Integrative molecular and spatial analysis reveals evolutionary dynamics and tumor-immune interplay of in situ and invasive acral melanoma.
In acral melanoma (AM), progression from in situ (AMis) to invasive AM (iAM) leads to significantly reduced survival. However, evolutionary dynamics during this process remain elusive. Here, we report integrative molecular and spatial characterization of 147 AMs using genomics, bulk and single-cell transcriptomics, and spatial transcriptomics and proteomics. Vertical invasion from AMis to iAM displays an early and monoclonal seeding pattern. The subsequent regional expansion of iAM exhibits two distinct patterns, clonal expansion and subclonal diversification. Notably, molecular subtyping reveals an aggressive iAM subset featured with subclonal diversification, increased epithelial-mesenchymal transition (EMT), and spatial enrichment of APOE+/CD163+ macrophages. In vitro and ex vivo experiments further demonstrate that APOE+CD163+ macrophages promote tumor EMT via IGF1-IGF1R interaction. Adnexal involvement can predict AMis with higher invasive potential whereas APOE and CD163 serve as prognostic biomarkers for iAM. Altogether, our results provide implications for the early detection and treatment of AM.
Pubmed ID: 38759655 RIS Download
Research resources used in this publication
- RSEM (RRID:SCR_000262) (software resource)
- RStudio (RRID:SCR_000432) (software resource)
- pheatmap (RRID:SCR_016418) (software resource)
- QuPath (RRID:SCR_018257) (data processing software)
- CellChat (RRID:SCR_021946) (software resource)
- Cellpose (RRID:SCR_021716) (software resource)
- CellPhoneDB (RRID:SCR_017054) (database)
- Harmony (RRID:SCR_022206) (software resource)
- infercnv (RRID:SCR_021140) (software resource)
- Seurat (RRID:SCR_016341) (software resource)
- Cell Ranger (RRID:SCR_017344) (software resource)
- DESeq2 (RRID:SCR_015687) (software resource)
- survival (RRID:SCR_021137) (software resource)
- CIBERSORT (RRID:SCR_016955) (software resource)
- clusterProfiler (RRID:SCR_016884) (software resource)
- Pyclone (RRID:SCR_016873) (software resource)
- GISTIC (RRID:SCR_000151) (software resource)
- CNVkit (RRID:SCR_021917) (software resource)
- Sequenza (RRID:SCR_016662) (data analysis software)
- STAR (RRID:SCR_004463) (software resource)
- ape (RRID:SCR_017343) (software resource)
- dndSCV (RRID:SCR_017093) (software resource)
- GSVA (RRID:SCR_021058) (data analysis software)
- Integrative Genomics Viewer (RRID:SCR_011793) (software resource)
- ANNOVAR (RRID:SCR_012821) (software resource)
