G1 Cell Cycle Research Articles

Abstract P2-26-23: Transcriptomic modification induced by the first cycle of neoadjuvant chemotherapy impacts response to treatment in triple negative breast cancer (TNBC)

Abstract Background Despite adequate neoadjuvant chemotherapy, TNBC remains poor prognosis. Non-responding patient have 25-40% risk of relapse at 5 years. pCR is therefore currently considered as a major goal in TNBC and new tools of early prediction of residual disease should be identified. TransTep is a phase 2 monocentric clinical trial which aims to identify transcriptomic profile of triple-negative cancer cells associated with early tumor chemoresistance, as identified by FDG PET after the first course of neoadjuvant chemotherapy. Twenty patients were included between January 2015 and October 2017, with stage II or III of the UICC classification (except stage T4d). All patients received neoadjuvant chemotherapy with anthracyclines and taxanes sequentially, none of them had a dose-dense chemotherapy. Six patients obtained metabolic response (Delta SUV < -30%) after one cycle of anthracycline. Methods Total RNA was extracted from biopsies (HES > 30%) and used to prepare libraries thanks to TruSeq RNA library Prep kit (Illumina) and sequenced on NextSeq500 device. Results Transcriptomic expression analysis between tumors before chemotherapy and tumors after one course of chemotherapy showed that tumors showing a significant decrease of their Delta SUV (←30%) had a much higher gene expression variation than tumors with a Delta SUV >-30%. These tumors presented, after one course of chemotherapy, a decrease of cell cycle, DNA replication and Fanconi anemia pathway related genes, while they harbored an increase of genes belonging to immunity related pathways such as natural killer cell mediated toxicity, TH17 cell differentiation, or chemokine signaling pathway. As patients had a surgery after neoadjuvant chemotherapy, we had Chevalier tumor response. As observed with FDG PET data, patients with a good response according to Chevalier (class 1) criteria presented a much higher transcriptomic modification after one course of chemotherapy. Patients with a little gene expression modification were classified as Chevalier 3. When we focused on pathways impacted by chemotherapy in tumors classified as Chevalier 1, we observed a significant decrease of cell cycle, DNA replication and DNA repair pathways related gene after one course of chemotherapy, whereas a high number of genes belonging to immunity related genes (NK cells, antigen processing and presentation, or chemokine signaling pathway) were increased. Conclusion Our results tend to indicate that transcriptomic tumor response after one course of chemotherapy could forecast final response to treatment. Moreover, it seems that one cycle of anthracycline-based chemotherapy is able to get hot some breast tumors, and that this tumor warming could be a marker of good response to the full treatment. In the following months, we will test whether transcriptomic could predict progression free survival and/or overall survival of patients. We will also look for the best early marker of response between PET FDG and tumor transcriptomic modifications. Based on these results, a new trial will be organized. A therapeutic adaptation depending on the transcriptomic or metabolic data will be proposed to increase pCR rate and prognosis of patients. Moreover, with years and therapeutic innovations, patient managment obviously evolves. This was recently the case with a new standard of care in triple negative breast cancer with combination of platinum salt and immunotherapy. Therefore, a new trial, similar to TRANSTEP, will be carried out with this new standard of care. Citation Format: Isabelle Desmoulins, David Chardin, Corentin Richard, Laurent Arnould, ALEXANDRE COCHET, Olivier Humbert, Romain Boidot. Transcriptomic modification induced by the first cycle of neoadjuvant chemotherapy impacts response to treatment in triple negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-26-23.

Abstract P6-14-11: Exosome-mediated Circ-CRSP1 promotes tumor proliferation and metastasis through stabilizing ELAVL1 protein and suppresses anti-tumor immune response in regulating the progression of Triple-Negative Breast Cancer

