Determinants of p53 DNA binding, gene regulation, and cell fate decisions.

The extent to which transcription factors read and respond to specific information content within short DNA sequences remains an important question that the tumor suppressor p53 is helping us answer. We discuss recent insights into how local information content at p53 binding sites might control modes of p53 target gene activation and cell fate decisions. Significant prior work has yielded data supporting two potential models of how p53 determines cell fate through its target genes: a selective target gene binding and activation model and a p53 level threshold model. Both of these models largely revolve around an analogy of whether p53 is acting in a "smart" or "dumb" manner. Here, we synthesize recent and past studies on p53 decoding of DNA sequence, chromatin context, and cellular signaling cascades to elicit variable cell fates critical in human development, homeostasis, and disease.

Encouraging medical students to become surgeons? Impact of psychological and surgical factors on career choice at medical school.

Aim: Training decisions are viewed as a problem by the majority of medical students.In the present study we compared sociodemographic and psychological characteristics of students who are interested in surgical training to those who preferred a non-surgical specialty. Furthermore, we examined whether students who wish to be trained as surgeons performed better than their non-surgical counterparts in a course designed to acquire skills in minimally invasive surgery. Method: From October 2020 to January 2021 we performed a cross-sectional survey among 116 medical students prior to their year of practical training at Christian-Albrechts University in Kiel. Based on their intended field of specialization, the students were divided into a non-surgical and a surgical group. Sociodemographic and psychological characteristics such as self-efficacy expectations, resilience and stress perception were evaluated and compared between groups. Simultaneously, we compared their surgical performance in two laparoscopic exercises and their self-assessment as surgeons. Statistical differences between the training groups were determined by the Mann-Whitney U test or Pearson's Chi square test. Results: Ninety-two students participated in the study, of whom 64.1% intended to train in a non-surgical specialty and 35.9% in a surgical specialty. Students who wished to be trained as surgeons had higher general self-efficacy expectations (p<0.001) and greater resilience (p=0.009). However, on comparison they had a lower stress level (p=0.047). The inter-group comparison of training results and self-assessment as surgeons revealed no unequivocal differences in surgical performance. Conclusion: Interest in surgical specialties is correlated, among other factors, with the strength of psychological skills such as general self-efficacy expectations, resilience and stress perception. Early attention to these psychological resources in academic training might assist medical students in future career choices.

Gene regulation by the tumor suppressor p53 - The omics era.

The transcription factor p53 is activated in response to a variety of cellular stresses and serves as a prominent and potent tumor suppressor. Since its discovery, we have sought to understand how p53 functions as both a transcription factor and a tumor suppressor. Two decades ago, the field of gene regulation entered the omics era and began to study the regulation of entire genomes. The omics perspective has greatly expanded our understanding of p53 functions and has begun to reveal its gene regulatory network. In this mini-review, I discuss recent insights into the p53 transcriptional program from high-throughput analyses.

p53 and MYC-regulated squalene epoxidase as Achilles heel in colorectal cancer.

The transcription factors p53 and MYC are often considered non-druggable targets, but their dysregulation can generate new dependencies and treatment opportunities in cancer cells. The p53 and MYC-regulated squalene epoxidase (SQLE) has been identified as a potential Achilles heel in colorectal cancer. This is of great interest because the FDA-approved anti-fungal SQLE inhibitor Terbinafine could be repurposed to treat colorectal cancer patients.

Principles of oncology taught in a one-week course.

BACKGROUND: Growing challenges in oncology require evolving educational methods and content. International efforts to reform oncology education are underway. Hands-on, interdisciplinary, and compact course formats have shown great effectiveness in the education of medical students. Our aim was to establish a new interdisciplinary one-week course on the principles of oncology using state-of-the-art teaching methods. METHODS: In an initial survey, medical students of LMU Munich were questioned about their current level of knowledge on the principles of oncology. In a second two-stage survey, the increase in knowledge resulting from our recently established interdisciplinary one-week course was determined. RESULTS: The medical students' knowledge of clinically important oncological topics, such as the diagnostic workup and interdisciplinary treatment options, showed a need for improvement. Knowledge of the major oncological entities was also in an expandable state. By attending the one-week course on the principles of oncology, students improved their expertise in all areas of the clinical workup in oncology and had the opportunity to close previous knowledge gaps. In addition, students were able to gain more in-depth clinical knowledge on the most common oncological entities. CONCLUSION: The interdisciplinary one-week course on the principles of oncology proved to be an effective teaching method to expand the knowledge of the future physicians to an appropriate level. With its innovative and interdisciplinary approach, the one-week course could be used as a showcase project for the ongoing development of medical education in Germany.

