Clinical and pathologic description of the familial kindred

The proband (III2), a 53-year-old female of Italian descent, was evaluated at the Sinai Health System, Toronto, after she presented with two months of bloating and vague abdominal pain. Abdominal computed tomography (CT) imaging revealed two exophytic masses with evidence of necrosis; a large 5.8 cm × 6 cm mass along the posterolateral aspect of the lesser curvature of the stomach (Fig. 1a) and a single lobulated mass, 4 cm × 3.8 cm in the proximal jejunum (Fig. 1b). Pathologic and immunohistochemical analysis demonstrated positivity for DOG1 and CD117 (KIT), negative CD34 staining. The gastric tumor demonstrated DOG1 and CD117 (KIT) positivity, with focal CD34 staining. The diagnosis was consistent with GIST for both tumors on final pathology. Physical examination revealed no signs of nevi, lentigines, nodules, pigmentation defects, or stigmata for neurofibromatosis type 1. Past medical history was significant for multiple uterine fibroids, ovarian cysts, and vertebral body hemangioma.

Fig. 1: Radiologic presentation of multifocal GIST in proband (a, b) and probands mother (c–f) with histologic features (g–l).

a Axial contrast-enhanced CT image through the upper abdomen demonstrates a lobulated exophytic solid mass arising from the lesser curvature of the stomach (arrows). The mass is entirely exoenteric, without significant intraluminal component. b Axial contrast-enhanced CT image through the lower abdomen demonstrates a second lobulated exophytic solid mass (arrows) arising from the distal jejunum (black tab). The mass is intimately associated with the adjacent jejunum and lies within the small bowel mesentery. c Coronal contrast-enhanced CT image demonstrates a dominant mesenteric heterogeneous solid mass in the lower abdomen, likely arising exophytically from the distal ileum (arrows). An intraluminal nodule is seen in the jejunum on the left side of the abdomen (black tab). Other small exophytic small bowel nodules are also present (white tabs). d Coronal contrast-enhanced demonstrates further numerous small bowel lesions (arrows). e Sagittal contrast-enhanced image demonstrates achalasia with a dilated esophagus (arrows) due to hypertrophy of the interstitial cells of Cajal. f Axial contrast-enhanced CT image through the upper abdomen demonstrates a lobulated exophytic solid mass arising from the lesser curvature of the stomach (arrows). The mass is entirely exoenteric, without significant intraluminal component. g Low power image (12.5×, H&E) showing hyperplasia of interstitial cells of Cajal along the nerve plexuses of the small bowel and a microscopic tumorlet. h Immunohistochemical study for CD117 highlights the GIST tumorlet and hyperplastic interstitial cells of Cajal. i Higher power view of tumorlet and hyperplastic interstitial cells of Cajal adjacent to the small mural ganglion (H&E, 100×), (arrow indicates ganglion). j Macroscopic GIST infiltrating the wall of the small bowel (H&E, 25×). k High power image of GIST showing classic spindle cell morphology, with fascicular architecture, fibrillary, eosinophilic cytoplasm, and blunt-ended, oval nuclei (H&E, 200×). l Medium power image of GIST showing largely negative CD34 in tumor cells, with strong positivity in blood vessels (100×).

The proband’s 83-year-old mother (II4) had an incidental finding of a small bowel mesenteric mass. She had a 6-month history of weight loss due to esophageal achalasia previously requiring dilatations. Past medical history was significant for frequent urticarial episodes, multiple drug allergies, and chronic constipation. Previous surgery included a total abdominal hysterectomy and bilateral salpingo-oophorectomy for fibroids. CT of the abdomen revealed two enhancing small bowel masses, including an enhancing nodule in the proximal jejunum and an enteric enhancing mass in the distal ileum/ proximal ileum (Fig. 1c, d). There were also large lower abdominal mesenteric masses that contained coarse calcifications. She underwent laparotomy where a 15 cm × 15 cm small bowel lobulated mesenteric GIST, a protruding second 5 cm × 4 cm mass, and numerous (>50) smaller GISTs were found along the length of the small bowel. Pathology revealed a background of diffuse hyperplasia of the interstitial cells of Cajal, numerous small tumorlets, and typical spindle cell morphology with low mitotic activity (Fig. 1f–j). Immunohistochemical studies showed that the tumors expressed CD117 (KIT), DOG-1, and SMA and were largely negative for CD34, S100 protein, and desmin, consistent with a pathological diagnosis of GIST (Fig. 1l).

The proband and her mother were started on imatinib in the preoperative setting but were found to be intolerant to the drug and manifested a severe diffuse macular papular rash after 8 weeks of therapy. In the proband (patient III2), the lesions coalesced into erythematous plaques on her trunk, upper and lower extremities, interdigital folds, and perianal region, with a hyperkeratotic and scaling appearance to some lesions. Patient II4 had accompanying periorbital and lower extremity edema, along with distal upper limb paresthesia. Skin biopsy confirmed lichenoid dermatitis with lymphoeosinophilic infiltrate consistent with a drug-mediated skin reaction. This was consistent with a CTCAE Grade 3 event for both the proband and her mother. In both relatives, imatinib was withheld, and symptoms resolved with steroid treatment. The tumor responses to imatinib for the proband and her mother were consistent with stable disease. The proband showed minimal interval reduction in the size of the stomach lesion after 3 months that stabilized on follow-up imaging consistent with stable disease. Following imatinib, she underwent resection of the tumors in the stomach and small bowel. The proband has no disease recurrence 11 years from diagnosis on active surveillance. The proband’s mother (II4) also demonstrated stable disease on post-treatment imaging. Imaging was performed earlier than planned due to drug-mediated skin reactions. The patient’s mother underwent small bowel resections for her dominant and symptomatic smaller lesion.

