Chromosomal Shattering

By Perry McLimore, MD., JD.

Introduction

Our DNA is located on chromosomes in the cell’s nucleus. Human beings possess 23 pairs or 46 chromosomes within a cell. All normal cells in the human body contain 46 chromosomes.

DNA is composed of 4 nucleotides: Adenine, Guanine, Thymine, and Cytosine, or A, G, T, and C. The sequence of these 4 nucleotides is different from gene to gene making it unique. A gene is a segment of DNA that encodes for a particular protein. That protein functions in a specialized manner that supports the life of the cell. There are many thousands of genes in a cell.

Depending on what genes are turned on or off is responsible for what a cell does. Some cells function in the eye while other cells are toenails. Both cells contain the same DNA or 46 chromosomes. The eye cell has certain genes turned on and off that is different from the toenail cell. This is called differentiation.

Cells divide through a process called mitosis. All the cell’s DNA or chromosomes replicate at the beginning of mitosis. When the cell divides into two daughter cells, each one has the same 46 chromosomes. Unfortunately, during DNA replication and cell division, mistakes can happen. These errors cause DNA mutations. The mistakes or mutations may be comprised of one nucleotide (A, G, T, or C) involving one gene, or may include long stretches of the chromosome encompassing multiple genes.

When genes are mutated, several consequences may occur. The gene may be turned off, which means its protein is not synthesized. This results in abnormal cell function or cell death. Sometimes a gene is turned on, or the protein it encodes is produced at higher levels than normal. Either one can cause the cell to be aberrant or die. Many times the mutation causes an irregular or malformed protein. The etiology is one or more of the nucleotides mutates, such as a C is inserted into the DNA where it should be an A. The abnormal protein will induce cellular dysfunction. For example, sickle cell disease is caused by a single nucleotide mutation. A T is inserted where there should be an A. This occurs in the hemoglobin gene in the red blood cell, and the result is a malformed hemoglobin protein. The irregular hemoglobin protein results in the red blood cell collapsing in a shape that resembles a sickle. Mutations in the DNA of genes cause many different diseases, cancers, or death.

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Gene Mutations

Genes or chromosomal DNA can mutate in many different ways or by multiple distinctive mechanisms.

Point mutations exchange a single nucleotide for another. The gene’s sequence of Adenine, Guanine, Thymine, and Cytosine becomes atypical. An aberrant protein becomes synthesized as a consequence. The point mutation may be silent, which means the abnormal protein still functions normally. However, a point mutation may cause the protein encoded for to be dysfunctional resulting in disease (sickle cell disease), cancer, or cell death.

Insertions occur when one or more nucleotides are inserted into the DNA or gene. Produced is an aberrant protein. Similarly, deletions of one or more nucleotides from the gene may happen. Deletions can be affecting only one gene or involving significant pieces of a chromosome affecting many genes.

Amplifications or gene duplications are multiple copies of the same gene. The protein in the gene encodes experiences increased synthesis. The elevated concentration of the protein can cause disease or cancer. Possibly, aneuploidy may happen during mitosis. This means the cell is missing a chromosome or has an extra chromosome. People with an extra chromosome 21 (trisomy) have Down’s syndrome.

Chromosomal translocation is the interchange of a section of one chromosome with a part of another different chromosome. Depending on the size of the translocation, this mutation may cause havoc in the cell.

Interstitial deletions involve an intra-chromosomal removal of nucleotides of the DNA from a single chromosome. When this happens, one gene irregularly opposes another distant gene.

Chromosomal inversions are segments of a chromosome that become inverted or backward.

Chromosomal translocation, interstitial deletion, and chromosomal inversion potentially connect separate genes. A fusion protein results, which means part of the protein comes from one gene, and part of the protein comes from another gene. Fusion proteins function abnormally and are known to cause cancer.