Abstract Background: Triple-negative breast cancer (TNBC) is one of the most malignant subtype of breast cancer. Lacking targetable molecular drivers, chemotherapy is almost the only effective systematic treatment for TNBC. Compared with other types of breast cancer, TNBC shows a higher long-term recurrence rate and worse prognostic outcome, and its main cause of death is tumor metastasis. Therefore, there is an urgent clinical need to explore underlying molecular mechanisms and find novel targets for therapeutic intervention, as well as biomarkers for early clinical diagnosis. Materials & Methods: To explore the signal pathways and target molecules related to tumor immunity by bioinformatics analysis of tissue samples [TNBC (n = 55), Her2 (n = 39), Luminal B (n = 30), Luminal A (n = 29), healthy (n = 11)]. Co-culture experiment was conducted to study the effect of TNBC-derived exosome-mediated molecules on the proliferation and migration of breast cancer. qRT-PCR assay was used to confirm the expression level of Circ-CRSP1 in tumor tissues, breast cancer cells, exosomes of breast cancer cells and serum exosomes of breast cancer patients. Overexpression and knockout experiments investigated the role of Circ-CRSP1 in promoting the proliferation and migration of TNBC cells. Protein molecular docking technique was used to predict the possible targeting binding protein ELAVL1, and molecular experiments and nude mice model were used to study the mechanism of Circ-CRSP1-ELAVL1 complex in tumor immunity. Results: TNBC-derived exosome-mediated molecular transmission promotes the proliferation and migration of breast cancer, and may promote distant metastasis of breast cancer by changing the tumor microenvironment (TME) before metastasis. Bioinformatics analysis of TNBC tumor samples confirmed that TNBC is strongly associated with tumor immune-related biological processes and signal pathways. Circ-CRSP1 is highly expressed in TNBC tumor tissues, TNBC cells, exosome derived from TNBC cells and serum exosomes of TNBC patients, and is related to the poor clinical prognosis of TNBC patients. Overexpression of Circ-CRSP1 enhanced the proliferation and migration ability of TNBC cells, and the expression levels of EMT and cell-cycle related genes altered. Circ-CRSP1 binds to protein ELAVL1 at the physical level. The target gene of Circ-CRSP1-ELAVL1 complex is involved in the immune response, and the overexpression of Circ-CRSP1 significantly down-regulates the expression level of immune-related genes. Conclusion: Exosome-mediated Circ-CRSP1 promotes the transport of ELAVL1 from nucleus to cytoplasm through targeted binding with ELAVL1, and then regulates cytoplasmic proliferation and metastasis and inhibits the stability and translation of anti-tumor immune-related gene mRNA, thus finally promotes the proliferation, invasion and metastasis of TNBC. This study can further understand the mechanism of circRNA in the growth and metastasis of TNBC from the theoretical level, further explore the feasibility of Circ-CRSP1 as a molecular target for gene therapy, and provide theoretical basis and pre-clinical data for Circ-CRSP1 in serum exosomes as a high risk screening index and prognostic marker for TNBC patients. Citation Format: Sujin Yang, Jinhai Tang. Exosome-mediated Circ-CRSP1 promotes tumor proliferation and metastasis through stabilizing ELAVL1 protein and suppresses anti-tumor immune response in regulating the progression of Triple-Negative Breast Cancer. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-14-11.

Abstract OT1-02-02: A phase 1/2 study to evaluate the safety and efficacy of EP0062, an oral Selective Androgen Receptor Modulator (SARM), for the treatment of AR+/HER2-/ER+ advanced breast cancer

Abstract There is growing interest in targeting the androgen receptor (AR) in advanced/metastatic breast cancer. It has been recently demonstrated preclinically that AR activation, rather than AR suppression, exerts potent antitumor activity across a number of ER+/AR+ breast tumors, including those resistant to standard-of-care endocrine therapy and CDK4/6 inhibitors (Hickey et al, Nature Medicine 2021 27: 310-320). Mechanistically, agonist activation of AR altered the genomic distribution of ER and essential co-activators resulting in repression of ER-regulated cell cycle genes and upregulation of AR target genes, including known tumor suppressors. EP0062 is an oral, non-steroidal, SARM currently being developed for the treatment of AR+/HER2-/ER+ advanced breast cancer. The efficacy and safety of EP0062 has previously been investigated in a Phase 1 clinical trial of AR+/HER2–/ER+ advanced breast cancer, and demonstrated that EP0062 has acceptable tolerability with evidence of clinical efficacy (LoRusso et al. Clinical Breast Cancer 2022 22;1 67-77). This new study is designed to further extend the evaluation of EP0062 as a potential therapy for AR+/HER2–/ER+ advanced breast cancer. The primary aim of the study is to assess tolerability and identify an optimal RP2D dose. The study will also explore the relationship between efficacy of EP0062 and AR expression, to establish a threshold for future patient selection, and undertake an initial evaluation of the safety and efficacy of EP0062 in combination with established standard of care therapies. The study will recruit up to 128 patients with AR+/HER2-/ER+ advanced breast cancer. Module A is a dose finding cohort to investigate safety, tolerability, PK and PD and to define the maximum tolerated dose (MTD) and/or Recommended Phase II Dose (RP2D). Dose finding will be based on a 3+3 design and is expected to recruit up to 32 patients. Once potential recommended doses are identified, approximately 60 evaluable patients will be randomised to two different dose cohorts in Module B in order to further optimise the RP2D dose, by further evaluation of safety and tolerability, as well as prospectively evaluate the relationship between efficacy and AR expression. In Module C, EP0062 will be combined with select standard of care targeted therapies in patients with relapsed AR+/HER2-/ER+ advanced breast cancer to confirm safety and explore efficacy. This will include approximately 36 patients across a number of single arm expansion cohorts. The key inclusion criteria are as follows: • Post-menopausal women, ≥18 years • ECOG performance status of 0 to 1 • Locally advanced or metastatic breast cancer • ER+, HER2- as per ASCO CAP guidelines • AR+, as defined as ≥ 10% AR nuclei staining by IHC • Endocrine-sensitive defined as greater than 3 years endocrine treatment prior to recurrence if recurrence occurred in the adjuvant setting, or ≥ 6 months treatment and response if recurrence occurred from primary treatment in the advanced setting • Relapsed, defined as clear and documented evidence of disease progression following ≥ 1 lines and ≤2 prior lines of previous endocrine therapy and ≤ 2 lines of chemotherapy in the advanced/metastatic setting • Measurable disease defined by RECIST version 1.1, or measurable bone-only disease EP0062 will be dosed to progression. Endpoints include incidence of DLTs during Cycle 1 of EP0062 treatment (28 days), MTD, RP2D (Module A), incidence and severity of AEs and SAEs, plasma PK parameters, Clinical Benefit Rate (complete response, partial response, or stable disease) at 24 weeks, ORR, duration of response, PFS, OS and quality of life. Clinic follow-up will be at 2 and 4 weeks, then every 4 weeks until disease progression. Recruitment is scheduled to initiate in Q4 2022. Citation Format: Elgene Lim, Erika Hamilton, Carlo Palmieri, Hendrik-Tobias Arkenau, Sue Brook, Geoff Fisher, Andrew Mazur. A phase 1/2 study to evaluate the safety and efficacy of EP0062, an oral Selective Androgen Receptor Modulator (SARM), for the treatment of AR+/HER2-/ER+ advanced breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr OT1-02-02.

