Genome mosaicism

This presentation is fetures the basic introduction to Genome mosaicism in humans and nature, with some examples of its harmful effects on humans, with

1. Surender Rawat M. Sc. Microbial Biotechnology Mahrishi Dayanand University Rohtak , Haryana Human mosaicism : A new approach to study Genomics

2. CONTENTS Introduction Mosaicism Causes of Mosaicism Chimerism Difference between Mosaic and chimera Somatic Mosaicism Germline Mosaicism Gonosomal Mosaicism Point mutations and small insertions and deletions Reversion mosaicism Detection of mosaicism Refrences

3. Introduction GENOME - The  genome is the genetic material of an organism . MOSAICISM - Mosaicism is a condition in which cells within the same person have a different genetic makeup. The phenomenon was discovered by  Curt Stern. In 1936, he demonstrated that recombination, normal in meiosis, can also take place in mitosis.  When it does, it results in somatic (body) mosaics. These are organisms which contain two or more genetically distinct types of tissue.

4. Mosaicism Named after the intricate images created by the craftsman from small pieces of coloured tiles. The coexistence of two or more genetically distinct cell populations derived  originally from a single zygote.  Mosaics may arise at any stage of development, from the two-cell stage onward, or in any tissue which actively proliferates thereafter.  The phenomenon is commonly observed in many species of animals and plants and  may be caused by somatic mutation or chromosomal  nondisjunction .  An individual animal or plant may exhibit  mosaicism , or it may occur in a culture of a single cell- or tissue-type obtained from an individual.

5.  When eye colours vary between the two eyes, or within one or both eyes, the condition is called  heterochromia  iridis  (= 'different coloured iris').  Changes may take place in the dividing cells leading up to iris formation in the embryo. Heterochromia  iridis EXAMPLES

6. Calico Cats These females are heterozygous  for the X-linked  colour genes: the genes for their coat colours are carried on the X chromosome. X-inactivation causes groups of cells to carry either one or the other X-chromosome in an active state. EXAMPLES

7. Mosaic gynandromorph of  Papilio androgeus FEMALE MALE MOSAIC GYNANDROMORPH A  gynandromorph  is an organism that contains both male and female characteristics. While the organism is only a few cells large, one of the dividing cells does not split its sex chromosomes typically. This leads to one of the two cells having sex chromosomes that cause male development and the other cell having chromosomes that cause female development.

8. We - Humans Use of aCGH and SNP chips has allowed detection of events that were missed by karyotyping Scientists analyzed the genomes of a bunch of iPSC lines and then compared them to the “parental” fibroblast cells from which they had been made CNV arose specifically during the iPSC production process CNVs varied from one cell to another even though all the cells came from a single person . Mosaicism for small for small intragenic CNV was detected in 10% of 30 molecularly diagonised Subjects and extensive genomic CNVs have been found in clonal isolates of embryonic stem cell. In addition, varying levels of mosaicism have reported in somatic human tissues including the skin, Brain, blood and induced pluripotent stem cells “means not all your cells have the same DNA”

9. CAUSES OF MOSAICISM Mosaicism may result from: Unusual events in cell division (mitosis). A gene mutation during development De novo pre zygotic mutation De novo post zygotic mutation A chromosomal mutation during development X-inactivation: one X chromosome is randomly switched off in cells of a female mammal Numerical or structural abnormalities of chromosomes Deletion Aneuploidy

10. Chimerism Chimerism — the presence of two or more cell lines that are derived from different zygotes in an organism . A 52-year-old woman from Boston was told that she was not the biological mother of her children, after years of raising them. The woman who claimed to have given birth to her children had a set of genes completely different from those of two of her three children. but the DNA of the children matched their father’s DNA. After working for nearly two years on the case, doctors came up with an answer to the problem: the woman was a “human chimera.”

11. DIFFERENCE BETWEEN MOSAICS AND CHIMERA MOSAICS Cells in the organism have same genetic origins Nearly all loci are identical in the different cell populations as all cells are derived from the same zygotic genotype Somatic mutations make us all mosaic CHIMERA A single organism composed of genetically distinct cells. In chimerism there are divergent genotypes all across the genome. Chimeras can be artificially produced: organ transplants, chimera of diffferent animals

12. Example of some diseases caused due to Genome Mosaicism Cancer Heterochromia iridis Lines of Blaschko Neurofibromatosis type 1 Proteus syndrome Osteogenesis imperfecta type II The cells in our body do not all contain identical genomes, which has implications for health and disease.

