Advances in Precision Medicine Approaches for Colorectal Cancer: From Molecular Profiling to Targeted Therapies

Abstract

Precision medicine is transforming colorectal cancer treatment through the integration of advanced technologies and biomarkers, enhancing personalized and effective disease management. Identification of key driver mutations and molecular profiling have deepened our comprehension of the genetic alterations in colorectal cancer, facilitating targeted therapy and immunotherapy selection. Biomarkers such as microsatellite instability (MSI) and DNA mismatch repair deficiency (dMMR) guide treatment decisions, opening avenues for immunotherapy. Emerging technologies such as liquid biopsies, artificial intelligence, and machine learning promise to revolutionize early detection, monitoring, and treatment selection in precision medicine. Despite these advancements, ethical and regulatory challenges, including equitable access and data privacy, emphasize the importance of responsible implementation. The dynamic nature of colorectal cancer, with its tumor heterogeneity and clonal evolution, underscores the necessity for adaptive and personalized treatment strategies. The future of precision medicine in colorectal cancer lies in its potential to enhance patient care, clinical outcomes, and our understanding of this intricate disease, marked by ongoing evolution in the field. The current reviews focus on providing in-depth knowledge on the various and diverse approaches utilized for precision medicine against colorectal cancer, at both molecular and biochemical levels.

1. Overview of Colorectal Cancer and Precision Medicine

Colorectal cancer, often termed bowel or colon cancer, is a prevalent and life-threatening disease that primarily affects the colon or rectum, which are parts of the digestive system. It is a multifaceted disease with a complex interplay of genetic, environmental, and lifestyle factors contributing to its development, with a substantial impact on public health worldwide. This cancer typically develops from the growth of abnormal cells in the lining of the colon or rectum and may take several years to progress from benign polyps to invasive cancer (Figure 1). Colorectal cancer is a multifaceted disease with a complex interplay of genetic, environmental, and lifestyle factors contributing to its development.¹

Figure 1.

Multi-factorial model of colorectal cancer progression and development (adapted from “The Hit-Model of Colorectal Cancer”; Biorender (2020)).

Risk factors for colorectal cancer include age, family history, genetics, and certain lifestyle choices (Figure 2). The risk of developing colorectal cancer increases significantly with age, making regular screenings crucial for individuals over 50 years old. Family history of the disease, especially among first-degree relatives, can also elevate the risk. Inherited genetic mutations, such as those seen in Lynch syndrome or familial adenomatous polyposis, can substantially increase the susceptibility to colorectal cancer.^2,3 Additionally, lifestyle choices, such as a diet high in red and processed meats, low fiber intake, tobacco use, excessive alcohol consumption, and physical inactivity, are modifiable factors that can contribute to the development of colorectal cancer. The symptoms of colorectal cancer can be subtle in the early stages, making it imperative to recognize the potential warning signs. Common symptoms may include changes in bowel habits, blood in the stool, unexplained weight loss, fatigue, and abdominal discomfort. Timely recognition of these symptoms can lead to early diagnosis, improving the prognosis of the disease. Screening tests, including colonoscopies, fecal occult blood tests, and sigmoidoscopies, are instrumental in detecting colorectal cancer at an early, more treatable stage.⁴

Figure 2.

Risk factors of colorectal cancer (age < family history < genetic alterations < lifestyle practices).

Colorectal cancer can be staged into different categories, with stage 0 representing the earliest, localized form of the disease and stage IV indicating metastatic cancer that has spread to distant organs. Treatment strategies for colorectal cancer depend on the cancer’s stage and may include surgery, chemotherapy, radiation therapy, targeted therapies, and immunotherapy.⁵ Surgical removal of the tumor is often the primary treatment for localized cancer, while advanced stages may require a combination of treatments to manage the disease. Personalized treatment plans tailored to the patient’s specific condition are crucial to improve outcomes and reduce side effects. Preventing colorectal cancer is a priority in public health, and lifestyle modifications can play a significant role in risk reduction. Furthermore, individuals with a family history of colorectal cancer or certain genetic predispositions may benefit from genetic counselling and early screenings.^6,7

Precision medicine, heralded as a paradigm shift in cancer treatment, represents a transformative approach to the management of cancer. Unlike traditional one-size-fits-all treatments, precision medicine tailors therapies to the unique genetic and molecular characteristics of each patient’s tumor (Figure 3). This shift acknowledges the inherent heterogeneity of cancer and the critical role that genomic information plays in guiding treatment decisions. By understanding the genetic makeup of the cancer, oncologists can prescribe more effective and less toxic therapies, thus offering new hope for patients.⁸

Figure 3.

Precision medicine (discovery, diagnosis, and decisions) in treatment of oncological disease. (Reprinted from ref (9) under a Creative Common License, CC BY 4.0, MDPI 2023.)

One of the fundamental tenet of precision medicine in cancer treatment is the identification of specific genetic alterations driving the growth and spread of tumors. Advances in genomic sequencing technologies have made it possible to analyze the DNA of cancer cells in unprecedented detail. Through techniques like next-generation sequencing, scientists can pinpoint mutations and alterations in the cancer genome that may be amenable to targeted therapies.⁹ For instance, the discovery of the BCR-ABL fusion gene in chronic myeloid leukemia (CML) led to the development of the ground-breaking drug imatinib, which revolutionized CML treatment and drastically improved patient outcomes. In addition to targeting genetic alterations, precision medicine also considers the patient’s individual characteristics, including their age, overall health, and treatment preferences. This holistic approach recognizes that each patient’s response to treatment may vary based on factors beyond their tumor’s genetic makeup. Therefore, precision medicine involves a comprehensive evaluation of both the tumor and the patient, allowing oncologists to make more informed decisions about the most suitable therapy.¹⁰

One notable aspect of precision medicine is its potential to reduce the reliance on traditional chemotherapy, which often comes with severe side effects due to its indiscriminate action on rapidly dividing cells. Targeted therapies and immunotherapies, two key components of precision medicine, aim to attack cancer cells specifically while sparing healthy tissues. For example, monoclonal antibodies like trastuzumab have revolutionized the treatment of HER2-positive breast cancer by selectively targeting the HER2 receptor on cancer cells, leading to improved outcomes and reduced side effects.^10,11

Despite the remarkable progress in precision medicine, challenges remain. Not all cancers have well-defined, targetable genetic alterations, and resistance to targeted therapies can develop over time. Furthermore, the cost and accessibility of genomic sequencing can limit its widespread adoption. However, ongoing research efforts, collaborative initiatives, and technological advancements continue to expand the applications of precision medicine, making it an exciting and evolving frontier in cancer treatment.¹²

2. Molecular Profiling of Colorectal Cancer

Molecular profiling of colorectal cancer has emerged as a pivotal tool for understanding the underlying genetic and molecular alterations that drive the development and progression of this malignancy. Colorectal cancer is a highly heterogeneous disease, and advances in genomic technologies have revealed a complex landscape of genetic mutations, epigenetic modifications, and altered signaling pathways that contribute to its pathogenesis. Through comprehensive molecular profiling, researchers can identify specific genetic aberrations, such as mutations in genes like APC, KRAS, and TP53, which not only inform prognosis but also guide treatment decisions¹³ (Figure 4). This personalized approach to cancer management is vital in an era where one size does not fit all, offering tailored therapeutic strategies that can lead to improved patient outcomes. Furthermore, molecular profiling has paved the way for the development of targeted therapies for colorectal cancer. By characterizing the molecular fingerprint of an individual patient’s tumor, clinicians can determine the most appropriate treatment options, including the use of monoclonal antibodies targeting proteins like EGFR and VEGF.^14,15 Additionally, advancements in immunotherapy have harnessed the power of the immune system to combat colorectal cancer with immune checkpoint inhibitors demonstrating promising results in specific molecular subtypes. As research continues to expand our understanding of the intricate genetic and molecular alterations in colorectal cancer, molecular profiling will play an increasingly central role in guiding treatment decisions, monitoring disease progression, and ultimately improving the precision and efficacy of therapies for this challenging malignancy.^16,17

Figure 4.

Various identified colorectal cancer related gene-products: (A) APC (OMIM: 611731); (B) KRAS (OMIM: 190070); (C) TP53 (OMIM: 191170); (D) SMAD4 (OMIM: 600993); (E) PIK3CA (OMIM: 171834); (F) BRAF (OMIM: 164757); (G) PTEN (OMIM: 601728).

2.1. Genomic Alterations in Colorectal Cancer

Colorectal cancer, which is a complex and heterogeneous disease, is characterized by a multitude of genomic alterations that underlie its development and progression. Genomic studies have unveiled a diverse landscape of genetic mutations and structural variations in this cancer, shedding light on the molecular intricacies of the disease (Table 1). Key genomic alterations in colorectal cancer include mutations in genes like APC, KRAS, and TP53.¹⁸ The APC gene, for example, is frequently inactivated early in the development of colorectal cancer, leading to the dysregulation of the Wnt signaling pathway and the formation of benign polyps that may evolve into cancer. Mutations in KRAS and TP53, on the other hand, contribute to uncontrolled cell growth and resistance to apoptosis, respectively, promoting tumor growth and metastasis.¹⁹

Table 1. List of Various Identified Gene Mutations Responsible for the Incidence of Colorectal Cancer.

