title: Glycine Receptor Activity in β Cells Is Downregulated in Type 2 Diabetes and After High Glucose Culture

status: Public on Dec 02 2024

city: Edmonton

first: Patrick

middle: E.

last: MacDonald

state: Alberta

address: 6-040 Li Ka Shing Centre

department: Pharmacology

institute: University of Alberta

summary: Objectives: Glycine acts in an autocrine positive feedback loop in human β cells through its ionotropic receptors (GlyRs). In type 2 diabetes (T2D), islet GlyR activity is impaired by unknown mechanisms. We sought to investigate if the GlyR dysfunction in T2D is replicated by hyperglycemia per se, and to further characterize its action in β cells and the islets.   Methods: GlyR-mediated currents were measured using whole-cell patch-clamp in human β cells from donors with or without T2D, or after high glucose culture. We also correlated glycine-induced current amplitude with transcript expression levels through patch-seq. The expression of the GlyR α1, α3, and β subunit mRNA splice variants was compared between islets from donors with and without T2D, and after high glucose culture. Insulin secretion from human islets was measured in the presence or absence of the GlyR antagonist strychnine.  Results: Gene expression of GlyRs was decreased in islets from T2D donors along with smaller GlyR-mediated currents in the β cells. Glycine-induced currents are also reduced in islets from donors without diabetes after 48 hours of culture in high glucose, along with reducedα1 subunit expression and increased  α3 subunit expression. Glycine-evoked currents are highly heterogeneous between different β cells within and between donors; inversely correlated with donor HbA1c; and significantly correlated to the expression of 99 different transcripts. Finally, glucose-stimulated insulin secretion is decreased in the presence of strychnine.

overall_design: Isolated human islets were dispersed to single cells, and whole cell patch clamp electrophysiology was performed. Following, the cells were collected and sent for scRNA-seq (SmartSeq).

first: Amanda

last: Schukarucha Gomes

first: Aliya

middle: F

last: Spigelman

first: Kunimasa

last: Suzuki

first: Jasmine

last: Maghera

first: Theodore

last: dos Santos

first: Cara

last: Ellis


title: Changes in adaptive immunity and increased neuroinflammation are key processes in ageing EAE: a road to develop new therapeutic strategies for elderly MS patients

status: Public on Dec 01 2024

city: Barcelona

first: María

middle: Dema

last: Etxezarreta

state: Barcelona

address: Passeig de la Vall d'Hebron, 119-129 Edifici Collserola - Laboratorio 150Passeig de la Vall d'Hebron, 119-129

department: Clinic neuroimmunology

country: Spain

institute: VHIR

type: Expression profiling by high throughput sequencing

summary: Characterisation of the impact of ageing on the peripheral immune response in EAE

overall_design: Gene expression profiling analysis of RNA-seq data comparing aged to young mice at three timepoints

last: Dema Etxezarreta

first: Herena

last: Eixarch Auhfinger

first: Carmen

last: Espejo Ruiz


title: transcriptomic analysis of murine chronic proximal thoracic aortic aneurysms

city: Beijing

first: Jianqing

last: Deng

address: 6 Fucheng Road, Haidian District

department: Department of Cardiovascular Surgery

country: China

institute: The Sixth Medical Center of PLA General Hospital

summary: This study aimed to establish a chronic proximal thoracic aortic aneurysm(cPTAA) model by combining periaortic elastase application and 90-day oral 3-aminopropionitrile fumarate salt(BAPN) administration.Transcriptome Sequencing was performed using Illumina Novaseq platform in 7 murine cPTAAs or 5 sham-operated proximal thoracic aortas.The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed the differentially expressed genes were most enriched in immune and inflammation related pathways.

overall_design: 7 murine cPTAAs or 5 sham-operated proximal thoracic aortas underwent RNA-seq.

first: Jiaying

last: Li

first: Ming

last: Yang

first: Cangsong

last: Xiao


title: Investigation of gene expression in glioma cell lines

status: Public on Nov 30 2024

city: Tübingen

first: Ghazaleh

last: Tabatabai

address: Otfried-Müller-Straße 2

country: Germany

institute: Hertie-Institut für klinische Hirnforschung

summary: Gene expression in glioma cell lines

overall_design: To analyze gene expression of glioma cell lines, we perferomd gene expression profiling.

first: Lara

middle: A

last: Haeusser

first: Laurence

last: Kuhlburger

first: Daniel

last: Merk


title: Involvement of NK cells and Fc gamma receptors in different kidney allograft rejection types

city: Pittsburgh

first: Elodie

last: Bailly

state: PA

address: BST 200 lothrop street

department: Surgery

country: USA

institute: Starzl Transplant Institute

summary: To investigate the involvement of FCGR3A and FCGR2C signaling and NK cell activation during antibody-mediated rejection, we analyzed transcriptomic data obtained by bulk RNA sequencing of kidney allograft FFPE biopsies diagnosed with either antibody-mediated rejection, T-cell mediated rejection or normal biopsies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for antibody-mediated rejection versus T-cell mediated rejection or normal biopsies, seeking NK-cell and FCGR-related transcripts

first: Parmjeet

last: Randhawa

first: Yuchen

last: Huang

first: Diana

last: Metes


title: Functional Variant Discovery Identifies SPRY2 as a Genetic Mechanism Linking Wood Smoke with Asthma

city: Denver

first: Arnav

last: Gupta

state: CO

address: 1400 Jackson St. K720

department: Pulmonary and Critical Care

institute: National Jewish Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Climate change is impacting human health through a historic rise in wildfire smoke across the United States and the world. Whereas the deleterious effects of wildfire smoke and associated air pollution on asthma outcomes are well-established epidemiologically, genetic risks and molecular mechanisms of how wildfire smoke affects asthma are unknown. This knowledge gap hinders the identification of high-risk individuals and the creation of targeted therapies or recommendations to protect these individuals. Here, we employ a genetic approach to identify common variant (minor allele frequency > 0.05) exposure-conditional genetic risk variants that localize with genomic responses to wood smoke particles (WSP), a model of wildfire smoke exposure, and associate with asthma in the Genetic Epidemiology Research on Aging (GERA) cohort. Our novel approach used nascent transcriptional signatures derived from WSP-exposed Beas-2B airway epithelial cells to reduce the genome sequence for discovery and allow a permutation-based statistical approach to identify 52 candidate SNPs. We applied biologic and bioinformatic filters to prioritize variants for direct testing of allele-dependent transcriptional regulatory function in plasmid reporters. The rs3861144 variant identified by this approach controls WSP responses of airway epithelial cells to SPRY2, which we showed is involved in mechanical injury repair in cell culture. Our results demonstrate that wildfire particulates contribute to asthma risk at the molecular level, and we have identified mechanistic targets and genetic variant candidates to apply for clinical risk prediction and development of targeted therapies for high-risk individuals.

overall_design: ATAC-seq profiling of live airway epithelial cells obtained from 3 healthy non-smoking adult donors. Cells were dissociated from cytology brushes and processed for ATAC-seq directly without treatment or manipulation. RNA-seq analysis of Beas-2B airway epithelial cells transfected with scrambled control (siCTRL) or SPRY2-targeting siRNA (siSPRY2) and exposed to wood smoke particles (WSP, 1 mg/ml) for 2 and 4 hours.

first: Amber

last: Dahlin

first: Alejandra

last: Macario

first: Fabienne

last: Gally

first: Michael

middle: R

last: Weaver

first: Lynn

last: Sanford

first: Margaret

last: Gruca

first: Robin

middle: D

last: Dowell

last: Cho

first: Scott

middle: T

last: Weiss

first: Sarah

middle: K

last: Sasse

first: Anthony

middle: N

last: Gerber


title: Molecular pathological mechanism of DIQUAT-induced multi-organ injury

city: Fuzhou

first: Zhimin

last: Chen

address: Chazhong Road NO.20

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

summary: Diquat is one of the most commonly used pesticides in recent years, and its improper use can lead to acute poisoning and loss of life. This study employed single-cell and single-cell nucleus transcriptome sequencing on mouse lung, liver, and kidney tissues induced by diquat to unveil the molecular pathophysiology of multi-organ damage caused by diquat exposure. In this research, we emphasize a novel hepatic cell subpopulation associated with detoxification and metabolic dysregulation following diquat exposure in the liver. Furthermore, a robust and intricate immune-inflammatory response is a prominent feature in the lungs, while a time-dependent shift from glomerular infiltration to tubular injury pattern is the main characteristic in the kidneys. This study underscores distinct injury features in multiple organs, significantly enhancing our understanding of diquat-induced multi-organ damage. Relevant molecules and pathways identified may serve as potential novel molecular targets.

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: Effect of dietary increased Vitamin a on urothelial regeneration after Cyclophosphamide induced injury in mice

status: Public on Nov 26 2024

city: Ljubljana

first: Brina

last: Dragar

address: Vrazov trg 2

department: Institute of Cell Biology

country: Slovenia

institute: University of Ljubljana, Faculty of Medicine

summary: Vitamin A, predominantly present as all-trans retinol, is an essential nutrient with wide-ranging physiological roles in embryonic development, vision, immunity, reproduction, cell differentiation and proliferation, apoptosis and maintenance of epithelial integrity. In this study the effects of an increased dietary Vitamin A on the regeneration of urinary bladder urothelial cells after severe cyclophosphamide (CP)-induced injury are investigated, focusing on proliferation, apoptosis and differentiation. After one week on a vitamin A-enriched diet, a high dose of CP (150 mg/kg) was administered to mice to induce acute urothelial injury. The effects of increased vitamin A intake on urothelial regeneration were analysed one and three days after the injury at both the RNA and protein levels using RNA sequencing, qPCR, immunohistochemistry and scanning electron microscopy. RNA sequencing revealed that the vitamin A-enriched diet upregulated two KEGG signalling pathways related to cell proliferation: the cell cycle and the PI3K-Akt pathway. We confirmed this by qPCR, which showed a significantly upregulated expression of the genes Itga3 and Areg, both of which are part of the PI3k-Akt signaling pathway. Furthermore, immunohistochemistry demonstrated increased proliferation rates in the urothelium of mice fed a vitamin A-enriched diet. Although RNA sequencing revealed significantly higher gene expression in apoptosis in mice on the vitamin A-enriched diet, this was not conformed by qPCR. Similarly, no significant effect of the vitamin A-enriched diet was observed on the expression of markers for highly differentiated urothelial cells, such as uroplakins, Krt20 and the percentage of the urothelial surface covered with microridges. Our results suggest that a vitamin A-enriched diet may accelerate urothelial regeneration by promoting cell proliferation in the early stages of regeneration.

overall_design: To investigate the effect of Vitamin A on urothelial regeneration we established the mouse model of acute cystitis, where mice were fed with a vitamin A-enriched diet (a diet containing 36× higher amount of Vitamin A in the form of retinyl palmitate) prior the cyclophosphamide injection. Half of the mice ate a normal diet. We examined early stages of regeneration, so we collected mice's urinary bladders 1 and 3 days after injection of cyclophosphamide (or saline in the case of control mice).

