Transcriptomics analysis and its applications in cancer

Cancer is a collection of diseases that combined are one of the leading causes of deaths worldwide. Although great strides have been made in finding cures for certain cancers, the heterogeneity caused by both the tissue in which cancer originates and the mutations acquired in the cell’s DNA results in unsuccessful treatments for some patients. The genetic alterations caused by carcinogenics or by random mutations acquired during normal cell division promotes changes in the cell’s metabolism. These changes are usually reflected in abnormal gene expression that can be studied to understand the underlying mechanisms giving rise to cancer as well as suggest treatments that can exploit each tumor’s specific vulnerabilities. RNA-Seq is a technology that allows the identification and quantification of the genes that are being expressed inside the cell in a given moment. RNA-Seq has several characteristics and advantages that allow a diversity of applications to exist. For example, apart from quantifying gene expression, it can be used to detect different variants of the same gene, has base pair resolution which is informative of the gene sequence, and can also be used to quantify other RNA molecules besides messenger RNA (mRNA), such as microRNAs. The two main aims of this work are to provide computational methods for data analysis of RNA-Seq and to show specific applications of RNA-Seq that can shed light into cancer mechanisms. In Publications I and IV we developed the Sequence Processesing Integration and Analysis (SePIA) and the Fusion Gene Integration (FUNGI) toolsets that facilitate the creation of reproducible pipelines for investigating different aspects of the cancer transcriptome. SePIA’s utility is showcased with the analysis of datasets from two public data repositories. One of the analysis shows a standard RNA-Seq analysis, while the second one produced a pipeline for mRNA-microRNA integration. The second toolset, FUNGI, is aimed specifically at finding reliable gene fusions with oncogenic potential. To demonstrate FUNGI’s features, we analyzed 107 in-house samples and processed over 400 public samples from a public data repository. FUNGI allowed us to detect fusions in ovarian cancer with a higher prevalence than previously recognized. Additionally, we identified a fusion gene that has not been reported before in ovarian cancer, but that can be targeted with a drug currently in clinical trials. In Publication II we investigated the role of alternative splicing in diffuse large B-cell lymphoma and were able to show that isoform-level instead of gene-level is better at discriminating between subtypes. Additionally, specific isoforms, such as APH1A, KCNH6, and ABCB1, were correlated with survival. In Publication III, we used RNA-Seq to complement the phasing of genetic variants with somatic mutations in tumor suppressor genes. In this study we found enrichment of haplotype combinations that suggest that haploinsufficiency of tumor suppressor genes is enriched in cancer patients. SePIA and FUNGI are tools that can be used by the community to explore their datasets and contribute to the acquisition of knowledge in the field of cancer genetics with next generation sequencing. The applications of RNA-Seq studies included in this dissertation showed that RNA-Seq can be effectively used to aid in the classification of cancer subtypes, and that RNA-Seq can be used in combination with DNA sequencing to explore gene expression mediated by genetic variation in cancer.Syöpä on kokoelma sairauksia, jotka yhdessä ovat yksi suurimmista kuolemaan johtavista syistä maailmanlaajuisesti. Vaikka monien syöpien hoidossa on tapahtunut suuria edistysaskelia, joidenkin potilaiden kohdalla hoidot epäonnistuvat koska kudos, josta kasvain saa alkunsa, sekä muutokset, joita kertyy solun DNA:han, aiheuttavat suuria eroavaisuuksia sekä kasvainten kesken, että niiden sisällä. Karsinogeenien aiheuttamat tai normaalin solunjakautumisen yhteydessä sattumalta tapahtuvat muutokset solun perimässä aiheuttavat muutoksia solun aineenvaihdunnassa. Nämä muutokset heijastuvat yleensä epänormaalina geenien ilmentymisenä, joita tutkimalla voidaan selvittää syövän syntyyn vaikuttavia mekanismeja ja ehdottaa hoitoja, jotka kohdistuvat yksittäisen kasvaimen erityisiin heikkouksiin. Tämän väitöskirjatyön päätavoitteina on ollut kehittää laskennallisia menetelmiä geenien ilmentymisen analysointiin sekä osoittaa käytännössä, miten niiden avulla saadaan lisätietoa syövän syntymekanismeista. Tätä varten kehitimme kaksi työkalupakettia, jotka edesauttavat luotettavasti toistettavien työnkulkujen luomista sýövän transkriptomin, eli sen kaikkien RNA-molekyylien, tutkimiseen. Näiden työkalujen avulla pystyimme vakioimaan transkriptiodatan analyysin ja tunnistamaan sellaisia poikkeuksia geenisekvensseissä tai muutoksia geenien ilmentymisessä, joilla on merkitystä syövän etenemisessä tai jotka liittyvät syövän eri alatyyppeihin

