Humara Naz Majeed, Aftab Ahmad Science Reviews - Biology, 2024, 3(3), 1-15
1
Emerging Bioengineering Approaches for Cancer and
Tumor Therapy
Humara Naz Majeed*, PhD and Aftab Ahmad
1
, PhD
*Dr. Humara Naz Majeed (Corresponding Author)
Department of Biochemistry, Government College Women University, Faisalabad, Pakistan; drhumaranaz@gcwuf.edu.pk
https://orcid.org/0000-0002-9393-1941
1
Dr. Aftab Ahmad
Department of Biochemistry/US-Pakistan Centre for Advance Studies in Agriculture and Food Security (USPCAS-AFS), University
of Agriculture Faisalabad, Pakistan; aftab.ahmad@uaf.edu.pk
https://orcid.org/0000-0002-2792-9771
https://doi.org/10.57098/SciRevs.Biology.3.3.1
Received September 21, 2024. Revised October 06, 2024. Accepted October 07, 2024
Abstract: Cancer has become a significant socioeconomic burden globally, with millions of new cases and deaths
each year. The promising field of bioengineering has recently undergone significant advancements, providing
new methods for combating cancer. Increasing attention has been directed toward understanding the molecular
mechanisms of human diseases, supported by the availability of various genetic tools and rapid technological
advancements. These developments have enabled the use of the latest gene therapy techniques for cancer
treatment, including gene editing, gene deletion, and correcting defective genes through methods such as
TALENs, Zinc fingers, RNAi, CRISPR, site-directed mutagenesis (SDM), and enzyme therapy to modulate
catalytic activity. In addition, bioengineering vaccines like mRNA vaccines, bioinformatics, computational tools,
artificial intelligence (AI), nanotechnology, and chemotherapy are emerging as significant cancer treatment
strategies. Among these, gene editing and gene therapy have gained particular attention in recent years and are
often used in combination with other therapeutic approaches. The engineering of enzymes and advancements
in nanotechnology have also significantly progressed. AI and bioinformatics have contributed to more precise
diagnosis, prediction, and prognosis, enabling tailored treatment of cancer and tumors. Imaging and
radiotherapy, enhanced by AI, have improved surgical outcomes, even from remote locations. Precision
oncology has emerged, using bacteria and viruses to target tumors directly. In this review, we discuss recent
advancements and challenges in various cancer therapies.
Keywords: Bioengineering, Gene therapy, CRISPR-Cas9, RNAi, Enzyme therapy, Chemotherapy, Bioinformatics,
Computational tools, Artificial Intelligence, Cancer and Tumor
Introduction
Cancer has a long historical presence in human-
ity, with the earliest known cases dating back to
around 1500 BCE (Beg and Parveen, 2021). The inci-
dence and mortality rates of cancer have continued to
rise globally, with approximately 19.3 million new
cases and 10 million deaths recorded in 2020, as per
Global Cancer Statistics (Sung et al., 2020). Despite the
availability of conventional cancer treatments like radi-
ation, chemotherapy, and surgery, these approaches
often prove insufficient and fail to fully eradicate the
disease, as evidenced by the increasing cancer inci-
dence and mortality rates (Qian et al., 2021). While
significant research has focused on understanding mo-
lecular mechanisms, immunotherapy, and signaling
pathways such as PI3K/AKT/mTOR, many cancers
remain resistant to treatment, necessitating the devel-
opment of new therapeutic strategies (Hosseini et al.,
2019; Zahoor et al., 2019); however, the drug resistance
and cancer recurrence necessitate new therapeutic ap-
proaches (Schirrmacher, 2019).
Cancer is now one of the greatest threats to
human health globally. The International Agency
for Research on Cancer (IARC), under the World
Health Organization (WHO), reports that many
countries lack adequate resources to properly
Humara Naz Majeed, Aftab Ahmad Science Reviews - Biology, 2024, 3(3), 1-15
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manage the disease, with only 39% of countries hav-
ing basic cancer management services. Cancer is
currently the second leading cause of death world-
wide, accounting for approximately 9.3 million
deaths annually, with one in six deaths attributed to
the disease. It is predicted that by 2030, 26 million
new cancer cases will emerge, leading to 17 million
probable deaths. By 2050, the number is expected to
increase significantly, particularly in low- to mid-
dle-income countries, where 61% of all new cancer
cases are projected to occur. In the United States
alone, 611,720 cancer-related deaths have been re-
ported in 2024, with over two million new cases ex-
pected this year (Hobbs, 2024). These alarming sta-
tistics highlight the urgent need to improve clinical
treatments, enhance bioengineering of enzymes
and drugs, develop advanced drug delivery sys-
tems, and refine therapeutic techniques such as
nanotechnology and chemotherapy to combat can-
cer more effectively worldwide (Binns and Low,
2024).
