Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs

APOBEC3 mutagenesis drives therapy resistance in breast cancer

Acquired genetic alterations drive resistance to endocrine and targeted therapies in metastatic breast cancer; however, the underlying processes engendering these alterations are largely uncharacterized. To identify the underlying mutational processes, we utilized a clinically annotated cohort of 3,880 patient samples with tumor-normal sequencing. Mutational signatures associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) enzymes were prevalent and enriched in post-treatment hormone receptor-positive cancers. These signatures correlated with shorter progression-free survival on antiestrogen plus CDK4/6 inhibitor therapy in hormone receptor-positive metastatic breast cancer. Whole-genome sequencing of breast cancer models and paired primary-metastatic samples demonstrated that active APOBEC3 mutagenesis promoted therapy resistance through characteristic alterations such as RB1 loss. Evidence of APOBEC3 activity in pretreatment samples illustrated its pervasive role in breast cancer evolution. These studies reveal APOBEC3 mutagenesis to be a frequent mediator of therapy resistance in breast cancer and highlight its potential as a biomarker and target for overcoming resistance.

Colorectal Tumors in Diverse Patient Populations Feature a Spectrum of Somatic Mutational Profiles

Admixed populations, including the Hispanic/Latino/a community, are underrepresented in cancer genetic/genomic studies. Leveraging the Latino Colorectal Cancer Consortium (LC3) and other existing datasets, we analyzed whole-exome sequencing data on tumor/normal pairs from 718 individuals with colorectal cancer to map somatic mutational features by ethnicity and genetic similarity. Global proportions of African, Asian, European, and Native American genetic ancestries were estimated using ADMIXTURE. Associations between these proportions and somatic mutational features were examined using logistic regression. APC, TP53, and KRAS were the top three mutated genes across all participants and in the subset of Latino individuals in LC3. In analyses examining recurrently mutated genes, tumors from patients of Latino ethnicity had fewer KRAS and PIK3CA mutations compared with tumors from non-Latino patients. Genetic ancestry overall was associated with CDC27 mutation status, and African genetic ancestry was associated with SMAD2 mutation status. In exome-wide analyses, African genetic ancestry was significantly associated with higher odds of mutation in KNCN and TMEM184B. Native American genetic ancestry was associated with a lower frequency of microsatellite instability-high tumors. The SBS11 mutational signature was associated with Native American genetic ancestry as well as Latino ethnicity. In an independent replication dataset, MSK-IMPACT, estimates of association were largely consistent in direction but nonsignificant. A meta-analysis of LC3 and MSK-IMPACT showed that African genetic ancestry was significantly associated with KRAS mutation status and MSI status. This work facilitates precision medicine initiatives by providing insights into the contribution of genetic ancestry to molecular features of colorectal tumors. Significance: Analysis of tumors from various populations can broadly characterize genomic landscapes and enhance precision medicine strategies.

Functional screening of somatic mutant events in extranodal natural killer/T-cell lymphoma with adrenal involvement

Background

Extranodal natural killer/T-cell lymphoma (ENKTL) involving the adrenal glands is extremely rare, and only a few cases have been reported. However, the genetic alterations, clinicopathological features and prognosis of these patients have not yet been fully elucidated.

Methods

Profiling of tumor mutations in ENKTL patients with adrenal involvement was conducted by whole-genome sequencing, and the predisposing genes and driver mutation gene variants were verified through Sanger sequencing. Immunohistochemical analysis of markers for the diagnosis and tumor microenvironment competent were performed to identify histopathological features. In addition, we searched the Surveillance, Epidemiology, and End Results (SEER), PubMed, Embase, and Scopus databases to perform a population-based study to compare the prognosis between adrenocortical carcinoma (ACC) patients and adrenal ENKTL patients using Kaplan-Meier survival curves and log-rank tests and analyzed the prognostic factors affecting the overall survival (OS) of adrenal ENKTL patients via univariate and multivariate Cox regression analyses.

Results

We screened 15892 somatic single-nucleotide variants (SNVs), 364 somatic insertions and deletions (INDELs), and four driver mutation genes, namely, TET2, STAT3, FAS, and TP53. In addition, immunohistochemical analysis revealed that tumor cells were positive for CD3, CD43, CD56, TIA1, granzyme B, CD2, CD4, and CD7. The immunohistochemistry for detecting components of the tumor microenvironment reveled the infiltration of tumor-associated macrophages (CD68, CD163) and tumor-associated fibroblasts (vimentin, SMA) in the tumor sample. According to our population-based analysis, Kaplan-Meier survival curves revealed that ENKTL patients with adrenal involvement had a significantly poorer prognosis than did patients with ACC (p<0.001), and chemotherapy was a significant prognostic factor for OS in ENKTL patients with adrenal involvement according to Cox multivariate analysis (hazard ratio = 0.318; p=0.027).

Conclusions

The metastasis of ENKTL to the adrenal gland may be due to gene mutations caused by genetic variations, which may provide new therapeutic targets for this disease. The prognosis of adrenal ENKTL patients is markedly worse than that of ACC patients, and chemotherapy may serve as an independent factor of OS in adrenal ENKTL patients. However, our findings still need to be validated in additional studies.

Clinicopathological features and genetic mutation spectrum of primary anastomosing hemangioma arising from the kidney

Background

Renal anastomosing hemangioma (RAH) is a rare benign renal tumor, and its clinicopathologic characteristics and genetic mutation spectrum related to its mechanisms of pathogenesis are unclear.

Methods

We carried out whole-genome sequencing (WGS) on RAH samples to explore the genetic mutation spectrum and verified the results by Sanger sequencing. Immunohistochemical analysis was also performed to reveal the histopathological characteristics and the tumor microenvironment components. Moreover, a population-based study was conducted after searching the PubMed, EMBASE, and Ovid SP databases to systematically summarize the clinicopathologic features of patients with RAH.

Results

WGS analysis revealed 10532 somatic single-nucleotide variants (SNVs), 6705 somatic insertions and deletions (INDELs), and mutations in 32 predisposing genes and 10 driver genes, among which the mutations in 8 of the predisposing genes, CNTNAP2, NCOA2, FAT1, MET, TJP2, MAML2, SRGAP3, and CSMD3, and the mutation site in the driver gene HIP1 were confirmed by Sanger sequencing. Moreover, the immunohistochemical profile of the tumor microenvironment revealed that the expression content of tumor-associated macrophages (CD163, CD68) and fibroblasts (SMA) differs between cancerous and precancerous tissues which may regulate the disease development. On the basis of our population-based analysis, we summarized the clinicopathological features of 100 patients with RAH and identified significant differences in age (p=0.001), tumor site (p<0.001), tumor focality (p<0.001), largest tumor diameter (p=0.001) and surgical approach (p=0.010) between patients with RAH with end-stage renal disease (ESRD) and those without ESRD.

Conclusions

The distinct phenotypes of RAH may be associated with the different genetic mutation spectra identified in our study. The presence or absence of comorbid ESRD varies among patients with RAH. However, additional studies are required to validate our results.

Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response

Identifying host genetic factors modulating immune checkpoint inhibitor (ICI) efficacy is experimentally challenging. Our approach, utilizing the Collaborative Cross mouse genetic resource, fixes the tumor genomic configuration while varying host genetics. We find that response to anti-PD-1 (aPD1) immunotherapy is significantly heritable in four distinct murine tumor models (H2: 0.18-0.40). For the MC38 colorectal carcinoma system, we map four significant ICI response quantitative trait loci (QTLs) with significant epistatic interactions. The differentially expressed genes within these QTLs that define responder genetics are highly enriched for processes involving antigen processing and presentation, allograft rejection, and graft vs. host disease (all p < 1 × 10-10). Functional blockade of two top candidate immune targets, GM-CSF and IL-2RB, completely abrogates the MC38 transcriptional response to aPD1 therapy. Thus, our in vivo experimental platform is a powerful approach for discovery of host genetic factors that establish the tumor immune microenvironment propitious for ICI response.

Genomic and transcriptomic landscapes of metastatic neuroendocrine neoplasms from distinct primary sites and their clinical implications

Neuroendocrine neoplasms (NENs) encompass a highly heterogeneous group of neoplasms with varying prognoses and molecular alterations. Molecular profiling studies have furthered our understanding of NENs, but the majority of previous studies have focused on primary tumors and on mutational landscapes using DNA sequencing data. Here, we describe the genomic and transcriptomic landscapes of 28 metastatic NENs across different primary anatomical sites (PASs) and their potential clinical implications. Although our cohort is small, our analyses provide further insights on the molecular commonalities and distinctions between metastatic NENs of different PASs. Comparison to several reference transcriptome data sets revealed that despite considerable whole genome and transcriptome variability in NENs, the metastatic NENs are still more like each other than other cancer types. Our study also highlights the potential utility of NEN transcriptome data for molecular classification and clinical decision making.

Identification of minimal residual disease using the clonesight test for ultrasensitive ctDNA detection to anticipate late relapse in early breast cancer

BACKGROUND

Early-stage breast cancer (BC) diagnosis significantly reduces mortality, yet relapse remains a concern due to undetectable minimal residual disease (MRD). Liquid biopsies offer real-time insights into tumor dynamics, aiding MRD detection and therapy response evaluation. However, MRD detection is challenging due to low tumor DNA levels in circulation.

