Genome Analysis in Sick Neonates and Infants: High-yield Phenotypes and Contribution of Small Copy Number Variations.

OBJECTIVE: To delineate the diagnostic efficacy of medical exome, whole exome, and whole genome sequencing according to primary symptoms, the contribution of small copy number variations, and the impact of molecular diagnosis on clinical management. STUDY DESIGN: This was a prospective study of 17 tertiary care centers in Japan, conducted between April 2019 and March 2021. Critically ill neonates and infants less than 6 months of age were recruited in neonatal intensive care units and in outpatient clinics. The patients underwent medical exome, whole exome, or whole genome sequencing as the first tier of testing. Patients with negative results after medical exome or whole exome sequencing subsequently underwent whole genome sequencing. The impact of molecular diagnosis on clinical management was evaluated through contacting primary care physicians. RESULTS: Of the 85 patients, 41 (48%) had positive results. Based on the primary symptoms, patients with metabolic phenotypes had the highest diagnostic yield (67%, 4/6 patients), followed by renal (60%, 3/5 patients), and neurologic phenotypes (58%, 14/24 patients). Among them, 4 patients had pathogenic small copy number variations identified using whole genome sequencing. In the 41 patients with a molecular diagnosis, 20 (49%) had changes in clinical management. CONCLUSIONS: Genome analysis for critically ill neonates and infants had a high diagnostic yield for metabolic, renal, and neurologic phenotypes. Small copy number variations detected using whole genome sequencing contributed to the overall molecular diagnosis in 5% of all the patients. The resulting molecular diagnoses had a significant impact on clinical management.

Highly recurrent H3F3A mutations with additional epigenetic regulator alterations in giant cell tumor of bone.

Recurrent H3F3A and IDH2 mutations have been reported in giant cell tumor of bone (GCTB). However, the reported incidences have varied, and other molecular genetic alterations have not been identified due to the small number of cases analyzed with comprehensive methods. Moreover, the relative sensitivities of Sanger sequencing and next-generation sequencing (NGS) for the detection of H3F3A mutations in DNA extracted from archival formalin-fixed paraffin-embedded (FFPE) samples for clinical diagnosis have not been assessed. To address these issues, we conducted whole-exome sequencing of 7 GCTBs and integrated the previously published genomic sequencing data of 6 GCTBs. We subsequently performed targeted sequencing of an additional 39 GCTBs, including 2 atypical cases and an extremely rare case of primary malignant transformation of GCTB. We also evaluated the sensitivity of Sanger sequencing for detecting H3F3A mutations in FFPE samples that are usually used for clinical diagnosis. H3F3A glycine hotspot mutations were the most frequently detected mutations (96%) in the 52 GCTBs by NGS. Of the 50 hotspot mutations, p.G34W was observed in 48 cases and p.G34L/G34R was detected in one. One of two atypical GCTB cases with wild-type H3F3A had a H3F3B mutation (p.G34V). Other mutated genes were not recurrent. Sanger sequencing did not detect H3F3A mutations in 10 of 15 H3F3A NGS mutation-positive FFPE samples. In conclusion, we confirmed that H3F3A is the most frequently mutated GCTB driver gene, and that H3F3A mutations are not present in atypical GCTBs. Sanger sequencing was much less sensitive than targeted NGS for detecting H3F3A mutations in FFPE samples.

Comprehensive mutation profiling of mucinous gastric carcinoma.

Mucinous gastric carcinoma (MGC) is a unique subtype of gastric cancer with a poor survival outcome. Comprehensive molecular profiles and putative therapeutic targets of MGC remain undetermined. We subjected 16 tumour-normal tissue pairs to whole-exome sequencing (WES) and an expanded set of 52 tumour-normal tissue pairs to subsequent targeted sequencing. The latter focused on 114 genes identified by WES. Twenty-two histologically differentiated MGCs (D-MGCs) and 46 undifferentiated MGCs (U-MGCs) were analysed. Chromatin modifier genes, including ARID1A (21%), MLL2 (19%), MLL3 (15%), and KDM6A (7%), were frequently mutated (47%) in MGC. We also identified mutations in potential therapeutic target genes, including MTOR (9%), BRCA2 (9%), BRCA1 (7%), and ERBB3 (6%). RHOA mutation was detected only in 4% of U-MGCs and in no D-MGCs. MYH9 was recurrently (13%) mutated in MGC, with all these being of the U-MGC subtype (p = 0.023). Three U-MGCs harboured MYH9 nonsense mutations. MYH9 knockdown enhanced cell migration and induced intracytoplasmic mucin and cellular elongation. BCOR mutation was associated with improved survival. In U-MGCs, the MLH1 expression status and combined mutation status (TP53/BCL11B or TP53/MLL2) were prognostic factors. A comparative analysis of driver genes revealed that the mutation profile of D-MGC was similar to that of intestinal-type gastric cancer, whereas U-MGC was a distinct entity, harbouring a different mutational profile to intestinal- and diffuse-type gastric cancers. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Comparative Analysis of Site-Specific N-glycosylation of LAMP1 from Breast Cancer Tissues.

