Landscape and function of multiple mutations within individual oncogenes.

Sporadic reports have described cancer cases in which multiple driver mutations (MMs) occur in the same oncogene1,2. However, the overall landscape and relevance of MMs remain elusive. Here we carried out a pan-cancer analysis of 60,954 cancer samples, and identified 14 pan-cancer and 6 cancer-type-specific oncogenes in which MMs occur more frequently than expected: 9% of samples with at least one mutation in these genes harboured MMs. In various oncogenes, MMs are preferentially present in cis and show markedly different mutational patterns compared with single mutations in terms of type (missense mutations versus in-frame indels), position and amino-acid substitution, suggesting a cis-acting effect on mutational selection. MMs show an overrepresentation of functionally weak, infrequent mutations, which confer enhanced oncogenicity in combination. Cells with MMs in the PIK3CA and NOTCH1 genes exhibit stronger dependencies on the mutated genes themselves, enhanced downstream signalling activation and/or greater sensitivity to inhibitory drugs than those with single mutations. Together oncogenic MMs are a relatively common driver event, providing the underlying mechanism for clonal selection of suboptimal mutations that are individually rare but collectively account for a substantial proportion of oncogenic mutations.

Whole-genome landscape of adult T-cell leukemia/lymphoma.

Adult T-cell leukemia/lymphoma (ATL) is an aggressive neoplasm immunophenotypically resembling regulatory T cells, associated with human T-cell leukemia virus type-1. Here, we performed whole-genome sequencing (WGS) of 150 ATL cases to reveal the overarching landscape of genetic alterations in ATL. We discovered frequent (33%) loss-of-function alterations preferentially targeting the CIC long isoform, which were overlooked by previous exome-centric studies of various cancer types. Long but not short isoform-specific inactivation of Cic selectively increased CD4+CD25+Foxp3+ T cells in vivo. We also found recurrent (13%) 3'-truncations of REL, which induce transcriptional upregulation and generate gain-of-function proteins. More importantly, REL truncations are also common in diffuse large B-cell lymphoma, especially in germinal center B-cell-like subtype (12%). In the non-coding genome, we identified recurrent mutations in regulatory elements, particularly splice sites, of several driver genes. In addition, we characterized the different mutational processes operative in clustered hypermutation sites within and outside immunoglobulin/T-cell receptor genes and identified the mutational enrichment at the binding sites of host and viral transcription factors, suggesting their activities in ATL. By combining the analyses for coding and noncoding mutations, structural variations, and copy number alterations, we discovered 56 recurrently altered driver genes, including 11 novel ones. Finally, ATL cases were classified into 2 molecular groups with distinct clinical and genetic characteristics based on the driver alteration profile. Our findings not only help to improve diagnostic and therapeutic strategies in ATL, but also provide insights into T-cell biology and have implications for genome-wide cancer driver discovery.

Feasibility and clinical utility of comprehensive genomic profiling of hematological malignancies.

Identification of genetic alterations through next-generation sequencing (NGS) can guide treatment decision-making by providing information on diagnosis, therapy selection, and prognostic stratification in patients with hematological malignancies. Although the utility of NGS-based genomic profiling assays was investigated in hematological malignancies, no assays sufficiently cover driver mutations, including recently discovered ones, as well as fusions and/or pathogenic germline variants. To address these issues, here we have devised an integrated DNA/RNA profiling assay to detect various types of somatic alterations and germline variants at once. Particularly, our assay can successfully identify copy number alterations and structural variations, including immunoglobulin heavy chain translocations, IKZF1 intragenic deletions, and rare fusions. Using this assay, we conducted a prospective study to investigate the feasibility and clinical usefulness of comprehensive genomic profiling for 452 recurrently altered genes in hematological malignancies. In total, 176 patients (with 188 specimens) were analyzed, in which at least one alteration was detected in 171 (97%) patients, with a median number of total alterations of 7 (0-55). Among them, 145 (82%), 86 (49%), and 102 (58%) patients harbored at least one clinically relevant alteration for diagnosis, treatment, and prognosis, respectively. The proportion of patients with clinically relevant alterations was the highest in acute myeloid leukemia, whereas this assay was less informative in T/natural killer-cell lymphoma. These results suggest the clinical utility of NGS-based genomic profiling, particularly for their diagnosis and prognostic prediction, thereby highlighting the promise of precision medicine in hematological malignancies.