Abstract P2-21-02: Longitudinal tumor-immune microenvironment changes in patients with clinical luminal A early breast cancer treated with neoadjuvant palbociclib and endocrine therapy: results from the Swedish randomized PREDIX Luminal A trial

Abstract Introduction: The use of preoperative CDK4/6 inhibitors combined with endocrine treatment remains investigational in breast cancer (BC), while their effect on tumor-immune microenvironment (TIME) in luminal BC is the subject of few published studies. The aim of this study was to characterize the treatment-induced changes of TIME at a spatial proteomic and bulk tumor transcriptomic level in clinical luminal A BC patients treated with neoadjuvant palbociclib and endocrine treatment. Methods: The PREDIX Luminal A phase II randomized clinical trial (NCT02592083) included patients with stage 2-3 BC and IHC-defined luminal A biology (ER+ and PR+, HER2-, low proliferation) treated with preoperative ET (tamoxifen or aromatase inhibitor) with or without the addition of CDK4/6i palbociclib, based on the early change of Ki67 levels. A core biopsy was obtained at baseline, after 10 weeks of treatment (on-treatment) and at surgery. The study was closed after the inclusion of 10 patients due to slow accrual. By using formalin-fixed paraffin-embedded tissue from all timepoints, we performed the GeoMx® Digital Spatial Profiling (DSP, NanoString, Seattle, WA, USA) for the spatial profiling of 27 immune cell and tumor markers (immune cell profiling core and pan-tumor panels) both at intra-epithelial and stromal tissue segments. Upon data normalization, a linear mixed model was adopted for differential marker expression assessment between the different timepoints and treatment arms, using the DSP Suite® software. RNA was also extracted from fresh-frozen biopsies and the nCounter® Breast Cancer 360™ panel (NanoString) was used for gene expression profiling of 776 targets and data analysis was performed using the nSolver® software. Results: A total of 7 patients received palbociclib + ET and 3 were treated with ET only. All patients experienced an on-treatment radiological partial response while no patient achieved pathological complete response. While ET suppressed the ER axis in both palbociclib-treated and untreated patients, treatment with palbociclib additionally led to cell-cycle arrest as evidenced by a decrease in proliferation and downregulation of cell-cycle gene pathways. Immune-related protein markers were enriched in the stroma segments and pan-tumor markers were enriched in the intra-epithelial segments at all timepoints. In palbociclib-treated patients, immune cell markers (e.g. CD45, CD68, CD20, CD4, HLA-DR) were significantly enriched in on-treatment samples (n=3) both in tumor and stromal segments, while these expression changes were reversed between on-treatment and surgery. In the ET-treated patients immune markers reflecting e.g. T-, B- and/or antigen-presenting-cells were significantly enriched at the operation samples (n=2), in the intra-epithelial but not in the stromal areas. This finding was confirmed also at the gene level, where immune-related pathways (e.g. chemokine and cytokine activity and receptor binding) were upregulated in the palbociclib-treated patients on-treatment but they were partially abrogated at surgery. The ET-only treated patients presented with enhanced immune activation gene sets at both on- and post-treatment timepoints Conclusion: The findings of this small hypothesis-generating study indicate an upregulation of immune function during treatment with palbociclib and ET and an altered tumor microenvironment. The prognostic and potential therapeutic implications of sensitizing tumors to subsequent chemotherapy and immunotherapy need to be further investigated in larger studies. Citation Format: Ioannis Zerdes, Dimitrios Salgkamis, Alexios Matikas, Lars Selander, Kang Wang, Evangelos Tzoras, Emmanouil Sifakis, Susanne Agartz, Xinsong Chen, Mats Hellström, Johan Hartman, Jonas Bergh, Theodoros Foukakis, Thomas Hatschek. Longitudinal tumor-immune microenvironment changes in patients with clinical luminal A early breast cancer treated with neoadjuvant palbociclib and endocrine therapy: results from the Swedish randomized PREDIX Luminal A trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-21-02.