METHODS

This prospective study included 20 HR + BC patients who had completed at least 5 years of adjuvant endocrine therapy (ET). Plasma samples were collected every 6 months over a median follow-up period of 2 years. Tumor-specific somatic variants identified through tumor tissue sequencing served as biomarkers for a patient-informed circulating tumor DNA (ctDNA) assay (CloneSight), which utilized a multiplex PCR-based next-generation sequencing (NGS) workflow.

RESULTS

ctDNA was detected in patients who experienced clinical relapse, with positivity observed up to 68 months (5.7 years) prior to overt recurrence, highlighting its potential for early relapse identification. In non-relapsed patients, ctDNA remained undetectable in 93% of cases, reflecting a potential high level of specificity. The assay detected ctDNA in 50% of relapsed patients, while no ctDNA signal was identified in the majority of non-relapsed cases.

CONCLUSION

Our exploratory findings indicate that CloneSight could be a promising tool for MRD detection and relapse prediction, providing a cost-effective, patient-informed approach to ctDNA monitoring. The ability of this approach to detect relapse prior to clinical recurrence suggests its potential relevance in improving patient monitoring. These findings suggest that ctDNA-based MRD assays could play a role in future surveillance strategies for HR + BC, though further studies in larger cohorts are needed to confirm their clinical applicability.

In vivo functional screens reveal KEAP1 loss as a driver of chemoresistance in small cell lung cancer

Exquisitely chemosensitive initially, small cell lung cancer (SCLC) exhibits dismal outcomes owing to rapid transition to chemoresistance. Elucidating the genetic underpinnings has been challenging owing to limitations with cellular models. As SCLC patient-derived xenograft (PDX) models mimic therapeutic responses, we perform genetic screens in chemosensitive PDX models to identify drivers of chemoresistance. cDNA overexpression screens identify MYC, MYCN, and MYCL, while CRISPR deletion screens identify KEAP1 loss as driving chemoresistance. Deletion of KEAP1 switched a chemosensitive SCLC PDX model to become chemoresistant and resulted in sensitivity to inhibition of glutamine metabolism. Data from the IMpower133 clinical trial revealed ~6% of patients with extensive-stage SCLC exhibit KEAP1 genetic alterations, with activation of a KEAP1/NRF2 transcriptional signature associated with reduced survival upon chemotherapy treatment. While roles for KEAP1/NRF2 have been unappreciated in SCLC, our genetic screens revealed KEAP1 loss as a driver of chemoresistance, while patient genomic analyses demonstrate clinical importance.

Artificial intelligence in variant calling: a review

Artificial intelligence (AI) has revolutionized numerous fields, including genomics, where it has significantly impacted variant calling, a crucial process in genomic analysis. Variant calling involves the detection of genetic variants such as single nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and structural variants from high-throughput sequencing data. Traditionally, statistical approaches have dominated this task, but the advent of AI led to the development of sophisticated tools that promise higher accuracy, efficiency, and scalability. This review explores the state-of-the-art AI-based variant calling tools, including DeepVariant, DNAscope, DeepTrio, Clair, Clairvoyante, Medaka, and HELLO. We discuss their underlying methodologies, strengths, limitations, and performance metrics across different sequencing technologies, alongside their computational requirements, focusing primarily on SNP and InDel detection. By comparing these AI-driven techniques with conventional methods, we highlight the transformative advancements AI has introduced and its potential to further enhance genomic research.

DirectHRD enables sensitive scar-based classification of homologous recombination deficiency

Homologous recombination deficiency (HRD) is a predictive biomarker for efficacy of PARP (poly ADP-ribose polymerase) inhibition and platinum chemotherapy for cancer patients but remains challenging to detect. The discovery of patients without pathogenic mutations in known HR genes but exhibiting genomic scars indicative of HRD led to the FDA approval of the first scar-based HRD test. Despite advancements in whole genome sequencing (WGS) and integration of large training datasets with machine learning models, current methods lack the sensitivity required for detecting HRD scars in low tumor purity samples, especially in liquid biopsies. Here, we describe DirectHRD, a genomic scar-based HRD classifier based on WGS. Compared to other WGS-based methods, DirectHRD exclusively utilizes a highly specific type of HRD scar-small deletions with microhomology-and its associated signatures in a probabilistic framework. We applied DirectHRD to 501 tumor and 90 cell-free DNA (cfDNA) samples from 4 cancer types: breast, ovarian, prostate, and pancreas. Among all 501 tumor biopsies, DirectHRD achieved 100% detection of HRD with high specificity (>90%). Across all 90 cfDNA samples, the method achieved an area under the curve of 0.87 and demonstrated the ability to detect HRD at tumor fractions as low as 1%, making it 10 times more sensitive than state-of-the-art methods.

Germline Pathogenic DROSHA Variants Are Linked to Pineoblastoma and Wilms Tumor Predisposition

PURPOSE

DROSHA, DGCR8, and DICER1 regulate miRNA biogenesis and are commonly mutated in cancer. Although DGCR8 and DICER1 germline pathogenic variants (GPV) cause autosomal dominant tumor predisposition, no association between DROSHA GPVs and clinical phenotypes has been reported.

EXPERIMENTAL DESIGN

After obtaining informed consent, sequencing was performed on germline and tumor samples from all patients. The occurrence of germline DROSHA GPVs was investigated in large pediatric and adult cancer datasets. The population prevalence of DROSHA GPVs was investigated in the UK Biobank and Geisinger DiscovEHR cohorts.

RESULTS

We describe nine children from eight families with heterozygous DROSHA GPVs and a diagnosis of pineoblastoma (n = 8) or Wilms tumor (n = 1). A somatic second hit in DROSHA was detected in all eight tumors analyzed. All pineoblastoma tumors analyzed were classified as miRNA processing-altered 1 subtype. We estimate the population prevalence of germline DROSHA loss-of-function variants to be 1:3,875 to 1:4,843 but find no evidence for increased adult cancer risk.

CONCLUSIONS

This is the first report of DROSHA-related tumor predisposition. As pineoblastoma and Wilms tumor are also associated with DICER1 GPVs, our results suggest that the tissues of origin for these tumors are uniquely tolerant of general miRNA loss. The miRNA processing-altered 1 pineoblastoma subtype is associated with older age of diagnosis and better outcomes than other subtypes, suggesting DROSHA GPV status may have important clinical and prognostic significance. We suggest that genetic testing for DROSHA GPVs be considered for patients with pineoblastoma, Wilms tumor, or other DICER1-/DGCR8-related conditions and propose surveillance recommendations through research studies for individuals with DROSHA GPVs.

Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling

Shallow genome-wide cell-free DNA sequencing holds great promise for noninvasive cancer monitoring by providing reliable copy number alteration (CNA) and fragmentomic profiles. Single-nucleotide variations (SNVs) are, however, much harder to identify with low sequencing depth due to sequencing errors. Here, we present Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), which leverages RCA and consensus calling based on genome-wide long-read nanopore sequencing to enable simultaneous multimodal tumor fraction (TF) estimation through SNVs, CNAs, and fragmentomics. The efficacy of NanoRCS is tested on 18 cancer patient samples and seven healthy controls, demonstrating its ability to reliably detect TFs as low as 0.24%. In vitro experiments confirm that SNV measurements are essential for detecting TFs below 3%. NanoRCS provides an opportunity for cost-effective and rapid sample processing, which aligns well with clinical needs, particularly in settings where quick and accurate cancer monitoring is essential for personalized treatment strategies.

TET2 gene mutation status associated with poor prognosis of transition zone prostate cancer: a retrospective cohort study based on whole exome sequencing and machine learning models

Background

Prostate cancer (PCa) in the transition zone (TZ) is uncommon and often poses challenges for early diagnosis, but its genomic determinants and therapeutic vulnerabilities remain poorly characterized.

Methods

Tumor mutational landscape was characterized in nine patients with TZ PCa, identifying somatic variants through whole-exome sequencing (WES). Novel candidate variants relevant to driver gene were selected using rare-variant burden analysis. Kaplan-Meier curves with log-rank testing and Cox regression models were applied to evaluate the prognostic significance of selected mutant driver gene and clinicopathological characteristics in a cohort of 132 patients with TZ PCa. Significant prognostic determinants were integrated into a validated nomogram for individualized prediction of 3-, 4-, and 5-year biochemical recurrence-free survival (BRFS) and overall survival (OS) probabilities. Eight machine learning algorithms were employed to develop BRFS and OS prediction models in a cohort.

Results

A total of 5,036 somatic single nucleotide variants (SNVs) and 587 somatic insertion and deletion (INDELs) were discovered. Among eight driver gene mutations which were verified through Sanger sequencing, TET2 gene, with high mutation frequency and potential targeted drug relevance (bromodomain inhibitors and DOT1L inhibitors) was selected for further validation. Retrospective cohort study demonstrated that TET2 mutant status was significantly associated with Gleason score (p = 0.004) and distant metastasis (p = 0.002). Furthermore, TET2 mutant status was significantly correlated with inferior BRFS and OS and served as an independent predictor. Comparative evaluation of eight algorithms revealed the GBM model achieved superior discriminative ability for BRFS (AUC for 3-year: 0.752, 4-year: 0.786, 5-year: 0.796). The predictive model based on the GBM machine learning algorithm achieved the best predictive performance for OS (AUC for 3-year: 0.838, 4-year: 0.915, 5-year: 0.868). The constructed predictive nomogram provided evidence that TET2 mutant status integration conferred statistically significant improvements in model accuracy and clinical predictive value.

