title: Effect of overexpression of KDM6B on gene expression in human periodontal ligament stem cells

status: Public on Jul 31 2024

city: Jinan

first: Qiaohui

last: Ying

state: Shandong

address: No.44-1 Wenhua Road West, 250012, Jinan, Shandong, China

department: Department of Orthodontics

country: China

institute: Shandong University

type: Expression profiling by high throughput sequencing

summary: In this study, we identify histone demethylase KDM6B as a critical regulator of osteogenic differentiation in mechanically stimulated periodontal ligament stem cells (PDLSCs). Prior sequencing initiatives and research have underscored KDM6B's mechanosensitivity and illuminated how advanced glycation end-products (AGEs) inhibit KDM6B, thereby impairing stem cell differentiation capabilities. Significant H3K27Me3 enrichment was observed at the transcriptional regions of osteogenic markers (ALP, RUNX2, BMP2, COL1A1) in pluripotent stem cells, with KDM6B essential for the demethylation of H3K27Me3. Moreover, KDM6B was found to activate several critical genes within both the canonical and non-canonical Wnt pathways, enhancing TCF and NFATC family gene expression and facilitating antioxidative responses, matrix adhesion, and intercellular interactions in PDLSCs. Collectively, our data establish a molecular framework that illustrates the cooperative role of lineage-specific histone modifiers in osteogenic differentiation, highlights KDM6B's function in eradicating repressive histone marks, and delineates a reciprocal enhancement loop involving KDM6B and the Wnt signaling pathways.

overall_design: To explore the role of KDM6B in regulating osteogenic differentiation, we established fifth-generation human periodontal ligament stem cells. In the experimental group, overexpression was achieved using KDM6B-pcDNA. The control group was treated with empty pcDNA vector, and total RNA was extracted for RNA sequencing 24 hours post-treatment.

first: Minqi

last: Li

first: Jie

last: Guo

first: Yujun

last: Jiang


title: Molecular mechanisms of Target organ damage in youth with primary hypertension [bisulfite-Seq]

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

country: USA

institute: Cincinnati Children's Hospital Medical Center

type: Methylation profiling by high throughput sequencing

summary: High blood pressure or Primary Hypertension is associated with target organ damage (TOD) in both adults and youth, where TOD predicts the adverse cardiovscular (CV) events. The mechanisms involved in blood pressure mediated TOD are limitedly understood in onset of  TOD. To understand this,  first using RNA sequencing, we identified candidate differentially expressed genes  in circulating PBMCs of study participants with and without hypertension and elevated  left ventrivlar mass index . Next, through miRNA and whole genome bisulphite sequencing of circulating PBMCs we determined the epigenetic regulators of TOD. Also, using LCMS, serum proteomics, the key circulatory protein involved in advancing CV- TOD events was identified. In conclusion,  multiomics approach was utilized to define the circulatory regulators involved in BP mediated CV-TOD.

overall_design: The design and methods of the SHIP AHOY (Study of High Blood Pressure in Pediatrics, Adult Hypertension Onset in Youth) project have been discussed elsewhere.1 Briefly, in the current cross-sectional study, youth aged 11 to less than 19 years with BP levels (N=397) across the BP distribution, were enrolled at five clinical sites (Cincinnati, Houston, Philadelphia, Rochester, and Seattle) from 2015 to 2017 from pediatric specialty clinics (four nephrology clinics, and one joint nephrology and cardiology clinic). Efforts were made to achieve body mass index (BMI) balance across BP groups by periodically checking differences in BMI percentile among groups and actively recruiting normotensive obese controls. Out of 397 subjects, 132 adolescents of both sexes and all races with normal (Cut off: SBP <80th%), and high- systolic blood pressure (Cut off: SBP >90th%), and then stratified by with or without TOD, like Low LVMI (Left ventricular mass index) (Cut off: <38.6 gm/m2.7), and High LVMI (Cut off: >38.6 gm/m2.7), were selected in the present study cohort. Urine and Blood samples (for PBNCs and serum) were collected to investigate genetic, epigenetic, and proteomics changes that influence the development of hypertensive TOD in youth.  We excluded youth with symptomatic severe hypertension, on antihypertensive or lipid-lowering medication in the past 6 months, with diabetes mellitus (type 1 or 2), kidney disease, or other chronic medical conditions. All study participants and their parents provided written informed consent and assent according to local investigational review board requirements.

first: Tammy

middle: M

last: Brady

first: Kalyani

last: Ananthamohan

first: Mohammed

last: Arif

first: Stephen

last: Daniels

first: Bonita

last: Falkner

first: Michael

last: Ferguson

first: Joseph

middle: T

last: Flynn

first: Coral

last: Hanevold

last: Hooper

first: Julie

last: Inglefinger

first: Marc

last: Lande

first: Lisa

middle: J

last: Martin

first: Meyer

last: SK

first: Mark

last: Mitsnefes

first: Bernard

last: Rosner

first: Joshua

middle: A

last: Samuels

first: Gina

last: Kuffel

last: Zilliox

first: Richard

middle: C

last: Becker

first: Elaine

last: Urbina

first: Sakthivel

last: Sadayappan


title: Imbalance of Intestinal Flora Activates Inflammatory Response Contributing to Acute Lung Injury

city: Chongqing

first: Xia

last: Chen

address: Jiangbei

institute: The 958th Army Hospital of the Chinese People's Liberation Army

summary: Seawater drowning is a leading cause of accidental injury and death, and the resulting acute lung injury (ALI) is a serious clinical syndrome for which there are no effective treatments. This aim is to investigate the potential mechanism of seawater drowning-induced ALI.

overall_design: To investigate the potential mechanism of seawater drowning-induced ALI.


title: Initial TCR Signal Strength Imprints GATA3 and Tbet Expression Driving T-helper Cell Fate Decisions

city: Doha

first: Nicholas

last: van Panhuys

state: State

address: Po Box 26999

department: Translational Medicine

country: Qatar

institute: Sidra Medicine

summary: With the exception of the T-helper 2 (Th2) subset, cytokine driven pathways provide a robust mechanistic explanation for the observed outcomes of CD4+ T-cell differentiation. Using a quantitative model of activation, we studied the integration of TCR-signal-strength with cytokine signalling during Th2 differentiation. Upon the initial activation of Th-naïve cells, TCR signalling was found to set early expression levels for the master regulators of differentiation Tbet and GATA3, independent of the presence of polarizing cytokines. Subsequently cytokine stimuli modulated transcription factor (TF) expression levels to tune the outcome of differentiation. Here, weak TCR signalling was sufficient to drive the early upregulation of GATA3 and induce Th2 differentiation, in an IL-4 independent manner. Th1 differentiation was however shown to require additional cytokine signalling input, either in the form of autocrine IFNγ or exogenous IL-12. Using mathematical modelling we demonstrate that T-helper differentiation occurs along a continuum of states. Set by the relative co-expression of regulatory TFs, where effector cytokine production is controlled in a probabilistic manner determined by the relative levels GATA3 and Tbet expressed. Together, our data indicate TCR signalling inputs drive an early bifurcation in the T-helper differentiation pathway. Together, the integration of TCR signal strength with cytokine inputs act as a mechanism for the detection of immuno-evasive parasitic infections, whilst providing an additional checkpoint to prevent aberrant Th1 associated immunopathology.

overall_design: To analyse outcomes of differentiation induced in CD4+ T cells by varying TCR signal strength during activation. Naïve TCR transgenic 5CC7 CD4+ T cells activated for 4 days with P13.9 APCs loaded with specific concentrations of pPCC (0.01uM, 0.1uM, 1.0uM and 10.0uM) had RNA isolated and sequenced for analysis. Naïve CD4+ T cell and P13.9 cells are included for comaprisons. Three samples per condition are included.

first: Mohammad-Ameen

last: Al-Aghbar

first: Taushif

last: Khan

first: Meritxell

last: Espino Guarch

first: Douglas

last: Palmer


title: Aneuploidy induces premature aging in yeast due to defects in Ribosome Quality Control [RNASeqData]

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

summary: Premature aging is a hallmark of Down syndrome, caused by trisomy of human chromosome 21;  but the reason is unclear and difficult to study in humans.  We used an aneuploid model in wild yeast to show that chromosome amplification disrupts nutrient-induced cell-cycle arrest, quiescence entry, and healthy aging, across genetic backgrounds and amplified chromosomes.  We discovered that these defects are due in part to aneuploidy-induced dysfunction in Ribosome Quality Control (RQC).  Aneuploids entering quiescence display aberrant ribosome profiles, accumulate RQC intermediates, and harbor an increased load of protein aggregates. Although they have normal proteasome capacity, aneuploids show signs of ubiquitin dysregulation, which impacts cyclin abundance to disrupt arrest.  Remarkably, inducing ribosome stalling in euploids produces similar aberrations, while up-regulating limiting RQC subunits or proteins in ubiquitin metabolism alleviates many of the aneuploid defects.  Our results raise major implications for other aneuploidy disorders including Down syndrome.

overall_design: Euploid and select aneuploid Saccharomyces cerevisiae strains (haploids with one additional copy of chromosome IV, XII, XIV, or XV). We cultured each strain in rich media, and allowed cultures to exhaust glucose and enter quiescence. Samples for RNAseq were harvested at log-phase (proliferative growth) and at days 1, 3, and 7 after start of experiment to quantify differential gene expression as euploid and aneuploid cultures enter quiescence. Each strain and timepoint was measured in biological duplicate. An equivalent amount of Schizosaccharomyces pombe was doped into each S. cer sample for downstream normalization.

middle: P

first: Leah

middle: E

last: Escalante


title: Metabolic conditioning enhances human bmMSC cell therapy of doxorubicin-induced heart failure

city: Toulouse

first: Thomas

last: FARGE

state: Occitanie

address: 1 Avenue jean pouilles

country: France

institute: INSERM

summary: The therapeutic potential of bone marrow mesenchymal stromal cells (bmMSCs) in addressing heart failure need improvement for a better engraftment and survival. This study explores the role of metabolic sorting for human bmMSC on coculture in vitro and on doxorubicin-induced heart failure mice models. Using functional, epigenetic and gene expression approaches on cells sorted on the mitochondrial membrane potential referring their metabolic status, we demonstrated that bmMSC selected for their glycolytic metabolism presented proliferative advantage and resistance to oxidative stress favoring cell engraftment. Therapeutic use of glycolytic bmMSC rescued left ventricular ejection fraction and decrease fibrosis in mice model of acute heart failure. Metabolic changes were also related to epigenetic histone modifications as lysine methylation. Targeting LSD1 (lysine-specific demethylase 1) as a conditioning agent for enhancing the metabolic profile of bmMSC, we decipher the interplay between glycolysis and cell functionality. Our study leads to elucidate novel strategies for optimizing bmMSC-based therapies in treating heart failure and highlight the metabolic properties of bmMSCs as a promising target for more effective cardiovascular regenerative therapies.

overall_design: Mesenchymal stromal cells (MSCs) from human bone marrow were sorted based on their Tetramethylrhodamine (TMRM) fluorescence. The low and high populations were isolated into separate tubes, and RNA purification was carried out directly to obtain the highest quality RNAseq data.

