title: B cell leukemia co-opts a hematopoietic stem cell-CD4 T cell tolerance program that facilitates relapse [CITE-Seq]

city: Minneapolis

first: Allison

middle: M.

last: Haaning

state: MN

address: 117 Pleasant St. SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Despite advances in immune therapies, leukemic relapse is still a major obstacle to long-term survival. Using a murine model of B cell leukemia (B-ALL), we show that B-ALL co-opts a hematopoetic stem cell (HSC)-driven program to induce immune-suppressive type-1 regulatory (Tr1) CD4 T cells. The immune-suppressive function of Tr1s that protects healthy HSCs is utilized by B-ALL to evade T-cell surveillance. Using single-cell approaches, we show that B-ALL induces a Tr1 phenotype in all CD4 T cells irrespective of their initial polarization state. Unlike exhausted T cells, Tr1s do not have epigenetic silencing of effector cytokines. Both IL10R- and PDL1-blockade mitigate Tr1 expansion upon treatment with the tyrosine kinase inhibitor nilotinib. However, PDL1-blockade alone expands Th1-memory CD4s and effector CD8s that prevent relapse. We find a similar population of CD4 Tr1s in human B-ALL patients, which correlate with worse prognosis. Thus, B-ALL co-opts an HSC-driven program to induce Tr1s that suppress anti-leukemia T cell responses, which facilitates relapse.

overall_design: For the scATAC-seq study, CD45.1+ mice were injected with CD45.2+ CD4 T cells from a leukemia-specific TCR transgenic mouse (HV1 CD4 T cells) via the tail vein, followed by a challenge with LM138 leukemia cells via the tail vein the next day. HV1 CD4 T cells from leukemic CD45.1+ mice at days 9, 13, and 17 post-leukemia challenge were sorted. As a control, HV1 CD4 T cells from naïve leukemia-specific TCR transgenic mice were also sorted. Nucleii from the sorted T cells were isolated and captured on the 10x Chromium, and library preparation was generated using the Chromium Next GEM Single Cell ATAC library kit (ver. 1.1), following the manufacturer’s recommendations. For the scRNA-seq study, CD45.1+ mice were injected with CD45.2+ HV1 CD4 T cells via the tail vein, followed by a challenge with LM138 leukemia cells via the tail vein the next day. Some of the CD45.1+ mice were treated with the tyrosine kinase inhibitor nilotinib five days/week for one week starting at day 14 post-leukemia-establishment, as well as treatment with an isotype control or IL10R blocking or PDL1 blocking antibody on days 14, 16 and 18 post-leukemia-establishment. A 50:50 mixture of CD45.2+ HV1 CD4 T cells as well as CD44+ CD8 T cells were sorted from the indicated experimental treatment arms. The sorted T cells were labeled with treatment arm-specific hashtag oligonucleotide (HTO) antibodies, as well as CITE-Seq antibody derived oligonucleotide tag (ADT) antibodies to CD4, CD39, CD4b, PD1, TIM3 and LAG3. Cells were captured and single cell sequencing for gene expression (GEX), sample-specific hashtag and protein feature barcodes, and T-cell receptor (TCR) repertoires was performed using the 10X Genomics Chromium Next GEM Single Cell 5' (ver. 1.1) reagents, resulting in three (GEX, HTO/ADT, and TCR) libraries.

first: Hrishi

last: Venkatesh

first: Sean

middle: I

last: Tracy

first: Todd

last: Knutson

first: Yinjie

last: Qiu

first: Michael

middle: A

last: Farrar


title: Restoration of CD56dim NK Cells by Methotrexate Contributes to the Treatment of Juvenile Idiopathic Arthritis

status: Public on Dec 31 2025

city: 广州

first: zhanying

last: wu

state: 广东

address: 803, Building 2, Jinxiyuan, Zengbian, Xinzao Town, Panyu District, Guangzhou, China

country: China

institute: GZHMU

type: Expression profiling by high throughput sequencing

summary: Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease in childhood. To elucidate the mechanism of methotrexate (MTX) treatment-induced JIA clinical remission, we conducted single-cell RNA sequencing (scRNA-seq) analysis of peripheral blood mononuclear cells (PBMCs) obtained from a female JIA patient before and after MTX treatment. Besides, we integrated our data with public bulk RNA-seq data. We found that the proportion of the CD56dim NK subsets was restored after MTX treatment, suggesting that CD56dim NK subsets are mainly involved in MTX treatment-induced JIA clinical remission. Differential expression analysis showed that the NK cell-mediated cytotoxicity pathway was riched in CD56dim NK subsets. Furthermore, bulk RNA-seq results showed that MTX-treated NK-92 cell lines were also enriched for NK cell-mediated cytotoxicity pathways. Our data highlight the importance of CD56dim NK subsets in MTX treatment-induced JIA clinical remission.

overall_design:
We conducted single-cell RNA sequencing (scRNA-seq) analysis of peripheral blood mononuclear cells (PBMCs) obtained from a female JIA patient before and after MTX treatment. Besides, we conducted bulk RNA-seq of NK-92 cell lines with or without MTX treatment for further validation.

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Zhanying

last: Wu

first: Wenliang

last: Zhang


title: Effect of B cell deficiency in mice during Acientobacter baumannii respiratory infection

city: Oxford

first: Aminul

last: Islam

state: OH

address: 700 E High street

department: Microbiology

country: USA

institute: Miami University

summary: Role of B cells against pulmonary infection caused by Acinetobacter baumannii is poorly understood. In this study we performed RNA-seq of whole lung tissue to compare the gene expression profile of WT C57BL/6 and B cell deficient mice (muMT) at 4 hours post infection (4hpi). We also compared the gene expression profile of naive WT and muMT mice. Here we report that naive WT mice had significantly higher expression of numerous genes related to antimicrobial peptide production, leukocyte chemotaxis and activation. We also found that the B cell deficiency lead to higher expression of genes associated with  decreased pulmonary respiratory rate, increased pulmonary ventillation rate, and increased recruitment of pulmonary eosinophils at 4hpi. This observation suggests a higher pulmonary infammatory response in B cell deficient mice. Taken together, this study expands our current understanding about the role of B cells in controlling A. baumannii at the early stages of respiratory infection.

overall_design: WT and muMT mice were intranasally infected with 10^8 cfu of Acinetobacter baumannii AB5075 strain. At 4 hours post infectiopn, lung tissues were aseptically harvested and total RNA was extracted from the lungs for RNA-sequencing. Lung tissues were also harvested from uninfected mice for RNA-sequencing.  We then performed comparative gene expression profiling analysis using the data obtained from RNA-seq.

first: Luis

last: Actis

first: Timothy

last: Wilson


title: Generation of hiPSC-derived brain microvascular endothelial cells using a combination of directed differentiation and transcriptional reprogramming strategies

city: New York

first: Andrew

last: Sproul

state: NY

address: 650 West 168th Street

institute: Columbia Univeristy

summary: The blood-brain barrier (BBB), formed by specialized brain microvascular endothelial cells (BMECs), regulates brain function in health and disease. In vitro modeling of the human BBB is  limited by the lack of robust protocols to generate BMECs from iPSCs. Here, we report generation of reprogrammed BMECs (rBMECs) through a combination of hiPSC differentiation into BBB-primed endothelial cells (bpECs) and subsequent reprogramming with two BBB transcription factors, FOXF2 and ZIC3. rBMECs express a subset of the BBB gene repertoire including tight junctions and transporters, exhibit higher paracellular barrier properties, and have lower tracer diffusion and transcellular transport compared to primary hBMECs, and can be activated by oligomeric Ab42 . We then generated an hiPSC 3D microfluidic system that incorporates rBMECs, pericytes and astrocytes using the MIMETAS platform. This novel 3D system closely resembles the in vivo BBB at structural, functional and transcriptome levels, and can be used to study pathogenic mechanisms of neurological diseases.

overall_design: Invastigate FOXF2 and ZIC3 transcription factor effectes on differentiation of brain microvascular endothelial cells.

first: Ugur

last: Akcan

first: Aomeng

last: Cui

first: Dritan

last: Agalliu


title: mRNA expression quantitative Analysis of mesenchymal stem cells (MSCs) treated with  CaP@Sr-MOF compared with control I

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

summary: The goals of this study are to evaluate the mRNA expressions of genes in mesenchymal stem cells treated with CaP@Sr-MOF

overall_design: There are 6 samples for mesenchymal stem cells ( control and CaP@Sr-MOF-treated)

first: L

first: Z


title: Cold-inducible brown fat thermogenesis enhances MHC class I expression and antitumor immunity in ovarian cancer.

city: Shanghai

first: Haiou

last: Liu

address: No.128, Shengyang road, Yangpu distinct, Shanghai, P. R. China.

institute: Fudan University

summary: Brown adipose tissue (BAT) thermogenesis, induced by cold exposure or β3-adrenergic receptors (β3AR) agonist, decreases tumor glucose availability and arrests tumor progression. However, the effect of BAT activation on tumor metabolic reprogramming, the tumor microenvironment (TME), and the possibility of in combination with immunotherapy has not been defined. Here, we found that cold-inducible BAT thermogenesis promoted an anti-Warburg metabolic shift that reshaped TME characterized by accumulation of tumor-infiltrating CD8+ T cells (CD8+ TILs) with effector-like and memory phenotype and proinflammatory macrophages. Consistently, combination treatment with anti-PD-1 and cold exposure or β3AR agonist, strongly inhibited tumor growth or complete regressions across multiple preclinical mouse models. Therefore, BAT thermogenesis by cold exposure or β3aR agonist, highlighting a promising therapeutic approach to increase tumor immunogenicity and improve immunotherapy efficacy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor tissues, sorted tumor cells, and sorted CD8+T cells from HM1 tumors under 30 °C and 4 °C.

first: Kankan

last: Cao


title: scRNAseq of EMT6.5 mammary tumors 24 hours after vehicle or treatment with the TLR2/6 agonist AXA-042

city: Bonn

first: Tobias

last: Bald

address: Venusberg-Campus 1

department: Institute for Experimental Oncology

country: Germany

institute: University Hospital Bonn

summary: Cancer immunotherapies targeting the adaptive immune system have revolutionized the treatment for many cancer patients. However, a considerable fraction of patients does not benefit from targeting only the adaptive arm of the immune system. Here, we demonstrate that priming the innate immune system via systemic delivery of a novel synthetic TLR2/6 agonist, AXA-042, represents a rational strategy to boost anti-tumor immunity. TLR2 and TLR6 expression in mouse and human was predominantly confined to tumor-infiltrating myeloid immune cells. Activation of TLR2-signalling induced a pro-inflammatory phenotype in myeloid immune cells with increased cytokine production which resulted in strong T cell dependent anti-tumor immune responses. Systemic delivery of AXA-042 was well tolerated in mouse and non-human primates, demonstrated innate response engagement and anti-tumor efficacy as monotherapy and in combination with checkpoint inhibitors across a wide range of preclinical mouse models. Preclinical efficacy and safety studies provide evidence that priming and re-shaping the innate immune system with the systemic administration of a TLR2 agonist may represent a promising approach for cancer patients. AXA-042 has completed GLP toxicology studies and is currently in clinical development (ACTRN12622000993796) in advanced solid tumors.