Conclusion

Our study elucidated the distinct genetic basis of prostate cancer in the transition zone and identified TET2 mutation as an independent prognostic determinant in TZ PCa. However, the limited sample size of this study necessitates cautious interpretation of these findings, and further validation in larger cohorts is warranted to confirm their generalizability.

A frameshift-generated cancer neoepitope that controls tumor burden in prophylaxis as well as therapy

Insertion or deletion of one or two base pairs within a coding region causes a frameshift, which has the potential to generate neoepitopes (InDel-generated neoepitopes) that lack a self-counterpart and are entirely novel. Despite the obvious appeal of InDel-generated neoepitopes, and the demonstration of such candidate neoepitopes that can elicit a CD8 T-cell response, no InDel-generated neoepitopes that actually control tumors in vivo have been reported thus far. Here, in a mouse colon carcinoma line, we identify 11 InDels, only one of which generates a neoepitope that elicits tumor control in vivo in models of prophylaxis as well as therapy. Although this neoepitope has no self-counterpart, it has a low affinity (IC50 33,937.60 nM) for its MHC I allele. Despite its low affinity for MHC I, this neoepitope elicits antitumor activity in vivo through CD8 T cells. Furthermore, CD8 T cells elicited by this InDel-generated neoepitope, like the neoepitopes created by point mutations, show notably less exhaustion than classical immunogenic epitopes. Ironically, this InDel-generated neoepitope follows the same rules as noted for most of the tumor control-mediating neoepitopes generated by point mutations that have a poor affinity for MHC I alleles.

Single-cell RNA sequencing reveals important role of monocytes and macrophages during mucopolysaccharidosis treatment

Mucopolysaccharidosis (MPS) encompasses a heterogeneous group of lysosomal storage diseases resulting from mutations in genes encoding lysosomal enzymes responsible for the degradation of mucopolysaccharides, also known as glycosaminoglycans (GAGs). Current therapeutic strategies for MPS include hematopoietic stem cell transplantation (HSCT), enzyme replacement therapy (ERT), and symptomatic therapy. This study investigated dynamic changes in MPS type II (MPS-II) through genomic and single-cell sequencing in a patient undergoing ERT. Analysis of peripheral blood mononuclear cells (PBMCs) from one MPS-II patient of 10 year old at different disease stages through scRNA-seq identified various immune cell types, including natural killer (NK) cells, NKT cells, CD4 + and CD8 + T cells, CD14 + and CD16 + monocytes, and B cells. Monocytes and macrophages were significantly reduced during the severe stage of MPS-II but increased during the recovery stage following ERT. Notably, monocyte subtype mono3 was exclusively expressed in the severe stage, while mono1_2, a subtype of mono1, was absent during the severe stage and exhibited distinct biological functions. These findings suggest that monocytes and macrophages play critical roles in the pathogenesis of MPS-II and in the response to ERT. Pseudotime, Gene Ontology, and cell-communication analyses revealed unique functions for the different cellular subtypes. Notably, key molecules mediating cellular interactions during ERT in MPS-II included CXCR3, PF4, APP, and C5AR1 in macrophages, RPS19 in T cells, HLA-DPB1 in B cells, ADRB2 in NK cells, and IL1B, C5AR1, RPS19, and TNFSF13B in monocytes. Overall, integrative analysis delineated the expression dynamics of various cell types and identified mutations in MPS-II, providing a comprehensive atlas of transcriptional programs, cellular characterizations, and genomic variation profiles in MPS-II. This dataset, along with advanced integrative analysis, represents a valuable resource for the discovery of drug targets and the improvement of therapeutic strategies for MPS-II.

Isolation and Characterization of the Adamantinomatous Craniopharyngioma Primary Cells with Cancer-Associated Fibroblast Features

Backgrounds: Adamantinomatous craniopharyngiomas (ACPs) are benign intracranial tumors that behave aggressively due to their location, infiltration of the surrounding nervous tissue and high capacity for recurrence. In this study, we aimed to construct ACP primary cell models for further investigation of tumorigenic and recurrent mechanisms. Methods: Primary cells were isolated from primary (one case) and recurrent (one case) ACP. Short tandem repeat (STR) analysis was used to clarify the identity of the ACP primary cells we isolated. Whole exome sequencing (WES), immunofluorescence (IF) and immunohistochemistry (IHC) were performed on primary cells and corresponding ACP tissues, to determine the mutational profile and to clarify the tissue origin and phenotypic of primary cells. Transcriptome RNA-seq was performed to obtain the gene expression characteristics of ACP primary cells. Subsequently, a heterotopic ACP xenograft mouse model was established to confirm the tumorigenesis capacity of ACP primary cells. Results: ACP primary cells were successfully cultured. The genetic variants were similar to the original tumor tissue, and they owned expression of cancer-associated fibroblast (CAF) markers (FSP1/S100A4, Vimentin) and nuclear translocation β-catenin. Meanwhile, they had an high level expression of extracellular matrix components (Fibronectin). The tumor formation ability of ACP primary cells was verified. The transcriptional signatures of ACP primary cells were also explored. Conclusions: We successfully isolated and characterized ACP primary cells that acquired multiple CAF features and demonstrated stable propagation through dozens of passages. These PDC models laid the foundation for further research on ACP.

The tandem duplicator phenotype may be a novel targetable subgroup in pancreatic cancer

Tandem duplicator phenotype (TDP) consists of distinct genomic rearrangements where tandem duplications are randomly distributed. In this study, we characterized the prevalence and outcomes of TDP in a large series of prospectively sequenced tumors from patients with pancreatic ductal adenocarcinomas (PDAC). Whole-genome sequencing (WGS) was performed in 530 PDAC cases from the PanCuRx Initiative, COMPASS and PanGen/POG trials in Canada. Of 530 cases, 52 were identified as TDP (9.8%; 13 resected, 39 advanced). Etiological subgroups of TDP included BRCA1 (n = 9), CCNE1 (n = 4), and unknown (n = 39). Presence of TDP was not prognostic in resected specimens (p = 0.77) compared with non-HRD and non-TDP cases, described as typicals. In advanced cases, when stratified for only classical subtype cases, platinum therapy was correlated with longer response in non-BRCA1 TDP vs. typicals (p = 0.0036). There was no difference in overall survival between TDP and typicals (p = 0.5).TDP represents a potential novel targetable subgroup for chemotherapy selection in PDAC.

Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors

Cancer genomics consortia have identified somatic drivers of breast cancer subtypes. However, these studies have predominantly included older, non-Black women, and the related socioeconomic status (SES) data are limited. Increased representation and depth of social data are crucial for understanding how health inequity is intertwined with somatic landscapes. Here, we conducted targeted sequencing on primary tumors from the Carolina Breast Cancer Study (N = 357; 52% Black; 47% <50) and compared the results with The Cancer Genome Atlas (N = 948; 18% Black; 27% <50). Race (Black vs. non-Black), age, and SES were evaluated in association with mutations, copy number alterations, and aneuploidy using generalized linear models. Pathway dysfunction was also assessed by aggregating mutation and copy number alterations. Adjusting for age, Black participants (N = 350) were significantly more likely to have TP53 and FAT1 mutations and less likely to have PIK3CA, CDH1, DDR2, and GATA3 mutations than non-Black participants. Younger participants had more GATA3 alterations and fewer KMT2C, PTEN, MAP3K1, and CDH1 alterations. Black participants had significant enrichment for MYC (8q) and PIK3CA (3q26) amplifications and higher total aneuploidy, but age was not associated with copy number variation. SES was associated with different patterns of alteration in Black versus non-Black women. Overall, Black participants showed modest differences in TP53, PIK3CA, and other alterations that further varied by SES. Race is a social construct, and varying distributions of etiologic factors across social strata may predispose Black, young, and low SES women to cancer subtypes characterized by these alterations. Significance: The collection and analysis of DNA sequencing with comprehensive socioeconomic factor associations in a large Black breast cancer patient cohort could help uncover mechanisms by which social conditions contribute to tumor biology.

Establishment and characterization of novel cancer cachexia-inducing cell line, Aku60GC, of scirrhous gastric cancer

Cancer cachexia is a pathological state characterized by severe weight loss, skeletal muscle depletion, and adipose tissue reduction. Cancer cachexia is observed in gastric cancer (GC) with a higher incidence over 80%. Approximately 80% patients with advanced GC including scirrhous gastric cancer (SGC), which has the worst prognosis among all GC, are affected with cachexia. The exact pathophysiology in SGC cancer cachexia remains elusive, and therapeutic approaches for the cancer cachexia have not been established. Patient-derived cancer cachexia models are promising for elucidating the underlying mechanisms of disease progression and developing novel treatments, none of which originate from SGC. Therefore, we established a novel cancer cachexia-inducing cell line, designated Aku60GC, through stepwise selection of a patient-derived SGC cell line, HSC-60. Subcutaneous implantation of the Aku60GC cells into nude mice resulted in weight loss, muscle atrophy, and adipose tissue depletion with high reproducibility, accompanied by elevation of the circulating cytokines IL-8 and IL-18. Compared to parental HSC-60 cells, Aku60GC cells exhibited additional genomic changes, such as AKT2 and CCNE1 gains, a somatic mutation of RUNX1, and accelerated growth. Thus, our results demonstrate that the Aku60GC cell line is a valuable resource for research on cancer cachexia in SGC.

