Novus Biologicals | Antibody News

We at Novus Biologicals offer many antibodies relevant to cancer research. Among the areas covered by our antibody catalogue are the nuclear matrix proteins, which include the heterogeneous nuclear ribonucleoproteins (hnRNPs). hnRNP antibodies were recently used in a new study in gastric cancer treatment.

The nuclear matrix is a filamentous and complex network of proteins and RNA fibrils, comprising the fibrous nuclear lamina and numerous nuclear pores. The matrix acts to provide a structural framework for the organisation of chromatin (the genetic component of the cell). Once thought to be a fairly static structure, antibody studies have shown matrix proteins play a dynamic role, interacting freely with chromatin. HnRNP proteins, for example, are involved in various nuclear activities, including pre-mRNA processing, mRNA translation and transcription.

The human nuclear cell matrix has been shown to be tumour specific. The human nuclear matrix of tumor cells is distinctly different from that of normal cells. Changes within the structure relate closely to DNA duplication and transcription. This has led to them becoming useful biomarkers in cancer studies.

Recently, a team from Xiamen University, China, studied the expression of nuclear matrix proteins before and after HMBA-induced differentiation of gastric tumour cells. 15 proteins were identified, of which 8 were down-regulated and 7 up-regulated. Antibody assays revealed that nucleophosmin, prohibitin, hnRNP A2 and hnRNP B1 were among the proteins that were significantly inhibited.

The antibody results confirmed that specific nuclear matrix proteins are altered during human gastric cancer cell differentiation. Furthermore, they proved the important role the NMP antibody database can play in uncovering the mechanisms regulating cancer cell differentiation and proliferation.

A large number of antibody assays are devoted to the study of nuclear excision repair (NER) proteins. However, there are a number of other DNA repair pathways, many of which are instigated by NER and share the same proteins. DNA repair antibodies are widely used in cancer research; our antibody catalogue at Novus Biologicals has more than 16 subsections devoted to DNA repair.

NER is subdivided into global repair, which repairs damage to any part of the DNA structure, and transcription-coupled repair, which preferentially recognises damage in an area where simultaneous transcription is occurring. The mechanism by which this occurs is still not fully understood, though it is known that XPC is essential. Antibody studies have shown that damage recognition and repair can be initiated by blocking RNA polymerase II, assisted by the Cockayne’s syndrome genes ERCC8 and ERCC6.

We at Novus Biologicals have 127 antibody products devoted to the area of mismatch repair. They are of importance in certain cancers specific cancers. For example, MLH1 is frequently mutated in cases of hereditary nonpolyposis colon cancer. It is a homologue of the E. coli mismatch repair gene mutS.

Mismatch repair proteins recognise and repair incorrect insertions and deletions of base pairs, such as guanine–thymine or adenine-cytosine. These mismatches can occur through replication errors, oxidation, methylation, spontaneous deamination and as intermediates of homologous recombination (HR).

Mismatch repair involves excision of the faulty base pair, replacing it with the correct sequence. It is often instigated through NER, though HR and BER (base excision repair) are also involved. BER antibodies are often used in brain cancer studies – BER is the main mismatch pathway in the brain.

Our antibody database at Novus Biologicals provides research tools for the forefront of cancer research. Recently, a mouse study using 53BP1 and BRCA1 antibodies showed that deletion of 53BP1 greatly lessened the incidence of tumour development in mice carrying the mutated BRCA1 gene.

The BRCA1 protein is important in the homologous recombination (HR) DNA repair pathway, repairing the replication-associated chromosome breaks which can occur during cell division. If the HR pathway becomes inactive through BRCA1 mutation, the cell relies on alternative repair pathways. However, these are more mutagenic than BRCA1, and can cause formation of abnormal chromosome structures, increasing the risk of cancer. 53BP1 is a binding protein, known to localise to DNA repair sites, in particular double-strand breaks. However, it is not thought to be mutagenic.

A study carried out by Nussenzweig et al, of the National Cancer Institute of America, set out to look at ways to inhibit tumour formation in a strain of BRCA-1 defective mice, which produce breast tumours similar to those seen in humans. A much lower incidence of tumour development had been noted in mice where 53BP1 was also defective, so in vitro antibody studies were performed. These showed that inactivation of 53BP1 restored HR to Brca1-deficient cells.

