Unknown primary tumors

A cross-cohort computational framework to trace tumor tissue-of-origin based on RNA sequencing

Carcinoma of unknown primary (CUP) is a type of metastatic cancer with tissue-of-origin (TOO) unidentifiable by traditional methods. CUP patients typically have poor prognosis but therapy targeting the original cancer tissue can significantly improve patients' prognosis. Thus, it's critical to develop accurate computational methods to infer cancer TOO. While qPCR or microarray-based methods are effective in inferring TOO for most cancer types, the overall prediction accuracy is yet to be improved. In this study, we propose a cross-cohort computational framework to trace TOO of 32 cancer types based on RNA sequencing (RNA-seq). Specifically, we employed logistic regression models to select 80 genes for each cancer type to create a combined 1356-gene set, based on transcriptomic data from 9911 tissue samples covering the 32 cancer types with known TOO from the Cancer Genome Atlas (TCGA). The selected genes are enriched in both tissue-specific and tissue-general functions. The cross-validation accuracy of our framework reaches 97.50% across all cancer types. Furthermore, we tested the performance of our model on the TCGA metastatic dataset and International Cancer Genome Consortium (ICGC) dataset, achieving an accuracy of 91.09% and 82.67%, respectively, despite the differences in experiment procedures and pipelines. In conclusion, we developed an accurate yet robust computational framework for identifying TOO, which holds promise for clinical applications. Our code is available at http://github.com/wangbo00129/classifybysklearn .

SEOM-GECOD clinical guideline for unknown primary cancer (2021)

Cancer of unknown primary site (CUP) is defined as a heterogeneous group of tumors that appear as metastases, and of which standard diagnostic work-up fails to identify the origin. It is considered a separate entity with a specific biology, and nowadays molecular characteristics and the determination of actionable mutations may be important in a significant group of patients. In this guide, we summarize the diagnostic, therapeutic, and possible new developments in molecular medicine that may help us in the management of this unique disease entity.

A Systematic Review of Cancer of Unknown Primary in the Head and Neck Region

Background

Despite the vivid progress in molecular and genetic profiling, extensive diagnosis and multiple therapeutic modalities, cancers of unknown primary in the head and neck region continue to be a formidable challenge.

Aim

The purpose of the review is to present the most recent and well-established findings concerning cancers of unknown primary (CUPs) in the head and neck patients and consequently to provide medical specialists with essential information regarding the biology, pathology, histology, diagnosis and treatment of CUP in the head and neck region.

Material and Methods

The Medline/PubMed database was searched by using the following keywords “CUP”, “cancer of unknown primary”, “CUP biology”, “head and neck”. The references of the publications of interest were also screened for relevant papers. There were no limitations in regard to the publication date.

Conclusion

Unique biology and pathophysiology prompt the management of CUP to be demanding. The vivid rise in HPV-related CUPs during the last 20 years has put more focus on this phenomenon. New findings concerning the enigmatic biology of CUP provide fundaments for targeted therapy. Despite the availability of various diagnostic methods, the diagnosis of CUP continues to be a time-consuming, strenuous process that eventually provides answers. It remains controversial as to what combination of treatment methods is the most effective. There is no consensus on the value of combining chemotherapy with radiotherapy. Highly specific surgical treatments for particular histological types of CUP produce more satisfactory results. It is paramount to establish reliable guidelines concerning the diagnosis and treatment of CUP patients.

miRNA landscape in primary tumors and matched metastases in gastrointestinal stromal tumors

Aim: Gastrointestinal stromal tumor management is extremely challenging, particularly the metastatic disease. The underlying mechanism in metastasis spread remains largely unknown. We aimed to characterize miRNAs involved in the metastatic process in gastrointestinal stromal tumor. Material & methods: Eight primary tumors and 18 synchronous metastases were analyzed through miRNA Taqman arrays or assays. Results: miRNAs profiles revealed similar expression in primary site and metastases. Pair-wise correlation coefficient between primary tumor and metastases was significant for each patient (p < 0.0001 for all profiled patients). Conclusion: Our study, the largest including primary tumors and metastases so far performed, highlighted perpetuation of miRNAs features in metastatic lesions and that the primary origin appears to be the main determinant of the metastases miRNA profile.

The impact of the patient's condition, diagnostic procedures and treatment on the survival of carcinoma of unknown primary site patients

Introduction

Carcinoma of unknown primary site (CUP) refers to 1–5% of all head and neck neoplasms. Very often, the primary site remains difficult to determine. Squamous cell carcinoma is the most frequent histopathological type diagnosed in the head and neck region. According to statistics, a primary site is usually located in the oropharynx.

Study objective

The study presents diagnostic difficulties and the methods of diagnosing and the therapy of CUP and primary sites in patients treated in the region of Lower Silesia and Silesia. The aim of the study was to show a retrospective analysis of 233 CUP patients to assess how clinical features, diagnosis and treatment affect the survival of patients.

Material and methods

The diagnostics of patients included panendoscopy with specimen collection (nasoendoscopy, laryngoscopy, esophagoscopy, brochoscopy), computed tomography examination of the neck, chest, abdomen and pelvis minor, as well as positron emission tomography examination. Tonsilletomy was performed in 37 patients. Neck dissection was carried out in 109 subjects and 165 patients were treated bt radiotherapy, and 135 by chemotherapy.

