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Global Translational Medicine Computational advances in cancer liquid biopsy

4. Repetitive elements (REs) remains a challenge, particularly in complex, repetitive
genomic regions. From a computational point of view, the
An intriguing perspective in the field of cfDNA hurdle of precisely assessing somatic TE activity lies in the
epigenomics is represented by transposable elements (TEs), difficulty of determining the exact genomic insertion sites
which are major components of eukaryotic genomes. TEs of elements that share very similar sequences, are repeated
are known for their ability to mobilize to new genomic in hundreds of thousands of genomic locations, and are
locations, affecting gene expression regulation and often embedded within one another.
inducing the formation of double-strand breaks, genomic
rearrangements, and epigenetic modifications. For these reasons, the contribution of TEs in cfDNA is still
poorly characterized, but increasing efforts are being devoted to
Utilizing TE DNA sequences in liquid biopsies offers
a range of benefits. Cancer cells harbor multiple copies maximizing the potential of this material. Recently, an alignment-
of TEs, which inevitably result in a higher concentration free, genome-wide method was developed for analyzing cfDNA
of TE DNA released into the blood compared to single- repeat landscapes, which appeared to be broadly altered in
copy genes. The high prevalence of RE DNA within various human cancers. The authors were able to predict patients
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cfDNA reduces the requirement for large quantities of with early-stage cancer and identify the tumor tissue of origin,
biological fluids and template DNA, making RE DNA and as the specific RE alterations varied among different tumor
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its expression products, such as long-interspersed nuclear types. Alu elements, the most abundant non-autonomous
element-1 (LINE-1) ORF2, prime candidate biomarkers TEs, are hypomethylated during tumor progression, similar to
for liquid biopsies in cancer patients. In particular, TE LINE-1s. Alu elements also mirror the modified fragmentation
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DNA sequences are useful in two key areas: quantifying patterns observed in the cfDNA of cancer patients, making
total cfDNA and evaluating cfDNA integrity. 70,71 them valuable for developing techniques aimed at early cancer
detection using cfDNA. By integrating LINE-1 methylation,
Massive global hypomethylation of TEs has been Alu-derived cfDNA concentrations, and Alu index, Park et
documented in physiological conditions such as aging, al. were able to distinguish cancer patients from healthy
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and pathological conditions, such as cancer, resulting individuals. In addition, Douville et al. developed a classifier
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in retroelement reactivation and subsequent genomic whose most important feature was the underrepresentation of
instability, which is associated with poor prognosis. the AluS subfamily in cfDNA from patients with solid cancers
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Although this phenomenon has been documented in only compared to controls.
a few cancer types, it appears that each tumor displays a
distinct methylation pattern, reflected in the autonomous cfRNA sequencing data derived from TEs and other
LINE-1 methylation profile detectable in cfDNA. repeat elements is another promising, yet underexplored,
Methylation is one of the strategies employed by our bodies application in the realm of liquid biopsy. In a recent
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to silence potentially propagating, active, and autonomous study, Reggiardo et al. presented a novel technique
LINE-1 elements. Indeed, extensive research has focused that allows for the in-depth characterization of disease-
on the methylation levels of these retrotransposons as specific, repeat-derived cfRNAs. Leveraging a highly
potential epigenetic markers for cancer. The ability to sensitive RNA-seq protocol coupled with single-molecule
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detect LINE-1 tumor-specific hypomethylation patterns in nanopore sequencing, the authors were able to detect
cfDNA could establish LINE-1 as a valuable biomarker for both coding and non-coding RNAs and provide accurate
tumor screening and tissue-of-origin identification. While characterization of protein-coding RNA, long non-coding
these pioneering works have shown promising results, RNA, LINE, short interspersed nuclear element (SINE),
further efforts are needed to address the critical limitations and LTR-derived cfRNAs characterization. The technique
related to LINE-1 hypomethylation in cfDNA to determine allows the classification of cancer patients, revealing the
its applicability as a biomarker in clinical practice. The value and utility of broadly characterizing the so-called
activity of the few “hot” LINE-1 elements varies depending “junk” fraction of the genome.
on the individual tumor type, stage, and the timeframe in
the clonal evolution of the tumor. Additional studies on 5. Transcriptomics
patients with different tumor types and stages, as well as Transcriptome analysis of CTCs has been performed for
asymptomatic patients and cancer-free controls, should several cancer types, 78-80 both at the bulk and single-cell
be conducted to evaluate intratumoral and intertumoral levels, showing that CTCs are a heterogeneous population
heterogeneity. between and within patients. This technology has greatly
Despite continuous technological advancements, contributed to discovering signal pathways involved in
comprehensively capturing the entire range of TE-mediated metastasis, resistance to chemotherapy, and epithelial-to-
structural variants with high sensitivity and specificity mesenchymal transition (EMT).

Volume 3 Issue 3 (2024) 5 doi: 10.36922/gtm.3063