- Strelka (RRID:SCR_005109) (software resource)
- VARSCAN (RRID:SCR_006849) (software resource)
- GATK (RRID:SCR_001876) (software resource)
- SAMTOOLS (RRID:SCR_002105) (software resource)
- BWA-MEM2 (RRID:SCR_022192) (data analysis software)
Additional research tools detected in this publication
None foundAntibodies used in this publication
- PE anti-human CD325 (N-Cadherin) (RRID:AB_10660824)
- PE anti-human CD163 (RRID:AB_1134002)
- PE anti-Apo E (RRID:AB_2801139)
- Brilliant Violet 510(TM) anti-human CD14 (RRID:AB_2561379)
- APC/Cyanine7 anti-human CD45 (RRID:AB_2566376)
- Brilliant Violet 421(TM) anti-mouse/human CD324 (E-Cadherin) (RRID:AB_2750483)
- Mouse Anti-Human HLA-DR Monoclonal Antibody, PE-Cy7 Conjugated, Clone G46-6 (RRID:AB_1727528)
- Recombinant Anti-CDKN2A/p16INK4a antibody [EPR1473] - BSA and Azide free (ab186932) (RRID:AB_2895712)
- Recombinant Anti-N Cadherin antibody [EPR1791-4] - BSA and Azide free (RRID:AB_2928049)
- Anti-CD86 antibody [EP1158-37] - BSA and Azide free (RRID:AB_3073666)
- Mouse Anti-Apolipoprotein E Monoclonal Antibody, Unconjugated, Clone D6E10 (RRID:AB_302668)
- Brilliant Violet 421(TM) anti-human CD163 (RRID:AB_2562462)
- ANTI-HU COLLAGEN IV(AKYP0083)-BX042—ALEXA FLUOR™ 647 FOR PHENOCYCLER (RRID:AB_2927676)
- ANTI-HU HLA-DR(AKYP0063)-BX033—ALEXA FLUOR™ 647 FOR PHENOCYCLER (RRID:AB_3080864)
- ANTI-HU CD11C(AKYP0051)-BX024—ALEXA FLUOR™ 647 (RRID:AB_3083459)
- KI67-BX047 (B56)—ATTO 550-RX047 Kit (RRID:AB_2895046)
- CD8-BX026 (C8/144B)—ATTO 550-RX026 (RRID:AB_2915960)
- Anti-Hu CD3e(AKYP0062)-BX045—Alexa Fluor™ 647 for PhenoCycler (RRID:AB_2936080)
- Anti-Hu CD163(AKYP0114)-BX069—Atto 550 for PhenoCycler (RRID:AB_2935895)
- PAN-CYTOKERATIN-BX019 (AE-1/AE-3)—ALEXA FLUOR™ 488-RX019 (RRID:AB_2909509)
- Anti-Hu CD4(AKYP0048)-BX003—Alexa Fluor™ 647 for PhenoCycler (RRID:AB_3094499)
- CD20-BX007 (L26)—ALEXA FLUOR™ 750-RX007 (RRID:AB_2915939)
- p44/42 MAP kinase (phosphorylated Erk1/2) (RRID:AB_331646)
- Phospho-Akt (Ser473) Antibody (RRID:AB_329825)
- Fibronectin/FN1 (E5H6X) Rabbit mAb (RRID:AB_2924220)
- N-Cadherin (D4R1H) XP Rabbit Antibody (RRID:AB_2687616)
- Anti-Hu CD68(AKYP0050)-BX015—Alexa Fluor™ 647 for PhenoCycler (RRID:AB_2935894)
- E-Cadherin (4A2) (RRID:AB_2728770)
- CD68 Antibody (RRID:AB_2904190)
- ApoE (pan) (D7I9N) Rabbit mAb (RRID:AB_2798191)
- E-CADHERIN-BX014 (4A2C7)—ATTO 550-RX014 Kit (RRID:AB_2895057)
- CD163 antibody [10D6], prediluted (RRID:AB_1280790)
Associated grants
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This is a list of tools and resources that we have found mentioned in this publication.
