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Category: Genetics

Mitochondrial DNA not just from moms but also from dads?

If one wants to trace down lineage, that person could turn to the cell’s powerhouse, the mitochondrion. This organelle contains its own special set of DNA believed as inherited solely from mothers across generations.  Thus, looking at the mitochondrial DNA (by mtDNA genealogical DNA testing) could help track down lineage, and for this reason, help determine ancestral or familial connection. Recently though, a team of scientists reported that the mitochondrial DNA is not solely inherited from the mothers. New empirical evidence of biparental inheritance of mitochondrial DNA implicates the need to rectify the long-held notion that the inheritance of mitochondrial genome is exclusively matrilineal or female line.

 

 

Mitochondrial DNA

The mitochondrion (plural: mitochondria), reckoned as the powerhouse of the cell, generates metabolic energy, especially the form of adenosine triphosphate (ATP). And it does so through the process referred to as cellular respiration. Apart from that, the organelle is also described as semi-autonomous since it has its own genetic material distinct from that found in the nucleus. The nucleus contains more genes organized into chromosomes and in charge for almost all of the metabolic processes in the body. On the contrary, the genetic material in the mitochondrion – referred to as mitochondrial DNA – is relatively fewer in number. It carries the genetic code for the manufacturing of RNAs and proteins necessary to the various functions of the mitochondrion, such as energy production.

 

(Recent news on the evolutionary origin of mitochondria, read: Prokaryotic Ancestor of Mitochondria: on the hunt)

 

(You may also want to read: Mitochondrial DNA – hallmark of psychological stress)

 

Mitochondrial inheritance

In humans, the mitochondrial DNA is believed to be inherited solely from the mother. This notion stems from the events that happen at fertilization. The sperm contains on its neck a helix of mitochondria that power up the tail to swim toward the ovum. And when the sperm finally makes its way into the ovum, it leaves its neck and tail on the cell surface of the ovum. Mitochondria that are brought into the ovum would eventually be inactivated and disintegrated. Thus, the mitochondria in the ovum are the only ones that the zygote eventually inherits. A human ovum has an average of 200,000 mtDNA molecules.1 For this, certain traits and diseases involving mitochondrional DNA implicate maternal origin.

 

 

 

Inheritance of mitochondrial DNA– not exclusive

mitochondrial dna eve
The theory of Mitochondrial Eve is based on the exclusivity of human mitochondrial DNA inheritance to the female line, which when traced would lead to only one most recent woman, “Eve”. (Image credit: Ludela, Creative Commons Attribution-Share Alike 3.0 Unported)

 

The theory of Mitochondrial Eve holds that tracing the matrilineal lineage of all recent human beings would lead to all lines converging to one woman referred to as “Eve“. The theory is based on the exclusivity of human mitochondrial DNA inheritance to female line. Nevertheless, independent empirical findings and clinical studies challenge this precept.

 

For instance, Schwartz and Vissing2 reported the case of a 28-year-old man with mitochondrial myopathy. Accordingly, the patient had a mutation (a novel 2-bp mtDNA deletion in ND2 gene). Normally, the gene encodes for a subunit of the enzyme complex I of the mitochondrial respiratory chain. Thus, the faulty gene affected the production of such enzyme, which, in turn, led to the patient’s severe, lifelong exercise intolerance. Furhter, Schwartz and Vissing2 pointed out that the patient’s mitochondrial myopathy was paternal in origin.

 

Recently, a team of researchers observed paternal inheritance of mitochondrial DNA, but this time, on 17 people from three different families.3 They sequenced their mitochondrial DNAs and they discovered father-to-offspring transmission.

 

 

Conclusion

The mitochondrial DNA is said to be a mother’s legacy to her offspring. However, recent studies indicate that the father could also transmit it to his progeny. Somehow, paternal mitochondrial DNA gets into the ovum. Rather than disintegrated or inactivated, it gets expressed. Mitochondrial DNA from the fathers may not be as rare as once thought.  If more studies will corroborate soon, this could debunk Mitochondrial Eve theory. It might also render mtDNA genealogical DNA testing questionable. And, we may also need to start looking to the other side of our lineage to fathom hereditary diseases arising from faulty mitochondrial DNA.

 

 

— written by Maria Victoria Gonzaga

 

 

References:

 

1 Mitochondrial DNA. (2018). Biology-Online Dictionary. Retrieved from https://www.biology-online.org/dictionary/Mitochondrial_DNA

 

2 Schwartz, M. & Vissing, J. (2002). “Paternal Inheritance of Mitochondrial DNA”. New England Journal of Medicine. 347 (8): 576–580.

