Gefitinib and erlotinib target the ATP cleft in the tyrosine kinase EGFR, which is overexpressed in 40-80 percent of non-small-cell lung cancer (NSCLC) and many other epithelial cancers. However, the application of gefitinib is ultimately limited by the emergence of mutations and other molecular mechanisms conferring drug resistance. Furthermore, it has been considered that acquired resistance to gefitinib is associated with a clinically significant risk of accelerated disease progression. We previously established a new gefitinib-resistant NSCLC cell line, HCC827GR, which harbors the T790M mutation. Using HCC827GR, we found that the inhibition of adenosine A2a receptors of NSCLC regulated cancer proliferation and exacerbation, indicating that adenosine A2a receptors may be new targets for a novel strategy in NSCLC therapy. These findings suggest that multilayered crosstalk between G-protein coupled receptors (GPCRs) and EGFR may play an important role in regulating downstream signaling molecules that are implicated in the development of gefitinib-resistant NSCLC.

Liquid biopsy is defined as a non-invasive blood test that detects features of tumor cells, which are shed into the blood stream from the primary tumor and/or metastatic sites. This method is developing based on research on circulating tumor cells (CTCs) and the circulating free/fragments of tumor DNA (cfDNA). CfDNA can be detected in the absence of detectable CTCs, and has been shown to increase with the disease condition. The detection of cfDNA can be used for tumor genotyping, monitoring of the tumor burden, and monitoring minimal residual diseases, and recent results showed that cfDNA is a highly specific biomarker with intermediate sensitivity. Liquid biopsy with cfDNA is promising, and is becoming an alternative to re- biopsy. However, there are some caveats: it has not been elucidated which patients and tumor types can be accessed with cfDNA. Further research is warranted.

Bone and soft-tissue sarcomas comprise a rare, complex, and heterogeneous group of tumors for which it is difficult for even experienced pathologists to provide a conclusive diagnosis. The number of diagnoses made using genetic analysis has increased since the detection of fusion genes in several soft-tissue tumors in the 1990s. Moreover, other specific genetic aberrations have been reported in various bone and soft-tissue tumors. In addition, molecular therapeutic targets have been sought in advanced cases of soft-tissue and bone tumors similar to other organ malignancies. To enable the pathological diagnosis of bone and soft-tissue tumors, it is necessary to combine histological diagnosis with immunohistochemistry and gene analysis findings including fusion gene or other genetic aberrations. In this review, we describe the fusion genes recently reported in bone and soft-tissue tumors such as solitary fibrous tumor, aneurysmal bone cyst, nodular fasciitis, CIC-DUX4 fusion gene-positive small round cell tumors, or BCOR-CCNB3-positive sarcoma as well as other genetic aberrations in dedifferentiated liposarcoma, malignant rhabdoid tumor, cartilaginous tumor, Langerhans cell histiocytosis chondroblastoma, or giant cell tumor of the bone. We also demonstrate their association with pathological diagnosis.

The genomic instability in colon cancer can be divided into at least 2 major types: chromosomal instability (CIN) and microsatellite instability(MSI). Although there are some overlaps between the 2 types, these are thought to be mutually exclusive. Colorectal tumors progress through a series of histopathologic grades, ranging from dysplastic crypts through small benign tumors to malignant cancers. This progression is the result of a series of genetic changes that involve activation of oncogenes and inactivation of tumor suppressor genes, ie, the CIN pathway. In contrast, MSI develops as a result of epigenetic silencing of MLH1 in sporadic tumors-in a background of methylation of CpG islands in gene promoters-and in tumors that frequently show BRAF mutation. Several tumor prognostic factors have been identified for colorectal cancer, including, tumor budding and molecular factors. In this review, we discuss the genetic mechanisms of colorectal cancer and the relationship of these alterations with emerging biomarkers for pathological diagnosis, patient prognosis, and the prediction of treatment responses.

Breast cancers contain variable histologies as well as biology. Gene expression profiling and cluster analyses have been performed since the beginning of the 21st century. The use of intrinsic subtype classification has replaced histological classification of breast carcinomas, as it frequently yields the same results. For examples, around 80% of triple negative (estrogen receptor-, progesterone receptor-, and HER2-negative) cancers are of the basal-like subtype. In daily practice, adjuvant therapy is selected based on histological features, but the results of ordinal cluster analyses and histological intrinsic subtypes are not always the same for individual cases. With advanced genetic analysis, new concepts have been elucidated, ie, the molecular identification of claudin-low breast cancer. Proposals of a new classification system and a new therapeutic approach are expected in the future.

