Estimating tongue deformation during laryngoscopy using a hybrid FEM-multibody model and intraoperative tracking - a cadaver study

Throat tumour margin control remains difficult due to the tight, enclosed space of the oral and throat regions and the tissue deformation resulting from placement of retractors and scopes during surgery. Intraoperative imaging can help with better localization but is hindered by non-image-compatible surgical instruments, cost, and unavailability. We propose a novel method of using instrument tracking and FEM-multibody modelling to simulate soft tissue deformation in the intraoperative setting, without requiring intraoperative imaging, to improve surgical guidance accuracy. We report our first empirical study, based on four trials of a cadaveric head specimen with full neck anatomy, yields a mean TLE of 10.8 ± 5.5 mm, demonstrating methodological feasibility.

Comprehensive landscape of tRNA-derived fragments in lung cancer

Transfer RNA (tRNA)-derived fragment (tRDF) is a novel small non-coding RNA that presents in different types of cancer. The comprehensive understanding of tRDFs in non-small cell lung cancer remains largely unknown. In this study, 1,550 patient samples of non-small cell lung cancer (NSCLC) were included, and 52 tRDFs with four subtypes were identified. Six tRDFs were picked as diagnostic signatures based on the tRDFs expression patterns, and area under the curve (AUC) in independent validations is up to 0.90. Two signatures were validated successfully in plasma samples, and six signatures confirmed the consistency of distinguished expression in NSCLC cell lines. Ten tRDFs along with independent risk scores can be used to predict survival outcomes by stages; 5a_tRF-Ile-AAT/GAT can be a prognosis biomarker for early stage. Association analysis of tRDFs-signatures-correlated mRNAs and microRNA (miRNA) were targeted to the cell cycle and oocyte meiosis signaling pathways. Five tRDFs were assessed to associate with PD-L1 immune checkpoint and correlated with the genes that target in PD-L1 checkpoint signaling pathway. Our study is the first to provide a comprehensive analysis of tRDFs in lung cancer, including four subtypes of tRDFs, investigating the diagnostic and prognostic values, and demonstrated their biological function and transcriptional role as well as potential immune therapeutic value.

Abstract 5865: Analysis of RNA sequencing data to advance our understanding of colorectal cancer health disparity in Native Hawaiians

Background Colorectal cancer (CRC) is the third deadliest cancer among Americans. Native Hawaiians (NH) as a unique ethnic group in the US, exhibit many disproportionate health issues. In particular, they suffer from both elevated CRC incidence and mortality rates. This study aimed to investigate if genetic differences could contribute to disparities observed between NH and White CRC patients by defining the association between unique NH-genetic differences and CRC outcomes.

Methods Paired tumor and adjacent normal biospecimens of NH CRC patients were collected from the Hawaii Tumor Registry (HTR), and gene expression and mutation were examined by RNA sequencing. Genomic data of CRC Whites was extracted from The Cancer Genome Atlas (TCGA) database as a comparative cohort. Differential expressed genes (DEGs) were identified for both NH and TCGA cohorts via DESeq2 with FDR q-value < 0.05 and a cutoff of 2-fold change. MutTecT2 and GATK were used to identify significant somatic mutations. Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression with 10-fold cross validation was performed to predict genetic risk factors for early detection, and Ingenuity Pathway Analysis (IPA) was processed for canonical pathways and network discovery. Univariate Cox proportional regression was performed to identify DEGs related to patient survival; multivariable Cox regression model with stepwise fitting generated a prognostic index (PI), and the prediction value was examined by the Area Under the Receiver Operating Characteristic Curve (AUC). A nomogram was developed by integrating PI and clinicopathologic factors; calibration curves were provided to internally validate the performance, and discriminative ability was appraised by concordance index.

Results In total, 2096 DEGs were identified between NH tumor and normal groups, 1740 transcripts and 78 carrying mutations were unique to NH compared to the TCGA Whites cohort. A set of 23 genes including 10 NH specific DEGs were identified as genetic risk factors for detecting NH with CRC, and the AUC was 99.8%. A 9 gene-signature prognostic model including 5 NH specific DEGs was built with high survival prediction capability (AUC=0.99), and Kaplan-Meier curve showed that the low PI group had a better survival than the high PI group in NH with CRC (Logrank P=3.6E-05). After adjustment by age, gender, and tumor grade, the prognostic 9 gene-signature was still significant (P=0.0059). By integrating the above signatures with prognostic clinicopathologic features, a nomogram was constructed to stratified patients with overall survival rates for 3, 10, and 20 years.

Conclusion This study demonstrated that CRC tumors from NH patients differ from White patients in their gene expression patterns and mutations, particularly those associated with clinical outcomes, which reinforced the necessity of NH race-specific biomedical research.

