| 1. |
- Larsson, Ludvig
(author)
-
Mapping Transcriptomes in Tissues
- 2023
-
Doctoral thesis (other academic/artistic)abstract
- Over the past few decades, the advent of pioneering biotechnological methods has allowed scientists to analyze the molecular components of multicellular organisms with remarkable precision. The field of transcriptomics has witnessed a rapid development of technologies for gene expression profiling of biological samples. These gene expression profiles offer crucial insights into biological processes that underlie organism development, homeostasis, and disease-causing dysregulation. Modern transcriptomics technologies can profile samples at various degrees of precision and resolution, and when combined, they contribute to a comprehensive understanding of the complex molecular mechanisms that shape entire organisms. Some of these molecular mechanisms occur at the microscopic scale, controlled by communication between nearby cells. Other mechanisms depend on coordinated efforts between large networks of cells organized into tissues and organs. Cells, tissues and organs represent hierarchical levels of structural organization, and each level plays a vital role in the proper functioning of the organism. Gene expression profiling technologies yield comprehensive data that can be harnessed to explore and characterize biological phenomena within and across these structural levels. The central theme of this thesis revolves around the use of experimental technologies and computational methods in the field of transcriptomics to enhance our understanding of multicellular life. Particular attention is directed at a technology known as Visium, which has held an important position in the field in recent years. The research articles included in this thesis demonstrate the applications of Visium and related technologies in biological research.In article I, we present a computational toolbox for processing, analyzing, and visualizing Visium data, assembled into an open-source package written in the R programming language. The package facilitates the characterization of gene expression profiles in tissue sections and seamlessly integrates expression data with corresponding histological images. This computational framework was used extensively for the data analyses presented in articles II, III and IV and the articles listed in the extended list of publications.In article II, we report one of the first spatiotemporal, transcriptomics atlases of the developing human heart. The atlas encompasses three developmental time points during the first trimester, and is constructed from gene expression data from isolated cells and intact tissue sections. Joint analysis of this data enabled characterization of the transcriptomic profiles and the cellular composition of anatomical domains within the heart, illuminating biological processes that underlie cardiac morphogenesis in humans.Article III constitutes a study of the transcriptomic landscape of the murine colon generated using spatially resolved transcriptomics. By folding the organ into a roll, we successfully obtained tissue sections covering the entire colon, enabling organ-wide transcriptomic profiling. Sections were acquired from a healthy colon and a colon recovering from damage due to treatment with a tissue-damaging substance. Data-driven analysis of the healthy colon unveiled a previously undiscovered molecular regionalization from the proximal to distal parts. In the recovering colon, we observed dramatic alterations in the distal tissues, while the proximal parts remained more similar to the healthy colon. In the injured distal colon, we mapped multiple gene expression programs associated with distinct biological responses to tissue injury.In article IV, we introduce an experimental protocol that makes the Visium method compatible with fresh frozen tissue samples with low RNA quality. The protocol was tested on human prostate cancer, lung, colon, small intestine and pediatric brain tumor tissue samples, as well as mouse brain and cartilage tissue samples. Together, these tissue samples represented a wide selection of specimens with varying composition and RNA quality. Through comparative analyses, we demonstrated that the proposed experimental protocol surpassed the standard Visium protocol in performance for samples with low to moderate RNA integrity.Finally, in article V, we present an updated R package for Visium data analysis. This R package builds upon the work presented in article I, but offers a more versatile and efficient computational framework. The package features web-based tools for interactive data exploration, image processing methods and methods to map cell types in tissue sections. Additionally, it includes several spatially aware analysis methods that incorporate information about distances between measurements to investigate biological phenomena that exhibit spatial patterns.
|
|
| 2. |
- Marco Salas, Sergio, 1996-, et al.
(author)
-
Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows
-
Other publication (other academic/artistic)abstract
- The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10X Genomics capable of mapping hundreds of genes in situ at a subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore 25 Xenium datasets generated from multiple tissues and species comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open source computational tools, when applied to Xenium datasets, in tasks including preprocessing, cell segmentation, selection of spatially variable features and domain identification. This study serves as the first independent analysis of the performance of Xenium, and provides best-practices and recommendations for analysis of such datasets.
|
|
| 3. |
- Noerenberg, Daniel, et al.
(author)
-
Genetic Characterization of Primary Mediastinal B-Cell Lymphoma : Pathogenesis and Patient Outcomes
- 2024
-
In: Journal of Clinical Oncology. - : American Society of Clinical Oncology (ASCO). - 0732-183X .- 1527-7755. ; 42:4, s. 452-466
-
Journal article (peer-reviewed)abstract
- PurposePrimary mediastinal large B-cell lymphoma (PMBCL) is a rare aggressive lymphoma predominantly affecting young female patients. Large-scale genomic investigations and genetic markers for risk stratification are lacking.Patients and MethodsTo elucidate the full spectrum of genomic alterations, samples from 340 patients with previously untreated PMBCL were investigated by whole-genome (n = 20), whole-exome (n = 78), and targeted (n = 308) sequencing. Statistically significant prognostic variables were identified using a multivariable Cox regression model and confirmed by L1/L2 regularized regressions.ResultsWhole-genome sequencing revealed a commonly disrupted p53 pathway with nonredundant somatic structural variations (SVs) in TP53-related genes (TP63, TP73, and WWOX) and identified novel SVs facilitating immune evasion (DOCK8 and CD83). Integration of mutation and copy-number data expanded the repertoire of known PMBCL alterations (eg, ARID1A, P2RY8, and PLXNC1) with a previously unrecognized role for epigenetic/chromatin modifiers. Multivariable analysis identified six genetic lesions with significant prognostic impact. CD58 mutations (31%) showed the strongest association with worse PFS (hazard ratio [HR], 2.52 [95% CI, 1.50 to 4.21]; P < .001) and overall survival (HR, 2.33 [95% CI, 1.14 to 4.76]; P = .02). IPI high-risk patients with mutated CD58 demonstrated a particularly poor prognosis, with 5-year PFS and OS rates of 41% and 58%, respectively. The adverse prognostic significance of the CD58 mutation status was predominantly observed in patients treated with nonintensified regimens, indicating that dose intensification may, to some extent, mitigate the impact of this high-risk marker. By contrast, DUSP2-mutated patients (24%) displayed durable responses (PFS: HR, 0.2 [95% CI, 0.07 to 0.55]; P = .002) and prolonged OS (HR, 0.11 [95% CI, 0.01 to 0.78]; P = .028). Upon CHOP-like treatment, these patients had very favorable outcome, with 5-year PFS and OS rates of 93% and 98%, respectively.ConclusionThis large-scale genomic characterization of PMBCL identified novel treatment targets and genetic lesions for refined risk stratification. DUSP2 and CD58 mutation analyses may guide treatment decisions between rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone and dose-adjusted etoposide, prednisone, vincristine, cyclophosphamide, doxorubicin, and rituximab.
|
|