first: Tadeja

last: Kuret

first: Daša

last: Zupančič


title: Embryonic myeloid cells orchestrate niche cell homeostasis critical for the establishment of the definitive HSC pool

status: Public on Nov 20 2024

city: Heidelberg

first: Jonas

last: Metz

address: Im Neuenheimer Feld 580

institute: DKFZ

summary: The lifelong replenishment of blood cells relies on the function of definitive HSCs that migrate to the bone marrow during development. This process is tightly controlled by the bone marrow microenvironment. Embryonic macrophages emerge before the onset of definitive hematopoiesis, seed into discrete tissues and contribute to specialized resident macrophages throughout life. However, the functional impact of embryonic macrophages on HSCs or the niche remains unknown. Here, by taking advantage of a lineage tracer mouse tool we show that bone marrow macrophages consist of two ontogenetically distinct cell populations from embryonic and adult hematopoiesis. Mice lacking embryonic myeloid cells have decreased HSC numbers in the bone marrow accompanied by an increase of stem cells in the liver of neonate mice. The emergence of HSCs from embryonic sources is unperturbed because pre-HSC and HSC numbers are normal, suggesting a key role for embryo-derived myeloid cells in orchestrating HSC trafficking around birth. We show here that the establishment of a normal cellular niche space in the bone marrow critically depends on embryonic myeloid cells that are important for the development of mesenchymal stromal cells, but not other non-hematopoietic niche cells, providing evidence for a specific role for embryo-derived myeloid cells in the establishment of a normal niche environment pivotal for HSC homing.

overall_design: RNA-sequencing of mesenchymal stroma cells of 14 weeks old mice

first: Gülce

last: Perçin

first: Konstantin

last: Riege

first: Julia

last: Fröbel

first: Stephan

last: Culemann

first: Mathias

last: Lesche

first: Susanne

last: Reinhardt

first: Thomas

last: Höfer

first: Steve

last: Hoffmann

first: Claudia

last: Waskow


title: Temporal dynamics of gene expression in Campylobacter jejuni biofilm formation

first: Manca

last: Volk

address: Jamnikarjeva 101

institute: Biotechnical faculty, University of Ljubljana

summary: Campylobacter jejuni, an important pathogen of bacterial gastrointestinal infections, forms biofilms that are crucial for its survival in different environments. We used RNA sequencing to investigate the changes in gene expression at different stages of biofilm formation (16 h, 24 h, 48 h and 72 h). The results showed that early biofilms (16 h and 24 h biofilms) show increased expression of genes involved in cysteine and methionine amino acid metabolism, while mature biofilms (48 h and 72 h biofilms) show decreased expression of capsular polysaccharides and lipooligosaccharides. Both early and mature biofilms are characterized by increased expression of genes involved in flagella formation, leucine amino acid metabolism and oxidative stress response, and decreased expression of genes involved in energy metabolism, iron acquisition and transmembrane transport. Thus, we provide a deeper understanding of the molecular mechanisms of C. jejuni biofilm maturation, environmental resistance and the dynamic nature of gene expression that facilitates adaptation to biofilm-associated lifestyles

overall_design: Gene expression profilling analysis using data obtained from RNA-seq of C. jejuni biofilms cells taken at 16 h, 24 h, 48 h, and 72 h compared to 16 h planktonic cells. Four biological replicates are included for each condition.

first: Anja

last: Klančnik

first: Marko

last: Petek

first: Špela

last: Baebler


title: Next Generation Thiazolyl Ketone Inhibitors of Cytosolic Phospholipase A2 α: from Synthesis to Chemotherapeutic Mechanism of Action

status: Public on Nov 19 2024

city: Trondheim

first: Felicity

middle: Jayne

last: Ashcroft

address: Hogskoleringen 5

department: Biology

country: Norway

institute: NTNU

summary: Eicosanoids participate in the pathologies of inflammation and carcinogenesis and limiting their production by inhibiting group IVA cytosolic phospholipase A2 (cPLA2α) is a potential approach to cancer treatment. Here we report the synthesis of a new generation of thiazolyl ketone inhibitors of cPLA2α starting from compound GK470 (AVX235), and the discovery of a more potent and selective lead, GK420 (AVX420), with significant chemotherapeutic properties. A cancer cell line screen revealed the selective growth inhibitory effects of AVX420 in acute leukemias, uncovering a novel function of cPLA2α to promote cancer cell survival during oxidative stress by epigenetic control of tumour suppressor gene transcription. Moreover, we showed that in sensitive cells, AVX420 increased intracellular reactive oxygen species (ROS) and instigated a transcriptional response resulting in cell death.  Our study suggests AVX420 has the potential to treat acute leukemias, and other cancers with specific adaptations to a high ROS burden.

overall_design: To investigate the effect of cPLA2alpha inhibition on cell survival signaling in CCRF-CEM cells, we treated cells with either vehicle (VEH CTRL) or the cPLA2alpha inhibitor AVX420 (AVX420) for 1 hour and 6 hours and extracted total RNA and ribsome-associated RNA, or for 16 hours and extracted just total RNA. As a positive control for translational repression, cells were treated with the mTOR inhibior Torin-1 for 1 hour and both the total and ribosome-associated RNA were extracted. Experiments were performed in duplicates (Biorep 1 and Biorep 2)

first: Nur

last: Mahammad

first: Berit

last: Johansen


title: NR4A1 suppresses breast cancer growth by repressing c-Fos-mediated lipid and redox dyshomeostasis (ChIP-seq)

status: Public on Nov 18 2024

first: Sunwang

last: Xu

address: Chazhong Road 20th

institute: The First Affiliated Hospital of Fujian Medical University

summary: The precise function of NR4A1 as a transcriptional regulator in cancer remains under investigation. To investive the biological functions and molecular mechanims by which NR4A1 suppresses breast cancer growth, we perform RNA sequence analysis in NR4A1-knockout and control MCF7 cell lines  to identify the alterated signaling pathway and celluar possesses in breast cancer. Besides, we also performed ChIP sequences by c-Fos ChIP in in NR4A1-knockout and control MCF7 cell lines to investigate the competitive function of NR4A1 on c-Fos binding to genome.

overall_design: NR4A1 knockout MCF7 cells and parental control MCF7 cells were generated and processed to ChIP-seq by antibody against c-Fos .

first: Cen

last: Jiang


title: Total RNA-seq from mice of NAc and mPFC

status: Public on Nov 27 2024

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

summary: Total RNA-seq approach identified mRNAs  and non-coding RNAs in the mouse NAc after Cocaine CPP conditioning and in the mPFC after social defeat stress.

overall_design: Adult male C57Bl6J mice were subjected to cocaine (7.5 mg/kg, i.p.) conditioned place preference conditioning procedure, experienced social defeat stress by aggressive male CD1 mice, or stayed in home cage as no stimulation control. The NAc and mPFC tissue were dissected out at 15 min after emotional experiences. The RNAs were then subjected to total RNA-seqencing processes with BGI Genomics.

first: Setefano

first: Makoto

last: Taniguchi

first: Christopher

last: Cowan

first: Rose

middle: M

last: Akiki


title: NR4A1 suppresses breast cancer growth by repressing c-Fos-mediated lipid and redox dyshomeostasis (RNA-seq)

overall_design: NR4A1 knockout MCF7 cells and parental control MCF7 cells were generated and the total RNA was isolated and subjected to RNA-seq


title: Cathepsin L as a dual-target to mitigate muscle wasting while enhancing anti-tumor efficacy of anti-PD-L1

status: Public on Nov 15 2024

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

summary: Immune checkpoint inhibitors (ICIs) have revolutionized cancer therapy; however, their use is frequently associated with immune-related adverse events (irAEs). In this study, anti-PD-L1 therapy exacerbates muscle wasting in tumor-bearing male mice despite its anti-tumor efficacy, accompanied by an accumulation of CD8+ T cells in muscle. Single-cell RNA sequencing identifies these cells as tissue-resident memory-like CD49a+ CD8+ T cells. While CD8+ T cell depletion prevents muscle wasting, it compromises the anti-tumor efficacy of anti-PD-L1. To resolve this paradox, we identify cathepsin L (CTSL) as a dual-target capable of suppressing both tumor progression and CD8+ T cell-mediated muscle wasting, through integrative transcriptomic analysis. Pharmacological inhibition of CTSL not only mitigates anti-PD-L1-induced muscle wasting but also further suppresses tumor growth, potentially via downregulation of BNIP3. Here, we show that CTSL is a dual-action target to uncouple anti-tumor efficacy from muscle-specific irAEs, offering a strategy to improve clinical outcomes of ICIs.

overall_design: To identify effective therapeutic targets for both cachexia and muscle-related immune-related adverse events (irAEs), we generated RNA-seq data from muscles in a tumor bearing mouse model treated with IgG, anti-PD-L1, and anti-CD8a

first: Nayoung

last: Song


title: Endogenous IFITM2 Involvement in Endocytosis to Regulate Neurogenesis

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose: To gain  futher insight into how IFITM2 regulates the neurogenesis ,RNA-seq was used to analyze the genome-wide changes resulting from the cerebral cortices of E13 IFITM2 conditional knock out mice and littermate wild-type.
Methods: Total RNA from E13 telencephalic tissue of wild-type(WT) and Ifitm2fl/fl;Nestin-Cre mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, total RNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 6000 platform in Annoroad Genomics
Approximately  one thousand transcripts showed differential expression between the wild-type(WT) and Ifitm2fl/fl;Nestin-Cre mice brain cortex, with a fold change ≥1.5 and p value <0.05. These results reflected IFITM2 plays a role in cortex development.
Conclusions:  RNA-seq based transcriptome characterization would provide a overall understanding how IFITM2 gene regulated the neurogenesis.

overall_design: Total mRNA profiles of E13 wild type (WT) and Ifitm2 fl/fl;Nestin-Cre mice were generated by deep sequencing, in triplicate,  using Illumina HiSeq 6000.

first: Yuqing

last: Lv


title: Clonal analysis of murine development reveals novel positional programs directing lineage progression

status: Public on Nov 14 2024

city: Vienna

first: Sergey

last: Isaev

address: Spitalgasse, 4

department: Department of Neuroimmunology

country: Austria

institute: Medical University of Vienna

summary: Embryonic development is commonly viewed through a tree model of cell differentiation, which does not adequately represent the precise spatial and temporal modulation of cell multipotency underlying morphogenesis. Identifying the mechanisms conditioning and executing these fate decisions is a major aim of developmental biology. Here we develop an integrated approach, combining in vivo single-cell high-throughput clonal lineage tracing with machine learning, to systematically decompose continuous spectra of clonal fate biases in mammalian embryos traced from neurulation to mid-gestation stages. The reconstructed patterns of recurrent clonal variation were used to reveal gene programs driving dynamic biasing and spatiotemporal control over clonal composition, with axial skeletogenesis and peripheral neurogenesis serving as example models of clonally patterned systems. Experimental mosaic combinatorial perturbations targeting the Hedgehog signaling pathway caused the formation of novel clone types, giving proof of concept that custom cell type assemblages could be programmed in vivo starting from a well-defined progenitor cell. Altogether, our work demonstrates an effective practical approach for interrogating programs guiding clonal lineage specification.