overall_design: Female Balb/c mice bearing orthotopic EMT6.5 mammary tumors received a single intravenous treatment of saline or AXA-042 (10 μg/mouse), 10 days after implantation of 1x105 cells, when tumors were ~300mm3. Mice were culled 24h later and tumors recovered for single cell transcriptomic analysis.

first: Robin

middle: L

last: Anderson

first: Dillon

last: Corvino

first: Anna

last: Galkin


title: Under pressure: Pressure loads can modify endothelial cell flow responses

city: Seattle

first: Christian

middle: J

last: Mandrycky

state: WA

address: 850 Republican St

department: Bioengineering

institute: University of Washington

summary: Blood flow within the vasculature is a critical determinant of endothelial cell (EC) identity and functionality, yet the intricate interplay of various hemodynamic forces and their collective impact on endothelial and vascular responses are not fully understood. Specifically, the role of hydrostatic pressure in the context of flow response is understudied, despite its known significance in vascular development and disease progression. To address this gap, we developed in vitro models to investigate how pressure influences EC responses to flow. Our study demonstrates that elevated pressure conditions significantly modify shear-induced flow alignment and increase endothelial cell density, a phenomenon often observed in vascular diseases. Utilizing both bulk and single-cell RNA sequencing, we found that while flow is the primary driver of transcriptional changes from static conditions, pressure distinctly modulates this flow response by upregulating gene sets linked to arterial cell phenotypes. When compared to early vascular development stages, pressure was notably associated with gene sets that promote the formation of early hemogenic endothelial cells. Our findings emphasize the necessity of an integrative approach to endothelial cell mechanotransduction, one that encompasses the effects induced by pressure alongside other hemodynamic forces.

overall_design: To investigate the effect of pressure conditions on endothelial cells responses to fluid shear stress, we cultured human pulmonary artery endothelial cells in microfluidic channels under different hemodynamic conditions. For static control conditions, cells were either cultured in a well plate (culture format = "wells") or in a microfluidic channel without flow. In all other samples, cells were exposed to controlled fluid shear stress (0, 5, 10, dyne/cm2) and pressure (0, 20, 60 mmHg) conditions for 24 hours to determine if pressure conditions modify the endothelial cell response to fluid shear stress.

first: Ying

last: Zheng


title: The effect of E2F proteins on thymic hypo- and hyper-plasia

city: Nashville

first: Seung Woo

last: Kang

state: TN

address: MRBIV 10475, 2215 Garland Avenue

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

summary: Deletion of E2F binding sites with CRISPR-Cas9 revealed a dynamic regulation of Foxn1 transcription and its direct effect on the thymic size and function.

overall_design: With CRISPR-Cas9, we deleted two E2F binding sites of Foxn1 proximal promotor. We compared the dataset to wild-type total thymic stromal scRNAseq dataset (GSE264402).


title: 10X Visium Spatial transcriptomics of murine small intestine 6 and 14 days post Heligmosomoides polygyrus infection with or without LXR agonist GW3965

city: Solna

first: Ning

last: He

address: Solnavägen 1

country: Sweden

institute: Karolinska Institutet

summary: In this dataset, we investigate the murine proximal small intestine spatial transcriptomic profile at the day 6 and day 14 post Heligmosomoides polygyrus infection and compare the genes alteration with and without LXR activation by sythetic ligand GW3965 diet.

overall_design: Wild type male C57BL/6JRj mice purchased from Janvier-lab were under standard of GW3965 diet for 10 days then mice were infected with 200 L3 Heligmosomoides polygyrus via oral gavage. At day 6 and day 14 post infection, proximal small intestine (4~6cm) was collected from each mouse. To prepare the swissroll, the small intestine was rolled from the proximal to the distal and frozen in OCT. Cryo-sectioned (10µm) and placed on the 10X visium provided slide with a barcoded square (6.5mm x 6.5mm). Libraries were prepared according to 10X Visium spatial transcriptomics protocol and submitted for sequensing

first: Xinxin

last: Luo

first: Ludvig

last: Larsson

first: Eduardo

last: Villablanca


title: Deciphering the Neurological Puzzle in ALG13-CDG Through Cutting-Edge Brain Organoid Modeling.

city: New York City

first: Rameen

last: Shah

address: 1425 Madison Avenue

institute: Mount Sinai

summary: Asparagine-linked glycosylation 13 (ALG13) is an X-linked congenital disorder of glycosylation (CDG). Our study addresses the urgent need for deeper insights into ALG13-CDG characterized by significant gaps in our understanding of its pathobiology and the absence of effective treatment options. Despite extensive research on various CDG, investigations into ALG13-CDG have been hindered by the lack of observable glycosylation defects in patient samples, particularly in blood and fibroblasts. However, the profound neurological symptoms associated with ALG13-CDG strongly suggest a primary impact on the brain. To test this hypothesis, we established a brain model of ALG13-CDG using induced pluripotent stem cells derived from fibroblasts, which were subsequently differentiated into human cortical cortical organoids(hCOs). Contrary to previous reports of random X-inactivation in individuals with ALG13-CDG, we observed X-inactivation skewing within ALG13-CDG cell lines. Our multi-omics approach, encompassing single-cell RNA-seq, proteomics, glycoproteomic, and metabolomics analyses, revealed significant reductions in glycosylation and expression of key proteins essential for axon growth, neuronal migration, and synaptic plasticity. Additionally, alterations in protein abundances associated with neuronal migration and nucleotide synthesis were also observed, along with distinctive changes in genes linked to epilepsy risk and lipid metabolism. Metabolomic analyses ALG13-CDG hCOs showed elevated GlcNAc levels and decreased nucleotide synthesis metabolites. Importantly, our study sheds light on the previously unrecognized protein glycosylation defect in ALG13-CDG, offering valuable insights into the brain-related disturbances underlying the disease pathology. Furthermore, our findings hold promise for guiding the clinical management of seizures in ALG13-CDG patients, addressing a critical unmet medical need.

overall_design: 3 ALG13-CDG cortical brain organoids and 3 control brain organoids were seperated into a single cell suspension using Neurosphere Dissociation Kit and ran through scRNAseq

first: Silvia

last: Radenkovic


title: Ube4a liver-specific knockout effect on fasted liver

city: Shenzhen

first: FengFeng

last: Rao

address: 1088 Xueyuan Road

institute: Southern University of Science and Technology

summary: Ectopic deposition of free fatty acids (FFAs) causes lipotoxicity in metabolic disorders such as obesity/diabetes. How intracellular FFAs are sensed and detoxified remains unclear. We identify a cytosol-facing FA-sensing machinery that synchronizes lipid droplet (LD) dynamics with FFA abundance. Specifically, an Ubxn4-Ube4a E3 complex located at the ER-LD interface restricts LD growth via non-degradative ubiquitylation of the acyl-CoA synthetases FATP1/4, thereby disrupting Fatp interaction with diacylglycerol O-acyltransferase 2 (Dgat2) to avoid premature triglyceride synthesis and storage into LD. Unsaturated FA binds to Ubxn4’s UAS domain, competitively displacing the E3 ligase Ube4a to autonomously promote Fatp-Dgat2 complexation and LD growth. Cellular UBE4A deletion accelerates LD growth, whereas mice with hepatocyte-specific Ube4a deletion are predisposed to hepatic steatosis, fibrosis, and hepatocellular carcinoma. Thus, FFA levels and LD expansion are coordinately monitored via ubiquitylation-modulated coupling between FA activation and acyltransfer, thereby maintaining lipid homeostasis to avoid metabolic anomalies.

overall_design: The hepatocyte specific knock out of Ube4a mice (Ube4a LKO) were generated in a C57BL6/J background by cross-breeding Ube4a flox/flox mice generated through homologous recombination with Albumin-Cre mice (Jax: 003574). 5 Ube4a flox/flox mice and 7 Ube4a LKO mice were fasted overnight for 16h. We then performed gene expression profiling analysis using data obtained from RNA-seq of livers from these mice.


title: Impact of Depletion or Overexpression on Gene Expression in Triple Negative Breast Cancer

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

summary: Triple-negative breast cancer (TNBC), known for its aggressiveness and high lethality, presents a significant challenge in terms of treatment. Its heterogeneity and absence of hormone receptors or HER2 expression further limit the availability of targeted therapies. Breast cancer stem cells (BCSCs), recognized for their role in fueling TNBC malignancy, are now being targeted as a vulnerability for TNBC treatment. In this study, we analyzed the transcriptome of BCSCs and identified Kinesin Family Member 20A (KIF20A) as an essential gene for BCSC survival and TNBC tumorigenesis. Depletion or pharmacological inhibition of KIF20A impairs BCSC viability, tumor initiation, and development both in vitro and in vivo. Mechanistically, KIF20A regulates BCSC stemness by modulating the oxidative phosphorylation (OXPHOS) pathway in mitochondria. Our findings underscore the importance of targeting KIF20A as a strategy to exploit BCSC vulnerability in TNBC.

overall_design:
To investigate the function of KIF20A in triple negative breast cancer, we established MDA-MB231 cells depleted or overexpressing KIF20A.
We then performed gene expression profiling analysis using data obtained from RNA-seq.
We performed comparative gene expression profiling analysis of RNA-seq data in MDA-MB231 cells.

first: Yayoi

last: Adachi

first: Qing

last: Zhang

first: Lin

last: Xu


title: Age-dependent alterations in the human striatum identify a PPP1R15B-miR-196a node as a modifier of Huntington’s disease phenotypes

city: Saint Louis

first: Victoria

middle: A.

last: Church

state: MO

address: 660 Euclid

institute: Washington University School of Medicine

summary: Polyglutamine expansion in Huntingtin (HTT) causes its aggregation and progressive loss of striatal neurons in Huntington’s disease (HD). HD is a mostly adult-onset neurodegenerative disorder with no disease-modifying therapies. Here we found that human striatal aging is associated with a global upregulation of genes involved in translation, including the translation and proteostasis regulator PPP1R15B (R15B). We used the R15B inhibitor Raphin1 to investigate if the age-associated changes could modify HD pathology. R15B inhibition rescued early learning and late motor deficits in HDYAC128 mice. In striatal medium spiny neurons directly reprogrammed from fibroblasts of symptomatic HD patients (HD-MSNs), Raphin1 reduced the formation of mutant HTT aggregates and neuronal death. Genetic knockdown of R15B also protected HD-MSNs from neurodegeneration whereas its overexpression exacerbated disease phenotypes. Moreover, both human striatum and reprogrammed MSNs exhibited age-dependent decline of miR-196a, a microRNA that directly targets non-conserved sites in human R15B 3’UTR and overexpressing miR-196a lowered mutant HTT aggregation. This work identifies age-dependent alterations in miR-196a and its target R15B and demonstrates the therapeutic potential of reversing these changes in diverse models and readouts of HD. We propose miR-196a and R15B as disease-modifying targets in HD.

overall_design: To determine the effect of Raphin1 on HD-MSNs, we treated HD-MSNs or control MSNs with Raphin1 for two weeks. We then obtained RNA-sequencing reads and compared the effect of drug treatment in HD-MSNs.

