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This article introduces an advanced Koopman mode decomposition (KMD) technique—coined Featurized Koopman Mode Decomposition (FKMD)—that uses delay embedding and a learned Mahalanobis distance to enhance analysis and prediction of high-dimensional dynamical systems. The delay embedding expands the observation space to better capture underlying manifold structures, while the Mahalanobis distance adjusts observations based on the system's dynamics. This aids in featurizing KMD in cases where good features are not a priori known. We show that FKMD improves predictions for a high-dimensional linear oscillator, a high-dimensional Lorenz attractor that is partially observed, and a cell signaling problem from cancer research. [ABSTRACT FROM AUTHOR]

Oncocytic follicular cell-derived thyroid neoplasms, formerly known as Hurthle cell tumors, are characterized by expansile nodular growths of thyroid follicular epithelium displaying abundant granular eosinophilic cytoplasm. The topic of oncocytic [...], * Context.--Oncocytic thyroid tumors displaying a papillary growth pattern are rare and may cause diagnostic problems. Objective.--To examine the clinicopathologic features of a series of 32 follicular cell-derived tumors composed of cells with oncocytic cytoplasm and displaying papillary architecture. Design.--Thirty-two cases were collected and studied to assess clinicopathologic features, including immunohistochemical and molecular testing for BRAF V600E. Results.--The patients were 26 women and 6 men, aged 17 to 77 years. The nodules ranged from 0.3 to 6.0 cm. Eighteen cases showed features of oncocytic hyperplastic nodules and were identified against a background of thyroid follicular nodular disease; 4 cases showed features of oncocytic follicular adenoma; and 10 cases corresponded to carcinomas with oncocytic and papillary features. Nuclear features of papillary thyroid carcinoma were absent or exceedingly rare. All cases were negative for HBME-1 and cytokeratin 19 (CK19) and wild type for BRAF V600E. Follow-up in 25 patients showed that all patients with hyperplastic nodules and oncocytic follicular adenomas were alive and well and free of disease from 7 to 20 years. One patient with oncocytic follicular carcinoma showed metastases and died of tumor at 16 months; 2 patients with carcinoma had metastases and recurrence at 6 and 7 years; and 5 patients with invasive tumors were free of disease from 5 to 10 years. Conclusions.--Oncocytic thyroid tumors with papillary features can span a spectrum from benign hyperplastic, to encapsulated neoplastic, to invasive malignant lesions. Owing to their papillary features, it is important not to confuse them for other types of thyroid tumors, such as oncocytic papillary thyroid carcinoma. (Arch Pathol Lab Med. 2024;148:997-1006; doi: 10.5858/arpa.2023-0309-OA)

Understanding of the biology, pathology, and natural history of cystic lesions of the pancreas has expanded dramatically. As recently as the 1970s, all tumors of the pancreas with cystic morphology [...], * Context.--Macroscopic precursor lesions of the pancreas represent a complex clinical management problem. Molecular characterization of pancreatic cysts has helped to confirm and refine clinical and pathologic classifications of these lesions, inform our understanding of tumorigenesis in the pancreas, and provide opportunities for preoperative diagnosis. Objective.--To review the pathologic classification of macroscopic cystic lesions of the pancreas: intraductal papillary mucinous neoplasms (IPMNs), mucinous cystic neoplasms (MCNs), intraductal oncocytic papillary neoplasms (IOPNs), and intraductal tubulopapillary neoplasms (ITPNs), and to describe our current state of understanding of their molecular underpinnings, relationship to invasive carcinomas, and implications for diagnosis and prognostication. Data Sources.--We assessed the current primary literature and current World Health Organization Classification of Digestive System Tumours. Conclusions.--Macroscopic cystic lesions of the pancreas are morphologically and molecularly diverse. IPMNs and MCNs share mucinous cytoplasm with papillae. MCNs are defined by ovarian-type stroma. IOPNs have granular eosinophilic cytoplasm, prominent nucleoli, and complex, arborizing papillae. ITPNs demonstrate complex, back-to-back tubules and anastomosing papillae and lack prominent intracellular mucin. IPMNs and MCNs are characterized by driver mutations in KRAS/ GNAS (IPMNs) and KRAS (MCNs), with later driver events in RNF43, CDKN2A, SMAD4, and TP53. In contrast, IOPNs and ITPNs have recurrent rearrangements in PRKACA/PRKACB and MAPK-associated genes, respectively. The recurrent alterations described in cysts provide an opportunity for diagnosis using aspirated cyst fluid. Molecular characterization of IPMNs shows a striking spatial and mutational heterogeneity, challenging traditional models of neoplastic development and creating challenges to interpretation of cyst fluid sequencing results. (Arch Pathol Lab Med. 2024;148:980-988; doi: 10.5858/arpa.2023-0358-RA)

Intraductal papillary neoplasm of the bile duct (IPNB) is a precursor lesion of cholangiocarcinoma. (1-3) Since the concept of this neoplasm was proposed almost 20 years ago, (4) it has [...], * Context.--Intraductal papillary neoplasm of the bile duct (IPNB) is classified into types 1 and 2 based on criteria proposed in 2019. Recent studies investigated the clinicopathologic and molecular features of IPNB, which contributed to a more detailed understanding of this undercharacterized neoplasm. Objective.--To summarize driver gene mutations, radiologic tumor evolution, and a potentially unique pattern of tumor progression in IPNB. Data Sources.--Data were derived from a literature review and personal clinical and research experiences. Conclusions.--In contrast to de novo cholangiocarcinoma, type 1 IPNB often has mutations in APC, CTNNB1, STK11, and GNAS. These molecular features are shared with intraductal papillary mucinous neoplasm of the pancreas; however, the frequencies of individual gene abnormalities differ between these 2 neoplasms. A radiologic review of sequential images suggested that type 1 IPNB is a slow-growing neoplasm, with an ~1-cm increase in size every 2 to 3 years, and remains in a noninvasive state for many years. A similar papillary neoplasm may develop in the biliary tree years after the complete surgical resection of IPNB. The second neoplasm has the same genetic abnormalities as the first neoplasm, indicating intrabiliary implantation rather than multifocal lesions. In contrast to type 1 IPNB, most cases of type 2 IPNB have invasive malignancy at the initial presentation. Type 2 IPNB shares many clinicopathologic and molecular features with de novo cholangiocarcinoma, questioning the distinctness of this tumor entity. The molecular mechanisms underlying malignant transformation in IPNB warrant further study. (Arch Pathol Lab Med. 2024;148:989-996; doi: 10.5858/arpa.2022-0407-RA)

