Association of metabolic and genetic heterogeneity in head and neck squamous cell carcinoma with prognostic implications: integration of FDG PET and genomic analysis

A study on metabolic characteristics and metabolic markers of gastrointestinal tumors

Tumor cells have significant heterogeneity in metabolism and are closely related to prognosis, gene mutation, and subtype. However, this association has not been demonstrated in reports of gastrointestinal tumors. In this study, we constructed four metabolic subtypes and identified four gene signatures using the expression data and clinical information of 252 metabolism-related genes from TCGA and NCBI databases for gastric adenocarcinoma (STAD) and colorectal cancer (COAD and READ). MC1 had the worst prognosis compared to other classifications. GSig1 was mainly related to drug metabolism and was the highest in MC1 with the worst prognosis, while the other subtypes were mainly related to glucose metabolism pathways. This difference also existed in other different malignant tumors. In addition, metabolic typing was associated with chemotherapeutic drug response and tumor heterogeneity, which indicated that monitoring metabolic typing could contribute to drug efficacy and gene-targeted therapy. In conclusion, we identified differences among subtypes in clinical characteristics such as prognosis and revealed the potential function of metabolic subtype in response to chemotherapeutic agents and oncogene mutations. This work highlighted the potential clinical meaning of metabolic subtype and characteristics in drug therapy and prognosis assessment of malignant tumors.

Prognostic impact of an integrative analysis of [18F]FDG PET parameters and infiltrating immune cell scores in lung adenocarcinoma

Background

High levels of ¹⁸F-fluorodeoxyglucose (¹⁸F-FDG) tumor uptake are associated with worse prognosis in patients with non-small cell lung cancer (NSCLC). Meanwhile, high levels of immune cell infiltration in primary tumor have been linked to better prognosis in NSCLC. We conducted this study for precisely stratified prognosis of the lung adenocarcinoma patients using the integration of ¹⁸F-FDG positron emission tomography (PET) parameters and infiltrating immune cell scores as assessed by a genomic analysis.

Results

Using an RNA sequencing dataset, the patients were divided into three subtype groups. Additionally, 24 different immune cell scores and cytolytic scores (CYT) were obtained. In ¹⁸F-FDG PET scans, PET parameters of the primary tumors were obtained. An ANOVA test, a Chi-square test and a correlation analysis were also conducted. A Kaplan–Meier survival analysis with the log-rank test and multivariable Cox regression test was performed to evaluate prognostic values of the parameters. The terminal respiratory unit (TRU) group demonstrated lower ¹⁸F-FDG PET parameters, more females, and lower stages than the other groups. Meanwhile, the proximal inflammatory (PI) group showed a significantly higher CYT score compared to the other groups (P = .001). Also, CYT showed a positive correlation with tumor-to-liver maximum standardized uptake value ratio (TLR) in the PI group (P = .027). A high TLR (P = .01) score of ¹⁸F-FDG PET parameters and a high T follicular helper cell (TFH) score (P = .005) of immune cell scores were associated with prognosis with opposite tendencies. Furthermore, TLR and TFH were predictive of overall survival even after adjusting for clinicopathologic features and others (P = .024 and .047).

Conclusions

A high TLR score was found to be associated with worse prognosis, while high CD8 T cell and TFH scores predicted better prognosis in lung adenocarcinoma. Furthermore, TLR and TFH can be used to predict prognosis independently in patients with lung adenocarcinoma.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13550-022-00908-9.

A Genomic Information Management System for Maintaining Healthy Genomic States and Application of Genomic Big Data in Clinical Research

Improvements in next-generation sequencing (NGS) technology and computer systems have enabled personalized therapies based on genomic information. Recently, health management strategies using genomics and big data have been developed for application in medicine and public health science. In this review, I first discuss the development of a genomic information management system (GIMS) to maintain a highly detailed health record and detect diseases by collecting the genomic information of one individual over time. Maintaining a health record and detecting abnormal genomic states are important; thus, the development of a GIMS is necessary. Based on the current research status, open public data, and databases, I discuss the possibility of a GIMS for clinical use. I also discuss how the analysis of genomic information as big data can be applied for clinical and research purposes. Tremendous volumes of genomic information are being generated, and the development of methods for the collection, cleansing, storing, indexing, and serving must progress under legal regulation. Genetic information is a type of personal information and is covered under privacy protection; here, I examine the regulations on the use of genetic information in different countries. This review provides useful insights for scientists and clinicians who wish to use genomic information for healthy aging and personalized medicine.

