title: Expression of the transcription factor ZBTB16 in porcine testes and molecular mechanisms for its regulation in porcine immature spermatogonia self-renewal [CUT&Tag]

city: 咸阳市

first: YouJie

last: Cui

state: 陕西省

address: 西北农林科技大学北校西南区

institute: 西北农林科技大学动物科技学院

summary: ZBTB16, a transcription factor, plays a critical role in the self-renewal and differentiation of mouse primordial germ cells. However, the subcellular localization of ZBTB16 in the porcine testis and its molecular mechanism in regulating the self-renewal of immature porcine germ cells remain unclear. Using immunofluorescence co-staining, we examined the subcellular localization of ZBTB16 and its co-localization with molecular markers for immature porcine germ cells (DBA, ZBTB16, UCHL1) and the proliferation marker Ki67 in the testes of pigs at 7, 30, 70, and 90 days of age. The results showed that ZBTB16-positive cells in the four age groups of pig testes highly overlapped with SALL4/UCHL1-positive cells and partially overlapped with DBA-positive cells, indicating that ZBTB16 is predominantly expressed in immature porcine germ cells, including pig primordial germ cells, spermatogonial stem cells, and undifferentiated spermatogonia. Furthermore, the immunofluorescence co-staining of ZBTB16 and Ki67 revealed that ZBTB16-positive cells in pig testes at different developmental stages exhibited proliferative activity, but with significant fluctuations. RNA-seq analysis identified 5931 differentially expressed genes in ZBTB16-knockdown immature porcine germ cells, while CUT&Tag analysis identified 5409 ZBTB16 target genes, with 2084 of them overlapping with the differentially expressed genes. ZBTB16 preferentially bound to gene promoters. Knockdown of ZBTB16 expression resulted in the suppression of mRNA levels of target genes involved in the self-renewal of immature germ cells. Additionally, we found that ZBTB16 regulates the self-renewal of immature porcine germ cells through the PI3K/AKT/mTOR pathway. These findings reveal the expression pattern of ZBTB16 in the porcine testis and its regulation of target genes and pathways involved in the self-renewal of immature germ cells. This contributes to the understanding of the function and regulatory network of the transcription factor ZBTB16 in porcine germ cell development and spermatogenesis, and holds significant implications for unraveling the molecular mechanisms underlying porcine germ cell development and sperm production.

overall_design:
Firstly, we plan to select porcine testicular tissues at 7, 30, 70, and 90 days of age for paraffin embedding. Immunofluorescence double staining will be conducted using molecular markers for undifferentiated germ cells, such as ZBTB16, SALL4, UCHL1, and DBA, to investigate the expression and localization of ZBTB16 in different age groups of porcine testes. Qualitative and quantitative analysis will be performed to determine the co-localization of ZBTB16 with other germ cell molecular markers.Next, primary porcine immature spermatogonia will be collected, and a library of ZBTB16-bound target genes in porcine immature spermatogonia will be established using ZBTB16 antibodies and CUT&Tag technology. Through systematic analysis of the sequencing results, ZBTB16-bound target genes in porcine immature spermatogonia will be identified, and their associated pathways will be predicted using bioinformatics software.Subsequently, siRNA sequences targeting the porcine Zbtb16 gene will be designed and synthesized. The efficiency of Zbtb16 knockdown will be evaluated by transfecting immortalized porcine immature spermatogonia lines and performing qPCR. The siRNA with the highest knockdown efficiency will be selected. The designed oligos will be packaged into lentiviruses, and primary porcine immature spermatogonia will be transduced with Zbtb16-shRNA using lentiviral transduction. RNA-seq analysis will then be performed.
Finally, the CUT&Tag data will be combined with the RNA-seq data for integrated analysis. Key genes and pathways related to the regulation of porcine immature spermatogonia self-renewal by ZBTB16 will be identified and experimentally validated. In addition, cross-species analysis will be conducted by downloading mouse ZBTB16 ChIP-seq and RNA-seq data to identify conserved and differential target genes and associated pathways regulated by ZBTB16 in mouse and porcine immature spermatogonia self-renewal.


title: Transcriptomic Analysis Reveals Distinct Strategies of Two Potato Cultivars Against Phytophthora infestans and Identifies StWRKY26 as a Positive Regulator of Late Blight Resistance

status: Public on Jun 30 2025

city: Chengdu

first: Ben

last: Ma

address: Huimin Street 211

country: China

institute: Sichuan Agricultural University

type: Expression profiling by high throughput sequencing

summary: Late blight caused by Phytophthora infestans seriously threatens world’s potato production. Understanding the responsive mechanism of potato to P. infestans infection and exploring key regulators would be advantageous for improving the late blight resistance. Here, we assess the late blight resistance of various potato cultivars from Liangshan Yi Autonomous Prefecture and identified Chuan Liang Shu 10 (CLS) with strong resistant, while Bu Wu Yu (BWY) is highly susceptible. Comparative transcriptomics between these two cultivars upon P. infestans inoculation reveal that CLS activates defense pathways rapidly, while BWY prioritizes energy towards growth and development pathways, resulting in distinct late blight resistances. Specifically, the resistance of CLS might be contributed by enhanced oxidation-reduction process and SA signaling. Clustering analysis of the expression patterns for transcription factors (TFs) demonstrates that the WRKY family members play important roles in late blight resistance of CLS, among which StWRKY26 is identified as a positive regulator of late blight resistance. Silencing of StWRKY26 in CLS significantly compromise its intrinsic resistance to P. infestans. Our study enriches the knowledge of transcriptional responses of potato under P. infestans infection and provide candidate genes for breeding potato cultivars with strong late blight resistance.

overall_design:
Two 'Solanum tuberosum L' Potato Cultivars Against Phytophthora infestans
Cultivars: CLS, WYY.
WYY and BWY are equivalent.

first: Jingye

last: Fu

first: Li

last: Zhu

first: Yuhan

last: Zhang

first: Yuxin

last: Li

first: Shuaibin

last: Tian

first: Luyao

last: Wang

first: Hongjiang

last: Liu

first: Guocheng

last: Wei

first: Liping

last: Yu

first: Changhe

first: Lang

last: Yan

first: Peihua

first: Yan

first: Yangmei

first: Xiyao

first: Qiang


title: Establishment and Validation of Immune-Related Genes Diagnostic Model in Autoimmune Thyroiditis Based on RNA-seq

city: Harbin

first: li

last: jia

state: Asia

address: No. 157, Health Care Road, Nangang District

institute: Harbin Medical University

summary: Our study used a cross-sectional survey as its foundation. Peripheral blood samples were taken from target subjects, which chosen by sampling. Ten cases were chosen as Training-set samples and eighty cases as Validation-set samples from all the samples. Following RNA sequencing (RNA-seq) of the Training-set samples, the result obtained was used as the Training-set to construct the diagnostic model. The Validation-set was made up of the model genes' expression in the Validation-set sample, which was detected by quantitative reverse transcription PCR (RT-qPCR). Utilizing bioinformatics technology, downloaded AIT sequencing datasets from the GEO database, combined and analyzed them to create the Test-set. Based on the Training-set, Validation-set, and Test-set, the diagnostic model's performance was thoroughly reviewed and assessed from a variety of angles. In addition to offering guidance for the diagnosis and prevention of AIT, which also effectively lowers the financial burden on patients and conserves scarce medical resources, this study may show the potential value of IRGs in the diagnosis of AIT to provide new insights for exploring the mechanism of AIT pathogenesis. It was anticipated that the diagnostic model will give researchers new tools for early prevention and diagnosis of AIT, help them identify populations with high risk efficiently, and support them in the hierarchical control of disease risk.

overall_design: The diagnostic model was constructed and internally verified using the sequencing results that served as the Training-set. Five healthy individuals were matched as the Control group based on age, gender, BMI and home place after selecting five representative AIT patients as the AIT group. Trizol extracted total RNA from peripheral blood of total ten samples. The RNA concentration was measured on NanoDrop 2000/2000C (Thermo Fisher Scientific, Waltham, MA, USA). These RNA samples were subsequently subjected to RNA-seq on the DNBSEQ platform following standard procedures (Bgi Genomics Co., Ltd, Shenzhen, China).

first: Jia

first: Xin

last: Hou

first: Meng

last: Zhao

first: Honglei

last: Xie

first: Yue

last: Su

first: Haowen

last: Pan

first: Zongyu

last: Yue

first: Zexu

first: Peng


title: Daunorubicin-induced T cell remodeling facilitates a high antitumor response to PD-1 blockade therapy by promoting the expansion and effector function of CD8+ prolifeating T cells [scRNA-Seq]

city: Shanghai

first: Qinlan

address: Chongqingnan R.280

institute: Shanghai Jiaotong University

summary: We showed that chemotherapy agent doxorubicin-pretreated CD8+ proliferating T cells had enhanced cytolytic activity against tumors after anti-PD-1 treatment in vitro. Doxorubicin-plus-anti-PD-1 treatment promoted the activation and expansion of endogenous tumor-reactive CD8+ proliferating T cells and efficiently suppressed tumor growth in multiple mice tumor models. The single-cell RNA-sequencing and TCR-sequencing demonstrated that doxorubicin-plus-anti-PD-1 combination altered the metabolic reprogramming and activation of CD8+ proliferating T cells and markedly elevated the clonally expansion and effector function of proliferating T cells as compared with anti-PD-1 monotherapy, presenting increased expression of genes associated with T cell activation, proliferation, cytolytic activity, memory and mitochondrial metabolism. Strikingly, doxorubicin-plus-anti-PD-1 combination promoted the expression and activity of T cell activation transcription factor Nfat, which was reduced following PD-1 blockade therapy. Together, our findings show that the novel chemoimmunotherapy remodels CD8+ proliferating T subset, improves responsiveness to anti-PD-1 therapy.

overall_design: Expression profiling by high throughput sequencing Transcripyional expression profiling by RNA sequencing

first: Jin


title: Effect of Daunorubicin on T cell activation [RNA-Seq]

summary: To determine the effect of DNR on T cell activation ,we treated T cells with DNR and analyzed their functions.

overall_design: Comparative gene expression profiling analysis of RNA-seq for T cells after treated with DNR.


title: Comprehensive analysis of Bulk RNA-seq and Single-nuclei RNA-seq reveals the origin of high-grade serous “ovarian” carcinoma [snRNA-seq]

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

summary: High grade serous ovarian cancer (HGSOC) is characterized by late stage, rapid progression, easy drug resistance, high mortality and recurrence rate.Tubal secretory cells have always been considered as the origin cells of HGSOC,due to the high heterogeneity of the latter,the type and mechanism of cell origin is poorly confirmed.Combined with single-nuclei RNA sequencing(snRNA-seq) and Bulk tissue transcriptome sequencing,we expounded the composition of epithelial cell subgroups of fallopian tubes and HGSOCs.