first: V

first: A

middle: S

last: Yoo


title: The role of the circadian transcriptional network in the aging Drosophila eye

city: West Lafayette

first: Sarah

last: McGovern

state: IN

address: Department of Biochemistry

department: Biochemistry

institute: Purdue University

summary: The circadian rhythm controls 24-hour periodic behaviors and physiology, and is observed across animal kingdoms including animals, plants, and fungi. The circadian clock is synchronized with the solar day, maintaining a robust 24-hour periodicity in consistent environmental conditions. Despite this robustness, behaviors that desynchronize the circadian clock with the solar day (e.g., shift working, sleep deprivation) have been widely implicated as being detrimental to human health. Additionally, the circadian rhythm in humans shows both an altered phase and a decrease in amplitude with aging. The circadian clock is synchronized by light at the highest level via direct innervation from the eyes to the suprachiasmatic nucleus in the hypothalamus. During aging, visual function decreases, which can result in decreased circadian photoreception, linking loss in visual function with decreased circadian rhythmicity. Despite these links between aging, alterations in circadian rhythm, and age-related decline in visual function, much remains unknown about the complex interplay between these processes. To profile transcriptome-wide rhythmic changes in photoreceptors during aging, photoreceptor nuclei were collected from young (D10) and old (D50) flies every four hours and used for nuclear RNA-seq.

overall_design: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 400 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated Zeitgeber times (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by RNA isolation and purification.

first: Gaoya

last: Meng

first: Vikki

last: Weake


title: A genome-wide CRISPRa screening to functionalize lncRNAs in CDK4/6i response [activation_RNAseq]

city: Pittsburgh

first: Da

last: Yang

address: 308 Salk Pavilion

institute: University of Pittsburgh

summary: RNA-seq data for candidate genes identified from CRISPR activation screen for regulation of CDK4/6i response

overall_design: Total RNA-seq data for candidate genes activation in MCF-7 cells

first: Yifei

last: Wang

first: Yueshan

last: Zhao

first: Min


title: Virus-Host Interactions Gets Lousy: P1vir Phage Development Upon Impaired RNA Global Regulation in E. coli Cells

city: Gdańsk

first: Grzegorz

last: Cech

state: Pomorskie

address: Wita Stwosza 59

department: Department of Bacterial Molecular Genetics, Department of Bacterial Molecular Genetics, University of Gdańsk

country: Poland

institute: Faculty of Biology, University of Gdańsk

summary: Bacteriophage P1 is one of the most commonly studied phages in molecular biology, and P1vir, its virulent derivative, has been widely used in almost every biotechnological laboratory as a useful genetic tool. Phage development depends on many host proteins and the cellular physiological state. In many cases, metabolic control is assessed by efficient and energy-saving riboregulation, and one of the major cellular hub of the global RNA regulation is the Hfq protein. Despite the fact that this factor was discovered as host factor necessary for Qβ bacteriophage replication, the role of Hfq in phage biology has not been extensively studied. We have found that deletion of the hfq gene resulted in impaired development of P1vir, suggesting its important role, but not indispensability, in the phage biology. We demonstrate global changes in the host-virus transcriptome during the infection. We have found that at different times after infection of the wild type strain (10 and 20 min), numerous hosts genes have been downregulated. On the other hand, in the Δhfq mutant, relatively small number of genes has been downregulated. Furthermore, numerous viral genes have been downregulated in the Δhfq mutant, comparing to the wild-type cells. Our results demonstrate that deficiency in global RNA regulation severely affects phage P1vir development. Thus, observed impaired P1vir development can be explained by abolition of proper cell re-programming during infection and/or impaired phage gene expression. The Hfq protein, as a global RNA hub, occurs in Escherichia coli and its homologues are present in other bacteria and archeons. Therefore, we anticipate that our results put new light on Hfq as a global phage regulator.

overall_design: To obtain a widespread and holistic overview of the virus–host interactions, we analyzed the transcriptome of both, the P1vir phage and the hfq and wild type hosts during the infection. Total RNA sequencing was performed to assess the changes in gene expression pattern at  0, 10 and 20 min of P1vir infection as wel as 0 min with no phage added.

first: Anna

last: Kloska

first: Jakub

last: Giełdon

last: Węgrzyn

first: Agnieszka

last: Szalewska-Pałasz


title: Identification of the Role of Vitamin D and VDR in Human Endometrial Stromal Cells

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: In women undergoing in vitro fertilization, higher vitamin D status has been associated with improved live birth rates. Among women with polycystic ovarian syndrome (PCOS), vitamin D has been associated with improvements in spontaneous ovulation. Vitamin D receptor (VDR) is a nuclear receptor activated by 1,25 dihydroxyvitamin D which is the most active metabolite of vitamin D. Mice that lack the vitamin D receptor exhibit arrested follicular development, uterine hypoplasia, prolonged estrous cycles, and subfertility. Also, one study of mice reported that the vitamin D receptor is expressed in gonadotropin-releasing hormone (GnRH) neurons, which might suggest a role for vitamin D in hypothalamic signaling. Since the vitamin D receptor knockout mouse is sub fertile with uterine hyperplasia, the most likely cause of vitamin D deficiency may be due to estrogen production by the ovary or estrogen responsiveness of the uterus. So, in this study, we want to identify the effect of vitamin D on human endometrial stromal cells associated with female reproduction.

overall_design: Experimental Design: There are 4 groups, and 12 samples in total. All RNAs will be extracted from the human endometrium stromal cell line (T-HESC). 1) Non-targeting siRNA transfection (control) - treated with vehicle (n=3), treated with 1,25-dihydroxyvitamin D3 (n=3) 2) VDR siRNA transfection (VDR knockdown) -  treated with vehicle (n=3), treated with 1,25-dihydroxyvitamin D3 (n=3)  Data Analysis Strategy: Dr. Tianyuan Wang from the informatics group will help us with the analysis.  1) Remove adaptor 2) Require unique mapping and allow 1 mismatch 3) Remove duplicated reads 4) Down-sampling to the appropriate sequencing depth for each 5) Compare between different groups (siNT vs siVDR, Vehicle vs ligand (1,25-dihydroxyvitamin D3))

first: MyeongJin

last: Yi

first: Tianyuan

first: Francesco

last: DeMayo


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT and cry1 cry2 in blue light or WT, cry2 and prr5 at ZT11 in 12/12 white light condition Transcriptomes

city: SH

first: chen

last: shi

address: Fenglin Road

institute: CSA Center for Excellence in Molecular Plant Science

summary: Analysis of differential differential gene expression regulated by CRYs and PRR5.

overall_design: mRNA profiles of Col-0 and cry1 cry2 grown under continuous blue light for 7 days before harvest or Col-0, cry2 and prr5 grown in 1/2 MS under 12/12 white light for 7 days then harvested at ZT11 were generated by deep sequencing, in triplicate, using novelseq 6000

first: Chen

last: Shi

first: Hongtao

last: Liu


title: CLK and CYC CUT&RUN in aging Drosophila photoreceptors

first: Sarah

last: McGovern

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Rhythmic changes in the transcriptome are widespread during aging in Drosophila photoreceptors. To investigate the mechanisms underyling these rhythmic changes, we performed CUT&RUN in photoreceptors of the core transcriptional activators that control the circadian rhythm, CLK and CYC, in both young and old flies across the circadian day.

overall_design: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 200 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated Zeitgeber times (ZT4, ZT12, ZT16). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by CUT&RUN (dx.doi.org/10.17504/protocols.io.zcpf2vn). For CUT&RUN, 1 ug of either anti-GFP antibody, or IgG was used.  MNase digestion was performed for 5 min using 1 ug of antibody.

first: Gaoya

first: Makayla

last: Marlin


title: B cell leukemia co-opts a hematopoietic stem cell-CD4 T cell tolerance program that facilitates relapse [scATAC-Seq]

city: Minneapolis

first: Allison

last: Haaning

address: 117 Pleasant St. SE

institute: University of Minnesota

summary: Despite advances in immune therapies, leukemic relapse is still a major obstacle to long-term survival. Using a murine model of B cell leukemia (B-ALL), we show that B-ALL co-opts a hematopoetic stem cell (HSC)-driven program to induce immune-suppressive type-1 regulatory (Tr1) CD4 T cells. The immune-suppressive function of Tr1s that protects healthy HSCs is utilized by B-ALL to evade T-cell surveillance. Using single-cell approaches, we show that B-ALL induces a Tr1 phenotype in all CD4 T cells irrespective of their initial polarization state. Unlike exhausted T cells, Tr1s do not have epigenetic silencing of effector cytokines. Both IL10R- and PDL1-blockade mitigate Tr1 expansion upon treatment with the tyrosine kinase inhibitor nilotinib. However, PDL1-blockade alone expands Th1-memory CD4s and effector CD8s that prevent relapse. We find a similar population of CD4 Tr1s in human B-ALL patients, which correlate with worse prognosis. Thus, B-ALL co-opts an HSC-driven program to induce Tr1s that suppress anti-leukemia T cell responses, which facilitates relapse.

overall_design: For the scATAC-seq study, CD45.1+ mice were injected with CD45.2+ CD4 T cells from a leukemia-specific TCR transgenic mouse (HV1 CD4 T cells) via the tail vein, followed by a challenge with LM138 leukemia cells via the tail vein the next day. HV1 CD4 T cells from leukemic CD45.1+ mice at days 9, 13, and 17 post-leukemia challenge were sorted. As a control, HV1 CD4 T cells from naïve leukemia-specific TCR transgenic mice were also sorted. Nucleii from the sorted T cells were isolated and captured on the 10x Chromium, and library preparation was generated using the Chromium Next GEM Single Cell ATAC library kit (ver. 1.1), following the manufacturer’s recommendations. For the scRNA-seq study, CD45.1+ mice were injected with CD45.2+ HV1 CD4 T cells via the tail vein, followed by a challenge with LM138 leukemia cells via the tail vein the next day. Some of the CD45.1+ mice were treated with the tyrosine kinase inhibitor nilotinib five days/week for one week starting at day 14 post-leukemia-establishment, as well as treatment with an isotype control or IL10R blocking or PDL1 blocking antibody on days 14, 16 and 18 post-leukemia-establishment. A 50:50 mixture of CD45.2+ HV1 CD4 T cells as well as CD44+ CD8 T cells were sorted from the indicated experimental treatment arms. The sorted T cells were labeled with treatment arm-specific hashtag oligonucleotide (HTO) antibodies, as well as CITE-Seq antibody derived oligonucleotide tag (ADT) antibodies to CD4, CD39, CD4b, PD1, TIM3 and LAG3. Cells were captured and single cell sequencing for gene expression (GEX), sample-specific hashtag and protein feature barcodes, and T-cell receptor (TCR) repertoires was performed using the 10X Genomics Chromium Next GEM Single Cell 5' (ver. 1.1) reagents, resulting in three (GEX, HTO/ADT, and TCR) libraries.

first: Hrishi

last: Venkatesh

first: Sean

last: Tracy

first: Todd

middle: P

last: Knutson

first: Yinjie

last: Qiu

middle: M

first: Michael

last: Farrar


title: B cell leukemia co-opts a hematopoietic stem cell-CD4 T cell tolerance program that facilitates relapse

