Promoter swapping of truncated PDGFRB drives Ph-like acute lymphoblastic leukemia.

Philadelphia chromosome (Ph)-like acute lymphoblastic leukemia (ALL) is a subset of ALL that demonstrated a high treatment failure rate. One of the hallmarks of Ph-like ALL is PDGFRB gene fusion, with fusion partner proteins often harboring dimerization domains and enhancing the kinase activity of PDGFRB. We determined a novel oncogenic PDGFRB fusion gene, NRIP1::PDGFRB, from a pediatric patient with ALL, encoding a protein with the carboxy-terminal kinase domain of PDGFRB, without the partner peptide. We confirmed the oncogenic potential of NRIP1::PDGFRB in vitro and the efficacy of all ABL1-specific inhibitor generations, including imatinib, dasatinib, nilotinib, and ponatinib, in suppressing this potential. PDGFRB activation mechanism may include juxtamembrane domain truncation in the predicted peptide. In conclusion, we determined a novel fusion gene pattern in Ph-like ALL.

Sleeping Beauty transposon mutagenesis identified genes and pathways involved in inflammation-associated colon tumor development.

Chronic inflammation promotes development and progression of colorectal cancer (CRC). To comprehensively understand the molecular mechanisms underlying the development and progression of inflamed CRC, we perform in vivo screening and identify 142 genes that are frequently mutated in inflammation-associated colon tumors. These genes include senescence and TGFß-activin signaling genes. We find that TNFα can induce stemness and activate senescence signaling by enhancing cell plasticity in colonic epithelial cells, which could act as a selective pressure to mutate senescence-related genes in inflammation-associated colonic tumors. Furthermore, we show the efficacy of the Cdk4/6 inhibitor in vivo for inflammation-associated colonic tumors. Finally, we functionally validate that Arhgap5 and Mecom are tumor suppressor genes, providing possible therapeutic targets for CRC. Thus, we demonstrate the importance of the inactivation of senescence pathways in CRC development and progression in an inflammatory microenvironment, which can help progress toward precision medicine.

[Evaluation of Low-dose Whole-body FDG PET with SiPM-based PET/CT Scanner: Visual and Semi-quantitative Analyses Using Random Sampling from Full-dose Scan Data].

PURPOSE: Sensitivity and count rate performance of the latest PET/CT scanners with a silicon photomultiplier (SiPM) have been substantially improved compared to scanners with a photomultiplier tube (PMT), thereby promising a low-dose whole-body PET scan with maintaining image quality. However, it is ethically difficult to verify the low-dose protocol in actual clinical settings. In this study, we investigated the effect of dose reduction on reconstructed images by using a low-dose simulation technique, i.e., reducing the number of events from the acquired data. METHOD: For 21 subjects who underwent whole-body 18F-FDG PET examination with an SiPM-based PET/CT scanner, Biograph Vision (Siemens Healthineers, Erlangen, Germany), at a dosage of 3.5 MBq/kg and a continuous bed motion speed of 1.1 mm/sec (the standard protocol in our hospital), the number of events in acquired list data (100%; "full-dose") was reduced to 50%, 25%, 12.5%, and 6.25% ("low-dose"). The low-dose reconstructed images were evaluated visually and physically with reference to the full-dose images. The physical evaluation was performed by calculating differences in SUVmax at abnormal uptake (n=54) between the full-dose and low-dose images. RESULT: The 25% data images were visually acceptable, and the difference in SUVmax between the 100% and 25% data images was 9.8±13.5%. CONCLUSION: Our results suggest that Biograph Vision is a feasible method to reduce conventional dose with the potential use of 25% data images.

Oncogenic structural aberration landscape in gastric cancer genomes.