Glycosylation changes in cancer proteins have been associated with malignant transformation. However, techniques for analyzing site-specific glycosylation changes in target proteins obtained from clinical tissue samples are insufficient. To overcome these problems, we developed a targeted N-glycoproteomic approach consisting of immunoprecipitation, glycopeptide enrichment, LC/MS/MS and structural assignment using commercially available analytical software followed by manual confirmation. This approach was applied to the comparative site-specific glycosylation analysis of lysosome-associated membrane glycoprotein 1 (LAMP1) between breast cancer (BC) tumors and normal tissues adjacent to tumors. Extensive determination of glycan heterogeneity from four N-glycosylation sites (Asn84/103/249/261) in LAMP1 identified 262 glycoforms and revealed remarkable diversity in tumor glycan structures. A significant increase in N-glycoforms with multiple fucoses and sialic acids at Asn84/249 and high-mannose-type glycans at Asn103/261 were observed in the tumor. Principal component analysis revealed that tumors of different subtypes have independent distributions. This approach enables site-specific glycopeptide analysis of target glycoprotein in breast cancer tissue and become a powerful tool for characterizing tumors with different pathological features by their glycan profiles.

Comprehensive Membrane N-Glycoproteomics Using Human Breast Cancer Cell Line Pairs.

Aberrant glycosylation of membrane proteins is a hallmark of cancer and a useful molecular marker for the diagnosis of breast cancer (BC). However, the molecular mechanisms by which altered glycosylation affects the malignant transformations associated with BC are poorly understood. Accordingly, we performed comparative membrane N-glycoproteomics using the human BC cell line pair, Hs578T, and its syngeneic normal cell line, Hs578Bst. A total of 359 N-glycoforms derived from 113 proteins were identified in both cell lines, of which 27 were found only in Hs578T cells. Significant changes in N-glycosylation were found in the lysosome-associated membrane protein 1 (LAMP1), the integrin family, and laminin. Confocal immunofluorescence microscopy images revealed the accumulation of lysosomes in the perinuclear space in cancer cells, which could be associated with marked changes in LAMP1 glycosylation, such as a decreased level of polylactosamine chains. Overall, the alterations in glycosylation may be involved in changes in the adhesion and degradation of BC cells.

Targeted O-glycoproteomics for the development of diagnostic markers for advanced colorectal cancer.

Aberrant glycosylation is a prominent feature of cancer, that can be used as targets to improve the existing cancer biomarkers, and help to assess metastasis risks, and therapeutic effects. We developed a targeted O-glycoproteomics method using serum specimens, and evaluated its utility in identifying advanced colorectal cancer (CRC) markers. To this end, we combined consecutive lectin affinity purification using Maclura pomifera lectin (MPL), jacalin, and Sambucus nigra lectin, which have affinities for the following O-glycans, that have received attention as cancer-related antigens, Tn (GalNAc-Ser/Thr), Sialyl Tn (Siaα2-6GalNAc-Ser/Thr), T (Galß1-3GalNAc-Ser/Thr), Sialyl T (Siaα2-3Galß1-GalNAc-Ser/Thr), and di-Sialyl T (Siaα2-3Galß1-3[Siaα2-6] GalNAc-Ser/Thr), with a unique O-glycoproteomics approach. A total of 2,068 O-glycoforms derived from 265 proteins were identified in healthy individuals and patients with advanced CRC, of which 44 CRC-specific O-glycoforms were extracted. Particularly, five glycoproteins with T, Sialyl T, and di-Sialyl T antigens in specific peptide regions were evaluated quantitatively and statistically. We found that fibulin-2 (FBLN2) (aa330-349)/T antigen (area under the curve [AUC] = 0.92); macrophage colony-stimulating factor 1 (CSF1) (aa370-395)/(T + di-Sialyl T) (AUC = 0.94); macrophage mannose receptor 1 (MRC1) (aa1083-1101 and aa1215-1229)/T (AUC = 0.96 and 0.99); fibrinogen alpha chain (FGA) (aa354-367, aa511-527 and aa559-573)/Sialyl T (AUC = 0.98, 0.90 and 0.94); and complement component C7 (C7) (aa692-701)/di-Sialyl T (AUC = 1.00), can have high diagnostic efficacy to strategically predict advanced CRC groups. Hence, they could be promising markers for detection of advanced CRC, and provide new clinical test indicators along with lectins, such as MPL and jacalin. Our O-glycoproteomics platform provides a novel tool and resource, for researchers and clinicians seeking to better understand and treat advanced CRC.