Total knee arthroplasty without patella resurfacing leads to worse results in patients with patellafemoral osteoarthritis Iwano Stages 3-4: a study based on arthroplasty registry data.

PURPOSE: To determine whether the preoperative degree of degeneration of the patellofemoral joint really affects the outcome of total knee arthroplasty (TKA) surgery without patella resurfacing and thus to establish a parameter that might serve as a guiding factor to decide whether or not to perform retropatellar resurfacing. It was hypothesized that patients with preoperative mild patellofemoral osteoarthritis (Iwano Stages 0-2) would significantly differ from patients with preoperative severe patellofemoral osteoarthritis (Iwano Stages 3-4) in terms of patient-reported outcome (Hypothesis 1) and revision rates/survival (Hypothesis 2) after TKA without patella resurfacing. METHODS: Application of a retrospective-comparative design on the basis of Arthroplasty Registry data that included patients with primary TKA without patella resurfacing. Patients were allocated to the following groups based on preoperative radiographic stage of patellofemoral joint degeneration: (a) mild patellofemoral osteoarthritis (Iwano Stage ≤ 2) and (b) severe patellofemoral osteoarthritis (Iwano Stages 3-4). The Western Ontario and MacMaster Universities Osteoarthritis Index (WOMAC) score was assessed preoperative and 1 year postoperative (0: best, 100 worst). In addition, implant survival was calculated from the Arthroplasty Registry data. RESULTS: In 1209 primary TKA without patella resurfacing, postoperative WOMAC total and WOMAC subscores did not differ significantly between groups, but potentially suffered from type 2 error. Three-year survival was 97.4% and 92.5% in patients with preoperative mild and severe patellofemoral osteoarthritis, respectively (p = 0.002). Five-year survival was 95.8% vs. 91.4% (p = 0.033) and 10-year survival was 93.3% vs. 88.6% (p = 0.033), respectively. CONCLUSIONS: From the study findings, it is concluded that patients with preoperative severe patellofemoral osteoarthritis have significantly higher risks for reoperation than do those with preoperative mild patellofemoral osteoarthritis-when treated with TKA without patella resurfacing. Hence, it is recommended that patella resurfacing be applied in patients with severe Iwano Stage 3 or 4 patellofemoral osteoarthritis during TKA. LEVEL OF EVIDENCE: III, Retrospective comparative.

Multi-omics analysis identifies RFX7 targets involved in tumor suppression and neuronal processes.

Recurrently mutated in lymphoid neoplasms, the transcription factor RFX7 is emerging as a tumor suppressor. Previous reports suggested that RFX7 may also have a role in neurological and metabolic disorders. We recently reported that RFX7 responds to p53 signaling and cellular stress. Furthermore, we found RFX7 target genes to be dysregulated in numerous cancer types also beyond the hematological system. However, our understanding of RFX7's target gene network and its role in health and disease remains limited. Here, we generated RFX7 knock-out cells and employed a multi-omics approach integrating transcriptome, cistrome, and proteome data to obtain a more comprehensive picture of RFX7 targets. We identify novel target genes linked to RFX7's tumor suppressor function and underscoring its potential role in neurological disorders. Importantly, our data reveal RFX7 as a mechanistic link that enables the activation of these genes in response to p53 signaling.

Differences in perceptions of capability, autonomy, and expectations between residents and surgical team members in executing EPAs in Ethiopian medical education.

