Special thanks to my resident Dr Babar Yasin for preparing the
ADAPTED FROM THE ABOVE ARTICLE FROM Seminar in diagnostics
Pathology 30 (2013) 375-381
Angelo P. Dei Tos, MD
Department of Pathology, Treviso General
Hospital, Piazza Ospedale,1 31100 Treviso, Italy
The marriage of Molecular
Genetics and soft tissue
More accurate deﬁnition of disease entities
and validation of classiﬁcation schemes.
Improved diagnostic accuracy.
Identiﬁcation of molecular predictive and
Discovery and validation of therapeutic
Nucleic acids (RNA and DNA), either via
hybridization on a slide(i.e., ﬂuorescent in
On isolated DNA or RNA via polymerase chain
reaction (PCR) techniques (i.e.,reverse
transcriptase PCR and quantitative PCR)It is MANDAOTORY that the results get
interpreted in context with morphology.
Genetic assessement is an
important ADJUNCT not a
Soft tissue tumors are heterogeneous group of
neoplasm which can be :
Challenge for Pathologists
Diagnostic inaccuracy affects the
treatment and development of new
drugs as clinical trials depend upon
Rare group of diseases (< 2% of all cancers)
Extremely heterogenous. Over 100 subtypes
are being described.
Usual features of malignancy (?) are not always
applicable to these.
Histologically worrisome leisons may
actually be benign e.g. Nodular fascitis
Cytollogically innocent neoplasm may
behave aggressively e.g. Low-Grade
Distinguishing speciﬁc subtypes of
Supporting diagnosis in non-canonical
Distinguishing sarcomas from benign
Molecular genetics has proved diagnostically
useful in two relatively large groups of
mesenchymal malignancies: round cell
sarcomas and pleomorphic sarcomas.
Round cell sarcomas include :
Desmo-plastic small round cell tumor
Poorly differentiated round cell synovial
Minority of cases of round cell liposarcoma
The demonstration by FISH of
EWSR1,SS18, and FOXO1 rearrangements in
EWS, PDSS, and
ARMS, respectively, or, alternatively, of
speciﬁc chimerical transcriptsby PCR-based
techniques is of great help for achieving
EWSR1 FISH results need to be
interpreted in context with
morphology and IHC findings.
Sub classification is very important.
myogenic differentiation in pleomorphic
sarcomas is associated with a less favorable
Another important point is the
distinction, among retroper-itoneal
sarcomas, of dedifferentiated
liposarcoma (DDLPS) from other
pleomorphic sarcomas, most often
The recognition of DDLPS is based on the
identiﬁcation of a well-differentiated
lipogenic component associated with a high-
grade, most often non-lipogenic, sarcoma.
Core biopsies usedfor diagnostic purposes
may leave the lipogenic component
DDLPS exhibit better out- comes when
compared to other pleomorphic
sarcomas, and its accurate recognition may
lead to adopt a more aggressive surgical
strategy. (Locally aggressive)
Detection of MDM2 ampliﬁcation by FISH or
quantitative RT-PCR certainly represents a useful
The MDM2 gene (as well as CDK4 and HMGA2) maps at
the 13q12–15 chromosome region and is ampliﬁed in
both well-differentiated and dedifferentiated
MDM2 testing is also potentially useful in
distinguishing between myxoid liposar-coma (MDM2
negative) and WD/DDPLS with myxoid change.
The separation of the two conditions again allows
adoption of proper treatment in consideration of the
high sensitivity of myxoid liposarcoma to the marine-
derived alkaloid named trabectedin.
The combination of morphological criteria
and genetics validates the recognition of rare
diseases even when arising at non-canonical
This is particularly true for referral centers
wherein challenging cases tend inevitably to
Molecular genetics has greatly
Contributed to the identiﬁcation of primary
Ewing sarcoma of the skin, kidney, and dura
mater, as well as of viscerally located
Morphological appearance of mesenchymal
lesions does not always reﬂect the clinical
The distinction of sarcomas from benign
mimics most often relies on morphology.
In a minority of cases molecular genetics may
also prove diagnostically helpful.
