title: Landscape of Transcription Termination in Arabidopsis Revealed by Single-molecule Nascent RNA Sequencing

first: Weipeng

last: Mo

state: Guangdong

address: 58 Zhongshaner Rd

department: The First Affiliated Hospital

institute: Sun Yat-sen University

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

overall_design: Refer to individual Series


title: First multiomics association study of trace element and mineral concentration and RNA sequencing profiles in human cancers

status: Public on Sep 21 2024

city: Moscow

first: Arsenia

last: Alekseeva

address: 8-2 Trubetskaya str.

country: Russia

institute: I.M. Sechenov First Moscow State Medical University

type: Expression profiling by high throughput sequencing

summary: The integration of various types of omics data is an important trend of contemporary molecular oncology. In this regard, high-throughput analysis of trace and essential elements in cancer biosamples is an emerging field that has not yet been sufficiently addressed. For the first time, we simultaneously obtained RNA sequencing gene expression and mass spectrometry essential and trace element profiles for a set of human cancer samples. The biosamples were formalin-fixed, paraffin-embedded primary tumor tissue blocks: 67 for colorectal cancer patients and 17 for different solid cancer types. The levels of 45 trace elements and minerals, Ag, Al, As, Au, B, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Fe, Ga, Ge, Hg, I, K, La, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Pd, Pt, Rb, Sb, Sc, Se, Si, Sn, Sr, Te, Ti, Tl, Zn, U, V, W, Zr, were assessed using inductively-coupled plasma mass-spectrometry. The expression levels were profiled for 36596 known human genes, and the activation levels were assessed for 10520 intracellular molecular pathways. For the concentrations of essential elements Ca, Cu, Fe, K, Mg, Na, P, and Zn we detected statistically significant correlations on both gene expression and pathway activation levels, both for colorectal cancer and for pan-cancer level of data analysis. We hope the first-in-class database provided here will be a valuable resource for multiomics cancer research.

overall_design: To explore the association between trace element and mineral concentration and gene expression and transcriptomic pathaway activation levels, we conducted a comprehensive analysis of 85 human cancer biosamples, including colorectal and other solid tumor types. RNA sequencing and inductively-coupled plasma mass-spectrometry (ICP-MS)were used to profile gene expression and trace element and mineral concentration.

first: Maria

last: Suntsova

first: Marianna

last: Zolotovskaia

first: Anton

last: Buzdin


title: CRISPR activation screens identify the SWI-SNF ATPases as suppressors of ferroptosis [NGS3716_CUT&RUN]

status: Public on Sep 22 2024

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

country: USA

institute: Genentech

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Ferroptosis is an iron-dependent cell death mechanism characterized by an accumulation of toxic lipid peroxides and membrane rupture. The glutathione dependent enzyme, GPX4 (glutathione peroxidase 4), prevents ferroptosis by reducing these lipid peroxides into non-toxic lipid alcohols. Ferroptosis induction by GPX4 inhibition has emerged as a vulnerability of cancer cells, thus highlighting the need to identify ferroptosis regulators that may be exploited therapeutically. Through genome-wide screens and a series of genetic, genomic, and quantitative imaging approaches, we identify the SWI-SNF ATPases BRM and BRG1 as ferroptosis suppressors. Mechanistically, they directly bind to and catalytically increase chromatin accessibility at NRF2 target loci, thus boosting NRF2 transcriptional output. This primes cells to counter lipid peroxidation and confers resistance to GPX4 inhibition and ferroptosis. Importantly, we demonstrate that the BRM/BRG1-ferroptosis connection can be leveraged to enhance the paralog dependency of BRG1-mutant lung cancer cells on BRM, especially in lines that are less sensitive to BRM inhibition or degradation. Our data reveal ferroptosis induction as a potential avenue for broadening the efficacy of BRM degraders/inhibitors and define a specific genetic context for exploiting GPX4 dependency.

overall_design: Cut and Run

first: Kamakoti

middle: P

last: Bhat

first: Xin

last: Ye

first: Musaddeque

last: Ahmed

first: Michal

last: Kabza

first: Jinchu

last: Vijay


title: Transcription analysis of GW and SFZ lychees under lychee downy blight stress

city: Guangzhou

first: Liu

last: Hailun

address: Tianhe District

country: China

institute: Guangdong Academy of Agricultural Sciences

summary: Lychee (Litchi chinensis Sonn.) is a popular fruit worldwide. Lychee downy blight, caused by Peronophythora litchii (P. litchii), is one of the major diseases in lychee. In this study, we conducted a P. litchii infection experiment on the lychee leaves of GW and SFZ, and analyzed the mRNA in the treated leaves using transcriptome RNA sequencing technology. Our research will provide a preliminary basis for the prevention and control of lychee downy blight.

overall_design: The leaves from GW and SFZ were treated with P. litchii or mock (sterile water). The gene expression profiling analysis was performed based on data derived from RNA-seq of the treated samples.

first: Hailun

last: Liu


title: CRISPR activation screens identify the SWI-SNF ATPases as suppressors of ferroptosis [NGS3788_scRNA-seq]

overall_design: scRNA sequencing of BRM-inducible KP4 cells treated with or without doxycycline to induce BRM overexpression.

first: Caroline

middle: K

last: Vilas

first: Steffen

last: Durinck


title: Integration of GWAS and transcriptome analysis to identify temperature-dependent genes involved in germination of Brassica napus L.

city: Hang Zhou

first: Guangyu

last: Wu

state: Zhejiang

address: No. 866 Yuhangtang Road

institute: Zhejiang University

summary: Global climate changes on one aspect of extreme temperature records would suddenly reset environmental growth conditions for field-grown crops, which severely affects agronomic and commercial traits. Taking the cold-season preferable crop rapeseed Brassica napus L. for example, low-temperature shocks change endogenous regulatory networks and cause phenotypic damages during most lifespan. Here we screened out two genetic breeding elites with different temperature-dependent germination rates, core germplasms with good germination performance and genetic loci and candidate genes potentially involved in low-temperature tolerant functions for the pre-breeding purpose of cold-tolerant germination. By using the phenotype of the germination index of 273 core germplasms under normal temperature and 10 transcriptomic datasets of cold-tolerant Jia You (JY) 1621 and cold-sensitive JY1605 elite cultivars on three timepoints during germination process, we successfully identified clustered genes of early and late temperature response germination (ETRG and LTRG) genes and several cold-tolerant (CDT) and temperature-insensitive (TPI) candidate regulators. This study performed comprehensive multi-omics research on potential cold-responsive genes for the rapeseed improvement of cold tolerance germination.

overall_design: we conducted a comprehensive transcriptome sequencing using JY1621 and JY1605 materials under normal- (25 ℃) and low- (8 ℃) temperature conditions. Dry seeds (ZT0), germinating seeds after 8 hours (8H on ZT8) and germinating seeds after 36 hours (36H on ZT12) of JY1621 and JY1605 grown at 25 ℃ and 8 ℃ conditions were collected in three biological replications.

first: Ruisen

last: Wang

first: Xiangtan

last: Yao

first: Yang

last: Zhu


title: Targeting Bradykinin Signaling Pathway: PLGA/BK Microspheres as a Therapeutic Strategy for Delaying Intervertebral Disc Degeneration

city: Lanzhou

first: Xuewen

last: Kang

state: Gansu

address: No. 82, Cuiying Gate, Chengguan District, Lanzhou City, Gansu Province

institute: Lanzhou University Second Hospital

summary: Intervertebral disc degeneration(IVDD) is a common spinal condition with limited effective treatments available. This study aims to investigate the impact of poly(lactic-co-glycolic acid)/Bradykinin (PLGA/BK) microspheres on IVDD and its underlying mechanisms. We collected nucleus pulposus samples from both healthy and degenerated human intervertebral discs and conducted immunohistochemical analyses, revealing reduced BK expression in degenerated tissues. Subsequently, we used BK to treat nucleus pulposus cells and conducted Bulk RNA sequencing (RNA-seq), identifying BK's involvement in cellular senescence, extracellular matrix metabolism, and the PI3K signaling pathway. Further experiments using tert-butyl hydroperoxide (TBHP)-induced cell senescence showed that BK treatment reduced senescence, enhanced extracellular matrix synthesis, and inhibited degradation, along with activation of the PI3K pathway. These effects were mediated through B2R (BK receptor 2) and the downstream PI3K pathway. Following this, we developed sustained-release BK microspheres with an optimized manufacturing process. In vitro co-culture experiments showed no observable toxicity. We established an IVDD model in rat tail vertebrae through fine needle puncture, administering local injections of BK sustained-release microspheres. Using various experimental methods, including X-ray, MRI, histopathology, and immunohistochemistry, we found that these microspheres could slow the progression of IVDD. This study highlights the potential of injectable PLGA/BK microspheres to regulate cellular senescence and extracellular matrix metabolism via the B2R and PI3K pathways, ultimately delaying IVDD.

overall_design: Experimental Design for Bulk RNA-Seq In this study, bulk RNA sequencing (RNA-seq) was employed to explore the effects of bradykinin (BK) on nucleus pulposus cells (NPCs). The experimental design involved two groups of cultured NPCs: a control group and a BK-intervention group. The goal was to examine how BK affects gene expression, focusing on its potential role in regulating cellular senescence and extracellular matrix metabolism.  Grouping and Treatment Control Group: NPCs without any treatment, serving as the baseline. BK Group: NPCs treated with 10 μM BK to assess its influence on gene expression. RNA Extraction and Bulk RNA-Seq Total RNA was extracted from both groups of NPCs using an RNA extraction kit. Bulk RNA-seq was performed on the extracted RNA to capture the complete transcriptome profiles. The workflow included:  RNA Extraction: High-quality RNA was extracted and subjected to strict quality control. Library Construction: Libraries were prepared from the extracted RNA and sequenced using the Illumina NovaSeq platform, generating paired-end 150 bp reads. Sequencing: Bulk RNA-seq was conducted to capture the entire transcriptome of NPCs from both the control and BK-treated groups. Bioinformatics Analysis Quality Control: The raw sequencing data underwent stringent quality control, including removal of adapters, low-quality reads, and ambiguous bases using fastp. Reference Genome Alignment: Clean reads were aligned to the reference genome using HISAT2 for precise mapping. Gene Expression Quantification: Gene expression levels were quantified, and differences in expression between the two groups were calculated using RSEM. Differential Expression Analysis: DESeq2 was used to identify differentially expressed genes (DEGs) with significance thresholds of FDR ≤ 0.05 and |log2 fold change| ≥ 1.

