Intra-tumoral heterogeneity of KRAS and BRAF mutation status in patients with advanced colorectal cancer (aCRC) and cost-effectiveness of multiple sample testing

KRAS mutation status is established as a predictive biomarker of benefit from anti-EGFr therapies. Mutations are normally assessed using DNA extracted from one formalin-fixed, paraffin-embedded (FFPE) tumor block. We assessed heterogeneity of KRAS and BRAF mutation status intra-tumorally (multiple blocks from the same primary tumor). We also investigated the utility and efficiency of genotyping a 'DNA cocktail' prepared from multiple blocks. We studied 68 consenting patients in two randomized clinical trials. DNA was extracted, from ≥2 primary tumor FFPE blocks per patient. DNA was genotyped by pyrosequencing for KRAS codons 12, 13 and 61 and BRAF codon 600. In patients with heterogeneous mutation status, DNA cocktails were prepared and genotyped. Among 69 primary tumors in 68 patients, 7 (10.1%) showed intratumoral heterogeneity; 5 (7.2%) at KRAS codons 12, 13 and 2 (2.9%) at BRAF codon 600. In patients displaying heterogeneity, the relevant KRAS or BRAF mutation was also identified in 'DNA cocktail' samples when including DNA from mutant and wild-type blocks. Heterogeneity is uncommon but not insignificant. Testing DNA from a single block will wrongly assign wild-type status to 10% patients. Testing more than one block, or preferably preparation of a 'DNA cocktail' from two or more tumor blocks, improves mutation detection at minimal extra cost.     

Prognostic significance of DNA aneuploidy and p21 ras oncoprotein expression in colorectal cancer and their role in the determination of treatment modalities

The purpose of the present study was to investigate the prognostic significance of DNA ploidy, S-phase fraction and p21 ras oncoprotein expression in patients with colorectal cancer and to correlate these factors with the clinical behavior of the tumors and their response to therapy. Of 79 patients with colorectal cancer 57% (45/79) had early stage disease. Forty-one percent (32/79) had aneuploid tumors while 30% (24/79) of the tumors had a high (>10%) S-phase fraction. p21ras oncoprotein expression was detected in 38% (30/79) of tumors. Patients with aneuploid tumors had a worse prognosis than patients with diploid tumors (p=0.0002). Similarly, patients with high S-phase fraction tumors had a shorter survival than those with low S-phase fraction tumors (p=0.005). No such difference was found between p21 raspositive and p21 ras-negative tumor subgroups. In early stage colorectal cancer, aneuploidy was closely correlated with disease outcome (p=0.029). Early stage patients with diploid tumors who received radiotherapy and chemotherapy had a better prognosis than patients with aneuploid tumors. In conclusion, DNA ploidy is a significant and independent prognostic factor in colorectal cancer. Aneuploidy and genetic alteration of the p21 ras oncoprotein are important in determining the biological aggressiveness of colorectal cancer. Furthermore, DNA ploidy may identify those subgroups of patients with early stage disease who may benefit from more aggressive treatment.     

Utility of Genomic Analysis in Differentiating Synchronous and Metachronous Lung Adenocarcinomas from Primary Adenocarcinomas with Intrapulmonary Metastasis

Distinguishing synchronous and metachronous primary lung adenocarcinomas from adenocarcinomas with intrapulmonary metastasis is essential for optimal patient management. In this study, multiple lung adenocarcinomas occurring in the same patient were evaluated using comprehensive histopathologic evaluation supplemented with molecular analysis. The cohort included 18 patients with a total of 52 lung adenocarcinomas. Eleven patients had a new diagnosis of multiple adenocarcinomas in the same lobe (n = 5) or different lobe (n = 6). Seven patients had a history of lung cancer and developed multiple new tumors. The final diagnosis was made in resection specimens (n = 49), fine needle aspiration (n = 2), and biopsy (n = 1). Adenocarcinomas were non‐mucinous, and histopathologic comparison of tumors was performed. All tumors save for one were subjected to ALK gene rearrangement testing and targeted Next Generation Sequencing (NGS). Using clinical, radiologic, and morphologic features, a confident conclusion favoring synchronous/metachronous or metastatic disease was made in 65% of patients. Cases that proved challenging included ones with more than three tumors showing overlapping growth patterns and lacking a predominant lepidic component. Genomic signatures unique to each tumor were helpful in determining the relationship of multiple carcinomas in 72% of patients. Collectively, morphologic and genomic data proved to be of greater value and achieved a conclusive diagnosis in 94% of patients. Assessment of the genomic profiles of multiple lung adenocarcinomas complements the histological findings, enabling a more comprehensive assessment of synchronous, metachronous, and metastatic lesions in most patients, thereby improving staging accuracy. Targeted NGS can identify genetic alterations with therapeutic implications.     