Computational framework for systematic and scalable analysis of deep sequencing transcriptomics data

High-throughput technologies have had a profound impact in transcriptomics. Prior to microarrays, measuring gene expression was not possible in a massively parallel way. As of late, deep RNA sequencing has been constantly gaining ground to microarrays in transcriptomics analysis. RNA-Seq promises several advantages over microarray technologies, but it also comes with its own set of challenges. Different approaches exist to tackle each of the required processing steps of the RNA-Seq data. The proposed solutions need to be carefully evaluated to find the best methods depending on the particularities of the datasets and the specific research questions that are being addressed. In this thesis I propose a computational framework that allows the efficient analysis of RNA-Seq datasets. The parallelization of tasks and organization of the data files was handled by the Anduril framework on which the workflow was implemented. Particular emphasis was bestowed on the quality control of the RNA-Seq files. Several measures were taken to prune the data of low quality bases and reads that hamper the alignment step. Furthermore, various existing processing algorithms for transcript assembly and abundance estimation were tested. The best methods have been coupled together into an automated pipeline that takes the raw reads and delivers expression matrices at isoform and gene level. Additionally, a module for obtaining sets of differentially expressed genes under different conditions or when measuring an experiment across a time course is included

Public Passenger Transportation in Colombia: Is it an area of Competition Law, administrative law, free competition? Or, on the contrary: is it a public service, subject to the laws of the free, arbitrary and self-sufficient market?

El transporte público individual, y colectivo, de pasajeros, se ha transformado dentro del derecho. Ha pasado de ser un servicio público de regulación y garantía por parte del derecho administrativo, a ser considerado, posteriormente, como un derecho fundamental, considerado a la fecha como un derecho fundamental esencial. Las ramas del derecho clásico, como lo son el derecho administrativo y el derecho constitucional, han sido garantes de su prestación eficiente. En este momento la evolución del servicio, las necesidades de los ciudadanos, la expansión de las ciudades, las nuevas tecnologías, la protección del medio ambiente y los retos urbanísticos; nos generan mayores desafíos que son abordados por el Derecho de la Competencia, el Derecho de los Mercados y el Derecho a la Ciudad. Este trabajo revisa los antecedentes, las nociones del transporte como servicio público, su evolución y plantea como reto la multidisciplinariedad del fenómeno, así como la necesidad de actuar de manera coordinada entre las ramas del derecho para asegurar el cumplimiento eficiente del mismo.Individual and collective public transportation of passengers has been transformed within the law. It has gone from being a public service regulated and guaranteed by administrative law, to being considered, subsequently, as a fundamental right, and as to this day an essential fundamental right. The branches of classical law, such as administrative law and constitutional law, have been guarantors of its efficient provision. At this time the evolution of the service, the needs of citizens, the expansion of cities, the new technologies, the environmental protection and urban challenges generate greater hurdles which are the ones addressed by the Competition Law, Market Law and the Right to the City branches. This work reviews the background, the notions of transportation as a public service, its evolution and poses the challenging and multifaceted character of this phenomenon, as well as the need to act in a coordinated manner between the branches of law to ensure its efficient compliance

