title: A robust circulating microRNA signature for diagnosis and early detection in pancreatobiliary cancer

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

summary: Purpose: Oncologists for pancreatobiliary cancer (PBca) demand a new circulating biomarker superior to carbohydrate antigen 19-9 (CA19-9). This study aimed to identify the serum microRNA signature composed of reproducible and disease-related microRNAs with clinical bioinformatics.   Methods: This multicenter study enrolled patients with treatment-naïve PBca and healthy participants. Optimized serum processing condition was evaluated with t-distributed stochastic neighbor embedding (t-SNE) visualization. The serum microRNA candidates were selected in disease association with Weighted Gene Coexpression Network Analysis (WGCNA). A microRNA signature, combination of multiple serum microRNAs, was examined in exploratory, validation and independent validation set. Biology of the diagnostic miRNAs was evaluated using human pancreatic cancer cells.  Results: The 284 (healthy 150, PBca 134) of 827 serum samples were processed within 2hr of time-to serum collection, distributed at the same area of t-SNE map, assigned to exploratory set. The 193 optimized samples were assigned to validation (healthy 50, PBca 47) or independent validation set (healthy 50, PBca 46). Index-1 was a combination of the 5 serum microRNAs having disease-association on WGCNA, showed a sensitivity/specificity >80% and an AUC outperforming CA19-9 in exploratory, validation and independent validation set. The AUC of Index-1 for detecting T1 tumor was superior to CA19-9 (0.856 vs. 0.649, p = 0.038). Human pancreatic cancer cells had intra- and extracellular expression of miR-665, a component of Index-1. Transfection of miR-665 to a human pancreatic cancer cell inhibited cell growth.   Conclusions: A serum microRNA signature, Index-1, was useful for detecting PBca, which would improve the early diagnosis of PBca.

overall_design: 284 (healthy 150, PBca 134) serums were analyzed in the training set, and 93 serums were assigned to validation (healthy 50, PBca 47) or independent validation set (healthy 50, PBca 46). Tripricate analyses per a sample.

first: Shuichi

last: Mitsunaga

first: Masafumi

last: Ikeda

first: Makoto

last: Ueno

first: Satoshi

last: Kobayshi

first: Masahiro

last: Tsuda

first: Ikuya

last: Miki

first: Takamichi

last: Kuwahara

first: Kazuo

last: Hara

first: Yukiko

last: Takayama

first: Yutato

last: Matsunaga

first: Keiji

last: Hanada

first: Akinori

last: Shimizu

first: Hitoshi

last: Yoshida

first: Tomohiro

last: Nomoto

first: Kenji

last: Takahashi

first: Hidetaka

last: Iwamoto

first: Hideki

last: Iwama

first: Etsuro

last: Hatano

first: Kohei

last: Nakata

last: Nakamura

first: Hiroko

last: Sudo

first: Atsushi

last: Ochiai


title: DNA methylation profiles of mice embryos (E7.5) of the control group and arsenic group

status: Public on Jan 22 2025

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

country: Japan

institute: National Institute for Environmental Studies

type: Methylation profiling by high throughput sequencing

summary: The control or gestationally arsenic exposed F1 males (C3H strain) and C57BL/6 strain (B6) females were crossed and F2 male embryos were obtained on embryonic day 7.5 (E7.5). The DNA methylomes of the embryos were investigated by RRBS method.

overall_design: Comparative DNA methylation analysis of RRBS data for control group and arsenic group

first: K


title: Multi-omics Analysis Unveils Metabolic Inflexibility Manifesting as Impaired Branched Amino Acid and Enhanced Fatty Acid Degradation in a Mouse Model of Diabetic Cardiomyopathy [RNA-seq]

city: Wuhan

first: Li

last: Zhou

address: Tongji Hospital Research Building, Wuxian Road, Caidian District, Wuhan, Hubei Province, People's Republic of China

department: Division of Cardiology, Departments of Internal Medicine

country: China

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

type: Expression profiling by high throughput sequencing

summary: Diabetic cardiomyopathy (DbCM) is an important clinical syndrome of diabetes and cause great burden to the people's life and health. Understanding its intrinsic epigenetic and metabolic alterations is critical to develop drugs for the treatment of DbCM. Multiple omics technology provides a feasible way for parsing the epigenetic characteristics and metabolic signatures associated with DbCM. The heart isolated from Male db/db mice and db/m mice were used for the analysis of high-throughput sequencing. Non-targeted metabolomics and amino acid-targeted metabolomics analyses were performed to detect the metabolites in plasma and heart tissues. Additionally, RNA-seq, proteomics, and ATAC-seq were employed to elucidate the underlying transcriptional-metabolic regulatory network mechanism in DbCM.

overall_design: Cardiac mRNA profiles of 24-week old db/m and db/db mice


title: Contribution of hypoxia-inducible 1alpha to pathogenesis of sarcomeric hypertrophic cardiomyopathy

city: Munich

first: Sarala Raj

last: Murthi

address: Lazarettstr. 36

country: Germany

institute: German Heart Center

summary: Aims: Hypertrophic cardiomyopathy (HCM) caused by autosomal-dominant mutations in genes coding for structural sarcomeric proteins, is the most common inherited heart disease. HCM is associated with progressive myocardial hypertrophy, fibrosis, ventricular dysfunction, and arrhythmias. Hypoxia together with hypoxia-inducible transcription factor-1a (HIF1A) is the central master regulators of cellular hypoxia response and associated with HCM. Yet their exact role remains to be elucidated. Therefore, the effect of a cardiomyocyte-specific Hif-1a knockout (cHif1aKO) was studied in an established α-MHC719/+ HCM mouse model that exhibits the classical features of human HCM. Results: HIF-1α protein and HIF downstream targets were upregulated in left ventricular tissue of α-MHC719/+ mice. Cardiomyocyte-specific abolishment of Hif-1a did not cause cardiac abnormalities in wild type (WT) mice and resulted in amelioration of disease phenotype in α-MHC719/+ mice, as evidenced by decreased left ventricular wall thickness, reduced myocardial fibrosis, reduced disordered SRX/DRX state and diminished ROS production. In addition, cHif1aKO induced normalization of pro-hypertrophic and pro-fibrotic left ventricular remodeling signaling evidenced on whole transcriptome and proteomics analysis in α-MHC719/+ mice. Proteomics of serum samples from patients with early onset HCM compared to age-and gender-matched healthy controls revealed significant upregulation of HIF targets IGF2, LTBP1, RECK and downregulation of WDR1. Innovation and Conclusion: Overall, these results demonstrate for the first time that HIF signaling is involved in mouse and human HCM pathogenesis. Cardiomyocyte-specific knockout of Hif-1a attenuates disease phenotype in the HCM α-MHC719/+ mouse model. Targeting HIF-1α might serve as a therapeutic option to mitigate HCM disease progression.

overall_design: The effect of cardiomyocyte-specific HIF-1α knockout was studied in the established α-MHC719/+ HCM mouse model that exhibits classical features of human HCM. Disease phenotype was analyzed by echocardiography, histopathology, immunohistochemistry, and determination of oxidative stress. Whole transcriptome and proteome analysis and subsequently pathway analysis were performed. Furthermore, serum proteomic analysis was carried out in patients affected by HCM to validate the contribution of HIF-1α signaling in human HCM. All animal procedures were performed in accordance with the Directive 2010/63/EU of the European Parliament and approved (Project Number: 55.2-1-54-2532-242-2015) by the local legislation on protection of animals (Government of Upper Bavaria, Munich, Germany).

first: Sarala

last: Raj Murthi

first: Andreas

last: Petry

first: Bachuki

last: Shashikadze

first: Jan

middle: B

last: Stöckl

first: Manuel

last: Schmid

first: Gianluca

last: Santamaria

first: Karin

last: Klingel

first: Damir

last: KraÄun

first: Xinpei

last: Chen

first: Sabine

last: Bauer

first: Joachim

middle: P

last: Schmitt

first: Florian

last: Flenkenthaler

first: Josh

last: Gorham

first: Christopher

middle: N

last: Toepfer

first: David

last: Potěšil

first: Pavel

last: Hruška

first: Zbyněk

last: Zdráhal

first: Zsuzsanna

last: Mayer

first: Mathieu

last: Klop

first: Luisa

last: Lehmann

first: Yishi

last: Qin

first: Laura

last: Papanakli

first: Nadine

last: Spielmann

first: Alessandra

last: Moretti

first: Thomas

last: Fröhlich

first: Peter

last: Ewert

first: Stefan

last: Holdenrieder

first: Jonathan

middle: G

last: Seidman

first: Christine

middle: E

first: Agnes

last: Görlach

first: Cordula

middle: M

last: Wolf


title: Asxl1 mutation enhances differentiation in CSF3R-mutated myeloproliferative neoplasms [RNA-Seq]

city: Portland

first: Julia

last: Maxson

state: Oregon

address: 3181 SW Sam Jackson Park Rd

country: USA

institute: Oregon Health and Science University

summary: Mutations in the epigenetic regulator Additional Sex Combs-Like 1 (ASXL1) are frequently observed in chronic neutrophilic leukemia (CNL). This disease is classically driven by activating mutations in Colony Stimulating Factor 3 Receptor (CSF3R), which promote the overproduction of neutrophils that characterizes this disease. Despite high rates of co-occurrence, the interplay between ASXL1 and CSF3R mutations in hematopoiesis and leukemia development remains poorly understood. Here, we present a new mouse model with both Asxl1Y588X and Csf3rT621I mutations, which recapitulates features of human CNL. Csf3r-mutant mice exhibit an age-associated depletion of hematopoietic stem and progenitor cells, which is reversed by the addition of Asxl1Y588X. This combination of mutations causes an expansion of myeloid-biased stem cells. As the mice age they develop neutrophilia, but leukemia is rare, suggesting additional mutations may be required for transformation. Using models of myeloid differentiation, we find that ASXL1 truncation enhances CSF3RT618I-driven neutrophil differentiation by downregulating MYC programs and activating inflammatory pathways associated with mature myeloid cell production. Moreover, cells with both mutations had increased priming of neutrophil-associated enhancers and reduced priming of enhancers associated with monocytic differentiation. Mutant ASXL1 is known to decrease genome-wide abundance of a repressive histone mark—H2AK119ub. While we see the expected decrease in H2AK119ub in Asxl1-mutant cells, this effect is reversed when CSF3R is also mutated, suggesting a complex interplay between these mutations in regulating chromatin dynamics during hematopoiesis. Our findings highlight context-dependent effects of ASXL1 mutation in myeloid disorders and provide insights into the mechanisms underlying neutrophil differentiation in ASXL1-mutant CNL.

overall_design: RNAseq in HoxB8 cells overexpression of Asxl1 truncation and overexpression of CSF3R T618I mutation, each single mutation and control.

first: Lucie

last: Darmusey

first: Anna

last: Bagley

first: Thai

last: Nguyen


title: Asxl1 mutation enhances differentiation in CSF3R-mutated myeloproliferative neoplasms [ATAC-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ATACseq in HoxB8 cells CRISPR modified for Asxl1 truncation and overexpression of CSF3R T618I mutation, each single mutation and control.


title: Transcriptome Analysis Reveal Molecular Targets of Erythrocyte Invasion Phenotype Diversity in Natural Plasmodium falciparum Isolates from Cameroon.

