A5024648764- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Cell Image Analysis Techniques
- T-cell and B-cell Immunology
- Immunotherapy and Immune Responses
- MicroRNA in disease regulation
- RNA Research and Splicing
- RNA regulation and disease
- Cutaneous Melanoma Detection and Management
- Evolution and Genetic Dynamics
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Breast Cancer Treatment Studies
- Skin Protection and Aging
- Cancer Immunotherapy and Biomarkers
- melanin and skin pigmentation
- Cancer Cells and Metastasis
- RNA Interference and Gene Delivery
- Epigenetics and DNA Methylation
- Atherosclerosis and Cardiovascular Diseases
- Sperm and Testicular Function
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Prostate Cancer Diagnosis and Treatment
- Urologic and reproductive health conditions
- Mast cells and histamine
KTH Royal Institute of Technology
2018-2025
Science for Life Laboratory
2018-2025
XLAB (Slovenia)
2024
To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics multiplexed ion beam imaging from a series human cSCCs matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating epidermal states, tumor-specific keratinocyte (TSK) population unique to cancer, which localized fibrovascular niche. Integration data mapped ligand-receptor networks specific types, revealing...
Cutaneous malignant melanoma (melanoma) is characterized by a high mutational load, extensive intertumoral and intratumoral genetic heterogeneity, complex tumor microenvironment (TME) interactions. Further insights into the mechanisms underlying are crucial for understanding progression responses to treatment. Here we adapted technology of spatial transcriptomics (ST) lymph node biopsies successfully sequenced transcriptomes over 2,200 tissue domains. Deconvolution combined with traditional...
Abstract Defining the transition from benign to malignant tissue is fundamental improving early diagnosis of cancer 1 . Here we use a systematic approach study spatial genome integrity in situ and describe previously unidentified clonal relationships. We used spatially resolved transcriptomics 2 infer copy number variations >120,000 regions across multiple organs, tissues. demonstrate that genome-wide variation reveals distinct patterns within tumours nearby using an organ-wide focused on...
In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding complex biological systems. However, splicing variants and full-length sequence heterogeneity cannot be characterized at spatial resolution current transcriptome profiling methods. To that end, we introduce isoform transcriptomics (SiT), an explorative method for characterizing variation using long-read sequencing. We show in mouse brain how SiT can used profile...
The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed transcriptomics variable, diversity, joining (VDJ) sequences (Spatial VDJ), a method that maps B cell T receptor in human tissue sections. Spatial VDJ captures match canonical distributions amplifies clonal confirmed by orthogonal methods. found congruency between paired chains, computational framework predict pairs, linked the expansion distinct...
Previous large-scale studies have uncovered many features that determine the processing of microRNA (miRNA) precursors; however, they been conducted in vitro. Here, we introduce MapToCleave, a method to simultaneously profile thousands distinct RNA structures living cells. We find miRNA precursors with stable lower basal stem are more efficiently processed and also higher expression vivo tissues from 20 animal species. systematically compare importance known novel sequence structural test...
ABSTRACT In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding complex biological systems. However, splicing variants and fulllength sequence heterogeneity cannot be characterized at spatial resolution current transcriptome profiling methods. To that end, we introduce Spatial Isoform Transcriptomics (SiT), an explorative method for characterizing isoform variation heterogeneity. We show in mouse brain how SIT can...
Abstract The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed Spatial Transcriptomics VDJ sequences (Spatial VDJ), which maps immunoglobulin TR antigen receptors in human tissue sections. captures matching canonical T, B, plasma cell distributions amplifies clonal confirmed by orthogonal methods. confirm congruency between paired receptor chains, develop a computational framework predict pairs, link the...
While triple-negative breast cancer (TNBC) is known to be heterogeneous at the genomic and transcriptomic levels, spatial information on tumor organization cell composition still lacking. Here, we investigate TNBC architecture including its microenvironment using transcriptomics a series of 92 patients. We perform an in-depth characterization stroma integrative approach combining histomorphological transcriptomics. Furthermore, detailed molecular tertiary lymphoid structures leads identify...
<title>Abstract</title> While triple negative breast cancer (TNBC) is known to be heterogeneous at the genomic and transcriptomic levels, spatial information on tumor organization cell composition still lacking. Here, we investigated TNBC architecture including its microenvironment using transcriptomics a series of 92 patients. We performed an in-depth characterization stroma integrative approach combining histomorphological transcriptomics. Furthermore, detailed molecular tertiary lymphoid...
Abstract Background Tertiary lymphoid structures (TLS) are ectopic organs playing a role in adaptive antitumor immune response. They were shown to be associated with favorable outcome and appears promising biomarker for response checkpoint inhibitors (ICI). Yet, there is no consensus their detection quantification. Here we aimed derive specific TLS signature using high resolution spatial transcriptomics data from large series of triple negative breast cancer (TNBC) samples assess its...
Abstract Defining the transition from benign to malignant tissue is fundamental improve early diagnosis of cancer. Here, we provide an unsupervised approach study spatial genome integrity in situ gain molecular insight into clonal relationships. We employed spatially resolved transcriptomics infer copy number variations >120 000 regions across multiple organs, and tissues. demonstrate that genome-wide variation reveals distinct patterns within tumours nearby tissue. Our results suggest a...
Abstract Spatial and genomic heterogeneity of tumors is the key for cancer progression, treatment, survival. However, a technology direct mapping clones in tumor tissue based on point mutations lacking. Here, we propose Tumoroscope, first probabilistic model that accurately infers their high-resolution localization by integrating pathological images, whole exome sequencing, spatial transcriptomics data. In contrast to previous methods, Tumoroscope explicitly addresses problem deconvoluting...
Abstract Defining the transition from benign to malignant tissue is fundamental improve early diagnosis of cancer. We provide an unsupervised approach (SpatialInferCNV) study spatial genome integrity, in situ, gain molecular insight into clonal relationships. employed spatially resolved transcriptomics (Visium, 10x Genomics) infer copy number variations &gt;120 000 regions across multiple organs, tissues and tumors, including three whole axial prostates. used this information deduce...