrophils are most abundant and immediate-responding circulating immune cells in our body, our study advances the path for understanding the general process of mechano-transduction, and mechano-modulatory applications with mechanically enhanced neutrophils.

overall_design:
Neutrophils were mobilized to lung of 8-10 weeks old male Catchup (heterozygous) or non-labelled C57BL/6-background mice by exposure to 1mg/ml of nebulized LPS (Sigma, Escherichia coli O55:B5) inside the fumigation chamber. 20 ug of anti-Ly6G-BV421 antibody (Biolegend, #127628) was i.v. injected 2 minutes before sacrifice. Lungs were perfused with 10 ml of PBS through right ventricle of heart and collected for PMN isolation, biochemical, and histopathological analyses. For PMN isolation, a single cell suspension was prepared by digestion of minced lung lobes with collagenase A (1 mg/ml; Millipore-Sigma # SCR103) at a 370C shaking water bath for 45 min. Digested lung samples were passed through 16-17G needle and filtered through 40 um cell strainer (Thermo Fisher, #08-771-1). Red blood cells were removed by using RBC lysis buffer (Thermo Fisher, #00-4333-57). A single cell suspension prepared from Catchup (heterozygous) mice were directly subjected to flow sorting for separation of td-Tomato-positive or double td-Tomato and anti-Ly6G-BV421-positive PMN. PMN, labelled with td-Tomato (or anti-Ly6G-AF-594) and td-Tomato and anti-Ly6G-BV-421 (or anti-Ly6G-AF-594 and anti-Ly6G-BV-421), were sorted in a sterile environment by MoFlo Astrios and MoFlo Astrios EQ (Beckman Coulter) cell sorter equipped with 405, 488, 561 and 635 nm lasers, and collected in RPMI-1640 medium (Thermo Fisher #72400047). Both the sorters are Gates were initially established on forward and side scatter, based on granularity and relative size. Aggregates were gated out accordingly. Selective gates were drawn to sort the single positive and dual positive PMN. Software SUMMIT, 6.1 (Beckman Coulter) was used for sorting and analysis.
Cpp is control dual stained vascular
LPSpp is LPS treated dual stained vascular
LPSp is LPS treated single stained transmigrated to lung

first: Amitabha

last: Mukhopadhyay

first: Asrar

middle: B

last: Malik

first: Yulia

last: Komarova


title: RNA-seq and ChIP-seq in mouse MLL-AF9 leukmemia cells with CRISPR knockout of Sgf29

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: This dataset examined the effect of Sgf29 knockout in mouse MLL-AF9 cells. The gene expression profiling (RNA-seq) and the chromatin targeting of SGF29 (TST-ChIP-seq) are reported.

overall_design: Cas9-expressing mouse MLL-AF9 leukemia cells were transduced with sgCtrl and sgSgf29. RNAseq: The total RNA was extracted using the RNeasy Mini Kit (74104, QIAGEN) and submitted for RNA-seq at Novogene (PE150, NovoSeq6000). H3K9ac ChIP-seq: anti-H3K9ac antibody (61663, Active Motif) cautured genomic DNA was submitted for ChIP-seq at Novogene (PE150, NovaSeq6000). TST-ChIP-seq:  SGF29-TST cautured genomic DNA was submitted for ChIP-seq at Novogene (PE150, NovaSeq6000).

first: Chun-Wei

last: Chen

first: Lu

last: Yang

first: Anthony

last: Chan


title: Identification of potential miRNA–mRNA regulatory network contributing to cytarabine resistance HL60 cells

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Identification of potential miRNA–mRNA regulatory network contributing to cytarabine resistance HL60 cells [miRNA-seq]

overall_design: Total RNA was isolated from parental HL60 and cytarabine resistant HL60 (R-HL60) cells. Subsequently, miRNAs were detected using small RNA sequencing. The miRNAs with ≥ 2-fold difference in expression between HL60 and R-HL60 cells were screened out.


title: Rice transcriptional repressor OsTIE1 controls anther dehiscence and male sterility by regulating JA biosynthesis

status: Public on Dec 02 2023

city: Beijing

first: Yuxing

last: Fang

address: Peking University

institute: Peking University

summary: The coordination of pollen viability, stamen filament elongation and anther dehiscence is essential for the successful pollination and reproduction in angiosperms. The hormone jasmonic acid (JA) are crucial for these processes. However, the tight regulation of JA biosynthesis during stamen development is still largely unknown. Here, we demonstrate that the rice (Oryza sativa) ERF-associated amphiphilic repression (EAR) motif-containing protein TCP INTERACTOR CONTAINING EAR MOTIF PROTEIN1 (OsTIE1) tightly regulates JA biosynthesis by repressing TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATINGCELLFACTORS (TCP) transcription factor OsTCP1/PCF5 during stamen development. The loss of OsTIE1 function in ostie1 mutants causes male sterility. The ostie1 mutants display inviable pollen, the early stamen filament elongation and the precocious anther dehiscence. JA biosynthesis is activated earlier and JA level is precociously increased in anthers of ostie1. The expression of OsTIE1 is developmentally regulated during stamen development. OsTIE1 is localized in nuclei and has transcriptional repression activity. We further show that OsTIE1 directly interacts with OsTCP1, and overexpression of OsTCP1 caused early anther dehiscence resembling that of ostie1. The expression of genes encoding key enzymes of JA biosynthesis including Oryza sativa lipoxygenase (OsLOX) genes is regulated by the OsTIE1-OsTCP1 complex. Our findings discover that the OsTIE1-OsTCP1 module plays critical roles in stamen development by finely tuning JA biosynthesis, and provides a new foundation to create male sterile plants for hybrid seed production.

overall_design: To determine the molecular mechanisms that OsTIE1 affected the anther development, we collected anthers of stage 10 and stage 12 from ostie1-1 and WT control for RNA sequencing (RNA-Seq) analysis

first: Genji

last: Qin


title: Understanding the cell fate and behavior of progenitors at the origin of the mouse cardiac mitral valve

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

country: France

institute: INSERM

summary: Congenital heart malformations include mitral valve defects, which remain largely unexplained. During embryogenesis, a restricted population of endocardial cells within the atrioventricular canal undergoes an endothelial-to-mesenchymal transition to give rise to mitral valvular cells. However, the identity and fate decisions of these progenitors as well as the behavior and distribution of their derivatives in valve leaflets remain unknown. We used single-cell RNA sequencing (scRNA-seq) of genetically labeled endocardial cells and microdissected mouse embryonic and postnatal mitral valves to characterize the developmental road. We defined the metabolic processes underlying the specification of the progenitors and their contributions to subtypes of valvular cells. Using retrospective multicolor clonal analysis, we describe specific modes of growth and behavior of endocardial cell-derived clones, which build up, in a proper manner, functional valve leaflets. Our data identify how both genetic and metabolic mechanisms specifically drive the fate of a subset of endocardial cells toward their distinct clonal contribution to the formation of the valve.

overall_design: Cells were isolated from enbryos from Tie2crex Rosa26 tdTomato female mice after microdissection of the AVC and embryonic mitral valves. At least 60 embryos were used for each stage of development Cells were then FACS sorted using tomato as a reporter and used in 10X chromium

first: Batoul

last: Farhat

first: Ignacio

last: Bordeu

first: Bernd

last: Jagla

first: Hugo

last: Blanc

first: Karine

last: Loulier

first: Benjamin

middle: D

last: Simons

first: Emmanuel

last: Beaurepaire

first: Jean

last: Livet

first: Michel

last: Pucéat


title: Transcriptome analysis of SAP30BP knockdown cells

city: Hirakata

first: Rei

last: Yoshimoto

state: Osaka

address: 45-1 Nagaotoge-cho

department: Faculty of Agriculture

country: Japan

institute: Setsunan University

summary: Examination of transcriptome of SAP30BP knockdown cells by Ribosomal RNA depleted RNA-Seq

overall_design: Ribosomal RNA depleted RNA-Seq

first: Kazuhiro

last: Fukumura


title: Temporal genome-wide fitness analysis of Mycobacterium marinum during infection reveals genetic requirement for virulence and survival in amoebae and microglial cells

status: Public on Dec 01 2023

city: Geneva

first: Thierry

last: Soldati

address: 30 quai Ernest Ansermet, Sciences II

country: Switzerland

institute: University of Geneva

summary: Tuberculosis remains the most pervasive infectious disease and the recent emergence of multiple or even fully drug-resistant strains increases the risk and emphasizes the need for more efficient and better drug treatments. A key feature of mycobacteria pathogenesis, conserved between the human pathogen Mycobacterium tuberculosis and the model pathogen Mycobacterium marinum, is the metabolic switch to lipid catabolism during infection and altered expression of virulence genes in coordination with different stages of infection. This study aims at identifying genes that are involved in the establishment and maintenance of the infection. To achieve this, we have applied Transposon Sequencing (Tn-Seq) to M. marinum, an unbiased genome-wide strategy that combines saturation insertional mutagenesis and high throughput sequencing. This approach allowed us to precisely identify the localization and relative abundance of insertions in pools of transposon mutants. The essentiality of genes and the positive and negative fitness cost of mutations were quantitatively compared between in vitro growth and different stages of infection in two evolutionary distinct host phagocytes, the amoeba Dictyostelium discoideum and the murine BV2 microglial cells. We found that 57% of TA sites in the M. marinum genome were disrupted and that 568 genes (10.2%) were essential for M. marinum, which is comparable to previous Tn-Seq studies on M. tuberculosis and M. bovis. Major pathways involved in the survival of M. marinum during infection of D. discoideum were related to DNA damage repair, vitamin metabolism, the type VII secretion system (T7SS) ESX-1 and the Mce1 lipid transport system.