Gene	Significance of the Gene	Type of Mutation	Expression of the Gene	Effect on Colorectal Cancer linked Metabolic Pathway	Mechanism of Action	References
APC	Tumor Suppressor Gene	Truncating Mutation (e.g., Nonsense, Frameshift)	Underexpressed	Wnt/β-catenin pathway	Loss of APC leads to uncontrolled cell growth, as it fails to regulate β-catenin levels in the cell, resulting in increased cell proliferation.	(20)
KRAS	Oncogene	Point Mutation (e.g., G12D, G13A)	Overexpressed	MAPK Signaling Pathway	Mutations in KRAS lead to constitutive activation of the MAPK pathway, promoting uncontrolled cell proliferation and survival.	(21)
TP53	Tumor Suppressor Gene	Various Mutations (e.g., Missense, Nonsense, Frameshift)	Underexpressed	Cell Cycle Regulation	Loss of TP53 function allows for the unchecked growth of damaged cells, increasing the risk of tumorigenesis.	(22)
SMAD4	Tumor Suppressor Gene	Deletion, Missense, Nonsense, Frameshift	Underexpressed	TGF-β Signaling Pathway	Loss of SMAD4 disrupts the regulation of cell differentiation and growth in the TGF-β pathway, contributing to cancer development.	(23)
BRAF	Oncogene	Point Mutation (e.g., V600E)	Overexpressed	MAPK Signaling Pathway	Mutations in BRAF, such as V600E, lead to overactive MAPK signaling, driving uncontrolled cell division and tumor growth.	(24)
PIK3CA	Oncogene	Point Mutation (e.g., H1047R)	Overexpressed	PI3K/Akt Signaling Pathway	Mutations in PIK3CA enhance PI3K/Akt signaling, promoting cell survival and growth through the activation of downstream effectors.	(25)
PTEN	Tumor Suppressor Gene	Deletion, Missense, Nonsense, Frameshift	Underexpressed	PI3K/Akt Signaling Pathway	Loss of PTEN results in increased PI3K/Akt signaling, leading to enhanced cell survival and growth, and contributing to carcinogenesis.	(26)

Beyond point mutations, genomic alterations in colorectal cancer also encompass chromosomal instability (CIN) and microsatellite instability (MSI). CIN results in widespread changes in the number and structure of chromosomes, creating genomic chaos within the tumor cells.²⁷ In contrast, MSI is characterized by a high frequency of mutations in short repetitive DNA sequences, primarily caused by defects in the DNA mismatch repair system. These genomic instability patterns have important implications for prognosis and treatment selection. MSI-high tumors, for instance, are more responsive to immunotherapy as they exhibit an increased mutational load and higher levels of immune cell infiltration. Understanding the diverse genomic alterations in colorectal cancer is pivotal for tailoring treatment strategies and improving patient outcomes, as it allows for the selection of therapies that specifically target the genetic drivers of the disease while minimizing the toxic effects on normal cells.^28,29

2.1.1. Key Driver Mutations and Signaling Pathways

One of the most prominent driver mutations in colorectal cancer occurs in the Adenomatous Polyposis Coli (APC) gene. Loss of function mutations in APC are considered an early event in colorectal carcinogenesis. APC normally serves as a tumor suppressor by regulating the Wnt signaling pathway. Mutations in APC lead to uncontrolled activation of the Wnt pathway, resulting in excessive cell proliferation and the formation of benign polyps that can eventually progress to cancer.^20,30 Another common driver mutation is found in the Kirsten rat sarcoma viral oncogene homologue (KRAS) gene. Activating mutations in KRAS are often associated with resistance to antiepidermal growth factor receptor (EGFR) therapies. The KRAS protein is a key player in the EGFR signaling pathway, and mutations in this gene lead to continuous activation of downstream signaling, promoting cell survival and proliferation.³¹

The tumor protein p53 (TP53) gene is also frequently mutated in colorectal cancer. TP53 is a critical tumor suppressor gene that is responsible for monitoring DNA damage and orchestrating cell cycle arrest or apoptosis in the presence of genetic instability. Mutations in TP53 lead to an impaired DNA damage response, allowing for the accumulation of additional mutations and the progression of the cancer. The mitogen-activated protein kinase (MAPK) signaling pathway is another central player in colorectal cancer.³² Activation of this pathway, often through mutations in KRAS or BRAF, contributes to uncontrolled cell growth and survival. Mutations in the BRAF gene, particularly the V600E mutation, are associated with poor prognosis and resistance to targeted therapies. In addition to these driver mutations, colorectal cancer can exhibit both chromosomal instability (CIN) and microsatellite instability (MSI). CIN results in widespread changes in the number and structure of chromosomes, contributing to genomic chaos. MSI, on the other hand, is characterized by a high frequency of mutations in short repetitive DNA sequences, primarily due to defects in the DNA mismatch repair system. MSI-high tumors are more responsive to immunotherapies due to their increased mutational load.^33,34

Understanding the interplay of these key driver mutations and signaling pathways is essential for developing targeted therapies that can disrupt the specific mechanisms driving the growth and progression of colorectal cancer. By targeting these genetic alterations and disrupted pathways, researchers and clinicians are striving to improve treatment options and outcomes for individuals affected by this challenging malignancy.³⁵

2.1.2. Microsatellite Instability and DNA Mismatch Repair Deficiency

Microsatellite instability (MSI) and DNA mismatch repair deficiency (dMMR) represent critical molecular features in colorectal cancer, playing a central role in the pathogenesis and clinical management of this disease. MSI is characterized by a high frequency of mutations in microsatellites, short repetitive DNA sequences scattered throughout the genome. dMMR, on the other hand, results from the loss of function in the DNA mismatch repair system, a crucial mechanism responsible for correcting errors in DNA replication.³⁶ Both MSI and dMMR can significantly influence the prognosis and therapeutic strategies for colorectal cancer patients. The DNA mismatch repair system comprises a set of proteins responsible for detecting and repairing errors that occur during DNA replication. When this system is intact, it corrects any mismatches between the two strands of DNA, ensuring the faithful transmission of genetic information. In colorectal cancer, the loss of function of one or more mismatch repair genes, such as MLH1, MSH2, MSH6, or PMS2, leads to dMMR. As a result, errors in DNA replication accumulate, leading to an increased mutational load in the tumor cells. This phenomenon is particularly relevant in the context of colorectal cancer, where dMMR is seen in approximately 15% of cases.^37,38

The presence of MSI and dMMR in colorectal cancer has several important clinical implications. First, it is associated with a more favorable prognosis. MSI-high tumors tend to have a lower propensity for invasion and metastasis, resulting in improved overall survival for affected patients.³⁹ Furthermore, MSI-high tumors often exhibit a distinct histological and molecular profile with increased lymphocytic infiltration within the tumor microenvironment, suggesting a heightened immune response against the tumor. Perhaps most importantly, MSI and dMMR status can dictate treatment choices.⁴⁰ Immunotherapies targeting immune checkpoint proteins, such as programmed cell death protein 1 (PD-1) and programmed death-ligand 1 (PD-L1), have shown remarkable efficacy in MSI-high colorectal cancer. These therapies harness the body’s immune system to attack cancer cells, exploiting the higher mutational burden in MSI-high tumors. The approval of pembrolizumab, a PD-1 inhibitor, for the treatment of dMMR or MSI-high colorectal cancer has provided a ground-breaking option for patients with these molecular features.^37,41

2.2. Proteomic Approaches and Biomarker Discovery

Proteomic approaches have emerged as valuable tools in the study of colorectal cancer, enabling a deeper understanding of the complex molecular landscape of this disease and the discovery of potential biomarkers for improved diagnosis, prognosis, and treatment strategies.⁴² Colorectal cancer is a highly heterogeneous malignancy, and proteomics offers a comprehensive means to analyze the intricate network of proteins that drive its development and progression. One of the primary goals of proteomic research in colorectal cancer is to identify potential biomarkers that can aid in early detection and accurate diagnosis. The search for biomarkers often involves the analysis of protein expression patterns in tissue samples, blood, or other bodily fluids.⁴³ By comparing the proteomic profiles of cancer patients with those of healthy individuals or patients with other diseases, researchers aim to pinpoint specific proteins that are over- or under-expressed in colorectal cancer. Such proteins can serve as diagnostic biomarkers, offering a noninvasive and sensitive means of identifying the disease at an earlier, more treatable stage.^44,45

Proteomics also plays a crucial role in prognostic and predictive biomarker discovery for colorectal cancer. By investigating the proteomic profiles of tumors, researchers can identify molecular signatures associated with disease aggressiveness, likelihood of recurrence, and response to specific treatments.⁴⁶ This information helps clinicians tailor treatment plans to individual patients, enhancing the prospects for successful outcomes. For example, proteomic studies have revealed biomarkers associated with resistance to certain targeted therapies, such as those directed at the epidermal growth factor receptor (EGFR), guiding the selection of more effective treatment options.^47,48 In addition to diagnosis and prognosis, proteomic approaches contribute to a deeper understanding of the underlying biology of colorectal cancer. They shed light on the molecular pathways, protein–protein interactions, and post-translational modifications that govern cancer cell behavior. Such insights can lead to the development of new therapeutic strategies, including the identification of druggable targets and the design of novel therapies. Proteomics is particularly valuable in the era of personalized medicine, where treatment decisions are increasingly based on the unique molecular characteristics of a patient’s tumor.⁴⁹

2.2.1. Proteomic Methodologies in Biomarker Discovery

Among the various avenues of molecular investigation, proteomic methodologies have emerged as crucial tools in unraveling the intricate molecular landscape of colorectal cancer and identifying biomarkers for precise diagnostics and targeted therapies.⁵⁰