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Purpose: This study has been focused on assessing the Open Science scenario of cancer research during the period 2011–2021, in terms of the derived scientific publications and raw data dissemination. Methods: A cancer search equation was executed in the Science Citation Index-Expanded, collecting the papers signed by at least one Spanish institution. The same search strategy was performed in the Data Citation Index to describe dataset diffusion. Results: 50,822 papers were recovered, 71% of which belong to first and second quartile journals. 59% of the articles were published in Open Access (OA) journals. The Open Access model and international collaboration positively conditioned the number of citations received. Among the most productive journals stood out Plos One, Cancers, and Clinical and Translational Oncology. 2693 genomics, proteomics and metabolomics datasets were retrieved, being Gene Expression Omnibus the favoured repository. Conclusions: There has been an increase in oncology publications in Open Access. Most were published in first quartile journals and received higher citations than non-Open Access articles, as well as when oncological investigation was performed between international research teams, being relevant in the context of Open Science. Genetic repositories have been the preferred for sharing oncology datasets. Further investigation of research and data sharing in oncology is needed, supported by stronger Open Science policies, to achieve better data sharing practices among three scientific main pillars: researchers, publishers, and scientific organizations. [ABSTRACT FROM AUTHOR]

ABSTRACT Currently, the majority of methods to monitor cancer treatment through the analysis of body fluids are based on a highly selective detection of single molecules or cells. In this study, we are considering the analysis of the aqueous medium of liquid samples, that is, water, itself, using aquaphotomics and near‐infrared spectroscopy (NIR) for spectral data acquisition and processing, within cancer research. Water, as a molecular system, is a rich source of information about the current state of a patient, which can be extracted from near‐infrared spectra of liquid samples via simple algorithms based on multivariate data analysis. The reported results, obtained ex vivo of body fluids, demonstrate the potential of aquaphotomics in cancer research. [ABSTRACT FROM AUTHOR]

Clinical practice guidelines are widely used in oncology to guide clinical decision making and inform health policy and planning. In recent years, the National Comprehensive Cancer Network and the American Society of Clinical Oncology, as well as other international groups, have developed resource‐stratified guidelines to guide clinicians and policymakers on cancer diagnosis and management in settings with various levels of resource constraints. Current methods for developing resource‐stratified guidelines rely heavily on supporting evidence originating from high‐income countries. In this commentary, the authors discuss limitations of the existing methods to develop resource‐stratified guidelines and offer perspective on ways to strengthen the guidelines and their evidence base. Pulling from conceptual frameworks in the health policy domain, the authors outline a more inclusive approach to evidence synthesis that seeks to integrate the growing volume of cancer research emerging from low‐ and middle‐income countries. The authors also introduce a revised evidence framework that provides transparency into the generalizability of evidence within the guidelines. These changes have the potential to enhance resource‐stratified guidelines and bring us one step closer to the goal of evidence‐based guidelines that are appropriate for diverse settings and unique patient populations across the world. [ABSTRACT FROM AUTHOR]

Microsatellite instability (MSI), a phenomenon caused by deoxyribonucleic acid (DNA) mismatch repair system deficiencies, is an important biomarker in cancer research and clinical diagnostics. MSI detection often involves next-generation sequencing data, with many studies focusing on DNA. Here, we introduce a novel approach by measuring microsatellite lengths directly from ribonucleic acid sequencing (RNA-seq) data and comparing its distribution to detect MSI. Our findings reveal distinct instability patterns between MSI-high (MSI-H) and microsatellite stable samples, indicating the efficacy of RNA–based MSI detection. Additionally, microsatellites in the 3′-untranslated regions showed the greatest predictive value for MSI detection. Notably, this efficacy extends to detecting MSI-H samples even in tumors not commonly associated with MSI. Our approach highlights the utility of RNA-seq data in MSI detection, facilitating more precise diagnostics through the integration of various biological data. [ABSTRACT FROM AUTHOR]

Precision oncology promises individually tailored drugs and clinical care for patients with cancer: That is, "the right drug, for the right patient, at the right dose, and at the right time." Although stratification of the risk for treatment resistance and toxicity is key to precision oncology, there are multiple ways in which such stratification can be achieved, for example, genetic, functional pathway based, among others. Moving toward precision oncology is sorely needed in the case of acute lymphoblastic leukemia (ALL) wherein adult patients display survival rates ranging from 30% to 70%. The present study reports on the pathway activity signature of adult B-ALL, with an eye to precision oncology. Transcriptome profiles from three different expression datasets, comprising 346 patients who were adolescents or adults with B-ALL, were harnessed to determine the activity of signaling pathways commonly disrupted in B-ALL. Pathway activity analyses revealed that Ph-like ALL closely resembles Ph-positive ALL. Although this was the case at the average pathway activity level, the pathway activity patterns in B-ALL differ from genetic subtypes. Importantly, clustering analysis revealed that five distinct clusters exist in B-ALL patients based on pathway activity, with each cluster displaying a unique pattern of pathway activation. Identifying pathway-based subtypes thus appears to be crucial, considering the inherent heterogeneity among patients with the same genetic subtype. In conclusion, a pathway-based stratification of the B-ALL could potentially allow for simultaneously targeting highly active pathways within each ALL subtype, and thus might open up new avenues of innovation for personalized/precision medicine in this cancer that continues to have poor prognosis in adult patients compared with the children. [ABSTRACT FROM AUTHOR]

Purpose: The primary goal of this study was to assess the growth, most influential articles, countries, journals, authors, and papers published in the field of global oral cancer. Research articles on oral cancer, published between 1989 and 2022, were identified through the Web of Science database to achieve this. Methods: A comprehensive dataset comprising 7,178 documents was meticulously extracted from the Web of Science, forming the basis for scientometric analysis. A refined subset of 4,901 documents was judiciously selected following a rigorous screening process for meticulous, in-depth analysis. Results: The field has witnessed a remarkable publication surge, with the United States taking the lead in productivity. The journal Oral Oncology has become the foremost publication, renowned for its prolific output and widespread citation. This trend highlights the growing importance and interest in this domain, with researchers and experts worldwide contributing to the expanding body of knowledge. The United States' dominance in productivity suggests its strong commitment to advancing research in the field, while Oral Oncology's recognition underscores its influential role in disseminating cutting-edge findings and fostering scientific progress. Conclusion: This scientometric analysis is a valuable resource for researchers, funding agencies, industry, and institutions, offering guidance and insights. Clinical trial number: Not Applicable. [ABSTRACT FROM AUTHOR]

