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iBlog, iBack, iGene January 7, 2009

Posted by ramunas in cancer genetics, familial cancer, genetic testing, hereditary cancer, personal, research.
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I am back. 2008 were quite important for me – graduated clinical genetics and virtually shifted from traditional-pediatrics based genetics and focused solely to cancer and adult onset disease, also half-sunk in molecular lab – working in best equipped lab with cool people is great. This month will try to handle pyrosequencing and Illumina genotyping, wow.

And defented my long-rolled PhD in tumor cell kinetics and T regulatory cells (enjoy the power of Open Access).

Do you know that 4154delA mutation of BRCA1 gene seems to originated in the Eastern Baltic Sea region of the Northern Europe? Read my and colleagues articles.

Research is the best way to find new health improving strategies. Such example could be  CIMBA –  “Consortium of Investigators of Modifiers of BRCA1/2″) – an international initiative to identify genetic modifiers of cancer risk in BRCA1 and BRCA2 mutation carriers. The goal is to find SNPs which could be important in modifing BRCA mutation effects and thus important in clinic for correct genetic risk stratification. A newly formed Baltic Familial Breast Ovarian Cancer Consortium (BFBOCC) currently is activelly recruiting patients from Lithuania and Latvia for the involvement in CIMBA (contact person for LT – me).

Spare time (hm, a night:) is a good for website developing – www.genetika.lt – is my new website in constant progress in lithuanian language to help translate cancer genetics in understandable manner for patients and doctors. This lovely header is creation of this weekend with the genuine help of Gimp buddy:

Von Hippel-Lindau (VHL) disease – a rare tumor predisposing disorder, where targeted surveillance and early diagnostics is crucial for the improved patients survival – is no longer an  “incognito” in my country – developed genetic testing and counseling service will help for these families to get the best from current medical practice. More about VHL.

And for 2009 several new genetic testing are scheduled to come – Familial Adenomatous Polyposis, Multiple Endocrine Neoplasia syndrome (type I and II), Neurofibromatosis type II and Li-Fraumeni syndrome – developing National Hereditary Childhood Cancer Research Platform.

Thats for now – greetings from Vilnius, European Capital of Culture 2009.

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Complexity of Breast Cancer August 20, 2008

Posted by ramunas in breast cancer, cancer genetics, familial cancer, genetic testing, hereditary cancer, research.
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This is an exciting time in the study of hereditary factors involved in breast cancer susceptibility. Breast cancer for a long time was classified according histology. Now genetics play a significant role and better knowledge ensures better management and treatment.

Hereditary breast cancer (HBC) accounts for as much as 10% of the total BC burden. Only about 30 percent of these cases will be found to be due to a germline mutations in well known BRCA1 and/or BRCA2 genes, but the rest won’t have these mutations. Less than 10 percent of remaining HBC will fall into other rare conditions – and here we can see breast cancer as heterogeneous disease (ref.):

Cowden, Li-Fraumeni syndromes, heterozygosity for Ataxia telangiectasia-mutated gene (ATM) or for CHEK2 1100delC or other rare conditions Nijmegen breakage syndrome (NBS1), familial diffuse gastric cancer (CDH1), Peutz-Jeghers syndrome (STK11), Fanconi anemia (BRIP1, PALB2), Bloom syndrome (BLM)) contribute sligthly – there is consensus for ten most important genes involved in HBC (ref.)

An estimated additional 15–20% of those affected with BC will have one or more first- and ⁄ or second-degree relatives with BC (familial or polygenic breast cancer). Therefore, when these numbers are combined, familial BC risk accounts for approximately 20–25% of the total BC burden (see figure).

Here we’re talking about so called low-penetrance susceptibility genes and variants (SNPs), like rs2981582 in FGFR2, rs889312 in MAP3K1, rs3803662 in TNRC9, rs1801270 in CASP8 and many more, most of which were hot topics in the recent years. Particular alleles (particular “letter” variants of these digitalized “rs” SNPs) only increase risk slightly (twice or so) and are intense study object now, but they sooner or later will enter clinical practice.

Resistance to chemotherapy and role of BRCA2 February 22, 2008

Posted by ramunas in BRCA, cancer genetics, hereditary cancer, ovarian cancer, research.
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Tumor resistance to chemotherapy is an often failure of successive treatment (together with adverse effects).