overall_design: To probe for genetic requirements at different stages of infection, we submitted a transposon insertion library of Mycobacterium marinum to selection by infection of Dictyostelium discoideum or BV2 microglial cells in 3 to 8 replicates, quantified the insertion frequency in each sample (TnSeq), and subsequently compared them to the frequency in the initial library.

first: Louise

last: Lefrançois

first: Jahn

last: Nitschke

first: Huihai

last: Wu

first: Gaël

last: Panis

first: Julien

last: Prados

first: Rachel

last: Butler

first: Tom

middle: A

last: Mendum

first: Nabil

last: Hanna

first: Graham

last: Stewart


title: Structural basis of H2A.Z recognition and H4K20 methylation by SUV420H2

city: Shenzhen

first: Zengqi

last: Wen

state: Guangdong

address: No 66, Gongchang Road, Guangming District

department: School of Medicine

institute: Sun Yat-sen University

summary: DNA replication ensures the accurate transmission of genetic information during cell cycle. The interaction between histone methyltransferase SUV420H1 and histone variant H2A.Z plays a critical role in the licensing of early replication origins. However, the mechanism by which SUV420H1 preferentially recognizes H2A.Z-nucleosome and deposits H4 lysine 20 dimethylation (H4K20me2) on DNA replication origins remains elusive. Here, we determined the cryo-EM structures of SUV420H1 bound to H2A.Z-nucleosome or H2A-nucleosome. Our structures show that the SUV420H1 catalytic domain (CD) directly interacts with histone H4 and nucleosomal DNA, whereas a SUV420H1 arginine-rich motif (ARM) anchors to the acidic patch of the nucleosome. The N-terminal aminal acid residues of H4 (Aa 1-24) forms a lasso-shaped structure sandwiched between SUV420H1 CD and nucleosome. The lasso-shaped structure stabilizes the SUV420H1-nucleosome interaction and precisely projects the H4 K20 residue into the SUV420H1 catalytic center. Further analyses revealed a crucial role of SUV420H1 KR-loop (aminal acid residues 214-223), which spatially lies closely to H2A.Z specific residues D97/S98, in dictating the preference for H2A.Z-nucleosome. SUV420H1 K219A/R220A mutations reduced the activity of SUV420H1 for H4K20me2 modification, the preference of SUV420H1 for H2A.Z-nucleosome, and the efficiency of DNA replication initiation. Collectively, our findings elucidate how SUV420H1 preferentially recognizes H2A.Z-nucleosome to deposit H4K20me2 modification and shed light on therapeutic strategies targeting the DNA replication initiation.

overall_design: SNS-seq, BrdU-IP-seq and CUT&Tag were performed in wild type and SUV420H1 knockout or mutant cells, two replicates were used for each test.


title: Single-Cell Morphological and Transcriptome Analysis Unveil Inhibitors of Polyploid Giant Breast Cancer Cells In Vitro

city: Pittsburgh

first: Yu-Chih

last: Chen

state: Pennsylvania

address: 5115 Centre Ave

institute: UPMC Hillman Cancer Center/University of Pittsburgh

summary: Considerable evidence suggests that breast cancer therapeutic resistance and relapse can be driven by polyploid giant cancer cells (PGCCs). The number of PGCCs increases with the stages of disease and therapeutic stress. Given the importance of PGCCs, it remains challenging to eradicate them. To discover effective anti-PGCC compounds, there is an unmet need to rapidly distinguish compounds that kill non-PGCCs, PGCCs, or both. Here, we establish a single-cell morphological analysis pipeline with a high throughput and great precision to characterize dynamics of individual cells. In this manner, we screen a library to identify promising compounds that inhibit all cancer cells or only PGCCs (e.g., regulators of HDAC, proteasome, and ferroptosis). Additionally, we perform scRNA-Seq to reveal altered cell cycle, metabolism, and ferroptosis sensitivity in breast PGCCs. The combination of single-cell morphological and molecular investigation reveals promising anti-PGCC strategies for breast cancer treatment and other malignancies.

overall_design: Breast cancer cells were treated with and without Docetaxel. The populations were sorted based on nucleus size as polyploid and non-polyploid cells.  Drop-Seq.


title: A single cell RNAseq benchmark experiment embedding "controlled" cancer heterogeneity

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: Single-cell RNA sequencing (scRNA-seq) has emerged as a vital tool in tumor research, enabling exploration of molecular complexities at the individual cell level. It offers new technical possibilities for advancing tumor research and is anticipated to yield significant breakthroughs. However, deciphering meaningful insights from scRNA-seq data poses challenges, particularly in cell annotation and tumor subpopulation identification. Efficient algorithms are needed to unravel the intricate biological processes of cancer. To address these challenges, benchmarking datasets are essential to validate bioinformatics tools focusing on the analysis of single-cell omics in oncology. Here, we present a 10XGenomics scRNA-seq experiment, providing a controlled heterogeneity environment using lung cancer cell lines characterised by expressing seven different driver genes (EGFR, ALK, MET, ERBB2, KRAS, BRAF, ROS1), which are characterised by the presence of partial overlaps in their functional pathways. Furthermore, PBMC from a healthy donor were also sequenced

overall_design: PC9 (EGFR Del19, activating mutation, PMID: 21167064; A549 (KRAS p.G12S, growth and proliferation,  PMID: 20358631; NCI-H596 (HTB178, MET Del14 , enhanced protection from apoptosis and cellular migration PMID: 35636967; NCI-H1395 (CRL5868, BRAF p.G469A, gain of function, resistant to all tested MEK +/− BRAF inhibitors, PMID: 32540409; DV90 (ERBB2 p.V842I, increases kinase activity, PMID: 23220880; HCC78 (SLC34A2-ROS1 Fusion, ROS1 inhibitors have antiproliferative effect PMID: 22919003; CCL.185.IG (EML4-ALK Fusion-A549 Isogenic Cell, https://www.atcc.org/products/ccl-185ig); White cell from donor buffy coat (PBMC). All cell lines were purchased and cultured as suggested by the manufacturer. scRNA-seq was done using 10XGenomics platform.

first: Maddalena

last: Arigoni

first: Maria

middle: L

last: Ratto

first: Federica

last: Riccardo

first: Francesca

last: Cordero

first: Marco

last: Beccuti

first: Luca

last: Alessandri


title: Transciptome profile of TrmB and TbsP, Genome-wide binding of TbsP (HVO_2861) in Haloferax volcanii

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 124 Science Dr

institute: Duke University


title: RNAseq analysis of two Drosophila mitochondrial complex I deficiency models

city: London

first: Debbra

middle: Y.

last: Knorr

address: 125 Coldharbour Lane

country: United Kingdom

institute: King's College London

summary: RNAseq was performed from Drosophila head tissue of two mitochondrial complex I deficiency models. The NDUFS1 homolog ND-75 was knocked down in Drosophila neurons using nSybGal4. Heads were collected from control of ND-75 knockdown flies and used for RNAseq analysis.

overall_design: nSybGal4 flies were crossed to either w[1118] control flies or ND-75 RNAi flies (HMS00853). Heads were collected from 20 progeny for each genotype with 4 biological replicates.

first: Joseph

last: Bateman

middle: Y

first: Lucy

last: Granat


title: Transciptome profile of TrmB and TbsP in Haloferax volcanii [RNA-seq]

summary: The hypersaline-adapted archaeon Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. The transcriptional regulator TrmB maintains the rod shape in the related species Halobacterium salinarum by activating the expression genes involved in gluconeogenesis. Here we investigated the role of TrmB in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name TrmB suppressor, or TbsP. TbsP is required for adhesion to abiotic surfaces and maintains wild-type cell morphology and motility. To better understand the roles of TrmB and TbsP, we conducted expression profiling in ∆trmB, ∆tbsP, ∆trmB∆tbsP in response to glucose availability. TrmB and TbsP jointly regulate the transcription of gapII, fbp, and ppsA.

overall_design: Transcripome profiling (RNA-seq) of TrmB and TbsP in the halophilic archaeon Haloferax volcanii in the presence and absense of glucose after 24 hours.