Conclusions

Tonsillectomy is required in CUP patients with the negative results of biopsy and imaging tests. It gives a possibility of detecting the primary site and improves the results of treatment and survival of CUP patients.Combination therapy, including surgical treatment and chemoradiotherapy, gives the best therapeutic results in CUP patients. The general condition of patient and younger age have an impact on prognosis and survival.

Where do these guests come from? A diagnostic approach for metastatic lymph nodes

Objective

In cases presenting with lymphadenopathies (LAP) without a primary focus detected by simple radiological methods, the primary tumor can be diagnosed by a histopathological evaluation of the metastatic lymph nodes. We aimed to discuss the nonhematological malignancies presenting with lymphadenopathies and the histopathological results for primary tumors.

Material and Methods

In this retrospective study, cases diagnosed with metastasis in excisional lymph nodes between January 2013 and June 2016 were assessed for a histopathological diagnostic approach.

Results

Among 632 lymph node biopsies, a total of 21 cases, involving 12 male and 9 female patients with a mean age of 57.23 y (range, 33-92 y), of nonhematological solid tumors were included. The most common localizations of the involved lymph nodes were inguinal (n=8), axillary (n=6), cervical (n=4), and supraclavicular (n=3) region. The most common primary tumors were malignant melanoma (n=6), breast carcinoma (n=4), ovarian carcinoma (n=2), squamous cell carcinoma (n=2), and germ cell tumor (n=2). Others were papillary thyroid carcinoma, renal cell carcinoma, urothelial carcinoma, prostate adenocarcinoma, and endometrial adenocarcinoma.

Conclusion

Nonhematological malignancies presenting with lymphadenopathies are one of the most complicated cases for clinicians. The histopathological evaluation of the excisional metastatic lymph node biopsies is an important method because of cost effectiveness and easy applicability.

SEOM clinical guideline on unknown primary cancer (2017)

Cancer of unknown primary site is a histologically confirmed cancer that manifests in advanced stage, with no identifiable primary site following standard diagnostic procedures. Patients are initially categorized based on the findings of the initial biopsy: adenocarcinoma, squamous-cell carcinoma, neuroendocrine carcinoma, and poorly differentiated carcinoma. Appropriate patient management requires understanding several clinical and pathological features that aid in identifying several subsets of patients with more responsive tumors.

An integrated tool for determining the primary origin site of metastatic tumours

Aims

Cancers of unknown primary sites account for 3%–5% of all malignant neoplasms. Current diagnostic workflows based on immunohistochemistry and imaging tests have low accuracy and are highly subjective. We aim to develop and validate a gene-expression classifier to identify potential primary sites for metastatic cancers more accurately.

Methods

We built the largest Reference Database (RefDB) reported to date, composed of microarray data from 4429 known tumour samples obtained from 100 different sources and divided into 25 cancer superclasses formed by 58 cancer subclass. Based on specific profiles generated by 95 genes, we developed a gene-expression classifier which was first trained and tested by a cross-validation. Then, we performed a double-blinded retrospective validation study using a real-time PCR-based assay on a set of 105 metastatic formalin-fixed, paraffin-embedded (FFPE) samples. A histopathological review performed by two independent pathologists served as a reference diagnosis.

Results

The gene-expression classifier correctly identified, by a cross-validation, 86.6% of the expected cancer superclasses of 4429 samples from the RefDB, with a specificity of 99.43%. Next, the performance of the algorithm for classifying the validation set of metastatic FFPE samples was 83.81%, with 99.04% specificity. The overall reproducibility of our gene-expression-classifier system was 97.22% of precision, with a coefficient of variation for inter-assays and intra-assays and intra-lots <4.1%.

Conclusion

We developed a complete integrated workflow for the classification of metastatic tumour samples which may help on tumour primary site definition.

The Reverse Transcriptase Encoded by LINE-1 Retrotransposons in the Genesis, Progression, and Therapy of Cancer

In higher eukaryotic genomes, Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons represent a large family of repeated genomic elements. They transpose using a reverse transcriptase (RT), which they encode as part of the ORF2p product. RT inhibition in cancer cells, either via RNA interference-dependent silencing of active LINE-1 elements, or using RT inhibitory drugs, reduces cancer cell proliferation, promotes their differentiation and antagonizes tumor progression in animal models. Indeed, the non-nucleoside RT inhibitor efavirenz has recently been tested in a phase II clinical trial with metastatic prostate cancer patients. An in-depth analysis of ORF2p in a mouse model of breast cancer showed ORF2p to be precociously expressed in precancerous lesions and highly abundant in advanced cancer stages, while being barely detectable in normal breast tissue, providing a rationale for the finding that RT-expressing tumors are therapeutically sensitive to RT inhibitors. We summarize mechanistic and gene profiling studies indicating that abundant LINE-1-derived RT can “sequester” RNA substrates for reverse transcription in tumor cells, entailing the formation of RNA:DNA hybrid molecules and impairing the overall production of regulatory miRNAs, with a global impact on the cell transcriptome. Based on these data, LINE-1-ORF2 encoded RT has a tumor-promoting potential that is exerted at an epigenetic level. We propose a model whereby LINE1-RT drives a previously unrecognized global regulatory process, the deregulation of which drives cell transformation and tumorigenesis with possible implications for cancer cell heterogeneity.

