Yosuke Tanaka

Cancer genome analysis relies on standard human reference genomes, but detecting somatic alterations in highly repetitive or individual-specific regions remains challenging. We developed the Personalized Reference genome-based Cancer Genome Analysis Pipeline (PRCGAP, https://github.com/yos-sk/PRCGAP), to our knowledge, the first comprehensive pipeline integrating haplotype-resolved analyses of somatic point mutations, structural variants, copy number, and DNA methylation on personalized diploid reference genomes, with each variant phased and annotated by genomic features. We applied PRCGAP to eight tumor-normal cell line pairs and three newly collected pediatric B-cell acute lymphoblastic leukemia (B-ALL) clinical samples. PRCGAP recovered most standard reference-based variants (86.7–96.4% across variant types), validated by orthogonal short-read sequencing, while additionally detecting variants that standard references missed (23.4% of SNVs and 32.6% of SVs). Notably, PRCGAP uncovered variants in centromeric and telomeric regions, and somatic single-nucleotide variants were enriched in centromere dip regions, the putative kinetochore formation sites. Using PRCGAP outputs, we identified L1 retrotransposition source sites absent from standard references and showed that a B-ALL IGH:: DUX4 fusion arose from a DUX4 pseudogene within an internal D4Z4 repeat unit, rather than the canonical full-length DUX4 gene. Within a single haplotype-resolved framework, PRCGAP opens regions of the cancer genome that are inaccessible to standard references.

Supplementary Table 1. Data summary of patients on dialysis. Supplementary Table 2. Significantly mutated genes in tumor in patients on dialysis. Supplementary Table 3. Data summary of patients not on HD. Supplementary Table 4. Genes sepcific to ACD. Supplementary Table 5. Gene list of pure PT cells. Supplementary Table 6. Genes sepcific to the cyst cluster. Supplementary Table 7. Recurrently mutated genes detected in LMD.

Supplementary Figure 1: a, Frequencies of mutations identified in ACD-RCC (left), ESRD-ccRCC (middle), and sporadicccRCC (right). Supplementary Figure 2: a, UMAP plot of the transcriptomes of tumours from HD patients. Supplementary Figure 3: a, eGFR in the expression-defined cluster groups. The green and pink groups correspond to the groups shown in Figure 3a. Supplementary Figure 4: a, Representative images of each marker via mIHC. Supplementary Figure 5: a, Spatial expression patterns of PT genes and DT genes in the renal cortex of patients not on HD. Scale bar, 2 mm.

Patients with end-stage renal disease (ESRD) are at increased risk of acquired cystic kidney disease (ACKD) and renal tumors, but the molecular basis of such disorders remains elusive. In this study, we performed spatial immunogenomic analyses on 268 specimens from 43 patients with ACKD and associated tumors. The molecular landscape of ESRD-associated tumors is different from that of sporadic renal cell carcinoma. Single-cell and spatial analyses have shown that ACKD is under an inflammatory environment and that the renal cysts in ACKD are derived from proximal tubular cells that have survived the destructive effects of inflammation. Interestingly, we revealed that cysts are formed by clonal expansion and that paracrine activation of the MET tyrosine kinase pathway by the surrounding environment nurtures cysts. Collectively, our results identify the oncogenic mechanisms of ESRD-associated renal tumors and will pave the way for improving the prognosis of patients with ESRD.Significance:We elucidated the molecular basis of renal cancer arising in patients with ESRD and show that the inflammatory environment of ESRD gives rise to field cancerization.See related commentary by Sager et al., p. 426

Supplementary Figure 6: a, Expression patterns of PT-related gene sets in UMAP plots of the integrated scRNA-seq data of the renal cortex of 5 HD patients with ACD-RCC. Supplementary Figure 7: a, Inferred CNV profiles of cyst cells with macrophages used as references. The yellow and green clusters in each figure represent heterogeneous expression clusters of cells within the same cyst. Supplementary Figure 8: a, Expression levels of HGF (macrophage) and MET (cyst) genes in UMAP plots of the integrated scRNA-seq data.