One of the fundamental proteomic techniques employed in the study of colorectal cancer is mass spectrometry (MS). MS enables the high-throughput identification and quantification of proteins, offering a comprehensive view of the proteome. This technology has been pivotal in characterizing the proteomic alterations associated with colorectal cancer initiation, progression, and metastasis.⁵¹ By analysis of tissue, blood, or other biological samples, MS allows the identification of potential protein biomarkers that can serve as indicators of disease presence, progression, or response to treatment. In addition to MS, advancements in gel-based and gel-free separation techniques have enhanced the depth and accuracy of proteomic analyses in colorectal cancer. Two-dimensional gel electrophoresis (2D-GE) and liquid chromatography (LC) coupled with MS have proven to be instrumental in resolving complex protein mixtures, enabling the detection of subtle changes in protein expression patterns associated with colorectal cancer. These methodologies facilitate the identification of dysregulated proteins that may serve as diagnostic or prognostic markers, guiding personalized treatment strategies.^52,53

Furthermore, the integration of proteomic data with other omics disciplines, such as genomics and transcriptomics, enhances the holistic understanding of colorectal cancer biology. Integrative analyses provide a more comprehensive view of the molecular alterations underlying colorectal cancer, aiding in the identification of novel biomarkers with potential clinical relevance. The identification and validation of such biomarkers are essential steps toward developing targeted therapies and improving patient outcomes in colorectal cancer.^54,55

2.2.2. Protein Signatures and Expression Profiles

One of the key applications of protein signatures in colorectal cancer is the development of diagnostic biomarkers. Researchers use proteomics techniques to compare the protein expression profiles of cancerous tissues with healthy tissues. This approach helps identify proteins that are over- or under-expressed in colorectal cancer. These differentially expressed proteins can serve as diagnostic biomarkers, providing a more accurate and less invasive method for the early detection of the disease. For example, carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA 19-9) are commonly used protein biomarkers for monitoring colorectal cancer.⁵⁶

Proteomic studies also contribute to the discovery of prognostic and predictive markers in colorectal cancer. By examining the protein expression patterns within tumors, researchers can identify signatures associated with disease aggressiveness, metastatic potential, and the likelihood of recurrence.⁵⁷ This information allows clinicians to predict patient outcomes more accurately and make informed decisions about the most suitable treatment strategies. Additionally, the identification of predictive protein markers can guide treatment choices, improving the efficacy of therapies, such as targeted agents or immunotherapies. Moreover, protein signatures provide insights into the underlying molecular pathways and networks involved in colorectal cancer.⁵⁸ Researchers can analyze the interactions between proteins and identify specific signaling pathways that are dysregulated in the disease. This knowledge is crucial for the development of targeted therapies that aim to disrupt these pathways and stop the progression of colorectal cancer. For example, the identification of the epidermal growth factor receptor (EGFR) pathway as a key player in colorectal cancer has led to the development of targeted therapies like cetuximab and panitumumab.^59,60

2.2.3. Phosphoproteomics and Protein Interaction Networks

Phosphoproteomics is a comprehensive study of protein phosphorylation, a critical post-translational modification that regulates the activity and function of proteins in cells. In colorectal cancer, aberrant phosphorylation events can drive various oncogenic processes, including cell proliferation, survival, and migration.⁶¹ The analysis of phosphorylation patterns in tumor tissues can reveal specific targets and signaling pathways that are dysregulated, leading to a better understanding of the molecular drivers of the disease. For instance, the dysregulation of proteins involved in the Wnt signaling pathway, often through phosphorylation events, is a hallmark of colorectal cancer and contributes to uncontrolled cell growth and tumor progression.⁶²

In conjunction with phosphoproteomics, the study of protein interaction networks helps to uncover the complex web of interactions between proteins in colorectal cancer cells. These networks elucidate the relationships between proteins involved in key signaling pathways and cellular processes, shedding light on the cross-talk and crosstalk between various pathways.⁶³ Understanding these interactions is pivotal for recognizing potential therapeutic targets and developing more effective treatment strategies. For instance, identifying proteins that interact with the EGFR can help pinpoint downstream effectors and signaling partners that contribute to tumor growth and survival.⁶⁴

Moreover, the integration of phosphoproteomics and protein interaction networks can provide a systems-level view of colorectal cancer biology. Phosphorylation events on proteins can influence their interactions with other proteins, modulating the entire signaling network.⁶⁵ This holistic approach allows researchers to unravel the intricate molecular mechanisms that underpin tumor development and progression. In the context of personalized medicine, it also facilitates the identification of patient-specific signaling alterations, enabling the design of tailored therapeutic interventions that target the specific dysregulated pathways.⁶⁶

2.3. Lipidomic and Metabolomic Approaches

The exploration of lipidomic and metabolomic approaches has emerged as a pivotal dimension in the quest for effective biomarker discovery within the realm of precision medicine for colorectal cancer. Lipidomics, the study of lipid profiles within biological systems, and metabolomics, the comprehensive analysis of small molecules, offer unique insights into the dynamic interplay of cellular processes that underlie cancer initiation, progression, and response to treatment. By elucidating the intricate alterations in lipid and metabolite landscapes associated with colorectal cancer, these approaches contribute to a more holistic understanding of the disease at the molecular level.⁶⁷

Lipidomic analyses in colorectal cancer have revealed significant perturbations in lipid composition including alterations in phospholipids, glycolipids, and sphingolipids. These changes are implicated in various cellular functions, such as membrane structure, cell signaling, and energy storage.^68,69 Characterizing these lipidomic signatures provides a window into the complex lipid metabolism of colorectal cancer cells, offering potential biomarkers that can aid in early detection, prognosis, and therapeutic stratification. Metabolomic investigations, on the other hand, focus on the global profiling of metabolites including amino acids, organic acids, and nucleotides. Metabolomic alterations in colorectal cancer reflect the dynamic shifts in cellular metabolism associated with cancer, offering valuable information on the tumor microenvironment and host responses. Metabolomic biomarkers have the potential to serve as indicators of disease progression, therapeutic response, and the identification of specific metabolic vulnerabilities that can be targeted for precision interventions.⁷⁰

Integration of lipidomic and metabolomic data with other omics disciplines, such as genomics and proteomics, enriches the complexity of molecular information available for biomarker discovery. The synergistic analysis of multiomics data sets enhances the identification of robust and reliable biomarkers with clinical relevance, providing a more comprehensive molecular portrait of colorectal cancer. This integrative approach is fundamental in advancing precision medicine, as it allows for a deeper understanding of the interconnected molecular networks driving colorectal cancer pathogenesis.^71,72 While lipidomic and metabolomic approaches hold immense potential, challenges persist in translating these findings into clinically actionable biomarkers. Standardization of sample preparation, analytical techniques, and data interpretation is essential to ensure the reproducibility and reliability of the results across different research settings. Additionally, the development of user-friendly and high-throughput technologies is crucial for the practical implementation of lipidomic and metabolomic biomarkers in routine clinical practice.^73,74

2.4. Nanomedicine and Protein Corona

Nanomedicine, the application of nanotechnology in the field of medicine, has emerged as a ground-breaking approach with the potential to revolutionize biomarker discovery for precision medicine against colorectal cancer. Engineered nanoparticles with their unique physical and chemical properties, offer versatile platforms for targeted drug delivery, imaging, and diagnostics. By leveraging these nanoparticles, researchers can enhance the specificity and efficacy of therapeutic interventions while simultaneously providing opportunities for the identification of novel biomarkers associated with colorectal cancer.⁷⁵

One critical aspect of nanomedicine in the context of biomarker discovery is the phenomenon known as the “protein corona.″ Upon exposure to biological fluids, nanoparticles rapidly adsorb a layer of proteins, forming a dynamic corona that influences their interactions with cells and tissues.⁷⁶ The protein corona serves as a bridge between nanoparticles and the biological environment, dictating their fate, cellular uptake, and biological responses. Understanding the intricacies of the protein corona is essential in deciphering the molecular signatures associated with colorectal cancer and identifying potential biomarkers that may be indicative of disease status or treatment response.^77,78 The protein corona’s role in modulating the biodistribution and cellular interactions of nanoparticles has implications for the development of precision medicine strategies.^79,80 By analyzing the composition of the protein corona in the context of colorectal cancer, researchers can gain insights into the tumor microenvironment, identify specific molecular markers associated with cancer cells, and optimize the design of nanoparticles for enhanced targeting and therapeutic delivery. This personalized approach holds the potential to improve the efficacy of nanomedicine-based treatments while minimizing off-target effects.⁸¹

Furthermore, the protein corona’s dynamic nature adds an additional layer of complexity to biomarker discovery. As nanoparticles interact with various biological fluids, including blood and interstitial fluid, the composition of the protein corona may evolve over time, reflecting the dynamic changes in the tumor microenvironment.^82,83 Monitoring these changes can provide real-time information about the disease progression, enabling the development of adaptive and personalized treatment strategies for colorectal cancer patients.^84,85 Despite the tremendous potential of nanomedicine and the protein corona in biomarker discovery, challenges remain in translating these findings into clinical applications. Standardization of nanoparticle characterization, corona analysis, and data interpretation is crucial for ensuring the reproducibility and reliability of the results across different studies. Additionally, addressing safety concerns and potential immunogenicity associated with nanoparticle exposure is paramount for the clinical translation of nanomedicine-based precision medicine approaches^86,87