overall_design: We collected human cancer-free fallopian tubes from three perimenopausal women undergoing hysterectomy with bilateral salpingo-oophorectomy due to benign uterine diseases, sectioned them into infundibulum/fimbriae, ampulla, and isthmus based on morphology, then performed 10X genomics single-nucleus RNA-seq (snRNA-seq) analyses.Beside, we also collected 4 individual HGSOC(High-Grade Serous Ovarian Cancer) samples and performed 10X genomics single-nucleus RNA-seq (snRNA-seq) analyses

first: Wei


title: High expression of the structural maintenance of chromosomes 5/6 complex is associated with the positive prognosis and doxorubicin susceptibility of colon cancer

city: Jinan

first: Xiaoxia

last: Gong

state: Shandong

address: No. 6699 Qingdao, Huaiyin District

institute: Shandong First Medical University

summary: Despite the exponential growth in colon cancer publications, our understanding of the tumorigenesis and progression problem is still limited. This study manifested the structural maintenance of chromosomes 5/6 complex (SMC5/6 complex) may serve as a prospective and novel biomarker for molecular diagnosis and therapeutics in patients with colon cancer. Dyregulation of SMC5/6 components is revealed to be dramatically correlated with the poor prognosis. Besides, ectopic expression of SMC5/6 components obviously impaired proliferation and migration capacity of colon cancer cells in vitro, and leaded to a restraint of the xenografted tumor growth in vivo. Moreover, overexpressed SMC5/6 components helped to enhance the doxorubicin (DOX) susceptibility of colon cancer cells by promoting apoptosis. The purpose of this article is to explore the clinical significance and molecular mechanism of SMC5/6 complex in colon cancer.

overall_design: To analyze the biological mechanism of SMC5/6 complex that inhibit cell growth and promote DOX induced apoptosis, exon transcriptome sequencing (RNA-seq) of HCT116 with NSE4A and SMC5 overexpression were performed, as well as the vector-transfected (Con) HCT116 as the background value. HCT116 cells were transfected with the plasmid of vector, NSE4A-flag, and SMC5-flag respectively. 24 hours later, the transfected cells were divided into two portion, and one portion of cells were treated with DOX, while the other were not. The cells were cultured for 24 hours later, total RNA was extracted using Trizol reagent (Thermo Fisher, Waltham, MA, USA) according to the manufacturer`s instructions. Lastly, the concentration, quality and integrity of the total RNA were determined using a Nano Drop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). The total RNA that had a standard of concentration 200ng/ml, mass 10mg and RNA integrity number (RIN) 8.0 was subjected to RNA-seq. Different gene and transcript expression was analyzed used TopHat and Cufflinks according to the protocol of the software.

first: Hao


title: Pannexin 1 Channels Control Cardiomyocyte Metabolism and Neutrophil Recruitment During Non-Ischemic Heart Failure

city: Charlottesville

first: Caitlin

last: Pavelec

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

country: USA

institute: University of Virginia School of Medicine

summary: Pannexin 1 (PANX1), a ubiquitously expressed ATP release membrane channel, has been shown to play a role in inflammation, blood pressure regulation, and myocardial infarction. However, a possible role of PANX1 in cardiomyocytes in the progression of heart failure has not yet been investigated. We generated a novel mouse line with constitutive deletion of PANX1 in cardiomyocytes (Panx1MyHC6). PANX1 deletion in cardiomyocytes had no effect on unstressed heart function but increased the glycolytic metabolism and resulting glycolytic ATP production, with a concurrent decrease in oxidative phosphorylation, both in vivo and in vitro. In vitro, treatment of H9c2 cardiomyocytes with isoproterenol led to PANX1-dependent release of ATP and Yo-Pro-1 uptake, as assessed by pharmacological blockade with spironolactone and siRNA-mediated knock-down of PANX1. To investigate non-ischemic heart failure and the preceding cardiac hypertrophy we administered isoproterenol, and we demonstrate that Panx1MyHC6 mice were protected from systolic and diastolic left ventricle volume increases as a result of cardiomyocyte hypertrophy. Moreover, we found that Panx1MyHC6 mice showed decreased isoproterenol-induced recruitment of immune cells (CD45+), particularly neutrophils (CD11b+, Ly6g+), to the myocardium. Together these data demonstrate that PANX1 deficiency in cardiomyocytes increases glycolytic metabolism and protects against cardiac hypertrophy in non-ischemic heart failure at least in part by reducing immune cell recruitment. Our study implies PANX1 channel inhibition as a therapeutic approach to ameliorate cardiac dysfunction in heart failure patients.

overall_design: Isolation of cardiomyocyte or use of whole heart tissue from Panx1fl/fl or Panx1MyHC6 male mice either untreated or after administration of isoproterenol (15mg/kg/day) for 14 days

first: Norbert

last: Leitinger


title: Transposable elements function as mechanical sensors [ChIP-seq]

city: Durham

first: Tongyu

last: Sun

state: NC

address: 307 research drive

institute: Duke university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transposable elements (TEs), comprising almost half of the genome, are tightly controlled by intrinsic factors. However, how TEs are modulated by extrinsic mechanical forces remains unknown. To address this question, we culture human embryonic stem cells on hydrogels with different rigidity and comprehensively analyze the changes in transcriptome, epigenome and genome architecture of TEs, and find that TEs are able to sense mechanical forces. Upon sensing changes in substrate rigidity, a majority of TEs exhibit elevated or declined transcription, accompanied by corresponding chromatin state alterations. Moreover, mechanotransducer YAP binds directly to a subset of TEs, especially LTR7/HERV-H, and its loss partly recapitulates effects of soft substrate on TEs. Notably, mechanical forces are required for TEs’ chromatin interaction through YAP and CTCF cooperation. Functionally, mechano-sensing TE-enhancer directs definitive endoderm formation through the regulation of distal target, FAM189A2. Overall, our results demonstrate that TEs are mechanical sensors, and that TE-enhancers dictate cell fate.

overall_design: Cells were cultured on the hydrogels with different rigidity, and were collected for RNA-seq, ChIP-seq and HiCAR.

first: Yarui

last: Diao


title: Transposable elements function as mechanical sensors [CUT&RUN]


title: Gene expression differences between TILs that are reactive to tumor cells and TILs that are not reactive

city: Seoul

first: INWON

last: LEE

address: 25, Misagangbyeonjungang-ro 7beonan-gil, Hanam-si, Gyeonggi-do

country: South Korea

institute: NeogenTC

summary: Clinical significance of tumor-infiltrating lymphocytes (TILs) was demonstrated in many tumor types. In the clinical trials, immune check point inhibitors showed significant clinical efficacy in some tumor types with high mutation burden such as melanoma, bladder cancer, and smoking-induced lung cancer, while there were little effects in cancers with lower mutation rates such as breast cancer. Recently, selection and adoptive transfer of autologous mutation-specific TILs showed successful regression of metastatic tumors in an estrogen receptor-positive breast cancer patient. In this study, we analyzed gene expression profiles in cultured TILs that are reactive or non reactive against autologous breast cancer cells. We cultured TILs and cancer cells derived from breast tumor tissues obtained from the surgery. Reactivity of TILs against cancer cells was determined by interferon gamma (IFN-γ) ELISA analysis after co-culture of TILs and cancer cells for 24 hours. The total RNA was purified from cultured TILs (post-REP TILs) using RNeasy kits. The gene expression library is generated by Illumina TruSeq RNA library prep kit and sequenced.

overall_design: TILs that are reactive to autologous breast cancer cells (n=5), TILs that are not reactive to autologous breast cancer cells (n=9)


title: METTL14 promotes retinal neovascularization via m6A-modification on MXD1 mRNA in oxygen induced retinopathy

city: Beijing

first: xinyuan

last: chen

address: No.17, Hougou Hutong, Dongcheng District, Beijing

institute: Beijing Eye Research Institute

summary: In this study, we explored the effects and underlying mechanisms of methyltransferase-like 14 (METTL14) in microglia cell line (HMC3 cells), which are crucial for the pathogenesis of Retinopathy of Prematurity (ROP). Our results showed that the expression of METTL14 was increased in HMC3 cells after hypoxia stimulation. MeRIP-seq and RNA-seq were performed to explore the underlying mechanisms.

overall_design: MeRIP-seq and RNA-seq were performed between sh-NC and sh-METTL14 HMC3 cells with hypoxia

first: Xianyang

last: Liu


title: Multilineage origins of lymphatic muscle cells with transcriptional parallels to venous smooth muscle

city: Boston

first: Guillermo

last: Arroyo Ataz

address: 670 Albany Street

institute: Boston University

summary: Lymphatic muscle cells (LMCs) have distinct contractility compared to vascular smooth muscle cells covering blood vessels (SMCs). Additionally, we found LMC and SMC populations to be partially derived from WT1-expressing progenitors. To learn more about the potential differences between WT1-derived cells and their counterparts, as well as the potential differences between LMCs and SMCs, we performed scRNAseq on popliteal lymphatics and veins of WT1 reporter mice.

overall_design: Popliteal lymphatic vessels and vein were specifically isolated by a surgical method.

last: Arroyo-Ataz

first: Pin-Ji

last: Lei

first: Julia

last: Breda

first: Sarah

last: Mazzilli

first: Dennis

last: Jones


title: Myeloid mimicry mediates hyperprogression in patients with renal medullary carcinoma treated with nivolumab plus ipilimumab

city: Houston

first: Pavlos

last: Msaouel

state: Texas

address: 1155 Pressler Street, Unit 1374

department: Genitourinary Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: Renal medullary carcinoma (RMC) is a rare but highly aggressive malignancy that mainly afflicts young individuals of African descent and has few treatment options. Despite the approval of combination immune checkpoint therapy (ICT) for other kidney cancers, its efficacy against RMC remains elusive. We conducted a prospective clinical trial of nivolumab plus ipilimumab in patients with RMC. Enrollment was halted for futility after a prespecified interim analysis revealed that all 10 patients experienced rapid disease progression with 5/10 meeting radiological criteria for hyperprogression. Median progression-free survival was only 1.38 months (95% confidence interval (CI): 1.28, 1.60). To elucidate the underlying mechanisms, we analyzed high-quality single-cell RNA sequencing data from RMC patients before and after nivolumab plus ipilimumab treatment. Our analysis suggested that ICT-triggered interferon gamma upregulation induces RMC tumor cells to activate key myeloid regulators such as the CEBPB / p300 complex that promote tumor cell proliferation leading to hyperprogression. Using an immunocompetent somatic mosaic genetically engineered mouse model of RMC, we confirmed that combination ICT induced hyperprogression of primary and metastatic tumors compared with IgG control by hijacking myeloid-affiliated transcriptional circuits. Blocking of this “myeloid mimicry” adaptive mechanism using a selective inhibitor of p300 induced sensitivity to combination ICT in our animal model of RMC. These findings provide novel insights into RMC adaptation to ICT and demonstrate that inhibiting master myeloid regulators can elicit antitumor responses to ICT thus informing the next generation of immunotherapy strategies targeting hyperprogression.

overall_design:
We collected samples from a total of 15 patients. 9 patients provided samples for single-cell RNA (scRNA) sequencing, and 6 other patients provided samples for bulk-RNA sequencing. The scRNA samples consisted of fresh tumor biopsy tissues from 7 immunotherapy-naïve patients with Renal Medullary Carcinoma (RMC), and tissues from 2 patients with RMC collected immediately after aggressive progression on nivolumab plus ipilimumab. The bulk-RNA samples included 3 baseline samples and 3 samples from patients with RMC collected after aggressive progression on nivolumab plus ipilimumab treatment.
contributor: Moon Shots Cancer Genomics Laboratory (CGL)
contributor: MD Anderson institutional Advanced Genomics Technology Core (AGTC)