city: Bamenda

first: Ines

last: Ngoh

state: North west region

address: Bambili

department: Microbiology & Parasitology

country: Cameroon

institute: University of Bamenda

summary: Further understanding of the molecular mediators of alternative RBC invasion phenotypes in endemic malaria parasites will support malaria blood stage vaccine or drug development. This study investigated the prevalence of SA-dependent and SA-independent RBC invasion pathways in endemic P. falciparum parasites from Cameroon and compared the schizont stage transcriptomes in these two groups with the goal of uncovering the wider repertoire of transcriptional variation associated with the use of alternative RBC invasion pathway phenotypes. Two-colour flow cytometry-based invasion-inhibition assay against RBCs treated with neuraminidase, trypsin and chymotrypsin and deep RNA sequencing of schizont stages harvested in the first ex-vivo replication cycle in culture were employed in this investigation. RBC invasion phenotypes were determined for 63 isolates from asymptomatic children with uncomplicated malaria. Approximately 80% of the isolates invaded neuraminidase-treated but not chymotrypsin-treated RBCs, representing sialic acid (SA)-independent pathways of RBC invasion. The schizont transcriptome profiles of 16 isolates with invasion phenotypes revealed a total of 5136 gene transcripts, with 85% of isolates predicted at schizont stages. Two distinct transcriptome profile clusters belonging to SA-dependent and SA-independent parasites were obtained by data reduction with principal component analysis. Differential analysis of gene expression between the two clusters implicated in addition to the well characterized adhesins, the up-regulation of genes encoding proteins mediating merozoite organelle discharges and several conserved, virulent, merozoite associated and exported proteins. The latter majority of which have been shown to have structural and physiological relevance to RBC surface remodelling and immune evasion in malaria and thus, have potential as anti-invasion targets.

overall_design:
To uncover the wider repertoire of transcriptional variation associated with the use of alternative RBC invasion pathway phenotypes, we harvested enriched schizont stages in the first ex-vivo replication cycle of P. falciparum isolates in culture.
We subjected to two-colour flow cytometry-based invasion-inhibition assay (against RBCs treated with neuraminidase, trypsin and chymotrypsin) to obtain RBC invasion pathway phenotypes and deep RNA sequencing to obtain transcriptome profiles.
Then, we compared transcriptome profiles of isolates with sialic acid-dependent and sialic acid-independent pathway phenotypes.

first: Karim

last: Mane

first: Alfred

last: Amambua-Ngwa


title: Antigen-driven CD8+ T cell clonal expansion is a prominent feature of MASH in humans and mice [mouse]

city: Aurora

first: Matthew

middle: Alan

last: Burchill

state: Colorado

department: Department of Medicine

institute: University of Colorado - Anschutz Medical Campus

summary: Metabolic dysfunction-associated steatoheptaitis (MASH) is a chronic liver disease caused by prolonged poor diet. During MASH-induced chirrosis in humans and diet-induced MASH in murine models, T cells accumulated in the liver but their function in MASH is unresolved. We aimed to evaluated differences in T cell phenotype and T cell receptor (TCR) repertoire in T cells from the livers of diseased humans and murine models. This set contains mouse sequencing data.

overall_design: 6-8 week old male C57BL/6 mice were put on a High-Fat, High-Cholesterol (HFHC) diet for 25 or 31 weeks or a chow control diet. Reversal mice were placed on HFHC diet for 26 weeks and then fed a chow diet for 5 weeks. From all samples, CD3+ cells were enriched from the liver prior to sequencing. All samples were analyzed with 5' scRNAseq and enrichment for T cell receptor (TCR) sequences.

first: Abbigayl

last: Burtis

first: Diestiny

last: DeNicola

first: Megan

last: Ferguson

first: Radleigh

last: Santos

first: Clemencia

last: Pinilla

first: Michael

middle: S

last: Kriss

first: David

middle: J

last: Orlicky

first: Beth

middle: A

last: Tamburini

first: Austin

last: Gillen


title: Iron metabolism in a mouse model of hepatocellular carcinoma

city: Ulm

first: André

last: Lechel

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine I

institute: University hospital Ulm

summary:
Background & Aims: Liver cancer is the sixth most frequently diagnosed type of cancer and the third leading cause of cancer-related mortality worldwide. One of the most frequently effected pathways in liver carcinoma is the p53 signalling pathway. Emerging evidence indicates that deregulation of p53 leads to several metabolic disorders that are pivotal during cancer progression.
Methods: We induced chronic liver disease and subsequent liver carcinoma formation by chronic injection of CCl4 (16 weeks treatment) in p53f/f and p53LKO mice. We characterized major differences between HCC from p53f/f and HCC from p53LKO mice. In addition, we characterized differences between HCC and ICC, both from p53LKO mice.  Results: We show that Conclusions: Dysregulation of Notch signaling is involved in tumor differentiation. Loss of Rbpj triggers the formation of combined HCC-iCCA which is associated by a pro-tumorigenic environment.
Results: We show that all liver cancers that develop on a p53-deficient background have an iron-poor phenotype with a “low hepcidin and high Tfr1” signature, while iron deficiency at the systemic level is restricted to female mice. In addition to iron, liver tumorigenesis correlated with significant deficits of selenium, zinc and manganese, accompanied by changes in their key metabolic players.
Conclusions: Our work demonstrates a pivotal role for p53 in a complex network controlling tumor development and micronutrient metabolism, locally in the liver cancers, and at a systemic level along with highlighting sex-specific differences underlying liver cancer development and the distribution of trace elements.

overall_design: Total RNA was isolated from murine liver carcinoma, and the quality was analyzed by a bioanalyzer. Agilent Mouse Gene Expression Microarrays 8x60K were used.

first: Umesh

last: Tharehalli

first: Yuexin

last: Chen

first: Maja

last: Vujić Spasić

first: Dilay

last: Yilmaz

first: Paul

last: Knoop


title: Mouse jejunum in a bidirectional nutrient supply model

city: Hangzhou

first: Jian

last: Zhang

address: Yuhangtang Road, Xihu District, Hangzhou, Zhejiang Province

institute: Zhejiang University

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

overall_design: Refer to individual Series


title: Disruption of BCAAs degradation is the primary mechanism of diabetic cardiomyopathy revealed by integrated transcriptome and metabolome analysis

city: Chengdu

first: Yanxia

last: Wu

state: sichuan

address: LinYin street in Wuhou district

institute: Sichuan University

summary: Diabetic cardiomyopathy (DCM) is a unique form of cardiomyopathy observed in diabetic patients, and in this study we aimed to gain a comprehensive understanding of the underlying mechanisms of DCM by integrating transcriptomics and metabolomics

overall_design: Male Sprague-Dawley rats were administered a single dose of streptozotocin to induce DCM and the diastolic and systolic function of the heart were evaluated through echocardiography and heart hemodynamics. The cardiac structure was determined using echocardiography and wheat germ agglutinin staining. A comprehensive analysis of global alterations in genes and metabolites within the DCM animal model at the heart level was conducted by integrating transcriptomics and metabolomics

first: Wanxiang

last: Jiang

first: Junlong

last: Wang

first: Jinliang

last: Yang


title: Ldb1 establishes multi-enhancer networks to regulate gene expression (TT-seq)

city: Philadelphia

first: Siqing

state: PENNSYLVANIA

address: 3401 Civic Center Blvd

department: Department of Pediatrics, Division of Hematology

institute: Children’s Hospital of Philadelphia

summary: How enhancers specifically connect to gene promoters is still unclear. Besides the CTCF/cohesin machinery, only a small set of nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops. Utilizing multiple degron systems, we demonstrate that most endogenous LDB1-mediated contacts can form in the absence of CTCF, cohesin and YY1. Furthermore, an engineered/forced, LDB1-driven chromatin loop can form in the absence of cohesin. Yet, in a fraction of cases cohesin driven extrusion may promote LDB1 anchored loops. Leveraging the dynamic reorganization of nuclear architecture during the transition from mitosis to G1 phase, we establish a relationship between LDB1-dependent interactions in the context of TAD organization and gene activation. Tri-C and Region Capture Micro-C reveal that LDB1 organizes multi-enhancer networks to activate transcription. This establishes LDB1 as direct driver of connectivity between regulatory elements.

overall_design: Transient transcriptome sequencing (TT-seq) in LDB1-AID cells (untreated and 4 hour auxin-treated conditions).

first: Nicholas

last: Aboreden

first: Gerd

last: Blobel


title: Artificial Biomarker-based Feedback-regulated Personalized Precise Thrombolysis with Lower Hemorrhagic Risk

city: Chongqing

first: Wen

last: Zeng

address: Gaotanyan street

department: Department of Cell Biology

institute: Army Medical University

summary: Intravenous thrombolysis possesses critical defects in efficiency and post-thrombolysis hemorrhage due to the current empirical body weight-based medication strategy. However, the inherent heterogeneity of thrombi, instead of body weight, endows thrombi different thrombolysis resistance and affect the thrombolytic outcome. The lack of methods for perceiving thrombolysis resistance has severely hindered the precise medication of vascular embolization. Here, we described the relationship between the thrombin heterogeneity in thrombi and the thrombolysis resistance of thrombi, and created an artificial biomarker-based nano-patrol system to perceive and report the thrombolysis resistance of thrombi taking advantage of the specific recognition and allosteric ability of aptamer-based DNA structure. The nano-patrols are able to accomplish thrombolysis resistance-matched personalized precise therapy through the NIR-Ⅱ laser-regulated synergistic thrombolytic effect, according to the feedback signal from artificial biomarkers. This new strategy depicted enhanced thrombolytic efficiency than alteplase for rats, mini pigs and clinical thrombi, achieved recanalization in thrombotic model where alteplase encountered failure. Moreover, the nano-patrol system remarkably reduced the infarct volume and the hemorrhagic transformation risk (0.12-fold of alteplase) of cerebral thrombosis. This nano-patrol system developed new tool for the assessment of thrombolysis resistance and personalized precise thrombolysis with lower hemorrhagic risk.

overall_design: Inject the corresponding drug (saline, rt-PA, Nano-patrol+NIR) 4.5 hours after modeling, and take brain tissue for testing three days later

first: Hao

last: Tian

first: Lang

last: Li


title: WHIM syndrome–linked CXCR4 mutations impair lymphoid progenitor specification in mice

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

summary: Both cell-intrinsic cues and niche-derived cell-extrinsic cues drive lineage  the specification of hematopoietic multipotent progenitors (MPPs) in the bone marrow, comprising multipotent MPP1 cells and lineage-restricted MMP2, MPP3, and MPP4 cells.  WHIM syndrome is a rare congenital immunodeficiency caused by gain-of-function mutations in the gene encoding the chemokine receptor CXCR4 and characterized by an increase in the number of myeloid cells that are produced in but fail to exit from the bone marrow. Here, we found that CXCR4 signaling regulated the localization and fate of MPPs. Knock-in mice bearing a WHIM syndrome–associated CXCR4 mutation phenocopied the myeloid-skewing of bone marrow in patients. Myeloid rewiring of lymphoid-primed MPPs (MPP4s) in the mice was associated with enhanced mechanistic target of rapamycin (mTOR) signaling and overactive Oxphos metabolism. The fate of these MPP4 cells was also affected by molecular changes established at the MPP1 level. Mutant MPP4 displayed altered localization in the bone marrow relative to perivascular structures, suggesting that extrinsic cues also contribute to their myeloid skewing. Chronic treatment with the CXCR4 antagonist AMD3100 or the mTOR inhibitor Rapamycin rescued the lymphoid capacities of mutant progenitors including MPP4, demonstrating a pivotal role for the CXCR4-mTOR axis in regulating MPP4 fate. Our study thus provides mechanistic insights into how CXCR4 signaling regulates the lymphoid potential of MPPs.