1. Gene Therapy
Recent studies have shown that gene therapy
holds significant promise for correcting defective
genes responsible for cancer. Techniques such as ri-
bonucleic acid interference (RNA i) and clustered
regularly interspaced short palindromic re-
peat/CRISPR-associated nuclease 9 (CRISPR/Cas9)
genome editing system have garnered considerable
attention globally.
I. DNA based Gene Therapy
Unlike traditional cancer treatments, DNA-
based gene therapy focuses on editing the genetic
material of cancer patients by replacing defective
genes with functional ones or modifying existing
sequences.
a. Gene Editing through CRISPR/Cas9 and
Cancer
The CRISPR/Cas9 system has emerged as a
powerful genetic engineering tool, widely applied
to manipulate nucleases for editing specific genes in
cancer cells. Oncoproteins such as Myc, CycE, and
their regulator archipelago (ago) are known to con-
trol cellular growth through the polyubiquitination-
mediated protein degradation pathway. Mutations
in the archipelago (ago) gene have been linked to
breast and ovarian cancers in humans (Zahoor et al.,
2019; Vo et al., 2018). The CRISPR-Cas9 technique
enables precise gene editing in oncogenes and the
restoration of tumor suppressor genes, presenting a
promising strategy for cancer treatment (Hosseini et
al., 2019a; Gemayel et al., 2024; Carrera-Pacheco et
al., 2024).
Clustered Regularly Interspaced Short Palin-
dromic Repeats (CRISPR) and CRISPR-associated
protein 9 (CRISPR/Cas9) is a cutting-edge genetic
technique considered one of the most advanced
tools for cancer treatment (Ma et al., 2024; Guo et al.,
2022). This system allows for the editing of genes for
a range of purposes, including both knock-out and
knock-in operations. The CRISPR/Cas9 system
originates from the bacterial adaptive immune re-
sponse against invading bacteriophages, first dis-
covered in E. coli in 1987 (Li et al., 2022). It operates
via a single-guide RNA (sgRNA), which is specifi-
cally designed to complement the target site of in-
terest. This guide RNA directs the Cas9 endonucle-
ase to create a double-stranded break (DSB) at the
precise location within the DNA sequence (Ruan et
al., 2022). CRISPR-Cas9 offers highly efficient, site-
specific gene correction and editing (Ma et al., 2024).
Unlike earlier techniques such as Zinc-Finger
Nucleases (ZFN) and Transcription Activator-Like
Effector Nucleases (TALEN), which require modifi-
cation of the endonucleases for each specific target,
the CRISPR/Cas9 system only requires altering the
guide RNA (gRNA) for different target sites. This
distinctive feature of CRISPR/Cas9, where the en-
donucleases remain unchanged, makes it more cost-
effective compared to conventional methods like
TALEN and ZFN (Jiang et al., 2019). Furthermore,
the ability to design specific gRNAs for various tar-
get sites enhances both the accuracy and target
specificity of the system, making it more precise
than previous approaches (Jiang et al., 2019).
The scope of the CRISPR/Cas9 system has
significantly expanded in the medical field, particu-
larly in cancer treatment. The American Society for
Cancer reports that breast cancer is the leading
cause of death in the U.S. (Binns and Low, 2024) and
other parts of the world (Siegel et al., 2024).
CRISPR/Cas9 has been employed to modify T cells,
enhancing their ability to inhibit tumors (Zhao et al.,
2018; Guo et al., 2018; Choi et al., 2019). Moreover,
CRISPR/Cas9 targeting the Ptch1 gene has shown
success in treating brain tumors (Vo et al., 2018). In
vertebrate models, such as mice, CRISPR/Cas9 has
been applied to target tumorigenesis-related genes
(Ratan et al., 2018). A notable application includes
Science Reviews - Biology, 2024, 3(3), 1-15 Humara Naz Majeed, Aftab Ahmad
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treating tyrosinemia type I in mouse hepatocytes
caused by Fah mutation, which was corrected using
CRISPR/Cas9 (Xu et al., 2020). Furthermore, multi-
plexed gene-editing techniques using
CRISPR/Cas9 have been employed in mouse mod-
els to inhibit tumor growth by targeting multiple
genes, achieving high accuracy without significant
off-target effects (Liang et al., 2023).