first: V

last: Jacques

first: S

last: Benaouadi

first: T

last: Farge

first: F

last: Savagner


title: Bombyx mori UFBP1 regulates apoptosis and promotes BmNPV proliferation by affecting the expression of ER chaperone BIP

city: hefei

first: Meng

middle: hao

state: An hui

address: An hui Agricultural

department: College of life

institute: An hui Agricultural

summary: Ubiquitin-fold modifier 1 (UFM1) is attached to protein substrates through the sequential activity of an E1 (UBA5)-E2 (UBC1)-E3 (UBL1) cascade. UFBP1 is a conserved UFL1-interacting protein in mammals. However, there is no study on UFBP1 in silkworm yet. In this study, we identified a UFBP1 ortholog in B. mori genome. Spatio-Temporal expression profiles showed that BmUFBP1 expression was highly in midgut, fatbody, and at the moth stage. BmUFBP1 knockdown inhibited ER-stress induced ER chaperone expression and BmNPV proliferation, while BmUFBP1 overexpression increased BmNPV proliferation. Furthermore, RNA sequencing and experimental verification identified the HSP70 family member BmBIP as the BmUFBP1 downstream target in regulating BmNPV proliferation. Overall, these results suggest that BmUFBP1 facilitates BmNPV proliferation via ATF6-BIP signaling.

overall_design: siNC siUFBP1

first: Haonan

last: Meng


title: A Promising Natural G6PD Inhibitor for Potential Therapeutic Strategies in DLBCL

first: Sanxiu

last: He

state: -- None selected --

address: Department of Hematology Oncology

institute: Chongqing University Cancer Hospital

summary: Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin lymphoma, has a high degree of clinical and biological heterogeneity. Although most patients can be cured with R-CHOP immunochemotherapy,30-40% of patients have progression or recurrence after treatment. Therefore, there is an urgent need to find new treatments to improve the survival rate of this group of patients. Natural small molecule drugs have unique advantages as anticancer agents due to their low toxicity and multiple targets. This project aims to explore potentially effective natural compounds as new therapeutic strategies for DLBCL. We found that Cinobufagin is a potentially effective therapeutic agent for DLBCL. Glucose 6 phosphate dehydrogenase (G6PD), a risk factor for poor prognosis in DLBCL, was a direct target of Cinobufagin. By inhibiting the enzyme activity of G6PD, Cinobufagin could inhibit DNA synthesis and the production of reductive NADPH, thereby inducing ROS accumulation and apoptosis of DLBCL cells. Our findings provide new strategies for the treatment of DLBCL.

overall_design: Effect of 40 nM Cinobufagin treatment for 24h on transcriptome expression of OCI-LY1 cells


title: LAIR1 prevents excess inflammatory tissue damage in S. aureus skin infection and Cutaneous T-cell Lymphoma [abscess]

city: Saint Louis

first: Hannah

last: Dorando

state: Missouri

address: 660 South Euclid Avenue, Campus Box 8118-0020-07

institute: Washington University in St. Louis

summary: Patients with cutaneous T cell lymphoma (CTCL) experience high morbidity and mortality due to S. aureus skin infections and sepsis, but the causative immune defect is unclear. We propose that high levels of LAIR2 in CTCL suppress LAIR1 inhibitory signaling, promoting inflammation and tissue damage, which increases S. aureus susceptibility. Mice do not have a LAIR2 homolog, so we used Lair1 KO mice to model LAIR2 overexpression. In a model of subcutaneous S. aureus skin infection, Lair1 KO mice had  significantly larger abscesses and areas of dermonecrosis compared to WT. Lair1 KO exhibited a pattern of increased inflammatory responses in infection and sterile immune stimulation, including increased production of proinflammatory cytokines and myeloid chemokines, neutrophil ROS, and collagen/ECM remodeling pathways. Notably, compared to WT, Lair1 KO infected skin had a similar bacterial burden and neutrophils and monocytes had equivalent S. aureus phagocytosis. These findings support a model in which lack of LAIR1 signaling results in an excessive inflammatory response that does not improve infection control. CTCL tissues harbored similar patterns of increased cytokine and collagen production, suggesting that high levels of LAIR2 in CTCL recapitulates Lair1 KO, causing inflammatory tissue damage and compromising host defense against S. aureus infection.

overall_design: To investigate the impact of LAIR1 loss in S. aureus skin and soft tissue infection, we collected skin punch biopsies from 2 WT and 2 Lair1 KO mice 48 hours-post infection with S. aureus. We then performed gene expression profiling analysis from RNA-seq of these lesions.

first: Jacqueline

last: Payton


title: Pharmacokinetic modeling and gene sequencing reveal the interplay between B vitamins and probiotics

city: nanjing

first: Lan

last: Sang

address: Longmian Avenue 639

institute: China Pharmaceutical University

summary: The pharmacological significance of B vitamins, essential for various metabolic processes, and the therapeutic potential of probiotics in gastrointestinal health have been well-documented. However, the interactions between these entities remain poorly understood. In this study, we endeavored to elucidate the potential interplay between B vitamins and probiotics utilizing liquid chromatography-triple quadrupole mass spectrometry, pharmacokinetic modeling, and 16S rRNA gene sequencing. Employing healthy and pseudo-germ-free rat models, we revealed that probiotics significantly improve the absorption of B1, B3, B5, and B12, and that the gut microbiota played a mediating role in this enhanced absorption of B vitamins by probiotics. High-throughput genetic sequencing uncovered a synergistic effect of B vitamins and probiotics in modulating the gut microbiota, particularly increasing the abundance of Verrucomicrobia and Akkermansia. Furthermore, in vitro experiments demonstrated that probiotics used in this study had a relatively minor influence on the production and permeability of B vitamins, while B vitamins did not significantly contribute to the growth, auto-aggregation, and adhesion of probiotics. In summary, a complex network connection exists between B vitamins and probiotics, wherein the gut microbiota emerges as a pivotal factor that cannot be overlooked.

overall_design: 40 male SD rats were randomly divided into five groups with eight rats in each group: Control, Model, VB (Vitamin B complex), Probiotics, and VB+Probiotics (the combination of vitamin B complex and probiotics). The rats were sacrificed and ileocecal valves were collected for each group(n=5) for the 16S rRNA sequencing to evaluate the

first: Ying

last: Zhu


title: Nuclear factors NF-YC3 and NF-YBs positively regulate arbuscular mycorrhizal symbiosis in tomato

city: Taipei

first: Shu-Yi

last: Yang

address: Life Science Building, NTU. No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: Institute of Plant Biology

summary: The involvement of nuclear factor Y (NF-Y) in transcriptional reprogramming during arbuscular mycorrhizal symbiosis has been demonstrated in several plant species. However, a comprehensive picture is lacking. We showed that the spatial expression of NF-YC3 was observed in cortical cells containing arbuscules via the cis-regulatory element GCC boxes. Moreover, NF-YC3 promoter was transactivated by the combination of CYCLOPS and autoactive CCaMK via GCC boxes. Knockdown of NF-YC3 significantly reduced the abundance of all intraradical fungal structures and affected arbuscules size. BCP1, SbtM1, and WRI5a, whose expression was correlated with NF-YC3 level, might be downstream of NF-YC3. NF-YC3 interacted with one of three NF-YBs, NF-YB3a, NF-YB5c, or NF-YB3b, in yeast and in planta, and interacted with NF-YA3a in yeast. Spatial expression of three NF-YBs was observed in all cell layers of roots under both mock and mycorrhizal conditions. Knockdown of three NF-YBs collectively, but not individually, reduced the fungal colonization level, suggesting that there might be functional redundancy of NF-YBs to regulate AM symbiosis. Collectively, our data suggest that NF-YC3 and NF-YBs positively regulate AM symbiosis in tomato, and arbuscule-related NF-YC3 may be important downstream gene of common symbiosis signaling pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tomato (Solanum lycopersicum cv. Micro-Tom) composite plants transformed with empty vector (EV, pK7GWIWG II-RedRoot) and nf-yc3 RNAi construct in the hairy roots and colonized without (mock) or with AM fungi Rhizophagus irregularis

first: Yi-Ru

last: Su


title: Molecular mechanisms of Target organ damage in youth with primary hypertension [bulk RNA-Seq 2]

first: Kwangmin

last: Choi

overall_design: The design and methods of the SHIP AHOY (Study of High Blood Pressure in Pediatrics, Adult Hypertension Onset in Youth) project have been discussed elsewhere  (Mendizabal B, et al., 2018, Hypertension . 2018 Sep;72(3):625-631.). Briefly, in the current cross-sectional study, youth aged 11 to less than 19 years with BP levels (N=397) across the BP distribution, were enrolled at five clinical sites (Cincinnati, Houston, Philadelphia, Rochester, and Seattle) from 2015 to 2017 from pediatric specialty clinics (four nephrology clinics, and one joint nephrology and cardiology clinic). Efforts were made to achieve body mass index (BMI) balance across BP groups by periodically checking differences in BMI percentile among groups and actively recruiting normotensive obese controls. Out of 397 subjects, 132 adolescents of both sexes and all races with normal (Cut off: SBP <80th%), and high- systolic blood pressure (Cut off: SBP >90th%), and then stratified by with or without TOD, like Low LVMI (Left ventricular mass index) (Cut off: <38.6 gm/m2.7), and High LVMI (Cut off: >38.6 gm/m2.7), were selected in the present study cohort. Urine and Blood samples (for PBNCs and serum) were collected to investigate genetic, epigenetic, and proteomics changes that influence the development of hypertensive TOD in youth.  We excluded youth with symptomatic severe hypertension, on antihypertensive or lipid-lowering medication in the past 6 months, with diabetes mellitus (type 1 or 2), kidney disease, or other chronic medical conditions. All study participants and their parents provided written informed consent and assent according to local investigational review board requirements.

first: Tammy

last: Brady

first: Kalyani

last: Ananthamohan

first: Mohammed

last: Arif

first: Stephen

last: Daniels

first: Bonita

last: Falkner

first: Michael

last: Ferguson

first: Joseph

last: Flynn

first: Coral

last: Hanevold

last: Hooper

first: Julie

last: Inglefinger

first: Marc

last: Lande

first: Lisa

last: Martin

first: Meyer

last: SK

first: Mark

last: Mitsnefes

first: Bernard

last: Rosner

first: Joshua

last: Samuels

first: Gina

last: Kuffel

last: Zilliox

first: Richard

last: Becker

first: Elaine

last: Urbina

first: Sakthivel

last: Sadayappan


title: PTBP1 mediates Sertoli cell actin cytoskeleton organization through regulating alternative splicing of actin regulators

city: URBANA

first: Ullas

middle: Valiya

last: Chembazhi

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: UIUC

summary: Spermatogenesis is a biological process within the testis that produces haploid spermatozoa for the continuity of species. Sertoli cells are somatic cells in the seminiferous epithelium that orchestrate spermatogenesis. Cyclic reorganization of Sertoli cell actin cytoskeleton is vital for spermatogenesis but the underlying mechanism remains largely unclear. Here we report that RNA-binding protein PTBP1 controls Sertoli cell actin cytoskeleton reorganization by programming alternative splicing of actin cytoskeleton regulators. This splicing control enables ectoplasmic specializations, the actin-based adhesion junctions, to maintain the blood-testis barrier and support spermatid transport and transformation. Of particular, we show that PTBP1 promotes actin bundle formation by repressing the inclusion of exon 14 of Tnik, a kinase present at the ectoplasmic specialization. Our results thus reveal a novel mechanism wherein Sertoli cell actin cytoskeleton dynamics is controlled post-transcriptionally by utilizing functionally distinct isoforms of actin regulatory proteins and PTBP1 is a key player in generating such isoforms.