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

overall_design: Refer to individual Series


title: Targeting the FOXP3–T-bet interaction to restore Treg stability in IFN-γ–driven autoimmunity

first: Weiqi

last: Zhang

address: 280 South Chongqing Road, Shanghai, China

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

summary: Regulatory T cell (Treg) stability is maintained by dynamic remodeling of the FOXP3 transcriptional complex, and its disruption leads to Treg dysfunction and immune dysregulation. However, how specific FOXP3 mutations alter the dynamic remodeling of the FOXP3-complex and thereby contribute to pathogenic Treg reprogramming in IPEX syndrome remains unclear. Here, by uncovering the distinctive pathogenesis of FOXP3V408M mutation in IPEX syndrome, we demonstrate that the FOXP3–T-bet interaction fine-tunes Treg function by repressing IFN-γ production, thereby preventing Th1-driven inflammation. Using an AI-driven virtual screening approach, we identified a first-in-class small molecule, 430C10, that directly binds FOXP3 and reinforces its interaction with T-bet. 430C10 robustly suppressed Treg-derived IFN-γ production and alleviated IFN-γ-driven tissue inflammation in FOXP3V408M knock-in mice as well as in models of acute colitis. Collectively, these findings establish the FOXP3–T-bet interaction as a central checkpoint governing Treg stability and IFN-γ-driven Th1 pathology, providing proof-of-concept that pharmacologic stabilization of FOXP3–T-bet interaction can mitigate IFN-γ–driven immune disorders.

overall_design: For single-cell RNA-seq of the human samples, we used Ficoll-purified PBMCs from the son (PT) and mother (MOM).

first: Xinnan


title: Targeting melanoma cell-intrinsic beta2 integrin inhibits ICAM-1-mediated tumor progression

city: Boston

first: Shannan

last: Ho Sui

address: 401 Park Drive

institute: Harvard

summary: Integrin b2 is an essential mediator of immune cell activation and trafficking via interaction with intercellular adhesion molecule (ICAM)-1. Expression of b2 integrins is thought to be restricted to cells of the hematopoietic lineage. Here we demonstrate nonhematopoietic expression and CD44-dependent induction and activation of integrin b2 by malignant melanoma cells. Tumor cell-b2 in patient primary melanomas correlates with sentinel lymph node metastases, mediates adhesion to ICAM-1, and promotes tumor progression in preclinical models of human and murine melanoma. Consistently, inhibition of melanoma cell-intrinsic b2 integrin using blocking antibodies or CRISPR/Cas9-based b2 gene knockout potently suppresses ICAM-1-dependent melanoma cell adhesion, tumor growth, and metastatic dissemination. Melanoma cell-b2:ICAM-1 interaction stimulates downstream Wnt pathway components, including non-canonical Wnt5a, the pharmacologic inhibition of which reverses protumorigenic melanoma-b2 integrin activity. This work identifies a tumor cell-intrinsic integrin b2:ICAM-1 protumorigenic axis as a bona fide cancer therapeutic target in melanoma.

overall_design: CRISPR/Cas9-based integrin b2 gene knockout (KO) and respective control YUMM5.2 melanoma cell variants were generated and inoculated subcutaneously into immunodeficient nonobese diabetic/severe combined immunodeficiency (NOD/SCID) IL-2Rg(-/-) KO (NSG), C57BL/6, or ICAM-1tm1Jcgr KO C57BL/6 mice. Total mRNA was sequenced from freshly harvested control and b2 integrin KO tumor biospecimens from each strain (n=2-4 per group).


title: BRD4 Regulates Gemcitabine Efficacy by Modulating Autophagy Activity in Osteosarcoma Cells [Patient samples]

first: Lei

last: Guo

summary: Therapeutic options for metastatic or recurrent osteosarcoma are limited. Gemcitabine and 12 docetaxel combination is used as second-line therapy for this disease. Bromodomain-containing 13 protein 4 (BRD4) plays essential roles in regulating autophagy in several human diseases and is 14 overexpressed in osteosarcoma. Thus, in the current study, we investigated whether BRD4 is 15 involved in the modulation of gemcitabine-induced autophagy in osteosarcoma. We confirmed 16 that gemcitabine induced autophagic flux in LM7 and CCH-OS-D human osteosarcoma cell lines. 17 Furthermore, we found that gemcitabine induced BRD4 protein and mRNA expression in a time-18 dependent manner in LM7 cells and also in CCH-OS-D cells but only at the mRNA level. Moreover, 19 gemcitabine induced CCAAT/enhancer binding protein beta (C/EBPβ), a transcription factor 20 known to regulate autophagy. We further showed that C/EBPβ induction was mediated by BRD4 21 as inhibition of BRD4 blocked its induction. Furthermore, we demonstrated that gemcitabine-22 induced C/EBPβ bound to BRD4. Because inhibition of BRD4 diminished autophagic flux, we 23 conclude that BRD4 may act as an epigenetic regulator of gemcitabine-induced autophagy in 24 osteosarcoma via C/EBPβ. Additionally, because inhibition of BRD4 in gemcitabine treated 25 osteosarcoma cells led to different outcomes, our data suggests the potential for the BRD4- 26 C/EBPβ interaction to define gemcitabine-induced autophagy outcome in osteosarcoma.

overall_design: RNAseq analyses was performed with human osteosarcoma tumors collected from patients treated at the University of Texas MD Anderson Cancer Center following IRB approval. No normal samples were included.

first: Jyothishmathi

last: Swaminathan

first: Nancy

last: Gordon

first: Lin

last: Xu

first: Vidya

last: Gopalakrishnan


title: scRNAseq of the BM immunophenotypic HSC fraction with tracing random DNA-barcode 20 weeks after transplantation

city: minato-ku

first: Tsuyoshi

last: Fukushima

state: tokyo

address: siroganedai 4-6-1

department: Cell therapy

country: Japan

institute: Institute of Medical Science

summary: Random DNA barcode could identified the functional atributes in  immunophenotypic HSC fraction. Combined scRNA-seq with tracing random DNA-barcode could identifed specific molecular signature of the theses functional atributes.

overall_design: HSCs were transduced random DNA barcode and transplantaed to lethal-irradiated mice. BM immunophenotypic HSCs were isolated by FACS 20 weeks after transplantation and analyzed using scRNA-seq.

first: Trine

last: Kristiansen

first: David

middle: T

last: Scadden


title: Ezh2 in NK cell functional regulation

city: Hangzhou

first: Xinhua

last: Liu

state: Zhejiang

address: NO.2318, Yuhangtang road

department: School of Basic Medicine

institute: Hangzhou Normal University

summary: Improving the function of immune cells in tumor microenvironment remains a major challenge in cancer treatment. EZH2 serves as the catalytic subunit of PRC2 that mediates gene repression via catalyzing H3K27me3 at specific genetic loci. Many studies have provided evidence showing that the tumor cell-intrinsic mechanisms of Ezh2-driven oncogenesis and tumor progression. However, the function of EZH2 in tumorigenesis by regulating the tumor immune microenvironment remains poorly understood. Here we used Cre-ERT2/Ezh2fl/fl mouse model to investigate the function and molecular mechanism of Ezh2 in tumor immune microenvironment. Tamoxifen-induced deletion of Ezh2 before tumor cells inoculation resulted in reduced tumor growth and lung metastasis in different tumor xenograft models. Neutralizing natural killer (NK) cells function by anti-NK1.1 antibody completely blocked Ezh2-KO-caused tumor repressive effect. To investigate the mechanism by which EZH2 modulates NK cell function, we profiled >4000 mouse lung NK cells using single-cell RNA sequencing to produce a comprehensive transcriptional landscape and compared WT or Ezh2-/- NK cells development, fate decision and function. We found that deletion of Ezh2 significantly promotes the maturity and function of NK cell. Mechanistically, Ezh2 deletion upregulated the expression of genes related to NK cell maturation and adhesion to tumor cells through reprograming chromatin architecture. Our findings suggest that EZH2 depletion will elevate the tumor-killing of NK cells, which may provide an alternative strategy for cancer immune therapy.

overall_design: ChIP-seq, ATAC-seq, Hi-C and RNA-seq for bone marrow (BM)-induced NK cells from Ezh2-/- and WT mice.

first: Zhe

first: Qiumin

last: Huang

first: Wei

last: Du

first: Yan

last: Jin


title: The multidirectional in-situ osteogenesis pattern based on biomimetic mineralized dual-crosslinked Fibrinogen-GelMA microspheres in the maxillary sinus region II

city: Chang chun

first: huixin

last: Lv

address: 1500 Tsinghua Road

institute: School and Hospital of Stomatology, Jilin University

summary: Dental defects in the posterior maxillary region seriously affect facial contours, as well as physiological functions. When bone height in the maxillary posterior region is extremely insufficient, the difficulty of dental prosthodontics is greatly increased. Autogenous bone replacement of exogenous bone grafting materials is often inadequate, resulting in the insufficient alveolar bone height. It is still necessary to study the mechanism of bone regeneration in this region and explore new treatment methods to ensure the quality of bone reconstruction. The development of mesenchymal stem cell (MSCs) biology and bioengineering has greatly advanced the field of regenerative medicine. MSCs from different tissue sources have different biological processes and differentiation abilities. Our previous studies confirmed that MSCs derived from human maxillary sinus membrane (hMSM) can be cultured in vitro. The lamina propria layer derived MSCs (hLMSCs) and periosteum layer derived MSCs (hPMSCs) from hMSM were isolated and expanded using explant cell culture method. In this study, further study about the biological characteristics of hLMSCs and hPMSCs under the three dimensional biomimetic microenviroment based on biomimetic mineralized dual-crosslinked Fibrinogen-GelMA microspheres are compared using RNA sequencing. According to RNA sequencing and subsequent functional verification, Both hLMSCs and hPMSCs were up-regulated the osteo-related signaling pathways, such as PI3K-AKT signaling pathway. The osteogenetic functions of hLMSCs could be improved by hPMSCs, and the most related signaling pathway pointed to PI3K-AKT signaling pathway. It seems that both hLMSCs and hPMSCs serve as good MSCs potential candidates for bone regeneration. And It also indicates that hLMSCs and hPMSCs are valuable in vitro tools for preclinical studies and future exploration of the origin osteogenesis machenism in maxillary sinus region.

overall_design:
To discover the biological characteristics of hLMSCs and hPMSCs and evaluate their osteogenic capabilities, we isolated and cultured the two cells in vitro, and processed osteogenic induction on them in the three dimensional biomimetic microenviroment based on biomimetic mineralized dual-crosslinked Fibrinogen-GelMA microspheres .
We performed gene expression profiling analysis using data obtained from RNA-seq of hLMSCs. Each group contained three samples.
We then compared the differential expression genes between the RNA-seq data of hLMSCs and hPMSCs-induced hLMSCs, and their osteogenic induced patterns, respectively. Each group contained three samples.

first: Huixin

first: Zhuoran

last: Wang

first: Yihan

first: Yangyang

last: Li

first: Xiuyu

first: Jingxia

last: Chen

first: Siyu

first: Sheng

first: Jingjie

last: Zhai

first: Yanmin

last: Zhou


title: Combining SHP2 inhibition with CX3CR1 inhibition shrinks tumors and normalizes the tumor microenvironment

