High frequency of chromosome 14 deletion in early-onset colon cancer

Frequent aneuploidy in primary human T cells after CRISPR-Cas9 cleavage

Multiple clinical trials of allogeneic T cell therapy use site-specific nucleases to disrupt T cell receptor (TCR) and other genes^1-6. In this study, using single-cell RNA sequencing, we investigated genome editing outcomes in primary human T cells transfected with CRISPR-Cas9 and guide RNAs targeting genes for TCR chains and programmed cell death protein 1. Four days after transfection, we found a loss of chromosome 14, harboring the TCRα locus, in up to 9% of the cells and a chromosome 14 gain in up to 1.4% of the cells. Chromosome 7, harboring the TCRβ locus, was truncated in 9.9% of the cells. Aberrations were validated using fluorescence in situ hybridization and digital droplet PCR. Aneuploidy was associated with reduced proliferation, induced p53 activation and cell death. However, at 11 days after transfection, 0.9% of T cells still had a chromosome 14 loss. Aneuploidy and chromosomal truncations are, thus, frequent outcomes of CRISPR-Cas9 cleavage that should be monitored and minimized in clinical protocols.

Emerging glioneuronal and neuronal tumors: case-based review

Glioneuronal and neuronal tumors (GNTs) are rare heterogeneous central nervous system tumors characterized by slow growth and favorable outcomes, but are often associated with diagnostic difficulties. A thorough analysis of three rare and recently recognized GNTs was performed in the context of clinicopathological features and molecular genetic characterization. The current spinal diffuse leptomeningeal glioneuronal tumor (DLGNT) was characterized with oligodendroglioma-like tumor with chromosome 1p/19q codeletion without IDH mutations and KIAA1549:BRAF fusion. The current occipital multinodular and vacuolating neuronal tumor (MVNT) was characteristic of the variable-sized vague nodules consisted of gangliocytic tumor cells with intracytoplasmic and pericellular vacuolation and the next-generation sequencing (NGS) revealed MAP2K1 p.Q56_V60del. A diffuse glioneuronal tumor with oligodendroglioma-like features and nuclear clusters (DGONC) of the amygdala was characterized by oligodendroglia-like cells and nuclear clusters, and monosomy 14. From the current cases and literature review, we found that DLGNT commonly occurs in the spinal cord and can make mass and more commonly have KIAA1549:BRAF fusion; MVNT is a neoplasm rather than malformation and MAP2K1 deletion is one of the hallmarks of this tumor; although DGONC may require a methylation profile, we can reach a diagnosis through its unique histology, monosomy 14, and exclusion diagnosis without a methylation profile.

Prognosis biomarker and potential therapeutic target CRIP2 associated with radiosensitivity in NSCLC cells

Radiotherapy plays a major role in non-small cell lung cancer (NSCLC) treatment. The curative efficacy of advanced NSCLC is unsatisfactory because of its radioresistance to conventional radiotherapy. The biomarkers which can be used to diagnose radiosensitivity or predict for prognosis are beneficial in promoting curative effects. In this study, NSCLC cell lines with acquired radioresistance to X-rays were obtained through fractionated irradiation. The differentially expressed proteins (DEPs) between the self-established radioresistant NSCLC cell line A549-R11 and control (A549-CK) were measured by proteomic analysis. Among the detected DEPs, CRIP2, ARHGDIB, and PADI3 were validated to be up-regulated in radioresistant cells, in mRNA and protein levels. Further analysis of bioinformatics deciphered that CRIP2, as a potential biomarker for diagnosis and a key biomarker for prediction of prognosis, may impact the X-ray radiosensitivity of NSCLC by regulating the occurrence of apoptosis and cell cycle arrest; as such, it may serve as a potent therapeutic target to facilitate NSCLC radiotherapy. CRIP2 and other DEPs may shed new light on the recognition of complex factors associated with radiation-responsiveness and finally be beneficial in the advancement of personalized therapies and precision medical treatment.

