Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.

During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the Spike gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the Spike and nsp12 genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.

Multidisciplinary approach on divergent outcomes in spinal muscular atrophies: comparing DYNC1H1 and SMN1 gene mutations.

Spinal Muscular Atrophy (SMA) emerges as a prominent genetic neuromuscular disorder primarily caused by variants in the survival motor neuron (SMN) gene. However, it is noteworthy that alternative variants impacting DYNC1H1 have also been linked to a subtype known as spinal muscular atrophy lower extremity predominant (SMA-LED). This observation underscores the complexity of SMA and highlights the necessity for tailored, gene-specific management strategies. Our study elucidates how similar approaches to managing SMA can yield distinct outcomes, emphasizing the imperative for personalized gene-based interventions in effectively addressing these conditions. Two patients were referred for further management due to clinical suspicion of type-3 SMA. The definitive diagnosis was confirmed through the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) technique, as well as whole-exome sequencing (WES). The analysis revealed deletions in exon-7 and 8 of SMN1 in the first patient and a likely pathogenic mutation (NM_001376.5(DYNC1H1):c.1867 T > C (NP_001367.2: p.Phe623Leu)) in DYNC1H1 in the second patient. Both patients presented with lower limb muscle weakness. However, while the first patient exhibited a gradual increase in severity over the years, the second patient displayed no progressive symptoms. The management was adjusted accordingly based on the genetic findings. Our observation underscores the complexity of SMA and highlights the necessity for tailored, gene-specific management strategies. Our study elucidates how similar approaches to managing SMA can yield distinct outcomes, emphasizing the imperative for personalized gene-based interventions in effectively addressing these conditions.

Aberrant SOX10 and RET expressions in patients with Hirschsprung disease.

BACKGROUND: HSCR is a complex genetic disorder characterized by the absence of ganglion cells in the intestine, leading to a functional obstruction. It is due to a disruption of complex signaling pathways within the gene regulatory network (GRN) during the development of the enteric nervous system (ENS), including SRY-Box Transcription Factor 10 (SOX10) and REarranged during Transfection (RET). This study evaluated the expressions of SOX10 and RET in HSCR patients in Indonesia. METHODS: Total RNA of 19 HSCR ganglionic and aganglionic colons and 16 control colons were analyzed using quantitative real-time polymerase chain reaction for SOX10 and RET with GAPDH as the reference gene. Livak's method (2-ΔΔCT) was used to determine the expression levels of SOX10 and RET. RESULTS: Most patients were males (68.4%), in the short aganglionosis segment (78.9%), and had undergone transanal endorectal pull-through (36.6%). There were significant upregulated SOX10 expressions in both ganglionic (2.84-fold) and aganglionic (3.72-fold) colon of HSCR patients compared to controls' colon (ΔCT 5.21 ± 2.04 vs. 6.71 ± 1.90; p = 0.032; and ΔCT 4.82 ± 1.59 vs. 6.71 ± 1.90; p = 0.003; respectively). Interestingly, the RET expressions were significantly downregulated in both ganglionic (11.71-fold) and aganglionic (29.96-fold) colon of HSCR patients compared to controls' colon (ΔCT 12.54 ± 2.21 vs. 8.99 ± 3.13; p = 0.0004; and ΔCT 13.90 ± 2.64 vs. 8.99 ± 3.13; p = 0.0001; respectively). CONCLUSIONS: Our study shows aberrant SOX10 and RET expressions in HSCR patients, implying the critical role of SOX10 and RET in the pathogenesis of HSCR, particularly in the Indonesian population. Our study further confirms the involvement of SOX10-RET within the GNR during the ENS development.

Long-term functional outcomes of patients with Hirschsprung disease following pull-through.