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: NF1 loss increases RAS-MAPK signaling in myeloid cell dominant benign nerve tumors that cause significant clinical burden, in which MEK inhibitor therapy is only partially effective. We studied SHP2 inhibition, which targets RAS-MAPK and has additional immunomodulatory effects, in a validated preclinical model system and found that both MEK and SHP inhibitors shrank tumor volume and tumor immune compartments. However, neither inhibitor was durable or efficacious in all mice. To identify druggable targets, paraspinal tumors from mice treated for 30 days with either vehicle, MEK inhibitor, or SHP2 inhibitor were collected, dissociated to achieve single-cell suspension and transcriptionally profiled.

overall_design: Nf flox/flox;DhhCre mice were treated for 30 days with 1.5 mg/kg/day of the MEK inhibitor PD-032590, 10mg/kg/day of the SHP2 inhibitor RMC-4550, or vehicle control. Mice were anesthetized with isoflurane, perfused with ice cold phosphate-buffered saline (PBS) lacking calcium and magnesium. Paraspinal tumors were collected within 5 minutes of death and stored in L-15 medium until tissue was cut into 1-mm3 pieces and placed into dissociation medium in 50 mL tubes containing 20 mL L-15 medium, 10 mg collagenase type I, and 50 mg Dispase II in a 37°C incubator for 2 hours, with 170 rpm shaking. The dissociation process was stopped by adding 30 mL DMEM containing 10% FBS. Samples were centrifuged at 800g for 5 minutes at 4°C. Supernatants were removed and cell pellets were resuspended into 50 mL of 1× PBS containing 0.1% BSA. Suspensions were sequentially filtered with 70 μm, 40 μm, and 20 μm cell strainers and centrifuged at 600g for 5 minutes at 4°C. Pellets were resuspended into 100 μL of 1× PBS/0.1% BSA. Trypan blue–negative viable cells were counted to determine the cell concentration for droplet-based scRNA-seq.

first: Niousha

last: Ahmari

first: Leah

last: Kershner

first: Nancy

last: Ratner


title: Analysis of A375 and SKMEL-103 cells after treatment with with DMSO as control or BAY-850

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

summary: To identify the gene expression changes in NRAS mutant cell line SKMEL-103, and BRAF mutant cell line A375 upon BAY-850 treatment, we analyzed these cell line with either control DMSO or BAY-850 treatment via RNA sequencing.

overall_design: SKMEL-103 and A375 cells were plated, samples were either treated with DMSO or BAY-850 (5-micromolar for 24 hours), cells were harvested and were used to prepare the total RNA, followed by RiboRNA depletion with random priming and RNASeq Illumina Hi-Seq 2500 platform, with three biological replicates for each sample.


title: Efficacy of melflufen in relapsed and refractory multiple myeloma patients with mutated or deleted TP53

city: Helsinki

first: Philipp

last: Sergeev

address: Tukholmankatu 8

country: Finland

institute: University of Helsinki

summary: Despite the development of several new treatments for multiple myeloma (MM) clinical challenges remain for patients with relapsed/refractory disease. This is especially so for the high-risk subgroup of patients with del(17p) who have poor response and significantly shorter survival compared to patients without this aberration.  Here, we report the clinical efficacy of melphalan flufenamide (melflufen) in patients with del(17p) from the OCEAN randomized, open label, head-to-head, phase III clinical trial. In the del(17p) subgroup, melflufen plus dexamethasone treatment resulted in favorable progression free survival compared to the pomalidomide plus dexamethasone arm. To understand the superior efficacy of melflufen in TP53 mutated MM, we compared drug response between melflufen and melphalan in primary MM cells from patients with del(17p)/TP53 mutated disease. In line with the clinical data ex vivo sensitivity to melfufen was independent of the TP53 mutation status. To better understand the mechanism of action of melflufen, we investigated DNA damage, apoptosis kinetics and mitochondrial function in TP53 wild type and double mutant (TP53-/-) myeloma cells after treatment with melflufen, melphalan or cyclophosphamide. Melflufen demonstrated superior in vitro efficacy in comparison to the other two alkylators. Comparison of gene expression profiles and DNA damage pathway alterations upon drug treatment in the TP53 wild type and double mutant MM cell lines revealed qualitative differences between melflufen and melphalan. Our insights into the molecular mechanisms of melflufen activity in mutant TP53 genetic background support its clinical efficacy and application in the del(17p) and mutant TP53 MM patient population.

overall_design: TP53 wildtype and TP53 null AMO1 myeloma cells were treated with melflufen, melphalan or DMSO for various time points and their RNA collected for RNAseq analysis

first: Thorsten

last: Stühmer

first: Umair

last: Munawar

first: Tobias

last: Heckel

last: Bischler

first: Klara

last: Acs


title: Astrocyte-microglia signaling controls developmental thalamocortical synapse refinement

city: Durham

first: Kristina

last: Sakers

address: 307 Research Dr

institute: Duke University

summary: Synapse formation and elimination are two crucial processes that concurrently take place in the developing brain. Astrocytes and microglia have been shown to control both processes. However, it is largely unknown how these two major glial cell types of the central nervous system (CNS) communicate to balance synapse formation and elimination. Astrocytes secrete a synaptogenic protein called Hevin/SPARCL1, which induces the formation and plasticity of thalamocortical synapses in the mouse visual cortex. Hevin does so by physically localizing to synaptic clefts and bridging the thalamic axon/cortical dendrite via its interactions with presynaptic Neurexin1a and postsynaptic Neuroligin1b. Here, we found that in addition to this synaptogenic function, Hevin directly signals to microglia cells by interacting with Toll-like Receptors (TLRs) TLR4 and TLR2. This signaling occurs when Hevin is proteolytically cleaved producing an active C-terminal fragment. This fragment is sufficient to upregulate TLR2 expression in microglia and increase microglia phagocytic activity in vivo. This signaling is required for proper refinement of thalamocortical synapses in early postnatal development and for early life ocular dominance plasticity.

overall_design: Microglia were isolated from P7-P9 mouse forebrains via Magnetic Activated Cell-Sorting using Cd11b microbeads. 40-80k cells were plated in each well of a 96 well tissue culture plate. Cells were treated with recombinant proteins at 500nM final concentration. LPS treatment was done at a final concentration of 50ng/mL. OxPAPC treated cells was performed at a final concentration of 15ug/mL. Control cells received additional growth media equivalent to the treatment volume. Microglia were cultured for 6 hours after treatment and then collected and pelleted. RNA was extracted from the cell pellets. RNA was sent to MedGenome for RNA-sequencing library generation and sequencing. Libraries were generated using the Illumina TruSeq stranded mRNA kit and then sequenced on a NovaSeq.

first: Juan

last: Ramirez

first: Evelyn

last: Hardin

first: Crystal

last: Colon-Ortiz

first: Richa

last: Hanamsagar

first: Carina

last: Block

first: Sandeep

middle: K

last: Singh

first: Staci

middle: D

last: Bilbo

first: Cagla

last: Eroglu


title: Epigallocatechin gallate ameliorates retinal pigment epithelial cell damage  via the CYFIP2 /AKT pathway

city: Harbin

first: sijia

last: li

address: 157 Health Road, Nangang District, Harbin City, Heilongjiang Province

institute: Harbin Medical University

summary: Based on the transcriptional data of mice, analyze the important role and regulation mechanism of E target gene CYFIP2 in Age-related macular degeneration

overall_design: We divided the mice into the Y control group, the old control group and the old treatment group, and the retinal tissue was taken for transcriptome sequencing. The total number of samples was 9, and there were duplicate samples.

first: Sijia

last: Li

first: Dawei

last: Sun


title: Potential role of uracil in the antigenic variation of the malaria parasite Plasmodium falciparum

city: Budapest

first: Richard

last: Izrael

state: Pest

address: Magyar tudosok korutja 2

department: Institute of Molecular Life Sciences

country: Hungary

institute: HUN-REN Research Center for Natural Sciences

summary: The high diversity in the genome of the malaria parasite, Plasmodium falciparum is a key contributor to its dominant presence as a terribly infectious agent for centuries. It provides the antigenic diversity to evade the host immune system and allows for the rapid emergence of multidrug resistant parasite strains. Here, we propose the involvement of uracil, a non-canonical base in the DNA, as an intermediary in the diversification of variant surface antigens (VSA). We generated an inducible PfUNG-iKO strain, which revealed the essential nature of uracil base excision repair, a unique feature of the malaria parasite. Furthermore, our proprietary U-DNA-Seq revealed structured enrichment of uracil across the major VSA families, the var and rif/stevor gene families. These results suggest that uracilation and its subsequent removal plays a pivotal role in the parasite life cycle. Their essential nature also brings forth questions about an orchestrated molecular mechanism on the DNA level to maintain the genetic variability.

overall_design: In the current study, we carried out immunprecipitation using a catalytically inactive uracil DNA-glycosylase and sequenced the regions that are enriched in uracilated in DNA fragments. Our goal was to characterize the genomic distribution within the late stage schizont parasites in wild-type and base excision repair mutant, uracil DNA-glycosylase knock-out parasites. The reads were sequenced using an NovaSeq 6000 platform. For reference: PMID 32956035.

first: Angéla

last: Békési

first: Márk

last: Hegedüs

first: Reem

last: El-Monla

first: Gergely

middle: N

last: Nagy

first: Réka

last: Babai

first: Rachel

last: Cerdan

first: Ana

middle: R

last: Gomes

first: Kai

last: Wengelnik

first: Beáta

middle: G

last: Vértessy


title: A genome-wide CRISPRa screening to functionalize lncRNAs in CDK4/6i response

first: Da

last: Yang

summary: Aberrant cell cycle regulation is one of central hallmarks for cancer, and cyclin-dependent kinase inhibitors (CDKi) have showed promising clinical outcome in treating ER+/HER2- breast cancer patients. There are also increasing pre-clinical and clinical studies trying to expand the usage of CDKi to more cancer types. However, the underlying mechanism of high individual variability in clinical response remains unclear. LncRNAs are a group of long non-coding RNAs, which have emerged as regulators and biomarkers for cancer therapeutic outcome. In this study, we first performed a CRISPR activation screen of 9744 lncRNAs in breast cancer cells treated with Palbociclib. We identified 144 and 152 lncRNAs that lead to Palbociclib sensitivity and resistance (FDR<0.05), respectively. Further pharmacogenomic analysis from 41 breast cancer cell lines suggested 34 lncRNAs as potential regulators for Palbociclib response (p<0.05). Targeted screen of overlapped lncRNAs and positive control protein-coding genes was performed to further narrow down the hits. Interestingly, we observed a significant association between cancer cell proliferation and Palbociclib response from both screens. Experimental validation of the screen demonstrated that activation of lncRNA CSS1, CSS2 and CSS3 lead to Palbociclib sensitivity. Mechanically, RNA-seq analysis suggested that they may promote cell cycle progression and downregulate cancer stemness. Collectively, our study characterized novel lncRNAs involved in CDK4/6i response which can act as biomarkers for CDK4/6i treatment in cancer patients.