La aplicación del contrato electrónico y el deber de idoneidad, Sullana, 2022

La investigación tuvo como objetivo general analizar si la aplicación del contrato electrónico es suficiente para garantizar el deber de idoneidad, Sullana, 2022. La investigación mantuvo un enfoque cualitativo, de tipo básico, nivel descriptivo, haciendo uso de la teoría fundamentada. Para la obtención de los datos de información se empleó la guía de entrevista y guía de análisis documental, los mismos que fueron validados por tres expertos, aplicándose el primero a 10 abogados especialistas en derecho civil y comercial y el segundo a 6 resoluciones emitidas por INDECOPI. De los resultados obtenidos se concluyó que, la aplicación del contrato electrónico no es suficiente para garantizar el deber de idoneidad, debido a la ausencia de elementos de seguridad jurídica ante su suscripción, tal como la dificultad de acceso a la justicia, la adecuada tutela judicial y el aprovechamiento por parte de los proveedores ante vacíos legales

Recent Development in the Preharvest 1-MCP Application to Improve Postharvest Fruit Quality

1-Methylcyclopropene (1-MCP), an ethylene action inhibitor, is routinely applied to fruit as a postharvest treatment prior to cold storage to extend fruit storability and posterior shelf life. Nevertheless, preharvest 1-MCP applied as a liquid spray to trees is a novel treatment for maintaining fruit quality throughout the postharvest in some crops and can be a very useful tool for improving handling operations in packing houses. This chapter aims to provide an overview of not only employing 1-MCP as a preharvest treatment in different crops, but also of its effect on the biochemical and physico-chemical parameters that influence fruit postharvest quality, storage capacity, and chilling injury development. It also intends to address the main factors related to the preharvest 1-MCP application effect, such as application time, optimum concentrations, and its combination with other preharvest treatments

Actividad diaria de forrajeo en Polybia diguetana Buysson 1905 (Hymenoptera, Vespidae, Polistinae)

It is important to study the foraging activity of Polistinae in order to understand their impact on ecosystems. In this work we describe the activity of one nest in post-emergence state of Polybia diguetana in relation to temperature and relative humidity. The study area is a university campus in Mérida, México, with warm sub - humid climate. Sampling were taken in the following dates of 2019: January 30 and 31, February 5 and 6 and April 9 and 10, the 9 it rained from 9:00 to 11:45 hours. A video lasting 3:40 min was taken every half an hour, beginning at 7:30 and finishing at 14:45. Eighty-three videos were recorded with an accumulated time of 308.5 minutes. When the video recording was beginning, temperature (°C) and relative humidity (%) were measured at a distance of 3 meters from the nest. Partial correlation analysis were carried out, with temperature and relative humidity as independent variables and wasp departures and arrivals frequencies as response variables, April 9th was excluded from this analysis for excluding the effect of the rain. In the rainy days the highest frequency of arrivals and departures was at 7:30, when the temperature was the highest and the humidity the lowest. In other days departure frequency was higher at 11:00 and arrivals at 14:00. Temperature was positively correlated to departures (r=0.21, p=0.05) and arrivals (r= 0.44, p<0.0001). Relative humidity was c orrelated to arrivals only (r=-0.27, p=0.01). Temperature was the main factor influencing foraging activity, and humidity did in lesser degree. The pattern was different in the rainy day, due to raises in humidity and the risk of being impacted by raindrops.Es importante estudiar la actividad de forrajeo de Polistinae para entender mejor su impacto en los ecosistemas. En este trabajo se describe la actividad de un nido en fase de post-emergencia de Polybia diguetana en relación a la temperatura y humedad relativa. El área de estudio fue un campus universitario en Mérida, México, con clima cálido subhúmedo. Se muestreó en las siguientes fechas de 2019: enero 30 y 31, febrero 5 y 6, y abril 9 y 10, el 9 llovió de 9:00 a 11:45 horas. Se tomó un video del nido de 3:40 min de duración cada media hora, iniciando a las 7:30 y finalizando a las 14:45 horas. En total fueron filmados 83 videos con una duración acumulada de 308,5 minutos. Se midió la temperatura (°C) y humedad relativa a tres metros del nido al iniciar cada video. Se realizaron análisis de correlación parcial con temperatura y humedad como variables independientes y frecuencias de despegues y aterrizajes como dependientes, el 9 de abril se excluyó del análisis por el posible efecto de la lluvia. En el día lluvioso los aterrizajes y despegues fueron más frecuentes a las 7:30 que hubo la temperatura más alta y la humedad relativa más baja; en los otros días los despegues fueron más frecuentes a las 11:00 y los aterrizajes a las 14:00. La temperatura se correlacionó positivamente tanto con los despegues (r=0,21, p=0,05) como con los aterrizajes (r =0,44, p<0,0001). La humedad relativa se correlacionó negativamente con los aterrizajes (r= -0,27, p=0,01). La temperatura fue el factor que más influyó las actividades de forrajeo, la humedad relativa lo hizo en menor medida. La presencia de lluvias modificó el patrón, tanto por el aumento en la humedad relativa como por el riesgo de impacto sobre las forrajeras