A decade of accumulated evidence has led to significant progress and a paradigm shift in ovarian tumor pathology. Now, ovarian carcinoma is widely recognized as a heterogeneous group of neoplasms with regard to histogenesis and underlying molecular mechanisms. Ovarian carcinoma is, therefore, divided into 2 clinicopathologic groups: type 1 and type 2 tumors. Type 1 tumors arise in association with benign neoplastic conditions (adenoma-carcinoma sequence). They include endometriosis-related ovarian neoplasias, such as clear cell carcinoma and low-grade endometrioid carcinoma, which are derived from atypical endometriosis or adenofibroma, as well as mucinous carcinoma and low-grade serous carcinoma, which are commonly associated with mucinous and serous borderline tumors, respectively. In contrast, type 2 tumors, which arise de novo directly from the normal epithelium, include high-grade serous and endometrioid carcinoma, carcinosarcoma, and undifferentiated carcinoma. Notably, the hypothesis that most high-grade serous ovarian carcinoma is not of ovarian origin and, rather, is associated with serous tubal intraepithelial carcinoma (STIC), which is mostly found on the fimbrial end of the fallopian tube in up to 70% of cases of high-grade serous carcinoma, is universally accepted. Understanding ovarian carcinoma molecular pathogenesis should aid in developing effective therapeutic strategies for these particular tumors.

Gastric cancer has been classified based on the pathological characteristics including microscopic configuration and growth pattern. Although these classifications have been used in studies investigating prognosis and recurrence pattern, they are not considered for decisions regarding the therapeutic strategy. In the ToGA study, trastuzumab, an anti-HER2 monoclonal antibody, demonstrated clinical efficacy for gastric cancer with HER2 overexpression or HER2 gene amplification. Based on these findings of the ToGA study, the definition of HER2-positive gastric cancer was established. Thereafter, several molecular targeted agents, including agents targeting other receptor tyrosine kinases, have been investigated in gastric cancer. However, to date no biomarker, except HER2, has been established. Based on the recent technological development in the field of gene analysis, a comprehensive molecular evaluation of gastric cancer was performed as part of The Cancer Genome Atlas (TCGA) project, and a new molecular classification was proposed that divided gastric cancer into the following 4 subtypes: tumors positive for Epstein-Barr virus, microsatellite instability tumors, genomically stable tumors, and tumors with chromosomal instability. Each subtype has specific molecular alterations including gene mutation and amplification, DNA methylation, and protein overexpression. Additionally, some subtypes were suggested to be correlated with the clinicopathological characteristics or as targets of some molecular targeted agents that are currently under development. The new molecular classification is expected to be a roadmap for patient stratification and clinical trials on molecular targeted therapies in gastric cancer.

Since 1981, cancer has been the leading cause of death in Japan, and its upward trend remains continuing until now. In 2013, approximately 365,000 Japanese died of cancer, and the ratio of the number of cancer-related deaths to the total number of deaths was 28.8%, implying that approximately 1 out of 3.5 deaths in Japan are caused by cancer. In recent years, immunotherapies are rapidly developed and recognized as an important anti-cancer treatment modality in addition to surgery, chemotherapy, and radiotherapy. In particular, the"immune checkpoint blockade therapy"has been attracting tremendous attention because of its potent clinical efficacy in the treatment of advanced cancers. The fundamental mechanism of the therapy is the induction of anti-tumor immune responses by disrupting the immunosuppressive mechanisms in the tumor milieu. Antibodies for the immune checkpoint blockade have been approved as clinical drugs in some countries, including in Japan, and a large number of clinical trials are currently in progress to further expand its application. However, several critical issues remain, one of which is the identification of biomarkers associated with clinical benefits or adverse events. In this review, we discuss recently reported genome-based biomarkers predictive for clinical benefits of immune checkpoint blockade therapies, namely activation of b-catenin signaling pathway and DNA mismatch repair deficiency.

The development of a genomic landscape of gliomas has led to the internally consistent, molecularly-based classifiers. However, development of a biologically insightful classification to guide therapy is still ongoing. Further, tumors are heterogeneous, and they change and adapt in response to drugs. The challenge of developing molecular classifiers that provide meaningful ways to stratify patients for therapy remains a major challenge for the field. Therefore, by incorporating molecular markers into the new World Health Organization (WHO) classification of tumors of the central nervous system, the traditional principle of diagnosis based on histologic criteria will be replaced by a multilayered approach combining histologic features and molecular information in an "integrated diagnosis", to define tumor entities as narrowly as possible. We herein review the current status of diagnostic molecular markers for gliomas, focusing on IDH mutation, ATRX mutation, 1p/19q co-deletion, and TERT promoter mutation in adult tumors, as well as BRAF and H3F3A aberrations in pediatric gliomas, the combination of which will be a promising endeavor to render molecular genetics as a best evidence in the glioma diagnositics.

Companion diagnostics (CoDx) will likely continue to rapidly increase in number and application to disease areas including solid tumors, for example EGFR for gefitinib and ALK fusion gene for crizotinib in non-small-cell lung cancer; KRAS against the use of cetuximab and panitumumab in colorectal cancer; HER2 for trastuzumab in breast cancer. CoDx are an indispensable part of personalized medicine and pharmacogenomics. In CoDx development, there are still many challenges, such as the business model promoting cooperation between diagnostics and pharmaceutical companies, and also the regulations related to CoDx. The FDA notice on the development of CoDx in 2011 recommended the co-development of a new drug and CoDx as the best practice, and the Ministry of Health, Labour and Welfare in Japan also issued a statement in 2013. In addition, the recent discovery of many novel variants in the DNA sequence, advances in sequencing and genomic technology, and improved analytic methods have enabled the impact of germline and somatic mutations to be determined using multiplex diagnosis. The complex challenges to develop CoDx necessitate a close collaboration among academic institutions, regulatory authorities, and pharmaceutical companies. [Review].