first: Rylee

last: Hackley

first: Preeti

last: Bhanap

first: Mar

last: Martinez Pastor


title: Shaping immune landscape of colorectal cancer by cholesterol metabolites [C57BL/6]

city: Shanghai

first: Haochen

last: Yang

state: Shanghai

address: 320 Yue-yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Cancer immunotherapies have achieved unprecedented success in clinic, but they remain largely ineffective in some major types of cancer, such as colorectal cancer with microsatellite stability (MSS CRC) (Picard et al., 2020). It is therefore important to study tumor microenvironment of resistant cancers for developing new intervention strategies. In this study, we identify a metabolic cue that determines the unique immune landscape of MSS CRC. Through secretion of distal cholesterol precursors, which directly activate RORgt, MSS CRC cells can polarize T cells toward Th17 cells that have well-characterized pro-tumor functions in colorectal cancer. Analysis of large human cancer cohorts revealed an asynchronous pattern of the cholesterol biosynthesis in MSS CRC, which is responsible for the abnormal accumulation of distal cholesterol precursors. Inhibiting the cholesterol biosynthesis enzyme Cyp51 by ketoconazole, a clinically approved drug, reduced the levels of intratumoral distal cholesterol precursors and suppressed tumor progression through a Th17-modulation mechanism in preclinical MSS CRC models. Our study therefore reveals a novel immune-modulation mechanism of oncometabolites and an invention strategy for the difficult-to-treat MSS CRC.

overall_design: Use AOM/DSS induced CRC model of C57BL/6 mice and take paired tumor and colon tissue to perform RNA-seq.

first: Yibing

last: Bai

first: Tongzhou

last: Li

first: Qingshu

last: Wang

first: Weiqiang

last: You

first: Zhigang

first: Zheng-Jiang

last: Zhu

first: Chenqi

last: Xu


title: Disruption of H3K36 methylation provokes cellular plasticity to drive aberrant glandular formation and squamous carcinogenesis

city: Philadelphia

first: Brian

middle: C.

last: Capell

state: PA

address: 421 Curie Boulevard Biomedical Research Building 1020 Biomedical Research Building 1020

department: Dermatology

institute: University of Pennsylvania


title: Disruption of H3K36 methylation provokes cellular plasticity to drive aberrant glandular formation and squamous carcinogenesis (Spatial Transcriptomics)

summary: To investigate the role H3K36 methylation in stratifying epithelia

overall_design: A mutant histone "H3K36M" was expressed in the keratin-14 expressing tissues of mice

first: Eun

last: Ko

last: Anderson

first: Carina

last: D'souza

first: Jonathan

last: Zou

first: Sijia

last: Huang

first: Sohyun

last: Cho

first: Faizan

last: Alawi

first: Stephen

last: Prouty

first: Vivian

last: Lee

first: Sora

last: Yoon

first: Keegan

last: Krick

first: Yoko

last: Horiuchi

first: Kai

last: Ge

first: John

middle: T

last: Seykora

middle: C


title: Disruption of H3K36 methylation provokes cellular plasticity to drive aberrant glandular formation and squamous carcinogenesis (RNA-Seq)

first: Amy


title: Disruption of H3K36 methylation provokes cellular plasticity to drive aberrant glandular formation and squamous carcinogenesis (CUT&RUN)


title: Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments [scRNA-Seq]

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

institute: Ospedale Pediatrico Bambino Gesù

summary: Brain tumors are the leading cause of cancer-related death in children. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of pediatric brain cancer are limited and hard to establish. We present a protocol that enables efficient generation, expansion and biobanking of pediatric brain cancer organoids. Utilizing our protocol, we have established patient-derived organoids (PDOs) from ependymomas, medulloblastomas, low-grade glial tumors and patient-derived xenograft organoids (PDXOs) from medulloblastoma xenografts. PDOs and PDXOs recapitulate histological features, DNA methylation profiles and intratumor heterogeneity of the tumors from which they were derived. We also showed that PDOs can be xenografted. Most interestingly, when subjected to the same routinely applied therapeutic regimens, PDOs respond similarly to the patients. Taken together, our study highlights the potential of PDOs and PDXOs for research and translational applications for personalized medicine.

overall_design: Cells from the three different samples (tumor and 2 PDOs) have been next integrated based on the reciprocal PCA (“RPCA”) approach, performed with FindIntegrationAnchors (settings: 5000 genes selected for data integration) and IntegrateData function in Seurat. Unsupervised cluster analysis was performed by exploiting the shared nearest neighbor (SNN) modularity clustering algorithm implemented in Seurat function FindClusters. Differentially expressed genes across the cell clusters were annotated using the wilcox test in Seurat function FindAllMarkers.


title: Genome-wide binding of TbsP (HVO_2861) in Haloferax volcanii [CHIP-seq]

last: Schmid

summary: The hypersaline-adapted archaeon Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. The transcriptional regulator TrmB maintains the rod shape in the related species Halobacterium salinarum by activating the expression genes involved in gluconeogenesis. Here we investigated the role of TrmB in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name TrmB suppressor, or TbsP. TbsP is required for adhesion to abiotic surfaces and maintains wild-type cell morphology and motility. We identified TbsP binding sites in the presence and absence of glucose to better understand the role of TbsP. TbsP does not bind DNA in response to glucose availability. The sole binding site near a metabolic enzyme-coding gene is upstream of gapII.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of TbsP in the halophilic archaeon Haloferax volcanii in the presence and absense of glucose.

first: Sungmin

last: Hwang

first: Rylee

last: Hackley


title: Astrocyte-produced HB-EGF limits autoimmune CNS pathology

city: Erlangen

first: Mathias

last: Linnerbauer

address: Schwabachanlage 6

department: Neurology

country: Germany

institute: University Hospital Erlangen


title: Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Pressure Stimuli: A Transcriptomic Study in Human Cartilage Explants

city: Lausanne

first: Dominique

middle: P.

last: Pioletti

state: Vaud

address: EPFL

department: STI IBI

institute: EPFL

summary: During daily activities, cartilage encounters complex biophysical cues upon loading. Foremost among these is the coupled stimulation of hydrostatic pressure (HP) and loading-induced temperature increase (T), which encompasses both mechanical and thermal aspects of biophysical stimulations in cartilage. While prior research on this subject has been initiated in our laboratory, the detailed mechanisms of combined HP-T effects on chondrocytes in their natural environment remain largely unexplored. Using a custom bioreactor, we applied both isolated and combined HP-T stimuli to cartilage explants obtained from a non-inflammatory adolescent knee joint. Tissue and cellular responses were evaluated through histochemical staining and transcriptomic analyses, employing bulk RNA-sequencing complemented with signaling enrichment analyses. Our findings reveal that the thermal component of the coupled HP-T stimulation predominantly regulates the chondrocytes' transcriptional profile during the stimulation period. When coupled with HP stimulation, a peak in chondroinduction was observed. This coupling process notably boosted chondroprotection in a synergistic manner, as demonstrated by the corresponding enhanced negative regulation of apoptotic processes and increased levels of Heat Shock Protein 70 (HSPA). Our study suggests that the upregulation in protein translation and processing, triggered by thermal stimulation, may serve as an adaptive mechanism in chondrocytes to mechanical simulations, thereby contributing to the observed synergy during the coupling of these two biophysical stimuli. The results highlight the potential of integrating thermal stimulation, a natural accompanying process during cartilage deformation, in tissue engineering, cell therapy or physiotherapy.

overall_design: Using a previously developed customized bioreactor, various biophysical stimulation protocols were administered for 1.5 hours daily over five consecutive days. Four experimental groups were considered and the specific stimulation details for each group are: (1) Control group (“C”): Maintained at a steady 32.5 ℃ within the bioreactor, replicating the resting knee temperature, with no applied hydrostatic pressure (HP) or temperature increase. (2) Isolated pressure group (“P”): While kept consistently at 32.5 ℃, samples underwent sinusoidal cyclic HP loading with a 5 MPa amplitude at 1 Hz. (3) Isolated temperature increase group (“T”): Samples were exposed to a gradual temperature rise from 32.5 ℃ to 38.7 ℃ without any HP loading. This temperature profile mirrors the intra-articular temperature evolution observed during a 1.5-hour jogging. (4) Coupled HP-T stimulation group (“PT”): Samples were concurrently subjected to a 5 MPa cyclic HP loading (as in the “P” group) and a temperature increase from 32.5 ℃ to 38.7 ℃ (as in the “T” group) for the entire 1.5-hour stimulation duration. In each group, the stimulation medium was replaced every other day. Samples of all conditions were harvested immediately after the last stimulation and processed accordingly to the analysis described below.


title: Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments [array]

type: Methylation profiling by genome tiling array

overall_design: Generated methylation data were compared to brain tumor classifier v11b4-v11b6 (Capper et al, 2018), while the most recent classifier version v12.5 was consulted for tumor subtype annotation. High-density DNA methylation arrays also allowed for determining copy number alterations.