overall_design: CRISPR activation sgRNA library targeting lncRNAs was transduced in MCF-7 cells and treated with Palbociclib before sequencing to determine sgRNA distribution

first: Yifei

last: Wang

first: Zehua

first: Yueshan

last: Zhao

first: Min

last: Zhang


title: RNA-Seq analysis of WT and Phlpp1-deficient alveolar macrophages in bleomycin-induced PF model

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

summary: The purpose of this study is to detect differentially expressed genes in wild-type (WT) and Phlpp1-deficient alveolar macrophages (AMs) 7 days after bleomycin. We performed gene expression profiling of AMs of broncho-alveolar lavage fluid (BALF) from mice that were intratracheally instilled with saline or bleomycin. Gene expression differences between the two samples could be found using transcriptome profiling (RNA-seq) analysis. RNA profiles were generated by deep sequencing, using Illumina. AMs were stained to confirm the surface expression of CD11c and Siglesc-F. Cells with purity >98% were used for subsequent experiments. We identified several differentially expressed genes in the two groups of cells.

overall_design: Expression profiling by high throughput sequencing

first: Yuyu

last: Jiang

first: Yunkai


title: Irgm1-Ifi35 Axis Promotes Renal Cancer Cell Immune Evasion Through Reprogramming the Differentiation of Myeloid-derived Suppressor Cell.

first: Lu

last: Chen

address: No.197, Ruijin Road II

department: Department of Urology

institute: Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital

summary: The management of cancers has been revolutionized by PD-1 blockade. However, most renal cell carcinoma (RCC) patients do not respond to anti-PD-1 antibodies. Here, we conducted anti-PD-1 treatment using a mouse model of RCC. We identified an immune-resistant subpopulation with high expression of immunity-related GTPase Irgm1 using a DNA barcoding system integrated with single-cell RNA sequencing. Next, the results of CyTOF analysis demonstrated a significant increase in Ly6ClowLy6G-CCL5+ M2-type macrophages after immunotolerance. These macrophages were differentiated from MDSCs and exhibited greater immunosuppressive capabilities than MDSC precursors. We also established contact between high-Irgm1 tumor cells and MDSC differentiation. We identify the tumor-secreted IFN-induced protein Ifi35 as an inhibitor for the differentiation of MDSCs, and Irgm1 facilitates the autophagic degradation of Ifi35 through p62-dependent selective autophagy, which results in the generation of MDSC-derived strongly immunosuppressive macrophages. We further demonstrated that Ifi35 in combination with anti-PD-1 antibody have synergistic therapeutic benefits for RCC.

overall_design: Tumor cells from tumor-bearing mouse model before and after were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of GFP signal and analyzed using scRNA-seq

first: Ao

first: Hai

last: Huang

first: Kiat Shenq

last: Lim

first: Qi

first: Junhui

last: Su

first: Xiaoqun

first: Menghui

first: Yueheng

last: Li

first: Xinjue

last: Dong

first: Yuqi

first: Qingquan

first: Danfeng

last: Xu


title: PHLPP1 Cut&Tag profiling of  bone marrow derived macrophage

summary: Purpose: To transcriptome widely reveal genes regulation by PHLPP1, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) analysis of wild-type (WT) BMDMs. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. WT BMDMs were stimulated with IL-4 (20ng/ml) for 4 hours. Results: We carried out a CUT&Tag assay using antibodies against PHLPP1, and found the global influence of PHLPP1 in regulating genes of transcription regulatory regions of key genes for pro-fibrosis macrophage effector function.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) analysis for PHLPP1-binding DNA  in WT  BMDMs stimulated with IL-4.


title: mRNA expression quantitative Analysis of mesenchymal stem cells (MSCs) treated with  CaP@Sr-MOF compared with control II

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

summary: The goals of this study are to evaluate the mRNA expressions of genes in mesenchymal stem cells treated with CaP@Sr-MOF

overall_design: There are 6 samples for mesenchymal stem cells ( control and CaP@Sr-MOF-treated)

first: L

first: Z


title: Phlpp1-deficient macrophages

first: Xingguang

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

overall_design: Refer to individual Series


title: BRD4 Regulates Gemcitabine Efficacy by Modulating Autophagy Activity in Osteosarcoma Cells [Cell lines]

city: Dallas

first: Lei

last: Guo

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

overall_design: RNAseq analyses was performed using human osteosarcoma cell lines. Differenetial gene expression between these cell lines was determined in the absence of any treatment.

first: Jyothishmathi

last: Swaminathan

first: Nancy

last: Gordon

first: Lin

first: Vidya

last: Gopalakrishnan


summary: To identify chromatic alterations by Phlpp1 deficiency in BMDMs, we performed ATAC-sequencing. We identified regions of chromatin that were altered in Phlpp1 deficiency BMDMs after exposure to IL-4 for 4 h.

overall_design: ATAC-seq to profile the chromatin accessibility in WT and Phlpp1-deficient BMDMs with IL-4 (20ng/ml) for 4 h.

first: Yuyu

first: Yunkai


title: Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Phlpp1-deficient Bone Marrow Derived macrophage Transcriptomes

summary: Purpose: The purpose of this study is to detect activated or silenced genes during wild type (WT) and Phlpp1-deficient bone marrow derived macrophages (BMDMs). Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. WT and Phlpp1 deficient BMDMs were stimulated with IL-4 (20ng/ml) for 12 and 24 hours, of which RNA profiles were generated by deep sequencing, using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA  between WT and Phlpp1 deficient BMDMs.

overall_design: mRNA profiles of WT and Phlpp1 deficient BMDMs were generated by deep sequencing.


title: Targeting the FOXP3–T-bet interaction to restore Treg stability in IFN-γ–driven autoimmunity [CUT&Tag/ATAC-seq]

first: Weiqi

summary: IPEX syndrome is a rare spontaneous autoimmune disease caused by the deficiency or mutations of FOXP3, the dominant transcription factor of regulatory T cells (Tregs). Here, by exploring the pathogenic mechanism of IPEX syndrome, we identified for the first time that FOXP3 physically interacted with T-bet to repress IFNγ production in Tregs. This interaction, independent of T-bet abundance, was essential for restraining IFNγ-mediated Th1 immune response and preventing Treg perturbation. Notably, FOXP3 p.V408M mutation disrupted FOXP3-T-bet interaction, unleashing T-bet-driven IFNγ excessive production and Treg perturbation characterized by impaired suppressive activity on extrinsic Th1 immune response.

overall_design: We used splenic CD4+CD25+ Treg cells sorted from Foxp3WT and Foxp3V408M mice for Foxp3 and T-bet CUT&Tag and ATAC-seq.

first: Xinnan

first: Zheng

last: Bao

first: Siyuan

last: Qiang


title: ERα mediated gene state switching regulates the extent of the single-cell estrogen response [scRNA-seq]

first: Christopher

last: Day

address: 111 TW Alexander Dr.

department: ERBL

institute: NIH/NIEHS

summary: Gene regulation is complex, involving the coordination of hundreds of proteins to initiate transcription.  At individual loci, transcriptional initiation is stochastic, resulting in short periods of nascent RNA synthesis known as transcriptional bursts.  To understand how altered Estrogen Receptor α (ERα) function and cofactor recruitment regulates transcriptional bursting, we utilized single molecule imaging of estrogen responsive genes in Bisphenol A (BPA) treated cells. We observe that cells treated with BPA exhibited TFF1 burst initiation rates and sizes which were indistinguishable from cells induced with Estradiol (E2). However, we observed a 50% reduction in the number of active alleles in BPA treated cells.  This effect is gene specific, as GREB1 was unperturbed.  Although we observed no difference in chromatin accessibility, the TFF1 promoter exhibited an altered structure which coincided with reduced ERα and cofactor binding.  Lastly, deletion of the enhancer locus removed the BPA effect, indicating that enhancer function was perturbed.  Our results demonstrate gene specific effects of altered ERα recruitment and function which lead to a reduction of transcriptionally permissive states. Our work supports the model that the initial estrogen response occurs from alleles in primed transcriptionally permissive states with additional inactive alleles contributing to the cellular response over time.

overall_design: CUT&Tag, ATAC-seq and RNA-seq of MCF7 cells treated with E2 and BPA. Time course scRNA-seq of MCF7 cells treated with E2.

first: Pelin

last: Yesar

first: Gloria

last: Adedoyin

first: Brian

last: Bennett

first: Joseph

last: Rodriguez


title: Disease type and Pathogenic Mechanism induced by PM2.5 in five Human Systems using omics and Human Disease Database [IOSE+Nthy]

city: chongqin

first: xiaomeng

last: li

state: nanchong

address: 266 Fangzheng Avenue, Shuitu Street

institute: Chinese Academy of Sciences

summary: PM2.5 can harm various systems in the human body. However, due to the limitations of epidemiology and toxicology, the disease types, shared and specific pathogenic mechanisms induced by PM2.5 in various human systems are not comprehensive and in-depth revealed. Thus, this study conducted an analysis on the aforementioned issues in respiratory, circulatory, endocrine, female, and male urogenital systems. According to this study, PM2.5 was more likely to induce pulmonary emphysema, reperfusion injury, malignant neoplasm of thyroid, endometriosis of ovary, nephritis in above each system respectively. FOS, extracellular matrix, urogenital system development, extracellular matrix structural constituent conferring tensile strength, and ferroptosis was the most important co-existing gene, cellular component, biological process, molecular function, and pathway in five systems targeted by PM2.5. Furthermore, BTG2, BIRC5, NFE2L2, TBK1, and STAT1 were significantly uniquely targeted by PM2.5 in each system respectively. Important disease related cellular component, biological process, and molecular function were highly specially induced by PM2.5, such as response to wounding, blood vessel morphogenesis, body morphogenesis, negative regulation of response to endoplasmic reticulum stress, and response to type I interferon were the top 1 uq-existing biological processes in each system respectively. PM2.5 highly specially acted on the key disease related pathway, such as PD-L1 expression and PD-1 checkpoint pathway in cancer (respiratory), cell cycle (circulatory), apoptosis (endocrine), antigen processing and presentation (female), and neuroactive ligand-receptor interaction (male). This study provides a new analysis method to clarify PM2.5-related disease types, which is an important supplement to epidemiological investigation. Furthermore, this study has clarified the risks of PM2.5 exposure, elucidated the pathogenic mechanisms, and provided scientific support for promoting precise prevention and treatment of PM2.5-related diseases.

overall_design: To investigate the pathogenic molecular mechanism of Female urogenital and endocrine diseases induced by PM2.5, we performed transcriptome sequencing on IOSE and Nthy cell models.


