Investigating somatic variants and pathways in mismatch repair-deficient (dMMR) colorectal carcinoma in South Africa.

AIMS: Colorectal carcinoma (CRC) is a common cause of morbidity and mortality worldwide, and an emerging public health problem in sub-Saharan Africa. Several authors have described an increased frequency of mismatch repair-deficient (dMMR) CRC in sub-Saharan Africa, but these tumours remain poorly characterised molecularly. We sought to interrogate the somatic molecular genetic landscape of dMMR CRC in a cohort of young patients to better inform Lynch syndrome (LS) screening strategies and personalised medicine approaches in our setting. METHODS: 32 patients (aged <60 years) were identified with dMMR CRC. DNA was extracted from selected formalin-fixed paraffin-embedded (FFPE) tissue resection samples and subjected to amplicon-based next-generation sequencing (NGS). RESULTS: Pathogenic or likely pathogenic variants were detected in the corresponding MMR gene in 14 of 18 (78%) MLH1/PMS2-deficient tumours, 5 of 8 (63%) MSH2/MSH6-deficient tumours, 1 of 4 (25%) tumours with isolated MSH6 loss and 0 of 2 tumours with isolated PMS2 loss. Previously unreported variants were identified in MLH1 (three) and MSH2 (one). Cases with a variant allele frequency suggesting a germline mutation were identified in MLH1 (eight), MSH2 (two) and MSH6 (one). Only one MMR gene variant was detected in more than one patient (MLH1 p.Q510*). Four POLE/POLD1 exonuclease domain variants were identified, one of which was previously unreported. CONCLUSION: The spectrum of disease-causing MMR gene variants in our population necessitates NGS testing for LS screening. This study also highlights the role of somatic testing on readily available FFPE samples to generate data on the epidemiology of CRC in different settings.

SARS-CoV-2 Viral Replication Persists in the Human Lung for Several Weeks after Symptom Onset.

Rationale: In the upper respiratory tract, replicating (culturable) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is recoverable for ∼4-8 days after symptom onset, but there is a paucity of data about the frequency and duration of replicating virus in the lower respiratory tract (i.e., the human lung).Objectives: We undertook lung tissue sampling (needle biopsy) shortly after death in 42 mechanically ventilated decedents during the Beta and Delta waves. An independent group of 18 ambulatory patients served as a control group.Methods: Lung biopsy cores from decedents underwent viral culture, histopathological analysis, electron microscopy, transcriptomic profiling, and immunohistochemistry.Measurements and Main Results: Thirty-eight percent (16 of 42) of mechanically ventilated decedents had culturable virus in the lung for a median of 15 days (persisting for up to 4 wk) after symptom onset. Lung viral culture positivity was not associated with comorbidities or steroid use. Delta but not Beta variant lung culture positivity was associated with accelerated death and secondary bacterial infection (P < 0.05). Nasopharyngeal culture was negative in 23.1% (6 of 26) of decedents despite lung culture positivity. This hitherto undescribed biophenotype of lung-specific persisting viral replication was associated with an enhanced transcriptomic pulmonary proinflammatory response but with concurrent viral culture positivity.Conclusions: Concurrent rather than sequential active viral replication continues to drive a heightened proinflammatory response in the human lung beyond the second week of illness and was associated with variant-specific increased mortality and morbidity. These findings have potential implications for the design of interventional strategies and clinical management of patients with severe coronavirus disease (COVID-19).

Mucoepidermoid carcinoma of the bronchus in two children: Case reports.

Childhood mucoepidermoid carcinomas (MEC) of the bronchus are rare. They present with non-specific symptoms and signs making diagnosis delayed. We present two children with bronchial MEC managed in a tertiary children's hospital in Cape Town, South Africa. The first was a 11-year male with recurrent haemoptysis and the second child was a 6-year female with recurrent unifocal pneumonia. Chest CT scan and bronchoscopy with biopsy confirmed the diagnosis. Both patients underwent treatment, including surgery and are doing well. It is important to exclude endobronchial lesions when children present with recurrent respiratory symptoms, since early diagnosis will enable lung-sparing treatment.