As you know, BRCA2 mutations are associated with an increase in breast and ovarian cancer risk, as the gene’s normal function is to repair damaged DNA. But these cancer-causing faults are bad news for the tumour itself, as they also render it sensitive to DNA-damaging chemotherapy drugs like cisplatin. Unfortunately, many BRCA2 tumours develop resistance to cisplatin (ref.).

(BRCA2 repairs a stretch of DNA; source)

Interestingly, the researchers found that, when exposed to cisplatin, some ovarian cancer cells develop secondary mutations on their BRCA2 gene that restore the gene’s ability to repair DNA (via). This is called positive mutation in general genetics – a mutation which improves adaptive properties of a cell (if we look from a cancer cell perspective).

The discovery raises the possibility that blocking BRCA2 function in such patients might allow doctors to overcome drug resistance and continue with cisplatin treatment. And maybe this mechanism will be true to other DNA-repair genes such as BRCA1, which may help explain drug resistance to a variety of cancers (via).

Another study finds the similar mechanism involved in resistance to PARP (Poly(ADP-Ribose) polymerase) inhibitors, a new class of drugs which are known to be more effective in BRCA1/2 mutation cases, because they work by selectively killing cells which have no functioning BRCA gene.

These observations have implications for understanding drug resistance in BRCA mutation carriers as well as in defining functionally important domains within BRCA2 (ref.). Sure, therefore it is featured by Nature.

Prostate Cancer | Old&New SNPs and deCODEPrCa February 15, 2008

Posted by ramunas in cancer genetics, familial cancer, genetic testing, hereditary cancer, prostate cancer, research, sporadic cancer.
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This week was undoubtfully very important in elucidation of genetic predisposition to prostate cancer. Three teams (two public and one private) reported their SNP studies in Nature Genetics.

A two-stage genome-wide association study (GWAS), lead by well known Cancer Research UK researchers dr. Rosalind Eeles and Douglas F Easton, was performed on Australian and UK men and confirmed previously associated genetic variants (SNP’s) to prostate cancer at 8q24, occurring in three distinct blocs, which were best “tagged” by SNPs rs6983267, rs1016343 and rs4242384 (as you know, our genome is fragmented and genetic information passes through generations by distinct “blocks” of DNA, called haplotypes, and which can be “marked/tagged” by representative spots, called “tag SNP” – a kind of genetic folksonomy marks) and 17q (a strongest association with rs7501939 (at 17q12) and rs1859962 (at 17q24) . Also several genetic variants on seven new loci on chromosomes 3 (rs2660753), 6 (rs9364554), 7 (rs6465657), 10 (rs10993994), 11 (rs7931342), 19 (rs2735839) and X (rs5945619) were identified, which could explain ~6% of the genetic risk for prostate cancer (a highly significant SNP rs10993994 in MSMB (beta-microseminoprotein) gene proximal promoter constitutes ~2% of risk).

Constantly innovative deCODE based on own results issued predisposition to prostate cancer test deCODE PrCa of 8 SNPs for $500, which is the second commercially available genetic test for prostate cancer after Focus5 test offered by Proactive Genomics. Two new SNP’s single-letter variations (rs721048 on chromosome 2 and rs5945572 on the X chromosome are also included in deCODEme genotyping service, and subscribers can check it out now.

These two SNPs confer relatively modest increases in risk – of approximately 20% and 15% per copy carried, respectively – but because they are also quite common they are each believed to contribute to about 5% of prostate cancer cases (via).

“The genetic testing market is highly competitive. No sooner does one company launch a first-of-its-kind test than another launches a similar one”, Hsien at EyeOnDNA notes about this new test.

Other study also confirms previously reported loci on 8q24 and 17q chromosomes and identifies new SNPs on 7 (rs10486567), 10 (rs10993994; strongest association) and 11 (rs10896449) chromosomes (overal 7 SNPs). Individual population attributable risk (PAR) for prostate cancer for each of the seven independent loci ranged from 8% to 20%.

These findings help clarify genetic structure of prostate cancer, shed light on plausible candidates gene regions and have implications for risk counseling, which can be of clinical importance when cumulative risk is appreciated.

Interestingly, all studies were performed using Illumina bead-chips platform.

Note: to associate any SNP with some condition a strict statistics must be applied: the results must meet or at least approach the “standart of genome-wide significance” with P value <10 minus 7 (0.00000001).

