Inference of the life cycle of environmental phages from genomic signature distances to their hosts

The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids

Clinical and pathological features of Merkel cell carcinoma: A 4-year follow-up observational retrospective study in Spain

Background: Merkel cell carcinoma (MCC) is a malignant skin cancer with a 5-year survival rate of approximately 50%. Knowledge of MCC has increased in recent years mostly due to improved diagnosis techniques. In Spain there is lack of information regarding the incidence and tumour characteristics, and the treatment approaches are not standardised. The objective of this study was to provide information of the clinical and epidemiological characteristics of MCC patients in Spain. Methods: Retrospective, observational study involving 192 patients from 25 Spanish hospitals. Evaluated vari ables included overall survival and incidence rate of Merkel cell polyomavirus, in patients diagnosed from 2012 to 2016. Results: The Spanish incidence rate was estimated 0.32/100,000 inhabitants/year, with variations according to geographical regions, being slightly higher in areas with greater sunlight exposure. In total, 61.5% of tumours showed expansive growth (progressive growth of the tumour), 78.6% showed localisation in UV-exposed skin. 97.4% of patients were diagnosed by excisional biopsy. Surgery was the first line treatment in 96.6% of patients, radiotherapy in 24.6%, and chemotherapy in 6.3%. These treatments were not mutually exclusive. Median overall survival was 38.3 months (78.4% at 12 months and 60% at 24 months). MCPyV was present in 33.8% of patients. Conclusion: The incidence of MCC in Spain is one of the highest in Europe, with a slight predominance in men. The sample has shown that a biopsy is available for diagnosis in most cases. Moreover, the treatment is surgical when the tumour is localized and is associated with lymphadenectomy, and/or it is radiotherapy if widespread

Impact of SARS-CoV-2 Infection on Patients with Cancer: Retrospective and Transversal Studies in Spanish Population

