Biology subjects

Shiraishi, Y.

Publications and source records attributed to Shiraishi, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Antibody-mediated VWF targeting reconstitutes ADAMTS13 metalloproteinase activity and prevents thrombocytopenia in mice

ADAMTS13 (a multidomain metalloproteinase) cleaves von Willebrand factor (VWF), thereby preventing the accumulation of ultra-large VWF multimers that promote platelet-rich thrombus formation. Severe ADAMTS13 deficiency causes thrombotic thrombocytopenic purpura (TTP). In immune-mediated TTP (iTTP), anti-ADAMTS13 autoantibodies inhibit ADAMTS13 activity, often by targeting non-catalytic domains that mediate substrate recognition. We developed ADAMTS13 mimetics by fusing the ADAMTS13 metalloproteinase domain to anti-human VWF A2 domain antibodies, aiming to replace native substrate-recognition domains with antibody-mediated substrate targeting while removing major autoantibody-targeted ADAMTS13 domains. The resulting mimetics bound to the recombinant VWF A2 domain and showed proteolytic activity toward both the recombinant VWF A2 domain and FRETS-VWF73 substrate. Kinetic analysis showed that the mimetics had not only lower kcat values than ADAMTS13 but also lower Km values, thereby maintaining overall catalytic efficiency. Importantly, ADAMTS13 mimetics retained VWF A2-cleaving activity in the presence of a spacer domain-directed anti-ADAMTS13 autoantibody both in vitro and in vivo. In an iTTP mouse model, ADAMTS13 mimetics prevented recombinant VWF-induced thrombocytopenia, whereas the parental anti-VWF A2 domain antibody did not. Platelet-preserving activity was also observed in ADAMTS13-deficient mice. In further analyses, some mimetics showed reduced binding to a conformationally restricted VWF A2 domain, resulting in reduced cleavage activity. Antibody binding correlated with platelet recovery in the iTTP mouse model, suggesting that epitope accessibility and antibody-mediated positioning contribute to in vivo activity. These findings demonstrate that antibody-mediated substrate targeting can reconstitute the VWF-cleaving activity of the ADAMTS13 metalloproteinase domain and suggest that ADAMTS13 mimetics represent a potential therapeutic approach for iTTP.

biochemistry↗

bioRxiv2026

Calibrated ADAMTS13 inhibition prevents cardiovascular shear coagulopathy

Mechanical circulatory support essential for managing severe heart failure frequently triggers bleeding complications, driven by shear stress-induced over-proteolysis of von Willebrand factor (VWF) by ADAMTS13. Inhibiting ADAMTS13 presents a rationale to treat this condition, known as acquired von Willebrand syndrome (AVWS). However, conventional therapeutic strategies remain limited due to the risk of triggering thrombotic thrombocytopenic purpura. Here we show that HA10, a humanized anti-ADAMTS13 antibody, preserves a residual level of ADAMTS13 activity above the thrombosis-associated threshold. Multimodal structural and biophysical analyses--including NMR, SAXS, and SANS--revealed that HA10 bound to the disintegrin-like domain of ADAMTS13, dynamically competing with VWF while leaving 10- 20% residual enzymatic activity. The therapeutic efficacy and safety of HA10 were verified in non-human primate models of AVWS. Our findings establish a novel paradigm of enzymatic calibration rather than complete blockade, offering a mechanistically targeted and safe therapeutic approach for cardiovascular bleeding.

biochemistry↗

bioRxiv2026

Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes

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.

bioinformatics↗

bioRxiv2026

A Wnt-responsive fibrocartilage progenitor system coordinates postnatal mandibular condylar cartilage growth