***************************************************************
Raw data is not provided due to patient privacy concerns.
***************************************************************

first: Jianfeng

last: Chen

first: Xinmiao

last: Yan

first: Jianjun

last: Gao

first: Linghua

last: Wang

first: Giannicola

last: Genovese


title: Transposable elements function as mechanical sensors [RNA-seq]

last: Sun

summary: Transposable elements (TEs), comprising almost half of the genome, are tightly controlled by intrinsic factors. However, how TEs are modulated by extrinsic mechanical forces remains unknown. To address this question, we culture human embryonic stem cells on hydrogels with different rigidity and comprehensively analyze the changes in transcriptome, epigenome and genome architecture of TEs, and find that TEs are able to sense mechanical forces.  Upon sensing changes in substrate rigidity, a majority of TEs exhibit elevated or declined transcription, accompanied by corresponding chromatin state alterations. Moreover, mechanotransducer YAP binds directly to a subset of TEs, especially LTR7/HERV-H, and its loss partly recapitulates effects of soft substrate on TEs. Notably, mechanical forces are required for TEs’ chromatin interaction through YAP and CTCF cooperation. Functionally, mechano-sensing TE-enhancer directs definitive endoderm formation through the regulation of distal target, FAM189A2. Overall, our results demonstrate that TEs are mechanical sensors, and that TE-enhancers dictate cell fate.


title: Decoding CD4+ T cell transcriptome in giant cell arteritis: novel pathways and altered cross-talk with monocytes [methylation]

city: Armilla

first: Bioinformatics Unit

last: IPBLN-CSIC

state: GRANADA

address: Avda. del Conocimiento, 17. Instituto de Parasitología y Biomedicina Lopez-Neyra. Bioinformática

country: Spain

institute: IPBLN-CSIC

type: Methylation profiling by genome tiling array

summary: Objectives: Giant cell arteritis (GCA) is an autoimmune large-vessels vasculitis with complex etiology. Although the pathogenic mechanisms remain poorly understood, a central role for CD4+ T cells has been demonstrated. In this context, delineating the transcriptome signatures of GCA CD4+ T cells will yield new insights into its pathogenesis.     Methods: Transcriptome analysis was conducted on CD4+ T cells from 70 patients with GCA with different disease activity (active patients before treatment and patients in remission with and without glucocorticoid treatment), along with 28 healthy controls. The study also evaluated potential impacts of DNA methylation on gene expression alterations and assessed cross-talk communication with CD14+ monocytes.     Results: This study has uncovered a substantial number of genes and pathways potentially contributing to the pathogenicity of CD4+ T cells in GCA. Specifically, CD4+ T cells from GCA patients with active disease exhibited altered expression levels of genes involved in multiple immune-related processes, including various interleukins (IL) signaling pathways. Notably, IL-2, a decisive interleukin for regulatory T cells homeostasis, was among the most significant. Additionally, impaired apoptotic pathways appear to be crucial in GCA development. Our findings also suggest that histone-related epigenetic pathways may be implicated in promoting an inflammatory phenotype in GCA active patients. Finally, our study observed altered signaling communication, such as the Jagged-Notch signaling, between CD4+ T cells and monocytes that could have pathogenic relevance in GCA.  Conclusions: Our study suggests the participation of novel cytokines and pathways and the occurrence of a disruption of monocyte-T cell crosstalk driving GCA pathogenesis.

overall_design: DNA methylation and gene expression profiling analysis of Illumina Infinium EPIC array and RNA-seq data sets for CD4+ T cells  in healthy individuals and giant cell arteritis patients within three different clinical status : a) active (n=17): newly diagnosed patients before starting GC treatment; b) in remission with treatment (n=26): patients in disease remission while receiving low doses of prednisone (≤ 10mg/day) for a minimum of 1 month; c) in remission without treatment (n=27): patients in remission without any treatment for at least 1 month. Remission was considered when individuals presented absence of GCA-related symptoms along with normal acute phase reactants.

first: Elkyn

last: Estupiñán-Moreno

first: José

last: Hernández-Rodríguez

first: Tianlu

last: Li

first: Laura

last: Ciudad

first: Eduardo

last: Andrés-León

middle: C

last: Terron-Camero

first: Sergio

last: Prieto-González

first: Georgina

last: Espígol-Frigolé

first: Maria

last: Cid

first: Ana

last: Márquez

first: Javier

last: Martín

first: Esteban

last: Ballestar

first: Lourdes

last: Ortiz-Fernández


title: Decoding CD4+ T cell transcriptome in giant cell arteritis: novel pathways and altered cross-talk with monocytes

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

overall_design: Refer to individual Series


title: H3S10-phosphorylation spreading in mitosis stably preserves 3D chromatin structure and functions

city: Bengaluru

first: Dimple

last: Notani

state: Karnataka

address: GKVK

country: India

institute: National Centre for Biological Sciences

summary: Gene regulatory landscape of a cell is faithfully recapitulated in daughter cell despite widespread loss of epigenetic marks, transcription and 3D chromatin structure during cell division. How a cell remembers its gene regulatory landscape through mitosis is poorly understood. Recently, a histone modification that spreads on chromatin was postulated to be a preserver of chromatin state. Unlike most histone modifications, mitotic cells gain H3S10p but its mitotic bookmarking roles are unknown. Here, we show that as the cell loses its interphase-specific chromatin structure, spreading of H3S10p occurs throughout active chromatin domains. The level of spreading is proportional to the activity of a domain. H3S10pmarked chromatin domains are formed earlier post mitosis. Further, within the domains, promoters but not enhancers are hyper-marked by H3S10p. Using mitosis specific expression of H3S10 and its mutants (H3S10A and H3S10D), we reveal that the loss of mitotic H3S10p causes widespread opening of promoters, resulting in abrupt transcription in the next interphase. We propose that H3S10p spreading preserves the 3D-chromatin epigenetic memory where it acts as a rheostat to fine-tune gene transcription in recently divided cells.

overall_design: ChIP-seq in HeLa/MCF-7, for H3S10p- upon 24 hours of DMSO/nococdazole treatment. ChIP-seq in S10, S10A and S10D HeLa lines, for HA, H3 and H3S10p- upon Doxycycline induction for 8h following an early S synchronisation with Thymidine for 24h; then followed by mitotic arrest with Nocodazole for 12h. ATAC-seq and RNA-seq in S10, S10A and S10D HeLa lines- upon Doxycycline induction for 8h following an early S synchronisation with Thymidine for 24h; then followed by mitotic arrest with Nocodazole for 12h and a final release into next interphase for 7h.

first: D

first: S

last: Meel


title: High-throughput explorations of Drosophila models of AKT1 variants associated with juvenile ovarian granula cell tumors provide insights into their pathogenesis mechanisms.

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

country: France

institute: CNRS/Université Paris Cité

summary: To investigate the effect of AKT1 mutants discovered in juvenile granulosa-cell tumors, we generated UAS-AKT1 transgenic flies (Drosophila melanogaster), expressing either the human wild type or a mutant form of AKT1. Next, we performed high-throughput analyses of the transcripts deregulated after mild over-expression of human WT and mutated AKT1 variants in Drosophila follicular cells. Site-specific transformation of pUASTattB-AKT1-3xFLAG constructs into the 51C fly line (y1 M{vas-int.Dm}ZH-2A w*; M{3xP3-RFP.attP'}ZH-51C)(Reference BDSC Stock # 24482) was performed by Bestgene, Inc. (CA, U.S.A.).

overall_design: Comparative of genes dysregulated in follicular cells expressing mutant form of AKT1 compared to WT AKT1 or empty Landing pad (#24482 fly stock) after RNAseq experiment

first: Anne

middle: L

first: Reiner

last: Veitia

first: Alain

last: Zider

first: Bérangère

last: Legois

first: Laetitia

last: Herman

first: Sandra

last: Claret


title: Cyclin-dependent kinase 8 reprograms primary and secondary metabolic pathways at high levels of jasmonate defense

city: East Lansing

first: Qiang

last: Guo

state: MI

address: 612 Wilson Rd

department: MSU-DOE Plant Research Laboratory

institute: Michigan State University

summary: The plant hormone jasmonate (JA) stimulates innate immunity by triggering the degradation of JASMONATE ZIM-DOMAIN (JAZ) proteins, which in turn reconfigure metabolic pathways to produce various defense-related molecules and cellular structures. However, the mechanisms by which JA shifts metabolism to thwart invading organisms remain largely unknown. Here, we employed a JAZ-deficient mutant (jazD) that exhibits heightened chemical defense and strong growth and reproduction inhibition to interrogate this question. Characterization of a genetic suppressor of jazD that rescues its growth phenotype identified a mutation in CYCLIN-DEPENDENT KINASE 8 (CDK8) as the causal mutation. Genetic epistasis analyses revealed that CDK8 in jazD not only contributes to its robust resistance to insect herbivory and necrotrophic pathogens, but also imposes strong inhibitory effects on shoot growth and seed production. Metabolic phenotypes of jazD cdk8 discerned from transcriptomic and metabolomic analyses showed that CDK8 specifically boosts JA-mediated anti-pathogen branch of specialized metabolism. CDK8-mediated resource allocation to defense sinks upon JAZ deficiency was associated with alteration in central carbon metabolism, upregulation of respiration, as well as increased production of proteinogenic amino acids. Our data establish CDK8 as a key regulator of defense-associated primary and secondary metabolism under JA-mediated stress conditions and provide a potential approach to unlink anti-insect defense to growth and reproduction.

overall_design: Analysis of Col-0 (wildtype), cdk8-1, jazD, and jazDcdk8-1 (four genotypes), with three biological replicates per genotype - 12 samples in total.


title: m6A sequencing of vitreous bodies of diabetic retinopathy patients

city: Wu'xi

first: Yu

last: Xin

state: Jiangsu

address: 1800 Lihu Road

institute: Jiangnan University

summary: As the most prevalent, abundant and conserved internal cotranscriptional modification in eukaryotic RNAs, N6-methyladenosine (m6A) plays vital role in the progression of different types of human diseases, including cancers. m6A RNA methylation have been reported to affects the physiological and pathological progressions of hematopoietic, central nervous and reproductive systems. As diabetic retinopathy is one of the most importent microvascular complication of diabetes, in this work, MeRIP-seq was employed to investigate the RNA m6A levels in the vitreous body samples of diabetic retinopathy and control groups.  A group of mRNAs were suggested with significantly fluctuated transcription and m6A levels, and they would be inverstigated in the further work to understand the mechanisam of the progression of diabetic retinopathy.

overall_design: During pars plana vitrectomy, vitreous bodies of diabetic retinopathy patients (DR group, 90 eyes) and  non-diabetic retinopathy patients (NC group, 90 eyes, including rhegmatogenous retinal detachment, macular hole, epimacular membrane) were collected. To enrich the RNA, samples of each group were combined (30 samples were mixed) as DR_1-3 and NC_1-3.  Comparative gene expression profiling and m6A modification analysis using RNA-Seq data of two groups were performed.