BRCA1 mutations in cancer stem cells February 1, 2008

Posted by ramunas in BRCA, breast cancer, cancer genetics, hereditary cancer, research.
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BRCA1 mutations are the most common cause of hereditary breast cancer and germline mutations carriers have a greatly increased lifetime incidence of breast and ovarian cancer. However, the molecular mechanisms responsible for this tissue-specific malignancy are still unknown.

A new study published in PNAS may explain why women with a mutation in the BRCA1 gene face up to an 85 percent lifetime risk of breast cancer.

The study, in mice and in human breast cancer cells, found that BRCA1 is involved in the stem cells differentiating into other breast tissue cells. When BRCA1 is missing, the stem cells tend to accumulate unregulated and develop into cancer. Researchers detected clusters of expanded stem cells in breast tissue isolated from women carrying BRCA1 mutations, and found that women with these expanded stem cells had a particularly high chance of developing breast cancer (via).

“If larger studies confirm these findings, it could potentially lead to a test to identify BRCA1 carriers at particularly high risk of developing breast cancer. This might help them and their physicians make a more informed decision about preventative measures such as prophylactic mastectomy,” says senior study author.

(image source: BRCA1 protein)

A New Tumor Markers & Targets January 3, 2008

Posted by ramunas in breast cancer, liver cancer, prostate cancer, pten, research.
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Yes, there are some already in 2008!

STAT5b – a key regulator of tumorigenesis and mediator of cytokine-growth factor signaling pathway through Janus kinases and signal transducers-activators (JAK/STAT). STAT5b phosphorylation and activation is mediated by several kinases known to be overexpressed in breast cancer, such as epidermal growth factor receptor, HER2, and c-Src. Breast tumor kinase (Brk), also known as protein tyrosine kinase 6, is a nonreceptor tyrosine kinase expressed in more than 60% of breast cancers. STAT5b as well as Brk were established as potential target for breast cancer therapy [ref.] Interestingly, knock-out mouse with defect in this signaling system have dwarfism and are immunodeficient.

Also STAT5 is overexpressed in almost all recurrent prostate cancers that are resistant to hormone therapy and suggest it as a potential drug target in prostate cancer, particularly resistant to other therapies (via).

– NUMB – article in Nature describe a previously unknown function for human NUMB tumour suppressor as a regulator of tumour protein p53. NUMB prevents ubiquitination and degradation of p53 and regulate p53-dependent phenotypes. In breast cancers there is frequent loss of NUMB expression and NUMB-defective breast tumours display poor prognosis (ref.).

– The EGF (epidermal growth factor) gene 61* G allele polymorphism (SNP) G/G genotype is associated with almost threefold risk for development of hepatocellular carcinoma in liver cirrhosis through modulation of EGF levels (ref.)

– Loss of PTEN expression due to gross mutations is significantly associated with the basal-like cancer (BBC) subtype in human sporadic and BRCA1-associated hereditary breast cancers, article in Nature reports. Interestingly, hereditary mutations in PTEN are responsible for so called rare PTEN-hamartoma tumors syndromes: Cowden syndrome (macrocephaly; skin, intestine, breast and thyroid neoplasias), Bannayan-Riley-Ruvalcaba sydrome, Proteus syndrome, and Proteus-like syndrome.

RASSF1A A133S polymorphism is associated with breast cancer pathogenesis in general and modifies breast cancer age of onset in BRCA1/2 mutations carriers – it was associated with earlier onset of breast cancer compared with those individuals with either a BRCA1/2 mutation or the A133S polymorphism alone (36.0 versus 42.0 years old, P = 0.002) (ref.)

– Colony stimulating factor-1 (CSF1) circulating levels confer a 33% increased risk of postmenopausal breast cancer and is associated with an 85% reduced risk of premenopausal breast cancer (ref.)

– more?

Who will catch the COBRA? December 17, 2007

Posted by ramunas in breast cancer, cancer genetics, familial cancer, research.
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I expect very exciting news about recently discovered cofactor of BRCA1 (COBRA1) – a member of the negative elongation factor (NELF) complex, a BRCA1-interacting protein. Cofactor of BRCA1 (COBRA1) was first identified as a protein that binds to the breast cancer susceptibility gene product BRCA1. It modulates estrogen-dependent and independent transcription and suppresses the growth of breast cancer cells. Its expression is significantly reduced in metastatic and recurrent breast cancer, pointing to a tumor suppressor function in breast cancer development [ref.].

Furthermore, a lack of COBRA1 expression in breast carcinoma may serve as a useful indicator for poor prognosis (ref).