Functional characterization of a candidate tumor suppressor gene, Mirror Image Polydactyly 1, in nasopharyngeal carcinoma

Mirror Image Polydactyly 1 (MIPOL1) is generally associated with congenital anomalies. However, its role in cancer development is poorly understood. Previously, by utilizing the functional complementation approach, microcell-mediated chromosome transfer (MMCT), a tumor suppressor gene, MIPOL1, was identified. MIPOL1 was confirmed to be downregulated in nasopharyngeal carcinoma (NPC) cells and tumor tissues, and re-expression of MIPOL1 induced tumor suppression. The aim of the current study is to further elucidate the functional tumor suppressive role of MIPOL1. In our study, with an expanded sample size of different clinical stages of NPC tumor tissues, we further confirmed the downregulation of MIPOL1 in different cancer stages. MIPOL1 re-expression down-regulated angiogenic factors and reduced phosphorylation of metastasis-associated proteins including AKT, p65, and FAK. In addition, MIPOL1 was confirmed to interact with a tumor suppressor, RhoB, and re-expression of MIPOL1 enhanced RhoB activity. The functional role of MIPOL1 was further validated by utilizing a panel of wild-type (WT) and truncated MIPOL1 expression constructs. The MIPOL1 tumor-suppressive effect can only be observed in the WT MIPOL1-expressing cells. In vitro and nude mice in vivo functional studies further confirmed the critical role of WT MIPOL1 in inhibiting migration, invasion and metastasis in NPC. Overall, our study provides strong evidence about the tumor-suppressive role of MIPOL1 in inhibiting angiogenesis and metastasis in NPC.

[Epidemiology, treatment and prognosis of colorectal cancer in young adults in sub-Saharan Africa]

Colorectal cancer is the most common digestive cancer. The objectives of this study was to analyse the frequency, aetiologies, and the therapeutic and progressive aspects of colorectal cancer in young adults in Burkina Faso. This study was a 10-years descriptive study conducted in 2 regional hospitals in Burkina Faso. It included all patients aged 20 to 45 years admitted to these two hospitals for colon cancer or rectal cancer during the study period. A total of 116 patients were included, which was 39.2% of all patients admitted for colorectal cancer during the same period. The average age of the included patients was 35.4 years old. There were 70 male patients (60.3%). Seven patients had a history of chronic inflammatory bowel disease, and six had a family history of colon cancer. The average consultation time was 6.2 months. In 25 cases (19.9%), the cancer was discovered in the context of an abdominal emergency. Ninety-two patients (79.3%) were diagnosed at stage 3 or stage 4 according to the TNM Staging System. The most common histological type was adenocarcinoma (103 cases, 88.9%). Therapeutically, surgery was performed on 87 patients (75%) and chemotherapy was used in 37 cases (31.9%). Sixteen patients received radiotherapy. The intra operative mortality rate was 4.6%. The 5-year survival rate was 17%. In conclusion, colorectal cancer in young adults occurs without obvious risk factors in Burkina Faso. Mortality remains high because of the limited therapeutic arsenal.

Left-sided early onset colorectal carcinomas: A sporadic neoplasm with aggressive behavior

BACKGROUND

Early onset (≤50y) colorectal carcinomas (EO-CRCs) are increasing in incidence according to epidemiological data. We investigated clinical-pathological, molecular features and outcomes of 62 left sided EO-CRCs (EOLS-CRCs) and compared them to a group of late onset (≥65) LS-CRCs (LOLS-CRCs).

MATERIALS AND METHODS

Samples were evaluated for pathological features and microsatellite instability (MSI). Overall survival (OS), disease free survival (DFS) and disease specific survival were evaluated in both groups.

RESULTS

Five out 62 (8%) EOLS-CRCs showed MSI phenotype. Interestingly these cases were aged 26-39y. Most EOLS-CRCs present at advanced stage and this was statistically significant when compared to LOLS-CRCs. OS was better in EOLS-CRCs whilst DFS showed a worst profile in EOLS-CRCs either in low and high stages even though young patients were treated more often with adjuvant chemotherapy compared to older ones at the same disease stage.

CONCLUSIONS

Most EOLS-CRCs are sporadic non Lynch, microsatellite stable (MSS) CRCs. Our data show that when compared with LOLS-CRCs the early group represents an aggressive disease with worst outcome underlining a possible different carcinogenic pathway.