Citation Format: Yuanyuan Fu, Devin Takahashi, Vedbar Khadka, Masaki Nasu, Mayumi Jijiwa, Heather Borgard, Peiwen Fei, Youping Deng. Analysis of RNA sequencing data to advance our understanding of colorectal cancer health disparity in Native Hawaiians [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5865.

Abstract 1241: Six potential biomarkers for non-small cell lung cancer diagnosis and prognosis

tRNA-derived fragment (tRDF) is novel small non-coding RNA that presences in different types of cancer tissue. More evidence has shown that tRDFs are associated with cancer progression through cell proliferation. In this study, we took advantage of public database and small RNA sequencing to investigate the diagnosis and prognosis potential of tRDFs as a biomarker for non-small cell lung cancer. We collected 1028 patient samples including adenocarcinoma from TCGA, GEO, and plasma. We gathered all fragments upstream sequences and 5’-tRF, to be categorized as 5’-tRDF and fragments 3’-tRF and downstream sequences, to be categorized as 3’-tRDF. 52 tRDFs were identified that were common in TCGA and GEO, and clustering results separated two GEO with TCGA as distinct expression pattern. 11 differentially expressed tRDFs were screened out from the GEO data and exhibited excellent diagnostic value. The AUC of two independent validations was up to 0.90. Six tRDFs, 5P_tRNA-Gly-TCC-1-1, 5a_tRF-Ile-AAT/GAT, 3P_tRNA-Arg-TCG-1-1, and 3P_tRNA-Arg-TCT-4-1, 5P_tRNA-Asn-GTT-2-3, 5a_tRF-Asp-GTC, were named as tRDF signatures and exhibited the same excellent diagnosis ability, and combination had better performance than individual tRDFs. Plasma data validated the diagnostic characteristics of two signatures, 3P_tRNA-Arg-TCG-1-1 and 5P_tRNA-Asn-GTT-2-3, that could serve as novel diagnostic biomarkers. We investigated the relationship between signatures and prognosis by stages and following-up times in TCGA-LUAD. 5a_tRF-Ile-AAT/GAT were identified to be a significant prognostic value with survival time on 36 months and 24 months among early stages patients. 3P_tRNA-Arg-TCT-4-1 was identified to associate with survival outcome within 12 and six months in early stages. We also assessed the role of tRDFs in transcriptional and post-transcriptional events. 3’-tRDFs showed more correlation with miRNA than 5’-tRDFs. A correlation analysis showed signatures, 5a_tRF-Asp-GTC, dominated the most correlation with miRNAs. Enrichment results of six tRDFs signatures presented PI3K-Akt, MAPK, and endocytosis signaling pathways are associated with tRDF target miRNAs. We also analyzed the signaling pathway characteristic of the six signatures tRDFs-target genes and found the tRDFs correlated genes are significantly activated in the cell cycle, oocyte meiosiss. Five signatures were assessed to associate with PD-L1 immune checkpoint and correlated with the genes that targets in PD-L1 checkpoint signaling pathway. Our study is the first to provide a comprehensive analysis of tRDFs as biomarkers in lung cancer, investigating the diagnostic and prognostic values of tRDFs, and demonstrated their biological function and transcriptional role as well as potential immune therapeutic value. This work highlights the potential clinical utility of tRDFs in lung cancer therapy and provides evidence of tRDF-target treatment in lung cancer.

Citation Format: Zitong Gao, Mayumi Jijiwa, Masaki Nasu, Heather Borgard, Jinwen Xu, Ting Gong, Shaoqiu Chen, Yuanyuan Fu, Youping Deng. Six potential biomarkers for non-small cell lung cancer diagnosis and prognosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1241.

Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies

DNA methylation is associated with transcriptional repression, genomic imprinting, stem cell differentiation, embryonic development, and inflammation. Aberrant DNA methylation can indicate disease states, including cancer and neurological disorders. Therefore, the prevalence and location of 5-methylcytosine in the human genome is a topic of interest. Whole-genome bisulfite sequencing (WGBS) is a high-throughput method for analyzing DNA methylation. This technique involves library preparation, alignment, and quality control. Advancements in epigenetic technology have led to an increase in DNA methylation studies. This review compares the detailed experimental methodology of WGBS using accessible and up-to-date analysis tools. Practical codes for WGBS data processing are included as a general guide to assist progress in DNA methylation studies through a comprehensive case study.