2.5. Gut Microbiome as Biomarker

The gut microbiome, a complex community of microorganisms residing in the gastrointestinal tract, has emerged as a compelling and influential factor in the landscape of precision medicine against colorectal cancer. Extensive research has revealed that the composition and function of the gut microbiome play a pivotal role in modulating various aspects of colorectal cancer, including carcinogenesis, tumor progression, and response to therapy.⁸⁸ As a dynamic and interactive component of the host’s physiology, the gut microbiome holds great potential as a biomarker for precision medicine in the battle against colorectal cancer. Numerous studies have demonstrated that alterations in the gut microbiome composition are associated with the development and progression of colorectal cancer.^89,90 Imbalances in microbial diversity, shifts in specific bacterial populations, and changes in the abundance of certain microbial metabolites have been linked to colorectal cancer risk. The identification of these microbiome signatures provides valuable insights into the intricate interplay between the gut microbiome and the host’s immune and metabolic systems, paving the way for the development of microbiome-based biomarkers.⁹¹

In the context of precision medicine, the gut microbiome holds promise as a prognostic and predictive biomarker for colorectal cancer. Research indicates that distinct microbiome profiles may influence treatment responses and patient outcomes. Understanding the interindividual variability in the gut microbiome allows for the tailoring of therapeutic strategies to individual patients, optimizing the efficacy of treatments and minimizing adverse effects. Moreover, the gut microbiome’s potential role in mediating the metabolism of certain drugs further underscores its significance in the realm of precision medicine.^92,93 The gut microbiome’s influence extends beyond conventional treatments, with implications for emerging immunotherapeutic strategies in colorectal cancer. Recent studies suggest that the gut microbiome composition can impact the response to immune checkpoint inhibitors, a class of immunotherapies that show promise in colorectal cancer treatment. Harnessing the predictive power of the gut microbiome allows for the identification of responders and nonresponders to immunotherapy, guiding clinicians in the selection of the most suitable and effective treatment modalities.^94,95

However, challenges persist in realizing the full potential of the gut microbiome as a biomarker for precision medicine in colorectal cancer. Standardizing methodologies for microbiome analysis, addressing interindividual variability, and establishing causal relationships between microbial signatures and colorectal cancer outcomes are critical steps. Additionally, considering the dynamic nature of the gut microbiome, longitudinal studies are essential for capturing temporal changes and understanding the impact of interventions on microbial communities.^96,97

3. Identification of Actionable Biomarkers

The identification of actionable biomarkers for colorectal cancers represents a critical pursuit in modern oncology, given the urgent need for more precise diagnostic and therapeutic strategies.⁹⁸ Comprehensive research endeavors have unveiled a plethora of potential candidates, including genetic alterations, epigenetic modifications, and protein expressions, that have demonstrated the potential to guide therapeutic decisions and prognostic assessments (Table 2, Figure 5). Among these, microsatellite instability (MSI), a hallmark of colorectal cancer, has emerged as a pivotal biomarker with therapeutic implications, as it enables the identification of patients who may respond favorably to immune checkpoint inhibitors, thereby reshaping the treatment landscape. Moreover, the discovery of specific mutations in the KRAS and BRAF genes has been instrumental in steering personalized treatment approaches, permitting the administration of targeted therapies such as cetuximab and panitumumab, which have shown efficacy in subsets of colorectal cancer patients with these mutations. As we delve deeper into the genomic intricacies of colorectal cancer, ongoing research is anticipated to unearth additional biomarkers and therapeutic targets, ultimately ushering in a new era of precision medicine for this debilitating disease.^99,100

Table 2. List of Various Colorectal Cancer Associated Biomarkers.

Biomarkers	Significance	Role in Colorectal Cancer	References
CEA (Carcinoembryonic Antigen)	Diagnostic and Prognostic	CEA is a blood marker used in screening and monitoring colorectal cancer. Elevated CEA levels may indicate the presence of the disease, and it can be used to assess treatment response and disease recurrence.	(101)
KRAS Mutation	Predictive and Prognostic	KRAS mutation status is important for predicting response to anti-EGFR targeted therapies. Mutations in KRAS are associated with resistance to these treatments, impacting treatment choices and prognosis.	(25)
BRAF Mutation	Prognostic	BRAF V600E mutations are associated with poor prognosis in colorectal cancer. Identifying this mutation helps in stratifying patients for more aggressive treatment strategies.	(24)
Microsatellite Instability (MSI)	Diagnostic and Prognostic	MSI status helps in identifying a subset of colorectal cancer patients with a better prognosis and predicting their response to immunotherapies. It is also used in diagnosing Lynch syndrome.	(102)
TP53 Mutation	Prognostic	TP53 mutations are associated with more aggressive tumor behavior and poor prognosis in colorectal cancer. Understanding TP53 status helps guide treatment planning.	(22)
EGFR Expression	Predictive and Prognostic	Assessing EGFR expression can help in predicting response to anti-EGFR targeted therapies. Higher EGFR expression may indicate a better response to these treatments.	(103)
Mismatch Repair (MMR) Proteins	Diagnostic and Prognostic	Abnormal expression of MMR proteins is associated with MSI and can help diagnose Lynch syndrome. It is also used to determine MSI status and guide therapy choices.	(104)

Figure 5.

Various identified actionable biomarkers of colorectal cancer.

In tandem with genetic and molecular biomarkers, the exploration of noncoding RNA species, such as microRNAs and long noncoding RNAs, has expanded the spectrum of actionable biomarkers for colorectal cancers. These noncoding RNAs exhibit aberrant expression patterns in colorectal cancer tissues, often correlating with disease stage, metastatic potential, and patient outcomes.^105,106 By scrutinizing their regulatory functions, researchers have discerned their role in the intricate molecular networks underlying colorectal carcinogenesis. For instance, microRNA-21 has been implicated in promoting tumor growth and metastasis through the suppression of tumor suppressor genes. Consequently, targeting these noncoding RNAs holds promise as a therapeutic strategy, with ongoing clinical trials assessing the efficacy of RNA-based therapeutics. Overall, the identification of actionable biomarkers for colorectal cancers not only promises to refine disease classification and prognosis but also holds the potential to revolutionize treatment approaches, ushering in a new era of personalized and targeted interventions, ultimately improving the clinical management and outcomes for patients with this prevalent and heterogeneous malignancy.^107,108

3.1. Predictive Biomarkers for Treatment Response

One of the most well-established predictive biomarkers in colorectal cancer is the mutation status of the Kirsten rat sarcoma viral oncogene homologue (KRAS) gene. Mutations in KRAS are associated with resistance to antiepidermal growth factor receptor (EGFR) therapies, such as cetuximab and panitumumab. Therefore, determining the KRAS mutation status of a patient’s tumor is crucial in guiding the selection of the most appropriate treatment. Additionally, other biomarkers related to the EGFR pathway, such as NRAS and BRAF mutations, also influence treatment response and can further refine treatment decisions.¹⁰⁹

Microsatellite instability (MSI) and DNA mismatch repair deficiency (dMMR) represent another group of predictive biomarkers in colorectal cancer. Tumors with high levels of MSI or dMMR are more likely to respond to immune checkpoint inhibitors, such as programmed cell death protein 1 (PD-1) inhibitors.^110,111 This is because these tumors tend to have a higher mutational load and increased levels of immune cell infiltration, making them more susceptible to immunotherapies. The identification of MSI or dMMR status helps select patients who are most likely to benefit from immunotherapy, highlighting the importance of these biomarkers in treatment decisions. Additionally, emerging biomarkers related to specific molecular alterations are being investigated as potential predictors of treatment response in colorectal cancer.¹¹² For example, alterations in the BRAF gene, particularly the V600E mutation, are associated with a poor prognosis and limited response to conventional therapies. Targeted agents, such as BRAF inhibitors, are being explored as potential treatment options for patients with BRAF-mutated colorectal cancer. Other molecular alterations, such as HER2 amplification, are also under investigation as potential biomarkers for targeted therapies.¹⁰⁴

3.1.1. RAS and BRAF Mutations

RAS and BRAF mutations are significant genetic alterations in colorectal cancer, playing a crucial role in the disease’s pathogenesis and clinical management. Understanding the impact of these mutations is essential for tailoring treatment strategies and predicting disease outcomes.¹¹³ Mutations in the RAS gene family, which includes KRAS and NRAS, are among the most common genetic alterations in colorectal cancer. These mutations are typically found in approximately 40–50% of cases and are associated with resistance to antiepidermal growth factor receptor (EGFR) therapies, such as cetuximab and panitumumab. RAS proteins are key components of the EGFR signaling pathway, and mutations in these genes lead to constitutive activation of downstream signaling, promoting cell proliferation and survival. Therefore, the presence of RAS mutations is a critical predictive biomarker, guiding treatment decisions and helping to avoid ineffective therapies.^114,115

In addition to RAS mutations, alterations in the BRAF gene, particularly the V600E mutation, are another important genetic event in colorectal cancer. BRAF mutations are observed in approximately 5–10% of colorectal cancer cases and are associated with poor prognosis.¹¹⁶ The BRAF V600E mutation leads to constitutive activation of the mitogen-activated protein kinase (MAPK) pathway, driving uncontrolled cell growth and tumor progression. Patients with BRAF-mutated colorectal cancer often have a more aggressive disease course and a limited response to conventional therapies. Identifying BRAF mutations is crucial for tailoring treatment strategies, as alternative therapeutic options, such as BRAF inhibitors, are being explored in clinical trials to target this specific mutation.¹¹⁷

