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Research Article
Multiscale heterogeneity in gastric adenocarcinoma evolution is an obstacle to precision medicine
Röcken, Christoph
Dept. of Pathology, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Germany
Corresponding Author
ORCiD: https://orcid.org/0000-0002-6989-8002
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Declarations:
Declarations
- This study involved human subjects.
- The author confirmed that all appropriate ethical guidelines for the use of human subjects have been followed, any necessary IRB and/or ethics committee review has been obtained, and information about the IRB/ethics committee is included in the manuscript.
- The author has confirmed that all necessary patient/participant consent or assent has been obtained and the appropriate institutional forms have been archived. If the IRB/ethics committee waived the requirement for patient/participant consent or assent, an explanation for the waiver is included in the text.
- The author has confirmed that a statement listing potential conflicts of interest or lack thereof is included in the text.
Purpose: Cancer is a somatic evolutionary disease. Using multiregional whole exome sequencing, we tested the effect of somatic evolution on intratumoral heterogeneity and its putative clinical and biological implications in adenocarcinomas of the stomach and gastroesophageal junction (GC).
Patients and Methods: The study comprised a prospective discovery cohort of 9 and a validation cohort of 463 GCs. Multiregional whole-exome sequencing was done using 48 tumor samples (range: 3-10 tumor samples/patient) of the discovery cohort.
Results: In total, the discovery cohort harbored 16,537 non-synonymous mutations (mutations/sample: median n=159; mutations/patient: median n=369). Intratumoral heterogeneity of somatic mutations and copy number variants were present in all tumors of the discovery cohort. 53-91% of the non-synonymous mutations were not present in each patient’s sample; 399 genes harbored 2-4 different non-synonymous mutations in the same patient; 175 genes showed copy number variations, the majority being heterogeneous, including CD274 (PD-L1). Multi-sample tree-based analyses provided evidence for branched evolution being most complex in a microsatellite instable GC. The analysis of the mode of evolution showed a high degree of heterogeneity in deviation from neutrality within each tumor. Studies on the validation cohort showed that the subclonal loss of SMAD4 is an independent predictor for poor patient outcome in Caucasian patients.
Conclusions: Neutral and non-neutral somatic evolution shape the mutational landscape in GC. It leads to complex spatial intratumoral heterogeneity and may have profound effects on patient management. It provides crucial information for an individualized understanding of clinical prognosis and therapeutic options in GC patients.
Keywords
Gastric cancer, intratumoral heterogeneity, evolution, SMAD4, TP53
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This is a list of supplementary files associated with this preprint. Click to download.
- GastricCancerEvolutionSupplementCCR.docx
Supplemental Results and Figures
- RockenetalSupplTable1Primersequencesfinal.xlsx
Supplemental Table 1 Primer sequences used for Sanger sequencing, pyrosequencing and ddPCR™.
- RockenetalSupplTable2Vaildationfinal.xlsx
Supplemental Table 2 Sanger sequencing, pyrosequencing and ddPCR™ were used to validate single nucleotide variations detected by whole exome sequencing.
- RockenetalSupplTable3SequencingStatisticsfinal.xlsx
Supplemental Table 3 Sequencing statistics.
- RockenetalSupplTable4VARSnonsynoynmousfinal.xlsx
Supplemental Table 4 List of non-synonymous mutations found in the discovery cohort.
- RockenetalSupplTable5VARSsynonymousfinal.xlsx
Supplemental Table 5 List of synonymous mutations found in the discovery cohort.
- RockenetalSupplTable6CCFfinal.xlsx
Supplemental Table 6 List of cancer cell fraction (CCF) non-synonymous mutations
- RockenetalSupplTable7purityploidyfinal.xlsx
Supplemental Table 7 List of purity- and ploidy status of the discovery cohort
- RockenetalSupplTable8mutiplemutationsfinal.xlsx
Supplemental Table 8 List of genes with ≥2 non-synonymous mutations per case.
- RockenetalSupplTable9primaryvslymphnodefinal.xlsx
Supplemental Table 9 List of genes with non-synonymous mutations present in the primary tumor of case #5 and its lymph node metastases.
- RockenetalSupplTable10Comparisonfinal.xlsx
Supplemental Table 10 Comparison of the prevalence of the single nucleotide variations discovered in our test cohort with published data on gastric cancer (3,5,7,53).
- RockenetalSupplTable11mutationsandmorefinal.xlsx
Supplemental Table 11 List of genes with non-synonymous mutations present in ≥2 gastric cancers of the discovery cohort.
- RockenetalSupplTable12CNVfinal.xlsx
Supplemental Table 12 Distribution of the copy number variants (CNVs), i.e. homozygous or heterozygous deletion and amplification among the 48 tumor samples of the discovery cohort.
- RockenetalSupplTable13Pathwaysfinal.xlsx
Supplemental Table 13 Pathway analysis including copy number variation on the discovery cohort.
- RockenetalSupplTable14.docx
Supplemental Table 13 Multivariate analysis
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This is a preprint. It has not completed peer review.
Research Article
Multiscale heterogeneity in gastric adenocarcinoma evolution is an obstacle to precision medicine
Röcken, Christoph
Dept. of Pathology, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Germany
Corresponding Author
ORCiD: https://orcid.org/0000-0002-6989-8002
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 2
Posted 21 Sep, 2020
No community comments so far
No comments provided
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Oncology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Declarations:
Declarations
- This study involved human subjects.
- The author confirmed that all appropriate ethical guidelines for the use of human subjects have been followed, any necessary IRB and/or ethics committee review has been obtained, and information about the IRB/ethics committee is included in the manuscript.
- The author has confirmed that all necessary patient/participant consent or assent has been obtained and the appropriate institutional forms have been archived. If the IRB/ethics committee waived the requirement for patient/participant consent or assent, an explanation for the waiver is included in the text.
- The author has confirmed that a statement listing potential conflicts of interest or lack thereof is included in the text.
Purpose: Cancer is a somatic evolutionary disease. Using multiregional whole exome sequencing, we tested the effect of somatic evolution on intratumoral heterogeneity and its putative clinical and biological implications in adenocarcinomas of the stomach and gastroesophageal junction (GC).
Patients and Methods: The study comprised a prospective discovery cohort of 9 and a validation cohort of 463 GCs. Multiregional whole-exome sequencing was done using 48 tumor samples (range: 3-10 tumor samples/patient) of the discovery cohort.
Results: In total, the discovery cohort harbored 16,537 non-synonymous mutations (mutations/sample: median n=159; mutations/patient: median n=369). Intratumoral heterogeneity of somatic mutations and copy number variants were present in all tumors of the discovery cohort. 53-91% of the non-synonymous mutations were not present in each patient’s sample; 399 genes harbored 2-4 different non-synonymous mutations in the same patient; 175 genes showed copy number variations, the majority being heterogeneous, including CD274 (PD-L1). Multi-sample tree-based analyses provided evidence for branched evolution being most complex in a microsatellite instable GC. The analysis of the mode of evolution showed a high degree of heterogeneity in deviation from neutrality within each tumor. Studies on the validation cohort showed that the subclonal loss of SMAD4 is an independent predictor for poor patient outcome in Caucasian patients.
Conclusions: Neutral and non-neutral somatic evolution shape the mutational landscape in GC. It leads to complex spatial intratumoral heterogeneity and may have profound effects on patient management. It provides crucial information for an individualized understanding of clinical prognosis and therapeutic options in GC patients.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5