KSNM60 in Clinical Nuclear Oncology

Since the foundation of the Korean Society of Nuclear Medicine in 1961, clinical nuclear oncology has been a major part of clinical nuclear medicine in Korea. There are several important events for the development of clinical nuclear oncology in Korea. First, a scintillating type gamma camera was adopted in 1969, which enabled to perform modern oncological gamma imaging. Second, Tc-99 m generator was imported to Korea since 1979, which promoted the wide clinical use of gamma camera imaging by using various kinds of Tc-99 m labeled radiopharmaceuticals. Third, a gamma camera with single photon emission tomography (SPECT) capability was first installed in 1980, which has been used for various kinds of tumor SPECT imaging. Fourth, in 1994, clinical positron emission tomography (PET) scanner and cyclotron with a production of F-18 fluorodeoxyglucose were first installed in Korea. Fifth, Korean Board of Nuclear Medicine was established in 1995, which contributed in the education and manpower training of dedicated nuclear medicine physicians in Korea. Finally, an integrated PET/CT scanner was first installed in 2002. Since that, PET/CT imaging has been a major imaging tool in clinical nuclear oncology in Korea. In this review, a brief history of clinical nuclear oncology in Korea is described.

PET Imaging for Head and Neck Cancers

Head and neck cancers are commonly encountered cancers in clinical practice in the United States. Fluorine-18-fluorodeoxyglucose (¹⁸F-FDG) PET/CT has been clinically applied in staging, occult primary tumor detection, treatment planning, response assessment, follow-up, recurrent disease detection, and prognosis prediction in these patients. Alternative PET tracers remain investigational and can provide additional valuable information such as radioresistant tumor hypoxia. The recent introduction of ¹⁸F-FDG PET/MR imaging has provided the advantage of combining the superior soft tissue resolution of MR imaging with the functional information provided by ¹⁸F-FDG PET. This article is a concise review of recent advances in PET imaging in head and neck cancer.

An Epithelial-Mesenchymal Transition Hallmark Gene-Based Risk Score System in Head and Neck Squamous-Cell Carcinoma

Background

Epithelial-to-mesenchymal transition (EMT) program plays a critical role in cancer. Thus, we attempted to generate a risk score system according to the expression pattern of different EMT hallmark genes in head and neck squamous-cell carcinoma (HNSC).

Methods

Differentially expressed EMT hallmark genes were screened to generate a risk score (RS) on TCGA HNSC dataset. The relative prognostic value of the RS compared to clinicopathological characteristics was explored using multivariable Cox analysis. Functional enrichment analysis was performed to reveal the biological characteristics. An external dataset was applied to validate the prognostic value of the RS.

Results

Nine genes constituted the EMT hallmark gene-based RS, which is significantly associated with poor prognosis and could successfully divide patients with HNSC into high- and low-risk groups. The RS was also an independent prognostic indicator compared to routine clinical factors.

Conclusion

We proposed and validated a nine-EMT hallmark gene-based risk score system in HNSC.