 

3 Luo, S.,  Valencia, C.A.,  Zhang, J., Lee, N., Slone, J., Gui, B., Wang, X.,  Li, Z.,  Dell, S., Brown, J., Chen, S.M.,  Chien, Y., Hwu, W., Fan, P.,  Wong, L.,  Atwal, P.S., & Huang, T. (2018). Biparental Inheritance of Mitochondrial DNA in Humans. Proceedings of the National Academy of Sciences 201810946. DOI:10.1073/pnas.1810946115

SELFISH GENE – selfish to persist

What is a selfish gene? A selfish gene is not a gene that makes an individual selfish. In fact, it may even be involved in the demonstration of a selfless act, a mark of altruism. Selfish gene elements (or selfish DNA) are nucleotide sequences that make copies of itself within the genome. They are regarded as unhelpful as they are of no use since they do not make a protein product. Sometimes, they may even cause harm. However, selfish genes have a vital impact on the survival of the species as a whole.

 

 

 

Selfish gene as a concept in evolution

Richard Dawkin coined the term selfish gene. He also proposed a gene-centric view of evolution in his book “The Selfish Gene”, which he wrote and published in 1976. An excerpt of his book states: “Genes are competing directly with their alleles for survival, since their alleles in the gene pool are rivals for their slot on the chromosomes of future generations. Any gene that behaves in such a way as to increase its own survival chances in the gene pool at the expense of its alleles will, by definition, tautologously, tend to survive. The gene is the basic unit of selfishness.” 1

 

Selfish gene, defined

Selfish gene - illustrated by vix maria
Selfish gene has a vital impact on the survival of the species as a whole. [Illustrator: Vix Maria]

 

Dawkin defined gene as a piece of chromosome that is sufficiently short to live and function long enough. A gene, he delineates, “functions as a significant unit of natural selection”.1 Based on this notion, genes tend to be selfish in a way that they would compete for their survival. They spread by forming replicas that ought to be passed on across generations. And we, as living beings, are only their vessel and an ephemeral vehicle that conveys them to the next vessel.

 

The genes are the immortals…. They are the replicators and we are the survival machines. When we have served our purpose we are cast aside. But genes are denizens of geological time: genes are forever. – Robert Dawkin1

 

Accordingly, a selfish gene would compete for its seat (loci) on the organism’s genome. Those that efficiently make copies of themselves would likely increase in number and survive in the gene pool whereas those that are less effective in the competition would tend to decrease in number.

 

 

Selfish gene and altruism

In spite of its reputation as egoistic, a selfish gene favours altruism, especially, if the act would help its replicas in other members of its species survive. Many animals – from mere ants to the more intricate humans – display altruism, which refers to a set of acts depicting a seemingly selfless behavior for the benefit or well-being of others. Hence, even if the altruistic act would eventually harm an individual, it would still prove beneficial to a selfish gene since more of its replicas in other members could wind up persisting.

 

 

 

Selfish gene elements

Selfish gene elements (sometimes referred to as selfish DNA) are nucleotide sequences that make copies of itself within the genome. They do not necessarily add up to the reproductive success of or confer significant advantage to the organism. Sometimes, they may even cause harm.

 

Recently, researchers have sequenced for the first time two selfish genes from the fungus Neurospora intermedia. A fungal spore that carries the selfish gene known as the “spore killer” would kill the sibling spores lacking the gene. 2

 

Another example of a selfish gene element is that found by the UCLA researchers in a strain of the roundworm Caenorhabditis elegans. They found a pair of selfish genes, one that encodes for a poison and the other that encodes for its antidote. The offspring that does not inherit the gene for the antidote dies while still an embryo because it fails to protect itself from the poison (toxin) produced by the mother. 3

 

 

 

Implications

These studies on selfish genes implicate that there might be many more of them and are probably just hiding in plain sight. Discovering them could one day lead to important uses. For instance, selfish genes could be used as genetic control that would deter the development of pesky parasites at the molecular level.