Structural variants (SVs) are responsible for driver events in gastric cancer (GC); however, their patterns and processes remain poorly understood. Here, we examine 170 GC whole genomes to unravel the oncogenic structural aberration landscape in GC genomes and identify six rearrangement signatures (RSs). Non-random combinations of RSs elucidate distinctive GC subtypes comprising one or a few dominant RS that are associated with specific driver events (BRCA1/2 defects, mismatch repair deficiency, and TP53 mutation) and epidemiological backgrounds. Twenty-seven SV hotspots are identified as GC driver candidates. SV hotspots frequently constitute complexly clustered SVs involved in driver gene amplification, such as ERBB2, CCNE1, and FGFR2. Further deconstruction of the locally clustered SVs uncovers amplicon-generating profiles characterized by super-large SVs and intensive segmental amplifications, contributing to the extensive amplification of GC oncogenes. Comprehensive analyses using adjusted SV allele frequencies indicate the significant involvement of extra-chromosomal DNA in processes linked to specific RSs.

PATIENT DOSIMETRY SURVEY OF PEDIATRIC DIAGNOSTIC AND THERAPEUTIC CARDIAC CATHETERISATION IN JAPAN.

To propose reference values for air-kerma at the reference point (Ka,r), air-kerma area product (PKA), fluoroscopy time (FT) and number of cine images (CI) for four age groups in Japan, a nationwide questionnaire was posted to 132 pediatric catheterisation of certified facility in Japan, using the conventional post system, to which 43 facilities responded. For diagnostic cardiac angiography, reference values were as follows: Ka,r: 86, 102, 165 and 264 mGy; PKA: 9.3, 9.5, 16 and 34 Gy.cm2; FT: 33, 29, 26 and 30 min and CI: 1904, 1966, 2405 and 1871 images. For therapeutic cardiac angiography, reference values were as follows: Ka,r: 107, 163, 103 and 202 mGy; PKA: 7.5, 18, 7 and 24 Gy.cm2; FT: 56, 52, 42 and 30 min and CI: 3886, 3232, 2212 and 4316 images for less than 1, 1-5, 6-10 and 11-15 y, respectively. To optimal patient exposure from diagnostic and therapeutic cardiac catheterisation, it is therefore necessary to establish reference values for pediatric cardiac catheterisation examinations for four age groups.

Multiancestry genomic and transcriptomic analysis of gastric cancer.

Gastric cancer is among the most common malignancies worldwide, characterized by geographical, epidemiological and histological heterogeneity. Here, we report an extensive, multiancestral landscape of driver events in gastric cancer, involving 1,335 cases. Seventy-seven significantly mutated genes (SMGs) were identified, including ARHGAP5 and TRIM49C. We also identified subtype-specific drivers, including PIGR and SOX9, which were enriched in the diffuse subtype of the disease. SMGs also varied according to Epstein-Barr virus infection status and ancestry. Non-protein-truncating CDH1 mutations, which are characterized by in-frame splicing alterations, targeted localized extracellular domains and uniquely occurred in sporadic diffuse-type cases. In patients with gastric cancer with East Asian ancestry, our data suggested a link between alcohol consumption or metabolism and the development of RHOA mutations. Moreover, mutations with potential roles in immune evasion were identified. Overall, these data provide comprehensive insights into the molecular landscape of gastric cancer across various subtypes and ancestries.

Bevacizumab beyond Progression for Newly Diagnosed Glioblastoma (BIOMARK): Phase II Safety, Efficacy and Biomarker Study.

We evaluated the efficacy and safety of bevacizumab beyond progression (BBP) in Japanese patients with newly diagnosed glioblastoma and explored predictors of response to bevacizumab. This phase II study evaluated a protocol-defined primary therapy by radiotherapy with concurrent and adjuvant temozolomide plus bevacizumab, followed by bevacizumab monotherapy, and secondary therapy (BBP: bevacizumab upon progression). Ninety patients received the protocol-defined primary therapy (BBP group, n = 25). Median overall survival (mOS) and median progression-free survival (mPFS) were 25.0 and 14.9 months, respectively. In the BBP group, in which O6-methylguanine-DNA methyltransferase (MGMT)-unmethylated tumors predominated, mOS and mPFS were 5.8 and 1.9 months from BBP initiation and 16.8 and 11.4 months from the initial diagnosis, respectively. The primary endpoint, the 2-year survival rate of the BBP group, was 27.0% and was unmet. No unexpected adverse events occurred. Expression profiling using RNA sequencing identified that Cluster 2, which was enriched with the genes involved in macrophage or microglia activation, was associated with longer OS and PFS independent of the MGMT methylation status. Cluster 2 was identified as a significantly favorable independent predictor for PFS, along with younger age and methylated MGMT. The novel expression classifier may predict the prognosis of glioblastoma patients treated with bevacizumab.

