CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

Hematopoietic stem cell transplantation for purine nucleoside phosphorylase deficiency with two novel mutations: a case report and review of literature

PURPOSE

We report the case of a 6-year-old boy who presented with muscular hypertonia, impaired growth, and recurrent infections, who was diagnosed with purine nucleoside phosphorylase (PNP) deficiency with two novel mutations in the PNP gene. He underwent a hematopoietic stem cell transplantation (HSCT) from an unrelated donor, and we observed the clinical outcome.

METHODS

We retrospectively analyzed the clinical manifestations and outcomes of this patient who underwent HSCT. We analyzed the results of whole exome sequencing (WES) on the patient.

RESULTS

The patient experienced repeated serious respiratory and gastrointestinal infections since birth and presented with neurological symptoms. He was found to have two novel pathogenic mutations in the PNP gene through WES. One hemizygous variant was c.385dup (p.Ile129Asnfs*6) in exon 4. The other was a heterozygous deletion in exon 2-6. He underwent HSCT with clinical improvement.

CONCLUSIONS

We presented a patient with two novel mutations in the PNP gene and clinical improvement following an allo-HSCT.

Clinicopathologic features of histologic transformation in lung adenocarcinoma after treatment with epidermal growth factor receptor-tyrosine kinase inhibitors

BACKGROUND

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) may lead to drug resistance, and the underlying mechanism may involve histologic transformations to small cell carcinoma (SCC), squamous cell carcinoma (SqCC), and sarcomatoid carcinoma (SC). Although there are reports regarding these transformations, comprehensive analyses are limited.

METHODS

A total of 233 patients with primary lung adenocarcinoma treated with EGFR-TKIs were reviewed. Among them, 26 patients (11.1 %) showed histologic transformation.

RESULTS

Eleven patients (42.3 %) showed SCC and SqCC transformations respectively, and four patients (15.4 %) showed SC transformation. The median time from TKI initiation to transformation was 19.8 months (6.8-51.4) for SCC, 45.3 months (2.4-101.5) for SqCC, and 11.8 months (6.8-15.7) for SC. The median overall survival (OS) was 41.8 months (12.5-78.9), 72.6 months (18.8-112.7), and 23.7 months (17.4-34.4), respectively. The survival from transformation was 12.3 months (2.1-28.3), 16.9 months (0.7-43.2), and 11.4 months (1.6-23.5), respectively. The most common mutations were TP53, PTEN, and RB1 in SCC; TP53 and RB1 in SqCC; and TP53 and KMT2D in SC. SC transformation had the worst OS, followed by SCC and SqCC (p < 0.001). This prognosis difference was also reflected in the time to transformation after EGFR-TKI treatment (p = 0.005). However, survival after transformation was not associated with tumor subtypes (p = 0.536).

CONCLUSIONS

The analysis of mutation profiles and survival outcomes revealed that the transformation subtype affects prognosis. Additionally, the time taken to undergo transformation is critical for patient outcomes.

Biopsy-derived organoids in personalised early breast cancer care: Challenges of tumour purity and normal cell overgrowth cap their practical utility

The ability to establish organoids composed exclusively of tumour rather than healthy cells is essential for their implementation into clinical practice. Organoids have recently emerged as a powerful tool to expand patient material in culture and generate modifiable 3D models derived from humans or animal models. For translational research, they enable the creation of model systems for an ever-increasing number of cell types and diseases. And in personalised medicine, they potentially allow for functional drug testing with high predictive power in certain settings. We found that using biopsy material from untreated, early-stage primary breast cancer patients poses significant challenges for consistently culturing tumour cells as organoids. Specifically, we observed frequent outgrowth of genetically normal, non-cancerous epithelial cells. We analysed >100 biopsy samples from early-stage breast cancer and present our large collection of >70 organoid lines. We also show methods of assessing successful tumour cell culture in a time, and cost-efficient manner, proving a high rate (>85%) of normal cell overgrowth in early-stage breast cancer organoids. Finally, we show a number of successful attempts to culture cancer organoids from mastectomy-derived tissue of advanced, metastatic breast cancer. We conclude that the usefulness of organoids from early breast cancer for translational research and personalised medicine, especially guidance of adjuvant or post-surgical maintenance therapy, is strongly limited by the low success rate of culturing cancerous cells under organoid conditions.

Development of a TaqMan-based dosage analysis PCR assay for the molecular diagnosis of 22q11.2 deletion syndrome

A hemizygous 1.5-3.0-Mb microdeletion of human chromosome 22q11.2 with the loss of multiple genes including histone cell cycle regulator (HIRA) causes 22q11.2 deletion syndrome (22q11.2 DS), a common disorder with variable manifestations including congenital malformations affecting the heart, palate and kidneys in association with neurodevelopmental, psychiatric, endocrine and autoimmune abnormalities. The aim of this study was to develop a TaqMan-based dosage analysis PCR (TaqMan qPCR) for use as a rapid, cost-effective test for clinically suspected patients fulfilling previously described criteria for molecular diagnosis of 22q11.2 DS in a lower middle-income country where the cost of testing limits its use in routine clinical practice. Nineteen patients were recruited with informed consent following ethical approval from the Ethics Review Committee, Lady Ridgeway Hospital for Children, Colombo. Dosage analysis of extracted DNA was performed using a TaqMan qPCR assay by amplifying regions within the target (HIRA) and control (testin LIM domain protein (TES)) genes of suspected patient (P) and unaffected person (N) samples. For detection of a deletion, the normalized value (HIRA/TES dosage) of a P sample was compared with that of an N sample. A ratio of P:N of 0.5 confirmed the presence of a deletion while a ratio of 1.0 refuted this. Seven of the 19 patients were found to have a HIRA deletion, confirming the diagnosis of 22q11.2 DS, with these results being in complete agreement with those of fluorescence in situ hybridization (FISH) (performed in nine of the 19 cases) and whole-exome sequencing (all 19 samples tested). This TaqMan qPCR assay was able to reliably distinguish HIRA-deleted cases from non-deleted ones. The assay was both cheaper and faster compared to commercially available alternatives in our setting, including FISH and multiple ligation-dependent probe amplification.

Meningiomas: Sex-specific differences and prognostic implications of a chromosome X loss

BACKGROUND

Meningiomas are the most common primary intracranial tumors in adults. Several studies proposed new stratification systems with a more accurate risk prediction than the WHO grading, eg, based on methylation and copy-number variations (CNVs). Yet, common shortcomings in these analyses are either a lack of stratification by sex of patients or excluding the gonosomes from CNV assessment.

METHODS

Within this study, DNA methylation array data from 7424 meningioma samples as well as targeted sequencing, clinical annotations, and morphology subtyping of 796 samples were examined for differences between females and males regarding mutations, methylation classes, CNVs, and histology.

RESULTS

Meningiomas from females accounted for about 53% of the malignant tumors and present a loss of one X chromosome in 57% of these malignant cases. In the group of benign tumors, females comprised about 75% of the patients. Therein, a loss of one X chromosome was detected in only about 10% of the cases but was associated with a significantly worse progression-free survival.

CONCLUSIONS

Although genomic instability is a common feature of malignant meningiomas, particularly loss of the X chromosome in tumors of female patients in otherwise histologically and molecularly low-risk tumors confers higher risk. Hence, the gonosomal copy-number status can be leveraged for increased diagnostic accuracy.

Role of genomic analysis in the classification of well differentiated hepatocellular lesions

BACKGROUND

The distinction of focal nodular hyperplasia (FNH) and hepatocellular adenoma (HCA) from well-differentiated hepatocellular carcinoma (WD-HCC) in noncirrhotic liver can be challenging. High-grade dysplastic nodule (HGDN) in cirrhosis can have overlapping features with WD-HCC. In some cases, HCA diagnosis is evident but glutamine synthetase (GS) staining is indeterminate for β-catenin activation, which does not allow reliable risk assessment. This study examines the role of genomic analysis in better categorization of WD hepatocellular lesions (WDHL).

DESIGN

Genomic analysis using capture-based NGS assay was done in 23 WDHLs that could not be definitely classified based on morphology, reticulin stain and IHC, and were designated as 'atypical hepatocellular neoplasms' (AHNs). GS staining was classified as diffuse homogeneous (moderate to strong staining in >90 % of tumor cells), diffuse heterogeneous (50-90 %), not diffuse (<50 %) and borderline (not clear if more or less than 50 %).

