>Magister Scientiae - MSc / Molecular genetics: strategies to indentify congenital cataract genes in captive-bred Vervet monkeys Zandisiwe Emilia Magwebu MSc thesis, Department of Medical Biosciences, University of the Western Cape The present study describes molecular aspects of inherited congenital cataract in captive-bred Vervet monkeys. Congenital cataracts are lens opacities that are present at birth or soon after birth and include hereditary cataracts or cataracts caused by infectious agents. The MRC Primate Unit is housing a colony of captive-bred Vervet monkeys in which 7.5% is suffering from congenital cataract. However, the parents of the affected individuals were asymptomatic. Six families within the colony have been identified to be affected by two types of morphologies (Ysutural and total cataract). Based on the evidence provided above, it was speculated that the colony was affected with autosomal recessive cataract. The main aim of this study was to facilitate a strategy for managing breeding programs by minimizing cataract occurrences in captive-bred Vervet monkeys. Integrated combination of clinical, molecular and bioinformatic strategies were used to identify and assess reciprocal candidate susceptibility genes for cataracts. The genes that are known to be responsible for most human congenital cataract cases were prioritized. The genes include Heat shock transcription factor 4 (HSF4), Crystalline Alpha A (CRYAA), glucosaminyl (N-acetyl) transferase 2 (GCNT2) and Lens intrinsic membrane protein 2 (LIM2). Twenty two subjects were selected based on their morphology (5 carriers, 5 controls and 12 cataracts). 2ml of blood was collected for Deoxyribonucleic acid (DNA) extraction. Coding exons and flanking regions were screened by polymerase chain reaction (PCR) amplification and sequenced. The CLC DNA workbench was used for results analysis. The screening of four genes revealed 20 sequence variants which were not present in the control individuals. Sequencing of HSF4 revealed three mutations: R116R, L245>L and P421>L in exon 5, 10 and 14, respectively. The coding exons for CRYAA showed two sequence variants: S134W and K166N in exon 3. Twelve mutations were identified in exon one of all three GCNT2 transcripts (A, B and C). These mutations include: G212G, H256>H, M258>V, N275>N, V16>I, Y122>F, S15>S, S24>N, S38>S, I118>I, D194>D and Y373>Y which was found in exon three of all transcripts. There were no mutations in LIM2, however, three single nucleotide polymorphisms (SNPs) were identified in exon 2 (P66>P) and 3 (I118>T and A127>T). The above mutations were conserved when aligned with other species. The sequence variations vary among the families and those individuals with the same or different cataract phenotype. Based on these findings, it can be concluded that the four candidate genes harbour mutations that are responsible for both phenotypes. The effect of these mutations in Vervet monkeys is not yet understood, however, their impact will be further investigated. For future studies, it will be of absolute importance to screen the entire family to verify that indeed cataract formation in this colony is inherited in an autosomal recessive manner.

The Himalayan Mountain range encompasses an unparalleled landscape featuring some of the planet’s highest peaks, including Mount Everest. In the heart of this massive orographic barrier lies Nepal, sandwiched in the historically geostrategic position between the Tibetan plateau to the north and India in the south. Until recently, Nepalese and Tibetan populations remained poorly characterized genetically, partly because of their inaccessible geographical locations. In the present study, the genetic diversity of these two Himalayan populations is evaluated using different marker systems, including mitochondrial DNA (mtDNA) and Short Tandem Repeats (STRs) in the autosomes as well as on the Y-chromosome (Y-STR). While autosomal STRs are distributed throughout the genome and are biparentally inherited, the Y-chromosome and mtDNA are haploid markers and provide the paternal and maternal histories of the population, respectively. Fifteen autosomal STR loci were typed in 341 unrelated individuals from three Nepalese populations (188), namely Tamang (45), Newar (66) and Kathmandu (77), and a general collection from Tibet (153). These samples were also sequenced for the mtDNA control region and all of them were subsequently assigned to 75 different mtDNA haplogroups and sub-haplogroups by screening their diagnostic sites in the coding region using Restriction Fragment Length Polymorphism analysis and/or sequencing, thus achieving an unprecedented level of resolution. The results from the autosomal and mtDNA data suggest a Northeast Asian origin for the Himalayan populations, with significant genetic influence from the Indian subcontinent in Kathmandu and Newar, corroborating our previous Y-chromosome study. In contrast, Tibet displays a limited Indian component, suggesting that the Himalayan massif acted as a natural barrier for gene flow from the south. The presence of ancient Indian mtDNA lineages in Nepal implies that the region may have been inhabited by the earliest settlers who initially populated South Asia. In addition, seventeen Y-STR loci were analyzed in 350 Tibetan males from three culturally defined regions of historical Tibet: Amdo (88), Kham (109) and U-Tsang (153). The results demonstrate that the 17 Y-STR loci studied are highly polymorphic in all the three Tibetan populations examined and hence are useful for forensic cases, paternity testing and population genetic studies.