MEDIATOR SUBUNIT17 is required for transcriptional optimization of root system architecture in Arabidopsis.

Sucrose and auxin are well-known determinants of root system architecture (RSA). However, the factors that connect the signaling pathways evoked by these two critical factors during root development are poorly understood. In this study, we report the role of MEDIATOR SUBUNIT17 (MED17) in RSA and its involvement in the transcriptional integration of sugar and auxin signaling pathways in Arabidopsis (Arabidopsis thaliana). Sucrose regulates root meristem activation through the TARGET OF RAPAMYCIN-E2 PROMOTER BINDING FACTOR A (TOR-E2FA) pathway, and auxin regulates lateral root (LR) development through AUXIN RESPONSE FACTOR-LATERAL ORGAN BOUNDARIES DOMAIN (ARF-LBDs). Both sucrose and auxin play a vital role during primary and LR development. However, there is no clarity on how sucrose is involved in the ARF-dependent regulation of auxin-responsive genes. This study establishes MED17 as a nodal point to connect sucrose and auxin signaling. Transcription of MED17 was induced by sucrose in an E2FA/B-dependent manner. Moreover, E2FA/B interacted with MED17, which can aid in the recruitment of the Mediator complex on the target promoters. Interestingly, E2FA/B and MED17 also occupied the promoter of ARF7, but not ARF19, leading to ARF7 expression, which then activates auxin signaling and thus initiates LR development. MED17 also activated cell division in the root meristem by occupying the promoters of cell-cycle genes, thus regulating their transcription. Thus, MED17 plays an important role in relaying the transcriptional signal from sucrose to auxin-responsive and cell-cycle genes to regulate primary and lateral root development, highlighting the role of the Mediator as the transcriptional processor for optimal root system architecture in Arabidopsis.

Cell cycle of microalga Isochrysis galbana arrested by neurotoxin β-N-methylamino-l-alanine and corresponding molecular mechanisms

The phycotoxin β-N-methylamino-l-alanine (BMAA) has attracted attention due to its risks to marine organisms and human health. In this study, approximately 85 % of synchronized cells of the marine microalga Isochrysis galbana were arrested at the cell cycle G1 phase by BMAA at 6.5 μM for a 24-h exposure. The concentration of chlorophyll a (Chl a) gradually decreased, while the maximum quantum yield of PSII (Fv/Fm), the maximum relative electron transport rate (rETRmax), light utilization efficiency (α) and half-saturated light irradiance (Ik) reduced early and recovered gradually in I. galbana exposed to BMAA in 96-h batch cultures. Transcriptional expression of I. galbana analyzed at 10, 12, and 16 h disclosed multiple mechanisms of BMAA to suppress the microalgal growth. Production of ammonia and glutamate was limited by the down-regulation of nitrate transporters, glutamate synthase, glutamine synthetase, cyanate hydrolase, and formamidase. Diverse extrinsic proteins related to PSII, PSI, cytochrome b6f complex, and ATPase were influenced by BMAA at transcriptional level. Suppression of the DNA replication and mismatch repair pathways increased the accumulation of misfolded proteins, which was reflected by the up-regulated expression of proteasome to accelerate proteolysis. This study improves our understanding of the chemical ecology impacts of BMAA in marine ecosystems.

Differential regulation of H3K9/H3K14 acetylation by small molecules drives neuron-fate-induction of glioma cell

Differentiation therapy using small molecules is a promising strategy for improving the prognosis of glioblastoma (GBM). Histone acetylation plays an important role in cell fate determination. Nevertheless, whether histone acetylation in specific sites determines GBM cells fate remains to be explored. Through screening from a 349 small molecule-library, we identified that histone deacetylase inhibitor (HDACi) MS-275 synergized with 8-CPT-cAMP was able to transdifferentiate U87MG GBM cells into neuron-like cells, which were characterized by cell cycle arrest, rich neuron biomarkers, and typical neuron electrophysiology. Intriguingly, acetylation tags of histone 3 at lysine 9 (H3K9ac) were decreased in the promoter of multiple oncogenes and cell cycle genes, while ones of H3K9ac and histone 3 at lysine 14 (H3K14ac) were increased in the promoter of neuron-specific genes. We then compiled a list of genes controlled by H3K9ac and H3K14ac, and proved that it is a good predictive power for pathologic grading and survival prediction. Moreover, cAMP agonist combined with HDACi also induced glioma stem cells (GSCs) to differentiate into neuron-like cells through the regulation of H3K9ac/K14ac, indicating that combined induction has the potential for recurrence-preventive application. Furthermore, the combination of cAMP activator plus HDACi significantly repressed the tumor growth in a subcutaneous GSC-derived tumor model, and temozolomide cooperated with the differentiation-inducing combination to prolong the survival in an orthotopic GSC-derived tumor model. These findings highlight epigenetic reprogramming through H3K9ac and H3K14ac as a novel approach for driving neuron-fate-induction of GBM cells.

