Proteins involved in cell

communication as target in
cancer treatment.
Introduction
• Proteins are often called the workhorses of cells, the machinery that
makes cells go.
• They act as key players in the many chemical reactions constantly
occurring in cells
• Collect cellular garbage
• Provide structure
• Repair damaged DNA
• ETC
 Cancer signaling networks
• Cancer is driven by genetic and epigenetic alterations that allow cells to overproliferate
and escape mechanisms that normally control their survival and migration.
• Many of these alterations map to signaling pathways that control cell growth and
division, cell death, cell fate, and cell motility, and can be placed in the context of
distortions of wider signaling networks that fuel cancer progression, such as changes in
the tumor microenvironment, angiogenesis, and inflammation.
• Mutations that convert cellular proto-oncogenes to oncogenes can cause
hyperactivation of these signaling pathways, whereas inactivation of tumor suppressors
eliminates critical negative regulators of signaling.
• An examination of the PI3K-Akt and Ras-ERK pathways illustrates how such alterations
dysregulate signaling in cancer and produce many of the characteristic features of
tumor cell
Cold Spring Harb Perspect Med. 2015 Apr; 5(4): a006098.
 Cancer signaling
networks
• The figure illustrates the wide variety of
intra- and intercellular signals affected in
cancer, focusing on Ras-ERK and PI3K-Akt
signaling.
• It is by no means comprehensive; many
more pathways are involved and there
are other stromal cells involved in
paracrine signaling.
• Oncoproteins are indicated with yellow
highlighting; tumor suppressors are
indicated with dashed outlines.
• Arrows do not necessarily indicate direct
interactions in this figure.

Cold Spring Harb Perspect Med. 2015 Apr; 5(4): a006098.

 An "interactome"
of protein–protein
interactions detected
in two head and
neck cancer cell
lines and one
normal cell line.
To created a map of how the
interacting proteins—also
called protein complexes—
function in key
communication networks, or
pathways, in those cells.

Credit: From Science. October 1, 2021. doi: 10.1126/science.abf2911.

 Cell cycle proteins as promising targets in
cancer therapy
• Cancer is characterized by uncontrolled proliferation resulting from
aberrant activity of various cell cycle proteins; therefore, cell cycle
regulators are considered attractive targets in cancer therapy.
• Cyclin-dependent kinases with transcriptional functions, as well as
PARP inhibitors, which are highly successful in targeting
BRCA1/BRCA2-mutant tumours

Tobias Otto et al. Nat Rev Cancer. 2017 January 27; 17(2): 93–115. doi:10.1038/nrc.2016.138.
 Cell cycle progression and major regulatory proteins
• Mitogenic signals activate complexes of
cyclins and cyclin-dependent kinases
(CDKs) that promote progression from the
G1 phase into S phase mainly by
phosphorylating the retinoblastoma
protein (RB) and subsequent activation of
transcription by the E2F family of
transcription factors.
• Growth-inhibitory signals antagonize G1-S
progression by upregulating CDK inhibitors
of the INK4 and CIP/KIP families.
• Progression through S phase and from G2
phase into mitosis (M phase) is also
controlled by cyclin-CDK complexes,
together with a variety of other proteins,
such as Polo-like kinase 1 (PLK1) and
Aurora kinases (Aurora A/B).
• Cells can also exit the cell cycle and enter a
reversible or permanent cell cycle arrest
(G0 phase).
• DNA damage is sensed by several
specialized proteins and triggers cell cycle
arrest via checkpoint kinase 2 (CHK2) and
Red and blue ovals denote positive and negative regulators of cell cycle progression, respectively. p53 in G1 phase or via checkpoint kinase 1
(CHK1) in S or G2 phase.
Tobias Otto et al. Nat Rev Cancer. 2017 January 27; 17(2): 93–115. doi:10.1038/nrc.2016.138.
 Regulation of G1-S cell cycle transitions is controlled by multiple proteins &
pathways
Red and blue ovals
denote positive
and negative
regulators of cell
cycle transitions,
respectively.