Ataxia Telangiectasia Mutated (ATM) gene helps to repair DNA damage and that increased cancer risks are associated with having a mutation in an ATM gene. ATM gene is newer compared to other known hereditary cancer genes. We present a rare care of 66-year-old female with extensive personal and family history of breast and pancreatic cancer had negative imaging surveillance until recent systemic imaging showed new pancreatic head 2.5x2.5 cm mass. Endoscopic ultrasound confirmed invasion of superior mesenteric vein with near confluence. No regional adenopathy was seen. She was felt to be borderline resectable and neoadjuavant chemotherapy was planned. She had a personal history of right breast cancer diagnosed in 1998 status post lumpectomy and axillary lymph node dissection and adjuvant chemotherapy with CMF regimen x 5 cycles and radiation therapy and endocrine therapy with tamoxifen for 5 years. In 2011 she was also diagnosed with rectal well to moderately differentiated adenocarcinoma status post abdominoperitoneal resection on 3/15/2011, 36 lymph nodes were negative, but the surgical circumferential radial margin was positive. She underwent adjuvant radiation therapy with total dose of 45 Gy. There was recurrence in vaginal and bladder wall adenocarcinoma in 2014 for which patient underwent an anterior exenteration. Pathology felt this was endocervical origin of malignancy and patient received megace therapy for 3 years based on hormone receptor positive status. For new diagnosis of pancreatic adenocarcinoma, she was started on Gemcitabine and Abraxane chemotherapy. Given extensive personal and family history of malignancy, she was referred to genetic counsellor. Hereditary cancers panel at invitae laboratory was positive for a heterozygous pathological variant in the ATM gene deletion (exons 62-63). ATM gene is associated with an increased risk for autosomal dominant breast, pancreatic and prostate cancer. Close relatives (children, siblings, and each parent) have up to a 50% chance of being a carrier of this variant. It is essential for treating physicians to educate patients and family members on the risk for subsequent malignancies.

Sexual assault investigations utilize both physical and biological evidence to aid in the investigation. Physical evidence may include fingerprints, hair, fibers, stains, soil, and glass. Biological evidence may include semen, saliva, vaginal secretions, menstrual blood, and skin. Semen, often found in small or trace quantities, is of great importance when trying to identify the perpetrator. From the semen sample, DNA profiles using autosomal short tandem repeats (aSTRs) (gold standard in forensic science) or Y-chromosome short tandem repeats (Y-STRs) can be obtained and can be used to identify a perpetrator through comparison to suspect reference samples or by searching the profile against a DNA database (CODIS). Obtaining DNA profiles can be challenging when assaults are reported many days after the incident. The amount of semen will decrease as the time frame increases due to various factors such as drainage from the vagina. To potentially overcome this obstacle and improve the recovery of profiles from extended interval samples, it may be possible to develop novel collection and analysis methods using individual or few sperm cells. Small quantities of sperm cells may still be present in extended interval samples that may otherwise fail to provide a DNA profile using conventional methods. The work presented here focuses on the development of these novel analysis methods using micromanipulation techniques and enhanced amplification strategies for the analysis of individual sperm cells to determine if a full DNA profile is present. The developed methods will be applied to the analysis of extended interval post coital samples.

No description available.