overall_design:
All of the samples are mice with additional layer of clonal information gotten via lentiviral injection with unique expressed barcodes (TREX system) at E7.5 and E8.5 days. Mice 1-7, 31-33 are control mice, sample 34 is a combination of three different mice, and mice 8-19 are mice with additional mosaic knock-outs via added gRNAs within the lentiviral construction.
All of the samples are mice with additional layer of clonal information gotten via lentiviral injection with unique expressed barcodes (TREX system) at E7.5 and E8.5 days. Mice 1-7 are control mice, and mice 8-19 are mice with additional mosaic knock-outs via added gRNAs within the lentiviral construction.

first: Alek

last: Erickson

first: Igor

last: Adameyko

first: Peter

last: Kharchenko


title: The role of the LysR-type transcription factor PacR in regulating nitrogen metabolism in Anabaena sp. PCC7120

status: Public on Nov 05 2024

city: Turku

first: Yagut

last: Allahverdiyeva

address: Tykistönkatu 6A

department: Life Sciences

country: Finland

institute: Turku University

summary: Deletion of the global transcription factor PacR in Anabaena triggers heterocyst formation even in NO3- containing medium, likely due to impaired NO3- uptake and disrupted NH4+ assimilation in the GOGAT cycle. This phenotype may be exacerbated by reduced PSI-yield and reduced expression of ferredoxin, which may lead to less reducing equivalents for nitrogen uptake and fixation. These results highlight PacR’s role as a global regulator of carbon metabolism and photosynthesis while also establishing its involvement in regulating nitrogen metabolism.

overall_design: To investigate the effect of PacR-deletion in Anabaena sp. PCC7120, we used a ΔpacR strain and a control strain which expressed PacR. We took samples directly before changing the nitrogen source from NH4+ to NO3- as well as 1h after and 12h after the shift. RNA was extracted from 3 biological replicates per timepoint and strain. We then performed differential expression anaysis between the strains and between the timepoints for each strain.

first: Elisa

last: Werner

first: Tuomas

last: Huokko

first: Lauri

last: Nikkanen

first: Anita

last: Santana-Sánchez

first: Brad

last: Koch

first: Antonia

last: Herrero

last: Allhaverdiyeva


title: An RNase III-processed sRNA coordinates sialic acid metabolism of Salmonella enterica during gut colonization

city: Shanghai

first: Chuan

last: Wang

address: 131 # Dong An Road

institute: Fudan University

summary: To study the biological function of the novel 3′ UTR-derived sRNA, ManS, originating from a S. enterica-specific genomic island, STM1127-STM1131, we conducted RNA-pulse expression combined with RNA sequencing to screen for mRNAs repressed by ManS. Additionally, we compared the transcriptomic changes between wild-type and ManS-deleted strains during N-acetylmannosamine (ManNAc) metabolism.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: RNA-pulse Expression Combined with RNA Sequencing:The 80-nt full-length ManS sequence was cloned downstream of the PBAD promoter in a plasmid, and its expression was induced with L-arabinose for 10 minutes in a Salmonella ManS-deleted strain grown in M9CA medium supplemented with 0.1% ManNAc at OD600 ~0.5. An empty pBAD plasmid served as a control under the same conditions. Total RNA was isolated and treated with DNase I, and non-stranded libraries were prepared for RNA sequencing.Comparing Transcriptomic Changes between Wild-Type and ManS-Deleted Strains during N-Acetylmannosamine Metabolism:Wild-type and ManS-deleted Salmonella strains were grown in M9CA medium supplemented with 0.1% ManNAc to an OD600 of ~0.5. Total RNA was isolated and treated with DNase I, and stranded libraries were prepared for RNA sequencing to compare the transcriptomic changes between the two strains.

first: Cheng

last: Bei

first: Qian

last: Gao


title: NAT10 is identified as a novel driver for brain metastasis

status: Public on Nov 24 2024

city: New Haven

first: Qin

last: Yan

state: CT

address: 310 Cedar Street

department: Pathology

institute: Yale University

summary: Metastatic breast cancer remains a major cause of cancer related deaths in women and there are few effective therapies against this advanced disease. Using in vivo and in vitro genetic screens, we identified NAT10 as a driver for breast cancer brain metastassis. Here, we profile the transcriptome of metastatic breast cancer cells MDA-MB-231-BrM3 following NAT10 knockdown, aiming to identify the downstream effectors of NAT10.

overall_design: RNA-seq analyses in human breast cancer cell line MDA-MB-231-BrM3 with shCtrl or shNAT10.

first: Jocelyn

last: Chen

first: Wesley

middle: L

last: Cai


title: A microfluidic bone marrow chip for the safety profiling of biologics in pre-clinical drug development

status: Public on Nov 04 2024

city: Basel

first: Daniel

last: Marbach

address: Grenzacherstrasse 124

department: pRED Pharmaceutical Sciences

country: Switzerland

institute: F. Hoffmann - La Roche Ltd

summary: The overall objective of the study is to evaluate a bone marrow microfluidic system for its ability to predict expected hematopoietic liabilities of immunotherapeutics. The human bone marrow model consists of a zirconium oxide/hyaluronic acid scaffold, primary human stromal cells, and primary human CD34+ hematopoietic stem and progenitor cells. RNA sequencing was used to investigate changes in gene expression signatures of mesenchymal stromal cells when cultured on the ceramic scaffold, when cultured in a hematopoietic culture medium, and when cultured in the microfluidic system.

overall_design: Single donor mesenchymal stromal cells purchased from StemCell Technologies (Cat# 70071) were expanded for two passages in stromal cell culture medium according to the manufacturer's recommendations. The cells were then seeded at 500,000 cells per ceramic scaffold and cultured in 24-well plates for 8 days. The seeded ceramic scaffolds were then either continuously cultured in stromal cell culture medium or switched to hematopoietic cell culture medium after 10 days. Scaffolds cultured in hematopoietic cell culture medium were either continuously cultured under static culture conditions in 24-well plates or placed in the microfluidic system under flow for 24 days.

first: Leopold

last: Koenig

first: Inga

last: Clausen

first: Desirée

last: Schubert


title: Responses to checkpoint inhibition in metastatic TNBC driven by divergent myeloid phenotypes

status: Public on Oct 31 2024

city: Cleveland

first: Lily

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: Due to scarcity of effective therapeutic targets, metastatic TNBC (mTNBC) has shorter survival times compared to other advanced breast cancer subtypes. Although chemo-immunotherapy with immune checkpoint inhibitors (ICIs) in PD-L1+ mTNBC has shown promise, survival benefit remains modest. Therefore, it is crucial to gain improved insight into the mechanisms underlying response and resistance   to checkpoint inhibition in mTNBC. We employed single cell-RNA-sequencing, single cell secretomics, and flow cytometry to identify transcriptomic and proteomic peripheral immune cell signatures associated  with response and non-response to anti-PD-1/PD-L1 therapy and chemotherapy in mTNBC. Transcriptomic analysis revealed divergent transcriptional programming of CD33+ myeloid cells between responders and non-responders, even in pretreatment PBMC samples. This divergence, in responders, was characterized by an immune-promoting CD33+ cell phenotype involving IL-1b signaling versus, in non-responders, an immunosuppressive phenotype marked by IL-1b inhibition. These baseline differences expanded during the course of treatment. Differences in CD33+ cell phenotype resulted in functional differences in lymphocyte activities between responders and non-responders. To confirm this causal role of myeloid cells, we depleted CD33+ cells in pre-treatment samples from non-responders, which led to a rescue of T cell effector function. Our findings highlight CD33+ cell phenotype as a key determinant of response to chemo-immunotherapy, which can be assessed from peripheral blood. This offers a valuable tool in the context of metastatic TNBC, in which tissue sampling is often challenging.

overall_design: Single cell RNAseq was performed on peripheral blood mononuclear cells isolated from metastatic Triple negative breast cancer patients. Sample names are descriptive in that P# is the deidentified patient number followed by the sample timepoint base (baseline), res (responder), prog, (progressive disease).

first: Avia

last: Wilkerson

first: Ivan

middle: J

last: Salendra Singh

first: Patricia

last: Rayman

first: Hana

last: Husic

first: Paul

middle: C

last: Pavicic Jr

first: Jennifer

last: Powers

first: Zahraa

last: Al-Hilli

last: Ko

first: Timothy

last: Chan

first: Tyler

last: Alban

first: Alberto

last: Montero

first: C

last: Diaz-Montero


title: Astrocyte Fabp7 modulates seizure threshold and activity-dependent gene expression in mouse brain

status: Public on Nov 06 2024

city: Spokane

first: Jason

middle: Robert

last: Gerstner

state: WA

address: 412 E Spokane Falls BLVD

department: Translational Medicine and Physiology

institute: Washington State Univ. Spokane

summary: Patients with epilepsy often experience increased frequency of seizures at night. Given the crucial role glial cells play in modulating neuronal excitability, we hypothesize that circadian changes in glia may affect changes in seizure threshold. Fatty acid binding protein 7 (Fabp7) is expressed in brain astrocytes and is involved in the transport of fatty acids, signal transduction, and gene transcription. Its mRNA expression levels rise and fall in a circadian rhythm and is necessary for normal sleep regulation. We examined if Fabp7 influences electrically induced seizure threshold and differential gene expression in wild type (WT) vs. Fabp7 knockout (KO) mice with and without seizure.

overall_design: Male C57/BL6N (WT) and KO mice were maintained on a 12/12 hour light/dark cycle. Seizure thresholds were measured by administering a regularly increasing, once per day, electroshock stimulus. Seizure type, either general (GEST) or maximal (MEST) electroshock seizure threshold, was determined by the mouse’s behavioral and motor response to the stimulus. Hippocampal/cortical tissue was taken at the time of MEST for mRNA-Seq / differential expression (DE) analysis.

first: Micah

last: Lefton

first: Flores

last: Flores

first: Yuji

last: Owada

first: Christopher

last: Davis

first: Thomas

last: Ferraro

first: Yool

last: Lee

first: Wheaton

last: Schroeder


title: Individual RNA-seq for different prostate cancer cells and Lucap145.2 PDX treated by JQ1, AZD5153,ENZ or by FOXA1 and BRD4 gene knockdown

status: Public on Oct 23 2024

city: sacramento

first: Xiong

last: Zhang

state: CA

address: 4645 2nd Ave

institute: University of California, Davis

summary: Gene expression profile of different prostate cancer PDX tumor, and cell models to study tumorigenic programs.

overall_design: RNA-seq for 42D, H660, Lucap145.2 with different treatments.

first: Yatian

last: Yang

first: Hong-wu

last: Chen


title: Activation of the innate immune system accelerates growth in cooperation with oncogenic Ras.

