Wednesday, April 10, 2013


So there we were, heralding the onset of a new dawn, drunk into a stupor with the insight of two men, Watson and Crick, who had just seen the X-ray diffraction images, projected by a woman named Rosalind Franklin. The fabled cloaked life of what made humans tick had been revealed. The DNA that carried the codes that made us, us, had been discovered. Now there was no end to the treatments that this knowledge would spawn. All those inimical diseases would be eradicated. Ah but that was such a long time ago, back at the dawn of genetic time in 1953.

And then again, our senses took leave, spread across the vast vistas of exotic thoughts of human life extensions into two or even three centuries. Oh yes, there were expert scientists who paid no heed to the term exaggeration. And on and on they boasted till there was no place on the front pages of the newspapers. Ah yes, a consortium of intellectuals had finally mapped the entire genome of a human being. A big and grand achievement worth celebrating indeed! They had found between 25,000 and 30,000 active genes on the DNA helix, not the 100,000+ that had been predicted. Well now! There would be little in the way of barriers in achieving the cures of cancer and other lamentable chronic diseases. Yes, truly the era of modern medicine was here. The Human Genome Project after 10 years and $3 billion had succeeded and every thing would be wonderful soon. That was 50 years after Watson and Crick, in 2003. A lot has transpired since then.

Every new discovery details a new path towards winning the war against disease, but every new discovery also brings with it questions. When I was 10, I thought there was nothing left to discover. When I was 20 that was really true. In my 30s it was really, really true, but then as time elapsed, none of it was true. Discoveries will keep coming as we try to figure out the mechanisms that keep us alive and eventually put us to a permanent sleep, "where dreams may come." Somewhere in there is the holy grail of a real understanding and if one would just stand a little far back, one can see that the intricacies are infinite.

The intricacies are infinite, because humans are constantly at war and peace simultaneously with their environment and life is in a flux of the ravages of storms and the glistening smooth calm of a silent sea.

And that brings me to the little pixies that create ruckus in our lives and simultaneously protect us. Sound familiar from a few paragraphs ago?

We’ve all heard the term Epigenetic, here “epi” the prefix means “upon” and quite literally that is true. The epi on the genetics is the rule of the meek over the mighty. Victor Ambros and colleagues Rosalind Lee and Rhonda Feinbaum discovered the first miRNA in 1993. The microRNA with only 18-24 nucleotides in their arsenal can wreak havoc on the function of a gene. In other words, put a miRNA on top of a gene and it can accelerate its function, decelerate it or completely silence it. Yup, the tiny maestros within, stand and shake their arms with aplomb!

Now that is called oomph! 

They do that by base pairing with the target messenger RNA or mRNA and inhibit heir expression through translation, or destruction. Humans have around 400 or so miRNA genes encoding their behavior ~ the guards, guarding. And if that wasn’t enough each miRNA sequence can mess with dozens if not hundreds of genes at one time, or the power of one! To boot, about 30% of the genes or more seem to be driving under this influence. These supervisory “little beings” if we can call them that, have taken on the responsibility of life and death decisions in the affairs of humans. They act as specific regulators of gene expression. In humans 3% of human genes encode for miRNAs, and up to 30% of human protein coding genes may be regulated by miRNAs. 

(The biogenesis and function of miRNAs. a Primary miRNAs (pri-miRNA) are transcribed from longer encoding DNA sequences (miRNA genes). The pri-miRNA contains one or more stem-loop structures of about 70 bases. In the nucleus, the ribonuclease enzyme Drosha excises the stem-loop structure to form the precursor miRNA (pre-miRNA). b After export into the cytoplasm, the pre-miRNA is cleaved by the ribonuclease Dicer to generate a short RNA duplex (miRNA:miRNA*). The mature single-stranded miRNA is incorporated into the RNA-induced silencing complex (RISC), while the complementary strand (miRNA*) is usually rapidly degraded. The miRNA incorporated into the silencing complex can bind to the target messenger RNA by base pairing, causing inhibition of protein translation and/or degradation of the target messenger RNA) Stephanie Sasson et al. Virchows Arch. 2008 January; 452(1): 1–10

Naturally, we as humans can’t sit around and party all day in oblivion. So we have created a set of double-stranded synthetic miRNA called siRNA or small interfering RNA that have the ability to degrade the mRNA. And they can target specific ones to achieve the purpose of silencing or activating to cool down an active oncogene or heat up the tumor suppressor gene. Human ingenuity is always nearby to exploit and defend its turf.