first: Jun

last: Shao

first: Lu

last: Ye

first: Shujing

last: Cui


title: Transcriptome-wide profiles and ac4c modification profile in RA FLS with NAT10 knockdown

city: Guangzhou

last: Kuang

address: No.58 Zhongshan Er Road Guangzhou

institute: The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China)


title: PIEZO1 promotes odontoblast-mediated reactionary dentinogenesis via Ca2+-SEMA3A axis

city: Wuhan

first: Pei

last: Huang

state: Hubei

address: 237 Luoyu Road

department: School and Hospital of Stomatology

institute: Wuhan University

summary: The odontoblasts are specialized cells responsible for dentin synthesis and nociceptive signal detection in response to external stimuli. Recent studies have shown that the mechanosensitive ion channel PIEZO1 is involved in bone formation and remodeling through the influx of calcium ions, and it is abundantly expressed in odontoblasts. However, the specific role of PIEZO1 in reactionary dentinogenesis by odontoblasts and the underlying mechanisms still remain elusive. In this study, we found intense PIEZO1 expression in the plasma membrane and cytoplasm of odontoblasts in human and mouse mandibular molars, and human odontoblast-like cells (hOBLCs). In hOBLCs, PIEZO1 positively regulated DSPP, DMP1, and COL1A1 expression through the Ca2+/PI3K-Akt/SEMA3A signaling pathway. Additionally, exogenous SEMA3A supplementation effectively reversed reduced mineralization capacity in PIEZO1-knockdown hOBLCs. In vivo, Piezo1 expression peaked at day 7 and returned to baseline at day 21 in a wild-type (WT) mice dentin injury model, with Sema3a presenting a similar expression pattern. To investigate the specific role of PIEZO1 in reactionary dentinogenesis, mice with a conditional knockout of PIEZO1 in odontoblasts were generated, and no significant differences of teeth phenotypes were observed between the control and conditional knockout (cKO) mice. Nevertheless, cKO mice exhibited reduced reactionary dentin formation, and decreased Sema3a and Dsp positive staining after dentin injury, indicating impaired dental pulp repair mediated by odontoblasts. In summary, these findings suggest that PIEZO1 enhances mineralization capacity of hOBLCs in vitro via the Ca2+/Akt/SEMA3A signaling pathway and contributes to dental pulp repair through enhancing reactionary dentinogenesis in vivo.

overall_design:
To investigate the signaling pathways involved in the regulation of PIEZO1 on odontoblasts, we established human odontoblast-like cells (hOBLCs) in which PIEZO1 was either activated by Yoda1 or knocked down by small interfering RNA (siRNA) sequences.
We then performed gene expression profiling analysis using data obtained from RNA-seq of hOBLCs under different treatments.

first: Zhuan

last: Bian

first: Liuyan

last: Meng


title: Single-cell analysis of the nervous system at small and large scales with instant partitions.

city: New York

first: Paul

last: Frazel

state: NY

address: 435 E 30th St

institute: NYU Langone Medical Center

summary: Single-cell RNA sequencing is a new frontier across all biology, particularly in neuroscience. While powerful for answering numerous neuroscience questions, limitations in sample input size, and initial capital outlay can exclude some researchers from its application. Here, we tested a recently introduced method for scRNAseq across diverse scales and neuroscience experiments. We benchmarked against a major current scRNAseq technology and found that PIPseq performed similarly, in line with earlier benchmarking data. Across dozens of samples, PIPseq recovered many brain cell types at small and large scales (1,000-100,000 cells/sample) and was able to detect differentially expressed genes in an inflammation paradigm. Similarly, PIPseq could detect expected and new differentially expressed genes in a brain single cell suspension from a knockout mouse model; it could also detect rare, virally-labelled following AAV-targeting and gene knockdown. Finally, we used PIPseq to investigate gene expression in a nontraditional model species, the little skate (Leucoraja erinacea). In total, PIPSeq was equally able to detect gene expression changes across models and species, with an added benefit of large scale capture and sequencing of each sample.

overall_design: Multiple dissociated single cell or single nucleus brain samples from mice of various ages and genotypes were processed with instant partitions (PIPseq)

first: Shane

last: Liddelow


title: ac4c modification profile in RA FLS with NAT10 knockdown

summary: Fibroblast-like synoviocytes (FLS) exhibit aggressive phenotype, proliferation and decreased cell-contact inhibition,and play a critical role in pathogenesis of rheumatoid arthritis (RA). However, the mechanism underlying these phenotype remains unknown. In this study, we explore the function of ac4c modification in modulating RA FLS aggressive behavior, and reveal the underlying molecular mechanism.

overall_design: To investigate the molecular mechanism of ac4c modification in RA FLS, NAT10 was knockdown by lentivirus infection containing NAT10 shRNA.

first: Di

last: Liu


title: Sterile alpha motif domain-containing protein 9 is an RNA binding protein impacting ribosome biogenesis and interferon signaling

city: Nashville

first: Jason

middle: Ross

last: Schwartz

state: TN

address: 2220 Pierce Ave

department: Pediatrics, Ped Hematology/Oncology

institute: Vanderbilt University Medical Center

summary: Inherited bone marrow failure syndromes often result from pathogenic mutations in genes that are important for ribosome function, namely, Diamond-Blackfan anemia, Shwachman-Diamond syndrome, and dyskeratosis congenita. Germline mutations in SAMD9 were identified in recent years as a frequent genetic lesion resulting in inherited bone marrow failure and monosomy 7, some patients even have severe multisystem syndromes that include myelodysplasia such as MIRAGE and ataxia-pancytopenia syndromes. The association of germline SAMD9 mutations and bone marrow failure is clear, but to date, there is no reliable method to predict if a novel SAMD9 mutation is pathogenic unless it is accompanied by an obvious family history and/or clinical syndrome. The difficulty with pathogenicity prediction is, in part, due to the incomplete understanding of the biological functions of SAMD9. Here, we used a SAMD9-targeted, inducible CRISPRa/i system to better understand the transcriptional changes that result from SAMD9 transcriptional manipulation. We also used cross-linking and solid phase purification to demonstrate that SAMD9 is an RNA binding protein, and that it is likely through this RNA binding function that SAMD9 affects ribosome biogenesis and subsequently global protein translation and cell proliferation. Thus, ribosome dysfunction contributes to SAMD9-related bone marrow failure like other classical inherited bone marrow failure syndromes.

overall_design: Three different isogenic K562 cell lines (parental, [VPR]-D9, [KRAB]-D9) were analyzed by RNA sequencing. Comparisons were made between no treatment conditions and IFN, doxycycline, or a combination of both.

last: Hoover

first: Marisol

last: Ramirez-Solano

first: Qi

middle: R


title: Decoding CD4+ T cell transcriptome in giant cell arteritis: novel pathways and altered cross-talk with monocytes [RNA-seq]

first: Bioinformatics Unit

last: IPBLN-CSIC

summary: Objectives: Giant cell arteritis (GCA) is an autoimmune large-vessels vasculitis with complex etiology. Although the pathogenic mechanisms remain poorly understood, a central role for CD4+ T cells has been demonstrated. In this context, delineating the transcriptome signatures of GCA CD4+ T cells will yield new insights into its pathogenesis.   Methods: Transcriptome analysis was conducted on CD4+ T cells from 70 patients with GCA with different disease activity (active patients before treatment and patients in remission with and without glucocorticoid treatment), along with 28 healthy controls. The study also evaluated potential impacts of DNA methylation on gene expression alterations and assessed cross-talk communication with CD14+ monocytes.   Results: This study has uncovered a substantial number of genes and pathways potentially contributing to the pathogenicity of CD4+ T cells in GCA. Specifically, CD4+ T cells from GCA patients with active disease exhibited altered expression levels of genes involved in multiple immune-related processes, including various interleukins (IL) signaling pathways. Notably, IL-2, a decisive interleukin for regulatory T cells homeostasis, was among the most significant. Additionally, impaired apoptotic pathways appear to be crucial in GCA development. Our findings also suggest that histone-related epigenetic pathways may be implicated in promoting an inflammatory phenotype in GCA active patients. Finally, our study observed altered signaling communication, such as the Jagged-Notch signaling, between CD4+ T cells and monocytes that could have pathogenic relevance in GCA. Conclusions: Our study suggests the participation of novel cytokines and pathways and the occurrence of a disruption of monocyte-T cell crosstalk driving GCA pathogenesis.

first: Elkyn

last: Estupiñán-Moreno

first: José

last: Hernández-Rodríguez

first: Tianlu

last: Li

first: Laura

last: Ciudad

first: Eduardo

last: Andrés-León

last: Terron-Camero

first: Sergio

last: Prieto-González

first: Georgina

last: Espígol-Frigolé

first: Maria

last: Cid

first: Ana

last: Márquez

first: Javier

last: Martín

first: Esteban

last: Ballestar

first: Lourdes

last: Ortiz-Fernández


title: Analysis of circRNA expression in human hepatocellular carcinoma.

first: YUE NING

last: WANG

state: Guangdong

address: 651 Dongfeng Road East

institute: Sun Yat-Sen University Cancer Centre

summary: CircRNA expression profiles were sucessfully contructed in 68 hepatocellular carcinoma tissues and 55 adjacent noncancerous tissues using a custom microarray containing probes for 814 circRNAs and 108 differentially expressed circRNAs were identified.

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 68 hepatocellular carcinoma cases, followed up more than three years, was used to acquire circRNA expression profiles and identify differentially expressed circRNAs.

first: Ji

last: Liu

first: Meiyin

last: Zhang

first: Huiyun

last: Wang


title: Microglial apolipoprotein E particles contribute to neuronal senescence and synaptotoxicity

city: Chongqing

first: Hongsheng

address: 1 Yixueyuan Road

institute: Chongqing Medical University

summary: Apolipoprotein E (apoE) plays a pivotal role in the pathogenesis of Alzheimer’s disease (AD). In the brain, apoE is predominantly expressed and secreted by astrocytes, but is dramatically up-regulated in microglia under AD-associated conditions. Although the function of astrocytic apoE has been widely investigated, whether and how apoE particles derived from different types of glia differ in biological features and function remains elusive. Here, we show that apoE particles derived from astrocytes and microglia exhibit dissimilar sizes. Microglial apoE particles impaired neurite growth and synapses and promoted neuronal senescence, whereas GPNMB-deficient microglial apoE particles abolished these detrimental effects. These findings provide direct evidence supporting that microglia-derived apoE particles contribute to neuronal senescence and toxicity.

overall_design: To explore how apoE particles affect transcriptome of neurons, we  treated primary neurons with apoE particle  for 24h. We then performed gene expression profiling analysis using data obtained from RNA-Seq of two treatment. Comparative gene expression of RNA-seq data for primary neuron treated with microglia apoE particle and astrocytic apoE particle.

first: Lujian

last: Cai

first: Yingjun

last: Zhao


title: mRNA expression profiles of engineered chondrocyte sheets

city: Salt Lake City

first: Makoto

last: Kondo

state: UT

department: Molecular Pharmaceutics

institute: University of Utah

summary: Cartilage injury does not naturally repair and lead to osteoarthritis.  Engineered chondrocyte sheets are readily transplantable and create neocartilage in vivo.  This experiment compares global mRNA profiling of adult and juvenile chondrocyte sheets.

overall_design: Examination of mRNA profiles of engineeredchondrocyte sheets created from adult cartilage and juvenile cartilage.

first: Keisuke

last: Matsukura

first: Adam

middle: J

last: Ford

first: Nicolas

middle: F

last: Metzler

first: Travis

middle: G

last: Maak

first: Douglas

middle: T

last: Hutchinson

first: Angela

middle: A

first: Masato

last: Sato

first: David

middle: W

last: Grainger

first: Teruo

last: Okano


title: Effect of GATA4 overexpression on gene expression during odontogenic differentiation of human dental pulp stem cells

first: Yan

address: Luoyu Road 237

summary: The odontogenic differentiation of human dental pulp stem cells (HDPSCs) is associated with reparative dentinogenesis. Transcription factor GATA binding protein 4 (GATA4) is proved to be essential for osteoblast differentiation and bone remodeling. This study clarified the function of GATA4 in HDPSCs odontoblast differentiation.

