Concurrent DNA Copy‐Number Alterations and Mutations in Genes Related to Maintenance of Genome Stability in Uninvolved Mammary Glandular Tissue from Breast Cancer Patients

Somatic mosaicism for DNA copy‐number alterations (SMC‐CNAs) is defined as gain or loss of chromosomal segments in somatic cells within a single organism. As cells harboring SMC‐CNAs can undergo clonal expansion, it has been proposed that SMC‐CNAs may contribute to the predisposition of these cells to genetic disease including cancer. Herein, the gross genomic alterations (>500 kbp) were characterized in uninvolved mammary glandular tissue from 59 breast cancer patients and matched samples of primary tumors and lymph node metastases. Array‐based comparative genomic hybridization showed 10% (6/59) of patients harbored one to 359 large SMC‐CNAs (mean: 1,328 kbp; median: 961 kbp) in a substantial portion of glandular tissue cells, distal from the primary tumor site. SMC‐CNAs were partially recurrent in tumors, albeit with considerable contribution of stochastic SMC‐CNAs indicating genomic destabilization. Targeted resequencing of 301 known predisposition and somatic driver loci revealed mutations and rare variants in genes related to maintenance of genomic integrity: BRCA1 (p.Gln1756Profs*74, p.Arg504Cys), BRCA2 (p.Asn3124Ile), NCOR1 (p.Pro1570Glnfs*45), PALB2 (p.Ser500Pro), and TP53 (p.Arg306*). Co‐occurrence of gross SMC‐CNAs along with point mutations or rare variants in genes responsible for safeguarding genomic integrity highlights the temporal and spatial neoplastic potential of uninvolved glandular tissue in breast cancer patients.     

BRCA1 Mutations in Familial Ovarian Cancer

BRCA1 mutation research in ovarian and breast cancer 17q21-linked families has yielded a large number of germline sequence variations. Somatic mutations have been uncommonly reported. We screened 81 probands with primary ovarian, peritoneal, or fallopian tube carcinoma for BRCA1 mutations. The study group was intentionally biased by the inclusion of 29 probands with a family history of ovarian and/or breast carcinoma, 13 probands diagnosed on or before age 45, seven individuals with a metachronous breast cancer and 51 tumors with BRCA1 LOH. Tumor and/or germline DNA was screened by modified techniques of single-strand confirmation polymorphism analysis, and abnormal banding patterns were sequenced to confirm mutations. Twenty-one (25.9%) BRCA1 sequence variations were identified. Eight mutations were somatic including seven null mutations. Apart from classical hereditary ovarian/breast cancer, a family history of ovarian/breast cancer defines a subset of ovarian cancer individuals with a significant likelihood of either a germline or a somatic BRCA1 gene sequence variation.     

Germline and somatic polymerase ϵ and δ mutations define a new class of hypermutated colorectal and endometrial cancers

Polymerases ? and δ are the main enzymes that replicate eukaryotic DNA. Accurate replication occurs through Watson–Crick base pairing and also through the action of the polymerases' exonuclease (proofreading) domains. We have recently shown that germline exonuclease domain mutations (EDMs) of POLE and POLD1 confer a high risk of multiple colorectal adenomas and carcinoma (CRC). POLD1 mutations also predispose to endometrial cancer (EC). These mutations are associated with high penetrance and dominant inheritance, although the phenotype can be variable. We have named the condition polymerase proofreading‐associated polyposis (PPAP). Somatic POLE EDMs have also been found in sporadic CRCs and ECs, although very few somatic POLD1 EDMs have been detected. Both the germline and the somatic DNA polymerase EDMs cause an ‘ultramutated’, apparently microsatellite‐stable, type of cancer, sometimes leading to over a million base substitutions per tumour. Here, we present the evidence for POLE and POLD1 as important contributors to the pathogenesis of CRC and EC, and highlight some of the key questions in this emerging field. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.     