title: Astrocyte-produced HB-EGF limits autoimmune CNS pathology [WGBS]

summary: Central nervous system (CNS) resident cells such as microglia, oligodendrocytes and astrocytes are gaining increasing attention in respect to their contribution to CNS pathologies including Multiple Sclerosis (MS). Several studies have demonstrated the involvement of pro- inflammatory glial subsets in the pathogenesis and propagation of inflammatory events in MS and its animal models. However, it has only recently become clear that the underlying heterogeneity of astrocytes and microglia can not only drive inflammation, but also lead to its resolution through direct and indirect mechanisms. Failure of these tissue-protective mechanisms may potentiate disease and increase the risk of conversion to progressive stages of MS, for which currently available therapies are limited. Using proteomic analyses of cerebrospinal fluid specimens from MS patients in combination with experimental studies, we here identify Heparin-binding EGF-like growth factor (HB-EGF) as a central mediator of tissue-protective and anti-inflammatory effects important for the recovery from acute inflammatory lesions in CNS autoimmunity. Hypoxic conditions drive the rapid upregulation of HB-EGF by astrocytes during early CNS inflammation, while pro-inflammatory conditions suppress trophic HB-EGF signaling through epigenetic modifications. Finally, we demonstrate both anti-inflammatory and tissue-protective effects of HB-EGF in a broad variety of cell types in vitro and use intranasal administration of HB-EGF in acute and post-acute stages of neuroinflammation to attenuate disease in a preclinical mouse model of MS. Altogether, we identify astrocyte-derived HB-EGF and its epigenetic regulation as a novel modulator of autoimmune CNS inflammation and potential therapeutic target in MS.

overall_design: Whole Genome Bisulfite Sequencing (WGBS) of FACS sorted naive astrocytes and from peak experimental autoimmune encephalomyelitis (EAE)

first: Veit

last: Rothhammer

first: Maja

last: Jagodic

first: Lara

last: Kular

first: Ewoud

last: Ewing

first: Maria

last: Needhamsen

first: Yanan

last: Han


title: Antisense oligonucleotide-mediated disruption of HTT caspase-6 cleavage site ameliorates the phenotype of YAC128 Huntington disease mice

city: Leiden

first: Elsa

last: Kuijper

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

summary: In Huntington’s Disease, cellular toxicity is particularly caused by toxic protein fragments generated from the mutant huntingtin (HTT) protein. By modifying the HTT protein, we aim to reduce proteolytic cleavage and ameliorate the consequences of mutant HTT without lowering total HTT levels. To that end, we use an antisense oligonucleotide (AON) that targets HTT pre-mRNA and induces partial skipping of exon 12, which contains the critical caspase-6 cleavage site. Here, we show that AON-treatment can partially restore the phenotype of YAC128 mice, a mouse model expressing the full-length human HTT gene including 128 CAG-repeats. Wild-type and YAC128 mice were treated intracerebroventricularly with AON12.1, scrambled AON or vehicle starting at 6 months of age and followed up to 12 months of age, when MRI was performed and mice were sacrificed. AON12.1 treatment induced around 40% exon skip and protein modification. The phenotype on body weight and activity, but not rotarod, was restored by AON treatment. Genes differentially expressed in YAC128 striatum changed towards wild-type levels and striatal volume was preserved upon AON12.1 treatment. However, scrambled AON also showed a restorative effect on gene expression and appeared to generally increase brain volume.

overall_design: RNAseq data from striatum obtained from YAC128 mice treated with aCSF, scrambled AON or AON12.1 and aCSF-treated wild-type mice of about 12 months of age.

first: Willeke

last: van Roon-Mom

first: Yavuz

last: Ariyurek

first: Hailiang

last: Mei


title: Gene expression profile at single cell level of 72 hpf heart cells from wild-type, tnnt2a mutant, and Tnnt2a degron zebrafish larvae.

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Heart cells are responsive to cardiac contractions and hemodynamic forces.  We use single cell RNA sequencing (scRNA-seq) to compare tnnt2a mutants with Tnnt2a degrons, both conditions leading to cardiac contraction defects.

overall_design: For each condition, 100 hearts were dissected, dissociated, and analyzed using scRNA-seq.

first: Thomas

last: Juan

first: Bárbara

last: Cardoso

first: Héloïse

last: Athéa

first: Nana

last: Fukuda

first: Marga

last: Albu

first: Mario

last: Looso

first: Didier

last: Stainier


title: Srsf2P95H/+  mutation exacerbates Asxl1Y588XTg-induced leukemogenesis

city: San Antonio

first: Pinpin

last: Sui

state: TX

address: 8403 Floyd Curl Dr., STRF

department: Molecular Medicine

institute: UT health San Antonio

summary: Additional sex comb-like 1 (ASXL1) is frequently mutated in a spectrum of myeloid malignancies and is associated with poor prognosis. Cancer genome sequencing found that AXL1 mutations frequently co-occur with splicing factors’ mutations (SRSF2, U2AF1, ZRZR2 and SF3B1) in myeloid malignancies. Several studies have reported that Patients with both ASXL1 and splicing mutations have a significantly worse prognosis than those with a single type of mutation, but the mechanisms largely remain to be elucidated. Here we constructed an ASXL1 and SRSF2 co-mutated mouse model and found that Srsf2P95H/+ mutation exacerbated Asxl1Y588XTg-induced leukemogenesis. Mechanistically, the co-existence of ASXL1 mutation and SRSF2 mutation altered the function of hematopoietic stem and progenitor cells and resulted in skewed myeloid differentiation.

overall_design: RNA-seq for bone marrow  Lin-cKit+Sca-1+ cells from WT (n=4), Asxl1Y588XTg (n=4), Srsf2P95H/+ (n=4) and  Asxl1Y588XTg;SRSF2P95H/+ (n=3) mice.

first: Guo

last: Ge

first: Feng-Chun

last: Yang


title: Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [DNA-seq_distribution]

city: Seattle

first: John

middle: K.

last: Lee

state: Washington

address: 1100 Fairview Ave N Rm E2-430

institute: Fred Hutch Cancer Research Ctr

summary: Available genetically-defined cancer models are limited in genotypic and phenotypic complexity and underrepresent the heterogeneity of human cancer. Herein, we describe a combinatorial genetic strategy applied to an organoid transformation assay to rapidly generate diverse, clinically relevant models of bladder and prostate cancer. Importantly, the clonal architecture of the resultant tumors can be resolved using single-cell or spatially resolved next-generation sequencing to uncover polygenic drivers of cancer phenotypes.

overall_design: 2-step PCR was performed on prostate organoid cells transduced with a pooled lentivirus containing candidate oncogenic events to amplify the oncogenic barcode region, helping deconvolute distribution of each oncogenic event transduced in the cells. The distributions of oncogenic barcode were retrieved in each sample. Th distribution was used to determine if each oncogenic events were evenly distributed in the transduced cells.

first: Shan

last: Li

first: Alicia

last: Wong

first: Huiyun

last: Sun


title: Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [scDNA-seq_MOI]

overall_design: scDNA sequencing was performed on the prostate organoid cells transduced with different MOI of the pooled lentivirus containing candidate oncogenic events. Different cell population with different virus copy number were retrieved to compare the transduction efficiency in each MOI group.


title: Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [scDNA-Seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: scDNA sequencing was performed on the bladder/prostate tumors generated by transducing the bladder urothelial cells with a pooled lentivirus containing candidate oncogenic events, in order to deconvolute the clonality and heterogenity formed in the generated tumors. Different cell populations were identified in each tumor samples with enriched candidate factors in each population.


title: Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations

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

overall_design: Refer to individual Series


title: Ketogenic diet therapy for pediatric epilepsy is associated with alterations in the human gut microbiome that confer seizure resistance in mice

city: Los Angeles

first: Gregory

last: Lum

state: California

address: 610 Charles E Young Drive, East

department: Integrative Biology and Physiology

institute: UCLA

summary: To investigate the effects of transplanted pre-ketogenic diet (pre-KD) and post-ketogenic diet (post-KD) human fecal microbiota on recipient germ-free swiss webster brain gene expression profiles

overall_design: Comparative gene expression profiling analysis of RNA-seq data from hippocampal and frontal cortex of germ-free swiss webster WT mice transplanted with pre-KD or post-KD human fecal microbiota

first: Elaine

last: Hsiao


title: Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [bulk DNA-Seq]

overall_design: 2-step PCR was performed on laser captured section of FFPF samples of bladder tumors generated by transducing the bladder urothelial cells with a pooled lentivirus containing candidate oncogenic events to amplify the oncogenic barcode region, helping deconvolute oncogenic events involved in initiating the tumors. The distributions of oncogenic barcode were retrieved in each sample. The overlapping enriched factors for different histology were identified to be potentially invovled in the histology initiation.


title: Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [RNA-Seq]

overall_design: Bulk RNA-seq was performed on laser captured section of FFPF samples of bladder tumors with different histology generated by transducing the bladder urothelial cells with a pooled lentivirus containing candidate oncogenic events to profile the transcriptome of tumors with different phenotypes. Analysis was performed to compare transcriptome profile of the tumors from different histology group.


title: Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection

city: New York

first: Pushkala

last: Jayaraman

state: New York

address: 1 Gustave Levy Pl

department: Charles Bronfman Institute of Personalized Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Background: Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms.   Methods: Using measurements of ~4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N= 437), we identified 413 higher plasma abundances of protein targets and 40 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p <0.05). Of these, 62 proteins were validated in an external cohort (p <0.05, N =261).   Results: We demonstrate that COVID-AKI is associated with increased markers of tubular injury (NGAL) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p <0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2, trefoil factor 3, transmembrane emp24 domain-containing protein 10, and cystatin-C indicating tubular dysfunction and injury.   Conclusions: Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.

overall_design:
We used serum protein measurements from patients hospitalized with COVID-19. We defined an AKI cohort using proteomic data acquired at the last available timepoint during the hospital course for all individuals. Controls were defined as individuals who developed AKI stage 1 or did not develop AKI during their hospital course. We used the SomaScan discovery platform to quantify levels of protein expression. See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data and associated metadata including detailed description for process workflow.