Background: Entrustable Professional Activities (EPAs) are units of professional practice that are defined as tasks or responsibilities that are entrusted to an unsupervised execution by a trainee. In 2021, a framework of 29 EPAs was developed for surgical residency training programs in Ethiopia, with the goal of residents being able to perform independently by the time they graduate. However, studies show that surgical residents lack confidence and are unable to execute EPAs autonomously upon graduation, and concerns have been raised about graduate competencies in EPA execution. The goal of this research is to assess how surgical team members judge/perceive residents' performance in executing these EPAs autonomously at the time of graduation and how residents rate their own capability and autonomy in executing EPAs in order to systematically introduce and implement EPAs in Ethiopian medical education. Methods: A survey was conducted in the Departments of Surgery at four residency training institutions in Ethiopia. All eligible surgical team members and final-year general surgery residents were invited to participate. Surgical team members were asked to rate the observed performance of a group of graduating surgical residents in each of the 29 EPAs, and residents were asked to rate their own capability in executing EPAs. The analysis focused on variations in performance ratings between surgical team members and residents, as well as across surgical team members. Results: A total of 125 surgical team members and 49 residents participated in this study. Residents rate their competence in performing these EPAs higher than surgical team members, mean 4.2 (SD = 0.63) vs. 3.7 (SD = 0.9). A statistically significant difference in perceptions of capability, autonomy, and expectations in executing EPAs was observed between the two groups of study (p = 0.03, CI: 0.51-0.95), as well as within surgical team members (p < 0.001). Conclusions: Differences in perceptions of capability, autonomy, and expectations between residents and surgical team members, as well as within faculty members, were seen in executing EPAs. There were concerns about graduate surgical residents' competence to execute EPAs autonomously at the time of graduation. Surgical team members perceived that a set of graduating surgical residents are not yet safe to perform these EPAs independently (without supervision) and still requires distant supervision.

The landscape of human p53-regulated long non-coding RNAs reveals critical host gene co-regulation.

The role of long non-coding RNAs (lncRNAs) in p53-mediated tumor suppression has become increasingly appreciated in the past decade. Thus, the identification of p53-regulated lncRNAs can be a promising starting point to select and prioritize lncRNAs for functional analyses. By integrating transcriptome and transcription factor-binding data, we identified 379 lncRNAs that are recurrently differentially regulated by p53. Dissecting the mechanisms by which p53 regulates many of them, we identified sets of lncRNAs regulated either directly by p53 or indirectly through the p53-RFX7 and p53-p21-DREAM/RB:E2F pathways. Importantly, we identified multiple p53-responsive lncRNAs that are co-regulated with their protein-coding host genes, revealing an important mechanism by which p53 may regulate lncRNAs. Further analysis of transcriptome data and clinical data from cancer patients showed that recurrently p53-regulated lncRNAs are associated with patient survival. Together, the integrative analysis of the landscape of p53-regulated lncRNAs provides a powerful resource facilitating the identification of lncRNA function and displays the mechanisms of p53-dependent regulation that could be exploited for developing anticancer approaches.

Physiological media advance cell culture experiments.

The metabolism plays a fundamental role in cellular signaling pathways, but commonly used cell culture media do not reflect physiological metabolite concentrations. The metabolic control hub mammalian target of rapamycin complex 1 (mTORC1) kinase is an illuminating example that it is about time to advance our cell culture to become more physiological and relevant.

Contrast mechanisms in pump-probe microscopy of melanin.

Pump-probe microscopy of melanin in tumors has been proposed to improve diagnosis of malignant melanoma, based on the hypothesis that aggressive cancers disaggregate melanin structure. However, measured signals of melanin are complex superpositions of multiple nonlinear processes, which makes interpretation challenging. Polarization control during measurement and data fitting are used to decompose signals of melanin into their underlying molecular mechanisms. We then identify the molecular mechanisms that are most susceptible to melanin disaggregation and derive false-coloring schemes to highlight these processes in biological tissue. We demonstrate that false-colored images of a small set of melanoma tumors correlate with clinical concern. More generally, our systematic approach of decomposing pump-probe signals can be applied to a multitude of different samples.

Coordinating gene expression during the cell cycle.

Cell cycle-dependent gene transcription is tightly controlled by the retinoblastoma (RB):E2F and DREAM complexes, which repress all cell cycle genes during quiescence. Cyclin-dependent kinase (CDK) phosphorylation of RB and DREAM allows for the expression of two gene sets. The first set of genes, with peak expression in G1/S, is activated by E2F transcription factors (TFs) and is required for DNA synthesis. The second set, with maximum expression during G2/M, is required for mitosis and is coordinated by the MuvB complex, together with B-MYB and Forkhead box M1 (FOXM1). In this review, we summarize the key findings that established the distinct control mechanisms regulating G1/S and G2/M gene expression in mammals and discuss recent advances in the understanding of the temporal control of these genes.

Evaluation of malnutrition in patients undergoing major abdominal surgery using GLIM criteria and comparing CT and BIA for muscle mass measurement.