Genomic determinants of patterns of failure in metachronous oligometastatic castration-sensitive prostate cancer.

238 Background: Oligometastatic castration-sensitive prostate cancer (omCSPC) represents an early state along the progression of metastatic disease in which patients experience improved outcomes compared to those with higher disease burden. Despite the generally more indolent nature, much heterogeneity still exists with some patients experiencing a more aggressive clinical course unexplained by clinical features alone. Here we correlate tumor genomics with modes of progression (MOP) and patterns of failure (POF) following treatment for omCSPC. Methods: We performed an international multi-institutional retrospective study of men treated for metachronous omCSPC, who underwent tumor next generation sequencing (NGS) with at least 1 year of follow-up. Descriptive POF and MOP were reported with respect to presence of genomic alterations in pathways of interest. Genomic pathways of interest included TP53, SPOP, WNT ( APC, CTNNB1, RNF43), DNA double strand break repair, cell cycle genes ( Rb1, CCND1–3, CDKN1B, and CDKN2A), and PI3K/AKT/mTOR. MOP were defined as oligoprogression (1-3 lesions), polyprogression (≥4 lesions), or long-term control (LTC, no radiographic progression at last follow-up). POF included location of lesions at first failure. Overall survival (OS) was calculated by the Kaplan-Meier method. Genomic associations with patterns/modes of failure were compared with chi-square test. Results: 221 patients were included for analysis with the majority having either 1 (47.5%) or 2 (27.3%) metastatic lesions at oligometastasis. 5-yr OS was associated with MOP 92% vs 89% vs 69% (p<0.01) for LTC, oligo- and polyprogression respectively. TP53 mutations were associated with significantly lower rates of LTC (24.4% vs 46%, p<0.01) and cell cycle mutations associated with high rates of polyprogression (36.7% vs 15.7%, p<0.01). With respect to POF, bone failure was significantly more common within tumors harboring mutations in TP53 (41.2% vs 23.1%, p=0.01) and less common with SPOP mutations (4.2% vs 27.8%, p=0.02). Finally, visceral failures were more common in tumors harboring either WNT pathway (20% vs 5.1%, p<0.01) or SPOP (17.4% vs 5.2%, p=0.04) mutations. Notably, SPOP and WNT pathway mutations cluster together (p<0.01). Conclusions: Tumor genomics provides novel insight into patterns of failure and modes of progression following treatment for metachronous omCSPC. Patients with TP53 and cell cycle mutations have a higher likelihood of progression and TP53, SPOP, and WNT pathway mutations may have a role in metastatic organotropism.

LncRNA DANCR counteracts premature ovarian insufficiency by regulating the senescence process of granulosa cells through stabilizing the interaction between p53 and hNRNPC

BackgroundPremature ovarian insufficiency (POI) is one of the common women reproductive endocrine diseases which adversely impacts female fertility, but the etiology and pathogenesis still remain elusive. Recently increasing researches focus on the roles of lncRNA in POI. LncRNA DANCR was involved in cell differentiation and multiple cancers. It’s highly expressed in ovary while the role of DANCR in POI is still unknown.ResultsHere, we identify a new POI related lncRNA DANCR, which negatively contributes to ovarian granulosa cells aging and follicular atresia. DANCR is proved to be decreasingly expressed in POI patients’ granulosa cells. Additionally, Dancr knockout (Dancr−/−) mice were constructed and characterized with POI phenotypes and fertility decline, compared with Dancr+/+ mice. Further, in vitro experiments indicated that DANCR knockdown in granulosa cells led to cell aging and series of aging-related changes including proliferation inhibition, cell cycle G1 arrest and DNA damage. Mechanism research revealed DANCR binds with hNRNPC and p53, while DANCR knockdown attenuates the binding of hNRNPC and p53, thus enhancing protein level of p53 and promoting granulosa cells aging significantly.ConclusionThe newly identified lncRNA DANCR inhibits p53-dependent granulosa cells aging by regulating hNRNPC-p53 interaction, and eventually counteracting POI. This provides new insights into the pathogenesis of POI and provides a potential target for future diagnosis and treatment.

Systemic Hypoxemia Induces Cardiomyocyte Hypertrophy and Right Ventricular Specific Induction of Proliferation.