status: Public on Oct 29 2024

city: Zurich

first: Fabienne

last: Brutscher

address: Winterthurerstrasse 190

department: Department of Molecular Life Sciences

institute: University of Zurich

summary: Innate immunity in Drosophila acts as an organismal surveillance system that measures external stimuli or cellular fitness and triggers context-specific responses to fight infections and maintain tissue homeostasis. However, uncontrolled activation of innate immune pathways can be detrimental to the system. In mammals, innate immune signaling is often overactivated in malignant cells and contributes to tumor progression. Drosophila tumor models have been instrumental in the discovery of interactions between pathways that promote tumorigenesis, but little is known about whether and how the Toll innate immune pathway interacts with oncogenes. Here we use a Drosophila epithelial in vivo model to investigate the interplay between Toll signaling and oncogenic Ras.

overall_design: Total RNA was extracted from approximately 50 control or 30 tumor eye-antennal discs (EAD) per sample from larvae at 96 h AED (after egg deposition). We generated mRNA sequencing libraries from four different samples, each in biologically independent triplicates:  (1) Control EADs (LacZ), (2) Control EADs after Toll pathway activation (Dorsal), (3) Tumor EADs (RasLacZ) and (4) Tumor EADs after Toll pathway activation (RasDorsal).

first: Federico

last: Germani

first: George

last: Hausmann

first: Lena

last: Jutz

first: Konrad

last: Basler


title: Individual ChIP-seq for BRD4 and H3K27ac

summary: Genome-wide measurements of histone modifications and transcripton factors binding in Luca145.2 PDX tumor and 42D cell models to studyBRD4 and H3K27ac regulate the tumorigenic programs

overall_design: ChIP-seq for different histone marks and transcriptional factors in 42D cell and LuCaP145.2.


title: ATAC-seq for LuCaP145.2 tumors treated with 50 mg/kg JQ1 or 10 mg/kg AZD5153 for 7 days

summary: Genome-wide measurements of chromatin accessibility in prostate cancer cells to study the tumorigenic programs.


title: OP3: single-cell multimodal dataset in PBMCs for perturbation prediction benchmarking

status: Public on Oct 22 2024

city: Somerville

first: Daniel

last: Burkhardt

state: Massachusetts

address: 101 South Street 6th Floor

institute: Cellarity

summary: The Open Problems Perurbation Prediction (OP3) dataset is to-date the largest single-cell small molecule perturbation dataset in primary tissue with multiple donor replicates. Compounds are dosed in cultured peripheral blood mononuclear cells (PBMCs), enabling the robust computation of perturbation effects on gene expression across four distinct cell type populations: T-cells, B-cells, NK cells, and Myeloid cells. This dataset is the basis for the OP3 benchmark, which evaluates machine learning models on the task of extrapolation perturbation effects into unseen cell types.

overall_design: We used scRNA-seq to measure the impact of 146 small molecules on human peripheral blood mononuclear cells (PBMCs). Each compound was dosed in triplicate across three donors, two male and one female. We complemented this data by also profiling PBMCs from the same three donors at baseline with joint multimodal snRNA-seq/scATAC-seq.

first: Artur

last: Szałata

first: Andrew

last: Benz

first: Robrecht

last: Cannoodt

first: Mauricio

last: Cortes

last: Fong

first: Sunil

last: Kuppasani

first: Richard

last: Lieberman

first: Tianyu

last: Liu

first: Javier

last: Mas-Rosario

first: Rico

last: Meinl

first: Jalil

last: Nourisa

first: Jared

last: Tumiel

first: Tin

last: Tunjic

first: Mengbo

last: Wang

first: Noah

last: Weber

first: Hongyu

last: Zhao

first: Benedict

last: Anchang

first: Fabian

last: Theis

first: Malte

last: Luecken

middle: B


title: Paired tumour biopsy gene expression data from patients with solid tumours, before and after combination treatment.

city: London

first: Rose

last: Hodgson

address: 2 Monnery Road

country: United Kingdom

institute: MiNA Therapeutics

summary: Gene expression quantification of PanCancer IO genes from paired tumour biopsies from 24 patients with pan-cancer solid tumours, before and after treatment with MTL-CEBPA and pembrolizumab.

overall_design: Normalised, transformed gene counts of nCounter Nanostring PanCancer IO panel (770 genes) of paired tumour biopsies from 24 patients with solid tumours, before treatment (Screening) and 6 weeks after treatment (C2D16) with MTL-CEBPA and pembrolizumab.

first: Bríd

last: Ryan


title: Transcriptomic atlas of the morphologic development of the fungal pathogen Coccidioides reveals key phase-enriched transcripts [ChIP-Seq]

status: Public on Oct 21 2024

city: San Francisco

first: Christina

last: Homer

address: 513 Parnassus Ave, S472

institute: University of California, San Francisco

summary: Coccidioides spp. are highly understudied but significant dimorphic fungal pathogens that can infect both immunocompetent and immunocompromised people. In the environment, they grow as multicellular filaments (hyphae) that produce vegetative spores called arthroconidia. Upon inhalation by mammals, arthroconidia undergo a process called spherulation. They enlarge and undergo numerous nuclear divisions to form a spherical structure, and then internally segment until the spherule is filled with multiple cells called endospores. Mature spherules rupture and release endospores, each of which can form another spherule, in a process thought to facilitate dissemination. Spherulation is unique to Coccidioides and its molecular determinants remain largely unknown. Here, we report the first high-density transcriptomic analyses of Coccidioides development, defining morphology-dependent transcripts and those whose expression is regulated by Ryp1, a major regulator required for spherulation and virulence. Of approximately 9000 predicted transcripts, we discovered 273 transcripts with consistent spherule-associated expression, 82 of which are RYP1-dependent, a set likely to be critical for Coccidioides virulence. ChIP-Seq revealed 2 distinct regulons of Ryp1, one shared between hyphae and spherules and the other unique to spherules. Spherulation regulation was elaborate, with the majority of 227 predicted transcription factors in Coccidioides displaying spherule-enriched expression. We identified provocative targets, including 20 transcripts whose expression is endospore-enriched and 14 putative secreted effectors whose expression is spherule-enriched, of which 6 are secreted proteases. To highlight the utility of these data, we selected a cluster of RYP1-regulated, arthroconidia-associated transcripts and found that they play a role in arthroconidia cell wall biology, demonstrating the power of this resource in illuminating Coccidioides biology and virulence.

overall_design: We generated arthroconidia and grew them as spherules (39˚C, 10% CO2) or hyphae (room temp, no additional CO2) in the specified media. At each timepoint, RNA was harvested and the transcriptome was analyzed by RNA-Seq. We have included 3 timecourses of WT spherules, 1 full and 1 limited timecourse of the ryp1∆ mutant which cannot form the spherule morphology but was subjected to spherulation or hyphal growth conditions. For samples labeled as originating from Figure S4, we also performed ChIP-Seq on the same biological samples using a polyclonal anti-Ryp1 antibody.

first: Mark

last: Voorhies

first: Keith

last: Walcott

first: Elena

last: Ochoa

first: Anita

last: Sil


title: Transcriptional response to mechanical wounding stress in Oryza sativa

city: Montpellier

first: Anne-Sophie

last: PETITOT

address: 911 avenue Agropolis

department: UMR DIADE

country: France

institute: IRD

summary: To understand the dynamics and global gene reprogramming in the early response to mechanical wounding in rice, the transcriptional response to mechanical injury was analyzed. A time-course experiment revealed the highly dynamic nature of the wound response in rice. Mechanical wounding triggered extensive gene expression reprogramming in the locally wounded leaf, affecting various physiological processes, including defense mechanisms and potentially tissue repair and regeneration. The rice response to mechanical wounding displayed both differences and similarities compared to the response to jasmonate treatment. These results highlight the importance of early JA signaling in response to mechanical stress in rice. This analysis provides an overview of the global transcriptional response to mechanical stress in rice, offering valuable insights for future studies on rice's response to injury, insect attack, and abiotic stresses.

overall_design: To decipher the molecular responses to wounding in rice leaves, a time-course experiment was performed in wild type rice. Rice leaves were submitted to mechanical wounding.

first: Antony

last: Champion

last: Petitot

first: Hieu

last: Nguyen

first: Julie

last: Orjuela


title: Charting the regulatory landscape of TP53 on transposable elements in cancer [ChIP-seq]

status: Public on Oct 20 2024

city: Saint Louis

first: Ting

last: Wang

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in Saint Louis

summary: The relationship between p53 and transposable elements (TEs) has been obscure. Thus, comprehensive profiling of TE-derived transcripts dynamics under the regulation of p53 provides valuable resources for more clarity in p53’s roles in cancer. In this study, we created three cancer cell lines with p53 genetic status as the only variable and combined long-read RNA-seq and short-read RNA-seq to define TE and TE-derived transcripts’ regulatory dynamics. We identified in total 2,503 transcripts that use TE as potential promoters, among which, 141 to 210 are activated by p53. We found ERVs to be a main driver of potential promoters, followed by LINEs. Epigenomic profiling including chromatin accessibility and DNA methylation provided additional support for active promoter potential for p53 upregulated TE-derived transcripts. Short-term restoration of p53 partially recovered chronic p53-regulated TE-derived transcript profile but gain of function TP53 mutations, R175H and R273H, did not show evidence to act via TE network. Overall, we provide a controlled isogenic cancer cell line system with TP53 mutation status as the only genetic variable, deliver a high confidence TE and TE-derived transcript atlas and comprehensively identify active TE promoters that are direct and indirect targets of p53.

overall_design: To investigate p53 regulation on TE, we used three pairs of cancer cell lines, A549, HCT116 and RKO. Each pair has one sample with endogenous WT TP53 and one sample with CRISPR knock down of TP53. With lentiviral transduction, we introduced WT TP53, mutant TP53 R175H, mutant TP53 R273H and empty vector to cells with TP53 KO background. All cells are treated with either doxorubicin for p53 activation or dmso as control. We then did gene expression analysis using RNA-seq. Using both short-read RNA-seq and long-read RNA-seq, we created an atlas detailing TE-derived transcripts. Transcript-level differential expression analysis was then conducted for high-confidence TE-derived transcripts.

first: Xuan

last: Qu

first: Yonghao

last: Liang

first: Chad

last: Tomlinson

first: Xiaoyun

last: Xing

first: Heather

last: Schmidt


title: Charting the regulatory landscape of TP53 on transposable elements in cancer [WGBS]

type: Methylation profiling by high throughput sequencing


title: Transcriptomic atlas of the morphologic development of the fungal pathogen Coccidioides reveals key phase-enriched transcripts [RNA-seq]


title: Charting the regulatory landscape of TP53 on transposable elements in cancer [ATAC-seq]

summary: Comprehensive profiling of transposable element (TE)-derived transcripts dynamics under the regulation of p53 provides valuable resources for more clarity in p53 pleiotropic roles in cancer. In this project, we created three cancer cell lines with p53 genetic status as the only variable and used long-read RNA-seq to profile TE and TE-derived transcripts’ regulatory dynamics. By using both short-read RNA-seq and long-read RNA-seq, novel TE-derived transcripts as a function of p53 status were accurately profiled for the first time. We identified in total 2503 transcripts that use TE as potential promoters, among which, 141 to 210 are activated by p53 across three cancer cell lines. We found ERVs to serve as potential driving promoters, followed by LINEs. Epigenomic information from chromatin accessibility and DNA methylation provided additional support for active promoter potential for p53 upregulated TE-derived transcripts. Short-term restoration of p53 partially recovered chronic p53-regulated TE-derived transcriptional profile; whereas gain of function TP53 mutations, R175H and R273H, did not show evidence to act via TE network. Overall, in this paper, we provide a controlled isogenic cancer cell line system with TP53 mutation status as the only genetic variable, deliver a high confidence TE and TE-derived transcript atlas, and comprehensively identify active TE promoters that are direct and indirect targets of p53.