 

 

— written by Maria Victoria Gonzaga

 

 

 

References:
1 Dawkins, R. (2016). The Selfish Gene: 40th Anniversary edition (4th ed). Oxford University Press. ISBN 0191093076.
2 Uppsala University. (2018, October 15). Unravelling the genetics of fungal fratricide. ScienceDaily. Retrieved from www.sciencedaily.com/releases/2018/10/181015113524.htm
3 University of California – Los Angeles Health Sciences. (2017, May 11). Study of worms reveals ‘selfish genes’ that encode a toxin, and its antidote: Discovery could suggest new ways to stop the spread of disease. ScienceDaily. Retrieved from www.sciencedaily.com/releases/2017/05/170511141937.htm

Longest recorded trans-Pacific migration of a whale shark

Whale shark is a slow moving carpet shark and known as the largest extant fish species. It has a very huge mouth yet it feeds almost exclusively on plankton and small fishes. In marine biodiversity records whale shark showed the longest migratory path. Migratory behavior of marine species has been subject for research studies since it is important for optimizing growth and foraging opportunities. It also caters the breeding ground at discrete geographical locations and identification of different habitats across several jurisdictions. Also, it serves as the key for spatial planning and international policy management for ecosystem resources. Furthermore, gene flow, connectivity and population status are essentials for the marine conservation especially for migratory species.

 

Whale shark Migratory Route

On September 16, 2011 three female whale shark were tag using satellite transmitter model SPOT 253C. The tag specifies battery life wherein transmission occurs only when the animal is swimming near surface to maximize battery life. One female whale shark named Anne remained in Panamanian waters for 116 days then to eastern Pacific for 226 days. Then transmission began again at Hawaii after 235 days of silence then continued to Marshall Islands for about 268 days. But then transmission were interrupted again when the Anne reach the Mariana Trench.

 

So, the whale shark Anne travelled a long distance of 20,142 km approximately from Panama to Mariana Trench. Throughout this period Anne spent the entire time above thermocline with a temperature ranging from 15.1–35 °C. The route taken by Anne followed primarily westward North Equatorial Current similar to other whale that has been tracked previously. These results show that long periods without transmission do not necessarily entails tag shedding. Thus, this unusual long distance travelled of Anne and the intervals between detection offers evidence both tracking and genetic studies. It also suggests that whale shark is capable of long-distance travel.

 

Whale shark can migrate from Eastern Pacific to Western Indo-Pacific connecting two ocean basin using North Equatorial Current. It also imply that a potential passageway to reach Philippine Sea into South China Sea to get to Indian Ocean. Moreover, the results of this record are consistent to the genetic studies showing potential dispersal of whale shark. Overall, these two tracks showed by Anne expose the complexity of management of endangered species crossing multiple jurisdictions. Yet, the protection and conservation programs focused only at the local level rather than across Pacific.

 

Source: Prepared by Joan Tura from BMC Marine Biodiversity Records

Volume 11:8, April 19, 2018

A fatal rare disease can now be treated with a historic first FDA-approved gene-silencing drug

Scientists are excited over a gene-silencing drug that recently won an approval from the US Food and Drug Administration (FDA). This approval is historic because it is the first of its kind. The drug works by silencing genes that otherwise lead to the production of damaged proteins associated with certain diseases. The drug is called patisiran and it recently got its approval for use to treat the hereditary transthyretin amyloidosis, a fatal rare hereditary condition associated with damaged nerves.

 

 

 

Gene basis of hereditary transthyretin amyloidosis

The hereditary transthyretin amyloidosis is a rare and fatal hereditary condition that manifests as an autosomal dominant neurodegenerative disease. Because it is dominant, this means that the offspring inheriting the defective autosomal gene will acquire the condition. A defective transthyretin (TTR) gene located on human chromosome 18q12.11 is the genetic cause. The most common type of mutation is the replacement of valine by methionine at position 30.

 

A normal, functional TTR gene codes for transthyretin (TTR) protein that is involved in the transportation of thyroxine (thyroid hormone) and retinol (vitamin A). TTR protein is produced mainly in the liver, and is then secreted into the bloodstream. TTR proteins from a defective TTR gene tend to misfold and stick together, forming amyloids. This building-up of amyloids in tissues is called amyloidosis. In hereditary transthyretin amyloidosis, pathogenic amyloids form especially in the peripheral nervous system, which may eventually lead to a progressive sensory and motor polyneuropathy.