Genomic landscape of colorectal carcinoma in sub-Saharan Africa.

Our understanding of the molecular classification of colorectal carcinoma (CRC) has evolved significantly over the past two decades. Tumours can be broadly categorised as microsatellite stable (MSS), microsatellite instability (MSI) or CpG island-methylator phenotype. Prognostic and predictive information is provided by these categories. The overwhelming majority of the data on which these categories are based have originated from Europe and North America. There is a dearth of information represented from Africa and indigenous African patients. However, some small studies and preliminary data have shown significant differences in all of these groups. The prevalence of MSI in Africa is consistently reported as almost double that of European and North American data. Interestingly, BRAF V600E mutations and MLH1 promotor hypermethylation seem to be uncommon in Africa. The high proportion of MSI tumours is only partly accounted for by germline mutations in mismatch repair genes (Lynch syndrome), suggesting that there are likely to be other mechanisms at play. Within the MSS group, preliminary data suggest that the typical molecular pathways (Wingless/Integrated pathway activation) may not be as dominant in Africa. The purpose of this review is to summarise the current state of the molecular genetic landscape of CRC in Africa and provide insights into areas for further study.

Placental pathology in women with HIV.

Recognizing the importance of placental features and their unique functions can provide insight into maternal health, the uterine environment during the course of pregnancy, birth outcomes and neonatal health. In the context of HIV and antiretroviral therapy (ART), there have been great strides in the prevention of mother to child transmission of HIV. However, there is still paucity of data on the impact of HIV/ART exposure on placental pathology and studies available only examine specific patterns of placental injury, further justifying the need for a more defined and comprehensive approach to the differential diagnoses of HIV/ART-exposed placentae. The purpose of this review is to consolidate findings from individual studies that have been reported on patterns of placental injury in the context of HIV/ART exposure. In both the pre- and post-ART eras HIV and/or ART has been associated with placental injury including maternal vascular malperfusion as well as acute and chronic inflammation. These patterns of injury are further associated with adverse birth outcomes including preterm birth and current evidence suggests an association between poor placental function and compromised fetal development. With the ever increasing number of pregnant women with HIV on ART, there is a compelling need for full incorporation of placental diagnoses into obstetric disease classification. It is also important to take into account key elements of maternal clinical history. Lastly, there is a need to standardize the reporting of placental pathology in order to glean additional insight into the elucidation of HIV/ART associated placental injury.

T-Cell Homeostatic Imbalance in Placentas From Women With Human Immunodeficiency Virus in the Absence of Vertical Transmission.

BACKGROUND: Implementation of universal antiretroviral therapy (ART) has significantly lowered vertical transmission rates but has also increased numbers of human immunodeficiency virus (HIV)-exposed uninfected children, who remain vulnerable to morbid effects. In the current study, we investigated whether T-cell alterations in the placenta contribute to altered immune status in HIV-exposed uninfected. METHODS: We analyzed T cells from term placenta decidua and villous tissue and paired cord blood from pregnant women living with HIV (PWH) who initiated ART late in pregnancy (n = 21) with pregnant women not living with HIV (PWNH) (n = 9). RESULTS: Placentas from PWH showed inverted CD4/CD8 ratios and higher proportions of tissue resident CD8+ T cells in villous tissue relative to control placentas. CD8+ T cells in the fetal capillaries, which were of fetal origin, were positively correlated with maternal plasma viremia before ART initiation, implying that imbalanced T cells persisted throughout pregnancy. In addition, the expanded memory differentiation of CD8+ T cells was confined to the fetal placental compartment and cord blood but was not observed in the maternal decidua. CONCLUSIONS: T-cell homeostatic imbalance in the blood circulation of PWH is reflected in the placenta. The placenta may be a causal link between HIV-induced maternal immune changes during gestation and altered immunity in newborn infants in the absence of vertical transmission.

Differential impact of antiretroviral therapy initiated before or during pregnancy on placenta pathology in HIV-positive women.