Patient-Derived Bladder Cancer Organoids as a Valuable Tool for Understanding Tumor Biology and Developing Personalized Treatment

Bladder cancer (BC) is a heterogeneous disease with high recurrence rates and variable treatment responses. To address these clinical challenges, the world's first bladder cancer patient-derived organoids (PDOs) biobank is established based on an Asian population. Thirty-six BC-PDOs are generated from 56 patients and demonstrated that the BC-PDOs can replicate the histological and genomic features of parental tumors. Drug screening tests are conducted with a broad spectrum of conventional chemotherapeutic and targeted therapy drugs and identified differential drug sensitivities among the BC-PDOs. These in vitro results are consistently supported by the PDO xenograft animal studies and patients' clinical treatment outcomes, thereby verifying the predictive power of PDOs for drug responses in BC patients. By analyzing the genetic profiles of the PDOs, specific driver genes that correlate with drug sensitivity to two stand-of-care chemotherapeutics, cisplatin, and gemcitabine, are identified. Additionally, the practicality of PDOs in investigating the tumor microenvironment has been demonstrated. This study underscores the utility of PDOs in advancing the understanding of bladder cancer and the development of personalized therapeutic strategies. The BC-PDOs biobank provides an ideal preclinical platform for supporting the development of personalized treatment strategies for BC patients. This study also provides insights into the potential mechanisms of drug resistance, paves the way for subsequent region-specific research, and demonstrates the possibility of using PDO-related models to direct future research in developing drugs targeting tumor microenvironments.

Evolutionary Pressures Shape Undifferentiated Pleomorphic Sarcoma Development and Radiotherapy Response

Radiotherapy is an integral component in the treatment of many types of cancer, with approximately half of patients with cancer receiving radiotherapy. Systemic therapy applies pressure that can select for resistant tumor subpopulations, underscoring the importance of understanding how radiation impacts tumor evolution to improve treatment outcomes. We integrated temporal genomic profiling of 120 spatially distinct tumor regions from 20 patients with undifferentiated pleomorphic sarcomas (UPS), longitudinal circulating tumor DNA analysis, and evolutionary biology computational pipelines to study UPS evolution during tumorigenesis and in response to radiotherapy. Most unirradiated UPSs displayed initial linear evolution, followed by subsequent branching evolution with distinct mutational processes during early and late development. Metrics of genetic divergence between regions provided evidence of strong selection pressures during UPS development that further increased during radiotherapy. Subclone abundance changed after radiotherapy with subclone contraction tied to alterations in calcium signaling, and inhibiting calcium transporters radiosensitized sarcoma cells. Finally, circulating tumor DNA analysis accurately measured subclone abundance and enabled noninvasive monitoring of subclonal changes. These results demonstrate that radiation exerts selective pressures on UPSs and suggest that targeting radioresistant subclonal populations could improve outcomes after radiotherapy. Significance: Radiotherapy mediates tumor evolution by leading to the expansion of resistant subclonal cancer cell populations, indicating that developing approaches to target resistant subclones will be crucial to improve radiotherapy response.

RNA neoantigen vaccines prime long-lived CD8+ T cells in pancreatic cancer

A fundamental challenge for cancer vaccines is to generate long-lived functional T cells that are specific for tumour antigens. Here we find that mRNA-lipoplex vaccines against somatic mutation-derived neoantigens may solve this challenge in pancreatic ductal adenocarcinoma (PDAC), a lethal cancer with few mutations. At an extended 3.2-year median follow-up from a phase 1 trial of surgery, atezolizumab (PD-L1 inhibitory antibody), autogene cevumeran1 (individualized neoantigen vaccine with backbone-optimized uridine mRNA-lipoplex nanoparticles) and modified (m) FOLFIRINOX (chemotherapy) in patients with PDAC, we find that responders with vaccine-induced T cells (n = 8) have prolonged recurrence-free survival (RFS; median not reached) compared with non-responders without vaccine-induced T cells (n = 8; median RFS 13.4 months; P  =  0.007). In responders, autogene cevumeran induces CD8+ T cell clones with an average estimated lifespan of 7.7 years (range 1.5 to roughly 100 years), with approximately 20% of clones having latent multi-decade lifespans that may outlive hosts. Eighty-six percent of clones per patient persist at substantial frequencies approximately 3 years post-vaccination, including clones with high avidity to PDAC neoepitopes. Using PhenoTrack, a novel computational strategy to trace single T cell phenotypes, we uncover that vaccine-induced clones are undetectable in pre-vaccination tissues, and assume a cytotoxic, tissue-resident memory-like T cell state up to three years post-vaccination with preserved neoantigen-specific effector function. Two responders recurred and evidenced fewer vaccine-induced T cells. Furthermore, recurrent PDACs were pruned of vaccine-targeted cancer clones. Thus, in PDAC, autogene cevumeran induces de novo CD8+ T cells with multiyear longevity, substantial magnitude and durable effector functions that may delay PDAC recurrence. Adjuvant mRNA-lipoplex neoantigen vaccines may thus solve a pivotal obstacle for cancer vaccination.

A neoantigen vaccine generates antitumour immunity in renal cell carcinoma

Personalized cancer vaccines (PCVs) can generate circulating immune responses against predicted neoantigens1-6. However, whether such responses can target cancer driver mutations, lead to immune recognition of a patient's tumour and result in clinical activity are largely unknown. These questions are of particular interest for patients who have tumours with a low mutational burden. Here we conducted a phase I trial (ClinicalTrials.gov identifier NCT02950766) to test a neoantigen-targeting PCV in patients with high-risk, fully resected clear cell renal cell carcinoma (RCC; stage III or IV) with or without ipilimumab administered adjacent to the vaccine. At a median follow-up of 40.2 months after surgery, none of the 9 participants enrolled in the study had a recurrence of RCC. No dose-limiting toxicities were observed. All patients generated T cell immune responses against the PCV antigens, including to RCC driver mutations in VHL, PBRM1, BAP1, KDM5C and PIK3CA. Following vaccination, there was a durable expansion of peripheral T cell clones. Moreover, T cell reactivity against autologous tumours was detected in seven out of nine patients. Our results demonstrate that neoantigen-targeting PCVs in high-risk RCC are highly immunogenic, capable of targeting key driver mutations and can induce antitumour immunity. These observations, in conjunction with the absence of recurrence in all nine vaccinated patients, highlights the promise of PCVs as effective adjuvant therapy in RCC.

Increased Synthetic Cytotoxicity of Combinatorial Chemoradiation Therapy in Homologous Recombination Deficient Tumors

PURPOSE

Homologous recombination deficient (HRD) tumors are exquisitely sensitive to platinum-based chemotherapy and when combined with radiation therapy (RT), leads to improved overall survival in multiple cancer types. Whether a subset of tumors with distinct molecular characteristics demonstrate increased benefit from cisplatin and RT (c-RT) is unclear. We hypothesized that HRD tumors, whether associated with BRCA mutations or genomic scars of HRD, exhibit exquisite sensitivity to c-RT, and that HRD may be a significant driver of c-RT benefit.

METHODS AND MATERIALS

Sensitivity to c-RT was examined using isogenic and sporadic breast cancer cell lines. HRD was assessed using 4 assays: RT-induced Rad51 foci, a DR-GFP reporter assay, a genomic scar score (large-scale state transitions [LST]), and clonogenic survival assays. Whole-genome sequencing of 4 breast tumors from a phase 2 clinical trial of neoadjuvant c-RT in triple-negative breast cancer was performed and HRD was defined using HRDetect.

RESULTS

BRCA1/2 deficient cell lines displayed functional HRD based on the Rad51 functional assay, with c-RT to RT or cisplatin interaction ratios (IR) of 1.11 and 26.84 for the BRCA1 isogenic pair at 2 μM cisplatin and 6 Gy, respectively. The highest LST lines demonstrated HRD and synthetic cytotoxicity to c-RT with IR at 2 Gy and cisplatin 20 μM of 7.50, and the lowest LST line with IR of 0.65. Of 4 evaluable patients in the phase 2 trial, one achieved a pathologic complete response with corresponding HRD based on multiple genomic scar scores including HRDetect and LST scores, compared with patients without a pathologic complete response.

CONCLUSIONS

HRD breast cancers, whether identified by BRCA1/2 mutation status, functional tests, or mutational signatures, appear to be significantly more sensitive to c-RT compared with isogenic controls or tumors without HRD mutational signatures. HRD tumors may be exquisitely sensitive to c-RT which warrants further clinical investigation to guide a precision oncology approach.

Molecular Classification of Endometrial Cancers Using an Integrative DNA Sequencing Panel

BACKGROUND AND OBJECTIVES

Adoption of molecular classification in endometrial cancer (EC) into clinical practice remains challenging due to complexity in coordination of multiple assays. We aimed to develop a simple molecular technique to classify ECs into four subgroups using our custom-designed targeted sequencing panel.

METHODS

Patients with newly diagnosed ECs were prospectively recruited from three cancer centres in Ontario, Canada. Using our panel, 181 ECs were sequenced. Variants were analysed for pathogenicity and clinicopathologic information was collected through medical records retrospectively.