Tobias Otto et al. Nat Rev Cancer. 2017 January 27; 17(2): 93–115. doi:10.1038/nrc.2016.138.
Regulation of G1-S cell cycle transitions is controlled by multiple proteins &
pathways
• Entry into the cell cycle is typically induced in response to mitogenic signals that activate signalling pathways such as
the RAS pathway.
• These pathways eventually impinge on transcriptions factors such as MYC, AP-1 or β-catenin and lead to induction of
a number of cell cycle proteins including D-type cyclins.
• Formation of active complexes of D-type cyclins and cyclin-dependent kinases (CDKs) 4 and 6 drives phosphorylation
of the RB (retinoblastoma) protein and is antagonized by the INK4 family (p16INK4A and p15INK4B) in response to
senescence-inducing or growth-inhibitory signals, such as the transforming growth factor β (TGFβ).
• Upon RB phosphorylation, E2F transcription factors are able to activate transcription of a plethora of S phase-
promoting genes, including cyclins E1 and E2.
• Cyclin E-CDK2 complexes are kept inactive by interaction with inhibitors p27KIP1 and p21CIP1 that are regulated by
growth-inhibitory signals and the p53-dependent G1 DNA damage checkpoint.
• Activation of cyclin E-CDK2 involves several mechanisms including the sequestration of p27KIP1 and p21CIP1 by cyclin
D-CDK4/6 complexes, and phosphorylation of p27KIP1 by cyclin E-CDK2 kinase. Active cyclin E-CDK2 complexes
further phosphorylate RB, as well as many other targets culminating in S phase entry.

Tobias Otto et al. Nat Rev Cancer. 2017 January 27; 17(2): 93–115. doi:10.1038/nrc.2016.138.
 Regulation of G2-M cell cycle transitions is controlled by multiple proteins &
pathways
Red and blue ovals denote positive and negative regulators of
cell cycle transitions, respectively.

Tobias Otto et al. Nat Rev Cancer. 2017 January 27; 17(2): 93–115. doi:10.1038/nrc.2016.138.
Regulation of G2-M cell cycle transitions is controlled by multiple proteins &
pathways
• During G2 phase, the MuvB complex associates with the transcription factor FOXM1 and
binds promoters containing cell cycle genes homology region (CHR) elements, thereby
inducing transcription of genes required for entry into and progression through mitosis (M
phase), including B-type cyclins.
• Activation of cyclin B-CDK1 kinase requires phosphorylation of CDK1 at Thr-161 by the
cyclin H-CDK7 complex (CAK, CDK activating kinase) as well as dephosphorylation of Thr-
14 and Tyr-15 on CDK1 by cell division cycle 25 (CDC25) family phosphatases, the latter
process being antagonized by protein kinases MYT1 and WEE1.
• Activation of CDK1 is prevented in response to activation of the CHK1-dependent G2 DNA
damage checkpoint. Upon recovery from DNA damage, Polo-like kinase 1 (PLK1) is
essential to re-activate CDK1.
• Activation of cyclin A/B-CDK1 complexes is required and sufficient for entry into mitosis.
Tobias Otto et al. Nat Rev Cancer. 2017 January 27; 17(2): 93–115. doi:10.1038/nrc.2016.138.
Deregulation of cell cycle proteins in human cancers
• The frequencies of genetic
alterations within genes
encoding major cell cycle
regulators across 25 types of
human cancers.
• Each cancer type is denoted by a
symbol with unique shape and
colour below the graph (for
symbol legend, see FIG. 3d).
• For each cancer type, the TCGA
data set with the highest
number of tumours was
selected.
• The figures summarize genetic
alterations from 48 (for
lymphoma) to 1105 (for breast
cancer) individual tumours
• Genetic alterations include amplifications (red bars), deletions (blue bars), point mutations (green bars) and multiple (median of 479 individual
alterations (grey bars).
Tobias Otto et al. Nat Rev Cancer. 2017 January 27; 17(2): 93–115. doi:10.1038/nrc.2016.138.
tumours per cancer type).
 Cell cycle proteins & cancer therapy: summary
• Many cell cycle proteins are overexpressed or overactive in human cancers, in particular
D-type and E-type cyclins, cyclin-dependent kinases (CDK4, CDK6 and CDK2), Polo-like
kinase 1 (PLK1) and Aurora kinases (Aurora A and B).
• In transgenic mice, overexpression of several of these cell cycle proteins induces or
contributes to tumorigenesis, revealing their prominent oncogenic roles.
• Some of these cell cycle proteins are also required for tumorigenesis and their ablation in
mice impairs tumour formation induced by specific genetic lesions or by carcinogen
treatment, as demonstrated for several cyclins (D1, D2, D3 and A2) and CDKs (CDK4,
CDK6, CDK2 and CDK1), as well as for checkpoint kinase 1 (CHK1).
• Importantly, in some cases the continued presence of a cell cycle protein has been shown
to be also required for tumour maintenance and progression, e.g. for cyclin D1, D3 and
CDK4, thereby providing a clear rationale for targeting these proteins in cancer treatment.