overall_design: Investigate the role of PTBP1 in Sertoli cell function

last: Valiya Chembazhi

first: Auinash

last: Kalsotra

first: Wenyan

last: Mei


title: The Orphan G Protein-Coupled Receptor GPR52 is a Novel Regulator of Breast Cancer Multicellular Organization

status: Public on Jul 26 2025

city: New York

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: G protein-coupled receptors (GPCRs) are the largest class of membrane-bound receptors and transmit critical signals from the extracellular to intracellular spaces. Transcriptomic data of resected breast tumors shows that low mRNA expression of the orphan GPCR GPR52 correlates with reduced overall survival in breast cancer patients, leading to the hypothesis that loss of GPR52 supports breast cancer progression. CRISPR-Cas9 was used to knockout GPR52 in human triple-negative breast cancer (TNBC) cell lines MDA-MB-468 and MDA-MB-231, and in the non-cancerous breast epithelial cell line, MCF10A. Loss of GPR52 was found to be associated with increased cell-cell interaction in 2D cultures, altered 3D morphology and increased propensity to organize and invade collectively in Matrigel. Furthermore, GPR52 loss was associated with features of EMT in MDA-MB-468 cells. To determine the in vivo impact of GPR52 loss, MDA-MB-468 cells were injected into zebrafish and loss of GPR52 was associated with a greater total cancer area compared to control cells. RNA-sequencing analyses of GPR52-null MDA-MB-468 cells and resected breast tumors reveal an increased cAMP signaling signature. Consistently, we found that treatment of wild-type cells with forskolin, which stimulates production of cAMP, induces some phenotypic changes associated with GPR52 loss, and inhibition of cAMP production rescued some of the GPR52 KO phenotypes. Overall, our results reveal GPR52 loss as a potential mechanism by which breast cancer progression may occur and support the investigation of GPR52 agonism as a therapeutic option in breast cancer.

overall_design: To determine the effect of GPR52 loss in breast cancer cells, we knocked out GPR52 using CRISPR-Cas9 in the MDA-MB-468 cell line. We compared the parental MDA-MB-468 cells cultured in triplicate in a 6-well plate to three populations of GPR52 KO MDA-MB-468 cells generated from a GPR52-targeted guide RNA (sgRNA1). (The generation of indels in these KO lines was confirmed by Sanger sequencing)

first: Sarah

last: Hanif

first: Bhavneet

last: Bhinder

first: Kristy

last: Brown

first: Olivier

last: Elemento


title: LAIR1 prevents excess inflammatory tissue damage in S. aureus skin infection and Cutaneous T-cell Lymphoma [BMDM]

first: Hannah

last: Dorando

overall_design: To investigate the impact of LAIR1 loss on the macrophage immune response to S. aureus, we treated bone marrow-derived macrophages from 3 WT and 3 Lair1 KO mice with PBS or PAM3CSK4 for 6 hours. We then performed gene expression profiling analysis from RNA-seq of these cells.

first: Jacqueline

last: Payton


title: Molecular mechanisms of kidney injury in diabetic mice based on single-cell sequencing techniques

city: Shenzhen

first: qiu

middle: zhong

last: guo

state: Guangdong

address: No. 53 Aixin Rd, Longgang Central City

institute: Longgang District People's Hospital

summary: To investigate the pathogenic molecular mechanisms and signaling pathways of early diabetic kidney disease. We performed single-cell RNA sequencing on kidney tissue of early type 1 diabetic mice.

overall_design: The 4-week-old male C57BL/6J mice were randomly divided into two groups: normal group ( n=1 ) and type 1 diabetic group ( n=2 )

first: Yan

last: Li

first: Qiao-an

last: Zheng

first: Zhuo

last: Wang

first: Zhong-qiu

last: Guo


title: Molecular mechanisms of Target organ damage in youth with primary hypertension [bulk RNA-Seq 3]

first: Kwangmin

last: Choi

first: Tammy

last: Brady

first: Kalyani

last: Ananthamohan

first: Mohammed

last: Arif

first: Stephen

last: Daniels

first: Bonita

last: Falkner

first: Michael

last: Ferguson

first: Joseph

last: Flynn

first: Coral

last: Hanevold

last: Hooper

first: Julie

last: Inglefinger

first: Marc

last: Lande

first: Lisa

last: Martin

first: Meyer

last: SK

first: Mark

last: Mitsnefes

first: Bernard

last: Rosner

first: Joshua

last: Samuels

first: Gina

last: Kuffel

last: Zilliox

first: Richard

last: Becker

first: Elaine

last: Urbina

last: Sadayappan


title: Negative effect of gst-35 on the health span of Caenorhabditis elegans through lysosomal dysfunction via the pmk-1 and skr genes

city: Shanghai

first: Gao

last: yehui

address: No. 1239 Siping Road, Yangpu District

institute: Tongji University

summary: As global life expectancy continues to increase, shifting our focus from solely extending lifespans to actively pursuing healthy ageing is crucial. GSTA1-3 members of the alpha class of glutathione S-transferase are involved in diverse biological processes, including metabolism and immune regulation, indicating their influence on human health and lifespan. We used Caenorhabditis elegans as a model organism to examine the impact of gst-35, an orthologous gene of mammalian GSTA1, GSTA2, and GSTA3, on healthy ageing. Our findings indicated that gst-35 overexpression had deleterious effects on various physiological aspects of nematodes. The overexpression specifically caused a significant reduction in nematode lifespan, inhibited nematode development and growth, and substantially diminished reproduction, physical fitness, and stress resistance. Conversely, gst-35 knockout in nematodes showed a partial improvement in physical fitness and stress resistance. Comprehensive RNA-sequencing transcriptome analysis revealed that gst-35 overexpression perturbed metabolic homeostasis. Additionally, gst-35 overexpression induceds lysosomal dysfunction via pmk-1 and skr, affecting the process of healthy ageing. These findings unravel the intricate role of gst-35 in the ageing process, contributing to the expanding knowledge in the field of healthy ageing research.

overall_design: To investigate the specific mechanism by which gst-35 affects the health cycle of nematodes, we used N2, PHX6971 (knockout), and PHX7528 (overexpression) nematode strains to detect changes in gene transcription levels on the fifth day of adult nematodes.

first: Yehui

last: Gao


title: Combined treatment of uterine leiomyosarcoma with gamma secretase inhibitor MK-0752 and chemotherapeutic agents de-creases cellular invasion and increases apoptosis

city: Neward

first: Nataki

middle: C.

last: Douglas

state: NJ

address: 185 S Orange Ave, MBS E569

department: Ob-Gyn and Women's Health

institute: Rutgers-New Jersey Medical

summary: Uterine leiomyosarcoma (uLMS) is a rare and aggressive malignancy with treat-ments that have limited efficacy and often have significant toxicities. We previously demonstrated the presence of Notch signaling in uLMS as well as decreased cell viability and Notch expression after inhibition using the gamma secretase inhibitor, MK-0752. The aim of this study was to assess the combination of MK-0752 and chemotherapeutics commonly used for the treatment of uLMS. Using two human uLMS cell lines, SK-UT-1B and SK-LMS-1, we investigate the role of MK-0752 alone and in combination with docetaxel and gemcitabine. We demonstrated synergism between MK-0752 and docetaxel and gemcitabine using MTT assays. These synergistic combinations were used in transwell invasion assays, cell cycle flow cytometry, and proliferation assays. We found decreased invasion and an increase in the apoptotic sub-G1 cell cycle population after combination treatment. The combinations of MK-0752 with gemcitabine and docetaxel is a potential novel therapeutic approach for uLMS.

overall_design:
SK-LMS-1 and SK-UT-1B cells were exposed to the IC30 of MK-0752 alone, MK-0752 in combination with gemcitabine and docetaxel, or DMSO volue control for 72 hours, at which time cells were harvested and RNA extraction was performed
Comparative gene and pathway analysis was performed on data obtained from RNA seq of both cells lines and treatment combinations

first: Abedin

last: Yasmin

first: Fife

last: Alexander

first: Murphy

last: Trystn

first: Zhao

last: Qingshi

first: Einstein

last: Mark

first: Dougals

last: Nataki


title: Colorectal cancer cell supermeres isolation methods

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify the best method for isolating supermeres and their small RNA cargo from colorectal cancer cells

overall_design: Test 2 methods for isolation of secreted carriers of extracellular small RNA from colorectal cancer cells

first: Robert

last: Coffey

first: Kasey

last: Vickers

first: Jeffrey

last: Franklin

first: Danielle

last: Michell

first: Clark

last: Massick


title: Effect of DAZAP1 deletion on gene expression in Cal27 cell line during progression of oral squamous cell carcinoma

city: Nanjing

first: Jiayi

last: Zhang

address: Hanzhong Road 140#

institute: Nanjing Medical University

summary: Tumor invasion and metastasis are the underlying cause of clinical refractoriness in oral squamous carcinoma (OSCC). Energy metabolism reprogramming has been identified as a vital process mediating tumor metastasis, indicating an urgent need for in-depth investigate into the specific mechanisms of tumor energy metabolism. Here, we identify an RNA-binding protein, DAZ associate protein 1 (DAZAP1), as a tumor-promoting factor to play an important role in OSCC progression. In vitro assays demonstrated that DAZAP1 was significantly upregulated in OSCC, while enhanced the migration and invasion of OSCC cells as well as epithelial-mesenchymal transition (EMT). RNA-seq analysis and experimental validation showed that DAZAP1 can regulate mitochondrial energy metabolism in OSCC. Mechanistically, we found that DAZAP1 underwent liquid-liquid phase separation (LLPS) to accumulate in the nucleus and enhanced cytochrome-c oxidase 16 (COX16) expression via regulating pre-mRNA alternative splicing, thereby promoted OSCC invasion and mitochondrial respiration. Finally, we observed a significant positive correlation between DAZAP1 and COX16, and high expression of these two proteins were both closely associated with poor prognosis in OSCC patients. Together, our study reveals a novel regulatory mechanism of DAZPA1 in mitochondrial metabolism and tumor development of OSCC by phase separation, suggesting the potential role of DAZAP1 in developing therapeutic strategies against OSCC invasion and metastasis.

overall_design: Cal27 cells were transfected by DAZAP1-KD and negative control (NC) sequence to knockdown DAZAP1 expression level, three NC transfected samples and three DAZAP1-KD transfected samples were analyzed.


title: Colorectal cancer cell supermeres

overall_design: Test culture conditions for sampling secreted carriers of extracellular small RNA from colorectal cancer cells


title: Glioblastoma cell supermeres

summary: To identify small RNAs coming out of glioblastoma cells in supermeres and other carriers

overall_design: 17 samples, 4 control and 13 experimental, replicates

first: Charest

last: Al

first: Vickers

last: Kasey

first: Franklin

last: Jeff

first: Massick

last: Clark

first: Michell

last: Danielle

first: Coffey

last: Robert


title: Aneuploidy induces premature aging in yeast due to defects in Ribosome Quality Control [MoBYSeqData]

first: Audrey

last: Gasch

overall_design: Haploid euploid and aneuploid (carrying one additional copy of chromosome XII) yeast strains were transformed with a barcoded CEN plasmid library. For each strain, we took samples at the start of the experiment (Time 0), 24 hours after start (Day 1), and 28 days after start (Day 28) to quantify the effects of gene duplication on chronological aging. Each strain was measured in biological triplicate (3 replicates from 2 independent transformations of the plasmid library).