OBJECTIVE: To examine the association between timing of antiretroviral treatment (ART) initiation in HIV-infected women and placental histopathology. DESIGN: A nested substudy in a larger cohort of HIV-infected women which examined the association between ART status and birth outcomes. METHODS: Placentas (n = 130) were examined for histopathology from two ART groups: stable (n = 53), who initiated ART before conception and initiating (n = 77), who started ART during pregnancy [median (interquartile range) 15 weeks gestation (11-18)]. Using binomial regression we quantified associations between ART initiation timing with placental histopathology and pregnancy outcomes. RESULTS: One-third of all placentas were less than 10th percentile weight-for-gestation and there was no significant difference between ART groups. Placental diameter, thickness, cord insertion position and foetal-placental weight ratio were also similar by group. However, placentas from the stable group showed increased maternal vascular malperfusion (MVM) (39.6 vs. 19.4%), and decreased weight (392 vs. 422 g, P = 0.09). MVM risk was twice as high [risk ratios 2.03 (95% confidence interval: 1.16-3.57); P = 0.01] in the stable group; the increased risk remaining significant when adjusting for maternal age [risk ratios 2.04 (95% confidence interval: 1.12-3.72); P = 0.02]. Furthermore, MVM was significantly associated with preterm delivery and low birth weight (P = 0.002 and <0.0001, respectively). CONCLUSION: Preconception initiation of ART was associated with an increased MVM risk, and may contribute to placental dysfunction. The association between MVM with preterm delivery and low birth weight suggests that a placenta-mediated mechanism likely links the putative association between long-term use of ART and adverse birth outcomes.

Renal dysfunction, rod-cone dystrophy, and sensorineural hearing loss caused by a mutation in RRM2B.

More than two decades ago, a recessive syndromic phenotype affecting kidneys, eyes, and ears, was first described in the endogamous Afrikaner population of South Africa. Using whole-exome sequencing of DNA from two affected siblings (and their carrier parents), we identified the novel RRM2B c.786G>T variant as a plausible disease-causing mutation. The RRM2B gene is involved in mitochondrial integrity, and the observed change was not previously reported in any genomic database. The subsequent screening revealed the variant in two newly presenting unrelated patients, as well as two patients in our registry with rod-cone dystrophy, hearing loss, and Fanconi-type renal disease. All patients with the c.786G>T variant share an identical 1.5 Mb haplotype around this gene, suggesting a founder effect in the Afrikaner population. We present ultrastructural evidence of mitochondrial impairment in one patient, to support our thesis that this RRM2B variant is associated with the renal, ophthalmological, and auditory phenotype.

Clinicopathologic Characterization of Children With B-Cell Non-Hodgkin Lymphoma Over 10 Years at a Tertiary Center in Cape Town, South Africa.

BACKGROUND: We characterized B-cell non-Hodgkin lymphoma (NHL) cases over 10 years at a tertiary children's hospital to contribute to the body of knowledge on pediatric lymphoma in developing countries with a high human immunodeficiency virus (HIV) burden. METHODS: A retrospective cohort study was carried out using clinical and laboratory records of children newly diagnosed with B-cell NHL from January 2005 to December 2014. RESULTS: Seventy-five children ≤15 years of age were included. The majority had Burkitt lymphoma (n=61). Overall, (n=19) were HIV positive and 16% (n=12) had concurrent active tuberculosis. Bulky disease was present in 65.7% (n=46) and 30.1% (n=22) were classified as Lymphomes Malins B risk group C. The 5-year survival estimates for HIV-negative and HIV-positive children were similar in our cohort: 81% versus 79% for event-free survival and 85% versus 83.9% for overall survival. Of 3 children with Burkitt lymphoma, HIV, and Lymphomes Malins B group C, 2 died within 1 year. CONCLUSIONS: Irrespective of HIV status, the survival of children in our B-cell NHL cohort compares favorably with cure rates in developed nations, although advanced disease remains associated with a poor prognosis. Characterization of childhood NHL cases contributes to accurate risk stratification and tailored treatment.

Characteristics and Outcomes of Autoimmune Hepatitis from a Tertiary Paediatric Centre, Cape Town, South Africa.

