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Neuroblastomas require novel therapies that are based on the exploitation of their biological mechanism. To address this need, we analyzed the DNA methylation and expression datasets of neuroblastomas, extracted a candidate gene characterizing the aggressive features, and conducted functional studies. Based on the DNA methylation data, we identified a subgroup of neuroblastoma cases with 11q loss of heterozygosity with extremely poor prognosis. PHGDH, a serine metabolism-related gene, was extracted as a candidate with strong expression and characteristic methylation in this subgroup as well as in cases with MYCN amplification. PHGDH inhibition suppressed neuroblastoma cell proliferation in vitro and in vivo, indicating that the inhibition of serine metabolism by PHGDH inhibitors is a therapeutic alternative for neuroblastoma. Inhibiting the arginine metabolism, which is closely related to serine metabolism using arginine deiminase, had a combination effect both in vitro and in vivo, especially on extracellular arginine-dependent neuroblastoma cells with ASS1 deficiency. Expression and metabolome analyses of post-dose cells confirmed the synergistic effects of treatments targeting serine and arginine indicated that xCT inhibitors that inhibit cystine uptake could be candidates for further combinatorial treatment. Our results highlight the rational therapeutic strategy of targeting serine/arginine metabolism for intractable neuroblastoma., 神経芽腫の新たな診断法と治療戦略を創出 --がん細胞の生存戦略「がん代謝」を逆用する--. 京都大学プレスリリース. 2022-11-02.

Acute erythroid leukemia (AEL) is a unique subtype of acute myeloid leukemia characterized by prominent erythroid proliferation whose molecular basis is poorly understood. To elucidate the underlying mechanism of erythroid proliferation, we analyzed 121 AEL using whole-genome, whole-exome, and/or targeted-capture sequencing, together with transcriptome analysis of 21 AEL samples. Combining publicly available sequencing data, we found a high frequency of gains and amplifications involving EPOR/JAK2 in TP53-mutated cases, particularly those having >80% erythroblasts designated as pure erythroid leukemia (10/13). These cases were frequently accompanied by gains and amplifications of ERG/ETS2 and associated with a very poor prognosis, even compared with other TP53-mutated AEL. In addition to activation of the STAT5 pathway, a common feature across all AEL cases, these AEL cases exhibited enhanced cell proliferation and heme metabolism and often showed high sensitivity to ruxolitinib in vitro and in xenograft models, highlighting a potential role of JAK2 inhibition in therapeutics of AEL.Significance:This study reveals the major role of gains, amplifications, and mutations of EPOR and JAK2 in the pathogenesis of pure erythroleukemia. Their frequent response to ruxolitinib in patient-derived xenograft and cell culture models highlights a possible therapeutic role of JAK2 inhibition for erythroleukemia with EPOR/JAK2-involving lesions.This article is highlighted in the In This Issue feature, p. 369

Supplementary Figure from Amplified EPOR/JAK2 Genes Define a Unique Subtype of Acute Erythroid Leukemia

Supplementary Table from Amplified EPOR/JAK2 Genes Define a Unique Subtype of Acute Erythroid Leukemia

XLS file - 75KB, Details of signature and expression analyses.

PDF file - 126KB, Analyses of two patients with detectable SF3B1 mutations in CD19+, CD34+ and CD14+ fractions.

Supplementary table 1-9

Lollipop plot of NUP93 comparing EMPD and PanCancer Atlas dataset

Supplementary Tables S1-S13. Supplementary Table S1. Clinical information and the summary of experiments performed on each sample. Supplementary Table S2. List of genes and regions captured for targeted deep sequencing. Supplementary Table S3. dbSNP ID list for which target baits were designed. Supplementary Table S4. Non-silent mutations detected in a validation cohort by targeted deep sequencing. Supplementary Table S5. Validated non-silent somatic mutations by PCR-based deep sequencing. Supplementary Table S6. Validated silent/non-silent somatic mutations used for clonal analysis of multiple samples from PBL001. Supplementary Table S7. Significantly hypo-/hyper-methylated gene sets in PBL compared to normal pancreas. Supplementary Table S8. Fusion genes detected by whole transcriptome sequencing in PBL. Supplementary Table S9. Genes with a significant differential expression between PBL and normal pancreatic samples. Supplementary Table S10. Significant gene set enrichment in comparison between PBL and normal pancreas. Supplementary Table S11. List of differentially expressed genes in each gene cluster identified by hierarchical clustering. Supplementary Table S12. Top 20 significantly enriched pathways in each gene cluster. Supplementary Table S13. Gene coefficients of PC1 and PC2.

