Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer Genomics

Interventional Oncology: 2024 Update

Interventional Oncology (IO) stands at the forefront of transformative cancer care, leveraging advanced imaging technologies and innovative interventions. This narrative review explores recent developments within IO, highlighting its potential impact facilitated by artificial intelligence (AI), personalized medicine and imaging innovations. The integration of AI in IO holds promise for accelerating tumour detection and characterization, guiding treatment strategies and refining predictive models. Imaging modalities, including functional MRI, PET and cone beam CT are reshaping imaging and precision. Navigation, fusion imaging, augmented reality and robotics have the potential to revolutionize procedural guidance and offer unparalleled accuracy. New developments are observed in embolization and ablative therapies. The pivotal role of genomics in treatment planning, targeted therapies and biomarkers for treatment response prediction underscore the personalization of IO. Quality of life assessment, minimizing side effects and long-term survivorship care emphasize patient-centred outcomes after IO treatment. The evolving landscape of IO training programs, simulation technologies and workforce competence ensures the field's adaptability. Despite barriers to adoption, synergy between interventional radiologists' proficiency and technological advancements hold promise in cancer care.

A clinical evaluation of an ex vivo organ culture system to predict patient response to cancer therapy

Introduction

Ex vivo organ cultures (EVOC) were recently optimized to sustain cancer tissue for 5 days with its complete microenvironment. We examined the ability of an EVOC platform to predict patient response to cancer therapy.

Methods

A multicenter, prospective, single-arm observational trial. Samples were obtained from patients with newly diagnosed bladder cancer who underwent transurethral resection of bladder tumor and from core needle biopsies of patients with metastatic cancer. The tumors were cut into 250 μM slices and cultured within 24 h, then incubated for 96 h with vehicle or intended to treat drug. The cultures were then fixed and stained to analyze their morphology and cell viability. Each EVOC was given a score based on cell viability, level of damage, and Ki67 proliferation, and the scores were correlated with the patients' clinical response assessed by pathology or Response Evaluation Criteria in Solid Tumors (RECIST).

Results

The cancer tissue and microenvironment, including endothelial and immune cells, were preserved at high viability with continued cell division for 5 days, demonstrating active cell signaling dynamics. A total of 34 cancer samples were tested by the platform and were correlated with clinical results. A higher EVOC score was correlated with better clinical response. The EVOC system showed a predictive specificity of 77.7% (7/9, 95% CI 0.4-0.97) and a sensitivity of 96% (24/25, 95% CI 0.80-0.99).

Conclusion

EVOC cultured for 5 days showed high sensitivity and specificity for predicting clinical response to therapy among patients with muscle-invasive bladder cancer and other solid tumors.

A molecular approach integrating genomic and DNA methylation profiling for tissue of origin identification in lung-specific cancer of unknown primary

BACKGROUND

Determining the tissue of origin (TOO) is essential for managing cancer of unknown primary (CUP). In this study, we evaluated the concordance between genome profiling and DNA methylation analysis in determining TOO for lung-specific CUP and assessed their performance by comparing the clinical responses and survival outcomes of patients predicted with multiple primary or with metastatic cancer.

METHODS

We started by retrospectively screening for CUP patients who presented with both intra- and extrathoracic tumors. Tumor samples from included patients were analyzed with targeted sequencing with a 520-gene panel and targeted bisulfite sequencing. TOO inferences were made in parallel via an algorithm using genome profiles and time interval between tumors and via machine learning-based classification of DNA methylation profiles.

RESULTS

Four hundred patients were screened retrospectively. Excluding patients definitively diagnosed with conventional diagnostic work-up or without available samples, 16 CUP patients were included. Both molecular approaches alone enabled inference of clonality for all analyzed patients. Genome profile enabled TOO inference for 43.8% (7/16) patients, and the percentage rose to 68.8% (11/16) after considering inter-tumor time lag. On the other hand, DNA methylation analysis was conclusive for TOO prediction for 100% (14/14) patients with available samples. The two approaches gave 100% (9/9) concordant inferences regarding clonality and TOO identity. Moreover, patients predicted with metastatic disease showed significantly shorter overall survival than those with multiple primary tumors.

CONCLUSIONS

Genome and DNA methylation profiling have shown promise as individual analysis for TOO identification. This study demonstrated the feasibility of incorporating the two methods and proposes an integrative scheme to facilitate diagnosing and treating lung-specific CUPs.