[Genetic dissection of the molecular mechanism of malignant lymphoma using advanced genomic technology].

Malignant lymphomas are a group of heterogeneous lymphoid malignancies, consisting of over 70 subtypes, which are classified according to their cell of origin. Classically, disease classification has been based on cellular morphology and immunophenotype. Due to the advancement of next-generation sequencing (NGS) technology, many comprehensive genomic studies have clarified the landscape of somatic alterations in these lymphomas, which has drastically improved our understanding of their molecular pathogenesis. Consequently, a new framework has been proposed for disease classification based on such somatic alterations and/or gene expression characteristic of each lymphoma subtype. Additionally, the results from the genomic studies have also established an important basis for the development of new targeted therapies and prognostic biomarkers. In the future, NGS-based gene panels will be covered by health insurance, and cancer precision medicine is expected to become more prevalent in this field. This paper outlines the analytical methods used in genomic studies by primarily focusing on NGS technology, and describes the results of major genomic and single-cell studies for various subtypes of malignant lymphoma.

Clinical practice guidance for next-generation sequencing in cancer diagnosis and treatment (Edition 1.0).

In Japan, the social (medical) health-care system is on the way to being developed to advance personalized medicine through the implementation of cancer genomic medicine, known as "cancer clinical sequencing," which uses a next-generation sequencer. However, no Japanese guidance for cancer genomic testing exists. Gene panel testing can be carried out to help determine patient treatment, confirm diagnosis, and evaluate prognostic predictions of patients with mainly solid cancers for whom no standard treatment is available. This guidance describes how to utilize gene panel testing according to the type of cancer: childhood cancer, rare cancer, carcinoma of unknown primary, and other cancers. The level of evidence classification for unified use in Japan is also detailed. This guidance establishes the basic principles of the quality control of specimens, requirements of medical institutions, informed consent, handling of data during the postanalysis stage, and treatment options based on the evidence level. In Japan, gene panel testing for cancer treatment and diagnosis is recommended to comply with this guidance. This is a collaborative work of the Japanese Society of Medical Oncology, Japan Society of Clinical Oncology, and the Japanese Cancer Association.

Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis during pregnancy.

An 11-week pregnant, 32-year-old Japanese woman who had recovered from infectious mononucleosis visited our center due to fever, anorexia, and bilateral hypochondrial pain. Blood tests revealed leukopenia, thrombocytopenia and elevated ferritin. She was diagnosed with hemophagocytic lymphohistiocytosis (HLH). A high viral load of the Epstein-Barr virus (EBV) was recognized, indicating EBV-HLH. She was treated with a single dose of dexamethasone to protect the fetus. However, the disease was uncontrollable, necessitating etoposide and cyclosporine administration. Remission was obtained with these medications, and she has remained in remission for the 10 months since completion of chemotherapy. Although the occurrence of EBV-HLH during pregnancy is rare, it is possible that a change in cellular immunity associated with the pregnancy may contribute to EBV-HLH development.

[IgE-κ type multiple myeloma achieving complete response with novel agents].

IgE multiple myeloma (MM) is a rare subtype of MM characterized by an aggressive and poor prognosis. Although novel agents have improved the prognosis of MM, there are few case reports of IgE MM treated with these agents. A 53-year-old male patient presented with pain in the right rib and was diagnosed with IgE-κ MM. He was treated with multidrug chemotherapy, including bortezomib and lenalidomide, and underwent autologous stem-cell transplantation (ASCT). Finally, he achieved a complete response after the initiation of pomalidomide. In previous reports, majority of patients with refractory IgE MM treated with novel agents had a poor prognosis. In contrast, patients who were treated with novel agents from the beginning and underwent ASCT had a long-term survival. Overall, the use of novel agents as the first-line therapy is expected to improve IgE MM prognosis.

[Induction treatment with bortezomib-cyclophosphamide-dexamethasone (CyBorD) for newly diagnosed transplant-eligible patients with multiple myeloma].