Pancreatoblastoma is a rare pediatric pancreatic malignancy for which the molecular pathogenesis is not understood. In this study, we report the findings of an integrated multiomics study of whole-exome and RNA sequencing as well as genome-wide copy number and methylation analyses of ten pancreatoblastoma cases. The pancreatoblastoma genome was characterized by a high frequency of aberrant activation of the Wnt signaling pathway, either via somatic mutations of CTNNB1 (90%) and copy-neutral loss of heterozygosity (CN-LOH) of APC (10%). In addition, imprinting dysregulation of IGF2 as a consequence of CN-LOH (80%), gain of paternal allele (10%), and gain of methylation (10%) was universally detected. At the transcriptome level, pancreatoblastoma exhibited an expression profile characteristic of early pancreas progenitor-like cells along with upregulation of the R-spondin/LGR5/RNF43 module. Our results offer a comprehensive description of the molecular basis for pancreatoblastoma and highlight rational therapeutic targets for its treatment.Significance: Molecular genetic analysis of a rare untreatable pediatric tumor reveals Wnt/IGF2 aberrations and features of early pancreas progenitor-like cells, suggesting cellular origins and rational strategies for therapeutic targeting. Cancer Res; 78(4); 865–76. ©2017 AACR.

Purpose:Extramammary Paget disease (EMPD) is an uncommon skin malignancy whose genetic alterations are poorly characterized. Previous reports identified mutations in chromatin remodeling genes and PIK3CA. In order to unambiguously determine driver mutations in EMPD, we analyzed 87 EMPD samples using exome sequencing in combination with targeted sequencing.Experimental Design:First, we analyzed 37 EMPD samples that were surgically resected using whole-exome sequencing. Based on several in silico analysis, we built a custom capture panel of putative driver genes and analyzed 50 additional formalin-fixed, paraffin-embedded samples using target sequencing. ERBB2 expression was evaluated by HER2 immunohisotochemistry. Select samples were further analyzed by fluorescence in situ hybridization.Results:A median of 92 mutations/sample was identified in exome analysis. A union of driver detection algorithms identified ERBB2, ERBB3, KMT2C, TP53, PIK3CA, NUP93, AFDN, and CUX1 as likely driver mutations. Copy-number alteration analysis showed regions spanning CDKN2A as recurrently deleted, and ERBB2 as recurrently amplified. ERBB2, ERBB3, and FGFR1 amplification/mutation showed tendency toward mutual exclusivity. Copy-number alteration load was associated with likelihood to recur. Mutational signatures were dominated by aging and APOBEC activation and lacked evidence of ultraviolet radiation. HER2 IHC/fluorescence in situ analysis validated ERBB2 amplification but was underpowered to detect mutations. Tumor heterogeneity in terms of ERBB2 amplification status was observed in some cases.Conclusions:Our comprehensive, unbiased analysis shows EMPD is characterized by alterations involving the PI3K–AKT pathway. EMPD is distinct from other skin cancers in both molecular pathways altered and etiology behind mutagenesis.

Supplementary Figures S1-S10. Supplementary Figure S1. Depths and coverages of targeted deep sequencing. Supplementary Figure S2. Sequencing coverages and numbers of mutations detected by WES. Supplementary Figure S3. Tumor subclonal populations in multiple samples from PBL001 estimated by PyClone. Supplementary Figure S4. Mutational signatures of primary and metastatic PBL. Supplementary Figure S5. SNP array-based copy number analysis of PBL. Supplementary Figure S6. Targeted deep sequencing based allele-specific copy number analysis of chromosome 11. Supplementary Figure S7. Bisulfite Sanger sequencing of ICR1 on chromosome 11p15.5. Supplementary Figure S8. Relative expression levels of IGF2 in CN-LOH-negative samples. Supplementary Figure S9. Aberrant activation of Wnt signaling pathway in PBL009. Supplementary Figure S10. Global DNA methylation profile of PBL.