A recent study suggests that systemic hypoxemia in adult male mice can induce cardiac myocytes to proliferate. The goal of the present experiments was to confirm these results, provide new insights on the mechanisms that induce adult cardiomyocyte cell cycle reentry, and to determine if hypoxemia also induces cardiomyocyte proliferation in female mice. EdU-containing mini pumps were implanted in 3-month-old, male and female C57BL/6 mice. Mice were placed in a hypoxia chamber, and the oxygen was lowered by 1% every day for 14 days to reach 7% oxygen. The animals remained in 7% oxygen for 2 weeks before terminal studies. Myocyte proliferation was also studied with a mosaic analysis with double markers mouse model. Hypoxia induced cardiac hypertrophy in both left ventricular (LV) and right ventricular (RV) myocytes, with LV myocytes lengthening and RV myocytes widening and lengthening. Hypoxia induced an increase (0.01±0.01% in normoxia to 0.11±0.09% in hypoxia) in the number of EdU+ RV cardiomyocytes, with no effect on LV myocytes in male C57BL/6 mice. Similar results were observed in female mice. Furthermore, in mosaic analysis with double markers mice, hypoxia induced a significant increase in RV myocyte proliferation (0.03±0.03% in normoxia to 0.32±0.15% in hypoxia of RFP+ myocytes), with no significant change in LV myocyte proliferation. RNA sequencing showed upregulation of mitotic cell cycle genes and a downregulation of Cullin genes, which promote the G1 to S phase transition in hypoxic mice. There was significant proliferation of nonmyocytes and mild cardiac fibrosis in hypoxic mice that did not disrupt cardiac function. Male and female mice exhibited similar gene expression following hypoxia. Systemic hypoxia induces a global hypertrophic stress response that was associated with increased RV proliferation, and while LV myocytes did not show increased proliferation, our results minimally confirm previous reports that hypoxia can induce cardiomyocyte cell cycle activity in vivo.

Opposing Roles of FACT for Euchromatin and Heterochromatin in Yeast.

DNA is stored in the nucleus of a cell in a folded state; however, only the necessary genetic information is extracted from the required group of genes. The key to extracting genetic information is chromatin ambivalence. Depending on the chromosomal region, chromatin is characterized into low-density "euchromatin" and high-density "heterochromatin", with various factors being involved in its regulation. Here, we focus on chromatin regulation and gene expression by the yeast FACT complex, which functions in both euchromatin and heterochromatin. FACT is known as a histone H2A/H2B chaperone and was initially reported as an elongation factor associated with RNA polymerase II. In budding yeast, FACT activates promoter chromatin by interacting with the transcriptional activators SBF/MBF via the regulation of G1/S cell cycle genes. In fission yeast, FACT plays an important role in the formation of higher-order chromatin structures and transcriptional repression by binding to Swi6, an HP1 family protein, at heterochromatin. This FACT property, which refers to the alternate chromatin-regulation depending on the binding partner, is an interesting phenomenon. Further analysis of nucleosome regulation within heterochromatin is expected in future studies.

Cspg4high microglia contribute to microgliosis during neurodegeneration

Microglia play a critical role in the pathogenic process of neurodegenerative diseases, such as Parkinson's disease (PD) and Alzheimer's disease (AD). Upon pathological stimulation, microglia are converted from a surveillant to an overactivated phenotype. However, the molecular characters of proliferating microglia and their contributions to the pathogenesis of neurodegeneration remain unclear. Here, we identify chondroitin sulfate proteoglycan 4 (Cspg4, also known as neural/glial antigen 2)-expressing microglia as a specific subset of microglia with proliferative capability during neurodegeneration. We found that the percentage of Cspg4+ microglia was increased in mouse models of PD. The transcriptomic analysis of Cspg4+ microglia revealed that the subcluster Cspg4high microglia displayed a unique transcriptomic signature, which was characterized by the enrichment of orthologous cell cycle genes and a lower expression of genes responsible for neuroinflammation and phagocytosis. Their gene signatures were also distinct from that of known disease-associated microglia. The proliferation of quiescent Cspg4high microglia was evoked by pathological α-synuclein. Following the transplantation in the adult brain with the depletion of endogenous microglia, Cspg4high microglia grafts showed higher survival rates than their Cspg4-counterparts. Consistently, Cspg4high microglia were detected in the brain of AD patients and displayed the expansion in animal models of AD. These findings suggest that Cspg4high microglia are one of the origins of microgliosis during neurodegeneration and may open up a avenue for the treatment of neurodegenerative diseases.

Targeted long-read sequencing of the Ewing sarcoma 6p25.1 susceptibility locus identifies germline-somatic interactions with EWSR1-FLI1 binding

Ewing sarcoma (EwS) is a rare bone and soft tissue malignancy driven by chromosomal translocations encoding chimeric transcription factors, such as EWSR1-FLI1, that bind GGAA motifs forming novel enhancers that alter nearby expression. We propose that germline microsatellite variation at the 6p25.1 EwS susceptibility locus could impact downstream gene expression and EwS biology. We performed targeted long-read sequencing of EwS blood DNA to characterize variation and genomic features important for EWSR1-FLI1 binding. We identified 50 microsatellite alleles at 6p25.1 and observed that EwS-affected individuals had longer alleles (>135bp) with more GGAA repeats. The 6p25.1 GGAA microsatellite showed chromatin features of an EWSR1-FLI1 enhancer and regulated expression of RREB1, a transcription factor associated with RAS/MAPK signaling. RREB1 knockdown reduced proliferation and clonogenic potential and reduced expression of cell cycle and DNA replication genes. Our integrative analysis at 6p25.1 details increased binding of longer GGAA microsatellite alleles with acquired EWSR-FLI1 to promote Ewing sarcomagenesis by RREB1-mediated proliferation.