Tobias Otto et al. Nat Rev Cancer. 2017 January 27; 17(2): 93–115. doi:10.1038/nrc.2016.138.
 Cell cycle proteins & cancer therapy: summary
• Kinases involved in cell cycle checkpoint function such as CHK1 and WEE1 also
constitute potential therapeutic targets.
• Their inhibition compromises checkpoint function, causes excessive DNA damage
and eventually leads to apoptosis, particularly in cells with compromised p53
function.
• CDK4/6-selective inhibitors, such as palbociclib, ribociclib and abemaciclib, have
shown significant benefits in clinical studies, particularly in breast cancer, but also in
non-small cell lung cancer, melanoma and head and neck squamous cell carcinoma.
• Importantly, following demonstration of a substantial improvement in progression-
free survival, combination of palbociclib and letrozole received accelerated approval
for first-line treatment of patients with advanced ER+ HER2- breast cancer.

Tobias Otto et al. Nat Rev Cancer. 2017 January 27; 17(2): 93–115. doi:10.1038/nrc.2016.138.
 Cell cycle proteins & cancer therapy: summary
• Inhibitors of PLK1, such as rigosertib and volasertib, have also shown
encouraging results in clinical phase II/III studies for patients with
myelodysplastic syndromes and acute myelogenous leukaemia, respectively,
and several phase III trials are currently ongoing.
• Compounds targeting Aurora A, particularly alisertib, have been extensively
studied in preclinical models and demonstrated synergy with many other
targeted therapies, leading to tumour regression in a variety of cancer
models.
• Moreover, clinical studies revealed encouraging activity of alisertib in
peripheral T-cell lymphoma, non-Hodgkin lymphoma, non-small cell lung
cancer and breast cancer
Tobias Otto et al. Nat Rev Cancer. 2017 January 27; 17(2): 93–115. doi:10.1038/nrc.2016.138.
 Targeting cancer stem cell pathways for cancer therapy
• Since cancer stem cells (CSCs) were first identified in leukemia in 1994, they have been
considered promising therapeutic targets for cancer therapy.
• These cells have self-renewal capacity and differentiation potential and contribute to
multiple tumor malignancies, such as recurrence, metastasis, heterogeneity, multidrug
resistance, and radiation resistance.
• The biological activities of CSCs are regulated by several pluripotent transcription
factors, such as OCT4, Sox2, Nanog, KLF4, and MYC.
• Molecules, vaccines, antibodies, and CAR-T (chimeric antigen receptor T cell) cells have
been developed to specifically target CSCs, and some of these factors are already
undergoing clinical trials.

Yang, L., Shi, P., Zhao, G. et al. Targeting cancer stem cell pathways for cancer therapy. Sig Transduct Target Ther 5, 8 (2020).
https://doi.org/10.1038/s41392-020-0110-5
 Targeting cancer stem cell pathways for cancer therapy
Important regulators of cancer stem cells
1. Intracellular signaling pathways, such as Wnt, NF-κB (nuclear factor-κB),
Notch, Hedgehog, JAK-STAT (Janus kinase/signal transducers and
activators of transcription), PI3K/AKT/mTOR (phosphoinositide
3-kinase/AKT/mammalian target of rapamycin), TGF (transforming growth
factor)/SMAD, and PPAR (peroxisome proliferator-activated receptor),
2. Extracellular factors, such as vascular niches, hypoxia, tumor-associated
macrophages, cancer-associated fibroblasts, cancer-associated
mesenchymal stem cells, extracellular matrix, and exosomes.