Pleuropulmonary blastoma (PPB) is a rare pediatric malignancy whose pathogens are poorly understood. Recent reports suggest that germline mutations in the microRNA-processing enzyme DICER1 may contribute to PPB development. To investigate the genetic basis of this cancer, we performed whole-exome sequencing or targeted deep sequencing of multiple cases of PPB. We found biallelic DICER1 mutations to be very common, more common than TP53 mutations also found in many tumors. Somatic ribonuclease III (RNase IIIb) domain mutations were identified in all evaluable cases, either in the presence or absence of nonsense/frameshift mutations. Most cases had mutated DICER1 alleles in the germline with or without an additional somatic mutation in the remaining allele, whereas other cases displayed somatic mutations exclusively where the RNase IIIb domain was invariably affected. Our results highlight the role of RNase IIIb domain mutations in DICER1 along with TP53 inactivation in PPB pathogenesis. Cancer Res; 74(10); 2742–9. ©2014 AACR.

PDF file - 1805KB, Supplementary Table S1. List of primers used for validation of somatic mutations detected by whole-exome sequencing. Supplementary Table S2. Primers for DICER1 sequencing of all coding exons. Supplementary Table S3. Primers for DICER1 sequencing of all coding exons in paraffin embedded samples. Supplementary Table S4. Primers for TP53, UBA2, PDCD2L, CTNNB1, and GPR182. Supplementary Table S5. List of mutated genes detected by whole-exome sequencing. Supplementary Table S6. Allele frequency of DICER1 mutations in cases with unknown somatic status. Supplementary Table S7. Recurrent mutations detected by whole-exome sequencing. Supplementary Figure S1. Analyzing processes using Genomon. Supplementary Figure S2. Mean coverage of whole-exome sequencing in primary tumor, relapse tumor, and control samples. Supplementary Figure S3. Mean coverage of whole exome sequencing with GC contents in primary tumor, relapse tumor and control samples. Supplementary Figure S4. Detected mutations of DICER1 by Sanger sequencing. Supplementary Figure S5. Distribution of genetic lesions with 14 samples in PPB cases. Supplementary Figure S6. Common amplification lesion at 19q13.11.

Azacitidine is a mainstay of therapy for MDS-related diseases. The purpose of our study is to elucidate the effect of gene mutations on hematological response and overall survival (OS), particularly focusing on their post-treatment clone size. We enrolled a total of 449 patients with MDS or related myeloid neoplasms. They were analyzed for gene mutations in pre- (n=449) and post- (n=289) treatment bone marrow samples using targeted-capture sequencing to assess the impact of gene mutations and their post-treatment clone size on treatment outcomes. In Cox proportional hazard modeling, multi-hit TP53 mutation (HR, 2.03; 95% CI, 1.42-2.91; P

Germ line DDX41 variants have been implicated in late-onset myeloid neoplasms (MNs). Despite an increasing number of publications, many important features of DDX41-mutated MNs remain to be elucidated. Here we performed a comprehensive characterization of DDX41-mutated MNs, enrolling a total of 346 patients with DDX41 pathogenic/likely-pathogenic (P/LP) germ line variants and/or somatic mutations from 9082 MN patients, together with 525 first-degree relatives of DDX41-mutated and wild-type (WT) patients. P/LP DDX41 germ line variants explained ∼80% of known germ line predisposition to MNs in adults. These risk variants were 10-fold more enriched in Japanese MN cases (n = 4461) compared with the general population of Japan (n = 20 238). This enrichment of DDX41 risk alleles was much more prominent in male than female (20.7 vs 5.0). P/LP DDX41 variants conferred a large risk of developing MNs, which was negligible until 40 years of age but rapidly increased to 49% by 90 years of age. Patients with myelodysplastic syndromes (MDS) along with a DDX41-mutation rapidly progressed to acute myeloid leukemia (AML), which was however, confined to those having truncating variants. Comutation patterns at diagnosis and at progression to AML were substantially different between DDX41-mutated and WT cases, in which none of the comutations affected clinical outcomes. Even TP53 mutations made no exceptions and their dismal effect, including multihit allelic status, on survival was almost completely mitigated by the presence of DDX41 mutations. Finally, outcomes were not affected by the conventional risk stratifications including the revised/molecular International Prognostic Scoring System. Our findings establish that MDS with DDX41-mutation defines a unique subtype of MNs that is distinct from other MNs.