A model was suggested whereby, when both BRCA1 and 53BP1 are present at replication breaks, BRCA1 displaces 53BP1 allowing HR to progress unimpeded. In BRCA1-deficient cells, 53BP1 binding at the site disrupts the action of other HR proteins, allowing repair to occur via a mutagenic pathway. When 53BP1 is blocked, HR can occur normally. In other words, deletion of both proteins allows a tumour-free HR pathway. Therefore, if the BRCA1 gene seems to be mutagenic, a possible therapy to prevent tumor growth would be to blcok 53BP1.

With questions also raised over secondary mutations causing resistance to chemotherapy drugs, it is an exciting time for our antibody catalogue.

We at Novus Biologicals have over 230 products in our antibody catalogue devoted to nucleotide excision repair. NER is a multi-stage sequential process involving over 30 proteins, all of which have been widely studied. Being the primary method to repair DNA damage caused by agents ranging from UV radiation to chemotherapy drugs, our NER antibody database is widely used by cancer research groups.

The first stage of NER is damage recognition and demarcation. There are two main pathways: global genomic repair and transcription-coupled repair. Global repair involves the xeroderma pigmentosum complementing proteins XPC and DDB1 (XPE), and the RD23B–centrin 2 complex, which recognise the damage by forming a heterotrimeric complex. Transcription-coupled repair occurs in genes that are being actively transcribed by RNA pol II. The Cockayne’s Syndrome Factors ERCC8 and ERCC6 act to inhibit transcription so repair of the gene can be initiated. Following this stage, the NER pathway is common to both mechanisms.

The second stage involves the two excision repair cross-complementing (ERCC) proteins ERCC5 (XPG; 3′-endonuclease) and ERCC4, which is a complex of XPF 5′-endonuclease and ERCC1. Excision is accomplished by unwinding and bubble-formation of the strand containing the damage, an oligonucleotide of around 29 nucleotide units. A dual incision is then made on either side of this, and the oligonucleotide removed, after which resynthesis and ligation ny DNA polymerase completes the repair. The size of the bubble and positions of incision points will vary depending on the extent of the damage.

Some changes have been made to nomenclature, which can cause confusion. The XPD, XPB, XPF and XPG excision repair complementing factors are today known as ERCC 2 – 5. We always include alternative names in our antibody catalogue, so antibodies can be easily found.

The mammalian DNA repair process encompasses a large number of protein pathways, and forms an important part of our antibody catalogue. The past 30 years have seen tremendous advances in the understanding of these mechanisms, with Wood et al recently compiling an updated inventory of at least 150 human DNA-repair proteins. This added considerably to the scope of the antibody database of us at Novus Biologicals.

Among the major repair pathways for mammalian DNA are: simple damage reversal; recombination repair; base excision repair (BER) and nucleotide excision repair (NER).

The last has been of much interest to cancer research groups, since it is the predominant method by which the cell maintains genomic integrity. Disruptions in the repair pathway can allow mutations to proliferate, which would normally be excised and repaired. In addition, elevated levels of NER proteins are seen in chemo-resistant tumor cells (i.e. those resistant to chemotherapy drugs, in particular the ones that work by disrupting the DNA of tumor cells.)

NER pathways are specific to particular types of DNA damage (known collectively as lesions). These range from simple base methylations, to inter-strand adduct formation causing major helical distortions. NER consists of 4 stages: Recognition and demarcation of the damaged DNA; excision and removal of the lesion area; synthesis of a new, replacement section using the undamaged strand as a template, and incorporation of this section into the existing downstream sequence.

The excision repair cross-complementing (ERCC), and xeroderma pigmentosum (XP) families of proteins govern nucleotide excision repair via several protein complexes. Recently, Bhagwat et al ran specific antibody studies targeted to human ERCC1-XPF, to clarify the role these proteins play in chemo-resistant tumour cells. Previously, no human antigen-specific antibody data for this gene was available.