Yang, L., Shi, P., Zhao, G. et al. Targeting cancer stem cell pathways for cancer therapy. Sig Transduct Target Ther 5, 8 (2020).
https://doi.org/10.1038/s41392-020-0110-5
 Eg: Biomarkers Of Cancer Stem Cells In Breast
Cancers
Cancers Markers Function

• ALDH: An enzyme that plays a role in cell resistance

CD29 , +
• CD44: A glycoprotein involves in cell migration and self-renewal
CD49f+ • CD90: A glycoprotein participates in T cell adhesion and signal
transduction
CD90+,
Breast • CD133: A transmembrane glycoprotein that maintains lipid
CD133 +
composition in cell membranes
ALDH+, • CD24: A marker that promotes blood flow in the tumor during
metastasis
ESA+/CD44+/CD24,
• CD49f: A membrane proteins of the integrin family that plays an
CD44 /CD24 + −
important role in cell surface adhesion and signaling

Yang, L., Shi, P., Zhao, G. et al. Targeting cancer stem cell pathways for cancer therapy. Sig Transduct Target Ther 5, 8 (2020).
https://doi.org/10.1038/s41392-020-0110-5
 Eg: Biomarkers Of Cancer Stem Cells In AML
Cancers Markers Function

CD34: It plays a role in the attachment of stem cells to bone marrow extracellular or
CD34+, stromal cells
CD38−, CD38: An intracellular Ca2+ mobilization messenger, prognostic markers for patients
CD90+, with chronic lymphocytic leukemia
CD71+, CD71: A transferrin receptor is important for nerve development
CD19+, CD19: A class of signal transduction molecules regulate B lymphocyte differentiation
AML
CD20+, CD20: The protein plays a role in the development and differentiation of B cells into
CD44+, plasma cells
CD10+, CD10: It inhibits a variety of peptide hormones, include glucagon, encephalin,
CD45RA+, oxytocin, and bradykinin
CD123+ CD45RA: A class of leukocyte activation regulators
CD123: An interleukin-specific subunit of a heterodimeric cytokine receptor

Yang, L., Shi, P., Zhao, G. et al. Targeting cancer stem cell pathways for cancer therapy. Sig Transduct Target Ther 5, 8 (2020).
https://doi.org/10.1038/s41392-020-0110-5
 Wnt/β-catenin pathway in cancer stem cells
• The canonical Wnt/β-catenin pathway regulates the
pluripotency of CSCs and determines the differentiation
fate of CSCs.
• In the absence of Wnt signaling, β-catenin is bound to the
Axin complex, which contains APC and GSK3β, and is
phosphorylated, leading to ubiquitination and proteasomal
degradation through the β-Trcp pathway.
• However, the complex (TAZ/YAP), the long noncoding
RNA TIC1 and proteins (TRAP1 and TIAM1) regulate the
β-Trcp pathway.
• In the presence of Wnt signaling, the binding of LRP5/6
and Fzd inhibits the activity of the Axin complex and the
phosphorylation of β-catenin, which makes β-catenin enter
the nucleus, and then bind to TEF/TCF to form a complex,
which then recruits cofactors to initiate downstream gene
expression.
• Some proteins (DKK2 (Dickkopf-related protein 2),
DACT1, CDH11, GECG, PKM2, EZH2, CD44v6, MYC,
and TERT), microRNAs (miR-1246, miR-9, miR-92a,
miR-544a, and miR-483-5p), and long noncoding RNAs
(lncR-β-catm and lncR-TCF7) regulate the activation of
the Wnt/β-catenin pathway in CSCs

Yang, L., Shi, P., Zhao, G. et al. Targeting cancer stem cell pathways for cancer therapy. Sig Transduct Target Ther 5, 8 (2020).
https://doi.org/10.1038/s41392-020-0110-5
 Hedgehog signaling pathway in cancer stem cells
• The Hedgehog pathway plays a key role in stem
maintenance, self-renewal, and regeneration of CSCs.
• The secreted Hh protein acts in a concentration- and time-
dependent manner to initiate a series of cell responses,
such as cell survival, proliferation, and differentiation.
• After receiving the Shh signal, the transmembrane protein
receptor PTCH relieves the inhibition of the
transmembrane protein SMO, which induces Gli1/2 to
detach from SUFU and enter the nucleus to regulate
downstream gene transcription.
• During activation of the Hh pathway, some proteins (IL-6,
IL-27, Fbxl17 (F-box and leucine-rich repeat protein 17),
PPKCI, RARα2, RUXN3, SCUBE2, HDAC6 (histone
deacetylase 6), USP48, CK2α, WIP1, GALNT1, VASH2
(Vasohibin 2), BCL6, FOXC1 (forkhead box C1), and
p65), microRNAs (miR-324-5p, miR-122, and miR-326),
and the long noncoding RNA HDAC2 are involved in the
Hedgehog pathway to affect CSC growth