OBJECTIVES: To describe the clinical characteristics, biochemical and histological features, outcomes and predictors of prognosis of children with autoimmune hepatitis (AIH) from a paediatric centre in South Africa. METHODS: Thirty-nine children diagnosed with AIH at Red Cross War Memorial Children's Hospital between 2005 and 2015 were included. Relevant patient's data were retrieved from the hospital's medical records and database. Liver biopsy slides were reviewed. Ethical approval was obtained. Data were analysed using SPSS. RESULTS: Females were 29 (74%). Mean age at presentation was 7.27 ± 3.35 years and the mean follow-up was 4.5 ± 2.4 years. Jaundice was present in 97% of patients at presentation. An acute presentation was observed in 26 (67%) even though cirrhosis was detected in 22 (56%). Autoantibody screening was completed in 35 patients, 20 (57%) were AIH-1, 1 (3%) was AIH-2 and 14 (40%) were seronegative AIH. Of the 25 patients who underwent magnetic resonance cholangiography 17 (68%) had associated autoimmune sclerosing cholangitis. The remission rate was 79%. However, 11 children relapsed later. One child required liver transplantation and one demised. Seronegative and seropositive patients have comparable characteristics and outcomes. While a higher alanine transaminase (ALT) level at presentation is a significant predictor of remission, a lower ALT level and cirrhosis are significant risk factors for unfavourable outcome. Overall survival rate was 97%. CONCLUSION: AIH responds well to therapy with excellent survival. Hence, it should be considered in any child presenting with viral screen negative hepatitis and start therapy timeously to prevent disease progression.

Clear Cell Sarcoma of the Kidney.

Clear cell sarcoma of the kidney is an uncommon malignant pediatric renal neoplasm that typically presents in the 2- to 3-year age group and has a propensity for aggressive behavior and late relapses. Histologically, this tumor exhibits a great diversity of morphologic patterns that can mimic most other pediatric renal neoplasms, often leading to confusion and misdiagnosis. Until recently, adjunct immunohistochemical and molecular genetic tests to support the diagnosis were lacking. The presence of internal tandem duplications in BCL-6 coreceptor (BCOR) and a translocation t(10;17) creating the fusion gene YWHAE-NUTM2B/E have now been well accepted. Immunohistochemistry for BCOR has also been shown to be a sensitive and specific marker for clear cell sarcoma of the kidney in the context of pediatric renal tumors. Improved intensive chemotherapy regimens have influenced the clinical course of the disease, with late relapses now being less frequent and the brain having overtaken bone as the most common site of relapse.

Renal disease in Cockayne syndrome.

BACKGROUND: Cockayne Syndrome (CS) is a rare autosomal recessive multi-systemic disorder, characterized; by developmental delay, microcephaly, severe growth failure and sensorial impairment. Renal complications have been reported but remain underinvestigated. The objective of this study was to perform a review of renal disease in a cohort of CS patients. METHODS: We retrospectively collected relevant clinical, biochemical and genetic data from a cohort of 136 genetically confirmed CS patients. Blood pressure (BP), proteinuria, albuminemia, uric acid, creatinine clearance, renal ultrasounds and renal biopsy result were analysed. RESULTS: Thirty-two patients had a renal investigation. We found that 69% of investigated patients had a renal disorder and/or an elevated BP. Fifteen out of 21 patients (71% of investigated patients) had an increased BP, 10 out of 16 patients (62% of investigated patients) presented with proteinuria and 4 of them had a nephrotic syndrome. Thirteen patients out of 29 (45%) had a decreased Glomerular Filtration Rate (GFR), 18 out of 25 patients (72%) had a hyperuricemia. No correlation with the genetic background or clinical types of CS was found, except for the renal clearance. CONCLUSIONS: Renal disease, increased blood pressure and hyperuricemia were highly prevalent in our study. We believe that CS patients should benefit from a nephrological follow-up and that anti-uric acid drug and Angiotensin-converting enzyme (ACE) inhibitor should be discussed in these patients.

Reliability of Histopathology for the Early Recognition of Fibrosis in Traction Alopecia: Correlation with Clinical Severity.