Due to the considerable success of cancer immunotherapy for leukemia, the tumor immune environment has become a focus of intense research; however, there are few reports on the dynamics of the tumor immune environment in leukemia. Here, we analyzed the tumor immune environment in pediatric B cell precursor acute lymphoblastic leukemia by analyzing serial bone marrow samples from nine patients with primary and recurrent disease by mass cytometry using 39 immunophenotype markers, and transcriptome analysis. High‐dimensional single‐cell mass cytometry analysis elucidated a dynamic shift of T cells from naïve to effector subsets, and clarified that, during relapse, the tumor immune environment comprised a T helper 1‐polarized immune profile, together with an increased number of effector regulatory T cells. These results were confirmed in a validation cohort using conventional flow cytometry. Furthermore, RNA transcriptome analysis identified the upregulation of immune‐related pathways in B cell precursor acute lymphoblastic leukemia cells during relapse, suggesting interaction with the surrounding environment. In conclusion, a tumor immune environment characterized by a T helper 1‐polarized immune profile, with an increased number of effector regulatory T cells, could contribute to the pathophysiology of recurrent B cell precursor acute lymphoblastic leukemia. This information could contribute to the development of effective immunotherapeutic approaches against B cell precursor acute lymphoblastic leukemia relapse., Tumor immune environment characterized by a T helper 1‐polarized immune profile was observed in recurrent B cell precursor acute lymphoblastic leukemia. Regulatory T cells were activated in recurrent B cell precursor acute lymphoblastic leukemia.

This article employs conversation analysis to investigate the workings of the so-called ‘nominative’ particle ga in storytelling sequences in naturally occurring Japanese conversation. Drawing on prior research, it is suggested that conversational stories are a natural habitat for ga—which is routinely found in the course of stories—in story initiations, within background information, in the articulation of the key sequence of events leading to the climax, as well as in the delivery of the climax itself. The current study looks at storytellers' deployment of ga for projecting and implementing a context-dependent mapping of a NP onto a Predicate, in interaction with story-recipients. Typically produced in the form NP ga Predicate, the mapping can be said to be demonstrably directed toward evoking or invoking varying types and degrees of identification or association of the NP with the Predicate. The identification or association appears to be profoundly shaped by the local interactional context as well as having a critical impact on the development of the story-telling sequence.

目的：フィリピン大学看護学部の都市と地方での地域看護学実習に参加し、フィールドワークを行った学生の学びと成長を明らかにする。方法：研修参加者３名にグループインタビューを実施した。逐語録を作成し、文脈の意味まとまり毎に要約しカテゴリー化した。結果：29 コード、12 サブカテゴリー、５カテゴリーを抽出した。【看護観の広がり】、【フィリピンの健康問題と保健医療サービスの特徴の理解】、【異文化の理解】の３カテゴリーと、特徴的な【人としての生き方の学び】、【将来へのきっかけと今後の決意】の２カテゴリーから構成されていた。考察：自己が主体的に関与するフィールドワークによる様々な経験から【人としての生き方の学び】、【将来へのきっかけと今後の決意】という人としての内面的成長の成果が認められた研修であった。本研修での学びが今後の様々な学習場面で関連づけられ、日本とフィリピンの文化の理解を更に促すと考える。

Clonal hematopoiesis (CH) in apparently healthy individuals is implicated in the development of hematological malignancies (HM) and cardiovascular diseases. Previous studies of CH analyzed either single-nucleotide variants and indels (SNVs/indels) or copy number alterations (CNAs), but not both. Here, using a combination of targeted sequencing of 23 CH-related genes and array-based CNA detection of blood-derived DNA, we have delineated the landscape of CH-related SNVs/indels and CNAs in 11,234 individuals without HM from the BioBank Japan cohort, including 672 individuals with subsequent HM development, and studied the effects of these somatic alterations on mortality from HM and cardiovascular disease, as well as on hematological and cardiovascular phenotypes. The total number of both types of CH-related lesions and their clone size positively correlated with blood count abnormalities and mortality from HM. CH-related SNVs/indels and CNAs exhibited statistically significant co-occurrence in the same individuals. In particular, co-occurrence of SNVs/indels and CNAs affecting DNMT3A, TET2, JAK2 and TP53 resulted in biallelic alterations of these genes and was associated with higher HM mortality. Co-occurrence of SNVs/indels and CNAs also modulated risks for cardiovascular mortality. These findings highlight the importance of detecting both SNVs/indels and CNAs in the evaluation of CH. Analysis of single-nucleotide variants and copy number alterations gives a more complete picture of clonal hematopoiesis and its impact on hematological malignancy and cardiovascular disease.