overall_design: ATACseq was performed on MPP1 and MPP4 HSPC from WT, heterozygous (1013) or homozygous (2026) Cxcr4 mutatnt mouse strains

first: Severine

last: Lecourt

first: Vincent

last: Rondeau

first: Karl

last: Balabanian


title: Identification of a global gene expression signature associated with the genetic risk of catastrophic fracture in iPSC-derived osteoblasts from Thoroughbred horses

city: Herts

first: Esther

last: Palomino Lago

address: Hawkshead Lane, North Mymms, Hatfield

department: Deptartment of Clinical Sciences and Services

country: United Kingdom

institute: Royal Veterinary College

summary: Bone fractures are a significant problem in Thoroughbred racehorses. The risk of fracture is influenced by both genetic and environmental factors. To determine the biological processes that affected in genetically susceptible horses, we utilised polygenic risk scoring to establish induced pluripotent stem cells (iPSCs) from horses at genetically high and low risk. RNA-sequencing on iPSC-derived osteoblasts revealed 112 genes that were significantly differentially expressed. 43 of these genes have known roles in bone, 27 are not yet annotated in the equine genome and 42 currently have no described role in bone. However, many of the proteins encoded by the known and unknown genes have reported interactions. Functional enrichment analyses revealed that the differentially expressed genes were overrepresented in progresses regulating the extracellular matrix and pathways known to be involved in bone remodelling and bone diseases. Gene set enrichment analysis also detected numerous biological processes and pathways involved in glycolysis that had a higher expression in the iPSC-osteoblasts from horses with low polygenic risk scores for fracture.Therefore, the differentially expressed genes may be relevant for maintaining bone homeostasis and contribute to fracture risk. A deeper understanding of the consequences of mis-regulation of these genes and the identification of the DNA variants which underpin their differential expression may reveal more about the molecular mechanisms which are involved in equine bone health and fracture risk.

overall_design: Skin fibroblasts that were used in this study had previously been scored for their polygenic risk for fracture and were selected to represent horses with low and high risk scores. Equine iPSC clones were derived in either duplicate or triplicate for each sample and have previously been characterized for their ability to form embryoid bodies, express pluripotency markers, and differentiate into derivatives of endoderm, ectoderm and mesoderm. All of the iPSC lines used in this study were differentiated into osteoblasts capable of producing a mineralised matrix and expressing osteoblast associated genes. RNA-sequencing was performed on 14 lines of iPSC-osteoblasts derived from six different horses (three with a low PRS (L1-3) and three with a high PRS (H1-H3) for fracture).

last: Lago

first: Deborah

last: Guest

first: Amy

middle: C

last: Ross

first: Alyce

last: McClellan


title: Variation in Bile Acid Synthesis Capacity: A Key Factor in Differentiating Lipid Deposition Patterns in Goldfish Breeds

city: YangZhou

first: Jianqiao

address: 48 Wenhui East Road

institute: Yangzhou University

summary: In our previous study, we observed distinct lipid deposition pattern between Crane-top red goldfish (HDH) and Pearl-scale goldfish (PS), yet the regulatory mechanisms remained unclear. In this study, a comprehensive comparison between HDH and PS was conducted to elucidate the mechanisms driving this difference. Our findings revealed that the hepatopancreas lipid content, as well as the levels of triglyceride and total cholesterol, were significantly higher in HDH than in PS. Conversely, the total bile acid level was significantly higher in PS than in HDH. Transcriptome and proteome analysis identified 3174 differentially expressed genes (DEGs) and 816 differentially expressed proteins (DEPs) between HDH and PS, respectively, which were primarily enriched in pathways associated with PPAR signaling, primary bile acid biosynthesis, steroid hormone biosynthesis, Taurine metabolism, and carbohydrate digestion and absorption. Notably, DEGs and DEPs related to bile acid synthesis were found to play a key role in the observed difference between HDH and PS. Specifically, the CYP27A1 gene and EBP, MSMO1, CYP7B1, and HSD3B7 proteins were up-regulated in PS goldfish, indicating an enhanced bile acid synthesis capacity. Additionally, the abundance of Cetobacterium, which is closely associated with host lipid deposition, was significantly higher in PS intestine than in HDH.

overall_design: To unravel the mechanisms underlying the differences in lipid deposition patterns between Crane-top red goldfish (HDH) and Pearl-scale goldfish (PS), the hepatopancreas of HDH and PS was analyzed transcriptomically.

first: Xiaojing

last: Dong

first: Xuedi

last: Du


title: Modeling and drug targeting of a myeloid neoplasm with atypical 3q26/MECOM rearrangement using patient-specific iPSCs [RNA-seq]

city: Kyoto

first: Yoshinori

last: Yoshida

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

institute: Kyoto University

summary: Structural variations involving enhancer hijacking induce aberrant oncogene expression and cause tumorigenesis. A rare translocation, t(3;8)(q26.2;q24), is associated with MECOM and MYC rearrangement, resulting in dismal prognosis. The most recent World Health Organization classification recognizes myeloid neoplasms with MECOM rearrangement as acute myeloid leukemia (AML) with defining genetic abnormalities. To date, patient-derived induced pluripotent stem cell (iPSC) models have helped elucidate the pathogenic processes of human diseases and serve as a valuable platform for drug discovery. However, their utility in cancer biology remains unclear. In this study, we generated iPSC lines from patients with myelodysplastic syndromes (MDS) harboring t(3;8)(q26.2;q24) and differentiated them into hematopoietic progenitor cells to model the pathophysiology of MDS with t(3;8)(q26.2;q24). Our iPSC model reproduced the primary patient's MECOM expression changes and histone H3 lysine 27 acetylation (H3K27ac) patterns in MECOM promoter/enhancer and MYC blood enhancer cluster (BENC). Notably, MDS-iPSCs exhibited H3K27ac activation at the MECOM promoter, even in the pluripotent state, with higher MECOM expression than control iPSCs, indicating that the aberrant histone acetylation of MDS cells could not be completely reset after reprogramming. Furthermore, we revealed the apoptotic effects of the bromodomain and extra-terminal motif (BET) inhibitor JQ1 on iPSC-derived MDS cells by suppressing activated MECOM, suggesting BET inhibitors as potential novel therapeutic drugs for MDS/AML carrying t(3;8)(q26.2;q24). Our study demonstrates the usefulness of iPSC models for uncovering the precise mechanism of enhancer hijacking due to chromosomal structural changes and discovering potential therapeutic drug candidates for cancer treatment.

overall_design: We generated iPSC lines derived from MDS clones and iPSC lines derived from normal T cells of a patient with t(3;8)(q26.2;q24). Two groups were compared: Isogenic normal iPSC-derived HPCs (n=3) and MDS-iPSC-derived HPCs (n=3).

first: Momoko

last: Nakamura

first: Kazuhisa

last: Chonabayashi

first: Megumi

last: Narita

first: Yasuko

last: Matsumura


title: RAD51 knockout in murine liver (11-week)

city: Suzhou

first: Changshun

last: Shao

state: Jiangsu

address: No.199 Renai Road

department: Institute for Translational Medicine

institute: Soochow University

summary: RAD51 is a highly conserved DNA repair protein and is indispensable for the execution of homologous recombination, thereby participating in maintaining genomic stability. Since constitutive Rad51 knockout mice exhibit embryonic lethality, the physiological functions of RAD51, and the consequences of lacking it, are largely unknown. We herein demonstrated a critical role of RAD51 in postnatal liver development and regeneration. RAD51 is highly expressed during liver development and during regeneration following hepatectomy and hepatic injury, and is also elevated in liver-related diseases. We generated hepatocyte-specific Rad51 deletion mouse model (Rad51-CKO) to evaluate the function of RAD51 in liver development and regeneration.RAD51 deletion in postnatal hepatocytes results in aborted mitosis, global polyploidization, oxidative stress and cellular senescence. Remarkable liver fibrosis occurs as early as in 3-month-old Rad51fl/fl; Alb-Cre+/+ mice.The senescence-associated secretory phenotype in the livers of Rad51-CKO mice creates a niche that favors the activation and propagation of hepatic progenitor cells (HPCs) in which Rad51 is spared due to lack of Alb-Cre expression. The Rad51 functional HPCs and immature hepatocytes can thus proliferate vigorously, acquire increased malignancy, and eventually give rise to HCC. Our results thus demonstrate a novel function of RAD51 in liver development, homeostasis and tumorigenesis. The RAD51-CKO mice represent a unique genetic model for premature liver senescence, fibrosis, impaired regeneration and hepatocellular carcinogenesis.

overall_design: Liver tissue samples taken from three independent hepatocyte-specific Rad51 deletion mice and three wild-type  littermate controls (11-week-old) were used for RNA-Seq.

first: Wenqing

last: Bu


title: Asxl1 mutation enhances differentiation in CSF3R-mutated myeloproliferative neoplasms [Cut & Tag]

first: Julia

last: Maxson

overall_design: CUT and TAG against H3K4me1, H3K27me3, H2AK119ub in HoxB8 cells CRISPR modified for Asxl1 truncation and overexpression of CSF3R T618I mutation, each single mutation and control.

first: Lucie

last: Darmusey

first: Anna

last: Bagley

first: Thai

last: Nguyen


title: Differential transcriptomic profile of Piscirickettsia salmonis LF-89 and EM-90 during an in vivo spatial separation co-culture in Atlantic salmon

city: Ås

first: Gabriela

last: Carril

address: Oluf Thesens vei 30

country: Norway

institute: Norwegian University of Life Sciences

summary: Salmonid Rickettsial Syndrome (SRS), caused by Piscirickettsia salmonis, is the most important disease in the Chilean aquaculture industry since it induces the highest mortality rates among infectious diseases. P. salmonis is a facultative intracellular bacterium comprising two genetically distinct groups (LF-89 and EM-90) in Chile. Previous data suggest that their cohabitation triggers the expression of virulence effectors, which could be related to a higher pathogenicity in salmon during a co-infection. Therefore, we evaluated whether the physical contact between two isolates from LF-89 and EM-90 was needed to activate this effect. Through a spatially separated in vivo co-culture inside Atlantic salmon followed by RNA-seq analysis, we compared the differential expressed genes (DEGs) with our previous results from an in vivo mixed co-culture. Data showed that LF-89 presented a similar virulence factor profile compared to the mixed co-culture. In contrast, EM-90 had more downregulated DEGs and the flagellar-related genes observed during mixed co-culture were absent. Hence, the synergistic effect related to increased pathogenicity to the host may be driven by the physical co-localization of both LF-89 and EM-90 P. salmonis isolates.