overall_design: To investigate the function of GATA4 in the regulation of odontogenic differentiation, we established human dental pulp stem cells in which GATA4 has been overexpressed by overexpression lentivirus

first: Zhang

last: Yan

first: Meng

last: Liuyan


title: Overexpression of NtPhyA gene improves tobacco cold resistance under low temperature stress

city: Guiyang

first: Jiajun

last: Luo

state: Guizhou

address: Guizhou University, Guiyang, Guizhou Province

institute: GUIZHOU university

summary: Overexpression of NtPhyA gene under low temperature stress improved the cold resistance of tobacco. The transcriptome analysis found that NtPhyA affected the biosynthesis of lysine, metabolism of ascorbic acid and aldehyde acid, metabolism of glutathione, inositol phosphate metabolism, glycolysis/gluconeogenesis, TCA cycle, plant hormone signal transduction, metabolism of secondary metabolites and other pathways.

overall_design: 6 samples were analyzed, including 2 plant materials, each with three replicates.


title: The SRC Family Kinase, YES1, is a modulator of centrosome homeostasis, chromosomal stability, and therapeutic response in triple negative breast cancer

city: Cleveland

first: Ruth

last: Keri

state: Ohio

address: 9620 Carnegie Ave

institute: Cleveland Clinic Foundation

summary: Triple negative breast cancer (TNBC) is a collection of heterogeneous disease with limited therapeutic options. One commonality of TNBCs is their distinct molecular profiles and increased chromosomal instability (CIN), both of which contribute to its difficulty to treat, but also offer points of leverage for therapeutic intervention. To capitalize on this vulnerability, we focused on Src Family Kinases (SFKs), a group comprised of 9-11 non-receptor tyrosine kinases that interact with upstream signaling partners to regulate cell phenotypes such as adhesion, motility, survival, and mitosis. We found that treatment with pan-SFK inhibitors leads to abnormal nuclear phenotypes and DNA double strand breaks, both characteristics of CIN, in TNBC cell lines. However, previous clinical studies demonstrated that pan-SFK inhibition resulted in significant toxicities and minimal efficacy in TNBC patients. Therefore, we sought to identify which, if any, of the SFK members may be a specific vulnerability in TNBC that was essential for maintenance of genomic integrity, mitotic progression, and cell survival. The SFK, YES1, was identified to be one of the most highly expressed SFKs in basal breast cancer, with high YES1 expression being correlated with poor patient outcomes. Using genomic depletion and pharmacologic inhibition, we demonstrated that sustained YES1 activity was essential for bipolar spindle formation, regulation of centrosome number, and maintenance of chromosomal stability. Combination treatment utilizing CIN-inducing therapies have been considered to improve treatment efficacy or re-sensitize tumor cells to certain drugs by inducing profound mitotic defects, maladaptive CIN, and cell death. Thus, we evaluated YES1 inhibition in combination with Taxols as an innovative drug treatment regimen that improves TNBC patient outcomes. We found that paclitaxel and the selective YES1 inhibitor, CH695355, synergized in both in vitro and in vivo TNBC models. Moreover, use of this inhibitor re-sensitized Taxol resistant TNBC cells to paclitaxel, a common obstacle in TNBC treatment. Our studies demonstrate that YES1 is a previously understudied component of genomic stability-regulating pathways in TNBC. More broadly, our data suggests that YES1 may be a therapeutically targetable vulnerability with the ability to be paired with other DNA damaging or mitotic inhibitors to improve treatment efficacy in TNBC.

overall_design: RNA-seq study of MDA-MB-231 and SUM159 cells transfected with non-targeting siRNA (siNS) or siRNA targeting YES1 (siYES) in technical (4) replicates.

first: Katrina

middle: M

last: Piemonte

first: Natasha

last: Ingles-Martinez

first: Salendra

last: Singh

first: Kristen

last: Weber-Bonk

first: Mitchell

last: Valentine


title: Tracking spatio-temporal dynamics of the endothelial niche during fetal hematopoiesis

city: Freiburg

first: Nina

last: Peltokangas

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: The emergence of the hematopoietic system occurs in temporal waves across different tissues during mouse development. During these waves, the endothelial niche serves as a source of hematopoietic cells and provides molecular cues that potentially shape the tissue-specific lineage output. Although the endothelial-to-hematopoietic transition in the aorta-gonad-mesonephros is well understood, a systematic analysis of hematopoietic progenitors and their endothelial niche across fetal tissues is lacking. Here, we leverage single-cell RNA-sequencing of micro-dissected fetal tissues during their peak of hematopoietic activity to systematically compare hematopoietic progenitors and the endothelial niche. We predict stage-specific interactions accompanying the transition of yolk sac endothelium to primitive and definitive hematopoietic fates and reveal distinct roles for fetal liver vascular niches. Furthermore, we provide in vitro evidence that lipid signaling by sphingosine-1-phosphate producing erythrocyte progenitors supports hematopoietic stem cell expansion in fetal liver. Our resource deciphers the temporal waves of hematopoietic development within distinct vascular niches.

overall_design: Single-cell RNA-sequencing was performed on hematopoietic (c-Kit+, CD34+) and endothelial (CD31+) cells isolated from micro-dissected fetal tissues (yolk sac = YS, aorta-gonad-mesonephros = AGM, placenta = PL, fetal liver = FL) between embryonic day (E) 8.5-14.5. For all samples, dead cells were excluded via Zombie staining. The lineage (Lin) cocktail used included: CD3e, B220, Gr-1, Ter119, SiglecH and CD19.

first: Dominic

last: Grün


title: MeRIP-seq Analysis of the Lumbar Spinal Cord in the Mouse Model of Bone Cancer Pain

city: Changsha

first: Xinran

last: Hou

state: Hunan

address: Xiangya Road 87

institute: Central South University

type: Methylation profiling by high throughput sequencing

summary: Bone cancer pain (BCP), in which the majority is caused by metastasis from other cancer sites, is the most common type of chronic cancer pain and is not fully understood. The role of posttranscriptional modification in the pathogenesis of bone cancer pain has not been reported. Thus, in the present study, we performed MeRIP-seq to explore changes in m6a modification of transcripts and to provide a landscape of dysregulated transcripts in the spinal cord of bone cancer pain.

overall_design: Comparative m6a profiling analysis of spinal cord in bone cancer pain mice and sham-operated mice at 21 days after femoral inoculation of Lewis lung carcinoma cells

first: Jie

last: Hu

first: Zhuofeng

last: Ding

first: Zongbin

last: Song


title: STING Signaling Contributes to Celastrol-induced Pyroptosis of Female Germline Stem Cells by Upregulating NLRP3

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: The expression profile data was obtained byRNA-Seqdata.

overall_design: Celastrol-treated and control FGSCs mRNA profiles of 12h were generated by deep sequencing, in triplicate.

first: Lu

last: Wang


title: Transcriptome-wide profiles in RA FLS with NAT10 knockdown

first: Yu

last: Kuang

first: Di

last: Liu


title: DEK facilitates regeneration in Stroke-Injured and Aging Brain via triggering Quiescence Exit of Neural Stem Cell

city: Hangzhou

first: sunli

last: cai

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: Quiescent neural stem cells (NSCs) in the adult mammalian brain can, upon activation, generate neurons and glial cells that contribute to complex sensory and cognitive functions during damage repair or aging. However, the specific and sustainable determinants of quiescent NSC activation remain unclear. Here, we present DEK as the primary activator of NSC quiescence in mice, functioning via the inhibition of downstream Notch signaling pathway. Overexpression of DEK in adult NSCs triggers quiescence exit, facilitating neurogenesis, eventually leading to either the rejuvenation of aged brains or the improved damage repair in a stroke-injured model. Meanwhile, persistent DEK overexpression from embryonic stages deprives NSCs of the ability to enter quiescence, leading to the ultimate depletion of the adult NSC reservoir, causing atrophy of hippocampus and deficits in spatial learning. Our findings establish a new narrative for quiescence exit of NSCs by DEK, potentially applicable when treating neurodegenerative diseases and brain injury.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of subventricular zone neural stem cells with AAV9-GFAP-GFP (Control) or AAV9-GFAP-DEK-GFP (DEK cOE) infection.

first: Sunli

last: Cai

first: Yunwen

last: Gu


title: RNA-seq of equine alveolar macrophages and blood monocyte-derived macrophages exposed to an inflammatory stimulus

city: Guelph

first: Heng

last: Kang

state: Ontario

address: 50 Stone Rd E

department: Pathobiology

country: Canada

institute: University of Guelph

summary:
The obejective was to investigate how equine alveolar macrophages (AMs) and monocyte-derived macrophages (MDMs) response to a stimuli which contained fungal spores, lipopolysaccharide, and silica microsphere (FLS), and whether different responses existed between AMs and MDMs.
RNA-seq was used to profile gene expression of AMs and MDMs from six clinically healthy horses were incubated with and without FLS for six hours.

overall_design: Differential gene expression analysis between control and FLS-exposed AMs, and MDMs, respectively. In additon, a comparison between AMs and MDMs in their gene expression change affected by FLS.

first: Gary

middle: K

last: Lee

first: Dorothee

last: Bienzle

first: Jutta

last: Hammermueller

first: Luis

last: Castro

first: Brandon

last: Lillie

first: Janet

last: Beeler-Marfisi


title: Developmentally Conserved CDX2 Cells from Human Term Placenta Drive Cardiovascular Regeneration

status: Public on Jun 29 2025

first: Hina

last: Chaudhry

state: USA

department: Cardiology

institute: Mount Sinai Hospital

summary: We report a population of multipotent cells isolated from term human placentas that exhibit clonal expansion, migratory capacity, and a gene expression profile indicating immune privilege. These cells, expressing the developmental regulator CDX2, previously known only for its role in early placentation, differentiate into cardiomyocytes and vascular cells. Building on our prior findings that murine Cdx2 cells improved cardiac function in mice after myocardial infarction (MI), we isolated CDX2⁺ cells from placentas of 180 healthy pregnancies. These human CDX2 cells spontaneously generate cardiac and vascular lineages in vitro, in vivo, and express transcriptomic signatures associated with cardiogenesis, vasculogenesis, immune modulation, and chemotaxis. When administered to NOD/SCID mice after MI, the cells restore cardiac function. Additionally, CDX2 cells can be clonally propagated while retaining cardiovascular differentiation potential. Our findings support the therapeutic potential of placental CDX2 cells as an ethically accessible and regenerative strategy for cardiovascular disease.

overall_design: Human CDX2mCherry-positive cell samples, both freshly isolated (n=2) and expanded at passage 3 (n=3), were thawed for analysis (total n=5). Cell counts were assessed using the Cellaca Cell Counter (Nexcelom Bioscience, Lawrence, MA, USA) in conjunction with NucBlue for staining cell nuclei and propidium iodide (PI) for identifying dead cells. Samples were then processed with the Chromium X platform (10x Genomics, Pleasanton, CA, USA), following the manufacturer’s protocols, to target the capture of approximately 3,000 cells per sample for downstream analysis. Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ Gene Expression Kit. Library quality was assessed using the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified via Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). Additional quantification was performed using qPCR (Applied Biosystems, Carlsbad, CA, USA) before sequencing on an Illumina platform, adhering to 10x Genomics' recommended sequencing configurations

first: Sangeetha

last: Vaddake-Madathil

first: Esmaa

last: Bouhamida

first: Prabhu

last: Mathiyalagan


title: Spatial transcriptomic analysis of transplanted vascularized lung organoids