Background: Chronic kidney disease is frequently associated with persistent inflammation, which results in fibrosis in the stroma, a reduced number of renal tubules, the formation of multiple cystic lesions, ultimately terminating in renal failure and hemodialysis. Given the high incidence of renal cell carcinoma (RCC) in hemodialysis patients, suggesting a relationship between tissue remodeling by chronic inflammation and carcinogenesis. However, little is known about the genetic background of cancer development from remaining tubules and cystic lesions in hemodialysis patients. Method: We enrolled 5 patients under hemodialysis who were accompanied by acquired cystic kidney disease and underwent radical nephrectomy for RCC. Surgical specimens were fixed with alcohol-based solution and paraffin-embedded, and after H&E staining, subjected to laser capture microdissection (LCM) to collect remaining tubules and cysts containing approximately 200 cells. DNA was extracted and analyzed for somatic mutations and copy number alteration by whole-exome sequencing. Result: In total, we collected 161 LCM samples, including 118 from proximal tubules, 17 from collecting ducts, and 26 from cysts. Median variant allele frequencies of detected mutations were 0.237 in proximal tubules, 0.133 in collecting duct, and 0.381 in cysts, indicating larger clonal expansion in proximal tubules and cysts than in collecting ducts. Proximal tubules and cysts contained recurrent mutations in FAT1 (11% and 8%, respectively), STAG2 (5% and 8%), and PTEN (3% and 4%), whereas no recurrent driver mutations were identified in collecting ducts. In copy number analysis, 26% of proximal tubules, 35% of collecting ducts, and 80% of cysts had copy number alterations. Of note, samples from cysts had more copy number alterations compared to remaining tubules (on average, 2.3 vs. 1.1). Proximal tubules had recurrent copy number gains of chromosomes 3, 7, 10, 18, and 20, and loss of chromosome 22 and samples from collecting ducts showed gains of chromosome 7 and loss of chromosome 18. In cysts, gains of chromosomes 2, 3, 7, 10, 12, and 16 and loss of chromosomes 15, 16, 21, and 22 were frequently observed. Copy number profile in cysts was similar to that of papillary RCC and acquired cystic disease-associated RCC. Conclusion: In the end-stage cystic kidney, proximal tubules and cysts showed an enrichment of driver mutations commonly found in papillary RCC and RCC with acquired cystic disease, reflecting the fact that the incidence of these two types of RCC increases as the duration of dialysis becomes longer. In addition, clear cell RCC drivers, such as VHL mutation and loss of chromosome 3, were not observed, possibly explaining the rare occurrence of clear cell RCC in hemodialysis patients. Since cysts had more frequent copy number alterations than remaining tubules, cysts in the end-stage kidney might be precursor lesions of RCC. Citation Format: Kosuke Ieiri, Nobuyuki Kakiuchi, Tomonori Hirano, Tomomi Nishimura, Koichi Watanabe, Hiroko Tanaka, Satoru Miyano, Dai Takamatsu, Keisuke Monji, Eiji Kashiwagi, Masaki Shiota, Junichi Inokuchi, Masatoshi Eto, Seishi Ogawa. Genomic analysis of end-stage renal disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6066.