first: Xiaoming

last: Qiu

first: Yizhi

last: Zhang

first: Ziyan

last: Wei

first: Zhangbin

last: Luo

first: Zhuanping


title: Landscape of Transcription Termination in Arabidopsis Revealed by Single-molecule Nascent RNA Sequencing [FLEP-seq]

first: Weipeng

last: Mo

summary: The dynamic process of transcription termination produces transient RNA intermediates, such as the full-length readthrough, 5’ and 3’ cleavage products, and polyadenylated nascent RNAs, which are difficult to distinguish from each other via short-read sequencing methods. Here, we used single-molecule nascent RNA sequencing to characterize these various forms of transient RNAs during termination at genome-wide scale in Arabidopsis. Our data revealed a wide range of termination windows (defined as the median readthrough distance) among genes, ranging from ~50 nt to over 1000 nt. The ends of termination windows precisely match the peak of Pol II occupancy and co-localize with termination factors. We also discovered a termination mechanism shaped by the downstream tRNA genes, suggesting that elongating Pol II can be expelled by Pol III activity. Mutation of the exonuclease AtXRN3 leads to a drastic accumulation of 3’ cleaved readthrough RNAs. Moreover, readthrough transcription in atxrn3 with delayed termination can run into downstream genes to produce normally spliced and polyadenylated mRNAs in the absence of their own transcription initiation. Our results revealed the diverse termination patterns in Arabidopsis, and our method is applicable to study the global termination landscape in a broad range of species.

overall_design: Nanopore nascent RNA sequencing to study the termination landscape

first: Jixian

last: Zhai


title: Kidney injury induced by sodium oxalate

city: Fuzhou

first: Zhimin

last: Chen

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

summary: In order to reveal the molecular physiological damage mechanism of kidney induced by oxalic acid, single cell sequencing was performed on the kidney of mice with control group and oxalic acid induced acute kidney injury.

overall_design: Harvested cells at the required densities were combined with gel beads  containing the barcoded information along with a mixture of cells and  enzymes. Oil surfactant droplets in a microfluidic double-cross system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence. The cDNA fragment was then reverse transcribed before the sample was labeled. The gel beads and the oil droplets are ruptured and PCR amplification was performed using the generated cDNA as a template. The products of all GEMs were mixed and a standard sequencing library is constructed. The cDNA was first enzymatically digested into fragments of about 200300 base pairs (bp), together with the library building process of traditional secondgeneration sequencing such as sequencing junction and primers. Finally, the DNA library was generated by PCR amplification

first: Yanfang

last: Xu


title: Direct transdifferentiation of tumorigenic melanoma cells to non-tumorigenic neuron-like cells

city: Heidelberg

first: Yiman

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

summary: Melanoma is an aggressive skin cancer and is highly lethal at advanced stages despite the availability of a variety of established therapeutic options due to the high tumorigenicity and metastatic capacity of melanoma cells. However, there is evidence that changing the lineage of cancer cells leads to a drastic reduction of their tumorigenic potential. Different approaches have been developed to change the phenotype of a cell from one lineage to another, a process called transdifferentiation. In this study, we investigated whether melanoma cells can be transdifferentiated into neurons and how that affects their properties and characteristics. For this reason, we ectopically overexpressed the neuron-specific transcription factors Ascl1, Brn2, Myt1L and NeuroD1 in melanoma cells. We could show that melanoma cells could be transdifferentiated into neuron-like cells that expressed neuronal markers and showed a neuron-like morphology. RNA sequencing and DNA methylation assay were used to further reveal the underlying mechanism. Moreover, the transdifferentiated cells had a significantly reduced tumorigenic and metastatic potential and were more sensitive to radiotherapy compared with their parental counterparts. We conclude that transdifferentiation of cancer cells into terminally differentiated cells could represent a new therapeutic alternative for the treatment of malignant melanoma.

overall_design: All melanoma cell lines were transduced with pLU-EF1aL-rtTA3-iCherry. The cells were then selected for mCherry fluorescence using cell sorter BD FACSAria from the Flow Cytometry Core Facility of the DKFZ. Successfully transduced cells were hereafter termed Melanoma-M2. Then the cells were sequentially transduced with the expression constructs for the factors Brn2, Myt1L and NeuroD1 and afterwards treated with 3 different antibiotics (blasticidin, hygromycin and G418) in order to select for cells transduced with the respective constructs. The selected cells were infected with Ascl1 and after induction with doxycycline (1 µg/ml) subjected to selection with puromycin. Melanoma-M2 Cells infected with and selected for all four transcriptional factors were named Melanoma-4F.

first: Jochen

last: Utikal

first: Daniel

last: Novak


title: Vasopressin V2 Receptor, Tolvaptan, and ERK1/2 Phosphorylation in the Renal Collecting Duct

city: Bethesda

first: Lihe

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary: Activation of ERK1 and ERK2 is essential in regulation of a wide variety of cellular and physiological processes. In native inner medullary collecting ducts, vasopressin (AVP) working through the V2 subtype vasopressin receptor (V2R)-mediated activation of Gαs, inhibits ERK1 and ERK2 activity. However, it has been reported that V2R can signal independently of Gαs through the activation of β-arrestin, which activates ERK1 and ERK2. Vaptans, V2R antagonists that function as so-called “inverse agonists”, have the potential of promoting cell proliferation via β-arrestin-dependent ERK activation. Here we use the mpkCCD cell line which natively expresses V2R to investigate the effects of AVP, the V2-selective analog dDAVP, and tolvaptan on ERK1 and ERK2 phosphorylation and activation. We demonstrated that ERK1 and ERK2 phosphorylation in mpkCCD cells was significantly reduced by either AVP or dDAVP, in contrast to the increases seen in non-collecting duct cells overexpressing V2R. We also found that tolvaptan has a strong effect to increase ERK1 and ERK2 phosphorylation in the presence of dDAVP and that the tolvaptan effect to increase ERK1 and ERK2 phosphorylation is absent in PKA-null mpkCCD cells. Thus, it appears that the tolvaptan effect to increase ERK activation is PKA-dependent and, therefore, not mediated by the β-arrestin pathway. Overall, the studies show that AVP decreases and that tolvaptan increases ERK1 and ERK2 activation in cells expressing V2R at endogenous levels, and provide no evidence for a role for β-arrestin in the regulation of ERK1 and ERK2 activity.

overall_design: Here we use the mpkCCD cell line to address the following questions regarding the endogenously expressed V2 vasopressin receptor: 1) What are the effects of AVP and dDAVP on ERK1 and ERK2 phosphorylation/activation? 2) What is the effect of tolvaptan on ERK1 and ERK2 phosphorylation/activation in the presence and absence of dDAVP? 3) What is the role of PKA in vasopressin-mediated regulation of ERK1 and ERK2 phosphorylation/activation and on the effect of tolvaptan?


title: BEX2 is poor prognostic factor and required for cancer stemness in gastric cancer

city: Natori, Miyagi

first: Keiichi

last: Tamai

address: 1-47, Nodayama, Shiote, Medeshima

country: Japan

institute: Miyagi Cancer Center


title: BEX2 is poor prognostic factor and required for cancer stemness in gastric cancer [GCIY_siBEX2]

summary: To investigate the BEX2 signaling, GCIY cells were knocked down using siRNA against BEX2.

overall_design: BEX2-knocked down GCIY cells

first: Akihiro

last: Yasumoto


title: Direct transdifferentiation of tumorigenic melanoma cells to non-tumorigenic neuron-like cells (methylation)

first: Aniello

last: Federico


title: Alarmin-loaded extracellular lipid droplets induce airway neutrophil infiltration during type 2 inflammation

city: Hangzhou

first: Heping

address: 18 Shilongshan Road

institute: Westlake University

summary: Group 2 innate lymphoid cells (ILC2s) play a crucial role in allergic diseases by coordinating a complex network of various effector cell lineages involved in type 2 inflammation. However, their function in regulating airway neutrophil infiltration, a deleterious symptom of severe asthma, remains unknown. Here, we observed ILC2-dependent neutrophil accumulation in the bronchoalveolar lavage fluid (BALF) of allergic mice models. Chromatography followed by proteomics analysis identified the alarmin high mobility group box-1 (HMGB1) in the supernatant of lung ILC2s initiated neutrophil chemotaxis. Genetic perturbation of Hmgb1 in ILC2s reduced BALF neutrophil numbers and alleviated airway inflammation. HMGB1 was loaded onto the membrane of lipid droplets (LDs) released from activated lung ILC2s. Genetic inhibition of LD accumulation in ILC2s significantly decreased extracellular HMGB1 abundance and BALF neutrophil infiltration. These findings unveil a previously uncharacterized extracellular LD-mediated immune signaling delivery pathway by which ILC2s regulate airway neutrophil infiltration during allergic inflammation.

overall_design: Bone marrow neutrophils and lung ILC2s were isolated from wildtype (WT) mice in homeostasis for in vitro stimulation and Bulk RNA-seq. ILC-enriched population (CD45+CD3-CD19- cells) was purified from the lungs of Il5cre/+Hilpda+/+ and Il5cre/+Hilpdaflox/flox mice at day 3 after IIL-33 treatment for scRNA-seq.

first: Zebing

last: Rao

first: Shaorui

last: Liu

first: Zhicheng

last: Li


title: Landscape of Transcription Termination in Arabidopsis Revealed by Single-molecule Nascent RNA Sequencing [BS-seq]

type: Methylation profiling by high throughput sequencing

overall_design:
Nanopore nascent RNA sequencing to study the termination landscape
BS_seq profiling of WT and xrn3 mutant seedlings


title: Whole transcriptomes analyses of control and Rictor knockout intestinal epithelial cells

city: Beijing

first: Meng

middle: zhen

address: 2 West Yuanmingyuan Road

department: College of biological science

institute: China Agricultural University

summary: To explore the molecular mechanisms of mTORC2, RNA sequencing was performed to analyze the geome-wide change of Rictor knockout intestinal epithelial cells compared to those of control intestinal epithelial cells.

overall_design: Methods: Total mRNA was extracted from control and Rictor knockout intestinal epithelial cells. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina NovaSeq 6000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays.

first: Lu

last: Yu

first: Zhengquan

first: Mengzhen


title: Transcriptomic analyses for grape peel color regulation under different grafting conditions

city: Wuhan

first: Wenying

last: Zhong

address: Shizi Street No.1

institute: Huazhong Agricultural University

summary: According to the field observation result, the grafting treatment used in this study was found that 101-14MG rootstocks grafted with Crimson Seedless had a positive influence on fruit coloring. Combined metabolomic and transcriptomic analyses were conducted with different treatment grape of own rooted Crimson Seedless cultivar, and grafted 101-14MG, 110R, SO4 rootstocks with Crimson Seedless cultivar. Peonidin 3-O-glucoside, Delphinidin 3-O-glucoside, Cyanidin 3-O-glucoside, Malvidin 3-O-glucoside, Petunidin 3-O-glucoside were identified as the pigments responsible for the purplish red color peels. The results showed that the grafting material of rootstock 101-14MG could promote the accumulation of anthocyanins in grapefruit in advance. Transcriptome analysis revealed the anthocyanins biosynthetic related genes from the upstream (phenylalanine ammonia-lyase) to the downstream (anthocyanidin 3-O-glucosyltransferase, anthocyanidin synthase) were almost upregulation during anthocyanins increased. However, all these genes were highly expressed in samples G715 (Crimson Seedless/ Crimson Seedless), suggested that self-grafting rootstocks might have an earlier response to fruit color-related metabolism. A transcription factors-scale protein interaction (PPI) analysis showed that MYB4, MYB44, MYB80, and dead-box RNA helicases might be the core regulatory genes. Our results provide global transcriptional changes in grape peel color regulation under different grafting conditions for improving the breeding process.