The distinction between RAS and BRAF mutations is crucial for treatment decisions in colorectal cancer. Patients with wild-type RAS and BRAF genes have a better chance of responding to anti-EGFR therapies. In contrast, the presence of RAS mutations or the BRAF V600E mutation is an indicator of treatment resistance and a more aggressive disease course. Therefore, comprehensive molecular profiling of colorectal tumors is necessary to determine the mutation status of RAS and BRAF and guide the selection of the most appropriate treatment strategy.¹¹⁸

3.1.2. HER2 Amplification

HER2, or human epidermal growth factor receptor 2, is a protein that plays a crucial role in cell growth and proliferation. Amplification or overexpression of the HER2 gene is most famously associated with breast cancer but is increasingly recognized in other malignancies, including colorectal cancer.¹⁰³

HER2 amplification is observed in a subset of colorectal cancer patients, usually accounting for around 3–5% of the cases. This amplification is typically detected through various molecular testing methods, such as fluorescence in situ hybridization (FISH) or immunohistochemistry (IHC).¹¹⁹ HER2-positive colorectal cancer is often characterized by a more aggressive clinical course, including a higher risk of disease recurrence and poor patient prognosis. The presence of HER2 amplification in colorectal cancer also has significant therapeutic implications. Patients with HER2-positive colorectal cancer may be candidates for targeted therapies. For example, drugs that have been developed to target HER2, such as trastuzumab, pertuzumab, and adostrastuzumab emtansine (T-DM1), have shown efficacy in breast cancer treatment. In recent years, there has been growing interest in exploring the use of these drugs for colorectal cancer patients with HER2 amplification.^120,121

Clinical trials and studies have shown promising results with anti-HER2 therapies in HER2-positive colorectal cancer. These targeted therapies aim to disrupt the signaling pathways driven by HER2 overexpression, ultimately inhibiting tumor growth and improving patient outcomes. However, it is important to note that not all patients with HER2 amplification respond to these therapies, and ongoing research is aimed at better understanding the subset of patients who are most likely to benefit from these treatments.¹²²

3.2. Prognostic Biomarkers for Risk Assessment

3.2.1. Tumor Microenvironment Factors

The tumor microenvironment encompasses various cellular and molecular components, including immune cells, fibroblasts, blood vessels, and extracellular matrix, all of which influence tumor behavior and patient outcomes.¹²³ One critical aspect of the tumor microenvironment is immune cell composition. In colorectal cancer, the presence of specific immune cell populations, such as tumor-infiltrating lymphocytes (TILs), can have a profound impact on the prognosis. High levels of TILs, particularly cytotoxic T cells, are associated with better outcomes and a favorable response to therapy. Tumors with a robust immune response tend to exhibit slower growth and a lower risk of metastasis. Consequently, the assessment of TIL levels in colorectal tumors has emerged as a promising prognostic biomarker, helping clinicians predict patient outcomes and inform treatment decisions.^124,125

Furthermore, the role of the stromal component within the tumor microenvironment is increasingly recognized. Cancer-associated fibroblasts (CAFs) are a major component of the stroma and play a crucial role in promoting tumor growth and invasion. The presence of abundant CAFs within the tumor microenvironment is linked to a worse prognosis in colorectal cancer. CAFs secrete factors that facilitate tumor progression, including extracellular matrix remodelling, angiogenesis, and immune evasion. Assessing the extent of CAF infiltration in the tumor microenvironment provides additional prognostic information and may guide therapeutic strategies, such as the development of CAF-targeted therapies.^126,127 Vascularization within the tumor microenvironment is another key factor that influences the prognosis in colorectal cancer. Tumor angiogenesis, driven by factors such as vascular endothelial growth factor (VEGF), supports the growth and spread of cancer cells. High micro vessel density within the tumor microenvironment is often associated with a more aggressive disease course and a poorer prognosis. Prognostic biomarkers related to angiogenesis, such as VEGF expression levels, help identify patients at higher risk and inform the potential benefits of antiangiogenic therapies in colorectal cancer treatment.¹²⁸

3.2.2. Immune Checkpoint Markers

One of the most studied immune checkpoint markers in colorectal cancer is programmed cell death protein 1 (PD-1) and its ligand programmed death-ligand 1 (PD-L1). Elevated PD-L1 expression on tumor cells can act as a prognostic biomarker, indicating a more aggressive tumor phenotype and a higher likelihood of disease recurrence. Tumors with high PD-L1 expression may escape immune recognition and elimination by inhibiting T-cell activity.^129,130 As a result, patients with such tumors often have a poorer prognosis. However, the presence of high PD-L1 expression may also predict better responses to immune checkpoint inhibitor therapies, which have shown promise in treating colorectal cancer with high PD-L1 expression. Similarly, cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), another immune checkpoint marker, is associated with immune regulation and is currently being investigated as a prognostic biomarker in colorectal cancer. Tumors with high CTLA-4 expression may indicate immune escape mechanisms and a more aggressive phenotype. Clinical trials are exploring the potential benefits of targeting CTLA-4 with immune checkpoint inhibitors to improve treatment outcomes in colorectal cancer patients.^131,132

The assessment of immune checkpoint markers as prognostic biomarkers also extends to tumor-infiltrating lymphocytes (TILs), which play a crucial role in antitumor immunity. The presence of a higher number of activated cytotoxic T cells among TILs in colorectal tumors is generally associated with a more favorable prognosis, suggesting that an effective immune response is mounted against the cancer. Such a finding is indicative of the tumor’s susceptibility to immune-based therapies, including immune checkpoint inhibitors, which can enhance the antitumor immune response.¹³³

4. Targeted Therapies in Precision Medicine

4.1. EGFR Inhibitors and RAS Pathway Targeting

The use of EGFR inhibitors and the RAS pathway as targeted therapy in precision medicine for colorectal cancer exemplifies the growing shift toward personalized treatment strategies. Colorectal cancer is a genetically heterogeneous disease, and understanding the genetic alterations in the RAS pathway is pivotal for tailoring therapy to individual patients. EGFR (epidermal growth factor receptor) is a transmembrane protein that plays a significant role in regulating cell growth and differentiation.¹³⁴ EGFR inhibitors, such as cetuximab and panitumumab, target this receptor, aiming to block downstream signaling and inhibit tumor cell proliferation. However, the effectiveness of these therapies is contingent on the mutation status of the RAS pathway, which includes genes, such as KRAS and NRAS. RAS mutations, particularly in KRAS, are commonly associated with resistance to EGFR inhibitors in colorectal cancer. Activating mutations in KRAS lead to persistent downstream signaling, rendering the blockade of EGFR less effective. Therefore, the RAS mutation status is a critical predictive biomarker in precision medicine for colorectal cancer. Patients with wild-type (nonmutated) RAS genes are more likely to benefit from EGFR inhibitors, whereas those with RAS mutations are typically unresponsive to these therapies.^135,136

Precision medicine in colorectal cancer involves identifying patients with wild-type RAS genes and administering EGFR inhibitors as part of their treatment regimen. This approach helps improve response rates, enhances the effectiveness of treatment, and reduces the risk of unnecessary side effects in patients who are unlikely to benefit from these targeted therapies.^137,138 However, it is essential to note that precision medicine is an ever-evolving field and ongoing research is uncovering further complexities within the RAS pathway. For example, specific mutations, such as the NRAS mutation, can also influence the treatment response. Moreover, acquired resistance mechanisms, such as secondary mutations in RAS genes, can develop during therapy, limiting the long-term effectiveness of EGFR inhibitors.¹³⁹

4.2. VEGF Inhibition and Anti-angiogenic Therapies

Colorectal cancer, like many other malignancies, relies on the development of new blood vessels, a process known as angiogenesis, to supply nutrients and oxygen to the growing tumor. Targeting this angiogenic process has become a key focus in the treatment of colorectal cancer.¹⁴⁰ VEGF is a major driver of angiogenesis and is often overexpressed in colorectal cancer. The binding of VEGF to its receptors triggers a cascade of events leading to the formation of new blood vessels, promoting tumor growth, and facilitating metastasis. As a result, VEGF has become an attractive target for antiangiogenic therapy.¹⁴¹ Antiangiogenic therapies for colorectal cancer primarily consist of drugs that inhibit VEGF or its receptors. Bevacizumab, a monoclonal antibody that targets VEGF, is one of the most widely used antiangiogenic agents in the treatment of colorectal cancer. By neutralizing VEGF, bevacizumab impedes angiogenesis, depriving the tumor of its blood supply and hindering its ability to grow and spread.¹⁴²

The use of antiangiogenic therapy in precision medicine is particularly relevant when considering predictive biomarkers. High levels of VEGF within the tumor microenvironment are often associated with a worse prognosis and a more aggressive disease course.¹⁴³ Therefore, understanding the molecular factors contributing to VEGF overexpression is vital in tailoring treatment strategies. Moreover, antiangiogenic therapies may be most effective in patients with specific genetic profiles or molecular characteristics that indicate an increased reliance on angiogenesis for tumor progression.^144,145 Precision medicine in the context of antiangiogenic therapy may involve the identification of patients who are more likely to benefit from these treatments, such as those with high VEGF expression or specific angiogenic signatures. Additionally, the combination of antiangiogenic therapy with other targeted agents, such as EGFR inhibitors, has been explored to enhance treatment efficacy further, particularly in patients with wild-type RAS genes.¹⁴⁶