first: Leah

last: Escalante


title: MITOCHONDRIAL ANTIOXIDANTS ABATE SARS-COV-2 LETHALITY IN MICE

city: Philadelphia

first: Joseph

middle: W

last: Guarnieri

state: PA

address: 3501 Civic Center Blvd

department: Center for Mitochondrial and Epigenomic Medicine

institute: Children's Hosptial of Philadelphia

summary: SARS-CoV-2 infection inhibits mitochondrial oxidative phosphorylation (OXPHOS), elevates mitochondrial reactive oxygen species (mROS) which activates HIF-1α shifting metabolism toward glycolysis, and causes release of mtDNA which activates the innate immune system. To determine if mitochondrially targeted antioxidants could mitigate these viral effects, we combined in mice hACE2 with mitochondrially-targeted-catalase (mCAT) and showed that SARS-CoV-2 infected hACE2-mCAT mice had decreased weight loss; decreased circulating levels of mtDNA, IL-1β, and INF-β; and decreased lung HIF-1α and nucleocapsid protein levels. RNA-sequencing of infected lungs revealed that mCAT upregulated OXPHOS gene expression and downregulated glycolytic, innate immune, and HIF-1α-target gene expression. The mitochondrial antioxidant drug EUK8 had the same effect as mCAT potentially providing a pharmacological therapy for COVID-19 which is not subject to viral mutational resistance.

overall_design: RNA sequencing analysis on hACE2-transgenic (hACE2) and mitochondrial targeted catalase (mCAT)-transgenic hACE2 mice (hACE2-mCAT), intranasally infected with 2.5x10^4 PFU of the SARS-CoV-2 Washington Variant (WA1) or a mock-control. 4 days-post-infection (dpi) RNA was collected using TRIzol™ Reagent (Invitrogen, 15596026) from 5 infected and 3 uninfected hACE2 and hACE2-mCAT lung samples. The RNA was assessed by NanoDrop spectrophotometer (ThermoFisher Scientific) and quantified by Qubit Flex (Thermofisher Scientific) using the Qubit RNA HS Assay Kit (Thermofisher Scientific, Q32855). The RNA was diluted to 1.43 ng/ul and reverse transcribed into cDNA using the Ion Torrent™ NGS Reverse Transcription Kit (Cat. No. A45003). The RNA library was prepared using the Ion Torrent S5 Chef and Ion AmpliSeq Kit for Chef DL8 (Thermofisher Scientific, A29024) and sequenced using the Ion Torrent S5 Sequencer and Ion 540 Kit (Thermofisher Scientific, A30011).

first: Gabrielle

last: Widjaja

first: Douglas

last: Wallace


title: Gammaherpesvirus infection alters transfer RNA splicing and triggers tRNA cleavage

city: Santa Cruz

first: Todd

last: Lowe

state: CA

address: 1156 High Street

department: Biomolecular Engineering and Bioinformatics

institute: University of California Santa Cruz

summary: Transfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. Moreover, mounting evidence supports a noncanonical role for tRNA cleavage products in the control of gene expression during diverse conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus, MHV68, leads to altered tRNA transcription, suggesting that tRNA regulation may play an important role in mediating viral replication or the host response. To better understand how viral infection alters tRNA expression, we combined Ordered Two Template Relay (OTTR) with tRNA-specific bioinformatic software called tRAX to profile full-length tRNAs and fragmented tRNA-derived RNAs (tDRs) during infection with the model gammaherpesvirus, MHV68. We find that OTTR-tRAX is a powerful sequencing strategy for combined tRNA/tDR profiling, and reveal that MHV68 infection triggers pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tDRs. Fragments of virally-encoded tRNAs (virtRNAs), as well as virtRNA base modification signatures are also detectable during infection. We further dissected the biogenesis pathway of an MHV68-induced cleavage product from a pre-tRNA. Our data shows that pre-tDR-Tyr expression is dependent on the tRNA splicing factor, TSEN2, and that pre-tDR-Tyr expression is inhibited by the kinase, CLP1, which regulates tRNA splicing. Significantly, our findings suggest that CLP1 kinase is required for infectious gammaherpesvirus production, offering new insight into the importance of tRNA processing during viral infection.

overall_design: MC57G mouse fibroblasts were mock-infected or infected with MHV68-MR (mutant revertant) or MHV68-R443I (muSOX mutant) for 24 h at an MOI=5. Deacylated and PNK-treated RNA was used for Ordered Two Template Relay to generate small RNA libraries in biological triplicate. Sequencing data was analyzed by tRNA expression analysis (tRAX) software for accurate tRNA and tRNA-derived RNA mapping and differential expression analysis.

first: Aidan

last: Manning

first: Mahmoud

last: Bashir

first: Ariana

middle: R

last: Jimenez

first: Heather

last: Upton

first: Kathleen

middle: L

last: Collins

first: Jessica

last: Tucker


title: Molecular mechanisms of Target organ damage in youth with primary hypertension [smallRNA-Seq 2]

city: Cincinnati

first: Kwangmin

last: Choi

address: 333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: High blood pressure or Primary Hypertension is associated with target organ damage (TOD) in both adults and youth, where TOD predicts the adverse cardiovscular (CV) events. The mechanisms involved in blood pressure mediated TOD are limitedly understood in onset of  TOD. To understand this,  first using RNA sequencing, we identified candidate differentially expressed genes  in circulating PBMCs of study participants with and without hypertension and elevated  left ventrivlar mass index . Next, through miRNA and whole genome bisulphite sequencing of circulating PBMCs we determined the epigenetic regulators of TOD. Also, using LCMS, serum proteomics, the key circulatory protein involved in advancing CV- TOD events was identified. In conclusion,  multiomics approach was utilized to define the circulatory regulators involved in BP mediated CV-TOD.

first: Tammy

last: Brady

first: Kalyani

last: Ananthamohan

first: Mohammed

last: Arif

first: Stephen

last: Daniels

first: Bonita

last: Falkner

first: Michael

last: Ferguson

last: Flynn

first: Coral

last: Hanevold

last: Hooper

first: Julie

last: Inglefinger

first: Marc

last: Lande

first: Lisa

last: Martin

first: Meyer

last: SK

first: Mark

last: Mitsnefes

first: Bernard

last: Rosner

first: Joshua

last: Samuels

first: Gina

last: Kuffel

last: Zilliox

first: Richard

last: Becker

first: Elaine

last: Urbina

first: Sakthivel

last: Sadayappan


title: The role of ASAH1 in Triple negative breast cancer (TNBC) growth and progression

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

summary: N-acylsphingosine amidohydrolase (ASAH1) expression is elevated in many cancer types including breast cancer. Therefore, we analyzed the role of ASAH1 in TNBC. Inhibition of ASAH1 expression in TNBC cell lines resulted in decreased tumor growth and metastasis

overall_design: MDA-MB-231 cell expressing either non-specific (NS) shRNA or two independent ASAH1 shRNA (ASAH1 #1 and ASAH1 # 2)  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: ZFP57 is a regulator of postnatal growth and life-long health

city: Cambridge

first: Kevin

middle: Richard

last: Costello

state: Cambridgeshire

address: Genetics Building Downing St.

department: Department of Genetics

country: United Kingdom

institute: Univerity of Cambridge

summary: Early-life factors, including nutrition, shape long-term health outcomes. Despite the essential role of lactation in maternal nutritional support, the influence of epigenetic factors on lactation and postnatal growth remains poorly understood. Zinc-finger protein 57 (ZFP57), is an epigenetic regulator of genomic imprinting, a process that directs gene expression based on parental origin, playing a vital role in mammalian prenatal growth.   Here, we identify a novel function of ZFP57 in the mammary glandI, where it serves as a key modulator of postnatal resource control, independently of imprinted genes.   ZFP57 regulates multiple aspects of mammary gland functions, including ductal branching and cellular homeostasis. Its absence leads to significant differential gene expression, related to alveologenesis, lactogenesis and milk synthesis, associated with delayed lactation and altered milk composition. This results in life-long impacts on offspring including the development of metabolic syndrome.  Cross-fostering reveals intricate dynamics between mother and offspring during lactation.  Pups raised by a dam of a different genotype than their birth mother exhibit exacerbated metabolic features in adulthood, providing additional novel insight into the programming of offspring long-term health by maternal context.  This study deepens our understanding of the interplay between epigenetic factors, lactation, and postnatal resource control.

overall_design: Mammary tissue from Wild type and ZFP57 KO mice were collected at various stages during pregancy and sorted into descreet cell population. RNA from each of these cell types were the harvested and sequenced to profile in impact ZFP57 KO has on transcriptional regulation of mammary cells during pregancy

first: Geula

last: Hanin

first: Boshra

last: Alsulaiti

first: Hugo

last: Tavares

first: Nozomi

last: Takahashi

first: Liudmila

last: Mikheeva

first: Anjuli

middle: K

last: Freeman

first: Shrina

last: Patel

first: Albert

last: Koulman

first: Anne

last: Ferguson-Smith


title: Integrate multi-omics analysis of LINC01767 in HCC

city: Harbin

first: Shao

last: Lan

address: No.92, Xidazhi Street, Nangang District

institute: Harbin Institute of Technology

summary: Hepatocellular carcinoma (HCC) is a significant contributor to cancer-related mortality rates worldwide. In previous studies, LINC01767, a type of ncRNAs, has been identified as playing a crucial role in the metastasis of colorectal cancer to the liver and was included in the diagnostic signature of HCC. No study of LINC01767 in HCC was published. We conducted a multi-omics analysis to examine the roles of LINC01767 in HCC at the first time. We employed bioinformatic analysis to evaluate its diagnostic and prognostic performance, as well as its correlation with clinical characteristics. We further used RNA sequencing and bioinformatic analysis to reveal the underlying mechanism, including its sensitivity to drugs. Our findings suggest that LINC01767 is a potential diagnostic marker and a stable independent OS predictor for HCC. It may associate with cancer stem cells in HCC, the RNA-seq and bioinformatic analysis identified its regulatory gene net and the potential sensitive drug including the PD1. The in vitro experiment verified it would influence the growth and clone formation of Huh7 cell.

overall_design: We conducted the RNA sequencing of 6 samples，including 3 control and 3 treatment. The sample was liver cancer cell line Huh7.and the control  sample was Huh7 transfected with blank plasimd named NC1,NC2,NC3,while the treatment samples were Huh7 trasfected with LINC01767-overexpression plasimd;,named OE1,OE2,OE3

first: Wenqin

last: Wang


title: Enhancing Tumor Targeting of Antitumor Drugs through Anlotinib-Mediated Modulation of Extracellular Matrix and RhoA/ROCK Signaling Pathway

first: Xuedan

last: Han

address: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road. Nanjing , China.