overall_design: RNA-seq  experiments and analyses for the samples from r different grafting conditions

first: Haixia


title: Sequencing study of NBV-MB control group and MENK-NBV-MB group

city: Jinzhou

first: Jing

last: Tian

state: Liaoning

address: Linghe District

institute: Jinzhou Medical University

summary: RAW264.7 cells were divided into NBV-MB control group and MENK-NBV-MB group. Macrophages infected with NBV-MB were treated with MENK prophylactic intervention. The purpose of this study was to explore the immunological mechanism of MENK regulation of macrophages against NBV-MB, provide data support for MENK to become a new drug or vaccine adjuvant for NBV, and provide new ideas for clinical reovirus prevention and treatment

overall_design: Divide RAW264.7 cells into the NBV-MB control group and the MENK-NBV-MB group. The NBV-MB group is infected with RAW264.7 cells at a multiplicity of infection (MOI) of 30, while the MENK concentration is 10 mg/ml. Extract total RNA from the cells using the Trizol method, and quantify the total RNA precisely with the Qubit RNA assay kit. After processing, convert the total RNA samples into libraries suitable for sequencing on the Illumina® platform. Utilize RNA-Seq technology to detect transcriptome levels in the three sample groups.


title: Molecular profiles, sources and lineage restrictions of stem cells in an annelid regeneration model

city: Vienna

first: Alexander

middle: Wilhelm

last: Stockinger

address: Dr. Bohr Gasse 9

department: Max Perutz Labs Vienna

country: Austria

institute: University of Vienna

summary: Regeneration of missing body parts can be observed in diverse animal phyla, but it remains unclear to which extent these capacities rely on shared or divergent principles. Research into this question requires detailed knowledge about the involved molecular and cellular principles in suitable reference models. By combining single-cell RNA sequencing and mosaic transgenesis in the marine annelid Platynereis dumerilii, we map cellular profiles and lineage restrictions during posterior regeneration. Our data reveal cell-type specific injury responses, re-expression of positional identity factors, and the re-emergence of stem cell signatures in multiple cell populations. Epidermis and mesodermal coelomic tissue produce distinct putative posterior stem cells (PSCs) in the emerging blastema. A novel mosaic transgenesis strategy reveals both developmental compartments and lineage restrictions during regenerative growth. Our work supports the notion that posterior regeneration involves dedifferentiation, and reveals molecular and mechanistic parallels between annelid and vertebrate regeneration.

overall_design: To understand how individual cell types in Platynereis respond to injury and change their transcriptomes during regeneration, we performed a single-cell RNA sequencing timecourse at multiple post-injury timepoints. Samples were obtained by dissociating and storing Platynereis tissues using the "ACME" protocol (Garcia-Castro et al.), followed by library preparation on the 10X genomics Chromium platform. Data were then processed using Seurat (Butler et al.).


title: Role of Piezo1-mediated mechanotransduction in osteocyte differentiation

status: Public on Sep 20 2024

city: Boston

first: Yizhong

last: Hu

state: MA

address: 190 Longwood Ave.

institute: Harvard School of Dental Medicine

summary: Mechanical force is a fundamental regulator of bone development and homeostasis. Mechanosensitive osteocytes are the most abundant bone cells that form interconnected dendrites to respond to mechanical stimuli and interact with the bone-forming osteoblasts and the bone-remodeling osteoclasts. However, the molecular mechanisms underlying osteocyte maturation and dendrite formation remain unclear. By generating a Piezo1 "knock-out" osteocyte cell line, we identified a key role of Piezo1-mediated mechanotransduction in osteocyte differentiation. QRT-PCR analysis revealed delayed osteocyte differentiation in the Piezo1 KO cells relative to WT cells. By performing bulk RNA sequencing of WT and Piezo1 KO OCY454 cells at early (D1), intermediate (D14), and late (D28) stages of differentiation allowed for the identification of key signaling pathways in driving normal osteocyte dfiferentiation, as well as  those regulated by Piezo1 mechanotransduction.

overall_design: To mechanistically investigate the role of Piezo1 in osteocyte differentiation, we generated a Piezo1 "knock-out"  (KO) osteocyte cell line using CRISPR-Cas9 gene editing. Exon 19 through exon 21 from the OCY454 cell line were deleted, confirmed by sanger sequencing, qRT-PCR, western blot, and immunofluroescent staining. WT and Piezo1 KO OCY454 cells were differentiated for 1 (basal), 14, and 28 days at 37C and collected for bulk RNA-sequencing analysis. Two replicates were performed for each group.

middle: J

first: Yu

last: Jin

first: Yuchen

first: Yingzi

last: Yang


title: Expression data from Triple Negative Breast Cancer (TNBC) cell lines cultured in 2D and 3D.

city: Ciudad de México

first: Mercedes

last: Olvera-Valencia

state: Mexico

address: San Fernando

department: Investigación básica

country: Mexico

institute: Instituto Nacional de Cancerología

summary:
Development of a reliable method for human triple-negative breast cancer organotypic culture: Improving imaging and genomic studies in 3D cultures
The primary objectives of this study are to develop an advanced three-dimensional cell culture system to better model the tumor microenvironment in triple-negative breast cancer (TNBC),  analyze the differences in molecular and cellular behavior between two-dimensional (2D) and 3D cultures, and  investigate the impact of these differences on key oncogenic signaling pathways, specifically PI3K and β-catenin.

overall_design: For RNA extraction and hybridization on Human Clariom D Affymetrix microarrays. 10 experiments of TNBC cell lines were used; 6 in 2D cell cultured and 4 in 3D cell culture using the Solid Hanging drop method.

first: Carlos

last: Perez-Plasencia


title: The molecular dissection of TRIM25‘s RNA-binding mechanism provides key insights into its antiviral activity

city: Glasgow

first: Louisa

last: Iselin

state: Lanarkshire

address: 464 Bearsden Road

country: United Kingdom

institute: University of Glasgow

summary: TRIM25 is an RNA-binding ubiquitin E3 ligase with central but poorly understood roles in the innate immune response to RNA viruses. The link between TRIM25’s RNA binding and its role in innate immunity has not been established. Thus, we utilized a multitude of biophysical techniques to identify key RNA-binding residues of TRIM25 and developed an RNA-binding deficient mutant (TRIM25-m9). Using iCLIP2 in virus-infected and uninfected cells, we identified TRIM25’s RNA sequence and structure specificity, that it binds specifically to viral RNA, and that the interaction with RNA is critical for its antiviral activity.

overall_design: iCLIP of wild-type and RNA binding mutant TRIM25 in either mock or SINV infected (9h, MOI 3) conditions. All SINV infected samples and mock WT samples were performed in triplicate with matching triplicate SMI samples. Mock TRIM25-M9 IP was performed in duplicate.

first: Lucia

last: Alvarez

first: Alfredo

last: Castello

first: Janosch

last: Hennig


title: Responses of grapevine cells to physiological doses of ethanol, among which induced resistance to heat stress

city: Castanet-Tolosan

first: Alice

last: DIOT

state: Occitanie

address: 24 Chem. de Borde Rouge

country: France

institute: LRSV

summary: Grapevine is a plant of agronomic interest, which is able to cope with several stresses: heat, drought, and hypoxia, among others. A recent study showed very low oxygen levels inside grape berries, linked to ethanol content. Other studies have established the link between ethanol and tolerance to various stresses: heat stress, drought, and high salinity. The causes of such tolerance induced by ethanol are not well understood. In our study, three-week-old Gamay calli were characterised for their endogenous O2 levels (78 ± 43 µM at 2.1 mm inside the callus) and endogenous ethanol concentration (406 ± 2 µM). Subsequently, a transcriptomic study of these cells was conducted, at 6 and 24 hours post-treatment with 1 mM ethanol. After 6 hours post-treatment, ethanol addition led to 386 Differentially Expressed Genes (DEGs) compared to the controls. Analyses of the gene classes modulated by ethanol showed that many genes involved in heat response were up-regulated, notably the small Heat Shock Proteins (sHSP). Next, we showed that grape cells primed with ethanol experienced less pigment leakage due to heat stress compared to the controls. This result was further supported by a similar observation in Arabidopsis seedlings, for which heat stress-induced electrolyte leakage was reduced by ethanol priming. his study confirms previous observations regarding the beneficial role of ethanol priming in protecting plants against heat stress and provides a comprehensive set of RNA-seq data to further decipher the mechanisms involved in such adaptation. The small heat shock proteins seem involved in this chemical priming response.

overall_design:
To identify the molecular pathways differentially regulated by a physiological dose of ethanol in Vitis vinifera (cv. Gamay Fréaux var. Teinturier) cell cultures, we carried out a genome-wide transcriptomic analysis by RNA-seq.
RNA was extracted from grapevine calli treated with 100 µL of either a 1 mM ethanol solution or a control solution. Prior to treatment, the grapevine cell cultures were grown for three weeks under controlled conditions, with a 16-hour day/8-hour night photoperiod, temperatures of 25°C during the day and 20°C at night, and a light intensity of 150 μmol/m²/s. Samples were collected at either 6 or 24 hours after the control or ethanol treatment.

last: Diot

first: Guillaume

last: Madignier

first: Ellie

last: Maza

first: Anis

last: Djari

first: DiValentin

last: Olivia

first: Chen

last: Yi

first: Blanchet

last: Simon

first: Christian

last: Chervin


title: Transcriptome data for comparing gene expressions of goldfish with normal and celestial-eye

first: Rongni

last: Li

state: beijing

address: 18 Jiaomen Road, Fengtai District, Beijing

department: Fisheries Science Institute

institute: Beijing Academy of Agriculture and Forestry Sciences

summary: The goldfish strains with celestial-eye (CE) are popular among ornamental fish customers. The CE phenotype consists of enlarged and protuberant eyes, and the eye balls were turned upward during the development, which were suitable for top viewing in pots. Genome and transcriptome data were obtained to comparative analysis for indentifying the causal mutations of CE in goldfish.

overall_design: The 3 goldfish with normal eyes (R) were from a fish farm fron Jiangsu Province of China, while the 3 goldfish with CE (C) were from a fish farm from Beijing of China. When they were 1 winter year's old, they were euthanized and total RNA were extracted from their eye balls for RNA-seq.

last: li

first: Jingyi


title: RNA sequencing of spheroids from HUVECs for differences in Cis- and Trans-signaling of IL-11

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

institute: University Medical Center Freiburg

summary: Cytokines of the IL-6 family, such as IL-11, may influence angiogenesis. Our experiments showed opposite angiogenic effects on HUVECs depending on cis- or transsignaling of IL-11. Spheroids from the 3D angiogenesis model (spheroid sprouting assay) were lysed in QIAzole buffer by vigorous vortexing. The transcriptomic changes were analyzed by RNA sequencing.