Sporadic carcinoma of the colon-rectum in young patients: a distinct disease? A critical review

INTRODUCTION

Colon carcinoma is rare in patients under 40 years but incidence is increasing. Results regarding outcome of this age group have been controversial and difficult to interpret. Some authors have reported a worse prognosis related to advanced stage at diagnosis and cancer-aggressive behavior. We tried to assess whether sporadic colon carcinoma in young patients is a distinct disease with different etiology and how this reflects on outcome.

METHODS

Most relevant papers published and indexed on PubMed in the last 20 years were reviewed. Epidemiological data were retrieved from the Surveillance, Epidemiology and End Results database and discussed.

DISCUSSION

Stage-specific analyses adjusted for age have demonstrated that prognosis is related to tumor stage regardless of age. Advanced stage is partly due to tumor biology and to delayed diagnosis. Younger patients show a better performance status that allows aggressive multimodal treatment.

CONCLUSION

Colon carcinoma in young adults appears to be a distinct disease characterized by biological aggressiveness, but prognosis is not worse due to a better performance status at time of surgical intervention.

Network cluster analysis of protein-protein interaction network identified biomarker for early onset colorectal cancer

Colorectal cancer (CRC) is a major cause of morbidity and mortality throughout the world. However, the genetic alterations and molecular mechanism of the early onset CRCs are not fully investigated. The present study aimed to characterize early onset CRC by analyzing its gene expression compared with normal controls and to identify network-based biomarkers of early onset CRC. The gene expression profiles of early onset CRC were downloaded from Gene Expression Omnibus and the differentially expressed genes (DEGs) in CRC patients were identified. Then, a protein-protein interaction (PPI) network was constructed and the clusters in PPI were analyzed by ClusterONE. Furthermore, the gene ontology functional analysis and pathway enrichment analysis were conducted to the modules in PPI network. A systems biology approach integrating microarray data and PPI was further applied to construct a PPI network in CRC. Total 631 DEGs were identified from the early onset CRC compared to healthy controls. These genes were found to be involved in several biological processes, including cell communication, cell proliferation, cell shape and apoptosis. Five functional modules which may play important roles in the initiation of early onset CRC were identified from the PPI network. Functional annotation revealed that these five modules were involved in the pathways of signal transduction, carcinogenesis and metastasis. The hub nodes of these five modules, CDC42, TEX11, QKI, CAV1 and FN1, may serve as the biomarkers of early onset CRC and have the potential to be targets for therapeutic intervention. However, further investigations are still needed to confirm our findings.

Age at onset should be a major criterion for subclassification of colorectal cancer

An important proportion of early-onset colorectal cancer (CRC) does not show a hereditary component with limited knowledge about its molecular basis and features. We analyzed a subset of patients with early-onset CRC and compared them with patients with late-onset CRC. We analyzed the microsatellite instability and CpG island methylator phenotype (CIMP) in both populations and classified them into four molecular subtypes. We analyzed the differential features between groups. Only 12 of 81 early-onset cases (15%) showed microsatellite instability, 10 of which (83%) were Lynch syndrome cases; microsatellite instability cases in elderly patients were sporadic. Early-onset microsatellite-stable cases showed different tumor locations and more family history of cancer than the elderly. Microsatellite instability/CIMP-high early-onset CRC was associated with Lynch syndrome, whereas the elderly cases were associated with BRAF mutations. Early-onset microsatellite-stable/CIMP-high CRCs were more frequently mucinous and right sided than elderly cases, with a high incidence of Lynch syndrome neoplasms; early-onset microsatellite stable/CIMP-low/0 differed from elderly cases in location, stages, incidence of multiple primary neoplasms, and the familial component. The clinical and familial differences observed between early- and late-onset CRC when considering the different carcinogenetic pathways underline that the age at onset criterion should be considered when classifying CRC.