BACKGROUND & AIMS: GLIM criteria have become a worldwide standard for diagnosing malnutrition. They emphasize the measurement of muscle mass but do not provide clear recommendations for the use of different diagnostic tools and cut-offs. Measurements of body composition by using computerized tomography (CT) and bioelectrical impedance analysis (BIA) are both easily accessible in hospitalized patients. However, there is sparse data regarding the comparison for GLIM diagnosis of malnutrition and its prognostic impact for postoperative outcome in patients undergoing major abdominal surgery for cancer. METHODS: We retrospectively analysed 260 patients undergoing major abdominal surgery between January 2017 and December 2019. Patients were prospectively screened and assessed for malnutrition with Nutritional Risk Score (NRS) and Subjective Global assessment (SGA). Body composition was analysed with CT scan and BIA within 30 days before surgery. GLIM criteria were retrospectively determined referring to the Fat free Mass from BIA (FFMBIA) and Muscle Mass from axial CT scan at lumbar level 3 (MMCT). The prevalence of GLIM - malnutrition according to BIA and CT was evaluated. Multivariate logistic regression analysis was used to determine association between malnutrition and outcome parameters. ROC-curves specified sensitivity and specificity of the different tools and areas under the curve were calculated. RESULTS: From 260 patients in total, 179 patients (68.8%) had a confirmed malnutrition according to MMCT, 178 patients (68.5%) were malnourished according to SGA (grade B or C), whereas 66 patients (25.4%) were diagnosed with malnutrition using FFMBIA. The risk for developing a complication was significant associated with both methods, FFMBIA (OR 2.116, 95% CI 1.185-3.778, p = 0.01) and MMCT (OR 2.028, 95% CI 1..188-3.463, p = 0.009). Sensitivity for the prediction of overall complications was: MMCT 76.3%, FFMBIA 31.9%, and SGA 73.3%; specificity: MMCT 40.0%, FFMBIA 81.6%, and SGA 36.8%. CONCLUSION: When using GLIM criteria, the method for measuring muscle mass is pivotal resulting in considerable differences in prevalence, sensitivity, and specificity. GLIM criteria are predictive for the risk of developing complications in patients undergoing major abdominal surgery. With the pre-existing cut-offs, BIA seems to diagnose patients at an more advanced stage of malnutrition and indicates an advanced deterioration of nutritional status.

TargetGeneReg 2.0: a comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation.

In recent years, our web-atlas at www.TargetGeneReg.org has enabled many researchers to uncover new biological insights and to identify novel regulatory mechanisms that affect p53 and the cell cycle - signaling pathways that are frequently dysregulated in diseases like cancer. Here, we provide a substantial upgrade of the database that comprises an extension to include non-coding genes and the transcription factors ΔNp63 and RFX7. TargetGeneReg 2.0 combines gene expression profiling and transcription factor DNA binding data to determine, for each gene, the response to p53, ΔNp63, and cell cycle signaling. It can be used to dissect common, cell type and treatment-specific effects, identify the most promising candidates, and validate findings. We demonstrate the increased power and more intuitive layout of the resource using realistic examples.

p53-mediated AKT and mTOR inhibition requires RFX7 and DDIT4 and depends on nutrient abundance.

In recent years the tumor suppressor p53 has been increasingly recognized as a potent regulator of the cell metabolism and for its ability to inhibit the critical pro-survival kinases AKT and mTOR. The mechanisms through which p53 controls AKT and mTOR, however, are largely unclear. Here, we demonstrate that p53 activates the metabolic regulator DDIT4 indirectly through the regulatory factor X 7 (RFX7). We provide evidence that DDIT4 is required for p53 to inhibit mTOR complex 2 (mTORC2)-dependent AKT activation. Most strikingly, we also find that the DDIT4 regulator RFX7 is required for p53-mediated inhibition of mTORC1 and AKT. Our results suggest that AMPK activation plays no role and p53-mediated AKT inhibition is not critical for p53-mediated mTORC1 inhibition. Moreover, using recently developed physiological cell culture media we uncover that basal p53 and RFX7 activity can play a critical role in restricting mTORC1 activity under physiological nutrient conditions, and we propose a nutrient-dependent model for p53-RFX7-mediated mTORC1 inhibition. These results establish RFX7 and its downstream target DDIT4 as essential effectors in metabolic control elicited by p53.

Simultaneous expression of MMB-FOXM1 complex components enables efficient bypass of senescence.