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

summary: To  investigate the cell-cell interactions among the transplanted vascularized organoids, we utilized a Slide-seq-based spatial transcriptomics platform to unbiasedly map the spatial distribution of ligand-receptor pairs.

overall_design: Transplanted organoids were freshly collected, immersed in the O.C.T. compound, and immediately frozen on the dry ice. 10X10 Curio Seeker Spatial transcriptomic was performed following the manufacturer’s instruction. This technique was developed based on the Slide-seq technology for high-resolution genome-wide expression analysis at a resolution of 10um diameter in each spot that was densely packed and randomly deposited. Briefly, 5 scrolls of tissue sections of 10um thickness were collected to derive an RNA integrity number (RIN) to test the tissue’s RNA quality. All organoids’ RIN numbers were higher than 8 to pass the quality test. One 10um thickness tissue section was placed on the Curio Seeker tile and mounted with 30um section of CryoCube. Then, the section was processed for hybridization, reverse transcription, and tissue clearance to yield Curio Seeker Bead resuspension. On the second day, 11 cycles of PCR was utilized for second-string synthesis and cDNA amplification. The purified cDNA was applied for Tagmentation with Dual Indexing Primer V2 and consequent library cleanup and QC. The final library was applied for NGS sequencing with NovaSeq6000 following the recommended sequencing depth.

first: Mingxia

first: Yifei

last: Miao

first: Cheng

last: Jiang


title: Ras-related protein 2 limits vascular smooth muscle cell phenotypic switching and abdominal aortic aneurysm development

city: Nanjing

first: Shanshan

last: Luo

state: Jiangsu province

address: Long Mian Avenue 109

department: Pharmacy

institute: 南京医科大学

summary: Abdominal aortic aneurysm (AAA) and the attendant catastrophic event of rupture remain a leading cause of death.  During AAA, VSMCs lost contractile-related phenotype, with reduced levels of actin alpha 2, smooth muscle (ACTA2), transgelin (TAGLN) and calponin 1 (CNN1)) , and obtain ability to secrete matrix metalloproteinases to degrade the extracellular matrix and weaken the arterial wall, which potentiate the rupture of the aneurysm. Angiotensin 2 (Ang II) can induce phenotype transition of VSMCs，while the underlying mechanism remains elusive. Here we found Ang II treatment could reduce expression of R-Ras2, thus reducing the phosphorylation and nuclear translocation of TFII-I, as a result, the gene expression of ACTA2, TAGLN and CNN1 were inhibited and VSMCs lost the contractile phenotype.

overall_design: RNA-seq profile of HASMCs stimulated with PBS or Ang II

first: Yong

last: Ji

first: Ke

last: Zhong


title: Targeting AEBP1 to mitigate pro-tumor activity of cancer-associated fibroblasts and increase therapeutic efficacy to anti-PD-1

status: Public on Jun 28 2025

city: South San Francisco

first: Heyuan

last: Li

state: California

address: 213 E Grand Ave

institute: Merck Research Laboratories

summary: Cancer-associated fibroblasts (CAFs) are one of the components in tumor microenvironment (TME) that can facilitate tumor progression, invasion, and metastasis directly through tumor-CAF interactions, or indirectly by crosstalking with tumor infiltrating immune cells and inducing immunosuppressive TME. Indeed, high stromal signature has been associated with reduced therapeutic efficacy and resistance to Immune Checkpoint Blockade. AEBP1 is highly expressed in myofibroblast cells whose expression is further upregulated in activated fibroblasts and the extracellular matrix (ECM)-producing CAFs. AEBP1 has two alternatively spliced isoforms that the extracellular isoform binds to collagen and promotes collagen remodeling, and the intracellular isoform modulates transcription and signaling. We observed expression of both isoforms of AEBP1 in primary human CAFs.  Our data showed that combined knock out (KO) of both isoforms of AEBP1 by gene editing technology decreased CAF proliferation, collagen gel contractility and CAF-mediated tumor cell proliferation in vitro. Pan AEBP1 KO mouse fibroblasts also showed reduced activity in vitro and in vivo in the co-implantation mouse model.  We found that knocking out both isoforms of AEBP1 downregulated the collagen biosynthesis and ECM organization related pathways in both mouse fibroblasts and primary human CAFs through RNA sequencing studies. In addition, loss of AEBP1 in fibroblasts impacted tumor cell phenotypes resulting in significant decrease of tumor cells with,with epithelial-mesenchymal transition signature in the co-implantation mouse model. Furthermore, AEBP1 KO in CAFs enhanced the anti-PD-1 induced effector T cell activity and the anti-PD-1 efficacy in this co-implantation model. Altogether, our results demonstrate that AEBP1 is important in regulating CAF function in the TME.  Inhibiting AEBP1, therefore, may be a novel strategy in targeting CAF tumor-supporting activity and overcoming cancer resistance to anti-PD-1 immunotherapy.

overall_design: RNAseq profiling of wild-type NIH3T3 cell line and three clonal derivatives with AEBP1 knocked out.

first: Suchitra

last: Natarajan

first: Khoa

last: Nguyen

first: Elysia

last: Saputra

first: Cindy

first: Gukhan

last: Kim

first: Yu

last: Liu

first: Hong

last: Sun

first: Ramli

last: Muhammad

first: Ling

first: William

last: Monis

first: Wendy

last: Blumenschein

first: Dewan

last: Hossain

first: Aleksandra

last: Olow

first: Xin

last: Yu


title: Nuclear Argonaute:miRNA complexes recognize target sequences within chromatin and silence gene expression

city: Dallas

first: David

middle: Reid

last: Corey

state: Texas

address: 6001 Forest Park Rd.

institute: UT Southwestern Medical Center

summary: RNA interference (RNAi) in mammalian cells involves recognition of mRNA in the cytoplasm and inhibition of translation. Both protein RNAi factors and miRNAs, however, are present in mammalian cell nuclei. It is unclear how this nuclear localization affects endogenous gene expression. Here, we use chimeric eCLIP to identify complexes of Argonaute 2 (AGO2) and miRNAs. We identify the most abundant miRNAs associated with chromatin and their chromatin-associated RNA targets. Chimeric eCLIP revealed that High mobility group AT-Hook 2 (HMGA2) was the most compelling target for miRNA-mediated gene binding. There are four confirmed let-7 miRNA sites within the 3’-UTR in the cytoplasm or nucleus and three within chromatin-associated RNA. The expression of mature HMGA2 mRNA was repressed by let-7 in the cytoplasm and nucleus.  let-7 had little effect splicing or transcription. Our data validate chimeric eCLIP as a powerful method for experimentally identifying promising miRNA:RNA interactions. Rather than a solely cytoplasmic event, binding of RNAi factors to mRNA targets may begin in the nucleus through a mechanism that can reduce RNA levels in both the cytoplasm and the nucleus. miRNA-mediated silencing of mRNAs may be influenced by both nuclear and cytoplasmic interactions.

overall_design: Argonaute 2 (AGO2) miR-eCLIP in HCT116 whole cell, cytoplasm and chromatin, and HCT116 NLS-AGO2 whole cell samples.

first: Cristina

last: Hofman

first: Jiaxin

last: Hu

first: Rut

last: Bryl

first: Victor

last: Tse


title: The 5’-end codon bias minimizes fitness costs to facilitate the persistent dissemination of mcr-3 and investigation of novel MCR inhibitors

city: Nagoya

first: Yihao

last: Zhang

state: Aichi

address: 65 Tsurumaichō, Showa Ward

department: Graduate School of Medicine

country: Japan

institute: Nagoya University

summary: Background: The rapid evolution and dissemination of mobilized colistin resistance gene (mcr) family has revealed as a severe threat to the global public health. Nevertheless, dramatic reduction in the prevalence of mcr-1, the major member of mcr family, was observed after the withdrawal of colistin in animal fodder in China since 2017, demonstrating that colistin acts as a selective stress to promote the dissemination of mcr-1. As the second largest lineage, mcr-3 was firstly discovered in 2017 and has been identified from numerous sources. However, whether the spreading of mcr-3 is driven by colistin remains unknown.  Methods: To this end, we investigated the global prevalence of mcr-3 from 2005 to 2022 by an up-to-date systematic review, along with a nation-wide epidemiological study to establish the change of mcr-3 prevalence in China before and after 2017. To investigate the fitness cost imposed by MCR-3 upon bacterial host, in vitro and in vivo competitive assays were employed, along with morphological study and fluorescent observation. Moreover, by replacing non-optimal codons with optimal codons, synonymous mutations were introduced into the 5’-coding region of mcr-3 to study mechanisms accounting for the distinct fitness cost conferred by MCR-1 and MCR-3. Furthermore, by combining AlphaFold and molecular dynamics (MD) simulation, we provided a complete characterization on the putative lipid A binding pocket localized at the linker domain of MCR-3. Crucially, inhibitors targeting at the putative binding pocket of MCR-1 or MCR-3 were identified from small molecules library using the pipeline of virtual screening.  Findings: The global prevalence of mcr-3 increased continuously from 2005 to 2022. The average prevalence was 0.18% during 2005-2014 and rapidly increased to 3.41% during 2020-2022. The prevalence of mcr-3 in China increased from 0.79% in 2016 to 5.87% in 2019. We found that the fitness of mcr-3-bearing E. coli and empty plasmid control was comparable but higher than that of mcr-1-positive strain. Although the putative lipid A binding pocket of MCR-3 was similar to that of in MCR-1, mcr-3 occupies remarkable codon bias at the 5’-end of coding region that disrupted the stability of mRNA, further reduced its protein expression in E. coli, resulting in the low fitness burden of bacterial host. Moreover, the 5’-end codon usage frequency appeared as a critical factor related with the evolution of mcr family. Furthermore, based on the similar lipid A binding pocket among MCR family protein, we identified three novel MCR inhibitors targeting at such pocket by screening from small-molecule library, which effectively restored the colistin susceptibility of mcr-bearing E. coli.  Interpretation: For the first time, we found that the prevalence of mcr-3 increased continuously during 2016-2019 in China, demonstrating that the withdrawal of colistin in husbandry failed to prevent the dissemination of mcr-3. Our study evidenced that the 5’-end codon bias appeared as a crucial regulator upon the fitness cost conferred by horizontally transferred genes. Most importantly, the putative lipid A binding pocket verified from current study was a promising target site for designing inhibitors against mcr-positive strains.

