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aao4277.
CHAPTER ELEVEN
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Proteomic biomarker technology
for cancer immunotherapy
Reilly Fankhausera, Nicholas DePatiea, Rachel Berrymana, Olivia M. Lucero
and Rajan P. Kulkarni
a
Department of Dermatology, Oregon Health & Science University (OHSU), Portland, OR, United States
b
Oregon Health & Science University, Knight Cancer Institute, Portland, OR, United States
c
Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute (KCI), Portland, OR, United States
d
Operative Care Division, Department of Veterans Affairs Portland Health Care System, Portland, OR, United States
a,b,c,d
a,b
,
Contents
1. Introduction and background 358
2. Proteomic technologies 362
2.1 Immunohistochemical and immunofluorescence approaches 362
2.2 Multiplexed immunohistochemistry (mIHC) 363
2.3 Quantitative multiplexed fluorescence immunohistochemistry 365
2.4 Cyclic immunofluorescence 366
2.5 Nanostring digital spatial profiler (DSP) 366
2.6 Mass cytometry imaging 370
2.7 Multiplexed immunoimaging with nanostars 372
2.8 Affinity technologies: Antibody and aptamer-based 372
2.9 Mass spectrometry 378
2.10 Flow cytometry 380
2.11 Mass cytometry; cytometry by time of flight (CyTOF) 381
2.12 Western blotting and ELISA 382
3. Proteomic analysis of immune-related adverse events 383
3.1 SERPA & SEREX for antigen/autoantibody detection 384
4. Discussion and future directions 386
References 388
Abbreviations
CAR-T chimeric antigen receptor T cell
CODEX codetection by indexing
CTA cancer testis antigens
CyCIF cyclic immunofluorescence
CyTOF cytometry by time of flight
DAB diaminobenzidine
DSP digital spatial profiler
ELISA enzyme-linked immunosorbent assay
Engineering Technologies and Clinical Translation Copyright © 2022 Elsevier Inc.
All rights reserved.https://doi.org/10.1016/B978-0-323-90949-5.00007-3
357
358 Reilly Fankhauser et al.
ESI electrospray ionization
FCM flow cytometry
FFPE formalin-fixed paraffin-embedded
FISH fluorescence in situ hybridization
GVAX cancer vaccine composed of cells designed to express granulocyte-macrophage
colony-stimulating factor (GM-CSF)
H&E hematoxylin and eosin
HNSCC head and neck squamous cell carcinoma
HPV human papillomavirus
HRP horseradish peroxidase
ICB immune checkpoint blockade
IF immunofluorescence
IHC immunohistochemistry
IMC imaging mass cytometry
irAE immune related adverse event
MALDI matrix-assisted laser desorption/ionization
MC mass cytometry
MIBI multiplexed ion beam imaging
mIHC multiplexed immunohistochemistry
MMR mismatch repair
MS mass spectrometry
MSI microsatellite instability
MS-I mass spectrometry-imaging
NGS next generation sequencing
NKT natural killer T cell
OS overall survival
PAGE polyacrylamide gel electrophoresis
PDAC pancreatic ductal adenocarcinoma
PEA proximity extension assay
PLA proximity ligation assay
PSA prostate specific antigen
SEREX serological analysis of antigens by recombinant expression cloning
SERPA serum proteome analysis
SERS surface enhanced Raman spectroscopy
SNP single-nucleotide polymorphism
SOMAmer slow off-rate modified aptamer
t-CyCIF tissue cyclic immunofluorescence
TGCT testicular germ cell tumors
TIL tumor-infiltrating lymphocyte
1. Introduction and background
Immunotherapies, which invigorate the patient’s immune system to attack tumor
cells, have emerged as a central treatment modality in cancer therapy. A wide variety of
methods are used to stimulate the immune system, including monoclonal antibodies,
adoptive cell transfer, immune checkpoint inhibitors, cancer vaccines, cytokines, and
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immunomodulators [1]. Immunotherapies commonly target surface molecules called
immune checkpoints, which mainly act to prevent an overactive autoimmune response,
but are also co-opted by tumors to evade destruction by the immune system. Antibodies
that target immune-inhibitory axes to stimulate the immune system, immune checkpoint
blockade (ICB), have become the most popular immunotherapies in clinical practice, as
seen by the expansion of indications for the use of FDA-approved immune checkpoint
inhibitors since the approval of anti-CTLA-4 antibodies (Ipilimumab) in 2011 and antiPD-1 antibodies (pembrolizumab and nivolumab) in 2014 [2]. The estimated percentage
of patients in the U.S. with cancer who are eligible for ICB rose from 1.54% of cancer
patients in 2011 to 46.63% in 2018 [3]. The success of PD-1/PD-L1 and CTLA-4 ICB
has spurred a keen interest in targeting alternative co-stimulatory and co-inhibitory axes,
including 4-1BB (CD137), ICOS (CD278), OX40 (CD134), VISTA (B7-H5), TIM-3,
and LAG-3 (CD223) [4, 5]. Response to anti-PD-1/PD-L1, anti-CTLA-4, or a combination thereof is still limited to a subset of patients. Response rates vary widely, ranging
from pancreatic cancer that does not respond to single-agent anti-CTLA-4 or anti-PD-1
[6, 7] to an overall response rate of 58% when anti-PD-1 and anti-CTLA-4 are combined
to treat metastatic melanoma [8]. However, this combinatorial approach comes at the
cost of increased toxicity [8]. Among patients treated with the same cancer type, response
rates are highly variable [9].
While “releasing the brakes” on these immune-inhibitory molecules may help induce
an antitumor response, this immune stimulation is not restricted to the tumor bed. As
such, administering these therapeutics can skew a patient toward an autoimmune reaction elsewhere in the body, as observed with the high rate of immune-related adverse
events (irAEs) associated with immunotherapy. These off-target effects include pneumonitis, colitis, hypophysitis, myocarditis, and dermatitis. The incidence and severity of
irAEs are highly variable and are dependent upon treatment modality, cancer type,
and disease setting [10]. Some reports indicate ipilimumab (anti-CTLA-4) use across
multiple cancer types can cause an irAE of any grade in up to 72% of patients [11].
Up to 66% of patients treated with anti-PD-1 ICB will experience any grade of irAE
[12]. irAEs of any grade are more common among patients placed on combination
anti-PD-1/anti-CTLA-4 to treat advanced melanoma and have been reported at
between 91% and 96% [13, 14]. In one study, the severity of irAEs associated with combination ipilimumab plus nivolumab was such that 72% of the patients required steroids,
and 36% of patients were hospitalized for an irAE, sometimes occurring months after
therapy discontinuation [13]. In rare cases, these irAEs can be fatal [15]. The current standard of care for treating these irAEs is to withhold the potentially life-saving treatment
and administer prednisone to control the autoimmune reaction. Data on the effects of
corticosteroid administration in human tumors is mixed [16] and is likely dependent
on cancer type, treatment modality, and even tumor location. Studies in mice have
359Proteomic biomarker technology for cancer immunotherapy
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