Introduction: The majority of patients with pancreatic cancer are inoperable at the time of diagnosis and even those cases with successful tumor resection for early-stage tumors frequently had second tumors within the remaining pancreas shortly after the surgery, contributing to a poor clinical outcome. Moreover, synchronous multiple pancreatic cancers were often reported. One of the long-standing issues about such synchronous and/or metachronous multiple pancreatic cancers is their clonal origins. In this study, we aimed to reveal the origin of multiple pancreatic cancers using an unbiased detection of somatic mutations in primary and metachronous cancers as well as adjacent precursor lesions. Methods: Serially obtained formalin-fixed paraffin-embedded surgical specimens from 18 patients who had undergone curative surgery for an early-stage pancreatic cancer were subjected to laser microdissection for the enrichment of tumor and precancerous lesions, from which DNA was extracted and analyzed for somatic mutations using whole-exome sequencing (WES) with matched normal DNA. Based on shared and private mutations across different samples, we interrogated history of clonal evolution of these lesions. Results: We analyzed 18 patients with multiple pancreatic cancers of 2 metachronous and synchronous, 14 metachronous, and 2 synchronous tumors. In metachronous cases, pathology for primary cancer were margin-negative in all patients, and the median interval between the initial and second surgery was 38.9 months (7 - 85 months). In addition, a total of 20 pancreatic intraepithelial neoplasia (PanIN) from 5 of these cases were analyzed. We identified a median of 66 (range: 31-232) and 20 (14-42) somatic mutations in cancer and PanIN lesions, respectively. None of the patients have known pathogenic germline variants. All samples had one or more driver mutations. In most cases (N=17), sharing many somatic mutations, multiple tumors had a common clonal origin. In another synchronous case, the synchronous tumors shared only one mutation, suggesting that they were clonally independent tumors. By contrast, none of the mutations other than hotspot KRAS mutations were shared between precursor and cancer lesions. While multiple independent clones were observed in precancerous lesions, most of multiple cancers originated from a common ancestor. Moreover, negative pathology of the margins at the initial surgery suggested that those multiple lesions arose from distant dissemination or metastasis, rather than contiguous, intraductal invasion. Conclusions: In conclusion, our study suggests that even early pancreatic cancer might be disseminated within the pancreas and contribute to synchronous and metachronous cancers. Citation Format: Tomonori Hirano, Nobuyuki Kakiuchi, Yasuhide Takeuchi, Tomomi Nishimura, Toshihiko Masui, Kazuyuki Nagai, Takayuki Anazawa, Sachiko Minamigushi, Hironori Haga, Norimitsu Uza, Hiroshi Seno, Yuzo Kodama, Atsuhiro Masuda, Takeshi Tanaka, Seishi Ogawa, Hiroko Tanaka, Satoru Miyano. Origin of synchronous or metachronous multiple pancreatic cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1511.

Introduction: The epithelial cells of the endometrium undergo rapid proliferation and shedding each month under the influence of estrogen and progesterone. Recent studies have demonstrated pervasive driver mutations in the endometrium with ageing. However, previous observations have been limited to the microscopic scale, and it is still unclear how clonal expansion occurs over the entire endometrium and what driver mutations are responsible therein. To address these issues, we performed multisampling of the endometrium with extensive spatial mapping. Methods: We collected multiple endometrial glands from normal endometrium in a 5mm lattice in 19 patients who underwent hysterectomy (3-31 samples per case), followed by DNA extraction, detected somatic mutations by whole exome sequencing, to identify large clones that spread across samples based on shared mutations. Results: In total, 216 bulk endometrial glands were analyzed. The number of detected somatic mutations per sample ranged from 6 to 98 (mean±SD: 37.8±16.0), and most of the samples had at least one known driver gene mutation (mean±SD: 4.38±2.27). The mutational signature analysis revealed the predominance of the age-related SBS1 and SBS5 signatures. dN/dS analysis identified 21 genes that were positively selected in normal endometrium, including PIK3CA, PIK3R1, KRAS, PPP2R1A, ARHGAP35, and FBXW7, most of which are also known as driver genes for endometrial cancer. The number of mutations and their frequency for each driver gene did not differ by background diseases: endometriosis, endometriosis-associated ovarian cancer and other non-endometrial related diseases. We found clones showing a large expansion involving multiple samples in 8 cases, most of which harbored one or more driver mutations, such as PIK3CA and KRAS. The size of the largest clone carrying a KRAS mutation, which was found in a 32-year-old woman with cervical cancer, spanned as long as 10 mm in diameter. This suggests that clonal expansion in the endometrium could be very rapid even in healthy women, which contrasts to the observations that clonal expansion in other organs is usually seen in aged individuals. Conclusion: We confirmed the high frequency of driver mutations in the normal endometrium, most of which overlapped to those found in endometrial cancers, suggesting that these driver genes are involved in the early phase of the development in the endometrial cancer. Some of the driver-mutated clones expanded in macroscopic size. Our findings provide an interesting insight into the clonal structure and underlying genetic variation in the normal endometrium. Citation Format: Koichi Watanabe, Nobuyuki Kakiuchi, Shiro Takamatsu, Sachiko Kitamura, Mana Taki, Koji Yamanoi, Ryusuke Murakami, Ken Yamaguchi, Junzo Hamanishi, Hiroko Tanaka, Satoru Miyano, Masaki Mandai, Seishi Ogawa. Clonal expansion with driver mutations in normal human endometrium [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 128.