Mitochondrial DNA variants in inclusion body myositis characterized by deep sequencing

Muscle pathology in inclusion body myositis (IBM) typically includes inflammatory cell infiltration, muscle fibers with rimmed vacuoles and cytochrome c oxidase (COX)‐deficient fibers. Previous studies have revealed clonal expansion of large mitochondrial DNA (mtDNA) deletions in the COX‐deficient muscle fibers. Technical limitations have prevented complete investigations of the mtDNA deletions and other mtDNA variants. Detailed characterization by deep sequencing of mtDNA in muscle samples from 21 IBM patients and 10 age‐matched controls was performed after whole genome sequencing with a mean depth of mtDNA coverage of 46,000x. Multiple large mtDNA deletions and duplications were identified in all IBM and control muscle samples. In general, the IBM muscles demonstrated a larger number of deletions and duplications with a mean heteroplasmy level of 10% (range 1%‐35%) compared to controls (1%, range 0.2%‐3%). There was also a small increase in the number of somatic single nucleotide variants in IBM muscle. More than 200 rearrangements were recurrent in at least two or more IBM muscles while 26 were found in both IBM and control muscles. The deletions and duplications, with a high recurrence rate, were mainly observed in three mtDNA regions, m.534‐4429, m.6330‐13993, and m.8636‐16072, where some were flanked by repetitive sequences. The mtDNA copy number in IBM muscle was reduced to 42% of controls. Immunohistochemical and western blot analyses of IBM muscle revealed combined complex I and complex IV deficiency affecting the COX‐deficient fibers. In conclusion, deep sequencing and quantitation of mtDNA variants revealed that IBM muscles had markedly increased levels of large deletions and duplications, and there were also indications of increased somatic single nucleotide variants and reduced mtDNA copy numbers compared to age‐matched controls. The distribution and type of variants were similar in IBM muscle and controls indicating an accelerated aging process in IBM muscle, possibly associated with chronic inflammation.     

Clinical Implications of Microsatellite Instability in T1 Colorectal Cancer

Purpose

The estimation of regional lymph node metastasis (LNM) risk in T1 colorectal cancer is based on histologic examination and imaging of the primary tumor. High-frequency microsatellite instability (MSI-H) is likely to decrease the possibility of metastasis to either regional lymph nodes or distant organs in colorectal cancers. This study evaluated the clinical implications of MSI in T1 colorectal cancer with emphasis on the usefulness of MSI as a predictive factor for regional LNM.

Materials and Methods

A total of 133 patients who underwent radical resection for T1 colorectal cancer were included. Genomic DNA was extracted from normal and tumor tissues and amplified by polymerase chain reaction (PCR). Five microsatellite markers, BAT-25, BAT-26, D2S123, D5S346, and D17S250, were used. MSI and clinicopathological parameters were evaluated as potential predictors of LNM using univariate and multivariate analyses.

Results

Among 133 T1 colorectal cancer patients, MSI-H, low-frequency microsatellite instability (MSI-L), and microsatellite stable (MSS) colorectal cancers accounted for 7.5%, 6%, and 86.5%, respectively. MSI-H tumors showed a female predominance, a proximal location and more retrieved lymph nodes. Twenty-two patients (16.5%) had regional LNM. Lymphovascular invasion and depth of invasion were significantly associated with LNM. There was no LNM in 10 MSI-H patients; however, MSI status was not significantly correlated with LNM. Disease-free survival did not differ between patients with MSI-H and those with MSI-L/MSS.

Conclusion

MSI status could serve as a negative predictive factor in estimating LNM in T1 colorectal cancer, given that LNM was not detected in MSI-H patients. However, validation of our result in a different cohort is necessary.     