RESULTS

Of 181, 86 (48%) were mismatch repair deficient (MMRd), of which 62 (72%) harboured MLH1 promoter methylation and 24 (28%) had pathogenic variants in MMR genes. Of single classifiers, three (1.8%) had pathogenic POLE (POLEmut), 15 (9%) had TP53 mutations (p53abn) and 61 (37%) had no specific molecular profile subtype (NSMP). Sixteen (9%) had more than one molecular classifying feature, with eight (4%) MMRd-p53abn, six (3%) POLEmut-MMRd, one (0.5%) POLEmut-MMRd-p53abn and one (0.5%) POLEmut-p53abn. When MMRd group was further subclassified according to mechanism of MMR loss, MLH1 promoter methylated group had worse outcomes than those with somatic MMR pathogenic variants.

CONCLUSIONS

Our panel can classify ECs into four subgroups through a simplified process and can be implemented reflexively in clinical practice.

VOYAGER: an international consortium investigating the role of human papilloma virus and genetics in oral and oropharyngeal cancer risk and survival

Head and neck cancer (HNC) is the sixth most common cancer globally. Incidence and survival rates vary significantly across geographic regions and tumor subsites. This is partly due to differences in risk factor exposure, which includes tobacco smoking, alcohol consumption and human papillomavirus (HPV) infection, alongside detection and treatment strategies. The VOYAGER (human papillomaVirus, Oral and oropharYngeal cAncer GEnomic Research) consortium is a collaboration between five large North American and European studies which generated data on 10,530 participants (7,233 cases and 3,297 controls). The primary goal of the collaboration was to improve understing of the role of HPV and genetic factors in oral cavity and oropharyngeal cancer risk and outcome. Demographic and clinical data collected by the five studies were harmonized, and HPV status was determined for the majority of cases. In addition, 999 tumors were sequenced to define somatic mutations. These activities generated a comprehensive biomedical resource that can be utilized to answer critical outsting research questions to help improve HNC prevention, early detection, treatment, and surveillance.

Inferring cell trajectories of spatial transcriptomics via optimal transport analysis

The integration of cell transcriptomics and spatial position to organize differentiation trajectories remains a challenge. Here, we introduce SpaTrack, which leverages optimal transport to reconcile both gene expression and spatial position from spatial transcriptomics into the transition costs, thereby reconstructing cell differentiation. SpaTrack can construct detailed spatial trajectories that reflect the differentiation topology and trace cell dynamics across multiple samples over temporal intervals. To capture the dynamic drivers of differentiation, SpaTrack models cell fate as a function of expression profiles influenced by transcription factors over time. By applying SpaTrack, we successfully disentangle spatiotemporal trajectories of axolotl telencephalon regeneration and mouse midbrain development. Diverse malignant lineages expanding within a primary tumor are uncovered. One lineage, characterized by upregulated epithelial mesenchymal transition, implants at the metastatic site and subsequently colonizes to form a secondary tumor. Overall, SpaTrack efficiently advances trajectory inference from spatial transcriptomics, providing valuable insights into differentiation processes.

Genomic mediators of acquired resistance to immunotherapy in metastatic melanoma

Although some patients with metastatic melanoma experience durable responses to immune checkpoint inhibitors (ICIs), most exhibit intrinsic or acquired resistance to these therapies. Here, we compare somatic genomic profiles from matched pre-treatment and post-resistance tumor biopsies in patients (n = 25) with metastatic melanoma who exhibited heterogeneous ICI responses to nominate additional mediators of acquired resistance. We find that several acquired resistance tumors exhibit defects in B2M or JAK1/2, consistent with prior findings. We also discover resistance-associated mutations in SEC24C and SEC24D in 3 patients. SEC24 has an essential role in the trafficking of the dsDNA sensor STING and has been linked to interferonopathies. Melanoma cells engineered to express the SEC24C mutations observed in patients exhibit diminished STING signaling, including decreased type I interferon production, antigen presentation, and a reduced capacity to activate cytotoxic T cells. This study nominates a role for aberrant STING trafficking in acquired resistance to ICIs.

A Multi-Center Real-World Study of Clinicopathologic Characteristics and Efficacy of the Malignant Mesothelioma in Chinese Population

OBJECTIVE

Malignant mesothelioma (MM) is a rare malignant tumor. To explore the clinicopathological characteristics and efficacy of Chinese population with MM in the real-world.

METHODS

Two hundred and forty-eight patients diagnosed with MM between September 2007 and August 2024 from three large medical centers (Beijing Hospital, Peking University Cancer Hospital, and Chinese Academy of Medical Sciences Cancer Hospital) were retrospectively analyzed. Kaplan-Meier and Cox regression were performed. Breast cancer gene 1-associated protein 1 (BAP1) status was evaluated.

RESULTS

Chinese population with MM had a lower diagnostic age, higher proportion of youth and female, more advanced stage and lower expression of characteristic markers. The median progression-free survival (mPFS) and median overall survival (mOS) were 8.90 and 25.60 months for the first-line treatment, and 3.28 and 19.50 months for the second-line. The first-line immunotherapy provided a relatively higher objective response rate (33.3% vs. 20.5%, p = 0.402) and a trend to prolong mPFS (12.10 vs. 9.20 months, p = 0.345) and mOS (NA vs. 23.90, p = 0.185) compared with chemotherapy. Bevacizumab combined with chemotherapy relatively prolonged mPFS (10.47 vs. 7.93 months, p = 0.074) and mOS (31.30 vs. 23.20 months, p = 0.673) than chemotherapy alone. Carboplatin relatively improved mPFS than cisplatin (10.87 vs. 8.87 months, p = 0.185). Age and histologic type were predictors for PFS, and gender, histologic subtype, and CK5/6 were prognosis factors for OS. Briefly, 17.78% patients existed BAP1 deletions and correlated with OS benefit.

CONCLUSION

Chinese population with MM present unique clinicopathologic characteristics and could benefit from the first-line immunotherapy and bevacizumab combined with chemotherapy. Gender, histologic subtype, and CK5/6 are prognosis factors for OS. BAP1 deletions correlate with OS benefit.

Immunogenomic determinants of exceptional response to immune checkpoint inhibition in renal cell carcinoma

Immune checkpoint inhibitors can lead to 'exceptional', durable responses in a subset of persons. However, the molecular basis of exceptional response (ER) to immunotherapy in metastatic clear cell renal cell carcinoma (mccRCC) has not been well characterized. Here we analyzed pretherapy genomic and transcriptomic data in treatment-naive persons with mccRCC treated with standard-of-care immunotherapies: (1) combination of programmed cell death protein and ligand 1 (PD1/PDL1) and cytotoxic T lymphocyte-associated protein 4 inhibitors (IO/IO) or (2) combination of PD1/PDL1 and vascular endothelial growth factor (VEGF) receptor inhibitors (IO/VEGF). In the IO/IO cohort, clonal neoantigen load was significantly higher in persons with ER. In the IO/VEGF cohort, ER participants displayed strong enrichment of B cell receptor signaling-related pathways, tertiary lymphoid structure (TLS) signatures and evidence of increased metabolic activity. Our results suggest that ER may be related to clonal neoantigen-driven cytotoxic T cell responses and TLS formation in tumor microenvironments. Therapeutic combinations that elicit both T cell-directed and B cell-directed antitumor immunity may be important to achieve exceptional benefit to IO-based treatment in ccRCC.

Adenomas from individuals with pathogenic biallelic variants in the MUTYH and NTHL1 genes demonstrate base excision repair tumour mutational signature profiles similar to colorectal cancers, expanding potential diagnostic and variant classification applications

BACKGROUND

Colorectal cancers (CRCs) from people with biallelic germline likely pathogenic/pathogenic variants in MUTYH or NTHL1 exhibit specific single base substitution (SBS) mutational signatures, namely combined SBS18 and SBS36 (SBS18+SBS36), and SBS30, respectively. The aim was to determine if adenomas from biallelic cases demonstrated these mutational signatures at diagnostic levels.

METHODS

Whole-exome sequencing of FFPE tissue and matched blood-derived DNA was performed on 9 adenomas and 15 CRCs from 13 biallelic MUTYH cases, on 7 adenomas and 2 CRCs from 5 biallelic NTHL1 cases and on 27 adenomas and 26 CRCs from 46 non-hereditary (sporadic) participants. All samples were assessed for COSMIC v3.2 SBS mutational signatures.

RESULTS

In biallelic MUTYH cases, SBS18+SBS36 signature proportions in adenomas (mean±standard deviation, 65.6 %±29.6 %) were not significantly different to those observed in CRCs (76.2 % ± 20.5 %, p-value=0.37), but were significantly higher compared with non-hereditary adenomas (7.6 % ± 7.0 %, p-value=3.4 × 10-4). Similarly, in biallelic NTHL1 cases, SBS30 signature proportions in adenomas (74.5 %±9.4 %) were similar to those in CRCs (78.8 % ± 2.4 %) but significantly higher compared with non-hereditary adenomas (2.8 % ± 3.6 %, p-value=5.1 × 10-7). Additionally, a compound heterozygote with the c.1187G>A p.(Gly396Asp) pathogenic variant and the c.533G>C p.(Gly178Ala) variant of unknown significance (VUS) in MUTYH demonstrated high levels of SBS18+SBS36 in four adenomas and one CRC, providing evidence for reclassification of the VUS to pathogenic.

CONCLUSIONS

SBS18+SBS36 and SBS30 were enriched in adenomas at comparable proportions to those observed in CRCs from biallelic MUTYH and biallelic NTHL1 cases, respectively. Therefore, testing adenomas may improve the identification of biallelic cases and facilitate variant classification, ultimately enabling opportunities for CRC prevention.