Flow cytometric analysis of DNA aneuploidy in primary and metastatic human solid tumors

DNA histograms were measured by flow cytometry for 656 human solid tumors (365 primary and 291 metastatic). The proportion of aneuploid cells in cell suspensions obtained by mechanical disaggregation was significantly higher than those obtained after enzymatic disaggregation (collagenase + DNAse) of the same tumor. A strong correlation was observed between the values of DNA-indices measured after staining with propidium iodide and with 4',-6-diamidino-2-phenylindole (r = 0.97). Aneuploid cells were observed in 430 tumors (66%); 30 of these had two aneuploid stemlines, and two had three aneuploid stemlines. The overall frequency of aneuploidy was 61% among primary and 71% among metastatic tumors. The median value of the DNA index was 1.67 for 224 primary aneuploid tumors and 1.68 for 206 metastatic aneuploid tumors. For most diseases, the largest proportion of aneuploid primary and metastatic tumors had DNA-indices in the hypertriploid region. No major differences in frequency and degree of aneuploidy was observed between primary and metastatic tumors. For carcinomas of the bladder and prostate, frequency of aneuploidy was higher among poorly differentiated, than among moderately and well-differentiated tumors. For carcinomas of the breast and for sarcomas, tumors with DNA-indices of greater than 2.0 were observed mostly in the poorly differentiated group. For patients with carcinomas of the bladder and prostate most tumors at earlier stages of disease were diploid; whereas most tumors at later stages of disease were aneuploid. For patients with carcinomas of the ovary, colon, and kidney, no relationship between stage of disease and aneuploidy was evident.     

Clinical Analysis of 152 Cases of Multiple Primary Malignant Tumors in 15,398 Patients with Malignant Tumors

ObjectivesIn this study, the etiology, clinical characteristics, and prognosis of multiple primary malignant tumors (MPMTs) were investigated. Furthermore, we analyzed the treatment factors associated with MPMTs.MethodsFrom 15,398 patients with malignant tumors presenting to The First Hospital of Jilin University, China, between January 2010 and December 2013, we identified and analyzed patients with MPMTs. Data were obtained retrospectively from the hospital database.ResultsThe prevalence of MPMTs in this study was 0.99% (152/15398): 51 cases were synchronous MPMTs, and 101 cases were metachronous MPMTs. The mean time between the first and second primary cancer was 43.1 months. In this population, MPMTs were observed more frequently in patients with head and neck tumors (5.65%) and urinary tumors (4.19%); the prevalence of MPMTs in these patients was over 4-fold greater than the prevalence of MPMTs in all patients (0.99%). There were no cases of MPMTs in 132 cases of nervous system tumors and 404 cases of multiple myeloma. Nearly 50% (45.4%) of patients with MPMTs did not receive chemotherapy or radiotherapy before the second primary cancer was diagnosed. Eighty-five patients with MPMTs were followed for more than 2 years, and the 2-year cumulative survival rate was 40.8%.ConclusionsIn this study, the prevalence of MPMTs was 0.99% (152/15398), which is consistent with the Chinese literature. Patients with head and neck tumors or urinary tumors are at greater risk of developing MPMTs. In addition to radiotherapy or chemotherapy, this study suggests that other factors may contribute to MPMTs.     

Growth in short term primary cell cultures derived from pregnancy-dependent mammary tumors.