BACKGROUND: Hirschsprung disease (HSCR) is a common congenital disorder presenting with functional obstruction due to aganglionosis of the colon. There are numerous types of pull-through surgery for managing HSCR, such as transabdominal endorectal (Soave), Swenson, Duhamel, transanal endorectal pull-through (TEPT), and laparoscopic (Georgeson) approach. Here, we aimed to describe the long-term outcome of patients with HSCR who underwent transabdominal Soave, Duhamel, and TEPT in our institution. METHODS: We performed a cross-sectional analysis for patients who underwent Duhamel, Soave, and TEPT at our institution from January 2012 to December 2015. Long-term functional outcome was determined by bowel function score (BFS). The BFS was obtained by interviewing patients who had completed at least three years of follow-up. RESULTS: Twenty-five patients were included in this study who underwent transabdominal Soave (n = 8), Duhamel (n = 4), and TEPT (n = 13). There were 24 patients with short aganglionosis type. The median age of HSCR diagnosis was 10 (IQR = 1-39) months, while the median age of pull-through surgery was 17 (IQR = 7-47) months. The median follow-up of BFS level for HSCR patients after pull-through was 72 (IQR, 54-99) months. There were 11 patients with good BFS level and 10 patients with normal BFS level. Additionally, 50% of Duhamel patients had poor BFS level, while 50% of Soave patients had good BFS level, and 54% of TEPT patients had normal BFS level (p = 0.027). As many as 50% of Duhamel patients showed daily soiling and required protective aids, while 38.5% of TEPT had staining less than 1/week and no change of underwear required, and 50% of Soave patients revealed no soiling, respectively (p = 0.030). Furthermore, 75% of Duhamel patients had accidents, while 75% of Soave and 46.2% of TEPT patients had no accidents (p = 0.035). CONCLUSION: Our study shows that the type of definitive surgery might affect the long-term bowel functional outcome; particularly, the TEPT approach might have some advantages over the transabdominal Soave and Duhamel procedures.

The impact of NRG1 expressions and methylation on multifactorial Hirschsprung disease.

BACKGROUND: Hirschsprung disease (HSCR) is a complex genetic disorder characterized by the lack of ganglion cells in the intestines. A current study showed that the NRG1 rare variant frequency in Indonesian patients with HSCR is only 0.9%. Here, we investigated the impact of NRG1 expressions and methylation patterns on the pathogenesis of HSCR. METHODS: This cross-sectional study determined NRG1 type I (HRGα, HRGß1, HRGß2, HRGß3, HRGγ, and NDF43 isoforms), type II and type III expressions in both ganglionic and aganglionic colons of 20 patients with HSCR and 10 control colons by real-time polymerase chain reaction (qPCR). For methylation studies, we treated the extracted gDNA from 16 HSCR patients' and 17 control colons with sodium bisulfate and analyzed the methylation pattern of NRG1 exon 1 with methylation-specific PCR. The samples were collected and analyzed at our institution from December 2018 to December 2020. RESULTS: NRG1 types I, II and III expressions were upregulated (17.2-, 3.2-, and 7.2-fold, respectively) in the ganglionic colons compared with control colons (type I: 13.32 ± 1.65 vs. 17.42 ± 1.51, p < 0.01; type II: 13.73 ± 2.02 vs. 16.29 ± 2.19, p < 0.01; type III: 13.47 ± 3.01 vs. 16.32 ± 2.58, p = 0.03; respectively); while only type I (7.7-fold) and HRGß1/HRGß2 (3.3-fold) isoforms were significantly upregulated in the aganglionic colons compared to the controls (type I: 14.47 ± 1.66 vs. 17.42 ± 1.51, p < 0.01; HRGß1/HRGß2: 13.62 ± 3.42 vs 14.75 ± 1.26, p = 0.01). Moreover, the frequency of partially methylated NRG1 was higher in the ganglionic (81%) and aganglionic (75%) colons than in the controls (59%). CONCLUSIONS: Our study provides further insights into the aberrant NRG1 expression in the colons of patients with HSCR, both ganglionic and aganglionic bowel, which might contribute to the development of HSCR, particularly in Indonesia. Furthermore, these aberrant NRG1 expressions might be associated with its methylation pattern.