Organoid technology has been developed rapidly in the past decade, which involves the exploration of the mechanism of development, regeneration and various diseases, and intersects among multiple disciplines. Thousands of literature on 3D-culture or organoids have been published in the research areas of cell biology tissue engineering, nanoscience, oncology and so on, resulting in it being challenging for researchers to timely summarize these studies. Bibliometric statistics is a helpfulway to help researchers clarify the above issues efficiently andmanage the whole landscape systematically. In our study, all original articles on organoids were included in the Web of Science database from January 2009 to May 2024, and related information was collected and analyzed using Excel software, "bibliometrix" packages of the R software, VOSviewer and CiteSpace. As results, a total of 6222 papers were included to classify the status quo of the organoids and predict future research areas. Our findings highlight a growing trend in publications related to organoids, with the United States and Netherlands leading in this field. The University of California System, Harvard University, Utrecht University and Utrecht University Medical Center have emerged as pivotal contributors and the key authors in the field include Clevers, H, Beekman, JM and Spence JR. Our results also revealed that the research hotspots and trends of organoids mainly focused on clinical treatment, drug screening, and the application of materials and technologies such as "hydrogel" and "microfluidic technology" in organoids. Next, we had an in-depth interpretation of the development process of organoid research area, including the emergence of technology, the translation from bench to bedsides, the profiles of the most widely studied types of organoids, the application of materials and technologies, and the emerging organoid-immune co-cultures trends. Furthermore,we also discussed the pitfalls, challenges and prospects of organoid technology. In conclusion, this study provides readers straightforward and convenient access to the organoid research field. [ABSTRACT FROM AUTHOR]

Research is central to achieving Europe's Beating Cancer Plan, and is the key focus of the European Commission's Mission on Cancer. To successfully tackle the challenges we face in cancer research, a coordinated effort of the entire Belgian scientific community is needed. It is for this reason the Belgian Cancer Research Alliance was proposed. The aim of BeCRA is to bring together various Belgian research institutes and associated care institutions and position them optimally at the EU level, with respect to the many research initiatives launched in the EBCP within the EU4Health program, the Mission on Cancer, Digital Europe programs and other EU projects. Members of BeCRA collaboratively plan the participation in certain cancer research activities to ensure optimal use of investment and sustained excellence of Belgian cancer research. Belgium cancer research has an excellent track record in fundamental, translational research and phase I, II, III clinical trials. However, translating outcomes from research to patients in the Belgian healthcare system has been less successful. Gaps in the collaboration between actors in the research field, have led to fragmentation hampering the development of fundamental and translational research. Moreover, actors from multi-disciplinary background, such as behavioural or psycho-social fields, are not systematically included in cancer research. More efficient coordination between the aforementioned actors is necessary. Academic hospitals and universities should be incentivized to collaborate across regions, as well as to put sufficient focus on research activities with a virtuous spiral ("bed-to bench" and "bench to bed" process), while supporting researchers focusing on patient-driven research. There is an urgent need for Belgium to determine how best to ensure it remains an attractive market so that patients have access to innovative care. This could include streamlining regulatory complexity, while establishing lean and harmonized clinical trial designs, procedures and networks. [ABSTRACT FROM AUTHOR]

Background: Cancer is a major public health challenge globally. However, little is known about the evolution patterns of cancer research communities and the influencing factors of their research capacity and impact, which is affected not only by the social networks established through research collaboration but also by the knowledge networks in which the research projects are embedded. Methods: The focus of this study was narrowed to a specific topic – 'synthetic lethality' – in cancer research. This field has seen vibrant growth and multidisciplinary collaboration in the past decade. Multi-level collaboration and knowledge networks were established and analysed on the basis of bibliometric data from 'synthetic lethality'-related cancer research papers. Negative binomial regression analysis was further applied to explore how node attributes within these networks, along with other potential factors, affected paper citations, which are widely accepted as proxies for assessing research capacity and impact. Results: Our study revealed that the synthetic lethality-based cancer research field is characterized by a knowledge network with high integration, alongside a collaboration network exhibiting some clustering. We found significant correlations between certain factors and citation counts. Specifically, a leading status within the nation-level international collaboration network and industry involvement were both found to be significantly related to higher citations. In the individual-level collaboration networks, lead authors' degree centrality has an inverted U-shaped relationship with citations, while their structural holes exhibit a positive and significant effect. Within the knowledge network, however, only measures of structural holes have a positive and significant effect on the number of citations. Conclusions: To enhance cancer research capacity and impact, non-leading countries should take measures to enhance their international collaboration status. For early career researchers, increasing the number of collaborators seems to be more effective. University–industry cooperation should also be encouraged, enhancing the integration of human resources, technology, funding, research platforms and medical resources. Insights gained through this study also provide recommendations to researchers or administrators in designing future research directions from a knowledge network perspective. Focusing on unique issues especially interdisciplinary fields will improve output and influence their research work. [ABSTRACT FROM AUTHOR]

ADCs represent a transformative class of medicine that combines the specificity of monoclonal antibodies with the potency of highly cytotoxic agents through linkers, aiming to enhance the therapeutic index of cytotoxic drugs. Given the complex molecular structures of ADCs, combining the molecular characteristics of small-molecule drugs and those of large-molecule biotherapeutics, there are several unique considerations when designing nonclinical-to-clinical PK/PD translation strategies. This complexity also demands a thorough understanding of the ADC's components – antibody, linker, and payload – to the overall toxicological, PK/PD, and efficacy profile. ADC development is a multidisciplinary endeavour requiring a strategic integration of nonclinical safety, pharmacology, and PK/PD modelling to translate from bench to bedside successfully. The ADC development underscores the necessity for a robust scientific foundation, leveraging advanced analytical and modelling tools to predict human responses and optimise therapeutic outcomes. This review aims to provide an ADC translational PK/PD framework by discussing unique aspects of ADC nonclinical to clinical PK translation, starting dose determination, and leveraging PK/PD modelling for human efficacious dose prediction and potential safety mitigation. [ABSTRACT FROM AUTHOR]

Over the course of the last 10 years, there has been a significant amount of advancement in the subject of nanotechnology, which has demonstrated a great deal of potential not only in the realm of technological fields but also in the realm of medical research. It is possible to see a broad variety of uses for zinc oxide nanoparticles (ZnO-NPs) in the field of cancer research, which is being conducted using nanotechnology. Despite the fact that scientific knowledge is continually expanding in terms of its comprehension of the molecular foundation of cancer cells, the number of people who are diagnosed with cancer continues to rise. The World Health Organisation (WHO) forecasted that the number of cancer cases will rapidly rise over the following ten years. ZnO-NPs have established themselves as a viable option for the treatment of cancer as a result of their capacity to trigger apoptosis in cancer cells. Due to the fact that ZnO nanoparticles have been shown to have anticancer, antibacterial, anti-diabetic, and anti-inflammatory activities, they have garnered a lot of interest in the field of biomedicine. The purpose of this study is to provide a summary of the recent research that have been conducted on the application of ZnO-NPS in the medical field. [ABSTRACT FROM AUTHOR]