Submitter states: The raw data files are .adat files and contain identifiable sample IDs that cannot be deidentified in the adat file.  Therefore the raw data files will not be provided.

first: Ishan

last: Paranjpe

first: Chen-Yang

last: Su

first: Sirui

last: Zhou

first: Steven

last: Chen

first: Ryan

last: Thompson

first: Diane

last: Del Valle

first: Ephraim

last: Kenigsberg

last: Zhao

first: Suraj

last: Jaladanki

first: Kumardeep

last: Chaudhary

last: Ascolillo

first: Akhil

last: Vaid

first: Arvind

last: Kumar

first: Edgar

last: Kozlova

first: Manish

first: Ross

last: O’Hagan

first: Samir

last: Kamat

first: Faris

middle: F

last: Gulamali

first: Justin

last: Kauffman

first: Hui

last: Xie

first: Joceyln

last: Harris

first: Manishkumar

last: Patel

first: Kimberly

last: Argueta

first: Craig

last: Batchelor

first: Kai

last: Nie

first: Sergio

last: Dellepiane

first: Leisha

last: Scott

first: Matthew

last: Levin

last: He

first: Mayte

last: Suarez-Farinas

middle: G

last: Coca

first: Lili

last: Chan

first: Evren

middle: U

last: Azeloglu

first: Eric

last: Schadt

first: Noam

last: Beckmann

first: Sacha

last: Gnjatic

first: Miram

last: Merad

first: Seunghee

last: Kim-Schulze

first: Brent

last: Richards

first: Benjamin

middle: S

last: Glicksberg

first: Alexander

middle: W

last: Charney


title: Molecular characterization of aged human eccrine gland cells using single-cell transcriptomic analysis

city: Kyoto

first: DUERNA

last: TIE

state: Kyoto

address: 54 Shogoin Kawara-machi, Sakyo

institute: Kyoto University Faculty of Medicine

summary: To uncover the natural cell heterogeneity state of healthy eccrine sweat gland (ESG) at the gene level, we obtained normal human skin tissue from three subjects without clinical evidence or a history of inflammatory or systemic skin disease and isolated the ESG performed single-cell (sc) RNA sequencing assay.

overall_design: The ESGs were stained with neutral red and then isolated from human skin tissue under a stereomicroscope using forceps.Then single cells of isolated ESGs were prepared and analyzed using scRNAseq.

first: Duerna

last: Tie

first: Yoshihiro

last: Ishida

first: Saeko

last: Nakajima

first: Kenji

last: Kabashima


title: A Molecular Signature Defining Exercise Adaptation and In Vivo Reprogramming in Skeletal Muscle

city: Fayetteville

first: Kevin

last: Murach

state: AR

address: 155 Stadium Dr.

department: Health, Human Performance, and Recreation

institute: University of Arkansas


title: A Molecular Signature Defining Exercise Adaptation and In Vivo Reprogramming in Skeletal Muscle [BiSulfite-seq]

summary: Methylome comparison to elucidate the effects of myc on molecular reprogramming in skeletal muscle tissue.

overall_design: Analyzed methylome from murine soleus muscle with myc overexpression (via tetracycline system of doxycycline-inducible gene expression) to late life murine exercise.

first: Ronald

last: Jones III


title: Astrocyte-produced HB-EGF limits autoimmune CNS pathology [RNA-Seq]

first: Mathias

last: Linnerbauer

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ACSA2 positive astrocytes during peak and late stage worsening of experimental autoimmune encephalomyelitis (EAE)

first: Veit

last: Rothhammer

first: Lena

last: Lößlein

first: Oliver

last: Vandrey


title: A Molecular Signature Defining Exercise Adaptation and In Vivo Reprogramming in Skeletal Muscle [RNA-seq]

summary: Transcriptome comparison to elucidate the effects of exercise on molecular reprogramming in skeletal muscle tissue.

overall_design: Compared transcriptomes from murine soleus and quad muscle with myc overexpression (via tetracycline system of doxycycline-inducible gene expression) to late life murine exercise.


title: Genetic factors underlying immune response to tick infestation of resistant and susceptible cattle unrevealed by omics data integration

city: Bagé

first: Robert

last: Domingues

state: Rio Grande do Sul

address: Av. General Osório 1737/302

department: Animal health

country: Brazil

institute: Embrapa

overall_design: Thirty-nine Braford cattle were artificially infected with approximately 20,000 cattle tick larvae (Rhipicephalus microplus). The animals belong to two contrasting phenotypic groups and represent biological replicates: 20 resistant and 19 susceptible. Skin biopsy samples were collected before infestation and 24 hours after infestation.

first: Carvalho

last: Wanessa Araújo

first: Gaspar

last: Emanuelle Baldo

first: Domingues

last: Robert

first: Regitano

last: Correia de Almeida

first: Cardoso

last: Fernando Flores


title: The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

summary: Polycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. In recent years, there is increasing evidence of the complexity of PRCs’ interaction networks and the interplay of these interactors with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a chromatin player able to counteract the deposition of the two PRCs epigenetic hallmarks in Arabidopsis thaliana. We demonstrated that UBP5 is a plant developmental regulator based on functional analyses of ubp5-CRISPR Cas9 mutant plants. UBP5 promotes H2A monoubiquitination erasure, leading to transcriptional de-repression. Furthermore, preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 gaining in ubp5 mutant plants suggest the existence of functional interplays between UBP5 and PRC2 in regulating epigenome dynamics. In summary, acting as an antagonist of the pivotal epigenetic repressive marks H2Aub and H3K27me3, UBP5 provides novel insights to disentangle the complex regulation of PRCs’ activities.

overall_design: Comparison of transcriptomes of Col-0 and ubp5 mutant seedlings using 3'RNA-seq (four biological replicates).

first: James

last: Godwin

first: Szymon

last: Swiezewski

first: Sara

last: Farrona


title: Spatial coupling of microbes and immune cells in solid malignancies.

first: Gregory

middle: L.

last: Beatty

address: 3400 Civic Center Blvd, South Pavilion, Rm 8-107

department: Medicine

summary: Microbes are an integral component of the tumor microenvironment (TME). However, mechanisms that direct microbial recruitment into tumors and the spatial relationship between intratumoral microbes and host cells remain poorly understood. Here, we show that microbes and immune cells have parallel spatial distribution and that the presence of intratumoral microbes is dependent on T cells. Analysis of human pancreatic ductal adenocarcinomas (PDAC) and lung adenocarcinomas (LUAD) revealed a spatially heterogeneous distribution of lipopolysaccharide (LPS) that is associated with T cell infiltration. Using mouse models of PDAC, we found that microbes were more abundant and diverse in tumors that were enriched in T cells compared to tumors that lacked T cells, despite no significant differences in the fecal microbiome. Consistent with these findings, we detected elevated levels of microbial genes in T cell-enriched tumor nests in human PDAC. Compared to microbe-poor tumor nests, microbe-enriched tumor nests displayed a higher number of myeloid cells, B cells, and plasma cells. Microbe-enriched tumor nests also showed upregulation of immune-related processes, including responses to bacteria, and receptors that mediate mucosal immune responses to microbes. Administration of antibiotics to tumor-bearing mice altered the phenotype and presence of intratumoral myeloid cells and B cells but did not alter T cell infiltration. In contrast, depletion of T cells reduced the presence of intratumoral microbes. Our results identify a novel coupling between microbes and the intratumoral immune landscape, with T cells shaping microbial presence and subsequent microbial-host interactions.

overall_design: RNA isolated from T cell-poor ("cold") tumors and T cell-enriched ("hot") tumors treated with or without anti-CD4 and CD8 antibodies or antibiotics were analyzed using QuantSeq 3' mRNA sequencing.

first: Yan

last: Li

first: Renee

middle: B

last: Chang

first: Jae

last: Lee


title: PTPN2 regulates metabolic flux to affect beta cell susceptibility to inflammatory stress

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

summary: Protein tyrosine phosphatase N2 (Ptpn2) is a type 1 diabetes (T1D) candidate gene identified from human genome-wide association studies. PTPN2 is highly expressed in human and murine islets and becomes elevated upon inflammation, suggesting that PTPN2 may be important for beta cell survival in the context of T1D. To test whether PTPN2 contributed to beta cell dysfunction in an inflammatory environment, we generated a beta cell-specific deletion of Ptpn2 in mice (Ptpn2 βKO). While unstressed animals exhibit normal metabolic profiles, streptozotocin (STZ) Ptpn2 βKO mice display marked increase in hyperglycemia and death due to exacerbated beta cell loss. Furthermore, cytokine treated Ptpn2 KO islets resulted in mitochondrial defects and reduced glucose-induced metabolic flux, suggesting beta cells lacking Ptpn2 are more susceptible to inflammatory stress associated with T1D due to compromised metabolic fitness.