Most mutations occur during mitosis or cell division when the DNA of chromosomes is replicating, or when the replicated chromosomes are being pulled into the two daughter cells. Mutations are probably more widespread than once thought; however, each cell contains DNA repair genes and proteins that fix the mutation before it can harm the cell. If the aberrancy is extensive, apoptosis or cell death occurs.

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Chromosome Shattering

Chromosome shattering or chromothripsis is a phenomenon where hundreds of chromosomal rearrangements or mutations occur on a chromosome in a single, catastrophic event. Such a huge episode overwhelms the cell’s DNA repair mechanisms leading to the haphazard juxtaposition of the fragments of the chromosome’s DNA back into the affected chromosome.i Many times this probably leads to apoptosis or cell death, but occasionally, the aberrant DNA is replicated during mitosis creating an abnormal clone of cells.ii Chromothripsis was first described in a patient with chronic lymphocytic leukemia in 2011.iii Subsequent investigation found chromothripsis in 2 to 3 percent of cancer cell lines and 25 percent of bone cancers.iv

Chromothripsis

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Cancer

Cancerous cells result from multiple genetic mutations (see above) or the loss of a chromosome or acquisition of more chromosomes than the standard 46.v This is called aneuploidy. These genetic alterations confer in the cancerous cell immortalization, loss of control by cell cycle mitigation, neovascularization (blood vessel growth), invasiveness, and metastatic potential.vi

Cancer is a disease of genetic or chromosomal instability. The current theory is cancer is a multi-step or a multi-mutation process that occurs over a substantial period. Colon polyps are an example. The polyp is present within the colon for years before it may develop into colon cancer. Chromosome shattering or chromothripsis is the exception to the prolonged, multi-step theory. This process is a sudden event of genetic or chromosomal mutations that can directly lead to a cancerous cell line. No doubt, cancer is related to chromosomal instability.vii Chromothripsis is the ultimate chromosomal instability.

One fact that is pertinent is humans possess certain genes in their chromosomes that promote the development of a cancerous cell. These genes are called proto-oncogenes or oncogenes. It is well established these genes can cause cancer. In addition, our chromosomal DNA contain tumor suppressor genes, which prevent a cell from becoming cancerous. There are numerous copies of these two types of genes on human chromosomes.

Characteristics of Chromothripsis

Below are the currently known features that signal chromosome shattering has occurred.

  • Present are many complex DNA rearrangements in localized regions of a chromosome or chromosome arm. Such findings support the theory that chromothripsis happens when DNA is condensed as in mitosis or cell division.viii
  • Low gene copy numbers with an alteration in between two states of gene encoding. This evidence supports the DNA rearrangements occurred in a short period.ix
  • Alternating regions where heterozygosity (two different DNA copies of the gene, called alleles) is retained with areas where heterozygosity is lost (only one DNA copy of the gene). Again, this observation suggests the DNA rearrangements or mutations happened when both parental copies of the chromosome were present (DNA replication). Such is seen only during mitosis or cell division.x
  • There is clustering of breakage points on the chromosome.xi
  • Randomness exists of the joining of DNA fragments along the resultant derivative, abnormal chromosome.xii

Breakdown and Repair of Chromosomal DNA

As above, chromothripsis is the shattering of distinct regions of a chromosome simultaneously in a single event. Subsequently, the DNA fragments are rejoined in an incorrect orientation. Entire lengths of chromosomal DNA involving multiple genes can be deleted. Such an event could produce double minute chromosomes, which are circular pieces of extra-chromosomal (away from the chromosome) DNA that can be encoded into its protein many times (amplification).xiii If the double minute chromosome contains an oncogene, then it will be encoded over and over, likely to create a cancerous cell.