 

 

 

Gene silencing by RNA interference

Normally, the cell performs what is now known as RNA interference (RNAi). It is also known as quelling, co-suppression, and post-transcriptional gene silencing. In this process, the RNA molecules inhibit the translation of a gene. They do so when they neutralize targeted mRNA molecules. RNAi is different from CRISPR, which is a gene-editing tool that makes use of a guide RNA. CRISPR is used to switch off a gene and has a potential therapeutic use to treat cancers. It also had FDA approval in 2016 for use in a clinical trial study. However, recent studies on CRISPR raised issues about its safety since it was found to cause unexpected mutations that involve large deletions and complex genomic rearrangement at target sites.2 To learn more about CRISPR, read: CRISPR caused gene damage? … Unlike CRISPR, the RNAi is presumed not to bring permanent changes to DNA.3

 

 

Patisiran as gene-silencing drug

Patisiran is RNA-based drug that recently received the first FDA approval for use as a gene-silencing tool. People with hereditary transthyretin-mediated amyloidosis can now be treated with it.  The drug interferes with the production of transthyretin. It doses so by preventing the mRNA involved in the translation of the gene that codes for the problematic protein. This is good news to people with such fatal rare condition. FDA has now approved a drug that can be administered to them. The downside, though, is the chillingly high cost. The cost of the therapy is estimated to be about $450,000 in a year.4

 

 

 

 

New therapeutic technologies that delve into the molecular and gene mechanisms hold so much promise especially in conditions that until now lack an efficacious treatment.  RNAi is a precise gene-silencing tool and scientists are excited in its historic FDA approval. This means that it is a glorious start for contemporary therapies involving targeted gene silencing and alterations. The cost of the therapy may be encumbering but it is still a step forward, certainly a scientific feat to reckon.

 

 

— written by Maria Victoria Gonzaga

 

 

 

References:
1 TRANSTHYRETIN; TTR. (n.d.). OMIM.org. Retrieved from https://omim.org/entry/176300
2 Gonzaga, M. V. (17 July 2018). CRISPR caused gene damage? Rise and pitfall of the gene-editor. Biology-Online.org. Retrieved from https://www.biology-online.org/crispr-caused-gene-damage-rise-pitfall-gene-editor/
3 Nield, D. (14 Aug. 2018). A First of Its Kind Gene-Silencing Drug Just Got Historic Approval From The FDA. ScienceAlert. Retrieved from https://www.sciencealert.com/first-drug-silencing-genes-approved-by-fda-for-disease-treatment
4 Lipschultz, B. & Cortez, M. (10 Aug. 2018). Rare-Disease Treatment From Alnylam to Cost $450,000 a Year. Bloomberg. Retrieved from https://www.bloomberg.com/news/articles/2018-08-10/alnylam-wins-first-u-s-drug-approval-in-rare-genetic-disease

Poor motherly care for newborn linked to a father’s gene?

Scientists from Cardiff University’s School of Biosciences reported that a father’s gene may have an impact on the quality of care that is furnished by the mother to her newborn offspring. One of the most crucial roles of a mother is being able to provide and attend to the needs of her offspring, especially during the time of conception up to the time of nursing the offspring. Good quality maternal care is essential to ensure a healthy development of the newborn and the recent study on mice suggests that a father’s gene may have an effect on the mother’s nurturing behavior towards her offspring before and after they are born.

 

 

Imprinting of genes

In humans, the zygote is a diploid cell that results from the union of two haploid sex cells. This means that the zygote will possess two copies of the genome, i.e. one coming from the mother and the other one from the father. The autosomal genes of the zygote would therefore occur in pairs or as two copies. Their expressions occur simultaneously except for a few genes whose expressions will depend on the parent-of-origin.  Depending on the parent source, one of the gene copies will be imprinted, which means it will be ”silent”. For example, a father’s gene that is imprinted will be “silent” and will not be expressed but the other copy of the gene (from the mother) will be expressed, or “vice versa“. This phenomenon is called genomic imprinting.  An imprinted gene is one in which the DNA is methylated. A methylated gene means that its expression is suppressed.1

 

 

Phlda2 gene – overview

Pleckstrin homology-like domain family A member 2 (Phlda2) gene is an example of a gene whose expression accords to the phenomenon of genomic imprinting. The gene is located in the cluster of imprinted genes on chromosome 11p15.5.2 It encodes for the Phlda2 protein. It was also found that only one copy of the Phlda2 gene is “switched on” and that the other copy of the gene that is “silent” comes from the father.3 In rodents, one of its physiological roles is identified to be associated with the regulation of the activity of the placental cells called spongiotrophoblasts, which are cells responsible for the production of placental hormones. It was reported that the Phlda2 gene controls their size, and therefore their hormone production activity. 3

 

 

 

Phlda2 gene – impact on mother’s behavior

Phlda2 gene activity may have an effect on the maternal care behavior

 