Introduction: Adjuvant chemotherapy (ACT) has a key role in the treatment of high-risk colorectal cancer (CRC) patients to prevent post surgical recurrence. However, the efficacy of ACT is offset by the development of complication such as peripheral neuropathy, which leads to compromised quality of life, while ACT is expected to prevent tumor recurrence in only 5% and 20% in Stage2 and 3 patients, respectively. Thus, there is an urgent need to develop a biomarker that accurately predicts the effect of ACT and therefore helps guide ACT eligibility. Methods: We enrolled a total of 3,023 cases with CRC, for whom targeted-capture sequencing was performed that covered 169 known or putative driver genes and 1,660 polymorphoic sites to detect somatic mutations and copy number alterations (CNAs), respectively. RNA sequencing was also performed to detect driver gene fusions and to profile gene expression. We identified, through univariate analysis, gene mutations/CNAs as well as clinical parameters using those cases who did not received ACT to establish a model that predict time to recurrence (TTR) using the Cox proportional hazard modelling. Thereafter, the model was applied to those who did receive ACT to assess the impact of the model in the prediction of TTR. Results: We identified a total of 32145 mutations and/or 44511 CNAs in 2970 (98%) out of 3,023 cases. Mutations were found in 55 driver genes, including 15 previously unknown drivers, such as MAP2K1, AKT1, and TCF7. According to the number of mutations, 278 casese were classified as hypermutated cases. The remaining ‘non-hypermutated cases’ (n=2692) were classified into APC-mutated, RNF43/ZNRF3-mutated, CTNNB1-mutated, RSPO-fusion(+) and other Wnt-mutation(−) cases. The TTR prediction model was constructed by repeating Cox regression 1000 times using randomly selected 80% of the non-hypermutated cases and variables identified in univariate analysis. Adopting those variables selected in >70% models, we established the final model including both genetic (mutations/CNAs) and clinical variables, based on which we classified patients into 4 risk groups, low/intermediate/high/very-high. Finally, by applying the classification to those who received ACT, we demonstrated that 18% of Stage2 and the majority of Stage3 cases with high/very-high risks were predicted to benefit from ACT, whereas most of the Stage2 and as many as 19% of Stage3 cases received ACT with no significant improvement of TTR. Approximately 5% of Stage1 cases belonged to the high-risk category and potentially benefit from ACT. Conclusions: On the basis of large-scale genotyping of clinically well-annotated CRC cases, we proposed molecular classification of CRC and established a model that enabled prediction of TTR and risk stratification, which was successfully used to identify cases who benefited (within Stage 2/3 cases) or will benefit (in Stage1 cases) from ACT to prolong TTR. Citation Format: Yoshikage Inoue, Nobuyuki Kakiuchi, Kenichi Yoshida, Yasuhito Nanya, Yasuhide Takeuchi, Yuichi Shiraishi, Kenichi Chiba, Tetusichi Yoshizato, Hiroko Tanaka, Satoshi Nagayama, Kazutaka Obama, Satoru Miyano, Seishi Ogawa. Genomic characterization and risk stratification of colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 978.