Non-Obese Type 2 Diabetes with a History of Being an Extremely Preterm Small-for-Gestational-Age Infant without Early Adiposity Rebound.

Adiposity rebound (AR), which is defined as a situation in which the body mass index (BMI) starts to increase after infancy, is a predictive marker of future development of type 2 diabetes. The patient was a 20-year-old male. He was born at 28 gestational weeks with a birthweight of 642 g (-3.20 standard deviation, small-for-gestational age [SGA]). AR during early childhood or obesity in later childhood was not observed. At the onset of type 2 diabetes (20 years of age), his BMI, body fat percentage, and body fat mass were within normal ranges (20.4, 18.4% and 10.8 kg, respectively). However, his muscle mass was 44.7 kg, with low muscle mass of the trunk and upper limbs, which was lower than the standard reference, indicating that myogenic insulin resistance was involved in the development of non-obese type 2 diabetes. This case report describes a patient with no presentation of AR and obesity during childhood, who was born extremely preterm SGA, developed non-obese type 2 diabetes with low muscle mass. We suggest that patients born extremely preterm SGA should be carefully observed for the development of type 2 diabetes, even if they did not have AR in early childhood or had not become obese.

Cranial shapes of Japanese preterm infants at one month of age using a three-dimensional scanner.

BACKGROUND: Recently, cranial shape measurements of preterm infants have been performed using handheld three-dimensional (3D) scanners and can now be objectively quantified. AIMS: To measure the cranial shapes of Japanese preterm infants at one month of age using a 3D scanner, compare these values with those of healthy term infants, and examine the risk factors for dolichocephaly. STUDY DESIGN: A multicenter, retrospective cohort study. SUBJECTS: Preterm infants born at <37 weeks of gestation and staying in the neonatal intensive care unit or visiting an outpatient clinic for a one-month checkup between April 2020 and March 2022. OUTCOME MEASURES: A 3D scanner was used to quantify cranial shape. Comparison was made with full-term, one-month-old infants. RESULTS: Ninety-four preterm infants (42 boys) and 165 full-term infants were enrolled. Preterm infants had a significantly lower cephalic index (77.9% and 85.0%, p < 0.01) and a higher incidence of dolichocephaly (54.3% and 13.3%, p < 0.01) compared to term infants. No significant difference in incidence of deformational plagiocephaly was found between the groups (41.5% vs. 47.3%, p = 0.44). The risk of dolichocephaly was significantly higher for female sex (odds ratio [OR], 3.32; 95% confidence interval, 1.30-8.50), cesarean section (OR, 4.07; 95% confidence interval, 1.23-13.5), and use of mechanical ventilation (OR, 4.66; 95% confidence interval, 1.09-20.0). CONCLUSIONS: Japanese preterm infants at the first month of life had longer heads than full-term infants; the risk factors identified were female sex, cesarean section, and use of mechanical ventilation.

Novel Physique Index for the Screening of Skeletal Dysplasia at Birth.

This study aimed to devise a novel physique index and investigate its accuracy in identifying newborns with skeletal dysplasia in comparison with head circumference (HC)/height (HT) ratio. The birth weight (W), HT, and HC at birth of 1500 newborns were retrospectively collected. The linear regression equations and coefficients of determination (R2) were determined. The formulated equation was corrected by the mean weight for gestational age at birth (Wcorr) as a novel physique index for screening skeletal dysplasia. The index accuracy was assessed using receiver operating characteristic (ROC) curves in 11 newborns by fetal ultrasound and compared with that of the HC/HT ratio. The R2 values between W and HT, (HT)2, and (HT) 3 were 0.978, 0.990, and 0.993, respectively. Those between W and HC, (HC)2, and (HC)3 were 0.974, 0.984, and 0.988, respectively. W/Wcorr × (HC/HT)3 was used as a novel physique index. Seven newborns had skeletal dysplasia. Our novel physique index had a higher area under the curve (AUC), sensitivity, and specificity than the HC/HT ratio (AUC: 1.00 vs. 0.86, sensitivity: 1.00 vs. 0.86, and specificity: 1.00 vs. 0.75, respectively). Our novel physique index was more accurate than HC/HT ratio and has the potential to accurately identify newborns with skeletal dysplasia.

Epigenetic landscape influences the liver cancer genome architecture.

The accumulations of different types of genetic alterations such as nucleotide substitutions, structural rearrangements and viral genome integrations and epigenetic alterations contribute to carcinogenesis. Here, we report correlation between the occurrence of epigenetic features and genetic aberrations by whole-genome bisulfite, whole-genome shotgun, long-read, and virus capture sequencing of 373 liver cancers. Somatic substitutions and rearrangement breakpoints are enriched in tumor-specific hypo-methylated regions with inactive chromatin marks and actively transcribed highly methylated regions in the cancer genome. Individual mutation signatures depend on chromatin status, especially, signatures with a higher transcriptional strand bias occur within active chromatic areas. Hepatitis B virus (HBV) integration sites are frequently detected within inactive chromatin regions in cancer cells, as a consequence of negative selection for integrations in active chromatin regions. Ultra-high structural instability and preserved unmethylation of integrated HBV genomes are observed. We conclude that both precancerous and somatic epigenetic features contribute to the cancer genome architecture.