summary: In this study, our research focused on investigating the impact of Anlotinib in enhancing the tumor targeting of antitumor drugs in vivo. Through RNA-sequencing and Label-free quantitative proteomics analysis, we discovered that Anlotinib effectively regulated the expression of extracellular matrix (ECM) genes and proteins, leading to a significant reduction in ECM stiffness. Our bioinformatic analysis indicated a potential positive relationship between the ECM pathways and gefitinib resistance, poor PD-1 treatment outcomes, as well as unfavorable prognosis in lung cancer patients following chemotherapy. To evaluate the efficacy of Anlotinib, we administered it in combination with anti-PD-1/PD-L1 agents, chemotherapeutic drugs, and gefitinib, and visualized their distribution using fluorescent labeling in various tumor types. Notably, our results demonstrated that Anlotinib substantially improved the drug targeting process by prolonging the retention time of antitumor drugs at the tumor site. Moreover, the combination therapy induced a notable loosening of the tumor tissue structure compared to the control group. This reduction in stiffness was further associated with decreased interstitial fluid pressures and tumor solid pressure. Additionally, we observed that Anlotinib effectively suppressed the RhoA/ROCK signaling pathway, inhibiting the formation of stress fibers. These findings strongly suggest that Anlotinib enhances the distribution and retention of antitumor drugs in tumors by modulating ECM expression and physical properties through the RhoA/ROCK signaling pathway. These valuable insights contribute to the development of combination therapies aimed at improving tumor targeting in cancer treatment.

overall_design:
In order to detect what pathways Anlotinib depends on affecting the hydraulic and solid pressure of tumor stroma. We established a cell line A549 treated with Anlotinib.
We then performed gene expression profiling analysis using date obtained from RNA-seq of A549 cells treated with Anlotinib or DMSO for 48 h

first: Lufeng

last: Zheng


title: Vitamin C modulates function and gene expression of mouse testis TM4 Sertoli cells

city: Hubei

first: Cai

middle: Xia

last: Yang

address: Jingzhou

institute: yangtze Universty

summary: Vitamin C (ascorbic acid, AA), as essential micro-nutrient and antioxidant, can affect multiple cellular processes. Previously, we showed that Vitamin C supplement could promote the proliferation and suppress apoptosis of porcine Sertoli cells, via modulating the global nucleic acid methylation levels to alter transcriptome and proteomics. Due to the differences between pig and rodent species, here we investigated the effects of Vitamin C on mouse TM4 Sertoli cells. Vitamin C (250µM) treatment of mouse TM4 Sertoli cells for 36h could significantly increase cell viability, promote cell proliferation and decrease the cell percentage with early apoptosis. Vitamin C (250µM, 36h) also significantly decreased ROS level, elevated mitochondrial function, altered the levels of nucleic acid N6-methylation (m6A) and modified the levels of histone H3 trimethylation (H3K4me3, H3K9Me3 and H3K36me3) of mouse TM4 Sertoli cells. Vitamin C (250µM, 36h) promoted the secretion of anti-müllerian hormone and Estrodiol, but decreased lactate metabolite in mouse TM4 Sertoli cells. RNA-seq identified 112 differentially expressed genes (DEGs) (74 up- and 38 down-regulated) (P≤0.05, |log2Fold Change|≥1) as induced by Vitamin C in mouse TM4 Sertoli cells. Gene enrichment analysis found multiple significantly enriched biological terms or pathways, including GO terms of regulation of response to biotic stimulus, homeostasis of number of cells, positive regulation of tumor necrosis factor production, GTPase activity, calmodulin binding etc., and KEGG signal pathways of calcium signal pathway, cGMP-PKG signaling pathway, steroid biosynthesis, arginine biosynthesis etc. 9 DEGs were selected for RT-qPCR validation and 8 of them showed the change trend consistent to RNA-seq. Taken together, Vitamin C (250µM, 36h) could modulate the functions of mouse TM4 Sertoli cells, through modifying the transcriptome to affect multiple signal pathways.

overall_design: To explore the effect of valine on testis of male mouse

first: Cai-Xia

first: Zhi-Qiang

last: Du


title: eIF4G2-dependent translation of pro-fibrotic mRNAs is essential for cardiac fibroblast activation

city: Rochester

first: feng

last: jiang

address: 601 Elmwood Ave box CVRI

department: Biochemistry and Biophysics

institute: University of Rochester

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

overall_design: Refer to individual Series


title: eIF4G2-dependent translation of pro-fibrotic mRNAs is essential for cardiac fibroblast activation (Polysome-Seq)

summary: RNA-binding proteins control gene expression in cardiac fibroblasts during TGFb-driven fibrotic responses, including the eukaryotic translation initiation factor 4G2 (eIF4G2), which was known to facilitate alternative mRNA translation during cellular stresses. However, the precise role of eIF4G2 in cardiac fibroblast activation in response to fibrotic stress remains unclear. In this study, we found increased eIF4G2 protein levels in the hearts of heart failure patients and myocardial infarcted mice, as well as in TGFb-treated immortalized human and primary mouse cardiac fibroblasts. Depletion of eIF4G2 led to predominant translational downregulation of genes that are enriched in focal adhesion and extracellular matrix pathways. eIF4G2 knockdown reduced the proliferation, migration, and collagen secretion of TGFb-treated cardiac fibroblasts. Mechanistically, we found that the translation of IGFBP7 mRNA relies on eIF4G2, which is crucial for ECM production in response to pro-fibrotic stimuli. The interaction between eIF4G2 and a DEAD box RNA helicase DDX24 can regulate IGFBP7 protein expression in cardiac fibroblasts. Together, these findings suggest that the TGFb-eIF4G2-IGFBP7 axis establishes a novel translational regulatory circuit that governs cardiac fibroblast activation. Furthermore, conditional knockout of Eif4g2 in POSTN-positive myofibroblasts reduced cardiac fibrosis in the myocardial infarction mouse model, thus improving cardiac function. Our study provides insights into the molecular mechanism of eIF4G2-mediated translational regulation of crucial physiological mRNAs during cardiac fibroblast activation.

overall_design: We performed polysome-seq on IHCF cells knockdown with scramble shRNA and eIF4G2 shRNA. Total RNA and polysome-associated RNA extracted from IHCF cells were subjected to RNA-seq. Biological triplicates were performed. Samples were subjected to DNA removal by DNase I and polyA enrichment before library construction by NGS Library Prep following the manufacturer's protocols. Paired-end sequencing was conducted at Novogene using NovaSeq6000 S4 with a depth of 20M reads/sample.

first: Eng-Soon

last: Khor

first: Feng

last: Jiang

first: Omar

middle: M

last: Hedaya

first: Jiangbin

last: Wu

first: Waihong

last: Tang


title: Small non-coding RNA profiles in sperms from depressive-like mice induced by chronic unpredictable mild stimulations

city: Qingdao

first: Jun-Jie

state: Shandong

address: Changcheng 700

department: Qingdao Agricultural University

institute: College of Life Sciences

summary: In this study, depressive-like mice induced by chronic unpredictable mild stimulation (CUMS) were used to investigate the impact of psychological stress on reproduction and alterations in sperm sncRNAs. The results showed that CUMS treatments for 4 weeks induced depressive behavior in male mice and significantly affected sperm quality. The results obtained from small RNA sequencing indicated that alterations occurred in the distribution and composition of small non-coding RNAs (sncRNAs), encompassing PIWI-interacting RNAs (piRNAs), rRNA-derived small RNAs (rsRNA), and tRNA-derived small RNAs (tsRNA). Furthermore, the offspring of male mice with depressive-like behavior have a significant reduction in survival rate at 21 days after birth, and those that did survive displayed an increased susceptibility to depression.

overall_design: The present study aims to investigate the alterations in sncRNAs in sperm from male depressive-like mice prepared by CUMS

first: Qiu-Yue

last: Zhai

first: Zhen-Hua

last: Song


title: Phosphatase, Mg2+/Mn2+ Dependent 1B (Ppm1b) regulates the self-renewal of HSCs through the Wnt/β-catenin pathway [scRNA-Seq]

city: Jinan

first: Zhiyuan

last: Lu

state: Shandong Province

address: No.6699, Qingdao Road, Huaiyin District

institute: Shandong First Medical University

summary: Hematopoietic stem cells (HSCs) have unique abilities to renew themselves and generate differentiated progenies of all blood cell lineages; however, how HSCs maintain the balance of self-renewal and lineage differentiation remains largely unknown. Herein, we showed that in mice the hematologic system deletion of Phosphatase, Mg2+/Mn2+ Dependent 1B (Ppm1b), a protein serine or threonine phosphatase highly expressed in HSCs, induces the suppression of phenotypic HSC expansion due to the blockage of cell cycle. Loss of Ppm1b impairs HSC self-renewal and hematopoietic reconstitution which were revealed by limiting dilution and BM transplantation assays. Through transcriptomic analysis, we observed that the Wnt/β-catenin pathway is downregulated in Ppm1b-deficient mice. Mechanistically, we provided evidence that Ppm1b interacted with β-catenin by performing a proximity ligation assay. Moreover, using an HN252 as a small molecule probe, we further found that Ppm1b inhibition suppressed the self-renewal of HSC and led to a decrease in common lymphoid progenitor cells, resulting in a reduction of B cells in the bone marrow and peripheral blood in turn. In the study we characterized an indispensable role of Ppm1b in regulating HSC self-renewal and B cell development via Wnt/β-catenin pathway.

overall_design: Single cell- and bulk RNA-seq were performed on Ppm1bCKO and Ppm1bfl/fl mouse Lsk cells isolated from the BM.

first: Hanzhi

last: Yu

first: Yanxia

last: Li

first: Mingjie

last: Liu


title: Phosphatase, Mg2+/Mn2+ Dependent 1B (Ppm1b) regulates the self-renewal of HSCs through the Wnt/β-catenin pathway


title: Kidney tissue pipeline for multi-omics and histological analysis

city: Hamburg

first: Sydney

last: Gies

state: Hamburg

address: Martinistraße 52

department: III. Medizinische Klinik und Poliklinik

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

summary: Biobanking of tissue from clinically obtained kidney biopsies for later analysis with multi-omic approaches, such as single cell technologies, proteomics, metabolomics and the different types of imaging, is an inevitable step to overcome the need of disease model systems and towards translational medicine. Hence, collection protocols that ensure integration into daily clinical routines by the usage of preservation media that do not require liquid nitrogen but instantly preserve kidney tissue for both clinical and scientific analyses are necessary. Thus, we modified a robust single nucleus dissociation protocol for kidney tissue stored snap frozen or in the preservation media RNAlater and CellCover. Using porcine kidney tissue as surrogate for human kidney tissue, we conducted single nucleus RNA sequencing with the widely recognized Chromium 10X Genomics platform. The resulting datasets from each storage condition were analyzed to identify any potential variations in transcriptomic profiles. Furthermore, we assessed the suitability of the preservation media for additional analysis techniques such as proteomics, metabolomics, and the preservation of tissue architecture for histopathological examination including immunofluorescence staining. In this study, we show that in daily clinical routines the preservation medium RNAlater facilitates the collection of highly preserved kidney biopsies and enables further analysis with cutting-edge techniques like single nucleus RNA sequencing, proteomics and histopathological evaluation. Only metabolome analysis is currently restricted to snap frozen tissue. This work will contribute to build tissue biobanks with well-defined cohorts of the respective kidney disease that can be deeply molecular characterized, opening up new horizons for the identification of unique cells, pathways and biomarkers for the prevention, early identification and targeted therapy of kidney diseases.

overall_design: This experimental study focused on cryopreserving pig kidney biopsies using three different methods: snap freezing in liquid nitrogen, preservation in RNAlater solution, and preservation in CellCover solution.