Phylogenetic analysis of congenital rubella virus from Indonesia: a case report.

BACKGROUND: Rubella is a common inherited infection resulting in congenital cataracts and a significant cause of permanent vision loss in developing countries. In 2016, Indonesia had the highest number of congenital rubella syndrome (CRS) cases globally. Here, we report the first genotype of the rubella virus extracted from the eye lens from a child with congenital cataracts due to CRS. CASE PRESENTATION: A female neonate was delivered by an elective caesarean delivery with normal birth weight at term from a 24-year-old mother in the rural setting. The baby presented with bilateral congenital cataracts, small-moderate secundum atrial septal defect, severe supravalvular pulmonary stenosis, and profound bilateral hearing loss. She also had microcephaly and splenomegaly. The patient's serology showed persistent positive IgG for rubella virus at the age of four years and four months. Following extraction during cataract surgery, viral detection of the lenses identified the presence of rubella. Phylogenetic analysis confirmed that the virus was grouped into genotype 1E. CONCLUSIONS: Our study reports the first phylogenetic analysis of the rubella virus extracted from the eye lens of a child with CRS in Indonesia. The detection of the rubella virus from eye lenses is remarkably promising. Our findings also emphasize the importance of molecular epidemiology in tracking the origin of rubella infection toward achieving virus eradication.

Autosomal dominant Emery-Dreifuss muscular dystrophy caused by a mutation in the lamin A/C gene identified by exome sequencing: a case report.

BACKGROUND: Emery-Dreifuss Muscular Dystrophy (EDMD) is an uncommon genetic disease among the group of muscular dystrophies. EDMD is clinically heterogeneous and resembles other muscular dystrophies. Mutation of the lamin A/C (LMNA) gene, which causes EDMD, also causes many other diseases. There is inter and intrafamilial variability in clinical presentations. Precise diagnosis can help in patient surveillance, especially before they present with cardiac problems. Hence, this paper shows how a molecular work-out by next-generation sequencing can help this group of disorders. CASE PRESENTATION: A 2-year-10-month-old Javanese boy presented to our clinic with weakness in lower limbs and difficulty climbing stairs. The clinical features of the boy were Gower's sign, waddling gait and high CK level. His father presented with elbow contractures and heels, toe walking and weakness of limbs, pelvic, and peroneus muscles. Exome sequencing on this patient detected a pathogenic variant in the LMNA gene (NM_170707: c.C1357T: NP_733821: p.Arg453Trp) that has been reported to cause Autosomal Dominant Emery-Dreifuss muscular dystrophy. Further examination showed total atrioventricular block and atrial fibrillation in the father. CONCLUSION: EDMD is a rare disabling muscular disease that poses a diagnostic challenge. Family history work-up and thorough neuromuscular physical examinations are needed. Early diagnosis is essential to recognize orthopaedic and cardiac complications, improving the clinical management and prognosis of the disease. Exome sequencing could successfully determine pathogenic variants to provide a conclusive diagnosis.

Challenge in diagnosis of late onset necrotizing enterocolitis in a term infant: a case report.

BACKGROUND: Necrotizing enterocolitis (NEC) is a common devastating inflammatory gastrointestinal disease and frequently occurs in premature infants. Here, we reported a case of late-onset NEC in a term neonate with good outcome after surgery for long-term follow-up. CASE PRESENTATION: Ten-week-old male came to emergency unit due to prolonged diarrhea and abdominal distention. He was born at gestational age of 40 weeks with birth weight and Apgar score of 2800 g and 7/8, respectively. He had no history of formula feeding. Two weeks before admitted to the hospital, the patient had frequent diarrhea with fever. He was found lethargic with abdominal distention, absence of bowel sounds and abdominal tenderness. Plain abdominal x-ray and CT scan showed gastric and intestinal dilatation and gasless colon, suggesting a small bowel obstruction, and bowel wall thickening indicating peritonitis, without any free subdiaphragmatic air (pneumoperitoneum). Moreover, the patient did not have a congenital heart disease. While in intensive medical treatment, he showed a continuous clinical deterioration. All findings were suggestive of intestinal inflammation with clinical deterioration, and we decided to perform an emergency exploratory laparotomy and found an ischemia along the jejunoileal with a perforation at 25 cm above the ileocecal valve. Subsequently, we performed a double-barrel ileostomy through a separate incision from the laparotomy. Histopathological findings confirmed the diagnosis of NEC. We closed the stoma at postoperative day 43. The patient was discharged uneventfully a month after stoma closure. CONCLUSION: Abdominal CT scan might be useful to establish an early recognition of late-onset NEC; thus, immediate surgical intervention might be performed to decrease its morbidity and mortality. Moreover, late-onset NEC in term neonates might occur without any risk factors or significant co-morbidities.