overall_design: RNA-seq of Ctrl and PTPN2-bKO islets with and without treatment of cytokines (4 total conditions).

first: Yong

last: Kim

first: Young

middle: J

first: Michelle

last: Guney

first: Tiffany

last: Zee

first: Gerad

last: Karsenty

first: Ernesto

last: Nakayasu

first: Lori

last: Sussel


title: circRNA-based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish (Danio rerio)

city: Erzurum

first: Selçuk

last: Özdemir

address: Atatürk University Faculty of Veterinary Medicine

country: Turkey

institute: Atatürk University

summary: Cypermethrin (CYP) and chlorpyrifos (CPF) are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish, which is non-target organisms. However, circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study, circRNAs were identified and characterized using RNA-seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up-regulated, 10 circRNAs were down-regulated in CYP brain samples compared to controls . In addition, it was found that 57 circRNAs are up-regulated and 3 circRNAs down-regulated in CPF brain samples compared to controls. Moreover, 62 circRNAs were down-regulated in the CYP samples, when CYP and CPF samples were compared. However, up-regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway, endocytosis mechanism, apoptosis and p53 signaling pathway. This study, which was conducted for the first time in terms of the subject of the study, could bring a different perspective especially to pesticide toxicity studies.

overall_design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish


title: Trancriptomic analysis of leukemic bone marrow cells with GFI1 wildtype, GFI1 SNP variant (GFI1-36N) and low level of GFI1 expression

city: Luebeck

first: Pradeep

middle: Kumar

last: Patnana

state: Schleswig-Holstein

address: Ratzeburger Allee 160

institute: Universitätsklinikum Schleswig-Holstein

summary: GFI1 is a transcriptional repressor protein that plays an essential role in HSCs development, lymphoid and myeloid differentiation and Acute Myeloid Leukaemic (AML) pathogenesis. Low expression levels of GFI1 is associated with a poor prognosis in AML development. In addition, a single nucleotide polymorphism (SNP) variant of GFI1 results in the generation of GFI1 protein with asparagine (N) instead of serine (S) at the 36th amino acid position, known as GFI136N. Expression of the GFI1-36N allele leads as well to poor prognosis and promotes AML development.   In this study, we demonstrated with the help of RNAseq transcriptomic analysis that the presence of GFI1-36N is associated with increased frequency of chromosomal aberrations and mutational burden in murine and human AML cells. In particular, GFI1-36N modulates DNA repair pathways, O6-methylguanine-DNA-methyltransferase (MGMT)-mediated repair and homologous recombination repair (HR). Mechanistically, GFI1-36N exhibits impaired binding to Ndrg1 promoter element compared to GFI1-36S (wild type), causing decreased NDRG1 levels, consequently leading to suppression of MGMT expression, imprinted at the transcriptome and proteome, thus leaving the AML cells vulnerable to DNA damaging agents.     Furthermore, we showed that a low expression level of GFI1 in leukemic cells is associated with high OXPHOS and enhanced glutamine metabolism. However, we hypothesise that the observed metabolic phenotype is mediated through FOXO1 protein. RNAseq transcriptomic analysis revealed higher Foxo1 mRNA expression levels with lower GFI1 expression, providing the first hint of Foxo1 as a potential target gene of GFI1 protein. The mRNA and protein levels of high Foxo1 with reduced GFI1 expression was confirmed by RT-PCR and western blot, respectively. In addition, CHIPseq and ATACseq analysis further proved that Foxo1 is a potential target gene of GFI1.  In summary, we show that GFI1 plays a role during DNA repair and metabolism and thus provides critical insights into a novel therapeutic option for AML patients carrying the GFI1-36N variant or having a low expression level of GFI1.

overall_design: The current study includes three mouse models: GFI1-KI mice, which express human GFI1 at the murine Gfi1 locus; GFI1-KD mice, expressing 10-20 % of the human GFI1 gene; and GFI1-36N mice, which express 36N variant of human GFI1 gene. The lineage depleted cells from GFI1-KI, GFI1-KD, and GFI1-36N mice were isolated and retrovirally transduced with MLL-AF9 oncogene, coexpressing GFP reporter protein. The GFP positive cells were FACS sorted and transplanted into lethally irradiated (7+3 Gy) C57BL/6 mice. The total bone marrow cells from the leukemic mice were serially transplanted into sublethally irradiated mice (3 Gy), and the total bone marrow cells from the quaternary transplanted leukemic mice were used for transcriptomic analysis. For the transcriptome analysis of temozolomide treated cells, leukemic bone marrow cells were treated with 50 µg/ml temozolomide 20 h before RNA isolation.

first: Cyrus

last: Khandanpour

first: Daria

last: Frank

first: Lanying

last: Wei


title: Loss of collagen X facilitates hypertrophic differentiation and endochondral ossification of human iPSC-derived chondrocytes

city: Sakyoku, Kyoto

first: takeshi

last: kamakura

address: Shogoin Kawaharacho 53

institute: Kyoto University

summary:
To investigate the role of collagen X in human chondrocytes, we established human induced pluripotent stem cells (hiPSC) with heterozygous (COL10A1+/-) or homozygous (COL10A1-/-) deletions of COL10A1 gene using dual guide RNAs and CRISPR/Cas9 system.
Several mutant clones were established from each of two standard hiPSCs and differentiated into hypertrophic chondrocytes by the previously reported 3D induction method.
Transcriptome analyses of chondrocyte pellets at the hypertrophic phase showed lower expression of proliferating-phase genes and higher expression of calcification-phase genes in COL10A1-/- pellets than in parental cell pellets.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSC-derived chondrocyte pellets and COL10A1 KO derivatives.

first: Takeshi

last: Kamakura

first: Yonghui

last: Jin

first: Junya

last: Toguchida


title: Spatial coupling of microbes and immune cells in solid malignancies [Cold_hot_tumors_mouse]

city: Philadelphia

first: Gregory

last: Beatty

institute: University of Pennsylvania

summary: Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Growing evidence shows that intratumoral microbes are associated with immune microenvironments in cancer. However, mechanisms that direct the recruitment of microbes to tumors remain poorly understood. Here, we show that intratumoral infiltration of  immune cells and microbes are heterogeneous, and the distribution of microbes within tumors are orchestrated by the spatial heterogeneity of intratumoral lymphoid populations. Analysis of human solid tumors revealed that the spatial distribution of immune cells, particularly CD8+ T cells, is markedly heterogeneous. Compared to T cell-poor (“cold”) tumor nests, T cell-rich (“hot”) tumor nests displayed a significantly higher number of myeloid cells, B cells, and plasma cells. We performed laser capture microdissection (LCM) followed by RNA sequencing to identify unique gene signatures that define tumor epithelium and stroma of cold and hot tumor nests. Cold tumor nests expressed genes that promote tumor proliferation and fibrosis, whereas hot tumor stroma and epithelium showed upregulation of immune-related processes, including responses to bacteria, and receptors that mediate mucosal immune responses to microbes, respectively. Consistent with these findings, we detected elevated levels of microbes within hot tumor nests in human pancreatic and lung cancers as well as in mouse models of pancreatic cancer. Intratumoral T cell infiltration plays a causal role in spatial distribution of bacteria in tumor. Our data implicate intratumoral immune heterogeneity in defining microbial spatial distribution and highlight a potential role for crosstalks between microbes, cancer cells, and the host immune system in shaping constituents of the tumor microenvironment (TME).

overall_design: RNA isolated from formalin-fixed, paraffin-embedded (FFPE) sections containing T cell-poor ("cold") and T cell-rich ("hot") tumors was analyzed using QuantSeq 3' mRNA sequencing.

first: Yan

last: Li

first: Renee

last: Chang

first: Jae

last: Lee

middle: L


title: Spatial coupling of microbes and immune cells in solid malignancies [LCM_cold_hot_tumor_nest]

summary: Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Although this spatial heterogeneity may reflect mutational variations in cancer cells, mechanisms that direct the recruitment of immune cells to distinct regions within a tumor remain poorly understood. Here, we show that microbial-host interactions define tumor nests enriched in immune cells, and the distribution of microbes within tumors parallels the spatial heterogeneity of intratumoral lymphoid and myeloid cell populations. Analysis of human solid tumors revealed that the spatial distribution of immune cells, particularly CD8+ T cells, is markedly heterogeneous. Compared to T cell-poor (“cold”) tumor nests, T cell-rich (“hot”) tumor nests displayed a significantly higher number of myeloid cells, B cells, and plasma cells. We performed laser capture microdissection (LCM) followed by RNA sequencing to identify unique gene signatures that define tumor epithelium and stroma of cold and hot tumor nests. Cold tumor nests expressed genes that promote tumor proliferation and fibrosis, whereas hot tumor stroma and epithelium showed upregulation of immune-related processes, including responses to bacteria, and receptors that mediate mucosal immune responses to microbes, respectively. Consistent with these findings, we detected elevated levels of microbes within hot tumor nests in human pancreatic and lung cancers. Our data implicate host immune responses to microbes in defining intratumoral immune heterogeneity and highlight a potential role for crosstalks between microbes, cancer cells, and the host immune system in regulating cancer immunogenicity.