RESULTS

The genomic profile provided additional information for the diagnosis and/or risk assessment enabling a benign diagnosis in 15/23 cases (66 %) and HCC in 4/23 cases (17 %), while the diagnosis remained as atypical in the remaining 4 cases. Of the 4 cases with final HCC diagnosis, findings were suspicious but not diagnostic based on morphology/IHC; additional changes like TERT promoter mutation (n = 2), AXIN mutation (n = 1), CDKN2A loss (n = 2) and copy number alterations (n = 3) helped to support HCC. Of the 15 cases with a final benign diagnosis, the status of β-catenin activation was unclear based on GS stain in 8 cases, 2 of which showed CTNNB1 exon 7 mutation, 1 showed CTNNB1 exon 8 mutation, while genomic changes in 5 cases did not show any evidence of Wnt activation. FNH-like features were seen in 2 cases, but the genomic changes excluded FNH (CTNNB1 and ARID1A mutation). The final diagnosis was unchanged from the initial diagnosis of AHN in 4/23 cases (17 %) as the molecular findings did not favor HCC.

CONCLUSION

Genomic changes were helpful in characterization of WDHLs, supporting HCC in 17 % of cases and clarifying β-catenin activation status in all 7 cases with borderline GS staining. Genomic changes are not specific but can provide diagnostic clues in selected challenging cases that cannot be classified on morphology and IHC. Given the significant treatment implications of distinguishing between HCC and benign/premalignant entities, routine use of genomic analysis in diagnostically challenging settings should be considered.

Genomic and immune profiling of breast cancer brain metastases

BACKGROUND

Brain metastases (BrM) arising from breast cancer (BC) are an increasing consequence of advanced disease, with up to half of patients with metastatic HER2 + or triple negative BC experiencing central nervous system (CNS) recurrence. The genomic alterations driving CNS recurrence, along with contributions of the immune microenvironment, particularly by intrinsic subtype, remain unclear.

METHODS

We characterized the genomic and immune landscape of BCBrM from a cohort of 42 patients by sequencing whole-exome DNA (WES) and total RNA libraries from frozen and FFPE BrM and FFPE extracranial tumors (ECT). Analyses included PAM50 intrinsic subtypes, somatic mutations, copy number variations (CNV), pathway alterations, immune cell type deconvolution, and associations with clinical outcomes RESULTS: Intrinsic subtype calls were concordant for the majority of BrM-ECT pairs (60%). Across all BrM and ECT samples, the most common somatic gene mutation was TP53 (64%, 30/47). For patients with matched FFPE BrM-FFPE ECT, alterations tended to be conserved across tissue type, although differential somatic mutations and CNV in specific genes were observed. Several genomic pathways were differentially expressed between patient-matched BrM-ECT; MYC targets, DNA damage repair, cholesterol homeostasis, and oxidative phosphorylation were higher in BrM, while immune-related pathways were lower in BrM. Deconvolution of immune populations between BrM-ECT demonstrated activated dendritic cell populations were higher in BrM compared to ECT. Increased expression of several oncogenic preselected pathways in BrM were associated with inferior survival, including DNA damage repair, inflammatory response, and oxidative phosphorylation CONCLUSIONS: Collectively, this study illustrates that while some genomic alterations are shared between BrM and ECT, there are also unique aspects of BrM including somatic mutations, CNV, pathway alterations, and immune landscape. A deeper understanding of differences inherent to BrM will contribute to the development of BrM-tailored therapeutic strategies. Additional analyses are warranted in larger cohorts, particularly with additional matched BrM-ECT.

Whole-exome sequencing provides assessment of homologous recombination deficiency for identification of PARPi-responsive ovarian tumors

BACKGROUND/OBJECTIVES

Homologous recombination repair deficiency (HRD) is frequently detected in gynecological cancers and is associated with sensitivity to poly-ADP ribose polymerase inhibition (PARPi). BRCA1/2 mutations have been approved as biomarkers for PARPi therapy, along with genomic patterns such as genomic loss of heterozygosity (gLOH) and large-scale transitions (LSTs). Clinical applications of various HRD assays are still under investigation. Here we validate the performance of a novel HRD assay based on whole-exome sequencing (WES).

METHODS

WES was used to evaluate gLOH, LST, and BRCA mutations and this data was compared to standard assays. An optimized genomic scar score (GSS) was based on combined gLOH and LST. A comprehensive HRD score was then developed, combining GSS and BRCA status. Survival data from 1661 PARPi-treated ovarian cancer patients was queried to optimize GSS and HRD scores associated with PARPi response.

RESULTS

A comparison of WES results to the OncoScan CNV assay and Myriad MyChoice assay showed high concordance for LOH values and GSS values, respectively. Median overall survival in PARPi-treated patients was 50.8 months for GSS-high, BRCA1/2-mut, 42.7 months for GSS-high, BRCA1/2-WT, and 36.6 months for GSS-low, BRCA1/2-WT patients with significant differences between each group. Combining the BRCA1/2-mut and WT GSS-high groups resulted in a median OS value of 47.8 months, significantly higher than the GSS-low BRCA1/2-WT group.

CONCLUSIONS

The use of a WES assay to assess BRCA results, along with a GSS method incorporating gLOH and LST, produced a HRD test that is predictive for PARPi therapy.

Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants

BACKGROUND

Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type-whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs).

METHODS

We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy.

RESULTS

Applied to 66 human samples Exo-C achieved 100% recall and 73% precision in detecting chromosomal translocations and SNVs. We further benchmarked its performance for inversions and CNVs and demonstrated its utility in detecting mosaic SVs and resolving diagnostically challenging cases.

CONCLUSIONS

Through several case studies, we demonstrate how Exo-C's multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders.

Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia

Pathogenic coding variants have been identified in thousands of genes, yet the mechanisms underlying the incomplete penetrance in individuals carrying these variants are poorly understood. In this study, in a cohort of 2009 craniofacial microsomia (CFM) patients of Chinese ancestry and 2625 Han Chinese controls, we identified multiple predicted pathogenic coding variants in SHROOM3 in both CFM patients and healthy individuals. We found that the penetrance of CFM correlates with specific haplotype combinations containing likely pathogenic-coding SHROOM3 variants and CFM-associated expression quantitative trait loci (eQTLs) of SHROOM3 expression. Further investigations implicate specific eQTL combinations, such as rs1001322 or rs344131, in combination with other significant CFM-associated eQTLs, which we term combined eQTL phenotype modifiers (CePMods). We additionally show that rs344131, located within a regulatory enhancer region of SHROOM3, demonstrates allele-specific effects on enhancer activity and thus impacts expression levels of the associated SHROOM3 allele harboring any rare coding variant. Our findings also suggest that CePMods may serve as pathogenic determinants, even in the absence of rare deleterious coding variants in SHROOM3 This highlights the critical role of allelic expression in determining the penetrance and severity of craniofacial abnormalities, including microtia and facial asymmetry. Additionally, using quantitative phenotyping, we demonstrate that both microtia and facial asymmetry are present in two separate Shroom3 mouse models, the severity of which is dependent on gene dosage. Our study establishes SHROOM3 as a likely pathogenic gene for CFM and demonstrates eQTLs as determinants of modified penetrance in the manifestation of the disease in individuals carrying likely pathogenic rare coding variants.

Clinicopathologic and Molecular Characterization of Gynecologic Carcinosarcomas With a Mesonephric-Like Carcinomatous Component

Carcinosarcoma with a mesonephric-like carcinomatous component (MLCS) is a rare subtype of gynecologic malignancy recently described in the literature. This study aims to expand the genomic characterization of MLCS by performing independent molecular analysis of the carcinomatous and sarcomatous components in a series of MLCS. Eight cases of gynecologic MLCS (endometrial, lower uterine segment, and ovarian) were identified and underwent clinicopathologic evaluation. Genomic DNA extraction and next-generation sequencing (NGS) were performed separately from the carcinomatous and sarcomatous components of 4 tumors, while 2 tumors underwent NGS of combined carcinomatous and sarcomatous components. The average age at diagnosis was 65.6 years (range 50 to 83 years). MLCS patients were diagnosed at FIGO stage I (n=3), stage II (n=2), stage III (n=2), and stage IV (n=1). The carcinomatous and sarcomatous components were observed to harbor the same single nucleotide variations. All cases had less than 10 mutations/Mb and were microsatellites stable. All cases (6/6, 100%) harbored KRAS point mutations in codon 12, including the following variants: p.G12D (n=2), p.G12A (n=2), and p.G12V (n=2). Five cases showed additional alterations in ARID1A (case 1), PTEN (case 2), PIK3CA (case 4), SPOP (case 6), TET1 (case 6), BUB1 (case 7), LYN (case 7) and PTPRD (case 7). The presence of both KRAS and PTEN / PIK3CA alterations suggests a combined endometrioid and mesonephric differentiation in MLCS.