结,直肠癌细胞核DNA含量的MSP分析研究

用显微分光光度计检测64例结、直肠癌及其对照肠粘膜细胞核DNA含量,并行细胞核DNA含量分布直方图型分析。淋巴细胞和对照肠粘膜细胞核DNA含量直方图属Ⅰ型。64例结、直肠癌中,56例(87.50%)DNA直方图为Ⅱ～Ⅳ型。与对照肠粘膜细胞比较,结、直肠癌细胞核平均DNA含量、平均核面积和>2C DNA含量的细胞百分率以及各项数值的标准差均明显增加。肠癌细胞核DNA含量直方图与Dukes’分期和分化程度无关。     

原代癌相关成纤维细胞和正常成纤维细胞特征比较及对结直肠癌细胞EMT影响

目的：观察原代癌相关成纤维细胞（ cancer associated fibroblasts, CAFs）和正常成纤维细胞（ normal fibroblasts, NFs）特征及其对结直肠癌细胞SW620上皮间质转化（ epithelial?mesenchymal transition, EMT）的影响。方法鉴定 NFs和 CAFs,比较两者活化和衰老程度。通过间接共培养实验观察两者对SW620细胞EMT和迁移能力影响。结果 NFs 和 CAFs 表达纤连蛋白（ Fibronectin ）和α?平滑肌动蛋白（α?smooth muscle actin,α?SMA）,不表达 E?钙黏蛋白（E?Cadherin）。 CAFsα?SMA 表达和衰老程度高于NFs。 CAFs促进SW620细胞E?Cadherin下调、波形蛋白（ vimentin）和Fibronectin上调, Wnt信号蛋白磷酸化的β?连环蛋白（Ser552, S552）和蓬乱蛋白（Dishevelled 3, DVL3）上调,促进其迁移。 NFs对SW620细胞EMT和迁移能力无影响。结论 CAFs活化和衰老程度大于NFs; CAFs促进结直肠癌细胞EMT、迁移和Wnt信号上调; NFs对结直肠癌细胞EMT和迁移能力无影响。     

High Frequency of RPL22 Mutations in Microsatellite‐Unstable Colorectal and Endometrial Tumors

Ribosomal Protein L22 (RPL22) encodes a protein that is a component of the 60S subunit of the ribosome. Variants in this gene have recently been linked to cancer development. Mutations in an A8 repeat in exon 2 were found in a recent study in 52% of microsatellite‐unstable endometrial tumors. These tumors are particularly prone to mutations in repeats due to mismatch repair deficiency. We screened this coding repeat in our collection of microsatellite‐unstable endometrial tumors (EC) and colorectal tumors (CRC). We found 50% mutation frequency for EC and 77% mutation frequency for CRC. These results confirm the previous study on the involvement of RPL22 in EC and, more importantly, reports for the first time such high mutation frequency in this gene in colorectal cancer. Furthermore, considering the high mutation frequency found, our data point toward an important role for RPL22 in microsatellite instability carcinogenesis.     

Higher Risk of Mismatch Repair-Deficient Colorectal Cancer in α1-Antitrypsin Deficiency Carriers and Cigarette Smokers

Microsatellite instability (MSI) is a genomic alteration observed in 15–30% of colorectal cancer (CRC). Two MSI phenotypes have been defined for CRC: MSI-H is characterized by MSI at ≥30% of the examined loci and MSI-L by MSI at 1–30% of the loci. An absence of MSI at any examined loci has been defined as a microsatellite stable (MSS) phenotype. Current data suggest the majority of MSI tumors are the result of defective DNA mismatch repair (MMR). In this study, we have determined the α₁-antitrypsin deficiency carrier (α₁ATD-ht) status of 161 CRC patients whose MSI phenotype and protein expression states had previously been determined. Cases were selected to enrich a larger number of MSI-H cases. Among 51 CRC patients with MSI-H tumors, the α₁ATD-ht rate was 21.6%; among 110 patients with MSI-L/MSS tumors, the rate was 9.1% (MSI-H vs MSI-L/MSS, P = 0.02); and among the 191 population-based controls the α₁ATD-ht rate was 9.4% (MSI-H vs controls, P = 0.02). The estimated relative risk of having MSI-H CRC among α₁ATD-ht was 3.1 after adjusting for age, gender, and smoking history. The risk of having MSI-H CRC among current and past smokers was 6.6 and 2.7, respectively. Patients who were α₁ATD-ht and smoked had a 20-fold increased risk of developing an MSI-H CRC compared to nonsmokers who were homozygous normal at the α₁ATD locus. Our findings suggest an etiologic link between α₁ATD alleles and development of CRC with defective MMR, and a synergistic effect between smoking and α₁ATD allele in the development of MSI-H CRC.     