overall_design: Spheroids from the spheroid sprouting assays were lysed in QIAzole buffer. A total of 12 samples from three independent spheroid assays were analyzed under the following conditions: VEGF, IL-11+VEGF, sIL-11R+VEGF, IL-11+sR+VEGF

first: Paulia

last: Liang

first: Felicitas

last: Bucher


title: BEX2 is poor prognostic factor and required for cancer stemness in gastric cancer [MKN1_siBEX2]

first: Keiichi

last: Tamai

summary: To investigate the BEX2 signaling, MKN1 cells were knocked down using siRNA against BEX2.

overall_design: BEX2-knocked down MKN1 cells

first: Akihiro

last: Yasumoto


title: Gut-derived indole propionic acid alleviates liver fibrosis by modulating pro-fibrogenic macrophage phenotype and biological function

city: Shanghai

first: Yuan-Yuan

last: Luo

address: Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China

institute: Tongji University

summary: Recently, gut metabolites have been recognized to play significant roles in liver diseases via the gut-liver axis. In this study, we investigate the regulatory effects of the tryptophan metabolite, indole-3-propionic acid (IPA), on immune cells during liver fibrogenesis using single-cell RNA sequencing (scRNA-seq).

overall_design: Single cells were isolated from the livers of fibrotic mice induced by CCl4, including both the IPA-treated and control groups.

first: Yuanyuan

first: Xin

last: Zeng


title: Single nucleus transcriptomes from post-synaptic targets of the corticospinal tract with respect to laterality.

city: New York

first: Benjamin

last: Fait

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: The spinal cord receives inputs from the cortex via corticospinal neurons (CSNs). While predominantly a contralateral projection, a less-investigated minority of its axons terminate in the ipsilateral spinal cord. We analyzed the spatial and molecular properties of these ipsilateral axons and their post-synaptic targets in mice and found they project primarily to the ventral horn, including directly to motor neurons. Barcode-based reconstruction of the ipsilateral axons revealed a class of primarily bilaterally-projecting CSNs with a distinct cortical distribution. The molecular properties of these ipsilaterally-projecting CSNs (IP-CSNs) are strikingly similar to the previously described molecular signature of embryonic-like regenerating CSNs. Finally, we show that IP-CSNs are spontaneously regenerative after spinal cord injury. The discovery of a class of spontaneously regenerative CSNs may prove valuable to the study of spinal cord injury. Additionally, this work suggests that the retention of juvenile-like characteristics may be a widespread phenomenon in adult nervous systems. This data is Smart-seq3 transcriptomic data from single nuclei of the post-synaptic targets of the corticospinal tract, as determined by AAV1-Cre monosynaptic tracing.

overall_design: AAV1-Cre was injected into the caudal forelimb area of the mouse motor cortices, driving nuclear sfGFP fluorescence in post-synaptic neurons in the spinal cord. These nuclei were sorted via FACS and sequenced using Smart-Seq3.

first: Eric

last: Schmidt


title: Dynamic evolution of TCF3-PBX1 leukemias at the single-cell level under chemotherapy pressure

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1E

department: School of Medicine, Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

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

overall_design: Refer to individual Series


title: PRAME induces genomic instability in uveal melanoma

city: Miami

first: Stefan

last: Kurtenbach

address: 1501 NW 10th Avenue

institute: University of Miami


title: Environmental dose of Bisphenol S exposure to brown adipose tissue accelerates aging

city: Chengdu

first: Man

last: Zhu

state: Sichuan

address: No. 4, Section 2, Jianshe North Road, Chenghua District, Chengdu City, Sichuan, China

department: School of Medicine

institute: University of Electronic Science and Technology of China

summary: Bisphenol S (BPS), a common industrial chemical, is increasingly recognized for its potential to disrupt physiological functions even at environmental doses. In this study, we investigated the effects of BPS exposure on lifespan and health span using Caenorhabditis elegans and mouse models. We found that BPS accumulates in brown adipose tissue (BAT), inducing BAT aging by triggering mitochondrial dysfunction, chronic inflammation, altered intercellular communication, cellular senescence, deregulated nutrient-sensing pathways, impaired macroautophagy, and loss of proteostasis. These changes accelerated aging in multiple organs, including the heart, liver, kidneys, lungs, and skeletal muscle. Notably, BAT transplantation experiments revealed that BAT from BPS-exposed mice induced accelerated aging in non-exposed mice, while BAT from non-exposed mice mitigated aging in BPS-exposed mice. In summary, this study is the first to demonstrate that environmental doses of BPS promote systemic aging by disrupting BAT energy metabolism.

overall_design: Transcriptome sequencing was conducted on total RNA extracted from BAT tissues of mice (veh group: n=8; BPS group: n=7), using the NovaSeq 6000 platform (Illumina) at the Beijing Genomic Institution (BGI, China).

first: Xue

last: Wen


title: The effect of Terc deficiency on differentiation and maturation of OCs during aging

first: Junjie

last: Gao

address: 600 Yishan Road

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


title: Candida albicans pathways that protect against organic peroxides and lipid peroxidation.

city: Gangneung-si

first: Kyunghun

last: Min

state: Gangwon

address: 7 Jukheon-gil

department: Department of Plant Science

country: South Korea

institute: Gangneung-Wonju National University

summary: Human fungal pathogens must survive diverse reactive oxygen species (ROS) produced by host immune cells. ROS can oxidize a range of cellular molecules including proteins, lipids, and DNA. Formation of lipid radicals by ROS can be especially damaging, as it leads to a chain reaction of lipid peroxidation that causes widespread damage to the plasma membrane. Most previous studies on antioxidant pathways in fungal pathogens have been conducted with hydrogen peroxide, so the pathways used to combat organic peroxides and lipid peroxidation are not well understood. The most well-known peroxidase in Candida albicans, catalase, only acts on hydrogen peroxide. We therefore characterized a family of four glutathione peroxidases (GPxs) that were predicted to play an important role in reducing organic peroxides. One of the GPxs, Gpx3 is also known to activate the Cap1 transcription factor that plays the major role in inducing antioxidant genes in response to ROS. Surprisingly, we found that the only measurable role of the GPxs is activation of Cap1 and did not find a significant role for GPxs in the direct detoxification of peroxides. Furthermore, a CAP1 deletion mutant strain was highly sensitive to organic peroxides and oxidized lipids, indicating an important role for antioxidant genes upregulated by Cap1 in protecting cells from organic peroxides. We identified GLR1 (Glutathione reductase), a gene upregulated by Cap1, as important for protecting cells from oxidized lipids, implicating glutathione utilizing enzymes in the protection against lipid peroxidation. Furthermore, an RNA-sequencing study in C. albicans measuring the transcriptional response for exposure to an organic peroxide showed upregulation of antioxidant and protein damage pathways. Overall, our results identify novel mechanisms by which C. albicans responds to oxidative stress resistance which open new avenues for understanding how fungal pathogens resist ROS in the host.

overall_design: We conducted RNA-sequencing to determine the transcriptional response of Candida albicans to the representative organic peroxide, tert-butyl hydroperoxide. For comparison, we also performed RNAseq with hydrogen peroxide. The strain used for this experiment is LLF100 which is a prototrophic, wild-type strain. The parental strain is SN152 which was derrived from SC5314. Cells were treated with 0.5mM t-BHP or H2O2 for 15 m (or no treatment for control samples), collected, and then submitted for RNAseq. Each condition was tested in triplicate.

first: Kara

last: Swenson

first: James

last: Konopka


title: Transcriptomic and proteomic analysis of Trametes versicolor interacting with a Hypholoma fasciculare mycelium foraging in soil

city: SWANSEA

first: Daniel

last: Eastwood

state: West Glamorgan

address: Wallace Building Science, Swansea University, Singleton Park Campus

department: Biosciences

institute: Swansea University

summary: The decomposition of large woody material is an important process in forest carbon cycling and nutrient release. Cord-forming saprotrophic basidiomycete fungi create non-resource limited mycelial networks between decomposing branches, logs and tree stumps on the forest floor where colonisation of new resource is often associated with the replacement of incumbent decay communities. Cord-forming species often dominate competition hierarchies in controlled paired antagonism experiments and have been shown to translocate resource to support colonisation and produce inhibitory metabolites. To date, antagonism experiments have mostly placed competing fungi in direct contact, while in nature cord-forming saprobes encounter colonised wood as mycelia in a network. Here we used soil-based microcosms that allowed foraging cord-forming Hypholoma fasciculare to encounter a wood block colonised by Trametes versicolor and conducted transcriptomic and proteomic analysis of the interaction. Cellular processes and metabolic responses to the competitive interaction were identified, where protein turnover featured strongly for both species. H. fasciculare demonstrated an exploitative profile with increased transcription of enzymes that targeted carbohydrate polymers of the substrate and in RNA and ribosome processing. T. versicolor showed a shift in signalling, energy generation and amino acid metabolism. Putative genes involved in secondary metabolite production were identified in both species. This study highlights the importance of ecologically-relevant experimental design when considering complex processes such as community development during wood decomposition

sample_organism:
Trametes versicolor
Hypholoma fasciculare

overall_design:
Beechwood microcosms were established with laboratory cultures of Hypholoma fasciculare and Trametes versicolor and species interactions conducted with single species controls
We conducted RNA-seq analysis using an Illumina HiSeq2500 on three replicates of H. fasciculare-T. versicolor interaction and three repicates of a single species control for each species at 14 h postcontact between the species
Comparative gene expression profiling analysis of RNA-seq data for interaction samples and singel speceis controls

first: Georgina

last: Powell

first: Lynne

last: Boddy

first: Ed

last: Dudley

first: Beth

last: Greenfield


title: Dynamic evolution of TCF3-PBX1 leukemias at the single-cell level under chemotherapy pressure [scRNA-seq]

summary: We have developed a mouse model in order to characterize in vivo chemotherapy resistance depending on niche. Global transcriptomics and phospho-proteomics at the single-cell level elucidated novel mechanisms of chemotherapy resistance depending on microenvironment, which might be suitable for pharmacological therapies. Comparison of the transcriptional profile of GFP+-sorted E2A-PBX1/preBCR+ leukemia cells in different tissues (bone marrow, spinal cord, lymph nodes, spleen) and after treatment with conventional chemotherapies prednisolone, daunorubicin compared to control (DMSO).

overall_design: scRNA-seq samples were generated from 5 tissues (bone marrow, spinal cord, brain, lymph nodes, spleen) from 3 mice (15 samples) developing E2A-PBX1/preBCR+ leukemia after treatment with conventional chemotherapies prednisolone, daunorubicin compared to control (DMSO) using the 10X Genomics Chromium platform and protocols.

first: Mari

last: Lahnalampi

first: Minna

last: Voutilainen

first: Jesús

last: Duque-Afonso

first: Sandra

last: Pennisi


title: Dynamic evolution of TCF3-PBX1 leukemias at the single-cell level under chemotherapy pressure [Bulk RNA-seq]

first: Merja

last: Heinäniemi

overall_design: RNAseq of GFP+ sorted blasts from bone marrow, spleen, lymph nodes and spinal cord (SC) from 3 mice treated with vehicle.