The deactivated protein variant of Cas9
(dCas9) is utilized by the CRISPR-Cas system to
bind DNA without causing double-strand breaks,
blocking transcriptional initiation and thereby
downregulating genes. This technique, known as
CRISPR interference (CRISPRi), has been applied in
cancer research to induce gene loss-of-function. For
instance, CASP8AP2 has been identified as an es-
sential viability factor in lung cancer, while syner-
gistic effects of ITGB5, TIMP1, and TMEM176B
genes on prostate cancer cell proliferation have
been observed. Activation of TMEM176B and
TIMP1, coupled with inhibition of ITGB5, has
shown potential in suppressing prostate cancer
growth (Yang et al., 2021; Myacheva et al., 2023).
CRISPRi has also been widely used for screening
various cancer-related factors across different or-
gans, helping to identify and improve cancer thera-
pies (Handly et al., 2020; Davies et al., 2021; Ahmed
et al., 2021; Cui et al., 2022). Thus, CRISPR/Cas9 has
proven highly effective in cancer and tumor re-
search (Ma et al., 2024).
b. RNA based Cancer Treatment
MicroRNAs (miRNAs) and small interfering
RNAs (siRNAs) represent short nucleic acid mole-
cule-based techniques with significant potential in
cancer treatment. siRNAs facilitate mRNA degrada-
tion in the cytoplasm by binding to RNA-induced
silencing complexes (RISC), which use siRNA or
miRNA as templates to locate and degrade target
mRNA via RNase activity. Both miRNAs and siR-
NAs have shown inhibitory effects on tumors and
cancer cells (Guan et al., 2019; Xiong et al., 2010).
miRNAs have the ability to block translation, exhib-
iting anticancer effects against liver, pancreatic, and
breast cancers. In vivo delivery of siRNAs has
demonstrated significant control over cancer metas-
tasis (Parvani et al., 2015). Notably, miRNA deliv-
ery using a three-helix structure has been effective
in reducing the size of malignant tumors in mice by
disrupting cancer-related gene expression. This ap-
proach simultaneously activates tumor-inhibiting
miRNAs while suppressing tumor-promoting miR-
NAs (Conde et al., 2016). RNA-based therapy, espe-
cially in combination with chemotherapy, has
shown remarkable specificity, targeting cancer cells
without affecting normal cellsa common issue in
chemotherapy alone. Such approaches, including
RNA-RNA co-delivery and drug combination ther-
apies, are gaining attention as promising cancer
treatment strategies (Beck et al., 2021; Cao et al.,
2024; Erdoğan et al., 2023; Espinoza et al., 2021;
Liang et al., 2023; Naseri et al., 2025).
Figure 1: Different Gene Therapy Approaches for Cancer Treatment
II. Site-Directed Mutagenesis
Site-directed mutagenesis (SDM) has
emerged as a crucial genetic tool for molecularly
characterizing gene products, such as enzymes or
proteins. It plays an essential role in modulating
specificity, activity, solubility, and stability of en-
zymes, as well as elucidating their biochemical
properties and dissecting their roles in signal trans-
duction (Pommier et al., 2003; Majeed et al., 2015;
Humara Naz Majeed, Aftab Ahmad Science Reviews - Biology, 2024, 3(3), 1-15
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Zeymer and Hilvert, 2018; Fu et al., 2024; Majeed et
al., 2024). The selection and identification of the spe-
cific site for SDM is critical to the process. Various
bioinformatics tools and software not only help in
identifying the precise mutagenesis site but also in
reproducing 3D structures before and after muta-
genesis (Majeed et al., 2024a; Steiner et al., 2012).
Databases like Swiss-model or NCBI can be used to
generate amino acid sequences for drawing 3D
structures. Through UCSF Chimera, the activity
and stability of enzymes, both in wild-type and mu-
tant forms, can be comprehensively studied. SDM
in glycosyltransferases, a family of enzymes respon-
sible for glycosylation, has been suggested to assist
in the development of cancer drugs (Majeed et al.,
2024).