Tyrosine kinase inhibitors (TKIs) are standard therapies for chronic myeloid leukemia (CML) that can eradicate Ph-positive leukemic cells. However, disease control is not achievable in a minority of cases, most commonly due to evolution of TKI-resistant clones. There have also been rare cases of emergence of Ph-negative clones with other cytogenetic abnormalities, and, less commonly, development of Ph-negative acute myeloid leukemia (AML), whose molecular pathogenesis is largely unknown. Here we report molecular features of a patient with Ph + CML who developed Ph-negative AML after showing a major molecular response to dasatinib. A 55-year-old man was diagnosed with CML. He achieved a complete cytogenetic response three months after dasatinib therapy but developed AML with normal karyotype 1 year later. After receiving induction and consolidation chemotherapy for AML, the patient achieved complete remission with no evidence of CML under maintenance with bosutinib. Targeted sequencing of serial bone marrow samples identified mutations in IDH2 and NPM1 in the Ph-negative AML cells, which had not been detected in CML cells. These results suggest that Ph-negative AML in this patient originated from a preleukemic population, which might have expanded during or after the successful elimination of CML clones with TKI therapy.

Context Pheochromocytoma and paraganglioma (PPGL) may appear as a complication of cyanotic congenital heart disease (CCHD-PPGL) with frequent EPAS1 mutations, suggesting a close link between EPAS1 mutations and tissue hypoxia in CCHD-PPGL pathogenesis. Objective Our aim is to further investigate the role of EPAS1 mutations in the hypoxia-driven mechanism of CCHD-PPGL pathogenesis, particularly focusing on metachronous and/or multifocal CCHD-PPGL tumors. Methods We performed whole-exome sequencing (WES) for somatic and germline mutations in 15 PPGL samples from 7 CCHD patients, including 3 patients with metachronous and/or multifocal tumors, together with an adrenal medullary hyperplasia (AMH) sample. Results We detected EPAS1 mutations in 15 out of 16 PPGL/AMH samples from 7 cases. Conspicuously, all EPAS1 mutations in each of 3 cases with multifocal or metachronous tumors were mutually independent and typical examples of parallel evolution, which is suggestive of strong positive selection of EPAS1-mutated clones. Compared to 165 The Cancer Genome Atlas non–CCHD-PPGL samples, CCHD-PPGL/AMH samples were enriched for 11p deletions (13/16) and 2p amplifications (4/16). Of particular note, the multiple metachronous PPGL tumors with additional copy number abnormalities developed 18 to 23 years after the resolution of hypoxemia, suggesting that CCHD-induced hypoxic environments are critical for positive selection of EPAS1 mutants in early life, but may no longer be required for development of PPGL in later life. Conclusion Our results highlight a key role of activated hypoxia-inducible factor 2α due to mutated EPAS1 in positive selection under hypoxic environments, although hypoxemia itself may not necessarily be required for the EPAS1-mutated clones to progress to PPGL.

To elucidate the molecular pathogenesis of pediatric germ cell tumors (GCTs), we performed DNA methylation array analysis, whole transcriptome sequencing, targeted capture sequencing, and single-nucleotide polymorphism array analysis using 51 GCT samples (25 female, 26 male), including 6 germinomas, 2 embryonal carcinomas, 4 immature teratomas, 3 mature teratomas, 30 yolk sac tumors, and 6 mixed germ cell tumors. Among the 51 samples, 11 were from infants, 23 were from young children, and 17 were from those aged ≥10 years. Sixteen of the 51 samples developed in the extragonadal regions. Germinomas showed upregulation of pluripotent genes and global hypomethylation. Pluripotent genes were also highly expressed in embryonal carcinomas. These genes may play essential roles in embryonal carcinomas given that their binding sites are hypomethylated. Yolk sac tumors exhibited overexpression of endodermal genes, such as GATA6 and FOXA2, the binding sites of which were hypomethylated. Interestingly, infant yolk sac tumors had different DNA methylation patterns from those observed in older children. Teratomas had higher expression of ectodermal genes, suggesting a tridermal nature. Based on our results, we suggest that KIT, TNFRSF8, and ERBB4 may be suitable targets for the treatment of germinoma, embryonal carcinomas, and yolk sac tumors, respectively., Yasuo Kubota et al. report a multi-omic analysis of pediatric germ cell tumors from 51 patients ranging in age from 2 months to 19 years. They identify unique methylation, expression, and mutational patterns for each of the main subtypes and propose potential target genes for treatments against the three main subtypes.