Twenty-nine transplant eligible newly diagnosed multiple myeloma (NDMM) patients have received Cyclophosphamide-Bortezomib-Dexamethasone (CyBorD) as induction treatment in our institute since November 2011. CyBorD is composed of CPA 300 mg/m2 p.o., Bor 1.3 mg/m2 i.v. or s.c., and Dex 40 mg/body p.o. on days 1, 8, 15, and 22. The median number of CyBorD cycles was 4 (range 2-6), except in one patient who progressed during the first cycle. Grade 4 neutropenia was observed in 2 patients, but none experienced grade 2 thrombocytopenia. Grade 3 non-hematologic adverse events were observed in two patients with varicella-zoster virus reactivation. Responses after CyBorD were ≥PR in 72%, ≥VGPR in 52%, ≥CR in 21%, and sCR in 21%. Autologous stem cells were harvested in 27 patients. Seventeen of these 27 patients received high-dose melphalan and autologous stem cell transplantation (ASCT) within 12 months after diagnosis. Patients with ≥CR increased to 59% after ASCT. Our data suggest the efficacy and the feasibility of administering CyBorD to transplant eligible NDMM patients.

[Graft-versus-host disease associated with lenalidomide maintenance after allogeneic transplantation for relapsed/refractory multiple myeloma].

Although allogeneic stem cell transplantation (allo-SCT) is a potentially curative treatment option for multiple myeloma (MM), it is not recognized as a standard of care because of the high associated incidences of both treatment related mortality and relapse. We administered lenalidomide (Len) as maintenance therapy for patients with MM undergoing allo-SCT who were at high risk of disease relapse. Graft-versus-host disease was induced by Len administration in two patients, but was manageable with dose reduction. Although Len has a direct anti-myeloma effect and can also induce tumor immunity against residual myeloma cells, it is important to identify how to optimize the safety and the effects of Len administration after allo-SCT. Further accumulation of data including those from prospective clinical trials is urgently needed.

[The clinical significance of decrease in CD138 positive cell ratio in multiple myeloma].

CD138 has been considered to be strongly expressed in multiple myeloma cells. However, CD138⁺ cells were decreased in some patients during the course of treatment. To clarify the clinical significance of this finding, we evaluated the correlations of CD138 levels with laboratory data employing flow cytometry. We found that CD138⁺ cells were decreased in 12 patients during treatment and were retained in the remaining 105 patients throughout their clinical courses. For nine (75%) patients in the CD138⁺ cells reduced group, median survival time was 25 months after the reduction in CD138⁺ cells was detected, and all nine died of myeloma. Furthermore, extramedullary lesions and specific cytogenetic abnormalities [del(17p), t(4;14), amplification of c-MYC] were observed in some patients when the number of CD138⁺ cells started to decrease. Interestingly, 2 of 3 patients who survived until the end of observation period showed re-increase in their CD138⁺ levels. Taking these observations together, it is unclear whether reduction of the number of CD138⁺ cells is associated with a poor prognosis and resistance to drugs. However, if treatment does not produce a reincrease in CD138⁺ levels, long term survival might be difficult to achieve.

Impacts of new agents for multiple myeloma on development of secondary myelodysplastic syndrome and acute myeloid leukemia.

The use of new agents (NAs) such as bortezomib, thalidomide, and lenalidomide has extended the survival of patients with multiple myeloma (MM). However, whether long-term treatment using NAs may increase the risk of second primary malignancies is a concern. Three hundred and thirty-three patients with MM were treated at our hospital from 1998 to 2013. Additional chromosomal abnormalities (CAs), associated with secondary myelodysplastic syndrome/acute myeloid leukemia, were observed in 13 of 152 users of NAs, but in 38 of 181 non-users of NAs. The cumulative CA incidence was higher in non-users of NAs. The CAs frequently observed were 13q-, 20q-, +8 in users of NAs, while -5/5q- and -7/7q- were detected in non-users of NAs. The total dose and treatment period of NAs did not differ between CAs-positive and -negative patients. However, a higher dose of melphalan was observed to have been used in patients who had CAs. Longer follow-up periods are necessary for an accurate risk assessment.

Comprehensive genetic profiling reveals frequent alterations of driver genes on the X chromosome in extranodal NK/T-cell lymphoma.