Postnatal growth of the mandibular condyle requires coordinated expansion of fibrocartilage and production of chondrocytes, yet the cellular populations that organize this process remain incompletely defined. Here we identify a Wnt-responsive fibrocartilage progenitor population that contributes to postnatal mandibular condylar cartilage growth. Using a direct Wnt activity reporter (R26-WntVis), inducible genetic lineage tracing (Axin2CreERT2), and single-cell transcriptomics, we define a Wnt-enriched progenitor-like cluster localized predominantly within the fibrocartilage zone. Lineage tracing demonstrates that Axin2-lineage cells expand laterally within fibrocartilage and generate vertically aligned chondrocytes in the chondrocartilage compartment, indicating bidirectional growth contribution in vivo. Conditional ablation of {beta}-catenin in Axin2-lineage cells results in depletion of the fibrocartilage compartment and premature activation of chondrogenic differentiation programs, whereas constitutive {beta}-catenin activation disrupts compartmental organization without enhancing proliferation. Mechanistically, we identify Foxm1 as a Wnt-associated proliferative mediator enriched in fibrocartilage, and genetic reduction of Foxm1 cooperates with {beta}-catenin deficiency to impair condylar growth. In parallel, {beta}-catenin loss derepresses TGF-{beta}-Smad signaling and enhances chondrogenic differentiation, indicating that canonical Wnt activity coordinates proliferative maintenance while restraining lineage commitment within the same cellular compartment. Together, these findings identify a Wnt-responsive fibrocartilage progenitor system that regulates postnatal mandibular condylar cartilage growth by coupling Foxm1-associated proliferative maintenance with suppression of TGF-{beta}-dependent chondrogenic differentiation during temporomandibular joint development. Graphical abstractWnt-responsive fibrocartilage progenitors coordinate postnatal mandibular condylar cartilage growth through Foxm1-dependent proliferative maintenance and suppression of TGF-{beta}-driven chondrogenic differentiation.

developmental biology↗

bioRxiv2026

Chromatin landscape and epigenetic heterogeneity of acute myeloid leukemia

Acute myeloid leukemia (AML) is an aggressive hematologic cancer characterized by proliferation of immature myeloblasts. It shows profound molecular heterogeneity, which has been primarily studied through genetic abnormalities, providing the basis for disease classification, prognostication, and therapeutic choice. However, genetic factors alone may not fully explain AML pathogenesis and diversity, while leaving the role of abnormal epigenome, particularly chromatin state, largely unexplored in a large cohort of patients. Here we show that AML is classified into 16 subgroups with distinct chromatin accessibility profiles based on ATAC-seq in 1,563 AML cases, including novel AML subgroups not previously recognized in conventional genomic classifications. By integrating multi-omics analyses of genome, transcriptome, and major histone marks, we show that these epigenetic subgroups exhibit unique features in clinical presentation, gene mutations, differentiation states, gene expression, and super-enhancer profiles, which are validated across independent cohorts. Single-cell sequencing demonstrates the presence of subgroup-specific ATAC signatures that are shared by all leukemic cells, confirming the definitive role of the epigenome in the ATAC-based classification. Mechanistically, each subgroup is associated with a distinct gene regulatory network centered on key transcription factors, where subgroup-specific super-enhancers play a pivotal role. These ATAC subgroups also have prognostic significance independent of genomic classification, and help reveal unexpected drug sensitivities. In summary, ATAC-based chromatin profiling in this large sample set, combined with multi-omics data, provides new insights into AML pathogenesis beyond genomic profiling and also serves as an invaluable resource for AML research.

cancer biology↗

bioRxiv2025

TMEM2 maintains hyaluronan turnover and cartilage homeostasis during early osteoarthritis progression

