Recently, single cell gene expression analysis was performed to help understand the complexity of cell populations. Single- cell analysis can analyze the diversity of individual cell populations as well as the tissue microenvironment, and is extremely useful for research on intercellular interactions in diseases and identifying specific marker genes. Recent advances in technology have made it possible to analyze hundreds of single cells in many cancer tissues, including stromal cells. In this paper, we introduce research examples of hepatocellular carcinoma by single cell transcriptome analysis.

Progress in genomic analysis are expected to improve the treatment outcome of cancers of unknown primary(CUP). We conducted a randomized phase Ⅱ trial of carboplatin plus paclitaxel versus site-specific therapy based on gene expression profiling(GEP)in patients with CUP. A phase Ⅱ trial was conducted in patients with CUP to evaluate the feasibility of site- specific therapy based on NGS-based primary site prediction from GEPs, including irGEP. We proposed the possibility of treatment with immune checkpoint inhibitors for CUP patients. Based on the results, a physician-led clinical trial of nivolumab for CUP was conducted with favorable results.

With the advent of immune checkpoint inhibitors, the importance of immunotherapy in cancer treatment has been widely recognized. However, it is also true that immune checkpoint inhibitors alone have limited therapeutic effects. Therefore, in addition to the combination among immune checkpoint inhibitors such as the combination therapy of anti-CTLA-4 antibody and anti-PD-1 antibody, the combinations with chemotherapy, radiotherapy, and molecular target drug are extensively being developed. In order to link the antitumor effect of the immune response equipped in the body to cancer treatment, it is necessary to understand and overcome the immunosuppressive environment that inhibits it. This article outlines the understanding of tumor immunity by the immune genome profiling of cancer tissues.

Based on the"neoantigen theory", the measurement of microsatellite instability(MSI)and tumor mutation burden(TMB) is one of the essential test items during cancer precision medicine, especially for the administration of immune checkpoint inhibitor. The conventional MSI test is consist of direct PCR method to amplify the microsatellite region using DNA derived from tumor specimen as a companion diagnostic(CDx)for pembrolizumab, while the recent comprehensive genomic profiling test such as FoundationOne CDx also evaluate the MSI status. TMB is counted and reported as the number of the mutation per 1 Mb(mut/Mb), and the over 10 mut/Mb is the universal cut off for pembrolizumab CDx.

How to efficiently suspect a germline gene variant(presumed germline pathogenic variant: PGPV)in comprehensive tumor-profiling tests using only cancer tissue(cells)as a sample is an important issue. This is because a few percent are derived from germline variants, which leads to the diagnosis of hereditary tumor syndromes and is useful information for the health management of patients and relatives. Clues include allele frequency, gene type, germline founder mutation, age of onset, present illness and past history, cancer type, family history, and tumor cell proportion. More than 97% of patients want to know such secondary findings before the test, but only about 23% of patients undergo confirmation tests even if PGPV is detected, and it is necessary to improve this in the future.

A 21-year-old man presented with bone marrow failure, short stature, fatty degeneration of the pancreas on CT images, and Shwachman-Bodian-Diamond syndrome (SBDS) gene abnormalities (exon 2: c.258+2T>C and deletion of exon 3). Thus, the patient was diagnosed with Shwachman-Diamond syndrome (SDS). In the clinical course, the patient developed acute myeloid leukemia (AML). Hematopoietic stem cell transplantation from the human-leukocytic-antigen-haploidentical father of the patient was performed. The patient was conditioned with 150 mg/m2 fludarabine, 6.4 mg/kg busulfan, and 4 Gy total body irradiation. Graft-versus-host disease prophylaxis included tacrolimus, micophenolate mofetil, and posttransplant cyclophosphamide. Although the patient achieved a complete remission on day 21, AML relapsed on day 434 after the transplantation. He died of sepsis. The prognosis of patients with SDS and AML is poor. Adult-onset cases must be recognized, and transplantation should be performed during bone marrow failure.