PE anti-human CD325 (N-Cadherin) (antibody)
RRID:AB_10660824
This monoclonal targets CD325
View all literature mentionsPE anti-human CD163 (antibody)
RRID:AB_1134002
This monoclonal targets CD163
View all literature mentionsBrilliant Violet 510(TM) anti-human CD14 (antibody)
RRID:AB_2561379
This monoclonal targets CD14
View all literature mentionsAPC/Cyanine7 anti-human CD45 (antibody)
RRID:AB_2566376
This monoclonal targets CD45
View all literature mentionsBrilliant Violet 421(TM) anti-mouse/human CD324 (E-Cadherin) (antibody)
RRID:AB_2750483
This monoclonal targets CD324
View all literature mentionsMouse Anti-Human HLA-DR Monoclonal Antibody, PE-Cy7 Conjugated, Clone G46-6 (antibody)
RRID:AB_1727528
This monoclonal targets HLA-DR
View all literature mentionsRecombinant Anti-CDKN2A/p16INK4a antibody [EPR1473] - BSA and Azide free (ab186932) (antibody)
RRID:AB_2895712
This recombinant monoclonal targets CDKN2A/p16INK4a
View all literature mentionsRecombinant Anti-N Cadherin antibody [EPR1791-4] - BSA and Azide free (antibody)
RRID:AB_2928049
This recombinant monoclonal targets N-cadherin
View all literature mentionsAnti-CD86 antibody [EP1158-37] - BSA and Azide free (antibody)
RRID:AB_3073666
This monoclonal targets CD86
View all literature mentionsMouse Anti-Apolipoprotein E Monoclonal Antibody, Unconjugated, Clone D6E10 (antibody)
RRID:AB_302668
This monoclonal targets Apolipoprotein E
View all literature mentionsBrilliant Violet 421(TM) anti-human CD163 (antibody)
RRID:AB_2562462
This monoclonal targets CD163
View all literature mentionsANTI-HU COLLAGEN IV(AKYP0083)-BX042—ALEXA FLUOR™ 647 FOR PHENOCYCLER (antibody)
RRID:AB_2927676
This monoclonal targets COLLAGEN IV
View all literature mentionsANTI-HU HLA-DR(AKYP0063)-BX033—ALEXA FLUOR™ 647 FOR PHENOCYCLER (antibody)
RRID:AB_3080864
This unknown targets HLA-DR
View all literature mentionsANTI-HU CD11C(AKYP0051)-BX024—ALEXA FLUOR™ 647 (antibody)
RRID:AB_3083459
This monoclonal targets CD11c/ITGAX
View all literature mentionsKI67-BX047 (B56)—ATTO 550-RX047 Kit (antibody)
RRID:AB_2895046
This monoclonal targets KI67
View all literature mentionsCD8-BX026 (C8/144B)—ATTO 550-RX026 (antibody)
RRID:AB_2915960
This monoclonal targets CD8
View all literature mentionsAnti-Hu CD3e(AKYP0062)-BX045—Alexa Fluor™ 647 for PhenoCycler (antibody)
RRID:AB_2936080
This monoclonal targets CD3e
View all literature mentionsAnti-Hu CD163(AKYP0114)-BX069—Atto 550 for PhenoCycler (antibody)
RRID:AB_2935895
This monoclonal targets CD163
View all literature mentionsPAN-CYTOKERATIN-BX019 (AE-1/AE-3)—ALEXA FLUOR™ 488-RX019 (antibody)
RRID:AB_2909509
This monoclonal targets Pan-Cytokeratin
View all literature mentionsAnti-Hu CD4(AKYP0048)-BX003—Alexa Fluor™ 647 for PhenoCycler (antibody)
RRID:AB_3094499
This monoclonal targets CD4
View all literature mentionsCD20-BX007 (L26)—ALEXA FLUOR™ 750-RX007 (antibody)
RRID:AB_2915939
This unknown targets CD20
View all literature mentionsp44/42 MAP kinase (phosphorylated Erk1/2) (antibody)
RRID:AB_331646
This polyclonal targets Erk1/2
View all literature mentionsPhospho-Akt (Ser473) Antibody (antibody)
RRID:AB_329825
This polyclonal targets Phospho-Akt (Ser473)
View all literature mentionsFibronectin/FN1 (E5H6X) Rabbit mAb (antibody)
RRID:AB_2924220
This monoclonal targets FN1
View all literature mentionsN-Cadherin (D4R1H) XP Rabbit Antibody (antibody)
RRID:AB_2687616
This monoclonal targets N-Cadherin
View all literature mentionsAnti-Hu CD68(AKYP0050)-BX015—Alexa Fluor™ 647 for PhenoCycler (antibody)
RRID:AB_2935894
This monoclonal targets CD68
View all literature mentionsE-Cadherin (4A2) (antibody)
RRID:AB_2728770
This monoclonal targets E-Cadherin
View all literature mentionsApoE (pan) (D7I9N) Rabbit mAb (antibody)
RRID:AB_2798191
This monoclonal targets APOE
View all literature mentionsE-CADHERIN-BX014 (4A2C7)—ATTO 550-RX014 Kit (antibody)
RRID:AB_2895057
This monoclonal targets E-CADHERIN
View all literature mentionsCD163 antibody [10D6], prediluted (antibody)
RRID:AB_1280790
This monoclonal targets CD163 antibody [10D6] prediluted
View all literature mentionsRSEM (software resource)
RRID:SCR_000262
Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data.