first: Colin

last: McCornack


title: Jasmonic acid signaling and glutathione coordinate plant recovery from high light stress

status: Public on Oct 15 2024

first: Mehmet

last: Kilic

address: FI-20014 TURUN YLIOPISTO

department: Molecular Plant Biology

institute: University of Turku

summary: High light (HL)-induced chloroplast retrograde signaling originates from the photosynthetic apparatus and regulates nuclear gene expression to enhance photoprotection and coordinate cell metabolism. Here, we analyzed the transcript profiles and accumulation of reactive oxygen species (ROS), stress hormones and small molecule antioxidants to investigate the signaling mechanisms operating under HL stress, and in particular during plant recovery (R) from stress under growth conditions. Exposure to HL for 15 min induced a number of singlet oxygen (1O2) and hydrogen peroxide (H2O2)-responsive genes and accumulation of an oxidative form of glutathione (GSSG) and ascorbate (DHA), the hallmarks of oxidative stress in cells. Prolonged exposure to HL resulted in accumulation of transcripts encoding oxylipin biosynthesis enzymes, leading to accumulation of 12-oxo-phytodienoic acid (OPDA) and jasmonic acid (JA). However, the expression of several JA-responsive genes, already induced by HL, peaked during the R-phase (R-sustained) together with accumulation of JA, reduced glutathione (GSH) and ascorbate (AsA), highlighting the critical role of JA signaling in restoring chloroplast redox balance following HL stress. The involvement of JA signaling in R-sustained gene expression was further confirmed by conducting experiments with JA receptor mutants (coi1). HL exposure of only 2 min was sufficient to induce some R-sustained genes, indicating rapid response of plants to changing light conditions. We propose that ROS production at HL induces the signaling cascade for early oxylipin biosynthesis and OPDA accumulation, while increased accumulation of JA in R-phase activates the genes that fully restore the glutathione metabolism, and ultimately allow recovery from short-term HL stress.

overall_design: Arabidopsis thaliana plants grown at  growth light (GL; 100 μmol photons m−2 s−1) were exposed to  high light (HL; 1000 μmol photons m−2 s−1) for 15 or 60 minutes. For recovery (R; at 100 μmol photons m−2 s−1), the plants exposed to 60 min of HL were returned to GL to recover for 15 or 60 minutes.

first: Eevi

last: Rintamäki

first: Peter

last: Gollan

first: Eva-Mari

last: Aro


title: Transcriptomic profiling of kidney transplant recipients [RNA-seq]

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

summary: RNA-seq data of peripheral blood mononuclear cells (PBMCs) from participants pre- and post- kidney transplant(Tx) was generated to study 1) gene expression difference between pre- and postTx, 2) gene expression difference between cytomegalovirus (CMV) seropositive and seronegative in preTx, 3) immune response regarding Tx and immunosuppression prophylaxes, and 4) how the gene expression and DNA methylation are associated.

overall_design: We collected  PBMC for RNA-seq from 37 kidney transplant patients with samples collected before and then 3 months after transplantation.

first: Harry

last: Pickering

first: Joanna

last: Schaenman

first: Elaine

last: Reed

first: Matteo

last: Pellegrini


title: Kidney transplant recipients

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

overall_design: Refer to individual Series


title: DNA methylation profiling of kidney transplant recipients

summary: Targeted bisulfite sequencing  data of peripheral blood mononuclear cells (PBMCs) from participants pre- and post- kidney transplant(Tx) was generated to study 1) methylation difference between pre- and postTx, 2) methylation difference between cytomegalovirus (CMV) seropositive and seronegative in preTx, 3) immune response regarding Tx and immunosuppression prophylaxes, and 4) how the gene expression and DNA methylation are associated.

overall_design: We collected  PBMC for targeted bisulfite sequencing  from 135  kidney transplant patients with samples collected before and then 3 months after transplantation.


title: Transcriptomics study reveals the underlying molecular mechanisms of circadian gene Bmal1 in rat nucleus pulposus cells

city: Xi'an

first: Liangwei

last: Mei

state: Shaanxi

address: 127 Changle West Road

department: Orthopaedics

institute: Xijing Hospital, the Fourth Military Medical University

summary: Intervertebral disc degeneration (IDD) is a major cause of low back pain (LBP), and the pathogenesis remains unknown. Recently, an autoregulating circadian rhythm was identiﬁed in intervertebral discs (IVDs), the abolition of which led to IDD. The genetic disruption of the mouse IVD molecular clock, speciﬁcally through the disruption of Bmal1, predisposes mice to IDD. However, the precise role of circadian gene Bmal1 in IDD remain elusive. In this study, RNA-seq was used to determine differentially expressed genes (DEGs) in rat nucleus pulposus cells (NPCs) treated with Bmal1 shRNA or its negative control lentivirus. GO and KEGG pathway analysis were also performed. In general, 6900 DEGs was identified. The anabolic genes, such as col2a1 and acan, showed significantly decreased expression, whereas catabolic genes, such as MMP-3 and MMP-13, showed significantly upregulated expression. GO analysis was performed to annotate the functions of the DEGs. The DEGs were primarily associated with the processes of cell transcription, behaviour, signal transduction, biological regulation, and protein binding. KEGG pathway analysis revealed that Bmal1 was related to multiple signalling pathways, such as p53, Hedgehog, Wnt, PI3K-Akt, mTOR, Hippo and MAPK. This study, for the first time, analyzes the transcriptome of NPCs in response to Bmal1 diminished, indicating that circadian gene Bmal1 is involved in the establishment and progression of IDD through its wide effects on the viability and function of NPCs.

overall_design: Expression profile of mRNAs in rat nucleus pulposus cells after transfection with Bmal1 shRNA or its negative control lentivirus

first: Jinghui

last: Huang


title: Stromal KITL/SCF promotes pancreas tissue homeostasis and restrains tumor progression.

status: Public on Oct 14 2024

city: New York

first: Mara

middle: H

last: Sherman

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Components of normal tissue architecture serve as barriers to tumor progression. Inflammatory and wound-healing programs are requisite features of solid tumorigenesis, wherein alterations to immune and non-immune stromal elements enable loss of homeostasis during tumor evolution. The precise mechanisms by which normal stromal cell states limit tissue plasticity and tumorigenesis, and which are lost during tumor progression, remain largely unknown. Here we show that healthy pancreatic mesenchyme expresses the paracrine signaling molecule KITL, also known as stem cell factor, and identify loss of stromal KITL during tumorigenesis as tumor-promoting. Genetic inhibition of mesenchymal KITL in the contexts of homeostasis, injury, and cancer together indicate a role for KITL signaling in maintenance of pancreas tissue architecture, such that loss of the stromal KITL pool increased tumor growth and reduced survival of tumor-bearing mice. Together, these findings implicate loss of mesenchymal KITL as a mechanism for establishing a tumor-permissive microenvironment.

overall_design: To assess the functional signifance of cell instrinsic KITL in panreatic mesenchymal cells, we generated Kitl knockdown and overexpression mouse pancretic stellate cell lines (mPSCs) using shRNA. We then performed gene expression profiling analysis using RNA-seq data obtained from all 4 samples with controls included (shCtrl, shKitl, Egfp OE, and Kitl OE).

first: Chet

last: Oon


title: Loss of smad7 promoted the stromal-myofibroblast transition of endometrium via autophagy

status: Public on Oct 11 2024

city: Chongqing

first: Jianguo

last: Hu

state: Chongqing

address: Linjiang Road, No. 76

department: Department of Obstetrics and Gynecology

institute: Chongqing Medical University Second Affiliated Hospital

summary: Background: Abnormal autophagy and TGFβ-SMAD3/7 signaling pathway plays an important role in intrauterine adhesions (IUA); however, the exact underlying mechanisms remain unclear. In this study, we aimed to detect whether SMAD7 effected IUA via regulating autophagy and TGFβ-SMAD3 signaling pathway.  Methods: The expression of p-SMAD3 and SMAD7 were detected by Immunohistochemistry. Endometrial fibrosis was detected by masson staining. The expression of protein related to autophagy and fibrosis was detected by western blot. The autophagic flux was monitored via Tandem mRFP-GFP-LC3 fluorescence system. Chip assay was used for SMAD3 binding site analysis. SMAD7 knockout mice were used to investigate the regulation of SMAD7 on intrauterine adhesions and autophagy.  Results: we observed that patients with IUA exhibited a lower expression of SMAD7. In endometrial stromal cells, the silencing of SMAD7 inhibited autophagic flux, whereas overexpressed SMAD7 promoted autophagic flux. We also found that SMAD7-mediated autophagic flux regulated stromal-myofibroblast transition. These phenotypes are regulated by the transforming growth factor (TGF)β-SMAD3 signaling pathway. We found that SMAD3 directly binds to the 3ʹ-untranslated region of transcription factor EB (TFEB) and inhibits its transcription. SMAD7 promoted autophagic flux by inhibiting SMAD3, thereby promoting the expression of TFEB. The endometria of SMAD7 knockout mice showed a fibrotic phenotype. Simultaneously, autophagic flux was inhibited. On administering the autophagy activator rapamycin, endometrial fibrosis of SMAD7 gene conditional knockout mice was partially restored.  Conclusions: The loss of SMAD7 promotes endometrial fibrosis by inhibited autophagic flux via the TGFβ-SMAD3 pathway. Therefore, this study reveals a potential therapeutic target for IUA.

overall_design: Uterine tissue of proestrus mice (SMAD7 knockout mice, WT) was used for RNA sequencing. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). The RNA integrity was assessed using Agilent Fragment Analyzer 5400 system (Agilent Technologies, CA, USA). Library construction and Illumina sequencing were completed by Shanghai Lifegenes Technology Co., Ltd。


title: Immunoprofiling of mouse prostate cancer infiltrate

status: Public on Oct 09 2024

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

summary: NK cells are effector cells that contribute to tumor immune surveillance. Due to their spontaneous ability to eliminate tumor cells, NK cell have been exploited for cancer treatment.  However, most cancers impair NK cell infiltration and hinder their cytotoxic capability. As a consequence, the efficacy of NK cell-based immunotherapies is still limited. Here we applied high dimensional single-cell RNA-seq to profile the transcriptional landscape of tumor-infiltrating NK in murine prostate cancer. We identified two subsets of tumor infiltrating NK cells. Tumor samples resulted to be abundantly infiltrated by the immunomodulatory subset at the expense of the cytotoxic one. Importantly, the anayles of the interaction network existing between NK cells and tumor cells revealed a deregulation of the autophagic process. Finally, genetic and pharmacological activation of autophagy rescues NK cell effector functions and confers to NK cells a superior ability in controlling tumor growth in vivo.