Inborn errors of immunity underlie clonal T cell expansions in large granular lymphocyte leukemia

BACKGROUNDT cell large granular lymphocyte leukemia (T-LGLL) is a lymphoproliferative disorder of cytotoxic T lymphocytes (CTLs), often with gain-of-function STAT3 mutations. T-LGLL represents a unique model for the study of persistent CTL expansions. Albeit autoimmunity is implied, various paradoxical observations led us to investigate whether immunodeficiency traits underpin T-LGLL.METHODSThis is a comprehensive immunogenomic study of 92 consecutive patients from a large T-LGLL cohort with full laboratory-clinical characterization (n = 271). Whole-exome profiling of variants associated with inborn errors of immunity (IEI) and somatic mutations in T cell lymphoid drivers was analyzed. Single-cell RNA-Seq and TCR-Seq in T-LGLL samples and RNA-Seq in T cell cancer cell lines were utilized to establish biological correlations.RESULTSLymphocytopenia and/or hypogammaglobulinemia were identified in 186 of 241 (77%) T-LGLL patients. Genetic screening for IEI revealed 43 rare heterozygous variants in 38 different immune genes in 34 of 92 (36%) patients (vs. 167/63,026 [0.26%] in controls). High-confidence deleterious variants associated with dominant, adult-onset IEIs were detected in 15 of 92 (16%) patients. Carriers showed atypical features otherwise tied to the cryptic IEI, such as earlier onset, lower lymphocyte counts, lower STAT3 mutational rate, and higher proportions of hypogammaglobulinemia and immune cytopenia/bone marrow failure than noncarriers. Somatic mutational landscape, RNA-Seq, and TCR-Seq analyses supported immune imbalance caused by the IEI variants and interactions with somatic mutations in T cell lymphoid drivers.CONCLUSIONSOur findings in T-LGLL reveal that maladaptive CTL expansions may stem from cryptic immunodeficiency traits and open the horizon of IEIs to clonal hematopoiesis and bone marrow failure.FUNDINGNIH; Aplastic Anemia and MDS International Foundation; VeloSano; Edward P. Evans Foundation; Instituto de Salud Carlos III; European Research Council; European Research Area Network on Personalised Medicine; Academy Finland; Cancer Foundation Finland.

Rational Design and Organoid-Based Evaluation of a Cocktail CAR-γδ T Cell Therapy for Heterogeneous Glioblastoma

Various challenges, including tumor heterogeneity and inadequate T cell infiltration, impede the progress of chimeric antigen receptor T cell (CAR-T) therapy for glioblastoma (GBM). To address these obstacles, a multiple step strategy is designed. Initially, literature review and bioinformatics analysis to screen a set of antigens that are heterogeneously expressed in GBM, which are designated as the target-bank, are leveraged. Then, according to the multiplex immunohistochemistry results of each patient's tumor sample, a personalized panel of antigens based on the principle that most cancer cells in tumor tissues can be covered from the target-bank is selected. To target these antigens, Vδ1 T cells are chosen as CAR vehicles because of its high tissue infiltration and off-the-shelf properties, and an optimized protocol for engineering CAR-Vδ1 T cells with high purity and cytotoxicity, low exhaustion, and cytokine release is developed. Next, the specific panel of cocktail CAR-Vδ1 T cells in the GBM organoids that are directly derived from the same patient's tumor is tested. The term "prof" cocktail therapy is coined to describe the approach using precise and rational combination of tumor antigens, organoid-based evaluation, and fitness of Vδ1 T cells. It may accelerate development of effective CAR-T drugs for heterogeneous solid tumors.

Analytical Validation of Next-Generation Sequencing-Based Comprehensive Liquid Biopsy Assay for Therapy Selection

Liquid biopsies are an increasingly important tool for the real-time monitoring of biomarkers, cancer recurrence, and disease burden in oncology practice. Tempus xF+ is a liquid biopsy assay that detects cell-free DNA in blood samples of patients with advanced solid tumors. The xF+ panel covers 523 genes spanning approximately 1.8 Mb of the human genome and can detect single-nucleotide variants and insertions-deletions in 522 genes. It also detects copy number gains in 7 genes and translocations (gene rearrangements) in 10 genes. Furthermore, the larger panel size allows for the calculation of blood tumor mutational burden. This work highlights the analytical validation performed for the xF+ assay, comparing it with a smaller panel liquid biopsy assay, calculating blood tumor mutational burden, and exploring its potential clinical utility.

A Strategy of Assessing Gene Copy Number Differentiation Between Populations Using Ultra-Fast De Novo Assembly of Next-Generation Sequencing Data

Gene duplication and loss play pivotal roles in the evolutionary dynamics of genomes, contributing to species phenotypic diversity and adaptation. However, detecting copy number variations (CNVs) in homoploid populations and newly-diverged species using short reads from next-generation sequencing (NGS) with traditional methods can often be challenging due to uneven read coverage caused by variations in GC content and the presence of repetitive sequences. To address these challenges, we developed a novel pipeline, ST4gCNV, which leverages ultra-fast de novo assemblies of NGS data to detect gene-specific CNVs between populations. The pipeline effectively reduces the variance of read coverage due to technical factors such as GC bias, providing a reliable CNV detection with a minimum sequencing depth of 10. We successfully apply ST4gCNV to the resequencing analysis of homoploid species Nelumbo nucifera and Nelumbo lutea (lotus). We reveal significant CNV-driven differentiation between these species, particularly in genes related to petal colour diversity such as those involved in the anthocyanin pathway. By highlighting the extensive gene duplication and loss events in Nelumbo, our study demonstrates the utility of ST4gCNV in population genomics and underscores its potential of integrating genomic CNV analysis with traditional SNP-based resequencing analysis.

Three-dimensional genome landscape of primary human cancers

Genome conformation underlies transcriptional regulation by distal enhancers, and genomic rearrangements in cancer can alter critical regulatory interactions. Here we profiled the three-dimensional genome architecture and enhancer connectome of 69 tumor samples spanning 15 primary human cancer types from The Cancer Genome Atlas. We discovered the following three archetypes of enhancer usage for over 100 oncogenes across human cancers: static, selective gain or dynamic rewiring. Integrative analyses revealed the enhancer landscape of noncancer cells in the tumor microenvironment for genes related to immune escape. Deep whole-genome sequencing and enhancer connectome mapping provided accurate detection and validation of diverse structural variants across cancer genomes and revealed distinct enhancer rewiring consequences from noncoding point mutations, genomic inversions, translocations and focal amplifications. Extrachromosomal DNA promoted more extensive enhancer rewiring among several types of focal amplification mechanisms. These results suggest a systematic approach to understanding genome topology in cancer etiology and therapy.

Synchronous bilateral Wilms tumors are prone to develop independently and respond differently to preoperative chemotherapy

Wilms tumor (WT) is the most common kidney cancer in infants and young children. The determination of the clonality of bilateral WTs is critical to the treatment, because lineage-independent and metastatic tumors may require different treatment strategies. Here we found synchronous bilateral WT (n = 24 tumors from 12 patients) responded differently to preoperative chemotherapy. Transcriptome, whole-exome and whole-genome analysis (n = 12 tumors from 6 patients) demonstrated that each side of bilateral WT was clonally independent in terms of somatic driver mutations, copy number variations and transcriptomic profile. Molecular timing analysis revealed distinct timing and patterns of chromosomal evolution and mutational processes between the two sides of WT. Mutations in WT1, CTNNB1 and copy-neutral loss of heterozygosity of 11p15.5 provide possible genetic predisposition for the early initiation of bilateral WT. Our results provide comprehensive evidence and new insights regarding the separate initiation and early embryonic development of bilateral WT, which may benefit clinical practices in treating metastatic or refractory bilateral WT.

Establishment of a high-risk pediatric AML-derived cell line YCU-AML2 with genetic and metabolic vulnerabilities

The prognosis of acute myeloid leukemia (AML) with KMT2A::MLLT3 rearrangement and MECOM overexpression and/or KRAS mutation is dismal, and the optimal treatment strategy remains unclear. However, to the best of our knowledge, a suitable model (such as a cell line or its xenograft model) for research on this subtype has not been established. We established a novel AML cell line, YCU-AML2, and its xenograft model harboring KMT2A::MLLT3 rearrangement, MECOM overexpression, and KRAS G12A mutation. YCU-AML2 xenograft mice models developed AML and mimicked the clinical phenotype of the original patient. YCU-AML2 expressed high sensitivity to MEK inhibitors, such as trametinib and selumetinib. Moreover, YCU-AML2 also exhibited high sensitivity to L-asparaginase with glutaminase activity, perhaps because of its reliance on oxidative phosphorylation via glutaminolysis as its main energy source. We believe that the YCU-AML2 cell line and its xenograft model can serve as models to explore the molecular pathogenesis of high-risk AML with KMT2A::MLLT3 rearrangement, MECOM overexpression, and/or KRAS mutation and develop new treatment strategies.

Multi‑omics analysis identifies different molecular subtypes with unique outcomes in early-stage poorly differentiated lung adenocarcinoma

INTRODUCTION

Early-stage poorly differentiated lung adenocarcinoma (LUAD) is plagued by a high risk of postoperative recurrence, and its prognostic heterogeneity complicates treatment and surveillance planning. We conducted this integrative multi-omics study to identify those patients with a truly high risk of adverse outcomes.