Structural Implications of β‐Cardiac Myosin Heavy Chain Mutations in Human Disease

Over 500 disease‐causing point mutations have been found in the human β‐cardiac myosin heavy chain, many quite recently with modern sequencing techniques. This review shows that clusters of these mutations occur at critical points in the sequence and investigates whether the many studies on these mutants reveal information about the function of this protein. Anat Rec, 297:1670–1680, 2014. © 2014 Wiley Periodicals, Inc.     

Somatic Mutations in Catalytic Core of POLK Reported in Prostate Cancer Alter Translesion DNA Synthesis

DNA polymerase kappa is a Y‐family polymerase that participates to bypass the damaged DNA known as translesion synthesis (TLS) polymerase. Higher frequency of mutations in DNA polymerase kappa (POLK) recently been reported in prostate cancer. We sequenced entire exons of the POLK gene on genomic DNA from 40 prostate cancers and matched normal samples. We identified that 28% of patients have somatic mutations in the POLK gene of the prostate tumors. Mutations in these prostate cancers have somatic mutation spectra, which are dominated by C‐to‐T transitions. In the current study, we further investigate the effect of p.E29K, p.G154E, p.F155S, p.E430K, p.L442F, and p.E449K mutations on the biochemical properties of the polymerase in vitro, using TLS assay and nucleotide incorporation fidelity, following site‐directed mutagenesis bacterial expression, and purification of the respective polymerase variants. We report that following missense mutations p.E29K, p.G154E, p.F155S, p.E430K, and p.L442F significantly diminished the catalytic efficiencies of POLK with regard to the lesion bypass (AP site). POLK variants show extraordinarily low fidelity by misincorporating T, C, and G as compared to wild‐type variants. Taken together, these results suggest that interfering with normal polymerase kappa function by these mutations may be involved in prostate carcinogenesis.     

mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome

A new algorithm and Web server, mutation3D ( http://mutation3d.org ), proposes driver genes in cancer by identifying clusters of amino acid substitutions within tertiary protein structures. We demonstrate the feasibility of using a 3D clustering approach to implicate proteins in cancer based on explorations of single proteins using the mutation3D Web interface. On a large scale, we show that clustering with mutation3D is able to separate functional from nonfunctional mutations by analyzing a combination of 8,869 known inherited disease mutations and 2,004 SNPs overlaid together upon the same sets of crystal structures and homology models. Further, we present a systematic analysis of whole‐genome and whole‐exome cancer datasets to demonstrate that mutation3D identifies many known cancer genes as well as previously underexplored target genes. The mutation3D Web interface allows users to analyze their own mutation data in a variety of popular formats and provides seamless access to explore mutation clusters derived from over 975,000 somatic mutations reported by 6,811 cancer sequencing studies. The mutation3D Web interface is freely available with all major browsers supported.     