Extranodal NK/T-cell lymphoma (ENKTCL) is an Epstein-Barr virus (EBV)-related neoplasm with male dominance and a poor prognosis. A better understanding of the genetic alterations and their functional roles in ENKTCL could help improve patient stratification and treatments. Here, we performed comprehensive genetic analysis of 177 ENKTCL cases to delineate the landscape of mutations, copy number alterations (CNAs), and structural variations, identifying 34 driver genes including six previously unappreciated ones, namely HLA-B, HLA-C, ROBO1, CD58, POT1, and MAP2K1. Among them, CD274 (24%) was the most frequently altered, followed by TP53 (20%), CDKN2A (19%), ARID1A (15%), HLA-A (15%), BCOR (14%), and MSN (14%). Chromosome X (chrX) losses were the most common arm-level CNAs in females (~40%), and alterations of four X-linked driver genes (MSN, BCOR, DDX3X, and KDM6A) were more frequent in males and females harboring chrX losses. Among X-linked drivers, MSN was the most recurrently altered, and its expression was lost in approximately one-third of cases using immunohistochemical analysis. Functional studies of human cell lines demonstrated that MSN disruption promoted cell proliferation and NF-κB activation. Moreover, MSN inactivation increased sensitivity to NF-κB inhibition in vitro and in vivo. In addition, recurrent deletions were observed at the origin of replication in the EBV genome (6%). Finally, by integrating the 34 drivers and 19 significant arm-level CNAs, non-negative matrix factorization and consensus clustering identified two molecular groups with different genetic features and prognosis irrespective of clinical prognostic factors. Together, these findings could help improve diagnostic and therapeutic strategies in ENKTCL.

Inter- and intra-tumor heterogeneity of genetic and immune profiles in inherited renal cell carcinoma.

Patients with von Hippel-Lindau disease (vHL) are at risk of developing spatially and temporally multiple clear cell renal cell carcinomas (ccRCCs), which offers a valuable opportunity to analyze inter- and intra-tumor heterogeneity of genetic and immune profiles within the same patient. Here, we perform whole-exome and RNA sequencing, digital gene expression, and immunohistochemical analyses for 81 samples from 51 ccRCCs of 10 patients with vHL. Inherited ccRCCs are clonally independent and have less genomic alterations than sporadic ccRCCs. Hierarchical clustering of transcriptome profiles shows two clusters with distinct immune signatures: immune hot and cold clusters. Interestingly, not only samples from the same tumors but also different tumors from the same patients tend to show a similar immune signature, whereas samples from different patients frequently exhibit different signatures. Our findings reveal the genetic and immune landscape of inherited ccRCCs, demonstrating the relevance of host factors in shaping anti-tumor immunity.

Single-Cell Analysis of the Multicellular Ecosystem in Viral Carcinogenesis by HTLV-1.

Premalignant clonal expansion of human T-cell leukemia virus type-1 (HTLV-1)-infected cells occurs before viral carcinogenesis. Here we characterize premalignant cells and the multicellular ecosystem in HTLV-1 infection with and without adult T-cell leukemia/lymphoma (ATL) by genome sequencing and single-cell simultaneous transcriptome and T/B-cell receptor sequencing with surface protein analysis. We distinguish malignant phenotypes caused by HTLV-1 infection and leukemogenesis and dissect clonal evolution of malignant cells with different clinical behavior. Within HTLV-1-infected cells, a regulatory T-cell phenotype associates with premalignant clonal expansion. We also delineate differences between virus- and tumor-related changes in the nonmalignant hematopoietic pool, including tumor-specific myeloid propagation. In a newly generated conditional knockout mouse model recapitulating T-cell-restricted CD274 (encoding PD-L1) gene lesions found in ATL, we demonstrate that PD-L1 overexpressed by T cells is transferred to surrounding cells, leading to their PD-L1 upregulation. Our findings provide insights into clonal evolution and immune landscape of multistep virus carcinogenesis. SIGNIFICANCE: Our multimodal single-cell analyses comprehensively dissect the cellular and molecular alterations of the peripheral blood in HTLV-1 infection, with and without progression to leukemia. This study not only sheds light on premalignant clonal expansion in viral carcinogenesis, but also helps to devise novel diagnostic and therapeutic strategies for HTLV-1-related disorders.

Use of eribulin as an earlier-line chemotherapy for patients with HER2-negative metastatic breast cancer.