METHODS

Whole-exome, RNA and whole methylome sequencing were carried out on 101 treatment-naïve early-stage poorly differentiated LUADs. Integrated analyses were conducted to disclose molecular characteristics and explore molecular subtyping. Functional validation of key molecules was carried out through in vitro and in vivo experiments.

RESULTS

Recurrent tumors exhibited significantly higher ploidy (p = 0.024), the fraction of the genome altered (FGA, p = 0.042), and aneuploidy (p < 0.05) compared to non-recurrent tumors, as well as a higher frequency of CNVs. Additionally, recurrent tumors showed hypomethylation at both the global level and in CpG island regions. Integrative transcriptomic and methylation analyses identified three molecular subtypes (C1, C2, and C3), with the C1 subtype presenting the worst prognosis (p = 0.024). Although frequently mutated genes showed similar mutation frequencies across the three subtypes, the C1 subtype exhibited the highest tumor mutation burden (TMB), mutant-allele tumor heterogeneity (MATH), aneuploidy, and HLA loss of heterozygosity (HLA-LOH), along with relatively lower immune cell infiltration. Furthermore, GINS1 and CPT1C were found to promote LUAD progression, and their high expression correlated with a poor prognosis.

CONCLUSIONS

This multi-omics study identified three integrative subtypes with distinct prognostic implications, paving the way for more precise management and postoperative monitoring of early-stage poorly differentiated LUAD.

MAD::NUT Fusion Sarcoma: A Sarcoma Class With NUTM1, NUTM2A, and NUTM2G Fusions and Possibly Distinctive Subtypes

NUT fusion-associated cancers are heterogeneous and include NUT carcinoma and an emerging group with non-BRD4/BRD3/NSD3 fusion partners. In this study, we characterized 11 tumors harboring MAD::NUT fusions (10/11 in female patients; median age: 48 years; range: 1-67 years), all histologically different from NUT carcinoma. Eight cases were identified via sequencing database review and 3 were diagnosed prospectively. Eight (73%) patients presented with multifocal disease, including 6 with disseminated peritoneal tumors; 3 (27%) presented with solitary colonic, pulmonary, or orbital masses. Nine (82%) tumors harbored NUTM1 fusions, with MXI1 (5/9; 56%), MXD4 (2/9; 22%), and MGA (2/9; 22%). One tumor each harbored MXD4::NUTM2G and MXI1::NUTM2A fusions. The 9 MXD4/MXI1-rearranged sarcomas were high-grade, with epithelioid-to-spindle cell cytomorphology, amphophilic cytoplasm, vesicular nuclei, and prominent nucleoli. Histologic features included infiltrative growth (7/7 assessable tumors), rhabdoid morphology (7/9; 78%), prominent collagen (3/9; 33%), multinucleated tumor cells (2/9; 22%), and myxoid stroma (1/9; 11%). MXD4/MXI1-rearranged sarcomas expressed desmin (3/7; 43%) and keratin(s) (3/7; 43%), and not p63 (6 tumors), CD34 (5 tumors), or S-100 (5 tumors). The adult MGA::NUTM1 fusion sarcoma exhibited some cytologic overlap with MXD4/MXI1-rearranged sarcomas but showed lower grade myxoid spindle cell regions, microcystic spaces, and S-100 expression. The pediatric MGA::NUTM1 fusion sarcoma was low-grade with CD34/S-100 coexpression. Immunohistochemistry demonstrated NUTM1 expression in NUTM1-rearranged sarcomas (5/5), and weak and no expression in NUTM2A- and NUTM2G-rearranged sarcomas, respectively. Gene expression profiling demonstrated sarcomas with MXD4/MXI1::NUTM1/NUTM2A/NUTM2G fusions clustered separately from NUT carcinoma. Follow-up was available for 9 patients (82%; median length: 1.8 years; range: 2 months to 8.2 years). Four of 7 patients with MXD4/MXI1-rearranged sarcomas died of disease (median survival: 1.3 years; range: 5 months to 4.8 years), 1 entered hospice at 2 months, 1 was alive with pericardial masses at 2.8 years, and 1 was alive with no evidence of disease at 8.2 years. The adult with the MGA::NUTM1 fusion sarcoma died of other causes at 4.5 years; the child was alive without disease at 11 months. We conclude that MAD::NUT fusions define a sarcoma class distinct from NUT carcinoma. Among this group, MGA::NUTM1 fusion sarcomas might represent a distinctive subset. NUTM1 immunohistochemistry does not reliably detect NUTM2A/NUTM2G-rearranged sarcomas.

Unusual Autosomal Dominant Inheritance of Oculocutaneous Albinism Type 4 (OCA-4): Clinical and Functional Features From A Chinese Family

Oculocutaneous albinism (OCA) is a complex genetic disorder characterized by reduced or absent pigmentation in the skin, hair, and eyes. Among the eight known subtypes, OCA-4 is caused by a mutation in SLC45A2, which plays a crucial role in melanin biosynthesis. While autosomal recessive inheritance is the most common pattern for all OCA subtypes, autosomal dominant cases are extremely rare. We report three patients from a Chinese family exhibiting autosomal dominant OCA-4. Clinical assessments evaluated pigmentation and ocular features in affected family members. Next-generation sequencing was performed to identify pathogenic variants, and functional studies in MNT-1 cells were performed to explore the variant's biological effects. Patients exhibited mild hypopigmentation and foveal hypoplasia, consistent with the OCA-4 phenotype. Genetic analysis identified a heterozygous c.208T>C (p.Tyr70His) variant in SLC45A2, the same variant that has been previously reported in association with autosomal dominant OCA-4. Functional studies demonstrated that this variant caused protein retention in the endoplasmic reticulum, resulting in reduced melanin production. This family represents the first documented cases of autosomal dominant OCA-4 in the Chinese population and only the second reported worldwide. Our findings confirm that the p.Tyr70His variant causes autosomal dominant OCA-4. This study deepens our understanding of OCA-4's genetic mechanisms and increases the complexity of its inheritance patterns in genetic counseling.

Rapid, Reliable, and Interpretable Copy Number Variant Curation Visualizations for Diagnostic Settings with SeeNV

Copy number variants (CNVs), structural alterations in the genome involving duplication or deletion of DNA segments, are implicated in various health conditions. Despite their clinical significance, accurate identification and interpretation of CNVs remain challenging, especially in the context of whole-exome sequencing (WES), which is commonly used in clinical diagnostic laboratories. Although WES offers economic advantages over whole-genome sequencing, it struggles with CNV detection because of technical noise introduced by laboratory and analytic processes. Manual curation of CNV calls generated by these tools is labor intensive and error prone. To address this, SeeNV, a command-line tool, is introduced to aid manual curation of CNVs at scale. SeeNV is one solution to these issues, developed in collaboration with and used by the Precision Diagnostics Laboratory at Children's Hospital Colorado. SeeNV generates static infographics for each CNV, incorporating sample and cohort sequencing coverage statistics, CNV population frequency, and, more, facilitating rapid and precise assessment. Using CNV calls identified in publicly available WES and whole-genome sequencing samples, users can rapidly and reliably curate CNV calls, needing only 4.3 seconds to curate a call, achieving 0.95 recall (analytical sensitivity) and 0.74 precision (positive predictive value). SeeNV is freely available for download on GitHub.

Clinicopathological and molecular features of so-called low-grade oncocytic fumarate hydratase-deficient renal cell carcinoma: a study of 5 cases

Low-grade oncocytic fumarate hydratase-deficient renal cell carcinoma (FHdRCC), resembling succinate dehydrogenase-deficient RCC morphologically, is a recently described uncommon variant of FHdRCC. We report five additional cases to enhance the understanding of this rare tumor type. These tumors had variably thick fibromuscular capsules with frequent intracapsular invasions and had prominently compact nests and/or tubules. The tumor cells were characterized by abundant dense eosinophilic cytoplasm imparting a ground glass-like appearance and by variable bubbly cytoplasm. Despite a predominantly low histology grade, focal nuclear pleomorphism was observed in two cases. Two cases showed FH negativity and 2SC positivity, while the remaining cases exhibited both FH and 2SC positivity. All cases were positive for PAX8, Vimentin, P504s, and SDHB, but negative for CD117, CA9, CK20, ALK, and cathepsin-K. CK7 and TFE3 positivity were seen in 2 and 4 of 5 cases, respectively. The whole exome sequencing and multiplex PCR-based next generation sequencing identified pathogenic or likely pathogenic FH mutations in three cases and failed in one case showing the FH-negative and 2SC-positive immunophenotype. The remaining case exhibiting both FH and 2SC positivity had a germline FH mutation of uncertain significance and single copy loss of chromosomes 1, 14, and 18. None of three cases who underwent FISH detections had TFE3 translocations. Follow-up time for the 5 cases ranged from 7 to 94 months (median 46 months; mean 52 months). All cases were alive without disease, except for case 4 being alive with a stable contralateral renal mass. While low-grade oncocytic FHdRCC has a relatively better prognosis than conventional FHdRCCs, further research is required to confirm this in the future.