overall_design: RNA isolated from cold and hot tumor nests of human pancreatic ductal adenocarcinoma was analyzed using SMARTer stranded total RNA sequencing.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Enterococcus durans A8-1 cells fermentation at MRS medium and MRS medium supplied with 60mg/L Na2SeO3

city: Xi'an

first: Bei

last: Han

state: Shaanxi

address: NO 76 Yanta West Road

department: School of Public Health

institute: Xi'an Jiaotong University

summary: There had a total number of 804 genes with transcript difference, including 482 up-regulated genes and 322 down-regulated genes. Enrichment analysis of those 804 different transcript gene sets was performed to explore the biological effects and the corresponding pathways that are significantly associated on GO and KEGG (Padj <0.05 as the threshold for significant enrichment). In the GO functional enrichment analysis, all differential genes were significantly enriched into 65 GO Terms, among them there had 50 GO terms belonging to BP (Biological Process). Among these BP 50 terms, organonitrogen compound metabolic process (44 genes), organonitrogen compound biosynthetic process (44 genes), and oxidation-reduction process (58 genes) had most different transcript gene sets. While in the MF (Molecular Function), there had 3 GO terms involved transcript changes, which including coenzyme binding (31 genes), structural constituent of ribosome (17 genes) and structural molecule activity (17 genes). In the KEGG pathways enrichment analysis, all differential genes were significantly enriched mainly into 4 pathways, including efq03010 (Ribosome, 30 genes), efq01212 (Fatty acid metabolism, 10 genes), efq00061 (Fatty acid biosynthesis, 10 genes), and efq02010 (ABC transporters, 19 genes), where efq03010 (Ribosome), efq01212 (Fatty acid metabolism), efq00061 (Fatty acid biosynthesis) were up-transcripted pathways, and efq02010 (ABC transporters) was the down-transcripted pathway. Based on transcriptome data analysis in selenium-enriched E. durans A8-1 compared with E. durans A8-1, a total of 19 genes were screened for significant up- transcripted that may be associated with selenium metabolic processes

overall_design: RNA was extracted from E. durans A8-1 grown in MRS broth containing 60 μg/ml selenite using a bacteria RNA kit (Tiangen Biotech Co. Ltd, Beijing, China). E. durans A8-1 grown in MRS broth without selenite was used as negative control, the control and treatment were all in triplicates. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Through qualified RNA samples, the cDNA library was constructed, and then transcriptome sequencing was performed at Novogen Co. Ltd (Beijing, China). The raw data passed the quality control and mapped to the reference genome, differential expression analysis of two groups (three biological replicates per group) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distributio. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value<0.05 found by DESeq were assigned as differentially expressed. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression. For the differentially expressed genes, the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment were analyzed.

first: Xiaohong

last: Tuo

first: Yi

last: Zhou

first: Lu

last: Shi


title: Distinct epicardial gene regulatory programmes drive development and regeneration of the zebrafish heart

city: Oxford

first: Paul

middle: Richard

last: Riley

address: IMS-Tetsuya Nakamura Building, Old Road Campus

institute: University of Oxford

summary: Unlike the adult mammalian heart, which has limited regenerative capacity, the zebrafish heart can fully regenerate following injury. Reactivation of cardiac developmental programmes is considered key to successfully regenerating the heart, yet the regulatory elements underlying the response triggered upon injury and during development remain elusive. Organ-wide activation of the epicardium is essential for zebrafish heart regeneration and is considered a potential regenerative source to target in the mammalian heart. Here we compared the transcriptome and epigenome of the developing and regenerating zebrafish epicardium by integrating gene expression profiles with open chromatin ATAC-seq data. We identified epicardial enhancer elements with specific activity during development or during adult heart regeneration. By generating gene regulatory networks associated with epicardial development and regeneration, we inferred genetic programmes driving each of these processes, which were largely distinct. We identified Wt1a, Wt1b, and the AP-1 subunits Junbb, Fosab and Fosb as central regulators of the developing network, whereas Hif1ab, Nrf1, Tbx2b and Zbtb7a featured as putative central regulators of the regenerating epicardial network. Targeting hif1ab, nrf1, tbx2b and zbtb7a using CRISPR/Cas9 in injured hearts resulted in elevated epicardial cell numbers infiltrating the wound and excess fibrosis after cryoinjury, illustrating the functional importance of these regulatory factors during zebrafish heart regeneration. Our work reveals striking differences between the regulatory blueprint deployed during epicardial development and regeneration. These findings underline that heart regeneration goes beyond the reactivation of developmental programmes and provide important insights into epicardial regulation.

overall_design: Bulk ATAC and RNA sequencing of purified zebrafish epicardial cells, either at 5 days-post-fertilization or at 3 days-post-cryoinjury or at 3 days-post-sham

first: Michael

last: Weinberger

first: Filipa

last: Simoes

first: Trishalee

last: Gungoosingh

first: Tatjana

last: Sauka-Spengler

middle: R


title: Spatial coupling of microbes and immune cells in solid malignancies [LCM_stroma_epithelium]

overall_design: RNA isolated from stromal and epithelial regions of human pancreatic ductal adenocarcinoma was analyzed using QuantSeq 3' mRNA sequencing.


title: Spatial coupling of microbes and immune cells in solid malignancies [Whole_slides]

overall_design: RNA isolated from formalin-fixed, paraffin-embedded (FFPE) blocks containing human pancreatic ductal adenocarcinoma was analyzed using QuantSeq 3' mRNA sequencing.


title: Faecalibacterium prausnitzii promotes intestinal epithelial IL-18 production through activation of the HIF1A pathway

status: Public on Nov 30 2023

city: GRONINGEN

first: Raphael

last: Fagundes Rosa

address: Hanzeplein 1

institute: University Medical Center Groningen

summary: In this study, we investigated the regulation of interleukin-18 (IL-18) expression, crucial for intestinal barrier integrity, in inflammatory bowel disease (IBD). Through experiments with Caco-2 cells, we demonstrated that HIF1α-mediated IL18 expression induced by F. prausnitzii was dependent on HIF1α, suggesting a potential role for butyrate-producing gut bacteria in promoting mucosal healing in IBD.

overall_design:
Wild-type Caco-2 and CRISPR/Cas9-engineered Caco-2-HIF1A-null cells were cocultured with Faecalibacterium prausnitzii in a 'Human oxygen-Bacteria anaerobic' in vitro system:

e.v.: CRISPR/Cas9-empty vector
cl.21: HIF1A-KO
2D: well-culture
Co-culture: co-cultures with F. prausnitzii in HoxBan system
Monoculture: monoculture in HoxBan system
monoculture YCFAinul: monoculture in HoxBan system supplemented with inulin
monoculture YCFAmuc: monoculture in HoxBan system supplemented with mucin
Poop + YCFAinul: stool coculture in HoxBan system supplemented with inulin
Poop + YCFAmuc: stool coculture in HoxBan system supplemented with mucin

and analyzed by RNA sequencing.

last: Fagundes

first: Gabriela

last: Bravo-Ruiseco

first: Shixian

last: Hu

first: Sarah

last: Kierans

first: Rinse

middle: K

last: Weersma

first: Cormac

last: Taylor

first: Gerard

last: Dijkstra

first: Hermie

last: Harmsen

first: Klaas

middle: N

last: Faber


title: ATACseq analysis of granulocyte-monocyte progenitor cells (GMPs) with GFI1 wildtype and low level of GFI1 expression

first: Pradeep

last: Patnana

summary: GFI1 is a transcriptional repressor protein that represses the transcription by mediating chromatin modifications such as histone demethylation, methylation and deacetylation of target genes. The genes with significant open chromatin configuration in the promoter and enhancer regions of GFI1-KI and GFI1-KD mice are identified in this study. This aids in the identification of unique additional genes that might be GFI1 protein's potential targets. We showed a significant open chromatin configuration of Foxo1 promoter and enhancer regions with reduced GFI1 expression. This gives additional support for hypothesising FOXO1 as a target gene of GFI1, along with the data from CHIPseq and RNAseq analysis.

overall_design: Two mouse models were employed in this study: GFI1-KI, in which murine Gfi1 is replaced by human GFI1, and GFI1-KD, in which mice express 10-20% human GFI1 rather than murine Gfi1. FACS sorting was used to isolate granulocyte monocyte progenitor cells (GMPs) of GFI1-KI and GFI1-KD mice, which were then processed for ATACseq analysis immediately after sorting.

first: Cyrus

last: Khandanpour

first: Xiaoqing

last: Xie

first: Daria

last: Frank

first: Lanying

last: Wei


title: CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation [CD34 ChIP-seq]