SDM is widely used for enzyme modification
to enhance catalytic efficiency. For example, terpe-
noids, known for their anti-inflammatory and anti-
tumor properties, and α-galactosidase, an enzyme
used in cancer diagnosis and therapy, have both
been improved through SDM to increase their cata-
lytic efficacy (Xu et al., 2014; Sarkar et al., 2022). Ad-
ditionally, a mutant superantigen,
SEC2(T20L/G22E), developed via SDM, has
demonstrated enhanced antitumor activity com-
pared to its native form in vitro (Wang et al., 2009).
A promising approach in cancer therapy, amino
acid deprivation therapy (AADT), inhibits cancer
cell proliferation by limiting amino acid availability
without affecting normal cells, which have lower
amino acid requirements. This makes AADT selec-
tive and non-toxic (Pokrovsky et al., 2022; Kumar et
al., 2022; Zhang et al., 2024).
Among targets for AADT, asparagine has
shown promise. L-asparaginase, an enzyme that hy-
drolyzes L-asparagine into L-aspartate and ammo-
nia, inhibits the availability of essential amino acids
in cancer cells, leading to cell death and reduced
proliferation (Butler et al., 2021). However, L-aspar-
aginase also accepts L-glutamine as a substrate,
which can lead to side effects like cerebral hemor-
rhage and neurological disorders due to decreased
glutamine levels (Van Trimpont et al., 2022; Feng-
min et al., 2023). Recent SDM efforts have improved
L-asparaginase’s activity, reducing its L-glutami-
nase activity and minimizing these side effects
(Zhang et al., 2024). Another recent breakthrough
includes the production of the anticancer com-
pound dehydroabietic acid through heterologous
expression in Saccharomyces cerevisiae via SDM (Ma
et al., 2024a). Nanobodies, traditionally produced
from camelid immune libraries, are widely used in
diagnostics and immunotherapy. However, due to
the complexity of animal-based procedures, recent
studies have utilized CDR grafting and SDM to pre-
pare genetically engineered nanobodies, such as
anti-CD20 nanobodies, for leukemia treatment.
SDM, when combined with other therapeutic tech-
niques, holds potential in treating cancer and tu-
mors (Gu et al., 2023; Heidari et al., 2024).
2. Enzyme Engineering/Therapy
Enzymes are essential biochemical catalysts,
facilitating specific reactions due to their protein-
based nature, which grants them high specificity to
distinguish substrates of similar structures. Their
catalytic efficiency is closely tied to the integrity of
their protein conformation (Tandon et al., 2021).
Mutations can compromise this efficiency, leading
to dysfunction in enzyme-related diseases, prompt-
ing the development of drugs targeting these com-
promised enzymes. In recent years, enzymes have
emerged as valuable tools for investigating and
treating various pathological conditions, including
cancer and metabolic deficiencies (Majeed et al.,
2024; Wang et al., 2024; Tvaroška, 2022). By utilizing
genetic engineering, enzymes can be modified to ac-
tivate under specific conditions, such as the hypoxic
or acidic environments found in tumor cells. Be-
sides creating new enzymes, existing enzymes can
be optimized for better activity through recombi-
nant DNA technology. This includes manipulating
molecular structures, altering amino acid sequences,
and introducing mutations via genetic engineering
(Majeed et al., 2024; Wang et al., 2024). These tech-
niques are crucial for enhancing desirable enzyme
traits, such as improving kinetic properties, increas-
ing thermal stability, adjusting optimal tempera-
tures, enhancing specificity, and eliminating allo-
steric regulations (Tandon et al., 2021).
Clinically and medically important com-
pounds are being produced by genetically introduc-
ing the gene encoding the desired product into var-
ious organisms, using genetic engineering tech-
niques (Fig. 2). This process has enabled the devel-
opment of several natural anticancer drugs through
enzyme engineering (Majeed et al., 2024; Wang et
al., 2024; Tvaroška, 2022). By bioengineering en-
zymes, researchers can assess the presence or ab-
sence of critical amino acids at catalytic sites, an ap-
proach made possible through methods such as do-
main swapping or site-directed mutagenesis (SDM).
These engineered enzymes are designed to target
and bind to specific structures and molecules found
Science Reviews - Biology, 2024, 3(3), 1-15 Humara Naz Majeed, Aftab Ahmad
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in cancer cells, enabling the precise delivery of ther-
apeutic agents directly to the cancerous tissues for
more effective treatment.