Whole-exome tumor-agnostic ctDNA analysis enhances minimal residual disease detection and reveals relapse mechanisms in localized colon cancer

In stage 2-3 colon cancer (CC), postsurgery circulating tumor DNA (ctDNA) assessment is crucial for guiding adjuvant chemotherapy (ACT) decisions. While existing assays detect ctDNA and help identify high-risk persons with CC for recurrence, their limited sensitivity after surgery poses challenges in deciding on ACT. Additionally, a substantial portion of persons with CC fail to clear ctDNA after ACT, leading to recurrence. In this study, we performed whole-exome sequencing (WES) of ctDNA at different time points in participants with relapsed CC in two independent cohorts, alongside transcriptomic and proteomic analyses of metastases, to enhance comprehension of progression mechanisms. A plasma WES-based tumor-agnostic assay demonstrated higher sensitivity in detecting minimal residual disease (MRD) compared to current assays. Immune evasion appears to be the primary driver of progression in the localized CC setting, indicating the potential efficacy of immunotherapy for microsatellite stability in persons with CC. Organoid modeling further supports the promising potential of targeted therapy in eradicating MRD, surpassing conventional treatments.

Rapid in vitro evolution of flucytosine resistance in Candida auris

The pan-antifungal-resistant pathogen Candida auris has been causing high-mortality infection outbreaks in hospitals and healthcare settings. The prodrug 5-fluorocytosine (5FC) is one of four chemical entities, but its clinical use as an antifungal drug has been limited owing to pronounced resistance. However, antifungal combination therapy with 5FC appears as a promising strategy for treating C. auris infections. Here, we show that a C. auris clinical isolate can rapidly acquire genetic mutations to mount 5FC resistance after only one to two passages under drug selection. We exploit a new bioinformatics workflow to identify genetic polymorphisms from RNA-seq data. Strikingly, we identify several mutations in the FUR1 gene encoding the 5-fluorouracil convertase that normally generates the active drug. A single nonsense mutation truncates the enzyme at residue Q30*, leading to 5FC resistance due to inactive Fur1. Whole-genome sequencing analysis revealed that an indel mutation in FCY2 also contributes to 5FC resistance. Furthermore, at least one out of seven adapted strains acquired enhanced 5FC tolerance without mutations in the 5FC conversion pathway. Thus, we demonstrate that FUR1 mutations are critical drivers of 5FC resistance in C. auris.IMPORTANCECandida auris is a high-priority human fungal pathogen, causing infection outbreaks of high mortality in healthcare settings. Antifungal combination therapy with 5-fluorocytosine (5FC) is one of the emerging approaches in treatment. However, acquired 5FC resistance traits have been a matter of concern. 5FC is taken up by fungal cells via a cytosine permease and further metabolized by a cytosine deaminase to 5-fluorouracil (5FU). 5FU is then converted by the Fur1 uracil phosphoribosyltransferase into a toxic antimetabolite that disrupts fungal RNA and DNA syntheses. Mutations in these proteins are commonly associated with 5FC resistance in fungal species. Here, we show that C. auris can rapidly develop resistance under 5FC selective stress owing to mutational inactivation of Fur1 function. Moreover, other mechanisms that bypass mutations in the 5FC conversion pathway may also contribute to 5FC resistance traits. Finally, we have developed a tailored bioinformatics workflow that facilitates the identification of polymorphisms associated with 5FC resistance in clinical isolates.

Genetic Etiology of Epilepsy: A Retrospective Study From a Single-Center Cohort

Next generation sequencing (NGS) technology has made significant progress in the genetic diagnosis and treatment of epilepsy. However, genetic studies on epilepsy with different etiologies remain relatively limited. In this study, whole-genome or whole-exome sequencing was performed on 158 unrelated patients with epilepsy of various etiologies, and the identified variants were analyzed for their association with 1356 seizure-related genes in the database. Additionally, the pathogenicity or likely pathogenicity of those variants associated with known epilepsy genes was evaluated. The results showed that pathogenic or likely pathogenic variants were detected in 31.65% (50/158) of the patients in our cohort study. Further analysis revealed significant differences in the diagnostic rates among different epilepsy categories: 29.60% (37/125) for idiopathic epilepsy and 39.39% (13/33) for symptomatic epilepsy. Moreover, the genes PRRT2, KMT2C, PRKRA, NOTCH3, NAGLU, and SCN1A were identified as potentially important for epilepsy, suggesting they could become key targets for clinical diagnosis and treatment. In conclusion, NGS technology demonstrates high diagnostic efficiency for epilepsy of different etiologies and highlights significant differences among various types. This provides novel genetic insights for the diagnosis and treatment of epilepsy.

Genetic characteristics associated with isolated Microtia revealed through whole exome sequencing of 201 pedigrees

Microtia is one of the most common congenital craniofacial malformations, characterized by the maldevelopment of the external and middle ear. While numerous genes have been implicated in syndromic forms of microtia, the genetic underpinnings of isolated microtia remain poorly understood. In this study, we conducted whole exome sequencing (WES) on 201 pedigrees with isolated microtia to investigate its genetic basis. Bioinformatics analysis identified 1362 deleterious variants corresponding to 332 candidate genes, including 40 previously associated with microtia-related phenotypes. Among these, variants in FOXI3, the most frequently identified pathogenic gene for isolated microtia so far, were detected. Remarkably, the remaining 39 genes, which have been recognized as pathogenic in syndromes with microtia, are also suggested to play a role in isolated microtia. However, the precise molecular mechanisms by which these genes contribute to microtia remain to be elucidated. Furthermore, through protein-protein interaction network analysis, functional annotation, and zebrafish expression profiling, we identified two novel genes, MCM2 and BDNF, as the most promising contributors to the pathogenesis of isolated microtia. Our findings, based on the largest WES study of isolated microtia pedigrees to date, provide new insights into the genetic architecture of isolated microtia and suggest promising avenues for future research.

Extrachromosomal DNA replication and maintenance couple with DNA damage pathway in tumors

Extrachromosomal DNA (ecDNA) drives the evolution of cancer cells. However, the functional significance of ecDNA and the molecular components involved in its replication and maintenance remain largely unknown. Here, using CRISPR-C technology, we generated ecDNA-carrying (ecDNA+) cell models. By leveraging these models alongside other well-established systems, we demonstrated that ecDNA can replicate and be maintained in ecDNA+ cells. The replication of ecDNA activates the ataxia telangiectasia mutated (ATM)-mediated DNA damage response (DDR) pathway. Topoisomerases, such as TOP1 and TOP2B, play a role in ecDNA replication-induced DNA double-strand breaks (DSBs). A subset of these elevated DSBs persists into the mitotic phase and is primarily repaired by the alternative non-homologous end joining (alt-NHEJ) pathway, which involves POLθ and LIG3. Correspondingly, ecDNA maintenance requires DDR, and inhibiting DDR impairs the circularization of ecDNA. In summary, we demonstrate reciprocal interactions between ecDNA maintenance and DDR, providing new insights into the detection and treatment of ecDNA+ tumors.

Benchmarking mouse contamination removing protocols in patient-derived xenografts genomic profiling

Patient-derived xenograft (PDX) models are widely used in cancer research. Genomic and transcriptomic profiling of PDXs are inevitably contaminated by sequencing reads originated from mouse cells. Here, we examine the impact of mouse read contamination on RNA sequencing (RNAseq), Whole Exome Sequencing (WES), and Whole Genome Sequencing (WGS) data of 21 PDXs. We also systematically benchmark the performance of 12 computational protocols for removing mouse reads from PDXs. We find that mouse read contamination increases expression of immune and stromal related genes, and inflates the number of somatic mutations. However, detection of gene fusions and copy number alterations is minimally affected by mouse read contamination. Using gold standard datasets, we find that pseudo-alignment protocols often demonstrate better prediction performance and computing efficiency. The best performing tool is a relatively new tool Xengsort. Our results emphasize the importance of removing mouse reads from PDXs and the need to adopt new tools in PDX genomic studies.

DeBasher: a flow-based programming bash extension for the implementation of complex and interactive workflows with stateful processes

BACKGROUND

Bioinformatics data analysis faces significant challenges. As data analysis often takes the form of pipelines or workflows, workflow managers (WfMs) have become essential. Data flow programming constitutes the preferred approach in WfMs, enabling parallel processes activated reactively based on input availability. While this paradigm typically follows a linear, acyclic progression, cyclic workflows are sometimes necessary in bioinformatics analyses. These cyclic workflows also present an opportunity to explore workflow interactivity, a feature not widely implemented in existing WfMs.