The behavior of cells in primary cultures derived from autonomous and pregnancy-dependent mouse mammary tumors was studied. Despite initial growth both dependent and autonomous mammary tumors produced only short-term primary cultures. Initial plating density had a marked effect on growth with only cultures plated at greater than or equal to 2 X 10(5) cells/cm2 showing any short-termed growth. Time lapse analysis showed that the lack of growth was due to failures of cytokinesis and increased death rate and intermitotic time in cultures plated at less than 2 X 10(5) cells/cm2. Using continuous label autoradiographic techniques, a partial synchronous wave of DNA synthesis was observed with newly plated and restimulated cultures. DNA synthesis reached a peak 24-48 hrs. after plating or restimulation and then dropped to low values for the next few days. Attempts to maintain the initial high rate of DNA synthesis or to induce another round of DNA synthesis by enriched media, increased serum concentrations, or other types of serum and plasma were at best only partially successful. Important hormones necessary for growth of mammary tissue in vivo may be necessary for sustained growth in vitro.     

Establishment of human colon carcinoma lines in nude mice.

After subcutaneous inoculation into nude mice of 24 human colon adenocarcinomas, growth, defined as histopathologically confirmed tumor growth which has been passed, was observed in 13 cases (54%). Tumors from metastatic sites showed higher take rates (58%) than tumors from primary sites or recurrent tumors (50%). Nine continuous tumor lines were established (69% of growing tumors) with metastatic tumors establishing more readily (100% of growing tumors) than primary tumors (40%). The average period in primary transplant was shorter for metastasis (8.3 weeks), than for primary tumors (18.5 weeks); total material 10.6 weeks. Average periods between passages were shorter than primary transplant times; these periods were shorter for metastases (6.6 weeks) than for primary tumors (9.4 weeks); total material 7.4 weeks. Of four growing tumors not established as continuous lines, three were primary and one a recurrent tumor, and the loss of tumor growth occurred in very early passages, not later than passage 3. All nude mouse-grown colon tumors were moderately well differentiated.     

DNA ploidy pattern and S-phase characteristics of metastatic melanoma

Samples of 130 metastatic melanomas from 92 patients were analyzed by DNA flow cytometry. DNA aneuploidy was observed in 67% of the patients. DNA indices were evenly distributed from 0.6 to 2.6 Tumors originating from primary lesions in the lower extremities were more frequently DNA aneuploid than those of other sites. S-phase fraction (SPF) was evaluable from 73 tumors. DNA aneuploid tumors had a significantly higher SPF than diploid tumors, and females had a higher SPF than males. Furthermore, distant metastases had a higher SPF than metastases in regional lymph nodes and in transit metastases, probably indicating a higher growth potential in metastases spreading to distant sites.     

DNA ploidy pattern and S-phase characteristics of metastatic melanoma.

Samples of 130 metastatic melanomas from 92 patients were analyzed by DNA flow cytometry. DNA aneuploidy was observed in 67% of the patients. DNA indices were evenly distributed from 0.6 to 2.6 Tumors originating from primary lesions in the lower extremities were more frequently DNA aneuploid than those of other sites. S-phase fraction (SPF) was evaluable from 73 tumors. DNA aneuploid tumors had a significantly higher SPF than diploid tumors, and females had a higher SPF than males. Furthermore, distant metastases had a higher SPF than metastases in regional lymph nodes and in transit metastases, probably indicating a higher growth potential in metastases spreading to distant sites.     

The nuclear DNA content of human breast carcinoma. Associations with clinical stage, axillary lymph node status, estrogen receptor status and outcome

Using Feulgen-DNA cytophotometry, the nuclear DNA content was determined in specimens from 169 female patients with unilateral primary carcinoma of the breast. The tumors were classified as either diploid (73 cases: 43%) or hyperdiploid (96 cases), according to the ploidy of the tumor cells. Statistically significant associations were found between the DNA content and other characteristics of the patients and their tumors. (1) In postmenopausal women, inoperable tumors were more likely to be hyperdiploid (P less than .005). (2) In patients with operable disease, diploid tumors were less likely to have metastasized to the axillary lymph nodes (P less than .005) and were also less likely to have four or more positive nodes (P = .0044). (3) Overall, 71% of the diploid tumors and 52% of the hyperdiploid tumors were estrogen-receptor (ER) positive. This difference in proportions was statistically significant (P less than .05), but when the patients were divided into premenopausal and post-menopausal groups, the proportions of ER-positive tumors were not significantly different in either group. (4) In 113 patients considered suitable for studies on outcome (mean length of follow-up of 27 months, with a range from 0 to 71 months), the rates of relapse were 3 of 55 diploid cases and 17 of 58 hyperdiploid cases. The rate of relapse was higher in the hyperdiploid group, irrespective of lymph node status.     