The daughter of the proband (IV3), a 34-year-old female, has been asymptomatic and reported no gastrointestinal tract symptoms on the last follow-up on March 2, 2021. She described intermittent skin manifestations and urticaria, and her upper limbs demonstrated numerous dark brown lentigines. A skin biopsy of a bothersome facial lesion that transiently filled with fluid revealed a diagnosis of cutaneous mastocytosis. An annular lesion on her upper back was also biopsy-proven to be consistent with the annular lichen planus. There was a prior history of a dermatofibroma removed from the left arm. The proband’s sister (III-3) has the KIT mutation but appears not affected at 58 years of age. Annual surveillance with CT enterography has continued on these family members without any detection of GIST. There is no standard approach to surveillance for surgically treated patients and/or a high-risk family member, but generally, follow-up schedules are tailored to the risk of recurrence. CT scan is the preferred modality despite radiation exposure, and in a family with syndromic GIST, we have opted for 6-monthly imaging for an extended period of at least 10 years in those affected and baseline scans with annual reviews for family members harboring the known mutation.

Gene panel and whole-genome sequencing identified candidate germline variants of interest in KIT and MSR1 genes

The proband, her mother, and her daughter all underwent WGS of germline DNA. Our analysis focused on the identification of pathogenic (or likely pathogenic) variants shared in the germline across multiple generations. A germline variant in KIT was detected (c.1965T>G; p.Asn655Lys) rs105751908 (NM_000222.2) in both the proband and her mother (Fig. 3a). Targeted testing of the same variant in KIT was found in the granddaughter not affected by GIST (IV3). Nonaffected relatives underwent germline gene panel analysis for the KIT variant if consent was provided (Fig. 2). All KIT variants found were heterozygous. Assessment of WGS data revealed also detected a stopgain variant in the MSR1 gene in all three generations of the kindred as a candidate germline variant of interest. The variant, located in exon 6 (c.877 C > T:p.Arg293*; rs41341748; chr8: 16012594), is predicted to result in a truncated non-functional protein product (Fig. 5a). We did not identify mutations associated with other germline GIST syndromes, including NF1, SDH genes or PDGFRA.

Fig. 2: Three generational pedigree.

Square, male; circle, female; strikethrough, deceased; white fill, no relevant disease; gray fill, declined assessment; black fill, GIST; grid fill, mastocytosis; cross-hatch fill, suspected GIST. The current age, age of tumor diagnosis, and age of death provided were known. Germline Asn655Lys KIT positive (+) and negative (−) genetic test results indicated. Arg293* MSR1 positive (+) genetic test results indicated. Definitions: ‘n’ refers to the presence of other relatives not specified; ‘2’ indicates two sisters or two children. Abbreviations: TAH total abdominal hysterectomy. There were no relevant familial conditions, including neurofibromatosis type 1, and cancers, including melanoma, breast carcinoma, leukemia, lymphoma, and non-GIST stromal tumors, sporadically associated with KIT carriers3.

Tumor genomic analysis reveals minimal somatic mutational events

Both whole-genome and panel-sequencing reported very low mutational burden in both the proband and her mother (<1mut/Mb). From WGS, only 6–7 coding changes were found in the mother’s two tumors, and 2-3 coding changes in the proband’s two tumors, none of which were shared. We identified the germline KIT and MSR1 variants in the somatic sequencing analysis for the proband and the proband’s mother. For the proband, somatic sequencing identified a variant allele fraction of 58% (KIT) and 63% (MSR1) within the one tumor and 61% (KIT) and 50% (MSR1) within the second tumor analyzed. For the proband’s mother, somatic sequencing demonstrated variant allele fractions of 47% (KIT) and 51% (MSR1) within one tumor and 55 and 57% within the second tumor analyzed for KIT and MSR1, respectively. A somatic hotspot variant, c.1679_1681del; p.Val560del, in the KIT gene was acquired in one of two tumors from patient II4 but was detected at a variant allele fraction of 1.1% (Fig. 3c). This somatic KIT variant was not detected in WGS, likely due to lower coverage that may be related to preservation, extraction and processing factors, that can all influence VAF detected.

Fig. 3: WGS of the germline.

a KIT c.1965T>G variant was detected in all three generations of the kindred. b Shared germline stopgain variant in the MSR1 gene. IGV screenshot depicting the c.877 C > T:p.Arg293* variant in MSR1, predicted to result in a stop gain mutation and truncated non-functional protein product. c IGV screenshot depicting hotspot KIT c.1679_1681del (p.Val560del) variant detected at 1.1% VAF in one of patient II4’s tumors.

Previous reports have suggested that deletions in chr14q, 22q, 1p, and 15q are associated with progression from microGISTs to malignant GISTs. We used the WGS data to detect copy number changes in our patient tumors. We found deletion of chromosome 1p shared across both of the mother’s tumor samples (Fig. 4a). The proband’s two tumors had unique copy events, which included 1p, 10p, and 15 loss in one tumor, and subclonal loss of chromosome 14 in the other tumor (Fig. 4b).

Fig. 4: Structural variants seen in the prob and and her mother.

a Chromosome 1p loss was seen in the proband’s mother (patient II4) in tumor 1 and tumor 2 (b) with an aberrant cell fraction of 79 and 74%, respectively. c Tumor 1 of the proband (patient III2) exhibited subclonal chromosome 14 loss, and Tumor 2 of patient III2 demonstrated chromosome 1p, 10p, and 15 loss (d) with aberrant cell fractions of 100 and 83%, respectively.