overall_design: A total of two samples; two mouse prostate samples (Tumor tissue, Normal tissue adjacent to tumor).

first: R

last: Carriero

first: M

last: Masetti

first: D

last: Di Mitri


title: Cathepsin L as a dual-target to mitigate muscle wasting while enhancing anti-tumor efficacy of anti-PD-L1 [Bulk2]

status: Public on Oct 08 2024

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

institute: Pusan National University

summary: Immune checkpoint inhibitors (ICIs) have revolutionized cancer therapy; however, their use is frequently associated with immune-related adverse events (irAEs). In this study, anti-PD-L1 therapy exacerbates muscle wasting in tumor-bearing male mice despite its anti-tumor efficacy, accompanied by an accumulation of CD8+ T cells in muscle. Single-cell RNA sequencing identifies these cells as tissue-resident memory-like CD49a+ CD8+ T cells. While CD8+ T cell depletion prevents muscle wasting, it compromises the anti-tumor efficacy of anti-PD-L1. To resolve this paradox, we identify cathepsin L (CTSL) as a dual-target capable of suppressing both tumor progression and CD8+ T cell-mediated muscle wasting, through integrative transcriptomic analysis. Pharmacological inhibition of CTSL not only mitigates anti-PD-L1-induced muscle wasting but also further suppresses tumor growth, potentially via downregulation of BNIP3. Here, we show that CTSL is a dual-action target to uncouple anti-tumor efficacy from muscle-specific irAEs, offering a strategy to improve clinical outcomes of ICIs.

overall_design: To identify effective therapeutic targets for both cachexia and muscle-related immune-related adverse events (irAEs), we generated RNA-seq data from muscles in a tumor bearing mouse model treated with IgG, anti-PD-L1, and anti-CD8a

first: Nayoung

last: Song


title: Transcriptomic analysis after SARS-CoV-2 mRNA vaccination reveals a specific gene signature in low-responder hemodialysis patients

city: Siena

first: Simone

last: Lucchesi

address: Viale Bracci, 16

institute: University of Siena

summary: Individuals with comorbidities, such as chronic kidney disease and hemodialysis patients (HDP), are particularly susceptible to severe COVID-19 and to its complications. Furthermore, their immune response to vaccines is impaired, requiring tailored vaccination strategies. In this study, we investigated through transcriptomic profiling the immune response heterogeneity of HDP vaccinated with two doses of mRNA BNT162b2 vaccine. Transcriptomic analyses were conducted in peripheral blood mononuclear cells (PBMC) collected from HDP and healthy controls (HC) before and 7 days after each dose. The HDP were stratified into high- and low-responders based on their humoral response after the second dose. Significant differences in gene expression related to B cell abundance and regulation, CD4 T cell proliferation, and inflammation pathways were observed at baseline and day 7 between HDP-low responders and HC, while the HDP high-responders displayed an intermediate expression profile for these genes. Results were consistent with the known immunologic alterations occurring in HDP cohorts related to lymphopenia, chronic inflammation, and dysregulated proliferation of CD4+. Our analyses identified an early transcriptional signature correlated with a diminished immune response in HDP low-responders, highlighting the importance of conducting a characterization of immunocompromised cohorts.

overall_design:
to investigate the immune response of hemodialysis patients (HDP) vaccinated with the mRNA BNT162b2 vaccine through transcriptomic profiling
Peripheral blood mononuclear cells (PBMC) were collected from HDP and healthy controls (HC) at baseline (day 0), at days 7, 21 (before the second dose) and 28 (7 days after the second dose) after two doses of mRNA BNT162b2 vaccine

first: Francesco

last: Santoro

first: Gabiria

last: Pastore

first: Jacopo

last: Polvere


title: Shared and divergent transcriptomic regulation in nucleus accumbens D1 and D2 medium spiny neurons by cocaine

first: Molly

middle: S

last: Estill

address: 1 Gustave L. Levy Place

institute: Mount Sinai School of Medicine

summary: Substance use disorders (SUDs) induce widespread molecular dysregulation in nucleus accumbens (NAc), a brain region pivotal for coordinating motivation and reward, which is linked to neural and behavioral disturbances promoting addiction. Despite the overlapping symptomatology of SUDs, different drug classes exert partly unique influences on neural circuits, cell types, physiology, and gene expression. To better understand common and divergent molecular mechanisms governing SUD pathology, we characterized the cell-type-specific restructuring of the NAc transcriptional landscape after psychostimulant or opioid exposure. We combined fluorescence-activated nuclei sorting and RNA sequencing to profile NAc D1 and D2 medium spiny neurons (MSNs) across cocaine exposure paradigms, including initial exposure, prolonged withdrawal after repeated exposure, and re-exposure post-withdrawal. Our analyses reveal that D1 MSNs display many convergent transcriptional responses across the two drugs, whereas D2 MSNs manifest highly divergent responses, with morphine causing far more adaptations in this cell type.

overall_design: Male double-transgenic mice expressing D1- or D2-specific nuclear-tagged GFP were generated by crossing LSL-eGFP::L10a (IMSR_JAX:022367) mice with either D1-Cre (MGI:3836633) or D2-Cre (MGI:3836635) mice. Cocaine hydrochloride (from the National Institute on Drug Abuse) were dissolved in 0.9% saline and administered intraperitoneally at doses of 20 mg/kg. In the cocaine cohort, mice received saline or cocaine each day for 10 days prior to withdrawal. As depicted in Figure 1A, after 30 days of homecage withdrawal, mice received challenge injections of saline, cocaine and were sacrificed 1 h later. Brains were extracted, the NAc was dissected, and samples underwent fluorescence-activated nuclei sorting to purify nuclei for D1 or D2 MSNs. RNA was then extracted from nuclei, and RNAseq was performed.

first: Caleb

last: Browne

first: Philipp

last: Mews

first: Xianxiao

last: Zhou

first: Leanne

last: Holt

first: Rita

last: Futamura

first: Li

last: Shen

first: Bin

last: Zhang

first: Eric

last: Nestler


title: USP22 promotes the proliferation and inhibits Sorafenib-induced ferroptosis of hepatocellular carcinoma cells through its deubiquitinase activity [ChIP-seq]

status: Public on Oct 03 2024

city: Tianjin

first: Bei

last: Lan

state: 天津Tianjin

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

summary: Hepatocellular carcinoma (HCC) remains one of the most lethal cancers, characterized by poor prognosis and low life expectancy. Unfortunately, there are very few molecular therapeutic options available for advanced HCC. Sorafenib is a current standard first-line treatment for advanced HCC, but drug resistance significantly limits its therapeutic efficacy. In this study, we identified ubiquitin-specific protease 22 (USP22) as the key regulator of HCC development and Sorafenib resistance. Analysis of TCGA databases revealed that USP22 is highly expressed in HCC tissues and is closely associated with poor patient prognosis. Our data further indicated that USP22 promotes the proliferation of HCC cells via deubiquitinating and stabilizing cyclin-dependent kinase 11B (CDK11B). Additionally, USP22 acts as a novel inducer of Sorafenib resistance and suppresses Sorafenib-triggered ferroptosis in HCC cells. It reduces the transcription of the transferrin receptor (TFRC) by decreasing H2BK120ub occupancy at TFRC transcription start site (TSS) downstream region, thereby inhibiting ferroptosis upon Sorafenib treatment. Finally, animal experiments confirmed the role of USP22 in promoting HCC cell growth and Sorafenib resistance in vivo. Taken together, our findings suggest that USP22 represents a promising prognostic biomarker and therapeutic target for HCC patients, particularly those with Sorafenib resistance.

overall_design: ChIP sequencing for H2BK120ub in Sorafenib-treated control and USP22 knockout HepG2 cells with Drosophila Schneider 2 cells (S2 cells) spike-in.

first: Xiaochen

last: Wang


title: Charting the regulatory landscape of TP53 on transposable elements in cancer [RNA-seq]

first: Ting

first: Xuan

last: Qu

first: Yonghao

last: Liang

first: Chad

last: Tomlinson

first: Xiaoyun

last: Xing

first: Heather

last: Schmidt


title: Immunologic changes are detectable in the peripheral blood transcriptome of clinically asymptomatic Chagas cardiomyopathy patients

status: Public on Oct 04 2024

city: Baltimore

first: Monica

last: Mugnier

state: MD

address: 615 N Wolfe St

department: MMI

institute: Johns Hopkins University

summary: Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, is a neglected parasitic disease that affects approximately 6 million individuals worldwide. Of those infected, 20-30% will go on to develop chronic Chagas cardiomyopathy (CCC), and ultimately many of these individuals will progress to advanced heart failure. The mechanism by which this progression occurs is poorly understood, as few studies have focused on early CCC. In this study, we sought to understand the physiologic changes associated with T. cruzi infection and the development of CCC. We analyzed gene expression in the peripheral blood of asymptomatic Chagas patients with early structural heart disease, Chagas patients without any signs or symptoms of disease, and Chagas-negative patients with and without early structural heart disease. Our analysis shows that early CCC was associated with a downregulation of various peripheral immune response genes, with gene expression changes suggestive of reduced antigen presentation and T cell activation. Notably, these genes and processes were distinct from those of early cardiomyopathy in Chagas-negative patients, suggesting that the processes mediating CCC may be unique from those mediating progression to other cardiomyopathies. This work highlights the importance of the immune response in early CCC, providing insight into the early pathogenesis of this disease. The changes we have identified may serve as biomarkers of progression and could inform strategies for the treatment of CCC in its early stages, before significant cardiac damage has occurred.

overall_design: We performed RNA sequencing of whole blood samples obtained from 10 Chagas-positive patients ( 4 stage IND, 6 stage early CCC), and 23 Chagas-negative patients ( 13 stage non-cardiomyopathy, 10 stage early cardiomyopathy)

first: Carolina

last: Duque

first: Jaime

last: So

first: Yagahira

middle: E

last: Castro-Sesquen

first: Kelly

last: DeToy

first: Sneider

last: Gutierrez

first: Fatemeh

last: Jahanbakhsh

first: Edith

last: Malaga Machaca

last: Miranda-Schaeubinger

first: Indira

last: Chakravarti

first: Virginia

last: Cooper

first: Mary

first: Luigi

last: Adamo

first: Rachel

last: Marcus

first: Kawsar

last: Talaat

first: Robert

last: Gilman


title: USP22 promotes the proliferation and inhibits Sorafenib-induced ferroptosis of hepatocellular carcinoma cells through its deubiquitinase activity

first: Bei

last: Lan

overall_design: Examination of gene expression changes in Sorafenib-treated control and USP22 knockout HepG2 cells

first: Yijie

last: Su


status: Public on Oct 02 2024

city: Philadelphia

first: Makarand

middle: V

last: Risbud

address: 1025 Walnut St.