first: Gaia

last: Gentile

first: Mira

last: Kusterer

first: Jesus


title: An accelerated Parkinson’s disease monkey model using AAV-α-synuclein plus Poly(ADP-ribose)

city: yunnan

first: wang

middle: yi

last: chao

state: postgraduation

address: Jingming South Road, Chenggong District, Kunming City, Yunnan Province

institute: Kunming University of Science and Technology

summary: The etiology of Parkinson’s disease (PD) remains elusive, and the limited availability of suitable animal models hampers research on pathogenesis and drug development. We report the development of a cynomolgus monkey model of PD that combines AAV-mediated overexpression of α-synuclein into the substantia nigra with injection of Poly(ADP-ribose) (PAR) into the striatum. Our results show that pathological processes were accelerated, including dopaminergic neuron degeneration, Lewy Bodies aggregation, and hallmarks of inflammation in microglia and astrocytes. Behavioral phenotypes, dopamine transporter imaging and transcriptomic profiling further demonstrate consistencies between the model and PD patients. This model can help to determine mechanisms underlying PD impacted by α-synuclein and PAR and aid in accelerated development of therapeutic strategies for PD.

overall_design: This paper can solve the limitations of the existing PD monkey model, including the drug-induced model cannot simulate Lewy body pathology in PD patients, and the current etiological PD model cannot simulate behavioral phenotype and glia inflammation. Our etiological monkey model utilizes PAR to accelerate pathological processes and behavioral phenotypes, which are closer to that of PD patients, which is significant for preclinical research on PD treatment strategies.


title: PRAME induces genomic instability in uveal melanoma [RNA-seq]

first: Stefan

last: Kurtenbach

summary: RNA-seq of uveal melanoma cell lines and uveal melanocytes

overall_design: PRAME was over-expressed or knocked down in uveal melanoma and uveal melanocyte cell lines

first: JW

last: Harbour


title: A novel Nilotinib derivative N-12 inhibits the proliferation and migration of colon cancer cells through the EMT signaling pathway

city: Lianyungang

first: Song

middle: meng

last: wei

address: China

institute: Jiangsu Ocean University

summary: Colon cancer ranks among the prevalent malignancies globally, and its proclivity for metastasis significantly contributes to the adverse prognostic outcomes observed in patients. The epithelial-mesenchymal transition (EMT) represents a critical biological process through which tumor cells gain migratory and invasive capabilities. Nilotinib is a selective inhibitor of tyrosine kinases, commonly utilized in the treatment of chronic myeloid leukemia (CML). Prior investigations have demonstrated that the Nilotinib derivative, N-12, exhibits significant antitumor properties. The objective of this study is to elucidate the inhibitory effects of N-12 on the progression of EMT in colon cancer cells. So, the human colon cancer cell line HCT116 was selected for experimentation. Initially, assessments of cell proliferation, migration and invasion were conducted utilizing MTT, colony formation, Edu and Transwell assays. Subsequently, the chick embryo chorioallantoic membrane model was employed to evaluate tumor size and its impact on angiogenesis in vivo. Thereafter, HCT116 cells treated with N-12 underwent RNA sequencing for analysis. Finally, the expression levels of EMT markers in colon cancer cells were determined by Western blot analysis. The results showed that N-12 significantly curtails the proliferation, migration, and invasion of colon cancer cells, and concurrently impedes tumor growth in vivo by influencing angiogenesis within the chick embryo chorioallantoic membrane. Furthermore, RNA sequencing and Western blot analyses have elucidated that the antitumor efficacy of N-12 is attributable to the inhibition of the EMT signaling pathway. These results underscore the therapeutic potential of N-12 in the management of colon cancer and delineate its mechanism of action.

overall_design: In order to investigate the role and mechanism of N_12 in colon cancer, we treated HCT116 cells with N_12 and without treatment. Then, we performed gene expression profiling analysis using RNA seq data from N_12 and DMSO cells.

first: Zirui

last: JIANG

first: Jing

last: JI


title: PRAME induces genomic instability in uveal melanoma [ChIP-Seq]

summary: ChIP-seq of histone marks and RNApol2 in uveal melanoma cell lines

overall_design: Mel202 and 92.1 cells were used for ChIP-seq of histone marks and RNA-pol2

first: J

middle: W


title: Loss of protein phosphatase 6 confers resistance to MAP kinase pathway inhibition in KRAS and BRAF mutant cells via NF-κB activation

city: Bethesda

first: Howard

last: Yang

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

summary: To understand the global impact of PPP6C loss on gene expression, we carried out RNA-seq analysis in parental and PPP6C KO SW620 cells under 2D and 3D culture conditions. SW620 WT (sgNT) and PPP6C KO (sgPPP6C#2, sgPPP6C#3) were cultured in normal petri dish (2D culture) or U-bottom plates (3D culture) for 3 days with three independent replicates for each cell sample. A total of 4,337 genes were found to be differentially expressed in the KO cells under at least one condition (FDR < 0.05, ≥ 2-fold change). Among these, 1,123 genes were significant up- or down-regulated in PPP6C KO cells under both 2D and 3D conditions. Unsupervised clustering analysis identified three large clusters of gene expression patterns: cluster 1 were upregulated in the PPP6C KO cells primarily under 2D conditions, cluster 2 were upregulated in the PPP6C KO cells under both 2D and 3D conditions, and cluster 3 gene were downregulated genes in the PPP6C KO cells under both 2D and 2D conditions. We next carried out gene set enrichment analysis (GSEA) using the hallmark gene set database to identified pathways that were significantly altered in PPP6C KO cells. Among the pathways upregulated in the PPP6C KO cells under both 2D and 3D conditions, the “TNFA-signaling_via_NFKB” gene set scored as the top one. Both “KRAS_signaling_up” and “PI3K_AKT_mTOR_signaling” gene sets were also significantly upregulated. PPP6C KO has opposite effects on cell proliferation in 2D monolayer vs. 3D tumor spheroid culture. We noticed that 383 genes in the PPP6C KO cells showed opposite changes in 2D vs. 3D conditions. Taken together, gene expression analysis indicates that multiple signaling pathways including the KRAS, PI3K and NF-κB pathways were perturbed in the in PPP6C KO cells and they could contribute to the cell’s decreased sensitivity to MEK inhibitors.

overall_design: mRNA profiles of PPP6C knockout in SW620 cells in 2D and 3D cultures.

first: Haibo

last: Zhang

first: Abigail

last: Read

first: Christophe

last: Cataisson

middle: H

first: Benjamin

middle: E

last: Turk

first: Stuart

last: Yuspa

first: Ji

last: Luo

first: Wei-Chun

last: Lee


title: Gene expression profile at single cell level of human Caco2 (hCaco2) cells expressing mouse CD300lf (mCD300lf) infected with murine norovirus (MNV)

status: Public on Sep 19 2024

first: Yuki

last: Matsushima

state: Maryland

address: Building 50, MSC 8026, 50 South Drive

department: LID/DIR/NIAID

institute: National Institutes of Health

summary: mCD300lf-hCaco2 cells infected with MNV were composed of multiple cell clusters with varying levels of viral RNA content. We used single cell RNA sequencing (scRNAseq) to analyze the diversity of mCD300lf-hCaco2 cells.

overall_design: mCD300lf-hCaco2 cells were infected with mock or MNV at MOI 5 for 0 hour, 4 hours, 8 hours or 12 hours and analyzed using scRNAseq.

first: Eric

middle: A

last: Levenson

first: Stanislav

last: Sosnovtsev

first: Kim

middle: Y

last: Green


title: RNA-sequencing of PBMC cultured with PolyI:C or LPS, from a pediatric cohort who received OM85 or placebo.

city: Perth

first: Niamh

last: Troy

address: Perth Children's Hospital, 15 Hospital Avenue Nedlands

country: Australia

institute: Telethon Kids Institute

summary: Bacterial-derived immune training agents are a showing promise in clinical studies for prevention of lower respiatory infections in high-risk infants but underlying mechanisms of this protective effect are unclear. To address this, we employed a systems-level analysis of transcriptional responses to immune stimuli (LPS and PolyI:C) in infants who participated in a clinical trial of one such agent called OM85 which was clinically effective. We identified key protected innate immune changes using a series of analytical approaches such as reduced inflammatory responses to LPS and enhanced antibacterial interferon responses potentially mediated through IRF7. We posit that immune training agents exemplified by OM85 potentially protect against infant severe lower respiratory infection principally via effects on innate immune responses targeting the bacterial components of the mixed respiratory viral/bacterial infections which are characteristic of this age group.

overall_design: Two participant groups; high-risk infants (aged 4-8 months) who received either OM85 or Placebo during their first winter of life as part of a previously published randomised controlled trial. Two timepoints; PBMC collected pre and post treatment period. Three in vitro stimulants: PBMC cultured with LPS, polyI:C or paired controls for 24 hours.

middle: M

first: Deborah

last: Strickland

first: Michael

last: Serralha

first: Emma

last: de Jong

first: Anya

last: Jones

first: James

first: Sally

last: Galbraith

first: Zahir

last: Islam

first: Parwinder

last: Kaur

first: Kyle

last: Mincham

first: Barbara

last: Holt

first: Peter

last: Sly

first: Anthony

last: Bosco

first: Patrick


title: Phytogenics from sage and lemon verbena promote growth, systemic immunity and disease resistance in Atlantic salmon (Salmo salar)

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

summary: Deciphering the dietary immunomodulatory effects of a feed additive rich in verbascoside and triterpenic compounds like ursolic (MPLE, NATAC Biotech SL, Spain) on the systemic immune response and disease resistance of Atlantic salmon (Salmo salar L.) smolts.

overall_design: Transcriptomic analysis was conducted in order to determine the differences on gene expression level between these two dietary strategies at head kidney specific level. The experimental design included two conditions: (1) fish fed basal diet with no phytogenic feed additives (MPLE) (control); (2) fish fed 0.1% inclusion of MPLE (10%, ursolic acid, 3% other triterpenic compounds; 2% verbascoside and <1% polyphenols) from sage and lemon verbena. After 133 days of feeding trial, total RNA were extracted invidually from Atlantic salmon (S. salar) head kidney fed basal diet or an experimental diet containing 0.1% inclusion. Total RNA samples were grouped into 3 pools (n= 6 fish for each condition). The transcriptomic analysis was done following a reference design using the control diet group as reference.

first: Ricardo

last: Salomón

first: Eva

middle: C

last: Vallejos-Vidal

first: Enric

last: Gisbert


title: Altered bone marrow myelopoiesis contributes to kidney injury [scRNA-seq]

city: Chicago

first: Eunsil

last: Hahm

address: 735 W Harrison St. , 753

institute: Rush University Medical Center

summary: The objectives of this study were to characterize bone marrow alteration in the context of kidney disease.