SePIA: RNA and small RNA sequence processing, integration, and analysis

Abstract Background Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed. Such studies would benefit from a computational workflow that is easy to implement and standardizes the processing and analysis of both sequenced data types. Results We developed SePIA (Sequence Processing, Integration, and Analysis), a comprehensive small RNA and RNA workflow. It provides ready execution for over 20 commonly known RNA-seq tools on top of an established workflow engine and provides dynamic pipeline architecture to manage, individually analyze, and integrate both small RNA and RNA data. Implementation with Docker makes SePIA portable and easy to run. We demonstrate the workflow’s extensive utility with two case studies involving three breast cancer datasets. SePIA is straightforward to configure and organizes results into a perusable HTML report. Furthermore, the underlying pipeline engine supports computational resource management for optimal performance. Conclusion SePIA is an open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA’s modular design enables robust customization to a given experiment while maintaining overall workflow structure. It is available at http://anduril.org/sepia

SePIA : RNA and small RNA sequence processing, integration, and analysis

Background: Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed. Such studies would benefit from a computational workflow that is easy to implement and standardizes the processing and analysis of both sequenced data types. Results: We developed SePIA (Sequence Processing, Integration, and Analysis), a comprehensive small RNA and RNA workflow. It provides ready execution for over 20 commonly known RNA-seq tools on top of an established workflow engine and provides dynamic pipeline architecture to manage, individually analyze, and integrate both small RNA and RNA data. Implementation with Docker makes SePIA portable and easy to run. We demonstrate the workflow's extensive utility with two case studies involving three breast cancer datasets. SePIA is straightforward to configure and organizes results into a perusable HTML report. Furthermore, the underlying pipeline engine supports computational resource management for optimal performance. Conclusion: SePIA is an open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA's modular design enables robust customization to a given experiment while maintaining overall workflow structure.Peer reviewe

A survey of best practices for RNA-seq data analysis.

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.This is the final published version. It first appeared at http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8

FUNGI : FUsioN Gene Integration toolset

Motivation: Fusion genes are both useful cancer biomarkers and important drug targets. Finding relevant fusion genes is challenging due to genomic instability resulting in a high number of passenger events. To reveal and prioritize relevant gene fusion events we have developed FUsionN Gene Identification toolset (FUNGI) that uses an ensemble of fusion detection algorithms with prioritization and visualization modules. Results: We applied FUNGI to an ovarian cancer dataset of 107 tumor samples from 36 patients. Ten out of 11 detected and prioritized fusion genes were validated. Many of detected fusion genes affect the PI3K-AKT pathway with potential role in treatment resistance.Peer reviewe