institute: Thomas Jefferson University

summary:
Transcriptional analysis of 24-month-old primary nucleus pulposus (NP) and annulus fibrosus (AF) mouse disc tissues from Sirt6fl/fl and Sirt6cKO mice, which harbor a mutation which constiuitively deletes Sirtuin 6 in aggrecan expressing cells.
SIRT6 loss causes intervertebral disc degeneration in mice by dysregulating senescence and SASP status

overall_design: Tissues from the nucleus pulposus (NP) and annulus fibrosus (AF) were harvested from the intervertebral discs of four Sirt6fl/fl and four Sirt6cKO mice at 24 months of age. NP and AF tissues were collected from lumbar and caudal discs in each animal for RNA extraction and hybridization using Affymetrix microarray.

first: Pranay

last: Ramteke


title: Cathepsin L as a dual-target to mitigate muscle wasting while enhancing anti-tumor efficacy of anti-PD-L1 [Bulk1]

status: Public on Oct 01 2024

first: Haeseung

last: Lee

overall_design: To identify effective therapeutic targets for both cachexia and muscle-related immune-related adverse events (irAEs), we generated RNA-seq data from lung and muscles in a tumor bearing mouse model.

first: Nayoung

last: Song


title: Gene expression profile at single cell level of mesenchymal cells and cancer-associated fibroblasts from mouse pancreas

status: Public on Sep 30 2024

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 2720 S Moody Ave

department: Department of Biology Medical Engineering

institute: Oregon Health Science University

summary: Pancreatic stellate cells (PSCs) are components of normal pancreatic mesenchyme, and give rise to cancer-associated fibroblasts during pancreatic tumorigenesis. We used single cell RNA sequencing (scRNA-seq) to analyze PSCs and PSC-derived CAFs from normal pancreas and pancreatic cancer tissues, respectively.

overall_design: PSCs and PSC-derived CAFs were isolated from healthy pancreas tissue and orthotopically implanted pancreatic cancer, respectively, by isolated GFP-positive (normal) and GFP-positive, PDPN-positive (tumor) cells from Rosa26-mTmG;Fabp4-Cre mice.

first: Xia

last: Zheng

first: Sherman

last: Mara


title: Single-cell muti-omics delineates the dynamics of distinct epigenetic codes coordinating mouse gastrulation

city: Guangzhou

first: fu

last: Ai

state: Guangdong

address: Jingxijiedao

institute: Southern Medical University

summary: Our study used CoBATCH to profile the H3K27ac and H3K4me1 states in mouse embryos at six continuous developmental stages ranging from Pre-Primitive Streak to Early Headfold stages, we comprehensively analyzed two histone markers and integrative scRNA-seq query dataset. Finally, we constructed a gene regulatory network centered on pivotal transcription factors and unraveled the mechanisms of how enhancers usage coordinates the transition of gene expression along lineage progression.

overall_design: The embryos were dissected at time points of E6.0, E6.5, E7.0, E7.25 and E7.5 and classified as pre-streak (Pre_Ps), Early Streak (ES), Mid-Streak (MS), Late Streak (LS), No Allantoic Bud (OB), and Early Headfold (EHF) stages according to their morphology. Embryos were digested with Collagenase I dissociation buffer at 37°C for 15-60 min to generate single-cell suspension. Single cells were subjected to single cell H3K27ac and H3K4me1 CoBATCH profiling.

first: Shanshan

first: Mingzhu

last: Fu


title: Distinct regulatory mechanisms by the nuclear Argonautes HRDE-1 and NRDE-3 in the soma of Caenorhabditis elegans.

city: Ann Arbor

first: Hector

last: Mendoza

state: MI

address: 1105 N University Ave

department: Molecular, Cellular and Developmental Biology

institute: University of Michigan

summary: Histone H3 lysine 9 methylation (H3K9me) and nuclear RNAi are two processes with roles in repression of repetitive elements and regulation of gene expression. Recently, they were also implicated in dosage compensation, a mechanism that accommodates for the differences in gene dosage between the biological sexes. In Caenorhabditis elegans, dosage compensation is achieved via epigenetic modifications on both X chromosomes of hermaphrodites, effectively dampening their expression by half to match the single X chromosome in males. This chromosome-wide process also relies on the anchoring and compaction of the X chromosomes near the nuclear lamina, mediated by the H3K9 histone methyltransferases MET-2, SET-25 and SET-32. H3K9me is also involved in gene silencing during nuclear RNAi, and recent evidence suggests that mutations in the nuclear RNAi machinery impact X chromosome compaction and dosage compensation. The nuclear Argonautes HRDE-1 and NRDE-3 are responsible for the recruitment of the H3K9 histone methyltransferases to targets in the germline and the soma, respectively, during nuclear RNAi. We investigated the impact of the loss of nuclear Argonautes and/or H3K9 methyltransferases on both dosage compensation and global gene expression during somatic development. Our immunofluorescence and bioinformatic analyses suggest that the nuclear RNAi and H3K9me pathways are involved in the packaging of the X chromosomes during dosage compensation, without consequence to their transcriptional output. Instead, mutant RNAi mutants exhibit global transcriptional differences, in which HRDE-1 and NRDE-3 affect expression of their native targets through different modes of regulation and different relationships between each nuclear Argonaute and H3K9 methylation.

overall_design: RNA-seq profiles of L1 larval stage C. elegans samples. The genotypes included are: N2 Bristol strain (wild-type), CSS419 set-32 (red11); met-2 (n4256) set-25 (n5021), EKM89 hrde-1 (tm1200), CSS415 set-32 (red11); hrde-1 (tm1200) met-2 (n4256) set-25 (n5021), WM156 nrde-3 (tm1116) and EKM205 set-32 (red11); met-2 (n4256) set-25 (n5021); nrde-3 (tm1116).

first: Eshna

last: Jash

first: Michael

last: Davis

first: Rebecca

middle: A

last: Haines

first: Sarah

last: VanDiepenbos

first: Györgyi

last: Csankovszki


title: Effect of depletion of SIRT6 in gene expression in Nucleus pulposus cells

summary: SIRT6 is a well known histone deactylase enzyme. Here, we report the effect of its depletion  in nucleus pulposus cells from rattus norvegicus. RNA seq was performed on control and sirt6 depelted cells via lentiviral transfection method. Downstream analysis includes upregulated and downregulated signalling molecules with respect to SIRT6 depletion.

overall_design: SIRT6 depletion was achieved via lentiviral transfection method via ShRNA on Nucleus pulposus cells derived from four(n=4) rats (rattus norvegicus) and submitted to RNA sequencing. Thereafter, comparative gene expression profiling was performed on SIRT6 depeleted cells(SIRT6KD/ShSirt6) vs their respective controls (SIRT6Ctrl/ShCtrl).


title: Oct4 overexpression and suppression of Notch signaling synergistically induce neurogenic competence in mammalian Muller glia.

status: Public on Sep 25 2024

city: Ann arbor

first: Thanh

last: Hoang

state: Michigan

address: 1000 wall street

institute: University of Michigan ann arbor

summary: scRNA-Seq and scMultiome (snRNA/ATAC) were performed on GFP+ cells from adult control and Rbpj-deleted mouse retinas with Gfap-Oct4 and Gfap-mCherry to profile changes in gene expression and chromatin accessibility

overall_design: scRNA-seq were prepared on dissociated retinal cells using the 10X Genomics Chromium Single Cell 3’ Reagents Kit v3.1 (10X Genomics, Pleasanton, CA). Libraries were constructed following the manufacturer’s instructions and were sequenced using Illumina NextSeq. Sequencing data were processed through the Cell Ranger 7.0.1 pipeline (10X Genomics) using default parameters. scMultiome was perfomed usinng 10x Genomics Multiome kit

first: Nguyet

last: Le

first: Sherine

last: Awad

first: Isabella

last: Palazzo

first: Seth

last: Blackshaw


title: Enhanced Spatial Transcriptomics Analysis of Mouse Lung Tissues Revealed Cell-Specific Gene Expression Changes Associated with Pulmonary Hypertension

city: St. Louis

first: Zhiyu

last: Dai

address: 4960 Childrens Place

institute: Washington University in St. Louis

summary: We developed a method that utilizes floating mounting of thin sections of fixed frozen mouse lung tissue onto Xenium slides for the fluorescent in situ hybridization (FISH) and imaging–based spatial transcriptomics analysis of gene expression using the Xenium platform provided by 10X Genomics. Spatial transcriptomics techniques provide a comprehensive view by merging gene expression data with spatial context within their native tissue architecture. However, the Xenium pipeline has been validated only for formalin-fixed paraffin-embedded (FFPE) and fresh frozen sections by 10X Genomics. Notably, many researchers prefer paraformaldehyde-fixed cryosections for immunohistochemistry and in situ hybridization. In our study, we assessed the compatibility of standard fixed frozen mouse lung sections with the Xenium protocol. Our findings reveal that these sections not only align well with the Xenium platform but also offer superb imaging and gene expression quantification, even with limited number of genes in the Xenium panel. This protocol can serve as a valuable resource for preparing various tissues where FFPE and fresh frozen samples present challenges.

overall_design: Total four mice lung sections were included. Two sections were from two Egln1Tie2Cre (KO) mice, and two sections were from littermate controls. Mouse lung was first fixed by 4% PFA through transcardial perfusion, dissected out, and further post-fixed in 4% PFA overnight at 4 °C. The lung was then cryoprotected, embedded in OCT compound, and sectioned on a cryostat into 10um thickness. Xenium slide is fully mounted with sections, and then take a note on tissue sections and layouts, and record the metadata information for each section (e.g. from which mouse, age, sex, genotypes etc). The slide is then stored in a slide mailer and kept at -80 °C up to three weeks. The predesigned 379-gene mouse panel of probes provided by 10x Genomics was used to conduct the high-resolution Xenium in Situ Analysis experiment.

first: Hanqiu

last: Zhao

first: Xiaokuang

last: Ma

first: Peng

last: Chen

first: Bin

last: Liu

first: Jing

last: Wei

first: John

last: Zhang

last: Fallon

first: Shenfeng

last: Qiu


title: A spatial transcriptomics study of splenic marginal zone lymphomas (SMZL) and spleen healthy donor

status: Public on Sep 17 2024

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

institute: IUCT-ONCOPOLE

summary:
Purpose: Spatial transcriptomics was used to characterize in depth splenic samples obtained from splenic marginal zone lymphomas
Methods: 4 frozen samples of spleen from SMZL patients, and 1 healthy donor were selected and thawed for performing a 10X genomics Visium Spatial assay.
Results: Tumor cells formed mainly patient specific-B cell clusters, while  T-cells from the 3 patients and healthy donors clustered together.
Conclusion: Single RNA-Seq unveils inter- and intra-patient heterogeneity.

overall_design: Spleen from SMZL patients, and 1 healthy donor were selected for performing a 10X genomics Visium Spatial assay.

first: Juan

middle: P

last: Cerapio Arroyo

first: Camille

last: Laurent

first: Jean-Jacques

last: Fournié


title: Gene expression in self-activating CAR-T cells with CD28 or 4-1BB costimulatory domain and G4S or Whilow218 linker.