Scientists from Cardiff University’s School of Biosciences found that female mice carrying pup embryos with two active Phlda2 genes, and thus with relatively higher Phlda2 levels and probably reduced placental hormone activity, exhibited decreased nursing and grooming of pups but with an increased focus in nest building. On the contrary, mothers carrying pup embryos with lower Phlda2 levels were more focused at nurturing their pups than on nest building. They also identified corresponding changes in the brain regions essential for maternal care behavior (particularly, hippocampus and hypothalamus) of the mothers during pregnancy. Their findings implicate that the Phlda2 gene activity may have an effect on the maternal care behavior of mice.3

 

 

Based on the recent findings, scientists speculate that Phlda2 gene activity may also have an impact in human pregnancies.  Many regard motherhood as an epitome of a woman’s existence. Apparently, there are instances when the quality of maternal care provided to the child is inadequate due to various factors. If these findings are relevant to humans, then, this is a potential aspect to probe in order to understand the biology of maternal care behavior – one that involves Phlda2 gene.

 

 

— written by Maria Victoria Gonzaga

 

 

References:
1 Genomic imprinting. (n.d.). Biology-Online Dictionary. Retrieved from https://www.biology-online.org/dictionary/Genomic_imprinting
2 PHLDA2 pleckstrin homology like domain family A member 2 [Homo sapiens (human)]. (8 July 2018). National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved from https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=ShowDetailView&TermToSearch=7262
3 Creeth, H.D.J., McNamara, G.I., Tunster, S.J., Boque-Sastre, R., Allen, B., Sumption, L., et al. (2018). Maternal care boosted by paternal imprinting in mammals. PLoS Biol, DOI: 10.1371/journal.pbio.2006599

Colon cancer : Independent prognostic genes and mechanisms

Colon Cancer is the third most deadly cancer worldwide. There were more than 1.4 million cases each year and 694,000 deaths globally. The treatment of colon cancer includes chemotherapy, surgery and radiation therapy. However, advances in diagnosis and treatment leads to development and improvement in survival. Numerous data point out that genetic changes function as vital role in the development of colon and rectal cancer. In which regulatory molecules mRNA affects various molecular and cellular target including cancer cells. That is why, development in research used mRNA as based diagnostic biomarkers for colon cancer in human. Furthermore, certain kind of mRNA used to predict survival in colon cancer patients. As well as a better knowledge of molecular mechanisms and associated gene is important for early diagnosis and treatment.

 

ULBP2 a novel prognostic biomarker in Colon Cancer

ULBP2 is a potential biomarker in colon cancer survival. Previous study shows that matrix metalloproteinase-9 reveals as an important marker for postoperative prognosis in colorectal cancer patients. Also extracellular matrix plays a vital role in cancer progression in which it provides structural and biochemical support in cells.  Despite from all of these, digestion is also considered to have a major role related to cancer preventive activity. Additionally, an in vitro of peptides gastrointestinal digestion can inhibit colon cancer cells proliferation and inflammation. Moreover, recent study showed that up and down regulated mRNAs are largely amass in extracellular matrix and digestion. As a result, it would entails that abnormality of extracellular matrix and digestion takes part in colon cancer progression.

 

Furthermore, the Wnt signaling pathway gives clinical importance on various diseases including colon cancer. Since alteration of this pathway are mostly observed in colorectal cancer with microsatellite instability. So, inhibiting this pathway might be helpful strategy for targeting chemotherapy-resistance cells. Also drug metabolism determined resistance of colorectal cancer resorcinol-based heat shock protein 90 inhibitors. Therefore, Wnt signaling and drug metabolism are both important pathway enriched by up and down regulated mRNAs.

 

Prognostic biomarkers are very important and have the power to change the course of disease if only knew beyond prognostic factors. In this research ULBP2 gene that encodes cell surface glycoprotein located at chromosome 6 demonstrates prognostic biomarker for colon cancer. High level of ULBP2 is deemed independent indicator for overall survival and identified as the sole outstanding mRNA.

 

Source: Prepared by Joan Tura from BMC Biological Research

Volume 51:10 March 29, 2018

CRISPR caused gene damage? Rise and pitfall of the gene-editor

CRISPR as a gene editing tool made a prodigious leap forward in science. In 2015, it was heralded as Science’s 2015 Breakthrough of the Year.1 It stymied other impressive contenders like Ebola vaccine. It supersedes other gene-editing predecessors, such as TALENs (transcription activator-like effector nucleases) and ZFNs (zinc finger nucleases). Unlike these two, CRISPR does not need a custom protein for every targeted DNA sequence. It does, however, require a guide RNA (gRNA). Even so, the process of designing a gRNA is easier and less time-consuming than creating a custom protein. For that, it is favoured over other gene-editing tools.