Figure 2: A brief summary of Enzyme Engineering
Genetic modifications in enzymes enable
them to restore target molecules for proper physio-
logical metabolism. While these treatments offer
significant advantages over previously established
therapeutic approaches due to their specificity, en-
zyme therapies also present several challenges. One
major issue is their short in vivo half-life, which can
lead to decreased specificity due to enzyme degra-
dation in the body. Additionally, the patient's im-
mune system may recognize the administered re-
combinant enzyme as a foreign neo-antigen, trig-
gering an immune response. This immune reaction
reduces therapeutic efficacy by generating anti-
drug antibodies, which either inhibit enzyme activ-
ity by binding to its catalytic site or block substrate
access. Such immune responses have been observed
in several studies. For example, glucocerebrosidase
treatments in Gaucher’s disease patients (Rosen-
berg et al., 1999), α-L-iduronidase therapy in
Hurler’s syndrome (Kakavanos et al., 2003), α-glu-
cosidase in Pompe’s disease, and α-galactosidase in
Fabry’s disease have all shown immune responses
against these enzymes (Amalfitano et al., 2001; Eng
et al., 2001). Despite these issues, ongoing research
is focused on developing novel biotechnological
strategies to enhance the efficacy and application of
enzyme therapies in the future (Radadiya et al.,
2020; Jadhav et al., 2020; Liu et al., 2021).
3. Bioengineering of Vaccines
mRNA-based therapies are emerging as a
highly effective approach for disease treatment. The
success of mRNA vaccines during the COVID-19
pandemic has laid the foundation for further ad-
vancements in this field, particularly in cancer im-
munotherapy (Cao et al., 2024a; Mir et al., 2024).
mRNA vaccines work by stimulating the innate im-
mune system, which then triggers an adaptive im-
mune response, targeting the disease (Cao et al.,
2024a; Mir et al., 2024). In recent developments,
mRNA vaccines have shown significant promise for
cancer treatment by expressing tumor antigens in
antigen-presenting cells (APCs), which subse-
quently activates both the innate and adaptive im-
mune systems (Li et al., 2023; Miao et al., 2021).
mRNA vaccines are gaining recognition for
their safety, potency, and cost-effectiveness, despite
certain limitations such as instability, in vivo ineffi-
ciency, and immunogenicity issues (Li et al., 2023;
Miao et al., 2021). Structural modifications of
mRNA are being explored to overcome these limi-
tations. The emergency authorization of COVID-19
mRNA vaccines, such as Comirnaty (BNT162b2)
and Spikevax (mRNA-1273), by the US FDA has
opened new possibilities for using mRNA technol-
ogy in cancer immunotherapy (Miao et al., 2021).
Over the past two years, mRNA vaccines have sig-
nificantly contributed to combatting SARS-CoV-2
Humara Naz Majeed, Aftab Ahmad Science Reviews - Biology, 2024, 3(3), 1-15
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and have provided a platform for ongoing research
into cancer vaccines (Li et al., 2023).
The key to mRNA vaccine success lies in its
practical mechanismunlike traditional vaccines
or viral vectors, mRNA vaccines prompt the body
to produce the necessary proteins directly after in-
jection. However, to maximize their efficacy against
cancer, improving mRNA vaccine delivery systems
in terms of safety and handling is crucial. Combina-
tion therapies have been suggested to enhance effi-
cacy (Tan et al., 2023; Duan et al., 2022).
mRNA vaccines are being increasingly studied
as an alternative approach for cancer prevention and
treatment (Beck et al., 2021). Large-scale production of
mRNA vaccines has helped reduce costs, but clinical
trials for cancer treatments remain focused on non-
replicating mRNAs (Lu and Robbins, 2016; Li et al.,
2019). Self-amplifying mRNAs (SAM), a more cost-ef-
fective approach, are advancing to the clinical trial
stage for cancer treatment (Tan et al., 2020; Liu et al.,
2021). These vaccines can stimulate a robust immune
response by encoding specific tumor-associated anti-
gens, utilizing self-amplifying RNA vectors, or com-
bining mRNA with adjuvants. Other strategies in-
clude gene editing tools, immune checkpoint inhibi-
tors, and novel delivery systems aimed at enhancing
the immune response against cancer cells (Beck et al.,
2021).