Combined Genetic Effects of RET and NRG1 Susceptibility Variants on Multifactorial Hirschsprung Disease in Indonesia.

BACKGROUND: Specific genetic variants at RET (rs2435357) and NRG1 (rs7835688, rs16879552) are associated with Hirschsprung disease (HSCR) in Indonesia. This study aimed to investigate the additional effect of RET rs2506030 on these variants to determine its potential interactions in HSCR patients of Indonesian ancestry. METHODS: Sixty HSCR patients and 122 non-HSCR controls were ascertained for this study and genotyped for RET rs2506030 using the TaqMan assay. RESULTS: RET rs2506030 was associated with HSCR both by case-control analysis (odds ratio = 1.68; P = 0.043) and the transmission disequilibrium test (P = 0.034). Furthermore, individuals with five or six risk alleles at RET rs2506030, rs2435357 and NRG1 rs7835688 showed ∼45-fold higher HSCR risk than those with 0 or 1 or 2 risk alleles. CONCLUSIONS: Disease risk of HSCR is increased by the combination of specific RET and NRG1 susceptibility variants.

Aberrant UBR4 expressions in Hirschsprung disease patients.

BACKGROUND: Recently, pathogenic alleles within ubiquitin N-recognin domain-containing E3 ligase 4 (UBR4) gene have been shown to be associated with Hirschsprung disease (HSCR). We determined the UBR4 expressions in Indonesian HSCR patients. METHODS: We analyzed the UBR4 expressions in the colons of HSCR patient and anorectal malformation (ARM) patient as control by real-time polymerase chain reaction (qPCR). RESULTS: Thirty-seven patients with non-syndromic HSCR and eighteen controls were involved in this study. qPCR revealed that the UBR4 expression was strongly decreased (0.77-fold) in the ganglionic group of patients with HSCR compared to the control group with ARM (ΔCT 2.43 ± 0.36 vs. 2.05 ± 0.69; p = 0.009), whereas the UBR4 expression was also significantly reduced (0.79-fold) in the aganglionic group of patients with HSCR compared to the control group with ARM (ΔCT 2.39 ± 0.46 vs. 2.05 ± 0.69; p = 0.044). However, the UBR4 expression change was not associated with gender (p = 0.35 and 0.80), nor with degree of aganglionosis both in ganglionic and aganglionic colons (p = 0.72 and 0.73), respectively. CONCLUSION: Our study demonstrates that expression of UBR4 is decreased in both aganglionic and ganglionic colon of HSCR patients.

The impact of down-regulated SK3 expressions on Hirschsprung disease.