Patients with end-stage renal disease (ESRD) are at increased risk of acquired cystic kidney disease (ACKD) and renal tumors, but the molecular basis of such disorders remains elusive. In this study, we performed spatial immunogenomic analyses on 268 specimens from 43 patients with ACKD and associated tumors. The molecular landscape of ESRD-associated tumors is different from that of sporadic renal cell carcinoma. Single-cell and spatial analyses have shown that ACKD is under an inflammatory environment and that the renal cysts in ACKD are derived from proximal tubular cells that have survived the destructive effects of inflammation. Interestingly, we revealed that cysts are formed by clonal expansion and that paracrine activation of the MET tyrosine kinase pathway by the surrounding environment nurtures cysts. Collectively, our results identify the oncogenic mechanisms of ESRD-associated renal tumors and will pave the way for improving the prognosis of patients with ESRD. Significance: We elucidated the molecular basis of renal cancer arising in patients with ESRD and show that the inflammatory environment of ESRD gives rise to field cancerization. See related commentary by Sager et al., p. 426

Platinum-based definitive chemoradiotherapy (dCRT) is the standard treatment for patients with unresectable locally advanced esophageal squamous cell carcinoma (ESCC) that invades the aorta, vertebral body or trachea; however, complete response rates remain low (11–25%), leading to poor survival. To evaluate the additive efficacy of the anti-PD-L1 antibody drug atezolizumab, we conducted a phase 2, multicenter, single-arm trial of 1 year of atezolizumab treatment following dCRT in 40 patients with unresectable locally advanced ESCC recruited from seven Japanese centers (UMIN000034373). The confirmed complete response (cCR) rate (primary end point) of the first consecutive 38 patients was 42.1% (90% CI 28.5–56.7%). Regarding the secondary end points, the median progression-free survival and 12-month progression-free survival rates of all 40 patients were 3.2 months and 29.6%, respectively, and the preliminary median overall survival with short-term follow-up and 12-month overall survival rate were 31.0 months and 65.8%, respectively. Other secondary end points evaluated included the cCR rate determined by an investigator’s assessment in the locoregionally recurrent ESCC cohort, cCR rate determined by central assessment, overall response rate and incidence of adverse events. No treatment-related death occurred during the study. Atezolizumab monotherapy after dCRT resulted in a promising cCR rate, although long-term survival data are required.

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.

Objective: Some of the most common causes of chronic cough include cough variant asthma (CVA), bronchial asthma (BA), and asthma–COPD overlap (ACO). Although there is some overlap in the etiology of these diseases, it is clinically important to attempt an early differential diagnosis due to treatment strategies and prognoses. Methods: Spirometry and impulse oscillometry (IOS) before and after bronchodilator inhalation were analyzed for clinically diagnosed CVA (cCVA, n = 203), BA (cBA, n = 222), and ACO (cACO, n = 61). Results: A significant difference in ΔFEV₁ was observed between cBA and cCVA (ΔFEV₁ improvement of 122.5 mL/5.4% and 65.7 mL/2.2%, respectively), but no difference was observed in ΔPEF, ΔV50, or ΔV25. Except for R20 (resistance at 20 Hz), significant differences between the three groups were observed in IOS. In IOS, cCVA and cBA showed comparable peripheral airway response to bronchodilator which was thought to be commensurate with changes in V50 and V25. cACO improved ΔFEV₁ improvement of 81.0 mL/6.2% and was distinguished by a downward respiratory system reactance (Xrs) waveform with a limited bronchodilator response. FEV₁/FVC, %FEV₁, and %V25 had relatively strong correlations with the three IOS parameters, X5 (reactance at 5 Hz), resonant frequency (Fres), and low-frequency reactance area (ALX), in the correlation between IOS and spirometers. Conclusion: Changes in IOS parameters were more sensitive in this study than changes in FEV₁ or the flow-volume curve. Considering the benefits and relevance of the two different tests, simultaneous IOS and spirometry testing were useful in the diagnosis of asthmatic cough.

Although transcriptome alteration is an essential driver of carcinogenesis, the effects of chromosomal structural alterations on the cancer transcriptome are not yet fully understood. Short-read transcript sequencing has prevented researchers from directly exploring full-length transcripts, forcing them to focus on individual splice sites. Here, we develop a pipeline for Multi-Sample long-read Transcriptome Assembly (MuSTA), which enables construction of a transcriptome from long-read sequence data. Using the constructed transcriptome as a reference, we analyze RNA extracted from 22 clinical breast cancer specimens. We identify a comprehensive set of subtype-specific and differentially used isoforms, which extended our knowledge of isoform regulation to unannotated isoforms including a short form TNS3. We also find that the exon–intron structure of fusion transcripts depends on their genomic context, and we identify double-hop fusion transcripts that are transcribed from complex structural rearrangements. For example, a double-hop fusion results in aberrant expression of an endogenous retroviral gene, ERVFRD-1, which is normally expressed exclusively in placenta and is thought to protect fetus from maternal rejection; expression is elevated in several TCGA samples with ERVFRD-1 fusions. Our analyses provide direct evidence that full-length transcript sequencing of clinical samples can add to our understanding of cancer biology and genomics in general.