overall_design: RNA-seq of E.coli K-12 carrying mcr-1 or mcr-3 resistant gene

first: Lujie

last: Liang

first: Guobao

last: Tian


title: Huangqin Decoction Exerts Antifungal Effects by Interfering with Energy Metabolism of Trichophyton rubrum with Glyoxylate Cycle as a Potential Target

city: Nanchang

first: Suqing

last: Yang

address: Nanchang

institute: Jiangxi Provincial People's Hospital (the First Affiliated Hospital of Nanchang Medical College)

summary:
Background: The dermatophyte Trichophyton rubrum (T. rubrum) is a highly specialized filamentous fungus that infects keratinized tissues and is the most common pathogen isolated from human dermatophytosis. The clinical treatment of the infections is challenging due to the prolonged treatment duration, limited efficacy, antifungal resistance and adverse effects of available drugs. Huangqin decoction (HQD) is a classical traditional Chinese medicine (TCM) formula, whose inhibitory efficiency against T. rubrum was disclosed in our previous study. However, the responsible mechanisms are not well understood.
Aim: This study aimed to elucidate the mode of action of Huangqin decoction (HQD) against T. rubrum as a whole by using transcriptome sequencing combined with verification of qRT-PCR and enzymatic activity assays.
Methods: By treating T. rubrum with HQD at minimum inhibitory concentration (MIC), the differentially expressed genes (DEGs) of T. rubrum in response to HQD based on transcriptome profiles were recognized. Gene function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed functions and signaling pathways modulated by the DEGs. The transcriptome results were validated by quantitative real-time PCR (qRT-PCR). The potential targets were further explored using enzymatic activity assays.
Results: At MIC, a total of 338 differentially expressed genes (DEGs) were detected in T. rubrum after HQD exposure compared with the control group (q-value < 0.05), of which 199 genes were significantly up-regulated and 139 genes were down-regulated. Gene function analysis indicated that COG functions of DEGs mainly covered “carbohydrate transport and metabolism” and “energy production and conversion”. The most frequently found GO terms were “metabolic process” and “catalytic activity”. KEGG enrichment analysis revealed that DEGs were predominately enriched in 6 pathways of “valine, leucine and isoleucine degradation”, “indole alkaloid biosynthesis”, “ABC transporters”, “synthesis and degradation of ketone bodies”, “starch and sucrose metabolism”, and “glyoxylate and dicarboxylate metabolism” (q-value < 0.05). Three KEGG pathways were closely related to energy metabolism, which was consistent with the COG and GO results. A subset of eight DEGs by the involvement of the biosynthesis and degradation of cell walls and energy metabolism including amino acid metabolism and the glyoxylate cycle were further confirmed by qRT-PCR and the results verified the transcriptome data. Enzymatic activity assays showed that compared to the control group, activities of citrate synthase (CS), aconitate hydratase (ACO) and isocitrate lyase (ICL) in the glyoxylate cycle were affected by HQD.
Conclusion: The overall evidence suggested that the interference of energy metabolism might contribute to the mode of action of HQD against dermatophyte pathogen T. rubrum, and the glyoxylate cycle may be the potential antifungal target of HQD against the fungi. Our study provides a theoretical basis for the mechanisms of HQD upon T. rubrum infections and offers an important insight regarding the glyoxylate cycle especially enzyme isocitrate lyase as indispensable targets of the herbal formulations.

overall_design: RNA-seq was performed in Trichophyton rubrum  (STRB012) treated with or without HQD to detect the differential genes that HQD may affect.

first: Su-Qing

first: Yi-Can

last: He

first: You-Jin

last: Ge

first: Bao-De

last: Shen

first: Chen-Ying


title: Identifying and Exploiting Combinatorial Synthetic Lethality by Characterizing Adaptive Kinome Rewiring of EGFRvIII-driven Glioblastoma

city: Birmingham

first: Benjamin

last: Lin

state: AL

address: 401F Wallace Tumor Institute

department: Pathology

institute: The University of Alabama at Birmingham

summary: GBM is an aggressive primary malignant brain tumor that has a poor prognosis. Molecular characterization of GBM has shown that EGFR mutations are present in over 50% of tumors. However, EGFR inhibitors have not shown clinical efficacy in contrast to other EGFR-driven neoplasms due to the unique EGFR biology found in GBM. We believe that upfront combinatorial therapy with EGFR inhibitors can overcome these challenges. To identify combinatorial drug targets, we temporally characterized drug induced EGFRvIII kinome rewiring in a cell line with an isogenic genetically engineered GBM EGFRvIII kinome. Kinomic characterization show that kinome rewiring has both shared and unique kinases after acquired resistance develops despite a common genetic origin. Additionally, we noted that the kinases altered in the acute setting are distinct from those in acquired resistance. By identifying these differential temporal kinomic vulnerabilities throughout the drug response process, we generated a kinase signature associated with inhibition of EGFR. Further molecular interrogation of these signature genes reveals that drug treatment induces an unexpected increase in Cdk6 protein but not mRNA despite a decrease in proliferation measured by both live cell counts and transcriptomics. Survival experiments with two cohorts of orthotopic allografts show that upfront combination inhibition of Cdk6, with abemaciclib, and EGFR, with neratinib, significantly prolonged median survival compared to neratinib alone. Our findings suggest that identifying and inhibiting targets with synthetic lethality in the upfront combinatorial setting is a viable approach for precision oncology and may help provide an avenue to overcome the resistance mechanisms that contributed to the failures of EGFR as a molecular target in GBM.

overall_design: Here we performed transcriptomic charecterization of an isogenic genetically engineered EGFRvIII kinome after treatment with EGFR TKI. Transcritomics was performed at 0, 4, 24, and 48 after treatment and also after acquired resistance developes.

first: Abigail

last: Shelton

first: Erin

last: Smithberger

first: Julia

last: Ziebro

first: Kasey

last: Skinner

first: Ryan

middle: E

last: Bash

first: Richard

last: Kirkman

first: Allie

last: Stamper

first: Madison

last: Butler

first: Alex

last: Flores

first: Steven

middle: P

last: Angus

first: Michael

last: East

first: Timothy

last: Cloughesy

last: Howton

first: Brittany

middle: N

last: Lasseigne

first: Christopher

middle: D

last: Willey

first: Gary

last: Johnson

first: Anita

middle: B

last: Hjelmeland

first: Frank

last: Furnari

first: C. Ryan

last: Miller


title: Overexpression of METTL3 leads to differential gene expression in the rat proximal tubular epithelial cell line NRK-52E

first: Yuhui

last: Zang

address: 163 Xianlin Road

institute: Nanjing University

summary: We generated the NRK-52E sublines overexpressing METTL3 (referred as to lv_Mettl3), and performed transcriptome sequencing to identify the differentially expressed genes compared to the control cell line (referred as to lv_nc).

overall_design: Total RNA was extracted from NRK-52E subline cells with TRIzol reagent. The RNA purity and integrity were analyzed with the Agilent Bioanalyzer 2100 (Agilent). The mRNA was purified from total RNA after removal of rRNA and sequenced on an Illumina Hiseq2500 system.

first: Yanyan

last: Sun

first: Jia

last: Ge

first: Wei

last: Zhang

first: Junfeng


title: Azanucleoside treatment leads to B cell leukemia in Rag1 deficient mice

city: Bethesda

first: Peter

last: Aplan

state: Maryland

address: 37 convent drive

department: Genetics

institute: CCR-NCI-NIH

summary: 5-Aza-4’-thio-2’-deoxycytidine (ATC) is an azanucleoside cytidine analog used in preclinical studies for solid tumors as a promising DNA methyltransferase 1 (DNMT1) inhibitor. Repeated treatment with ATC has previously been shown to result in acute lymphoblastic leukemia (ALL) of both B-cell and T-cell origin in mice. Herein, Rag1 knockout mice were treated with ATC to determine if ATC could be oncogenic in non-lymphoid cells. However, ATC treatment targeted early B progenitors and invariably led to B-lineage ALL, with a gene expression signature similar to human B cell precursor (BCP) ALL. Whole exome sequencing revealed numerous single base substitutions of cytosine, primarily C>G transversions at CpG dinucleotides, within genes important for BCP-ALL. Bisulfite sequencing and treatment with a non-covalent DNMT1 inhibitor indicated that methylated cytosines were preferred targets for mutagenesis. This study reveals that ATC exposure leads to both DNMT1 dependent and independent mutagenesis and provides a direct link from ATC exposure to complex mutation signature to malignant transformation

overall_design: We used Bulk RNA Sequencing for comparison between expression profiles between BCP-ALL and non-leukemic counterpart, we used Rag1 KO BCP ALL samples(N=6), CD19+B220+ sorted Rag1 BM cell samples (N=3) and B220+ sorted Rag1 BM cell samples (N=2).

first: Vijay

last: Negi

first: Ryan

last: Bertoli


title: Single-cell analysis of mesenteric lymphatic endothelial cells following lymphatic-specific deletion of ERG/FLI1

city: Daejeon

first: Myung Jin

last: Yang

institute: Institute for Basic Science

summary: To investigate the transcriptomic changes following dual deletion of transcription factors ERG and FLI1, lymphatic endothelial cells (LEC) from mesenteries of WT or double deleted mice were FACS sorted and single-cell RNA seq was performed.

overall_design: Mesenteric LEC of WT or ERG/FLI1 double deleted mice were sorted and single-cell libraries were generated.

first: Gou Young

last: Koh


title: RNA-seq revealed the transcriptome landscape of yak at different developmental stages.

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

summary: This study constructed a complete testicular transcriptome atlas using yak and bovine yak testes at different developmental stages, and explored the changes in gene expression during the sexual maturation process of yak testes. This study utilized RNA-seq technology to construct a transcriptome of yak testicular development, revealing the expression of genes related to spermatogenesis at different developmental stages.

overall_design: Construction of transcriptome map of yak testis

first: Shaoke

last: Guo

first: Mengli

last: Cao

first: Xian


title: RCOR2 downregulates RNF43 via LSD1-mediated histone demethylation in cancer cells

first: Lei

last: Bao

state: TX

address: 5323 Harry Hines Blvd, NB6.126

summary: RCOR2 and LSD1 directly co-binds to RNF43 gene. RCOR2 knockout does not affect LSD1 binding on RNF43 gene.

overall_design: Parental and RCOR2-KO MDA-MB-231 cells were subjected to CUT&RUN with anti-LSD1 antibody. CUT&RUN libraries with anti-normal rabbit IgG were used as input for analysis. Occupancy of RCOR2 and LSD1 on RNF43 gene was analyzed.

first: Weibo

last: Luo


title: RCOR2 downregulates CIITA via HDAC1-mediated histone deacetylation in cancer cells [ChIP-seq]

summary: RCOR2 and HDAC1 directly co-binds to CIITA gene. RCOR2 knockout does not affect HDAC1 binding on CIITA gene. RCOR2 has no binding on most MHCII genes.

overall_design: MDA-MB-231 cells overexpressing HA tagged RCOR2 were subjected to ChIP-seq with anti-HA antibody. Parental and RCOR2-KO MDA-MB-231 cells were subjected to ChIP-seq with anti-HDAC1 antibody. Occupancy of RCOR2 and HDAC1 on CIITA and MHCII genes were analyzed.


title: Effect of RCOR2 in cancer cell stemness and immune evasion

summary: To investigate the function of RCOR2 in cancer cell stemness and immune evasion, we established RCOR2-KO MDA-MB-231 cells by CRISPR-Cas9. We then performed gene expression profiling analysis using data obtained from RNA-seq of the parental cells as well as two independent KO cell lines. Two biological repeats were applied for each cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for parental and RCOR2-KO MDA-MB-231 cells.


title: LKB1-deficient NSCLC cells show vulnerability to high-dose AA-induced pyroptosis.

city: Guangzhou

first: Xiang-yu

address: China

institute: Nanfang Hospital,southern Medical University

summary: The deficiency of LKB1 in tumor cells impairs their ability to sense metabolic stress appropriately,ultimately leading to redox imbalance. LKB1-deficient NSCLC cells predominantly take up ascorbic acid. Inflammatory PCD, including necroptosis, pyroptosis and PANoptosis, could release inflammatory mediators and switch the inflammatory state of TIME. Previous study demonstrated that high-dose AA could promote lung cancer cell death, but the modality of cell death still remained unclear. To further investigated the precise modality of the above inflammatory PCD, we performed RNA sequencing on cells with deficient or intact LKB1 pretreated with high-dose AA or not and then analyzed the established different forms of programmed cell death signaling gene.