Comparative analysis of histopathological parameters, genome-wide copy number alterations, and variants in genes involved in cell cycle regulation in chordomas of the skull base and sacrum.

Chordomas are rare tumors of the axial skeleton that are refractory to conventional therapy. Few studies have compared the morphological and molecular characteristics of chordomas according to the skull base and sacral locations. Histopathological data and changes revealed by array comparative genomic hybridization (CGH) and next-generation sequencing (NGS) of cell cycle regulation genes were analyzed for 28 skull base (SBCs) and 15 sacral (SC) chordomas. All cases were conventional chordomas. SBCs were significantly more frequent in patients aged <40 years and SCs predominated in patients aged >60 years. Mitotic indices ≥2 mitoses/10 high-power fields were correlated with high degrees of nuclear atypia and Ki67 labeling indices ≥6%. We identified 321 genomic positions, and copy number variation losses were more frequent than gain. Moreover, we report a panel of 85 genetic variants of cell cycle genes and the presence of molecular clusters for chordoma as well in CGH as in NGS. These new data strengthen the view that the chordoma should not be considered as a single molecular entity.

Analyses of regulatory network and discovery of potential biomarkers for Korean rockfish (Sebastes schlegelii) in responses to starvation stress through transcriptome and metabolome

Whether in aquaculture or in nature, starvation stress limits the growth of fish. The purpose of the study was to clarify the detailed molecular mechanisms underlying starvation stress in Korean rockfish (Sebastes schlegelii) through liver transcriptome and metabolome analysis. Transcriptome results showed that liver genes associated with cell cycle and fatty acid synthesis were down-regulated, whereas those related to fatty acid decomposition were up-regulated in the experimental group (EG; starved for 72 days) compared to the control group (CG; feeding). Metabolomic results showed that there were significant differences in the levels of metabolites related to nucleotide metabolism and energy metabolism, such as purine metabolism, histidine metabolism and oxidative phosphorylation. Five fatty acids (C22:6n-3; C22:5n-3; C20:5n-3; C20:4n-3; C18:3n-6) were selected as possible biomarkers of starvation stress from the differential metabolites of metabolome. Subsequently, correlation between these differential genes of lipid metabolism and cell cycle and differential metabolites were analyzed, and observed that these five fatty acids were significantly correlated with the differential genes. These results provide new clues for understanding the role of fatty acid metabolism and cell cycle in fish under starvation stress. It also provides a reference for promoting the biomarker identification of starvation stress and stress tolerance breeding research.

Inflammation and DNA damage: cause, effect or both.

Inflammation is a biological response involving immune cells, blood vessels and mediators induced by endogenous and exogenous stimuli, such as pathogens, damaged cells or chemicals. Unresolved (chronic) inflammation is characterized by the secretion of cytokines that maintain inflammation and redox stress. Mitochondrial or nuclear redox imbalance induces DNA damage, which triggers the DNA damage response (DDR) that is orchestrated by ATM and ATR kinases, which modify gene expression and metabolism and, eventually, establish the senescent phenotype. DDR-mediated senescence is induced by the signalling proteins p53, p16 and p21, which arrest the cell cycle in G1 or G2 and promote cytokine secretion, producing the senescence-associated secretory phenotype. Senescence and inflammation phenotypes are intimately associated, but highly heterogeneous because they vary according to the cell type that is involved. The vicious cycle of inflammation, DNA damage and DDR-mediated senescence, along with the constitutive activation of the immune system, is the core of an evolutionarily conserved circuitry, whicharreststhe cellcycle to reduce the accumulation of mutations generated by DNA replication during redox stress caused by infection or inflammation. Evidence suggests that specific organ dysfunctions in apparently unrelated diseases of autoimmune, rheumatic, degenerative and vascular origins are caused by inflammation resulting from DNA damage-induced senescence.

The Phytochemical α-Mangostin Inhibits Cervical Cancer Cell Proliferation and Tumor Growth by Downregulating E6/E7-HPV Oncogenes and KCNH1 Gene Expression.

Cervical cancer is the fourth most common cancer among women worldwide. The main factor associated with the onset and progression of this neoplasia is the human papillomavirus (HPV) infection. The HPV-oncogenes E6 and E7 are critical drivers of cellular transformation, promoting the expression of oncogenes such as KCNH1. The phytochemical α-mangostin (AM) is a potent antineoplastic and antiviral compound. However, its effects on HPV oncogenes and KCNH1 gene expression remain unknown. This study evaluated the effects of AM on cell proliferation, cell cycle distribution and gene expression, including its effects on tumor growth in xenografted mice. AM inhibited cell proliferation in a concentration-dependent manner, being the most sensitive cell lines those with the highest number of HPV16 copies. In addition, AM promoted G1-cell cycle arrest in CaSki cells, while led to cell death in SiHa and HeLa cells. Of interest was the finding of an AM-dependent decreased gene expression of E6, E7 and KCNH1 both in vitro and in vivo, as well as the modulation of cytokine expression, Ki-67, and tumor growth inhibition. On these bases, we suggest that AM represents a good option as an adjuvant for the treatment and prevention of cervical cancer.