[EN] Background: Studies of patients with cancer affected by coronavirus disease 2019 (COVID-19) are needed to assess the impact of the disease in this sensitive population, and the influence of different cancer treatments on the COVID-19 infection and seroconversion. Material and Methods: We performed a retrospective analysis of all patients hospitalized with RT-PCR positive for COVID-19 in our region to assess the prevalence of cancer patients and describe their characteristics and evolution (Cohort 1). Concurrently, a transversal study was carried out in patients on active systemic cancer treatment for symptomatology and seroprevalence (IgG/IgM by ELISA-method) against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (Cohort 2). Results: A total of 215 patients (Cohort 1) were admitted to hospital with a confirmed COVID-19 infection between February 28 and April 30, 2020, and 17 died (7.9%). A medical record of cancer was noted in 43 cases (20%), 6 of them required Intensive care unit ICU attention (14%), and 7 died (16%). There were thirty-six patients (83%) who tested IgG/IgM positive for SARS-CoV-2. Patients on immunosuppressive therapies presented a lower ratio of seroconversion (40% vs. 8%; p = 0.02). In Cohort 2, 166 patients were included in a symptoms-survey and tested for SARS-CoV-2. Any type of potential COVID-19-related symptom was referred up to 67.4% of patients (85.9% vs. 48.2% vs. 73.9%, for patients on chemotherapy, immunotherapy and targeted therapies respectively, p < 0.05). The seroprevalence ratio was 1.8% for the whole cohort with no significant differences by patient or treatment characteristics. Conclusion: Patients with cancer present higher risks for hospital needs for COVID-19 infection. The lack of SARS-CoV-2 seroconversion may be a concern for patients on immunosuppressive therapies. Patients receiving systematic therapies relayed a high rate of potentially COVID-19-related symptoms, particularly those receiving chemotherapy. However, the seroconversion rate remains low and in the range of general population.We thank all the patients who consented to this study, and the frontline healthcare professionals who are involved in patients' care during this pandemic. We also thank the technical assistants: M. Portero Hernandez, A. Real Perez, and M. Ocasar Garcia. VGB's research work is partially supported by the Ministerio de Ciencia e Innovacion of Spain under grant No. PID2019-110442GB-I00.Garde-Noguera, J.; Fernández-Murga, ML.; Giner-Bosch, V.; Domínguez-Márquez, V.; García Sánchez, J.; Soler-Cataluña, JJ.; López Chuliá, F.... (2020). Impact of SARS-CoV-2 Infection on Patients with Cancer: Retrospective and Transversal Studies in Spanish Population. Cancers. 12(12):1-11. https://doi.org/10.3390/cancers12123513S1111212Munster, V. J., Koopmans, M., van Doremalen, N., van Riel, D., & de Wit, E. (2020). A Novel Coronavirus Emerging in China — Key Questions for Impact Assessment. New England Journal of Medicine, 382(8), 692-694. doi:10.1056/nejmp2000929Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineeringhttps://coronavirus.jhu.edu/map.htmlInforme Sobre la Situación COVID-19 en España a 6 April 2020. Equipo COVID-19. RENAVE. CNE. CNM (ISCIII). Informe COVID-19 nº21https://covid19.isciii.es/Report 13: Estimating the Number of Infections and the Impact of Non-Pharmaceutical Interventions on COVID-19 in 11 European Countrieshttps://spiral.imperial.ac.uk:8443/handle/10044/1/77731Rothan, H. A., & Byrareddy, S. N. (2020). The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. Journal of Autoimmunity, 109, 102433. doi:10.1016/j.jaut.2020.102433Liang, W., Guan, W., Chen, R., Wang, W., Li, J., Xu, K., … He, J. (2020). Cancer patients in SARS-CoV-2 infection: a nationwide analysis in China. The Lancet Oncology, 21(3), 335-337. doi:10.1016/s1470-2045(20)30096-6Sharpe, A. H., & Pauken, K. E. (2017). The diverse functions of the PD1 inhibitory pathway. Nature Reviews Immunology, 18(3), 153-167. doi:10.1038/nri.2017.108Fisher, R. A. (1922). On the Interpretation of χ 2 from Contingency Tables, and the Calculation of P. Journal of the Royal Statistical Society, 85(1), 87. doi:10.2307/2340521Mehta, C. R., & Patel, N. R. (1983). A Network Algorithm for Performing Fisher’s Exact Test in r × c Contingency Tables. Journal of the American Statistical Association, 78(382), 427. doi:10.2307/2288652Wilcoxon, F. (1945). Individual Comparisons by Ranking Methods. Biometrics Bulletin, 1(6), 80. doi:10.2307/3001968Kuderer, N. M., Choueiri, T. K., Shah, D. P., Shyr, Y., Rubinstein, S. M., Rivera, D. R., … de Lima Lopes, G. (2020). Clinical impact of COVID-19 on patients with cancer (CCC19): a cohort study. The Lancet, 395(10241), 1907-1918. doi:10.1016/s0140-6736(20)31187-9Zhang, L., Zhu, F., Xie, L., Wang, C., Wang, J., Chen, R., … Zhou, M. (2020). Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China. Annals of Oncology, 31(7), 894-901. doi:10.1016/j.annonc.2020.03.296Winter, A. K., & Hegde, S. T. (2020). The important role of serology for COVID-19 control. The Lancet Infectious Diseases, 20(7), 758-759. doi:10.1016/s1473-3099(20)30322-4Venkatesulu, B. P., Thoguluva Chandrasekar, V., Giridhar, P., Advani, P., Sharma, A., Hsieh, C. E., … Krishnan, S. (2020). A systematic review and meta-analysis of cancer patients affected by a novel coronavirus. doi:10.1101/2020.05.27.20115303Van Assen, S., Holvast, A., Benne, C. A., Posthumus, M. D., van Leeuwen, M. A., Voskuyl, A. E., … Bijl, M. (2010). Humoral responses after influenza vaccination are severely reduced in patients with rheumatoid arthritis treated with rituximab. Arthritis & Rheumatism, 62(1), 75-81. doi:10.1002/art.25033Rousseau, B., Loulergue, P., Mir, O., Krivine, A., Kotti, S., Viel, E., … Tournigand, C. (2012). Immunogenicity and safety of the influenza A H1N1v 2009 vaccine in cancer patients treated with cytotoxic chemotherapy and/or targeted therapy: the VACANCE study. Annals of Oncology, 23(2), 450-457. doi:10.1093/annonc/mdr141Di Cosimo, S., Malfettone, A., Pérez-García, J. M., Llombart-Cussac, A., Miceli, R., Curigliano, G., & Cortés, J. (2020). Immune checkpoint inhibitors: a physiology-driven approach to the treatment of coronavirus disease 2019. European Journal of Cancer, 135, 62-65. doi:10.1016/j.ejca.2020.05.026Bersanelli, M., Scala, S., Affanni, P., Veronesi, L., Colucci, M. E., Banna, G. L., … Liotta, F. (2020). Immunological insights on influenza infection and vaccination during immune checkpoint blockade in cancer patients. Immunotherapy, 12(2), 105-110. doi:10.2217/imt-2019-0200Pollán, M., Pérez-Gómez, B., Pastor-Barriuso, R., Oteo, J., Hernán, M. A., Pérez-Olmeda, M., … Fernández de Larrea, N. (2020). Prevalence of SARS-CoV-2 in Spain (ENE-COVID): a nationwide, population-based seroepidemiological study. The Lancet, 396(10250), 535-544. doi:10.1016/s0140-6736(20)31483-5Choe, P. G., Perera, R. A. P. M., Park, W. B., Song, K.-H., Bang, J. H., Kim, E. S., … Oh, M. (2017). MERS-CoV Antibody Responses 1 Year after Symptom Onset, South Korea, 2015. Emerging Infectious Diseases, 23(7), 1079-1084. doi:10.3201/eid2307.170310Cao, W.-C., Liu, W., Zhang, P.-H., Zhang, F., & Richardus, J. H. (2007). Disappearance of Antibodies to SARS-Associated Coronavirus after Recovery. 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Viure amb càncer colorectal

