Supplementary Material:
Supplementary Figure S1: H&E staining and mtDNA analysis of clear cell RCC and oncocytoma from a
single patient.
Supplementary Figure S2: H&E staining and representative electropherogram of biopsy and corresponding
tumor samples.
Supplementary Table S1: Clinical information on BMF oncocytoma patients.
Supplementary Table S2: Histology and mtDNA analysis of chromophobe RCC.
Supplementary Table S3: mtDNA analysis in non-oncocytic and non-chromophobe renal tumors.
Supplementary Table S4: Genetic analysis of FLCN and mtDNA in BHD tumors.
Supplementary Figure S1:
H&E staining and mtDNA analysis of clear cell RCC (ccRCC) and oncocytoma from a single patient
(BMF6). A and B, H&E staining of ccRCC and oncocytoma, respectively (100x magnification); C and D,
electropherogram showing mutations m.10952insC and m.G12923A in DNA extracted from oncocytoma,
which were absent from ccRCC and blood DNA.
Supplementary Figure S2:
H&E staining and representative electropherogram of biopsy and corresponding tumor samples (BMF8).
H&E staining shows histology of biopsy sample (100x magnification) (A) and corresponding tumor sample
after surgery (200x magnification) (B). C: Gel electrophoresis of PCR reactions showing amplification of
DNA extracted from biopsy samples. D: Sequencing electropherogram showing detection of heteroplasmic
mutation m.G4244A in tumor, biopsy, and blood DNA.
Supplementary Table S1:
Clinical information on BMF oncocytoma patients.
For every BMF oncocytoma patient, clinical history and pathology information about each tumor is given.
Availability and histology of nonneoplastic kidney parenchyma is also listed.
Patient
Family
history
Sex
Clinical history
BMF1
None
M
BMF2
None
F
BMF3
None
F
BMF4
None
M
BMF5
None
F
BMF6
None
M
BMF7
None
F
Patient underwent a left partial nephrectomy at NIH at age
67, where 5 oncocytomas were removed, the largest being
2.8 cm. At age 69, biopsies were taken at NIH of 2 right
renal masses, and both were diagnosed as oncocytoma. As
of age 75, imaging shows 2 right renal masses and 1 left
renal mass.
Patient underwent a right partial nephrectomy at NIH at age
54, where 5 tumors were removed, the largest being 6 cm;
all were diagnosed as tumors consistent with oncocytoma.
At age 55, the patient had a left partial nephrectomy at NIH
to remove 6 masses, all of which were oncocytoma. As of
age 60, imaging shows 4 masses in her right kidney and at
least 9 masses in her left kidney.
Patient underwent a right partial nephrectomy at NIH at age
48 for 4 masses, the largest being 3 cm, which were
diagnosed as oncocytic tumors consistent with
oncocytomas. As of age 51, imaging shows 6 solid lesions
in her left kidney and none remaining in her right kidney.
Patient underwent a left radical nephrectomy at an outside
hospital at age 62. The outside pathology report described
two oncocytomas (10 cm and 0.6 cm) and a small (0.3 cm)
separate area of oncocytosis; our pathologist at NIH
concurred. At age 63, he had a right partial nephrectomy at
NIH to remove 10 tumors, the largest of which was 3.5 cm,
8 of which were called oncocytoma and 2 were called
oncocytic tumors. At age 70, imaging shows 2 solid lesions
in his right kidney.
Patient underwent a right partial nephrectomy at NIH at age
71, where 2 masses (4.5 cm and 2.5 cm) were removed,
both of which were oncocytoma. Three years later, at age
74, she had a biopsy at NIH of a left renal mass that was
diagnosed as an oncocytoma.
Patient underwent first a right and then a left partial
nephrectomy at NIH at age 66. A right 3.4 cm renal mass
was diagnosed as oncocytoma, whereas one left mass was a
3.5 cm clear cell renal cell carcinoma and the other 4.0 cm
left mass was a cyst and oncocytoma. As of 2 years later, at
age 68, imaging shows one renal mass in the left kidney
and one in the right.
Patient underwent a left partial nephrectomy at NIH at age
69, for a 2.5 cm oncocytoma and a 0.7 cm
angiomyolipoma. Imaging information has not been
available for the last 8 years.
Nonneoplastic
kidney
parenchyma
Histology was not
available;
Genetic analysis
showed no mtDNA
mutation
Oncocytosis
not available
Oncocytosis
not available
not available
not available
Supplementary Table S2:
Histology and mtDNA analysis of chromophobe RCC.
Histologic subtype and mtDNA nucleotide changes are reported, where identified, in a total of 12
chromophobe RCC samples from 11 different patients plus one patient with multiple chromophobe RCCs.
Mutation load is given for each mutation: “hom” indicates homoplasmic and “het” heteroplasmic mutations.
Pathogenic prediction of missense mutations are indicated as PSIC score, given by PolyPhen-2. Site
variability scores are listed for each nucleotide change, as reported by the Human mitochondrial Database
(hmtdb: www.hmtdb.uniba.it, (Rubino et al. 2012)) for normal and patient samples, to identify previously
reported nucleotide changes. Column entitled “mitomap.org” reports description of nucleotide changes as
reported by mitomap.org.
Supplementary Table S3:
mtDNA sequence analysis in non-oncocytic and non-chromophobe renal tumors.
For each sample, somatic nucleotide changes and resulting amino acid change, affected gene, homoplasmy
(hom) or heteroplasmy (het) status and mutation load for heteroplasmic samples, and PSIC score from
prediction of pathogenic potential of missense mutations with PolyPhen-2 are listed. fs indicates frameshift
mutations. Hmtdb site variability scores for normal and patient samples are listed to identify previously
reported nucleotide changes (Rubino et al. 2012).
Supplementary Table S4:
Genetic analysis of FLCN and mtDNA in BHD tumors.
For BHD tumors of different histologies germline and somatic FLCN status is shown along with mtDNA
sequence data. “LOH” indicates somatic loss of heterozygosity at the FLCN locus. Homoplasmic (hom) or
heteroplasmic (het) status of mtDNA mutations is specified for each mutation together with the affected
genes and information on whether the nucleotide change has been previously reported (hmtdb site variability
score in normal and patient samples, (Rubino et al. 2012)). PSIC score of in silico prediction of pathogenic
potential with PolyPhen-2 is shown. Samples in which no somatic FLCN or mtDNA mutations were detected
are indicated as “ND”.
a
Mutation position is determined from the first nucleotide of the folliculin transcript, GenBank accession
number AF517523
b
Mutation m.297_348del50 is described in:
Bi R, Zhang AM, Zhang W, et al. The acquisition of an inheritable 50-bp deletion in the human mtDNA
control region does not affect the mtDNA copy number in peripheral blood cells. Hum Mutat. 2010;
31(5):538-43