title: Effect of B cell-intrinsic deletion of MLL1 on gene expression of germinal centre B cells during day 13 Trichuris muris infection

city: Clayton

first: Kim

last: Good-Jacobson

state: Victoria

address: Gr Fl Reception (Bldg 77) 23 Innovation Walk

country: Australia

institute: Monash University

summary: We measured the gene expression differences in germinal centre B cells from day 13 Trichuris muris-infected mice in which MLL1 is conditionally deleted in mature B cells

overall_design: RNA-sequencing of sort-purified germinal centre B cells (CD19+IgDloCD95hiCD38lo) from mesenteric lymph nodes of day 13 Trichuris muris-infected Cd23cre/+ and Mll1f/fCd23cre/+ mice.

first: Yan

last: Zhang

last: Jacobson


title: Distinct functions of wild-type and mutant Δ133p53α R273H differentially regulate glioblastoma aggressiveness and therapy-induced senescence

city: Bethesda

first: Josh

last: Stone

state: MD

address: 9000 Rockville Pike

department: CCR

institute: National Cancer Institue

summary: Mutations effects on p53 isoforms’ activities remain largely unknown, although they are mutated in 92% of TP53 mutant cancers. Therefore, exploring the effect of mutations on p53 isoforms activities is a critical, albeit unexplored area in the p53 field. Current glioblastoma treatments, including temozolomide chemotherapy and radiations, induce cellular senescence through a p53-dependent mechanism. Nevertheless, GBMs still have a poor 6.8% five-year survival indicating a need to better understand underlying mechanisms affecting the response to treatments. The progression from low-grade astrocytoma to glioblastoma is accompanied by TP53 mutations. Since Δ133p53α prevents cellular senescence, studying the impact of its mutation in glioblastoma is relevant to determine if it affects the progression and response to treatment of GBM cells. In this aim, we stably overexpressed wild-type (WT) Δ133p53α in WT glioblastoma multiforme (GBM) cells, and Δ133p53α R273H in R273H mutant GBM cells. We used mRNA-sequencing to identify mutant Δ133p53α-specific target genes. We examined proliferation, invasion, DNA repair, apoptosis, and senescence regulation by WT and mutant Δ133p53α. All results were confirmed by siRNA knock-down. Finally, using TCGA data, we investigated the association of the mutant Δ133p53α-specific target genes to clinical outcome of GBM and low-grade glioma (LGG) patients.   This study provides the first and most in-depth characterization of a mutant p53 isoform’s activities to date and demonstrate that mutant Δ133p53α R273H is an active contributor to glioblastoma carcinogenesis and response to treatment. Furthermore, by discovering the link between TP53 mutation and IL4I1/IDO1/AhR pathway, we show strong evidence of Δ133p53α R273H clinical relevance in mutant TP53 glioblastoma development and aggressiveness, and as a potential therapeutic target and biomarker.

overall_design: Wild-type (WT) Δ133p53α was stably overexpressed in two WT glioblastoma multiforme (GBM) cells (U87 and A172) and mutant Δ133p53α R273H in as stably overexpressed in two R273H mutant GBM cells (SF268 and SNB19). Each control or Δ133p53α overexpressing cells were either treated with DMSO, Temozolomide, or radiations. mRNA sequensing was then performed on threee independent experiments.

first: Jo

last: Sabastien

first: Mohammed

last: Khan

first: Izumi

last: Horikawa

first: Curtis

last: Harris


title: Prtg+ve Rhombic Lip Ventricular Zone Stem Cells Initiate and Maintain Group 3 Medulloblastoma [human_tumours_bulk]

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

summary: Total RNA sequencing was performed to understand the transcriptome alterations in Gr3-medulloblastoma lines induced by the indirect interactions of endothelial cells.

overall_design: Briefly, Group 3 medulloblastoma PDX (Med-411FH, Med-211FH) and cell lines (D425, MB002) were cocultured on a porous membrane insert (0.4µm) along with HUVEC (Human umbilical vein endothelial cells). The membrane allows the exchange of secreted factors. For the control condition, Medulloblastoma cells were plated alone on the insert. Post 72hrs of incubation, the cells were collected for RNA isolation.

first: M

middle: D

last: Taylor


title: Exosomes packaged chromatin with dynamic H3R26me2s modification prevents cellular inflammation by blocking the cGAS-STING pathway [RNA-seq]

city: Shanghai

first: Xiaoguang

last: Ren

address: 130 Dong-An Road

department: Department of Biochemistry and Molecular Biology

institute: Fudan University

summary:
Exosomes DNA derived from genomic and mitochondrial could modulate type I IFN expression by triggering the cGAS-STING pathway. However, the chromatin modification of secreted exosomes involved in this process is largely unknown. Here, we could detect the histone H3R26me and H3K27ac in the components of secreted exosomes, meanwhile, a global decrease of H3R26 symmetric dimethylation (H3R26me2s) accompanied by the lowering enrichment of H3K27ac, and this distribution pattern was able to be verified by decreased H3R26me2s leading to the reduction of H3K27ac. Furthermore, these fragmented chromatins trans-located into cytoplasmic could repress cGAS-STING induction of IFNβ1 expression, which is further packaged into the exosomes. Collectively, our findings elucidate a novel pathway that which cells can actively transport the chromatin fragments of altered histone arginine methylation to alleviate the stimulation by damaged DNA.
We perform RNA-seq  to analysis the changes of gene expression in cells treated with bleomycin.

overall_design: Xiaoguang Ren

first: Wei

first: Wenqiang


title: Cavefish Mount a Rapid and Sustained Regenerative Response Following Skeletal Muscle Injury

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

summary: This study seeks to investigate the temporal, genome-wide response of skeletal muscle following cardiotoxin injection within the skeletal muscle of the Astyanax mexicanus – comprised of the river-dwelling surface fish and troglobitic cavefish – providing novel insights into the evolutionary consequence of skeletal muscle regernation.

overall_design: Skeletal muscle from cavefish and surface fish were collected at multiple timepoints spanning a 24-hour cycle. Three fish were used at each timepoint.

first: Olsen

last: Luke

first: Sarah

last: Keaton

first: Hassan

last: Huzaifa

first: Rohner

last: Nicolas


title: Exosomes packaged chromatin with dynamic H3R26me2s modification prevents cellular inflammation by blocking the cGAS-STING pathway [CUT&Tag-seq]

summary:
Exosomes DNA derived from genomic and mitochondrial could modulate type I IFN expression by triggering the cGAS-STING pathway. However, the chromatin modification of secreted exosomes involved in this process is largely unknown. Here, we could detect the histone H3R26me and H3K27ac in the components of secreted exosomes, meanwhile, a global decrease of H3R26 symmetric dimethylation (H3R26me2s) accompanied by the lowering enrichment of H3K27ac, and this distribution pattern was able to be verified by decreased H3R26me2s leading to the reduction of H3K27ac. Furthermore, these fragmented chromatins trans-located into cytoplasmic could repress cGAS-STING induction of IFNβ1 expression, which is further packaged into the exosomes. Collectively, our findings elucidate a novel pathway that which cells can actively transport the chromatin fragments of altered histone arginine methylation to alleviate the stimulation by damaged DNA.
We perform ChIP-seq to analysis the changes of histone modification in cells treated with bleomycin.

last: Li

last: Yu


title: Exosomes packaged chromatin with dynamic H3R26me2s modification prevents cellular inflammation by blocking the cGAS-STING pathway.


title: All you can eat yeast: substitution of major hexose transporters by AtSWEET7 in Saccharomyces cerevisiae enables simultaneous utilization of multiple sugars

city: Urbana

first: Nurzhan

last: Kuanyshev

address: 1206 W Gregory Dr

department: CABBI

institute: University of Illinois at Urbana Champaign

summary: Yeast sugar transporters are highly evolved for optimized glucose transport, a major roadblock when it comes to utilizing non-glucose sugars in renewable feedstocks such as lignocellulosic biomass. The AtSWEET7p transporter has been identified for simultaneous transport of glucose and xylose, prevalent in plant cell wall hydrolysates. Here, we replaced endogenous hexose transporters with AtSWEET7 to construct an engineered Saccharomyces cerevisiae capable of multiple sugars with no glucose repression. The resulting strain (NKSW7-1) gained the capacity to simultaneously co-ferment glucose, xylose, mannose, and fructose in a synthetic medium, as well as the sugars in mixtures of bagasse hydrolysate and cane juice. Notably, the replacement of native sugar transporters by AtSWEET7 led to reprogramming of central carbon metabolism, activating glucose-repressed genes even in the presence of substantial amounts of glucose. Continuous culture experiments with the NKSW7-1 strain demonstrated feasibility of AtSWEET7 to disable glucose repression on other hexose or/and pentose sugar uptake. The broad transport capacity of AtSWEET7p can be utilized for achieving co-consumption of all sugars, especially in the case of emerging, underutilized, and renewable substrates.

overall_design: To enable multisugar consumption in Saccharomyces cerevisiae we substituted all major hexose transporters by AtSWEET7. We further evaluated its fermentation phenotype and transcirptional changes induced by AtSWEET7 integration. For transcriptome analysis we cultered control S. cerevisiae and AtSWEET7 expressing S. cerevisaie at 5 g/L glucose condition.

first: Degaulle

last: Dai

first: Jungyeon

last: Kim

first: Nam-Kyu

last: Kang

first: Ming-Hsun

last: Cheng

first: Vijay

last: Singh

first: Yong-Su

last: Jin


title: A Cocktail Factor Approach to Promote the Differentiation of mESC-Derived Oral Epithelium into Salivary Gland Progenitors

city: Beijing

first: Yifei

last: Zhang

address: Haidian

institute: Peking University

summary: The derivation of salivary gland (SG) progenitors from pluripotent stem cells (PSCs) presents significant potential for developmental biology and regenerative medicine. However, the existing protocols for inducing SG include limited factors, making it challenging to mimic the in vivo microenvironment of embryonic SGs. We reported a cocktail factor approach to enhance the differentiation of mouse embryonic stem cell (mESC)-derived oral epithelium (OE) into SG progenitors through a three-dimensional co-culture method. Upon confirming that the embryonic SG can promote the differentiation of mESC-derived OE, we performed RNA sequence analysis to identify factors involved in the differentiation of SG progenitors. Our findings highlight several efficient pathways related to SG development, with frequent appearances of four factors: IFN-γ, TGF-β2, EGF, and IGF-1. The combined treatment using these cocktail factors increased the expression of key SG progenitor markers, including Sox9, Sox10, Krt5, and Krt14. However, absence of any one of these cocktail factors did not facilitate differentiation. Notably, aggregates treated with the cocktail factor formed SG epithelial-like structures and pre-bud-like structures on the surface. In conclusion, this study offers a novel approach to developing a differentiation protocol that closely mimics the in vivo microenvironment of embryonic SGs. This provides a foundation for generating PSC-derived SG organoids with near-physiological cell behaviors and structures.

overall_design: To investigate the differentiate function during co-culture process, we performed RNA-seq tests for aggregates with or without co-culture for three replicates. Then we aimed to replace the co-culture with cocktail factors, so we performed RNA-seq tests for aggregates with or without cocktail factors for three replicates.