title: Targeting the FOXP3–T-bet interaction to restore Treg stability in IFN-γ–driven autoimmunity

last: Zhang

address: 280 South Chongqing Road, Shanghai, China

institute: Shanghai Jiao Tong University School of Medicine

summary: Regulatory T cell (Treg) stability is maintained by dynamic remodeling of the FOXP3 transcriptional complex, and its disruption leads to Treg dysfunction and immune dysregulation. However, how specific FOXP3 mutations alter the dynamic remodeling of the FOXP3-complex and thereby contribute to pathogenic Treg reprogramming in IPEX syndrome remains unclear. Here, by uncovering the distinctive pathogenesis of FOXP3V408M mutation in IPEX syndrome, we demonstrate that the FOXP3–T-bet interaction fine-tunes Treg function by repressing IFN-γ production, thereby preventing Th1-driven inflammation. Using an AI-driven virtual screening approach, we identified a first-in-class small molecule, 430C10, that directly binds FOXP3 and reinforces its interaction with T-bet. 430C10 robustly suppressed Treg-derived IFN-γ production and alleviated IFN-γ-driven tissue inflammation in FOXP3V408M knock-in mice as well as in models of acute colitis. Collectively, these findings establish the FOXP3–T-bet interaction as a central checkpoint governing Treg stability and IFN-γ-driven Th1 pathology, providing proof-of-concept that pharmacologic stabilization of FOXP3–T-bet interaction can mitigate IFN-γ–driven immune disorders.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene expression profile at single cell level of endothelial cells (ECs) from LPS-injected PPARD-ECWT or PPARD-ECKO mouse lung

city: Shatin

first: XiaoYu

last: TIAN

state: Hong Kong

address: Rm208, LKIBSB, Area 39, Chinese University of Hong Kong

country: Hong Kong

institute: Chinese University of Hong Kong

summary: Vascular hyperpermeability is one of the hallmarks of sepsis and endotoxemia, which contributes to tissue inflammation and organ dysfunction. The peroxisome proliferator-activated receptor delta (PPARδ) is an anti-inflammatory transcription factor, while its role in endothelial barrier function remains unclear. We use single cell RNA-sequencing analysis to profile the gene expression of mouse lung ECs regulated by PPARD in endotoxemia.

overall_design: Mouse received i.p. injection of LPS (5 mg/kg) for 18 h, and mouse lung CD45-CD326-CD144+CD31+ ECs were collected by flow cytometry sorting for scRNA-seq.

first: Xiao

middle: Y

last: Tian

first: Huiling

last: Hong


title: Surfactant Protein D promotes the inhibition of tumor growth and metastatic progression with a potential for therapeutic intervention

city: Odense M

first: Kim

last: Ravnskjaer

state: CA

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Pulmonary surfactant protein D (SP-D) is an endogenous innate immune factor known to be involved in several immune related diseases and has also been linked to lung adenocarcinoma cell growth. By analyzing single-cell, bulk, and spatial transcriptomics of human clinical samples, we have demonstrated significantly reduced expression in lung cancer cells compared to healthy cells, along with a distinct localization of SP-D expression in stromal areas adjacent to the tumor cells and at the periphery. Interestingly, a near-complete loss of SP-D expression was observed in metastatic tissue, suggesting its association with a more aggressive and metastatic phenotype. In this context, we show that SP-D re-expression in A549 adenocarcinoma cell line significantly decreased tumor growth and spontaneous metastasis formation in vivo and furthermore, that intranasal administration of recombinant SP-D signicantly reduced lung tumor burden. Mechanistically, we demonstrated that SP-D supresses interleukin 4 (IL4)/IL13 signaling pathways. Intriguingly, our data revealed that recombinant SP-D binds directly to the IL4 receptor, leading to the effective inhibition of the IL4 signaling pathway. Collectively, these findings demonstrate that SP-D acts as a tumor supressor inhibiting both tumor growth and metastatic progression potentially through blokage of the IL4/STAT6 signaling pathway. This provides a rationale of SP-D as a promising therapeutic agent for modulating crucial signaling pathways involved in cancer development and progression.

overall_design: A549 cells were treated in triplicates with recombinant human SP-D protein (10µg/ml) og vehicle for 48h.

first: Ali

last: Mohammadi

first: Grith

last: Soerensen

first: Mohammed

last: Inayatullah

first: Behzad

last: Mansoori

first: Mikkel

last: Terp


title: The multidirectional in-situ osteogenesis pattern based on biomimetic mineralized dual-crosslinked Fibrinogen-GelMA microspheres in the maxillary sinus region

first: huixin

last: Lv

summary: Dental defects in the posterior maxillary region seriously affect facial contours, as well as physiological functions. When bone height in the maxillary posterior region is extremely insufficient, the difficulty of dental prosthodontics is greatly increased. Autogenous bone replacement of exogenous bone grafting materials is often inadequate, resulting in the insufficient alveolar bone height. It is still necessary to study the mechanism of bone regeneration in this region and explore new treatment methods to ensure the quality of bone reconstruction. The development of mesenchymal stem cell (MSCs) biology and bioengineering has greatly advanced the field of regenerative medicine. MSCs from different tissue sources have different biological processes and differentiation abilities. Our previous studies confirmed that MSCs derived from human maxillary sinus membrane (hMSM) can be cultured in vitro. The lamina propria layer derived MSCs (hLMSCs) and periosteum layer derived MSCs (hPMSCs) from hMSM were isolated and expanded using explant cell culture method. In this study, further study about the biological characteristics of hLMSCs and hPMSCs under the three dimensional biomimetic microenviroment based on biomimetic mineralized dual-crosslinked Fibrinogen-GelMA microspheres are compared using RNA sequencing. According to RNA sequencing and subsequent functional verification, Both hLMSCs and hPMSCs were up-regulated the osteo-related signaling pathways, such as TGF-β signaling pathway. The osteogenetic functions of hLMSCs could be improved by hPMSCs, and the most related signaling pathway pointed to PI3K-AKT signaling pathway. It seems that both hLMSCs and hPMSCs serve as good MSCs potential candidates for bone regeneration. And It also indicates that hLMSCs and hPMSCs are valuable in vitro tools for preclinical studies and future exploration of the origin osteogenesis machenism in maxillary sinus region.

overall_design:
To discover the biological characteristics of hLMSCs and hPMSCs and evaluate their osteogenic capabilities, we isolated and cultured the two cells in vitro, and processed osteogenic induction on them in the three dimensional biomimetic microenviroment based on biomimetic mineralized dual-crosslinked Fibrinogen-GelMA microspheres .
We performed gene expression profiling analysis using data obtained from RNA-seq of hLMSCs and hPMSCs. Each group contained three samples.
We then compared the differential expression genes between the RNA-seq data of hLMSCs and hPMSCs-induced hLMSCs, and their osteogenic induced patterns, respectively. Each group contained three samples.

first: Huixin

first: Yihan

last: Wang

first: Zhuoran

first: Sheng

last: Chen

first: Xiuyu

last: Liu

first: Yanmin

last: Zhou


title: Disease type and Pathogenic Mechanism induced by PM2.5 in five Human Systems using omics and Human Disease Database [Sertoli]

first: xiaomeng

overall_design: To investigate the pathogenic molecular mechanism of Male urogenital diseases induced by PM2.5, we performed transcriptome sequencing on Sertoli cell models.


title: Upregulation of Siglec-6 induces mitochondrial dysfunction by promoting GPR20 expression in early-onset preeclampsia

city: 上海

first: 卢

last: 文静

state: 上海市

address: 高科西路2699号

department: 附属第一妇婴保健院

institute: 同济大学

summary: Preeclampsia (PE) is a pregnancy complication that seriously threatens maternal and fetal health, but its pathogenesis is unclear. A growing number of studies have revealed significant changes in the mitochondria of placental trophoblasts in PE, with abnormalities in mitochondrial content, morphology, and function, but the regulatory mechanisms are not clear. Siglec-6 belongs to the family of sialic acid-binding immunoglobulin-like lectins (Siglecs), and studies have demonstrated that the Siglecs family is capable of modulating the oxidative phosphorylation and energy metabolism of mitochondria. Our study revealed that Siglec-6, which is mainly localized in syncytiotrophoblasts (STB) and extravillous trophoblast (EVT), is abnormally up-regulated in EVT in early-onset PE (EO-PE). Siglec-6 inhibited trophoblast migration, invasion, and impaired mitochondrial function. Mechanistic studies revealed that Siglec-6 inhibits NF-κB activation by recruiting SHP1/SHP2, leading to an increase in GPR20 expression, which further suppresses the downstream c-AMP/PKA/ERK signaling pathway and causes mitochondrial dysfunction in trophoblast cells. Placenta-specific overexpression of Siglec-6 in an animal model causes impaired placental structure and vessel formation, leading to a PE-like phenotype in mice. We conclude that trophoblast upregulated Siglec-6 induced trophoblast mitochondrial dysfunction through the SHP1/SHP2-NF-κB-GPR20 signaling pathway, leading to diminished trophoblast migration, invasion, and ultimately mediating the development of PE. Our study provides new ideas for the pathogenesis of PE and may provide new targets for the prevention or treatment of PE.

overall_design: Comparative gene expressing profiling analysis of RNA-seq data for HTR8/SVneo cells overexpressing Siglec-6 and nagative control.

first: Hao

last: Ying

first: Yuanhui

last: Jia

first: Wenjing

last: Lu


first: Weiqi

last: Zhang

overall_design: For bulk RNA-seq, we sorted splenic CD4+CD25+ Treg cells from WT and V408M mice and treated with anti-CD3&CD28 for 18 hours (3 samples in each group, and each sample came from the spleens of 2-3 mice).

first: Xinnan


title: Codon Pair-Specific Translation Defects Induce Ribosome-Associated Quality Control to Avoid Proteotoxic Stress.

city: Bern

first: Jie

last: Wu

state: Bern

address: Freiestrasse 3

country: Switzerland

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences


title: EIF2AK2 regulates the apoptotic genes in pancreatic beta cell damage associated with diabetes mellitus

city: Changchun

first: Hanqing

last: Cai

institute: Jilin university

summary: This study revealed that the biological roles of EIF2AK2 in islet cell apoptosis and inflammation can be predicted by its regulatory network. These roles may be mediated via the modulation of apoptosis-related gene transcription and alternative splicing. This connection might be crucial for the pathogenesis and progression of DM.

overall_design: Bioinformatics analysis and full transcriptional sequencing (RNA-seq) were conducted on INS1 cells derived from the control and the EIF2AK2 upregulation groups to identify regulatedalternative splicing events (RASEs) and differentially expressed genes (DEGs). The DEGs and RASEs were subsequently validated via RT-qPCR.

first: Lili

last: Ning

first: Tong

first: Yuanyuan

first: Yan

last: Cheng

first: Maoguang

last: Yang


title: Transcrptiome profiling of aging mouse hearts following swimming trainning

city: Tampa

first: Wanling

last: xuan

state: FL

address: 12901 Bruce B Down Blvd

department: DPS

institute: University of South Florida

summary: To investigate the effects of swimming on cardiac aging

overall_design: To compare the transcrptiome profiling of cardiac tissue from  sedentary and swimming Mice.

last: Xuan


title: 3C-Seq of Conchiformibus steedae

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

summary: Chromosome conformation capture coupled to high-throughput sequencing (3C-Seq)

overall_design: 3C libraries were prepared as previously described (Lioy et al., 2021b, 2018; Marbouty et al., 2015b).

first: Tobias

last: Viehboeck


title: 3C-Seq of Simonsiella muelleri


title: PKC inhibition overcomes chemo-resistance in TNBC by restoring Aurora kinase B expression

summary: Triple negative breast cancer (TNBC) poses a significant challenge due to its high mortality rates, primarily attributed to resistance against chemotherapy regimens containing taxanes like paclitaxel. Overcoming this resistance is imperative for improving patient outcomes. In this context, the study aimed to identify more efficient combinatorial strategies to tackle with paclitaxel resistance in TNBC.

overall_design: Chemo-resistant TNBC cells (termed SUM159-R) were treated with paclitaxel(500nM)/enzastaurin(2.5uM) alone or in combination. 24h later, cell pellets were collected and subjected to RNA extraction,followed by sequencing.

first: Bing

first: Zhitong

last: Niu


title: 3C-Seq of Alysiella filiformis


title: Axon guidance genes are regulated by TDP-43 and RGNEF through the rate of long-intron processing.