C-CAT: The National Datacenter for Cancer Genomic Medicine in Japan.

SUMMARY: Since June 2019, under the umbrella of the national health insurance system, Japan has started cancer genomic medicine (CGM) with comprehensive genomic profiling (CGP) tests. The Ministry of Health, Labour and Welfare (MHLW) of Japan constructed a network of CGM hospitals (a total of 233 institutes as of July 1, 2022) and established the Center for Cancer Genomics and Advanced Therapeutics (C-CAT), the national datacenter for CGM. Clinical information and genomic data from the CGP tests are securely transferred to C-CAT, which then generates "C-CAT Findings" reports containing information of clinical annotation and matched clinical trials based on the CGP data. As of June 30, 2022, a total of 36,340 datapoints of clinical/genomic information are aggregated in C-CAT, and the number is expected to increase swiftly. The data are now open for sharing with not only the CGM hospitals but also other academic institutions and industries.

Genomic landscape of chemical-induced lung tumors under Nrf2 different expression levels.

The transcription factor Nrf2 plays a crucial role in the anti-oxidative stress response, protection of DNA from injury and DNA repair mechanisms. Nrf2 activity reduces cancer initiation, but how Nrf2 affects whole-genome alterations upon carcinogenic stimulus remains unexplored. Although recent genome-wide analysis using next-generation sequencing revealed landscapes of nucleotide mutations and copy number alterations in various human cancers, genomic changes in murine cancer models have not been thoroughly examined. We elucidated the relationship between Nrf2 expression levels and whole exon mutation patterns using an ethyl-carbamate (urethane)-induced lung carcinogenesis model employing Nrf2-deficient and Keap1-kd mice, the latter of which express high levels of Nrf2. Exome analysis demonstrated that single nucleotide and trinucleotide mutation patterns and the Kras mutational signature differed significantly and were dependent on the expression level of Nrf2. The Nrf2-deficient tumors exhibited fewer copy number alterations relative to the Nrf2-wt and Keap1-kd tumors. The observed trend in genomic alterations likely prevented the Nrf2-deficient tumors from progressing into malignancy. For the first time, we present whole-exome sequencing results for chemically-induced lung tumors in the Nrf2 gain or loss of function mouse models. Our results demonstrate that different Nrf2 expression levels lead to distinct gene mutation patterns that underly different oncogenic mechanisms in each tumor genotype.

Open reading frame dominance indicates protein-coding potential of RNAs.

Recent studies have identified numerous RNAs with both coding and noncoding functions. However, the sequence characteristics that determine this bifunctionality remain largely unknown. In the present study, we develop and test the open reading frame (ORF) dominance score, which we define as the fraction of the longest ORF in the sum of all putative ORF lengths. This score correlates with translation efficiency in coding transcripts and with translation of noncoding RNAs. In bacteria and archaea, coding and noncoding transcripts have narrow distributions of high and low ORF dominance, respectively, whereas those of eukaryotes show relatively broader ORF dominance distributions, with considerable overlap between coding and noncoding transcripts. The extent of overlap positively and negatively correlates with the mutation rate of genomes and the effective population size of species, respectively. Tissue-specific transcripts show higher ORF dominance than ubiquitously expressed transcripts, and the majority of tissue-specific transcripts are expressed in mature testes. These data suggest that the decrease in population size and the emergence of testes in eukaryotic organisms allowed for the evolution of potentially bifunctional RNAs.

Comparison of Radiofrequency and Cryoballoon Pulmonary Vein Ablation for the Early and Late Recurrence of Atrial Fibrillation.