Osteoarthritis (OA) is a degenerative joint disease characterized by progressive disruption of the cartilage extracellular matrix (ECM), yet the molecular mechanisms governing ECM turnover during disease initiation remain incompletely defined. Hyaluronan (HA) is a major structural component of articular cartilage, and its regulated turnover is essential for maintaining tissue integrity. Transmembrane protein 2 (TMEM2) is a cell-surface hyaluronidase capable of degrading high-molecular weight HA under physiological conditions, but its role in joint tissues has remained unclear. Here, we examine the spatiotemporal expression and functional contribution of TMEM2 in articular cartilage using single-cell transcriptomic analysis, histological approaches, and a chondrocyte-specific conditional knockout mouse model. Under physiological conditions, Tmem2 was predominantly expressed in non-calcified articular chondrocytes. Following joint destabilization, Tmem2 expression was transiently increased during early osteoarthritis, coinciding with reduced cartilage HA content, consistent with altered HA turnover. Importantly, genetic ablation of Tmem2 in chondrocytes markedly exacerbated osteoarthritis progression, resulting in accelerated cartilage delamination, increased chondrocyte apoptosis, reduced proliferative activity, and enhanced hypertrophic differentiation. These changes occurred without detectable abnormalities in the synovium, subchondral bone, or osteophyte formation, indicating a cartilage-intrinsic phenotype. Collectively, these findings identify TMEM2 as an important regulator of hyaluronan homeostasis within the cartilage ECM and provide in vivo genetic evidence that TMEM2- dependent HA turnover contributes to the maintenance of articular cartilage integrity during osteoarthritis progression.

molecular biology↗

bioRxiv2025

Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations

Centromeres are among the most diverse and dynamically evolving regions of the human genome and are commonly affected in various human cancers. However, organized into highly repetitive -satellite higher-order repeats (HORs), human centromere sequences have long resisted detailed genomic analysis. Although the development of long-read sequencing platforms has enabled the analysis of complete centromere sequences, their application to a large set of samples is still largely limited, preventing our understanding of centromere variation and haplotype structures across large human populations and the structural basis of centromere-involving translocations in cancer. Here we show that rare k-mers present in centromeric regions can serve as effective markers for dissecting the complexity of centromere structure, particularly that of active -satellite HOR arrays (aHOR arrays), across human populations and for understanding centromere-involving abnormalities in cancer. Based on rare k-mer-based clustering, centromere aHOR arrays are clustered into discrete haplogroups (aHOR-HGs) with distinct structural features. These k-mers were also used to develop a framework that enables the inference of haplogroups in a given sample based on short-read whole genome sequencing (WGS) data (ascairn). By applying ascairn to large-scale human population datasets (n > 3,300), we revealed the diversity of aHOR-HGs and their geographic histories across populations. The rare k-mer-based approach was also applied to investigate the structure of 1p/19q co-deletion, a highly recurrent centromere-involving translocation in IDH-mutated oligodendrogliomas. Analyzing short-read WGS data from 142 cases with 1p/19q co-deletion using rare k-mers, we showed that breakpoints of 1p/19q co-deletion were mapped to aHOR arrays in chromosomes 1 (D1Z7) and 19 (D19Z3), which was validated by long-read sequencing of two 1p/19q co-deletion-positive cases. Notably, the translocation preferentially involved haplogroups composed of haplotypes containing larger regions susceptible to rearrangement. These results highlight the role of rare k-mers in dissecting the complexity of centromere sequences and their evolutionary history as well as understanding centromere-involving abnormalities associated with human diseases.

genomics↗

bioRxiv2025

mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing

SummaryWe propose a new algorithm, "interval hashing," which distinguishes identical k-mers arising from different repeat sequences, particularly in complex repeat arrays such as alpha satellite HORs. We implement this algorithm as a fork of minimap2, named mm2-ivh. In local assembly of alpha satellite HORs, mm2-ivh accurately reconstructs more haplotypes than assemblers using standard minimizers. Availabilitymm2-ivh is available under the MIT license at https://github.com/ocxtal/mm2-ivh and runs on common Unix-compatible systems.

bioinformatics↗

bioRxiv2025

The Knock-In Atlas: A web resource for targeted protein trap by CRISPR/Cas9 in human and mouse cell lines

Various cell engineering techniques have been developed by leveraging the CRISPR-Cas9 technology, but large-scale resources for targeted gene knock-in are still limited. Here we introduce the Knock-in Atlas, a web resource for gene tagging by fluorescent proteins by inserting artificial exons in target gene introns. To produce knock-in cells efficiently and reproducibly, we carefully chose and catalogued guide RNAs (gRNAs) for targeting genes in the human and mouse genomes by taking the gRNA efficacy scores and protein structures around the insertion sites into account. As of August 2025, we have characterized knock-in cell lines for 350 proteins, with a focus on RNA binding proteins, by flow cytometry and confocal microscopy. The transfection and flow cytometry protocols were optimized for several cell lines including HEK293T, eHAP1, HeLa, THP-1, Neuro2a, mouse embryonic fibroblast (MEF) and mouse embryonic stem cell (mESC). A website has been launched to organize the results of initial characterization including flow cytometry data after transfection, confocal microscopy, and western blot results for the genes for which knock-in HEK293T cell lines were already made. The site also provides a database to organize the information of pre-designed gRNAs for the human and mouse genomes. .