overall_design: Bone marrow (BM) aspirates were collected from patients with chronic kidney disease (CKD). This study included adult patients with CKD (primary FSGS, secondary FSGS, or non-FSGS) who had previously undergone kidney transplant and have developed recurrence in the renal allograft (n=9, age>18 yrs, both genders, all races). Participation in this study was entirely voluntary. We excluded patients who have acute humoral or cell-mediated rejection, thrombocytopenia, leukocytopenia, hematocrit below 20% or a known reaction to Lidocaine. BM aspirates of healthy donors were purchased from Lonza Inc. and used as controls. BM samples were shipped overnight and processed the next day. From these samples, BM mononuclear cells (BM-MNCs) were isolated. The resulting BM-MNCs cells were cryopreserved in freezing medium for this subsequent scRNA-seq analysis. Scipio bioscience Asteria kit (REV-gel technology) and Cytonaut software was used for analysis.

first: Ryan

last: Spear


title: Altered bone marrow myelopoiesis contributes to kidney injury [RNA-seq]

overall_design: Mobilized apheresis products were collected from de-identified, healthy donors. Isolated CD34+ HSPCs were cultured in myeloid expansion medium for 10 days with or without TNFα supplement. For bulk ATAC and RNA sequencing, CD14+ monocytic cells were further isolated at day 10.


title: Altered bone marrow myelopoiesis contributes to kidney injury [ATAC-seq]

overall_design: Mobilized apheresis products were collected from de-identified, healthy donors. Isolated CD34+ HSPCs were cultured in myeloid expansion medium for 10 days with or without TNFα supplement. For bulk ATAC sequencing, CD14+ monocytic cells were further isolated at day 10. The cells were then thawed in a 37oC water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017).


title: A quantitative computational framework for allopolyploid single-cell data integration and core gene ranking in development [scRNA-seq]

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

summary: Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome divergent regulation in the context of cellular differentiation. However, analyzing single-cell data suffers from high error rates due to high-dimensionality, noise, and sparsity, and the errors stack up in polyploid analysis due to the increased dimensionality of comparisons between subgenomes of each cell, hindering deeper mechanistic understandings. Here, we developed a quantitative computational framework, pseudo-genome divergence quantification (pgDQ), for quantifying and tracking subgenome divergence directly at the cellular level. Further comparing with cellular differentiation trajectories derived from scRNA-seq data allowed for an examination of the relationship between subgenome divergence and the progression of development. pgDQ produces robust results and is insensitive to data dropout and noise, avoiding high error rates due to multiple comparisons of genes, cells, and subgenomes. A statistical diagonostic approach is proposed to identify genes that are central to subgenome divergence during development, which facilitates the integration of different data modalities, enabling the identification of factors and pathways that mediate subgenome-divergent activity during development. Case studies demonstrated that applying pgDQ to single cell and bulk tissue transcriptome data promotes a systematic and deeper understanding of how dynamic subgenome divergence contributes to developmental trajectories in polyploid evolution.

overall_design: Common wheat (Triticum aestivum cultivar ‘Chinese Spring’) seeds were surface-sterilized via a 10-min incubation in 30% H2O2 and then thoroughly washed five times with distilled water. The seeds were germinated in water for 3 days at 22 °C.The germinated seeds with residual endosperm were transferred to Hoagland solution and grown under 16 h light/ 8 h dark condition at 22 °C in greenhouse.The root tips (0.5 cm) of the seedlings were harvested for scRNA-seq experiment. The root tips were harvested and digested for 2 h at room temperature in digestion buffer (1.5% cellulase R10, 1.5% macerozyme R10, 0.3 M mannitol, 3 mM β-mercaptoethanol, 10 mM CaCl2, and 0.3% BSA). Single-cell suspensions were loaded onto 10× GENOMICS Chromium to capture approximately 6000 single cells following the manufacturer’s instructions for the 10× Genomics Chromium Single-Cell 3′ kit (V3). cDNA amplification, library construction, and sequencing on the Illumina NovaSeq 6000 platform (paired-end multiplexing run, 150 bp) were performed by LC-Bio Technology (HangZhou, China)

first: Yijing

last: Zhang


title: Evaluation of the impact of aging on lung tumor progression

first: Xueqian

last: Zhuang

address: 417 E 68th Street

institute: Memorial Sloan Kettering Cancer Center

summary: To understand the impact of aging on lung tumor progression, we isolated lung tumor cells from Kras LSL-G12D/+; Trp53 fl/fl (KP) mouse models at different stage of tumor progression and performed single-cell sequencing on them.

overall_design: Aged (> 2 years old) and young (12-16 weeks old) Kras LSL-G12D/+; Trp53 fl/fl (KP) mouse models with or without reporter alleles were infected by adenoviral Cre recombinase and tumor cells at different tumor development were isolated for single-cell mRNA sequencing

first: Simon

last: Joost

first: Tuomas

last: Tammela

first: Emily

middle: S

last: Wong


title: The G Protein-Coupled Receptor ADGRG6 Maintains Mouse Growth Plate Homeostasis by Negatively Regulating IHH Signaling

city: Los Angeles

first: Zhaoyang

last: Liu

state: California

address: 2250 Alcazar Street, CSA 103

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

summary: ADGRG6 is a cartilage-enriched G protein-coupled receptor (GPCR). Using molecular mouse genetics and spatial transcriptomics approaches, we demonstrated that Adgrg6 has a vital role in regulating chondrocyte differentiation and growth plate homeostasis by positively regulating the formation and/or maintenance of the PTHrP (+) cell population and negatively regulating the IHH signaling in postnatal growth plates.

overall_design: Spatial Transcriptomics (Visium, 10x Genimocs) was performed on Hindlimbs of P20 Col2Cre; Adgrg6f/f mutants and Cre (-) littermate (wild-type) controls

first: Chia-Lung

last: Wu

first: Yanshi

last: Chen

first: Fangzhou

last: Bian

first: Jingyu

last: He

last: Gray


title: Bulk RNAseq of adult Drosophila melanogaster whole brains with neuronal specific knock down of brummer.

city: Vancouver

first: Elizabeth

last: Rideout

state: BC

address: 2350 Health Sciences Mall

department: Department of Cell and Physiological Science

country: Canada

institute: University of British Columbia

summary: Lipids are essential for neuron development and physiology. Lipid droplets (LD) play a central role in coordinating cellular lipid distribution and metabolism in non-neuronal cells; however, there is no general consensus on a role for neuronal LD under normal physiological conditions. We have previously shown that neuronal LD exists in wildtype flies under normal physiological condition, and that the loss of a triglyceride lipase, brummer, increases neutral lipids in the brain (Wat et al., 2020). To investigate the importance of brummer in regulating neuronal metabolism and function in a sex-specific manner, we performed transcriptomic profiling in adult male and female whole brain with RNAi-mediated neuron-specific knock down of brummer.

overall_design: To assess the transcriptomic effects of brummer knock down in either males or females, we raised male and female flies with neuron-specific expression of RNAi targeting brummer transcripts (elav-GAL4>UAS-bmm-RNAi). Adult whole brains were dissected at day 5 to 6 after eclosion for transcriptomic profiling. We also profiled the transcriptome of whole brains from elav-GAL4>+ and +>UAS-bmm-RNAi males and females as controls.

first: Colin

last: Miller

first: Serena

last: Hollman

first: Charlotte

last: Chao


title: Technical considerations for placental tissue processing and the subsequent impact on genome-wide DNA methylation analysis

city: Washington

first: Kristen

last: Kocher

state: DC

address: 111 Michigan Ave NW

institute: Children's National Hospital

type: Methylation profiling by genome tiling array

summary: To assess the impact of postnatal processing on placental DNA methylation, array data from flash frozen placental tissue was compared to perfluorocarbon-immersed and formalin fixed paraffin embedded placental tissue. We observed tissue exposed to perfluorocarbon showed no significant DNA methylation differences when compared to unprocessed tissue, while formalin processing altered the quality and reliability of the data produced on the DNA methylation array platform. Placental DNA methylation allows for the study of gene-environment interactions that influence the fetal environment and development. Our study highlights that placental postprocessing techniques must be considered in the evaluation and interpretation of epigenetic studies.

overall_design: Matched samples exposed to various processing methods (flash frozen, exposure to perfluorocarbon MRI media, FFPE processing, and FFPE processing restored chemically using the Illumina Restore Protocol) from 6 term placentas were used to assess DNA methylation data quality

first: Julius

last: Ngwa

first: Kushal

last: Kapse

first: Surajit

last: Bhattacharya

first: Christopher

last: Rossi

first: Emmanuele

last: Delot

first: Adre

last: duPlessis

first: Catherine

last: Limperopoulos

first: Nickie

last: Andescavage


title: An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs [Cut & Tag]

status: Public on Sep 18 2024

city: SAN DIEGO

first: Lishuan

last: Wang

address: 9500 Gilman Drive

institute: UCSD

summary: The evidence that several signal and ligand-dependent pathways function by activating regulatory enhancer programs suggests that a “checkpoint” strategy may underline activation of some or even many diversely-regulated enhancers. Here, we report a molecular mechanism common to several acute signal- and ligand-dependent enhancer activation programs based on release of a shared eRNA transcription checkpoint. This requires recruitment of a DNA-PKcs-phosphorylated RING finger repressor, KAP1, functioning as a modulator, inhibiting its association with 7SK and E3 SUMO ligase activity on the CDK9 subunit of P-TEFb, facilitating formation of an activated P-TEFb complex, licensing eRNA elongation. Overcoming this checkpoint for signal-dependent enhancer activation occurs in diverse pathways including estrogen receptor α, NF-κB-regulated proinflammatory, androgen receptor and neuronal depolarization. Therefore, a specific strategy required to convert a basal state enhancer P-TEFb complex to an active state to release a conserved checkpoint is apparently employed by several functionally-important signal/ligand-regulated regulatory enhancers to implement the instructions of endocrine/paracrine system.

overall_design: For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM. For knock-down of KAP1 genes, the shRNA were employed.


title: LSD1 and CoREST2 Regulate STAT3 Activity to Promote Enteroendocrine Cell Differentiation in Mucinous Colorectal Cancer[scMultiome-seq]

city: Bloomington

first: Ahmed

last: Ghobashi

state: IN

institute: Indiana University

summary: Neuroendocrine cells have been implicated in therapeutic resistance and worse overall survival in many cancer types. Mucinous colorectal cancer (mCRC) is uniquely enriched for enteroendocrine cells (EECs), the neuroendocrine cell of the normal colon epithelium, as compared to non-mucinous CRC. Therefore, targeting EEC differentiation may have clinical value in mCRC. Here, single cell multi-omics was used to uncover epigenetic alterations that accompany EEC differentiation, identify STAT3 as a novel regulator of EEC specification, and discover a rare cancer-specific cell type with enteric neuron-like characteristics. Further experiments demonstrated that lysine-specific demethylase 1 (LSD1) and CoREST2 mediate STAT3 demethylation and regulate STAT3 chromatin binding. Knockdown of CoREST2 in an orthotopic xenograft mouse model resulted in decreased primary tumor growth and lung metastases. In culmination, these results provide rationale for new LSD1 inhibitors that target the interaction between LSD1 with STAT3 or CoREST2, which may improve clinical outcomes for patients with mCRC.