Development of an osteosarcoma model with MYCN amplification and TP53 mutation in hiPS cell-derived neural crest cells.

Mesenchymal stem cell- or osteoblast-derived osteosarcoma is the most common malignant bone tumor. Its highly metastatic malignant phenotypes, which are often associated with a poor prognosis, have been correlated with the modulation of TP53- and cell-cycle-related pathways. MYC, which regulates the transcription of cell-cycle modulating genes, is used as a representative prognostic marker for osteosarcoma. Another member of the MYC oncoprotein family, MYCN, is highly expressed in a subset of osteosarcoma, however its roles in osteosarcoma have not been fully elucidated. Here, we attempted to create an in vitro tumorigenesis model using hiPSC-derived neural crest cells, which are precursors of mesenchymal stem cells, by overexpressing MYCN on a heterozygous TP53 hotspot mutation (c.733G>A; p.G245S) background. MYCN-expressing TP53 mutated transformed clones were isolated by soft agar colony formation, and administered subcutaneously into the periadrenal adipose tissue of immunodeficient mice, resulting in the development of chondroblastic osteosarcoma. MYCN suppression decreased the proliferation of MYCN-induced osteosarcoma cells, suggesting MYCN as a potential target for a subset of osteosarcoma treatment. Further, comprehensive analysis of gene expression and exome sequencing of MYCN-induced clones indicated osteosarcoma-specific molecular features, such as the activation of TGF-β signaling and DNA copy number amplification of GLI1. The model of MYCN-expressing chondroblastic osteosarcoma was developed from hiPSC-derived neural crest cells, providing a useful tool for the development of new tumor models using hiPSC-derived progenitor cells with gene modifications and in vitro transformation.

Genetic analysis of grapevine root system architecture and loci associated gene networks.

Own-rooted grapevines and grapevine rootstocks are vegetatively propagated from cuttings and have an adventitious root system. Unraveling the genetic underpinnings of the adventitious root system architecture (RSA) is important for improving own-rooted and grafted grapevine sustainability for a changing climate. Grapevine RSA genetic analysis was conducted in an Vitis sp. 'VRS-F2' population. Nine root morphology, three total root system morphology, and two biomass traits that contribute to root anchorage and water and nutrient uptake were phenotyped. Quantitative trait loci (QTL) analysis was performed using a high density integrated GBS and rhAmpSeq genetic map. Thirty-one QTL were detected for eleven of the RSA traits (surface area, root volume, total root length, fresh weight, number of tips, forks or links, longest root and average root diameter, link length, and link surface area) revealing many small effects. Several QTL were colocated on chromosomes 1, 9, 13, 18, and 19. QTL with identical peak positions on chromosomes 1 or 13 were enriched for AP2-EREBP, AS2, C2C2-CO, HMG, and MYB transcription factors, and QTL on chromosomes 9 or 13 were enriched for the ALFIN-LIKE transcription factor and regulation of autophagy pathways. QTL modeling for individual root traits identified eight models explaining 13.2 to 31.8% of the phenotypic variation. 'Seyval blanc' was the grandparent contributing to the allele models that included a greater surface area, total root length, and branching (number of forks and links) traits promoting a greater root density. In contrast, V. riparia 'Manitoba 37' contributed the allele for greater average branch length (link length) and diameter, promoting a less dense elongated root system with thicker roots. LATERAL ORGAN BOUNDARY DOMAIN (LBD or AS2/LOB) and the PROTODERMAL FACTOR (PFD2 and ANL2) were identified as important candidate genes in the enriched pathways underlying the hotspots for grapevine adventitious RSA. The combined QTL hotspot and trait modeling identified transcription factors, cell cycle and circadian rhythm genes with a known role in root cell and epidermal layer differentiation, lateral root development and cortex thickness. These genes are candidates for tailoring grapevine root system texture, density and length in breeding programs.

Short-Term Starvation Weakens the Efficacy of Cell Cycle Specific Chemotherapy Drugs through G1 Arrest.

Short-term starvation (STS) during chemotherapy can block the nutrient supply to tumors and make tumor cells much more sensitive to chemotherapeutic drugs than normal cells. However, because of the diversity of starvation methods and the heterogeneity of tumors, this method's specific effects and mechanisms for chemotherapy are still poorly understood. In this study, we used HeLa cells as a model for short-term starvation and etoposide (ETO) combined treatment, and we also mimicked the short-term starvation effect by knocking down the glycolytic enzyme GAPDH to explore the exact molecular mechanism. In addition, our study demonstrated that short-term starvation protects cancer cells against the chemotherapeutic agent ETO by reducing DNA damage and apoptosis due to the STS-induced cell cycle G1 phase block and S phase reduction, thereby diminishing the effect of ETO. Furthermore, these results suggest that starvation therapy in combination with cell cycle-specific chemotherapeutic agents must be carefully considered.