DNA content in fresh versus paraffin-embedded tissue. Flow cytometric analysis of 100 tumors.

DNA ploidy analysis was determined on 100 consecutive tumors from a wide variety of sites using both fresh and paraffin-embedded tissue on the same specimen. The correlation coefficient (r) value between the methods was 0.85. Aneuploidy was detected by both methods in 51/100 (51%) of the cases. Fresh tissue analysis yielded 10 additional cases (overall 61% aneuploidy) not detected on corresponding paraffin-embedded sections, whereas paraffin-embedded analysis detected 4 additional cases (overall 55% aneuploidy) not revealed by fresh tissue analysis. Fresh tissue analysis produced lower coefficients of variation and resulted in a cleaner preparation with less cellular debris. Fresh tissue analysis was also superior to paraffin for the detection of hypodiploid, near-diploid and multiple peaks. Analysis of paraffin-embedded material allows examination of archival tissue and provides a more rapid means of long-term follow-up and statistical correlations for prognostic studies. Although the overall correlation of both methodologies for DNA analysis showed a minimal variation in results, in our experience fresh tissue analysis has an advantage and is preferable, when available, for ploidy analysis.     

Flow cytometric analysis of head and neck carcinoma DNA index and S-fraction from paraffin-embedded sections: comparison with malignancy grading

Archival, paraffin-embedded, pathology specimens representing pretreatment tissue biopsies from 73 patients with epidermoid carcinoma of the head and neck were analyzed for DNA Index and %S-phase cells by flow cytometry and were scored for quantitative histomorphology. The DNA fluorescence/light scatter size patterns derived from paraffin-embedded specimens were shown to be essentially the same as those from mechanically disaggregated, ethanol-fixed cells obtained from the same tissue specimen. Patterns ranged from lymphocyte-like to highly abnormal DNA Index cytokinetic patterns. The DNA Index values ranged from 0.70 to 3.50 (median 1.42), with an aneuploidy frequency of 63/73 (86%). DNA distribution %S ranged from 4% to 45% (mean 19), with the microscopic malignancy grading showing broad heterogeneity (mean 2.1, range 1.0-3.0, where 1.0-1.7 = well differentiated, 1.8-2.3 = moderately differentiated, 2.4-3.0 = poorly differentiated). Cross-comparison of these data showed that (1) the tumor %S was dependent on DNA Index (higher %S at higher ploidy), (2) low to high malignancy tumors were randomly distributed between diploid/near diploid tumors and high-degree DNA abnormality tumors, and (3) proliferative activity values broadly overlapped between low to high malignancy scored tumors. However, those carcinomas characterized by high DNA Index (greater than or equal to 1.50) and high %S-phase fractions (greater than or equal to 20) had a five fold higher incidence of high-degree malignancy, invasive tumors than diploid/near diploid (%S less than or equal to 19) tumors.     

Intratumoral variations in DNA ploidy and s-phase fraction in human breast cancer.

To study intratumoral DNA ploidy heterogeneity and S-phase fraction (SPF) variability, we prospectively collected five different samples from 48 breast carcinomas and each sample was analysed separately by flow cytometry. Aneuploidy rate was 89.6% after analysis of four or five samples. DNA ploidy heterogeneity, i.e., different samples classified as either DNA euploid or DNA aneuploid in the same tumor was seen in 17%, and DNA index heterogeneity, i.e., tumor populations with different DNA indices (DIs) seen in different samples was 44%. A statistical model defining SPF heterogeneity is proposed. SPF heterogeneity as defined by us was 71%, and as expected the SPF heterogeneity rate increased significantly with increasing number of analysed samples. Four or more samples are needed to detect the most deviant (highest) SPF values. An unrecognized intratumor heterogeneity of DNA ploidy and SPF may partly explain the conflicting results reported in the literature on the above prognostic indicators.     