overall_design: Investigating cellular heterogeneity of colon cancer in response to ISX9 using multimodal single-cell sequencing (scRNA-seq+scATAC-seq)

first: Heather

last: O'Hagan

last: Ladaika


title: LSD1 and CoREST2 Regulate STAT3 Activity to Promote Enteroendocrine Cell Differentiation in Mucinous Colorectal Cancer[CUT&RUN]

overall_design: Study the enrichment of STAT3 and CoREST2 using CUT&RUN


title: Transcriptome changes caused by PHF6 knockout in THP1 human AML cell line

city: Philadelphia

first: Vikram

middle: R

last: Paralkar

state: PA

address: 421 Curie Boulevard

department: Division of Hematology and Oncology, Department of Medicine

institute: University of Pennsylvania Perelman School of Medicine

summary: CRISPR Cas9 guided knockout (KO) of PHF6 in human THP1 AML cell line. We performed bulk RNA-Seq on knockout (PHF6 KO) and wildtype (CTRL) clones derived from THP1 cells transduced with lentiviral vectors encoding Cas9 protein and either PHF6 gRNAs or non-targeting gRNAs. Our results reveal that PHF6 knockout upregulates self-renewal gene sets and downregulates myeloid differentiation gene sets.

overall_design: RNA-Seq of PHF6 knockout and wildtype THP1 AML cells that were clonally selected and expanded after Cas9-gRNA lentiviral transduction.

first: Aishwarya

last: Pawar

first: Subin

last: George


title: Single-cell RNA sequencing analysis of Angiotensin II-induced mouse dissecting AAA samples

city: Wuhan

first: Jiahong

last: Xia

state: Hubei

address: JieFang Road 1277

department: Department of Cardiovascular Surgery

institute: Union Hospital, Tongji Medical College,  Huazhong University of Science and Technology

summary: Dissecting abdominal aortic aneurysm (AAA) is a life-threatening condition characterized by medial layer degeneration of the abdominal aorta. Complex, complicated, and extremely heterogeneous diseases like dissecting AAAs severely limit our ability to understand it. A thorough understanding of cell types and signaling pathways associated with the initiation and progression of dissecting AAA is essential for the development of medical therapy. Single-cell RNA sequencing (scRNA-seq) was performed on the abdominal aortas from ApoE-/- mice at days 28 post-Angiotensin II-induced mouse dissecting AAAs. According to the Angiotensin II-induced dissecting AAA model described in this study, alterations in cellular subpopulations, fractions, and transcriptome profiles are present.

overall_design: Examination of the transcriptomic profiles of the abdominal aortic single cells from ApoE-/- mice at days 28 post-Angiotensin II-induced mouse dissecting AAAs or normal abdominal aortas.

first: Ping

last: Ye

first: Sheng

last: Le


title: An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs [PRO-Seq]


title: Sense codon-misassociated eRF1 elicits widespread ribosome stalling subjected to quality control

city: Saitama

first: Peixun

last: Han

address: Hirosawa Wako

institute: Riken

summary: The ribosome-associated quality control (RQC) is a surveillance system for aberrant translation, sensing ribosome collisions. Although the molecular mechanism has been extensively studied, the endogenous targets of RQC in human cells were poorly understood. Here, starting from the study of codon specificity of eukaryotic termination factor eRF1, we unexpectedly find that misrecognition of UUA sense codon by eRF1 leads to ribosome collisions and provides the source of RQC substrates in humans. eRF1-selective Monosome-Seq and Disome-Seq reveal that eRF1 recruitment to ribosome was not restricted to the stop codons but also the sub-cognate sense codons, including the UUA codon. The UUA misrecognition by eRF1 causes ribosome collision without termination reaction. Remarkably, Disome-Seq with the depletion of ASCC3 and 4EHP, key factors in RQC, showed that ribosome stalled at UUA codons are the predominant sub-populations rescued by RQC. Failure to resolve ribosome collisions by RQC triggers p38 phosphorylation and upregulation of stress response transcription factor ATF3. This study presents the impact of sense codon misrecognition by the termination factor on translation homeostasis in human cells.

overall_design:
Ribosome profiling (including monosome and disome) data from HEK293 Flp-In T-REx cells overexpressing SBP-eRF1. Ribosome footprints were collected from input and IP samples.
Ribosome profiling (including monosome and disome) and RNA-seq data from HEK293 Flp-In TREx cells transfected with siRNA.

first: Mari

last: Mito

first: Shintaro

last: Iwasaki


title: 4-octyl itaconate attenuate experimental acute pancreatitis via inhibiting Sting signaling pathway and activating Nrf2 pathway in macrophages

city: Shanghai

first: Chuanyang

state: Shanghai

address: Shanghai Wujin Road 85#

institute: Shanghai Jiaotong University

summary: Acute pancreatitis (AP) is a common and severe inflammatory disease of the abdomen. Recent studies have shown that macrophages play a crucial role in AP. 4-octyl itaconate (4OI), a derivative of the cell metabolism intermediate itaconate (ITA), has demonstrated significant anti-inflammatory effects in various cell and disease models. In this study, we investigated the potential role and mechanism of 4OI in both in vivo and in vitro models of AP.After administering 25 mg/kg of 4OI to mice and inducing AP with caerulein or L-Arg, we found that 4OI significantly alleviated the severity of AP: serum amylase and lipase levels were significantly reduced, histopathological scores decreased, and levels of inflammatory factors were notably lower. Additionally, macrophage infiltration and M1 polarization were significantly reduced. Through in vitro experiments, we further explored the molecular mechanism by which 4OI inhibits the inflammatory response in macrophages. We discovered that 4OI reduces macrophage polarization to the pro-inflammatory M1 type and decreases the expression of inflammation-related genes. We also found that 4OI exerts its anti-inflammatory effects by promoting the Nrf2 signaling pathway and inhibiting the Sting signaling pathway. In conclusion, this study reveals the anti-inflammatory effects of 4OI in AP and its potential clinical therapeutic value.

overall_design: BMDMs were extracted from male wildtype C57BL/6 mice（6-8weeks，22-25g）,the cells were used for experiment 6 days of culture. Acinar cells were stimulated by caerulein (200nM) for 5 h before conditional medium(CM) collection. All samples were treated with CM (1:1) for 4h. CM_4OI group were additional treated with 200μM 4-octyl itaconate(4OI).

first: Jingpiao

last: Bao

first: Leheng

last: Liu

first: Rong

last: Wan


title: Molecular phenology regulating bud dormancy of the Yoshino-cherry tree

city: Fukuoka

first: Atsuko

last: Miyawaki-Kuwakado

address: 744 Motooka, Nishi-ku

department: Department of Biology, Faculty of Science

institute: Kyushu University

summary: We explored seasonal gene expression profiles in the Yoshino cherry trees (Cerasus × yedoensis ‘Somei-yoshino’) at three distinct sites, each situated at varying latitudes in Japan. Our goal was to gather molecular phenology data that could provide insights into mechanism of bud dormancy. The molecular phenology approach, which monitors the seasonal dynamics of global gene expression profiles in leaves and buds under natural conditions, enables the study of physiological responses to seasonal environmental changes at the molecular level.

overall_design: We characterized the seasonal dynamics of global transcriptomics every four weeks using apical buds and leaves throughout the year from June 2018 to April 2019. To monitor the molecular phenology, we collected samples from two individuals each at three study sites in Japan: Sapporo (nursery at Forestry and Forest Products Research Institute (FFPRI) Hokkaido, 42°59′ N, 141°23′ E; 146.5 m a.s.l.), Tsukuba (an arboretum of the FFPRI, 36°0′ N, 140°7′ E, 24 m a.s.l.) and Fukuoka (the biodiversity reserve on the Ito campus of Kyushu University; 33°35′ N, 130°12′ E, 20 to 57 m a.s.l.). RNA was extracted independently from bud and leaf and samples of each tree of Cerasus × yedoensis ‘Somei-yoshino’.

first: Qingmin

first: Keiko

last: Kitamura

first: Akiko

last: Satake


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Control and BET bromodomain Inhibitor-treated Uterine Leiomyosarcoma Cell Transcriptome

city: San Antonio

first: Azad

last: Khosh

state: TX

address: 7703 Floyd Curl Dr

institute: UTHSCSA

summary: We report that BET bromodomain inhibition alters multiple biological pathways in uterine leiomyosarcoma cells

overall_design: Examine the transcriptome alteration in uterine leiomyosarcoma cells with or without BET bromodomain inhibitors

first: Qiwei

last: Yang

first: Ali

last: Falahati

first: Ayman

last: Al-Hendy


city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

summary: Efficient targeted control of exon splicing is a major goal of functional genomic and therapeutic applications. Guide RNA-directed, deactivated (d)Cas CRISPR enzymes fused to splicing effectors represent a promising strategy due to the flexibility and presumed specificity of these systems. However, efficient, selective, and generalizable activation of targeted endogenous exons using this approach has not been reported. Here, we identify dCasRx-RBM25 as a potent activator of exons by screening over 300 dCasRx splicing factor fusions tethered to splicing reporters. dCasRx-RBM25 also strongly activates splicing of endogenous alternative exons, when recruited to downstream intron sequences using single guide RNAs. In transcriptome wide analyses we observe a high degree of specificity of dCasRx-RBM25 for endogenous exon targeting. We further leverage the guide array-processing activity of dCasRx to simultaneously target multiple endogenous exons for activation and repression by dCasRx-RBM25. Our results pave the way for versatile exon-resolution functional assays and splicing-directed therapeutic applications.

overall_design: This dataset consists of 12 RNA-seq files associated with the manuscript "Efficient, specific and combinatorial control of endogenous exon splicing with dCasRx-RBM25" characterizing the effect of dCasRx-RBM25, RBFOX1N-dCasRx-C, or dCasRx overexpression by co-transfection either with a non-targeting guide RNA, a gRNA targeting MAPT exon 10 for activation, or a gRNA targeting CD46 exon 13 for repression (for dCasRx-RBM25 only) on global gene expression and alternative splicing patterns in HEK293T cells. Each treatment was performed in two biological replicates.

first: Jack

middle: D

last: Li

first: Mikko

last: Taipale

first: Benjamin

last: Blencowe


title: Ischemia-preconditioning induced serum exosomal miR-133a-3p improved post-myocardial infarction repair via targeting LTBP1/TGF-β1/PPP2CA axis

city: Hefei

first: Hai-Juan

last: ZHU

state: Anhui

address: the 15th Yimin street

institute: Maternal and Child Medical Center of Anhui Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: This study found that IPC-induced serum exosomes inhibit myocardial fibrosis and improve cardiac function following MI by transferring miR-133a-3p, which targets LTBP1 and PPP2CA, to regulate the TGF-β signaling pathway in rats.

overall_design: Exosomes were obtained from the serum of adult rats in the control (Con-exo) and IPC (IPC-exo) groups. The samples for high -throughput sequencing were three in each group.