Background: Previous prospective studies have shown that eribulin improves the survival in patients with metastatic breast cancer (MBC). However, the optimal timing of its administration to achieve the longest extended survival and the efficacy of using eribulin monotherapy as earlier-line chemotherapy are yet unclear. Methods: We identified all consecutive female patients with MBC who received any chemotherapeutic intervention for metastatic disease at our institution between July 2012 and December 2017, excluding patients with HER2-positive disease. Those who received eribulin monotherapy for MBC were classified under the eribulin cohort, whereas those who never received eribulin were included in the non-eribulin (Non-E) cohort. Among the patients in the eribulin cohort, those who received eribulin as the first- or second-line chemotherapy for MBC were further classified under the earlier-line eribulin (EE), and otherwise classified under the later-line eribulin (LE) cohorts. The survival of patients was assessed using the log-rank test. A multivariable Cox proportional hazards model was used to assess the independent efficacy and timing of eribulin monotherapy. The inverse probability of treatment weighting (IPTW) estimate was utilized to compare the EE and LE cohorts. Results: Of the 507 patients who were initially screened, 226 were included after an intensive chart review: 93, 49, and 84 patients were included in the Non-E, EE, and LE cohorts, respectively. The eribulin cohort showed significantly longer overall survival than the Non-E cohort (30.3 vs. 22.2 months, p = 0.0217). No significant difference was observed in the progression-free survival of the EE and LE cohorts (3.4 vs. 4.4 months, p = 0.1337) after adjusting for clinically relevant factors using IPTW estimates. LE cohort showed good overall survival (OS) compared with patient group of Non-E and EE by log-rank testing (p = 0.0398), although multivariate analysis did not demonstrate eribulin administration timing as an independent prognostic factor of OS. OS was defined from the initiation of first-line chemotherapy date. Conclusions: Our data provided additional insights regarding the use of eribulin monotherapy as earlier-line chemotherapy. However, the optimal timing of eribulin monotherapy for MBC was not determined in the current study.

Phase 2 trial of daily, oral epigallocatechin gallate in patients with light-chain amyloidosis.

Previous studies have suggested that an increase in mitochondrial reactive oxygen species may cause organ damage in patients with light-chain (AL) amyloidosis; however, this damage can be decreased by antioxidant-agent treatment. Epigallocatechin gallate (EGCG), the major natural catechin in green tea, has potent antioxidant activity. Because EGCG has recently been reported to have a favorable toxicity profile for treating amyloidosis, we sought to examine the clinical efficacy and toxicity of EGCG in patients with AL amyloidosis. Fifty-seven patients were randomly assigned to the EGCG and observation groups and observed for six months. There were no increases in grade 3-5 adverse events and EGCG therapy was well tolerated. Although a decrease in the urinary albumin level was found in the EGCG group in patients with obvious albuminuria after treatment initiation, its antioxidant activity may not be sufficient to clarify the potential effect of EGCG in patients with AL amyloidosis. Because some of the biological markers responsible for organ damage were well correlated to the level of antioxidant potential in patients' plasma, the status of oxidative stress in the blood may indicate the extent of organ damage in clinical situations.

High-dose melphalan and autologous stem cell transplantation for systemic light-chain amyloidosis: a single institution retrospective analysis of 40 cases.

We report our retrospective analysis of 40 patients who received high-dose melphalan and autologous stem cell transplantation for systemic immunoglobulin light-chain (AL) amyloidosis. Between 2006 and 2013, 40 patients with AL amyloidosis were transplanted at our medical center. Their median age was 54 years (range 32-70 years): 18 were male. The dominant organs involved were the heart in 13 patients, and kidney in 22: and other organs were involved in five. The median melphalan dose administered was 129 (range 50-200) mg/m(2), and the median infused CD34(+) cells was 2.69 (range 1.17-11.26) × 10(6)/kg. Of the 40 patients, 30 are alive after a median follow-up of 42 (range 12-94) months, and the 4-year estimated overall survival rate was 74% (95% CI 56-86%). Four patients died ≤ 100 days post-ASCT (heart failure in three patients, bacteremia in one). The 4-year estimated survival of the patients with cardiac involvement was 54%, significantly lower than that of the other patients (91%). Hematological and organ responses were 52 and 50%, respectively. Careful patient selection and experienced management are important, especially for patients with cardiac involvement. It is also important to develop additional treatment for patients who do not achieve a hematological and/or organ response.