Familial primary hyperparathyroidism (HPT) is a rare disorder that is treated surgically and mostly occurs in association with tumor-susceptibility syndromes, like multiple endocrine neoplasia and the hyperparathyroidism-jaw tumor syndrome. Familial hypercalciuric hypercalcemia (FHH) is another cause of hereditary hypercalcemia that generally is considered to require no treatment and is genetically and pathophysiologically distinct from HPT. Inactivating mutations in the calcium receptor gene cause FHH, whereas the down-regulated expression of the CaR in HPT never has been coupled to CaR gene mutations. Family screening revealed a hitherto unknown familial condition with characteristics of both FHH and HPT. The hypercalcemia was mapped to a point mutation in the intracellular domain of the CaR gene that was coupled to relative calcium resistance of the PTH release by transient expression in HEK 294 cells. Unusually radical excision of parathyroid glands was required to normalise the hypercalcemia. The mildly enlarged parathyroid glands displayed hyperplasia with nodular components. Frequent allelic loss on especially 12q was found and contrasts to findings in HPT. Allelic loss was also seen in loci typical for primary HPT like 1p, 6q and 15q, but not 11q13. Quantitative mRNA analysis showed that the glands had mild increase in a proliferation index (PCNA/GAPDH mRNA ratio) and mild reduction in genes important to parathyroid cell function, like CaR, PTH, VDR and LRP2. A previously unrecognized variant of hypercalcemia is explored that could be one explanation for persistent hypercalcemia after apparently typical routine operations for HPT. It also raises the issue of possibilities to treat FHH with parathyroidectomy provided it is radical enough.

Autosomal recessive spastic ataxia of Charlevoix Saguenay (ARSACS) is an early onset neurodegenerative disorder resulting from mutations in the SACS gene that encodes the protein sacsin. Sacsin is a 520kDa multi-domain protein localised at the cytosolic face of the outer mitochondrial membrane with suggested roles in proteostasis and most recently in the regulation of mitochondrial morphology. An excessively interconnected mitochondrial network was observed as a consequence of reduced levels of sacsin protein following SACS knockdown in neuroblastoma cells as well as in an ARSACS patient carrying the common Quebec homozygous SACS mutation 8844delT. Moreover, it was suggested that sacsin has a role in mitochondrial fission as it was found to interact with mitochondrial fission protein Dynamin related protein 1 (Drp1). The aim of this thesis was to explore sacsin’s role in the regulation of mitochondrial morphology and dynamics in non-Quebec ARSACS patients and sacsin knockdown fibroblasts. This study shows that loss of sacsin function promotes a more interconnected mitochondrial network in non-Quebec ARSACS patients and in sacsin knockdown fibroblasts. Moreover, recruitment of the essential mitochondrial fission protein Drp1 to the mitochondria was significantly reduced in ARSACS patient cells and in sacsin knockdown fibroblasts. This reduced recruitment of Drp1 to mitochondria also occurred when cells were treated to induce mitochondrial fission. Furthermore, both the size and intensity of Drp1 foci localised to the mitochondria were significantly reduced in both sacsin knockdown and patient fibroblasts. Finally, reduced ATP production, decreased respiratory capacity of mitochondria and an increase in mitochondrial reactive oxygen species demonstrated impaired mitochondrial function in ARSACS patient and sacsin knockdown fibroblasts. These results suggest a role for sacsin in the stabilisation or recruitment of cytoplasmic Drp1 to prospective sites of mitochondrial fission similar to that observed by other mitochondrial fission accessory proteins.

Sacsin, which is mutated in the neurodegenerative disease Autosomal Recessive Spastic Ataxia of Charlevoix-Saguenay (ARSACS), is a 520 kDa modular protein with regions of homology to molecular chaperones and domains linking to the ubiquitin proteasome system. This suggests a role in proteostasis. Previously, sacsin has been shown to partially localise with mitochondria, and loss of sacsin results in elongated and dysfunctional mitochondria. Moreover, alterations in neurofilaments have recently been reported in a mouse model of ARSACS. Despite these findings, pathophysiological mechanisms of ARSACS are poorly understood. The aim of this thesis was to elucidate the cellular role of sacsin by determining how loss of its function leads to the observed mitochondrial and intermediate filament defects. This hoped to shed light on the mechanism of disease in ARSACS. The results indicate that the mitochondrial elongation seen in ARSACS is likely due to reduced mitochondrial localisation of the essential fission factor DRP1. This may be mediated by loss of function of a complex involving sacsin and dynactin-6, a subunit of the dynein-dynactin motor complex, which has previously been shown to be required for DRP1 mitochondrial recruitment. DRP1-mediated mitochondrial fission is necessary for mitochondrial quality control; hence a disruption to mitochondrial quality control is likely to occur in sacsin deficient cells, which may explain the mitochondrial dysfunction in ARSACS. Furthermore, sacsin null cells display a dramatic collapse and perinuclear bundling of the vimentin intermediate filament network. This is coupled with the displacement of cellular organelles, particularly mitochondria, early endosomes and the Golgi, which accumulate at the periphery of the vimentin bundle. These are characteristic features of aggresome formation, indicating an aggregation of misfolded protein, which occurs due to disrupted proteostasis. Further supporting this, the proteostasis components ubiquitin, HSP70, LAMP2 and p62 are recruited to the perinuclear vimentin bundles. In summary, the findings of this thesis indicate a role for sacsin in mitochondrial and protein quality control, the dysfunction of which is likely to be particularly detrimental in neurons. Mitochondrial dysfunction along with protein misfolding and aggregation are implicated in many neurodegenerative diseases, and ARSACS is no exception.

