1
IMMUNE CHECKPOINT
INHIBITOR BIOMARKERS
• Programmed cell death ligand 1 (PDL1)
immunohistochemistry (IHC) uses various
scoring systems and cutoffs for particular
antibody clones to quantify PDL1 expression as
a predictive biomarker for specic FDA
approved ICI. For example:
- The PDL1 pharmDX 22C3 immunostain is
a companion diagnostic for non small cell
lung carcinoma (NSCLC) patients eligible for
pembrolizumab immunotherapy.
- The tumor proportion score (TPS) is calcu-
lated by dividing the total number of PDL1
positive tumor cells by the total number of
tumor cells (
≥
1% positive cutoff).
- The combined positive score (CPS) is based
on dividing the number of PDL1 positive
cells (tumor cells, lymphocytes, macrophages)
by the number of tumor cells to predict
pembrolizumab efcacy in metastatic gastric
and gastroesophageal junctional carcinoma,
Issue 17 || February 2022
WHAT’S NEW IN
MOLECULAR GENETIC
PATHOLOGY 2022:
IMMUNE CHECKPOINT
INHIBITOR BIOMARKERS
AND SELECT SOLID
TUMORS
Patricia C. Tsang, MD
1
and Guoli Chen, MD
2
1
MedStar Washington Hospital Center, Pathology &
Laboratory Medicine, Washington, DC, USA
2
Geisinger Medical Laboratories, Geisinger Health,
Danville, Pennsylvania, USA
Corresponding Author: Patricia C. Tsang, MD
MedStar Washington Hospital Center, Pathology &
Laboratory Medicine, Washington, DC, USA
E-mail: patctsang@hotmail.com
ORCID
Patricia C. Tsang
https://orcid.org/0000-0003-0523-9793
Guoli Chen
https://orcid.org/0000-0002-4426-6156
Abstract
Predictive biomarker testing plays a critical role
in targeted immuno-oncology, including the use
of immune checkpoint inhibitors (ICI) for various
solid tumors. Molecular advancements in cancers
of the breast, kidney and brain have continued to
propel tumor classication and precision therapy.
GENE FUSION NOMENCLATURE
The HUGO Gene Nomenclature Committee has
released a new recommendation to denote gene
fusion with a double colon, e.g., BCR::ABL
(Leukemia 2021;35:3040).
bladder cancer and cervical cancer (Fig. 1). It
has the same cutoff of
≥
1%, using the 22C3
antibody clone.
- The PDL1 SP142 clone is an FDA approved
complementary diagnostic to predict response
of metastatic NSCLC to atezolizumab. The
evaluation is based on either the proportion
of tumor area occupied by PDL1 expressing
tumor inltrating immune cells of any
intensity or the percentage of PDL1 express-
ing tumor cells of any intensity.
• Decient mismatch repair (dMMR) / high mic-
rosatellite instability (MSI-H) is predictive of
ICI efcacy in colorectal cancers and other solid
tumors. While it is commonly tested by IHC,
assays based on PCR or next generation
sequencing (NGS) are available.
• High tumor mutational burden (TMB) may
also serve as a predictor of immunotherapy
response. TMB reects the number of somatic
mutations per megabase of tumor genomic
sequence. It can be determined by whole exome
sequencing (WES) or targeted sequencing of
gene panels (usually
≥
200 genes). Cutoff values
have not yet been unied and may vary in
respect to different assay platforms and ICI
drug targets. Recently, Foundation Medicine’s
FoundationOne
®
CDx, which includes MSI
and TMB assessment, was approved as a
companion diagnostic for pembrolizumab with
a cutoff of
≥
10 mutations per megabase,
regardless of solid tumor type.
BREAST CARCINOMA
• NGS can simultaneously detect alterations of
multiple genes involved in breast cancers.
Clinically actionable genomic changes include
ERBB2 (HER2) amplication (prevalence
~15%), BRCA1/BRCA2 mutations (5%–
10%), PIK3CA mutations (30%–40%) and
ETV6::NTRK3 fusion in secretory breast
carcinoma (< 0.2% of breast cancers).
- BRCA1 and BRCA2 inactivating mutations
carry a lifetime cumulative risk of 60% and
55% to develop breast cancer, respectively.
PathologyOutlines.com
WHAT’S NEW
IN PATHOLOGY?
Sponsored by an unrestricted grant from Geisinger Medical Laboratories: Dedicated to Laboratory Excellence
Fig. 1. Esophagogastric adenocarcinoma. (A) H&E
stain, 40 x. (B) PD-L1 22C3 immunostain demonstrat-
ing a combined positive score of close to 20% (posi-
tive: > 1%), indicating response to pembrolizumab.
A
B
2
Poly-ADP-ribose polymerase (PARP)
inhibitors are FDA approved targeted therapy
for BRCA1/BRCA2 associated breast cancer.
- API3K (phosphoinositide 3-kinase) inhibitor,
alpelisib, is FDA approved for advanced
breast cancers that are PIK3CA altered,
HER2 (-) and hormone receptor (+).
- Seen in ~30% of breast cancers, TP53
mutation is associated with an increased
likelihood of pathologic complete remission
following chemotherapy, while wild type
TP53 appears to induce cell cycle arrest
instead of cell death, resulting in residual
disease following chemotherapy (Trends
Cancer 2020;6:98).