Motivation Software is vital for the advancement of biology and medicine. Impact evaluations of scientific software have primarily emphasized traditional citation metrics of associated papers, despite these metrics inadequately capturing the dynamic picture of impact and despite challenges with improper citation. Results To understand how software developers evaluate their tools, we conducted a survey of participants in the Informatics Technology for Cancer Research (ITCR) program funded by the National Cancer Institute (NCI). We found that although developers realize the value of more extensive metric collection, they find a lack of funding and time hindering. We also investigated software among this community for how often infrastructure that supports more nontraditional metrics were implemented and how this impacted rates of papers describing usage of the software. We found that infrastructure such as social media presence, more in-depth documentation, the presence of software health metrics, and clear information on how to contact developers seemed to be associated with increased mention rates. Analysing more diverse metrics can enable developers to better understand user engagement, justify continued funding, identify novel use cases, pinpoint improvement areas, and ultimately amplify their software's impact. Challenges are associated, including distorted or misleading metrics, as well as ethical and security concerns. More attention to nuances involved in capturing impact across the spectrum of biomedical software is needed. For funders and developers, we outline guidance based on experience from our community. By considering how we evaluate software, we can empower developers to create tools that more effectively accelerate biological and medical research progress. Availability and implementation More information about the analysis, as well as access to data and code is available at https://github.com/fhdsl/ITCR_Metrics_manuscript_website. [ABSTRACT FROM AUTHOR]

Background Lack of diversity in the cancer research workforce persists, which the new requirement for all National Cancer Institute (NCI)–designated cancer centers to have a Plan to Enhance Diversity (PED) seeks to address. However, it is not well understood how different cancer centers are approaching the development and execution of these plans. Our objective was to assess how cancer centers are establishing and pursuing their PED. Methods We conducted a cross-sectional survey of members of the Cancer Center Diversity, Equity and Inclusion Network, which includes all NCI-designated cancer centers and several emerging centers. A total of 62 cancer centers (75% of those invited), including 58 NCI-designated cancer centers (81% of those with this designation), participated and completed a questionnaire that assessed PED leadership, major challenges, implementation strategies, and approach to evaluate PED progress. Results The most common PED challenge identified is recruiting diverse faculty (68% of centers), and the most common strategy currently used to address this is reviewing and revising faculty recruitment practices (67%). The most common approach centers are using to measure PED progress is shifts in demographics (68%), and data on the demographics of faculty, leadership, and trainees are available at 79%, 81%, and 75% of centers, respectively. Conclusions Almost all centers have established a PED leadership structure, however, there is considerable variation in the approaches used to realize PED goals and in the resources provided to support PED work. Realizing opportunities to share and implement common best practices and exemplar programs has the potential to elevate the impact of PED efforts nationally. [ABSTRACT FROM AUTHOR]

We consider two negative exponential (NE) populations with unknown location parameters and unknown but unequal scale parameters. We develop fixed-width confidence interval (FWCI) estimation strategies for comparing the location parameters. First, we formulate a unified multi-stage estimation strategy and derive the theory for an asymptotic second-order (s.o.) expansion of the coverage probability as well as s.o. efficiency. Next, we successively specialize by providing a range of asymptotics associated with (i) purely sequential, (ii) parallel piecewise sequential, (iii) accelerated sequential, and (iv) three-stage strategies. Theoretical findings are supplemented by simulations and real data illustrations from head and neck cancer research. [ABSTRACT FROM AUTHOR]

Adenocarcinomas of the stomach and gastroesophageal junction remain one of the most common malignant tumours in humans worldwide, often with a poor prognosis. Particularly in countries without upper gastrointestinal tract screening endoscopy, tumours that have been asymptomatic for a long time are only diagnosed at an advanced stage. This limits the therapeutic options. Often only palliative therapy concepts are available. Great progress has been made in the last two decades. The genetic basis of adenocarcinomas of the stomach and gastroesophageal junction has been deciphered and new targeted drugs have been developed. Cell and tissue‐based predictive diagnostics are becoming increasingly important in therapy planning. Here, surgical pathology forms an important link between basic research, clinical trials, and translation into clinical application. This review article summarizes the experiences made in translational tumour research, which point to the problems of spatial and temporal intratumoral heterogeneity of adenocarcinomas of the stomach and gastroesophageal, the development and continuous re‐assessment of therapeutically relevant cut‐off values, resistance mechanisms, tumour microenvironment, sexual dimorphism and the pitfalls molecular tumour boards may face. [ABSTRACT FROM AUTHOR]

In this Policy Review we discuss ten key pressure points in the NHS in the delivery of cancer care services that need to be urgently addressed by a comprehensive national cancer control plan. These pressure points cover areas such as increasing workforce capacity and its productivity, delivering effective cancer survivorship services, addressing variation in quality, fixing the reimbursement system for cancer care, and balancing of the cancer research agenda. These areas have been selected based on their relative importance to ensuring sustainable cancer services, persistence as key issues in the NHS, and their impact on delivering better and more equitable and affordable patient outcomes. Many of these pressure points are not acknowledged explicitly in any current discourse. The evidence we provide points to their impact on the ability to deliver world class cancer care, but also to their amenability to affordable solutions if given the relevant prioritisation and investment. The current narrative needs to move away from a technocentric approach to improving care, to one focused on understanding the complexity of cancer services and the wider health system to drive improvements in survival, quality of life, and experience for patients. [ABSTRACT FROM AUTHOR]

The role of the microbiome in cancer and its crosstalk with the tumor microenvironment (TME) has been extensively studied and characterized. An emerging field in the cancer microbiome research is the concept of the intratumoral microbiome, which refers to the microbiome residing within the tumor. This microbiome primarily originates from the local microbiome of the tumor-bearing tissue or from translocating microbiome from distant sites, such as the gut. Despite the increasing number of studies on intratumoral microbiome, it remains unclear whether it is a driver or a bystander of oncogenesis and tumor progression. This review aims to elucidate the intricate role of the intratumoral microbiome in tumor development by exploring its effects on reshaping the multileveled ecosystem in which tumors thrive, the TME. To dissect the complexity and the multitude of layers within the TME, we distinguish six specialized tumor microenvironments, namely, the immune, metabolic, hypoxic, acidic, mechanical and innervated microenvironments. Accordingly, we attempt to decipher the effects of the intratumoral microbiome on each specialized microenvironment and ultimately decode its tumor-promoting or tumor-suppressive impact. Additionally, we portray the intratumoral microbiome as an orchestrator in the tumor milieu, fine-tuning the responses in distinct, specialized microenvironments and remodeling the TME in a multileveled and multifaceted manner. [ABSTRACT FROM AUTHOR]

The chicken embryo chorioallantoic membrane (CAM) model has played a crucial role in various aspects of cancer research. The purpose of this study is to help researchers clarify the research direction and prospects of the CAM model. A bibliometric analysis was conducted on the top 100 most cited articles on use of the CAM model in tumour research, retrieved from the Web of Science Core Collection database. Tools such as Bibliometrix, VOSviewer, CiteSpace and Excel were utilized for the visualization network analysis. The 100 articles analysed were mainly from the USA, China and European countries such as Germany and France. Tumour research involving CAM model experiments demonstrated reliability and scientific rigor (average citation count = 156.2). The analysis of keywords, topics and subject areas revealed that the applications of this model ranged from the biological characteristics of tumours to molecular mechanisms and signaling pathways, to recent developments in nanotechnology and clinical applications. Additionally, nude mouse experiments have been more frequently performed in recent years. We conclude that the CAM model is efficient, simple and cost-effective, and has irreplaceable value in various aspects of cancer research. In the future, the CAM model can further contribute to nanotechnology research. [ABSTRACT FROM AUTHOR]