Interestingly, COBRA1 is overexpressed in the majority of primary upper gastrointestinal adenocarcinoma, what suggests COBRA1 as a novel oncogene in UGCs that regulate AP-1 binding and the expression of TFF1 in upper gastric epithelia [ref.].

One genome-wide study identified a total of 134 genes that were either activated or repressed upon small hairpin RNA-mediated reduction of COBRA1. Interestingly, many COBRA1-regulated genes reside as clusters on the chromosomes and have been previously implicated in cancer development.

It’s not too big gene – just 13 small exons, Venter and Watson have several SNPs in intronic regions. I am eager to know its involvement in cancer predisposition.

There is a great “streaming” from the North – Finnish studies of TopBP1 (topoisomerase IIbeta binding protein 1 which displays sequence homology as well as functional similarities with BRCA1) points to a novel breast cancer susceptibility gene, where CLSPN (involved in monitoring of replication and sensoring of DNA damage and cooperates with CHK1 and BRCA1) does not appear to be associated with susceptibility.

So, who will catch the COBRA? Maybe TRANSFOG.

SMAD7 | Colorectal Cancer October 31, 2007

Posted by ramunas in cancer genetics, colorectal cancer, genetic testing, research.
2 comments

A message is simple: variants (SNP’s) in SMAD7 gene (which is involved in TGF-beta and Wnt signaling; shown in red on the left side) influence colorectal cancer (CRC) risk.

Particulary association between rs4939827 and CRC was highly statistically significant. This study was performed by UK researchers and just published in Nature Genetics.

Just another SNP for future personalized genomic screen and risk assessment.

(image source)

Gene’s Mountains and Hills | Cancer October 21, 2007

Posted by ramunas in breast cancer, cancer genetics, colon cancer, research.
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A picture of huge (and ugly) macro-anatomical sample of cancer is an often finding in some chapters of textbook about cancer genetics. It has no educational value from a present personalized medicine perspective. A picture of expression profiling or mutated genes provides more relevant and contemporary understanding.

Here is how an individual colon cancer from a patient Mx38 looks like (source):

Kind of avantgarde picture in an early 20 century? Don’t worry – it will go mainstream soon like a pop-art cartoon…

A researchers team lead by notorious Bert Vogelstein (co-author of colorectal cancer mutagenesis model) performed (second) amazing study – they sequenced several individual cancers DNA:

In a systematic search of 18,191 genes representing more than 90 percent of the protein-coding genes in the human genome — about 5,000 more than in the first screen — the Johns Hopkins scientists found that most cancer-causing gene mutations are quite diverse and can vary from person to person. They found that an average 77 genes are mutated in an individual colon cancer and 81 in breast cancer. Of these, about 15 are likely to contribute to a cancer’s key characteristics, and most of these genes may be different for each patient (via).

These data suggest a genetic landscape dominated by genes that each are mutated in relatively few cancers:

“There are gene ‘mountains’ represented by those that are frequently altered and have been the focus of cancer research for years, in part because they were the only genes known to contribute to cancer,” says Bert Vogelstein, M.D., an investigator at the Howard Hughes Medical Institute and co-director of the Ludwig Center at Johns Hopkins. “Now, we can see the whole picture, and it is clear that lower peaks or gene ‘hills’ are the predominant feature.

It looks like “few mountains surrounded by many hills.”

Surprisingly, they found that an average 77 genes are mutated in an individual colon cancer and 81 in breast cancer. Of these, about 15 are likely to contribute to a cancer’s key characteristics, and most of these genes may be different for each patient.

Lot of texbooks state, that c.a. 7-8 genes are mutated in colon cancer. And they were ten-fold  wrong: mutations in 77 for colon and 81 genes for breast cancer are required to develop.

The scientists say that directing therapies at common pathways that are linked by both prevalent and rare gene mutations is a better approach than aiming treatments at specific genes. They also note that personalized cancer genomics paves the way for tailored therapies and diagnostics focusing on the alterations identified in a particular patient’s cancer. Many of the mutations identified by scientists could be important in developing individualized cancer vaccines and monitoring patients for early recurrence of their disease.

Exciting Discoveries of 2007 | Breast Cancer October 13, 2007

Posted by ramunas in breast cancer, cancer genetics, familial cancer, research.
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It seems that year 2007 is one of the most exciting year in breast cancer genetics. There have been at least 7 new genes strongly linked to breast cancer this year (and still there is some time left for discoveries).