overall_design:
To investigate the transcriptomic changes of P. salmonis in spatially separated co-cultures compared to mixed co-cultures of P. salmonis EM-90 and LF-89, we inserted dialysis bags with the bacterial cultures inside Atlantic salmon for 6 days. Then extracted the total RNA to perform an RNA-seq analysis comparing the transcriptomics profiles of both types of co-cultures

The GSM7508520-GSM7508522 (in GSE235725/PRJNA987513) raw data are being re-analyzed in the current study and the resulting processed data files are linked as Series supplementary files:

Sample Accns SRA Experiment   BioSample  processed_data_files
GSM7508520  SRX20775587  SAMN35982295  Sample_10_7-*.counts
GSM7508521  SRX20775588  SAMN35982294  Sample_11_8-*.counts
GSM7508522  SRX20775589  SAMN35982293  Sample_12_9-*.counts

first: Henning

last: Sørum


title: Exercise-induced methylation of the Serhl2 promoter and implication for lipid metabolism in rat skeletal muscle

city: Stockholm

first: Mutsumi

last: Katayama

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: DNA methylation is an epigenetic mark that influences cell programming and function. Environmental factors such as physical activity alter DNA methylation, with exercise-responsive methylation changes in various tissues including skeletal muscle.

overall_design: We used whole-genome methylated DNA immunoprecipitation (MeDIP) sequencing to determine the skeletal muscle DNA methylation signature in response to endurance swim training.

last: Krook

first: Juleen

middle: R

last: Zierath


title: Modeling and drug targeting of a myeloid neoplasm with atypical 3q26/MECOM rearrangement using patient-specific iPSCs


title: RAD51 knockout in murine liver (4-week)

overall_design: Liver tissue samples taken from three independent hepatocyte-specific Rad51 deletion mice and three wild-type (WT) littermate controls (4-week-old) were used for RNA-Seq.


title: Transcriptional profiling of mouse embryonic fibroblasts harboring the Fxn G127V mutation

city: Dallas

first: Marek

last: Napierala

state: TX

address: Marek Napierala

institute: University of Texas Southwestern Medical Center

summary: Friedreich's ataxia (FRDA) is a neurodegenerative disease caused by mutations in the frataxin (FXN) gene.  In this study, we immortalized mouse embryonic fibroblasts (MEFs) derived from G127V Fxn mutant mice and compared them to the wild-type (WT) MEFs. Mutant G127V MEFs demonstrated decreased cell proliferation and ATP production, as well as an increase in reactive oxygen species (ROS) production when compared to WT cells. These phenotypes are partially corrected by exogenous expression of frataxin. Surprisingly, extended passaging of immortalized G127V Fxn MEFs improves their proliferation, and alleviates ATP deficiency as well as decreases ROS levels despite persistent frataxin deficiency. We defined gene expression changes associated with phenotypic adaptation of G127V mutant MEFs by comparing transcriptional profiles of early and late passage G127V MEFs with WT cells.

overall_design: To investigate the molecular mechanisms underlying phenotypic adaptation associated with extended passages of immortalized mutant G127V MEFs, we purified RNA from WT (passage 8, WT17_P8 and WT18_P8), early passage mutant G127V (passage 6, Mut4Z_P6 and passage 9, Mut3J_P9) and late passage G127V (passage 19, Mut4Z_P19 and passage 26,  Mut3J_P26) MEFs. The extracted total RNAs from each sample were processed for transcriptome sequencing.

first: Shibani

last: Mukherjee

first: Achisha

last: Saikia

first: Jixue

last: Li

first: Larisa

last: Pereboeva

first: Daniel

last: Fil

first: Robert

last: Wilson

first: Maria

last: Grazia Cotticelli

first: Jill


title: 5G2 Mutant Mice Model Loss of a Commonly Deleted Segment of Chromosome 7q22  in  Myeloid Malignancies

city: Memphis

first: Michael

last: Walsh

address: 262 Danny Thomas

institute: St Jude Children's Research Hospital

summary: Monosomy 7 and del(7q) are among the most common and poorly understood genetic alterations in myelodysplastic neoplasms and acute myeloid leukemia. Chromosome band 7q22 is a minimally deleted segment in myeloid malignancies with a del(7q). However, the rarity of “second hit” mutations supports the idea that del(7q22) represents a contiguous gene syndrome. We generated mice harboring a 1.5 Mb germline deletion of chromosome band 5G2 syntenic to human 7q22 that removes Cux1 and 27 additional genes. Hematopoiesis is perturbed in 5G2+/del mice but they do not spontaneously develop hematologic disease. Whereas alkylator exposure modestly accelerated tumor development, the 5G2 deletion did not cooperate with KrasG12D, NrasG12D, or the MOL4070LTR retrovirus in leukemogenesis. 5G2+/del mice are a novel platform for interrogating the role of hemopoietic stem cell attrition/stress, cooperating mutations, genotoxins, and inflammation in myeloid malignancies characterized by monosomy 7/del(7q).

overall_design: RNA-seq analysis of mouse (HSCs) with or without deletions in chromosome band 5G2 (syntenic to human 7q22)

first: Tamara

last: Westover

first: Jeffery

last: Klco

first: Kevin

last: Shannon


title: Expression profiling of microRNAs enriched in small extracellular vesicles isolated from bone marrow plasma of patients with multiple myeloma, extramedullary disease, and plasma cell leukemia

city: Brno

first: Monika

last: Vlachová

address: Kamenice 753/5

country: Czech Republic

institute: Masaryk University

type: Non-coding RNA profiling by high throughput sequencing

summary: Multiple myeloma is a plasma cell malignancy characterized by the abnormal increase of monoclonal immunoglobulins. Despite great treatment advances, there are still patients experiencing migration of tumor cells from the bone marrow and progression of the disease into its aggressive forms including extramedullary disease or plasma cell leukemia. Although the exact molecular mechanisms are not known, several studies have confirmed the involvement of small extracellular vesicles-enriched microRNAs in multiple myeloma progression. Thus, we have performed the expression profiling of these molecules in bone marrow plasma of patients with multiple myeloma, extramedullary disease, and plasma cell leukemia using next-generation sequencing with the aim to identify new molecules involved in the disease pathogenesis. In total, 42 microRNAs were wound to be significantly deregulated among analyzed subgroups. The independent validation by RT-qPCR confirmed the elevated levels of miR-140-3p, miR-584-5p, miR-191-5p, and miR-143-3p in patients with multiple myeloma compared to extramedullary disease and/or plasma cell leukemia. Subsequent statistical analysis proved several significant correlations between clinical characteristics or flow cytometry parameters of patients and microRNAs’ expression. In addition, low levels of miR 140 3p, miR-191-5p, miR-744-5p, and miR-143-3p were associated with worse overall survival. These results indicate that deregulation of microRNAs could contribute to multiple myeloma progression. Nevertheless, the exact mechanisms have yet to be clarified.

overall_design: Expression miRNA (isolated from EVs) profile of multiple myeloma, extramedullary disease and plasma cell leukemia patients.


title: Coordination between transcriptional orientation and nucleoprotein complexes generate chromatin configuration of IgH locus [HiChIP]

city: Baltimore

first: Xiang

last: Qiu

address: 251 Bayview Blvd.

institute: National Institutes of Health

summary: In this study we combined epigenetic, transcriptional and recombinational assays of wild type and mutated Igh alleles to uncover structure function relationships between sequences that configure the locus for the first step of gene assembly.

overall_design: Chromatin struture of different pro-B cells

first: Fei

last: Ma

first: Noah

last: Ollikainen

first: Christopher

last: Dunn

first: Hansen

last: Du

first: Fatima

middle: Z

last: Braikia

first: Nina

last: Cui

first: Haley

last: Bianchi

first: Cuong

last: Nguyen

first: Jinshui

last: Fan

first: Supriyo

last: De

first: Ranjan

last: Sen


title: Quantitative Proteomics Identifies Profilin-1 as a Pseudouridine-Binding Protein

city: RIVERSIDE

first: Yinsheng

last: Wang

state: CA

address: 900 University Ave

department: Chemistry

institute: University of California, Riverside

summary: Pseudouridine (Ψ) is the most abundant RNA modification in nature; however, the exact biological functions of Ψ remain largely elusive. By employing an unbiased quantitative proteomics method, we identified multiple candidate reader proteins of Ψ in RNA, including a cytoskeleton protein profilin-1, whose mutations are linked with amyotrophic lateral sclerosis (ALS). We purified recombinant PFN1 and showed that it can bind directly and selectively to Ψ-containing RNA. We also found that PFN1 binds to thousands of transcripts in human cells, including a known Ψ site in the mRNA of TPI1. We showed that PFN1-Ψ interaction is crucial for regulating the stability and translation efficiency of TPI1 mRNA. Together, our data unveiled PFN1 as a reader protein of Ψ in RNA and illustrated the functions of PFN1-Ψ interaction in modulating the stability and translation efficiency of TPI1 mRNA, which provides new insights into the functions of Ψ in RNA biology and lays a strong foundation for the discovery of new mechanisms in disease pathogenesis

overall_design: Transcriptome-wide profiling analysis of FLAG-PFN1 in HEK293T cells

first: Songbo

last: Wei

first: Xiaoxia

last: Dai

first: Jun

last: Yuan

first: Shiyang

last: He

first: Kriti

last: Shah

first: Shiyuan

last: Guo

first: Zheng

last: Duan

first: Jernej

last: Murn


title: Coordination between transcriptional orientation and nucleoprotein complexes generate chromatin configuration of IgH locus [ChIP-Seq]

first: Xiang

last: Qiu

overall_design: ChIP-seq in different pro-B cells

first: Fei

last: Ma

first: Noah

last: Ollikainen

first: Christopher

last: Dunn

first: Hansen

last: Du


title: Modeling and drug targeting of a myeloid neoplasm with atypical 3q26/MECOM rearrangement using patient-specific iPSCs [ChIP-seq]

first: Yoshinori

last: Yoshida

summary: Structural variations involving enhancer hijacking induce aberrant oncogene expression and cause tumorigenesis. A rare translocation, t(3;8)(q26.2;q24), is associated with MECOM and MYC rearrangement, causing myeloid neoplasms with a dismal prognosis. The most recent World Health Organization classification recognises myeloid neoplasms with MECOM rearrangement as acute myeloid leukaemia (AML) with defining genetic abnormalities. Recently, the increasing use of induced pluripotent stem cell (iPSC) technology has helped elucidate the pathogenic processes of haematologic malignancies. However, its utility for investigating enhancer hijacking in myeloid neoplasms remains unclear. In this study, we generated iPSC lines from patients with myelodysplastic syndromes (MDS) harbouring t(3;8)(q26.2;q24) and differentiated them into haematopoietic progenitor cells to model the pathophysiology of MDS with t(3;8)(q26.2;q24). Our iPSC model reproduced the primary patient's MECOM expression changes and histone H3 lysine 27 acetylation (H3K27ac) patterns in the MECOM promoter and MYC blood enhancer cluster (BENC). Furthermore, we revealed the apoptotic effects of the bromodomain and extra-terminal motif (BET) inhibitor on iPSC-derived MDS cells by suppressing activated MECOM. Our study demonstrates the usefulness of iPSC models for uncovering the precise mechanism of enhancer hijacking due to chromosomal structural changes and discovering potential therapeutic drug candidates for cancer treatment.

