Genomic landscape of lymphatic malformations: a case series and response to the PI3Kα inhibitor alpelisib in an N-of-1 clinical trial

  1. Montaser F Shaheen  Is a corresponding author
  2. Julie Y Tse
  3. Ethan S Sokol
  4. Margaret Masterson
  5. Pranshu Bansal
  6. Ian Rabinowitz
  7. Christy A Tarleton
  8. Andrey S Dobroff
  9. Tracey L Smith
  10. Thèrése J Bocklage
  11. Brian K Mannakee
  12. Ryan N Gutenkunst
  13. Joyce Bischoff
  14. Scott A Ness
  15. Gregory M Riedlinger
  16. Roman Groisberg
  17. Renata Pasqualini
  18. Shridar Ganesan  Is a corresponding author
  19. Wadih Arap  Is a corresponding author
  1. University of Arizona Cancer Center, United States
  2. Division of Hematology/Oncology, Department of Medicine, University of Arizona College of Medicine, United States
  3. Foundation Medicine, Inc, United States
  4. Rutgers Cancer Institute of New Jersey, United States
  5. Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, United States
  6. University of New Mexico Comprehensive Cancer Center, United States
  7. Division of Hematology/Oncology, Department of Internal Medicine, University of New Mexico School of Medicine, United States
  8. Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, United States
  9. Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, United States
  10. Department of Pathology, University of Kentucky College of Medicine and Markey Cancer Center, United States
  11. Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, United States
  12. Department of Molecular and Cellular Biology, College of Science, University of Arizona, United States
  13. Vascular Biology Program, Boston Children’s Hospital, United States
  14. Department of Surgery, Harvard Medical School, United States
  15. Department of Pathology, Rutgers Robert Wood Johnson Medical School, United States
  16. Division of Medical Oncology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, United States
  17. Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, United States
5 figures, 1 table and 2 additional files

Figures

Mutational landscape and histopathology of lymphatic malformations (LMs).

(A) Oncoprint showing mutational landscape of 30 LM samples sequenced. (B) Lollipop plot showing spectrum of PIK3CA and NRAS mutations in this cohort. (C) Schema showing details of GOPC–ROS1 fusion identified in an NRAS and PIK3CA wild-type LM. (D) Representative histologic images for LMs with conventional and kaposiform histology. The relative frequencies of PIK3CA and NRAS mutations in the two histologic variants are plotted.

Imaging and histological analysis of lymphatic malformation (LM) patient.

(A) Baseline CT abdomen scan at the time of presentation demonstrating a large retroperitoneal/pancreatic LM. (B) CT abdomen scan 6 weeks after the initiation of alpelisib. (C) CT abdomen scan 1 year into the trial. (D, E) Hematoxylin and eosin (H&E)-stained photomicrographs of the LM showing dilated lymphatic channels percolating through visceral fat and associated patchy lymphocytic inflammation (×4 and ×20, respectively). (F) Immunohistochemistry utilizing an anti-P-6S antibody demonstrates PI3Ka pathway activation within the channels’ lining cells. (G) Anti-P-AKT positivity in the lining endothelium of lymphatic channels as well.

Alpelisib reduces lymphatic malformation-lymphatic endothelial cell (LM-LEC) viability.

(A) Logarithmic dose–response curve of alpelisib was performed using the xCELLigence RTCA system. 1, 3, 10, 30, and 100 nM (n = 5 replicates) of alpelisib were used to determine the concentration–response curve. The alpelisib half maximal inhibitory concentration (IC50) was calculated for LM-LEC at 24 hr after treatment as 4.72 × 10−9 M. Error bars are shown as mean +/- standard deviation (SD), which was automatically calculated for each data point by the xCELLigence RTCA system software (Version 2.0) based on five replicates per drug concentration. (B) Illustrative picture of LM-LEC clonogenic plaques at 24 hr after alpelisib treatment (4.72 × 10−9 M). Negative, no treatment; dimethyl sulfoxide (DMSO), vehicle control. Experiments were performed two times with similar results. LM-LEC colonies were stained with crystal violet (0.3%). (C) Colony count 24 hr after alpelisib treatment (4.72 × 10−9 M; n = 2 wells/condition). Error bars are shown as mean +/- SD calculated by GraphPad Prism by determining the square root of variance for each data point deviation relative to the mean.

RNA-seq analysis of lymphatic malformation (LM) samples from index patient (#9).