13. Somatic Mosaicism The non-germ cells of the body are heterogeneous: some have a mutation and some do not. The person may or may not be affected by the disorder caused by that mutation. Individuals will express the phenotype depending on how many and which cells are affected. Typically, individuals with somatic mosaicism exhibit a milder phenotype since only a proportion of cells contain the mutation and/or because the mutation is confined to a finite segment of the body. Clinical Information on Diseases: Cancer Down Syndrome - Lines of Blaschko

14. A classic example of somatic mosaicism . Cancer arises when cells grow uncontrollably, which can be caused by mutations in genes that prevent the cell from properly functioning within the cell cycle or prevent it from cell death at the proper time. Most cancers occur sporadically, meaning they are not due to an inherited predisposition. Some inherited cancer syndromes include breast and ovarian cancer (BRCA1/2 genes), colon cancer, retinoblastoma, and thyroid cancer. Since these mutations are only present in the cancer cells and not the rest of the cells in the body, the individual has somatic mosaicism  for these mutations. Cancer

15. Lines of Blaschko Blaschko lines or the lines of Blaschko are thought to represent pathways of epidermal cell migration and proliferation during the development of the fetus. These lines are invisible but many inherited and acquired diseases of skin manifest themselves according to these patterns creating the visual appearance of these lines.

16. Germline Mosaicism The diploid germ cell precursors in the gonad are heterogeneous: some have a mutation and some do not. A mosaic germline mutation is significant because it can be passed to offspring. Germline mosaicism can be observed with any inheritance pattern, but it is most commonly seen with autosomal dominant and X-linked disorders. Most individuals are unaware they possess a germline mutation until they have children that are affected. Clinical Information on Diseases: Osteogenesis imperfecta Ovarian dysgenesis

17. Germline Mosaicism

18. Osteogenesis imperfecta type II Sometimes known as  brittle bone disease Bone disorder characterized by brittle bones that are prone to fracture. People with OI are born with defective connective tissue, or without the ability to make it, usually because of a deficiency of Type-I collagen.  Eight types of OI can be distinguished. Most cases are caused by mutations in the  COL1A1  and  COL1A2 genes. Severe and usually lethal in the perinatal period Most cases die within the first year of life due to respiratory failure or  intracerebral hemorrhage

19. Gonosomal Mosaicsm A combination of germline and somatic mosaicism Example is Neurofibromatosis type 2 (NF2) is an autosomal dominant cancer syndrome Symptoms are dizziness; headache; facial weakness, numbness, or pain; ringing in the ears and progressive hearing loss. This disease is caused by inactivating mutations in the NF2 tumour -suppressor gene, located in 22q12, that normally gives rise to a product called Merlin. This peptide is thought to have a tumor-suppressive function Merlin's deficiency can result in unmediated progression through the cell cycle due to the lack of contact-mediated tumour suppression, sufficient to result in the tumors characteristic of NF II.

20. Point mutations and small insertions and deletions Recently, a range of disorders has been shown to be caused by mosaicism for point mutations, primarily using NGS technologies Non-overgrowth mosaic disorders like Benign keratinocytic epidermal nevi, which have been shown to be caused by mutations in fibroblast growth factor receptor 3 ( FGFR3), phosphatidylinositol‑4, -5‑bisphosphate 3‑kinase and different RAS family members. A series of mosaic overgrowth disorders was molecularly delineated, beginning with Proteus syndrome, which was shown to be due to AKT1 mutations

21. Proteus syndrome Causes skin overgrowth and a typical bone development, often accompanied by tumours over half the body. Proteus syndrome results from a mutation in the  AKT1  gene. The  AKT1  gene helps regulate cell growth and division (proliferation) and cell death. A mutation in this gene disrupts a cell's ability to regulate its own growth, allowing it to grow and divide abnormally. Increased cell proliferation in various tissues and organs leads to the abnormal growth characteristic of Proteus syndrome. Studies suggest that an  AKT1  gene mutation is more common in groups of cells that experience overgrowth than in the parts of the body that grow normally

22. Proteus syndrome

23. Chromosomal Mosaicism Chromosome  nondisjunction  is probably the principal cause of chromosomal aberration,  which in turn may lead to the development of  mosaicism . Chromosomal alterations (such as whole-chromosome aneuploidy , segmental aneuploidy (that is, aneuploidy of parts of chromosomes) and structural alterations) have been historically identified by cytogenetic analyses