BACKGROUND: Some Hirschsprung's disease (HSCR) patients showed persistent bowel symptoms following an appropriately performed pull-through procedure. The mechanism is presumed to be down-regulated small-conductance calcium-activated potassium channel 3 (SK3) expression in the HSCR ganglionic intestines. We aimed to investigate the SK3 expression's impact in HSCR patients after a properly performed pull-through surgery in an Indonesian population, a genetically distinct group within Asia. METHODS: We assessed SK3 gene expression in both the ganglionic and aganglionic colon of HSCR patients and controls colon by quantitative real-time polymerase chain reaction (RT-PCR). RESULTS: We ascertained fourteen sporadic HSCR patients and six anorectal malformation patients as controls. Quantitative RT-PCR showed that the SK3 expression was significantly lower (23-fold) in the ganglionic colon group compared to the control group (9.9 ± 4.6 vs. 5.4 ± 3.4; p = 0.044). The expression of SK3 in the aganglionic colon group was also significantly lower (43-fold) compared to the control group (10.8 ± 4.4 vs. 5.4 ± 3.4; p = 0.015). CONCLUSION: Our study shows that the down-regulated SK3 expression in ganglionic intestines might contribute to the persistent bowel symptoms following a properly performed pull-through surgery in Indonesian HSCR patients. Furthermore, this study is the first report of SK3 expression in a sample population of Asian ancestry.

NRG1 variant effects in patients with Hirschsprung disease.

BACKGROUND: Hirschsprung disease (HSCR) is a heterogeneous genetic disorder characterized by absence of ganglion cells along the intestines resulting in functional bowel obstruction. Mutations in neuregulin 1 (NRG1) gene have been implicated in some cases of intestinal aganglionosis. This study aims to investigate the contribution of the NRG1 gene to HSCR development in an Indonesian population. METHODS: We analyzed the entire coding region of the NRG1 gene in 54 histopathologically diagnosed HSCR patients. RESULTS: All patients were sporadic non-syndromic HSCR with 53/54 (98%) short-segment and 1/54 (2%) long-segment patients. NRG1 gene analysis identified one rare variant, c.397G > C (p.V133 L), and three common variants, rs7834206, rs3735774, and rs75155858. The p.V133 L variant was predicted to reside within a region of high mammalian conservation, overlapping with the promoter and enhancer histone marks of relevant tissues such as digestive and smooth muscle tissues and potentially altering the AP-4_2, BDP1_disc3, Egr-1_known1, Egr-1_known4, HEN1_2 transcription factor binding motifs. This p.V133 L variant was absent in 92 non-HSCR controls. Furthermore, the rs7834206 polymorphism was associated with HSCR by case-control analysis (p = 0.037). CONCLUSIONS: This study is the first report of a NRG1 rare variant associated with HSCR patients of South-East Asian ancestry and provides further insights into the contribution of NRG1 in the molecular genetic pathogenesis of HSCR.

Clinical profile of congenital rubella syndrome in Yogyakarta, Indonesia.

BACKGROUND: Congenital rubella syndrome (CRS) has many severe neurological manifestations and other systemic consequences. Although various studies have been done in Indonesia, there are no conclusive results on CRS incidence. The aim of this study was therefore to investigate the incidence, clinical manifestations and outcomes of CRS in Yogyakarta, Indonesia. METHODS: A descriptive study involving a review of congenital anomalies associated with CRS was carried out at Dr Sardjito Hospital, Yogyakarta, Indonesia, from July 2008 to June 2013. CRS was categorized according to the World Health Organization (WHO) classification. This study involved children aged <1 year old, and was conducted at the outpatient clinic, pediatric and neonatology wards. RESULTS: A total of 201 children met the criteria for suspected CRS during the 5 year study. Of those patients, 6% were classified as having laboratory-confirmed CRS, 21.4% as having clinically compatible CRS, and 72.6% as having discarded CRS (i.e. a suspected case that does not meet the criteria for CRS). The estimated incidence of laboratory-confirmed CRS and laboratory-confirmed and clinically compatible CRS in Yogyakarta, Indonesia during the study period was 0.05:1,000 and 0.25:1,000 live births, respectively. Of the laboratory-confirmed CRS patients, 83.3% of children had congenital heart disease (CHD), 75% had hearing impairment, 66.7% had congenital cataract and 50% had microcephaly. Furthermore, none of the mothers was vaccinated against rubella. CONCLUSIONS: The incidence of CRS in infants in Yogyakarta Indonesia is considered high, with most clinical manifestations being CHD, hearing impairment and congenital cataract. This emphasizes the necessity for epidemiological study of CRS in other hospitals and the importance of establishing a national rubella vaccination program in Indonesia.

