Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization.

Colorectal cancer (CRC) is the third most common cancer and the second most deathly worldwide. It is a very heterogeneous disease that can develop via distinct pathways where metastasis is the primary cause of death. Therefore, it is crucial to understand the molecular mechanisms underlying metastasis. RNA-sequencing is an essential tool used for studying the transcriptional landscape. However, the high-dimensionality of gene expression data makes selecting novel metastatic biomarkers problematic. To distinguish early-stage CRC patients at risk of developing metastasis from those that are not, three types of binary classification approaches were used: (1) classification methods (decision trees, linear and radial kernel support vector machines, logistic regression, and random forest) using differentially expressed genes (DEGs) as input features; (2) regularized logistic regression based on the Elastic Net penalty and the proposed iTwiner-a network-based regularizer accounting for gene correlation information; and (3) classification methods based on the genes pre-selected using regularized logistic regression. Classifiers using the DEGs as features showed similar results, with random forest showing the highest accuracy. Using regularized logistic regression on the full dataset yielded no improvement in the methods' accuracy. Further classification using the pre-selected genes found by different penalty factors, instead of the DEGs, significantly improved the accuracy of the binary classifiers. Moreover, the use of network-based correlation information (iTwiner) for gene selection produced the best classification results and the identification of more stable and robust gene sets. Some are known to be tumor suppressor genes (OPCML-IT2), to be related to resistance to cancer therapies (RAC1P3), or to be involved in several cancer processes such as genome stability (XRCC6P2), tumor growth and metastasis (MIR602) and regulation of gene transcription (NME2P2). We show that the classification of CRC patients based on pre-selected features by regularized logistic regression is a valuable alternative to using DEGs, significantly increasing the models' predictive performance. Moreover, the use of correlation-based penalization for biomarker selection stands as a promising strategy for predicting patients' groups based on RNA-seq data.

Genetic and microenvironmental intra-tumor heterogeneity impacts colorectal cancer evolution and metastatic development.

Colorectal cancer (CRC) is a highly diverse disease, where different genomic instability pathways shape genetic clonal diversity and tumor microenvironment. Although intra-tumor heterogeneity has been characterized in primary tumors, its origin and consequences in CRC outcome is not fully understood. Therefore, we assessed intra- and inter-tumor heterogeneity of a prospective cohort of 136 CRC samples. We demonstrate that CRC diversity is forged by asynchronous forms of molecular alterations, where mutational and chromosomal instability collectively boost CRC genetic and microenvironment intra-tumor heterogeneity. We were able to depict predictor signatures of cancer-related genes that can foresee heterogeneity levels across the different tumor consensus molecular subtypes (CMS) and primary tumor location. Finally, we show that high genetic and microenvironment heterogeneity are associated with lower metastatic potential, whereas late-emerging copy number variations favor metastasis development and polyclonal seeding. This study provides an exhaustive portrait of the interplay between genetic and microenvironment intra-tumor heterogeneity across CMS subtypes, depicting molecular events with predictive value of CRC progression and metastasis development.

Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical Practice.

Next-generation sequencing (NGS) has been implemented in clinical oncology for diagnosis, prognosis, and therapeutic guidance. Among the various NGS applications in molecular oncology, we focused on the following topics: laboratory standards for targeted gene panels (somatic mutations) and therapeutic guidance based on NGS of lung cancer and rare cancers, namely sarcomas and cancers of unknown primary. Multiple quality control checkpoints should be addressed in the pre-analytical phase for good quality and interpretation of the NGS results. It includes tumor size and cellularity, tissue processing and decalcification, tumor fraction, tumor viability, fixatives, and staining. Communication between clinicians and laboratory support is also essential. In lung cancer, all patients with non-squamous non-small cell lung cancer should be tested with a NGS panel, and it should include not only genes with approved targeted therapies (ALK, BRAF, EGFR, MET, NTRK, RET, and ROS1) but also genes with potentially actionable genomic alterations (HER2 and KRAS). Since there is a lack of extensive knowledge regarding the use of NGS in rare tumors performing comprehensive genomic profiling, NGS panels to better manage the disease are recommended. Moreover, other patients with other incurable solid tumors may benefit from being included in biomarker-driven clinical trials. Multidisciplinary tumor boards with the participation of experts with the ability to integrate genomic profiling data are essential to tailor the best strategy for each patient. Considering that there are no national guidelines, this article aims to guide laboratory and clinical practice for the use of NGS in the context of lung cancer, rare tumors, and cancer of unknown primary in Portugal.