Although preclinical studies of mRNA cancer
vaccines show promise, their efficacy in early clini-
cal trials remains limited. Additional challenges in-
clude manufacturing complexity, immunogenicity,
and stability. Nonetheless, with further develop-
ment, mRNA cancer vaccines hold significant po-
tential as a breakthrough in cancer treatment (Tan
et al., 2020; Liu et al., 2021; Li et al., 2019).
4. Chemotherapy
Traditional cancer treatment has predomi-
nantly focused on systemic therapies like chemo-
therapy, where drugs circulate through the blood-
stream to block or slow down the growth of cancer
cells. Chemotherapy is primarily employed in two
ways: to treat cancer by inhibiting its progression or
to reduce tumor size, often relieving painful symp-
toms (Sharma et al., 2024). However, the cytotoxic
nature of chemotherapy impacts healthy organ sys-
tems, particularly the kidneys and liver, and can
lead to irreversible side effects on the skin, heart,
and nerves, sometimes with fatal consequences
(Gustafson et al., 2013; Aslam et al., 2014; Sharma et
al., 2024). While some side effects are reversible
over time, chemotherapy also poses challenges such
as drug resistance, limited target specificity, and re-
duced efficacy against certain tumor cells. Combin-
ing chemotherapy with gene therapy has been sug-
gested as a way to enhance its success in cancer
treatment, with the addition of ultrasound technol-
ogy further improving outcomes (Peng et al., 2023;
Sharma et al., 2024).
Recent advances have explored using nano-
particles, specifically designed to target DNase, to
inhibit cancer cell proliferation and metastasis. This
approach has shown promise in controlling tumor
metastasis and improving chemotherapy outcomes
(Peng et al., 2023; Sharma et al., 2024). Despite the
drawbacks, significant progress has been made to
optimize chemotherapy, including the develop-
ment of next-generation black hole algorithms that
have shown potential in effectively managing and
treating cancer. While new state-of-the-art tech-
niques continue to emerge, the combination of
chemotherapy with other modern approaches of-
fers a cost-effective and efficient treatment strategy
(Dos Santos et al., 2024).
5. Nanotechnology
Nanomedicine has emerged as a rapidly ad-
vancing field in cancer treatment. Although chemo-
therapy remains a key option, its limitations have
spurred interest in alternative methods. Depending
on the type, stage, and nature of the cancer, differ-
ent strategies are employed. The rising incidence of
skin cancer, in particular, has prompted the explo-
ration of nanocarriers as an efficient therapeutic ap-
proach (Mongia et al., 2024).
Nanoparticles, which are less than 100 na-
nometers in diameter, are increasingly being recog-
nized for their potential in cancer treatment. Their
favorable properties, including a high surface-to-
volume ratio, heterogeneous nature, and enhanced
site specificity, make them suitable for standalone
treatments or in combination with other therapeutic
options. Various modifications have enabled the de-
velopment of versatile nanoparticles, including
coated, magnetic, metal, and silica variants. In addi-
tion, nanocarriers such as polyplexes, exosomes,
liposomes, and polymersomes are being employed
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to induce tumor cell death and stimulate an im-
mune response (Peer et al., 2020; Gavas et al., 2021).
Recent breakthroughs in nanotechnology
have led to the development of DNA nanostruc-
tures for the targeted delivery of cancer drugs.
These nanosystems are bioengineered for precision,
ensuring accurate delivery to specific tissues or lo-
cations. Engineered to recognize and bind to cancer
cells, these nanostructures represent a significant
advancement in targeted cancer therapy (Yadav et
al., 2024).
6. Cancer Therapy through Viral and Bacterial
Pathogens
Under challenging and often unavoidable cir-
cumstances, chemotherapy and radiotherapy re-
main the primary options for cancer treatment.
However, drug resistance has emerged as a signifi-
cant obstacle, with certain tumor tissues proving
difficult for drugs to penetrate deeply (Duong et al.,
2019). This has created a growing demand for alter-
native treatment options that demonstrate effective-
ness under specific conditions. Recently, bacterial-
based therapies and oncolytic viruses (OVs) have
been employed with success in combating cancer.
The principle behind this is that the tumor microen-
vironment is susceptible to bacterial colonization,
which in turn induces an immune response against
the tumor. Many bacteria can infiltrate and colonize
tumors, aiding in their eradication. Additionally,
OVs have shown the ability to specifically target
cancer cells, inducing apoptosis (Shalhout et al.,
2023).