molecular biology↗

bioRxiv2024

Identification and characterization of substrate- and product-selective nylon hydrolases

Enzymes have evolved to rapidly and selectively hydrolyze diverse natural and anthropogenic polymers, but only a limited group of related enzymes have been shown to hydrolyze synthetic polyamides. In this work, we synthesized and characterized a panel of 95 diverse enzymes from the N-terminal nucleophile hydrolase superfamily with 30-50% pairwise amino acid identity. We found that nearly 40% of the enzymes had substantial nylon hydrolase activity, in many cases comparable to that of the best-characterized nylon hydrolase, NylC. There was no relationship between phylogeny and activity, nor any evidence of prior selection for nylon hydrolase activity. Several newly-identified hydrolases showed significant substrate selectivity, generating up to 20-fold higher product titers with Nylon 6,6 versus Nylon 6. Finally, we determined the crystal structure and oligomerization state of a Nylon 6,6-selective hydrolase to elucidate structural factors that could affect activity and selectivity. These new enzymes provide insights into the widespread potential for nylon hydrolase evolution and opportunities for analysis and engineering of improved hydrolases. SignificanceNylons are common industrial polyamides with few recycling options. As an alternative to mechanical or chemical recycling, enzymes may provide a selective and energy-efficient route to deconstruct nylons from mixed waste. Several nylon hydrolases have been identified, most notably NylC, but these enzymes are all closely related and demonstrated similar activity and substrate range. In this work, we investigated a diverse set of enzymes and showed that nylon hydrolase activity is common, providing new insights into the evolution of microbial nylon hydrolysis. Unlike NylC, several enzymes demonstrated unprecedented substrate selectivity, preferentially hydrolyzing Nylon 6,6 compared to Nylon 6. These enzymes can be used to understand substrate selectivity in nylon hydrolysis and to engineer enzymes for nylon recycling from mixed waste.

biochemistry↗

bioRxiv2024

Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data

Genomic variants causing abnormal splicing play an important role in genetic disorders and cancer development. Among them, variants that cause formations of novel splice-sites (splice-site creating variants, SSCVs) are particularly difficult to identify and often overlooked in genomic studies. Additionally, these SSCVs, especially those found in deep intronic regions, are frequently considered promising candidates for treatment with splice-switching antisense oligonucleotides (ASOs), offering therapeutic potential for rare disease patients. To leverage massive transcriptome sequence data such as those available from the Sequence Read Archive, we developed a novel framework to screen for SSCVs solely using transcriptome data. We have applied it to 322,072 publicly available transcriptomes and identified 30,130 SSCVs. Utilizing this extensive collection of SSCVs, we have revealed the characteristics of Alu exonization via SSCVs, especially the hotspots of SSCVs within Alu sequences and their evolutionary relationships. Many of the SSCVs affecting disease-causing variants were predicted to generate premature termination codons and are degraded by nonsense-mediated decay. On the other hand, several genes, such as CREBBP and TP53, showed characteristic SSCV profiles indicative of heterogeneous mutational functions beyond simple loss-of-function. Finally, we discovered novel gain-of-function SSCVs in the deep intronic region of the NOTCH1 gene and demonstrated that their activation can be suppressed using splice-switching ASOs. Collectively, we provide a systematic approach for automatically acquiring a registry of SSCVs, which can be used for elucidating novel biological mechanisms for splicing and genetic variation, and become a valuable resource for pinpointing critical targets in drug discovery. Catalogs of SSCVs identified in this study are accessible on SSCV DB (https://sscvdb.io/).