Na área da oncologia clínica, a sequenciação de nova geração (NGS) foi implementada com o objetivo de contribuir para o diagnóstico, prognóstico e orientação terapêutica. A utilização de NGS em oncologia molecular é vasta, focalizando-se estas recomendações nas: normas laboratoriais para painéis genéticos direcionados (mutações somáticas) e na orientação terapêutica baseada em NGS de cancro do pulmão e cancros raros, nomeadamente sarcomas e cancros de origem desconhecida. Para que sejam obtidos resultados de NGS com a qualidade que permita a sua correta interpretação, devem ser abordados múltiplos controlos de qualidade na fase pré-analítica que disponibilizem informação sobre o tamanho e celularidade do tumor, processamento e descalcificação de tecidos, fração tumoral, viabilidade do tumor, fixadores e coloração utilizados. A comunicação entre os diferentes intervenientes no processo, em particular entre os clínicos e o laboratório também contribui, de forma inequívoca, para a interpretação dos resultados de NGS. Todos os doentes com cancro do pulmão de não pequenas células não escamoso devem ser testados com um painel de NGS, que deve incluir não só genes com terapias dirigidas aprovadas (ALK, BRAF, EGFR, MET, NTRK, RET e ROS1), mas também genes com alterações genómicas identificadas como potenciais alvos terapêuticos (HER2 e KRAS). Dada a escassez de evidência científica sobre a utilização de NGS em tumores raros, recomenda-se a realização de painéis genómicos abrangentes que poderão contribuir para uma melhor gestão da doença. Adicionalmente, outros doentes, com outros tumores sólidos incuráveis, podem beneficiar da inclusão em ensaios clínicos orientados por biomarcadores. A realização de reuniões multidisciplinares com a participação de diferentes especialistas capazes de integrar dados dos perfis genómicos são fundamentais para a escolha da melhor estratégia para cada doente. Considerando que não existem recomendações nacionais, este artigo visa orientar a prática laboratorial e clínica para a utilização de NGS em tumores do pulmão, raros e cancros de origem primária desconhecida em Portugal.

Influence of photobiomodulation therapy on the treatment of pulmonary inflammatory conditions and its impact on COVID-19.

We are currently facing a pandemic that continuously causes high death rates and has negative economic and psychosocial impacts. Therefore, this period requires a quick search for viable procedures that can allow us to use safe and non-invasive clinical tools as prophylactic or even adjuvant methods in the treatment of COVID-19. Some evidence shows that photobiomodulation therapy (PBMT) can attenuate the inflammatory response and reduce respiratory disorders similar to acute lung injury (ALI), complications associated with infections, such as the one caused by the new Coronavirus (SARS-CoV-2). Hence, the aim of the present study was to evaluate the influence of PBMT (infrared low-level laser therapy) on the treatment of ALI, one of the main critical complications of COVID-19 infection, in an experimental model in rats. Twenty-four male Wistar rats were randomly allocated to three experimental groups (n = 8): control group (CG), controlled ALI (ALI), and acute lung injury and PBM (ALIP). For treatment, a laser equipment was used (808 nm; 30 mw; 1.68 J) applied at three sites (anterior region of the trachea and in the ventral regions of the thorax, bilaterally) in the period of 1 and 24 h after induction of ALI. For treatment evaluation, descriptive histopathological analysis, lung injury score, analysis of the number of inflammatory cells, and expression of interleukin 1 ß (IL-1ß) were performed. In the results, it was possible to observe that the treatment with PBMT reduced inflammatory infiltrates, thickening of the alveolar septum, and lung injury score when compared to the ALI group. In addition, PBMT showed lower immunoexpression of IL-1ß. Therefore, based on the results observed in the present study, it can be concluded that treatment with PBMT (infrared low-level laser therapy) was able to induce an adequate tissue response capable of modulating the signs of inflammatory process in ALI, one of the main complications of COVID-19.

Malignant pericardial effusion as a primary manifestation of metastatic colon cancer: a case report.

BACKGROUND: Pericardial neoplastic involvement is rarely related to primary tumors of the pericardium and is most often caused by spread from other primary sites, such as lung and breast carcinomas, hematological malignancies (lymphoma and leukemia), and melanoma. Although pericardial metastasis from infradiaphragmatic tumors (such as colon cancers) are rare and poorly described in literature, any neoplasm has the potential to metastasize to the pericardium and heart by either contiguity, lymphatic, or hematological spread. CASE PRESENTATION: A 44-year-old previously healthy male Causasian patient had a sudden onset of dyspnea and wheezing. During investigation with echocardiogram, computed tomography and repeated pericardiocentesis, the cause of malignant pericardial effusion was confirmed as primary manifestation of metastatic colon cancer. The patient was treated with appropriate chemotherapy and presented satisfactory disease control. CONCLUSIONS: This report emphasizes the importance of considering the diagnostic hypothesis of occult neoplasia in a patient with pericardial effusion.

Sarcoma Metabolomics: Current Horizons and Future Perspectives.