Treballs d'Educació Farmacèutica als ciutadans. Unitat Docent d'Estades en Pràctiques Tutelades. Facultat de Farmàcia, Universitat de Barcelona. Curs: 2015-2016. Tutors: Jordi Casas Sánchez i Marian March Pujol

Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite

The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called 'RNASeq' and 'VariantSeq' to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, 'RNASeq' and 'VariantSeq' are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server-Side can be installed, via a Docker container, in the user's PC under any operating system or on remote servers, as a cloud solution. 'RNASeq' and 'VariantSeq' are both available as desktop (RCP compilation) and web (RAP compilation) applications. Each application has two execution modes: a step-by-step mode enables each step of the workflow to be executed independently, and a pipeline mode allows all steps to be run sequentially. 'RNASeq' and 'VariantSeq' also feature an experimental, online support system called GENIE that consists of a virtual (chatbot) assistant and a pipeline jobs panel coupled with an expert system. The chatbot can troubleshoot issues with the usage of each tool, the pipeline jobs panel provides information about the status of each computational job executed in the GPRO Server-Side, while the expert system provides the user with a potential recommendation to identify or fix failed analyses. Our solution is a ready-to-use topic specific platform that combines the user-friendliness, robustness, and security of desktop software, with the efficiency of cloud/web applications to manage pipelines and workflows based on command line interface software

Serum Phospholipids Fatty Acids and Breast Cancer Risk by Pathological Subtype

This study evaluates whether serum phospholipids fatty acids (PL-FAs) and markers of their endogenous metabolism are associated with breast cancer (BC) subtypes. EpiGEICAM is a Spanish multicenter matched case-control study. A lifestyle and food frequency questionnaire was completed by 1017 BC cases and healthy women pairs. Serum PL-FA percentages were measured by gas chromatography-mass spectrometry. Conditional and multinomial logistic regression models were used to quantify the association of PL-FA tertiles with BC risk, overall and by pathological subtype (luminal, HER2+ and triple negative). Stratified analyses by body mass index and menopausal status were also performed. Serum PL-FAs were measured in 795 (78%) pairs. Women with high serum levels of stearic acid (odds ratio (OR)T3vsT1 = 0.44; 95% confidence interval (CI) = 0.30-0.66), linoleic acid (ORT3vsT1 = 0.66; 95% CI = 0.49-0.90) and arachidonic to dihomo-γ-linolenic acid ratio (OR T3vsT1 = 0.64; 95% CI = 0.48-0.84) presented lower BC risk. Participants with high concentrations of palmitoleic acid (ORT3vsT1 = 1.65; 95% CI = 1.20-2.26), trans-ruminant palmitelaidic acid (ORT3vsT1 = 1.51; 95% CI = 1.12-2.02), trans-industrial elaidic acid (ORT3vsT1 = 1.52; 95% CI = 1.14-2.03), and high oleic to stearic acid ratio (ORT3vsT1 = 2.04; 95% CI = 1.45-2.87) showed higher risk. These associations were similar in all BC pathological subtypes. Our results emphasize the importance of analyzing fatty acids individually, as well as the desaturase activity indices