Tubular Dysfunction Mimicking Dent's Disease in 2 Infants Born with Extremely Low Birth Weight.

Two preterm infants, with extremely low birth weight born at gestational weeks 24 and 25, showed generalized proximal tubular dysfunction during their stay in the neonatal intensive care unit, including glucosuria, low molecular weight proteinuria, phosphaturia, uricosuria, enzymuria (elevated urine N-acetyl-ß-D-glucosaminidase), panaminoaciduria, and hypercalciuria, associated with renal calcification. Renal tubular acidosis was not present in either patient. DNA mutation analysis for Dent's disease, performed in patient 1, was negative. Although both patients had rickets of prematurity, tubular dysfunction persisted after its resolution. Patient 2, who had severe chronic lung disease, also had elevated serum creatinine, proteinuria, and hypertension, suggesting glomerular damage. In patient 1, low molecular weight proteinuria, enzymuria, panaminoaciduria, hypercalciuria, and renal calcification were still present at the age of 8 years. In patient 2, tubular dysfunction resolved except for ß2 microglobulinuria at the age of 5 years. While a reduced nephron number resulting in focal segmental glomerulosclerosis is well-known, generalized proximal tubular dysfunction can also occur in infants born preterm and/or with extremely low birth weight.

Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer.

Liver cancer, which is most often associated with virus infection, is prevalent worldwide, and its underlying etiology and genomic structure are heterogeneous. Here we provide a whole-genome landscape of somatic alterations in 300 liver cancers from Japanese individuals. Our comprehensive analysis identified point mutations, structural variations (STVs), and virus integrations, in noncoding and coding regions. We discovered mutational signatures related to liver carcinogenesis and recurrently mutated coding and noncoding regions, such as long intergenic noncoding RNA genes (NEAT1 and MALAT1), promoters, CTCF-binding sites, and regulatory regions. STV analysis found a significant association with replication timing and identified known (CDKN2A, CCND1, APC, and TERT) and new (ASH1L, NCOR1, and MACROD2) cancer-related genes that were recurrently affected by STVs, leading to altered expression. These results emphasize the value of whole-genome sequencing analysis in discovering cancer driver mutations and understanding comprehensive molecular profiles of liver cancer, especially with regard to STVs and noncoding mutations.

Genomic spectra of biliary tract cancer.

The incidence of biliary tract cancer (BTC), including intrahepatic (ICC) and extrahepatic (ECC) cholangiocarcinoma and gallbladder cancer, has increased globally; however, no effective targeted molecular therapies have been approved at the present time. Here we molecularly characterized 260 BTCs and uncovered spectra of genomic alterations that included new potential therapeutic targets. Gradient spectra of mutational signatures with a higher burden of the APOBEC-associated mutation signature were observed in gallbladder cancer and ECC. Thirty-two significantly altered genes, including ELF3, were identified, and nearly 40% of cases harbored targetable genetic alterations. Gene fusions involving FGFR2 and PRKACA or PRKACB preferentially occurred in ICC and ECC, respectively, and the subtype-associated prevalence of actionable growth factor-mediated signals was noteworthy. The subgroup with the poorest prognosis had significant enrichment of hypermutated tumors and a characteristic elevation in the expression of immune checkpoint molecules. Accordingly, immune-modulating therapies might also be potentially promising options for these patients.

Trans-ancestry mutational landscape of hepatocellular carcinoma genomes.

Diverse epidemiological factors are associated with hepatocellular carcinoma (HCC) prevalence in different populations. However, the global landscape of the genetic changes in HCC genomes underpinning different epidemiological and ancestral backgrounds still remains uncharted. Here a collection of data from 503 liver cancer genomes from different populations uncovered 30 candidate driver genes and 11 core pathway modules. Furthermore, a collaboration of two large-scale cancer genome projects comparatively analyzed the trans-ancestry substitution signatures in 608 liver cancer cases and identified unique mutational signatures that predominantly contribute to Asian cases. This work elucidates previously unexplored ancestry-associated mutational processes in HCC development. A combination of hotspot TERT promoter mutation, TERT focal amplification and viral genome integration occurs in more than 68% of cases, implicating TERT as a central and ancestry-independent node of hepatocarcinogenesis. Newly identified alterations in genes encoding metabolic enzymes, chromatin remodelers and a high proportion of mTOR pathway activations offer potential therapeutic and diagnostic opportunities.