bioinformatics↗

bioRxiv2023

SLC26A2-mediated sulfate metabolism is essential for the tooth development

The sulfate transporter gene SLC26A2 is responsible for diastrophic dysplasia, which represents skeletal dysplasia in humans. This highlights the importance of sulfate metabolism in skeletal formation. SLC26A2-related chondrodysplasia is also known to exhibit abnormalities in craniofacial and tooth development. Although the function of SLC26A2 in mammals has been investigated using genetic mouse models, the essential role of SLC26A2 during craniofacial and tooth development has not been elucidated. In this study, we demonstrate the pivotal roles of SLC26A2-mediated sulfate metabolism during tooth development. Analysis of Slc26a2 expression reveals that it is predominantly expressed in dental tissues, including odontoblasts and ameloblasts, during tooth development. Slc26a2 knockout mice (Slc26a2-KO-{Delta}exon2) exhibit a retrognathic upper jaw, small upper incisors, and hypoplasia of upper molars. Additionally, upper incisors and molars in Slc26a2-KO-{Delta}exon2 mice display flattened odontoblasts and nuclei that lack intracellular polarity. In contrast, tooth phenotype is not remarkable in lower incisors and molars. Furthermore, the expression of odontoblast differentiation markers, Dspp and Dmp1, is significantly decreased in the upper molars of Slc26a2-deficient mice. Ex vivo organ culture of tooth germs by implantation of Slc26a2-deficient tooth germs under the kidney capsule reveals hypoplasia of the dentin matrix as well as tooth root shortening. In vitro studies using human dental pulp stem cells (hDPSCs) show that the expression levels of Dspp and Dmp1 in shSlc26a2 knockdown cells are significantly decreased compared to control cells. Collectively, our data demonstrate that SLC26A2-mediated sulfate metabolism is essential for tooth development. This study may provide insight into the mechanisms underlying tooth abnormalities in patients with recessively inherited chondrodysplasias caused by mutations in the SLC26A2 gene.

developmental biology↗

bioRxiv2022

Predicting gene expression from cell morphology in human induced pluripotent stem cells

Purification is essential before differentiating human induced pluripotent stem cells (hiPSCs) into cells that fully express particular differentiation marker genes. High-quality iPSC clones are typically purified through gene expression profiling or visual inspection of the cell morphology; however, the relationship between the two methods remains unclear. We investigated the relationship between gene expression levels and morphology by analyzing live-cell phase-contrast images and mRNA profiles collected during the purification process. We employed this data and an unsupervised image feature extraction method to build a model that predicts gene expression levels from morphology. As a benchmark, we confirmed that the method can predict the gene expression levels from tissue images for cancer genes, performing as well as state-of-the-art methods. We then applied the method to iPSCs and identified two genes that are well-predicted from cell morphology. Although strong batch effects resulting from the reprogramming process preclude the ability to use the same model to predict across batches, prediction within a reprogramming batch is sufficiently robust to provide a practical approach for estimating expression levels of a few genes and monitoring the purification process.

bioengineering↗

bioRxiv2021

Systematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data

Many disease-associated genomic variants disrupt gene function through abnormal splicing. With the advancement of genomic medicine, identifying disease-associated splicing associated variants has become more important than ever. Most bioinformatics approaches to detect splicing associated variants require both genome and transcriptomic data. However, there are not many datasets where both of them are available. In this study, we developed a methodology to detect genomic variants that cause splicing changes (more specifically, intron retention), using transcriptome sequencing data alone. After demonstrating its high sensitivity and precision, we have applied it to 230,988 transcriptome sequencing data from the publicly available repository and identified 27,937 intron retention associated variants (IRAVs). In addition, by exploring positional relationships with variants registered in existing disease databases, we extracted 3,077 putative disease-associated IRAVs, which range from cancer drivers to variants linked with autosomal recessive disorders. The new in-silico screening framework proposed here provides a foundation for a platform that can automatically acquire medical knowledge making the most of massively accumulated publicly available sequencing data. Collections of IRAVs identified in this study are available through IRAVDB (https://iravdb.io/).