Objective Although the benefits of consumer involvement in research and health care initiatives are known, there is a need to optimize this for all people with cancer. This systematic review aimed to synthesize and evaluate the application of co-design in the oncology literature and develop recommendations to guide the application of optimal co-design processes and reporting in oncology research, practice, and policy. Methods A systematic review of co-design studies in adults with cancer was conducted, searching MEDLINE, CINAHL, Embase, and PsycINFO databases and included studies focused on 2 concepts, co-design and oncology. Results A total of 5652 titles and abstracts were screened, resulting in 66 eligible publications reporting on 51 unique studies. Four frameworks were applied to describe the co-design initiatives. Most co-design initiatives were designed for use in an outpatient setting (n = 38; 74%) and were predominantly digital resources (n = 14; 27%) or apps (n = 12; 23%). Most studies (n = 25; 49%) used a co-production approach to consumer engagement. Although some studies presented strong co-design methodology, most (n = 36; 70%) did not report the co-design approach, and 14% used no framework. Reporting was poor for the participant level of involvement, the frequency, and time commitment of co-design sessions. Consumer participation level was predominantly collaborate (n = 25; 49%). Conclusions There are opportunities to improve the application of co-design in oncology research. This review has generated recommendations to guide 1) methodology and frameworks, 2) recruitment and engagement of co-design participants, and 3) evaluation of the co-design process. These recommendations can help drive appropriate, meaningful, and equitable co-design, leading to better cancer research and care. [ABSTRACT FROM AUTHOR]

Three-dimensional (3D) spheroid models are crucial for cancer research, offering more accurate insights into tumour biology and drug responses than traditional 2D cell cultures. However, inconsistent and low-throughput spheroid production has hindered their application in drug screening. Here, we present an automated high-throughput platform for a spheroid selection, fabrication, and sorting system (SFSS) to produce uniform gelatine-encapsulated spheroids (GESs) with high efficiency. SFSS integrates advanced imaging, analysis, photo-triggered fabrication, and microfluidic sorting to precisely control spheroid size, shape, and viability. Our data demonstrate that our SFSS can produce over 50 GESs with consistent size and circularity in 30 min with over 97% sorting accuracy while maintaining cell viability and structural integrity. We demonstrated that the GESs can be used for drug screening and potentially for various assays. Thus, the SFSS could significantly enhance the efficiency of generating uniform spheroids, facilitating their application in drug development to investigate complex biological systems and drug responses in a more physiologically relevant context. [ABSTRACT FROM AUTHOR]

OBJECTIVE: In this discussion paper, we provide a narrative review of past and present occupational cancer studies in the journal with a viewpoint towards future occupational cancer research. METHOD: We reviewed all references in the journal that mentioned cancer according to relevance to etiology, cancer type, agent type, study design, and study population. RESULTS: The Scandinavian Journal of Work, Environment & Health has published over 300 manuscripts on occupational cancer over the 50 past years. Although studies of cancer represent the primary health outcome in the journal overall, the relative ranking of cancer manuscripts has declined somewhat over time. A large body of evidence from studies of occupation and industry was apparent both in early research and continuing in recent years. There are several examples of the utility of pooled multi-country collaborative studies. Studies also took advantage of available high-quality national population and cancer registers in Nordic countries. There have been notable shifts in focus with regard to the cancer types examined, with increases in publications examining female breast cancer over the decades. The interplay of studies of occupational and environmental cancer has also been apparent. CONCLUSIONS: The journal offers a unique viewpoint to consider the evolution of occupational cancer evidence over time. Studies of occupational cancer have played a central role in global cancer hazard identification efforts. Although much has been gained, there remains a need for renewed global support for occupational cancer research. Concerted efforts will be needed to ensure a future robust evidence-base for occupational and environmental cancer worldwide.

Abstract A critical aspect of simulation models used in cost-effectiveness analysis lies in accurately representing the natural history of diseases, requiring parameters such as probabilities and disease burden rates. While most of these parameters can be sourced from scientific literature, they often require calibration to align with the model’s expected outcomes. Traditional optimization methods can be time-consuming and computationally expensive, as they often rely on simplistic heuristics that may not ensure feasible solutions. In this study, we explore using Bayesian optimization to enhance the calibration process by leveraging domain-specific knowledge and exploiting structural properties within the solution space. Specifically, we investigate the impact of additive kernel decomposition and a stepwise approach, which capitalizes on the sequential block structure inherent in simulation models. This approach breaks down large optimization problems into smaller ones without compromising solution quality. In some instances, parameters obtained using this methodology may exhibit less error than those derived from naive calibration techniques. We compare this approach with two state-of-the-art high-dimensional Bayesian Optimization techniques: SAASBO and BAxUS. Our findings demonstrate that Bayesian optimization significantly enhances the calibration process, resulting in faster convergence and improved solutions, particularly for larger simulation models. This improvement is most pronounced when combined with a stepwise calibration methodology.