4.3. HER2-Targeted Therapies

Although HER2-targeted therapies have been well-established in breast cancer, their application in colorectal cancer is a more recent and evolving field. HER2 is a transmembrane receptor protein that regulates cell growth and division.¹⁴⁷ Overexpression or amplification of HER2 can drive uncontrolled cell proliferation and has been identified in a subset of colorectal cancer patients. The prevalence of HER2 amplification in colorectal cancer is estimated at around 3–5% of cases. HER2-positive colorectal cancer is associated with a more aggressive clinical course including a higher risk of disease recurrence and a poorer prognosis. The identification of HER2 amplification is a crucial step in precision medicine, as it may guide the selection of targeted therapies specifically designed to inhibit HER2 activity.^148,149

The use of HER2-targeted therapies in colorectal cancer has shown promise in clinical trials. Monoclonal antibodies like trastuzumab, pertuzumab, and ado-trastuzumab emtansine (T-DM1) have been tested in HER2-positive colorectal cancer patients.¹⁵⁰ These targeted therapies aim to block the HER2 pathway, slowing the growth and progression of cancer cells. Although the response rates may vary, HER2-targeted therapies offer a potential treatment option for patients with HER2-positive colorectal cancer, particularly for those who have exhausted other available treatments. Precision medicine plays a crucial role in the context of HER2-targeted therapy in colorectal cancer. Identifying patients with HER2 amplification or overexpression allows for a more tailored approach to treatment. By selecting those patients who are most likely to respond to HER2-targeted therapies, clinicians can improve the effectiveness of treatment and potentially enhance patient outcomes.^151,152 Furthermore, ongoing research continues to refine our understanding of HER2 as a therapeutic target in colorectal cancer, highlighting the potential for further advancements in precision medicine for this complex disease.¹¹

4.4. Immune Checkpoint Inhibitors and Immunotherapy

Colorectal cancer, like other malignancies, can evade the immune system’s surveillance by upregulating immune checkpoint proteins, which inhibit the immune response (Figure 6). Immunotherapies aim to counteract this evasion, reinvigorate the immune system, and improve patient outcomes.¹⁵³ One of the primary mechanisms targeted by immunotherapy is the interaction between programmed cell death protein 1 (PD-1) and programmed death-ligand 1 (PD-L1). High expression of PD-L1 on tumor cells can act as a predictive biomarker, indicating that the tumor has developed mechanisms to suppress the immune response. In colorectal cancer, the presence of PD-L1 expression is associated with a more aggressive tumor phenotype and worse prognosis. Immunotherapies that block the PD-1/PD-L1 interaction, such as pembrolizumab and nivolumab, have shown efficacy in a subset of colorectal cancer patients with PD-L1-positive tumors.¹⁵⁴ Another key target in immunotherapy for colorectal cancer is the microsatellite instability-high (MSI-H) or DNA mismatch repair deficient (dMMR) phenotype. Tumors with these characteristics accumulate many genetic mutations, making them more susceptible to immune recognition and attack. This heightened mutational load provides an opportunity for immunotherapies, such as immune checkpoint inhibitors targeting PD-1, to be more effective in MSI-H and dMMR colorectal cancer. Pembrolizumab was the first immune checkpoint inhibitor to receive FDA approval for the treatment of MSI-H or dMMR colorectal cancer, marking a significant advancement in precision medicine for this disease.^102,131

Figure 6.

Mechanism of immune checkpoint inhibitors in cancer therapy. (Reprinted from ref (119). Creative Commons Attribution - Non Commercial (unported, v3.0) License; Dove Medical Press Limited, 2018.)

The integration of immune checkpoint inhibitors and immunotherapy into precision medicine for colorectal cancer involves the identification of patients who are most likely to benefit from these treatments. Molecular testing methods, such as assessing PD-L1 expression, MSI status, and dMMR, play a pivotal role in patient selection. Tailoring treatment to the molecular characteristics of the tumor enhances the chances of therapeutic success and reduces the risk of exposing patients to ineffective treatments and unnecessary side effects.¹⁵⁵

5. Challenges and Considerations in Precision Medicine Implementation

5.1. Tumor Heterogeneity and Clonal Evolution

Colorectal cancer is a highly heterogeneous disease, not only among patients but also within individual tumors. This intratumoral heterogeneity arises from the presence of distinct genetic mutations, variations in gene expression, and differences in cellular phenotypes among cancer cells in the same tumor.¹⁵⁶ This diversity can be a formidable barrier to the success of precision medicine approaches. One of the primary consequences of tumor heterogeneity is the potential resistance to targeted therapies. In colorectal cancer, specific mutations, such as RAS mutations, can render certain targeted therapies ineffective. However, within a single tumor, different regions may harbor varying RAS mutation profiles. If treatment decisions are based on a single biopsy sample that does not represent the entire tumor’s genetic landscape, there is a risk of underestimating the presence of resistant subclones. As a result, targeted therapies may be less effective than anticipated, and patients could experience disease progression due to the survival and growth of undetected resistant subpopulations.^157,158

Clonal evolution further complicates the treatment of colorectal cancer. Over time, the genetic makeup of the tumor can change, with certain subclones acquiring new mutations that provide a growth advantage.¹⁵⁹ This evolution can lead to therapy resistance and the emergence of more aggressive tumor phenotypes. It is crucial for precision medicine to consider the dynamic nature of colorectal cancer and to adapt treatment strategies accordingly. To address these challenges, comprehensive molecular profiling, multiple biopsies, and the monitoring of genetic changes over time are essential components of precision medicine.^160,161 By obtaining a more complete understanding of tumor heterogeneity and clonal evolution, clinicians can better tailor treatments to target the full spectrum of genetic alterations within the tumor. Moreover, the use of liquid biopsies, which analyze circulating tumor DNA, can provide a more comprehensive picture of tumor genetic diversity, allowing for adjustments in treatment regimens as the tumor evolves.¹⁶²

5.2. Access to Next-Generation Sequencing Technologies

Next-generation sequencing (NGS) technologies have become a cornerstone of precision medicine for colorectal cancer, offering the ability to comprehensively analyze the genetic landscape of individual tumors. Colorectal cancer is a genetically complex disease, with various mutations contributing to its development and progression. NGS technologies have revolutionized our understanding of these genetic alterations, enabling tailored treatment strategies and personalized care.¹⁶³

One of the key advantages of NGS in colorectal cancer is its ability to simultaneously examine multiple genes and genetic mutations within a single test. This high-throughput capability allows for the identification of clinically relevant genetic alterations, such as mutations in KRAS, NRAS, BRAF, and other genes, which are critical for determining treatment options.^164,165 The identification of specific mutations or gene expression patterns in the tumor helps clinicians select the most appropriate targeted therapies or immunotherapies, enhancing treatment efficacy, and minimizing potential side effects. NGS also plays a pivotal role in uncovering rare or less common genetic alterations in colorectal cancer. Many of these rare mutations have significant implications for patient prognosis and treatment response.^166,167 For instance, NGS can detect mutations in the HER2 gene, which, when amplified or overexpressed, may make patients eligible for HER2-targeted therapies. By identifying rare genetic events that might not be captured with traditional testing methods, NGS broadens the scope of precision medicine and ensures that no potentially actionable mutations are overlooked. Furthermore, NGS can be applied to monitor disease progression and therapy response over time. This longitudinal approach is particularly valuable in colorectal cancer, where clonal evolution and the development of resistance mechanisms can occur. By periodically assessing the tumor’s genetic profile, clinicians can adapt treatment strategies as needed, ensuring that patients receive the most effective therapies at each stage of their disease.¹⁶⁸

5.3. Integration of Biomarker Testing into Clinical Practice

One of the pivotal biomarkers in colorectal cancer is the mutation status of the RAS gene family, including KRAS and NRAS. These mutations can confer resistance to antiepidermal growth factor receptor (EGFR) therapies, such as cetuximab and panitumumab.¹⁶⁹ Integrating RAS mutation testing into the diagnostic workup is crucial to determine whether these therapies are suitable for a patient. The identification of RAS mutations or wild-type status (nonmutated) guides the selection of treatment options, reducing the risk of exposing patients to ineffective therapies and unnecessary side effects.^170,171

Microsatellite instability (MSI) and DNA mismatch repair deficiency (dMMR) represent another set of biomarkers with critical implications for treatment. Tumors with high MSI or dMMR are more likely to respond to immune checkpoint inhibitors such as programmed cell death protein 1 (PD-1) inhibitors. Integrating MSI or dMMR testing into the diagnostic process helps identify patients who are more likely to benefit from immunotherapy, underscoring the importance of these biomarkers in guiding treatment decisions.¹⁷² Moreover, the integration of multiple biomarker tests is becoming increasingly common in precision medicine for colorectal cancer. Comprehensive molecular profiling that assesses a range of biomarkers, such as RAS mutation status, MSI/dMMR, HER2 amplification, and others, provides a more holistic view of the tumor’s genetic landscape. This integrated approach is essential for capturing the full spectrum of genetic alterations within the tumor, ensuring that no potentially actionable mutations are overlooked.¹⁷³

5.4. Drug Resistance and Drug Specificity

Drug resistance, a phenomenon in which cancer cells become refractory to the effects of therapeutic agents, poses a substantial obstacle to the success of precision medicine strategies. In the context of colorectal cancer, the development of resistance mechanisms can compromise the effectiveness of targeted therapies, limiting their long-term efficacy. Understanding the molecular basis of drug resistance is essential for devising strategies to overcome or prevent it, ensuring the sustained success of precision medicine interventions.^174,175