The utility of the hematoxylin and eosin staining in patients with suspected Hirschsprung disease.

BACKGROUND: While immunohistochemistry (IHC) methods have been widely conducted for the diagnosis of Hirschsprung disease (HSCR) in developed countries, there are very few studies on their use in developing countries where hematoxylin and eosin (HE) staining is a key element of the diagnosis of HSCR. We aimed to determine the accuracy of HE staining in the diagnosis of HSCR using S100 IHC as the reference standard in Indonesia. METHODS: All histopathology performed for the suspicion of HSCR patients from January 2013 to August 2015 in Dr. Sardjito Hospital, Yogyakarta, Indonesia, were retrospectively reviewed. RESULTS: Our study included 23 HSCR patients: 9 males and 14 females. The HE staining revealed 14 negative (absence of ganglion cells) cases (61%) and 9 positive (presence of ganglion cells) cases (39%). In S100 IHC, out of the 9 positive cases by HE staining, 6 (67%) were confirmed for having ganglion cells; and out of the 14 negative cases by HE staining, 12 (86%) were reported negative and 2 (14%) were positive by S100 IHC staining. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy rates of the HE staining were 80% (95% CI: 0.51-0.95), 75% (95% CI: 0.36-0.96), 85.7% (95% CI: 0.56-0.98), 66.7% (95% CI: 0.31-0.91), and 78.3% (95% CI: 0.58-0.90), respectively. CONCLUSIONS: Our study showed that HE staining has relatively moderate accuracy for the diagnosis of HSCR. The use of HE staining is still recommended for the diagnosis of HSCR given the limitation of resource allocation for more expensive IHC technologies in developing countries.

Accuracy of polymerase chain reaction-restriction fragment length polymorphism for RET rs2435357 genotyping as Hirschsprung risk.

BACKGROUND: Recently, the common RET rs2435357 variant has been shown to be strongly related to Hirschsprung disease (HSCR) in the Indonesian population. This association study was conducted in developed areas using high-throughput TaqMan polymerase chain reaction (PCR) assay. Although the TaqMan method is less time-consuming, it requires a special more expensive PCR machine and a highly skilled analyst. In this study, we analyzed the usefulness of the PCR-restriction fragment length polymorphism (RFLP) method for genotyping RET rs2435357 polymorphism in Indonesian HSCR patients given the limitation of resource allocation for more expensive technologies. MATERIALS AND METHODS: We compared our previous genotyping results of RET rs2435357 in 53 HSCR patients and 86 controls using the TaqMan PCR assay with the PCR-RFLP technique. Furthermore, we included an additional 40 HSCR patients and 50 controls and subsequently genotyped all subjects using the PCR-RFLP method. RESULTS: Compared with our previous genotyping data of RET rs2435357 using the TaqMan PCR assay, the PCR-RFLP method indicated 100% concordant results. The overall accuracy of the PCR-RFLP for RET rs2435357 genotyping was 100%. In addition, case-control analysis demonstrated that RET rs2435357 is significantly correlated with HSCR (P = 2.2 × 10(-13)) with an odds ratio of 5.1 (95% confidence interval = 3.2-8.1). The transmission disequilibrium test revealed that risk allele (T) at rs2435357 is significantly overtransmitted to probands at a transmission rate (τ) of 0.87 (P = 1.5 × 10(-6)). CONCLUSIONS: The PCR-RFLP method is reliable and affordable for genotyping of RET rs2435357 polymorphism in developing countries. Our results strengthen the proof that the RET rs2435357 variant is a genetic risk for HSCR in Indonesia.

The importance of prenatal diagnosis for the surgical strategy of giant cystic meconium peritonitis: A case report.