A Comparative Genomic Analysis of Parathyroid Adenomas and Carcinomas Harboring Heterozygous Germline CDC73 Mutations

CONTEXT

Parathyroid cancer has been linked to germline mutations of the Cell Division Cycle 73 (CDC73) gene. However, carriers harboring cancer-associated germline CDC73 mutations may develop only parathyroid adenoma or no parathyroid disease. This incomplete penetrance indicates that additional genomic events are required for parathyroid tumorigenesis.

OBJECTIVE

(1) Determine the status of the second CDC73 allele in parathyroid tumors harboring germline CDC73 mutations and (2) compare the genomic landscapes between parathyroid carcinomas and adenomas.

DESIGN

Whole-exome and RNA sequencing of 12 parathyroid tumors harboring germline CDC73 mutations (6 adenomas and 6 carcinomas) and their matched normal tissues.

RESULTS

All 12 parathyroid tumors had gained 1 somatic event predicted to cause a complete inactivation of the second CDC73 allele. Several distinctive genomic features were identified in parathyroid carcinomas compared to adenomas, including more single nucleotide variants bearing the C > G transversion and APOBEC deamination signatures, frequent mutations of the genes involved in the PI-3K/mTOR signaling, a greater number of copy number variations, and substantially more genes with altered expression. Parathyroid carcinomas also share some genomic features with adenomas. For instance, both have recurrent somatic mutations and copy number loss that impact the genes involved in T-cell receptor signaling and tumor antigen presentation, suggesting a shared strategy to evade immune surveillance.

CONCLUSION

Biallelic inactivation of CDC73 is essential for parathyroid tumorigenesis in carriers harboring germline mutations of this gene. Despite sharing some genomic features with adenomas, parathyroid carcinomas have more distinctive alterations in the genome, some of which may be critical for cancer formation.

Development and validation of a molecular classifier of meningiomas

BACKGROUND

Meningiomas exhibit considerable clinical and biological heterogeneity. We previously identified four distinct molecular groups (immunogenic, NF2-wildtype, hypermetabolic, proliferative) that address much of this heterogeneity. Despite the utility of these groups, the stochasticity of clustering methods and the use of multi-omics data for discovery limits the potential for classifying prospective cases. We sought to address this with a dedicated classifier.

METHODS

Using an international cohort of 1698 meningiomas, we constructed and rigorously validated a machine learning-based molecular classifier using only DNA methylation data as input. Original and newly-predicted molecular groups were compared using DNA methylation, RNA sequencing, copy number profiles, whole exome sequencing, and clinical outcomes.

RESULTS

We show that group-specific outcomes in the validation cohort are nearly identical to those originally described, with median PFS of 7.4 (4.9-Inf) years in hypermetabolic tumors and 2.5 (2.3-5.3) years in proliferative tumors (not reached in the other groups). Tumors classified as NF2-wildtype had no NF2 mutations, and 51.4% had canonical mutations previously described in this group. RNA pathway analysis revealed upregulation of immune-related pathways in the immunogenic group, metabolic pathways in the hypermetabolic group and cell-cycle programs in the proliferative group. Bulk deconvolution similarly revealed enrichment of macrophages in immunogenic tumours and neoplastic cells in hypermetabolic and proliferative tumours with similar proportions to those originally described.

CONCLUSIONS

Our DNA methylation-based classifier, which is publicly available for immediate clinical use, recapitulates the biology and outcomes of the original molecular groups as assessed using multiple metrics/platforms that were not used in its training.

Integrated proteogenomic characterization of ampullary adenocarcinoma

Ampullary adenocarcinoma (AMPAC) is a rare and heterogeneous malignancy. Here we performed a comprehensive proteogenomic analysis of 198 samples from Chinese AMPAC patients and duodenum patients. Genomic data illustrate that 4q loss causes fatty acid accumulation and cell proliferation. Proteomic analysis has revealed three distinct clusters (C-FAM, C-AD, C-CC), among which the most aggressive cluster, C-AD, is associated with the poorest prognosis and is characterized by focal adhesion. Immune clustering identifies three immune clusters and reveals that immune cluster M1 (macrophage infiltration cluster) and M3 (DC cell infiltration cluster), which exhibit a higher immune score compared to cluster M2 (CD4+ T-cell infiltration cluster), are associated with a poor prognosis due to the potential secretion of IL-6 by tumor cells and its consequential influence. This study provides a comprehensive proteogenomic analysis for seeking for better understanding and potential treatment of AMPAC.

Selective utilization of circulating tumor DNA testing enables disease monitoring in endometrial and ovarian carcinomas

OBJECTIVE

Biomarkers reflecting real-time response to therapy and recurrence are lacking. We assessed the clinical value of detecting cell-free circulating tumor DNA (ctDNA) mutations in endometrial cancer (EC) and ovarian cancer (OC) patients.

METHODS

EC/OC patients undergoing primary surgery were consented for tissue banking and 2-year serial blood draws. Tumor tissue DNA and plasma ctDNA underwent next generation sequencing using a targeted gene panel for somatic mutations.

RESULTS

Of 44 patients (24 EC, 17 OC, 2 synchronous endometrial and ovarian carcinomas [SEOC] and 1 endocervical adenocarcinoma [EA]) at least one somatic mutation was identified in tumor tissue in 40 (91%, 20/24 EC, all OC/SEOC/EA), and in preoperative plasma ctDNA in 12 (27%) patients (6/24 [25%] EC and 6/17 [35%] OC). Detection of preoperative ctDNA mutations was associated with advanced stage, higher preoperative CA125, and subsequent disease recurrence. In 5/12 (42%) patients with preoperative ctDNA mutations, examination/imaging suggested clinical stage I however final pathology revealed stage II/III. In 11 patients where serial timepoints were assessed during treatment for ctDNA and CA125, ctDNA clearance preceded normalization of CA125. Thirteen patients developed recurrent disease (4 EC, 8 OC, 1 EA); 8 in whom ctDNA mutations were detected postoperatively, and 4 followed through time of recurrence with ctDNA mutations identified 2-5 months prior to clinical/radiologic/biomarker progression in 3.

CONCLUSION

ctDNA can reflect larger tumor volume/metastases, treatment response and subsequent disease recurrence in EC and OC. Careful patient selection is critical to direct resources to patients most likely to benefit, considering disease burden and risk group.

Primary mucinous cystadenocarcinoma of the breast: A case report and literature review

Mucinous cystadenocarcinoma (MCA) is a rare breast cancer. The present study reports a case of primary MCA of the breast with a comprehensive evaluation of this rare tumour. A 51-year-old woman sought medical attention for a mass in the left breast. A core needle biopsy revealed an infiltrating adenocarcinoma with mucus secretion and papillary formation. The macroscopic appearance was of a greyish-white, tough and well-circumscribed solid mass, without a notable cyst. Microscopically, the tumour consisted of ducts and cysts of varying sizes. Varying degrees of branching papillary structures were observed in the lumen and cyst cavities. The tumour cells were highly columnar in shape, with high-grade nuclei arranged in a single-layer. Immunohistochemistry revealed that the tumour was a basal-like triple-negative breast cancer with a high proliferation index and tumour protein p53 diffuse strong expression. Mutations in breast cancer 1-associated RING domain 1 (BARD1), kinase domain containing receptor (KDR), mucin-6 (MUC6), tumour protein 53 (TP53) and breast cancer 1-interacting protein C-terminal helicase 1 (BRIP1) were identified using DNA analysis. The patient was followed up for 26 months and showed no signs of recurrence or metastasis. In conclusion, the current study presents a case of MCA of breast accompanied by mutations in the BARD1, KDR, MUC6, TP53 and BRIP1 genes, with no recurrence after a 26-month follow-up. Combining this case with a review of the literature helps us to better understand the clinicopathological and genetic characteristics of MCA, and guide treatment.

Comprehensive genomic characterization of early-stage bladder cancer

Understanding the molecular landscape of nonmuscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and treatment regimens. We performed a comprehensive genomic analysis of patients with NMIBC using whole-exome sequencing (n = 438), shallow whole-genome sequencing (n = 362) and total RNA sequencing (n = 414). A large genomic variation within NMIBC was observed and correlated with different molecular subtypes. Frequent loss of heterozygosity in FGFR3 and 17p (affecting TP53) was found in tumors with mutations in FGFR3 and TP53, respectively. Whole-genome doubling (WGD) was observed in 15% of the tumors and was associated with worse outcomes. Tumors with WGD were genomically unstable, with alterations in cell-cycle-related genes and an altered immune composition. Finally, integrative clustering of multi-omics data highlighted the important role of genomic instability and immune cell exhaustion in disease aggressiveness. These findings advance our understanding of genomic differences associated with disease aggressiveness in NMIBC and may ultimately improve patient stratification.

