Online Purchasing Account You are logged on as Guest. LoginRegister a New AccountShopping cart (Empty)
United States 

FISH Probes Generated by Nick Translation Provide a Valuable Tool for Kidney Cancer Classification

Posted By Jan-Henning Martens
Tags: Cancer, Molecular Biology, Screening

Renal cell carcinoma (RCC) is the most common type of kidney cancer in adults, responsible for approximately 90–95% of cases. The American Cancer Society’s estimates for kidney cancer in the United States are that about 62,700 new cases of kidney cancer (39,650 in men and 23,050 in women) occurred and that 14,240 people (9,240 men and 5,000 women) died from this disease in 2016. Kidney cancer is among the 10 most common cancers in both men and women. Overall, the lifetime risk for developing kidney cancer is about 1.6 % and this risk is higher in men than in women. Interestingly, kidney cancer is very uncommon in people aged below 45 with the average diagnostic age being 64. It is also noteworthy that the rate of new kidney cancers has been rising since the 1990s with little improvement on the development of successful treatments. RCC encompasses a heterogeneous group of tumors that is mainly categorized based on unique histopathological features. Major subtypes are clear cell RCC (ccRCC, ~75 %), papillary RCC (pRCC, ~15 %) and chromophobe RCC (chRCC, ~5%). Although RCC with unclassified histology (uRCC) constitute a significant portion of aggressive non-clear cell RCC (4–5 %), there is no standard therapy available yet and uRCC still presents a substantial diagnostic and management challenge as the largest molecularly uncharacterized RCC category with unknown oncogenic pathways as of to date.

Nick Translation

One of the most important methods deployed today to analyze genetic aberrations for classifying and diagnosing tumor subsets such as in uRCC is fluorescence in situ hybridization (FISH) using probes that are generated by nick translation. Nick translation was the first method ever devised for the in vitro labeling of DNA and has become a gold standard technique for the generation of sensitive, inexpensive and highly customizable probes in molecular biology. It is especially recommended for labeling of double stranded DNA larger than 1 kb for FISH. During the reaction, the DNA to be labeled is nicked by DNase I yielding a free 3′ hydroxyl end. DNA polymerase I then adds a new nucleotide to this end. The 5′-3′ exonuclease activity of the polymerase then moves the “nick” along the strand in the 3′ direction. The addition of a fluorescently or otherwise labeled nucleotide to the reaction results in probes that can be used in hybridization reactions to whole cells and tissue samples as well as DNA immobilized on Southern blots, colony lifts, etc.

uRCC Classification

In a recent study, Ying-Bei Chen and colleagues from the Memorial Sloan Kettering Cancer Center in New York, analyzed a cohort of 62 uRCC primary tumors by an integrated and step-wise approach, combining targeted cancer gene sequencing, RNA sequencing, single-nucleotide polymorphism (SNP) arrays, FISH, immunohistochemistry, and cell-based assays. Deploying a targeted next generation sequencing platform specific for all exons and selected introns of 230 oncogenes, tumor suppressor genes, and members of pathways deemed actionable by targeted therapies, they identified 29 recurrently mutated genes with NF2 (18 %), SETD2 (18 %) and BAP1 (13 %) being the three most frequently mutated genes. To further assess the NF2 status in uRCC, the authors of this study thoroughly analyzed chromosome 22q12 where NF2 resides and found that based on copy-number plots generated by the sequencing, 22q12 loss was evident in 14 cases (23%), among which 9 also carried NF2 mutations. This hemizygous 22q12 loss could be confirmed in all 14 cases by applying nick translated FISH probes that had been labeled with fluorochrome-conjugated dUTPs from Enzo. In addition to the NF2 loss, this uRCC subset showed dysregulated Hippo-YAP signaling, enrichment of SETD2 mutations, frequent 1p and 3p losses, aberrant histone methylation, and aggressive clinical behavior. Ying-Bei Chen and colleagues were also able to denote other uRCC subsets such as those characterized by mTORC1 hyperactivity and FH deficiency. In conclusion, this study yielded molecularly distinct subsets accounting for about 76% of the uRCC cohort cases investigated and uncovered unique oncogenic pathways to uRCC, which could have important future diagnostic, pathogenic and therapeutic implications for rare kidney cancer patients.