Objective Early recurrence (ER) after pulmonary vein isolation (PVI) for atrial fibrillation (AF) is expected to resolve within the recommended 3-month blanking period, irrespective of the ablation device used. To compare the occurrence and relationship of AF within the blanking period and subsequent late recurrence (LR) with radiofrequency (RF) and cryoballoon (CB) ablation. Methods A retrospective analysis of 294 patients (mean age=62±9, 70.0% male) undergoing PVI for drug-refractory paroxysmal AF was done. After categorizing the patients into the RF group (n=152) and the CB group (n=142), a group-wise comparison was done to investigate the impact of ER on LR throughout a 2-year follow-up. Results The groups were similar regarding the occurrence of ER (RF=22.4%, CB=24.6%, p=0.62), while LR was significantly higher in the RF group (p=0.003). ER was associated with LR in the RF group (p<0.01) but not in the CB group (p=0.08), while a significant independent association with an increased LR risk was observed [hazard ratio (HR) 6.12; 95% confidence interval (CI) 3.56-10.51, p<0.01]. RF ablation also significantly increased the risk of LR (HR=2.93; 95% CI=1.64-5.23, p<0.01). Conclusion A recurrence of atrial arrhythmia is more frequent with RF-PVI than with CB-PVI for patients with paroxysmal AF. ER and RF-ablation are strong predictors for LR after the 3-month blanking period.

Transcriptome and methylome analysis of CNS germ cell tumor finds its cell-of-origin in embryogenesis and reveals shared similarities with testicular counterparts.

BACKGROUND: CNS germ cell tumors (GCTs) predominantly develop in pediatric and young adult patients with variable responses to surgery, radiation, and chemotherapy. This study aimed to examine the complex and largely unknown pathogenesis of CNS GCTs. METHODS: We used a combined transcriptomic and methylomic approach in 84 cases and conducted an integrative analysis of the normal cells undergoing embryogenesis and testicular GCTs. RESULTS: Genome-wide transcriptome analysis in CNS GCTs indicated that germinoma had a transcriptomic profile representative of primitive cells during early embryogenesis with high meiosis/mitosis potentials, while nongerminomatous GCTs (NGGCTs) had differentiated phenotypes oriented toward tissue formation and organogenesis. Co-analysis with the transcriptome of human embryonic cells revealed that germinomas had expression profiles similar to those of primordial germ cells, while the expression profiles of NGGCTs were similar to those of embryonic stem cells. Some germinoma cases were characterized by extensive immune-cell infiltration and high expression of cancer-testis antigens. NGGCTs had significantly higher immune-cell infiltration, characterized by immune-suppression phenotype. CNS and testicular GCTs (TGCTs) had similar mutational profiles; TGCTs showed enhanced copy number alterations. Methylation analysis clustered germinoma/seminoma and nongerminoma/nonseminoma separately. Germinoma and seminoma were co-categorized based on the degree of the tumor microenvironment balance. CONCLUSIONS: These results suggested that the pathophysiology of GCTs was less dependent on their site of origin and more dependent on the state of differentiation as well as on the tumor microenvironment balance. This study revealed distinct biological properties of GCTs, which will hopefully lead to future treatment development.

NATIONWIDE SURVEY OF RADIATION EXPOSURE FOR RADIOFREQUENCY CATHETER ABLATION FOR PULMONARY VEIN ISOLATION AND NONPULMONARY VEIN ISOLATION IN JAPAN.

To propose typical values for the arrhythmia region between pulmonary vein isolation (PVI) and nonpulmonary vein isolation (non-PVI) in Japan. A nationwide questionnaire was posted to 343 facilities, to which 125 facilities (36.4%) responded. Results is the median for PVI and non-PVI were in terms of Ka,r (317 and 196 mGy), PKA (40.8 and 26.3 Gy.cm2), FT (43.0 and 27.3 min), and CI (326 and 102 images). When comparing PVI and non-PVI procedures, there were significant differences in Ka, r, PKA, FT, and CI (p < 0.05). In other words, by classifying into two types, PVI and non-PVI, we contributed to the establishment of typical values in Japan's RFCA.