Ronja Thallner,1 Christoph Gumbinger,1 Anja Hohmann,1 Antje Wick,1 Wolfgang Wick,1 Loraine Busetto1,2 1Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany; 2Institute for Medical Virology, Goethe University Frankfurt, University Hospital, Frankfurt am Main, GermanyCorrespondence: Loraine Busetto, Institute for Medical Virology, Goethe University Frankfurt, University Hospital, Paul-Ehrlich-Straße 40, Frankfurt am Main, 60590, Germany, Tel/Fax +49 69 6301-86103, Email busetto@med.uni-frankfurt.dePurpose: There is a lack of evidence regarding how patients with malignant brain tumor and their relatives experience participation in neurooncological clinical trials. Similarly, insights from the perspective of trial staff caring for this group of patients are missing. This study aims to investigate patient, relative and trial staff experiences regarding participation in clinical neurooncological trials.Methods: Within a qualitative exploratory study, 29 semi-structured interviews with brain tumor patients, relatives and trial staff were conducted and analyzed using reflexive thematic analysis (RTA) by Braun and Clarke. A patient researcher and patient council were involved in data analysis and interpretation.Results: Four themes were developed reflecting significant aspects of the trial experience: 1. “It all revolves around hope”; 2. “Trial participation: experiencing unique medical care”; 3. “Everyone’s roles are changing”; 4. “Communication as a possible area of conflict”. Experiencing trial participation and general medical treatment were found to be interconnected to such a degree that they were often not meaningfully distinguished by patients and relatives.Conclusion: In addition to assessing traditional endpoints for patient outcomes, we recommend increased emphasis on investigating the impact of the “soft” components constituting trial participation. Due to the interconnectedness of medical treatment and trial participation, we recommend further investigation in comparison to experiences in regular care. A deeper understanding of trial participation is needed to inform improvements for patient experiences and staff satisfaction alongside medical and scientific progress.Plain Language Summary: The treatment options available to patients with (malignant) brain tumors are currently very limited. Therefore, patients are sometimes offered to participate in a clinical trial. This means that they receive an experimental treatment (eg new medicine) for which it is not yet clear whether it works better than regular medical care. Currently, little is known about how this group of patients, their relatives and the hospital staff who care for them experience the participation in these clinical trials – which is what we aimed to explore in our study reported here.Based on interviews with patients, relatives and staff, we found that:trial participation mainly revolves around hope;trial participation entails experiencing unique medical care;trial participation significantly changes the previous roles of patients, relatives and staff;trial participation intensifies communication as a possible area of conflict.By providing information on how patients, relatives and staff make sense of their trial experiences, this study constitutes an important addition to the traditional focus of clinical trials on medical and scientific endpoints (eg progression-free survival). This may help clinicians and researchers involved in cancer research and treatment to understand why “unsuccessful” trials can still be perceived as positive by patients or how hopeful communication may support their patients even when perceived as “unrealistic” from the clinicians’ perspective. An in depth understanding of trial participation from the perspective of those affected is needed for improved care experiences alongside medical and scientific progress for cancer treatment.Keywords: cancer research, brain tumor, qualitative research, care experiences

Hanna Dilenko, Kateřina Bartoň Tománková, Lucie Válková, Barbora Hošíková, Markéta Kolaříková, Lukáš Malina, Robert Bajgar, Hana Kolářov&#x00E1Department of Biophysics, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech RepublicCorrespondence: Kateřina Bartoň Tománková, Department of Biophysics, Faculty of Medicine and Dentistry, Palacky University, Hněvotinska 3, Olomouc, 77900, Czech Republic, Tel +420 733 690 914, Email katerina.barton@upol.czAbstract: Photodynamic therapy (PDT) is a non-invasive therapy that has made significant progress in treating different diseases, including cancer, by utilizing new nanotechnology products such as graphene and its derivatives. Graphene-based materials have large surface area and photothermal effects thereby making them suitable candidates for PDT or photo-active drug carriers. The remarkable photophysical properties of graphene derivates facilitate the efficient generation of reactive oxygen species (ROS) upon light irradiation, which destroys cancer cells. Surface functionalization of graphene and its materials can also enhance their biocompatibility and anticancer activity. The paper delves into the distinct roles played by graphene-based materials in PDT such as photosensitizers (PS) and drug carriers while at the same time considers how these materials could be used to circumvent cancer resistance. This will provide readers with an extensive discussion of various pathways contributing to PDT inefficiency. Consequently, this comprehensive review underscores the vital roles that graphene and its derivatives may play in emerging PDT strategies for cancer treatment and other medical purposes. With a better comprehension of the current state of research and the existing challenges, the integration of graphene-based materials in PDT holds great promise for developing targeted, effective, and personalized cancer treatments.Keywords: graphene quantum dots, graphene oxide, cancer research, photosensitizers, drug delivery

Abstract Numerous algorithms have been proposed to identify cell types in single-cell RNA sequencing data, yet a fundamental problem remains: determining associations between cells and phenotypes such as cancer. We develop SCIPAC, the first algorithm that quantitatively estimates the association between each cell in single-cell data and a phenotype. SCIPAC also provides a p-value for each association and applies to data with virtually any type of phenotype. We demonstrate SCIPAC’s accuracy in simulated data. On four real cancerous or noncancerous datasets, insights from SCIPAC help interpret the data and generate new hypotheses. SCIPAC requires minimum tuning and is computationally very fast.

The importance of context Obesity is a driver of diverse pathologies, including cardiometabolic diseases and cancer, with endometrial cancer being among the most strongly associated (1, 2). However, the excess [...], Obesity is a known driver of endometrial cancer. In this issue of the JCI, Gomez-Banoy and colleagues investigated a cohort of patients with advanced endometrial cancer treated with immune checkpoint inhibitors targeting the interaction between programmed cell death receptor-1 (PD-1) and its ligand (PD-L1). Notably, a BMI in the overweight or obese range was paradoxically associated with improved progression-free and overall survival. A second paradox emerged from CT analyses of visceral adipose tissue, viewed as an unhealthy fat depot in most other contexts, the quantity of which was also associated with improved treatment outcomes. Though visceral adiposity may have value as a biomarker to inform personalized treatment strategies, of even greater impact would be if a therapeutic strategy emerges from the future identification of adipose- derived mediators of this putative anticancer immune-priming effect.

Introduction Xerostomia, the subjective feeling of dry mouth typically accompanied by hyposalivation (1-3), is a common but often overlooked condition that can profoundly impair an individual's quality of life. Xerostomia [...], Salivary gland dysfunction is a common side effect of cancer treatments. Salivary function plays key roles in critical daily activities. Consequently, changes in salivary function can profoundly impair quality of life for cancer patients. We discuss salivary gland anatomy and physiology to understand how anticancer therapies such as chemotherapy, bone marrow transplantation, immunotherapy, and radiation therapy impair salivary function. We discuss approaches to quantify xerostomia in the clinic, including the advantages and limitations of validated quality-of-life instruments and approaches to directly measuring salivary function. Current and emerging approaches to treat cancer therapy-induced dry mouth are presented using radiation-induced salivary dysfunction as a model. Limitations of current sialagogues and salivary analogues are presented. Emerging approaches, including cellular and gene therapy and novel pharmacologic approaches, are described.

Following the acquisition of oncogenic mutations, cells undergo senescence and acquire heightened secretory states termed senescence-associated secretory phenotypes (SASPs). Proteins identified in SASPs include a broad range of inflammatory and [...]

Introduction Metastases account for the vast majority of cancer-related deaths (1), however, why some cancers metastasize while others do not is poorly understood. Specific genetic alterations do not define metastatic [...], Metastasis is the leading cause of cancer-related deaths. It is unclear how intratumor heterogeneity (ITH) contributes to metastasis and how metastatic cells adapt to distant tissue environments. The study of these adaptations is challenged by the limited access to patient material and a lack of experimental models that appropriately recapitulate ITH. To investigate metastatic cell adaptations and the contribution of ITH to metastasis, we analyzed single-cell transcriptomes of matched primary tumors and metastases from patient-derived xenograft models of breast cancer. We found profound transcriptional differences between the primary tumor and metastatic cells. Primary tumors upregulated several metabolic genes, whereas motility pathway genes were upregulated in micrometastases, and stress response signaling was upregulated during progression. Additionally, we identified primary tumor gene signatures that were associated with increased metastatic potential and correlated with patient outcomes. Immune-regulatory control pathways were enriched in poorly metastatic primary tumors, whereas genes involved in epithelial-mesenchymal transition were upregulated in highly metastatic tumors. We found that ITH was dominated by epithelial-mesenchymal plasticity (EMP), which presented as a dynamic continuum with intermediate EMP cell states characterized by specific genes such as CRYAB and S100A2. Elevated expression of an intermediate EMP signature correlated with worse patient outcomes. Our findings identified inhibition of the intermediate EMP cell state as a potential therapeutic target to block metastasis.