 

 

The rise of a revolutionary gene-editing tool — CRISPR

CRISPR-Cas9 – a customizable tool that cuts and inserts small pieces of DNA at specific areas along a DNA strand. (Credit: Ernesto del Aguila III, National Human Genome Research Institute, NIH)

 

The discovery of CRISPR was indeed phenomenal. Short for clustered regularly interspaced short palindromic repeats, CRISPR swiftly opened avenues for biological and medical innovations. Initially identified as a family of viral DNA snippets, it was discovered to inherently protect bacteria against re-invading bacteriophages akin to our immune system’s adaptive immunity. This natural gene-editing system in bacteria has two key players: gRNA and Cas9 (CRISPR-associated enzyme). The gRNA finds and binds to specific DNA target. The Cas9 goes where the gRNA is, and then cuts the DNA target, disabling the latter. Now, scientists exploit it as a way to splice specific DNA targets and then replace them with a DNA that would yield the desired outcome. For instance, CRISPR can be used to correct physiological anomalies caused by gene mutations or defective genes.


CRISPR-Cas9 system. (Credit: marius walter, Wikimedia Commons under CC BY-SA 4.0 Int’l license)

 

 

 

CRISPR – a versatile gene-editing tool

CRISPR has been shown to have the potential to slow down the progression of cancers. It can switch off a gene in immune cells. The altered immune cells can be designed to fight cancer. In 2016, US FDA approved the clinical trial study where CRISPR technology would be used to cure patients with cancers. 2 Not only in biology and medicine, the use of CRISPR has also extended to agriculture and animal husbandry. Through it, the genes of crops and livestock can be improved. They can be made more resistant to certain diseases.

 

 

 

CRISPR causing gene damage?

One of the issues raised against CRISPR is ethical concerns. Similar to what was ethically raised against other gene-editing technologies, the concern is chiefly about the notion of bias and “playing God”. What are the standards that will define and permit judgment over a gene to be construed as either “good” or “bad”? But taking aside this issue, there is another issue being hurled against CRISPR. Marked of recent as “breaking news”, a study published in Nature warned about the possible pathogenic consequences of CRISPR when the researchers identified on-target mutagenesis in the form of large deletions and complex genomic rearrangements at target sites in mitotically active cells of mice and humans.3 This is not the first time that a study questioned the safety of CRISPR technology. In 2017, researchers from Columbia University reported that it led to hundreds of unexpected mutations. Nevertheless, this claim was retracted when they failed to replicate their results.4

 

 

CRISPR as a gene-editing tool wields so much potential beyond one can imagine. It is easy to use, feasible, and far-reaching. One can expect that issues would come along the way, and thus slow down its fast-paced utilization in different fields. It is a no-nonsense stumbling block for we belong in a community that moves forward through social discourse fueled by scientific nosiness and reasoning. Probing the dangers of CRISPR should be as extensive as exploring its benefits. We must be not too quick to adulate without first bringing out in the open its risks — especially ones that are as crucial as mutations and gene damage.

 

 

— written by Maria Victoria Gonzaga

 

 

References:

1 Science News Staff. (2015). And Science’s 2015 Breakthrough of the Year is…

ScienceMag.org. Retrieved from http://www.sciencemag.org/news/2015/12/and-science-s-2015-breakthrough-year

2 Reardon, S. (2016). First CRISPR clinical trial gets green light from US panel. Retrieved from

https://www.nature.com/news/first-crispr-clinical-trial-gets-green-light-from-us-panel-1.20137

3 Kosicki, M., Tomberg, K. & Bradley, A. (2018 July 16). Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nature Biotechnology. https://doi.org/10.1038/nbt.4192

4 Dockrill, P. (2018 July 16). BREAKING: CRISPR Could Be Causing Extensive Mutations And Genetic Damage After All. ScienceAlert.com. Retrieved from https://www.sciencealert.com/crispr-editing-causes-frequent-extensive-mutations-genetic-damage-target-deletion-site

Not Junk: ‘Jumping Gene’ Is Critical For Early Embryo

Jumping genes, also known as transposons, are gaining momentum. They are considered either as slacking junks or maleficent parasites in our genome. As such, they are largely taken for granted. However, it seems the tables have turned. There seem to be certain jumping genes that without them we would not move past our embryonic state.  Researchers from the University of California – San Francisco presented proof that certain jumping genes do perform a crucial role during the development of an embryo.  Without them, the embryo would not progress as it should.1