Oncolytic immunotherapy with nivolumab in muscle-invasive bladder cancer: a phase 1b trial

There is a critical unmet need for safe and efficacious neoadjuvant treatment for cisplatin-ineligible patients with muscle-invasive bladder cancer. Here we launched a phase 1b study using the combination of intravesical cretostimogene grenadenorepvec (oncolytic serotype 5 adenovirus encoding granulocyte-macrophage colony-stimulating factor) with systemic nivolumab in cisplatin-ineligible patients with cT2-4aN0-1M0 muscle-invasive bladder cancer. The primary objective was to measure safety, and the secondary objective was to assess the anti-tumor efficacy as measured by pathologic complete response along with 1-year recurrence-free survival. No dose-limiting toxicity was encountered in 21 patients enrolled and treated. Combination treatment achieved a pathologic complete response rate of 42.1% and a 1-year recurrence-free survival rate of 70.4%. Pathologic response was associated with baseline free E2F activity and tumor mutational burden but not PD-L1 status. Although T cell infiltration was broadly induced after intravesical oncolytic immunotherapy, the formation, enlargement and maturation of tertiary lymphoid structures was specifically associated with complete response, supporting the importance of coordinated humoral and cellular immune responses. Together, these results highlight the potential of this combination regimen to enhance therapeutic efficacy in cisplatin-ineligible patients with muscle-invasive bladder cancer, warranting additional study as a neoadjuvant therapeutic option. ClinicalTrials.gov identifier: NCT04610671 .

Context-dependent effects of CDKN2A and other 9p21 gene losses during the evolution of esophageal cancer

CDKN2A is a tumor suppressor located in chromosome 9p21 and frequently lost in Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). How CDKN2A and other 9p21 gene co-deletions affect EAC evolution remains understudied. We explored the effects of 9p21 loss in EACs and cancer progressor and non-progressor BEs with matched genomic, transcriptomic and clinical data. Despite its cancer driver role, CDKN2A loss in BE prevents EAC initiation by counterselecting subsequent TP53 alterations. 9p21 gene co-deletions predict poor patient survival in EAC but not BE through context-dependent effects on cell cycle, oxidative phosphorylation and interferon response. Immune quantifications using bulk transcriptome, RNAscope and high-dimensional tissue imaging showed that IFNE loss reduces immune infiltration in BE, but not EAC. Mechanistically, CDKN2A loss suppresses the maintenance of squamous epithelium, contributing to a more aggressive phenotype. Our study demonstrates context-dependent roles of cancer genes during disease evolution, with consequences for cancer detection and patient management.

Establishment and characterization of a novel patient-derived cell line from conventional central grade 3 chondrosarcoma, NCC-CS1-C1

Chondrosarcoma (CS) is a malignant tumor that produces cartilaginous matrix and is the second most common primary bone sarcoma. CS encompasses a range of histological subtypes, with high-grade conventional central CS being particularly rare, occurring at a rate of 1.81 cases per 1 million person-years. Complete surgical resection is the standard curative treatment for this subtype, as radiation therapy and chemotherapy have proven ineffective. High-grade conventional central CS is highly metastatic and prone to recurrence, resulting in a poor prognosis. Therefore, effective multidisciplinary treatment strategies are urgently needed. Patient-derived cell lines offer promising tools for exploring new therapeutic approaches. However, only two cell lines of high-grade CSs are currently available in public cell banks. In this study, we aimed to establish a novel cell line for high-grade conventional central CS. We successfully developed the NCC-CS1-C1 cell line using surgically resected tumor tissues from a patient with conventional central grade 3 CS. This cell line harbored an IDH1 mutation (p.R132S), commonly found in 50% of CS cases, and exhibited complex copy number variants. A high-throughput screening of 221 anti-cancer drugs identified five candidates-bortezomib, carfilzomib, doxorubicin, panobinostat, and romidepsin-that demonstrated low IC50 values, indicating potential efficacy in treating CS. These findings suggest that NCC-CS1-C1 is a valuable tool for both preclinical and basic research on high-grade conventional central CS.

Genomes and epigenomes of matched normal and tumor breast tissue reveal diverse evolutionary trajectories and tumor-host interactions

Normal tissues adjacent to the tumor (NATs) may harbor early breast carcinogenesis events driven by field cancerization. Although previous studies have characterized copy-number (CN) and transcriptomic alterations, the evolutionary history of NATs in breast cancer (BC) remains poorly characterized. Utilizing whole-genome sequencing (WGS), methylation profiling, and RNA sequencing (RNA-seq), we analyzed paired germline, NATs, and tumor samples from 43 individuals with BC in Hong Kong (HK). We found that single-nucleotide variants (SNVs) were common in NATs, with one-third of NAT samples exhibiting SNVs in driver genes, many of which were present in paired tumor samples. The most frequently mutated genes in both tumor and NAT samples were PIK3CA, TP53, GATA3, and AKT1. In contrast, large-scale aberrations such as somatic CN alterations (SCNAs) and structural variants (SVs) were rarely detected in NAT samples. We generated phylogenetic trees to investigate the evolutionary history of paired NAT and tumor samples. They could be categorized into tumor only, shared, and multiple-tree groups, the last of which is concordant with non-genetic field cancerization. These groups exhibited distinct genomic and epigenomic characteristics in both NAT and tumor samples. Specifically, NAT samples in the shared-tree group showed higher number of mutations, while NAT samples belonging to the multiple-tree group showed a less inflammatory tumor microenvironment (TME), characterized by a higher proportion of regulatory T cells (Tregs) and lower presence of CD14 cell populations. In summary, our findings highlight the diverse evolutionary history in BC NAT/tumor pairs and the impact of field cancerization and TME in shaping the genomic evolutionary history of tumors.

Proteogenomic Landscape of Breast Ductal Carcinoma Reveals Tumor Progression Characteristics and Therapeutic Targets

Multi-omics studies of breast ductal carcinoma (BRDC) have advanced the understanding of the disease's biology and accelerated targeted therapies. However, the temporal order of a series of biological events in the progression of BRDC is still poorly understood. A comprehensive proteogenomic analysis of 224 samples from 168 patients with malignant and benign breast diseases is carried out. Proteogenomic analysis reveals the characteristics of linear multi-step progression of BRDC, such as tumor protein P53 (TP53) mutation-associated estrogen receptor 1 (ESR1) overexpression is involved in the transition from ductal hyperplasia (DH) to ductal carcinoma in situ (DCIS). 6q21 amplification-associated nuclear receptor subfamily 3 group C member 1 (NR3C1) overexpression helps DCIS_Pure (pure DCIS, no histologic evidence of invasion) cells avoid immune destruction. The T-cell lymphoma invasion and metastasis 1, androgen receptor, and aldo-keto reductase family 1 member C1 (TIAM1-AR-AKR1C1) axis promotes cell invasion and migration in DCIS_adjIDC (DCIS regions of invasive cancers). In addition, AKR1C1 is identified as a potential therapeutic target and demonstrated the inhibitory effect of aspirin and dydrogesterone as its inhibitors on tumor cells. The integrative multi-omics analysis helps to understand the progression of BRDC and provides an opportunity to treat BRDC in different stages.

Real-World Performance of Integrative Clinical Genomics in Pediatric Precision Oncology

Despite significant improvement in the survival of pediatric patients with cancer, treatment outcomes for high-risk, relapsed, and refractory cancers remain unsatisfactory. Moreover, prolonged survival is frequently associated with long-term adverse effects due to intensive multimodal treatments. Accelerating the progress of pediatric oncology requires both therapeutic advances and strategies to mitigate the long-term cytotoxic side effects, potentially through targeting specific molecular drivers of pediatric malignancies. In this report, we present the results of integrative genomic and transcriptomic profiling of 230 patients with malignant solid tumors (the "primary cohort") and 18 patients with recurrent or otherwise difficult-to-treat nonmalignant conditions (the "secondary cohort"). The integrative workflow for the primary cohort enabled the identification of clinically significant single nucleotide variants, small insertions/deletions, and fusion genes, which were found in 55% and 28% of patients, respectively. For 38% of patients, molecularly informed treatment recommendations were made. In the secondary cohort, known or potentially driving alteration was detected in 89% of cases, including a suspected novel causal gene for patients with inclusion body infantile digital fibromatosis. Furthermore, 47% of findings also brought therapeutic implications for subsequent management. Across both cohorts, changes or refinements to the original histopathological diagnoses were achieved in 4% of cases. Our study demonstrates the efficacy of integrating advanced genomic and transcriptomic analyses to identify therapeutic targets, refine diagnoses, and optimize treatment strategies for challenging pediatric and young adult malignancies and underscores the need for broad implementation of precision oncology in clinical settings.

Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma

The introduction of immune checkpoint blockade (ICB) has markedly improved outcomes for advanced melanoma. However, many patients develop resistance through unknown mechanisms. While combination ICB has improved response rate and progression-free survival, it substantially increases toxicity. Biomarkers to distinguish patients who would benefit from combination therapy versus aPD-1 remain elusive. We analyzed whole-exome sequencing of pretreatment tumors from four cohorts (n = 140) of ICB-naïve patients treated with aPD-1. High genomic heterogeneity and low ploidy robustly identified patients intrinsically resistant to aPD-1. To establish clinically actionable predictions, we optimized and validated a predictive model using ploidy and heterogeneity to confidently identify (90% PPV) patients with intrinsic resistance to and worse survival on aPD-1. We further observed that three of seven (43%) patients predicted to be intrinsically resistant to single-agent PD-1 ICB responded to combination ICB, suggesting that these patients may benefit disproportionately from combination ICB. These findings highlight the importance of heterogeneity and ploidy, nominating an approach toward clinical actionability.