Introduction Phenotypic plasticity is a hallmark of cancer (1-3). In advanced prostate cancer, up to 15%-20% of patients develop resistance to androgen receptor-directed (AR-directed) therapies through conversion from an androgen-driven [...], Notch signaling can have either an oncogenic or tumor-suppressive function in cancer depending on the cancer type and cellular context. While Notch can be oncogenic in early prostate cancer, we identified significant downregulation of the Notch pathway during prostate cancer progression from adenocarcinoma to neuroendocrine (NE) prostate cancer, where it functions as a tumor suppressor. Activation of Notch in NE and Rb1/Trp53-deficient prostate cancer models led to phenotypic conversion toward a more indolent, non-NE state with glandular features and expression of luminal lineage markers. This was accompanied by upregulation of MHC and type I IFN and immune cell infiltration. Overall, these data support Notch signaling as a suppressor of NE differentiation in advanced prostate cancer and provide insights into how Notch signaling influences lineage plasticity and the tumor microenvironment (TME).

Rare cancers are defined by low incidence rates, and may lack evidence that supports uniform standards of care and relevant clinical guidelines. Rare cancers may represent up to 24% of all cancers, yet remain understudied and underappreciated in terms of their clinical and ultimately societal impact. The PLOS Rare Cancer Collection brings together a broad range of research endeavors that are being undertaken in rare cancers research ranging from basic biological evaluations to therapeutic drug development. This Overview presents a brief background to the Collection and highlights the contributions of included articles. [ABSTRACT FROM AUTHOR]

This review focuses on the intersection of artificial intelligence and genomic data in cancer research. It explores the types of genomic data used in the literature, the methodologies of machine learning and deep learning, recent applications, and the challenges associated with this field. Through an analysis of 47,586 articles and addressing seven research questions, the study reveals significant growth in this area over the past years. While there has been remarkable progress, ongoing attention is needed to address ethical considerations, interpretability of algorithms, and potential data biases, to ensure the reliable and responsible use of these advanced technologies. Overall, this paper provides a comprehensive overview of the current research landscape, offering insights into both the potential and challenges of AI in genomic data research. [ABSTRACT FROM AUTHOR]

This article examines the influence that digital life stories (DLS) can have on cancer research, using the PARCA1 project as an example. After describing the theoretical framework of DLS, we present the PARCA1 project. The PARCA1 project was anchored in the French context (Grand Est region) and aimed at producing knowledge on patients' experience of the cancer pathway through DLS. It involved 10 patients chosen to favor heterogeneity in profiles and experiences of illness. The paper describes the digital tool and the life stories methodology used to accompany the DLS. Next, it presents the methods and strategies used by participants to complete their DLS and the relationship between people with cancer and the accompanying researcher. Following this, we present (1) the impact of DLS on people with cancer, i.e., their progressive engagement in research, and (2) the impact on research, i.e., the methodological impact of people with cancer on research. In the discussion and conclusion, we explore how DLS can impact individuals who engage in them and their role in research. [ABSTRACT FROM AUTHOR]

Background: Lack of diversity in participants throughout the research process limits the generalizability of findings and may contribute to health disparities. There are unique challenges to recruitment of families to pediatric cancer research studies, especially for those from disadvantaged backgrounds. Thus, there is a need to evaluate the most effective recruitment and retention strategies to optimize equitable recruitment of diverse participants. Methods: The present study adapted and implemented methods outlined previously in the literature. These previous efforts were developed to address barriers to pediatric research, behavioral health intervention research and research with Black adolescents. Recruitment and retention strategies are described across four different time points: pre-approach, initial connection, building connection and follow-up. Eligible families of children with a pediatric cancer diagnosis were approached during a routine oncology visit. Once consented, enrollment and retention rates over three timepoints of data collection were recorded and evaluated. Results: Results indicated high rates of enrollment (86%) and retention (95%) for eligible participants. There were no trends in heightened attrition for any specific subgroup. Conclusions: The findings of this study are promising and suggest these recruitment and retention strategies may be useful in recruiting individuals from disadvantaged backgrounds. [ABSTRACT FROM AUTHOR]

Background: Despite the strong declining trends in incidence and mortality over the last decades, gastric cancer (GC) is still burdened with high mortality, even in high-income countries. To improve GC prognosis, several guidelines have been increasingly published with indications about the most appropriate GC management. The Italian Society of Digestive System Pathology (SIPAD) and Gastric Cancer Italian Research Group (GIRCG) designed a survey for both surgeons and patients with the purpose of evaluating the degree of application and adherence to guidelines in GC management in Italy. Materials and Methods: Between January and May 2022, a questionnaire has been administered to a sample of Italian surgeons and, in a simplified version, to members of the Patient Association "Vivere Senza Stomaco" (patients surgically treated for GC between 2008 and 2021) to investigate the diagnosis, staging, and treatment issues. Results: The survey has been completed by 125 surgeons and 125 patients. Abdominal CT with gastric hydro-distension before treatment was not widespread in both groups (47% and 42%, respectively). The rate of surgeons stating that they do not usually perform minimally invasive gastrectomy was 15%, but the rate of patients who underwent a minimally invasive approach was 22% (between 2011 and 2022). The percentage of surgeons declaring to perform extended lymphadenectomy (>D2) was 97%, although a limited lymph node dissection rate was observed in about 35% of patients. Conclusions: This survey shows several important discrepancies from surgical attitudes declared by surgeons and real data derived from the reports available to the patients, suggesting heterogeneous management in clinical practice and, thus, a not rigorous adherence to the guidelines. [ABSTRACT FROM AUTHOR]