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Hematopoietic stem and progenitor cell (HSPC) formation and lineage differentiation involve gene expression programs orchestrated by transcription factors and epigenetic regulators. Knockdown of the chromatin remodeler chromodomain-helicase-DNA-binding protein 7 (CHD7) expanded phenotypic HSPCs, erythroid, and myeloid lineages in zebrafish and mouse embryos. CHD7 acts to suppress hematopoietic differentiation in a cell autonomous manner in the embryo and adult. CHD7 chromatin immunoprecipitation in human CD34+ and mouse HSPCs revealed enrichment of binding motifs for hematopoietic transcription factors including Runx1 and GATA factors, and decreased Runx1 occupancy correlated with loss of CHD7 occupancy. CHD7 physically interacts with Runx1 and suppresses Runx1-induced expansion of HSPCs during development, providing both physical and genetic evidence for the Runx1-CHD7 interaction. CHD7 modulates Runx1 activity to provide proper timing and function of HSPCs as they emerge during hematopoietic development or mature in adults, representing a distinct and evolutionarily conserved control mechanism to ensure accurate hematopoietic lineage differentiation.

overall_design: ChIP sequencing of CHD7 and histone H3K27ac in human CD34+ cells, single replicates

first: Eirini

last: Trompouki

first: Brian

last: Abraham

first: Hsuan-Ting

last: Huang


title: Two-motif model illuminates DICER's cleavage preferences [DICER-rescue]

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: In humans, DICER is a key regulator of gene expression in animals through its production of miRNAs and siRNAs by processing miRNA precursors (pre-miRNAs), short-hairpin RNAs (shRNAs), and long double-stranded RNAs (dsRNAs). To advance our understanding of this process, we employed high-throughput assays using various shRNA variants and both wild-type and mutant DICER (DICERΔdsRBD). Our analysis revealed that DICER predominantly cleaves shRNAs at two positions, specifically at 21 (DC21) and 22 (DC22) nucleotides from the 5'-end. Our investigation identified two independent motifs, mWCU and YCR, that determine whether DICER cleaves at DC21 or DC22, depending on their locations in shRNA/pre-miRNAs. These motifs can work together or independently to determine the cleavage sites of DICER. Furthermore, our findings indicate that dsRBD enhances cleavage at DC21, and mWCU strengthens the interaction between dsRBD and RNA, leading to an even greater enhancement of DC21 cleavage. Conversely, YCR functions independently of dsRBD. Our study proposes a two-motif model that sheds light on the intricate regulatory mechanisms involved in gene expression by elucidating how DICER recognizes its substrate, providing valuable insights into this critical biological process.

overall_design: miRNA sequencing

first: Cong-Truc

last: Le

first: Trung-Duc

last: Nguyen

first: Tuan-Anh


title: Expression data from primary human healthy donor-derived CD14- cDC2s, CD14+ cDC2s and monocytes

city: Nijmegen

first: Jolanda

last: de Vries

address: Geert grooteplein Zuid 28

department: Tumor Immunology Department

institute: Radboud Institute for Molecular Life Sciences, Radboudumc

summary:
The human dendritic cell (DC) family has recently been expanded by CD1c+CD14+CD163+ DCs, introduced as DC3. DC3 are found in tumors and peripheral blood of cancer patients but which cells can serve as their pre-cursors remain unknown.
CD1c+CD14+ cells share similarities with both CD1c+ DCs (cDC2s) and CD14+ monocytes on transcriptomic and phenotypic level. To investigate whether CD14+ cDC2s are closer related to CD14- cDC2s or monocytes on transcriptomic level, we analyzed their RNA.

overall_design: To compare the myeloid populations on transcriptome level, RNA was isolated from FACS-sorted CD1c+CD14- DCs, CD1c+CD14+ cells and CD14+ monocytes from blood of four healthy donors and analyzed by Affymetrix microarrays.

first: Anouk

middle: M

last: Becker

first: Georgina

last: Florez-Grau

first: Ghaith

last: Bakdash

first: Rutger

last: Roring

first: Suzan

last: Stelloo

first: Michiel

last: Vermeulen

first: Martijn

last: Verdoes

first: I

last: De Vries


title: Long non-coding RNA PVT1 is overexpressed in cutaneous squamous cell carcinoma and exon 2 is critical for its oncogenicity

city: Uppsala

first: Andor

last: Pivarcsi

address: Husargatan 3

department: Department of Medical Biochemistry and Microbiology (IMBIM)

country: Sweden

institute: Uppsala University

summary:
Background
Cutaneous squamous cell carcinoma (cSCC) is one of the most common and fastest increasing forms of cancer worldwide with metastatic potential. Long non-coding RNAs (lncRNAs) are a group of RNA-molecules with essential regulatory functions for both physiological and pathological processes.
Objectives
To investigate the function and mode of action of lncRNA plasmacytoma variant translocation 1 (PVT1) in cSCC.
Methods
The expression level of PVT1 was quantified in healthy skin, benign skin diseases and cSCCs by qRT-PCR and single molecule in situ hybridization. The function of PVT1 in cSCC was investigated both in vivo (tumour xenograft) and in vitro (competitive cell growth assay, EdU-incorporation assay, colony formation assay and tumour spheroid formation assay) by CRISPR-Cas9-mediated PVT1 or PVT1 exon 2 knockout and by locked nucleic acid (LNA) GapmeR-mediated PVT1-knockdown. RNAseq-analysis was conducted to identify genes and processes regulated by PVT1.
Results
We identified PVT1 as a lncRNA upregulated in cutaneous squamous cell carcinoma in situ (cSCCIS) and cSCC and associated with oncogenic phenotype of cSCC. The increased expression of PVT1 in cSCC was regulated by MYC. Both CRISPR-Cas9-deletion of the entire PVT1 locus and LNA GapmeR-mediated knockdown of PVT1-transcript impaired malignant behaviour of cSCC cells which suggested that PVT1 is an oncogenic transcript in cSCC. Furthermore, knockout of PVT1 exon 2 inhibited cSCC tumour growth both in vivo and in vitro demonstrating that exon 2 is a critical element for the oncogenic role of PVT1. Mechanistically, we show that PVT1 is localized in the cell nucleus and acts as a suppressor of cellular senescence by inhibiting CDKN1A expression and preventing cell cycle arrest.
Conclusions
Our study reveals a previously unrecognized role for exon 2 of PVT1 in its oncogenic role and that PVT1 suppresses cellular senescence. PVT1 may be a biomarker and therapeutic target in cSCC.

overall_design: To investigate the regulatory effect of lncRNA PVT1 on cSCC cell transcriptome, wildtype (WT) cSCC cell line UT-SCC-7 and CRISPR-Cas9-mediated PVT1 exon2 knockout (PVT1 E2KO) UT-SCC-7 cell line were used for RNA-seq

first: Chen

last: Li


title: Spatial coupling of microbes and immune cells in solid malignancies

first: Gregory

last: Beatty

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

overall_design: Refer to individual Series


title: Two-motif model illuminates DICER's cleavage preferences [DICER-mutants]

overall_design: RNA sequencing


title: Human iPSC-derived renal collecting duct organoids model cystogenesis in ADPKD

status: Public on Nov 29 2023

first: Shin-Ichi

last: Mae

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

institute: Center for iPS Cell Research and Application, Kyoto University

summary: We established the expansion culture of human iPSC-derived ureteric bud tip cells (UBTCs), an embryonic precursor that give rise to collecting ducts (CDs), and succeeded in advancing the developmental stage of CD organoids. We used single cell RNA-sequencing (scRNA-seq) to dissect cell types in CD organoids.

overall_design: Day-21 CD organoids reconstituted from 2- or 6-week-cultured UBTCs were dissociated into single cells and analyzed using scRNA-seq.

first: Kenji

last: Osafune


title: Effects of Follicle Stimulating Hormone on Liver Metabolic Health After Loss of Ovarian Function

status: Public on Nov 28 2023

first: Paul

last: MacLean

department: Endocrinology, Metabolism, & Diabetes

institute: University of Colorado Anschutz Medical Campus

summary: Loss of ovarian function imparts increased susceptibility to obesity and metabolic disease. These effects are largely attributed to decreased estradiol (E2), but the role of increased follicle stimulating hormone (FSH) in modulating energy balance has not been fully investigated. Previous work that inhibited FSH activity in mice suggested this hormone may play a part in modulating body weight and energy expenditure after ovariectomy.  We used an alternate approach to experimentally isolate the individual and combined contributions of FSH and E2 in mediating energy imbalance and changes in tissue-level metabolic health.  Female Wistar rats were ovariectomized and given the GnRH antagonist degarelix to suppress FSH production. E2 and FSH were then added back individually and in combination for a period of 3 weeks.  Energy balance, body mass composition, and transcriptomic profiles of individual tissues were obtained.  In contrast to previous studies, ablation and replacement of FSH in our paradigm had no effect on body weight, body composition, food intake, or energy expenditure.  We did, however, observe organ-specific effects of FSH that produced unique transcriptomic signatures of FSH in retroperitoneal white adipose tissue. These included reductions in biological processes related to lipogenesis and carbohydrate transport.  Additionally, rats administered FSH had reduced liver triglyceride concentration (p<0.001), which correlated with FSH-induced changes at the transcriptomic level.  While not appearing to modulate energy balance after loss of ovarian function in rats, FSH may still impart tissue-specific effects in the liver and white adipose tissue that might affect the metabolic health of those organs.

overall_design: RNA was extracted from liver tissue from individual female ovariectomized wild-type Wistar rats receiving either degarelix-only (n=5) or degarelix+FSH (n=4) and subjected to RNA sequencing.

first: Andrew

middle: E

last: Libby