Acute erythroid leukemia (AEL) is a unique subtype of acute myeloid leukemia characterized by erythroid predominance and dysplasia. It is classified into two subtypes: pure erythroid (PEL) and erythroid/myeloid (EML) phenotypes. To understand the mechanism of the erythroid dominant phenotype of AEL and identify potential therapeutic targets for AEL, we analyzed 105 AEL and 214 non-AEL cases using whole-genome/exome and/or targeted-capture sequencing, with SNP probes for detecting copy number abnormalities. We also performed a transcriptome analysis of 12 AEL samples. Combining publicly available sequencing data, AEL was genetically clustered into four groups according to mutational status in TP53, STAG2, and NPM1 genes. Conspicuously, highly recurrent gains and amplifications affecting EPOR, JAK2, and/or ERG/ETS2 were recurrently detected in AEL cases, almost exclusively found in TP53-mutated cases. Among these, gains/amplifications of EPOR/JAK2 were more highly enriched in PEL than EML cases. Along with the activated STAT5 pathway, a common feature across all AEL cases, these AEL cases exhibited enhanced cell proliferation and heme metabolism, and they showed high sensitivity to ruxolitinib in in vitro and in xenograft models, highlighting the potential role of JAK2 inhibition in AEL therapeutics.

Variants of the t (8;21) (q22;q22) involving chromosome 8, 21, and other chromosomes account for about 3% of all t (8;21) (q22;q22) in patients with acute myeloid leukemia (AML). However, the prognosis of AML with variant t (8;21) remains unknown due to the scarcity of reported cases. Herein we report a case of AML with t (6;21;8) (p23;q22;q22). Fluorescence in situ hybridization confirmed a RUNX1-RUNX1T1 fusion signal on the derivative chromosome 8. This is the first report on a variant of t (8;21) involving the breakpoint 6p23. After induction chemotherapy, our patient achieved complete remission and has been stable for four years.

Molecular targeted therapies are now guideline-recommended treatments for unresectable non-small cell lung cancer( NSCLC) patients harboring driver gene mutations as a front-line treatment. Currently, 17 agents have been approved in Japan for the treatment of patients with NSCLC harboring EGFR mutation, ALK/ROS1/NTRK/RET fusions, BRAF V600E mutation, or MET exon 14 skipping mutation. In addition, many novel agents are being developed against NSCLCs with the other driver mutations such as EGFR or HER2 exon 20 insertion mutations and KRAS G12C mutation. In the era of personalized medicine, thoracic surgeons are expected to play an important role, as one of specialists for multidisciplinary treatments of NSCLCs, at the tumor boards/cancer boards, therefore, the knowledge of genetic testing and molecular targeted drugs is becoming essential for thoracic surgeons. In this review, from the standpoint of thoracic surgeons, we briefly summarize current topics on molecular testing in NSCLCs, approved molecular targeted drugs in Japan, acquired resistance mechanisms to these agents, and attempts to use molecular targeted drugs in adjuvant/neoadjuvant settings.

Human samples and health/clinical information are essential resources for both basic cancer research and cancer genomic medicine which stratifies subgroups of tumors and develops effective approaches to prevention, diagnosis and treatment of each cancer. For this purpose, a variety of population-based and disease-oriented cohort/biobanks are established as research platforms with a large number of cases with health/clinical record and biomaterials, including DNA, plasma/serum and tissue samples of high quality. In Japan, Tohoku Medical Megabank organization(ToMMo)and Japan Multi-Institutional Collaborative Cohort(J-MICC)are representative population-based cohorts, whereas Biobank Japan(BBJ)and National Center Biobank Network(NCBN)are major disease-oriented biobanks. Additional biobanks for rare cancers or childhood tumors have also been established and operated in these years. Cross-search programs for samples and information from the network of these Japanese biobanks has been established and being utilized for providing valuable information to researchers involved in basic sciences and cancer genomic medicine.

Cerebral cavernous malformations(CCMs)are vascular anomalies characterized by clusters of dilated capillaries and veins. They frequently cause epileptic seizures, hemorrhagic strokes, and focal neurological deficits. At present, CCMs can be treated only by surgical resection. However, the identification of germline and somatic mutations and the associated signaling pathways have improved our understanding of the underlying mechanisms; this has further led to testing of targeted molecular therapies for the disease. This review summarizes the current knowledge on the molecular pathogenesis of CCMs.