Comprehensive Genomic Profiling of Neuroendocrine Carcinomas of the Gastrointestinal System.

The neuroendocrine carcinoma of the gastrointestinal system (GIS-NEC) is a rare but highly malignant neoplasm. We analyzed 115 cases using whole-genome/exome sequencing, transcriptome sequencing, DNA methylation assays, and/or ATAC-seq and found GIS-NECs to be genetically distinct from neuroendocrine tumors (GIS-NET) in the same location. Clear genomic differences were also evident between pancreatic NECs (Panc-NEC) and nonpancreatic GIS-NECs (Nonpanc-NEC). Panc-NECs could be classified into two subgroups (i.e., "ductal-type" and "acinar-type") based on genomic features. Alterations in TP53 and RB1 proved common in GIS-NECs, and most Nonpanc-NECs with intact RB1 demonstrated mutually exclusive amplification of CCNE1 or MYC. Alterations of the Notch gene family were characteristic of Nonpanc-NECs. Transcription factors for neuroendocrine differentiation, especially the SOX2 gene, appeared overexpressed in most GIS-NECs due to hypermethylation of the promoter region. This first comprehensive study of genomic alterations in GIS-NECs uncovered several key biological processes underlying genesis of this very lethal form of cancer. SIGNIFICANCE: GIS-NECs are genetically distinct from GIS-NETs. GIS-NECs arising in different organs show similar histopathologic features and share some genomic features, but considerable differences exist between Panc-NECs and Nonpanc-NECs. In addition, Panc-NECs could be classified into two subgroups (i.e., "ductal-type" and "acinar-type") based on genomic and epigenomic features. This article is highlighted in the In This Issue feature, p. 587.

Prognostic biomarker study in patients with clinical stage I esophageal squamous cell carcinoma: JCOG0502-A1.

We undertook genomic analyses of Japanese patients with stage I esophageal squamous cell carcinoma (ESCC) to investigate the frequency of genomic alterations and the association with survival outcomes. Biomarker analysis was carried out for patients with clinical stage T1bN0M0 ESCC enrolled in JCOG0502 (UMIN000000551). Whole-exome sequencing (WES) was performed using DNA extracted from formalin-fixed, paraffin-embedded tissue of ESCC and normal tissue or blood sample. Single nucleotide variants (SNVs), insertions/deletions (indels), and copy number alterations (CNAs) were identified. We then evaluated the associations between each gene alteration with a frequency of 10% or more and progression-free survival (PFS) using a Cox regression model. We controlled for family-wise errors at 0.05 using the Bonferroni method. Among the 379 patients who were enrolled in JCOG0502, 127 patients were successfully analyzed using WES. The median patient age was 63 years (interquartile range, 57-67 years), and 78.0% of the patients ultimately underwent surgery. The 3-year PFS probability was 76.3%. We detected 20 genes with SNVs, indels, or amplifications with a frequency of 10% or more. Genomic alterations in FGF19 showed the strongest association with PFS with a borderline level of statistical significance of P = .00252 (Bonferroni-adjusted significance level is .0025). Genomic alterations in FGF4, MYEOV, CTTN, and ORAOV1 showed a marginal association with PFS (P < .05). These genomic alterations were all CNAs at chromosome 11q13.3. We have identified new genomic alterations associated with the poor efficacy of ESCC (T1bN0M0). These findings open avenues for the development of new potential treatments for patients with ESCC.

Non-Lead Protective Aprons for the Protection of Interventional Radiology Physicians from Radiation Exposure in Clinical Settings: An Initial Study.