Background: Giant cystic meconium peritonitis (MP) is a relatively rare entity. Prompt surgical treatment is required to manage the underlying etiology and reestablish the continuity of the intestines. Despite perinatal and postoperative care improvements, the overall mortality rate is still relatively high. We reported a giant cystic MP that was recognized using antenatal sonography (US). It was successfully treated with primary anastomosis. Case presentation: We presented a female newborn with a chief complaint of abdominal mass. The prenatal sonography showed an intraabdominal cyst at the 28th week of gestation. She was born at the gestational age of 38 weeks via vaginal delivery from a primigravid mother without complications, with a birth weight of 3275 g. Elective surgery was performed at the age of eight days, and a calcified 10 cm cyst was revealed along with severe adhesions. The cyst was found to communicate with the ileum located 30 cm proximal from the ileocecal junction. No malrotation and volvulus were found. The cyst and a portion of the ileum were resected, followed by a primary end-to-end anastomosis. Pathologic examination showed necrotic tissue lined with epithelial tissue with microcalcifications containing bilirubin pigments, consistent with cystic MP. The patient has uneventfully discharged on postoperative day 17. The patient has normal growth and development, except for delayed walking, at the last follow-up of two years of age. Conclusion: Giant cystic MP is a rare disorder that can be detected early using the antenatal US. Our case highlights the importance of early diagnosis for giant cystic MP using the antenatal US leads to prompt surgical treatment and a more favorable prognosis.

Phenotypes of a female patient with novel de novo frameshift ARX variant identified by whole-exome sequencing: a case report.

Variants in the aristaless-related homeobox (ARX) gene cause a diverse spectrum of phenotypes of neurodevelopmental disorders (NDD) in male patients. This article describes the role of genetic testing using whole-exome sequencing (WES) in detecting a novel de novo frameshift variant in the ARX gene in a female patient with autism, seizure, and global developmental delay. Case presentation: A 2-year-old girl with frequent seizures, global developmental delay, and autistic features was referred to our hospital. She was the second child of consanguineous non-affected parents. She had a high forehead, mildly prominent ears, and prominent nasal root. A generalized epileptiform discharge was noted in her electroencephalography. Brain MRI revealed corpus callosum agenesis, cerebral atrophy, and a left parafalcine cyst. The WES result showed a likely pathogenic variant identified as a novel de novo deletion in exon 4 of the ARX gene, which creates a frameshift variant. The patient is on dual therapy of antiepilepsy drugs, physiotherapy, speech therapy, occupational therapy, and oral motor exercises. Clinical discussion: Variants in the ARX gene can result in various phenotypes in males transmitted from asymptomatic carrier females. However, several reports showed that the ARX variants might cause phenotypes in females with milder symptoms than affected males. Conclusion: We report a novel de novo ARX variant in an affected female with a NDD. Our study confirms that the ARX variant might cause remarkable pleiotropy phenotypes in females. Moreover, WES could help to identify the pathogenic variant in NDD patients with diverse phenotypes.

Exome sequencing identifies novel genes and variants in patients with Hirschsprung disease.

BACKGROUND: Hirschsprung disease (HSCR) is a complex genetic disease characterized by the absence of ganglion cells in the intestines, leading to a functional obstruction in infants. At least 24 genes have been identified for the pathogenesis of HSCR. They contributed to approximately 72% of HSCR cases. We aimed to elucidate further the genetic basis of HSCR in Indonesia using the whole-exome sequencing (WES) approach. METHODS: WES was performed in 39 sporadic non-syndromic HSCR patients and 16 non-HSCR subjects as controls. Variants presented in controls were excluded, followed by in silico prediction tools and population allele frequency databases to select rare variants. We determined the minor allele frequency (MAF) using gnomAD (MAF <0.1%). RESULTS: We involved 24 (61.5%) males and 15 (38.5%) females. Most patients (62%) had short-segment aganglionosis and underwent the Duhamel procedure (41%). We identified several candidate novel variants in HSCR-related genes, including UBR4, GDNF, and ECE1. Moreover, we also identified some novel candidate genes, including a possible compound heterozygous variant in the MUTYH gene: the first variant, a known protein-truncating variant associated with colorectal cancer (CRC), p.Glu452Ter and the second variant is novel, p.Ala39Val. Moreover, the type of variants was not associated with the aganglionosis type. CONCLUSIONS: We identified several novel genes and variants, including the variant associated with CRC, that might contribute to the pathogenesis of HSCR. No genotype-phenotype associations were noted. Our study further confirms the complex network involved in enteric nervous system development and HSCR pathogenesis. LEVEL OF EVIDENCE: Level III.