A case of colonic mucinous adenocarcinoma in 19-year-old male patient

Colorectal cancer is rare in teenagers, especially without known risk factors. Colon cancer in young age is more likely to be diagnosed at advanced-stage, to present unfavorable tumor histology such as mucinous carcinoma, and poor outcome. We report a case of sporadic mucinous adenocarcinoma of the colon in a 19-year-old male patient without any risk factors. He complained of severe left abdominal pain that developed 1 month ago. He had a distended abdomen with severe tenderness on the left lower quadrant. A distal descending colon mass causing mechanical obstruction was observed on abdominal computed tomography. Emergency colonoscopy showed a large, fungating mass obstructing the lumen at 40 cm from the anal verge. Biopsy of the colonic mass suggested a mucinous adenocarcinoma. After decompression by colonic stent, the patient was transferred to the general surgery department for left hemicolectomy. The lesion was confirmed to be a mucinous adenocarcinoma (7.0×4.5 cm). For hereditary nonpolyposis colorectal cancer evaluation, immunohistochemical staining for MLH1 and MSH2 was normal. Reverse transcription polymerase chain reaction analysis did not detect microinstability in any of the markers tested. The patient had no familial history of cancer. Mucinous adenocarcinoma has high frequencies of poor differentiation, advanced tumor stage, loss of mismatch repair gene expression, and increased MUC2 expression. A mucinous histology is considerably more frequent in children and adolescent than in adults. Adequate invasive study is also necessary for young age patients.

Cysteine-rich intestinal protein 2 (CRIP2) acts as a repressor of NF-kappaB-mediated proangiogenic cytokine transcription to suppress tumorigenesis and angiogenesis

Chromosome 14 was transferred into tumorigenic nasopharyngeal carcinoma and esophageal carcinoma cell lines by a microcell-mediated chromosome transfer approach. Functional complementation of defects present in the cancer cells suppressed tumor formation. A candidate tumor-suppressor gene, cysteine-rich intestinal protein 2 (CRIP2), located in the hot spot for chromosomal loss at 14q32.3, was identified as an important candidate gene capable of functionally suppressing tumor formation. Previous studies have shown that CRIP2 is associated with development. To date, no report has provided functional evidence supporting a role for CRIP2 in tumor development. The present study provides unequivocal evidence that CRIP2 can functionally suppress tumorigenesis. CRIP2 is significantly down-regulated in nasopharyngeal carcinoma cell lines and tumors. CRIP2 reexpression functionally suppresses in vivo tumorigenesis and angiogenesis; these effects are induced by its transcription-repressor capability. It interacts with the NF-κB/p65 to inhibit its DNA-binding ability to the promoter regions of the major proangiogenesis cytokines critical for tumor progression, including IL6, IL8, and VEGF. In conclusion, we provide compelling evidence that CRIP2 acts as a transcription repressor of the NF-κB-mediated proangiogenic cytokine expression and thus functionally inhibits tumor formation and angiogenesis.

Distinct high resolution genome profiles of early onset and late onset colorectal cancer integrated with gene expression data identify candidate susceptibility loci

Background

Estimates suggest that up to 30% of colorectal cancers (CRC) may develop due to an increased genetic risk. The mean age at diagnosis for CRC is about 70 years. Time of disease onset 20 years younger than the mean age is assumed to be indicative of genetic susceptibility. We have compared high resolution tumor genome copy number variation (CNV) (Roche NimbleGen, 385 000 oligo CGH array) in microsatellite stable (MSS) tumors from two age groups, including 23 young at onset patients without known hereditary syndromes and with a median age of 44 years (range: 28-53) and 17 elderly patients with median age 79 years (range: 69-87). Our aim was to identify differences in the tumor genomes between these groups and pinpoint potential susceptibility loci. Integration analysis of CNV and genome wide mRNA expression data, available for the same tumors, was performed to identify a restricted candidate gene list.