Clinical and immunological characteristics of sarcomas patients with clonogenic tumors

Tumorigenesis is related to the generation of heterogeneous tumor cell population, which is the result of genetic and epigenetic alterations followed by clonal selections and subsequent expansion. In basic studies genetic, histological and morphological diversity of different clones within a patient's neoplasm and specifics of their interrelation with patient's immune system are investigated mostly on the models of tumors of epithelial origin. Mesenchymal tumors such as soft tissue and bone-derived sarcomas (STBS) have been poorly studied in this regard. The molecular genetic methods used to examine intratumoral heterogeneity do not currently provide insight into which portion of the identified subclones are able to grow autonomously. Limiting dilution cloning demonstrates the existence of self-regulating tumor cells in the population and can serve as an independent prognostic predictor of poor prognosis. Intratumoral heterogeneity results not only in differences in growth dynamics, gene expression, and phenotypic markers, but also in the resistance to treatment, especially immunotherapy, thus causing tumor eluding immune escape. The changes that accompany this process can be affected by the cellular immune system, resulting in an imbalance between populations. The variations in the population composition of immune system cells are now widely debated as a predictor of response to immunotherapy, which is of obvious interest for sarcomas, where the effectiveness of chemotherapy is low and the prognosis is unfavorable, especially in case of metastatic disease development. The search for new predictive markers of disease prognosis and treatment efficacy is an important task, to which this study is focused. Our results demonstrate that clonogenic tumor characteristics such as clonogenic potential is independent predictor of unfavorable prognosis in cases of cancer and correlate with the clinical characteristics of the tumor such as overall survival (OS) and progression free survival (PFS). It was found that patients with clonogenic sarcomas had a lower content of activated cytotoxic T-lymphocytes (CTL) with the CD3⁺CD8⁺HLA^-DR⁺ phenotype and an increased number of natural NK killers (p < 0.05) compared to nonclonogenic tumors. In addition, according to our data, a high neutrophil to lymphocyte ratio (NLR), a low value of major T-lymphocyte populations, and a higher number of natural killer cells (NK) in the blood can be negative prognostic factors for the immunotherapy of this disease.

Comprehensive analysis of DNA damage repair in squamous cell carcinoma subtypes

AIMS

Defective components resulting from DNA damage and repair mechanisms have been found to be underlying causes that affect the development and progression of different types of cancers, including squamous cell carcinoma (SCC). A more detailed classification of SCC is necessary for better application of DNA damage repair therapies.

MATERIALS AND METHODS

We aimed to characterize the molecular profile of SCC by developing a classification system based on DNA damage repair gene expression profiles. An integrative analysis was performed using a metadata set of 1374 SCC human samples from the UCSC Genome Browser. We then analyzed genomic alterations and mutations, and genes-TF-microRNA regulatory relationships and conducted enrichment, survival, and immune infiltration analyses.

KEY FINDINGS

This study was conducted on a total of 1374 SCC patients and 402 DNA damage repair genes. Two subtypes were established using consensus clustering, with 1143 patients being of the Non DDR subtype and 231 patients being of the DDR subtype. MATH, mutation burden, and heterogeneity were significantly higher in Non-DDR subtype than in DDR subtype. Next, a total of 1081 differentially expressed genes and 21 microRNAs were identified between the two subtypes and a genes-TF-microRNA regulatory network was constructed. In addition, stromal score, immune score and ESTIMATE score were significantly lower for the Non-DDR subtype, while tumor purity was significantly lower for the DDR subtype. In addition, five pathways associated with DNA damage repair were all enriched in the DDR subtype.

SIGNIFICANCE

Our study established two subtypes of SCC based on DNA damage repair, which may help to predict prognosis and determine the most suitable treatment for SCC patients.

Genetic alterations associated with 18F-fluorodeoxyglucose positron emission tomography/computed tomography in head and neck squamous cell carcinoma

•

¹⁸F-FDG PET/CT visualizes altered glucose metabolism which is underpinned by the alteration of specific genes and signaling pathways.

•

Our analysis of TCGA-HNSC data showed a positive correlation of FDG uptake with the total and non-silent mutation rates, genetic heterogeneity, and copy number alterations.

•

Significant higher FDG uptake was noted in patients with alterations in cell cycle (CDKN2A gene), or TP53 oncogenic signaling pathways (TP53 gene).

Background

We investigated the relationship between genetic alterations and ¹⁸F-FDG PET/CT findings in head and neck squamous cell carcinoma (HNSC).