Traction alopecia (TA) is hair loss caused by prolonged pulling or repetitive tension on scalp hair; it belongs to the biphasic group of primary alopecia. It is non-scarring, typically with preservation of follicular stem cells and the potential for regrowth of early lesions especially if traction hairstyles are stopped. However, the alopecia may become permanent (scarring) and fail to respond to treatment if the traction is excessive and prolonged. Hence, the ability to detect fibrosis early in these lesions could predict patients who respond to treatment. Histopathological diagnosis based on scalp biopsies has been used as a gold standard to delineate various forms of non-scarring alopecia and to differentiate them from scarring ones. However, due to potential discrepant reporting as a result of the type of biopsy, method of sectioning, and site of biopsy, histopathology often tends to be unreliable for the early recognition of fibrosis in TA. In this study, 45 patients were assessed using the marginal TA severity scoring system, and their biopsies (both longitudinal and transverse sections) were systematically assessed by three dermatopathologists, the aim being to correlate histopathological findings with clinical staging. Intraclass correlation coefficients were used to determine the level of agreement between the assessors. We found poor agreement of the identification and grading of perifollicular and interfollicular fibrosis (0.55 [0.23-0.75] and 0.01 [2.20-0.41], respectively), and no correlation could be drawn with the clinical severity score. Better methods of diagnosis are needed for grading and for recognition of early fibrosis in TA.

Collagenous gastritis: An unusual cause of generalized oedema in a child.

Collagenous gastritis is an uncommon gastrointestinal disease in children. Its cause remains uncertain. It may present as severe hypoproteinaemia manifesting as generalized oedema. We report a 15 months old female who presented with pica, generalized body oedema and diarrhoea. Diagnostic workup revealed gastric replacement of the lamina propria by hyalinized collagen on histology. This case seeks to highlight the need for early paediatric gastroenterology referral including oesophagogastroduodenoscopy with multiple tissue biopsies as part of a broad diagnostic workup in children with non-specific gastrointestinal symptoms to improve diagnostic yield and enable accurate histologic diagnosis, so that appropriate therapy can be timeously applied.

Exogenous lipoid pneumonia: an important cause of interstitial lung disease in infants.

Exogenous lipoid pneumonia (ELP), an important cause of interstitial lung disease, often goes unrecognized. We conducted a retrospective study of children with histologically confirmed ELP at Red Cross Children's Hospital, South Africa. Twelve children of Zimbabwean heritage aged 2.1-10.8 months were identified between 2012 and 2017. Repeated oral administration of plant-based oil for cultural reasons was reported by 10 of 11 caregivers. Cough (12/12), tachypnoea (11/12), hypoxia (9/12), and diffuse alveolar infiltrates on chest radiography (12/12) were common at presentation. Chest computed tomography revealed ground-glass opacification with lower zone predominance (9/9) and interlobular septal thickening (8/9). Bronchoalveolar lavage specimens appeared cloudy/milky, with abundant lipid-laden macrophages and extracellular lipid on Oil-Red-O staining (12/12), with polymicrobial (6/12) and Mycobacterium abscessus (2/12) co-infection. Antibiotics, systemic corticosteroids, and therapeutic lavage were interventions in all eight and five patients, respectively. Clinicians should consider ELP in children with non-resolving pneumonia in settings with similar practices.

The First Case of Riboflavin Transporter Deficiency in sub-Saharan Africa.

This report describes the first case of a child with genetically confirmed Brown-Vialetto-van Laere syndrome in sub-Saharan Africa. This is an extremely rare clinical condition that presents with an auditory neuropathy, bulbar palsy, stridor, muscle weakness, and respiratory compromise that manifests with diaphragmatic and vocal cord paralysis. It is an autosomal recessive condition for which the genetic mutation has only recently been linked to a riboflavin transporter deficiency. We describe an 11-month-old affected male infant. He has required long-term respiratory support and a gastrostomy tube to support feeding. With high-dose riboflavin supplementation, he had limited recovery of motor function. His respiratory chain enzyme studies were abnormal suggestive of mitochondrial (mt) dysfunction. In the setting of limited resources, recognition of this striking clinical phenotype is important to highlight, specifically regarding the genetic implications of the condition and the potentially remedial response to vitamin supplementation.