Cellular senescence is a stable cell cycle arrest that normal cells undergo after a finite number of divisions, in response to a variety of intrinsic and extrinsic stimuli. Although senescence is largely established and maintained by the p53/p21WAF1/CIP1 and pRB/p16INK4A tumour suppressor pathways, the downstream targets responsible for the stability of the growth arrest are not known. We have employed a stable senescence bypass assay in conditionally immortalised human breast fibroblasts (CL3EcoR) to investigate the role of the DREAM complex and its associated components in senescence. DREAM is a multi-subunit complex comprised of the MuvB core, containing LIN9, LIN37, LIN52, LIN54, and RBBP4, that when bound to p130, an RB1 like protein, and E2F4 inhibits cell cycle-dependent gene expression thereby arresting cell division. Phosphorylation of LIN52 at Serine 28 is required for DREAM assembly. Re-entry into the cell cycle upon phosphorylation of p130 leads to disruption of the DREAM complex and the MuvB core, associating initially to B-MYB and later to FOXM1 to form MMB and MMB-FOXM1 complexes respectively. Here we report that simultaneous expression of MMB-FOXM1 complex components efficiently bypasses senescence with LIN52, B-MYB, and FOXM1 as the crucial components. Moreover, bypass of senescence requires non-phosphorylated LIN52 that disrupts the DREAM complex, thereby indicating a central role for assembly of the DREAM complex in senescence.

p63 and p53: Collaborative Partners or Dueling Rivals?

The tumor suppressor p53 and its oncogenic sibling p63 (ΔNp63) direct opposing fates in tumor development. These paralog proteins are transcription factors that elicit their tumor suppressive and oncogenic capacity through the regulation of both shared and unique target genes. Both proteins predominantly function as activators of transcription, leading to a paradigm shift away from ΔNp63 as a dominant negative to p53 activity. The discovery of p53 and p63 as pioneer transcription factors regulating chromatin structure revealed new insights into how these paralogs can both positively and negatively influence each other to direct cell fate. The previous view of a strict rivalry between the siblings needs to be revisited, as p53 and p63 can also work together toward a common goal.

Transcription factor RFX7 governs a tumor suppressor network in response to p53 and stress.

Despite its prominence, the mechanisms through which the tumor suppressor p53 regulates most genes remain unclear. Recently, the regulatory factor X 7 (RFX7) emerged as a suppressor of lymphoid neoplasms, but its regulation and target genes mediating tumor suppression remain unknown. Here, we identify a novel p53-RFX7 signaling axis. Integrative analysis of the RFX7 DNA binding landscape and the RFX7-regulated transcriptome in three distinct cell systems reveals that RFX7 directly controls multiple established tumor suppressors, including PDCD4, PIK3IP1, MXD4, and PNRC1, across cell types and is the missing link for their activation in response to p53 and stress. RFX7 target gene expression correlates with cell differentiation and better prognosis in numerous cancer types. Interestingly, we find that RFX7 sensitizes cells to Doxorubicin by promoting apoptosis. Together, our work establishes RFX7's role as a ubiquitous regulator of cell growth and fate determination and a key node in the p53 transcriptional program.

A three-dimensional musculoskeletal model of the dog.

The domestic dog is interesting to investigate because of the wide range of body size, body mass, and physique in the many breeds. In the last several years, the number of clinical and biomechanical studies on dog locomotion has increased. However, the relationship between body structure and joint load during locomotion, as well as between joint load and degenerative diseases of the locomotor system (e.g. dysplasia), are not sufficiently understood. Collecting this data through in vivo measurements/records of joint forces and loads on deep/small muscles is complex, invasive, and sometimes unethical. The use of detailed musculoskeletal models may help fill the knowledge gap. We describe here the methods we used to create a detailed musculoskeletal model with 84 degrees of freedom and 134 muscles. Our model has three key-features: three-dimensionality, scalability, and modularity. We tested the validity of the model by identifying forelimb muscle synergies of a walking Beagle. We used inverse dynamics and static optimization to estimate muscle activations based on experimental data. We identified three muscle synergy groups by using hierarchical clustering. The activation patterns predicted from the model exhibit good agreement with experimental data for most of the forelimb muscles. We expect that our model will speed up the analysis of how body size, physique, agility, and disease influence neuronal control and joint loading in dog locomotion.

Mice Are Not Humans: The Case of p53.

Mouse models represent powerful tools in cancer research that have influenced much of our understanding of tumor development and our current anticancer strategies. Yet, central signaling pathways differ considerably between mouse and human, including gene regulatory networks (GRNs) of the most important tumor suppressor p53 and its oncogenic sibling p63.