• Multigenomic prognostic proling is being
used to predict the risk of breast cancer
recurrence. Commercial platforms include:
- Oncotype DX
®
(Genomic Health Inc.): 21
gene reverse transcription PCR assay for
predicting the likelihood of recurrence and
chemotherapy benet in hormone receptor
(+) patients on endocrine therapy.
- MammaPrint (Agendia, Inc.): 70 gene
expression prole by microarray for predict-
ing the risk of distant metastasis. Patients
with high clinical risk but low genomic risk
based on MammaPrint might not require
chemotherapy.
- EndoPredict
®
(Myriad Genetics): 11 gene
RNA expression prole for predicting the
risk of recurrence in hormone receptor (+) /
HER2 (-) patients who are node (+) or (-) on
endocrine therapy.
- Prosigna
®
(Veracyte): 50 gene reverse
transcription PCR assay for assessing the risk
of recurrence in 10 years for hormone
receptor (+) early stage breast cancer and
identifying the subset of patients who may
not benet from chemotherapy.
RENAL CELL CARCINOMA (RCC)
• In addition to recurrent VHL alterations and
3p deletion, clear cell RCC frequently carries
other genetic alterations. BAP1 or SETD2
mutated RCCs behave aggressively, while
PBRM1 mutations predict a poor prognosis in
localized RCC but a favorable outcome in
advanced disease.
• Chromosome 7 or 17 polysomy and trisomy are
the most common chromosomal changes in
type 1 papillary RCC. Type 2 tumors are
heterogeneous and may harbor CDKN2A
silencing, SETD2 mutations and other altera-
tions.
• Some hybrid oncocytic chromophobe tumors
(HOCT) are associated with Birt-Hogg-Dubé
syndrome (BHD) or renal oncocytosis, while
others are sporadic. BHD can be conrmed by
germline mutations in the FLCN tumor
suppressor gene.
• Renal cell neoplasms with TFE3, TFEB and
MITF rearrangements are now grouped
together as MiT family translocation RCC.
• Loss of SMARCB1 expression by IHC supports
a diagnosis of medullary carcinoma.
• Negative or abnormal IHC staining for
fumarate hydratase (FH), positive IHC staining
for 2-succino-cysteine (2SC) or FH gene
mutation supports FH decient RCC / heredi-
tary leiomyomatosis and RCC (HLRCC).
Succinate dehydrogenase (SDH) decient RCCs
are associated with germline mutations of the
SDH subunits (usually SDHB), as demonstrable
by negative SDHB IHC staining. Genetic
counseling is recommended for FH-decient or
SDH decient RCC.
• Molecular proling has helped to dene new
and emerging RCC variants, e.g., eosinophilic
solid and cystic RCC associated with tuberous
sclerosis (TSC1 or TSC2 gene alterations), RCC
with TSC/MTOR mutations, TCEB1 mutated
RCC, RCC with TFEB/6p21/VEGFA ampli-
cation and ALK rearranged RCC (Genes (Basel)
2021;12:1585).
BRAIN TUMORS
• Primary glioblastoma (GBM) may harbor 10q
loss of heterozygosity (LOH) (70%), EGFR
amplication (36%), CDKN2A deletion (31%)
and PTEN mutations (25%), all of which
denote aggressive disease.
• MGMT promoter hypermethylation (30%–
40% of primary GBM) predicts improved
response to alkylating agents and a lower risk of
tumor recurrence.
• Associated with improved survival, IDH1 or
IDH2 mutations are common in grades II and
III astrocytoma, oligodendroglioma and
secondary GBM, and uncommon in primary
GBM. When present, they help to distinguish
low-grade astrocytoma (~70%) from gliosis.
• Co-deletion of 1p / 19q (detectable by FISH /
PCR / microarray) is characteristic of oligoden-
droglioma (Fig. 2), predicting response to
conventional therapy. Equivocal FISH can be
subsequently assessed by LOH analysis via
PCR. ATRX loss of function mutations, which
correlate well with negative IHC, favor diffuse
astrocytoma over oligodendroglioma.
• Diffuse midline glioma is characterized by a
K27M substitution in the histone H3 genes,
H3F3A or HIST1H3B/HIST1H3C, resulting
in hypomethylation and H3 protein inactiva-
tion. These tumors may also harbor mutations
in TP53 (42%) or ACVR1 (24%) (EBioMedi-
cine 2021;69:103453).
• BRAF fusion, most commonly with
KIAA1549, is observed in 59%–90% of
pilocytic astrocytomas.
Dr. Tsang joined the Pathology Outlines
editorial board in 2019 and has been serving
as Deputy Editor in Chief for Clinical
Pathology for PathologyOutlines since 2020.
She works as Chair of Pathology & Laboratory
Medical Director at MedStar Washington
Hospital Center in Washington, D.C. She has
been practicing molecular pathology for more
than a decade.
Dr. Chen is currently an Associate and
Attending Pathologist at Geisinger Medical
Center, where he participates in the clinical,
academic and teaching services in surgical
pathology and molecular diagnostics. He has
been actively publishing and lecturing on
topics related to molecular pathology of solid
tumors.
Meet the Authors
Fig. 2. (A) Oligodendroglioma showing perinuclear
clearing and delicate capillary network (H&E stain, 20
x). Co-deletion of 1p (B) and 19q (C) by dual color
FISH. Target (orange) to control (green) signal ratio of
≤
0.8 indicates loss of the target allele.
A
B
C