overall_design: Chromatin Immunoprecipitation DNA-sequencing (CHIP-seq) for H3K27ac in iPSCs, HPCs derived from iPSCs, Patient HPCs, and K562.

first: Momoko

last: Nakamura

first: Kazuhisa

last: Chonabayashi

first: Megumi

last: Narita

first: Yasuko

last: Matsumura


title: Effects of the soil treatment with a corn gluten-derived protein hydrolysate on table grape berry transcriptome

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

summary: Protein hydrolysate (PH)-based biostimulants offer a cost-effective and sustainable approach for regulating physiological processes in plants to stimulate growth and improve quality characteristics and stress tolerance. The effectiveness of treatments using different categories of biostimulants on grapevine growth and development has been well-documented for foliar applications compared to soil applications. Considering table grapes, colour is an important quality trait that can be modulated by vineyard practice, including fertilization. In this context, we have evaluated the effects of an environmentally friendly biostimulant, a protein hydrolysate derived from corn gluten, on the berry developmental process of the Black magic table grape. When applied to the soil at veraison, the biostimulant increased the cluster weight, berry diameter, and colour just 14 days after application. The transcriptome analysis of berries carried out at the same sampling time point underlined that the treatment speeds up the ripening process.

overall_design:
To evaluate the effects of the treatment with a corn gluten-derived protein hydrolysate (GDPH, SURNAN®) on berry ripening, we applied veraison the products by ferti-irrigation to Black magic vines. As a control, we applied urea in the same mode (46% N) in a quantity to apply the same dose of nitrogen (N) applied with the protein hydrolysates (1.25 kg ha-1). The experiment was organized by a randomized complete block design comprising four plots (biological replicates) for each treatment. Each plot contained 7 vines. RNAseq analysis was carried out with a pool of berries sampled after 14 days from the 7 plants for three out of the four plots (biological replicates).
We sampled the berries after 14 days of treatment and we identified the by RNAseq analysis the differentially expressed transcripts between the berries of plants treated with the protein hydrolysates and the control plants.

first: Marika

last: Peli

first: Stefano

last: Ambrosini

first: Zeno

last: Varanini

first: Daniela

last: Sorio

first: Fabrizia

last: Pasquarelli


title: Coordination between transcriptional orientation and nucleoprotein complexes generate chromatin configuration of IgH locus

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

overall_design: Refer to individual Series


title: Coordination between transcriptional orientation and nucleoprotein complexes generate chromatin configuration of IgH locus [Directional RNA-Seq]

overall_design: RNA-seq of different pro-B cells

first: Fatima

last: Braikia

first: Nina

last: Cui

first: Haley

last: Bianchi

first: Cuong

last: Nguyen

first: Jinshui

last: Fan

first: Supriyo

last: De

first: Ranjan

last: Sen


title: Coordination between transcriptional orientation and nucleoprotein complexes generate chromatin configuration of IgH locus [Capture Hi-C]

first: Xiang

last: Qiu

overall_design: Chromatin structure of different pro-B cells

first: Fei

last: Ma

first: Noah

last: Ollikainen

first: Christopher

last: Dunn

first: Hansen

last: Du


title: Meningeal solitary fibrous tumor cell states phenocopy cerebral vascular development and homeostasis

city: San Francisco

first: David

last: Raleigh

address: 500 Parnassus

institute: UCSF

type: Methylation profiling by genome tiling array

summary: Meningeal solitary fibrous tumors (SFTs) are rare mesenchymal neoplasms that are associated with hematogenous metastasis, and the cell states and spatial transcriptomic architecture of SFTs are unknown. Here we use single-cell and spatial RNA sequencing to show SFTs are comprised of regionally distinct gene expression programs that resemble cerebral vascular development and homeostasis. Our results shed light on mechanisms underlying SFT biology in comparison to other central nervous system tumors and provide a framework for integrating single-cell and spatial transcriptomic data in human cancer samples.

overall_design: Genomic DNA underwent bisulfite conversion using the EZ DNA Methylation kit (Zymo Research, cat# D5004), followed by amplification, fragmentation, and hybridization to Infinium EPIC 850k Human DNA Methylation BeadChips (Illumina, cat# 20020530) according to manufacturer’s instructions at the Molecular Genomics Core at the University of Southern California (Los Angeles, CA). Bioinformatic analysis was performed in R (v4.2.1). DNA methylation data were preprocessed using the minifi pipeline (v1.47.0). In brief, probes were filtered and analyzed using normal-exponential out-of-band background correction, nonlinear dye bias correction, p-value with out-of-band array hybridization masking, and β value calculation (β=methylated/[methylated+unmethylated]).  Principal component analysis was performed on the β methylation values from minfi pre-processing pipeline in R. Variable probes were identified from the first three principal components (PCs). PCs greater than 4 contributed to less than 5% of β value variance. The top 2000 probes were selected for analysis by ranking the absolute gene loading score values within PCs and the tumors were projected along the first two PCs.

first: Kanish

last: Mirchia


title: 5-hydroxymethylated biomarkers in cell-free DNA predict occult colorectal cancer up to 36 months prior to diagnosis in the PLCO Cancer Screening Trial

city: Chicago

first: Xiaolong

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

summary: Purpose: Using the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial samples, we identified cell-free DNA (cfDNA) biomarker candidate genes bearing the epigenetic mark 5-hydroxymethylcytosine (5hmC) that detect occult colorectal cancer (CRC) up to 36 mo prior to clinical diagnosis. Methods: PLCO study subjects were matched by age, race, and sex as cases (n = 201, diagnosed with CRC within 36 mo of blood collection)  and controls (n = 402, no cancer diagnosis on follow-up, average 16.3 years after entering the study). Archived plasma samples (300 µL per study subject) were obtained from the National Cancer Institute (NCI), and we employed the sensitive 5hmC-Seal chemical labeling approach on 3 - 8 ng of extracted cfDNA. Following next-generation sequencing (NGS) and genome-wide mapping of 5hmC, we then conducted association studies and machine-learning modeling to analyze the genome-wide 5hmC profiles within training and validation groups that were randomly selected at a 2:1 ratio. Results: Robust genome-wide 5hmC profiles were successfully obtained from these decades-old samples. Association analyses using the Cox proportional hazards models suggested several epigenetic pathways relevant to CRC development distinguishing cases from controls. A weighted Cox model, comprised of 32-associated gene bodies, showed predictive detection value for CRC as early as 24-36 mo prior to overt tumor diagnosis. Furthermore, a trend for increased predictive power was observed for blood samples collected closer to CRC diagnosis. Notably, the 5hmC-based predictive model showed comparable performance regardless of sex and self-reported race/ethnicity, and significantly outperformed risk factors such as age and obesity assessed as BMI (body mass index).  Conclusion: An assay and machine learning modeling of 5hmC epigenetic signals on cfDNA revealed candidate biomarkers and a scoring algorithm with the potential to predict CRC occurrence despite the absence of clinical symptoms or the availability of effective predictors. Developing a minimally-invasive clinical assay that detects 5hmC-modified biomarkers holds promise for improving early CRC detection and ultimately patient outcomes. Future investigations to expand this strategy to prospectively collected samples are warranted.

overall_design:
To develop our biomarkers and prediction algorithm, we used samples obtained from the PLCO Cancer Screening Trial. Samples were taken from the intervention arm of the colorectal cancer study. "Cases" were defined as individuals who received a colorectal cancer diagnosis within 36 months of sample collection. "Controls" were defined as individuals who remained cancer-free until lost to follow-up. Cases were matched to Controls in a 1:2 case:control ratio and matched by age, sex, and race. Samples were provided with a masked identifier that was later unmasked to the our study team. NCI's Cancer Data Access System (CDAS) only permits that we provide the PLCO ID with the sequencing data; if GEO users wish to analyze the data, they will need to request information about the samples' case vs. control status and subject clinicodemographic information from CDAS.
Must contact NCI CDAS to unmask clinicopathologic characteristics

first: Diana

last: West-Szymanski

first: Zhou

last: Zhang

first: Xiao-Long

first: Krissana

last: Kowitwanich

first: Lu

last: Gao

first: Zifeng

last: Deng

first: Urszula

last: Dougherty

first: Craig

last: Williams

first: Shannon

last: Merkle

first: Matthew

last: Moore

first: Chuan

last: He

first: Wei

first: Marc

last: Bissonnette


title: FCRL4 and exhausted B cell signature in tumor infiltrating B cells from lung cancer

status: Public on Jan 21 2025

city: Moscow

first: Ekaterina

last: Serebrovskaya

address: Ostrovityanova st., 1

country: Russia

institute: Russian National Research Medical University

summary: Our understanding of the heterogeneity of tumor-infiltrating B cells (TIBs) evolves in parallel with the advances in high-dimensional flow cytometry and single-cell RNA sequencing (scRNA-seq). Subpopulations of TIBs have been described with diverse and even opposite roles in tumor control, based on surface molecule, cytokine and transcriptional factor expression. Furthermore, recently the predictive role of IgA and IgG expression in tumors was shown for melanoma and KRAS-mutated, but not KRAS wild type, lung adenocarcinoma. This may imply that B cells producing different immunoglobulin isotypes also acquire different functional characteristics that have unequal effects on tumor microenvironment (TME) and differentially affect tumor progression. To address this question, we performed comparative bulk transcriptome analysis of tumor-infiltrating surface-IgA+ (sIgA+) and sIgG+ memory B cells from lung adenocarcinoma (LUAD) tumors. We identified FCRL4, PDCD1 and RUNX2 among genes overexpressed in IgA+ B cells, which suggests exhausted, chronically antigen-stimulated phenotype. Using public scRNA-seq data, we showed that FCRL4-expressing memory TIBs form a distinct cluster of cells with transcriptomic profile characterized by upregulation of genes involved in IFNγ and IFNα responses. sIgG+ B cells, on the other hand, overexpress IL5RA, consistent with the role of IL-5 in class-switch recombination to IgG isotype. Moreover, based on the analysis of the TCGA LUAD cohort, we found that FCRL4 to CD20 expression ratio correlates with lower overall survival, further strengthening the view on FCRL4 as a marker of exhausted dysfunctional TIBs. Our findings support the initial hypothesis that IgA/IgG ratio in tumors is not merely an indication of cytokine environment in the TME, but also reflects the difference in the functional characteristics of the respective B cell populations.

overall_design: bulk RNA sequencing of sorted B cells from primary lung and renal cancer

last: Bryushkova

first: Evgeny

last: Shchoka

first: Daniil

last: Lukyanov

first: Marina

last: Gikalo

first: Dmitry

last: Chudakov


title: Premature neural differentiation in cerebral organoids derived from early-onset autism individuals in a birth cohort

city: Nanjing

first: Yuanlin

address: 101Longmian Avenue, Jiangning District

institute: Nanjing medical university

summary: Diversity clinical phenotypes of autism spectrum disorders (ASD), caused by heterogeneity of genetic and environmental factors, hampered the investigation in uncovering pathological mechanisms. Here we generated ASD patient-cerebral organoids from induced pluripotent stem cells (iPSCs) that reprogramed from the early-onset ASD individuals at around 2 years old with common clinical diagnosis in a prospective birth cohort, which was excluded typical autistic mutations and environmental exposures.