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

country: Italy

institute: University of Trieste

summary: Rho guanine nucleotide exchange factor (RGNEF) is a guanine nucleotide exchange factor (GEF) mainly involved in regulating the activity of Rho-family GTPases. It is a bi-functional protein, acting both as a guanine exchange factor and as an RNA binding protein. RGNEF is known to act as a destabilising factor of neurofilament light chain mRNA (NEFL). Most importantly, RGNEF inclusions in the spinal motor neurons of ALS patients co-localise with TDP-43, the major RNA binding protein aggregating in the brain and spinal cord of ALS patients. Therefore, it can be hypothesized that loss-of-function of both proteins, following their aggregation, may contribute to motor neuron death/survival in ALS patients. To further characterise their relationship, we compared the transcriptomic profiles of neuronal-like cells depleted of TDP-43 and RGNEF demonstrating that these two factors predominantly act in an antagonistic manner when regulating the expression of axon guidance genes. From a mechanistic point of view, our experiments show that the effect of these genes on the processivity of long introns can explain their action. Taken together, our results show that the loss-of-function of factors co-aggregating with TDP-43 can potentially affect the expression of commonly regulated neuronal genes in a very significant manner, acting as potential disease modifiers. This finding further highlights that neurodegenerative processes at the RNA level are the result of combinatorial interactions between different RNA binding factors that can co-aggregate in neuronal cells. A deeper study of these complex scenarios may lead to a better understanding of pathogenic mechanisms occurring in patients, where more than one specific protein may be aggregated in their neurons.

overall_design: Analysis of RGNEF-mediated transcription profile in human neuroblastoma (SH-SY5Y) cell line.

first: Sara

last: Cappelli

first: Emanuele

last: Buratti


title: Identification of potential targets of PPDPF in cholangiacarcinoma via transcriptome-wide RNA-seq

city: Changsha

first: Yidi

last: Guan

state: 湖南省

address: No.87 Xiangya road

institute: Xiangya hospital of central south university

summary: Tumor cells display profound changes in the branched-chain amino acid (BCAA) metabolism. However, how these changes are regulated and aids the development of tumor is not fully understood. Here, we have identified PPDPF as an amino acid-regulated protein after the extensive screening using Stable Isotope Labeling by Amino acids in Cell culture (SILAC). PPDPF is up-regulated in cholangiocarcinoma tissues and correlated with clinical features. PPDPF enhanced the tumorigenicity of cholangiocarcinoma cells by activating mTORC1 signaling pathway. The metabolic flux analysis revealed that PPDPF inhibits the catabolism of Leucine by preventing the interaction between MCCA and MCCB, thus leading to the elevation of BCAA content and the activation of mTORC1 signaling. Moreover, upon the amino acid starvation, the ariadne RBR E3 ubiquitin protein ligase 2 (ARIH2) and the OTU deubiquitinase 4 (OTUD4) cooperatively regulated the stability of PPDPF protein by modulating the ubiquitination of K48/62/99 in PPDPF protein. Additionally, IL10, secreted by the monocyte/macrophage, elevated the BCAA content in the cholangiocarcinoma cells, and stabilized PPDPF protein even in the amino acid starvation. Furthermore, knockout of PPDPF or restriction of leucine intake significantly inhibited the progression of tumor in a cholangiocarcinoma mouse model. Thus, our study discovered an unexpected role of PPDPF in the progression of cholangiocarcinoma by activating mTORC1signaling through inhibiting the catabolism of Leucine, and targeting PPDPF or lowing the dietary Leucine may have translational significance.

overall_design: To elucidate the molecular mechanism by which PPDPF promotes cholangiocarcinoma progression, we overexpressed PPDPF in human biliary cells(HIBEpiC) and subsequently extracted RNA from the cells for RNA-seq.

first: Zhi

last: Li

first: Yuezhen

last: Deng

first: Lunquan

last: Sun


title: Gene expression profile at single cell level of WT and med22-F0-KO zebrafish embryo heads

city: Laval

first: Kessen

last: Patten

state: Quebec (QC)

address: 531, Boul des Prairies

department: Centre Armand-Frappier Santé Biotechnologie

country: Canada

institute: Institut National de la Recherche Scientifique

summary: We used single cell RNA sequencing (scRNA-seq) to identify genes differentially expressed in med22-KO embryos compared with WT, with the aim of identifying new pathways involved in the associated pathology.

overall_design: Cells were extracted, isolated, and libraries prepared with the 10x Genomics manufactor kit, for sequencing using an Illumina Novaseq 60000

first: Léa

last: Lescouzères

first: Sabrina

last: Maher


title: Baicalein Alleviates Acute-on-Chronic Liver Failure by Promoting TREM2-dependent Macrophage Polarization

city: Guangzhou

first: Jia

last: Chen

state: Guangdong

address: The Third Affiliated Hospital of Sun Yat sen University, No. 600 Tianhe Road, Tianhe District, Guangzhou

department: Department of Infectious Diseases and Guangdong Key Laboratory of Liver Disease Research

institute: Third Affiliated Hospital of Sun Yat-sen University

summary: Liver tissues from C57BL/6 mice with an ACLF model, subjected to either baicalein treatment or saline treatment, were collected. Bulk-RNA sequencing of liver tissues was used to explore the potential molecular mechanism of baicalein in alleviating ACLF.

overall_design: Comparative gene expressionprofling analysis of RNA-seq data contains four samples. Two livers from saline group were named ”ACLF1“ and ”ACLF2",while another two livers from bacalein group were named "BA1" and "BA2".


title: HMGB1 regulates autophagy of placental trophoblast through MAPK/ERK signaling pathway

city: Chongqing

first: MIngrui

last: LI

address: No.1, Medical College Road

institute: Chongqing Medical University

summary: Objective: The purpose of this study is to investigate the role of high mobility group protein B1 (HMGB1) in placental development and its correlation with the occurrence of pregnancy diseases.Methods: A placenta-specific HMGB1 knockout mouse model was established using the Cre–loxP recombination system to explore the molecular mechanism of HMGB1 on placental development, including placental weight, fetal weight, and bone development. Then lentiviral system interference and overexpression of HMGB1 in human trophoblast cells were used to further evaluate the function of HMGB1.

overall_design: Transcriptome sequencing (three control replicates, three interference replicates) was performed after HMGB1 gene interference in HTR8/SVneo cells.


title: Characteristics and differences of genes in different meat cuts from Chalu black pigs

first: zhang

middle: ying

last: ying

state: Shanghai

address: Beidi Road No.2901

department: Institute of Animal Husbandry & Veterinary Science

institute: Shanghai Academy of Agricultural Sciences

summary: In this study, pork intramuscular fat (IMF) content and tenderness, myosin heavy chain (MYH) isoform expression was characterized in four cuts including longissimus dorsi muscle (LDM), trapezius muscle (TM), hamstring muscle (HM) and pork belly (PB). Then transcription expression profiles were compared in LDM, TM, HM and PB of Chulu black pig using RNA sequencing technologies (RNA-Seq). We profiled the transcriptome of HM, LDM, PB and TM isolated from pigs with approximately 100kg body weight and identified expressed 21280 transcription units. Of the them, 292-1589 DEGs genes were differentially expressed between four cuts. Using analysis of upset Venn graph, the 47, 305, 395 and 10 unique DEGs were respectively screened for HM, LDM, PB and TM. The enriched pathways in unique DEGs of HM mainly related to “organismal systems and inflammatory mediator regulation of TRP channels”, “neurotrophins signaling pathway” and “cellular senescence”. In unique DEGs of LDM, pathways included “glycolysis / Gluconeogenesis”, “carbon metabolism”, “HIF-1 signaling pathway”, “glucagon signaling pathway”, “pentose phosphate pathway” and “PPAR signaling pathway” were significantly enriched. In PB, the specific DEGs enriched in the human disease, cellular process and organismal systems pathways. Only two significantly enriched pathways including “inflammatory mediator regulation of TRP channels” and “axon guidance” were found in unique DEGs of TM. The findings suggested that the cuts differences of the pork are not only related to amino acid metabolism and lipid metabolism, but also closely associated with muscle fibers type and the formation of flavor precursor substances. The cut specific gene expression patterns finally decided the VOCs profile in pork constituting the unique aroma of each meat cuts of ChaLu black pork.

overall_design: The mRNA profiles of Longissimus dorsi muscle (LDM), trapezius muscle (TM), hamstring muscle (HM) and pork belly (PB) in Chalu black pig were generated by using RNA sequencing technologies (RNA-Seq). Forty cDNA libraries representing LDM, TM, HM, PB groups were constructed for mRNA transcriptome analysis.

first: Yingying

last: Zhang

first: Yongsong

last: Tan


title: Tetrathiomolybdate affect muscle function through ROS

first: Guolin

state: Hunan

address: 177 Lushan Road

department: College of Life Sciences

institute: Hunan Normal University

summary: To screen potential molecular regulator mediating tetrathiomolybdate(TM)-induced muscle function changes, we measured the transcriptome of gastrocnemius muscle in control and tetrathiomolybdate-treated mice with or without N-acetylcysteine (NAC) coadministration.

overall_design: Gene expression profiling analysis of RNA-seq data for 4 weeks administration of tetrathiomolybdate (TM) and/or N-acetylcysteine (NAC) in mice

first: Siyu

last: Lu

first: Fang

last: Wei

first: Yiming

last: Zhou


title: An Optimized Hepatocyte-like Cells Differentiation Protocol Using Machine Learning Assisted Approach and Multi-omics Analysis

first: Jian

last: Tu

address: #58 Zhongshan second road

institute: The First Affliated Hospitap of Sun Yat-sen University

type: Genome variation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: An Optimized Hepatocyte-like Cells Differentiation Protocol Using Machine Learning Assisted Approach and Multi-omics Analysis [WGS]

summary: The hepatocyte is a vital cell type responsible for numerous physiological processes in the body. We developed a machine learning-based AI algorithm to monitor morphological changes in hESCs during their differentiation into mature hepatocytes.Furthermore, we developed a modified strategy that safely and efficiently produces HLCs from hESCs.

overall_design: WGS are used to assess mutation burdens during HLCs differentiation process.

first: Zijun

last: Huo

first: Dung-Fang

last: Lee

first: Ruiying

last: Zhao

first: Yao

last: Yu


title: A time course of jellyfish metagenesis

first: Alison

last: Cole

department: Neurosciences and Developmental Biology

summary: A diversity of life cycle stages processed into single-cell RNA-seq libraries in order to characterize cell type diversity and relationships

overall_design: Embryos/animals were dissociated and cell suspensions were processed with a 10X Genomics Chromium Controller

first: Ulrich

last: Technau

first: Oliver

last: Link