first: Yongbo

last: Hou

first: Yuanyuan

last: Zhang

first: Ye

first: Junma

last: Yu

first: Shufang

last: He

first: Haijuan

last: Zhu


title: Full-length target sequences of GeoMx Digital Spatial Profiling probes reveal that gene-promiscuity predicts probe sensitivity to EDTA tissue decalcification

city: Wien

first: Andre

last: Oszwald

address: Währinger Gürtel 18-20

institute: Medical University of Vienna

summary:
GeoMx Digital Spatial Profiling (Nanostring) is a commercial spatial transcriptomics method to selectively analyze regions of interest within intact tissue sections. However, it is unclear how tissue decalcification affects the results of this assay, or if decalicified samples are comparable to untreated samples. For this purpose, we assembled a set of tissues that were subjected to progressive durations of incubation with ethylene-diamine-tetra-acetic (EDTA), and analyzed comparable regions of the tissue using GeoMx DSP. In the associated manuscript, we show that EDTA incubation attenuates signals, and distorts counts from a subset of probes. We determine the undisclosed full-length target sequences of probes used in the human whole transcriptome panel, updating target transcripts and genes, and identify that gene-promiscuous probes are particularly affected by normalization after EDTA incubation.
For the purpose of this study, we prepared series of non-calcified tissues that were incubated with EDTA for increasing time periods, and matched control samples from the same source tissue, which were left untreated. Specimens submitted for routine tissue analysis were collected for research purposes after approval of the ethics commission of the Medical University of Vienna (2167/2021, registered at https://ekmeduniwien.at/core/catalog/2022/) as graphically shown in Figure 1A). In the course of routine pathology workup, 24 clinical tissue specimens (Table S1) of different organs stemming from 20 patients were fixed in 7.5% buffered formalin for 2.0 to 3.5 (mean 3.3, median 3.0) days according to the laboratory’s routine procedure. At macroscopic dissection, an excess piece of tissue was removed and divided into 4 macroscopically similar samples. Tissues were then either processed immediately in a Tissue-Tek VIP® 6 AI (Sakura Finetek) or incubated at room temperature in EDTA solution (Tritiplex, Glatt-Koller, 403212270) for 1, 3, and 7 days before processing them analogous to the untreated tissue. Samples were embedded in paraffin blocks according to standard protocols using low-melting point Paraffin (Histo-Comp, ATS-200856).
Blocks were sectioned, stained with hematoxylin/eosin and scanned (Pannoramic 250 Flash II, 3DHistech) to confirm the content of equivalent histological structures among samples sourced from the same specimen. Areas for tissue microarray (TMA) cores were selected using the digital slide scans. Tissue microarrays were then assembled using an automated TMA device (TMA Grandmaster, 3DHistech) using 1mm punches and a recipient block of 5mm depth. TMA were tempered by alternating storage at 37°C, 4°C, and room temperature, for 5 times (2h each), following by a single incubation at 65°C for 10 minutes.
Slides were sectioned using a rotating microtome at 5µm thickness. One section was used for DSP analysis as outlined below, while an adjacent section was used for validation of the TMA cores using hematoxylin & eosin stain. DSP was performed according to protocols provided by Nanostring using the following standard parameters. In brief, sections were deparaffinized and subjected to heat-induced protein epitope retrieval (using retrieval buffer at pH 9, Thermo Fisher Scientific, 00-4956-58) for 15 minutes at 100°C using a steam cooker. Retrieval for mRNA was performed using proteinase K (Thermo Fisher Scientific, 25530049) at 1µg/ml for 15 minutes. Slides were then incubated with the human Whole Transcriptome Atlas (WTA) probe panel (Nanostring, NA-GMX-RNA-NGS-HuWTA-4, Lot HWTA21003) at 37°C in a humidified environment overnight. Sections were washed according to standard protocols and direct immunofluorescence was performed with antibodies against CD34 conjugated to Alexa-647 (Novus Biologicals, clone QBEnd-10, NBP2-34713AF647), Pan-cytokeratin conjugated to to Alexa532 (Novus Biologicals, clone AE1/AE3, NBP2-33200), CD45 conjugated to Alexa594 (clone 2B11 + PD7/26, Novus Biologicals, NBP2-34528), and a nuclear counterstain (Syto-13, Nanostring) DSP device run and library preparation were performed according to the manufacturers’ protocol. The library was sequenced using an Illumina NextSeq 550 sequencer with the specifications provided by Nanostring (paired-end reads at length 27, index length 8) at a library concentration of 1.6 pM using a NextSeq 550 High Output 75-cycle kit (Illumina, 20024906). Nuclei counts of regions of interest were obtained via the default automatic nuclear segmentation settings of the DSP device software.

overall_design: 24 clinical tissue specimens of different organs stemming from 20 patients; during routine workup, one excess piece of tissue per specimen was divided into 4 macroscopically similar samples. Samples were then either processed immediately or incubated at room temperature in EDTA solution for 1, 3, and 7 days before processing them analogous to the untreated sample. Tissue microarrays were assembled and analzysed using Nanostring GeoMx DSP.

first: André

first: Renate

last: Kain


title: c-Myc alone is enough to reprogram fibroblasts into functional macrophages [RNA-seq]

first: Guoyu

last: Chen

address: Xuhui District Yueyang Road 320

institute: PICB

summary:
Background Cell therapy based on macrophages is promising in solid tumors, but effective acquisition of macrophages is a challenge. Induced pluripotent stem cell (iPSC)-induced macrophages are a good source but are time-consuming and costly. Macrophages derived from somatic cells by reprogramming technologies have the potential to enable the development of cell-based therapies for numerous malignant diseases.
Methods The composition of CD45+ myeloid-like cell complex (MCC) was analyzed by flow cytometry and single-cell sequencing. The engraftment capacity of CD45+ MCC was evaluated by two transplantation assays. Regulation of c-myc on MafB was evaluated by ChIP-qPCR and promoter reporter and dual luciferase assays. The phenotype and phagocytosis of induced macrophages were explored by flow cytometry and immunofluorescence. Leukemia, breast cancer, and patient-derived tumor xenograft models were used to explore the anti-tumor function of induced macrophages.
Results Here we report on the establishment of a novel methodology allowing for reprogramming fibroblasts into functional macrophages with phagocytic activity by c-Myc overexpression. Fibroblasts with ectopic expression of c-Myc in iPSC medium rapidly generated CD45+ MCC intermediates with engraftment capacity as well as the repopulation of distinct hematopoietic compartments. MCC intermediates were stably maintained in suspension culture and continuously generated functional and highly pure-induced macrophage (iMac) just by M-CSF cytokine stimulation. Single-cell transcriptomic analysis of MCC intermediates revealed that c-Myc up-regulates the expression of MafB, a major regulator of macrophage differentiation, to promote macrophage differentiation. Characterization of the iMac activity showed NF-κB signaling activation and a pro-inflammatory phenotype. iMac cells display significantly increased in vivo persistence and inhibition of tumor progression in leukemia, breast cancer, and patient-derived tumor xenograft models.
Conclusions Our findings demonstrate that c-Myc alone is enough to reprogram fibroblasts into functional macrophages, supporting that c-Myc reprogramming strategy of fibroblasts could help circumvent long-standing obstacles to gaining “off-the-shelf” macrophages for anti-cancer immunotherapy.
Keywords c-Myc, fibroblast, macrophage, immunotherapy, reprogramming

overall_design: We performed transcriptome analysis in MEF, MCC and iMac using RNA-seq

first: Yanxin


title: N39 APOA1-tdTomato drug screen

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

summary: N39 organoids were subjected to different compounds to study the effect of different drugs on the intestinal epithelial.

overall_design: Organoids were grown in expansion medium and then subjected to drug exposure for one week in differentiation medium supplemented with drug compounds. Organoids were then lysed and RNA was extracted for RNAsequencing.

first: Jens

last: Puschhof

first: Joep

last: Beumer

first: Sam

last: Willemsen

first: Hans

last: Clevers


title: An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs [ATAC-Seq]

first: Lishuan

last: Wang


title: c-Myc alone is enough to reprogram fibroblasts into functional macrophages [scRNA-seq]

overall_design: A single-cell RNA sequencing of c-Myc-induced macrophage (iMac) was performed

last: Li


title: Multiple Evolutionary Pathways to Host Adaptation in the Fall Armyworm

city: Shenzhen

first: Mei

last: Luo

state: Gangdong

address: Dapeng

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

summary: During the over 300 million years of co-evolution between herbivorous insects and their host plants, a dynamic equilibrium of evolutionary arms race has been established. However, the co-adaptation between insects and their host plants is a complex process, often driven by multiple evolutionary mechanisms. We found that various lepidopteran pests that use maize as a host exhibit differential adaptation to the plant secondary metabolites, benzoxazinoids (BXs). Notably, the Spodoptera genus, including Spodoptera frugiperda (fall armyworm) and Spodoptera litura (cotton leafworm), demonstrate greater tolerance to BXs compared to other insects. Through comparative transcriptomic analysis of the midgut, we identified four candidate genes potentially involved in BXs detoxification in S. frugiperda. Subsequently, we confirmed two UGT genes, Sfru33T10 and Sfru33F32, as key players in BXs detoxification using CRISPR/Cas9 gene-editing technology. Phylogenetic analysis revealed that Sfru33T10 evolved independently within the Noctuidae family and is involved in the glycosylation of HDMBOA, while Sfru33F32 evolved independently within the Spodoptera genus and functions as a key detoxification enzyme responsible for the glycosylation of both DIMBOA and HMBOA. Our study demonstrates that the UGT gene family plays a crucial role in the adaptation of noctuid insects to maize, with multiple independent evolutionary events within the Noctuidae family and the Spodoptera genus contributing significantly to host adaptation.

overall_design: To investigate the gene expression profiles of FAW under different feeding conditions, fourth-instar larvae of each species were fed fresh maize leaves (W22) for 24 hours. Larvae fed with artificial feed (AF) served as controls. After the feeding period, midguts were rapidly dissected and frozen in liquid nitrogen for further analysis. Each treatment consisted of three biological replicates, with five midguts pooled per replicate.

first: Guirong

first: Bin

last: li


title: RNA Polymerase II coordinates histone deacetylation at active promoters

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

summary: Nucleosomes at actively transcribed promoters have specific histone post-transcriptional modifications and histone variants. These features are thought to contribute to the formation and maintenance of a permissive chromatin environment. Recent reports have drawn conflicting conclusions about whether these histone modifications depend on transcription. We used triptolide to inhibit transcription initiation and degrade RNA Polymerase II and interrogated the effect on histone modifications. Transcription initiation was dispensable for de novo and steady-state histone acetylation at transcription start sites (TSSs) and enhancers. However, at steady state, blocking transcription initiation increased the levels of histone acetylation and H2AZ incorporation at active TSSs. These results demonstrate that deposition of specific histone modifications at TSSs is not dependent on transcription and that transcription limits the maintenance of these marks.

overall_design: ChIP-seq and Cut&Tag for RNAP2, histone modifications, and H2AZ in T47D A12 breast cancer cells as well as a variety of other human cell lines

first: Kevin

last: Trotter

first: Trevor

middle: K

last: Archer