Breast cancer, a complex disease with a significant prevalence to form metastases, necessitates novel therapeutic strategies to improve treatment outcomes. Here, we present the results of a comparative molecular study of primary breast tumours, their metastases, and the corresponding primary cell lines using Desorption Electrospray Ionisation (DESI) and Laser-Assisted Rapid Evaporative Ionisation Mass Spectrometry (LA-REIMS) imaging. Our results show that ambient ionisation mass spectrometry technology is suitable for rapid characterisation of samples, providing a lipid- and metabolite-rich spectrum within seconds. Our study demonstrates that the lipidomic fingerprint of the primary tumour is not significantly distinguishable from that of its metastasis, in parallel with the similarity observed between their respective primary cell lines. While significant differences were observed between tumours and the corresponding cell lines, distinct lipidomic signatures and several phospholipids such as PA(36:2), PE(36:1), and PE(P-38:4)/PE(O-38:5) for LA-REIMS imaging and PE(P-38:4)/PE(O-38:5), PS(36:1), and PI(38:4) for DESI-MSI were identified in both tumours and cells. We show that the tumours' characteristics can be found in the corresponding primary cell lines, offering a promising avenue for assessing tumour responsiveness to therapeutic interventions. A comparative analysis by DESI-MSI and LA-REIMS imaging revealed complementary information, demonstrating the utility of LA-REIMS in the molecular imaging of cancer. [ABSTRACT FROM AUTHOR]

While cancer research and care have benefited from revolutionary advances in the ability to manipulate and study living systems, the field is limited by a lack of synergy to leverage the power of engineering approaches. Cancer engineering is an emerging subfield of biomedical engineering that unifies engineering and cancer biology to better understand, diagnose, and treat cancer. We highlight cancer engineering's unique challenges, the importance of creating dedicated centers and departments that enable translational collaboration, and educational approaches to arm a new generation of scientists with engineering expertise and a fundamental understanding of cancer biology to transform clinical cancer care. [ABSTRACT FROM AUTHOR]

Motivation Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited. Results Here, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of employing hypergraphs for representing annotated gene sets. Second, we validate the accuracy of DISHyper-predicted cancer genes using functional validation results and multiple independent functional genomics data. Third, our model predicts 44 novel cancer genes, and subsequent analysis shows their significant associations with multiple types of cancers. Overall, our study provides a new perspective for discovering cancer genes and reveals previously undiscovered cancer genes. Availability and implementation DISHyper is freely available for download at https://github.com/genemine/DISHyper. [ABSTRACT FROM AUTHOR]

Clinical research is the cornerstone of improvements in cancer care. However, it has been conducted predominantly in high-income countries with few clinical trials available in Brazil and other low-and-middle-income countries (LMIC). Of note, less than one-third of registered clinical trials addressing some of the most commonly diagnosed cancers (breast, lung and cervical) recruited patients from LMIC in the last years. The Institute Project CURA promoted the fourth CURA meeting, discussing barriers to cancer clinical research and proposing potential solutions. A meeting was held in São Paulo, Brazil, in June 2023 with representatives from different sectors: Brazilian Health Regulatory Agency (Anvisa), National Commission of Ethics in Research (CONEP), non-governmental organisations, such as the Latin American Cooperative Oncology Group, the Brazilian Society of Clinical Oncology (SBOC), Contract Research Organisations, pharmaceutical companies and investigators. A total of 16 experts pointed out achievements as shortening the time of regulatory processes involving Anvisa and CONEP, development of staff training programs, maintenance of the National Program of Oncological Attention (PRONON), and the foundation of qualified centres in North and Northeast Brazilian regions. Participants also highlighted the need to be more competitive in the field, which requires optimising ongoing policies and implementing new strategies as decentralisation of clinical research centres, public awareness campaigns, community-centered approaches, collaborations and partnerships, expansion of physicians-directed policies, exploring the role of the steering committee. Active and consistent reporting of the initiatives might help to propagate ongoing advances, increasing Brazilian participation in clinical cancer research. Engagement of all players is crucial to maintain continuous progress with further improvements in critical points including regulatory timelines and increments in qualified human resources which aligned with new educational initiatives focused on physicians and the general population will expand access to cancer clinical trials in Brazil. [ABSTRACT FROM AUTHOR]

Human gene research studies that describe wrongly identified nucleotide sequence reagents have been mostly identified in journals of low to moderate impact factor, where unreliable findings could be considered to have limited influence on future research. This study examined whether papers describing wrongly identified nucleotide sequences are also published in high-impact-factor cancer research journals. We manually verified nucleotide sequence identities in original Molecular Cancer articles published in 2014, 2016, 2018, and 2020, including nucleotide sequence reagents that were claimed to target circRNAs. Using keywords identified in some 2018 and 2020 Molecular Cancer papers, we also verified nucleotide sequence identities in 2020 Oncogene papers that studied miRNA(s) and/or circRNA(s). Overall, 3.8% (251/6647) and 4.0% (47/1165) nucleotide sequences that were verified in Molecular Cancer and Oncogene papers, respectively, were found to be wrongly identified. Wrongly identified nucleotide sequences were distributed across 18% (91/500) original Molecular Cancer papers, including 38% (31/82) Molecular Cancer papers from 2020, and 40% (21/52) selected Oncogene papers from 2020. Original papers with wrongly identified nucleotide sequences were therefore unexpectedly frequent in two high-impact-factor cancer research journals, highlighting the risks of employing journal impact factors or citations as proxies for research quality. [ABSTRACT FROM AUTHOR]

Lung cancer (LC) is a highly invasive malignancy and the leading cause of cancer-related deaths, with non-small cell lung cancer (NSCLC) as its most prevalent histological subtype. Despite all breakthroughs achieved in drug development, the prognosis of NSCLC remains poor. The mitogen-activated protein kinase signaling cascade (MAPKC) is a complex network of interacting molecules that can drive oncogenesis, cancer progression, and drug resistance when dysregulated. Over the past decades, MAPKC components have been used to design MAPKC inhibitors (MAPKCIs), which have shown varying efficacy in treating NSCLC. Thus, recent studies support the potential clinical use of MAPKCIs, especially in combination with other therapeutic approaches. This article provides an overview of the MAPKC and its inhibitors in the clinical management of NSCLC. It addresses the gaps in the current literature on different combinations of selective inhibitors while suggesting two particular therapy approaches to be researched in NSCLC: parallel and aggregate targeting of the MAPKC. This work also provides suggestions that could serve as a potential guideline to aid future research in MAPKCIs to optimize clinical outcomes in NSCLC. [ABSTRACT FROM AUTHOR]

Stable isotope-resolved metabolomics comprises a critical set of technologies that can be applied to a wide variety of systems, from isolated cells to whole organisms, to define metabolic pathway usage and responses to perturbations such as drugs or mutations, as well as providing the basis for flux analysis. As the diversity of stable isotope-enriched compounds is very high, and with newer approaches to multiplexing, the coverage of metabolism is now very extensive. However, as the complexity of the model increases, including more kinds of interacting cell types and interorgan communication, the analytical complexity also increases. Further, as studies move further into spatially resolved biology, new technical problems have to be overcome owing to the small number of analytes present in the confines of a single cell or cell compartment. Here, we review the overall goals and solutions made possible by stable isotope tracing and their applications to models of increasing complexity. Finally, we discuss progress and outstanding difficulties in high-resolution spatially resolved tracer-based metabolic studies. [ABSTRACT FROM AUTHOR]