 

 

 

Jumping genes — junk DNAs

Transposons are small segments of DNA  with a special capability. They create copies of the genetic material and then insert at random sites in the genome.2 For that, they are dubbed as “jumping genes” based on the “jumping” activities that they do. Some consider jumping genes as junk DNA because they tend to replicate needlessly multiple copies of DNAs that already exist. Some of these genetic copies could be noncoding (junk) DNAs. Our genome is comprised mostly of junk — about 98-99%! Only 1 or 2 % of it codes for the building blocks of proteins. Scientists presumed that these noncoding regions are unnecessary and therefore viewed as an evolutionary mess in our genome. Apparently, half of our genome is comprised of jumping genes, and the most common is the long interspersed nuclear element-1 (LINE1).1

 

 

Jumping genes — parasitic stowaways

While some people view jumping genes as slackers that add up to the pile of junk littering our genome, others see them as parasitic stowaways. Because they can “jump” at seemingly random sites in the genome, they could insert themselves where they might cause gene disruptions, deleterious mutations, and chromosomal rearrangements resulting in diseases, including cancer.3

 

 

LINE1 — a paradoxical jumping gene

LINE1 (a jumping gene) is crucial during embryonic development

 

Researchers from the University of California – San Francisco recently reported that LINE1 (a jumping gene) is crucial during embryonic development. LINE1 accounts for 20% or more of the human genome. It is a retrotransposon, meaning it is amplified by first transcribing a segment of DNA into RNA, and then reverse-transcribed into DNA. The extra DNA copy will then be inserted at a different site in the genome.2 This jumping gene apparently acts as a critical regulator during the early embryonic development. It appears indispensable for an embryo to develop past the two-cell stage.1 This finding seems paradoxical since LINE1 has been implicated in various diseases, particularly cancers.4 Nevertheless, the important role of LINE1 was revealed when it was eliminated from the fertilized eggs, and consequently, they all remained at the two-cell phase. Accordingly, the role of the jumping gene in embryonic development is associated with the LINE1 RNA forming a complex with Nucleolin and Kap1 (gene regulatory proteins). The complex is believed to regulate embryonic development by turning off the dominant genes orchestrating the embryo’s two-cell state as well as by turning on the genes that promote further cell divisions and development.1

 

 

 

Jumping genes are mostly underappreciated largely because they are believed to be contributors to a pile of genetic junk or as parasitic stowaways. Despite being regarded as such, recent findings poised them as crucial genes.   While most studies focus on the 1-2% of the genome performing a blatantly important role, i.e. to code for amino acids whereby a protein could be spectacularly built from, the recent study implicates that the jumping genes, too, deserve a spot in the research field.

 

 

 

— written by Maria Victoria Gonzaga

 

 

 

References:
1 University of California – San Francisco. (2018, June 21). Not junk: ‘Jumping gene’ is critical for early embryo: Gene that makes up a fifth of the human genome is not a parasite, but key to the first stages of embryonic development. ScienceDaily. Retrieved from www.sciencedaily.com/releases/2018/06/180621141038.htm
2 Transposon. (n.d.). Biology-Online Dictionary. Retrieved from https://biology-online.org/dictionary/Transposon
3 Chénais, B. (2013). Transposable elements and human cancer: A causal relationship? Biochimica et Biophysica Acta (BBA) – Reviews on Cancer, 1835 (1), 28-35. https://doi.org/10.1016/j.bbcan.2012.09.001
4 Burns, K. H. (2017). Transposable elements in cancer. Nature Reviews Cancer, 17, 415–424. https://www.nature.com/articles/nrc.2017.35

Immune characterization of Breast Cancer Metastases

Breast cancer is the occurrence of lumps or thickening of the surrounding tissues of the breast mostly in women. Yet it also occurs rarely in men. It leads to the changes in shape and appearance of the breast. As well as the changes of skin like peeling, scaling and crusting of the surrounding nipples. Nowadays, extensive support for breast cancer awareness has helped generate advances in treatment and diagnosis. In which survival rates increased while the death rates continuously declining. Due to some factors such as personalized approach for treatment, early detection and have better knowledge of the disease. In this particular research a tumor-infiltrating lymphocytes has been evaluated to convey prognostic information of the breast cancer metastases. Assess its levels, immune composition and ligand expression in metastatic lesions.