Schwannoma is a tumor that develops from the Schwann cells in the peripheral nervous system or cranial nerves. Gamma Knife radiosurgery has become an accepted treatment for schwannoma, with a high rate of tumor control. For sporadic or neurofibromatosis type 2-associated schwannoma resistant to radiotherapy, vascular endothelial growth factor(VEGF)-A/VEGF receptor(VEGFR)-targeted therapy(e.g., bevacizumab)may become the first-line therapy. However, some aspects of treatment with bevacizumab are problematic, such as the need for frequent parenteral administration, side effects, apparent drug resistance, and rebound tumor progression after cessation. In these situations, the gene product of the SH3PXD2A-HTRA1 fusion and several protein tyrosine kinase inhibitors may be supportive in preventing tumor progression because merlin inhibits signaling by tyrosine receptor kinases and there is activation of downstream pathways, including the Ras/Raf/MEK/ERK and PI3K/Akt/mTORC1 pathways. Although the tumor-microenvironment(TME)plays a key role in tumor growth, this physiological state is unclear in schwannoma. Tumor-associated macrophages may be a major component of the immunosuppressive cells in the TME of schwannoma. To impede tumor growth, the TME is also explored as a potential therapeutic target. Multimodal therapy is required to manage patients with refractory schwannoma. Furthermore, basic scientific research may be essential in achieving a novel treatment strategy.

Neurofibromatosis type 2(NF2)is a hereditary condition that causes bilateral vestibular schwannomas(VS), multiple schwannomas, and meningiomas. The prognosis is poor because the multiplicity of the tumors leads to a progressive decline in the quality of life, deafness, and death in an early age. NF2 is caused by a disorder in the tumor suppressor gene NF2, which encodes the merlin protein. Although it is an autosomal dominant disease, more than half of cases are presumed to be de novo caused by somatic mosaicism, the diagnosis rate of which has been improved by the recently introduced technology of targeted deep sequencing of DNA from multiple tissues. No chemotherapeutic drugs for treating NF2-related VS are available at present, and surgery and radiotherapy remain the only therapeutic options. Recently, a randomized, double-blind, multicenter clinical trial has started in Japan to verify the efficacy and safety of bevacizumab, a humanized monoclonal antibody that targets vascular endothelial growth factor, in treating NF2-related VS.

Meningiomas are one of the most common primary brain tumors. The majority of patients with meningiomas can undergo curative resection or remain asymptomatic for a lifetime, but a minority of them have tumors with cumbersome clinicopathological features causing life-threatening disease. Although several cytotoxic agents and hormonal therapies have been tried for refractory and unresectable meningiomas, there are no effective drugs available for meningiomas so far. In the last decade, due to the rapid progress in comprehensive genomic research for individual tumors, novel somatic and recurrent mutations were discovered in meningiomas. The discovered somatic mutations were mostly mutually exclusive with NF2 gene alterations, and importantly, several of these mutations, such as AKT1 and SMO, are potentially actionable mutations for precision/personalized medicine. In addition, immunotherapy is another attractive treatment option for refractory meningiomas due to the development of immune checkpoint inhibitors. Herein, we describe the possibility of precision medicine for meningiomas according to each molecular aberrancy and present the currently ongoing clinical trials including hormonal therapy, targeted kinase inhibitors, and immunotherapy.

About one-third of pediatric low-grade glioma and a half of pediatric high-grade glioma occur in the cerebrum. Pediatric hemispheric glioma may harbor diagnostic and therapeutically targetable genetic abnormalities, including BRAF V600E, H3.3 G34R/V, FGFR1 alternation, MYB or MYBL1 alternation, and NTRK/ALK/ROS1/MET fusion. In addition, the efficacy of molecular-targeted agents, such as BRAF inhibitors, MEK inhibitors, and NTRK inhibitors, against pediatric glioma with the relevant mutations has been demonstrated in several clinical trials. Furthermore, checkpoint inhibitors are considered a choice of treatment for hypermutated glioma, which is typically observed in patients with constitutional mismatch repair deficiency syndrome. Cancer gene panel testing, approved for insurance coverage in Japan in 2019, has been beneficial to pediatric cancer patients. However, to promote the clinical application of the recent molecular understanding of pediatric neuro-oncology, some issues have to be addressed. Herein, we review the genetic profiles of pediatric hemispheric glioma and introduce the current medical situation of precision medicine for pediatric patients with glioma in Japan.