An analysis of research biopsy core variability from over 5000 prospectively collected core samples

Factors correlated with biopsy tissue adequacy and the prevalence of within-biopsy variability were evaluated. Totally, 1149 research biopsies were performed on 686 patients from which 5090 cores were assessed. Biopsy cores were reviewed for malignant percentage (estimated percentage of cells in the core that were malignant) and malignant area (estimated area occupied by malignant cells). Linear mixed models and generalized linear mixed models were used for the analysis. A total of 641 (55.8%) biopsies contained a core with <10% malignant percentage (inadequate core). The chance of an inadequate core was not influenced by core order, though the malignant area decreased with each consecutive core (p < 0.001). Younger age, bone biopsy location, appendiceal tumor pathology, and responding/stable disease prior to biopsy increased the odds of a biopsy containing zero adequate cores. Within-biopsy variability in core adequacy is prevalent and suggests the need for histological tumor quality assessment of each core in order to optimize translational analyses.

Evaluation of New Immunohistochemical Approaches for the Study of Kidney Tumors in Geriatric

Kidney malignancies are among the most deadly genitourinary tumors. It is more common in males and is often seen in people aged 60-70 years old. The incidence rate of kidney cancer seems to be increasing. One reason for this may be the fact that imaging techniques, such as computed tomography scans are more commonly used. These tests may lead to the accidental detection of more kidney cancers. Fortunately, kidney cancer is often detected in the early stages, when the tumor is small and confined to the kidney. The objective of this study was the development of new diagnostic immunohistochemical methods. Clinical examination material of 134 people, including 94 (70%) males and 40 (30%) females, were used in this study. Immunohistochemical staining of tryptase was carried out in compliance with the requirements using Anti-Mast Cell Tryptase antibodies. Goat anti-mouse antibodies #AS-M1-HRP were used as secondary antibodies, visualized with ImmPACTTM DAB Peroxidase Substrate Kit (#SK-4105) according to the instructions of the manufacturer. The nuclei were counterstained with Mayer's hematoxylin, and the sections were embedded in a permanent mounting medium. The immunohistochemical study showed an increase in both tryptase- and chymase-positive mast cells in the renal parenchyma, compared with the control group. The number of mast cells with tryptase expression directly in the tumor was significantly less than the peritumoral localization. A similar pattern was observed for chymase-positive mast cells as the content of the tumor was more than 10 times higher than the intratumoral arrangement. The histological and immunological characteristics did not differ in different age groups. The immunohistochemical method of research in the diagnosis of renal tumors plays an important diagnostic and prognostic value. It can assist pathologists in difficult and ambiguous cases to correctly diagnose renal tumors. This will make it possible to prescribe the correct treatment and predict the course of malignant tumor growth in patients.

Overcoming the Challenges of High Quality RNA Extraction from Core Needle Biopsy

The use of gene expression profiling (GEP) in cancer management is rising, as GEP can be used for disease classification and diagnosis, tailoring treatment to underlying genetic determinants of pharmacological response, monitoring of therapy response, and prognosis. However, the reliability of GEP heavily depends on the input of RNA in sufficient quantity and quality. This highlights the need for standard procedures to ensure best practices for RNA extraction from often small tumor biopsies with variable tissue handling. We optimized an RNA extraction protocol from fresh-frozen (FF) core needle biopsies (CNB) from breast cancer patients and from formalin-fixed paraffin-embedded (FFPE) tissue when FF CNB did not yield sufficient RNA. Methods to avoid ribonucleases andto homogenize or to deparaffinize tissues and the impact of tissue composition on RNA extraction were studied. Additionally, RNA’s compatibility with the nanoString nCounter^® technology was studied. This technology platform enables GEP using small RNA fragments. After optimization of the protocol, RNA of high quality and sufficient quantity was obtained from FF CNB in 92% of samples. For the remaining 8% of cases, FFPE material prepared by the pathology department was used for RNA extraction. Both resulting RNA end products are compatible with the nanoString nCounter^® technology.

Defining the clinical genomic landscape for real-world precision oncology

Through the delivery of large international projects including ICGC and TCGA, knowledge of cancer genomics is reaching saturation point. Enabling this to improve patient outcomes now requires embedding comprehensive genomic profiling into routine oncology practice. Towards this goal, this study defined the biologically and clinically relevant genomic features of adult cancer through detailed curation and analysis of large genomic datasets, accumulated literature and biomarker-driven therapeutics in clinic and development. The characteristics and prevalence of these features were then interrogated in 2348 whole genome sequences, covering 21 solid tumour types, generated by the PCAWG project. This analysis highlights the predominant contribution of copy number alterations and identifies a critical role for disruptive structural variants in the inactivation of clinically important tumour suppressor genes, including PTEN and RB1, which are not currently captured by diagnostic assays. This study defines a set of essential genomic features for the characterisation of common adult cancers.