overall_design: The organoids were dissociated by trypLE (Life technology) into single cells. The cell debris and other aggregates were removed by an additional low-speed centrifugation. About 12,000 cells were captured and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 degrees Celsius for 45 min, followed by 85 degrees Celsius for 5 min and final hold at 4 degrees Celsius. cDNA was generated and then amplified, and quality was assessed using an Agilent2100. scRNA-seq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit V3 (10x Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 50000 reads per cell with a paired-end 150 bp (PE150) reading strategy.

first: Xiao

last: Han

first: Hao

last: Yuan

first: Yan

last: Liu


title: Gross transcriptomic analysis of Pseudomonas putida for diagnosing environmental shifts

city: Madrid

first: Ángeles

last: Hueso-Gil

state: Madrid

address: c/ Darwin 3

department: Systems Biology

country: Spain

institute: Centro Nacional de Biotecnología (CNB, CSIC)

summary: The biological regime of Pseudomonas putida (and any other bacterium) under given environmental conditions results from the hierarchical expression of sets of genes that become turned on and off in response to one or more physicochemical signals. In some cases, such signals are clearly defined, but in many others, cells are exposed to a whole variety of ill-defined inputs that occur simultaneously. Transcriptomic analyses of bacteria passed from a reference condition to a complex niche can thus expose both the type of signals that they experience during the transition and the functions involved in adaptation to the new scenario. In this article, we describe a complete protocol for generation of transcriptomes aimed at monitoring the physiological shift of P. putida between two divergent settings using as a simple case study the change between homogeneous, planktonic lifestyle in a liquid medium and growth on the surface of an agar plate. To this end, RNA was collected from P. putidaKT2440 cells at various times after growth in either condition, and the genome-wide transcriptional outputs were analysed. While the role of individual genes needs to be verified on a case-by-case basis, a gross inspection of the resulting profiles suggested cells that are cultured on solid media consistently had a higher translational and metabolic activity, stopped production of flagella and were conspicuously exposed to a strong oxidative stress. The herein described methodology is generally applicable to other circumstances for diagnosing lifestyle determinants of interest.

overall_design: 100 microL of an over night culture of Pseudomonas putida KT2440 was cultured in M9 minimal media supplemented with 0.2 % (v/w) citrate in the following conditions: 5 mL of liquid media during 6 hours, 12 hours or 24 hours incubation, and solid media (25 mL of 1.5% (v/w) agar plate) during 6 hours, 12 hours or 24 hours incubation. RNA was collected and sent for RNASeq service in two biological replicates per condition. Each time point ( 6, 12 and 24 hours) were used to contrast results for liquid and solid media in order to check what genes are transcribed differentially in cells exposed to a solid surface vs cells that live in a liquid media.

first: Belén

last: Calles

first: George

last: O'Toole

first: Víctor

last: de Lorenzo


title: Gene Expression Profiling of the hPheo1 Cell Line

city: Linköping

first: Mouna

last: Tababi

state: Östergötland

institute: Linköping University

summary:
We investigated the transcriptomic data generated from the hPheo1 cell line
We utilized microarrays to pinpoint distinct categories of genes that are either up-regulated or down-regulated, and to clarify the regulatory pathways in hPheo1 cell line.

overall_design: RNA was extracted from the hPheo1 cell line and hybridized using Affymetrix microarrays (HuGene-1_0-st-v1). Each group had three biological replicates

last: Tabebi

first: Oliver

last: Gimm

first: Peter

last: Söderkvist


title: Artificial Intelligence Prediction Across 12,000 Samples Shows Widespread Increased Gene-Gene Chromatin Interactions in Cancers that Constitute Therapeutic Vulnerabilities

city: Singapore

first: Fuying

last: Dao

address: 50 Nanyang Avenue

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Gene-gene chromatin interactions (GGIs) bring distal genes into close spatial proximity to permit strong co-expression, which could potentially contribute to cancer progression. High-throughput methods like Hi-C are impractical for very large cohort analyses, thus we developed AI4Loop, an Artificial Intelligence (AI) Deep Learning -based tool to predict GGIs using RNA-Seq data. Applying AI4Loop to 12,000 patient samples from The Cancer Genome Atlas (TCGA) database across 32 cancer types revealed that GGIs show increased cancer sub-type predictivity compared to RNA-Seq data and demonstrated oncogenic gains of GGIs in almost all cancers examined. To target the therapeutic vulnerability of gain of GGIs in cancers, using low-information RNA expression datasets from the CLUE database, we also constructed a drug-perturbation GGI atlas from 50,000 drug-treated samples to identify and repurposed compounds that disrupt oncogenic GGIs. Notably, we found that the antibiotics eperezolid and radezolid reduced cancer-acquired GGIs, which we confirmed with Hi-C experiment. This work showcases AI-directed research in epigenetics, enhances cancer biology predictivity and can promote wide-range drug repurposing in the future. This GEO submission contains the Hi-C data used to test the accuracy of AI4Loop when applied to compounds leading to loss of gene-gene interactions from the CLUE datasets.

overall_design: Hi-C, performed with the TOPO-Link Hi-C Kit from Dovetail in DMSO, Eperezolid, Radezolid, JQ1 and Trihexyphenidyl treated MCF7 cells for 8h

first: Benjamin

last: Lebeau

first: Prachi

last: Amuley

first: Wei Kit

last: Tan

first: Crystal Chia Yin

last: Ling

first: Kaijing

last: Chen

first: Xinya

last: Li

first: Chee Keong

last: Kwoh

last: Lin

last: Lv

first: Melissa Jane

last: Fullwood


title: The transcriptomic signature of age and sex is not conserved in human primary myocytes

city: Geelong

first: Séverine

last: Lamon

state: VIC

address: 1 Gheringhap St

department: School of Exercise and Nutrition Sciences

country: Australia

institute: Deakin University

summary: Human primary muscle cell (HPMC) lines derived from skeletal muscle biopsies are potentially powerful tools to interrogate the molecular pathways underlying fundamental muscle mechanisms. HPMCs retain their genome in culture, but many endogenous circulating factors are not present in the in vitro environment or at concentrations that do not mirror physiological levels. To address the assumption that HPMCs are valid models of age and sex-specificity in human muscle research, we examined to what extent HPMC lines maintain their source phenotypes in culture. A comparison of the transcriptomic signature of 30 human muscle biopsies (N = 10 young males, N = 10 young females, N = 10 old males) and their corresponding HPMCs indicated a near-complete lack of retention of the genes and pathways that were differentially regulated in vivo when compared to their in vitro equivalent, except for some genes encoded on the Y-chromosome. The diversity of the muscle cell population and the lack of sex- and age-dependent factors in the cellular milieu likely contribute to these observations, which call for caution when using HPMCs as an experimental model of human muscle sex or age. Nuclear single cell sequencing or HMPCs grown in 3D culture as organoids under strain might therefore provide a closer alternative to human muscle tissue.

overall_design: RNASeq profiling of human primary cell lines and tissue samples from the vastus lateralis muscle biopsies of 10 young males (ave age = 23.22), 10 older males (ave age = 67.50), and 10 young females (ave age = 26.90).

first: Megan

last: Soria

first: Ross

last: Williams

first: Annabel

last: Critchlow

first: Andrew

last: Garnham

first: Danielle

last: Hiam

first: Mark

last: Ziemann


title: Replication Protein A1 is essential for DNA damage repair during mammalian oogenesis

city: Amherst

first: Wei

last: Cui

state: Massachusetts

address: 240 Thatcher Road

institute: University of Massachusetts Amherst

summary: Persistence of unrepaired DNA damage in oocytes is detrimental and may cause genetic aberrations, miscarriage, and infertility. RPA, an ssDNA-binding complex, is essential for various DNA-related processes. Here we report that RPA plays a novel role in DNA damage repair during postnatal oocyte development after meiotic recombination. To investigate the role of RPA during oogenesis, we inactivated RPA1 (replication protein A1), the largest subunit of the heterotrimeric RPA complex, specifically in oocytes using two germline-specific Cre drivers (Ddx4-Cre and Zp3-Cre). We find that depletion of RPA1 leads to the disassembly of the RPA complex, as evidenced by the absence of RPA2 and RPA3 in RPA1-deficient oocytes. Strikingly, severe DNA damage occurs in RPA1-deficient germinal vesicle (GV)-stage oocytes. Loss of RPA in oocytes triggered the canonical DNA damage response mechanisms and pathways, such as activation of ATM, ATR, DNA-PK, and p53. In addition, the RPA deficiency causes chromosome misalignment at metaphase I and metaphase II stages of oocytes, which is consistent with altered transcript levels of genes involved in cytoskeleton organization in RPA1-deficient oocytes. Absence of the RPA complex in oocytes severely impairs folliculogenesis and leads to a significant reduction in oocyte number and female infertility. Our results demonstrate that RPA plays an unexpected role in DNA damage repair during mammalian folliculogenesis.

overall_design: Fully grown germinal vesicle (GV) oocytes were collected from PMSG-primed 4- to 5-week-old Control mice and Rpa1 oocyte-specific conditional knockout (OcKO) mice. Three biological replicates were prepared for each genotype (Control samples: 13, 14, 15; Rpa1 OcKO samples: 16, 17, 18) and each sample contained around 20 GV oocytes without any cumulus cells.


title: Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus

city: Shanghai

first: Dandan

last: Dong

address: 130 Dongan Road, Xuhui

institute: Fudan University Shanghai Cancer Center

summary: Genome wide association studies (GWASs) have identified numerous risk loci associated with prostate cancer, yet unraveling their functional significance remains elusive.  Leveraging our high-throughput SNPs-seq method, we pinpointed rs4519489 within the multi-ancestry GWAS-discovered 2p25 locus as a potential functional SNP due to its significant allelic differences in protein binding. Here, we conduct a comprehensive analysis of rs4519489 and its associated gene, NOL10, employing diverse cohort data and experimental models. Clinical findings reveal a synergistic effect between rs4519489 genotype and NOL10 expression on prostate cancer prognosis and severity. Through unbiased proteomics screening, we reveal that the risk allele A of rs4519489 exhibits enhanced binding to USF1, a novel oncogenic transcription factor (TF) implicated in prostate cancer progression and prognosis, resulting in elevated NOL10 expression. Furthermore, we elucidate that NOL10 regulates cell cycle pathways, fostering prostate cancer progression. The concurrent expression of NOL10 and USF1 correlates with aggressive prostate cancer characteristics and poorer prognosis. Collectively, our study offers a robust strategy for functional SNP screening and TF identification through high-throughput SNPs-seq and unbiased proteomics, highlighting the rs4519489-USF1- NOL10 regulatory axis as a promising biomarker or therapeutic target for clinical diagnosis and treatment of prostate cancer.

overall_design: To examine the potential enhancer functionality of the rs4519489 region, we performed chromatin immunoprecipitation sequencing (ChIP-seq) experiments for epigenetic markers in various cell lines and clinical specimens. Expanding ChIP-seq to include histone modifications in both normal and tumor prostate tissues from the CPGEA cohort confirmed enhancer/promoter activity at rs4519489, reinforcing its functional gene regulatory role. Subsequently, to assess the impact of NOL10 or USF1 knockdown on downstream gene expression, we performed RNA sequencing analysis to identify differentially expressed genes (DEGs) in LNCaP,DU145,PC3, and 22Rv1 cells treated with shRNA or siRNA targeting NOL10 or USF1.