RESULTS

We propose DeBasher, a tool that adopts the flow-based programming (FBP) paradigm, in which the workflow components are in control of their life cycle and can store state information, allowing the execution of complex workflows that include cycles. DeBasher also incorporates a powerful model of interactivity, where the user can alter the behavior of a running workflow. Additionally, DeBasher allows the user to define triggers so as to initiate the execution of a complete workflow or a part of it. The ability to execute processes with state and in control of their life cycle also has applications in dynamic scheduling tasks. Furthermore, DeBasher presents a series of extra features, including the combination of multiple workflows at runtime through a feature we have called runtime piping, switching to static scheduling to increase scalability, or implementing processes in multiple languages. DeBasher has been successfully used to process 131.7 TB of genomic data by means of a variant calling pipeline.

CONCLUSIONS

DeBasher is an FBP Bash extension that can be useful in a wide range of situations and in particular when implementing complex workflows, workflows with interactivity or triggers, or when a high scalability is required.

Identification of novel TCOF1 mutations in Treacher Collins syndrome and their functional characterization

BACKGROUND

Treacher Collins syndrome (TCS) is a congenital disorder primarily caused by the mutation in the Treacle Ribosome Biogenesis Factor 1 (TCOF1) gene. However, the significance of many TCOF1 mutations remains uncertain.

RESULTS

We report two novel mutations identified in two TCS families and assess their pathogenicity alongside two previously reported mutations. Both novel mutations, c.2115dupG (p.T706DfsTer52) and c.2142+23_2142+52 del (p.A715VfsTer31), result in truncated proteins lacking nuclear location signals (NLSs), which impedes their entry into the nucleus and reduces mRNA expression level. Notably, the mutation c.2142+23_2142+52 del, leading to the retention of a 62 bp intron and disrupting RNA splicing, represents the first documented case of intron retention in TCS patients. Additionally, the previously reported mutation c.136 C> G (p.L46V) hinders protein nuclear location, while mutation c.1719del (p.N574TfsTer22) significantly decreases mRNA levels.

CONCLUSIONS

Our research expands the spectrum of TCOF1 mutations and provides evidence clarifying their pathogenic nature. These findings are crucial for genetic counseling and prenatal diagnosis for TCS patients.

CAN-Scan: A multi-omic phenotype-driven precision oncology platform identifies prognostic biomarkers of therapy response for colorectal cancer

Application of machine learning (ML) on cancer-specific pharmacogenomic datasets shows immense promise for identifying predictive response biomarkers to enable personalized treatment. We introduce CAN-Scan, a precision oncology platform, which applies ML on next-generation pharmacogenomic datasets generated from a freeze-viable biobank of patient-derived primary cell lines (PDCs). These PDCs are screened against 84 Food and Drug Administration (FDA)-approved drugs at clinically relevant doses (Cmax), focusing on colorectal cancer (CRC) as a model system. CAN-Scan uncovers prognostic biomarkers and alternative treatment strategies, particularly for patients unresponsive to first-line chemotherapy. Specifically, it identifies gene expression signatures linked to resistance against 5-fluorouracil (5-FU)-based drugs and a focal copy-number gain on chromosome 7q, harboring critical resistance-associated genes. CAN-Scan-derived response signatures accurately predict clinical outcomes across four independent, ethnically diverse CRC cohorts. Notably, drug-specific ML models reveal regorafenib and vemurafenib as alternative treatments for BRAF-expressing, 5-FU-insensitive CRC. Altogether, this approach demonstrates significant potential in improving biomarker discovery and guiding personalized treatments.

A patient-derived T cell lymphoma biorepository uncovers pathogenetic mechanisms and host-related therapeutic vulnerabilities

Peripheral T cell lymphomas (PTCLs) comprise heterogeneous malignancies with limited therapeutic options. To uncover targetable vulnerabilities, we generate a collection of PTCL patient-derived tumor xenografts (PDXs) retaining histomorphology and molecular donor-tumor features over serial xenografting. PDX demonstrates remarkable heterogeneity, complex intratumor architecture, and stepwise trajectories mimicking primary evolutions. Combining functional transcriptional stratification and multiparametric imaging, we identify four distinct PTCL microenvironment subtypes with prognostic value. Mechanistically, we discover a subset of PTCLs expressing Epstein-Barr virus-specific T cell receptors and uncover the capacity of cancer-associated fibroblasts of counteracting treatments. PDXs' pre-clinical testing captures individual vulnerabilities, mirrors donor patients' clinical responses, and defines effective patient-tailored treatments. Ultimately, we assess the efficacy of CD5KO- and CD30- Chimeric Antigen Receptor T Cells (CD5KO-CART and CD30_CART, respectively), demonstrating their therapeutic potential and the synergistic role of immune checkpoint inhibitors for PTCL treatment. This repository represents a resource for discovering and validating intrinsic and extrinsic factors and improving the selection of drugs/combinations and immune-based therapies.

Neo-adjuvant pembrolizumab in stage IV high-grade serous ovarian cancer: the phase II Neo-Pembro trial

While immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, their efficacy in high-grade serous ovarian cancer (HGSOC) remains limited. Some patients, however, achieve lasting responses, emphasizing the need to understand how tumor microenvironment and molecular characteristics influence ICI response. The phase 2 Neo-Pembro study (NCT03126812) included 33 untreated stage IV HGSOC patients, who were scheduled for 6 cycles of carboplatin-paclitaxel and interval cytoreductive surgery. Pembrolizumab (pembro) was added from cycle two and continued for one year. The primary objective was to assess intratumoral immune activation using multiplexed immunofluorescence and immune-related gene expression. Our findings show immune activation, evidenced by an increase in CD3 + , CD8 + , CD8 + /FOXP3+ ratio, TNF-α and interferon-γ signaling. Treatment was well-tolerated. We observed major pathologic responses in 9/33 patients (27%, 95%CI 14-46), with pathologic response strongly associated with immune activation and OS. At a median follow-up of 52.8 months, 8/9 major responders were alive, with 6 patients recurrence-free. In contrast, 4/24 minor responders survived, including one recurrence-free. ctDNA clearance was observed in all major responders and was associated with prolonged PFS and OS. PD-L1 expression and homologous recombination deficiency were predictive of major response and may serve as biomarkers, warranting further exploration. These results suggest major responders may benefit from neo-adjuvant pembro.

Deep targeted sequencing of circulating tumor DNA to inform treatment in patients with metastatic castration-resistant prostate cancer

BACKGROUND

Intrinsic and acquired resistance to second-generation anti-androgens pose a significant clinical challenge in the treatment of metastatic castration-resistant prostate cancer (mCRPC). Novel biomarkers to predict treatment response and inform alternative treatment options are urgently needed.

METHODS

Deep targeted sequencing, with a prostate cancer-specific gene panel, was performed on circulating tumor DNA (ctDNA) and germline DNA from blood of mCRPC patients recruited in Denmark (n = 53), prior to starting first-line treatment with enzalutamide or abiraterone acetate, and for a subset of patients also at progression (n = 18). Likely clonal hematopoietic variants were filtered out. Genomic findings were correlated to clinical outcomes (PSA progression-free survival (PFS), overall survival (OS)). Intrinsic resistance candidate biomarkers were considered by enrichment analysis of nonresponders vs. responders. Genomic alterations at progression were considered as possible drivers of acquired resistance. Clinical actionability was assessed based on OncoKB and ESCAT.

RESULTS

Somatic alterations in PTEN, cell cycle regulators (CCND1, CDKN1B, CDKN2A, and RB1) and chromatin modulators (CHD1, ARID1A) were associated with significantly shorter PFS and OS, also after adjusting for ctDNA% in multivariate Cox regression analysis. The associations with poorer outcomes for alterations in PTEN and chromatin modulators were validated in an external dataset. Patients with primary resistance to enzalutamide/abiraterone had enrichment for BRAF amplification and CHD1 loss, while responders had enrichment for TMPRSS2 fusions. AR resistance mutations emerged in 22% of patients at progression. These were mutually exclusive with other alterations that may confer resistance (i.e., activating CTNNB1 mutations, combined TP53/RB1 loss). Clinically actionable alterations, primarily in homologous recombination repair genes, were found in 54.7% and 49.0% of patients (OncoKB and ESCAT, respectively), with few additional alterations detected at progression. Level I alterations were identified in 41.5% of patients employing OncoKB, however only in 13.2% based on ESCAT.

CONCLUSIONS

Our study identifies known and novel prognostic and predictive biomarker candidates in patients with mCRPC undergoing first-line treatment with enzalutamide or abiraterone acetate. It further provides real-world evidence of the significant potential of genomic profiling of ctDNA to inform treatment in this setting. Clinical trials are warranted to advance the implementation of ctDNA-based biomarkers into clinical practice.