Generally, DNA breaks are repaired by homologous recombination, which means there is a complementary open sequence of DNA to guide repair. With this process, there are only rare errors in the A, G, T, and C sequence of the DNA. In chromothripsis, repair seems to be mediated by non-homologous end joining (NHEJ) and microhomology-mediated break induced repair (MMBIR). Both systems do not utilize an open complementary sequence to guide DNA repair.xiv

Both NHEJ and MMBIR are associated with error-prone DNA repair. Complex deletions, amplifications, and translocations can easily happen. Why are these error-prone DNA repair mechanisms seen in chromothripsis? Possibly, the genes that encode for homologous recombination are disrupted. Likely, there are so many DNA breaks happening during chromothripsis that homologous recombination repair systems are overwhelmed. NHEJ and MMBIR repair mechanisms are recruited to rejoin the DNA fragments. DNA repair with both mechanisms lead to many gene mutations and chromosomal instability.xv

Mechanisms of Chromothripsis

There are several theories regarding the mechanism causing chromothripsis to occur.

Micronuclei

Micronuclei are vesicle-like structures that contain a chromosome or fragment of a chromosome enclosed in the cell’s nucleus. Micronuclei form when mitosis or cell division is not normal, and are seen in certain diseases.

The chromosomal DNA in micronuclei undergo defective replication. No DNA repair mechanism exists. Consequently, the DNA in the micronuclei that is not replicated typically breaks up. These DNA fragments may then be reincorporated back into a chromosome creating an abnormal chromosome. These irregular chromosomes may end up in the two daughter cell’s nucleus.xvi

Ionizing Radiation

If a strong enough dose of radiation hits the cell during mitosis, it could break up chromosomes into fragments. The problem is human beings are not

generally exposed to the amount of radiation it takes to disrupt chromosomes.xvii

Telomere Erosion or Breakage

A telomere is DNA located at the end of chromosomes. Telomeres serve a number of important functions for the chromosome. If a telomere erodes or is broken off, then the exposed ends of DNA will fuse together on homologous chromosomes. When the chromosomes are being pulled toward both daughter cells during mitosis, the chromosomes will break up in areas other than where they fused (anaphase bridging). The result is a rearranged, aberrant chromosome.xviii A rearranged chromosome is the hallmark of chromosome shattering. Telomere dysfunction has been associated with cancer.xix

Abortive Apoptosis

Apoptosis means cell dying or death. Endonucleolytic DNA breakage, or cleavage of DNA inside the chromosome, is a major component of apoptosis or cell death. If this cleavage is started then suddenly stopped (aborted) for whatever reason, the consequence will be the fragmentation of segments of a chromosome. Such fragmentation is what occurs in chromothripsis.xx It is known certain viruses may cause cancer development and some of these viruses can stop apoptosis.xxi

Replication Stress and Mitotic Errors

The activation of oncogenes can result in premature DNA replication termination during mitosis, and cause DNA breaks in an otherwise healthy cell.xxii If this happens, the DNA fragments may be rejoined abnormally, as is seen in chromothripsis. The aberrant chromosomes would enter the two daughter cells and could become cancerous. Mitotic errors are well documented. Mistakes during mitosis may cause aneuploidy, chromosome translocations, and the development of micronuclei. All these mistakes may create an abnormal chromosome and instability.

p53 Tumor Suppressor Gene

Patients with Li-Fraumeni Syndrome possess a mutated and inactivated p53 gene. It is sometimes called sarcoma, breast, leukemia, and adrenal gland syndrome because these patients very frequently develop cancer.xxiii This tumor suppressor gene assists in the control of cell division. It prevents cells with DNA damage from replicating and being perpetuated. If the DNA damage is extensive enough, p53 will cause apoptosis or cell death. If p53 is inactivated, the cells with DNA damage could replicate, divide, and grow, potentially causing cancer.xxiv

All these mechanism cause chromosome mutations, rearrangements, and instability observed in chromothripsis. Other processes could induce chromosome shattering. The exact method that creates chromothripsis has not yet been determined. It may be many different pathways could lead to this chromosome crisis.