Another critical consideration in precision medicine against colorectal cancer is drug specificity. While targeted therapies aim to selectively inhibit specific molecular pathways involved in cancer progression, achieving sufficient specificity presents a significant challenge. Off-target effects and unintended interactions with normal tissues can lead to adverse side effects and compromise the therapeutic window of precision medicine drugs.^176,177 Striking the right balance between targeting cancer-specific pathways and minimizing the impact on healthy tissues is crucial for the safety and success of precision medicine interventions. The molecular heterogeneity of colorectal cancer further complicates the landscape of drug specificity. colorectal cancer exhibits diverse molecular subtypes, each characterized by distinct genetic and epigenetic alterations. Tailoring precision medicine approaches to the specific molecular profile of an individual patient’s tumor requires a comprehensive understanding of the unique molecular characteristics of each subtype. The challenge lies in developing therapies that are effective across the spectrum of colorectal cancer subtypes while avoiding generalized approaches that may not be equally beneficial for all patients.^178,179

The evolution of resistance and issues related to drug specificity underscore the need for a dynamic and adaptable approach in precision medicine implementation against colorectal cancer. Continuous monitoring of a patient’s molecular profile throughout the course of treatment, incorporating real-time data, and utilizing advanced diagnostic technologies become crucial components of a successful precision medicine strategy.^180,181 Additionally, the integration of multiomics approaches, combining genomics, proteomics, and metabolomics, offers a more comprehensive understanding of the molecular landscape, aiding in the identification of potential resistance mechanisms and refining drug specificity.¹⁸² Collaborative efforts among researchers, clinicians, and pharmaceutical industries are essential for addressing these challenges. The development of innovative therapeutic strategies, such as combination therapies and personalized treatment regimens, holds promise in overcoming drug resistance and improving drug specificity. Furthermore, the incorporation of artificial intelligence and machine learning in analyzing vast data sets can assist in predicting and mitigating resistance patterns, enhancing the precision of treatment strategies tailored to individual patients.¹⁸³

5.5. Ethical and Regulatory Implications

Ethical and regulatory implications present considerable challenges in the application of precision medicine to colorectal cancer. While precision medicine holds tremendous promise in improving patient care and outcomes, it also raises complex ethical dilemmas and requires careful regulatory oversight to ensure the responsible and equitable use of advanced technologies and therapies.¹⁸⁴

One of the primary ethical challenges revolves around equitable access to precision medicine. As new targeted therapies and genetic testing technologies become available, there is a risk of creating disparities in access to these treatments. Not all patients or healthcare systems may have the same level of access to the latest precision medicine advancements, potentially exacerbating existing healthcare inequalities. Ensuring that the benefits of precision medicine are accessible to all patients, regardless of socioeconomic status or geographic location, is a crucial ethical consideration.^185,186 Moreover, issues related to informed consent and privacy are of paramount concern. Patients often undergo extensive molecular profiling to guide treatment decisions, and this generates a wealth of genetic and medical data. Striking a balance between advancing scientific knowledge and safeguarding the individual’s privacy is essential. Establishing robust data protection measures, informed consent processes, and secure information-sharing frameworks is imperative to alleviate these ethical concerns.¹⁸⁷ Ethical dilemmas arise regarding the storage, sharing, and use of these data, particularly in the context of research. Patients must be informed about the potential implications of sharing their data, including privacy concerns and the use of their information for future research. Ensuring that patients fully understand these implications and can provide informed consent is essential. Addressing these disparities requires a proactive approach in designing and implementing precision medicine strategies, ensuring that the benefits are accessible to diverse demographic groups. This involves considering factors such as socioeconomic status, geographic location, and cultural diversity to prevent the exacerbation of existing healthcare inequities.¹⁸⁸ The regulatory landscape in precision medicine is evolving to keep pace with scientific advancements.^189,190 Regulatory agencies, such as the U.S. Food and Drug Administration (FDA), are faced with the challenge of expeditiously reviewing and approving new targeted therapies and diagnostic tests. Balancing the need for swift access to innovative treatments with the requirement of rigorous safety and efficacy assessments is a significant regulatory challenge. The regulatory framework must adapt to the rapidly changing landscape of precision medicine, where treatments are increasingly tailored to specific genetic profiles.¹⁹¹ Collaboration between regulatory agencies, researchers, and industry partners is fundamental to streamline the approval process and bring innovative precision medicine approaches to patients in a timely manner.^192,193

Additionally, the responsible use of genetic information is a critical regulatory consideration. Genetic discrimination, where individuals could be discriminated against by employers or insurers based on their genetic makeup, is a potential concern. Legislation, such as the Genetic Information Nondiscrimination Act (GINA) in the United States, aims to protect individuals from genetic discrimination, but regulatory agencies must continue to enforce these protections and address any emerging challenges.¹⁹⁴

6. Future Directions and Emerging Technologies

6.1. Liquid Biopsies and Circulating Tumor DNA

Liquid biopsies, particularly the analysis of circulating tumor DNA (ctDNA), represent a transformative and emerging technology in the realm of precision medicine for colorectal cancer treatment. Colorectal cancer is traditionally diagnosed and monitored through tissue biopsies, but liquid biopsies offer a less invasive and more dynamic approach to understanding the genetic landscape of the disease¹⁹⁵ (Figure 7).

Figure 7.

Procedural representation of liquid biopsy analysis for colorectal cancer (modified using Biorender.com).

CtDNA refers to the small fragments of DNA shed by tumor cells in the bloodstream. These fragments carry genetic information about the tumor’s mutations, allowing for noninvasive and real-time assessment of the cancer’s genetic makeup. Liquid biopsies can detect and quantify ctDNA, providing valuable insights into the tumor’s genetic heterogeneity and evolution over time.¹⁹⁶ This technology can help identify specific mutations, including those associated with resistance to targeted therapies, which enable more precise treatment decisions. The potential applications of liquid biopsies in colorectal cancer are vast. First, liquid biopsies can be used for early cancer detection, providing a minimally invasive means to screen individuals at risk and monitor for recurrences in patients who have undergone treatment. Second, these tests can guide treatment decisions by assessing a patient’s response to therapy and detecting the emergence of treatment-resistant mutations. Additionally, liquid biopsies can identify minimal residual disease, offering the possibility of early intervention to prevent relapse.^197,198

The emergence of liquid biopsies in colorectal cancer reflects a shift toward more personalized and patient-centric care. Patients may benefit from reduced reliance on invasive tissue biopsies and more frequent monitoring of their disease through blood tests. However, challenges remain, including the need for further standardization and validation of liquid biopsy techniques. As technology continues to evolve and our understanding of ctDNA deepens, liquid biopsies hold the promise of transforming the way colorectal cancer is diagnosed, monitored, and treated, ultimately enhancing the precision of patient care.^199,200

6.2. Targeted Delivery Systems

The pursuit of precision medicine against colorectal cancer has led to significant advancements in targeted drug delivery systems, offering a sophisticated approach to enhance therapeutic efficacy while minimizing off-target effects. Targeted delivery systems aim to selectively deliver therapeutic agents to cancer cells by exploiting specific molecular markers or features that distinguish them from normal cells. In the context of colorectal cancer, where heterogeneity is a key factor, these systems play a crucial role in improving the precision and effectiveness of treatment strategies.^201,202

Nanoparticles, liposomes, and antibody-drug conjugates are examples of targeted delivery systems that have shown promise in the context of colorectal cancer precision medicine. Nanoparticles, often designed with specific surface modifications, can be engineered to carry therapeutic payloads directly to cancer cells. These nanoparticles can exploit features such as overexpressed receptors or unique cellular characteristics, allowing for selective drug release within the tumor microenvironment.^203,204 Liposomes, lipid-based vesicles, provide a versatile platform for encapsulating and delivering drugs, ensuring controlled release, and reducing systemic toxicity. Antibody-drug conjugates combine the specificity of monoclonal antibodies with potent cytotoxic drugs, enabling targeted delivery to cancer cells expressing specific antigens.²⁰⁵

One of the key advantage of targeted delivery systems in precision medicine for colorectal cancer is the potential to overcome drug resistance. By delivering therapeutic agents directly to cancer cells, these systems can bypass resistance mechanisms that may be present in normal cellular pathways.^206,207 Additionally, targeted delivery reduces exposure to healthy tissues, minimizing side effects and improving the overall safety profile of the treatment. Moreover, targeted delivery systems contribute to the personalization of colorectal cancer treatment by tailoring therapeutic interventions to the unique molecular profile of each patient’s tumor. The ability to customize the drug delivery system based on specific genetic or proteomic markers allows for a more precise and individualized approach. This personalized strategy is particularly relevant in the face of colorectal cancer’s molecular heterogeneity, ensuring that treatment is aligned with the distinct characteristics of each patient’s cancer.^208,209 Despite the considerable promise of targeted delivery systems, challenges persist in their widespread clinical implementation. Issues such as scalability, reproducibility, and the potential for immune responses to the delivery vehicles need to be addressed for these systems to transition from research laboratories to routine clinical practice. Moreover, optimizing the design of delivery systems to accommodate the dynamic changes within the tumor microenvironment is crucial for long-term efficacy.²¹⁰