Fibroid and myxoid areas.
Swirling whorled growth pattern.
Low to moderate cellularity.
Minimal nuclear pleomorphism.
Deceptively bland-looking spindle cell
mesenchymal malignancY with an aggressive
The differential diagnosis of LGFMS includes
benign lesions such as
perineurioma, neuroﬁbroma, cellular
myxoma, and nodular fasciitis, as well locally
aggressive neoplasms such as desmoid
MUC4 expression is
regarded as key
Identification of FUS
rearrangement via FISH
or identification of
via PCR is very useful.
Several attempts have been made to
determine the prognostic value of
molecular genetic findings.
Focused on Ewing sarcoma, alveolar
rhabdomyosarcoma, and synovial
No meaningful molecular prognostic
stratiﬁcation can be foreseen for
A notable exception is represented by
a molecular signature named
CINSARC, which allows better
separation of grade 2 sarcomas. This
attempt is based on the use of a
complex technique (CGH-array) and
requires availability of fresh
material, which hampers a large scale
clinical application of CINSARC.
Type of mutations involving both the KIT and
PDGFRA genes are associated with distinctive
Deletions occurring at the exon 11 of the KIT
gene are associated with more aggressive
disease, whereas mutations of exon 18 of the
PDGFRA gene generally identify a more
indolent clinical course.
Distinct mutation types in GIST reﬂect
different objective response rates (greater
for KIT exon 11 mutation and much lower for
so-called wild-type GIST).
presence of speciﬁc mutations in the exon 18
of the PDGFRA gene (D842V) predict primary
resistance to tyrosine kinase inhibitors.
Molecular assessement in GIST
assumes a central role in clinical
The identiﬁcation of the two speciﬁc
fusion products of CHOP/DDIT3 gene
with FUS and more rarely with
EWSR1 is extremely helpful in
distinguishing challenging examples
of myxoid liposarcoma from other
myxoid sarcomas and therefore to
apply the adequate therapeutic
Another examples is use of crizotinib in
inﬂammatory myoﬁbroblastic tumors wherein
assessment of the ALK gene may represent an
important diagnostic conﬁrmatory ﬁnding as
well as a key biomarker of prediction.
Molecular Genetics represents the
most valuable tool to identify and
validate new therapeutic targets.
Good examples are represented
by MDM2, ampliﬁed in
and potentially targetable by
Nutlin-A3, the mTOR pathway in
malignant PEComa and
FB in DFSP, and KDR in
Molecular pathology/genetics does not
represent an alternative but a complement
to surgical diagnostic pathology.
Considering the degree of molecular
promiscuity of EWSR1 gene aberrations, the
results of FISH analysis need to be
mandatorily evaluated in context with
morphology as EWSR1 aberrations are
described in a variety of unrelated entities.
ETV6–NTRK3/t(12;15) Infantile ﬁbrosarcoma
Acute myeloid leukemia
Secretory breast carcinoma
ALK gene fusions Inﬂammatory
Anaplastic large cell
Subsets of lung
FUS–ERG/t(16;21) Ewing sarcoma
Acute myeloid leukemia
ASPL–TFE3/t(X;17) Alveolar soft part sarcoma
Subset of pediatric renal
EWS–ATF1/t(12;22) and EWS-
Clear cell sarcoma
Genetics has certainly played a key role in
allowing a better understanding of many
The uniﬁcation of myxoid and round cell
liposarcoma within a single tumor entity
represents one of the best examples.
Genetics has greatly helped in recognizing the
close relationships between several tumors
such as giant cell ﬁbroblastoma and DFSP,
LGFMS and epithelioid sclerosing
ﬁbrosarcoma, and hemosiderotic
ﬁbrolipomatous tumor and myxoinﬂammatory
The deﬁnition of new entities has been
strongly supported by genetics.
The identiﬁcation of t(7;19)(q22;q13)
translocation in pseudomyogenic (epithelioid
The future classiﬁcations will include more
Genetic aberrations will also contribute to the
deﬁnition of the speciﬁc tumor entities.
The marriage between
Pathology and Genetics
not only proved to be
fruitful but also to be