Myeloproliferative neoplasms (MPNs) are characterized by activation of the JAK-STAT pathway due to driver mutations including JAK2V617F and MPLW515K/L, as well as to mutations in CALR. Driver mutations phosphorylate multiple STAT proteins that lead to proliferations, differentiations and cytokine secretions of various hematopoietic cells. However, hematopoietic cells carrying JAK2V617F, which causes excessive cellular proliferation and differentiation, do not necessarily have a clonal growth advantage in terms of hematopoietic repopulation. Alterations of epigenetic modifiers involving histone modifications and DNA methylations, which often co-exist with driver mutations and eventually upregulate several oncogenes, may play crucial roles in long-term clinical courses characterized by progression to myelofibrosis or acute leukemia in MPNs. In addition to JAK2 inhibition, molecules altered by abnormal epigenetic modifications may be worth exploring as potential new therapeutic targets in MPNs.

Chronic myelomonocytic leukemia (CMML) is one of the clonal myeloid neoplasms characterized by persistent monocytosis and dysplasia of myeloid lineage cells. Thus, CMML includes characteristics of both myelodysplastic syndromes and myeloproliferative neoplasms. Clinical features of CMML are quite heterogeneous. There are no disease-specific gene mutations although more than 90% of CMML patients have one or more gene mutations, and most mutations detected in CMML are also seen in other myeloid malignancies. Among these mutations, ASXL1 mutations negatively affect the disease outcome. Moreover, it has been clarified that the clonal architecture of CMML is characterized by linear accumulation of mutations. Recently, international consortium perspectives in diagnostic recommendations and response criteria were published, and clinical reports on CMML, including a new diagnostic method, molecularly integrated CMML-specific prognostic models and therapeutic trials, are increasing. However, despite the existence of several prognostic models of CMML, formal guidelines for the management of CMML are still lacking. An international consortium proposal of uniform guidelines for management of CMML based on a uniform prognostic scoring system is eagerly awaited.

Juvenile myelomonocytic leukemia (JMML) is a rare myelodysplastic/myeloproliferative disorder that occurs during infancy and early childhood; this disorder is characterized by hypersensitivity of the myeloid progenitor cells to granulocyte-macrophage colony-stimulating factor (GM-CSF) in vitro. JMML usually involves somatic and/or germline mutations in the genes of the RAS pathway, including PTPN11, NRAS, KRAS, NF1, and CBL, in the leukemic cells. Recently, additional genetic and/or epigenetic alterations have been identified in JMML, and these alterations appear to be prognostic indicators. Moreover, analyses of JMML stem cells and induced pluripotent stem cells (iPSCs) technology are expected to identify new targets for therapeutic interventions. Almost all patients with JMML experience an aggressive clinical course, and hematopoietic stem cell transplantation (HSCT) is the only curative treatment. The most suitable therapeutic regimen after diagnosis and the optimal conditioning regimen prior to HSCT have yet to be identified, though several clinical trials have been initiated worldwide. Taken together, these new findings indicate that genetic and/or epigenetic alteration-specific risk management may be introduced, and that suitable pre- or post-allogeneic HSCT treatments which are less toxic and can improve outcomes will be developed in the near future.

Acute myeloid leukemia (AML) is a form of blood cancer that is characterized by the rapid growth of abnormal myeloid cells. Although the general therapeutic strategy in patients with AML has not changed substantially in more than 30 years, remarkable progress has been achieved in understanding the pathogenesis of AML. Genome-wide analyses have revealed genetic mutations and epigenetic dysregulations that are present in AML cells. Studies of leukemia stem cells have clarified their complex properties and functions in the development of AML, and have also led to the recent identification of pre-leukemic hematopoietic stem cells that undergo clonal evolution in healthy people. Translation of these new findings into the clinical setting is just beginning. This article focuses on recent advances in basic research on the molecular pathogenesis of AML. New strategies under investigation, including epigenetic therapies and immunotherapies, to provide better therapeutic options for AML patients, are also summarized.

Elucidation of the molecular pathogenesis of neoplasms and application of emerging technologies for testing and therapy have resulted in a series of paradigm shifts in patient care, from conventional to personalized medicine. This has been promoted by companion diagnostics and molecular targeted therapy, tailoring the treatment to the individual characteristics of each patient. Precision oncology has been accelerated by integrating the enhanced resolution of molecular analysis, mechanism clarity, and therapeutic relevance through genomic knowledge. In its clinical implementation, there are laboratory challenges concerning accurate measurement using stored samples, differentiation between driver and passenger mutations as well as between germline and somatic mutations, bioinformatics availability, practical decision-making algorithms, and ethical issues regarding incidental findings. The medical laboratory has a new role in providing not only testing services but also an instructive approach to users to ensure the sample quality and privacy protection of personal genome information, supporting the quality of patient practice based on laboratory diagnosis.