status: Public on Sep 16 2024

city: Yokohama

first: Taku

last: Kouro

state: Kanagawa

address: 2-3-2 Nakao, Asahi-ku

department: Division of Cancer Immunotherapy

country: Japan

institute: Kanagawa Cancer Center Research Institute

summary: We observed self-activation of SKM-CAR-T cells which target novel mesothelioma antigen. CAR-T with CD28 costimulatory domain showed signs of exhaustion while those with 4-1BB costimulatory domain did not. Changes in the gene expression by substituting (G4S)4 linker in scFv portion to Whitlow 218 linker was investigated.

overall_design: We performed RNA-seq analysis of SKM-CAR-T cells with CD28 or 4-1BB each with (G4S)4 linker or Whitlow 218 linker together with T cells without transducing CAR.

first: Tetsuro

last: Sasada


title: Machine Learning Analysis of Circulating Alternative Spliced RNAs Reveal Segregation of Retained Intron Species with New-onset Type 1 Diabetes

status: Public on Sep 18 2024

city: Chicago

first: Raghavendra

middle: G

last: Mirmira

state: IL

address: 900 E. 57th Street

department: Medicine

institute: University of Chicago

summary: Distinct patterns of RNA splicing differentiated participants with T1D from healthy unaffected controls. Notably, certain splicing events, particularly involving retained introns, showed significant association with T1D. Machine learning analysis using these splicing events as features from the training cohort demonstrated high accuracy in distinguishing between T1D subjects and controls in the validation cohort.  Gene Ontology pathway enrichment analysis of the retained intron category showed evidence for a systemic viral response in T1D subjects.

overall_design: Examination of circulating alternative splicing patterns in subjects of  T1D and matched healthy subjects

first: Wenting

last: Wu

first: Bobbie-Jo

last: Webb-Robertson

first: G

last: Raghavendra


title: The Gq/11 family of G alpha subunits is necessary and sufficient for lower jaw development

status: Public on Sep 19 2024

city: Aurora

first: Stanley

middle: Michinobu

last: Kanai

state: CO

department: Craniofacial Biology

institute: University of Colorado Anschutz Medical Campus

summary: Development of the vertebrate jaw apparatus depends on highly conserved signaling pathways. Patterning of the lower jaw is driven by Endothelin receptor type A (Ednra) and secreted ligand Endothelin 1 (Edn1). The Ednra signaling pathway establishes the identity of lower jaw progenitors by regulating expression of numerous patterning genes, but the intracellular signaling mechanisms linking receptor activation to gene regulation remains poorly understood. As a first step towards addressing this question, we examined the function of the Gq/11 family of Gα subunits in zebrafish using pharmacological and genetic ablation of Gq/11 activity and transgenic induction of a constitutively active Gq protein in edn1-/- embryos. Loss of Gq/11 activity fully recapitulated the edn1-/- phenotype, with genes encoding for G11 being most essential. Furthermore, inducing Gq activity in edn1-/- embryos not only restored Ednra-dependent jaw structures and gene expression signatures but also caused homeosis of the upper jaw structures into a lower jaw-like structure. These results indicate that Gq/11 is necessary and sufficient to mediate the lower jaw patterning mechanism for Ednra.

overall_design: Zebrafish embryos were first treated with YM-254890 or DMSO (control) between 16 - 36 hours post fertilization (hpf). Then, cranial neural crest cells (NCCs) labeled with two transgenes, sox10:mRFP and fli1a:EGFP, were isolated at 36 hpf by fluorescence activated cell sorting (FACS). Isolated cranial NCCs were then analyzed by scRNA-seq.

first: Ezra

last: Lencer

first: James

middle: T

last: Nichols

first: David

last: Clouthier


title: Ctla-4 deficiency induces an inflammatory bowel disease-like phenotype in a zebrafish model [bulkRNA-seq]

city: Hangzhou

first: Qin

middle: Lu

last: lu

address: Gudun Road, Xihu District

institute: zhejiang university

summary: Inflammatory bowel disease (IBD) is a chronic and relapsing immune-mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood, but genetic factors have implicated in genome-wide association studies, including CTLA-4, an essential negative regulator of T cell activation. However, establishing a direct link between CTLA-4 and IBD has been challenging due to the early lethality of CTLA-4 knockout mice. In this study, we identified zebrafish Ctla-4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla-4-deficient (ctla-4-/-) zebrafish line. These mutant zebrafish exhibit reduced weight, along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation-related genes, disturbing immune system homeostasis. Moreover, single-cell RNA-sequencing analysis indicated increased Th2 cells and interleukin 13 expression, along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally, Ctla-4-deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly, supplementation with Ctla-4-Ig successfully alleviated intestinal inflammation in these mutants. Altogether, these findings offer substantial evidence linking CTLA-4 to IBD and establish a new model for investigating pathogenesis and potential treatments.

overall_design: Total RNAs were isolated from wild-type or ctla-4-/- intestines (three biological replicates) using TRIzol reagent following the manufacturer's instructions (Takara). cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit (NEB), and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio (Hangzhou, China).

first: Lulu

last: Qin

first: Chongbin

last: Hu

first: Ye

last: Chen

first: Lixin

last: Xiang

first: Jianzhong

last: Shao


title: TRKB Signaling Promotes Alveolar Capillary Angiogenesis Following Perinatal Hyperoxic Damage

status: Public on Sep 15 2024

city: Chengdu

first: Hua

last: He

state: Sichuan

address: 2222 Xinchuan Rd

institute: West China Second University Hospital Sichuan University

summary: Impaired angiogenesis characterized by the reduced proliferation of pulmonary endothelial cells leads to reduced capillary density in patients with bronchopulmonary dysplasia (BPD). In a mouse model of BPD, perinatal hyperoxic injury decreases the number of the recently identified lung capillary stem cells termed as general capillary (gCap) cells, along with the specific reduction of Ntrk2, which encodes for Tropomyosin receptor kinase B (TRKB) within this subpopulation. Herein, we determine whether TRKB signaling is required for perinatal gCap cell proliferation and further promoting pulmonary angiogenesis using the hyperoxia mouse BPD model. TRKB activation by BDNF treatment led to enhanced tube-forming ability of endothelial cells in vitro. In vivo treatment of mice with BDNF increased the proliferation of gCap cells and alleviated capillary loss caused by hyperoxic injury. Conversely, inhibition of TRKB signaling disrupted the tube formation of endothelial cells and exaggerated the vascular endothelial damage caused by hyperoxia. We further show that MAPK/ERK signaling might act downstream of TRKB to modulate pulmonary angiogenesis. These data indicate that TRKB signaling play a critical role in pulmonary angiogenesis upon perinatal lung injury, supporting the concept that TRKB activation might be a potential therapeutic for preserving endothelial cells for lung diseases associated with prematurity.

overall_design: We performed RNA-seq on MACS-sorted CD31+ lung endothelial cells isolated from mice maintained in room air (RA, 21% oxygen) or hyperoxia (HO, 75% oxygen). Mice were subjected to treatment on postnatal day 0, and lungs were harvested on postnatal day 7.


title: Ctla-4 deficiency induces an inflammatory bowel disease-like phenotype in a zebrafish model [scRNA-seq]

overall_design: intestine leukocyte (WT and KO (Ctla-4 deficiency) ) of the AB zebrafish were isolated by Ficoll-Hypaque (1.080 g/mL) density-gradient centrifugation and analyzed using scRNAseq.


title: Multiomic-based Immune Response Profiling in Migraine, Vestibular Migraine and Meniere's Disease

city: St Leonards

first: Jose Antonio

last: Lopez-Escamez

state: NSW

address: 10 Westbourne St

department: Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute

country: Australia

institute: The University of Sydney

summary: We analysed the immune profile of individuals with MI, VM, and MD using scRNAseq and scATACseq in PBMCs and to determine active biochemical pathways to identify new potential druggable molecular targets

overall_design: Blood samples were obtained from 24 Spanish participants with no diagnosed allergies or autoimmune diseases (eight patients with Meniere's Disease(MD), five with Vestibular Migraine (VM), five with Migraine (MI), and six healthy controls (HC)).

first: Jose

first: Pablo

last: Cruz-Granados


title: Multiomic-based Immune Response Profiling in Migraine, Vestibular Migraine and Meniere's Disease [scATAC-Seq]


title: Most adult gonadotrophs originate from postnatal pituitary stem cells during minipuberty.

status: Public on Sep 10 2024

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

institute: Francis Crick Institute

summary: In the first three weeks postnatally, the pituitary gland undergoes a period of rapid growth, due to both cell proliferation and endocrine cell size increase. SCs are initially the most proliferative, and lineage tracing experiments previously showed that neonatal SCs can give rise to all endocrine cell types. However, because the Cre drivers used for lineage tracing were relatively inefficient and relied on tamoxifen, a selective estrogen receptor modulator which perturbs normal physiology, we could not decipher SC contribution to organ growth. We have thus performed lineage tracing using a new, more efficient and physiologically neutral Sox2rtTA allele. When we traced early postnatal SCs using Sox2rtTA, we observed, similarly in both sexes, that most adult gonadotrophs derive from this neonatal SC population. These observations were confirmed and complemented by a single cell RNAseq dataset from postnatal day 3 (PND3) SOX9iresGFP XX and XY positive cells. From SOX9iresGFP cells, which comprise SCs and their immediate progeny, cell trajectories were inferred, and relevant gene regulatory networks predicted. Along with lineage tracing experiments, this dataset confirmed that SCs mostly differentiate into gonadotrophs postnatally. As animals develop, SC-derived gonadotrophs invade the gland, while the minor embryonic population remains confined ventrally. The discovery of a dual origin for gonadotrophs may help understand aspects of gonadotrophin regulation and mechanisms of diseases affecting puberty and fertility.

overall_design: FACsorted Sox9iresGFP positive cells from post-natal day 3 (PND3) males and females.

first: Daniel

last: Sheridan

first: Karine

last: Rizzoti


title: Upregulated expression of ubiquitin ligase TRIM21 promotes PKM2 nuclear translocation and astrocyte activation in experimental autoimmune encephalomyelitis

status: Public on Sep 12 2024

city: Xi'an

first: Zhe

last: Feng

address: No.620 West Chang'an Street

institute: Shaanxi Normal University

summary: Reactive astrocytes play critical roles in the occurrence of various neurological diseases such as multiple sclerosis. Activation of astrocytes is often accompanied by a glycolysis-dominant metabolic switch. We found that PKM2 displayed nuclear translocation in astrocytes of EAE mice, an animal model of multiple sclerosis. And we identified the ubiquitination-mediated regulation of PKM2 nuclear import by ubiquitin ligase TRIM21. To detect the expression of TRM21 in EAE mice, We used single-cell sequencing to analyze the expression  of TRM21 in EAE mice.

overall_design: In order to detect whether there were differences in the expression of TRIM21 in EAE mice at different stages, we compared normal mice with EAE mice in Peak and Chronic phases.

first: Luting

last: Yang

first: Chunqing

first: Xiaowen

first: Jie

last: Zhang

first: Yanxin

last: Xiao

first: Weitai

first: Tingting

last: Cui

first: Xin

first: Yang

first: Yaling

first: Yaping

last: Yan