Abstract PO-167: Predictive genetic risk factors and prognostic nomogram for colorectal cancer in Native Hawaiian population

Background While Native Hawaiians (NH) comprise a small portion of the US population, their numbers are expected to increase. Concerningly, NH exhibit disproportionate health issues, and specifically those with colorectal cancer (CRC) present elevated incidence and mortality above the US population. This study aims to identify race-specific genetic factors for CRC early detection and prognosis in this unique population. Methods Paired tumor and adjacent normal biospecimens from NH patients with primary CRC were collected from the Hawaii Tumor Registry (HTR), and RNA sequencing on 41 paired samples were performed to establish the first genome-wide transcriptome profiling dataset specifically for NH with CRC. RNAseq data of 18 paired samples and additional 212 cancer samples were taken from The Cancer Genome Atlas (TCGA) white patients. Differential expressed genes (DEGs) were identified for both NH and TCGA cohorts via DESeq2 with FDR q-value < 0.05 and a cutoff of 2-fold change. A diagnostic model was built by Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression with 10-fold cross validation, and Ingenuity Pathway Analysis (IPA) was processed for canonical pathways and network discovery. Univariate Cox proportional regression was performed to identify DEGs related to NH patient survival; multivariable Cox regression model with stepwise fitting generated a prognostic index (PI): PI=Σbi × expGenei (where expGene defines the gene expression and b equals the regression coefficient), and the prediction value was examined by the Area Under the Receiver Operating Characteristic (ROC) Curve (AUC). A nomogram was developed by integrating PI and clinicopathologic factors; calibration curves were provided to internally validate the performance, and discriminative ability was appraised by concordance index. Results In total, 2096 DEGs were identified between tumor and normal groups, and 1740 transcripts were unique to NH compared to the TCGA Whites cohort. A set of 23 genes including 10 NH specific DEGs was identified as genetic risk factors for detecting NH with CRC, and the AUC was 99.8%. A 9 gene-signature prognostic model including 5 NH specific DEGs was built with high survival prediction capability (AUC=0.99), and Kaplan-Meier curve showed that the low PI group had a better survival than the high PI group in NH with CRC (Logrank P=3.6E-05). After adjustment by age, gender, and tumor grade, the prognostic 9 gene-signature was still significant (P=0.0059). By integrating the above signatures with prognostic clinicopathologic features, a nomogram was constructed to stratified patients with overall survival rates for 3, 10, and 20 years. Conclusion Divergent DEGs and consequential pathways between NH and TCGA cohort reinforced the necessity of NH race specific biomedical research. The prognostic gene signature offered evidence that genomic data provided independent and complementary prognostic information, and the nomogram incorporating genetic and clinicopathological factors refined the prognosis of CRC for this unique population.

Citation Format: Yuanyuan Fu, Devin Takahashi, Vedbar Khadka, Masaki Nasu, Mayumi Jijiwa, Yu Chen, Heather Borgard, Youping Deng. Predictive genetic risk factors and prognostic nomogram for colorectal cancer in Native Hawaiian population [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PO-167.

The Function and Mechanism of Lipid Molecules and Their Roles in The Diagnosis and Prognosis of Breast Cancer

Lipids are essential components of cell structure and play important roles in signal transduction between cells and body metabolism. With the continuous development and innovation of lipidomics technology, many studies have shown that the relationship between lipids and cancer is steadily increasing, involving cancer occurrence, proliferation, migration, and apoptosis. Breast cancer has seriously affected the safety and quality of life of human beings worldwide and has become a significant public health problem in modern society, with an especially high incidence among women. Therefore, the issue has inspired scientific researchers to study the link between lipids and breast cancer. This article reviews the research progress of lipidomics, the biological characteristics of lipid molecules, and the relationship between some lipids and cancer drug resistance. Furthermore, this work summarizes the lipid molecules related to breast cancer diagnosis and prognosis, and then it clarifies their impact on the occurrence and development of breast cancer The discussion revolves around the current research hotspot long-chain non-coding RNAs (lncRNAs), summarizes and explains their impact on tumor lipid metabolism, and provides more scientific basis for future cancer research studies.

Multi-modal Framework for Image-guided Trans-oral Surgery with Intraoperative Imaging and Deformation Modeling

Treatment of throat cancers have improved due to minimally-invasive trans-oral approaches. Surgeons rely on preoperative imaging to guide their resection; however, large tissue deformations occur during trans-oral procedures due to placement of necessary retractors and laryngoscopes which hinders the surgeon's ability to accurately assess tumor extent and location of critical structures. We propose an image-guided framework utilizing intraoperative imaging and deformation modeling to improve surgeon accuracy and confidence. A CT-compatible laryngoscopy system previously developed was evaluated in this framework. Intraoperative images were acquired during laryngoscopy; force-sensing capabilities were enabled in the laryngoscope; and tracking of the scope and anatomic features was trialed. Tissue deformation and displacement were quantified and determined to be extensive, with values <; 4.6 cm in the tongue, <; 1.8 cm in bony structures, and <; 108.9 cm³ in airway volume change. Surgical navigation using intraoperative imaging and tracking was evaluated. Preliminary assessment of deformation modeling showed potential to supplement intraoperative imaging. Future work will involve streamlined integration of the components of this framework.