View all literature mentionsRStudio (software resource)
RRID:SCR_000432
Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).
View all literature mentionspheatmap (software resource)
RRID:SCR_016418
Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters.
View all literature mentionsQuPath (data processing software)
RRID:SCR_018257
Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.
View all literature mentionsCellChat (software resource)
RRID:SCR_021946
Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.
View all literature mentionsCellpose (software resource)
RRID:SCR_021716
Software tool used to precisely segment cells from wide range of image types and does not require model retraining or parameter adjustments. Generalist algorithm for cellular segmentation. Anatomical segmentation algorithm written in Python 3.
View all literature mentionsCellPhoneDB (database)
RRID:SCR_017054
Collection of publicly available data of curated receptors, ligands and their interactions. Integrates existing datasets that pertain to cellular communication and new manually reviewed information. Used to search for particular ligand or receptor or to interrogate single cell transcriptomics data.
View all literature mentionsHarmony (software resource)
RRID:SCR_022206
Software R package to project cells into shared embedding in which cells group by cell type rather than dataset specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. Used for integration of single cell data.
View all literature mentionsinfercnv (software resource)
RRID:SCR_021140
Software R package to infer copy number variation from single-cell RNA-seq data.
View all literature mentionsSeurat (software resource)
RRID:SCR_016341
Software as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.
View all literature mentionsCell Ranger (software resource)
RRID:SCR_017344
Software tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics.
View all literature mentionsDESeq2 (software resource)
RRID:SCR_015687
Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionssurvival (software resource)
RRID:SCR_021137
Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
View all literature mentionsCIBERSORT (software resource)
RRID:SCR_016955
Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.
View all literature mentionsclusterProfiler (software resource)
RRID:SCR_016884
Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.
View all literature mentionsPyclone (software resource)
RRID:SCR_016873
Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing.
View all literature mentionsGISTIC (software resource)
RRID:SCR_000151
Software to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, they improve the estimation of background rates for each category.
View all literature mentionsCNVkit (software resource)
RRID:SCR_021917
Software command line toolkit and Python library for detecting copy number variants and alterations genome wide from hight hroughput sequencing.
View all literature mentionsSequenza (data analysis software)
RRID:SCR_016662
Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
View all literature mentionsSTAR (software resource)
RRID:SCR_004463
Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
View all literature mentionsape (software resource)
RRID:SCR_017343
Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R.
View all literature mentionsdndSCV (software resource)
RRID:SCR_017093
Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets.
View all literature mentionsGSVA (data analysis software)
RRID:SCR_021058
Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner.
View all literature mentionsIntegrative Genomics Viewer (software resource)
RRID:SCR_011793
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
View all literature mentionsANNOVAR (software resource)
RRID:SCR_012821
An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)
View all literature mentionsStrelka (software resource)
RRID:SCR_005109
Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. The method employs a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, whilst leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. The method has superior accuracy and sensitivity on impure samples compared to approaches based on either diploid genotype likelihoods or general allele-frequency tests.
View all literature mentionsVARSCAN (software resource)
RRID:SCR_006849
A platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software)
View all literature mentionsGATK (software resource)
RRID:SCR_001876
A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)
View all literature mentionsSAMTOOLS (software resource)
RRID:SCR_002105
Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsBWA-MEM2 (data analysis software)
RRID:SCR_022192
Software tool for sequence mapping.The next version of BWA-MEM. Used for aligning sequencing reads against large reference genome.
View all literature mentions