Chromothripsis and Cancer

The hallmark of cancer is chromosomal instability and resultant mutations. The sudden breakage of much DNA in a chromosome with aberrant reassembly would create a lot of chromosomal instability and mutations. Chromothripsis has been known to cause oncogene amplification and loss of tumor suppressor genes.xxv When the number of chromosomes within a cell is abnormal (aneuploidy), micronuclei form. Aneuploidy is associated with tumor development, and micronuclei may be a cause of chromosome shattering.xxvi Patients with p53 mutations have been found to have chromothripsis mediated cancers.xxvii

Congenital Diseases

There are congenital diseases linked to chromothripsis. Bloom Syndrome is an inherited disorder characterized by short stature, facial rash, and a long, narrow face. A mutation in the BLM gene is the etiology. There is an elevated rate of DNA mutation and chromosomal instability. Patients with Bloom Syndrome are observed to have accumulations of micronuclei in their cells. Micronuclei is a possible cause of chromosome shattering.xxviii The BLM mutation is associated with a greatly increased risk of cancer. Leukemias, lymphomas, and carcinomas occur at an early age (in their twenties).

Fanconi Anemia is a genetic disease typified by short stature, skin pigmentation, and anemia from bone marrow failure. Patients with Fanconi Anemia possess dysfunctional DNA repair pathways due to a mutation in the FANCM gene. Increased micronuclei formation is observed, suggesting chromothripsis is happening. People with this disease have an extremely high risk of developing leukemia.xxix

Chromothripsis being Curative

There is an example of chromosome shattering curing a woman of a rare disease. As a child in the 1960s, the woman experienced repeated bacterial infections. An evaluation found low levels of white blood cells in her blood. The woman was the first described case of WHIM Syndrome. Manifestations of the disorder include warts, hypogammaglobulinemia (low antibody levels), infections, and myelokathexis (low white blood cells in the bloodstream due to retention in the bone marrow). There are 60 cases known.

Patients usually live into adulthood but suffer from lung scarring, hearing loss and other medical problems from repeated infections. They are susceptible to viruses that cause warts.

In 2003, researchers found WHIM patients had a defective CXCR4 gene. This gene encodes for a cell-surface protein or receptor that white blood cells utilize to recognize chemical messengers called chemokines. WHIM patients possess one normal copy of CXCR4 and a defective or mutated copy of the gene. The cell-surface protein or receptor becomes overactive. The result is white blood cells are retained in the bone marrow instead of being released into the blood.

The woman, who is currently 59 years old, brought her two daughters to be evaluated. She thought her children also had WHIM disease. Both daughters, after investigation, possessed the mutated CXCR4 gene.

When the physicians asked the woman how she was doing, she stated she had been fine since her thirties. Her response spiked the doctor’s interest.

Doing a little research, the investigators discovered the woman’s white blood cells no longer had the defective CXCR4 gene. In addition, the woman had one copy of chromosome 2 shorter than the other copy. Genomic analysis found the tell-tale signs of chromothripsis. Evidentially, a blood stem cell experienced chromosome shattering of chromosome 2 that got rid of the mutated CXCR4 gene. The stem cell survived and repopulated her bone marrow with “normal” white blood cells. The new white blood cells could now be released into the blood stream. The woman was cured.

Such is the first case of chromothripsis resulting in a cure of a disease. Further research is ongoing.xxx

Conclusion

Chromosome shattering or chromothripsis is a relatively newly described phenomenon. It was quickly associated with cancer. Chromothripsis is the exception to the theory that cancer formation is a multi-step process that evolves over a substantial period. Chromosome shattering, however, does not cause all cancers. There are many pathways that can create an cancerous cell.

Cancer is a disease of genomic or chromosomal instability. Chromothripsis represents extreme chromosomal instability, so it should not be a surprise it is linked to cancer and other diseases.

There is one example of chromosome shattering curing a rare disease. There are numerous disorders associated with abnormal genes, so such an event could happen again. Researchers should be diligent.

A single, catastrophic chromosomal episode has not been observed experimentally, but the circumstantial evidence of its occurrence is overwhelming. The exact mechanism of how chromothripsis happens has not yet been elucidated. There may be multiple processes that cause the phenomenon. More research is necessary.