Flow cytometric DNA analysis on fine needle aspiration biopsies of liver lesions

Flow cytometric DNA analysis on fine needle aspiration biopsies of liver lesions The DNA cell content of 39 fine needle aspiration biopsies (FNAs) from five benign liver lesions, nine hepatocellular carcinomas (HCCs), and 25 metastatic tumours was analysed in a prospective fashion by flow cytometry (FCM). All benign lesions were diploid. Aneuploidy was found in five (55.6%) HCCs and in nine (36%) metastatic tumours. DNA index (DI) differences were not significant. The S-phase fraction (SPF) was higher in the malignant tumours, both combined (P < 0.02) and separated primary and metastatic (P < 0.05). We could not demonstrate an association between diploidy and percentage of benign hepatocytes in the smears of malignant tumours. The serum alpha-fetoprotein (AFP) level did not correlate with ploidy, DI, or SPF in the HCCs. In conclusion, ploidy and DI do not discriminate between benign and malignant liver lesions, but the SPF is higher in malignant tumours. DNA analysis does not help to distinguish primary from metastatic liver tumours. The presence of benign hepatocytes in samples from malignant tumours does not seem to influence the analysis of ploidy by FCM.     

Low Incidence of Synchronous or Metachronous Tumors after Endoscopic Submucosal Dissection for Early Gastric Cancer with Undifferentiated Histology

Background

Gastric cancer with undifferentiated histology has different clinicopathologic characteristics compared to differentiated type gastric cancer. We aimed to compare the risk of synchronous or metachronous tumors after curative resection of early gastric cancer (EGC) via endoscopic submucosal dissection (ESD), according to the histologic differentiation of the primary lesion.

Methods

Clinicopathological data of patients with initial-onset EGC curatively resected via ESD between January 2007 and November 2014 in a single institution were reviewed. We analyzed the incidence of synchronous or metachronous tumors after ESD with special reference to the differentiation status of the primary lesion.

Results

Of 1,560 patients with EGC who underwent curative resection via ESD, 1,447 had differentiated type cancers, and 113 had undifferentiated type cancers. The cumulative incidence of metachronous or synchronous tumor after ESD was higher in the differentiated cancer group than in the undifferentiated cancer group (P = 0.008). Incidence of metachronous or synchronous tumor was 4.8% and 1.2% per person-year in the differentiated and undifferentiated cancer groups, respectively. The Cox proportional hazard model revealed that undifferentiated cancers were associated with a low risk of synchronous or metachronous tumors after adjusting for confounding variables (hazard ratio [95% confidence interval] = 0.287 [0.090–0.918]).

Conclusions

The rate of synchronous or metachronous tumors after curative ESD was significantly lower for undifferentiated cancers compare to differentiated cancers. These findings suggest that ESD should be actively considered as a possible treatment for undifferentiated type EGCs.     

Genomic analysis reveals low tumor mutation burden which may be associated with GNAQ/11 alteration in a series of primary leptomeningeal melanomas

Primary central nervous system melanoma is rare and characterized by a variable prognosis, and no current treatment guidelines exist. We describe the clinical course of a 70‐year‐old female patient diagnosed with primary leptomeningeal melanoma (LMN) whose case represents the diagnostic and management challenges of this tumor. Targeted genomic sequencing of 315 genes from this tumor revealed GNAQ Q209L mutation and low (4 mutations/Megabase) tumor mutation burden (TMB). Wild‐type NRAS, KIT, and BRAF were also observed. A cohort of 4,787 melanomas was subsequently analyzed to identify additional primary central nervous system melanomas, of which 10 additional tumors met pathologic criteria (0.21% of total melanoma cohort). These tumors were genomically assessed according to the same targeted sequencing panel, and 6 of the tumors were also found to harbor a GNAQ mutation. All 10 tumors had low (less than or equal to 2 mutations/Megabase) TMB indicating a potential trend between G‐protein‐coupled receptor (GPCR) alterations and low TMB in LMNs. GPCR alterations were found to significantly correlate with TMB across the cohort of 4,787 melanomas, supporting this potential finding in the limited LMN subset.     