Yang, L., Shi, P., Zhao, G. et al. Targeting cancer stem cell pathways for cancer therapy. Sig Transduct Target Ther 5, 8 (2020).
https://doi.org/10.1038/s41392-020-0110-5
 NF-κB signaling pathway in cancer stem cells
• NF-κB proteins are involved in the dimerization of
transcription factors, regulate gene expression, and
affect various CSC biological processes, including
inflammation, stress responses, growth, and
development of CSCs.
• The main physiological function of NF-κB is the
p50-p65 dimer.
• The active p50-p65 dimer is further activated by
post-translational modification (phosphorylation,
acetylation, or glycosylation) and transported into
the nucleus, which induces the expression of target
genes in combination with other transcription
factors.
• Some proteins (CD44, CD146, TNFRSF19, Bmi-1,
FOXP3, and SDF-1) and microRNAs (miR-221 and
miR-222) directly regulate the NF-κB pathway.
• Some proteins (PGE2, GIT-1 (G protein-coupled
receptor kinase-interacting protein 1), C-C
chemokine receptor 7 (CCR7), and TGF-β) and
miR-491 indirectly affect the NF-κB pathway via the
ERK and MAPK pathways in CSCs

Yang, L., Shi, P., Zhao, G. et al. Targeting cancer stem cell pathways for cancer therapy. Sig Transduct Target Ther 5, 8 (2020).
https://doi.org/10.1038/s41392-020-0110-5
 The microenvironment of cancer stem cells
• Proliferation, self-renewal, differentiation, metastasis, and tumorigenesis of CSCs in the CSC microenvironment.
• The CSC microenvironment is mainly composed of vascular niches, hypoxia, tumor-associated macrophages, cancer-
associated fibroblasts, cancer-associated mesenchymal stem cells, and extracellular matrix.
• These cells in response to hypoxic stress and matrix induce growth factors and cytokines (such as IL-6 and VEGF) to
regulate the growth of CSCs via Wnt, Notch, and other signaling pathways

Yang, L., Shi, P., Zhao, G. et al. Targeting cancer stem cell pathways for cancer therapy. Sig Transduct Target Ther 5, 8 (2020).
https://doi.org/10.1038/s41392-020-0110-5
Drug name Target Condition Phase Sample size NCT number Current status
Hedgehog inhibitors
Recurrent or refractory 31 NCT00939484 Completed, has results
medulloblastoma
Basal cell carcinoma 28 NCT01700049 Completed, has results
Sarcoma 78 NCT01700049 Completed, has results
Recurrent small-cell lung
  Vismodegib (GDC-0449) carcinoma II 168 NCT01700049 Completed, has results
Metastatic pancreatic
98 NCT01088815 Completed, has results
cancer
Ovarian cancer 104 NCT00739661 Completed, has results
Metastatic colorectal
199 NCT00636610 Completed, has results
cancer
Basal cell carcinoma 10 NCT01350115 Completed, has results
Relapsed
medulloblastoma 20 NCT01708174 Completed, has results
Acute myeloid leukemia 70 NCT01826214 Completed, has results
Pancreatic
20 NCT01431794 Completed, has results
adenocarcinoma
  Sonidegib (LDE225) II
Advanced or metastatic
9 NCT02151864 Completed
hepatocellular carcinoma
Recurrent plasma cell Active, not recruiting, has
28 NCT02086552
myeloma results
Advanced pancreatic
cancer 39 NCT01485744 Active, not recruiting
Advanced breast cancer I 12 NCT02027376 Completed, has results
Smoothened
  Glasdegib Acute myeloid leukemia II 255 NCT01546038 Completed, has results
Solid tumors 12 NCT01413906 Completed
Small-cell lung carcinoma 5 NCT00927875 Completed
Metastatic gastric,
gastroesophageal, 39 NCT00909402 Completed
  BMS-833923 (XL139) esophageal II
adenocarcinomas
Advanced or metastatic 53 NCT00670189 Completed
basal cell carcinoma
Leukemia 70 NCT01357655 Terminated, has results
Localized esophageal or
gastroesophageal 9 NCT02530437 Active, not recruiting
  Taladegib (LY2940680) junction cancer II
Small-cell lung carcinoma 26 NCT01722292 Terminated, has results
  LEQ-506 Solid tumors I 57 NCT01106508 Completed
  G-024856 BCC I      
Basal cell carcinomas 36 NCT02828111 Completed, has results
 CSC-directed immunotherapy in ongoing clinical trials
Trial description Condition Sample size Phase NCT Number Current status
CD19 CAR-T B cell leukemia and lymphoma II 80 NCT03398967 Recruiting