Historically, bacteria such as Streptococci and
Clostridia were among the first employed in cancer
therapy. Today, advancements in genetic engineer-
ing have led to the use of genetically modified bacte-
ria in cancer treatments (Yarahmadi et al., 2024). Bac-
terial species like Salmonella, Listeria, and Clostridium
are particularly promising because of their natural
ability to penetrate tumors, replicate, and shrink
them through various mechanisms (Duong et al.,
2019). Research has shown that Salmonella typhi-
murium can directly attack and kill tumor cells, pro-
liferating within the tumor until the cells undergo
apoptosis, necrosis, or rupture (Sarotra et al., 2016).
Numerous bacteria and viruses, including Bifidobac-
teria, Clostridium, Listeria monocytogenes, Salmonella
typhimurium, Bacillus, as well as oncolytic viruses like
vaccinia viruses, adenoviruses, reoviruses,
herpesviruses, and coxsackieviruses, have been
tested in various therapeutic strategies with remark-
able outcomes. These findings position them as key
players in the potential eradication of malignant tu-
mors (Kiaheyrati et al., 2024). Consequently, there is
increasing support for the development of strategies
that incorporate these specific bacteria and viruses,
either alone or in combination, to treat cancer in hu-
mans (Kiaheyrati et al., 2024; Ijaz et al., 2024; Cao et
al., 2024a).
7. Bioinformatics and Computational Tools
Bioinformatics tools have been extensively
applied in a broad range of research areas, particu-
larly in genomics and proteomics, to advance our
understanding of human cancers (Anashkina et al.,
2021). Long non-coding RNAs (lncRNAs), endoge-
nous RNA molecules of approximately 200 nucleo-
tide base pairs, have gained attention due to their
prominent role in humans, especially in embryonic
development and cancer progression (Gu et al.,
2021; Zhang et al., 2021). Research has demon-
strated that lncRNAs are significantly associated
with carcinogenesis (Chen et al., 2023; Statello, 2021;
Xu et al., 2022). Thanks to advances in bioinformat-
ics, new therapeutic tools, such as SINEUPs, are
emerging for RNA-based therapies (Stransky & Ga-
lante, 2010; Espinoza et al., 2021). These develop-
ments have helped elucidate the precise mecha-
nisms of lncRNA-regulated gene expression, shed-
ding light on key processes in cancer, including me-
tastasis, cell invasion, proliferation, and apoptosis
(Xu et al., 2020; Zhang et al., 2021; Erdoğan et al.,
2023).
More recently, dysregulation of lncRNAs has
been linked to gastric cancer (Naseri et al., 2025).
The use of high-throughput techniques has gener-
ated vast amounts of data, stored in databases and
repositories, such as the Stanford Microarray Data-
base and the Gene Expression Omnibus, which are
crucial for advancing cancer research (Hanauer et
al., 2007). Other tools, including Module Maps,
SLAMS (Stepwise Linkage Analysis of Microarray
Signatures), and COPA (Cancer Outlier Profile
Analysis), have also greatly contributed to this field
(Hanauer et al., 2007; Stransky & Galante, 2010).
Following the year 2000, The Cancer Genome Atlas
(TCGA) project emerged as an extension of the Hu-
man Genome Project, with the goal of developing a
comprehensive atlas of genetic changes associated
Humara Naz Majeed, Aftab Ahmad Science Reviews - Biology, 2024, 3(3), 1-15
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with cancer (Tomczak et al., 2015). Moreover, the
Cancer Biomedical Informatics Grid (caBIG), an
initiative of the National Cancer Institute (NCI), has
greatly enhanced the biological research commu-
nity’s access to data, contributing significantly to
cancer research and the development of precision
medicine (Fenstermacher et al., 2006).
Substantial advancements have been made
using in silico techniques, especially in genomics
and proteomics (Anashkina et al., 2021; Beg & Par-
veen, 2021). Recently, predictive models for protein
structures have been developed to assist in site-di-
rected mutagenesis (SDM). For instance, the use of
BLAST tools and the SWISS-Model Template Li-
brary (SMTL) allows for protein model building,
and visualization through UCSF Chimera has been
reported (Majeed et al., 2024a). Majeed and col-
leagues (2024a) performed SDM on the glycosyl-
transferase enzyme UGT71B8, comparing wild-
type and mutant forms, which opens new possibili-
ties for cancer treatment. Glycosyltransferases have
also been identified as promising targets in gastric
cancer therapy (Wang et al., 2024). In addition, bio-
informatics tools like PrDOS
(http://prdos.hgc.jp/cgi-bin/top.cgi) enable re-
searchers to determine enzyme disorder probabili-
ties, further enhancing cancer research (de Brevern,
2020).