The vast array of metabolic adaptations that cancer cells are capable of assuming, not only support their biosynthetic activity, but also fulfill their bioenergetic demands and keep their intracellular reduction-oxidation (redox) balance. Spotlight has recently been placed on the energy metabolism reprogramming strategies employed by cancer cells to proliferate. Knowledge regarding soft tissue and bone sarcomas metabolome is relatively sparse. Further characterization of sarcoma metabolic landscape may pave the way for diagnostic refinement and new therapeutic target identification, with benefit to sarcoma patients. This review covers the state-of-the-art knowledge on cancer metabolomics and explores in detail the most recent evidence on soft tissue and bone sarcoma metabolomics.

HERVs establish a distinct molecular subtype in stage II/III colorectal cancer with poor outcome.

Colorectal cancer (CRC) is one of the most lethal malignancies. The extreme heterogeneity in survival rate is driving the need for new prognostic biomarkers. Human endogenous retroviruses (hERVs) have been suggested to influence tumor progression, oncogenesis and elicit an immune response. We examined multiple next-generation sequencing (NGS)-derived biomarkers in 114 CRC patients with paired whole-exome and whole-transcriptome sequencing (WES and WTS, respectively). First, we demonstrate that the median expression of hERVs can serve as a potential biomarker for prognosis, relapse, and resistance to chemotherapy in stage II and III CRC. We show that hERV expression and CD8+ tumor-infiltrating T-lymphocytes (TILs) synergistically stratify overall and relapse-free survival (OS and RFS): the median OS of the CD8-/hERV+ subgroup was 29.8 months compared with 37.5 months for other subgroups (HR = 4.4, log-rank P < 0.001). Combing NGS-based biomarkers (hERV/CD8 status) with clinicopathological factors provided a better prediction of patient survival compared to clinicopathological factors alone. Moreover, we explored the association between genomic and transcriptomic features of tumors with high hERV expression and establish this subtype as distinct from previously described consensus molecular subtypes of CRC. Overall, our results underscore a previously unknown role for hERVs in leading to a more aggressive subtype of CRC.

Antimicrobial photodynamic therapy against Propionibacterium acnes biofilms using hypericin (Hypericum perforatum) photosensitizer: in vitro study.

Acne vulgaris is the most recurring skin condition in the world, causing great harm to the physical and psychological well-being of many patients. Antimicrobial photodynamic therapy (aPDT) has broad therapeutic applicability. The purpose was to evaluate in vitro the photodynamic inactivation against Propionibacterium acnes (P. acnes) biofilms by using different concentrations of hypericin (Hypericum perforatum) photosensitizer associated with different energies of low-level laser. The biofilms were placed in 96-well microplates with a 6.4-mm diameter surface, by using standard suspensions (2 × 107 CFU/mL) and grown in brain heart infusion broth (BHI) for 48 h in anaerobic chamber. Subsequently, the control group received application of 0.9% sterile saline solution for 3 min; the photosensitising groups received hypericin at concentrations of 5 and 15 µg/mL for 3 min; the laser groups received irradiation of energies of 3 and 5 J (660 nm, continuous output, 100 mW, 30 and 50 s and 100 J/cm2 and 166 J/cm2, respectively); the aPDT groups received 5 and 15 µg/mL concentrations of hypericin associated with energies of 3 and 5 J of low-level laser irradiation. After the biofilms were broken up and seeded for CFU counting. The results showed a reduction in P. acnes biofilms after aPDT emphasising that 15 µg/mL hypericin associated with 3 and 5 J laser irradiation reduced biofilms by 14.1 and 27.9%, respectively. In addition, all groups of aPDT demostrated statistically significant reductions. In vitro photodynamic inactivation against P. acnes biofilms using different concentration of hypericin photosensitizer associated with different energies of low-level laser promoted effective antimicrobial action.

Levels of Circulating Fibroblast Growth Factor 23 (FGF23) and Prognosis in Cancer Patients with Bone Metastases.

The fibroblast growth factor (FGF) signaling pathway plays a key role in tumorigenesis and is recognized as a potential therapeutic target. In this study, the authors aimed to assess the impact of serum FGF23 levels in the prognosis of patients with cancer and bone metastases from solid tumors. A cohort of 112 patients with cancer and metastatic bone disease were treated with bone-targeted agents (BTA). Serum baseline FGF23 was quantified by ELISA and dichotomized in FGF23high and FGF23low groups. Additionally, the association between FGF23 and overall survival (OS) and time to skeletal-related events (TTSRE) was investigated. Baseline characteristics were balanced between groups, except for the median urinary N-terminal telopeptide (uNTX) level. After a median follow-up of 26.0 months, a median OS of 34.4 and 12.2 months was found in the FGF23low and FGF23high groups, respectively (multivariate HR 0.18, 95% CI 0.07⁻0.44, p = 0.001; univariate HR 0.27, p = 0.001). Additionally, TTSRE was significantly longer for patients with FGF23low (13.0 vs 2.0 months, p = 0.04). Overall, this study found that patients with FGF23low at baseline had longer OS and TTSRE. Further studies are warranted to define its role as a prognostic biomarker and in the use of drugs targeting the FGF axis.