bioinformatics↗

bioRxiv2021

Combined landscape of single-nucleotide variants and copy-number alterations in clonal hematopoiesis

Implicated in the development of hematological malignancies (HM) and cardiovascular mortality, clonal hematopoiesis (CH) in apparently healthy individuals has been investigated by detecting either single-nucleotide variants and indels (SNVs/indels) or copy number alterations (CNAs), but not both. Here by combining 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 a general population of 11,234 individuals, including 672 with subsequent HM development. Both CH-related lesions significantly co-occurred, which combined, affected blood count, hypertension, and the mortality from HM and cardiovascular diseases depending on the total number of both lesions, highlighting the importance of detecting both lesions in the evaluation of CH.

cancer biology↗

bioRxiv2020

Precise characterization of somatic structural variations and mobile element insertions from paired long-read sequencing data with nanomonsv

We present our novel software, nanomonsv, for detecting somatic structural variations (SVs) using tumor and matched control long-read sequencing data with a single-base resolution. The current version of nanomonsv includes two detection modules, Canonical SV module, and Single breakend SV module. Using paired long-read sequencing data from three cancer and their matched lymphoblastoid lines, we demonstrate that Canonical SV module can identify somatic SVs that can be captured by short-read technologies with higher precision and recall than existing methods. In addition, we have developed a workflow to classify mobile element insertions while elucidating their in-depth properties, such as 5 truncations, internal inversions, as well as source sites for 3 transductions. Furthermore, Single breakend SV module enables the detection of complex SVs that can only be identified by long-reads, such as SVs involving highly-repetitive centromeric sequences, and LINE1- and virus-mediated rearrangements. In summary, our approaches applied to cancer long-read sequencing data can reveal various features of somatic SVs and will lead to a better understanding of mutational processes and functional consequences of somatic SVs.

bioinformatics↗

bioRxiv2020

Multi-sample Full-length Transcriptome Analysis of 22 Breast Cancer Clinical Specimens with Long-Read Sequencing

Although transcriptome alteration is considered as one of the essential drivers of carcinogenesis, conventional short-read RNAseq technology has limited researchers from directly exploring full-length transcripts, only focusing on individual splice sites. We developed a pipeline for Multi-Sample long-read Transcriptome Assembly, MuSTA, and showed through simulations that it enables construction of transcriptome from the transcripts expressed in target samples and more accurate evaluation of transcript usage. We applied it to 22 breast cancer clinical specimens to successfully acquire cohort-wide full-length transcriptome from long-read RNAseq data. By comparing isoform existence and expression between estrogen receptor positive and triple-negative subtypes, we obtained a comprehensive set of subtype-specific isoforms and differentially used isoforms which consisted of both known and unannotated isoforms. We have also found that exon-intron structure of fusion transcripts tends to depend on their genomic regions, and have found three-piece fusion transcripts that were transcribed from complex structural rearrangements. For example, a three-piece fusion transcript resulted in aberrant expression of an endogenous retroviral gene, ERVFRD-1, which is normally expressed exclusively in placenta and supposed to protect fetus from maternal rejection, and expression of which were increased in several TCGA samples with ERVFRD-1 fusions. Our analyses of real clinical specimens and simulated data provide direct evidence that full-length transcript sequencing in multiple samples can add to our understanding of cancer biology and genomics in general.

genomics↗

bioRxiv2019

Long read sequencing reveals a novel class of structural aberrations in cancers: identification and characterization of cancerous local amplifications

Here we report identification of a new class of local structural aberrations in lung cancers. The whole-genome sequencing of cell lines using a long read sequencer, PromethION, demonstrated that typical cancerous mutations, such as point mutations, large deletions and gene fusions can be detected also on this platform. Unexpectedly, we revealed unique structural aberrations consisting of complex combinations of local duplications, inversions and micro deletions. We further analyzed and found that these mutations also occur in vivo, even in key cancer-related genes. These mutations may elucidate the molecular etiology of patients for whom causative cancerous events and therapeutic strategies remain elusive.

genomics↗