As you may already know, BRCA1 and BRCA2, highly penetrant autosomal dominant breast cancer genes, were discovered in 1994 and 1995 respectively (a very informative article is written by Steven Narod, the most cited author in the world working in the breast cancer field). These known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks.

Then only in 2002, a new low-penetrance gene CHEK2 (particularly 1100delC mutation) was described with twofold increase of breast cancer risk in women and a tenfold increase of risk in men. There are data that it could be also multiorgan cancer susceptibility gene. And now starts “Golden 2007”:

  • Just recently (October 7th) a multicenter international study linked a new gene called HMMR to increased breast cancer risk and stated. It is mutated in about 10 percent of the population and mutations in HMMR gene can increase breast cancer risk by one third (ref.).

Interestingly, researchers used sophisticated computerized network-modeling tool that allows many different types of existing scientific data sources to be analyzed easily to identify genes that impact cancer development.

These in silico findings for three HMMR haplotype-tagging SNPs (htSNPs) were then verified on 2,475 women with breast cancer and 1,918 healthy women were studied in Israel and New York. Biotage Pyrosequencing genotyping platform was used. They also found, that HMMR gene, encoding a centrosome subunit, interacts with the well-known breast cancer gene BRCA1, which together with BRCA2, is mutated in about one of every 300 individuals, or less than 1 percent of the population.

The study found that women with a variation in the HMMR gene had a higher risk of breast cancer, even after accounting for mutations in the BRCA1 or BRCA2 genes. In particular, the risk of breast cancer in women under age 40 who carry the HMMR variation was 2.7 times the risk in women without this variation.

Overall, the risk of breast cancer was 23 percent higher in women who had one copy of genetic variant (the A-C-A haplotype: rs7712023-rs299290-rs10515860), and 46 percent higher in women who had inherited two copies. In addition, those women were diagnosed an average of 12 months younger than women from the control group, suggesting that HMMR is linked to early-onset breast cancer.

Interestingly, this breast cancer susceptibility gene functionally is oncogene, i.e. its overexpression may lead to centrosome amplification and genomic instability.

  • On May, in Science a new candidate breast-cancer susceptibility gene Rap80 (has 15 exons), was described (in three articles: 1, 2, 3), which is required for the normal DNA-repair function of the well-known breast cancer gene BRCA1.

Cancer-causing mutations in the BRCA1 protein fail to bind to the Rap80 ubiquitin-binding protein. Consequently BRCA1 is unable to identify DNA damage sites in the genome. When BRCA1 fails to fix DNA damage, cancer-causing mutations accumulate, spawning the development of breast and ovarian malignancies (via).

“Thus Rap80, by interacting with a BRCA1 region that is essential for BRCA tumor suppression, now becomes a candidate to investigate as another breast cancer disease gene in families that do not have BRCA1 and BRCA2 mutations, but have a history of breast and/or ovarian cancer,” say researchers. “In collaboration with other researchers we are currently looking to see if families that have a history of breast cancer, but lack BRCA1 and BRCA2 mutations, have any gene sequence changes in Rap80 (via).”

  • Another gene, mostly confined to sporadic breast cancer (probably), is infamous FoxP3, the hottest topic in immunology and marker of T regulatory cells (and one of candidate markers for my PhD work), but also acts as X-linked tumor suppressor gene. About 80 percent of the cancer tissues studied did not express the gene at all and it is found to be a represor of HER-2, a protein that typically marks a more aggressive form of breast cancer (also target of Trastuzumab (Herceptin) monoclonal antibody).
  • Two very important genome-wide association huge collaborative studies published on May by UK (Douglas Easton et al) and USA (Hunter D. et al) researchers, unexpectedly identified FGFR2 (fibroblast growth factor receptor), TNRC9, MAP3K1 and LSP1 genes as important breast cancer susceptibility loci.

The team found that women who carry one faulty copy of FGFR2 (four mutations) appear to have a 20% elevated risk of breast cancer, while those with two altered versions – one in six women – face up to a 60% greater chance of the illness (via).

“This is probably the most important paper on breast cancer genetics since the cloning of BRCA2 in 1995”. “This finding opens up new avenues of research into the causes and prevention of breast cancer by identifying a new biological pathway (rj: cell growth and signaling) relevant to risk of the disease” (ref.)

Researchers hesitate to advocate testing women for the FGFR2 gene. Hunter believes that “it is premature to recommend screening women for these variants” until scientists know more about other genetic risk factors (via).

If I’ve missed something, please remind it in the comments field.