Effective targeting of PDGFRA-altered high-grade glioma with avapritinib

PDGFRA is crucial to tumorigenesis and frequently genomically altered in high-grade glioma (HGG). In a comprehensive dataset of pediatric HGG (n = 261), we detect PDGFRA mutations and/or amplifications in 15% of cases, suggesting PDGFRA as a therapeutic target. We reveal that the PDGFRA/KIT inhibitor avapritinib shows (1) selectivity for PDGFRA inhibition, (2) distinct patterns of subcellular effects, (3) in vitro and in vivo activity in patient-derived HGG models, and (4) effective blood-brain barrier penetration in mice and humans. Furthermore, we report preliminary clinical real-world experience using avapritinib in pediatric and young adult patients with predominantly recurrent/refractory PDGFRA-altered HGG (n = 8). Our early data demonstrate that avapritinib is well tolerated and results in radiographic response in 3/7 cases, suggesting a potential role for avapritinib in the treatment of HGG with specific PDGFRA alterations. Overall, these translational results underscore the therapeutic potential of PDGFRA inhibition with avapritinib in HGG.

Systematic identification of genomic hotspots for high-yield protein production in CHO cells

The efficient and stable production of therapeutic proteins in Chinese hamster ovary (CHO) cells hinges on robust cell line development (CLD). Traditional methods relying on random transgene integration often result in clonal variability, requiring extensive and resource-intensive screening. To address this limitation, we established a systematic, multiomics-driven framework that integrates 202 RNA-sequencing datasets and whole-genome sequencing data to identify genomic "hotspot" loci for precise and high-yield transgene integration. From an initial pool of 20 candidate loci, 5 top-performing hotspots were validated using site-specific integration in CHO-DG44 cells via the CRISPR/Cas9 system with Recombinase-mediated cassette exchange (RMCE). These genomic hotspots achieved 2.2- to 15.0-fold higher relative specific productivity compared to previously known controls (Fer1L4 and Locus1 sites), across multiple therapeutic proteins, including a lysosomal storage disorder-related enzyme and an Immunoglobulin G (IgG)-related monoclonal antibody (mAb) expression. This study offers a transformative approach to CLD, achieving significant improvements in productivity, genomic stability, and efficiency, as well as paving the way for enhanced biopharmaceutical manufacturing.

hTERT and SV40LgT Renal Cell Lines Adjust Their Transcriptional Responses After Copy Number Changes from the Parent Proximal Tubule Cells

Primary mouse renal proximal tubule epithelial cells (moRPTECs) were immortalized by lentivirus transduction to create hTERT or SV40LgT (LgT) cell lines. Prior work showed a more pronounced injury and repair response in LgT versus hTERT cells after chemical challenge. We hypothesized that unique genomic changes occurred after immortalization, altering critical genes and pathways. RNA-seq profiling and whole-genome sequencing (WGS) of parent, hTERT, and LgT cells showed that 92.5% of the annotated transcripts were shared, suggesting a conserved proximal tubule expression pattern. However, the cell lines exhibited unique transcriptomic and genomic profiles different from the parent cells. Three transcript classes were quite relevant for chemical challenge response-Cyps, ion channels, and metabolic transporters-each important for renal function. A pathway analysis of the hTERT cells suggested alterations in intermediary and energy metabolism. LgT cells exhibited pathway activation in cell cycle and DNA repair that was consistent with replication stress. Genomic karyotyping by combining WGS and RNA-seq data showed increased gene copy numbers in chromosome 5 for LgT cells, while hTERT cells displayed gene copy losses in chromosomes 4 and 9. These data suggest that the exaggerated transcriptional responses of LgT cells versus hTERT cells result from differences in gene copy numbers, replication stress, and the unique selection processes underlying LgT or hTERT immortalization.

Molecular clustering on ctDNA improves the prognostic stratification of patients with DLBCL compared with ctDNA levels

ABSTRACT

Circulating tumor DNA (ctDNA) levels can help predict outcomes in diffuse large B-cell lymphoma (DLBCL), but its integration with DLBCL molecular clusters remains unexplored. Using the LymphGen tool in 77 DLBCL cases with both ctDNA and tissue biopsy, a 95.8% concordance rate in molecular cluster assignment was observed, showing the reproducibility of molecular clustering on ctDNA. A multicenter, prospective cohort of 166 patients with newly diagnosed DLBCL was analyzed for ctDNA levels and molecular clusters using cancer personalized profiling by deep sequencing. Patients with ctDNA levels of <2.5 log10 haploid genome equivalents (hGE)/mL had a 4-year progression-free survival (PFS) and overall survival (OS) of 71.7% and 85.7%, respectively, compared with 50.3% and 61.0% for those with higher ctDNA levels (P = .0018 and P = .0017). Recursive partitioning showed that patients with ctDNA levels of ≥2.5 log10 hGE/mL were further stratified by clusters ST2/BN2. In this group, ST2/BN2 patients associated with a favorable outcome with a 4-year PFS and OS of 87.5% and 100%, respectively, compared to 38.0% and 47.1% for other clusters (P = .003 and P = .001). Combining ctDNA levels and ST2/BN2 clusters improved outcome prediction. Low-risk patients (n = 51), characterized by ctDNA levels of <2.5 log10 hGE/mL and/or BN2/ST2 cluster, had a 4-year PFS and OS of 75.3% and 87.8%, respectively. High-risk patients (n = 115), with ctDNA levels of ≥2.5 log10 hGE/mL and no BN2/ST2 cluster, had a 4-year PFS and OS of 38.0% and 47.1%, respectively. Adding cluster assignment to ctDNA levels improved the model's C statistics (0.63 vs 0.59 for PFS; 0.68 vs 0.63 for OS). Liquid biopsy thus provides a multilayered approach for outcome prediction in DLBCL.

CIT tumor lines: A novel series of immunogenic squamous cell skin carcinoma cell lines derived from chemical carcinogenesis

Immunotherapy is now widely used to treat cancer, but its efficacy in many cancer types remains modest. To overcome current barriers, preclinical mouse models that faithfully recapitulate the diversity of cancer types, tumor genetics, mutation burdens, and neoantigen patterns of human tumors are essential. Currently, there are relatively few transplantable murine models of squamous cell carcinomas (SCC). Here we describe a novel series of 11 skin SCC tumor lines, the Carcinogen-Induced Tumor (CIT) lines, syngeneic to the FVB strain. The CIT lines were established from skin carcinomas induced by DMBA and TPA treatment, and harbor genetic drivers and overall tumor mutational burdens that recapitulate those found across multiple human SCCs. Each CIT line gives rise to tumors with a consistent immune infiltration pattern, ranging from T cell-rich "hot" tumors to T cell-poor "cold" tumors. Hot CIT lines exhibit partial responses to treatment with immune checkpoint inhibitors, and we have identified two neoantigens present in an immunotherapy-responsive CIT line. The CIT lines thus provide a valuable new series of preclinical models for studying anti-tumor immune responses and developing strategies to improve immunotherapy efficacy in SCCs.

Heterozygous deletion of 10q24.31-q24.33- a new syndrome associated with multiple congenital anomalies: case report and literature review

BACKGROUND

Congenital anomalies and neurodevelopmental disorders are complex conditions often requiring comprehensive diagnostic approaches. Next-generation sequencing (NGS), particularly whole-exome sequencing (WES), has greatly improved the detection of pathogenic variants, including copy number variations (CNVs), which account for up to 35% of genetic causes in neurological patients. Combining CNV and single nucleotide variant (SNV) analysis through WES enhances diagnostic accuracy, especially in cases with unclassified congenital anomalies.

CASE PRESENTATION AND LITERATURE REVIEW

This study reports a 14-year-old male patient with multiple congenital anomalies, including hypospadias, complete cleft palate, and recurrent pneumonia. His clinical presentation includes significant physical and intellectual developmental delays, autism-like symptoms, and spastic diplegia. Whole-exome sequencing (WES) was performed due to these complex symptoms, revealing a novel heterozygous deletion on chromosome 10q24.31-q24.33. Laboratory findings indicated agammaglobulinemia, leading to prophylactic antibiotic therapy and immunoglobulin replacement. Additional imaging studies showed cystic malformation of the middle lobe of the right lung, sliding hiatal hernia with prolapse of the gastric mucosa, and brain anomalies consistent with Joubert syndrome.

CONCLUSIONS

This case underscores the importance of genetic analysis in understanding the etiology of congenital anomalies and neurodevelopmental disorders, providing critical insights into the molecular mechanisms driving complex phenotypes. The identified chromosomal deletion contributes to the existing literature on genomic imbalances associated with similar phenotypes.

Analysis of the clinical application value of cfDNA methylation and fragmentation in early diagnosis of esophageal cancer

BACKGROUND

This study explores the clinical value of cfDNA methylation and fragmentation for the early diagnosis of esophageal cancer using liquid biopsy.

METHODS

Whole genome bisulfite sequencing and low-pass whole genome sequencing were utilized to detect cfDNA biomarkers, comparing 30 esophageal cancer patients with 10 healthy controls.