Integrated proteomic and glycoproteomic analysis reveals heterogeneity and molecular signatures of brain metastases from lung adenocarcinomas

Brain metastasis is a major cause of poor prognosis and death in lung adenocarcinoma (LUAD); however, the understanding of therapeutic strategies and mechanisms for brain metastases from LUAD (BM-LUAD) remains notably limited, especially at the proteomics levels. To address this issue, we conducted integrated proteomic and glycoproteomic analyses on 49 BM-LUAD tumors, revealing two distinct subtypes of the disease: BM-S1 and BM-S2. Whole exome sequencing analysis revealed that somatic mutations in STK11 and KEAP1, as well as copy number deletions on chr19p13.3, such as STK11, UQCR11, and SLC25A23, were more frequently detected in BM-S2. In BM-S1 tumors, we observed significant infiltration of GFAP + astrocytes, as evidenced by elevated levels of GFAP, GABRA2, GABRG1 and GAP43 proteins and an enrichment of astrocytic signatures in both our proteomic data and external spatial transcriptomic data. Conversely, BM-S2 tumors demonstrated higher levels of PD-1 immune cell infiltration, supported by the upregulation of PD-1 and LAG-3 genes. These findings suggest distinct microenvironmental adaptations required by the different BM-LUAD subtypes. Additionally, we observed unique glycosylation patterns between the subtypes, with increased fucosylation in BM-S1 and enhanced sialylation in BM-S2, primarily affected by glycosylation enzymes such as FUT9, B4GALT1, and ST6GAL1. Specifically, in BM-S2, these sialylation modifications are predominantly localized to the lysosomes, underscoring the critical role of N-glycosylation in the tumor progression of BM-LUAD. Overall, our study not only provides a comprehensive multi-omic data resource but also offers valuable biological insights into BM-LUAD, highlighting potential mechanisms and therapeutic targets for further investigation.

Single-cell epigenetic profiling reveals an interferon response-high program associated with BAP1 deficiency in kidney cancer

Renal cell carcinoma (RCC) is characterized by recurrent somatic mutations in epigenetic regulators, which stratify patients into clinically significant subgroups with distinct prognoses and treatment responses. However, the cell type-specific epigenetic landscape of RCC-broadly and in the context of these mutations-is incompletely understood. To investigate these open questions, we integrated single nucleus ATAC sequencing data from RCC tumors across four independent cohorts. In clear cell RCC tumors, we identified four shared malignant epigenetic programs related to angiogenesis, proximal tubule-like features, interferon (IFN) signaling, and one that lacked distinct genomic regions with increased accessibility. Among the mutated epigenetic regulators, BAP1 mutation exhibited the most significant impact on chromatin accessibility in tumor cells, and the associated epigenetic changes were linked to IFN response. We identify multiple potential sources of elevated IFN signaling in these lesions, such as increased immune infiltration and increased accessibility and expression of an IFN-associated ERV, ERV3-16A3_LTR. We find that the expression of ERV3-16A3_LTR may itself be a negative prognostic biomarker in ccRCC. Our findings highlight the convergence of malignant epigenetic programs across ccRCC tumors and suggest that BAP1 loss, potentially through ERV3-16A3_LTR dysregulation, is associated with an IFN response-high epigenetic program.

Whole-exome sequencing reveals genomic landscape of intrahepatic cholangiocarcinoma and identifies SAV1 as a potential driver

Intrahepatic cholangiocarcinoma (ICC) is the second most common primary hepatic malignancy after hepatocellular carcinoma, with poor prognosis and limited treatment options. The genomic features of ICC in Chinese patients remain largely unknown. In this study, we perform deep whole-exome sequencing of 204 Chinese primary ICCs and characterize genomic alterations and clonal evolution, and reveal their associations with patient outcomes. We identify six mutational signatures, including Signatures A and F, which are highly similar to previously described signatures linked to aristolochic acid and aflatoxin exposures, respectively. We also identify 13 significantly mutated genes in the ICC samples, including SAV1. We find that SAV1 was mutated in 2.9% (20/672) of 672 ICC samples. SAV1 mutation is associated with lower SAV1 protein levels, higher rates of tumor recurrence, and shorter overall patient survival. Biofunctional investigations reveal a tumor-suppressor role of SAV1: its inactivation suppresses Hippo signaling, leading to YAP activation, thereby promoting tumor growth and metastasis. Collectively, our results delineate the genomic landscape of Chinese ICCs and identify SAV1 as a potential driver of ICC.

Deciphering the toxicity of polyhexamethylene guanidine phosphate in lung carcinogenesis: Mutational profiles and molecular mechanisms

Polyhexamethylene guanidine (PHMG) is widely utilized in personal hygiene products due to its bactericidal, non-volatile, and hydrophilic properties. However, the long-term toxic effects and underlying mechanisms associated with respiratory exposure to the commonly used form, PHMG phosphate (PHMG-p), are still insufficiently understood. This study aims to elucidate the types of pulmonary lesions and the incidence of lung cancer associated with varying concentrations of PHMG-p and observation periods, along with the molecular mechanisms underlying this relationship. To assess these effects, CT scans and pathological analyses were conducted for up to 54 weeks following initial exposure to PHMG-p. Furthermore, to investigate the underlying causes of pulmonary toxicity, TGF-beta-activated kinase 1 was identified as a PHMG-p-binding protein, and its associated signaling pathways, including necroptosis, apoptosis, and MKK7, were explored. Somatic mutational signature, and gene ontology (GO) analyses were performed to investigate the genetic characteristics of PHMG-p-induced lung carcinogenesis. PHMG-p exposure led to somatic mutations in lung cancer-related genes, including TP53, SOS1, KMT2D, MDM2, ERBB2, SETD2, MET, ARID1A, RBM10, and CDKN2A as well as in genes such as RAB31, WASHC1, DDX11, ECD, STAB2, MUC2, and MUC5AC. The mutated genes were primarily associated with impaired DNA repair mechanisms. GO analysis highlighted the activation of pathways related to cell cycle checkpoints, necroptosis, MAPK, and idiopathic pulmonary fibrosis, while also revealing the suppression of signaling pathways associated with natural killer cells, GADD45, LXR/RXR activation, and IL-15 production. Gain-of-function experiments confirmed the oncogenic roles of PLAU and HMGA2, as well as the tumor-suppressive functions of TBX4 and GPX3. These findings suggest that PHMG-p activates necroptosis and MAPK signaling, increases the frequency of somatic mutations, and inhibits apoptosis, thus fostering an environment conducive to carcinogenesis. This underscores the importance of understanding the potential health risks associated with PHMG-p exposure and provides insights for future research and regulatory considerations regarding the safety of personal hygiene products.

Mutational landscape induced by chronic exposure to environmental PM10 and PM2.5 in A549 lung epithelial cell

Exposure to particulate matter (PM) has been linked to an increased risk of multiple diseases, primarily lung cancer, through various molecular mechanisms. However, the mutagenic potential of PM remains unclear. This study aimed to provide a comprehensive description of genetic mutations and mutagenic signatures resulting from chronic exposure to PM10 or PM2.5. Using whole exome sequencing, we identified driver mutations and mutational signatures in A549 cells, a lung epithelial cell model subjected to weekly exposure to either PM10 or PM2.5, for a period of 28 weeks. The number of single nucleotide variations, insertions, and deletions increased depending on the duration of exposure. PM10 generated the highest number of genomic alterations. Amplifications in SYK (oncogene) and mutations in NCOR1 (tumor suppressor gene) were prevalent in cells exposed to either PM10 or PM2.5; however, other mutations were exclusive, such as TP53 and ANK3 for PM10, and ERCC1 and ERCC2 for PM2.5. Different p53-related signaling pathways were most enriched by driver mutations upon exposure to both PM10 and PM2.5, particularly the glucose deprivation pathway. Exposure to either PM10 or PM2.5 resulted in high frequencies of C > A substitutions and one-base insertions/deletions in microhomology sites. The single-base substitution (SBS) signature SBS05, related to the nucleotide excision DNA repair pathway, contributed the most to both PM10-and PM2.5-exposed cells. The contribution of signature SBS18, related to oxidative stress, was observed in cells exposed to either PM10 or PM2.5, but a greater contribution was observed in PM2.5-exposed cells. In addition, SBS03 and SBS36, which are related to different DNA damage repair mechanisms, were observed more frequently in PM10-exposed cells. We assessed the mutagenic potential of PM10 and PM2.5, as a complete mixture, identifying mutated driver genes and mutational signatures generated by chronic PM exposure, which could contribute to the development of cancer, cardiovascular, and digestive diseases.

Widespread mutagenesis and chromosomal instability shape somatic genomes in systemic sclerosis

Systemic sclerosis is a connective tissue disorder characterized by excessive fibrosis that primarily affects women, and can present as a multisystem pathology. Roughly 4-22% of patients with systemic sclerosis develop cancer, which drastically worsens prognosis. However, the mechanisms underlying systemic sclerosis initiation, propagation, and cancer development are poorly understood. We hypothesize that the inflammation and immune response associated with systemic sclerosis can trigger DNA damage, leading to elevated somatic mutagenesis, a hallmark of pre-cancerous tissues. To test our hypothesis, we culture clonal lineages of fibroblasts from the lung tissues of controls and systemic sclerosis patients and compare their mutation burdens and spectra. We find an overall increase in all major mutation types in systemic sclerosis samples compared to control lung samples, from small-scale events such as single base substitutions and insertions/deletions, to chromosome-level changes, including copy-number changes and structural variants. In the genomes of patients with systemic sclerosis, we find evidence of somatic hypermutation or kategis (typically only seen in cancer genomes), we identify mutation signatures closely resembling the error-prone translesion polymerase Polη activity, and observe an activation-induced deaminase-like mutation signature, which overlaps with genomic regions displaying kataegis.