Radiation protection/evaluation during interventional radiology (IVR) poses a very important problem. Although IVR physicians should wear protective aprons, the IVR physician may not tolerate wearing one for long procedures because protective aprons are generally heavy. In fact, orthopedic problems are increasingly reported in IVR physicians due to the strain of wearing heavy protective aprons during IVR. In recent years, non-Pb protective aprons (lighter weight, composite materials) have been developed. Although non-Pb protective aprons are more expensive than Pb protective aprons, the former aprons weigh less. However, whether the protective performance of non-Pb aprons is sufficient in the IVR clinical setting is unclear. This study compared the ability of non-Pb and Pb protective aprons (0.25- and 0.35-mm Pb-equivalents) to protect physicians from scatter radiation in a clinical setting (IVR, cardiac catheterizations, including percutaneous coronary intervention) using an electric personal dosimeter (EPD). For radiation measurements, physicians wore EPDs: One inside a personal protective apron at the chest, and one outside a personal protective apron at the chest. Physician comfort levels in each apron during procedures were also evaluated. As a result, performance (both the shielding effect (98.5%) and comfort (good)) of the non-Pb 0.35-mm-Pb-equivalent protective apron was good in the clinical setting. The radiation-shielding effects of the non-Pb 0.35-mm and Pb 0.35-mm-Pb-equivalent protective aprons were very similar. Therefore, non-Pb 0.35-mm Pb-equivalent protective aprons may be more suitable for providing radiation protection for IVR physicians because the shielding effect and comfort are both good in the clinical IVR setting. As non-Pb protective aprons are nontoxic and weigh less than Pb protective aprons, non-Pb protective aprons will be the preferred type for radiation protection of IVR staff, especially physicians.

Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model.

BACKGROUND: Intra-tumor heterogeneity (ITH) encompasses cellular differences in tumors and is related to clinical outcomes such as drug resistance. However, little is known about the dynamics of ITH, owing to the lack of time-series analysis at the single-cell level. Mouse models that recapitulate cancer development are useful for controlled serial time sampling. RESULTS: We performed single-cell exome and transcriptome sequencing of 200 cells to investigate how ITH is generated in a mouse colorectal cancer model. In the model, a single normal intestinal cell is grown into organoids that mimic the intestinal crypt structure. Upon RNAi-mediated downregulation of a tumor suppressor gene APC, the transduced organoids were serially transplanted into mice to allow exposure to in vivo microenvironments, which play relevant roles in cancer development. The ITH of the transcriptome increased after the transplantation, while that of the exome decreased. Mutations generated during organoid culture did not greatly change at the bulk-cell level upon the transplantation. The RNA ITH increase was due to the emergence of new transcriptional subpopulations. In contrast to the initial cells expressing mesenchymal-marker genes, new subpopulations repressed these genes after the transplantation. Analyses of colorectal cancer data from The Cancer Genome Atlas revealed a high proportion of metastatic cases in human subjects with expression patterns similar to the new cell subpopulations in mouse. These results suggest that the birth of transcriptional subpopulations may be a key for adaptation to drastic micro-environmental changes when cancer cells have sufficient genetic alterations at later tumor stages. CONCLUSIONS: This study revealed an evolutionary dynamics of single-cell RNA and DNA heterogeneity in tumor progression, giving insights into the mesenchymal-epithelial transformation of tumor cells at metastasis in colorectal cancer.

Immunogenomic pan-cancer landscape reveals immune escape mechanisms and immunoediting histories.

Immune reactions in the tumor microenvironment are an important hallmark of cancer, and emerging immune therapies have been proven effective against several types of cancers. To investigate cancer genome-immune interactions and the role of immunoediting or immune escape mechanisms in cancer development, we analyzed 2834 whole genome and RNA sequencing datasets across 31 distinct tumor types with respect to key immunogenomic aspects and provided comprehensive immunogenomic profiles of pan-cancers. We found that selective copy number changes in immune-related genes may contribute to immune escape. Furthermore, we developed an index of the immunoediting history of each tumor sample based on the information of mutations in exonic regions and pseudogenes and evaluated the immunoediting history of each tumor. Our immuno-genomic analyses of pan-cancers have the potential to identify a subset of tumors with immunogenicity and diverse backgrounds or intrinsic pathways associated with their immune status and immunoediting history.