24. Mosaicism can result when that genetic lesion is completely or partially reverted, perhaps driven by selective pressure, in a subset of cells in the multicellular organism. For example, the phenomenon of revertant mosaicism has recently been described, in which a mutation was spontaneously directly corrected in a subset of cells in an affected organ. This phenomenon has been demonstrated in blood, muscle, liver and skin, of which skin is most dramatic, as the normal patches can be directly visualized among the abnormal patches. Reversion mosaicism

25. Detection of mosaicism Recent technological advances have provided us with tools to assess mosaicism on a much broader scale, in many disorders and in diverse tissues, with increasing resolution to detect smaller-scale mutations Different approaches used to study mosaicism include Cytogenetics Microarray DNA sequencing

26. Cytogenetics Cytogenetic analysis by study of banded metaphase chromosomes or by fluorescence in situ hybridization (FISH) is carried out in a cell‑ by ‑ cell manner, and recognition of mosaicism is therefore fairly straightforward. Mosaicism is recognized when cells within an individual are found to have divergent chromosome contents, such as monosomic or trisomic chromosomes in the karyotype of one cell and a normal karyotype in another. The cytogenetic detection of low-level mosaicism is challenging, as a sufficient number of cells must be counted

27. Microarray-based techniques Beginning in 2005, microarray-based techniques began to replace cytogenetic testing, with the introduction first of array-based comparative genomic hybridization ( aCGH ), which can analyse genomic copy number variants (CNVs). It is followed by genome-wide SNP arrays, which can analyse both SNPs and CNVs. The advantages of array-based testing (which typically analyses DNA extracted from whole blood) for mosaicism detection include: many cells are analysed simultaneously; different cell types are analysed ; cells of all cell cycle phases are analysed ; samples do not require culturing, which might itself cause mutations SNP arrays are much more sensitive than aCGH for mosaicism detection.

28. DNA sequencing Sanger-based sequencing can be extremely effective for many applications, but it is a low throughput technique. NGS is a high-throughput technique that is massively used nowadays. These digital data are more amenable to statistical approaches to distinguish mosaicism from sequencing errors. It also does not require genetic mapping data to identify causative genetic variants. For this reason, subtractive informatic approaches — in which two samples are informatically processed to identify only those positions in the genome that differ — can be coupled to NGS to identify mosaic alterations.

29. Conclusions and future perspectives The recognition of mosaic disorders is rapidly increasing. It can affect somatic tissues, the germ line or both. It can arise at various stages of development or adult life and can be caused by mutation from a normal genotype to a variant genotype or from a variant genotype to a normal genotype. Recent advances in genomic technologies have enhanced our ability to study the widespread nature of mosaicism in both healthy individuals and in patients with a wide range of disorders. Recent insights include: Identification of disease genes for disorders that are seen only as mosaics as they are lethal when constitutional the identification of chimerism by whole-genome tools recognition of the changing rates of mosaicism with increasing age represents a window on the ageing process.

30. Refrences Abyzov , A. et al. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature 492, 438–442 (2012). Biesecker and Nancy . A genomic view of mosaicism and human disease , Nature, 2013 Youssoufian & Pyeritz MECHANISMS AND CONSEQUENCES OF SOMATIC MOSAICISM IN HUMANS, Nature, 2002 Mardis , E. R. The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133–141 (2008). Happle , R. Mosaicism in human skin. Understanding the patterns and mechanisms. Arch. Dermatol . 129, 1460–1470 (1993). Lindhurst , M. J. et al. A mosaic activating mutation in AKT1 associated with the Proteus syndrome. New Engl. J. Med. 365, 611–619 (2011). Callum , P. et al. Gonosomal mosaicism for an NF1 deletion in a sperm donor: evidence of the need for coordinated, long-term communication of health information among relevant parties. Hum. Reprod . 27, 1223–1226 (2012). Maertens , O. et al. Molecular dissection of isolated disease features in mosaic neurofibromatosis type 1. Am. J. Hum. Genet. 81, 243–251 (2007). Conlin , L. K. et al. Mechanisms of mosaicism , chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis. Hum. Mol. Genet. 19, 1263–1275 (2010). Hook, E. B. Exclusion of chromosomal mosaicism : tables of 90%, 95% and 99% confidence limits and comments Shin, S. Y., Yoo , H. W., Lee, B. H., Kim, K. S. & Seo , E. J. Identification of the mechanism underlying a human chimera by SNP array analysis. Am. J. Med. Genet. A 158, 2119–2123 (2012). Conlin , L. K. et al. Utility of SNP arrays in detecting, quantifying, and determining meiotic origin of tetrasomy 12p in blood from individuals with Pallister –Killian syndrome. Am. J. Med. Genet. A 158, 3046–3053 (2012).