References

i Stephens P, Greenman C, Fu B, et al. “Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development.” Cell, 2011 Jan. 7; 144(1): 27-40.

ii Forment J, Kaidi A, Jackson S, “Chromothripsis and Cancer: Causes and Consequences of Chromosome Shattering.” Nature Reviews Cancer, 12: 663-670, 2012.

iii Stephens P, Greenman C, Fu B, et al. “Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development.” Cell, 2011 Jan. 7; 144(1): 27-40.

iv Ibid.

v Jones M, Jallepalli P, “Chromothripsis: Chromosomes in Crisis.” Dev Cell 13; 23(5): 908-917, Nov. 13, 2012.

vi Ibid.

vii Baker D, Jin F, Jeganathan K, van Deursen J, “Whole Chromosome Instability Caused by Bub I Insufficiency Drives Tumorigenesis through Tumor Suppressor Gene Loss of Heterozygosity.” Cancer Cell, 16: 475-486, 2009.

viii Maher C, Wilson R, “Chromothripsis and Human Disease: Piecing Together the Shattering Process.” Cell, 148: 29-32, 2012.

ix Korbel J, Campbell, P, “Criteria for Inference of Chromothripsis in Cancer Genomes.” Cell, 152: 1226-1236, 2013.

x Ibid.

xi Ibid.

xii Ibid.

xiii Jones M, Jallepalli P, “Chromothripsis: Chromosome in Crisis.” Dev Cell, 23(5): 908-917, Nov. 13, 2012.

xiv Ibid.

xv Ibid.

xvi Forment J, Kaidi A, Jackson S, “Chromothripsis and Cancer: Causes and Consequences of Chromosome Shattering.” Nature Review Cancer, 12: 663-670, 2012.

xvii Jones M, Jallepalli P, “Chromothripsis: Chromosome in Crisis.” Dev Cell, 23(5): 908-917, Nov. 13, 2012.

xviii Tubio J, Estavill X, “Cancer: When Catastrophe Strikes a Cell.” Nature, 470: 476-477, 2011.

xix Artandi S, Chang S, Lee S, et al. “Telomere Dysfunction Promotes Non-Reciprocal Translocations and Epithelial Cancers in Mice.” Nature, 406: 641-645, 2000.

xx Tubio J, Estavill X, “Cancer: When Catastrophe Strikes a Cell.” Nature, 470: 476-477, 2011.

xxi Ibid.

xxii Jones M, Jallepalli P, “Chromothripsis: Chromosome in Crisis.” Dev Cell, 23(5): 908-917, Nov. 13, 2012.

xxiii Ibid.

xxiv Bartek J, Lukas C, Lukas J, “Checking on DNA Damage in S Phase.” Nature Reviews Molecular Cell Biology, 5: 792-804, 2004.

xxv Forment J, Kaidi A, Jackson S, “Chromothripsis and Cancer: Causes and Consequences of Chromosome Shattering.” Nature Reviews Cancer, 12: 663-670, 2012.

xxvi Janssen A, Van der Burg M, Szuhai K, et al. “Chromosome Segregation Errors as a Cause of DNA Damage and Structural Chromosome Aberrations.” Science, 333: 1895-1898, 2011.

xxvii Li M, Fang X, Baker D, et al. “The ATM-P53 Pathway Suppresses Aneuploidy-Induced Tumorigenesis.” Proceedings of the National Academy of Sciences, 107: 14188-14193, 2011.

xxviii Rosin M, German J, “Evidence for Chromosome Instability in vivo in Bloom Syndrome: Increased Numbers of Micronuclei in Exfoliated Cells.” Human Genetics, 71: 187-191, 1985.

xxix Tischkowitz M, Hodgson S, “Fanconi Anaemia.” Journal of Medical Genetics, 40: 1-10, 2003.

xxx Kaiser J, “Shattered Chromosome Cures Woman of Immune Disease.” Science/AAAS News, February 5, 2015.

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