(A) The heatmap summarizes the results of the differential gene expression analysis. Up- and downregulated genes are shaded red and blue, respectively. (B) The volcano plot summarizes the distribution of genes that were differentially expressed. The vertical axis shows the p value and the horizontal shows the fold-change. The genes that were more than twofold changed and had an adjusted p value less than 0.05 are shaded red. Similar numbers of genes were up- or downregulated.

Graphical summary of the mutations found in genomic analysis of lymphatic malformation (LM) patient cohort (created with BioRender.com).

(A) The majority of LMs have driver mutations that are potentially targetable. (B) LMs with NRAS mutations had kaposiform histopathology. (C) An N-of-1 clinical trial is reported in a patient with a targetable PIK3CA mutation. (D) Comprehensive genomic analyses may reveal further actionable molecular insights.

Tables

Table 1
Clinical and histological features of lymphatic malformation cohort.
PatientAge(years)SexSubmitted clinical syndromeLocalized vs. multifocalLocation of LM(s)Specimen typeLM histologyPIK3CA or NRAS alteration% VAF
19MCLOVESMultifocalSuperficial soft tissuesExcisionConventionalPIK3CA E542K14
24FLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA E542K7
31FLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA H1047R11
417MLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA H1047R4
518MLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA H1047L4
68FKlippel–TrenaunayLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA H1047R9
79MLocalizedVisceralCore biopsyConventionalPIK3CA E545K7
83FLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA C420R5
923MLocalizedVisceralIncisional biopsyConventionalPIK3CA H1047R4
1016FPTEN-like hamartomaLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA H1047R3
113FCLOVESMultifocalSuperficial soft tissuesExcisionConventionalPIK3CA E545K12
121MMultifocalSuperficial soft tissuesExcisionConventionalPIK3CA H1047R2
134FLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA E542K6
145MLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA H1047R5
151FLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA E545K1
1614FMultifocalVisceralExcisionConventionalPIK3CA C420R14
172FCLOVESMultifocalSuperficial soft tissuesExcisionConventionalPIK3CA C420R38
1816FCLOVESLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA E453K32
1910FCLOVESMultifocalSuperficial soft tissuesExcisionConventionalPIK3CA H1047L15
209MLocalizedSuperficial soft tissuesExcisionConventionalPIK3CA H1047R5
219FMultifocalVisceralExcisionKaposiformNRAS Q61R5
228MMultifocalSuperficial soft tissuesExcisionKaposiformNRAS Q61R5
239FMultifocalVisceralExcisionKaposiformNRAS Q61R1
2445MMultifocalVisceralCore biopsyConventionalNRAS Q61R6
2510FLocalizedSuperficial soft tissuesCore biopsyKaposiformNRAS Q61R14
2617MMultifocalSuperficial soft tissuesExcisionConventionalWTNA
2724MLocalizedBoneCore biopsyConventionalWTNA
283MMultifocalSuperficial soft tissuesExcisionConventionalWTNA
2911FLocalizedSuperficial soft tissuesExcisionConventionalWTNA
309FLocalizedSuperficial soft tissues, boneBiopsyConventionalWTNA
  1. CLOVES – congenital lipomatous overgrowth, vascular anomalies, epidermal nevi, and skeletal anomalies; NA – not applicable; VAF – variant allele frequency of PIK3CA or NRAS.

Additional files

Supplementary file 1

Somatic coding mutations identified from whole-genome sequencing.

The genetic coding variants that exist in lymphatic malformation (LM) but do not exist in germline DNA. These pass MuTect2 quality filters (designed to call somatic variants only) and have three or more alternate reads. VAF, variant allele frequency; COSMIC, Catalogue Of Somatic Mutations In Cancer.

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  1. Montaser F Shaheen
  2. Julie Y Tse
  3. Ethan S Sokol
  4. Margaret Masterson
  5. Pranshu Bansal
  6. Ian Rabinowitz
  7. Christy A Tarleton
  8. Andrey S Dobroff
  9. Tracey L Smith
  10. Thèrése J Bocklage
  11. Brian K Mannakee
  12. Ryan N Gutenkunst
  13. Joyce Bischoff
  14. Scott A Ness
  15. Gregory M Riedlinger
  16. Roman Groisberg
  17. Renata Pasqualini
  18. Shridar Ganesan
  19. Wadih Arap
(2022)
Genomic landscape of lymphatic malformations: a case series and response to the PI3Kα inhibitor alpelisib in an N-of-1 clinical trial
eLife 11:e74510.
https://doi.org/10.7554/eLife.74510