Quantitative pathologic analysis of first and second primary cancers in double tumors of the lung

In spite of the frequent occurrence of double tumors of the lung, pathologic reports on these tumors are rare. In this study, 34 patients with double tumors (10 metachronous and 24 synchronous) were quantitatively analyzed; in all cases, both the first and second tumors had been completely resected and had adequate archival material. One aim of the study was to investigate whether there was a difference in the malignancy of the first and second tumors, as evaluated from their pathologic features. A second question was whether the length of the disease-free interval between the first and second tumors or the survival could be predicted on the basis of any of the investigated features. It was found that the first and second tumors, whether synchronous or metachronous, were strikingly similar: there was no difference in any of the quantitative pathologic features studied (epithelial percentage, DNA index, mean nuclear area and standard deviation of the nuclear area). It was not possible to predict by either univariate or multivariate analysis from any of the parameters either the length of the disease-free interval between the first and second tumors or the survival. These quantitative pathologic similarities suggest that the malignancy of the second tumor (synchronous as well as metachronous) is not higher than that of the first tumor. Thus, in the case of metachronous tumors, the fact that most of the second tumors (60%) are detected at a higher (inoperable) stage is probably caused by inadequate follow-up and not by increased malignancy.(ABSTRACT TRUNCATED AT 250 WORDS)     

Distal deletion of chromosome Ip in ductal carcinoma of the breast.

By use of recombinant DNA probes that correspond to genetic loci residing on human chromosome 1, DNA samples from 37 ductal breast carcinomas and constitutional DNA from the same individuals were tested for loss of heterozygosity. A high frequency (41%) of reduction to homozygosity was detected with the probe p1-79, which recognizes the highly polymorphic locus D1Z2, localized on 1p36. Loss of heterozygosity at other chromosome 1 loci was much less common, not exceeding a frequency of 10%, and was never observed in the absence of the D1Z2 loss. Somatic loss of heterozygosity at D1Z2 was more frequent in patients with a strong family history of breast cancer (60%), in patients with early diagnosis (before 45 years of age) (70%), and in those with multiple tumors or tumor foci (50%) than in patients with none of the characteristics of hereditary tumors (21%). No associations were observed between loss of heterozygosity and prognostic factors. These results suggest that inactivation of a tumor suppressor gene located on the distal portion of chromosome 1p, alone or combined with other genetic changes, may represent a fundamental step in the pathogenesis of ductal carcinoma of the breast.     

Integration of bovine leukemia virus DNA in the genomes of bovine lymphosarcoma cells

Integration of bovine leukemia virus (BLV) in the genomes of infected cells was investigated in cattle with enzootic bovine leukosis (EBL) and sporadic bovine leukosis (SBL). Southern blot hybridization of BLV cDNA to Eco RI and Xba I restriction fragments of EBL tumor DNAs revealed that: 1) one to four or more copies of proviral DNA were integrated per genome; 2) the restriction pattern of the integrated proviral DNA was the same in two or three different tumors from the same animals; and 3) different patterns were observed among tumors from four different animals. These findings suggest the monoclonal origin of different tumors in an individual animal and the existence of multiple chromosomal integration sites of BLV provirus. DNAs from several SBL tumors were also analyzed with the same restriction enzymes, but with both representative and cDNA3'-enriched's of BLV RNA. No hybridization bands reactive with representative BLV cDNA could be detected, while several bands appeared to hybridize with cDNA3'-enriched.     

Comparison of nuclear DNA content in primary and metastatic malignant melanoma.

The DNA patterns obtained from 23 primary malignant melanomas and 35 corresponding metastases were compared and found to differ in many cases. In eight cases the primary tumors and their metastases had a ploidy type I ("euploid") DNA pattern. One case had a type I primary tumor and both type I and type II metastases. Five cases had type I primary tumors and ploidy type II ("aneuploid") DNA pattern metastases. In five cases the primary tumors and corresponding metastases were type II, and in another four cases the primary tumors were type II, whereas the metastases were type I. We interpret these data as indicating that malignant melanomas (more often than adenocarcinomas) are composed of genetically heterogeneous tumor sublines that frequently give rise to heterogeneously composed metastases. Since we sometimes observed a change in the DNA content in malignant melanomas, it seems to be more difficult to obtain prognostic information from DNA analysis in malignant melanoma as compared to the more stable adenocarcinomas.