Mutations in the NSDHL gene,encoding a 3β‐hydroxysteroid dehydrogenase,cause CHILD syndrome

We report for the first time that CHILD syndrome (MIM 308050), an X‐linked dominant, male‐lethal trait characterized by an inflammatory nevus with striking lateralization and strict midline demarcation, as well as ipsilateral hypoplasia of the body is caused by mutations in the gene NSDHL located at Xq28 (NAD(P)H steroid dehydrogenase‐like protein) encoding a 3β‐hydroxysteroid dehydrogenase functioning in the cholesterol biosynthetic pathway. SSCA and genomic sequence analysis of NSDHL identified in 6 patients with CHILD syndrome, including one boy as well as a mother and her daughter, mutations potentially impairing protein function. This phenotype is distinct from, but shares various clinical and biochemical findings with chondrodysplasia punctata (CDPX2, MIM 302960). CDPX2 is due to mutations affecting a Δ8‐Δ7 sterol isomerase (EBP, emopamil binding protein, at Xp11.22 ‐ p11.23) that functions downstream of NSDHL in a later step of cholesterol biosynthesis. EBP was unaffected in the patients analyzed by us demonstrating that CHILD syndrome and CDPX2 are not caused by allelic mutations. Two mouse X‐linked dominant male‐lethal traits, bare patches (Bpa) and striated (Str) had previously been associated with mutations in Nsdhl. They provide animal models for the study of CHILD syndrome, a further human condition due to mutations in a gene of the cholesterol synthesis pathway. Am. J. Med. Genet. 90:339–346, 2000. © 2000 Wiley‐Liss, Inc.     

Putative Precursor Cancer Cells in Human Colorectal Cancer Tissue

Multistage carcinogenesis is an important concept in cancer biology. Each new stage is triggered by the acquisition of an additional genetic aberration, leading to clonal expansion of the cancer cell. The resulting tumor mass consists of cancer cells with all genetic aberrations, but may include precursor cells at some point of carcinogenesis. We analyzed six colorectal cancer tissues with APC, K-ras, and p53 mutations. From each sample, 40–50 areas (100×100×40μm) consisting only of cancer cells were microdissected, and genomic DNA was purified. Ratios of mutated and normal alleles were quantitated by the SNaPshot assay, a primer extension assay. In five tumor tissues, we identified cancer cell subpopulations corresponding to putative precursors, i.e., cells with mutations in one or two of the three genes. All samples were likely to be of monoclonal origin, and temporal sequences of the mutations could be deduced from the mutation patterns of putative precursors. The orders of mutation events were variable. However, the two carcinoma tissues accompanying adenoma regions started with the APC mutation, not contradicting the previous studies. The analysis also revealed considerable heterogeneity in allele ratios of one or two of the chromosomes. The current findings are promising to uncover the process of carcinogenesis directly from the tumor tissue of the patient.     

120例结直肠癌手术前后血清CEA RIA测定的临床观察

为了解结直肠癌患者血清中CEA的水平与该疾病的关系 ,采用RIA法对 12 0例结直肠癌患者手术前后的血清进行了CEA检测 ,同时检测了 2 4名正常人作为对照。结果显示 :正常组CEA为 9.84± 2 .4 4ng/mL ,术前患病组CEA为 38.85± 19.2 1ng/mL ,其中结肠癌组为 37.4 3± 18.5 8ng/mL ,直肠癌组为 39.72± 2 0 .6 7ng/mL ,正常组与患病组比较P <0 .0 1,结肠癌组与直肠癌组比较P >0 .0 5。术后 2个月内对 4 4例术前CEA阳性者进行监测 ,37例CEA降至 11.2 1± 3.6 5ng/mL ,7例因手术无法根治 ,CEA为 5 0 .6 3± 2 4 .38ng/mL。术后长达 6年随访监测有 4 1例复发 ,CEA水平为 4 3.12± 2 7.15ng/mL ,4 1例复发患者中 3年内复发率占 87.80 %。结论 :CEA水平检测对结直肠癌患者术前诊断 ,术后疗效评估及监测肿瘤复发与转移是一种简便易行的有效手段。     

TUSC3 promotes colorectal cancer progression and epithelial–mesenchymal transition (EMT) through WNT/β‐catenin and MAPK signalling

