what is the advantage of macro - dissection in testing for tumor - specific molecular markers from paraffin - embedded formalin - fixed tissue section ? ( please explain in 500 word )
Answers
Answer:
Abstract
Metabolite profiling has significantly contributed to a deeper understanding of the biochemical metabolic networks and pathways in cancer cells. Metabolomics-based biomarker discovery would greatly benefit from the ability to interrogate retrospective annotated clinical specimens archived as formalin-fixed, paraffin-embedded (FFPE) material. Mass spectrometry–based metabolomic analysis was performed in matched frozen and FFPE human prostate cancers as well as isogenic prostate cancer cell lines. A total of 352 and 460 metabolites were profiled in human tissues and cell lines, respectively. Classes and physical–chemical characteristics of the metabolites preserved in FFPE material were characterized and related to their preservation or loss following fixation and embedding. Metabolite classes were differentially preserved in archival FFPE tissues, regardless of the age of the block, compared with matched frozen specimen, ranging from maximal preservation of fatty acids (78%) to loss of the majority of peptides and steroids. Generally, FFPE samples showed a decrease of metabolites with functional groups, such as carboxamide. As an adjunct technique, metabolic profiles were also obtained in situ from FFPE tissue sections where metabolites were extracted in a manner that preserves tissue architecture. Despite the fact that selected metabolites were not retained after processing, global metabolic profiles obtained from FFPE can be used to predict biologic states and study biologic pathways. These results pave the way for metabolomics-based biomarker discovery/validation utilizing retrospective and clinically annotated FFPE collections.
Explanation:
please mark me as brainliest
Explanation:
Testing for tumor specific mutations on routine formalin-fixed paraffin-embedded (FFPE) tissues may predict response to treatment in Medical Oncology and has already entered diagnostics, with KRAS mutation assessment as a paradigm. The highly sensitive real time PCR (Q-PCR) methods developed for this purpose are usually standardized under optimal template conditions. In routine diagnostics, however, suboptimal templates pose the challenge
Methodology/Principal Findings
Tumor FFPE-DNA from 135 diagnostic and 75 low-quality control samples was obtained upon macrodissection, tested for fragmentation and assessed for KRAS mutations with dideoxy-sequencing and with two Q-PCR methods (Taqman-minor-groove-binder [TMGB] probes and DxS-KRAS-IVD). Samples with relatively well preserved DNA could be accurately analyzed with sequencing, while Q-PCR methods yielded informative results even in cases with very fragmented DNA (p<0.0001) with 100% sensitivity and specificity vs each other. However, Q-PCR efficiency (Ct values) also depended on DNA-fragmentation (p<0.0001). Q-PCR methods were sensitive to detect ≤1% mutant cells, provided that samples yielded cycle thresholds (Ct) <29, but this condition was met in only 38.5% of diagnostic samples. In comparison, FFPE samples (>99%) could accurately be analyzed at a sensitivity level of 10% (external validation of TMGB results)
Conclusions/Significance
Diagnostic targeted mutation assessment on FFPE-DNA is very efficient with Q-PCR methods in comparison to dideoxy-sequencing. However, DNA fragmentation/amplification capacity and tumor DNA content must be considered for the interpretation of Q-PCR results in order to provide accurate information for clinical decision making.
Introduction
Based on accumulated knowledge about tumor biology, newer drugs are meant to treat cancer in a more rational way than classic chemotherapy, i.e., by targeting specific molecules and pathways that are essential for promoting tumor growth, maintenance and metastasis. In this context, EGFR, a HER family receptor tyrosine kinase, has emerged as a major molecular target. Because EGFR was considered to be involved in the pathogenesis of most epithelial cancers [1], anti-EGFR drugs were anticipated to improve outcome for millions of patients worldwide. In fact, though, these drugs dramatically benefit only a small percentage of cancer patients, based on the alterations concerning EGFR itself (e.g., specific mutations targeted by small molecule tyrosine kinase inhibitors [TKIs]) or molecules in the EGFR effector pathways (for example, KRAS [official gene name: v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog; aliases: KRAS2, RASK2] mutations hampering therapeutic EGFR antibodies and possibly TKIs as well). Of note, success rates of as low as 5% correspond to hundreds thousands of patients worldwide for the major cancer types (breast, lung, colorectal).
Patient selection is required for drugs that are labeled for a certain molecular target when approved for clinical practice. A recent development in this context concerns two anti-EGFR antibodies, cetuximab and panitumumab, that have been labeled for use in metastatic colorectal cancer (CRC) under the condition that the tumor carries a wild-type KRAS gene [5], [6]. This decision was based on accumulating evidence showing that CRC patients with KRAS mutant tumors do not benefit from treatments with anti-EGFR antibodies Hence, patients with mutant KRAS tumors are not eligible for treatment with these drugs; the clinician must have the information on
Starting with the latter, diagnostic tests for the assessment of any marker at any molecular level (e.g., proteins – immunohistochemistry, mutations – DNA) are performed on routine diagnostic tumor material, i.e., formalin-fixed paraffin-embedded (FFPE) tumor tissue containing molecular templates suffering from protein cross-linking with formaldehyde. tissues are of inferior quality as compared to their frozen counterparts, these may still be useable for a lot of recently developed methods for nucleic acid investigation, even microarray profiling and wide genome scans, while the main advantage from using molecular FFPE templates is accurate correlation of results with tissue histology.