title: Phosphatase, Mg2+/Mn2+ Dependent 1B (Ppm1b) regulates the self-renewal of HSCs through the Wnt/β-catenin pathway [bulk RNA-Seq]

first: Zhiyuan

last: Lu

first: Hanzhi

first: Yanxia

first: Mingjie

last: Liu


title: eIF4G2-dependent translation of pro-fibrotic mRNAs is essential for cardiac fibroblast activation (RIP-Seq)

first: feng

last: jiang

overall_design: We performed RIP-seq on IHCF cells overexpressing scramble control and full-length eIF4G2. Total and eIF4G2-bound mRNAs extracted from IHCF cells were subjected to RNA-seq. Biological replicates were performed. Samples underwent DNA removal and polA enrichment before library construction using NEBNext UltraTM II RNA library Prep Kit for Illumina. Paired-end sequencing was conducted at Novogene using NovaSeq6000 S4 with a depth of 20M reads per sample.

first: Eng-Soon

last: Khor

first: Feng

last: Jiang

first: Omar

last: Hedaya

first: Jiangbin

last: Wu

first: Waihong

last: Tang


title: Comprehensively profiling of molecular landscape using mHSPC patient (scRNA-Seq).

city: Seoul

first: BYULA

last: JEE

address: 81 Irwon-Ro Gangnam-gu

department: Urology

country: South Korea

institute: Samsung medical center

summary: Although many treatment options have been adopted in patients with metastatic hormone sensitive prostate cancer (mHSPC), such as early docetaxel and AR-targeting therapy, there are currently no optimal biomarkers to guide treatment in these patients. To understand the transcriptomic features in mHSPC patients treated by either docetaxel or abiraterone acetate by performing whole transcriptome sequencing (WTS) and single cell RNA sequencing (scRNA-seq).

overall_design: Single-cell and bulk RNA-seq provide a comprehensive transcriptomic gene expression atlas for mHSPC.

first: Minyoung


title: Prtg+ve Rhombic Lip Ventricular Zone Stem Cells Initiate and Maintain Group 3 Medulloblastoma [blood_vessels_PDXs_tumours_bulk]

first: Vikas

last: Patil

summary: Transcriptome profile of Gr3-MB cells located distal and proximal to blood vessels in the PDXs.

overall_design: The experiment was performed as described previously with modifications (Kumar et al., 2019). Briefly, Group 3 medulloblastoma PDXs (Med-411FH, Med-211FH, BT2019051) were engrafted into NSG mice. Once the animal reaches humane endpoint, Hoechst 33342 (2.5mg/kg body weight) was injected through the tail vein and after 15 min the tumor was resected. Tumors cells were dissociated using enzyme-free cell dissociation solution (Millipore # S014C) and the single cell suspension was passed through a 70 micron cell strainer. The tumor cells are sorted based on Hoechst uptake using BD FACSAria III cell sorter.

first: M

last: Taylor


title: Prtg+ve Rhombic Lip Ventricular Zone Stem Cells Initiate and Maintain Group 3 Medulloblastoma


title: Clear Cell Renal Cell Carcinoma: high-throughput sequencing facilitates quantitative analysis of micro RNAs in the negative control and circSOD2-sh groups

city: guangzhou

first: Gaosheng

last: Yao

address: Zhongshan second road

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: As it turns out, circular RNAs (circRNAs) play a key role in various types of tumor progression, and they typically serve as sponges for microRNAs (miRNAs) to regulate the expression of downstream genes. However, the specific function and mechanism of circRNAs in human clear cell renal cell carcinoma (ccRCC) requires further study.Previous studies have proved that circSOD2 is up-regulated in ccRCC and plays a role in promoting tumor progression.In order to clearly verify the potential downstream miRNAs of circSOD2, 4 circSOD2-sh ccRCC cell samples and corresponding negative control samples were prepared, and miRNA sequencing was performed.

overall_design: Micro-RNA sequencing of negative control and circSOD2-sh treated 786O cells

first: Junhang

last: Luo

first: Jinhuan

last: Wei


title: Chronic sleep fragmentation reduces left ventricular contractile function and alters gene expression related to innate immune response and circadian rhythm in the mouse heart

first: Ling

last: Zhong

address: Wangfujing Street

department: Department of Endocrinology

institute: Peking Union Medical College Hospital

summary: Purpose: The purpose of this study was to comprehensively identify the gene expression changes that occur after chronic sleep fragmentation.    Method: We conducted total microarray analysis of the heart in mice following 5 weeks of sleep fragmentation.    Results: The microarray analysis revealed significant and dramatic gene expression changes in the mouse heart as a result of chronic sleep fragmentation.    Conclusion: This study provides valuable insights into the biological impact of chronic sleep fragmentation, shedding light on the molecular mechanisms involved.

overall_design: Microarray analysis was conducted on 21-week-old female C57BL/6N mice who were subjected to either 5 weeks of sleep fragmentation or left undisturbed.

first: Dongmei

last: Wang

first: Bo

last: Li

first: Xinghao

last: Yi

first: Yan

last: Xiao

first: Xuan

first: Ming

first: Shan

last: Gao


title: Comprehensively profiling of molecular landscape using mHSPC patient (RNA-Seq).

summary:
Although many treatment options have been adopted in patients with metastatic hormone sensitive prostate cancer (mHSPC), such as early docetaxel and AR-targeting therapy, there are currently no optimal biomarkers to guide treatment in these patients.
To understand the transcriptomic features in mHSPC patients treated by either docetaxel or abiraterone acetate by performing whole transcriptome sequencing (WTS) and single cell RNA sequencing (scRNA-seq).

last: Kang


title: Comprehensively profiling of molecular landscape using mHSPC patient

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

overall_design: Refer to individual Series


title: Transcriptomic Analysis Reveals the Responses of Dendritic Cells to Vdbp

city: Wuhan

first: Wenying

address: Shizi Street No.1

institute: Huazhong Agricultural University

summary: Our current study overexpressed Vdbp stably in DC to explore the function of this gene. CKK-8 results revealed Vdbp successfully inhibited viability of DC. Besides, we found overexpressing this gene greatly promoted apoptosis and obviously altered cell cycle distribution in DC. Moreover, RNA sequencing (RNA-seq) was carried out and numerous differently expressed genes (DEGs) were obtained. The results indicated that Vdbp globally mediated expression of mRNAs, which might translate into its potential functions. Finally, bio-informatics analysis illustrated that most DEGs were more uniformly enriched in immunity-related pathways. We believe that Vdbp regulates the function of DC by altering its cellular immunity.

overall_design: Examination the overexpression of Vdbp in DCs.

last: Zhao


title: Ad-SGE-DKK3 Gene Therapy Against Resistance to Immune Checkpoint Blockade in Malignant Mesothelioma

status: Public on Jul 30 2024

city: Houston

first: Sung Wook

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

overall_design: This phase 2 study evaluates the combination of Ad-SGE-Dickkopf-3 (DKK3) gene therapy and nivolumab in patients with chemotherapy-refractory epithelioid malignant pleural mesothelioma (MPM). This clinical study was based on our preclinical study to overcome primary immune resistance by combining Ad-SGE-DKK3 gene therapy with anti-PD-1 therapy through DKK3-driven immune modulation in mesothelioma. The study enrolled 12 patients between 2019 and 2022, who were refractory to pemetrexed-platin-based chemotherapy. Treatment involved CT-guided intratumoral injections of Ad-SGE-DKK3 and systemic nivolumab administration. The primary goal was to assess the objective response rate (ORR), with secondary and exploratory objectives focusing on safety, durable clinical benefit (DCB), survival, and biomarker changes. Of the enrolled patients, 75% completed the Ad-SGE-DKK3 treatment protocol. The study observed a 16.6% ORR with 41.7% maintaining stable disease, which reached 58.3% DCB rate. The median overall survival was 14.5 months, and the median progression-free survival was 4.5 months. Adverse events of grade 3 were noted in 41.7% of patients. Serial analysis of tumor biopsies and serum biomarkers indicated that patients with DCB had increased tumor-infiltrating CD8 T cells, decreased circulating memory CD8 T cells, and sustained lower concentrations of soluble mesothelin and M-CSF than progressors. The combination therapy demonstrated a favorable safety profile and promising efficacy in this patient population. ClinicalTrials.gov identifier: NCT04013334.

first: Hyun-Sung

last: Lee

first: Bryan

last: Burt

first: Sung


title: Long chain non-coding RNA-EN_181 potentially contributes to the protective role of N-acetylcysteine against non-alcoholic fatty liver disease in mice

city: Hangzhou

first: Wenwen

last: Yang

address: No.548 Binwen Road, Binjiang District

department: School of Life Science

institute: Zhejiang Chinese Medical University

summary:
Background: N-acetylcysteine (NAC), a scavenger of free radicals, possesses strong capability to improve high fat diet (HFD)-induced non-alcoholic fatty liver disease (NAFLD) in mice. However, the underlying mechanism(s) of NAC-ameliorated NAFLD are still not fully illustrated. This study was designed to clarify the involvement of long chain non-coding RNAs (lncRNAs) in the beneficial effects of NAC on NAFLD in HFD-induced obese mice.
Methods: C57BL/6J mice were arranged into normal fat diet (10% energy from fat), HFD (45% energy from fat), and HFD plus NAC (2 g/L in drinking water) groups, respectively. After 14-week intervention, the role of NAC was determined by immunohistochemistry and biochemical indexes in both plasma and liver. The profiles of hepatic lncRNAs were analyzed by whole transcriptome sequencing, and were further verified by quantitative real-time polymerase chain reaction (qRT-PCR). Meanwhile, the gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses were carried out to identify the functions of candidate lncRNAs. Furthermore, lncRNA-related ceRNA network was constructed in combination with miRNA and mRNA profiles by Cytoscape software.
Results: NAC treatment obviously rescued the deleterious alterations induced by HFD, including body and liver weight, hepatic triglyceride (TG), plasma alanine aminotransferase (ALT), plasma aspartate transaminase (AST), and liver histomorphology (H&E and Oil red O staining). Through whole transcriptome sequencing technology, 52167 (50758 known and 1409 novel) lncRNAs were detectable in liver samples. Our data revealed that the expressions of 175 lncRNAs were significantly changed by HFD but reversed by NAC treatment through cross-comparison. Among those lncRNAs, 5 lncRNAs, including lncRNA-NONMMUT148902.1 (NO_902.1), lncRNA-XR_001781798.1 (XR_798.1), lncRNA-NONMMUT141720.1 (NO_720.1), lncRNA-XR_869907.1 (XR_907.1), and lncRNA-ENSMUST00000132181 (EN_181), were selected based on the absolute value of log2 fold change (FC) being greater than 4, P-value ＜ 0.01, and P-adjust ＜ 0.01. Further qRT-PCR identified that lncRNA-NO_902.1, lncRNA-XR_798.1, and lncRNA-EN_181 were dramatically decreased by HFD while rescued by NAC treatment, consistent with the RNA-sequencing. Finally, we further screened and constructed a ceRNA network, including lncRNA-EN_181, 3 miRNAs, and 13 mRNAs, which was associated with the beneficial role of NAC in NAFLD.
Conclusions: This study identified for the first time that lncRNA-EN_181 might be a potential target in NAC-ameliorated NAFLD. The finding enhanced our understanding of biological mechanisms in the beneficial role of NAC.

overall_design: hepatic lncRNA profiles of 8-week old mice given normal fat diet (NFD), high fat diet (HFD) and high fat diet plus NAC (NAC+HFD).