Methods

Using mRNA-sequences of HNSC samples (480 patients) from the Cancer Genome Atlas (TCGA) portal, gene coexpression networks were constructed via a weighted correlation network analysis (WGCNA) algorithm, and their association with the tumor-to-blood signal ratio on ¹⁸F-FDG PET/CT data (21 patients) was explored. An elastic-net regression model was developed to estimate the PET tumor-to-blood ratio from the gene networks and to derive an FDG signature score (FDG_SS). The FDG_SS was evaluated with regard to clinical variables and general mutational profiles, as well as alterations to oncogenic signaling pathways.

Findings

The FDG_SS values differed across clinical stages (p = 0.027), HPV-status (p< 0.001), and molecular subtypes of HNSC (p< 0.001). Multivariate Cox regression demonstrated that FDG_SS was an independent predictor for overall (p = 0.019) and progression-free survival (p = 0.024). FDG_SS positively correlated with total mutation rate (p = 0.016), aneuploidy (p < 0.001), and somatic copy number alteration scores (p < 0.001). CDKN2A in the cell cycle pathway (q = 0.014) and the TP53 gene in the TP53 pathway (q = 0.005) showed significant differences between high and low FDG_SS patients.

Conclusion

FDG_SS based on the gene coexpression network was associated with the mutational landscape of HNSC. ¹⁸F-FDG PET/CT is therefore a valuable tool for the in vivo imaging of these cancers, being able to visualize the glucose metabolism of the tumor and allow inferences to be made on the underlying genetic alterations in the tumor.

Treatment-related changes in neuroendocrine tumors as assessed by textural features derived from 68Ga-DOTATOC PET/MRI with simultaneous acquisition of apparent diffusion coefficient

Background

Neuroendocrine tumors (NETs) frequently overexpress somatostatin receptors (SSTRs), which is the molecular basis for ⁶⁸Ga-DOTATOC positron-emission tomography (PET) and radiopeptide therapy (PRRT). However, SSTR expression fluctuates and can be subject to treatment-related changes. The aim of this retrospective study was to assess, which changes in PET and apparent diffusion coefficient (ADC) occur for different treatments and if pre-therapeutic ⁶⁸Ga-DOTATOC-PET/MRI was able to predict treatment response to PRRT.

Methods

Patients with histopathologically confirmed NET, at least one liver metastasis > 1 cm and at least two ⁶⁸Ga-DOTATOC-PET/MRI including ADC maps were eligible. ⁶⁸Ga-DOTATOC-PET/MRI of up to 5 liver lesions per patients was subsequently analyzed. Extracted features comprise conventional PET parameters, such as maximum and mean standardized uptake value (SUVmax and SUVmean) and ADC values. Furthermore, textural features (TFs) from both modalities were extracted. In patients with multiple ⁶⁸Ga-DOTATOC-PET/MRI a pair of 2 scans each was analyzed separately and the parameter changes between both scans calculated. The same image analysis was performed in patients with ⁶⁸Ga-DOTATOC-PET/MRI before PRRT. Differences in PET and ADC maps parameters between PRRT-responders and non-responders were compared using Mann-Whitney test to test differences among groups for statistical significance.

Results

29 pairs of ⁶⁸Ga-DOTATOC-PET/MRI scans of 18 patients were eligible for the assessment of treatment-related changes. In 12 cases patients were treated with somatostatin analogues between scans, in 9 cases with PRRT and in 2 cases each patients received local treatment, chemotherapy and sunitinib. Treatment responders showed a statistically significant decrease in lesion volume and a borderline significant decrease in entropy on ADC maps when compared to non-responders. Patients treated with standalone SSA showed a borderline significant decrease in mean and maximum ADC, compared to patients treated with PRRT. No parameters were able to predict treatment response to PRRT on pre-therapeutic ⁶⁸Ga-DOTATOC-PET/MRI.

Conclusions

Patients responding to current treatment showed a statistically significant decrease in lesion volume on ADC maps and a borderline significant decrease in entropy. No statistically significant changes in PET parameters were observed. No PET or ADC maps parameters predicted treatment response to PRRT. However, the sample size of this preliminary study is small and further research needed.