Some specifics for those who love specifics:

Colorectal Cancer: In Cancer Epidemiol Biomarkers Prev; 20(7); 1272–86. Hermann Brenner states, “A total of 160 miRNAs were found to be dysregulated in CRC. MiR-20a and miR-31 were found to be significantly upregulated in more than one study, and miR-143 and miR-145 were found to be significantly downregulated in CRC tissue in six or more studies. MiR-92a was significantly upregulated in CRC patients in two of the plasma-based studies and in CRC tissue in one of the tissue-based studies.”

Breast cancer: In Genome Biol. 2007;8(10): R214, Blenkiron  et al. state, Of 309 human miRNAs assayed, we identify 133 miRNAs expressed in human breast and breast tumors. We used mRNA expression profiling to classify the breast tumors as luminal A, luminal B, basal-like, HER2+ and normal-like. A number of miRNAs are differentially expressed between these molecular tumor subtypes and individual miRNAs are associated with clinicopathological factors.” (Supervised hierarchical clustering over selected miRNAs 

(Pearson correlation, average linkage). Heatmap colors represent relative miRNA expression as indicated in the color key for each panel. Brackets in the right margin indicate members of the same miRNA family. (a) Clustering of 51 tumor samples that could be classified as basal-like (red), HER2+ (pink), luminal A (dark blue), luminal B (light blue) or normal-like (green) over 38 miRNAs with Benjamini-Hochberg adjusted Kruskal-Wallis p < 0.05. (b) Clustering of 24 tumor samples classified as luminal A (dark blue) or luminal B (light blue) over 9 miRNAs with Benjamini-Hochberg adjusted Wilcoxon p < 0.05.)

Lung cancer: In Journal of Experimental & Clinical Cancer Research 2012, 31:54 Peng Guan states, “A total of 184 differentially expressed microRNAs were reported in the fourteen microRNA expression profiling studies that compared lung cancer tissues with normal tissues, with 61 microRNAs were reported in at least two studies. In the panel of consistently reported up-regulated microRNAs, miR-210 was reported in nine studies and miR-21 was reported in seven studies. In the consistently reported down-regulated microRNAs, miR-126 was reported in ten studies and miR-30a was reported in eight studies. Four up-regulated microRNAs (miR-210, miR-21, miR-31 and miR-182) and two down-regulated mcroiRNAs (miR-126 and miR-145) were consistently reported both in squamous carcinoma and adenocarcinoma-based subgroup analysis, with the other 14 microRNAs solely reported in one or the other subset… In conclusion, the top two most consistently reported up-regulated microRNAs were miR-210 and miR-21.”

Prostate Cancer: In Methods Mol Biol. 2011; 732:69-88, Tang et. al state, “As an example, profiling of miRNAs in four prostate cancer cell lines has revealed that a set of miRNAs were differentially expressed between androgen-dependent and androgen-independent metastatic prostate cancer cells. Among them, the differential expression of miR-205 and miR-200c were further validated by Northern blot analysis in these two types of prostate cancer cells.”

Epethelial-Mesenchymal Transition: In Journal of Hematology & Oncology 2012, 5:9, Oudai Hassan  et al. state, “Generally, the importance of miRNAs in cancer is emphasized by the fact that around 50% of all miRNA genes are positioned in the so called 'fragile sites', the cancer associated genomic regions which are repeatedly changed in cancer. The miRNA 143 and miRNA 145 are other two miRNAs that are assumed to play a role in EMT. In Prostate Cancer, miR-143 and miR-145 are deregulated in primary cancer compared with normal prostate tissue. The up-regulation of miR-143 in prostate cancer cells represses mesenchymal markers (vimentin and fibronectin) and increases the epithelial marker E-cadherin, while the up-regulation of miR-145 leads to the same effects except for vimentin."

Chronic Lymphocytic leukemia: In Proc Natl Acad Sci USA 99:15524–15529, Calin et al, “found that two miRNA genes, mir-15 and mir-16, were located within this 30-kb deletion. They subsequently analyzed the expression of miR-15 and miR-16 in blood samples from patients with CLL. Both miRNAs were absent or downregulated in the majority (68%) of cases when compared to normal tissue or lymphocytes. This finding suggested that these two miRNAs were causally involved in the pathogenesis of chronic lymphocytic leukemia.”

As equally as the miRNA are implicated as causal factors, their absence presages similar calamity, “A global decrease in miRNA levels has been observed in human cancers, indicating that small RNAs may have an intrinsic function in tumor suppression.”

Untangling the web of this deceitful malady called cancer, we learn a little and find out that we need a lot more to learn. For every one answer, more questions pop up, needing further investigation.

The human body is amazing evolving machinery. The beauty in it is the leaps of faith towards perfection and with each leap the unintended consequences leave us slightly more imperfect, more fallible, more in need of more information. Thus the cycle of profligate proliferation of the human race, like the viruses and their counterparts; bacteria, the race, is always on to survive the vicissitudes of out environment one piece of information at a time!

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