6.3. Artificial Intelligence and Machine Learning in Precision Medicine

Artificial intelligence (AI) and machine learning have emerged as powerful future technologies with the potential to revolutionize precision medicine for colorectal cancer treatment. The complex nature of colorectal cancer and the vast amount of available patient data make it an ideal candidate for the application of AI and machine learning algorithms to improve diagnosis, prognosis, and therapeutic decision-making.²¹¹

One of the most promising applications of AI in precision medicine for colorectal cancer is in the field of medical imaging. AI-powered image analysis can help radiologists and pathologists identify tumor features, such as size, location, and the presence of metastases, with higher accuracy and efficiency.²¹² This technology can aid in the early detection of colorectal cancer as well as in the assessment of disease progression and response to treatment, ultimately improving patient outcomes. Machine learning algorithms are also being used to integrate and analyze vast data sets, including genetic, molecular, clinical, and radiological information.^213,214 By identifying complex patterns within this data, machine learning can help clinicians predict patient prognosis, identify potential treatment targets, and tailor therapies to individual patients. These algorithms have the capacity to consider a wide range of variables and discover hidden correlations that may not be apparent through traditional methods, offering a more comprehensive and personalized approach to colorectal cancer treatment.^215,216

Furthermore, AI and machine learning can assist in the identification of new drug targets and development of novel therapies. By mining extensive databases of biological information, these technologies can uncover potential drug candidates and predict their efficacy in specific patient populations¹² (Figure 8). This approach has the potential to accelerate the drug discovery process and improve the development of targeted therapies for colorectal cancer. Despite the tremendous promise of AI and machine learning in precision medicine, several challenges must be addressed. Data privacy, regulatory considerations, and the need for rigorous validation of AI algorithms are paramount.^217,218 Additionally, the integration of AI into clinical practice requires healthcare professionals to be trained in the use of these technologies and to collaborate effectively with AI systems.²¹⁹

Figure 8.

Pictorial presentation of advantage of artificial intelligence and machine learning in precision medicine. (Reprinted from “Bioinformatics (AI vs Traditional Techniques), Ona, S. (2023); Biorender.com.)

6.4. Combination Therapies and Personalized Treatment Strategies

Combination therapies and personalized treatment approaches are emerging as promising technologies in precision medicine for colorectal cancer treatment. Colorectal cancer is a heterogeneous disease, and no single therapy is universally effective. To address this complexity, researchers are exploring the synergistic potential of combining multiple treatment modalities tailored to the individual patient’s genetic and molecular profile.²²⁰

Personalized treatment is at the forefront of this approach. By analyzing the genetic and molecular characteristics of a patient’s tumor, clinicians can identify specific driver mutations and aberrant pathways. This information is used to select targeted therapies that are most likely to be effective for that particular patient.²²¹ Precision medicine allows for a more individualized treatment strategy, minimizing exposure to ineffective therapies and optimizing the chances of therapeutic success. Combination therapies take this personalization to the next level. In colorectal cancer, a combination of targeted therapies may be used to simultaneously block multiple signaling pathways that drive the disease.²²² For instance, dual inhibition of the EGFR and HER2 pathways has shown promise in preclinical studies. Additionally, combining targeted therapies with immunotherapy can enhance the body’s immune response against the tumor, improving treatment outcomes. By tailoring combination therapies to a patient’s specific molecular profile, clinicians can optimize the chances of response while minimizing potential side effects.^223,224

While the potential of combination therapies and personalized treatment in colorectal cancer is promising, several challenges must be addressed. These include determining the optimal drug combinations, managing potential drug interactions and toxicities, and developing a deeper understanding of the specific genetic and molecular characteristics that predict the response to these combination regimens. Furthermore, the cost and accessibility of such personalized approaches must be considered to ensure equitable access to these advanced treatments.

6.5. Computational and Bioinformatics Approaches

The integration of computational and bioinformatics approaches has emerged as a transformative paradigm in advancing precision nanomedicine against colorectal cancer. Nanomedicine, with its targeted drug delivery systems and diagnostic platforms, presents an innovative avenue for personalized treatment strategies. Computational modeling and bioinformatics analyses play a pivotal role in optimizing the design and implementation of precision nanomedicine, facilitating a deeper understanding of the complex interactions between nanoparticles and the intricate molecular landscape of colorectal cancer.²²⁵

Computational modeling serves as a powerful tool in predicting and optimizing the behavior of nanoparticles within the biological milieu. Molecular dynamics simulations, for instance, allow researchers to explore the dynamic interactions between nanoparticles and biological components at the atomic level. These simulations provide insights into the stability, biodistribution, and cellular uptake of nanoparticles, guiding the rational design of delivery systems tailored to the unique characteristics of colorectal cancer. Computational approaches also aid in predicting the pharmacokinetics and pharmacodynamics of nanoparticle-based therapeutics, enhancing their precision and efficacy in targeted cancer therapy.^226,227

Bioinformatics, on the other hand, contributes to the interpretation and integration of large-scale omics data generated from nanomedicine studies. High-throughput technologies, such as next-generation sequencing and mass spectrometry, generate vast data sets that require sophisticated bioinformatics analyses to extract meaningful information.²²⁸ Integrating genomics, proteomics, and metabolomics data allows for a comprehensive understanding of the molecular alterations induced by nanomedicine in colorectal cancer cells. Bioinformatics approaches help identify potential biomarkers, unravel signaling pathways affected by nanoparticle interventions, and predict patient responses based on molecular profiles, thus enabling a more refined and personalized approach to treatment.^229,230

Moreover, the application of machine learning and artificial intelligence in computational and bioinformatics analyses enhances the predictive power of precision nanomedicine. These advanced techniques can analyze complex data sets to identify patterns, correlations, and predictive signatures associated with treatment response. Machine learning algorithms can aid in patient stratification, predicting optimal therapeutic regimens, and even anticipating the emergence of drug resistance, thereby contributing to the development of adaptive and personalized nanomedicine strategies against colorectal cancer.^231,232 Despite tremendous potential, challenges persist in the integration of computational and bioinformatics approaches in precision nanomedicine for colorectal cancer. Standardization of modeling methodologies, validation of predictive algorithms, and addressing the dynamic nature of tumor biology remain critical hurdles. Collaborative efforts between computational scientists, bioinformaticians, and experimental researchers are essential to bridge the gap between computational predictions and experimental validations, ensuring the reliability and reproducibility of precision nanomedicine strategies.^233,234

7. Future Progression and Challenges

The future of precision medicine in the fight against colorectal cancer holds great promise, driven by ongoing advancements in technology and a deeper understanding of the molecular complexities associated with this malignancy. One key avenue for progress lies in the refinement and expansion of molecular profiling techniques.^235,236 As high-throughput sequencing technologies continue to evolve, the ability to comprehensively analyze the genomic landscape of colorectal cancer tumors becomes more sophisticated. This evolving molecular characterization, encompassing genetic, epigenetic, and proteomic data, will contribute to a more nuanced understanding of the disease, allowing for the identification of novel targets and the development of tailored therapeutic strategies.²³⁷

In parallel, the integration of artificial intelligence and machine learning into the analysis of vast data sets is poised to revolutionize the field of precision medicine for colorectal cancer. These technologies can decipher intricate patterns within genomic and proteomic information, facilitating the identification of subtle correlations and predictive biomarkers. AI-driven algorithms hold the potential to enhance the accuracy of patient stratification, predict treatment responses, and uncover previously unrecognized molecular subtypes of colorectal cancer, thereby guiding clinicians toward more effective therapeutic interventions.^238,239 Despite these optimiztic prospects, challenges persist on the path to realizing the full potential of precision medicine in colorectal cancer. One notable hurdle involves the need for robust and standardized methodologies for biomarker discovery and validation. As the field advances, ensuring the reproducibility and reliability of identified biomarkers across diverse patient cohorts and clinical settings remains a priority.^240,241 Additionally, the integration of molecular profiling into routine clinical practice requires the development of user-friendly, cost-effective, and widely accessible diagnostic tools. Bridging the gap between cutting-edge research findings and routine patient care will be essential for the successful implementation of precision medicine strategies in colorectal cancer.^242,243

Moreover, the ethical considerations surrounding the use of genomic and proteomic data in clinical decision-making must be addressed. Safeguarding patient privacy, ensuring informed consent, and addressing potential biases in data interpretation are critical aspects that demand ongoing attention. As precision medicine evolves, a multidisciplinary approach involving clinicians, researchers, ethicists, and policymakers will be crucial in navigating these complex ethical landscapes.^244,245

8. Conclusion

Precision medicine is transforming the landscape of colorectal cancer treatment by leveraging an array of advanced technologies and biomarkers. Through the identification of key driver mutations, molecular profiling, and the integration of immune checkpoint inhibitors, precision medicine has begun to offer tailored treatment approaches for colorectal cancer patients. The utilization of liquid biopsies, artificial intelligence, and machine learning, along with combination therapies and personalized treatment strategies, promises to further enhance diagnostic accuracy, therapy selection, and patient outcomes in the future. However, ethical and regulatory considerations, as well as the challenges posed by tumor heterogeneity and clonal evolution, underscore the importance of the responsible and equitable implementation of these cutting-edge technologies in the field of colorectal cancer precision medicine.

Author Contributions

B.G.P. and S.B. - Conceptualization; K.S. and C.Y. - Original Draft; Investigation; Methodology; Data Curation; B.G.P. and R.M. - Editing. Methodology; B.G.P., S.S., and R.M. - Formal Analysis; Validation; Visualization; B.G.P. and S.B. - Review and Editing and Supervision.

The authors declare no competing financial interest.