Any gene or gene product associated with
cancer can be analyzed using bioinformatics tools,
and 3D structural validation can be achieved
through methods such as the Ramachandran plot.
In summary, bioinformatics and computational
tools have revolutionized cancer research by inte-
grating vast datasets, advanced software, and algo-
rithms, driving cancer research toward more tar-
geted and effective treatments (Altschul et al., 1997;
Waterhouse et al., 2018; Chauhan et al., 2020;
Majeed et al., 2015; Anashkina et al., 2021; Beg &
Parveen, 2021).
8. Artificial Intelligence
Over the past decade, artificial intelligence
(AI) has undergone significant evolution, now of-
fering advanced and innovative approaches for the
diagnosis and treatment of cancer. AI has revolu-
tionized early detection, enabling the prediction of
cancer onset and progression even in the earliest
stages, a development often referred to as precision
oncology. Through AI-enhanced imaging and
radiotherapy, healthcare professionals are now able
to more precisely delineate tumor boundaries and
cancerous cells. This precise targeting has led to sig-
nificant improvements in therapeutic outcomes
(Weerarathna et al., 2023). While human expertise
remains crucial, AI surpasses traditional methods in
several areas, particularly in cancer and tumor
treatment.
It has been suggested that an integrated ap-
proach combining multiple strategies such as radi-
odiagnosis, radiotherapy, ophthalmology, derma-
tology, pharmacology, chemotherapy, immuno-
therapy, nanotechnology, targeted therapy, and
surgery could provide even more effective cancer
treatments (Cabral et al., 2023; Weerarathna et al.,
2023).
Cancer is a complex disease caused by genetic
mutations, often resulting in uncontrolled cell prolif-
eration. Even among similar tumor types, character-
istics can vary greatly, making accurate predictions
challenging. AI, however, leverages genomics and
proteomics data to develop personalized medicine
approaches. For instance, the HER2 biomarker has
been effectively used in breast cancer patients, illus-
trating the utility of AI-based precision medicine
(Binns & Low, 2024). AI has made significant strides
in enhancing cancer detection accuracy, reducing
risk, improving prognosis and prediction at early
stages, and characterizing tumors. The use of AI al-
gorithms and sophisticated computing software con-
tinues to push the boundaries of what is possible in
cancer diagnosis and treatment (Binns & Low, 2024;
Weerarathna et al., 2023).
Challenges and Future Perspectives
Cancer continues to pose a significant threat
to global health, currently standing as the second
leading cause of death worldwide. The rising global
cancer burden demands a focus on developing pre-
cise, effective, and cost-efficient treatment strategies.
Significant progress has been made in understand-
ing the molecular mechanisms underlying cancer,
with gene therapy emerging as a promising tool for
its treatment. However, despite the progress, sev-
eral invisible risks remain under-examined. Off-tar-
get effects and side effects of nucleic acid-based
drugssuch as complications in the blood and di-
gestive systemsalong with the non-targeted de-
livery of nanoparticles, bacterial strains, and viruses,
Science Reviews - Biology, 2024, 3(3), 1-15 Humara Naz Majeed, Aftab Ahmad
9
need thorough investigation to ensure safety and ef-
ficacy.
Drugs like doxorubicin, widely used against
various cancer types, are known to cause several
side effects that warrant further research into safer
alternatives. Integrating bioinformatics tools and
artificial intelligence into cancer diagnosis and
treatment stages can offer significant advancements
in precision medicine. These tools can help process
large datasets from genomics and proteomics, en-
suring more accurate predictions of cancer progres-
sion and improving patient outcomes. However,
careful consideration must be given to optimizing
algorithms and software before moving forward
with personalized oncology.
To ensure success, there is a pressing need for
the optimization of emerging techniques for safe, af-
fordable, and precise cancer treatment. Further-
more, potential unforeseen issues, including ethical
concerns, must be carefully addressed as new ther-
apeutic technologies and methodologies continue
to evolve. The balance between innovation and pa-
tient safety should remain a top priority as we move
toward the future of cancer treatment.
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