Primary bone metastasis as first manifestation of an unknown primary tumour

Unknown primary tumour refers to a group of cancers for which the anatomical site of origin remains occult after detailed investigations. Thanks to sophisticated imaging, immunohistochemical testing and molecular-profiling tools, there is a more accurate approach to unknown primary cancer. Metastasis to bone is not a rare phenomenon, because any tumour can metastasise to bone, so it is a common clinical scenario. The role of clinical history, physical examination, laboratory tests, radiographic studies and immunohistochemistry is critical for a successful diagnostic strategy. Subsets of unknown primary cancers can be identified primarily on the basis of histopathological findings, the pattern of spread and serum markers. New immunohistochemical markers and tissue-of-origin profiles may establish presumable primary sites to unknown primary cancer on the basis of immunohistochemical and molecular patterns. We present a case of a 57-year-old woman without a cancer history, who had primary bone metastasis as the first manifestation of an occult primary tumour.

Systems biology of cancer: entropy, disorder, and selection-driven evolution to independence, invasion and "swarm intelligence"

Our knowledge of the biology of solid cancer has greatly progressed during the last few years, and many excellent reviews dealing with the various aspects of this biology have appeared. In the present review, we attempt to bring together these subjects in a general systems biology narrative. It starts from the roles of what we term entropy of signaling and noise in the initial oncogenic events, to the first major transition of tumorigenesis: the independence of the tumor cell and the switch in its physiology, i.e., from subservience to the organism to its own independent Darwinian evolution. The development after independence involves a constant dynamic reprogramming of the cells and the emergence of a sort of collective intelligence leading to invasion and metastasis and seldom to the ultimate acquisition of immortality through inter-individual infection. At each step, the probability of success is minimal to infinitesimal, but the number of cells possibly involved and the time scale account for the relatively high occurrence of tumorigenesis and metastasis in multicellular organisms.

Metastatic tumors to the gingiva and the presence of teeth as a contributing factor: a literature analysis

BACKGROUND

Gingiva that is prone to inflammation may serve as a pre-metastatic niche for the attraction of circulating malignant cells. The aim of this study is to analyze cases of metastatic lesions to the gingiva compared with cases metastasizing to other oral mucosal sites. The pathogenesis of gingival metastases is discussed, with emphasis on the role of inflammation.

METHODS

The English-language literature between 1916 and 2011 was searched for cases of metastatic lesions to the oral mucosa; only cases metastasizing in the oral mucosa, gingiva, and periodontium were included.

RESULTS

Two hundred seven cases were included. The gingiva was the most common site (60.4%), followed by tongue and tonsil. The most common primary sites were lung (24.2%), kidney (13.5%), skin (10.6%), and breast (8.7%). In 27%, the oral lesion was the first sign of a malignant disease. In most cases, the lesion appeared as an exophytic mass (96%) diagnosed clinically as a reactive gingival lesion. The presence of teeth was significantly associated with the development of gingival metastases: in 108 of 125 gingival metastases, the lesion was found adjacent to teeth (P <0.001; odds ratio = 8.2). The average life expectancy after diagnosis of the metastasis was 3.7 months.

CONCLUSIONS

The gingiva is the most common site for metastases to oral soft tissues, with strong association with the presence of teeth. This finding may be related to the role of inflammation in the attraction of metastatic cells to chronically inflamed gingiva.

Giant adenocarcinoma of unknown origin penetrating from the pelvic cavity to subcutaneous tissue: A case report and review of the literature

In this study, we present a case of a 43-year-old female patient who was admitted to our hospital due to a giant mass on the left buttock. Imaging tests revealed that the mass was a solid-cystic tumor with a large size of 143×430×180 mm, penetrating from the pelvic cavity to the subcutaneous tissue. Pathology tests indicated a metastatic mucinous adenocarcinoma which was most likely of gastrointestinal origin. However, there was no evidence to confirm the existence of malignant changes in the gastrointestinal tract.

Cancers of unknown primary origin: current perspectives and future therapeutic strategies

It is widely accepted that systemic neoplastic spread is a late event in tumour progression. However, sometimes, rapidly invasive cancers are diagnosed because of appearance of metastatic lesions in absence of a clearly detectable primary mass. This kind of disease is referred to as cancer of unknown primary (CUP) origin and accounts for 3-5% of all cancer diagnosis. There is poor consensus on the extent of diagnostic and pathologic evaluations required for these enigmatic cases which still lack effective treatment. Although technology to predict the primary tumour site of origin is improving rapidly, the key issue is concerning the biology which drives early occult metastatic spreading. This review provides the state of the art about clinical and therapeutic management of this malignant syndrome; main interest is addressed to the most recent improvements in CUP molecular biology and pathology, which will lead to successful tailored therapeutic options.