Results

The total fraction of the genome with aberrant copy number, the overall genomic profile and the TP53 mutation spectrum were similar between the two age groups. However, both the number of chromosomal aberrations and the number of breakpoints differed significantly between the groups. Gains of 2q35, 10q21.3-22.1, 10q22.3 and 19q13.2-13.31 and losses from 1p31.3, 1q21.1, 2q21.2, 4p16.1-q28.3, 10p11.1 and 19p12, positions that in total contain more than 500 genes, were found significantly more often in the early onset group as compared to the late onset group. Integration analysis revealed a covariation of DNA copy number at these sites and mRNA expression for 107 of the genes. Seven of these genes, CLC, EIF4E, LTBP4, PLA2G12A, PPAT, RG9MTD2, and ZNF574, had significantly different mRNA expression comparing median expression levels across the transcriptome between the two groups.

Conclusions

Ten genomic loci, containing more than 500 protein coding genes, are identified as more often altered in tumors from early onset versus late onset CRC. Integration of genome and transcriptome data identifies seven novel candidate genes with the potential to identify an increased risk for CRC.

Chromosome 14 transfer and functional studies identify a candidate tumor suppressor gene, mirror image polydactyly 1, in nasopharyngeal carcinoma

Chromosome 14 allelic loss is common in nasopharyngeal carcinoma (NPC) and may reflect essential tumor suppressor gene loss in tumorigenesis. An intact chromosome 14 was transferred to an NPC cell line using a microcell-mediated chromosome transfer approach. Microcell hybrids (MCHs) containing intact exogenously transferred chromosome 14 were tumor suppressive in athymic mice, demonstrating that intact chromosome 14 NPC MCHs are able to suppress tumor growth in mice. Comparative analysis of these MCHs and their derived tumor segregants identified 4 commonly eliminated tumor-suppressive CRs. Here we provide functional evidence that a gene, Mirror-Image POLydactyly 1 (MIPOL1), which maps within a single 14q13.1-13.3 CR and that hitherto has been reported to be associated only with a developmental disorder, specifically suppresses in vivo tumor formation. MIPOL1 gene expression is down-regulated in all NPC cell lines and in approximately 63% of NPC tumors via promoter hypermethylation and allelic loss. SLC25A21 and FOXA1, 2 neighboring genes mapping to this region, did not show this frequent down-regulated gene expression or promoter hypermethylation, precluding possible global methylation effects and providing further evidence that MIPOL1 plays a unique role in NPC. The protein localizes mainly to the nucleus. Re-expression of MIPOL1 in the stable transfectants induces cell cycle arrest. MIPOL1 tumor suppression is related to up-regulation of the p21(WAF1/CIP1) and p27(KIP1) protein pathways. This study provides compelling evidence that chromosome 14 harbors tumor suppressor genes associated with NPC and that a candidate gene, MIPOL1, is associated with tumor development.

[Early-onset colorectal carcinoma study]

Early-onset colorectal carcinoma (before the age of 45 years) are a distinct clinical group characterized by frequent distal location, poor cellular differentiation and aggressive evolution. A systematic study of early-onset cancers without familial predisposition in the context of the CIT program of "la Ligue Nationale Contre le Cancer" has been set up to characterize molecular mechanisms of carcinogenesis of these tumors. Preliminary results of transcriptome analysis show different gene-expression profiles among age. The next step will consist in validating a molecular signature specific for early-onset carcinoma. Genomic profile does not differ from that observed in late-onset colon cancers.

Associations between single nucleotide polymorphisms in double-stranded DNA repair pathway genes and familial breast cancer

PURPOSE

DNA damage recognition and repair play a major role in risk for breast cancer. We investigated 104 single nucleotide polymorphisms (SNP) in 17 genes whose protein products are involved in double-stranded break repair (DSBR).

EXPERIMENTAL DESIGN

We used a case-control design. Both the case individuals affected with breast cancer or with both breast and ovarian cancers and the controls had similar familial risk of breast cancer and were participants in a high-risk cancer registry.

RESULTS

We found that 12 of the polymorphisms are associated with breast or breast and ovarian cancers, most notably rs16888927, rs16888997, and rs16889040, found in introns of RAD21, suggesting that SNPs in other genes in the DSBR pathway in addition to BRCA1 and BRCA2 may affect breast cancer risk.

CONCLUSIONS

SNPs within or near several DSBR DNA repair pathway genes are associated with breast cancer in individuals from a high-risk population. In addition, our study reemphasizes the unique perspective that recruitment of cases and controls from family cancer registries has for gene discovery studies.