Palbociclib Rechallenge for Hormone Receptor–Positive/HER-Negative Advanced Breast Cancer: Findings from the Phase II BioPER Trial

Purpose: To assess the efficacy and exploratory biomarkers of continuing palbociclib plus endocrine therapy (ET) beyond pro-gression on prior palbociclib-based regimen in patients with hor-mone receptor-positive/HER2-negative (HR+/HER2-) advanced breast cancer (ABC).Patients and Methods: The multicenter, open-label, phase II BioPER trial included women who had experienced a progressive disease (PD) after having achieved clinical benefit on the immedi-ately prior palbociclib plus ET regimen. Palbociclib (125 mg, 100 mg, or 75 mg daily orally for 3 weeks and 1 week off as per prior palbociclib-based regimen) plus ET of physician's choice were administered in 4-week cycles until PD or unacceptable toxicity. Coprimary endpoints were clinical benefit rate (CBR) and percent-age of tumors with baseline loss of retinoblastoma (Rb) protein expression. Additional endpoints included safety and biomarker analysis.Results: Among 33 patients enrolled, CBR was 34.4% [95% confidence interval (CI), 18.6-53.2; P < 0.001] and 13.0% of tumors (95% CI, 5.2-27.5) showed loss of Rb protein expression, meeting both coprimary endpoints. Median progression-free survival was 2.6 months (95% CI, 1.8-6.7). No new safety signals were reported. A signature that included baseline mediators of therapeutic resistance to palbociclib and ET (low Rb score, high cyclin E1 score, ESR1 mutation) was independently associated with shorter median progression-free survival (HR, 22.0; 95% CI, 1.71-282.9; P = 0.018). Conclusions: Maintaining palbociclib after progression on prior palbociclib-based regimen seems to be a reasonable, investigational approach for selected patients. A composite biomarker signature predicts a subset of patients who may not derive a greater benefit from palbociclib rechallenge, warranting further validation in larger randomized controlled trials

Shared Oncogenic Pathways Implicated in Both Virus-Positive and UV-Induced Merkel Cell Carcinomas

Merkel cell carcinoma (MCC) is a highly malignant neuroendocrine tumor of the skin whose molecular pathogenesis is not completely understood, despite the role that Merkel cell polyomavirus can play in 55e90% of cases. To study potential mechanisms driving this disease in clinically characterized cases, we searched for somatic mutations using whole-exome sequencing, and extrapolated our findings to study functional biomarkers reporting on the activity of the mutated pathways. Confirming previous results, Merkel cell polyomavirus-negative tumors had higher mutational loads with UV signatures and more frequent mutations in TP53 and RB compared with their Merkel cell polyomavirus-positive counterparts. Despite important genetic differences, the two Merkel cell carcinoma etiologies both exhibited nuclear accumulation of oncogenic transcription factors such as NFAT or nuclear factor of activated T cells (NFAT), P-CREB, and P-STAT3, indicating commonly deregulated pathogenic mechanisms with the potential to serve as targets for therapy. A multivariable analysis identified phosphorylated CRE-binding protein as an independent survival factor with respect to clinical variables and Merkel cell polyomavirus status in our cohort of Merkel cell carcinoma patients.This work was supported by grants from Instituto de Salud-Carlos III (ISCIII); cofinanced by the European Union; (FEDER) (PI12/00357), and a Ramón and Cajal research program (MINECO; RYC-2013-14097) to JPV, Asociación Española Contra el Cáncer and ISCIII grants (RD06/0020/0107, RD012/0036/0060) to MAP, and Coordinated Project of Excellence inter-Institutos de investigación acreditados institutes (ISCIII; PIE15/00081) to MAP. The Ramón and Cajal research program also supports IV. SD was supported by the Torres Quevedo subprogram (MICINN; PTQ-12-05391)

Angiosarcomas: histology, immunohistochemistry and molecular insights with implications for differential diagnosis

Angiosarcomas (AS) represent a heterogenous group of tumors with variable clinical presentation. AS share an important morphologic and immunohistochemical overlap with other sarcomas, hence the differential diagnosis is challenging, especially in poorly-differentiated tumors. Although molecular studies provide significant clues, especially in the differential diagnosis with other vascular neoplasms, a thorough hematoxylin and eosin analysis remains an essential tool in AS diagnosis. In this review, we discuss pathological and molecular insights with emphasis on implications for differential diagnosis in cutaneous, breast, soft tissue and visceral AS