Subependymal giant cell astrocytoma(SEGA)is a low-grade brain tumor occurring specifically in patients with tuberous sclerosis complex(TSC). TSC is an autosomal dominant genetic disease affecting multiple body systems and with wide variability in presentation. SEGA usually arises around the caudothalamic groove near the foramen of Monro, and can therefore cause life-threatening complications due to hydrocephalus. SEGA develops due to complete loss of function of the TSC1/TSC2 complex through a two-hit mechanism of biallelic inactivation of the TSC1 or TSC2 gene, leading to activation of mammalian target of rapamycin(mTOR). Identification of a pathogenic variant in TSC1 or TSC2 is sufficient for the diagnosis of TSC. Individuals with SEGAs presenting with acute deterioration due to obstructive hydrocephalus should undergo urgent surgical treatment. mTOR inhibitors have been shown to prevent SEGA growth in patients with TSC. Treatment with mTOR inhibitors is primarily recommended for individuals with non-acute symptomatic or asymptomatic growing or large SEGAs and those who are not surgical candidates or prefer medical treatment over surgery. Long-term treatment with mTOR inhibitors efficiently reduced SEGAs and prevented hydrocephalus. The surgical risks, potential side effects of mTOR inhibitors, and effect on other TSC manifestations should be considered so that the best treatment option is selected.

Hemangioblastoma(HB)is a tumor that frequently occurs in von Hippel-Lindau(VHL)disease, a hereditary tumor disease. It is a benign tumor and excision is the first choice of treatment, but in VHL disease, where HB occurs frequently, the emergence of more promising molecularly-targeted therapeutic agents has been desired. In this paper, we first explain HB and VHL disease and then outline the function of the VHL gene and the mechanism of onset of VHL disease. After that, we explain the analysis technology and frequency of VHL gene abnormalities and finally describe HIF2α inhibitors, which are promising as molecularly-targeted therapeutic agents for VHL disease. As the medical system for personalized medicine/precision medicine is being developed in Japan, it is expected that HB and VHL diseases will attract attention as target diseases in the future.

Herein we discuss precision medicine for ependymoma. We reviewed the new molecular classifications of ependymoma, studies on the molecular mechanisms involved in carcinogenesis and proliferation, and the various studies exploring new therapeutic strategies. Of the nine molecular classifications of ependymoma, supratentorial ependymomas with ZFTA fusion, posterior fossa PFA group, and spinal ependymomas with MYCN amplification are treatment-resistant, and candidates for precision medicine. Precision medicine is considered to select a treatment method based on molecular biological information, but its application is thought to be difficult for ependymomas with few somatic mutations. Recent studies have shown that epigenetic mechanisms are involved in the development and growth of PFA ependymomas without recurrent somatic mutations. It has been found that ZFTA forms fusion genes with various genes other than the typical ZFTA-RELA fusion, and a common therapeutic target has been suggested for the genes downstream of it. Unfortunately, these findings have not yet been clinically applied to precision medicine for ependymoma, but newer discoveries are gradually accumulating. Further development of research is warranted.

Current treatment protocols for medulloblastomas(MBs)stratify patients into high and average risk groups according to their age, metastatic status, and residual tumor volume after resection. Recent genetic and molecular biological reserach revealed that MBs are classified into at least four core subgroups - WNT, SHH, Group 3, and Group 4 - based on differences in their cytogenetics, mutational spectra, and gene expression signatures, as well as in their clinical phenotypes and prognosis. Latest studies suggest more distinct subtypes of MBs by DNA methylation profiles. In addition to conventional clinical risk stratification, new molecular risk stratification using molecular subgroups/subtypes, cytogenetic features and copy number aberrations help understand the outcome of current standard and/or experimental therapies. To achieve further improvement in prognosis and reduce treatment-related adverse events, the efficiency and safety of low-dose craniospinal irradiation and novel molecular targeted drugs, including SMO inhibitors, cyclin-dependent kinases 4/6, or checkpoint kinase 1/2 inhibitors, have been examined with respect to the molecular properties of each tumor. The molecular information of each MB is indispensable for precision medicine of MBs, strongly promoting the development of advanced therapeutic strategies of MBs.