De novo mutation of the TSC2 gene in patient with Tuberous Sclerosis Complex-Associated Neuropsychiatric Disorders (TAND) Phenotype: a case report.

Tuberous sclerosis complex (TSC) is a neurocutaneous disease caused by a mutation in the TSC1 or TSC2 gene. There are several neuropsychiatric manifestations associated with TSC known as TSC-associated neuropsychiatric disorder (TAND). This article concerns neuropsychiatric manifestations in children with the TSC2 gene mutation, with genetic analysis findings using whole-exome sequencing. Case: A 17-year-old girl presented with TSC, absence and focal epilepsy, borderline intellectual functioning, organic psychosis, and renal angiomyolipoma. She was emotionally unstable and preoccupied with irrelevant fears. In the physical examination, we found multiple hypomelanotic maculae, angiofibroma, and a shagreen patch. The intellectual assessment result with the Wechsler Adult Intelligence Scale at 17 was borderline intellectual functioning. Brain MRI showed cortical and subcortical tubers in the parietal and occipital lobes. Whole-exome sequencing was conducted, and the result was a missense mutation in exon 39 of the TSC2 gene [NM_000548.5:c.5024C>T (NP_000539.2:p.Pro1675Leu)]. The Sanger sequencing of the patient's parents revealed no mutations in the TSC2 gene, confirming the patient's de novo mutation. The patient was given several antiepileptic and antipsychotic drugs. Clinical discussion: Neuropsychiatric manifestation is a common phenotype in the TSC variant, and psychosis is one of the rare TAND symptoms in children. Conclusions: The neuropsychiatric phenotype and genotype in TSC patients are rarely reported and evaluated. We reported a female child with epilepsy, borderline intellectual functioning, and organic psychosis associated with a de novo mutation of the TSC2 gene. Organic psychosis is a rare symptom of TAND which also manifested in our patient.

Neurological Manifestations of COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C) in Yogyakarta, Indonesia.

OBJECTIVE: This observational cohort study aims to provide data on pediatric patients with neurological manifestations associated with multisystem inflammatory syndrome in children (MIS-C) associated with coronavirus disease (Covid-19). METHODS: Patients aged <18 with neurologic symptoms and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from January, 2021 to January, 2022 at the Dr. Sardjito Hospital in Yogyakarta, Indonesia were evaluated. We used WHO diagnostic criteria to classify patients as MIS-C or non-MIS-C. Demographic information, symptoms, and outcomes were compared between MIS-C and non-MIS-C groups. RESULTS: Between January, 2021 and January, 2022, 74 pediatric patients were considered eligible. More than half of the patients were female (54.1%), and 24.3% presented with MIS-C. Length of hospitalization was significantly longer in MIS-C individuals (P=0.006). The commonest neurological findings were involuntary movements (43.2%) and paresis (27%). The commonest neuroimaging findings were meningoencephalitis (18.9%) and hydrocephalus (22.9%). Among all the variety of neurologic manifestations in non-MIS-C and MIS-C patients, a statistically significant result was found for fever (71.4% vs 100%; P=0.015), altered mental state (14.2% vs 50%, P=0.004), and paresis (33.9% vs 5.5%, P=0.030). CONCLUSION: MIS-C was found in 24% of our patients with acute neurologic symptoms, and most cases (51.8%) had positive SARS-CoV-2 antibody results.