From our fluorescently-labeled dUTPs and nick translation system for preparing FISH probes to our large in situ hybridization and microarray labeling portfolio, Enzo Life Sciences provides a complete set of genomic tools, some of which are described below.

Share this TechNote

Never miss a new TechNote!

Receive our TechNotes as soon as they are published.


Follow Us!

 
comments powered by Disqus

Reference:

  1. Y.-B. Chen, et al. Molecular analysis of aggressive renal cell carcinoma with unclassified histology reveals distinct subsets. Nat. Commun. (2016) 7: 13131.

Related Products

Nick translation DNA labeling system 

Nick translation  system for preparing FISH probes
FISH | Print as PDF
 
ENZ-42910 50 Reactions 288.00 USD
Do you need bulk/larger quantities?
 

Nick translation DNA labeling system 2.0 

Nick translation system for preparing FISH probes
ISH (in situ hybridization), FISH | Print as PDF
 
ENZ-GEN111-0050 50 tests 260.00 USD
Do you need bulk/larger quantities?
 

BIO-PROBE® Nick translation kit with bio-16-dUTP 

Dot Blot, ISH (in situ hybridization), Northern Blot, Southern Blot | Print as PDF
 
ENZ-42710-12 25 Reactions 360.00 USD
Do you need bulk/larger quantities?
 

BIO-PROBE® Nick translation kit with fluorescein-12-dUTP 

Dot Blot, ISH (in situ hybridization), Northern Blot, Southern Blot | Print as PDF
 
ENZ-42710-16 25 Reactions 355.00 USD
Do you need bulk/larger quantities?
 

BIO-PROBE® Random primed kit with bio-16-dUTP 

Dot Blot, ISH (in situ hybridization), Northern Blot, Southern Blot | Print as PDF
 
ENZ-42720-22 25 Reactions 360.00 USD
Do you need bulk/larger quantities?
 

BIO-PROBE® Random primed kit with fluorescein-12-dUTP 

Dot Blot, ISH (in situ hybridization), Northern Blot, Southern Blot | Print as PDF
 
ENZ-42720-26 25 Reactions 346.00 USD
Do you need bulk/larger quantities?
 

Aqua 431 dUTP 

≥93% (HPLC), FISH | Print as PDF
 
ENZ-42853 25 nmol 318.00 USD
Do you need bulk/larger quantities?
 

Green 496 dUTP 

≥93% (HPLC), FISH | Print as PDF
 
ENZ-42831 25 nmol 250.00 USD
Do you need bulk/larger quantities?
 

Green 500 dUTP 

≥93% (HPLC), FISH | Print as PDF
 
ENZ-42845 25 nmol 250.00 USD
Do you need bulk/larger quantities?
 

Gold 525 dUTP 

≥93% (HPLC), FISH | Print as PDF
 
ENZ-42843 25 nmol 318.00 USD
Do you need bulk/larger quantities?
 

Orange 552 dUTP 

≥93% (HPLC), FISH | Print as PDF
 
ENZ-42842 25 nmol 300.00 USD
Do you need bulk/larger quantities?
 

Red 650 dUTP 

≥93% (HPLC), FISH | Print as PDF
 
ENZ-42522 25 nmol 315.00 USD
Do you need bulk/larger quantities?
 

Cyanine 3-dUTP 

≥93% (HPLC) | Print as PDF
 
ENZ-42501 25 nmol 175.00 USD
Do you need bulk/larger quantities?
 

Cyanine 5-dUTP 

≥93% (HPLC) | Print as PDF
 
ENZ-42502 25 nmol 175.00 USD
Do you need bulk/larger quantities?
 