Young-onset colorectal cancer in patients with no known genetic predisposition: can we increase early recognition and improve outcome?

Early recognition of colorectal cancer (CRC) in young patients without known genetic predisposition is a challenge, and clinicopathologic features at time of presentation are not well described. We conducted the current study to review these features in a large population of patients with young-onset CRC (initial diagnosis at age <or=50 yr without established risk factors). We reviewed the records of all patients aged 50 years or younger diagnosed with a primary CRC at our institution between 1976 and 2002. Patients with inflammatory bowel disease, polyposis syndromes, or a known genetic predisposition for CRC were excluded. Data regarding clinical and pathologic features at time of initial presentation were abstracted by trained personnel. We identified 1025 patients, 585 male. Mean age at presentation was 42.4 years (standard deviation 6.4). Eight hundred eighty-six (86%) patients were symptomatic at time of diagnosis. Clinical features in symptomatic patients included rectal bleeding (51%), change in bowel habits (18%), abdominal pain (32%), weight loss (13%), nausea/vomiting (7%), melena (2%), and other (26%). Evaluation of asymptomatic patients was pursued with findings of anemia (14%), positive fecal occult blood test (7%), abdominal mass (2%), mass on digital rectal exam (2%), and other (80%). Site of primary tumor was colonic in 51% and rectal in 49%. Synchronous malignant lesions were noted in 1%. Mucinous and signet cell histology was seen in 11% and 2%, respectively. Tumor grade distribution was grade 1 (2%), grade 2 (54%), grade 3 (34%), and grade 4 (7%). The stage distribution was stage I (13%), stage II (21%), stage III (32%), and stage IV (34%). To our knowledge, the current study is the largest cohort of young-onset CRC patients with no known genetic predisposition for disease. Most patients were symptomatic, had left-colon or rectal cancers and presented with more advanced stage disease. Our findings should promote increased awareness and the aggressive pursuit of symptoms in otherwise young, low-risk patients, as these symptoms may represent an underlying colorectal malignancy.

Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays

BACKGROUND

The vast majority of human genes (>70%) are alternatively spliced. Although alternative pre-mRNA processing is modified in multiple tumors, alternative hyper-splicing signatures specific to particular tumor types are still lacking. Here, we report the use of Affymetrix Human Exon Arrays to spot hyper-splicing events characteristic of myasthenia gravis (MG)-thymoma, thymic tumors which develop in patients with MG and discriminate them from colon cancer changes.

METHODOLOGY/PRINCIPAL FINDINGS

We combined GO term to parent threshold-based and threshold-independent ad-hoc functional statistics with in-depth analysis of key modified transcripts to highlight various exon-specific changes. These denote alternative splicing in MG-thymoma tumors compared to healthy human thymus and to in-house and Affymetrix datasets from colon cancer and healthy tissues. By using both global and specific, term-to-parent Gene Ontology (GO) statistical comparisons, our functional integrative ad-hoc method allowed the detection of disease-relevant splicing events.

CONCLUSIONS/SIGNIFICANCE

Hyper-spliced transcripts spanned several categories, including the tumorogenic ERBB4 tyrosine kinase receptor and the connective tissue growth factor CTGF, as well as the immune function-related histocompatibility gene HLA-DRB1 and interleukin (IL)19, two muscle-specific collagens and one myosin heavy chain gene; intriguingly, a putative new exon was discovered in the MG-involved acetylcholinesterase ACHE gene. Corresponding changes in spliceosome composition were indicated by co-decreases in the splicing factors ASF/SF(2) and SC35. Parallel tumor-associated changes occurred in colon cancer as well, but the majority of the apparent hyper-splicing events were particular to MG-thymoma and could be validated by Fluorescent In-Situ Hybridization (FISH), Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and mass spectrometry (MS) followed by peptide sequencing. Our findings demonstrate a particular alternative hyper-splicing signature for transcripts over-expressed in MG-thymoma, supporting the hypothesis that alternative hyper-splicing contributes to shaping the biological functions of these and other specialized tumors and opening new venues for the development of diagnosis and treatment approaches.