title: RNA-seq of control and DOPAC-treated CD8+ T cells in vitro

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

summary: To investigate the effect of DOPAC on CD8+ T cells function, CD8+ T cells were treated with DOPAC for bulk RNA sequcecing.

overall_design: CD8+ T cells were stimulated for 48 h with αCD3/αCD28 in the absence or presence of DOPAC

first: Penghu

last: Han

first: Shuzheng

last: Chu

first: Yatai

first: Shiyang

first: Detian

last: Yuan


title: Non-linear heterochronic scaling of neurogenesis for species-specific dosing of cortical excitatory subtypes

city: Tokyo

first: Ikuo

middle: K

last: Suzuki

address: Bunkyo-ku, Hongo7-3-1

institute: The University of Tokyo

summary: All animals have specialized brain structures with a neuronal composition optimized for their survival and adaptation. The mammals share the laminar structure of the cerebral cortex, where a certain repertoire of excitatory neuron subtypes is arranged in specific tangential layers. However, the quantitative balance of subtypes is highly specialized in each species due to unknown developmental mechanisms. It is of particular interest to understand how the relatively conserved process of mammalian corticogenesis is modified in each species to achieve an optimized neuronal composition. Here, we show that fine-tuning the temporal progression of neurogenesis is the critical mechanism of the species-specific neuronal repertoire through our comparative study of mouse and rat cortical excitatory neurogenesis. Clonal tracing of individual progenitors revealed that rats produce more deep layer (DL) subtypes than mice, but both species produce essentially the same number of upper layer (UL) neurons. Such subtype-specific dosage optimization is mediated by the selective expansion of the early neurogenetic window for DL production in rats, as revealed by our neuronal birthdating and single cell transcriptomics. We found that the temporal neurogenetic status of the progenitors is encoded, at least in part, by Ccnd1 expression, as evidenced by the precocious UL production upon Ccnd1 knockdown in the rat mid-neurogenetic phase, when significant expression is maintained at levels comparable to the earlier phase in mice. Collectively, these results suggest that the closely related rodents, mouse and rat, construct their cortical structure with specific neuronal composition through the pinpointed specialization in developmental progression while maintaining the basic framework of the inside-out sequence of cortical excitatory neurogenesis. This study used mice and rats, the most common laboratory mammals with a close evolutionary relationship, to reveal the detailed molecular and cellular mechanisms behind the fine-tuning of cell composition in the cerebral cortex. Such a detailed comparison dissected the specialized and unchanged processes of corticogenesis during the evolutionary divergence of the two species. This further provides insights into the evolvability and developmental constraints of mammalian corticogenesis.

overall_design: Primary cells derived from rat embryonic cerebral cortex

first: Yuki

last: Yamauchi

first: Xuanhao

last: Zhou

first: Merve

last: Bilgic

first: Shuto

last: Deguchi

first: Tomonori

last: Nakamura

first: Yusuke

last: Kishi

first: Kazuo

last: Emoto


title: The Carbohydrate-Active Enzymes (CAZymes) required for cellulose deconstruction in Cellvibrio japonicus are part of an efficient cellodextrin uptake system

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

summary: Microbial deconstruction of plant polysaccharides is important for environmental nutrient cycling, and bacteria proficient at this process have extensive suites of polysaccharide-specific enzymes. In the Gram-negative saprophyte Cellvibrio japonicus, genome annotation suggests that 17 genes are predicted to encode Carbohydrate-Active enZymes (CAZymes) with roles in cellulose degradation, however previous work suggested that only a subset of these genes is essential. Building upon that work, here we identify the required and minimally sufficient set of enzymes for complete degradation of cellulose using a combination of transcriptomics, gene deletion analysis, heterologous expression studies, and metabolite analysis. We identified six CAZyme-encoding required for cellulose deconstruction in C. japonicus, which are cel3B, cel5B, cel6A, lpmo10B, cbp2D, and cbp2E. These genes encode for a β-glucosidase, an endoglucanase, a cellbiohydrolase, a lytic polysaccharide mono-oxygenase, and two carbohydrate-binding proteins, respectively. These CAZyme-encoding genes are essential for growth using insoluble cellulose by C. japonicus, and sufficient using soluble cellulose when heterologously expressed in Escherichia coli. Moreover, during C. japonicus grow using insoluble cellulose we detected no cellodextrins in the medium, which suggests that cello-oligosaccharide uptake is highly efficient. RNAseq analysis corroborates these results, as we observed several genes significantly up-regulated during growth on cellulose that encode TonB-dependent and ABC transporters. Our revised model of cellulose utilization by C. japonicus suggests a greater importance for the Cbp2D and Cbp2E proteins than previously thought and that rapid cellodextrin update by C. japonicus is a mechanism to maximize the energetic return on investment for the production and secretion of CAZymes.

overall_design: RNAseq profiling of wild-type Cellvibrio japonicus grown using insoluble filter paper under biomass containment with sampling during exponential growth and during stationary phase


title: Mapping cell-cell fusion at single-cell resolution

city: Austin

first: Amy

last: Brock

state: Texas

address: 107 W Dean Keeton St.

department: Biomedical Engineering

institute: The University of Texas at Austin

summary: Cell-cell fusion is a tightly controlled process in the human body known to be involved in fertilization, placental development, muscle growth, bone remodeling, and viral response. Fusion between cancer cells results first in a whole-genome doubled state, which may be followed by the generation of aneuploidies; these genomic alterations are known drivers of tumor evolution. The role of cell-cell fusion in cancer progression and treatment response has been understudied due to limited experimental systems for tracking and analyzing individual fusion events. To meet this need, we developed a molecular toolkit to map the origins and outcomes of individual cell fusion events within a tumor cell population. This platform, ClonMapper Duo (‘CMDuo’), identifies cells that have undergone cell-cell fusion through a combination of reporter expression and engineered fluorescence-associated index sequences paired to random barcode sets. scRNA-seq of the indexed barcodes enables the mapping of each set of parental cells and fusion progeny throughout the cell population. In triple negative breast cancer cells CMDuo uncovered subclonal transcriptomic hybridization and unveiled distinct cell-states which arise in direct consequence of homotypic cell-cell fusion. CMDuo is a platform that enables mapping of cell-cell fusion events in high-throughput single cell data and enables the study of cell fusion in disease progression and therapeutic response.

overall_design: scRNA-seq and targeted barcode sequencing for a longitudinal study on cell-cell fusion in HCC1806 and MDA-MB-231 cells. For each cell line, there is 1 'initial' population replicate, 4 replicates before flourescence-activated cell sorting to enrich for fusion or control cells ('pre-sort'), 4 replicates for the final enriched fusion populations ('fusion-enriched'), and 4 replicates for final parallel sorted controls ('ctrl').

first: Andrea

middle: L

first: Lan

last: Zheng

first: Kennedy

last: Howland

first: Andrew

last: Saunders

last: Ramirez

first: Patrik

last: Parker

first: Chisom

last: Iloegbunam

first: Daylin

last: Morgan

first: Tyler

last: Jost


title: Gene expression profiling of clear cell renal cell carcinoma with sarcomatoid transformation

city: Kuala Lumpur

first: Retnagowri

last: Rajandram

address: University of Malaya

country: Malaysia

institute: University of Malaya

summary: Renal cell carcinoma (RCC) with sarcomatoid transformation features a biphasic tumour with both sarcomatoid and carcinomatous components. Clear cell RCC (ccRCC) is the most common RCC subtype, frequently exhibits sarcomatoid transformation. The pathogenesis of sarcomatoid ccRCC remains unclear. This study aimed to identify the genes and pathways involved in sarcomatoid ccRCC using gene expression profiling. We analysed three distinct regions including sarcomatoid component, clear cell component and matched normal kidney tissue from formalin-fixed, paraffin-embedded (FFPE) tissue samples of four patients. RNA was extracted and gene expression profiles were analysed using the NanoString nCounter® PanCancer Pathways Panel on the NanoString nCounter® Analysis System. Data analysis was performed using NanoString nSolver™ Analysis Software. Significant gene expression differences were defined with a threshold of fold change ˃ 4 and P-value ˂ 0.05. Compared to normal kidney tissue, 17 genes were significantly different in the clear cell component, with 5 were upregulated and 12 downregulated. The most significantly upregulated and downregulated genes were GDF6 and SFRP1 respectively. In the sarcomatoid component, 85 genes showed differences, with 38 upregulated and 47 downregulated. COL11A1 and LRP2 were the most significantly overexpressed and underexpressed genes respectively. When comparing sarcomatoid component with clear cell component, there were 53 significantly dysregulated genes, including epithelial-mesenchymal transition markers such as MMP9 and FN1. Pathway analysis indicated that PI3K was the most frequently deregulated pathway in the sarcomatoid component, suggesting its role in sarcomatoid transformation. This study provides insights into the gene expression patterns in ccRCC with sarcomatoid transformation.

first: Yi

middle: X

last: Foong

first: Ning

middle: Y

last: Yap

first: Kein

last: Mun

first: Glenda

last: Gobe

first: Shanggar

last: Kuppusamy

first: Teng

last: Ong


title: KDM5C and KDM5D mutations have different and opposing consequences in ccRCC cells [Cut & Run]

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

institute: University Hospital Freiburg

summary: KDM5C is commonly mutated in ccRCC tumours in men but rarely in women. Introducing KDM5C mutation into two male and two female KDM5C wild type ccRCC cell lines caused different phenotypes and nonoverlapping transcriptional consequences, indicative of context-dependent functions of KDM5C. We identify that loss of the Y chromosome, harbouring the KDM5C homologue KDM5D, occurs in most male KDM5C mutant ccRCCs. Mutation of KDM5D in male 786-O cells prevented xenograft tumour formation and this phenotype was rescued by co-mutation of KDM5C. This unexpected antagonistic relationship between KDM5C and KDM5D is consistent with the co-occurrence of KDM5C mutation and loss of the Y chromosome in ccRCC. Transcriptional analyses showed that KDM5C and KDM5D regulate the expression of both overlapping as well as distinct sets of genes. Consistent with the tumour growth phenotype, KDM5D mutation induced the upregulation of putative tumour suppressor genes and downregulation of putative pro-proliferative genes. These transcriptional effects were also reversed by co-mutation of KDM5C. While KDM5C and KDM5D bind to at least some overlapping genomic sites, we identify that gene expression changes induced by KDM5C or KDM5D mutation are apparently unrelated to the direct functions of these proteins at the relevant gene promoters or enhancers. Our findings identify similarities and differences in KDM5C and KDM5D functions, challenging the idea that KDM5D in male cells functions equivalently to the second KDM5C allele in female cells, and implicate an interplay between KDM5C mutation and Y chromosome loss in ccRCC development in men.

overall_design: CUT&RUN-Seq for H3K4me1, H3K4me3, H3K27me3, H3K27ac, KDM5C, and KDM5D in human ccRCC cell lines with KDM5C, KDM5D, or KDM5C/KDM5D KO. IgG was used as a negative control. The experiments were performed in different sequencing runs, each with its own IgG control, as indicated by the file names. For exp1 and exp2, spike-in DNA from drosophila melanogaster was used. For exp3, spike-in DNA from E.coli was used.