first: Xiaobing

last: Dou

first: Songtao

first: Qinchao

last: Ding

first: Feiwei

last: Cao


title: Transcriptome sequence of Human bladder cancer cell line

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

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

summary: Circular RNAs (circRNAs) have been increasingly indicated to be important participants in the development and progression of various malignant tumors. In this study, we re-analyzed circRNA high-throughout sequencing from human bladder cancer tissues and paired adjacent normal tissues. Then, we discover that a circRNA hsa_circ_0000591, named as circMGA, is significantly downregulated in bladder cancer. FISH assay has been proved that hsa_circ_0008399 mainly located in cytoplasm. Transcriptome analysis was performed to find the potential genes that could be regulated by circMGA.

overall_design: Examination overexpression of circMGA in human bladder cancer

first: Jiayin

last: Sun

first: Hui

last: Zhang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Vehicle or R-2-HG Treating Mouse Peritoneal Macrophages Transcriptomes

first: Xiang

address: 399 Wanyuan Road, Minhang District, Shanghai

department: Children’s Hospital and Institute of Biomedical Sciences

summary:
Purpose: The goals of this study are to screen differentially expressed genes in mouse peritoneal macrophages treated by vehicle or R-2-HG and to explore potential mechanisms of how R-2-HG regulating the process of macrophage activation.
Methods: After RNA extraction, purification, and library construction, the samples were paired-end (PE) sequenced by Next-Generation Sequencing using an Illumina sequencing platform (Illumina HiSeq 2500). After sequencing, the filtered high-quality sequences (Clean Data) filtered from the original raw data were mapped to the Mus_musculus GRCm38.p4 (mm10) genome. Based on the mapped results, the expression level of each gene was calculated, and the samples of the different groups were subjected to further analysis for differences in expression, enrichment, and cluster analysis.
Results: The mRNA expression levels of only a few genes were changed after R-2-HG treatment in mouse peritoneal macrophages, but HIF1A was not included.
Conclusions:Regulating the macrophage activation by R-2-HG may not be due to its effect on gene transcription, and R-2-HG doses not affect the mRNA expression of HIF1A.

overall_design: mRNA profiles of mouse peritoneal macrophages treated with vehicle (Control) or R-2-HG (0.1mM) for 24h.

first: Yufeng

last: Zhou


title: DNA Methylation Profiles of Early Organogenesis-Stage Mouse Conceptuses after Exposure to Mono-2-Ethylhexyl Phthalate: Effects in the Absence and Presence of Neural Tube Defects

city: East Lansing

first: Karilyn

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

type: Methylation profiling by genome tiling array

summary: The goal of this study was to assess whether changes in DNA methylation were observed following MEHP treatment in mouse embryos. Explanted GD8 mouse embryos were exposed to 100 ug/ml mono-2-ethylhexyl phthalate (MEHP) or dimethyl sulfoxide (0.01%; control) in whole embryo culture for 24 h. On GD9 tissues were manually separated using watchmaker's forceps and placed for genomic DNA isolation. At that time, the presennce (positive) or absence (negative) of a neural tube defect in the mouse embryos was noted.

overall_design:
n=3 samples per group (CTL, MEHP), per tissue (EMB, VYS), per NTD status (neg, pos).
*** The raw data (pair files) are not included because they were lost due to disk corruption ***


title: TFCP2L1 promotes GPX4-mediated ferroptosis to inhibit breast cancer cell proliferation and metastasis via the PI3K/AKT signaling pathway

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary: Breast cancer represents the most prevalent form of malignant tumors among women. Despite the existence of numerous therapeutic methods, a significant portion of patients face a poor prognosis, highlighting the urgency in identifying new remedial targets. Here, we for the first time demonstrated that the CP2 family member TFCP2L1, a classical marker of embryonic stem cell maintenance, as a tumor suppressor in breast cancer. Patients with breast cancer have poorer prognoses when TFCP2L1 is expressed highly. Consistently, the expression of TFCP2L1 is higher in normal breast cells than those in breast cancer cell lines. Gain- and loss-of-function and xenograft tumor assay showed that overexpression of TFCP2L1 significantly inhibited both the proliferation and migration of breast cancer cells in vivo and in vitro. Conversely, the knockdown of TFCP2L1 promoted the proliferation and migration of breast cancer cells. Mechanistically, we found that TFCP2L1 suppresses breast cancer progression by directly inhibiting the expression of glutathione peroxidase 4 (GPX4), a key regulator of ferroptosis. Therefore, inhibition of GPX4 by RSL3, an inducer of ferroptosis was able to promote the function of TFCP2L1 in breast cancer cells. On the other hand, transcriptome high-throughput exhibited that TFCP2L1 negatively regulated the activity of PI3K/AKT signaling pathway. Administration of SC79, an AKT activator, was capable of partially restoring the negative effects of TFCP2L1 on GPX4 transcription. Together, TFCP2L1 functions by directly or indirectly regulating GPX4-mediated ferroptosis, and may serve as a novel biomarker and potential therapeutic target for breast cancer.

overall_design: Empty control group of Hs578T cells and the Hs578T cells with overexpression of TFCP2L1 were collected by using Trizol. Two repeat groups were set for each treatment group. These samples were sent to MajorBIO (Shanghai, China) company to do deep sequencing by using illumina Hiseq.


title: DNA Methylation and Transcriptomic Profiles of Early Organogenesis-Stage Mouse Conceptuses after Exposure to Mono-2-Ethylhexyl Phthalate: Effects in the Absence and Presence of Neural Tube Defects

summary: The goal of this study was to assess changes in gene expression and DNA methylation in response to embryonic exposures to the plasticizer metabolite, mono-2-ethylhexyl phthalate (MEHP). Because we previously observed increased incidence of neural tube defects (NTDs) in exposed embryos, we also stratified our samples by NTD status to examine changes in expression or methylation that may be associated with NTD progression in response to MEHP.

overall_design:
There are a total of 20 samples submitted for Affymetrix analysis of gene expression. Detailed information about tissue, exposure, and neural tube defect status is provided in the sample table below.
*** The raw data (CEL files) are not included because they were lost due to disk corruption ***


title: Transcriptome profiling of HOXA13 and HOXB13 expression knockdown in bladder cancer cell lines.

city: Bandar Sunway

first: Abhi

last: Veerakumarasivam

state: Selangor

address: Jalan Universiti

country: Malaysia

institute: Sunway University

summary: Homeobox genes HOXA13 and HOXB13 have been dysregulated in various human cancers, including bladder cancer. Our aim was to identify significant differentially expressed genes (DEGs) and molecular pathways upon the HOXA13 and HOXB13 knockdown in bladder cancer cell lines.

overall_design: Transcriptome profiles of HOXA13 or HOXB13 siRNA-transfected bladder cancer cells and negative control siRNA-transfected bladder cancer cells at different time points were generated in triplicates by RNA sequencing using Illumina HiSeq 2000.

first: Fee

last: Chin

first: Soon

last: Chan

first: Khatijah

last: Yusoff


title: Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 skeletal muscle knockout RNA-Seq of unloading-reloading protocol)

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: Muscle atrophy is a morbidity and mortality risk factor that happens with disuse, chronic disease, and ageing. Recovery from atrophy involves changes in protein synthesis and different cell types such as muscle fibers, and satellite and immune cells. Here we show that the previously uncharacterized gene and protein Zfp697 is a damage-induced regulator of muscle regeneration. Zfp697/ZNF697 expression is transiently elevated during recovery from muscle atrophy or injury in mice and humans. Sustained Zfp697 expression in mouse muscle leads to a gene expression signature of chemokine secretion, immune cell recruitment, and extracellular matrix remodeling. Myofiber-specific Zfp697 ablation hinders the inflammatory and regenerative response to muscle injury, compromising functional recovery. We uncover Zfp697 as an essential mediator of the interferon gamma response in muscle cells that functions primarily as an ncRNA-binding protein, most notably the pro-regenerative miR-206. This work identifies Zfp697 as an integrator of cell-cell communication necessary for tissue regeneration.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse gastrocnemius muscle from model of hindlimb unloading/reloading comparing wild-type and Zfp697 conditional skeletal muscle knockout (mKO) animals. Control mice were kept in conventional cages throughout the entire protocol. Experiment was performed in three replicates per condition.

first: Jorge

last: Correia

first: Paulo

last: Jannig

first: Maya

last: Gosztyla

first: Serge

last: Ducommun

first: Stine

last: Præstholm

first: Kyle

last: Dumont

first: Liu

last: Zhengye

first: Qishan

last: Liang

first: Daniel

last: Edsgärd

first: Olof

last: Emanuelsson

first: Paul

last: Gregorevic

first: Tomas

last: Venckunas

first: Marius

last: Brazaitis

first: Sigitas

last: Kamandulis

first: Johanna

middle: T

last: Lanner

first: Gene

last: Yeo

last: Ruas


title: TG6050, an oncolytic vaccinia virus encoding interleukin-12 and anti-CTLA-4 antibody induces tumor regression through profound tumor microenvironment remodeling and strong antitumor adaptive immune response [RNA-seq]

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

institute: Transgene SA

summary:
By their selective infection or replication into tumors, oncolytic viruses trigger profound modifications of tumor immune microenvironment with a massive infiltration and activation of T cells. This tumor warming up can be further amplified by the local delivery of powerful immunomodulatory molecules encoded into virus’ genome. Those properties are particularly of interest for tumor poorly infiltrated or infiltrated with anergic T cells to reverse patient’s unresponsiveness to immune checkpoint inhibitors (ICI).
TG6050 is a new oncolytic vaccinia virus encoding single-chain human Interleukin-12 (hIL-12) and full length anti-cytotoxic T-lymphocyte-associated antigen-4 (@CTLA-4) monoclonal antibody. Replication, oncolysis, selectivity, transgenes expression and functionality of TG6050 were characterized in vitro. Virus and IL-12 pharmacokinetics, antitumoral activities (alone or combined with ICI), and mechanism of action (MOA) were investigated in “hot” (highly infiltrated) and “cold” (poorly infiltrated) syngeneic murine tumor models. MOA was deciphered by monitoring both systemic and tumor immune responses, and tumor transcriptome analyses. Finally, TG6050 safety after repeated intravenous administrations was evaluated in cynomolgus monkeys and special attention was paid to the level of circulating IL-12 potentially associated with toxic effects.
In vitro or in vivo replication of TG6050 in tumor cells allows local expression of functional IL-12 and @CTLA-4. The expression of transgenes, together with the virus replication, translated into an antitumoral activity in both “cold and “hot” tumor murine models that was further amplified by combination with ICI. Analysis of tumor microenvironment (TME) after TG6050 treatment showed an increase of interferon gamma, CD8+ T cells, M1/M2 macrophages ratio and a drastic decrease of regulatory T cells. Those local modifications were observed together with an enhanced systemic and specific antitumor adaptive immune response. In toxicology studies, the virus did not produce any observable adverse effects in cynomolgus monkeys.
Conclusions: TG6050 allows the delivery of functional IL-12 and @CTLA-4 into tumor resulting in an excellent antitumor activity along with a shift towards an inflamed TME, and a boost of the systemic antitumor T-cells. Toxicological studies in macaques demonstrated the safety of TG6050. Together these results paved the way for clinical evaluation of TG6050 in metastatic non-small cell lung cancer (NCT05788926).

overall_design: CT26 or B16F10 tumours treated with the vaccinia virus mTG6050 expressing anti-CTLA-4 and IL-12 (COPTG19859), the empty vaccinia virus (COPTG19289), or untreated

first: Fadi

last: Azar

first: Jean-Baptiste

last: Marchand

first: Eric

last: Quéméneur