Characterization and validation of somatic mutation spectrum to reveal heterogeneity in gastric cancer by single cell sequencing

Single-cell multi-omics in the study of digestive system cancers

Digestive system cancers are prevalent diseases with a high mortality rate, posing a significant threat to public health and economic burden. The diagnosis and treatment of digestive system cancer confront conventional cancer problems, such as tumor heterogeneity and drug resistance. Single-cell sequencing (SCS) emerged at times required and has developed from single-cell RNA-seq (scRNA-seq) to the single-cell multi-omics era represented by single-cell spatial transcriptomics (ST). This article comprehensively reviews the advances of single-cell omics technology in the study of digestive system tumors. While analyzing and summarizing the research cases, vital details on the sequencing platform, sample information, sampling method, and key findings are provided. Meanwhile, we summarize the commonly used SCS platforms and their features, as well as the advantages of multi-omics technologies in combination. Finally, the development trends and prospects of the application of single-cell multi-omics technology in digestive system cancer research are prospected.

Applications of single‑cell omics and spatial transcriptomics technologies in gastric cancer (Review)

Gastric cancer (GC) is a prominent contributor to global cancer-related mortalities, and a deeper understanding of its molecular characteristics and tumor heterogeneity is required. Single-cell omics and spatial transcriptomics (ST) technologies have revolutionized cancer research by enabling the exploration of cellular heterogeneity and molecular landscapes at the single-cell level. In the present review, an overview of the advancements in single-cell omics and ST technologies and their applications in GC research is provided. Firstly, multiple single-cell omics and ST methods are discussed, highlighting their ability to offer unique insights into gene expression, genetic alterations, epigenomic modifications, protein expression patterns and cellular location in tissues. Furthermore, a summary is provided of key findings from previous research on single-cell omics and ST methods used in GC, which have provided valuable insights into genetic alterations, tumor diagnosis and prognosis, tumor microenvironment analysis, and treatment response. In summary, the application of single-cell omics and ST technologies has revealed the levels of cellular heterogeneity and the molecular characteristics of GC, and holds promise for improving diagnostics, personalized treatments and patient outcomes in GC.

Applications and Achievements of Single-Cell Sequencing in Gastrointestinal Cancer

Gastrointestinal cancer represents a public health concern that seriously endangers human health. The emerging single-cell sequencing (SCS) technologies are different from the large-scale sequencing technologies which provide inaccurate data. SCS is a powerful tool for deciphering the single-cell resolutions of cellular and molecular landscapes, revealing the features of single-cell genomes, transcriptomes, and epigenomes. Recently, SCS has been applied in the field of gastrointestinal cancer research for clarifying the origin and heterogeneity of gastrointestinal cancer, acquiring micro-environmental information, and improving diagnostic and treatment methods. This review outlines the applications of SCS in gastrointestinal cancer research and summarizes the most recent advances in the field.

Exposing structural variations in SARS-CoV-2 evolution

The mutation of SARS-CoV-2 influences viral function as residue replacements affect both physiochemical properties and folding conformations. Although a large amount of data on SARS-CoV-2 is available, the investigation of how viral functions change in response to mutations is hampered by a lack of effective structural analysis. Here, we exploit the advances of protein structure fingerprint technology to study the folding conformational changes induced by mutations. With integration of both protein sequences and folding conformations, the structures are aligned for SARS-CoV to SARS-CoV-2, including Alpha variant (lineage B.1.1.7) and Delta variant (lineage B.1.617.2). The results showed that the virus evolution with change in mutational positions and physicochemical properties increased the affinity between spike protein and ACE2, which plays a critical role in coronavirus entry into human cells. Additionally, these structural variations impact vaccine effectiveness and drug function over the course of SARS-CoV-2 evolution. The analysis of structural variations revealed how the coronavirus has gradually evolved in both structure and function and how the SARS-CoV-2 variants have contributed to more severe acute disease worldwide.

Intratumoral and intertumoral heterogeneity of HER2 immunohistochemical expression in gastric cancer

BACKGROUND

Given the high heterogeneity of tumor tissue in gastric cancer (GC), inaccurate detection of tumor biomarkers will inevitably hamper a precise diagnosis and selection of patients for targeted therapies. Human epidermal growth factor receptor 2 (HER2) has been widely accepted as an underlying treatment biomarker of GC. The objective of this study is to investigate the heterogeneity (both intratumoral and intertumoral) of HER2 expression in GC, and the relationship between heterogeneity and the clinicopathological features.

METHODS

A total of 618 patients with primary gastric adenocarcinoma were recruited, and two formalin-fixed paraffin-embedded (FFPE) tumor-containing blocks of each patient were selected for HER2 immunohistochemical (IHC) assay. Clinicopathological characteristics were recorded, and intratumoral and intertumoral heterogeneity of HER2 IHC expression was determined.

RESULTS

The results indicated that the dual-block assays significantly increased the HER2 overexpression (IHC 2+ and 3+) rate compared with the single paraffin block detection. Approximately 50 % of the cases showed intratumoral HER2 heterogeneity within a single tissue section, and 30.10 % of cases showed intertumoral heterogeneity between a patient's two blocks. Furthermore, intertumoral heterogeneity was associated with tumors of small size (P = 0.029) and distal location (P = 0.032) characters, while the intratumoral heterogeneity was correlated with poorly differentiated carcinomas. Laurén's diffuse type showed a notably higher intratumoral heterogeneity rate, and the mixed type exhibited higher intertumoral HER2 discordance between the dual-block cohorts (P < 0.001). Besides, HER2 heterogenous overexpression was not associated with age, gender, type of resection, lymphatic or venous invasion, perineural invasion or pTNM (P > 0.05) for both cohorts.

CONCLUSION

The research findings in this paper indicate that the intratumoral and intertumoral heterogeneity of HER2 overexpression is common in GC patients, and these variations are associated with certain clinicopathological features. We highly recommend multi-block HER2 assessment for accurate diagnosis of GC.