first: Marvin

last: Müller

first: Kyra

last: Zodel

first: Behnaz

last: Abhari

first: Francesca

last: Cuomo

first: Sheikh

last: Nizamuddin

first: Melanie

last: Boerries

first: Marc

last: Timmers

first: Ian

last: Frew


title: KDM5C and KDM5D mutations have different and opposing consequences in ccRCC cells [RNASeq_double_KO]

overall_design: bulk RNA-Seq of human 786-O ccRCC cell line with KDM5C, KDM5D, or KDM5C/KDM5D KO


title: KDM5C and KDM5D mutations have different and opposing consequences in ccRCC cells [RNASeq_single_KO]

overall_design: bulk RNA-Seq of human ccRCC cell lines with KDM5C or KDM5D KO


title: Determinants of response to BLU-222, a potent and highly selective CDK2 inhibitor, in CCNE1-aberrant ovarian and endometrial tumors

city: Cambridge

first: Maxine

last: Chen

address: 45 Sidney St.

institute: Blueprint Medicines

summary: To further refine our understanding of BLU-222 response in the context of CCNE1, Rb, and p16 expression, we analyzed BLU-222 induced gene expression changes in 18 ovarian cancer cell lines. This panel of responders (GI50 ≤200 nM) and non-responders (GI50 >200 nM) included CCNE1-amplified, CCNE1 CN-increased, and CCNE1-normal cell lines. Each cell line was treated with BLU-222 at its proliferative GI50 and differential mRNA expression analysis between BLU-222 treated cells and DMSO treated cells was performed for each cell line to calculate mRNA expression fold change and identify significantly differentially expressed genes.

overall_design: 18 ovarian cancer cell lines dosed with BLU-222, a CDK2 inhibitor, at cell line IC-50 or DMSO (3 replicates each).  Collected 24hr post dose.


title: Mapping cell-cell fusion at single-cell resolution [scRNA-seq]

first: Amy

last: Brock

first: Andrea

last: Gardner

first: Lan

last: Zheng

first: Kennedy

last: Howland

first: Andrew

last: Saunders

last: Ramirez

first: Patrik

last: Parker

first: Chisom

last: Iloegbunam

first: Daylin

last: Morgan

first: Tyler

last: Jost


title: Heart-specific gene silencing via single-AAV-delivered base editing [Amplicon-Seq]

city: Beijing

first: zhanzhao

last: liu

address: No. 38, Xueyuan Road

institute: peking university

summary: We used an adenine base editor to target the translation start site and mRNA splicing site of Camk2d in order to knock out CaMKIIδ. We found that editing the 5' splice site of intron 7 can lead to premature translation termination, effectively knocking out CaMKIIδ.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We first designed 10 sgRNAs, transfected them into Neuro2a cells using plasmids. After 48 hours, we extracted DNA and performed amplicon sequencing to detect the editing efficiency of each sgRNA. Then, we delivered the top 3 sgRNAs with the highest editing efficiency using a single AAV vector into mice to evaluate the editing efficiency in the heart and the knockout effect of CaMKIIδ. Finally, we split the single AAV vector into dual AAV vectors and compared the editing efficiency in the mouse heart between single AAV and dual AAV under the same total AAV dosage.


title: Heart-specific gene silencing via single-AAV-delivered base editing [RNA-Seq]

overall_design: In order to investigate the impact of editing the 5' splice site of Camk2d intron 7 using an adenine base editor on mRNA expression, we designated the edited mice as the experimental group and the unedited mice as the control group. We compared the changes in RNA expression in the hearts of both groups using RNA-seq.


title: DEF6 regulates renal ischemia reperfusion injury through suppressing the WWP2 mediated ubiquitination of PARP1

city: Wuhan

first: Tao

last: Qiu

address: No. 238 Jiefang Road, Wuchang District, Wuhan, China

institute: Renmin Hospital of Wuhan University

summary: Background: Renal ischemia-reperfusion injury (RIRI) stands as an unavoidable complication arising from kidney surgery, profoundly intertwined with its prognosis. The role of differentially expressed in FDCP 6 homolog (DEF6) in RIRI remains elusive, despite its confirmation as a potential therapeutic target for diverse diseases. Here, we investigated the mechanism by which DEF6 regulated RIRI. Methods: RNA sequencing data and IP-MS were used to identify the expression and potential targets of DEF6 through bioinformatics analysis. To elucidate the impact of DEF6 on RIRI, both an in vivo model of RIRI in mice and an in vitro model of kidney cell hypoxia/reoxygenation were established. Biochemical and histological analyses were used to investigate the influence of DEF6 on kidney damage mediated by RIRI. Results: We confirmed that DEF6 was upregulated during RIRI and had a close correlation with RIRI-related inflammation and apoptosis. Moreover, inhibition of DEF6 could mitigate RIRI-induced kidney damage, inflammation, and apoptosis. Through our comprehensive mechanistic investigation, we revealed that DEF6 interacts with poly ADP-ribose polymerase 1 (PARP1) and suppresses the ubiquitination of PARP1. Inhibition of DEF6 resulted in reduced cleaveage of PARP1, leading to a marked suppression of PARP1-mediated apoptosis activation. The aggravation effect on inflammation and apoptosis achieved through DEF6 was nullified by the inhibition of NF-κB and Bax/Bcl2 signaling activation through PARP1 deletion. Conclusions: The findings from our study indicate that DEF6 suppressed the WWP2 mediated ubiquitination of PARP1 and modulates the activation of NF-κB and Bax/Bcl2 pathway, thus involved in RIRI-induced inflammation and apoptosis. These results suggest that DEF6 holds promise as a potential therapeutic target for mitigating RIRI.

overall_design: RNA-seq profiling of wildtype HK2 cells(named V76) and their overexpressed derivatives (DEF6-OE, named 2225-OE) of differentially expressed genes.

first: Haochong

last: Hu

first: Yiting

last: Liu

first: Shangting

last: Han

first: Jiayu

last: Guo

first: Jiangqiao

last: Zhou


title: Biosensor capability of the endometrium is mediated in part, by altered miRNA cargo from conceptus-derived extracellular vesicles

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

institute: University of Leeds

summary: We tested the hypothesis that the biosensor capability of the endometrium is mediated in part, by the effect of different cargo contained in the extracellular vesicles secreted by the conceptus during the peri-implantation period of pregnancy. We transferredBos taurus taurusembryos of different origin:In vivo(high developmental potential (IV)),in vitro(intermediate developmental potential (IVF)), or cloned (low developmental potential (NT)), intoBos taurus indicusrecipients. Extracellular vesicles (EVs) recovered from Day 16 conceptus conditioned medium were characterized and their microRNA (miRNA) cargo sequenced alongside RNA sequencing of their respective endometria. There were substantial differences in the endometrial response toin vivoVsin vitroandin vivoVs cloned conceptuses (1153 and 334DEGs respectively) with limited differences betweenin vitroVs cloned conceptuses (36 DEGs). miRNA cargo was similar between all three groups (426 common cargo) differences betweenin vivoand cloned (8 miRNAs), andin vivoandin vitro(6 miRNAs) observed. Treatment of endometrial epithelial cells with mimic or inhibitors for miR-128 and miR-1298 changes to the proteomic content of target cells (96, and 85 respectively) of which mRNAs are altered in the endometriumin vivo(PLXDC2, COPG1, HSPA12A, MCM5, TBL1XR1, and TTF). In conclusion, we have determined that the biosensor capability of the endometrium is mediated in part, by its response to different EVs miRNA cargo produced by the conceptus during the peri-implantation period of pregnancy.

overall_design: Endometrium from day 16 pregnant cattle (bos taurus indicus) underwent RNA sequencing. Extracellular vesicles secreted by day 16 bovine (bos taurus taurus) conceptuses for 6 hours in culture medium underwent small miRNA sequencing. Conceptuses were produced by either in vivo (artificial insemination), in vitro fertilisation (IVF), or nuclear transfer techniques.

first: Tiago

last: de Bem

first: Haidee

last: Tinning

first: Elton

last: Vasconcelos

first: Flavio

last: Meirelles

first: Niamh

last: Forde


title: Comparison of transcriptional profiles of human psoriatic skin and skin from K14-CreER/GPX4flox mouse model.

city: PITTSBURGH

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

summary: Transcriptional profile of full thickness skin or epidermis only obtained from K14-CreER+/+;GPX4flox mouse model vs K14-CreER-/-;GPX4flox controls is analyzed and compared to transcriptional profile of epidermis plus papillary dermis obtained from patient-matched lesional vs perilesional psoriatic skin.

overall_design:
GPX4 was selectively deleted in a subset of K14+ keratinocytes of 8-10 week-old B6.K14-CreER+/+;GPX4flox male and female mice using tamoxifen injections. On day 15-18 after the initiation of tamoxifen injections, either full thickness skin (epidermis and dermis, 3 mice per group) or epidermis only (3 mice per group) were harvested from K14-CreER+/+;GPX4flox mice and K14-CreER-/-;GPX4flox control mice, and used for RNA-sequencing. In addition, clinical specimens composed of epidermis and superficial dermis were obtained from three patients suffering from psoriasis. Specifically, 3 lesional (from 2 males, 1 female) and 3 patient-matched perilesional (located 8 mm from the active lesion) specimens were obtained from the back, thigh or leg, and used for RNA-sequencing.
NOTE FROM SUBMITTER: Due to privacy rules and logistics we will only be uploading the processed raw counts file for the human data.

first: Yuri

last: Bunimovich

first: Kavita

last: Vats


title: Single-nucleus chromatin accessibility profiling identifies cell types and functional variants contributing to major depression

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

summary: We performed high-throughput snATAC-seq using the 10X Genomics Chromium platform on archived post-mortem dorsolateral prefrontal cortex (BA9) tissue in MDD subjects who died by suicide and neurotypical control subjects to identify cell-type specific differentially accessible chromatin regions. We further combined snATAC-seq with previously generated snRNA-seq data from the same subjects to generate high-resolution multi-modal accessibility and expression atlas of cortical cells. This identified accessible chromatin regions potentially regulating expression of genes. Further, MDD-associated genetic risk variants were examined for their allele-specific effects on chromatin accessibility and transcription factors binding sites in cell type speciifc manner, elucdiating target risk genes and pathways associated with MDD.

overall_design: 10X Genomics Chromium snATAC-seq was performed on nuclei extracted from BA9 of the post-mortem brain tissue of 44 MDD cases who died by suicide and 40 neurotypical controls. We multiplexed nuclei obtained from a pair of male (n=42) and female (n=42) subjects before 10x microfluidic capture and produced combined libraries. These libraries were demultiplexed using common variants and sex-specific chromatin accessibility signals. Unsupervised clustering was perfomed using accessibility measured in 500bp bins and pseudobulk differential accessibility analysis was performed between cases and controls for each cluster and each broad brain cell type. The library preparation was performed with the Chromium Single Cell ATAC v1.1 Chemistry. Paired-end sequencing was performed on the Illumina NovaSeq 6000. FASTQ files were produced with 10x cellranger-atac mkfastq. Alignments were generated with refdata-cellranger-arc-GRCh38-2020-A-2.0.0 and cellranger-atac count. 10x fragment files were converted to peak count matrices using ArchR [release_1.0.1].

first: Anjali

last: Chawla

first: Corina

last: Nagy