<p>Familial primary hyperparathyroidism (HPT) is a rare disorder that is treated surgically and mostly occurs in association with tumor-susceptibility syndromes, like multiple endocrine neoplasia and the hyperparathyroidism-jaw tumor syndrome. Familial hypercalciuric hypercalcemia (FHH) is another cause of hereditary hypercalcemia that generally is considered to require no treatment and is genetically and pathophysiologically distinct from HPT. Inactivating mutations in the calcium receptor gene cause FHH, whereas the down-regulated expression of the CaR in HPT never has been coupled to CaR gene mutations. </p><p>Family screening revealed a hitherto unknown familial condition with characteristics of both FHH and HPT. The hypercalcemia was mapped to a point mutation in the intracellular domain of the CaR gene that was coupled to relative calcium resistance of the PTH release by transient expression in HEK 294 cells. Unusually radical excision of parathyroid glands was required to normalise the hypercalcemia. The mildly enlarged parathyroid glands displayed hyperplasia with nodular components. Frequent allelic loss on especially 12q was found and contrasts to findings in HPT. Allelic loss was also seen in loci typical for primary HPT like 1p, 6q and 15q, but not 11q13. Quantitative mRNA analysis showed that the glands had mild increase in a proliferation index (PCNA/GAPDH mRNA ratio) and mild reduction in genes important to parathyroid cell function, like CaR, PTH, VDR and LRP2. </p><p>A previously unrecognized variant of hypercalcemia is explored that could be one explanation for persistent hypercalcemia after apparently typical routine operations for HPT. It also raises the issue of possibilities to treat FHH with parathyroidectomy provided it is radical enough.</p>

Familial primary hyperparathyroidism (HPT) is a rare disorder that is treated surgically and mostly occurs in association with tumor-susceptibility syndromes, like multiple endocrine neoplasia and the hyperparathyroidism-jaw tumor syndrome. Familial hypercalciuric hypercalcemia (FHH) is another cause of hereditary hypercalcemia that generally is considered to require no treatment and is genetically and pathophysiologically distinct from HPT. Inactivating mutations in the calcium receptor gene cause FHH, whereas the down-regulated expression of the CaR in HPT never has been coupled to CaR gene mutations. Family screening revealed a hitherto unknown familial condition with characteristics of both FHH and HPT. The hypercalcemia was mapped to a point mutation in the intracellular domain of the CaR gene that was coupled to relative calcium resistance of the PTH release by transient expression in HEK 294 cells. Unusually radical excision of parathyroid glands was required to normalise the hypercalcemia. The mildly enlarged parathyroid glands displayed hyperplasia with nodular components. Frequent allelic loss on especially 12q was found and contrasts to findings in HPT. Allelic loss was also seen in loci typical for primary HPT like 1p, 6q and 15q, but not 11q13. Quantitative mRNA analysis showed that the glands had mild increase in a proliferation index (PCNA/GAPDH mRNA ratio) and mild reduction in genes important to parathyroid cell function, like CaR, PTH, VDR and LRP2. A previously unrecognized variant of hypercalcemia is explored that could be one explanation for persistent hypercalcemia after apparently typical routine operations for HPT. It also raises the issue of possibilities to treat FHH with parathyroidectomy provided it is radical enough.