overall_design: Gene expression profiling analysis of RNA-sequencing of A549 cells with deficient or intact LKB1 pretreated with or without high-dose AA, 3 replicates for each group.

first: Xiangyu

first: Xuejun

first: Xiaoting

last: Cai

first: Zhongyi

last: Dong

first: Dehua

last: Wu

first: Xue

last: Bai


title: Microglial Replacement as a Drug Delivery Method for the Brain

city: Bronx

first: Rohan

last: Hofland

state: NY

address: 1945 Eastchester Rd, Apt 17D

institute: Albert Einstein College of Medicine

summary: Microglia, the central nervous system's (CNS) resident immune cells, show promise as vehicles for treating intractable neurological disorders. Microglia can be transiently ablated using a Colony Stimulating Factor 1 (CSF1r) inhibitor and can quickly repopulate their environment. They can also be genetically engineered in vitro. Given these properties, replacing native microglia with engineered ones could bypass the blood-brain barrier and revolutionize the way drugs are delivered to the CNS. However, most current strategies for microglia replacement use radiation or transgenic models, limiting clinical applicability. Here, without radiation or transgenics, we successfully replaced microglia within a portion of forebrain tissue of an adult immunocompetent mouse. These microglia were engineered to overexpress Brain-Derived Neurotrophic Factor (BDNF), for which we not only measured an increase within the transplanted region of tissue, but also demonstrated increased TrkB phosphorylation.  These transplanted microglia transcriptionally mirror endogenous repopulating microglia, retain immune functions, and effectively deliver BDNF to the brain parenchyma, demonstrating significant promise for clinical application.

overall_design: Single Cell RNA Sequencing of Cx3Cr1-Cre Csf1r fx/fx;DTA host animals transplanted with microglia infected with a lentivirus expressing a BDNF construct, or microglia without viral infection. These 4 mice (2 virus 2 no virus) are compared to 4 age matched controls with the same genetic background as the transplanted microglia without transplantation (WT)

first: Tiago

last: Gonçalves


title: Effect of decitabine on gene expression in THP-1 or decitabine-resistant THP-1 leukemia cells

first: Xueqin

last: Chen

address: No. 197 Ruijin 2nd Road

department: Ruijin Hospital

institute: Shanghai Jiao Tong University

summary: To globally evaluate transcriptome in THP-1 and decitabine-resistant THP-1 cells treated by decitabine, cells were treated with the IC90 dose of decitabine until 90% cell death was reached, then cultured in decitabine-free medium until confluence, followed by another round of decitabine treatment and the treatment cycles were repeated for 3 months to generate decitabine-resistant THP-1 cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of THP-1 or decitabine-resistant THP-1 cells treated with or without decitabine.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP-1 or decitabine-resistant THP-1 cells treated with or without 1μM decitabine for 6 days.

first: Min

last: Lu

first: Jiale

first: Yuntong

last: Li


title: Applications for estimation of in vivo toxicity point of departure for discovery stage molecule predictive safety assessment

city: Indianapolis

first: Andi

last: Dhroso

state: Indiana

address: 9330 Zionsville Rd

institute: Corteva

summary: Utilization of in vitro (cellular) techniques, like Cell Painting and transcriptomics-based methods could provide powerful tools for risk assessment and regulatory decision-making. However, using these models generates challenges translating in vitro concentrations to corresponding in vivo internal exposures. We tested whether in vivo (rat liver) transcriptional and apical points of departure (PODs) could be accurately predicted from in vitro (rat hepatocyte or human HepaRG) transcriptional PODs or HepaRG Cell Painting PODs using PBPK modeling. We compared two PBPK models, ADMET predictor and the httk R package, and found httk to predict the rat hepatocyte no observed transcriptional effect level (NOTEL)-derived PODs more accurately. Our findings suggest that a rat liver apical and transcriptome POD can be estimated utilizing a combination of in vitro transcriptome-based PODs coupled with PBPK modeling for IVIVE.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: RNAseq transcriptomics profiling on Rat primary hepatocytes and Human HepaRG after treatments with a set of agrochemicals, with known developmental toxicity endpoints, at multiple doses

first: Enrica

last: Bianchi

first: Eduardo

last: Costa

first: Joshua

last: Harrill


title: BICC1 is a genetic modifier for Polycystic Kidney Disease

city: Cleveland

first: Oliver

last: Wessely

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

summary: Autosomal dominant polycystic kidney disease (ADPKD) is primarily of adult-onset and caused by pathogenic variants in PKD1 or PKD2. Variable disease expression is incompletely understood with rare very early-onset PKD (VEO-PKD) presentations in utero or infancy. In animal models, the RNA-binding molecule Bicc1 has been shown to play a crucial role in the pathogenesis of PKD. To further investigate this, we first demonstrated that BICC1 physically binds to the proteins Polycystin-1 and -2 encoded by PKD1 and PKD2 via distinct protein domains. Furthermore, PKD was aggravated in loss-of-function studies in Xenopus and mice. These resulted in more severe disease when Bicc1 was depleted in conjunction with Pkd1, Pkd2 or Pkhd1., Finally, in a large human patient cohort, we identified several VEO-PKD patients that exhibited compound situations of PKD1, PKD2 and PKHD1 in conjunction with BICC1 as well as a sibling pair with a homozygous BICC1 mutation. Together these findings support the hypothesis that BICC1 cooperates with PKD1 and PKD2, and that BICC1 variants may aggravate disease severity highlighting RNA metabolism as an important new concept for disease modification in ADPKD.

overall_design: HEK cells were edited using CRISPR/Cas9 to knockout BICC1 or introduce a point mutation in S240P. Cells were grown under standard conditions and processed for RNA extraction and bulk mRNA sequencing.

first: Uyen

last: Tran

first: Lahoucine

last: Izem

first: R

last: Schweickart


title: Effect of STING-TRIM29 interaction inhibitor SB24011 on gene expression upon solo or co-treatment with STING agonist in Raw264.7 murine macrophage-like cells.

city: Seoul

first: Seung Bum

last: Park

address: 1 Gwanak-ro, Gwanak-gu

department: Chemistry

institute: Seoul National University

summary: SB24011 upregulates cellular STING levels through inhibition of STING-TRIM29 E3 ligase interaction. We performed gene expression profiling using RNA-seq in Raw264.7 cells, to investigate the effect of SB24011 on 1) STING downstream pathways upon combination with cGAMP, or 2) the novel gene expressions upon STING upregulation by SB24011.

overall_design: Comparative gene expression profiling analysis using RNA-seq, upon treatment of: 1) DMSO, 2) cGAMP, 3) SB24011, 4) cGAMP + SB24011, 5) cGAMP + 7a (negative analog of SB24011) in Raw264.7 cells.

first: Wansang

last: Cho

first: Solchan

last: Won

first: Yoona

last: Choi

first: Sihyeong

last: Yi

first: Jong

first: Jun-Gyu

first: Caroline

last: Kim

first: Chintam

last: Narayana

first: Ju

middle: H

first: Junhyeong

last: Yim

first: Young

middle: I

first: Dong-Sup

last: Lee

first: Seung


title: Role of Matrix Gla Protein in Brown Adipose Tissue Development

city: Los Angles

first: Kristina

last: Boström

address: 630 Charles E Young Dr S

department: Medicine Cardiology

institute: UCLA

summary:
To investigate matrix gla protein (Mgp) function in angiogenesis and adipogenesis in brown adipose tissue (BAT) of C57BL/6 mice. we dissected 5 pairs of BAT from 4 weeks male Mgp wild-type (WT) and  knock out (KO) mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 5 pairs of WT and KO mice.

overall_design: Comparative gene expression profiling between Mgp KO and WT  mice in brown adipose tissue .

first: Li

last: Zhang

first: Feiyang

last: Ma

first: Xiuju

last: Wu

last: Bostrom


title: Transcriptome of floating aggregate biofilms in Pseudomonas aeruginosa

status: Public on Jun 27 2025

city: Cambridge

first: Rahan

middle: Rudland

last: Nazeer

address: Hopkins Building, Downing Site, Tennis Court Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

summary: Pseudomonas aeruginosa is a critical priority pathogen, whose proclivity to establish chronic infections and to resist antibiotic treatment is intimately linked to its ability to form biofilms at the infection site. Recent developments in our understanding of these biofilms has pointed to the fact that the surface-bound biofilms recapitulated by in vitro models do not sufficiently capture the type of biofilms that occur in infection sites, such as the CF lung. This study aimed to develop a straightforward and medium throughput model for free floating biofilms, alongside a protocol that permits fractionating of the biofilm into its constituent parts. The RNA-seq investigation takes the cells fraction at three timepoints in biofilm development (and one point in a planktonic culture for comparison), to ask what genes are driving the development of these free floating aggregate biofilms.

overall_design: RNA-seq profiling of PAO1 cells at three biofilm timepoints (24, 48 and 72 h) as well as 5 h in planktonic culture.

middle: R

first: Welch

last: Martin


title: Single-cell RNA-seq of MEFs transduced with 4 factors (Nkx2-1, Foxa1, Foxa2, Gata6), 14 days after the transduction

city: Shinjyuku-ku

first: Makoto

last: Ishii

state: Tokyo

address: 35, Shinanomachi

institute: Keio University

summary: Single cell RNA-seq analyses of MEFs obtained from GFP/SP-C transgenic mice on CBA/Ca x C57BL/6 mixed background were transduced sets of 4 combination factors (Nkx2-1/Foxa1/Foxa2/Gata6) into induced pulmonary epithelial cell-like cells 14 days after the transduction. Abstract is as follows: pneumocyte differentiation has been achieved previously using embryonic stem cells or induced pluripotent stem cells. However, direct reprograming of somatic cells into pulmonary epithelial cells has not been achieved. Here, we report that a combination of three or four transcription factors (i.e., Nkx2-1, Gata6, and [Foxa1 and/or Foxa2]) directly reprogrammed mouse tail-tip fibroblast or embryonic fibroblast into differentiated induced pulmonary epithelial cell-like cells (iPUL cells). iPUL cells had a global gene expression profile similar to various kinds of pulmonary epithelial cells. Some iPUL cells showed lamellar body-like structures and expressed SP-C, consistent with the features of alveolar epithelial type II cells. Interestingly, intratracheal administration of iPUL cells rescued influenza virus-induced acute lung injury in mice. These findings demonstrate that functional pulmonary epithelial cell-like cells can be directly reprogrammed from differentiated somatic cells by defined factors. Reprograming of fibroblasts might provide a source of pulmonary epithelial cells for regenerative medicine.

overall_design: We generated pulmonary epithelial-like cells transduced 4 factors (Nkx2-1, Foxa1, Foxa2, Gata6) from mouse embryonic fibroblast and the cells were subjected to scRNA-Seq on the 10X Chromium System (10X Genomics, Pleasanton, CA) with the v3 chemistry. We sequenced (Read1=28 bp, Read2=98 bp and Readi7=8 bp) on a Illumina NovaSeq 6000 (Illumina, San Diego, CA).

first: Masaya

last: Yotsukura