Colorectal cancer (CRC) is one of the most common malignancies and is the second leading cause of cancer death in humans. Tumour suppressor candidate 3 (TUSC3) plays an important role in embryogenesis and metabolism. Deletion of TUSC3 often causes non‐syndromic mental retardation. Even though TUSC3 deregulation is frequently observed in epithelial cancers, the function of TUSC3 in CRC has remained unknown. In this study, we observed greater expression of TUSC3 at the mRNA and protein level in clinical colorectal tumour samples compared with paired normal tissues. Gain‐ and loss‐of‐function analyses were performed to evaluate the functional significance of TUSC3 in CRC initiation and progression. Immunoblotting, immunofluorescence, and co‐immunoprecipitation analyses were used to identify potential pathways with which TUSC3 might be involved. Overexpression of TUSC3 in CRC cells induced epithelial–mesenchymal transition (EMT) in CRC cells, accompanied by down‐regulation of the epithelial marker, E‐cadherin, and up‐regulation of the mesenchymal marker, vimentin. Increased proliferation, migration, and invasion, as well as accelerated xenograft tumour growth, were observed in TUSC3‐overexpressing CRC cells, while opposite effects were achieved in TUSC3‐silenced cells. In conclusion, our study demonstrated the oncogenic role of TUSC3 in CRC and showed that TUSC3 may be responsible for alternations in the proliferation ability, aggressiveness, and invasive/metastatic potential of CRC through regulating the MAPK, PI3K/Akt, and Wnt/β‐catenin signalling pathways. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.     

Key Enzymes of the Extracellular Matrix in Colorectal Cancer

The role of extracellular matrix enzymes in the development of distant metastases of colorectal cancer was studied. The expression of types 2 and 9 matrix metalloproteinases was evaluated in primary colorectal adenocarcinomas (264 patients) and their metastases in the lymph nodes (127 patients) and liver (109 patients). Increased expression of matrix metalloproteinase-9 was associated with the probable progress of tumor process and with a low level of histological differentiation of the tumor (p=0.048), deeper invasion of the tumor in the intestinal wall (p=0.012), unfavorable outcome (p=0.037), high risk of metastases in the liver, and worse overall and uneventful survival of patients with colorectal cancer (p=0.001 and p=0.01, respectively). High expression of matrix metalloproteinase-2 was less significant for the invasive potential and prognosis of colorectal tumors. It is suggested that matrix metalloproteinase-9 is an important marker for analysis of the postoperative prognosis and risk of metastases in the liver in patients with colorectal cancer. Translated from Byulleten’ Eksperimental’noi Biologii i Meditsiny, Vol. 147, No. 3, pp. 327–330, March, 2009     

Exome Resequencing Identifies Potential Tumor‐Suppressor Genes that Predispose to Colorectal Cancer

Inherited factors account for around one third of all colorectal cancers (CRCs) and include rare high penetrance mutations in APC, MSH2, MSH6, and POLE. Here, we sought novel tumor‐suppressor genes that predispose to CRC by exome resequencing 50 sporadic patients with advanced CRC (18 diagnosed ≤35 years of age) at a mean coverage of 30×. To help identify potentially pathogenic alleles, we initially sought rare or novel germline truncating mutations in 1,138 genes that were likely to play a role in colorectal tumorigenesis. In total, 32 such mutations were identified and confirmed, and included an insertion in APC and a deletion in POLE, thereby validating our approach for identifying disease alleles. We sought somatic mutations in the corresponding genes in the CRCs of the patients harboring the germline lesions and found biallelic inactivation of FANCM, LAMB4, PTCHD3, LAMC3, and TREX2, potentially implicating these genes as tumor suppressors. We also identified a patient who carried a germline truncating mutation in NOTCH3, part of the Notch signaling cascade that maintains intestinal homeostasis. Our whole exome analyses provided further gene lists to facilitate the identification of potential predisposition alleles.