RESULTS

Significant differences in cfDNA methylation and fragmentation were observed between cancerous and non-cancerous samples (p < 0.05). A volcano plot identified 822 differentially methylated markers (817 upregulated, 5 downregulated), with SOX17, SOX1, ZNF382, ZNF667-AS1, and TFPI2 highly associated with esophageal cancer. Fragmentation markers (EDM, FSD, FSR, TFBS, CNV) showed 95 % specificity and sensitivity, with EDM demonstrating the best performance.

CONCLUSION

Our study highlights the clinical potential of cfDNA methylation and fragmentation biomarkers for the early diagnosis of esophageal cancer.

Individualized patient tumor organoids faithfully preserve human brain tumor ecosystems and predict patient response to therapy

Tumor organoids are important tools for cancer research, but current models have drawbacks that limit their applications for predicting response to therapy. Here, we developed a fast, efficient, and complex culture system (IPTO, individualized patient tumor organoid) that accurately recapitulates the cellular and molecular pathology of human brain tumors. Patient-derived tumor explants were cultured in induced pluripotent stem cell (iPSC)-derived cerebral organoids, thus enabling culture of a wide range of human tumors in the central nervous system (CNS), including adult, pediatric, and metastatic brain cancers. Histopathological, genomic, epigenomic, and single-cell RNA sequencing (scRNA-seq) analyses demonstrated that the IPTO model recapitulates cellular heterogeneity and molecular features of original tumors. Crucially, we showed that the IPTO model predicts patient-specific drug responses, including resistance mechanisms, in a prospective patient cohort. Collectively, the IPTO model represents a major breakthrough in preclinical modeling of human cancers, which provides a path toward personalized cancer therapy.

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.

Presence of RB1 or Absence of LRP1B Mutation Predicts Poor Overall Survival in Patients with Gastric Neuroendocrine Carcinoma and Mixed Adenoneuroendocrine Carcinoma

PURPOSE

Neuroendocrine carcinomas (NECs) of the stomach are extremely rare, but fatal. However, our understanding of the genetic alterations in gastric NECs is limited. We aimed to evaluate genomic and clinicopathological characteristics of gastric NECs and mixed adenoneuroendocrine carcinomas (MANECs).

MATERIALS AND METHODS

Fourteen gastric NECs, three gastric MANECs, and 1,381 gastric adenocarcinomas were retrieved from the departmental next-generation sequencing database between 2017 and 2022. Clinicopathological parameters and next-generation sequencing test results were retrospectively collected and reviewed.

RESULTS

Gastric NECs and MANECs frequently harbored alterations of TP53, RB1, SMARCA4, RICTOR, APC, TOP1, SLX4, EGFR, BRCA2, and TERT. In contrast, gastric adenocarcinomas exhibited alterations of TP53, CDH1, LRP1B, ARID1A, ERBB2, GNAS, CCNE1, NOTCH, and MYC. Mutations of AKT3, RB1, and SLX4; amplification of BRCA2 and RICTOR; and deletion of ADAMTS18, DDX11, KLRC3, KRAS, MAX, NFKBIA, NUDT7, and RB1 were significantly more frequent in gastric NECs and MANECs than in gastric adenocarcinomas. The presence of LRP1B mutation was significantly associated with longer overall survival (OS), whereas RB1 mutation and advanced TNM stage were associated with shorter OS.

CONCLUSION

We identified frequently mutated genes and potential predictors of survival in patients with gastric NECs and MANECs.

MYC ecDNA promotes intratumour heterogeneity and plasticity in PDAC

Intratumour heterogeneity and phenotypic plasticity drive tumour progression and therapy resistance1,2. Oncogene dosage variation contributes to cell-state transitions and phenotypic heterogeneity3, thereby providing a substrate for somatic evolution. Nonetheless, the genetic mechanisms underlying phenotypic heterogeneity are still poorly understood. Here we show that extrachromosomal DNA (ecDNA) is a major source of high-level focal amplification in key oncogenes and a major contributor of MYC heterogeneity in pancreatic ductal adenocarcinoma (PDAC). We demonstrate that ecDNAs drive varying levels of MYC dosage, depending on their regulatory landscape, enabling cancer cells to rapidly and reversibly adapt to microenvironmental changes. In the absence of selective pressure, a high ecDNA copy number imposes a substantial fitness cost on PDAC cells. We also show that MYC dosage affects cell morphology and dependence of cancer cells on stromal niche factors. Our work provides a detailed analysis of ecDNAs in PDAC and describes a new genetic mechanism driving MYC heterogeneity in PDAC.

Genetic immune escape in cancer: timing and implications for treatment

Genetic immune escape (GIE) alterations pose a significant challenge in cancer by enabling tumors to evade immune detection. These alterations, which can vary significantly across cancer types, may often arise early in clonal evolution and contribute to malignant transformation. As tumors evolve, GIE alterations are positively selected, allowing immune-resistant clones to proliferate. In addition to genetic changes, the tumor microenvironment (TME) and non-genetic factors such as inflammation, smoking, and environmental exposures play crucial roles in promoting immune evasion. Understanding the timing and mechanisms of GIE, alongside microenvironmental influences, is crucial for improving early detection and developing more effective therapeutic interventions. This review highlights the implications of GIE in cancer development and immunotherapy resistance, and emphasizes the need for integrative approaches.

Establishing a cryopreserved biobank of living tumor tissues for drug sensitivity testing

The cryopreservation of cancer tissues to generate frozen libraries is a common practice used worldwide for storing patient samples for later applications. However, frozen samples stored by existing methods cannot be used for initiating living cell cultures, such as patient-derived tumor organoids (PDOs), which offer great potential for personalized treatment. To overcome this challenge, we developed a novel procedure for culturing PDOs using frozen live tumor tissues. We show that tumor specimens stored using this technique maintain their viability and can be successfully used to generate organoids even after long-term freezing, with an impressive success rate of 95.2 %. Importantly, we found that the structural features, tumor marker expression, and drug responses of organoids derived from frozen tissues are similar to those derived from fresh tissues. Moreover, organoids derived from frozen tissues can be routinely passaged and frozen, making them ideal for high-throughput drug screening at any time. Notably, cryopreserved tumor tissues can also be utilized in air-liquid interface (ALI) culture. This method allows for preserving the original tumor microenvironment, making it an invaluable resource for conducting tests on antitumor drug responses, including immune checkpoint inhibitors (ICIs). This innovation has the potential to enable the identification of potentially effective drugs for patients and facilitate the development of novel therapeutic drugs. Thus, we have established protocols for the long-term cryopreservation of cancer tissues to maintain their viability and microenvironment, which are useful for personalized therapy.

Gastric cancer genomics study using reference human pangenomes

A pangenome is the sum of the genetic information of all individuals in a species or a population. Genomics research has been gradually shifted to a paradigm using a pangenome as the reference. However, in disease genomics study, pangenome-based analysis is still in its infancy. In this study, we introduced a graph-based pangenome GGCPan from 185 patients with gastric cancer. We then systematically compared the cancer genomics study results using GGCPan, a linear pangenome GCPan, and the human reference genome as the reference. For small variant detection and microsatellite instability status identification, there is little difference in using three different genomes. Using GGCPan as the reference had a significant advantage in structural variant identification. A total of 24 candidate gastric cancer driver genes were detected using three different reference genomes, of which eight were common and five were detected only based on pangenomes. Our results showed that disease-specific pangenome as a reference is promising and a whole set of tools are still to be developed or improved for disease genomics study in the pangenome era.

LINC01235 Promotes Clonal Evolution through DNA Replication Licensing-Induced Chromosomal Instability in Breast Cancer

Despite the development of HER2-targeting drugs such as trastuzumab and T-DXd, treatment resistance is a substantial challenge, often leading to relapse and distant metastasis. Tumor heterogeneity in HER2-positive breast cancer drives the evolution of resistant clones following therapeutic stress. However, the targetable drivers of anti-HER2 treatment resistance are not thoroughly identified. This study aims to use neoadjuvant-targeted therapy cohorts and a patient-derived organoid in vitro treatment model to uncover the potential targetable drivers of anti-HER2 treatment resistance. it is found that LINC01235 significantly enhances DNA replication licensing and chromosomal instability, fostering clonal expansion and evolution, and ultimately increasing resistance to therapeutic interventions. LINC01235 regulates global H3K27ac, H3K9ac, and H3K36me3 modifications, promotes H2A.Z expression in regulatory regions, and increases the accessibility of DNA licensing factors to their promoter regions. XRCC5 is identified as a key component for maintaining genomic stability, crucial for LINC01235's role in replication licensing. Furthermore, therapeutic strategies targeting LINC01235, including the use of antisense oligonucleotides or ATR inhibitors, which showed promise in overcoming treatment resistance are explored. These findings underscore the pivotal role of LINC01235 in driving resistance mechanisms and highlight novel avenues for targeted therapies to improve the outcomes of patients with HER2-positive breast cancer.