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Eurasian Journal of
Medicine and Oncology Single-cell sequencing for lung cancer

environmental conditions using correlative approaches. imaging. For example, spatial ATAC–RNA-seq combines
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Single-cell proteomics refers to techniques capable of ATAC-seq, which studies chromatin accessibility, with
measuring protein expression levels within individual RNA-seq, which captures gene expression, within the same
cells. Furthermore, integrating transcriptomics and tissue section while preserving spatial information. This
proteomics provides deeper insights into gene expression method tags accessible chromatin regions and captures
and regulatory mechanisms. RNA, followed by spatial barcoding to map gene activity and
chromatin states across tissue regions. This approach offers
Cellular indexing of transcriptomes and epitopes by
sequencing (CITE-seq) is a high-throughput, droplet a comprehensive view of tissue-specific gene regulation and
complex biological processes. Notably, Nature listed spatial
microfluidics-based single-cell technology that integrates multi-omics technologies as one of the seven technologies
transcriptomic and proteomic data by simultaneously to watch in 2022, providing their invaluable insights into
measuring mRNA and proteins. This method uses tissue organization and intercellular communication. 39
antibodies labeled with oligonucleotide barcodes to
analyze proteins while capturing mRNA for sequencing. 3. Single-cell sequencing in lung cancer
Antibody-derived DNA tags (ADTs) contain PCR handles, research
antibody barcodes, and poly(A) tails, allowing antibodies
to bind specific target proteins on the cell surface. After The TME is a highly intricate and dynamic network made
cell sorting and lysis within droplets, the internal contents, up of tumor cells, immune cells, stromal cells, extracellular
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including mRNA and surface proteins, are released. matrix elements, and a variety of signaling molecules. It
mRNA is captured using Drop-seq beads, which are beads plays a crucial role in regulating tumor progression and
coated with oligo(dT) primers that specifically bind to response to therapy. Single-cell sequencing reveals cell
the poly(A) tails of mRNA. Simultaneously, antibody- types, phenotypic changes, and gene expression in lung
derived oligonucleotides (bound to surface proteins) cancer. 15,41
are also captured by these beads. A sequencing library is 3.1. Intratumor heterogeneity in lung cancer
generated using cDNA molecules and PCR amplification,
enabling the simultaneous quantification of mRNA and Intratumor heterogeneity is mainly associated with clonal
proteins through sequencing. Multi-omics approaches evolutionary trajectory, which is the main cause of drug
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allow the tracing of tumor cell clonal evolution, revealing resistance, metastatic progression, and adverse clinical
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epigenomic differences between primary and metastatic outcomes. scRNA-seq has become a pivotal technique
tumors. They also facilitate the study of key regulatory in elucidating the intratumor heterogeneity (ITH) in lung
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elements in the tumor immune microenvironment and cancer. Tian et al. analyzed approximately 5,000 single
uncover the epigenetic mechanisms of immune escape. cells from primary tumors and adjacent normal tissues
of 11 small cell lung cancer (SCLC) patients, discovering
In addition, spatial genomics is rapidly emerging, as heterogeneity in cell cycle, immune response, hypoxia,
disease development involves dynamic changes in cells epithelial-mesenchymal transition (EMT), and key
within specific spatial locations. Spatial omics enable the transcription factors (TCFs) such as achaete-scute family
study of cellular interactions with surrounding cells and BHLH TCF1 and neurogenic differentiation 1. Li et al.
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extracellular matrices. This allows for the identification used scRNA-seq to identify mixed-lineage tumor cells in
of different cellular subpopulations and gene expression non-SCLC, which co-expressed classical marker genes
states in distinct tissue regions. By providing spatial associated with adenocarcinoma (ADC), squamous cell
dimensional information, it deepens the understanding carcinoma, and neuroendocrine tumor, demonstrating
of these processes and their underlying mechanisms. high cellular plasticity. Patients with high mixed-lineage
Spatial multi-omics technologies are advancing rapidly features had worse prognoses, and aldo-keto reductase
in single-cell sequencing, integrating molecular data with family 1 member B (AKR1B1) was identified as a
spatial information to analyze gene expression patterns potential therapeutic target. Chan et al. found a highly
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and chromatin accessibility in tissue contexts. These heterogeneous SCLC population, including a recurrent
technologies allow researchers to study not only gene phospholipase C gamma 2 (PLCG2)-high subpopulation
expression but also cell–cell interactions and networks with stem-like, pro-metastatic traits linked to poor
within their native tissue environments. Some prominent prognosis, emphasizing the need for targeted therapies.
methods include array-based spatial transcriptomics,
microfluidic deterministic barcoding strategies, DNA 3.2. Epithelial cells
antibody tags, multiplex single-molecule fluorescent in situ Epithelial cells, the origin of malignant cells, show a
hybridization, in situ sequencing, and mass spectrometry complex heterogeneity and plasticity in lung cancer.
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Volume 9 Issue 2 (2025) 7 doi: 10.36922/ejmo.6883