CD123 CAR-T CD122+ myeloid malignancies II 45 NCT02937103 Recruiting

CD22 CAR-T Recurrent or refractory B cell malignancy I/II 45 NCT02794961 Unknown

CD22 CAR-T B-ALL I 15 NCT02650414 Recruiting
CD33 CAR-T Myeloid malignancies I/II 45 NCT02958397 Recruiting
CD33 CAR-T CD32+ acute myeloid leukemia I 11 NCT03126864 Active, not recruiting
CD38 CAR-T B-ALL II 80 NCT03754764 Recruiting
CD138 CAR-T Multiple myeloma II 10 NCT03196414 Recruiting
MUC1 CAR-T/PD- Advanced esophageal cancer I/II 20 NCT03706326 Recruiting
1 KO
EGFR IL-12 CAR-T Metastatic colorectal cancer I 20 NCT03542799 Not yet recruiting

MESO CAR-T Refractory–relapsed ovarian cancer I/II 20 NCT03916679 Recruiting

MESO-19 CAR-T Metastatic pancreatic cancer I 4 NCT02465983 Completed

LeY CAR-T Myeloid malignancies I/II 445 NCT02958384 Recruiting
MOv19-BBz CAR -
Recurrent high-grade serous ovarian cancer I 18 NCT03585764 Recruiting
T
LeY CAR-T Advanced cancer I 30 NCT03851146 Recruiting
EpCAM CAR-T Recurrent breast cancer I 30 NCT02915445 Recruiting
BCMA CAR-T Multiple myeloma II 80 NCT03767751 Recruiting
Mutated Collagen Proteins May Aid
Cancer Metastasis
• Another of the UCSF/UCSD studies focused on identifying protein–protein
interactions in breast cancer, while the third study combined findings from the first
two to provide a more universal analysis of cancer-wide pathways.
• Among the key findings of the latter study was the discovery of recurrent mutations
in proteins that are part of collagen, a main component of the extracellular matrix,
or ECM.
• The ECM provides a scaffold for collections of cells in the body, including tumors.
• The recurrent mutations in these collagen complexes, the researchers wrote,
“disrupt[ed] the extracellular matrix” in tumors, “thereby promoting proliferation” of
cancer cells.
• In mice, they reported, when these same mutated collagen proteins were present,
tumors were more likely to spread in the body.
Conclusion: Pushing Ahead on Pathways
• Based on previous studies implicating HER3 in head and neck cancers positive for the human
papillomavirus (HPV), the HER3 inhibitor used in the head and neck study is already being tested in
small clinical trials of patients with these cancers.
• But the study team believes these new findings may help identify people whose tumors are most likely to
shrink following HER3-inhibitor treatment. 
• There’s a strong interest among researchers to target the “particular axis” of HER3 and PIK3CA interactions
• Approximately 5% of all cancers have the specific PIK3CA mutation shown in the study to be susceptible to
blocking HER3 
• From a broader perspective, continued research is needed “to further improve functional maps and more
precisely define which [protein–protein] interactions are rewired in each tumor” 
• When proteins interact with each other, the resulting complexes “are not static structures, but rather
dynamically reassemble in response to the state of the cell,”
• So it will be helpful to understand the impact on these interactions of other factors that can affect cells,
• Tumor microenvironment, including inflammation and the presence of different types of immune cells.
• Maps constructed to direct treatment by interpreting the genomic data on tumors
• To use this approach to mapping network pathways “and make it systematic for the whole of cancer cell
biology.”
Thank you