 

Tumor-infiltrating lymphocytes as an Immunogenicity of Breast cancer

Evidences suggest the potential of tumor-infiltrating lymphocytes as biomarker in breast cancer metastatic stage. Even at onset of disease it proves as prognostic biomarker in human epidermal growth factor receptor positive with breast cancer. 94 patients have been studied retrospectively with metastatic breast cancer. Younger women showed significant lowered tumor-infiltrating lymphocytes compared to older patients above 50 years of age. Generally tumor-infiltrating lymphocytes are low but have been recognized significantly at high level with patients having this disease. Moreover, previous reports indicate that at secondary or recurrence of disease a lower tumor-infiltrating lymphocytes level occurs.

 

Analysis of the characteristics of tumor immune infiltrate differs across metastatic sites. It also suggests that cutaneous tissues might harbor permissive immune microenvironment for tumor growth. In which immune heterogeneity across metastatic sites need to be explored because it is relevant in treatment and immunotherapy. Other factors that are significant to tumor-infiltrating lymphocytes composition are those patients treated with multiple lines of chemotherapy. Indeed, heavily pretreated patients might have an impaired antitumor cytotoxic activity of the immune system.

 

Therefore, tumor-infiltrating lymphocytes showed strong prognostic value in breast cancer patients. Further examinations of its relevance as biomarker reflect a general activation of the immune system. Thus, it indicates that tumor-infiltrating lymphocytes is a simple method that effectively appreciates the immune activation status of tissue negative tumor. Certainly, given the availability of standardized method of the assessment, this immune marker is technically simple and clinically reliable. Finally, tumor-infiltrating lymphocytes provide novel hypothesis-generating data with regards to immune composition and complex interplay with breast cancer metastatic setting.

 

Source: Prepared by Joan Tura from Springer BMC Breast Cancer Research

Volume 20:62, 22 June 2018

Prognostic biomarkers in Pancreatic Cancer

Pancreatic cancer started at the tissue of the pancreas – an organ in the abdomen that lies behind the lower stomach.  Pancreas releases hormones that helps in maintaining the sugar level in the blood and assist in digestion. Pancreatic cancer is hardly detected at early stage and it is recorded as third deadliest cancer in the United States. Some of its symptom includes weight loss, diabetes, jaundice, blood clots, depression and fatigue. However, it is usually characterized at late stage that has been already metastasized. Current therapy of this disease involves adjuvant chemotherapy, surgical resection and radiotherapy. Yet despite of the advancement of the clinical management and therapy the outcome remains unsatisfactory to the patients. So, this novel research of prognostic biomarker helps pancreatic cancer treatment to maximize survival and avoid toxicity.

 

miRNAs as Prognostic Biomarkers for Pancreatic Cancer

Due to poor prognosis of pancreatic cancer early detection methods have been developed. To have an effective treatment options as well as the importance of critical biomarkers. However, miRNAs shows significance for early detection and diagnosis. It divulges to have great potentials as prognostic biomarkers in pancreatic cancer. miRNAs are small non-coding RNA with 18-22 nucleotides in length that have been known to be associated with tumorigenesis. It is also linked to apoptosis, cell cycle control, proliferation, chemoresistance, metastasis and invasion. This miRNAs modulates key targets and pathways in signaling as well as its unusual expression are associated with chemoresistance.

 

In terms of chemotherapeutic treatment of pancreatic cancer miRNAs elevated expression inhibits the anti-tumor activity. miRNAs is related to gemcitabine resistance by inhibiting tumor suppressor gene phosphatase and tensin homologue thereby activating the PI3K/AKT pathway.  It is also showed that miRNAs expression correlates with prolong overall survival benefits from chemotherapeutic treatment. Additionally, down regulation of miRNAs is responsible for progression of various malignancies including pancreas, breast, prostate, lung and liver cancer. It contains anti-cancer role via modulating targets implicated in cell cycle, apoptosis and DNA repair.

 

Therefore, it is clear that pancreatic cancer utilizes various mechanisms to maintain a highly resistant phenotype. miRNAs epigenetic controls allow cells to quickly adapt to the genotoxic stress caused by chemotherapy. It is also quickly modulates the mRNA translation in pancreatic cancer cells in response to chemotherapeutic treatment. As a result, various kinds of miRNAs showed great potentials as prognostic biomarkers in pancreatic cancer. Optimistically, these biomarkers will form a solid foundation to have better clinical treatment strategies.To avoid toxicity and enhance the survival rate benefits.

 

 

Source: Prepared by Joan Tura from Springer BMC Biomarkers Research

Volume 6:18, 2018