Bio-16-dUTP 

≥93% (HPLC) | Print as PDF
 
ENZ-42811 50 nmol 375.00 USD
Do you need bulk/larger quantities?
 

Cyanine 3-UTP (enhanced) 

≥93% (HPLC) | Print as PDF
 
ENZ-42505 250 nmol 310.00 USD
Do you need bulk/larger quantities?
 

Cyanine 5-UTP (enhanced) 

≥93% (HPLC) | Print as PDF
 
ENZ-42506 250 nmol 310.00 USD
Do you need bulk/larger quantities?
 

Digoxigenin-dUTP, alkali-stable 

Digoxigenin-labeled nucleotide suitable for non-radioactive labeling of DNA probes
≥93% (HPLC), ISH (in situ hybridization), Southern Blot | Print as PDF
 
ENZ-NUC113-0025 25 nmol 180.00 USD
Do you need bulk/larger quantities?
 

Digoxigenin-UTP, alkali-stable 

Digoxigenin-labeled nucleotide suitable for non-radioactive labeling of RNA probes
≥93% (HPLC), ISH (in situ hybridization), Northern Blot | Print as PDF
 
ENZ-NUC114-0250 250 nmol 210.00 USD
Do you need bulk/larger quantities?
 

Digoxigenin polyclonal antibody 

Species independent all-purpose immuno-tag.
ELISA, WB, ISH (in situ hybridization), TUNEL | Print as PDF
 
ENZ-ABS266-0100 100 µg 82.00 USD
Do you need bulk/larger quantities?
 

CYTAG® CGH Labeling kit 

Superior labeling efficiency and better dye incorporation results in less failed runs
CGH | Print as PDF
 
ENZ-42671-K010 2x10 Reactions Inquire for pricing
 
ENZ-42671-K100 2x100 Reactions Inquire for pricing
Do you need bulk/larger quantities?
 

CYTAG® TotalCGH Labeling kit 

Complete kit to digest and label DNA for CGH+SNP arrays
CGH | Print as PDF
 
ENZ-42674-0010 2x10 Reactions Inquire for pricing
 
ENZ-42674-0100 2x100 Reactions Inquire for pricing
Do you need bulk/larger quantities?
 

CGH labeling kit for BAC arrays 

CGH | Print as PDF
 
ENZ-42670 20 Reactions Inquire for pricing
Do you need bulk/larger quantities?
 

BIOSCORE® Screening and amplification kit (20 reactions) 

Print as PDF
 
ENZ-42440 1 Kit 490.00 USD
Do you need bulk/larger quantities?
 

BIOARRAY™ Single-round RNA amplification and biotin labeling system 

Improved data quality and  analysis results through greater biotin incorporation.
Print as PDF
 
ENZ-42420-10 10 Reactions 805.00 USD
Do you need bulk/larger quantities?
 

BIOARRAY™ Single-round RNA amplification and biotin labeling system (100 reaction) 

Improved data quality and analysis results through greater biotin incorporation.
Print as PDF
 
ENZ-42421-100 100 Reactions 6,195.00 USD
Do you need bulk/larger quantities?
 

BIOARRAY HIGHYIELD® RNA transcript labeling kit (T7) 

The gold standard in transcript labeling, for use with Affymetrix® GeneChip® microarrays.
Print as PDF
 
ENZ-42655-10 10 Reactions 845.00 USD
 
ENZ-42655-40 40 Reactions 2,645.00 USD
 
ENZ-42655-100 100 Reactions 4,955.00 USD
Do you need bulk/larger quantities?
 

BIOARRAY™ Low Input RNA Amplification and Biotin Labeling System 

Lower RNA Input with High Yield – High Quality Biotin-labeling
Print as PDF
 
ENZ-42422-0010 10 Reactions 758.00 USD
Do you need bulk/larger quantities?
 

Recommend this page

 
For Research Use Only. Not for use in diagnostic procedures.
Keep in touch

©2017 Enzo Life Sciences, Inc.,